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Crystal Structure Determination at the Center for X-Ray Crystallography: A Practical Guide

HIDE
 Title Page
 Dedication
 Acknowledgement
 Table of Contents
 List of Tables
 List of Figures
 Abstract
 Introduction
 Experimental work and data...
 Structure refinement with SHELXTL...
 Solution and refinement of a structure...
 Multimetal cluster structure...
 Solution of a crystal structure...
 Patterson method of structure...
 Synthesis, crystallization and...
 Appendices
 References
 Biographical sketch
 

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CRYSTAL STRUCTURE DETERMINATIO N AT THE CENTER FOR X-RAY CRYSTALLOGRAPHY: A PRACTICAL GUIDE By ALEXANDR EVGENIEVICH OBLEZOV A THESIS PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLOR IDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE UNIVERSITY OF FLORIDA 2003

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Copyright 2003 by Alexandr Evgenievich Oblezov

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I dedicate this work to my father Evgenii Vasilievich Oblezov and my mother Gulnara Khazipovna Kharisova.

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iv ACKNOWLEDGMENTS I thank Dr. Khalil A. Abboud for the opportunity to discover a world of crystallography under his advisement. Also I thank everyone who helped and supported me during my studies in the University of Florida.

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v TABLE OF CONTENTS page ACKNOWLEDGMENTS.................................................................................................iv LIST OF TABLES............................................................................................................vii LIST OF FIGURES.........................................................................................................viii ABSTRACT....................................................................................................................... xi CHAPTER 1 INTRODUCTION......................................................................................................1 2 EXPERIMENTAL WORK AND DATA COLLECTION........................................3 Equipment ............................................................................................................3 Selection and Preparation of Crystal for X-ray Analysis...........................................4 Examination of the System before Data Collection...................................................6 Checking of the Cooling System......................................................................6 Checking of the Goniometer.............................................................................7 Checking of the X-ray Generator.....................................................................8 Optical Alignment......................................................................................................8 Single Frame Diffraction..................................................................................9 Precise Optical Alignment................................................................................9 Determination of Cell Parame ters (Orientation Matrix)..........................................10 Measuring of Faces..................................................................................................11 Description of the First Method......................................................................12 Description of the Second Method.................................................................12 Full Data Collection.................................................................................................13 SAINT ..........................................................................................................14 3 STRUCTURE REFINEMENT WITH SHELXTL SOFTWARE PACKAGE........16 Introduction ..........................................................................................................16 XPREP ..........................................................................................................17 Introduction .......................................................................................17 Step by Step Description of Interactive Work with XPREP..........................18 XS ..........................................................................................................19 XP ..........................................................................................................20 XL ..........................................................................................................23 Work with name.ins File in a Text Editor................................................................24

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vi Applying of Absorption Correction.........................................................................25 XCIF ..........................................................................................................26 4 SOLUTION AND REFINEMENT OF A STRUCTURE WITH A LARGE DISORDER..............................................................................................................28 Experimental Section...............................................................................................28 Structure Solution and Refinement..........................................................................29 5 MULTIMETAL CLUSTER STRUCTURE SOLUTION.......................................43 Experimental Section...............................................................................................43 Structure Solution and Refinement..........................................................................44 6 SOLUTION OF A CRYSTAL STRU CTURE WITH PSEUDO SYMMETRY.....54 Experimental Section...............................................................................................54 Structure Solution and Refinement..........................................................................55 7 PATTERSON METHOD OF STRUCTURE SOLUTION.....................................64 Experimental Section...............................................................................................64 Structure Refinement................................................................................................64 8 SYNTHESIS, CRYSTALLIZATION AND STRUCTURE DETERMINATION OF AQUA-CHLORO-(1,4,8,11-TETRAA ZAUNDECANE)NICKEL(II) CHLORIDE..............................................................................................................70 Introduction ..........................................................................................................70 Experimental Section...............................................................................................70 Structure Description................................................................................................71 APPENDIX A CIF FILE OF STRUCTURE EL06..........................................................................73 B CIF FILE OF STRUCTURE XM54........................................................................93 C CIF FILE OF STRUCTURE CW10......................................................................122 D CIF FILE OF AQUA-CHLORO-( 1,4,8,11-TETRAAZAUNDECANE)NICKEL(II) CHLORIDE............................................................................................................133 LIST OF REFERENCES.................................................................................................147 BIOGRAPHICAL SKETCH...........................................................................................148

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vii LIST OF TABLES table page 2-1. Parameters of the “Hemis phere” and “Multirun” modes.........................................14 3-1. Sample name.ins file before running XS.................................................................20 3-2. Example of a string of an atom’s parameters...........................................................22 3-3. Sample of modify.cif file.........................................................................................26 4-1. Results of an orientation matrix collection of el 06.................................................29 4-2. File el06.ins............................................................................................................. .33 4-3. Setting of the “part” command in the el06.ins file...................................................38 5-1. Results of orientation ma trix collection for xm 54..................................................44 5-2. Information revealed with “bang” command...........................................................49 6-1. Results of orientation ma trix collection for cw 10...................................................55 7-1. Parameters of structure solution with XS.................................................................64 8-1. Selected bond lengths ( ) for the title compound....................................................71 8-2. Selected diamond style hydrogen bonds for the title compound [ and ]..............71

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viii LIST OF FIGURES figure page 2-1. Scheme of the Siemens SMART™/CCD system with 3–circle Siemens PLATFORM™ goniometer.2.....................................................................................4 2-2. The preferred orientation of a crystal on a glass fiber tip of a goniometer head........6 2-3. The low temperature control unit. 1) Cold probe display, 2) “Power” button, 3) “Liquid nitrogen start filli ng” button, 4) Level of n itrogen control display...............7 2-4. The image of the aligned crystal in VIDEO program frame......................................9 2-5. The scheme of the goniom eter manual control box.................................................10 3-1. Scheme of crystal struct ure solution with SHELXTL.............................................17 4-1. Scheme of the expected structure pr ovided by the Wagener group (generated by ACD/Structure Drawing Applet).............................................................................28 4-2. View of the structure at the start point of the refinement.........................................31 4-3. View of the structure afte r deleting all “noise” q peaks...........................................31 4-4. View of the structure after labeling elect ron density peaks. Color notation: black for C; dark blue for N; purple for P; light blue for Ru and H; light green for Cl. The color scheme is used for all figures in this chapter...........................................32 4-5. View of the structure afte r the first run of XL. Twen ty new electron density peaks were obtained...........................................................................................................34 4-6. View of the structure during the second run of refinement in XP...........................35 4-7. View of the structure after the second run of XL – new electron density peaks were determined................................................................................................................36 4-8. View of the structure afte r eliminating “noise” q peaks after the third run of XP...36 4-9. View of the structure after refinement with XL. New twenty electron density peaks were obtained...........................................................................................................39

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ix 4-10. View of the structure after elimina tion of “noise” q peak s and assigning real electron density to specific atom types....................................................................39 4-11. View of the structure incl uding disorder. Thermal ellipsoids of disordered part are treated in isotropic mode..........................................................................................41 4-12. View of the structure without the minor pa rt of the disorder. Thermal ellipsoids of disordered part are treated in isotropic mode...........................................................41 4-13. Scheme of the structure constructed acco rding to the final result of the structure solution and refinement............................................................................................42 5-1. Scheme of the ligands used for the synthesis of the cluster.....................................43 5-2. View of the structure as a result of structure solu tion, completed by program XS. Color notation: black for C; dark blue for Mn and N; light blue for H; red for O. The color scheme is used for all figures in this chapter...........................................45 5-3. View of the whole cluster at the first step of refinement.........................................46 5-4. View of the asymmetric unit after elimin ation of “noise” q electron density peaks.47 5-5. View of the cluster after eliminati on of “noise” q electron density peaks...............48 5-6. View of the asymmetric unit w ith labeled electron density peaks...........................49 5-7. View of the cluster with electron density peaks assigned to specific atom types as result of the first run of XP.......................................................................................50 5-8. View of the asymmetric unit after the fi rst run of XL. Twenty new electron density peaks were obtained.................................................................................................50 5-9. View of the asymmetric unit and three identical groups of q peaks........................51 5-10. View of the cluster at the end of refinement............................................................53 5-11. View of the Mn-O core of the cluster at the end of refinement...............................53 6-1. Scheme of the expected structur e provided by the McElwee-White group (generated by ACD/Structure Drawing Applet).......................................................54 6-2. View of the structure at the first run of XP..............................................................56 6-3. Pseudo symmetry of the structure............................................................................57 6-4. View of the structure. A) part of the st ructure as q peaks, B) part of the structure after labeling.............................................................................................................57

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x 6-5. View of the structure after the second r un of XL refinement. Color notation: black for C; dark blue for N; light blue for H; light green for Cl and W. The color scheme is used for all figures in this chapter...........................................................58 6-6. View of the structure afte r eliminating “noise” q peaks..........................................59 6-7. View of the structure with labeled electron density peaks.......................................59 6-8. View of the structure with elements of pseudo symmetry after refinement with XL. New twenty q electron density peaks were obtained...............................................60 6-9. View of the structure after deleting “noise” q peaks and relabeling of electron density peaks............................................................................................................61 6-10. View of the structure after one more cycle of refinement. Twenty new electron density peaks q peaks were obtained...................................................................62 6-11. View of the structure after dele ting “noise” q peaks and relabeling........................62 6-12. Final result of the struct ure solution and refinement................................................63 7-1. Pseudo symmetry of the structure............................................................................65 7-2. View of the structure afte r eliminating pseudo symmetry.......................................65 7-3. View of the structure afte r relabeling atoms. Color nota tion: black for C; dark blue for N; light blue for H; light green for Cl and W. The color scheme is used for all figures in this chapter...............................................................................................66 7-4. View of the structure after the first refinement with XL. Twenty new electron density peaks were obtained.....................................................................................66 7-5. View of the structure af ter elimination of “noise” q peaks at the second time of running XP...............................................................................................................67 7-6. View of the structure after relabeling q peaks..........................................................68 7-7. View of the structure after the second run of refinement.........................................68 7-8. View of the structure after eliminatio n of “noise” q peaks (third run of XP)..........69 8-1. View of an asymmetric unit of the title compound..................................................72 8-2. View of the two dimensional layer in the crystal structure of the title compound...72

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xi Abstract of Thesis Presen ted to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Master of Science CRYSTAL STRUCTURE DETERMINATIO N AT THE CENTER FOR X-RAY CRYSTALLOGRAPHY: A PRACTICAL GUIDE By Alexandr Evgenievich Oblezov December 2003 Chair: Daniel R. Talham Major Department: Chemistry Initial steps of working w ith sophisticated equipment and software of single structure X-ray determination are not obvious, bu t confusing. The main idea of this work is to show to an inexperienced user an operating guideline of Bruker SMART CCD diffractometer and SHELXTL structure soluti on and refinement software package. Detailed description of all ope rations is provided, as well as examples of step by step structure refinements of various structures.

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1 CHAPTER 1 INTRODUCTION Modern chemistry uses many different me thods to characterize structures of organic and inorganic compounds. These tec hniques can yield information about bonds and their nature in case of IR spectrometry; presence of specific st ructural fragments can be determined with mass-spectroscopy; da ta about functional gr oups can be obtained with NMR, but only single crystal X-ray di ffraction can give a de tailed picture of a structure. This method reveals informa tion about position and types of atoms, bond distances and angles betw een them, including those of hydrogen bonding and other significant data. Knowledge of this method is important to every chemist, especially those working in synthesis of new materials. Ability to cr ystallize, to select a good crystal, to collect data on X-ray diffractometer and then to re fine the structure is vital for inorganic chemists, but because of tremendous devel opment of single crystal X-ray structure determination technique in last decades, dealing with this method’s hardware and software is neither simple nor easy.1 This work is an attempt to write a practical guide for users of Bruker diffractometer2 and SHELXTL software,3 used in the Center for X-ray Crystallography of the University of Florida. Chapter 2 is the detailed description of the process of crystal preparation and work with the Bruker di ffractometer, including SMART software.2 Chapter 3 is a very short manual of SHELX TL software package, describing only the

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2 most used commands. The other chapters ar e thorough examples of step by step structure solution and refinement of various compounds.

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3 CHAPTER 2 EXPERIMENTAL WORK AND DATA COLLECTION The purpose of this chapter is to describe the detaile d processes of selecting a crystal, operating an X-ray machine, and working with SMART and SAINT data collection and reduction programs, respectively. Equipment The Bruker SMART™/CCD system with Bruker PLATFORM™ goniometer is used in the Crystallographic X -ray Center of the Un iversity of Florida for single crystal X-ray structure determination (Figure 21). X-ray diffraction experiments were performed on this equipment. The Bruker SMART™/CCD system includes: 1. CCD camera (area detector) 2. Camera Electronics Unit (CEU) 3. Frame Buffer computer 4. CCD cooling system with associated cold probe 5. X-ray generator and a sealed tube X-ray source 6. X-ray tube cooling system 7. Video camera, used for optical alignment of crystals. The X-ray tube is made of molybdenum. A graphite monochromating crystal is used to isolate X-rays with the wavelengt h of 0.71073. Resolution of the CCD detector is 512 pixels*512 pixels. The distance between the detector and center of the sphere of reflections, center of crystal, is variable and has a range of 30-200 mm. A personal computer with Windows operation system is us ed as a Frame Buffer. SMART is a data collection program used to opera te the system and to collect and analyze crystallographic data. Leika Stereo Zoom 7 microscope with standard polarizer was used in this work.

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4 Figure 2-1. Scheme of the Siemens SMAR T™/CCD system with 3–circle Siemens PLATFORM™ goniometer.2 Selection and Preparation of Crystal for X-ray Analysis The first step in X-ray single crystal stru cture determination is selecting a single crystal. Readers should be familiar with proper crystallization methods.1 A few requirements for a suitable crystal are the following: it must be single; it must be without visible defects; it must be of appropriate size-de pends on X-ray beam parameters. A selected single crystal, in theory, could be twinned and its structure could be determined but the process is complex. Twi nned crystals can be identified by using a microscope with a polarizer. It is reco mmended to use a microscope with large magnification and equipped with polarizer for the best result. Selection of suitable crystals starts with observation of a vial or dish, in which crystals were grown, under a microscope. At this point a student should judge the quality

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5 of crystals and types of crys tals present, according to their shapes and colors. Each crystal form should be studied as a separate project. Next step is to select one good single crystal and transfer it into a drop of oil placed on a microscopy glass slide. When the crystal is in a drop of oil, one can clean it and take a closer look to confirm that it is single. There are few signs that show a selected crystal is not single. First, the crysta l is not clearly transparent, coul d indicate that it is a stock of plates or needles. In this case only one solu tion is acceptable, choose another crystal. A second sign is that one or few small crystals are built into large one. This problem could be fixed by cutting the crystal. The third sign is a presence of hardly visible defects like fine lines in the body of a crystal, unusual geom etry of edges, etc. The solution in this case is also cutting. When a good single crysta l is selected, its size should not exceed dimensions of 0.5mm*0.5mm*0.5mm (size of the X-ray beam) if so it needs to be cut to appropriate size. Special procedures are required for work w ith air sensitive crystals. Those include working in glove box and preventing contact of crystals with ai r by putting an extra amount of grease or oil on them. Promptness is very important in work with air sensitive crystals. The next step is to mount the chosen cr ystal on a glass fiber tip of a goniometer head. The optimal orientation of a crystal on this tip can be reached by mounting the crystal with the larges t face along the fiber direction. Fixa tion of the crystal on the fiber tip could be made in two ways: by using epoxy and by using oil in cas e of collecting data at low temperatures.

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6 Figure 2-2. The preferred orientation of a cr ystal on a glass fiber tip of a goniometer head. Examination of the System before Data Collection Checking of the Cooling System It is essential to verify that the cooling system is working properly before mounting the goniometer head and starting data collecti on. Inspection of the nitrogen tank is the first step. A user must be sure that the am ount of nitrogen is sufficient to complete data collection if a low temperature data collection is the goal. The next step is to check the low temperature (LT) control unit to be sure th at liquid nitrogen is flowing (Figure 2-3). Temperature of -100 C is usually kept on the Siemens machine at the CXC. LT control panel should display “-100” if all parts of cooling system are working properly (1 on Figure 2-3). It’s possible that flow of liquid nitrogen has been turned off. The turned off “Power” green button on LT control unit (2 on Figur e 2-3) shows that. In this case a user should turn this button on. “LN2 Start Fil ling” red button (3 on Figure 2-3) operates the filling of a small reservoir with liquid nitrog en from the big tank. Three lamps: green, yellow and red in “Dewar/Cooler” part of LT control unit (4 on Figure 2-3) shows the level of liquid nitrogen in this reservoir: fu ll, half and empty. After checking the cooling system the goniometer head with mounted crystal may be installed on the goniometer.

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7 The goniometer head should be installed promp tly in order to avoid appearance of ice on the glass fiber. If the crystal is moun ted on the goniometer, the cooling system is checked, and then a user can proceed to th e next step, checking the goniometer. These operations require work with the SMART software, which is a powerful tool of collecting, analyzing and solv ing crystallographic data.2 Figure 2-3. The low temperature control unit. 1) Cold probe displa y, 2) “Power” button, 3) “Liquid nitrogen start filling” butt on, 4) Level of nitrogen control display. Checking of the Goniometer It is very important to be sure that the goniometer is working properly. Users can examine it by driving all axes to zero and verify ing that all the axes are indeed at zero. To do that run “GONIOMETER / Zero” in the SM ART program. If a user has doubts about preciseness of the determination of the zero positions at this point he/she can “home” axes by running “GONIOMETER / Home axis.” The values must be 2 = 29.18, = 30.77, = -157.83. In the case when the marks on axis are too far from home detectors user can use command “GONIOMETER / Manual” and drive axis “home” manually. It is highly recommended to start “GONIOM ETER / Home axis” again after using “Manual” command. Successful completion of these operations ensures that the goniometer works properly. It is important to mention a rare situation when the goniometer does not respond to commands fr om SMART program. Reloading of the

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8 goniometer interface must be completed in this case. A user can do it by turning off and after 5 minutes pause turning back on th e “Power” green button of the GGCS block. Checking of the X-ray Generator X-ray generator control panel shows the voltage and current used for the X-ray generation. The standard parameters are 50 kV and 40 mA for the Siemens system in the CXC. If the X-ray generator control panel displays values of parameters, which differ from the standard ones, they must be adjust ed to the standard (maximum power). This can be done by using “MODE,” “ ,” “ ” and “EDIT” buttons on the X-ray generator control panel. Also, these parameters can be modified in the SMART program by changing values of “GONIOMETER / Generator.” In general, maximum power is recommended, but sometimes it is project dependent. As soon as a user becomes sure that the system is working properly he/she ca n start optical alignment of the crystal and take single frame diffraction frames. Optical Alignment Quality of the data and quality of the structure determination depends on the alignment of a crystal. It must be at the ex act center of the X-ray beam and must stay in this center in spite of any rotation of the goniometer head. To align the crystal, run “GONIOMETER/Optical” in the SMART and st art the video capturing program, Bruker Advanced X-ray Solution VIDEO for 2000/NT, this depicts single shots and streaming video from the video camera installed on the goniometer. This vi deo capturing program has different grid patterns, wh ich are very helpful for precise alignment of crystals. The video camera is preinstalled so that it is focu sed on the point, which is the center of the X-ray beam. The goal of optical alignment is to adjust a crystal so that its center (geometrical center) falls in the cent er of the grid pattern, Figure 2-4.

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9 Figure 2-4. The image of the aligned crystal in VIDEO program frame. Single Frame Diffraction Before alignment of the crystal, it is useful to run single frame diffraction with command “ACQUIRE / Still.” It requires that a crystal be placed roughly in the center of the beam, in other words be visible in th e frame of the VIDEO program. The single frame yields a picture of di ffraction, which reveals the qual ity of crystals. A single crystal of good quality must produce a diffr action pattern series of bright, not overlapping, perfectly rounded s pots. A user can make a c onclusion about singularity of chosen crystal and its quality at this stage. In case of bad diffraction or absence of diffraction a new crystal should be tried. If a diffraction pict ure is acceptable, the user can proceed to precise optical alignment. Precise Optical Alignment A user can start alignment by pushing the “ ” and then the “AXIS PRINT” buttons on the manual box, Figure 2-5. This command will drive the and axes to the base position for optical alignment.4 The alignment of a crystal includes the following operations:

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10 1. According to streaming video, at the VIDE O program frame, adjust the sleds on the goniometer head to center the cr ystal in the cross lines – th e center of a grid pattern. 2. Push the “AXIS PRINT” button again to drive 180 degrees from its current position. If the cross lines ar e not centered on the crystal, move half the error using the goniometer head screw. Adjust only the screw that moves the pin with the crystal perpendicular to the axis of the video camera. 3. Repeat 2 until the crystal is centered in the cross lines for both positions of 4. Press “ ” button on the manual control box and the “AXIS PRINT.” The spindle will drive 90 degrees from the previous position. 5. Adjust the crystal in the same way as described in 1-3 for After the optical alignment of the crystal is completed, cell parameters of the crystal can be determined. Figure 2-5. The scheme of the goni ometer manual control box. Determination of Cell Parame ters (Orientation Matrix) The next step in single crystal structur e determination is to determine the cell parameters of the crystal. At this time, the user can set a project name – “Crystal Name,” “Title;” define a directory “Working director y” and “Data Directory” for this project; describe color and geometry of the crystal in fields “Crystal Color” and “Crystal Morphology” in “CRYSTAL / Edit Project.” Then a dark frame should be defined in “DETECTOR / Load dark” menu. It means to pr ovide the name of a file with recorded dark frames (background reading by the CCD de tector). These files differ in time of

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11 collecting the dark frame. A file with 10 s. dark frame is usually used at this stage. After editing the project and loading the dark fram e, the data collection of a matrix can be started. A user must close the safety wi ndows of the diffractometer, push “Reset” button on the control panel of the machine and start “ACQUIRE / Matrix” in SMART. After this short data collection, SMART au tomatically tries to obtain a solution of cell parameters from this data. A solution includes many parameters and the most important of them are Bravai s lattice type, and a, b, c, , SMART may show more than one possible solutions. In this ca se a user can choose one or let SMART do it automatically, but a user should be aware that if angles are not exact 90 but very close (e.g. 89.9 ) SMART may select a lower symmetry Br avais lattice type. At this point, decision about which solution to follow should be made. If a user decides to choose another solution than the one picked by SMART, he/she should run “CRYSTAL / Reduction Cell” and on the final stage choos e desired solution. The least-square refinement of the solution “CRYSTAL / LS ” deletes unsuitable peaks from the array and derives final number of peaks used for cel l parameters and an orientation matrix determination. This number of peaks is usuall y entered after the name of the project in the line “Title” of “CRYSTAL / Edit Project” for record keeping. Measuring of Faces In order to load face measuring routin e, run “CRYSTAL / Faces.” Also the VIDEO program should be started. There are two ways to measure faces which can be applied separately or simultane ously. The first one is based on driving to specific h k l faces and, if found on the crystal, measuring the faces.

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12 Description of the First Method 1. In “CRYSTAL / Faces” mode push “Ctr l + F.” In a new window “GONIOMETER Options” enter h k l indexes, usua lly low ones, and then push “OK.” 2. The goniometer rotates the crys tal so that the face corr esponding to the entered h k l indexes become parallel to the direction of video cam era and it is seen edge on. 3. Load the face measurement ruler pushing “F 12.” Measure size of the face in units of the ruler of VIDEO program. To c onvert these units to millimeters multiply them on 0.019. This coefficient based on magnification of the video camera. 4. Return to SMART window and push “E nter.” A new window “GONIOMETER Options” appears with two parameters, whic h can be changed. The first parameter is “Eyepiece Angle” – do not change in th is method of faces measurement. The second one – “Distance” is the distance of the face from the crystal center. A user should remember that the real size of th e face is a half of the measured crystal width and the real size should be entere d in the second line of the window. Press “OK” – the face is measured. 5. Press “Home” – a new window “Crystal Face s” with indexes of already measured faces and their sizes appears. The opposite face of the measured one with the same size should be entered here. For example if in step 4 face 1 0 1 was measured with width 0.05 mm, then enter -1 0 -1 and the same width 0.05mm. 6. Repeat 1-5 so that at least six faces were measured. The second method of measuring faces is to estimate “Eyepiece Angle” – the angle of rotation of the ruler on VIDEO program fram e, and then accept or refuse h k l indexes of faces derived by SMART. Description of the Second Method 1. Use the goniometer manual control box Figure 2-5 to rotate crystal so that a plane of a face of the crystal is seen edge on. 2. Switch to VIDEO program window and with command “F12” load the face measurement ruler. Push “Ctrl + Z,” in a new window “Options” in part “Reticule / Tilt” enter a tilt angle of th e ruler – the “Eyepiece Angle,” so that the ruler is perpendicular to an edge of this face. Measure the width of the face – “Distance” in units of the ruler. How to convert it to millimeters is described in the first method steps 3-5. Remember the “Eyepiece Angle” of the ruler. 3. Return to SMART window, push “AXIS PRINT” button on the manual control box. This command updates the angles of the goniometer position in the SMART

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13 window. Push “Enter” and in the wi ndow “Goniometer Options” enter the “Eyepiece Angle” and the width of the face – “Distance.” Then push “OK.” 4. SMART shows the calculated h k l indexes corresponding to this face. Sometime calculated indexes are not integers, so a us er should decide to accept these indexes and start to measure a new face, or to refuse proposed by SMART h k l indexes and repeat steps 1-4. The best way is to veri fy these indexes. To do this – proceed steps 1–5 from the first method using h k l indexes derived by SMART. If the indexes picked by SMART are correct the same face should be visible in VIDEO window. 5. Same as step 5 in the first method 6. Repeat 1–5 so that at leas t six faces were measured. When at least 6 faces were measured, th e frame model of the crystal appears in SMART window. Shape and proportions should be the same as those of the real crystal. After measuring faces, a user should enter th e sizes of the crystal in “CRYSTAL / Edit Project” window in fields “Maximum Dimension,” “Intermediate Dimension,” “Minimum Dimension.” The next step is a full data collection. Full Data Collection For collection of full data, a user should decide the exposure time to record every frame and the corresponding dark frame file in “DETECTOR / Load Dark.” Depending on quality and size of a crys tal this time may vary, usually from 20 to 50 seconds. The next step is to select mode of data collection. There are two: “ACQUIRE / Hemisphere” and “ACQUIRE / Multirun” (full s phere). If a crystal is high symmetry or good quality, “Hemisphere” mode should be appl ied, in other cases “Multirun” regime is more helpful. The difference between these tw o modes is in number of collected frames and angles of the goniometer, at which the frames are collected (Table 2-2). The last fifty frames in each mode are used to control possible low temperature alterations of a crystal, and collected at the same position of the goniometer as the first

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14 fifty frames. The time of recording every frame in field “Time” must be the same as defined in “DETECTOR / Load Dark” menu. These two modes can be edited in “ACQUIRE / Edit Hemisphere” or “ACQUIRE / Edit Multirun,” respectively. At this point a user can start data collection running “ACQUIRE / Hemisphere” or “ACQUIRE / Multirun.” Table 2-1. Parameters of the “Hemisphere” and “Multirun” modes. Mode Run Frame 2-Theta Omega Phi Chi Axis Width # Frames Time 1 001 -28.00 -28.00 0.00 54.70 2 -0.300 626 2 001 -28.00 -28.00 90.00 54.70 2 -0.300 455 3 001 -28.00 -28.00 180.00 54.70 2 -0.300 250 Hemispher4 001 -28.00 -28.00 0.00 54.70 2 -0.300 50 1 001 -28.00 -28.00 0.00 54.70 2 -0.300 600 2 001 -28.00 -28.00 120.00 54.70 2 -0.300 600 3 001 -28.00 -28.00 240.00 54.70 2 -0.300 600 Multirun 4 001 -28.00 -28.00 0.00 54.70 2 -0.300 50 SAINT After the first frame of diffraction data is recorded, a user can start program SAINT. Purpose of this program is to gath er data from each single frame, to integrate this data and extract the intensity data from the frames.5 1. To start a new project ru n “PROJECT / New.” In a new window “Open a new Project” define a directory where SMAR T records *.p4p files of the running data collection. Pick “name1.p4p” and push “OK.” 2. Initialize the process of integration of da ta by clicking “INITIALIZE.” This allows SAINT to read all of the crystal parameters from th e “namet.p4p” file (such as, crystal system, cell dimensions, orientation matrix etc.). 3. Push “EXECUTE” and conti nue to work in a new window “Basic SAINT menu for analyzing small molecule area detector frames.” Push button “INCREMENT LAST RUN” three times – it increases number of runs up to four. It must be the same number of runs as in setting of “Hemisphere” or “Multirun” mode, depending

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15 on which one is running. Also the number of frames in every run in this window must be the same as in running mode of full data collection (Table 2-2). 4. Define waiting time of frame files – “Maxim um wait for frame file (seconds).” It must not be less than time of collecting a single frame. Period of 111 seconds is used in the CXC. 5. In the field “Resolution limit for output” select “2 ” option and make it 56 deg. 6. Push “INTEGRATE+SORT+GLOBAL” button. The main outcome of running of program SAINT, which is used in following structure solution and refinement, is two files, namet.p4p and namet.raw located in “Work” subdirectory of defi ned before in SMART “CRYSTAL / Edit Project” working directory. These files are the re sult of whole experimental wo rk and are the start point of structure calculation and refinement in software package SHELXTL.

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16 CHAPTER 3 STRUCTURE REFINEMENT WITH SHELXTL SOFTWARE PACKAGE Introduction SHELXTL is the most widely used set of programs for crystal structure solution and refinement of small molecules. The following is a brief roadmap of using this package of programs. It is intended to be a qui ck reference for a crystal structure project. The complete manual of SHELXTL3 is large and very detailed. In this work, only programs and commands frequently used for structure solution and refinement are described. SHELXTL consists of the following programs: 1. XPREP – the main functions of this program are automatic space group determination, merging of datase ts and absorption corrections. 2. XS – the program for structure solu tion by Direct or Patterson methods. 3. XL – the least–squares structure refinement. 4. XP – the interactive graphic program, whic h allows visualization of the crystal structure and editing it. 5. XCIF – the program for CIF tables prepar ation after structure determination and refinement are completed. 6. XSHELL – a program intended for use by the less experienced users for the determination and refinement of crystal structures. The step by step process of crystal stru cture determination and refinement is depicted on Figure 3-1. The first step – work with SMART and SAINT programs as described in Chapter 2. The result of this work is the raw data file namet.raw and the parameter file namet.p4p. Step 3 is the star t point of working with SHELXTL. Before

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17 starting XPREP, a user should define a project in “PROJECT / New” by picking namet.raw or namet.p4p files and enteri ng “NAMET” as a title of the project. XPREP Introduction XPREP is the first step in structure solu tion. It is used to determine space groups, symmetry classes, to define unit-cell conten ts, to set up SHELXTL files and many others (step3 on Figure 3-1). XPREP is an interactiv e program that shows all possible solutions, proposes the optimal one and waits for user’s choice. In most cases, XPREP suggests correct options, which must always be checked by the user. Figure 3-1. Scheme of crystal st ructure solution with SHELXTL.

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18 Step by Step Description of Interactive Work with XPREP 1. Push “XPREP.” The first action is to determine the lattice type. Possible solutions are P A B C I F Obv Rev. The correct so lution should have “Lattice exceptions” parameters N(total), N(int/3sigma), Mean intensity and Mean (int/sigma) equal to zero or very low value. A user may accept the program’s solution or select a different one and then push “Enter.” The main menu of XPREP appears after determination of lattice type. It contains the following functions: [D] Read, modify or merge DATASETS [P] Contour PATTERSON section [H] Search for HIGHER metric symmetry [S] Determine or input SPACE GROUP [A] Absorption, powder, SIR, SAD, MAD etc. [M] Test for MEROHEDRAL TWINNING [L] Reset LATTICE type of original cell [C] Define unit-cell CONTENTS [F] Set up SHELXTL FILES [R] RECIPROCAL space displays [U] UNIT-CELL transformations [T] Change TOLERANCES [O] Self-rotation function [Q] QUIT program A user can choose a function which to st art or can follow XPREP default options (recommended). 2. In the main menu follow default opti on “[H] – Search for HIGHER metric symmetry.” Push “Enter” and XPREP show s all possible solutions and picks one of them. A user should pay attention to “R (sym)” parameter – for correct solution it must be the smallest. Select option and push “Enter” – XPREP returns to the main menu. 3. In the main menu follow default opti on “[S] – Determine or input SPACE GROUP” and push “Enter.” In new s ubmenu choose “[I] – INPUT known space group,” if space group is known or follow de fault option “[S] – Determine SPACE GROUP” and push “Enter.” New submenu with Bravais lattice types appears. It’s recommended to accept solution determined by the program. Push “Enter” and program returns to the main menu. 4. In the main, menu follow default opti on “[D] – Read, modify or merge DATASETS.” In this submenu always pick default options until returning to the main menu. 5. In main menu follow default option “[C] – Define unit-cell CONTENTS.” In a new submenu a user can choose “[F] – ne w formula” to enter exact formula of

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19 compound in unit cell or choose “[E] – EXIT to main menu” and leave to the main menu without making any alterations. Usually the exact formula of unit-cell contents is unknown until final stages of solution and refinement of crystal structure because synthesis might go unexp ected ways and the amount of solvent molecules in the unit cell is unpredictable. So usually users choose option “[E] – Exit to main menu.” 6. In main menu follow default option “[ F] – Set up SHELXTL FILES.” Enter a name of files – the name of current proj ect, but without “t” – “NAME.” Answer “[Y] – yes” on question “Do you wish to (over)write the intensity data file name.hkl?” 7. In main menu follow defau lt option [Q] – QUIT program. At this stage work with XPREP is completed and SHELXTL files are created. Because the title of new files name.ins and name.hkl (step 5 on Figure 3-1) is different from one of namet.p4p and namet.raw (step 2 on Figure 3-1) a new project “NAME” instead of “NAMET” should be started as described before. XS XS is a program for structure solution fr om X-ray diffraction data. It uses files name.ins and name.hkl (the result of running XPREP) to create structure solution file name.res which contains crystal data and atom list, as well as listing file name.lst (steps 4-6 on Figure 3-1). Before running program XS a user should decide what method of structure solution to use: Direct Methods or Patterson method and enter proper command in name.ins file as it shown in Table 3-1. If Direct Methods are se lected, a user should watch the parameter “Fourier and peak sear ch RE” during running XS. “RE” should be less than 0.250 if correct solu tion was obtained by running XPREP. In case of high value of “RE” parameter a user should check se lected options in XPREP or try Patterson method of structure solution. The next step of work is XP program (step 7 on Figure 31).

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20 Table 3-1. Sample name.ins file before running XS. TITL name in R-3 CELL 0.71073 33.8651 33.8651 28.2246 90.000 90.000 120.000 ZERR 15.00 0.0017 0.0017 0.0020 0.000 0.000 0.000 LATT 3 SYMM -Y, X-Y, Z SYMM -X+Y, -X, Z SFAC C H O S NI SB UNIT 240 1590 720 120 25.05 60 TEMP -100 TREF < for direct methods > PATT < for Patterson method > HKLF 4 END XP XP is the program with which users work most of the time of crystal structure determination (step 7 on Figure 3-1). XP is a very powerful program, which has a lot of functions.3 Only the most useful are described in this chapter. After XP is started, a new window with black screen and highlighted co mmand line appears. XP is an interactive program, which is operated with commands, entered on the command line. To create a connectivity table (s tart a session) enter command fmol It activates the project and shows a list of atoms in the asymmetric unit. XS can recognize automatically only heavy atoms, like dmetals, so at the first run of XP a user may see in the list of atoms heavy metals and a lot of “q” peaks of electron density not assigned to any atom type. The main idea of work with XP is to assign these peaks of electron density to specific atom types. Ma ny q electron density peaks are not real. They are “noise”. These “noise” peaks should be eliminated from the structure. Atoms and q peaks can be deleted with command kill < name/s of atom/s >

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21 For example “kill q1” – to delete only q1 pea k, “kill $c” – to delete all carbon atoms. A user can use command pick < name/s of atom/s> to select atoms, delete them or change their names. Alterations of names of atoms is also possible with command name < name of atom before > < name of atom after> Command proj allows users to see wire model of the studied structure. A user can check the number of bonds of atoms, as well as bond lengths a nd angles between them, using command bang < name/s of atom/s > This is key information for analyzing q peaks. Commands undo < name of atom 1 > < name of atom 2 > undo < type of atoms 1 > < type of atoms 2 > delete bonds or bond between atoms or t ypes of atoms respectively. Examples: undo c14 o22 undo $mn $n Commands link < name of atom 1 > < name of atom 2 > link < type of atoms 1 > < type of atoms 2 > create bond or bonds between atoms or types of atoms respectively. Current work can be saved in XP (step 12 in Figure 3-1) with command save < name of file > If a step of refinement is completed a user can save the results and create name.ins file (step 8 in Figure 3-1) with command

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22 file < name of file > After running XL (step 9 in Figure 3-1) and starting XP again a user can check whether electron density peaks are correctly assigned to atom types. Command info info < name/s of atom/s > shows many parameters of atoms (Table 3-2) the most important of which are x, y, z coordinates, occupation parameter and para meter “Ueq” – the thermal parameter or average displacement, which characterizes c onformity of assigned electron density to measured one. Table 3-2. Example of a string of an atom’s parameters. Name type X Y Z occupation Ueq. C1 1 0.35060 0.66220 0.26130 11.00000 0.05000 Command uniq < name/s of atom/s> is used for temporary selection of a se parated part of a structure. Command grow extends the structure if it has a symmetry elem ent, which splits molecule in two or more identical parts. Command hadd hadd attaches hydrogen atoms to other – target –atoms according to hybridization. Command telp creates name.plt file, which is used for ge nerating graphic file name.hgl with command draw

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23 More specific features and commands of progr am XP will be discussed in Chapters 4-8 upon consideration of certain problems of structure solution and refinement. XL As mentioned before, XL is a least-square s optimization program. It reads file name.ins created in XP and writes results of calculation into name.res file (step 9 on Figure 3-1). The full cycle of refinement c onsists of working with two programs – XP and XL. It is shown on Figure 3-1 as the cycle with steps 6-9. During running XL, a user should monitor the following parameters: R1 = (||F o | |F c ||) / |F o | wR2 = [ w(F o 2 F c 2 ) 2 ] / w F o 2 2 ]] 1/2 GooF = S = [ w(F o 2 F c 2 ) 2 ] / (n-p)] 1/2 where, w= 1/[ 2 (F o 2 )+(m*p)2+n*p], p = [max(F o 2 ,0)+ 2* F c 2 ]/3, m & n constants, F o– observed structure factor, F c – calculated structure factor. The exponential form of the structure factor: ) ( 2j j jlz ky hx i j hkle f F Parameters wR2 and R1 should decrease with ev ery run of XL if the solution of structure is correct. XL is the last step in crystal structure refinement. Th e final outcome of work of XL is name.cif file (ste p 10 on Figure 3-1), which contai ns all information about the collected data and the structure derived from this data.

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24 Work with name.ins File in a Text Editor Refinement of a structure includes also edit ing name.ins and name.res files in a text editor. There are many commands, which should be included in name.ins for refinement with a text editor. Command anis entered in a separate string switches refinement to the mode of anisotropic treatment of thermal vibration ellipsoids. Command hadd 137 -1.5 adds hydrogen atoms to methyl carbon atoms. Command omit < h k l > eliminates a specific h k l re flection. Command “omit” also used for elimination of reflections, detected beyond 2 =55 deg. reflection sphere, from least square optimization with XL. Thus separate string omit -3 55 must be added to the name.ins file be fore the first run of XL. Commands cgls and L.S. acta define which type of least-squa res refinement to use. On th e first stages of refinement “cgls” command is more useful, and on the fina l steps “L.S.” and “act a” should be used. At the final point of structur e refinement a user must pa y attention to the weighting scheme in name.res file. A name.ins file has a string before atoms listing with command

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25 WGHT After a cycle of refinement with XL in the name.res a new string with command WGHT appears after line with “end” command. So there are “WGHT” commands in name.res files and weighting scheme is balanced, when parameters of this command before and after XL refinement are the same. It can be reached by copying “parameters “after XL” in place of “parameters before XL.” The other commands will be introduced during consideration of specific cases of structure solution in Chapters 4-8. Applying of Absorption Correction At the end of refinement, when the exact formula of unit cell is determined, unit cell content should be correcte d, and then absorption correctio n should be applied. These two operations could be completed by running XPREP. For the first one in the main menu of XPREP a user should follow de fault option “[C] – Define unit-cell CONTENTS,” then in a new submenu he/she can choose “[F] – new formula” and enter exact formula of compound in unit cell. Af ter formula correction XPREP calculates new Z parameter (number of molecule s in unit cell). This numbe r must be equal to Z from International Crystallographic Tables6 for the space group of th is crystal structure. For absorption correction a user should choose option “[A] Absorption, powder, SIR, SAD, MAD etc.” in the main menu of XPREP, and then in a new submenu follow option “[F] – FACE-indexed absorption correct ion.” In a new submenu a user should follow options selected by the program until returning to the main menu. As a result of running XPREP, new name.i ns and name.hkl files would be created. New name.ins file with corre cted unit cell contents does not contain information about atoms – there is no atom listing. A user can repeat whole proce ss of refinement of

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26 structure or all information about each alre ady refined atom could be copied from unmodified name.res file. Parameters R 1, wR2, GooF improve (become smaller) after correction of the unit-cell formula and appl ying absorption correc tion, what leads to better refinement of a crystal structure. XCIF The main purpose of program XCIF (step 11 in Figure 3-1) is to create the tables, which is not a part of structure solution, but it is very important for organization of the results. Before running XCIF, name.cif file has to be edited in a text editor. The correct version of parameters, needed to be edited, is saved in a locally cr eated modify.cif file (Table 3-2) on every computer of the CXC. Table 3-3. Sample of modify.cif file. _cell_measurement_reflns_used _cell_measurement_theta_min 2.0 _cell_measurement_theta_max 28.0 _exptl_absorpt_correction_type integration to analytical _exptl_absorpt_process_details 'based on measured indexed crys tal faces, SHELXTL (Bruker 1998)' OR _exptl_absorpt_process_details 'multiscan (SADABS, Blessing 1995)' _diffrn_ambient_temperature 173(2) _diffrn_radiation_wavelength 0.71073 _diffrn_radiation_type MoK\a _diffrn_radiation_source 'normal-focus sealed tube' _diffrn_radiation_monochromator graphite _diffrn_measurement_device_type 'SMART CCD area detector' _diffrn_measurement_method '\w scans' _diffrn_detector_area_ resol_mean ? _diffrn_standards_number 0 _diffrn_standards_interval_count ? _diffrn_standards_interval_time ?

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27 _diffrn_standards_decay_% none _reflns_threshold_expression 'I>2\s(I)' _computing_data_collection 'Bruker SMART (Bruker 1998)' _computing_cell_refinement 'Bruker SMART & SAINT (Bruker 1998)' _computing_data_reduction 'Bruker SHELXTL (Bruker 2000)' _computing_structure_solution 'Bruker SHELXTL' _computing_structure_refinem ent 'Bruker SHELXTL' _computing_molecular_graphics 'Bruker SHELXTL' _computing_publication_material 'Bruker SHELXTL' After file name.cif is modified according to modify.cif, a user can run XCIF. In new window the main menu contains following options: 1. [S] Change structure code 2. [X] Print from SHELXTL XTEXT format file 3. [R] Use another CIF file to resolve ? items 4. [C] Set compound name for tables (currently 'name') 5. [N] Set next table number (currently 1) 6. [D] Set default directory for format files 7. [T] Crystal/atom tables from .cif 8. [F] Structure factor tables from .fcf 9. [Q] Quit. A user should go only through commands “[ C] Set compound name for tables,” “[T] Crystal/atom tables from .cif” and “[F] Structure factor tables from .fcf.” The result of work of XCIF is two file s name.rtf and name.sft, which need to be formatted in Microsoft Word by running locally created m acros “tbl” and “sft,” respectively. These macros are stored on every computer of the CXC. The structure refinement is completed. The result of the whole pr ocess is table files name.tbl.doc and name.sft.doc. Graphic files name.hgl should be inserted in Microsoft Word as pictures and it should be save d as name.drw.doc. The work is done.

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28 CHAPTER 4 SOLUTION AND REFINEMENT OF A STRU CTURE WITH A LARGE DISORDER This chapter focuses on structure refinement of a structure with a large portion of disorder over two positions. Experimental Section Crystals of structure “el06” were provid ed by the Wagener group. A scheme of the expected structure was given in the submission form, Figure 4-1. Figure 4-1. Scheme of the expected structur e provided by the Wagener group (generated by ACD/Structure Drawing Applet). Few pale yellow prism-like shaped crystals were selected for the analysis. Using our polarizing microscope, it wa s established that the crys tals are not twinned. One crystal with size 0.37*0.19*0.14 mm3 was selected and mounted on the glass fiber of the goniometer head. The crystal was aligned as described in Chapter 2 and an orientation matrix was determined using 10 sec/frame e xposure time, because the crystal diffracted well. The results of collecting the matrix after least-squares refinement are shown in Table 4-1.

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29 Table 4-1. Results of an orientat ion matrix collection of el 06. Orientation Matrix: -0.01094318 0.01455290 0.04128984 0.07639965 0.02656884 0.00842880 -0.03031138 0.06173897 -0.01331213 Lattice parameters & Standard deviations: 12.2226 14.5411 22.9325 90.058 99.354 89.983 4021.59 0.0021 0.0019 0.0052 0.015 0.011 0.013 1.16 Standard deviations corrected for GOF: 0.0017 0.0015 0.0041 0.012 0.009 0.010 0.92 Histograms: .00 .05 .10 .15 .20 .25 .30 .35 .40 .45 +Inf H 137 0 0 0 0 0 0 0 0 0 K 137 0 0 0 0 0 0 0 0 0 L 137 0 0 0 0 0 0 0 0 0 Omega 126 11 0 0 0 0 0 0 0 0 The conclusions from the result s in Table 4-1 are following: 1. The crystal is single and of good quality, be cause of all zeros in “Histograms.” 2. The number of peaks (137) confirms good diffraction of the crystal. 3. The crystal’s lattice is Monoclinic, but SM ART recognizes it as Triclinic, because =90.058, not exactly 90 deg. 4. Cell parameters are: a=12.2226 =90.058 b=14.5411 =99.354 c=22.9325 =89.983 A hemisphere of data was collected. The ma in results of full data collection were two files el06t.p4p and el06t.raw. Structure Solution and Refinement A new project “el06t” was created in SHELXTL and XPREP was started. In all steps of running XPREP, default options we re selected. XPREP determined Monoclinic crystal system and P21/c space group, because reflections 0 k 0 (k = odd) and h 0 l (l = odd) were unobserved. The results of runni ng XPREP were el06.ins and el06.hkl files.

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30 A new project “el06” was created and program XS was applied to el06.ins file, using Direct Methods. The RE parameter was 0.275, whic h is slightly higher than expected for this good quality crystal. The solution revealed the Ru and four P positions in addition to a set of q electron density peaks, as shown in Figure 4-2. At first look, a user can deduce that, according to the structure provided in the submission form, all P atoms were not correctly assigned. P2 and P3 should be chlorines and the rest of phosphorous atoms are “noise,” but strong peaks of electron density. From Figure 4-2 it is easy to see phenyl rings in the lower part of the structure (q peaks of the rings are la beled on the figure) and two “arms” connected to the Ru atom. All obvious “noise” q peaks were deleted with command “kill.” It is easy to determine “noise” q peaks in the lower part of the structure, because the real structure is clearly determined. After al l obvious “noise” q peaks were deleted the structure looked more understandable, Figure 43. According to the structure description from the submission form (Figure 4-1) it was known that in Figure 4-3: 1. Q3 and Q4 should be nitrogen atoms 2. P2 and P3 should be chlorine atoms. 3. There should be one iso-pentane ligand connected to Ru atom, but there are probably two in the figure. It could be a disorder. 4. Initially all disordered atoms should be eliminated. They should be found after the main part is determined. 5. Q1 more likely should be a phosphorous atom – P1. 6. Because of the suspected disorder of the upper part of the structure, Q6 could be electron density peak of the disordered position of P1. 7. The rest of the q peaks are carbon atoms. 8. Three cyclopentane ligands should be coordi nated to P1 atom. One of these three ligands is recognizable in the se quence of q peaks Q30-Q54-Q28-Q45.

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31 Atoms were relabeled according to the a bove mentioned observations, Figure 4-4. Figure 4-2. View of the structure at the start point of the refinement. Figure 4-3. View of the structure af ter deleting all “noise” q peaks.

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32 Figure 4-4. View of the structure after labeli ng electron density peak s. Color notation: black for C; dark blue for N; purple for P; light blue for Ru and H; light green for Cl. The color scheme is used for all figures in this chapter. After the atoms were labeled and sorte d, a new file el06.ins was written with command “file,” Table 4-2. This file was edited (added or changed commands highlighted in bold) in a text editor and then run with XL. After running XL, the solution with tw enty q peaks was obtained, Figure 4-5. Because of isotropic treatment of the atoms, the four q peaks – Q2, Q6, Q17, and Q20 are obviously “noise,” because they are a result of motion of the chlorine atoms. These four electron density peaks should be removed. Th e peaks Q4 and Q7 are also the result of anisotropy of Ru and should be deleted. Q5 is a part of the cy clopentane C50 –C54 and should be labeled as C54. One more cyclopentan e is recognizable alread y at this stage in the sequence of peaks C40-Q10-Q3-Q8-Q12. These atoms are labeled as C40-C41-C42C43-C44. Using command “info,” high th ermal vibration parameter of C24 was observed and thus deleted, because a more appropriate iso-pentane ligand shape had

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33 sequence of atoms C23-Q9-Q14-Q16 and C25. The other q peaks were deleted as “noise” and the atoms were labeled as shown on Figure 4-6. The atoms were sorted, filed and the structure was refined with XL. Table 4-2. File el06.ins TITL el06 in P2(1)/c CELL 0.71073 12.2221 14.5343 22.9264 90.000 99.364 90.000 ZERR 4.00 0.0007 0.0009 0.0014 0.000 0.001 0.000 LATT 1 SYMM -X, 0.5+Y, 0.5-Z SFAC C H N P CL RU UNIT 200 250 10 5 10 5 TEMP -100 omit -3 55 cgls 4 BOND FMAP 2 PLAN 20 FVAR 1.00000 RU1 6 0.26280 0.55940 0.29070 11.00000 0.05000 P1 4 0.13140 0.43830 0.28980 11.00000 0.05000 CL1 5 0.11000 0.66080 0.26670 11.00000 0.05000 CL2 5 0.41810 0.45590 0.31320 11.00000 0.05000 N2 3 0.36790 0.68080 0.20790 11.00000 0.05000 N5 3 0.40300 0.73470 0.29530 11.00000 0.05000 C1 1 0.35060 0.66220 0.26130 11.00000 0.05000 C3 1 0.43410 0.76530 0.19990 11.00000 0.05000 C4 1 0.45330 0.80360 0.26150 11.00000 0.05000 C5 1 0.42610 0.74260 0.35900 11.00000 0.05000 C6 1 0.51940 0.70140 0.39050 11.00000 0.05000 C7 1 0.54530 0.71430 0.45010 11.00000 0.05000 C8 1 0.47880 0.76540 0.48430 11.00000 0.05000 C9 1 0.38460 0.80490 0.44800 11.00000 0.05000 C10 1 0.36120 0.79660 0.38800 11.00000 0.05000 C11 1 0.59700 0.64620 0.35830 11.00000 0.05000 C12 1 0.50730 0.77130 0.55110 11.00000 0.05000 C13 1 0.25820 0.84860 0.35390 11.00000 0.05000 C14 1 0.34390 0.62310 0.15460 11.00000 0.05000 C14 1 0.25030 0.63840 0.11780 11.00000 0.05000 C15 1 0.23280 0.57990 0.06760 11.00000 0.05000 C16 1 0.31680 0.50320 0.06010 11.00000 0.05000

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34 C17 1 0.40780 0.50470 0.10150 11.00000 0.05000 C18 1 0.42950 0.55880 0.14790 11.00000 0.05000 C19 1 0.17360 0.71890 0.12120 11.00000 0.05000 C20 1 0.32160 0.45630 0.00150 11.00000 0.05000 C21 1 0.53450 0.55620 0.19350 11.00000 0.05000 C22 1 0.26760 0.58510 0.37120 11.00000 0.05000 C23 1 0.17460 0.61580 0.42360 11.00000 0.05000 C24 1 0.20100 0.64850 0.48960 11.00000 0.05000 C30 1 -0.03370 0.43460 0.28750 11.00000 0.05000 C50 1 0.10060 0.38040 0.21330 11.00000 0.05000 C51 1 0.20570 0.32570 0.20010 11.00000 0.05000 C52 1 0.16780 0.32930 0.12900 11.00000 0.05000 C53 1 0.05210 0.39370 0.11410 11.00000 0.05000 C40 1 0.19740 0.33190 0.34270 11.00000 0.05000 HKLF 4 END Figure 4-5. View of the structure after the fi rst run of XL. Twenty new electron density peaks were obtained.

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35 Figure 4-6. View of the structure during the second run of refinement in XP. After one more run of XL, the structure is shown in Figure 4-7. On this figure one more, in addition to two already existing, cyclopenta ne rings Q5-Q7-Q9-Q8-Q19 appeared. C30 should be deleted as a wrongly determined carbon atom (it has a high value of thermal parameter). Strong Q1 elect ron density peak is the second position of P1 disordered atom. Peaks Q10-Q13-Q15-Q 17 form the iso-pentane ligand, which is the second position of original C23-C24-C25-C26 and C27 iso-pentane ligand. It is easer to work with separate disordered parts during di fferent runs of refinement, so at this run only disorder of the iso-pent ane ligand was considered. Results of eliminating and relabeling of atoms are shown in Figure 4-8. The list of atoms wa s sorted and filed.

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36 Figure 4-7. View of the structure after the s econd run of XL – new electron density peaks were determined. Figure 4-8. View of the structur e after eliminating “noise” q peaks after the third run of XP.

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37 In case of disorder, command part can be used. Each part requires a “disorder” parameter – site occ upation factor in the string with FVAR command. This parameter shows th e distribution of electron dens ity of disordered atoms. Initial value of this parameter, entered by user, must be in the range of 0 to 1, usually it is 0.5. The occupation factor of disordered atoms should be changed from 11.00000 to X1.0 for original atom and –X1.0 for its count er part in the disorder, where X is the number of “disorder” para meter in the FVAR string. It is helpful to consider an example w ith a hypothetical diso rdered atom At01. Disorder means that the atom At01 can be found in two (in rare cases three and more) positions. It is possible because during crys tallization same atoms of a structure can occupy different positions. So there is At01’ electron density peak, which is the counter part of disorder of At01. In the listing of atoms, peak At 01 should be in “part 1,” At01’ in “part 2,” and the rest of the structure s hould be in “part 0.” The disorder parameter (initial value 0.5) should be entered in “FVAR” command string. The occupation parameter should be altered from 11.0000 to 21.0000 for At01, and from 11.0000 to -21.0000 for At01’. Details of setting of “parts” for EL06 st ructure are shown in Table 4-3. File el06.ins was edited, saved and the structure wa s refined with XL one more time. The results of the refinement and editing in XP of the structure are shown in Figures 4-9 and Figure 4-10. At this time, refinement was focused on the disorder of phosphorous and its

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38 cyclopentanes, so P1’ and C50’ atoms were f ound and set up as members of “part 2.” All atoms with labels containing primes were grouped in “part 2” and their disorder counterparts in “part 1.“ The whole picture of disorder was recognized as a result of two fold rotation around the Ru atom, with al l coordinated to it li gands, around C1-Ru1 bond with fixed 1,3-di(2,4,6-tri methyl)phenylimidazolidine. Table 4-3. Setting of the “part” command in the el06.ins file. File el06.ins before edition. File el06.i ns after edition and setting parts. TITL el06 in P2(1)/c CELL 0.71073 12.2221 14.5343 22.9264 90.000 99.364 90.000 ZERR 4.00 0.0007 0.0009 0.0014 0.000 0.001 0.000 LATT 1 SYMM -X, 0.5+Y, 0.5-Z SFAC C H N P CL RU UNIT 200 250 10 5 10 5 TEMP -100 omit -3 55 cgls 4 BOND FMAP 2 PLAN 20 WGHT 0.100000 FVAR 0.19969 RU1 6 0.26240 0.55911 0.29028 11.00000 0.03755 ……………………………………………………………. C22 1 0.52790 0.54853 0.18645 11.00000 0.07966 C23 1 0.26488 0.59514 0.36971 11.00000 0.15289 C24 1 0.32532 0.55821 0.41939 11.00000 0.14908 C25 1 0.27831 0.59499 0.47961 11.00000 0.19196 C26 1 0.36007 0.54663 0.51576 11.00000 0.21120 C27 1 0.21168 0.64094 0.49176 11.00000 0.15958 C23' 1 0.24040 0.48290 0.22160 11.00000 0.05000 C24' 1 0.14770 0.48740 0.17570 11.00000 0.05000 C25' 1 0.12260 0.42210 0.13350 11.00000 0.05000 C26' 1 0.01350 0.43680 0.08630 11.00000 0.05000 C30 1 0.00210 0.44730 0.32400 11.00000 0.05000 ……………………………………………………………. C54 1 0.07648 0.44929 0.16259 11.00000 0.14476 HKLF 4 END TITL el06 in P2(1)/c CELL 0.71073 12.2221 14.5343 22.9264 90.000 99.364 90.000 ZERR 4.00 0.0007 0.0009 0.0014 0.000 0.001 0.000 LATT 1 SYMM -X, 0.5+Y, 0.5-Z SFAC C H N P CL RU UNIT 200 250 10 5 10 5 TEMP -100 omit -3 55 cgls 4 BOND FMAP 2 PLAN 20 WGHT 0.100000 FVAR 0.19969 0.5 RU1 6 0.26240 0.55911 0.29028 11.00000 0.03755 ……………………………………………………………. C22 1 0.52790 0.54853 0.18645 11.00000 0.07966 part 1 C23 1 0.26488 0.59514 0.36971 21.00000 0.15289 C24 1 0.32532 0.55821 0.41939 21.00000 0.14908 C25 1 0.27831 0.59499 0.47961 21.00000 0.19196 C26 1 0.36007 0.54663 0.51576 21.00000 0.21120 C27 1 0.21168 0.64094 0.49176 21.00000 0.15958 part 2 C23' 1 0.24040 0.48290 0.22160 -21.00000 0.05000 C24' 1 0.14770 0.48740 0.17570 -21.00000 0.05000 C25' 1 0.12260 0.42210 0.13350 -21.00000 0.05000 C26' 1 0.01350 0.43680 0.08630 -21.00000 0.05000 part 0 C30 1 0.00210 0.44730 0.32400 11.00000 0.05000 ……………………………………………………………. C54 1 0.07648 0.44929 0.16259 11.00000 0.14476 HKLF 4 END

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39 Figure 4-9. View of the struct ure after refinement with XL New twenty electron density peaks were obtained. Figure 4-10. View of the struct ure after eliminatio n of “noise” q peaks and assigning real electron density to specific atom types.

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40 The next steps of refinement included: 1. changing of isotropic refinement to anisotropic refinement 2. determination the exact cell unit contents 3. applying absorption correction 4. finding or adding hydrogen atoms 5. refining the weighting scheme 6. more detailed consideration of the di sordered part and resolution of atoms All of these procedures, excep t the last one, are described in the Chapter 3. The rest of process of refinement of this st ructure was focused on disordered cyclopentane ligands. The main difficulty was to find and identify these ligands, because the disorder parameter was 0.38167. It means that the disordered part in 62% of the time is located in one position and the rest at the other one, which causes problems locating atoms in the second position. In order to resolve disorder ed parts, all cyclope ntane ligands were treated in isotropical mode. The cyclope ntane ligands C40-C44 and C30-C34 did not keep their shapes during refinement with XL compared to ligand C50-C54. In order to keep these ligands at constant geometrical shape, command same C50 > C54 was used and was placed in file el06.ins be fore lines of the atoms of the C30-C34 and C40-C44 cyclopentanes. Also four h k l peak s (0 4 0, 0 1 1, 0 4 4, 1 0 4) demonstrated the largest disagreement between Fc2 and F o2 (from el06.lst file) were omitted with command “omit.” This improved the refinement parameters wR2, R1 and GooF. At the final stage, carbon atoms were relabeled in order to keep number consequence without skips. The final result of the refinement is depicted in Figures 4-11 and 4-12. The scheme of the solved structure is shown on Fi gure 4-13. The CIF file for this structure is presented in Appendix A.

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41 Figure 4-11. View of the stru cture including disorder. Ther mal ellipsoids of disordered part are treated in isotropic mode. Figure 4-12. View of the structure without the minor part of the disorder. Thermal ellipsoids of disordered part are treated in isotropic mode.

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42 C N H2C CH2N C C Ru Cl Cl H C C H C H3C H3C P CH C H2CH2CH2H2C CH CH2CH2H2C H2C CH CH2H2C H2C C H2C H C C HC C C CH C H C C CH3CH3H3C CH3H3C H3C Figure 4-13. Scheme of the structure constr ucted according to the final result of the structure solution and refinement.

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43 CHAPTER 5 MULTIMETAL CLUSTER STRUCTURE SOLUTION Large clusters with many metal centers are typical projects for single crystal X-ray structure determination, but solution of this stru cture is not trivial. In this Chapter a Mn12 cluster’s structure solution is described. Experimental Section Brown crystals were provided by the Christou group. A scheme of the ligands (used for the synthesis of these crystals, as well as Mn(II) ) was gi ven in the submission form, Figure 5-1. One crystal with dimensions 0.20*0.12*0.05 mm3 was selected for the structure determination. The crystal was trea ted according to procedures described in Chapter 2. The results of collection of orie ntation matrix with 10 sec/frame dark frame file are presented in Table 5-1. H2C C HO CH2OH CH2OH H2C OH CH C HOO Figure 5-1. Scheme of the ligands used for the synthesis of the cluster

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44 Table 5-1. Results of orientati on matrix collection for xm 54. Orientation Matrix: 0.02926206 0.04185782 0.01827227 0.03962067 -0.01966710 -0.00947578 -0.01726891 0.02561772 -0.03705560 Lattice parameters & Standard deviations : 20.5462 18.9147 25.2994 90.027 111.174 90.053 9168.18 0.0094 0.0128 0.0127 0.053 0.054 0.041 7.47 Standard deviations corrected for GOF: 0.0073 0.0100 0.0099 0.041 0.042 0.032 5.80 Histograms: .00 .05 .10 .15 .20 .25 .30 .35 .40 .45 +Inf H 40 0 0 0 0 0 0 0 0 0 K 40 0 0 0 0 0 0 0 0 0 L 40 0 0 0 0 0 0 0 0 0 Omega 35 5 0 0 0 0 0 0 0 0 From Table 5-1 next conclu sions could be derived: 1. The selected crystal is single and of good quality, because of all zeros in “Histograms” section. 2. Number of peaks (40) reveals good diffraction of the crystal. 3. The crystal’s lattice is Monoclinic. 4. Cell parameters are: a=20.5462 =90.027 b=18.9147 =111.174 c=25.2994 =90.053 Full sphere mode was used for full data collection. The result of experimental work was two files xm54t.p4p and xm54t.raw. Structure Solution and Refinement A new project was defined and XPREP wa s started. All options selected by XPREP were accepted, except determination of crystal system, which the program recognized as Triclinic, because of the small value of R parameter for this lattice type (R=0 for Triclinic; R=0.125 for Monoclinic). The Monoclinic crystal system was

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45 selected and space group P21/c was determined, because reflections 0 k 0 (k = odd) and h 0 l (l = odd) were unobserved. Direct Methods were used for structure so lution in program XS. The value of RE parameter was 0.204, which indicated that solu tion and refinement could be completed without problems. View of the structure at the first time of running XP is presented in Figure 5-2. Manganese atoms were located by the program. Phenyl rings of biphenyl acetate ligands were easy to recognize in this figure (labeled q electron density peaks). Command “grow” was applied resulting in th e doubling of the structure (Figure 5-3) showing the complete cluster. Command “f use” can be used to eliminate all duplicate atoms and electron density peaks. Figure 5-2. View of the struct ure as a result of structur e solution, completed by program XS. Color notation: black for C; dark bl ue for Mn and N; light blue for H; red for O. The color scheme is used for all figures in this chapter.

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46 Figure 5-3. View of the w hole cluster at the firs t step of refinement. The “noise” electron density peaks were lo cated and deleted, according to the rules from Chapter 3. The result of the “cleaning” is shown in Figure 54. During the process of eliminating the “noise” q electron density peaks commands “grow” and “fuse” were used many times, in order to determine as ma ny “noise” q peaks as possible, according to octahedral coordination of all manganese atoms. The view of the w hole cluster at this stage is presented in Figure 5-5.

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47 Figure 5-4. View of the asymmetric unit afte r elimination of “noise” q electron density peaks. The next step was to assign atom types to the q electron density peaks, according to the schemes of ligands provided in the submi ssion form. There were only Mn, O, C, and H atoms in this cluster (hydrogen atoms were not in focus at this stage). The result of labeling of q peaks is shown in Figure 5-6 ( only labels of Mn and O atoms are shown for clear view). The structure of the cluster after the labeling is presented in Figure 5-7. The list of atoms was sorted and xm54.ins file was sa ved. This file was edited in a text editor (commands “omit -3 55” and “cgls” were adde d) as described in Chapter 3 and Chapter 4. This file was run with XL for the first time. During the leastsquires refinement wR2 parameter dropped from 0.37 to 0.33 during 5 cycl es, which was a sign that the structure refinement was on the right track.

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48 Figure 5-5. View of the cluste r after elimination of “nois e” q electron density peaks. The result of the first run of XL is presented in Figure 5-8. Many Q peaks were recognized as carbon atoms, which were elemen ts of the phenyl rings, Figure 5-9. Using command “info,” it was determined that all atom s of the cluster were successfully located (except hydrogen atoms). Low values of the q peaks confirmed that. Thus all attention was focused on the q peaks, which were not elements of the cluster, but solvent molecules. At the next step the structure re finement focused on three groups of q peaks: Q14-Q7-Q6, Q16-Q5-Q3, Q10-Q4-Q2. Command “bang” was used to get information about bonds and angles in these groups, Table 5-2.

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49 Table 5-2. Information revealed with “bang” command. Q4 Q2 1.114 Q4 Q10 1.460 174.3 Q2 Q5 Q3 1.088 Q5 Q16 1.480 179.3 Q3 Q7 Q6 1.111 Q7 Q14 1.524 169.0 Q6 Figure 5-6. View of the asymmetric unit with labeled electron density peaks.

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50 Figure 5-7. View of the cluste r with electron density peak s assigned to specific atom types as result of th e first run of XP. Figure 5-8. View of the asymme tric unit after the first run of XL. Twenty new electron density peaks were obtained.

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51 Figure 5-9. View of the asymmetric unit and three identical groups of q peaks. According to the values of the bond lengt h and the angles from Table 5-2 these groups of q electron density peaks are three ace tonitrile molecules with Q2, Q3, Q6 being nitrogen atoms. Information provided in th e submission form confirms this conclusion. These groups of q peaks were labeled as acet onitriles and the struct ure was refined with XL. As indicated, parameters of XL refi nement – all atoms (except hydrogen atoms) were determined correctly at that step. Following stages of refinement included: 1. finding and adding hydrogen atoms 2. changing of isotropic refinement to anisotropic refinement 3. determining the exact unit cell contents 4. applying absorption correction 5. balancing of the weighting scheme.

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52 All of these procedures are described in Chapter 3 and should not cause any problems in finishing the solution. Finally in asymmetric unit besides a half of cluster, 3 acetonitrile molecules were found, which resulted, according to the space group P21/c and Z=4, in twelve acetonitrile molecu les and two clusters in a unit cell. One of the acetonitrile molecules was disordered. Program Platon7 for Windows Taskbar v1.07 was used to eliminate the disordered solvent molecule. Command “SQUEEZE” was applied to calculate the tota l number of electrons in voids (volume where acetonitrile were eliminated). The result of r unning program Platon were new files name.ins and name.hkp, which were renamed to xm54.ins and xm54.hkl, respectively. File xm54.ins should be run through XL refinement one more time. The main idea of applying program Platon is to find out the ex act formula, according to electron count, of the disordered part and remove its contribu tion to the intensity da ta: consequently, to improve the structural parameters. The final view of the cluster (without so lvent molecules) as result of structure solution is presented in Figure 5-10. The Mn-O core of this cluster is presented in Figure 5-11. The CIF file for this structure is presented in Appendix B.

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53 Figure 5-10. View of the cluste r at the end of refinement. Figure 5-11. View of the Mn-O core of the cluster at the end of refinement.

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54 CHAPTER 6 SOLUTION OF A CRYSTAL STRUCTURE WITH PSEUDO SYMMETRY This chapter focuses on solution of a struct ure with pseudo symmetry. This type of symmetry can appear when a very heavy atom, su ch as tungsten in this project, exists in a structure. The intensity data of such a crys tal is usually dominated by scattering from the heavy metal. XS treats a heavy atom as sphe re and this action resu lts in appearance of additional pseudo symmetry, e.g. fold of rotation or mirror planes. A user should recognize and eliminate pseudo symmetry part of a structure during structure refinement. Experimental Section Red needles like crystals were provide d by the McElwee-White group. A scheme of the expected structure was drawn in the submission form, Figure 6-1. Figure 6-1. Scheme of the expected struct ure provided by the McElwee-White group (generated by ACD/Structure Drawing Applet). A crystal with dimensions 0.18*0.09*0.06 mm3 was selected and mounted on the goniometer head. The crystal was aligned and an orientation matrix was collected. The results of determining of the matr ix are presented in Table 6-1.

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55 Table 6-1. Results of orientati on matrix collection for cw 10. Orientation Matrix: 0.02881307 -0.05321006 -0.03430764 -0.01663550 -0.03776496 0.05264987 -0.10185793 -0.00892692 -0.01838870 Lattice parameters & Standard deviations : 9.3324 15.1843 15.2727 90.018 90.071 90.035 2164.23 0.0017 0.0025 0.0027 0.018 0.016 0.018 0.67 Standard deviations corrected for GOF: 0.0017 0.0026 0.0028 0.019 0.016 0.018 0.68 Histograms: .00 .05 .10 .15 .20 .25 .30 .35 .40 .45 +Inf H 97 0 0 0 0 0 0 0 0 0 K 97 0 0 0 0 0 0 0 0 0 L 97 0 0 0 0 0 0 0 0 0 Omega 85 10 1 1 0 0 0 0 0 0 Some conclusions can be derived from Table 6-1: 1. The selected crystal is single and of good quality, because of all zeros in “Histograms” section. 2. Number of peaks (97) reveals good diffraction of the crystal. 3. The crystal’s lattice is Orthorhombic. 4. Cell parameters are: a=9.3324 =90.018 b=15.1843 =90.071 c=15.2727 =90.035 After measuring the crystal’s faces, a he misphere data collection was completed. Structure Solution and Refinement All default options intended by XPRE P were correct and were used for determination of crystallographic parameters According to systematic absences of certain h k l reflections, space group Pna21 was established by XPREP. Direct Methods was used for structure solution in XS. It yielded RE=0.189, which wa s relatively low. The outcome of the first run of XP is s hown in Figure 6-2. The program recognized heavy atoms W1, Cl2, and Cl3, but it seems th at Cl2 and Cl3 were wrongly determined,

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56 according to the scheme of expected structure. In Figure 6-2, it is impossible to see any structure motif, because the majority of q electron density peaks forms a sphere surrounding W1. All q peaks, Cl2 and Cl3 we re deleted, and only W1 remained in the atom list, which was saved as cw10.ins file Regular corrections were completed, as described in Chapters 3-5. Figure 6-2. View of the struct ure at the first run of XP. After the first run of XL, the structur e presented in Figure 6-3 was obtained. Except for Q11, all peaks seem to have a mirror plane symmetry. This is pseudo symmetry. The real structure is only a half. Peaks from the right side of the structure depicted in Figure 6-3 were se lected and all q peaks from the left side were deleted. According to bond length, angles and the scheme of expected structure from the

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57 submission form, two conclusion were made : q electron density peaks Q2, Q6 were assigned as chlorines; Q9, Q18, Q16, Q15 peaks form a part of the ligand, coordinated to W1 with two nitrogen atoms (F igure 6-4 A). These peaks we re saved and the rest of q peaks was deleted. Saved q peaks were labele d as shown in Figure 6-4 B. The atoms were sorted and filed as cw10.ins file. Figure 6-3. Pseudo symmetry of the structure. A B Figure 6-4. View of the structure. A) part of the structure as q p eaks, B) part of the structure after labeling.

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58 Figure 6-5. View of the structure after the seco nd run of XL refinement. Color notation: black for C; dark blue for N; light blue for H; light green for Cl and W. The color scheme is used for all figures in this chapter. After running XL, a structure presented in Figure 6-5 was obtained. No ghost peaks from pseudo symmetry were observed, but more elements of the ligands appeared. During refinement, usually, more attention is pa id to q peaks with lower numbers, but in this case some of these peaks were eliminat ed. For example Q4, because it was not clear what kind of atom it could be. At the same time q peaks Q6, Q9, Q11 were saved, because it was obvious that they formed the isopropyl part of the ligand. The structure with all saved q peaks is presented in Figur e 6-6. The q peaks of this structure were labeled as shown in Figure 6-7. The atom lis t was sorted and filed. XL was run again and a structure, depicted on Figure 6-8 was obtained.

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59 Figure 6-6. View of the structure af ter eliminating “noise” q peaks. Figure 6-7. View of the structure w ith labeled electron density peaks.

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60 Figure 6-8. View of the structure with elem ents of pseudo symmetry after refinement with XL. New twenty q electr on density peaks were obtained. As it can be seen from Figure 6-8, pse udo symmetry of the structure appeared again. It is obvious that cyclohexane Q9 -Q7-Q13-Q14-Q10-Q12 is a mirror image of real cyclohexane Q2-Q3-Q5-Q6-Q8-Q4. The q peaks of the latter were saved and all other q peaks were deleted. The saved q peak s were labeled as shown in Figure 6-9. The list of atoms was sorted, saved, and run with XL. After this run of least-squares refinement all atoms except hydrogens were found, thus command “anis” was added to cw10.ins file, in order to switch refinement of thermal ellipsoids into anisotropic mode. After one more run of XL a structure, depi cted in Figure 6-10, was obtained. At this point, the important part of st ructure solution and refinement was finished. To prove it, all q peaks, except the most intense one Q1 were eliminated, Figure 6-11. Position of

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61 this Q1 peaks is not a position of a real atom. It is a “ noise” peak attributed to the anisotropy of the heavy W1 atom. The rest of refinement was regular and included: 1. finding and adding hydrogen atoms 2. changing of isotropic refinement to anisotropic refinement 3. determining of exact cell unit contents 4. applying absorption correction 5. balancing of the weighting scheme All these procedures are described in Chap ter 3, as well as in Chapters 4 and 5, and should not cause any problems in finishing th e solution. The final result of structure solution and refinement for this project is pres ented in Figure 6-12. The CIF file for this structure is presented in Appendix C. Figure 6-9. View of the structure after deleti ng “noise” q peaks and relabeling of electron density peaks.

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62 Figure 6-10. View of the structure after one more cycle of refinement. Twenty new electron density peaks q peaks were obtained. Figure 6-11. View of the structure afte r deleting “noise” q peaks and relabeling

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63 Figure 6-12. Final result of the structure solution and refinement.

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64 CHAPTER 7 PATTERSON METHOD OF STRUCTURE SOLUTION There are many cases in singl e crystal structure determin ation when Direct Method fails. Thus alternative met hod of structure solution – Patt erson Method – can be used. Knowledge of this method is important and help ful. This Chapter is focused on Patterson the Method of solution of the structure CW10, which was also solved and refined with Direct Methods in Chapter 6. Experimental Section All experimental procedures described in th e previous chapter, as well as work with program XPREP. Structure Refinement The result of running XPREP, file cw10.ins was edited; command “TREF” was substituted with command “PATT” in orde r to initiate Patterson method of structure solution. Modified cw10.ins f ile was run with XS. The results of running of XS are presented in Table 7-1. Table 7-1. Parameters of structure solution with XS. Patterson and peaksearch Patt. Sup. on vector 1 0.0325 0.5000 0.5000 Height 425. Length 8.92 PATFOM=99.9 Corr. Coeff.=90.2 SYMFOM=99.9 for 9 heavy atoms. During structure solution with Patters on Method XS established only the heavy atom positions. In case of this compound it was expected that XS could find out tungsten atom and may be chlorine atoms. Figure 7-1 proves this forecast. The very heavy atom W1 caused formation of pseudo symmetry, which is described in Chapter 6.

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65 Refinement of a structure (which starts with running XP at the fi rst time) in case of Patterson Method is exactly the same, as with Direct Methods of st ructure solution. All steps of refinement of CW10 structure are described in Chapter 6 and only figures and short descriptions of steps are presented in this Chapter. Figure 7-1. Pseudo symmetry of the structure. The result of eliminating pseudo symmetry and labeling presented in Figures 7-2 and Figures 7-3. Figure 7-2. View of the structure after eliminating pseudo symmetry

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66 Figure 7-3. View of the struct ure after relabeling atoms. Color notation: black for C; dark blue for N; light blue for H; light green for Cl and W. The color scheme is used for all figures in this chapter. Figure 7-4. View of the structur e after the first refinement w ith XL. Twenty new electron density peaks were obtained.

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67 After the first run of XL, structure, pr esented in Figure 7-4, was obtained, then “noise” q peaks were eliminated, Figure 7-5. Electron density q peaks were assigned to atoms’ types, Figure 7-6. Atoms list was sort ed and filed. The stru cture was refined with XL and the result of refinement is presented in Figure 7-7. On this figure motif of the whole molecule is recognizable. Detailed description of finalization of structure refinement and the final result of the re finement of cw10 compound is described in Chapter 6. The CIF file for this st ructure is presente d in Appendix C. Figure 7-5. View of the structur e after elimination of “noise” q peaks at the second time of running XP.

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68 Figure 7-6. View of the struct ure after relabeling q peaks. Figure 7-7. View of the structure af ter the second run of refinement.

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69 Figure 7-8. View of the structur e after elimination of “noise” q peaks (third run of XP). Figure 7-9. View of the structure after relabeling of atoms (third run of XP)

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70 CHAPTER 8 SYNTHESIS, CRYSTALLIZATION AN D STRUCTURE DETERMINATION OF AQUA-CHLORO-(1,4,8,11-TETRAAZAUNDE CANE)NICKEL(II) CHLORIDE Introduction Complexes of transition metals with long alkyl chains are widely used to build Langmuir-Blodgett monolayers with specific magnetic properties.8,9 The attempt to accomplish synthesis of nickel (II) pentaaz a macrocyclic complex with attached 1-dodecyl chain the same way as described in the paper of H.J. Choi and M.P. Suh10 was not successful. The result of this reacti on was aqua-chloro-(1,4,8,11-tetraazaundecane) nickel(II) chloride complex. Lavender prismatic crystals were collected and characterized by single-crystal Xray diffraction in the same wa y as described in previous chapters. The results of this structur e determination are published in Acta Crystallographica Section E11 and the CIF file for this compound is presented in Appendix D. Experimental Section Synthesis of aqua-chloro-(1,4,8,11-tetraa zaundecane)nickel (II) chloride was conducted according to the work of H.J. Choi and M.P. Suh10 with some modifications. To a refluxed solution of NiCl2*6H2O (1.2 g, 5 mmol) in MeOH (50 ml) were added 1,4,8,11-tetraazaundecane (0.8 g, 5 mmol). After 3 hours of refluxing the mixture, the solvent was evaporated a nd a light purple product of th e reaction was dissolved in EtOH (20ml). Slow evaporation of the solven t over five days, at room temperature,

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71 yielded light purple prismatic crystals. Structure solution and refinement was completed according to standard procedures described in Chapters 3 and 4. Structure Description In the title compound, nickel has octahe dral coordination (Figure 8-1), which results in elongation of Ni -N bonds compared to thos e in square planar 1,4,8,11tetrazaundecanenickel(II) cation:12 the average Ni-N bond in the title compound is 2.082(2) , when the average value of the Ni -N bonds in the cation is only 1.922(5) , Table 8-1. Table 8-1. Selected bond lengths ( ) for the title compound. Original data Data for square planar cation12 Ni1-N1 2.0788(14) Ni1-N2 2.0805(16) Ni1-N3 2.0825(13) Ni1-N4 2.0878(16) N1-C1 1.481(2) N2-C3 1.478(2) N2-C2 1.475(2) C1-C2 1.515(3) C3-C4 1.529(2) C4-C5 1.527(3) Ni1-N1 1.907(5) Ni1-N2 1.928(5) Ni1-N3 1.934(5) Ni1-N4 1.916(5) N1-C1 1.480(9) N2-C3 1.473(8) N2-C2 1.476(8) C1-C2 1.476(11) C3-C4 1.488(10) C4-C5 1.508(11) The protons of the coordinated water a nd the uncoordinated counterion Cl2 are involved in H-bonding with their inversion symmetry equivalents, creating a diamondshaped interaction, Table 8-2. As a result, H-bonding chains are formed along the b-axis, Figure 8-2. These chains ar e linked together by H-bonds be tween the amino protons on one hand and both, coordinate d and uncoordinated, chlorine ions, thus creating twodimensional layers in the ab-plane. Table 8-2. Selected diamond style hydroge n bonds for the title compound [ and ]. D-H...A d(D-H) d(H...A) d(D...A) <(DHA) O1-H1...Cl2 0.96 2.28 3.2359(13) 174.1 O1-H2...Cl2 #1 0.97 2.15 3.1066(14) 167.2

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72 Symmetry transformations used to genera te equivalent atoms: #1 -x,-y+1,-z Figure 8-1. View of an asymme tric unit of the title compound. Figure 8-2. View of the two dimensional laye r in the crystal structure of the title compound.

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73 APPENDIX A CIF FILE OF STRUCTURE EL06 data_el06 _audit_creation_method SHELXL-97 _chemical_name_systematic ; ? ; _chemical_name_common ? _chemical_melting_point ? _chemical_formula_moiety ? _chemical_formula_sum 'C41 H61 Cl2 N2 P Ru' _chemical_formula_weight 784.86 loop_ _atom_type_symbol _atom_type_description _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source 'C' 'C' 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'H' 'H' 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'N' 'N' 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'P' 'P' 0.1023 0.0942 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'Cl' 'Cl' 0.1484 0.1585 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'Ru' 'Ru' -1.2594 0.8363 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' _symmetry_cell_setting Monoclinic _symmetry_space_group_name_H-M P2(1)/c loop_ _symmetry_equiv_pos_as_xyz

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74 'x, y, z' '-x, y+1/2, -z+1/2' '-x, -y, -z' 'x, -y-1/2, z-1/2' _cell_length_a 12.2221(7) _cell_length_b 14.5343(9) _cell_length_c 22.9264(14) _cell_angle_alpha 90.00 _cell_angle_beta 99.3640(10) _cell_angle_gamma 90.00 _cell_volume 4018.4(4) _cell_formula_units_Z 4 _cell_measurement_temperature 173(2) _cell_measurement_reflns_used 137 _cell_measurement_theta_min 2.0 _cell_measurement_theta_max 28.0 _exptl_crystal_description needles _exptl_crystal_colour brown _exptl_crystal_size_max 0.37 _exptl_crystal_size_mid 0.19 _exptl_crystal_size_min 0.14 _exptl_crystal_density_meas 0 _exptl_crystal_density_diffrn 1.297 _exptl_crystal_density_method 'not measured' _exptl_crystal_F_000 1656 _exptl_absorpt_coefficient_mu 0.593 _exptl_absorpt_correction_t ype integration _exptl_absorpt_correction_T_min 0.8379 _exptl_absorpt_correction_T_max 0.9310 _exptl_absorpt_process_details 'based on measured indexed crys tal faces, SHELXTL (Bruker 1998)' _exptl_special_details ; ? ; _diffrn_ambient_temperature 173(2) _diffrn_radiation_wavelength 0.71073 _diffrn_radiation_type MoK\a _diffrn_radiation_source 'normal-focus sealed tube' _diffrn_radiation_monochromator graphite _diffrn_measurement_device_type 'SMART CCD area detector' _diffrn_measurement_method '\w scans'

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75 _diffrn_detector_area_ resol_mean ? _diffrn_standards_number 0 _diffrn_standards_interval_count ? _diffrn_standards_interval_time ? _diffrn_standards_decay_% none _diffrn_reflns_number 24710 _diffrn_reflns_av_R_equivalents 0.0728 _diffrn_reflns_av_sigmaI/netI 0.0977 _diffrn_reflns_limit_h_min -11 _diffrn_reflns_limit_h_max 15 _diffrn_reflns_limit_k_min -18 _diffrn_reflns_limit_k_max 18 _diffrn_reflns_limit_l_min -24 _diffrn_reflns_limit_l_max 29 _diffrn_reflns_theta_min 1.80 _diffrn_reflns_theta_max 27.50 _reflns_number_total 9077 _reflns_number_gt 5056 _reflns_threshold_expression 'I > 2\s(I)' _computing_data_collection 'Bruker SMART (Bruker 1998)' _computing_cell_refinement 'Bruker SMART & SAINT (Bruker 1998)' _computing_data_reduction 'Bruker SHELXTL (Bruker 2000)' _computing_structure_solution 'Bruker SHELXTL' _computing_structure_refinem ent 'Bruker SHELXTL' _computing_molecular_graphics 'Bruker SHELXTL' _computing_publication_material 'Bruker SHELXTL' _refine_special_details ; Refinement of F^2^ against ALL reflect ions. The weighted R-factor wR and goodness of fit S are based on F^2^, c onventional R-factors R are based on F, with F set to zero for negativ e F^2^. The threshold expression of F^2^ > 2sigma(F^2^) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflec tions for refinement. R-factors based on F^2^ are statistically about twice as large as t hose based on F, and Rfactors based on ALL data will be even larger. ; _refine_ls_structure_factor_coef Fsqd _refine_ls_matrix_type full _refine_ls_weighting_scheme calc _refine_ls_weighting_details 'calc w=1/[\s^2^(Fo^2^)+(0.0849P)^2^+0.0000P] where P=(Fo^2^+2Fc^2^)/3' _atom_sites_solution_primary direct

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76 _atom_sites_solution_secondary difmap _atom_sites_solution_hydrogens geom _refine_ls_hydrogen_treatment mixed _refine_ls_extinction_method none _refine_ls_extinction_coef ? _refine_ls_number_reflns 9077 _refine_ls_number_parameters 424 _refine_ls_number_restraints 158 _refine_ls_R_factor_all 0.1310 _refine_ls_R_factor_gt 0.0648 _refine_ls_wR_factor_ref 0.1746 _refine_ls_wR_factor_gt 0.1476 _refine_ls_goodness_of_fit_ref 1.009 _refine_ls_restrained_S_all 1.031 _refine_ls_shift/su_max 0.001 _refine_ls_shift/su_mean 0.000 loop_ _atom_site_label _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_adp_type _atom_site_occupancy _atom_site_symmetry_multiplicity _atom_site_calc_flag _atom_site_refinement_flags _atom_site_disorder_assembly _atom_site_disorder_group Ru1 Ru 0.26237(3) 0.05905(3) -0.209824(18) 0.04053(15) Uani 1 1 d . Cl1 Cl 0.41717(12) -0.04202(9) -0.18789(8) 0.0742(5) Uani 1 1 d A Cl2 Cl 0.10994(11) 0.16245(10) -0.23346(7) 0.0673(4) Uani 1 1 d A N1 N 0.4040(3) 0.2351(3) -0.20368(19) 0.0504(11) Uani 1 1 d . N2 N 0.3687(3) 0.1818(3) -0.29322(19) 0.0486(10) Uani 1 1 d . C1 C 0.3568(4) 0.1641(3) -0.2366(2) 0.0421(11) Uani 1 1 d A C2 C 0.4484(6) 0.3069(4) -0.2382(3) 0.0776(19) Uani 1 1 d A H2A H 0.5281 0.3178 -0.2236 0.093 Uiso 1 1 calc R . H2B H 0.4075 0.3655 -0.2368 0.093 Uiso 1 1 calc R . C3 C 0.4307(5) 0.2675(4) -0.3001(3) 0.0643(16) Uani 1 1 d A H3A H 0.3868 0.3099 -0.3286 0.077 Uiso 1 1 calc R . H3B H 0.5022 0.2544 -0.3134 0.077 Uiso 1 1 calc R . C4 C 0.3438(5) 0.1224(3) -0.3430(3) 0.0533(14) Uani 1 1 d A C5 C 0.2491(5) 0.1368(4) -0.3842(3) 0.0641(16) Uani 1 1 d . C6 C 0.2333(7) 0.0795(5) -0.4346(3) 0.089(2) Uani 1 1 d A

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77 H6A H 0.1686 0.0877 -0.4633 0.107 Uiso 1 1 calc R . C7 C 0.3063(10) 0.0137(6) -0.4436(4) 0.109(3) Uani 1 1 d . C8 C 0.4002(9) 0.0029(4) -0.4029(4) 0.102(3) Uani 1 1 d A H8A H 0.4515 -0.0435 -0.4096 0.122 Uiso 1 1 calc R . C9 C 0.4249(6) 0.0568(4) -0.3516(3) 0.0693(18) Uani 1 1 d . C10 C 0.5321(6) 0.0492(4) -0.3094(3) 0.086(2) Uani 1 1 d A H10A H 0.5826 0.0081 -0.3261 0.129 Uiso 1 1 calc R . H10B H 0.5178 0.0243 -0.2717 0.129 Uiso 1 1 calc R . H10C H 0.5660 0.1103 -0.3030 0.129 Uiso 1 1 calc R . C11 C 0.2890(10) -0.0454(6) -0.4990(4 ) 0.168(5) Uani 1 1 d A H11A H 0.2758 -0.1093 -0.4884 0.253 Uiso 1 1 calc R . H11B H 0.3553 -0.0425 -0.5179 0.253 Uiso 1 1 calc R . H11C H 0.2249 -0.0226 -0.5264 0.253 Uiso 1 1 calc R . C12 C 0.1671(5) 0.2108(5) -0.3761(3) 0.091(2) Uani 1 1 d A H12A H 0.1346 0.1978 -0.3406 0.137 Uiso 1 1 calc R . H12B H 0.1083 0.2123 -0.4107 0.137 Uiso 1 1 calc R . H12C H 0.2048 0.2704 -0.3718 0.137 Uiso 1 1 calc R . C13 C 0.4258(4) 0.2418(4) -0.1408(3) 0.0546(14) Uani 1 1 d A C14 C 0.3574(4) 0.2950(4) -0.1112(3) 0.0578(14) Uani 1 1 d . C15 C 0.3857(5) 0.3035(4) -0.0505(3) 0.0690(17) Uani 1 1 d A H15A H 0.3396 0.3395 -0.0299 0.083 Uiso 1 1 calc R . C16 C 0.4775(5) 0.2622(5) -0.0188(3) 0.0744(18) Uani 1 1 d . C17 C 0.5454(5) 0.2108(4) -0.0497(3) 0.0733(18) Uani 1 1 d A H17A H 0.6094 0.1816 -0.0286 0.088 Uiso 1 1 calc R . C18 C 0.5216(4) 0.2015(4) -0.1102(3) 0.0589(15) Uani 1 1 d . C19 C 0.5989(5) 0.1471(4) -0.1427(3) 0.0781(19) Uani 1 1 d A H19A H 0.6691 0.1361 -0.1162 0.117 Uiso 1 1 calc R . H19B H 0.6130 0.1820 -0.1773 0.117 Uiso 1 1 calc R . H19C H 0.5645 0.0880 -0.1555 0.117 Uiso 1 1 calc R . C20 C 0.5033(6) 0.2707(5) 0.0485(3) 0.101(2) Uani 1 1 d A H20A H 0.5484 0.3257 0.0592 0.152 Uiso 1 1 calc R . H20B H 0.5442 0.2161 0.0651 0.152 Uiso 1 1 calc R . H20C H 0.4338 0.2756 0.0645 0.152 Uiso 1 1 calc R . C21 C 0.2573(5) 0.3436(4) -0.1435(3) 0.0749(18) Uani 1 1 d A H21A H 0.2809 0.3969 -0.1645 0.112 Uiso 1 1 calc R . H21B H 0.2105 0.3641 -0.1152 0.112 Uiso 1 1 calc R . H21C H 0.2151 0.3013 -0.1721 0.112 Uiso 1 1 calc R . P1 P 0.1705(4) -0.0421(3) -0.15083(19) 0.0684( 14) Uani 0.382(3) 1 d P A 1 C22 C 0.2331(11) -0.0143(11) -0.2782(6) 0.063(4) Uiso 0.382(3) 1 d PD A 1 H22A H 0.2906 -0.0564 -0.2826 0.076 Uiso 0.382(3) 1 calc PR A 1 C23 C 0.1449(12) -0.0180(10) -0.3221(6) 0.066(4) Uiso 0.382(3) 1 d PD A 1 H23A H 0.0944 0.0321 -0.3250 0.080 Uiso 0.382(3) 1 calc PR A 1 C24 C 0.1222(14) -0.0850(11) -0.3617(8) 0.080(5) Uiso 0.382(3) 1 d PD A 1 C25 C 0.0171(12) -0.0763(11) -0.4075(7) 0.070(5) Uiso 0.382(3) 1 d PD A 1 H25A H -0.0199 -0.0180 -0.4016 0.105 Uiso 0.382(3) 1 calc PR A 1 H25B H -0.0328 -0.1276 -0.4029 0.105 Uiso 0.382(3) 1 calc PR A 1

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78 H25C H 0.0367 -0.0777 -0.4472 0.105 Uiso 0.382(3) 1 calc PR A 1 C26 C 0.1999(17) -0.1692(14) -0.3731(9) 0.083(6) Uiso 0.382(3) 1 d PD A 1 H26A H 0.2770 -0.1548 -0.3567 0.124 Uiso 0.382(3) 1 calc PR A 1 H26B H 0.1935 -0.1800 -0.4158 0.124 Uiso 0.382(3) 1 calc PR A 1 H26C H 0.1767 -0.2246 -0.3540 0.124 Uiso 0.382(3) 1 calc PR A 1 C27 C 0.0104(11) -0.0425(10) -0.1715(7) 0.060(4) Uiso 0.382(3) 1 d PD A 1 H27A H -0.0182 -0.0975 -0.1526 0.072 Uiso 0.382(3) 1 calc PR A 1 C28 C -0.0768(14) -0.0193(13) -0.2318(6) 0.084(5) Uiso 0.382(3) 1 d PD A 1 H28A H -0.0489 0.0297 -0.2556 0.100 Uiso 0.382(3) 1 calc PR A 1 H28B H -0.0959 -0.0746 -0.2566 0.100 Uiso 0.382(3) 1 calc PR A 1 C29 C -0.1736(13) 0.0134(15) -0.2028(9) 0.104( 7) Uiso 0.382(3) 1 d PD A 1 H29A H -0.2327 0.0423 -0.2316 0.125 Uiso 0.382(3) 1 calc PR A 1 H29B H -0.2053 -0.0370 -0.1818 0.125 Uiso 0.382(3) 1 calc PR A 1 C30 C -0.1180(19) 0.0764(17) -0.1646(13) 0.198(15) Uiso 0.382(3) 1 d PD A 1 H30A H -0.1638 0.0922 -0.1342 0.237 Uiso 0.382(3) 1 calc PR A 1 H30B H -0.1066 0.1333 -0.1866 0.237 Uiso 0.382(3) 1 calc PR A 1 C31 C -0.0097(12) 0.0414(10) -0.1354(6) 0.060( 4) Uiso 0.382(3) 1 d PD A 1 H31A H -0.0122 0.0243 -0.0939 0.072 Uiso 0.382(3) 1 calc PR A 1 H31B H 0.0491 0.0879 -0.1362 0.072 Uiso 0.382(3) 1 calc PR A 1 C32 C 0.1893(19) -0.1605(11) -0.1532(9) 0.070(7) Uiso 0.382(3) 1 d PD A 1 H32B H 0.2713 -0.1600 -0.1395 0.084 Uiso 0.382(3) 1 calc PR A 1 C33 C 0.162(3) -0.2426(15) -0.1103(10) 0.183( 14) Uiso 0.382(3) 1 d PD A 1 H33A H 0.2084 -0.2379 -0.0708 0.220 Uiso 0.382(3) 1 calc PR A 1 H33B H 0.0827 -0.2415 -0.1055 0.220 Uiso 0.382(3) 1 calc PR A 1 C34 C 0.1884(15) -0.3278(10) -0.1415(8) 0.080(5) Uiso 0.382(3) 1 d PD A 1 H34A H 0.2617 -0.3513 -0.1228 0.096 Uiso 0.382(3) 1 calc PR A 1 H34B H 0.1324 -0.3756 -0.1375 0.096 Uiso 0.618(3) 1 calc PR A 1 C35 C 0.190(2) -0.3116(12) -0.1992(8) 0.122( 8) Uiso 0.382(3) 1 d PD A 1 H35A H 0.1229 -0.3387 -0.2233 0.146 Uiso 0.382(3) 1 calc PR A 1 H35B H 0.2560 -0.3405 -0.2112 0.146 Uiso 0.382(3) 1 calc PR A 1 C36 C 0.1919(16) -0.2122(11) -0.2092(7) 0.089(6) Uiso 0.382(3) 1 d PD A 1 H36A H 0.1272 -0.1944 -0.2389 0.107 Uiso 0.382(3) 1 calc PR A 1 H36B H 0.2600 -0.1958 -0.2251 0.107 Uiso 0.382(3) 1 calc PR A 1 C37 C 0.212(2) -0.0092(15) -0.0740(11) 0.157( 10) Uiso 0.382(3) 1 d PD A 1 H37B H 0.2934 -0.0143 -0.0748 0.189 Uiso 0.382(3) 1 calc PR A 1 C38 C 0.210(2) 0.1040(15) -0.0759(9) 0.139(9) Uiso 0.382(3) 1 d PD A 1 H38C H 0.2705 0.1289 -0.0953 0.167 Uiso 0.382(3) 1 calc PR A 1 H38D H 0.1379 0.1276 -0.0965 0.167 Uiso 0.382(3) 1 calc PR A 1 C39 C 0.228(2) 0.1268(15) -0.0096(9) 0.097(8) Uiso 0.382(3) 1 d PD A 1 H39C H 0.2643 0.1873 -0.0011 0.116 Uiso 0.382(3) 1 calc PR A 1 H39D H 0.1575 0.1255 0.0065 0.116 Uiso 0.382(3) 1 calc PR A 1 C40 C 0.2972(19) 0.0548(16) 0.0117(10) 0.116( 8) Uiso 0.382(3) 1 d PD A 1 H40C H 0.3168 0.0564 0.0554 0.139 Uiso 0.382(3) 1 calc PR A 1 H40D H 0.3658 0.0542 -0.0061 0.139 Uiso 0.382(3) 1 calc PR A 1 C41 C 0.222(4) -0.026(2) -0.0093(13) 0.50( 5) Uiso 0.382(3) 1 d PD A 1

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79 H41C H 0.2572 -0.0861 0.0025 0.599 Uiso 0.382(3) 1 calc PR A 1 H41D H 0.1494 -0.0221 0.0046 0.599 Uiso 0.382(3) 1 calc PR A 1 P1' P 0.1333(2) -0.06759(17) -0.20942(12) 0.060 9(8) Uani 0.618(3) 1 d P A 2 C22' C 0.2660(8) 0.0868(7) -0.1314(4) 0.065(3) Uiso 0.618(3) 1 d PD A 2 H22B H 0.2135 0.1337 -0.1274 0.078 Uiso 0.618(3) 1 calc PR A 2 C23' C 0.3199(9) 0.0614(7) -0.0776(5) 0.085(3) Uiso 0.618(3) 1 d PD A 2 H23B H 0.3832 0.0233 -0.0773 0.102 Uiso 0.618(3) 1 calc PR A 2 C24' C 0.2948(12) 0.0834(10) -0.0252(7) 0.110(4) Uiso 0.618(3) 1 d PD A 2 C25' C 0.3701(13) 0.0410(11) 0.0264(6) 0.135(6) Uiso 0.618(3) 1 d PD A 2 H25D H 0.4100 -0.0110 0.0125 0.203 Uiso 0.618(3) 1 calc PR A 2 H25E H 0.3258 0.0193 0.0556 0.203 Uiso 0.618(3) 1 calc PR A 2 H25F H 0.4235 0.0872 0.0446 0.203 Uiso 0.618(3) 1 calc PR A 2 C26' C 0.1955(18) 0.1439(17) -0.0058(11) 0.197(12) Ui so 0.618(3) 1 d PD A 2 H26D H 0.2256 0.2016 0.0122 0.295 Uiso 0.618(3) 1 calc PR A 2 H26E H 0.1605 0.1092 0.0229 0.295 Uiso 0.618(3) 1 calc PR A 2 H26F H 0.1401 0.1574 -0.0407 0.295 Uiso 0.618(3) 1 calc PR A 2 C27' C -0.0205(12) -0.0592(10) -0.2032(7) 0.112(5) Uiso 0.618(3) 1 d PD A 2 H27B H -0.0252 -0.1249 -0.1909 0.134 Uiso 0.618(3) 1 calc PR A 2 C28' C -0.0029(12) -0.0205(14) -0.1350(7) 0.151(6) Uiso 0.618(3) 1 d PD A 2 H28C H 0.0116 -0.0718 -0.1064 0.181 Uiso 0.618(3) 1 calc PR A 2 H28D H 0.0599 0.0232 -0.1278 0.181 Uiso 0.618(3) 1 calc PR A 2 C29' C -0.1102(13) 0.0271(11) -0.1294(7) 0.133(5) Uiso 0.618(3) 1 d PD A 2 H29C H -0.1280 0.0211 -0.0890 0.160 Uiso 0.618(3) 1 calc PR A 2 H29D H -0.1079 0.0931 -0.1398 0.160 Uiso 0.618(3) 1 calc PR A 2 C30' C -0.1822(10) -0.0192(11) -0.1687(7) 0.120(5) Uiso 0.618(3) 1 d PD A 2 H30C H -0.2472 0.0207 -0.1818 0.143 Uiso 0.618(3) 1 calc PR A 2 H30D H -0.2084 -0.0734 -0.1488 0.143 Uiso 0.618(3) 1 calc PR A 2 C31' C -0.1383(15) -0.0505(14) -0.2209(7) 0.178(8) Uiso 0.618(3) 1 d PD A 2 H31C H -0.1713 -0.1104 -0.2346 0.214 Uiso 0.618(3) 1 calc PR A 2 H31D H -0.1553 -0.0053 -0.2534 0.214 Uiso 0.618(3) 1 calc PR A 2 C32' C 0.2095(12) -0.1715(8) -0.1633(5) 0.071(4) Uiso 0.618(3) 1 d PD A 2 H32A H 0.2866 -0.1814 -0.1714 0.086 Uiso 0.618(3) 1 calc PR A 2 C33' C 0.1356(9) -0.2616(7) -0.1736(4) 0.084(3) Uiso 0.618(3) 1 d PD A 2 H33C H 0.0557 -0.2464 -0.1832 0.101 Uiso 0.618(3) 1 calc PR A 2 H33D H 0.1570 -0.3003 -0.2055 0.101 Uiso 0.618(3) 1 calc PR A 2 C34' C 0.1627(11) -0.3075(7) -0.1149(5) 0.086(3) Uiso 0.618(3) 1 d PD A 2 H34C H 0.1063 -0.3545 -0.1101 0.104 Uiso 0.618(3) 1 calc PR A 2 H34D H 0.2363 -0.3374 -0.1105 0.104 Uiso 0.618(3) 1 calc PR A 2 C35' C 0.1626(10) -0.2356(7) -0.0725(5) 0.085(3) Uiso 0.618(3) 1 d PD A 2 H35C H 0.2110 -0.2519 -0.0350 0.102 Uiso 0.618(3) 1 calc PR A 2 H35D H 0.0866 -0.2247 -0.0643 0.102 Uiso 0.618(3) 1 calc PR A 2 C36' C 0.2063(10) -0.1508(7) -0.0997(5) 0.089(3) Uiso 0.618(3) 1 d PD A 2 H36C H 0.1571 -0.0976 -0.0963 0.107 Uiso 0.618(3) 1 calc PR A 2 H36D H 0.2815 -0.1357 -0.0788 0.107 Uiso 0.618(3) 1 calc PR A 2 C37' C 0.0987(7) -0.1192(6) -0.2835(4) 0.062(2) Uiso 0.618(3) 1 d PD A 2

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80 H37A H 0.0427 -0.1689 -0.2816 0.074 Uiso 0.618(3) 1 calc PR A 2 C38' C 0.2019(9) -0.1632(8) -0.3070(5) 0.098(4) Uiso 0.618(3) 1 d PD A 2 H38A H 0.2664 -0.1211 -0.3011 0.117 Uiso 0.618(3) 1 calc PR A 2 H38B H 0.2234 -0.2227 -0.2874 0.117 Uiso 0.618(3) 1 calc PR A 2 C39' C 0.1563(12) -0.1762(10) -0.3723(5) 0.098(5) Uiso 0.618(3) 1 d PD A 2 H39A H 0.2149 -0.1635 -0.3963 0.117 Uiso 0.618(3) 1 calc PR A 2 H39B H 0.1308 -0.2404 -0.3798 0.117 Uiso 0.618(3) 1 calc PR A 2 C40' C 0.0686(11) -0.1162(9) -0.3877(5) 0.099(4) Uiso 0.618(3) 1 d PD A 2 H40A H -0.0005 -0.1513 -0.4008 0.118 Uiso 0.618(3) 1 calc PR A 2 H40B H 0.0827 -0.0764 -0.4208 0.118 Uiso 0.618(3) 1 calc PR A 2 C41' C 0.0561(9) -0.0573(7) -0.3342(4) 0.085(3) Uiso 0.618(3) 1 d PD A 2 H41A H 0.1008 -0.0004 -0.3331 0.102 Uiso 0.618(3) 1 calc PR A 2 H41B H -0.0225 -0.0407 -0.3342 0.102 Uiso 0.618(3) 1 calc PR A 2 loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_23 _atom_site_aniso_U_13 _atom_site_aniso_U_12 Ru1 0.0413(2) 0.0373(2) 0.0432(2) -0.00019(19) 0.00733(16) -0.00204(18) Cl1 0.0656(9) 0.0490(8) 0.1162(14) 0.0245( 8) 0.0390(9) 0.0179(7) Cl2 0.0485(8) 0.0663(9) 0.0864(11) 0.0030( 8) 0.0086(7) 0.0120(7) N1 0.059(3) 0.041(2) 0.052(3) 0.006(2) 0.011(2) -0.014(2) N2 0.061(3) 0.035(2) 0.052(3) 0.001(2) 0.013(2) -0.0067(19) C1 0.039(3) 0.038(3) 0.050(3) 0.000(2) 0.009(2) 0.007(2) C2 0.103(5) 0.060(4) 0.078(5) -0.010(3) 0.038(4) -0.029(3) C3 0.085(4) 0.043(3) 0.067(4) 0.002(3) 0.018(3) -0.016(3) C4 0.068(4) 0.036(3) 0.061(4) -0.007(3) 0.026(3) -0.008(3) C5 0.073(4) 0.067(4) 0.056(4) -0.013(3) 0.022(3) -0.008(3) C6 0.112(6) 0.093(5) 0.066(5) -0.022(4) 0.020(4) -0.037(5) C7 0.172(10) 0.084(6) 0.082(6) 0.041(5) 0.056(6) -0.048(6) C8 0.175(9) 0.045(4) 0.109(7) -0.016(4) 0.091(6) -0.005(5) C9 0.108(5) 0.037(3) 0.075(4) 0.005(3) 0.050(4) 0.002(3) C10 0.098(5) 0.077(5) 0.094(5) 0.031(4) 0.048(4) 0.041(4) C11 0.296(14) 0.122(8) 0.104(7) -0. 075(6) 0.087(8) -0.074(8) C12 0.075(5) 0.129(6) 0.067(4) 0.003(4) 0.004(3) 0.015(4) C13 0.051(3) 0.050(3) 0.062(4) 0.008(3) 0.007(3) -0.013(3) C14 0.049(3) 0.061(4) 0.064(4) 0.007(3) 0.012(3) -0.004(3) C15 0.063(4) 0.078(4) 0.069(4) -0.016(3) 0.018(3) 0.003(3) C16 0.061(4) 0.099(5) 0.062(4) 0.022(4) 0.005(3) -0.001(4) C17 0.053(4) 0.091(5) 0.072(4) 0.017(4) -0.001(3) 0.007(3) C18 0.048(3) 0.064(4) 0.062(4) 0.018(3) 0.000(3) -0.003(3) C19 0.060(4) 0.086(5) 0.085(5) -0.026(4) 0.001(3) 0.008(3)

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81 C20 0.100(6) 0.139(7) 0.061(5) -0.029(5) 0.004(4) 0.003(5) C21 0.069(4) 0.070(4) 0.087(5) -0.007(4) 0.017(3) 0.009(3) P1 0.073(3) 0.074(3) 0.058(3) 0.006(2) 0.011(2) -0.032(2) P1' 0.0528(15) 0.0672(17) 0.0629(17) 0.0034(13) 0.0101(12) -0.0172(12) _geom_special_details ; All esds (except the esd in the dihe dral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. ; loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance _geom_bond_site_symmetry_2 _geom_bond_publ_flag Ru1 C22' 1.836(9) ? Ru1 C22 1.882(14) ? Ru1 C1 2.067(5) ? Ru1 Cl1 2.3835(14) ? Ru1 Cl2 2.3863(14) ? Ru1 P1 2.397(4) ? Ru1 P1' 2.425(2) ? N1 C1 1.352(6) ? N1 C13 1.426(7) ? N1 C2 1.466(6) ? N2 C1 1.353(6) ? N2 C4 1.424(6) ? N2 C3 1.481(6) ? C2 C3 1.513(8) ? C2 H2A 0.9900 ? C2 H2B 0.9900 ? C3 H3A 0.9900 ? C3 H3B 0.9900 ? C4 C5 1.384(8) ? C4 C9 1.412(7) ? C5 C6 1.413(8) ? C5 C12 1.502(8) ? C6 C7 1.347(11) ? C6 H6A 0.9500 ? C7 C8 1.365(11) ?

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82 C7 C11 1.520(10) ? C8 C9 1.406(10) ? C8 H8A 0.9500 ? C9 C10 1.500(9) ? C10 H10A 0.9800 ? C10 H10B 0.9800 ? C10 H10C 0.9800 ? C11 H11A 0.9800 ? C11 H11B 0.9800 ? C11 H11C 0.9800 ? C12 H12A 0.9800 ? C12 H12B 0.9800 ? C12 H12C 0.9800 ? C13 C14 1.393(7) ? C13 C18 1.394(7) ? C14 C15 1.384(8) ? C14 C21 1.500(8) ? C15 C16 1.372(8) ? C15 H15A 0.9500 ? C16 C17 1.392(8) ? C16 C20 1.529(8) ? C17 C18 1.376(8) ? C17 H17A 0.9500 ? C18 C19 1.517(7) ? C19 H19A 0.9800 ? C19 H19B 0.9800 ? C19 H19C 0.9800 ? C20 H20A 0.9800 ? C20 H20B 0.9800 ? C20 H20C 0.9800 ? C21 H21A 0.9800 ? C21 H21B 0.9800 ? C21 H21C 0.9800 ? P1 C32 1.739(16) ? P1 C37 1.82(2) ? P1 C27 1.938(14) ? C22 C23 1.350(15) ? C22 H22A 0.9500 ? C23 C24 1.329(17) ? C23 H23A 0.9500 ? C24 C25 1.526(18) ? C24 C26 1.60(2) ? C25 H25A 0.9800 ? C25 H25B 0.9800 ? C25 H25C 0.9800 ? C26 H26A 0.9800 ?

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83 C26 H26B 0.9800 ? C26 H26C 0.9800 ? C27 C31 1.516(15) ? C27 C28 1.638(15) ? C27 H27A 1.0000 ? C28 C29 1.523(15) ? C28 H28A 0.9900 ? C28 H28B 0.9900 ? C29 C30 1.368(15) ? C29 H29A 0.9900 ? C29 H29B 0.9900 ? C30 C31 1.474(16) ? C30 H30A 0.9900 ? C30 H30B 0.9900 ? C31 H31A 0.9900 ? C31 H31B 0.9900 ? C32 C36 1.493(16) ? C32 C33 1.616(16) ? C32 H32B 1.0000 ? C33 C34 1.492(16) ? C33 H33A 0.9900 ? C33 H33B 0.9900 ? C34 C35 1.347(15) ? C34 H34A 0.9900 ? C34 H34B 0.9900 ? C35 C36 1.464(15) ? C35 H35A 0.9900 ? C35 H35B 0.9900 ? C36 H36A 0.9900 ? C36 H36B 0.9900 ? C37 C41 1.491(18) ? C37 C38 1.645(16) ? C37 H37B 1.0000 ? C38 C39 1.538(16) ? C38 H38C 0.9900 ? C38 H38D 0.9900 ? C39 C40 1.386(16) ? C39 H39C 0.9900 ? C39 H39D 0.9900 ? C40 C41 1.524(18) ? C40 H40C 0.9900 ? C40 H40D 0.9900 ? C41 H41C 0.9900 ? C41 H41D 0.9900 ? P1' C37' 1.841(9) ? P1' C27' 1.912(13) ?

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84 P1' C32' 1.986(13) ? C22' C23' 1.352(12) ? C22' H22B 0.9500 ? C23' C24' 1.327(15) ? C23' H23B 0.9500 ? C24' C25' 1.507(17) ? C24' C26' 1.62(2) ? C25' H25D 0.9800 ? C25' H25E 0.9800 ? C25' H25F 0.9800 ? C26' H26D 0.9800 ? C26' H26E 0.9800 ? C26' H26F 0.9800 ? C27' C31' 1.437(14) ? C27' C28' 1.643(14) ? C27' H27B 1.0000 ? C28' C29' 1.505(14) ? C28' H28C 0.9900 ? C28' H28D 0.9900 ? C29' C30' 1.334(12) ? C29' H29C 0.9900 ? C29' H29D 0.9900 ? C30' C31' 1.461(15) ? C30' H30C 0.9900 ? C30' H30D 0.9900 ? C31' H31C 0.9900 ? C31' H31D 0.9900 ? C32' C36' 1.497(13) ? C32' C33' 1.586(12) ? C32' H32A 1.0000 ? C33' C34' 1.491(12) ? C33' H33C 0.9900 ? C33' H33D 0.9900 ? C34' C35' 1.426(12) ? C34' H34C 0.9900 ? C34' H34D 0.9900 ? C35' C36' 1.516(12) ? C35' H35C 0.9900 ? C35' H35D 0.9900 ? C36' H36C 0.9900 ? C36' H36D 0.9900 ? C37' C41' 1.496(11) ? C37' C38' 1.584(11) ? C37' H37A 1.0000 ? C38' C39' 1.522(13) ? C38' H38A 0.9900 ?

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85 C38' H38B 0.9900 ? C39' C40' 1.381(13) ? C39' H39A 0.9900 ? C39' H39B 0.9900 ? C40' C41' 1.524(12) ? C40' H40A 0.9900 ? C40' H40B 0.9900 ? C41' H41A 0.9900 ? C41' H41B 0.9900 ? loop_ _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_angle _geom_angle_site_symmetry_1 _geom_angle_site_symmetry_3 _geom_angle_publ_flag C22' Ru1 C22 155.7(5) . ? C22' Ru1 C1 101.7(3) . ? C22 Ru1 C1 102.2(5) . ? C22' Ru1 Cl1 92.1(3) . ? C22 Ru1 Cl1 82.1(5) . ? C1 Ru1 Cl1 93.18(13) . ? C22' Ru1 Cl2 88.7(3) . ? C22 Ru1 Cl2 97.6(5) . ? C1 Ru1 Cl2 85.43(13) . ? Cl1 Ru1 Cl2 178.50(5) . ? C22' Ru1 P1 61.4(3) . ? C22 Ru1 P1 94.6(4) . ? C1 Ru1 P1 163.01(17) . ? Cl1 Ru1 P1 86.07(12) . ? Cl2 Ru1 P1 95.42(12) . ? C22' Ru1 P1' 94.3(3) . ? C22 Ru1 P1' 62.4(4) . ? C1 Ru1 P1' 163.11(15) . ? Cl1 Ru1 P1' 91.48(7) . ? Cl2 Ru1 P1' 89.70(7) . ? P1 Ru1 P1' 33.66(12) . ? C1 N1 C13 127.6(4) . ? C1 N1 C2 113.8(4) . ? C13 N1 C2 118.2(4) . ? C1 N2 C4 127.7(4) . ? C1 N2 C3 113.5(4) . ? C4 N2 C3 118.1(4) . ? N1 C1 N2 106.8(4) . ?

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86 N1 C1 Ru1 127.3(4) . ? N2 C1 Ru1 125.3(3) . ? N1 C2 C3 103.2(4) . ? N1 C2 H2A 111.1 . ? C3 C2 H2A 111.1 . ? N1 C2 H2B 111.1 . ? C3 C2 H2B 111.1 . ? H2A C2 H2B 109.1 . ? N2 C3 C2 102.5(4) . ? N2 C3 H3A 111.3 . ? C2 C3 H3A 111.3 . ? N2 C3 H3B 111.3 . ? C2 C3 H3B 111.3 . ? H3A C3 H3B 109.2 . ? C5 C4 C9 122.4(5) . ? C5 C4 N2 120.1(5) . ? C9 C4 N2 117.2(5) . ? C4 C5 C6 117.2(6) . ? C4 C5 C12 121.7(5) . ? C6 C5 C12 121.1(7) . ? C7 C6 C5 122.5(8) . ? C7 C6 H6A 118.8 . ? C5 C6 H6A 118.8 . ? C6 C7 C8 118.8(7) . ? C6 C7 C11 121.5(11) . ? C8 C7 C11 119.5(10) . ? C7 C8 C9 123.4(8) . ? C7 C8 H8A 118.3 . ? C9 C8 H8A 118.3 . ? C8 C9 C4 115.6(7) . ? C8 C9 C10 123.0(7) . ? C4 C9 C10 121.3(6) . ? C9 C10 H10A 109.5 . ? C9 C10 H10B 109.5 . ? H10A C10 H10B 109.5 . ? C9 C10 H10C 109.5 . ? H10A C10 H10C 109.5 . ? H10B C10 H10C 109.5 . ? C7 C11 H11A 109.5 . ? C7 C11 H11B 109.5 . ? H11A C11 H11B 109.5 . ? C7 C11 H11C 109.5 . ? H11A C11 H11C 109.5 . ? H11B C11 H11C 109.5 . ? C5 C12 H12A 109.5 . ? C5 C12 H12B 109.5 . ?

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87 H12A C12 H12B 109.5 . ? C5 C12 H12C 109.5 . ? H12A C12 H12C 109.5 . ? H12B C12 H12C 109.5 . ? C14 C13 C18 120.6(5) . ? C14 C13 N1 120.2(5) . ? C18 C13 N1 118.9(5) . ? C15 C14 C13 117.9(5) . ? C15 C14 C21 120.3(5) . ? C13 C14 C21 121.7(5) . ? C16 C15 C14 122.9(6) . ? C16 C15 H15A 118.6 . ? C14 C15 H15A 118.6 . ? C15 C16 C17 117.9(6) . ? C15 C16 C20 121.1(6) . ? C17 C16 C20 121.0(6) . ? C18 C17 C16 121.3(6) . ? C18 C17 H17A 119.3 . ? C16 C17 H17A 119.3 . ? C17 C18 C13 119.2(5) . ? C17 C18 C19 120.0(5) . ? C13 C18 C19 120.7(5) . ? C18 C19 H19A 109.5 . ? C18 C19 H19B 109.5 . ? H19A C19 H19B 109.5 . ? C18 C19 H19C 109.5 . ? H19A C19 H19C 109.5 . ? H19B C19 H19C 109.5 . ? C16 C20 H20A 109.5 . ? C16 C20 H20B 109.5 . ? H20A C20 H20B 109.5 . ? C16 C20 H20C 109.5 . ? H20A C20 H20C 109.5 . ? H20B C20 H20C 109.5 . ? C14 C21 H21A 109.5 . ? C14 C21 H21B 109.5 . ? H21A C21 H21B 109.5 . ? C14 C21 H21C 109.5 . ? H21A C21 H21C 109.5 . ? H21B C21 H21C 109.5 . ? C32 P1 C37 105.9(10) . ? C32 P1 C27 97.0(9) . ? C37 P1 C27 110.5(10) . ? C32 P1 Ru1 120.9(7) . ? C37 P1 Ru1 107.6(8) . ? C27 P1 Ru1 114.3(5) . ?

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88 C23 C22 Ru1 131.6(12) . ? C23 C22 H22A 114.2 . ? Ru1 C22 H22A 114.2 . ? C24 C23 C22 126.2(15) . ? C24 C23 H23A 116.9 . ? C22 C23 H23A 116.9 . ? C23 C24 C25 117.9(14) . ? C23 C24 C26 127.6(15) . ? C25 C24 C26 114.0(14) . ? C31 C27 C28 98.9(9) . ? C31 C27 P1 96.4(10) . ? C28 C27 P1 134.4(12) . ? C31 C27 H27A 107.8 . ? C28 C27 H27A 107.8 . ? P1 C27 H27A 107.8 . ? C29 C28 C27 98.1(11) . ? C29 C28 H28A 112.1 . ? C27 C28 H28A 112.1 . ? C29 C28 H28B 112.1 . ? C27 C28 H28B 112.1 . ? H28A C28 H28B 109.8 . ? C30 C29 C28 98.5(15) . ? C30 C29 H29A 112.1 . ? C28 C29 H29A 112.1 . ? C30 C29 H29B 112.1 . ? C28 C29 H29B 112.1 . ? H29A C29 H29B 109.7 . ? C29 C30 C31 112.0(15) . ? C29 C30 H30A 109.2 . ? C31 C30 H30A 109.2 . ? C29 C30 H30B 109.2 . ? C31 C30 H30B 109.2 . ? H30A C30 H30B 107.9 . ? C30 C31 C27 104.1(11) . ? C30 C31 H31A 110.9 . ? C27 C31 H31A 110.9 . ? C30 C31 H31B 110.9 . ? C27 C31 H31B 110.9 . ? H31A C31 H31B 109.0 . ? C36 C32 C33 100.9(11) . ? C36 C32 P1 123.1(13) . ? C33 C32 P1 132.1(14) . ? C36 C32 H32B 96.5 . ? C33 C32 H32B 96.5 . ? P1 C32 H32B 96.5 . ? C34 C33 C32 103.7(12) . ?

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89 C34 C33 H33A 111.0 . ? C32 C33 H33A 111.0 . ? C34 C33 H33B 111.0 . ? C32 C33 H33B 111.0 . ? H33A C33 H33B 109.0 . ? C35 C34 C33 111.4(13) . ? C35 C34 H34A 109.3 . ? C33 C34 H34A 109.3 . ? C35 C34 H34B 109.3 . ? C33 C34 H34B 109.3 . ? H34A C34 H34B 108.0 . ? C34 C35 C36 109.3(13) . ? C34 C35 H35A 109.8 . ? C36 C35 H35A 109.8 . ? C34 C35 H35B 109.8 . ? C36 C35 H35B 109.8 . ? H35A C35 H35B 108.3 . ? C35 C36 C32 111.0(12) . ? C35 C36 H36A 109.4 . ? C32 C36 H36A 109.4 . ? C35 C36 H36B 109.4 . ? C32 C36 H36B 109.4 . ? H36A C36 H36B 108.0 . ? C41 C37 C38 101.0(14) . ? C41 C37 P1 152.5(18) . ? C38 C37 P1 103.7(15) . ? C41 C37 H37B 94.9 . ? C38 C37 H37B 94.9 . ? P1 C37 H37B 94.9 . ? C39 C38 C37 101.0(12) . ? C39 C38 H38C 111.6 . ? C37 C38 H38C 111.6 . ? C39 C38 H38D 111.6 . ? C37 C38 H38D 111.6 . ? H38C C38 H38D 109.4 . ? C40 C39 C38 99.5(15) . ? C40 C39 H39C 111.9 . ? C38 C39 H39C 111.9 . ? C40 C39 H39D 111.9 . ? C38 C39 H39D 111.9 . ? H39C C39 H39D 109.6 . ? C39 C40 C41 99.7(18) . ? C39 C40 H40C 111.8 . ? C41 C40 H40C 111.8 . ? C39 C40 H40D 111.8 . ? C41 C40 H40D 111.8 . ?

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90 H40C C40 H40D 109.6 . ? C37 C41 C40 97.6(16) . ? C37 C41 H41C 112.2 . ? C40 C41 H41C 112.2 . ? C37 C41 H41D 112.2 . ? C40 C41 H41D 112.2 . ? H41C C41 H41D 109.8 . ? C37' P1' C27' 90.8(5) . ? C37' P1' C32' 101.4(5) . ? C27' P1' C32' 113.0(6) . ? C37' P1' Ru1 111.0(3) . ? C27' P1' Ru1 126.9(5) . ? C32' P1' Ru1 109.3(4) . ? C23' C22' Ru1 139.8(9) . ? C23' C22' H22B 110.1 . ? Ru1 C22' H22B 110.1 . ? C24' C23' C22' 127.6(12) . ? C24' C23' H23B 116.2 . ? C22' C23' H23B 116.2 . ? C23' C24' C25' 114.2(12) . ? C23' C24' C26' 132.4(15) . ? C25' C24' C26' 113.3(14) . ? C24' C25' H25D 109.5 . ? C24' C25' H25E 109.5 . ? H25D C25' H25E 109.5 . ? C24' C25' H25F 109.5 . ? H25D C25' H25F 109.5 . ? H25E C25' H25F 109.5 . ? C24' C26' H26D 109.5 . ? C24' C26' H26E 109.5 . ? H26D C26' H26E 109.5 . ? C24' C26' H26F 109.5 . ? H26D C26' H26F 109.5 . ? H26E C26' H26F 109.5 . ? C31' C27' C28' 102.0(10) . ? C31' C27' P1' 159.6(13) . ? C28' C27' P1' 96.6(10) . ? C31' C27' H27B 93.6 . ? C28' C27' H27B 93.6 . ? P1' C27' H27B 93.6 . ? C29' C28' C27' 104.9(10) . ? C29' C28' H28C 110.8 . ? C27' C28' H28C 110.8 . ? C29' C28' H28D 110.8 . ? C27' C28' H28D 110.8 . ? H28C C28' H28D 108.8 . ?

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91 C30' C29' C28' 101.5(11) . ? C30' C29' H29C 111.5 . ? C28' C29' H29C 111.5 . ? C30' C29' H29D 111.5 . ? C28' C29' H29D 111.5 . ? H29C C29' H29D 109.3 . ? C29' C30' C31' 114.8(12) . ? C29' C30' H30C 108.6 . ? C31' C30' H30C 108.6 . ? C29' C30' H30D 108.6 . ? C31' C30' H30D 108.6 . ? H30C C30' H30D 107.5 . ? C27' C31' C30' 106.3(11) . ? C27' C31' H31C 110.5 . ? C30' C31' H31C 110.5 . ? C27' C31' H31D 110.5 . ? C30' C31' H31D 110.5 . ? H31C C31' H31D 108.7 . ? C36' C32' C33' 101.9(8) . ? C36' C32' P1' 106.4(9) . ? C33' C32' P1' 110.0(8) . ? C36' C32' H32A 112.6 . ? C33' C32' H32A 112.6 . ? P1' C32' H32A 112.6 . ? C34' C33' C32' 101.4(8) . ? C34' C33' H33C 111.5 . ? C32' C33' H33C 111.5 . ? C34' C33' H33D 111.5 . ? C32' C33' H33D 111.5 . ? H33C C33' H33D 109.3 . ? C35' C34' C33' 105.3(9) . ? C35' C34' H34C 110.7 . ? C33' C34' H34C 110.7 . ? C35' C34' H34D 110.7 . ? C33' C34' H34D 110.7 . ? H34C C34' H34D 108.8 . ? C34' C35' C36' 106.0(8) . ? C34' C35' H35C 110.5 . ? C36' C35' H35C 110.5 . ? C34' C35' H35D 110.5 . ? C36' C35' H35D 110.5 . ? H35C C35' H35D 108.7 . ? C32' C36' C35' 107.7(8) . ? C32' C36' H36C 110.2 . ? C35' C36' H36C 110.2 . ? C32' C36' H36D 110.2 . ?

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92 C35' C36' H36D 110.2 . ? H36C C36' H36D 108.5 . ? C41' C37' C38' 100.0(7) . ? C41' C37' P1' 118.1(7) . ? C38' C37' P1' 113.7(6) . ? C41' C37' H37A 108.2 . ? C38' C37' H37A 108.2 . ? P1' C37' H37A 108.2 . ? C39' C38' C37' 101.6(8) . ? C39' C38' H38A 111.5 . ? C37' C38' H38A 111.5 . ? C39' C38' H38B 111.5 . ? C37' C38' H38B 111.5 . ? H38A C38' H38B 109.3 . ? C40' C39' C38' 108.6(10) . ? C40' C39' H39A 110.0 . ? C38' C39' H39A 110.0 . ? C40' C39' H39B 110.0 . ? C38' C39' H39B 110.0 . ? H39A C39' H39B 108.4 . ? C39' C40' C41' 108.9(10) . ? C39' C40' H40A 109.9 . ? C41' C40' H40A 109.9 . ? C39' C40' H40B 109.9 . ? C41' C40' H40B 109.9 . ? H40A C40' H40B 108.3 . ? C37' C41' C40' 102.7(8) . ? C37' C41' H41A 111.2 . ? C40' C41' H41A 111.2 . ? C37' C41' H41B 111.2 . ? C40' C41' H41B 111.2 . ? H41A C41' H41B 109.1 . ? _diffrn_measured_fraction_theta_max 0.985 _diffrn_reflns_theta_full 27.50 _diffrn_measured_fraction_theta_full 0.985 _refine_diff_density_max 0.755 _refine_diff_density_min -0.428 _refine_diff_density_rms 0.084

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93 APPENDIX B CIF FILE OF STRUCTURE XM54 data_xm54 _audit_creation_method SHELXL-97 _chemical_name_systematic ; ? ; _chemical_name_common ? _chemical_melting_point ? _chemical_formula_moiety ? _chemical_formula_sum 'C184 H198 Mn12 N12 O42' _chemical_formula_weight 3908.82 loop_ _atom_type_symbol _atom_type_description _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source 'C' 'C' 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'H' 'H' 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'N' 'N' 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'O' 'O' 0.0106 0.0060 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'Mn' 'Mn' 0.3368 0.7283 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' _symmetry_cell_setting Monoclinic _symmetry_space_group_name_H-M P2(1)/c loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x, y+1/2, -z+1/2'

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94 '-x, -y, -z' 'x, -y-1/2, z-1/2' _cell_length_a 20.5435(15) _cell_length_b 18.8989(14) _cell_length_c 25.3111(19) _cell_angle_alpha 90.00 _cell_angle_beta 111.180(2) _cell_angle_gamma 90.00 _cell_volume 9163.2(12) _cell_formula_units_Z 2 _cell_measurement_temperature 173(2) _cell_measurement_reflns_used 40 _cell_measurement_theta_min 2.0 _cell_measurement_theta_max 28.0 _exptl_crystal_description plates _exptl_crystal_colour orange _exptl_crystal_size_max 0.20 _exptl_crystal_size_mid 0.12 _exptl_crystal_size_min 0.05 _exptl_crystal_density_meas 0 _exptl_crystal_density_diffrn 1.417 _exptl_crystal_density_method 'not measured' _exptl_crystal_F_000 4044 _exptl_absorpt_coefficient_mu 0.875 _exptl_absorpt_correction_t ype integration _exptl_absorpt_correction_T_min 0.8438 _exptl_absorpt_correction_T_max 0.9596 _exptl_absorpt_process_details 'based on measured indexed crys tal faces, SHELXTL (Bruker 1998)' _exptl_special_details ; ? ; _diffrn_ambient_temperature 173(2) _diffrn_radiation_wavelength 0.71073 _diffrn_radiation_type MoK\a _diffrn_radiation_source 'normal-focus sealed tube' _diffrn_radiation_monochromator graphite _diffrn_measurement_device_type 'SMART CCD area detector' _diffrn_measurement_method '\w scans' _diffrn_detector_area_ resol_mean ? _diffrn_standards_number 0

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95 _diffrn_standards_interval_count ? _diffrn_standards_interval_time ? _diffrn_standards_decay_% none _diffrn_reflns_number 81055 _diffrn_reflns_av_R_equivalents 0.1240 _diffrn_reflns_av_sigmaI/netI 0.1636 _diffrn_reflns_limit_h_min -26 _diffrn_reflns_limit_h_max 25 _diffrn_reflns_limit_k_min -24 _diffrn_reflns_limit_k_max 24 _diffrn_reflns_limit_l_min -32 _diffrn_reflns_limit_l_max 32 _diffrn_reflns_theta_min 1.06 _diffrn_reflns_theta_max 27.50 _reflns_number_total 20946 _reflns_number_gt 9314 _reflns_threshold_expression 'I > 2\s(I)' _computing_data_collection 'Bruker SMART (Bruker 1998)' _computing_cell_refinement 'Bruker SMART & SAINT (Bruker 1998)' _computing_data_reduction 'Bruker SHELXTL (Bruker 2000)' _computing_structure_solution 'Bruker SHELXTL' _computing_structure_refinem ent 'Bruker SHELXTL' _computing_molecular_graphics 'Bruker SHELXTL' _computing_publication_material 'Bruker SHELXTL' _refine_special_details ; Refinement of F^2^ against ALL reflect ions. The weighted R-factor wR and goodness of fit S are based on F^2^, c onventional R-factors R are based on F, with F set to zero for negativ e F^2^. The threshold expression of F^2^ > 2sigma(F^2^) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflec tions for refinement. R-factors based on F^2^ are statistically about twice as large as t hose based on F, and Rfactors based on ALL data will be even larger. ; _refine_ls_structure_factor_coef Fsqd _refine_ls_matrix_type full _refine_ls_weighting_scheme calc _refine_ls_weighting_details 'calc w=1/[\s^2^(Fo^2^)+(0.0803P)^2^] where P=(Fo^2^+2Fc^2^)/3' _atom_sites_solution_primary direct _atom_sites_solution_secondary difmap _atom_sites_solution_hydrogens geom _refine_ls_hydrogen_treatment mixed

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96 _refine_ls_extinction_method none _refine_ls_extinction_coef ? _refine_ls_number_reflns 20946 _refine_ls_number_parameters 1052 _refine_ls_number_restraints 0 _refine_ls_R_factor_all 0.1420 _refine_ls_R_factor_gt 0.0616 _refine_ls_wR_factor_ref 0.1969 _refine_ls_wR_factor_gt 0.1770 _refine_ls_goodness_of_fit_ref 1.001 _refine_ls_restrained_S_all 1.001 _refine_ls_shift/su_max 0.001 _refine_ls_shift/su_mean 0.000 loop_ _atom_site_label _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_adp_type _atom_site_occupancy _atom_site_symmetry_multiplicity _atom_site_calc_flag _atom_site_refinement_flags _atom_site_disorder_assembly _atom_site_disorder_group Mn1 Mn 1.01369(4) 0.02229(4) 0.45110(3) 0.0188(2) Uani 1 1 d . Mn2 Mn 1.03502(4) -0.13666(4) 0.48276(3) 0.0190(2) Uani 1 1 d . Mn3 Mn 0.86055(4) 0.07736(5) 0.38922(3) 0.0239(2) Uani 1 1 d . Mn4 Mn 0.80431(5) 0.18977(5) 0.45886(4) 0.0262(2) Uani 1 1 d . Mn5 Mn 1.17375(5) -0.02718(5) 0.49571(4) 0.0265(2) Uani 1 1 d . Mn6 Mn 0.87272(4) -0.12727(5) 0.41323(3) 0.0235(2) Uani 1 1 d . O1 O 0.95959(18) 0.07330(18) 0.38442(14) 0.0205(8) Uani 1 1 d . O2 O 1.04663(18) 0.13129(18) 0.49597(13) 0.0197(8) Uani 1 1 d . O3 O 1.11736(18) -0.13267(18) 0.46351(14) 0.0202(8) Uani 1 1 d . O4 O 0.97700(18) -0.08958(18) 0.41447(13) 0.0202(8) Uani 1 1 d . O5 O 1.09153(18) 0.01149(18) 0.42675(14) 0.0205(8) Uani 1 1 d . O6 O 1.06035(17) -0.02883(18) 0.52002(14) 0.0191(8) Uani 1 1 d . O7 O 0.7544(2) 0.2249(2) 0.37369(16) 0.0358(10) Uani 1 1 d . O8 O 0.7940(2) 0.1462(2) 0.32593(15) 0.0333(10) Uani 1 1 d . O10 O 0.78744(19) 0.08208(19) 0.42883(14) 0.0246(9) Uani 1 1 d . O11 O 0.7325(2) 0.1780(2) 0.49971(17) 0.0362(11) Uani 1 1 d . O12 O 0.8502(2) 0.2903(2) 0.49661(18) 0.0367(11) Uani 1 1 d . H12A H 0.8929 0.2846 0.5153 0.055 Uiso 1 1 calc R .

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97 H12B H 0.834(3) 0.327(4) 0.513(3) 0.06(2) Uiso 1 1 d . O13 O 0.9012(2) -0.2365(2) 0.40226(15) 0.0301(10) Uani 1 1 d . O14 O 1.01647(19) -0.24287(19) 0.45011(15) 0.0250(9) Uani 1 1 d . O15 O 0.8147(2) -0.1271(2) 0.31247(16) 0.0372(11) Uani 1 1 d . O16 O 0.83487(19) -0.0278(2) 0.36023(15) 0.0279(9) Uani 1 1 d . O17 O 0.7752(2) -0.1724(2) 0.42051(18) 0.0428(12) Uani 1 1 d . O18 O 1.09365(18) -0.17344(18) 0.55462(14) 0.0194(8) Uani 1 1 d . O19 O 1.2582(2) -0.0635(2) 0.47322(17) 0.0373(11) Uani 1 1 d . O20 O 1.1918(2) 0.0738(2) 0.53371(17) 0.0396(11) Uani 1 1 d . O21 O 0.9712(2) 0.2850(2) 0.32529(15) 0.0344(10) Uani 1 1 d . H21A H 0.9888 0.2890 0.3002 0.052 Uiso 1 1 calc R . O22 O 1.0331(2) -0.1833(2) 0.28786(16) 0.0351(11) Uani 1 1 d . H22A H 1.0318 -0.1926 0.2551 0.053 Uiso 1 1 calc R . C1 C 1.1095(3) -0.1460(3) 0.4054(2) 0.0244(13) Uani 1 1 d . H1A H 1.0919 -0.1948 0.3953 0.029 Uiso 1 1 calc R . H1B H 1.1560 -0.1431 0.4021 0.029 Uiso 1 1 calc R . C2 C 0.9847(3) -0.1019(3) 0.3604(2) 0.0231(13) Uani 1 1 d . H2A H 0.9552 -0.0677 0.3324 0.028 Uiso 1 1 calc R . H2B H 0.9675 -0.1500 0.3470 0.028 Uiso 1 1 calc R . C3 C 1.0847(3) -0.0175(3) 0.3730(2) 0.0229(13) Uani 1 1 d . H3A H 1.1305 -0.0139 0.3685 0.028 Uiso 1 1 calc R . H3B H 1.0512 0.0119 0.3431 0.028 Uiso 1 1 calc R . C4 C 1.0604(3) -0.0949(3) 0.3633(2) 0.0214(13) Uani 1 1 d . C5 C 1.0601(3) -0.1140(3) 0.3032(2) 0.0275(14) Uani 1 1 d . H5A H 1.0311 -0.0795 0.2751 0.033 Uiso 1 1 calc R . H5B H 1.1083 -0.1115 0.3032 0.033 Uiso 1 1 calc R . C7 C 1.0606(3) 0.1846(3) 0.4608(2) 0.0227( 13) Uani 1 1 d . H7A H 1.1016 0.1698 0.4518 0.027 Uiso 1 1 calc R . H7B H 1.0728 0.2293 0.4826 0.027 Uiso 1 1 calc R . C8 C 0.9850(3) 0.1354(3) 0.3651(2) 0.0230( 13) Uani 1 1 d . H8A H 0.9503 0.1496 0.3280 0.028 Uiso 1 1 calc R . H8B H 1.0287 0.1230 0.3592 0.028 Uiso 1 1 calc R . C9 C 0.9993(3) 0.1987(3) 0.4052(2) 0.0204( 12) Uani 1 1 d . C10 C 1.0228(3) 0.2611(3) 0.3764(2) 0.0259(13) Uani 1 1 d . H10A H 1.0368 0.3011 0.4034 0.031 Uiso 1 1 calc R . H10B H 1.0645 0.2462 0.3684 0.031 Uiso 1 1 calc R . C12 C 1.0658(3) -0.2244(3) 0.5838(2) 0.0227(13) Uani 1 1 d . H12D H 1.1026 -0.2363 0.6206 0.027 Uiso 1 1 calc R . H12C H 1.0538 -0.2684 0.5610 0.027 Uiso 1 1 calc R . C13 C 0.7664(3) -0.1264(3) 0.4522(2) 0.0307(14) Uani 1 1 d . C14 C 0.7091(3) -0.1299(4) 0.4771(3) 0.0394(16) Uani 1 1 d . H14A H 0.7030 -0.0807 0.4891 0.047 Uiso 1 1 calc R . C15 C 0.7338(4) -0.1748(4) 0.5311(3) 0.050(2) Uani 1 1 d . C16 C 0.6382(3) -0.1531(4) 0.4357(3) 0.0386(17) Uani 1 1 d . C17 C 0.6254(4) -0.2185(4) 0.4096(3) 0.069(3) Uani 1 1 d . H17A H 0.6631 -0.2509 0.4175 0.083 Uiso 1 1 calc R .

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98 C18 C 0.5826(4) -0.1059(5) 0.4243(3) 0.066(2) Uani 1 1 d . H18A H 0.5891 -0.0607 0.4419 0.079 Uiso 1 1 calc R . C19 C 0.7640(4) -0.2408(4) 0.5340(4) 0.062(2) Uani 1 1 d . H19A H 0.7701 -0.2603 0.5015 0.074 Uiso 1 1 calc R . C20 C 0.8104(3) -0.0616(3) 0.3129(2) 0.0252(13) Uani 1 1 d . C21 C 0.7799(3) -0.0164(3) 0.2594(2) 0.0265(14) Uani 1 1 d . H21B H 0.7691 0.0311 0.2717 0.032 Uiso 1 1 calc R . C22 C 0.7124(3) -0.0448(4) 0.2163(2) 0.0329(15) Uani 1 1 d . C23 C 0.7045(4) -0.1136(4) 0.1956(3) 0.056(2) Uani 1 1 d . H23A H 0.7423 -0.1460 0.2092 0.068 Uiso 1 1 calc R . C24 C 0.6420(5) -0.1353(5) 0.1554(3) 0.081(3) Uani 1 1 d . H24A H 0.6379 -0.1827 0.1421 0.098 Uiso 1 1 calc R . C25 C 0.5861(5) -0.0914(6) 0.1341(4) 0.078(3) Uani 1 1 d . H25A H 0.5437 -0.1078 0.1065 0.094 Uiso 1 1 calc R . C26 C 0.5924(4) -0.0232(6) 0.1534(3) 0.072(3) Uani 1 1 d . H26A H 0.5538 0.0082 0.1390 0.087 Uiso 1 1 calc R . C27 C 0.6549(4) 0.0011(4) 0.1943(3) 0.055(2) Uani 1 1 d . H27A H 0.6585 0.0487 0.2070 0.066 Uiso 1 1 calc R . C28 C 0.8356(3) -0.0049(3) 0.2331(2) 0.0296(14) Uani 1 1 d . C29 C 0.8538(3) 0.0649(3) 0.2256(3) 0.0407(17) Uani 1 1 d . H29A H 0.8328 0.1034 0.2376 0.049 Uiso 1 1 calc R . C30 C 0.9030(4) 0.0774(4) 0.2003(3) 0.0515(19) Uani 1 1 d . H30A H 0.9157 0.1246 0.1954 0.062 Uiso 1 1 calc R . C31 C 0.9329(4) 0.0222(4) 0.1826(3) 0.051(2) Uani 1 1 d . H31A H 0.9656 0.0312 0.1647 0.061 Uiso 1 1 calc R . C32 C 0.9156(3) -0.0481(4) 0.1906(2) 0.0427(18) Uani 1 1 d . H32A H 0.9368 -0.0863 0.1785 0.051 Uiso 1 1 calc R . C33 C 0.8678(3) -0.0612(4) 0.2160(2) 0.0373(16) Uani 1 1 d . H33A H 0.8567 -0.1086 0.2220 0.045 Uiso 1 1 calc R . C34 C 0.7518(3) 0.1939(3) 0.3294(2) 0.0320(15) Uani 1 1 d . C35 C 0.6922(3) 0.2093(4) 0.2739(3) 0.0396(17) Uani 1 1 d . H35A H 0.6624 0.1659 0.2658 0.048 Uiso 1 1 calc R . C36 C 0.6454(3) 0.2682(4) 0.2784(3) 0.0408(17) Uani 1 1 d . C37 C 0.5867(4) 0.2555(5) 0.2905(3) 0.072(3) Uani 1 1 d . H37A H 0.5759 0.2079 0.2964 0.086 Uiso 1 1 calc R . C38 C 0.5428(5) 0.3081(6) 0.2947(4) 0.090(3) Uani 1 1 d . H38A H 0.5014 0.2970 0.3015 0.108 Uiso 1 1 calc R . C39 C 0.5600(5) 0.3767(6) 0.2887(4) 0.081(3) Uani 1 1 d . H39A H 0.5314 0.4140 0.2934 0.097 Uiso 1 1 calc R . C40 C 0.6183(5) 0.3928(5) 0.2761(4) 0.094(3) Uani 1 1 d . H40A H 0.6297 0.4404 0.2712 0.113 Uiso 1 1 calc R . C41 C 0.6597(4) 0.3373(4) 0.2707(4) 0.069(2) Uani 1 1 d . H41A H 0.6995 0.3476 0.2614 0.083 Uiso 1 1 calc R . C42 C 0.7161(3) 0.2167(3) 0.2239(2) 0.0360(16) Uani 1 1 d . C43 C 0.6720(4) 0.1942(3) 0.1708(3) 0.0424(17) Uani 1 1 d . H43A H 0.6272 0.1761 0.1661 0.051 Uiso 1 1 calc R .

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99 C44 C 0.6926(4) 0.1979(4) 0.1251(3) 0.0469(19) Uani 1 1 d . H44A H 0.6620 0.1819 0.0891 0.056 Uiso 1 1 calc R . C45 C 0.7576(4) 0.2248(4) 0.1308(3) 0.051(2) Uani 1 1 d . H45A H 0.7716 0.2271 0.0989 0.061 Uiso 1 1 calc R . C46 C 0.8019(4) 0.2484(4) 0.1833(3) 0.0459(18) Uani 1 1 d . H46A H 0.8462 0.2676 0.1875 0.055 Uiso 1 1 calc R . C47 C 0.7812(4) 0.2437(3) 0.2298(3) 0.0399(17) Uani 1 1 d . H47A H 0.8119 0.2592 0.2659 0.048 Uiso 1 1 calc R . C48 C 0.7135(3) 0.1249(4) 0.5197(3) 0.0360(16) Uani 1 1 d . C49 C 0.6514(3) 0.1374(4) 0.5390(3) 0.0391(16) Uani 1 1 d . H49A H 0.6639 0.1793 0.5649 0.047 Uiso 1 1 calc R . C50 C 0.5874(3) 0.1580(4) 0.4896(3) 0.0402(17) Uani 1 1 d . C51 C 0.5782(4) 0.1389(4) 0.4337(3) 0.054(2) Uani 1 1 d . H51A H 0.6119 0.1106 0.4259 0.065 Uiso 1 1 calc R . C52 C 0.5181(5) 0.1624(5) 0.3894(4) 0.076(3) Uani 1 1 d . H52A H 0.5116 0.1506 0.3514 0.091 Uiso 1 1 calc R . C53 C 0.4695(5) 0.2018(5) 0.4003(6) 0.094(4) Uani 1 1 d . H53A H 0.4292 0.2168 0.3698 0.113 Uiso 1 1 calc R . C54 C 0.4771(5) 0.2202(5) 0.4542(5) 0.082(3) Uani 1 1 d . H54A H 0.4423 0.2479 0.4611 0.099 Uiso 1 1 calc R . C55 C 0.5351(4) 0.1987(4) 0.4983(4) 0.065(2) Uani 1 1 d . H55A H 0.5402 0.2118 0.5358 0.078 Uiso 1 1 calc R . C56 C 0.6408(3) 0.0761(3) 0.5739(3) 0.0321(15) Uani 1 1 d . C57 C 0.5940(4) 0.0230(4) 0.5504(3) 0.0449(18) Uani 1 1 d . H57A H 0.5663 0.0246 0.5111 0.054 Uiso 1 1 calc R . C58 C 0.5861(4) -0.0332(4) 0.5829(3) 0.055(2) Uani 1 1 d . H58A H 0.5541 -0.0701 0.5657 0.066 Uiso 1 1 calc R . C59 C 0.6246(4) -0.0356(4) 0.6405(3) 0.052(2) Uani 1 1 d . H59A H 0.6180 -0.0730 0.6631 0.063 Uiso 1 1 calc R . C60 C 0.6718(4) 0.0162(5) 0.6643(3) 0.068(2) Uani 1 1 d . H60A H 0.6997 0.0141 0.7034 0.082 Uiso 1 1 calc R . C61 C 0.6799(4) 0.0738(4) 0.6308(3) 0.0513(19) Uani 1 1 d . H61A H 0.7122 0.1106 0.6479 0.062 Uiso 1 1 calc R . C62 C 0.9582(3) -0.2692(3) 0.4213(2) 0.0271(14) Uani 1 1 d . C63 C 0.9577(3) -0.3494(3) 0.4118(2) 0.0340(15) Uani 1 1 d . H63A H 1.0077 -0.3643 0.4236 0.041 Uiso 1 1 calc R . C64 C 0.9233(3) -0.3697(3) 0.3502(2) 0.0323(15) Uani 1 1 d . C65 C 0.9318(4) -0.3270(4) 0.3080(3) 0.0498(19) Uani 1 1 d . H65A H 0.9558 -0.2832 0.3186 0.060 Uiso 1 1 calc R . C66 C 0.9067(5) -0.3459(4) 0.2522(3) 0.066(2) Uani 1 1 d . H66A H 0.9127 -0.3158 0.2243 0.079 Uiso 1 1 calc R . C67 C 0.8725(5) -0.4098(5) 0.2374(3) 0.075(3) Uani 1 1 d . H67A H 0.8547 -0.4234 0.1986 0.090 Uiso 1 1 calc R . C68 C 0.8635(4) -0.4542(4) 0.2768(3) 0.064(2) Uani 1 1 d . H68A H 0.8401 -0.4982 0.2658 0.077 Uiso 1 1 calc R . C69 C 0.8891(3) -0.4338(3) 0.3331(3) 0.0443(18) Uani 1 1 d .

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100 H69A H 0.8830 -0.4643 0.3607 0.053 Uiso 1 1 calc R . C70 C 0.9296(4) -0.3833(3) 0.4533(3) 0.0404(17) Uani 1 1 d . C71 C 0.9769(4) -0.4115(4) 0.5036(3) 0.058(2) Uani 1 1 d . H71A H 1.0255 -0.4112 0.5103 0.070 Uiso 1 1 calc R . C72 C 0.8819(6) -0.4402(4) 0.5341(4) 0.075(3) Uani 1 1 d . H72A H 0.8650 -0.4599 0.5612 0.090 Uiso 1 1 calc R . C73 C 0.8371(5) -0.4124(5) 0.4863(4) 0.073(3) Uani 1 1 d . H73A H 0.7885 -0.4128 0.4795 0.088 Uiso 1 1 calc R . C74 C 0.8609(4) -0.3827(4) 0.4461(3) 0.056(2) Uani 1 1 d . H74A H 0.8283 -0.3616 0.4131 0.067 Uiso 1 1 calc R . C75 C 0.9524(6) -0.4404(4) 0.5442(3) 0.074(3) Uani 1 1 d . H75A H 0.9842 -0.4598 0.5784 0.089 Uiso 1 1 calc R . C80 C 0.7258(4) -0.1480(5) 0.5783(3) 0.071(3) Uani 1 1 d . H80A H 0.7058 -0.1025 0.5776 0.085 Uiso 1 1 calc R . C81 C 0.7471(5) -0.1881(7) 0.6277(4) 0.098(4) Uani 1 1 d . H81A H 0.7396 -0.1699 0.6600 0.117 Uiso 1 1 calc R . C82 C 0.7776(5) -0.2513(7) 0.6315(5) 0.106(4) Uani 1 1 d . H82A H 0.7934 -0.2767 0.6663 0.127 Uiso 1 1 calc R . C83 C 0.7853(5) -0.2783(5) 0.5843(5) 0.082(3) Uani 1 1 d . H83A H 0.8057 -0.3237 0.5859 0.098 Uiso 1 1 calc R . C84 C 0.5616(5) -0.2388(6) 0.3734(4) 0.083(3) Uani 1 1 d . H84A H 0.5548 -0.2842 0.3561 0.099 Uiso 1 1 calc R . C85 C 0.5088(5) -0.1938(7) 0.3626(4) 0.083(3) Uani 1 1 d . H85A H 0.4640 -0.2083 0.3376 0.100 Uiso 1 1 calc R . C86 C 0.5157(4) -0.1273(7) 0.3857(3) 0.082(3) Uani 1 1 d . H86A H 0.4769 -0.0961 0.3762 0.098 Uiso 1 1 calc R . N1 N 0.7890(3) 0.1014(3) 0.0388(3) 0.0595(18) Uani 1 1 d . C87 C 0.7618(4) 0.0632(4) 0.0570(3) 0.0488(19) Uani 1 1 d . C88 C 0.7247(5) 0.0133(5) 0.0799(3) 0.083(3) Uani 1 1 d . H88A H 0.6798 0.0338 0.0774 0.124 Uiso 1 1 calc R . H88B H 0.7528 0.0034 0.1196 0.124 Uiso 1 1 calc R . H88C H 0.7165 -0.0308 0.0580 0.124 Uiso 1 1 calc R . N2 N 0.1288(4) 0.8773(3) 0.1512(3) 0.0605(19) Uani 1 1 d . C89 C 0.1666(5) 0.8956(4) 0.1307(3) 0.056(2) Uani 1 1 d . C90 C 0.2159(5) 0.9194(5) 0.1054(4) 0.083(3) Uani 1 1 d . H90A H 0.1906 0.9342 0.0662 0.124 Uiso 1 1 calc R . H90B H 0.2478 0.8806 0.1058 0.124 Uiso 1 1 calc R . H90C H 0.2428 0.9594 0.1271 0.124 Uiso 1 1 calc R . N3 N 0.3444(4) 0.5281(5) 0.1565(3) 0.090(3) Uani 1 1 d . C91 C 0.3585(4) 0.4723(6) 0.1746(3) 0.066(3) Uani 1 1 d . C92 C 0.3726(4) 0.3991(5) 0.1971(3) 0.073(3) Uani 1 1 d . H92A H 0.3879 0.4002 0.2385 0.110 Uiso 1 1 calc R . H92B H 0.4093 0.3780 0.1860 0.110 Uiso 1 1 calc R . H92C H 0.3299 0.3708 0.1817 0.110 Uiso 1 1 calc R . loop_

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101 _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_23 _atom_site_aniso_U_13 _atom_site_aniso_U_12 Mn1 0.0214(5) 0.0201(5) 0.0154(4) 0.0005( 3) 0.0072(4) 0.0009(4) Mn2 0.0217(5) 0.0215(5) 0.0142(4) 0.0012( 4) 0.0068(4) 0.0005(4) Mn3 0.0240(5) 0.0267(5) 0.0201(4) 0.0015(4) 0.0069(4) 0.0008(4) Mn4 0.0263(5) 0.0291(5) 0.0231(5) 0.0015( 4) 0.0090(4) 0.0046(4) Mn5 0.0261(5) 0.0290(5) 0.0219(5) 0.0005( 4) 0.0057(4) -0.0005(4) Mn6 0.0237(5) 0.0254(5) 0.0199(4) 0.0013( 4) 0.0061(4) -0.0017(4) O1 0.023(2) 0.021(2) 0.0163(19) -0. 0003(16) 0.0065(16) -0.0033(17) O2 0.022(2) 0.022(2) 0.0144(18) 0. 0010(16) 0.0052(16) 0.0005(17) O3 0.023(2) 0.022(2) 0.0167(18) -0 .0001(16) 0.0089(16) 0.0020(17) O4 0.025(2) 0.023(2) 0.0127(18) -0 .0008(16) 0.0066(16) 0.0040(17) O5 0.024(2) 0.022(2) 0.0155(19) -0 .0009(16) 0.0074(17) 0.0002(17) O6 0.021(2) 0.019(2) 0.0173(19) 0. 0024(16) 0.0068(17) -0.0010(16) O7 0.043(3) 0.035(3) 0.029(2) 0.004(2) 0.012(2) 0.009(2) O8 0.037(3) 0.039(3) 0.022(2) 0.00 36(19) 0.0085(19) 0.007(2) O10 0.026(2) 0.026(2) 0.023(2) -0.00 32(17) 0.0091(17) -0.0003(18) O11 0.033(3) 0.041(3) 0.041(3) 0.002(2) 0.021(2) 0.004(2) O12 0.035(3) 0.031(3) 0.043(3) -0.006(2) 0.013(2) 0.003(2) O13 0.034(3) 0.024(2) 0.029(2) -0.00 13(18) 0.007(2) -0.0012(19) O14 0.021(2) 0.025(2) 0.026(2) -0.00 54(18) 0.0056(18) -0.0020(18) O15 0.049(3) 0.028(3) 0.028(2) 0.001(2) 0.006(2) -0.002(2) O16 0.032(2) 0.030(2) 0.020(2) -0.00 32(18) 0.0070(18) -0.0038(19) O17 0.049(3) 0.042(3) 0.046(3) 0.012(2) 0.028(2) -0.005(2) O18 0.020(2) 0.023(2) 0.0159(19) 0. 0047(16) 0.0087(16) 0.0043(16) O19 0.036(3) 0.045(3) 0.035(2) 0.004(2) 0.018(2) -0.002(2) O20 0.036(3) 0.035(3) 0.043(3) 0.003(2) 0.008(2) -0.006(2) O21 0.048(3) 0.039(3) 0.019(2) 0.0153(19) 0.015(2) 0.002(2) O22 0.054(3) 0.033(3) 0.023(2) 0.0123(19) 0.020(2) -0.010(2) C1 0.027(3) 0.029(3) 0.019(3) -0.006(2) 0.010(3) 0.000(3) C2 0.023(3) 0.032(3) 0.014(3) -0.001(2) 0.006(2) 0.001(3) C3 0.030(3) 0.027(3) 0.014(3) -0.002(2) 0.012(3) 0.001(3) C4 0.029(3) 0.023(3) 0.016(3) -0.002(2) 0.012(3) 0.000(3) C5 0.035(4) 0.032(4) 0.019(3) 0.000(3) 0.014(3) 0.002(3) C7 0.029(3) 0.027(3) 0.014(3) 0.003(2) 0.011(3) -0.005(3) C8 0.034(3) 0.026(3) 0.009(3) 0.002(2) 0.009(2) 0.000(3) C9 0.026(3) 0.020(3) 0.018(3) 0.002(2) 0.011(2) 0.000(2) C10 0.035(4) 0.021(3) 0.026(3) 0.002(3) 0.016(3) 0.001(3) C12 0.026(3) 0.023(3) 0.018(3) 0.007(2) 0.008(3) 0.004(3) C13 0.025(3) 0.035(4) 0.030(3) 0.001(3) 0.008(3) -0.006(3) C14 0.031(4) 0.048(4) 0.039(4) -0.006(3) 0.013(3) 0.002(3)

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102 C15 0.034(4) 0.076(6) 0.042(4) 0.013(4) 0.017(4) -0.003(4) C16 0.032(4) 0.056(5) 0.032(4) 0.001(3) 0.017(3) -0.014(3) C17 0.071(6) 0.058(6) 0.064(5) 0.000(4) 0.006(5) -0.030(5) C18 0.064(6) 0.093(7) 0.051(5) -0.004(5) 0.034(5) 0.013(5) C19 0.060(5) 0.063(6) 0.064(6) 0.007(5) 0.024(4) -0.013(5) C20 0.017(3) 0.036(4) 0.024(3) 0.001(3) 0.008(3) -0.003(3) C21 0.030(3) 0.026(3) 0.021(3) 0.001(3) 0.006(3) -0.001(3) C22 0.033(4) 0.049(4) 0.018(3) 0.002(3) 0.009(3) -0.010(3) C23 0.053(5) 0.061(5) 0.042(4) 0.006(4) 0.001(4) -0.008(4) C24 0.064(6) 0.103(8) 0.056(5) 0.022(5) -0.004(5) -0.038(6) C25 0.044(6) 0.118(9) 0.057(6) 0.005(6) -0.001(4) -0.029(6) C26 0.029(5) 0.117(8) 0.055(5) 0.030(6) -0.004(4) 0.008(5) C27 0.051(5) 0.068(5) 0.045(4) 0.017(4) 0.015(4) 0.010(4) C28 0.031(4) 0.037(4) 0.015(3) 0.003(3) 0.002(3) 0.001(3) C29 0.052(5) 0.036(4) 0.038(4) 0.003(3) 0.020(3) -0.005(3) C30 0.061(5) 0.053(5) 0.044(4) 0.005(4) 0.023(4) -0.008(4) C31 0.043(5) 0.082(6) 0.031(4) 0.015(4) 0.017(3) -0.003(4) C32 0.043(4) 0.065(5) 0.021(3) -0.001(3) 0.012(3) 0.008(4) C33 0.042(4) 0.039(4) 0.028(3) 0.001(3) 0.008(3) -0.003(3) C34 0.034(4) 0.040(4) 0.022(3) 0.009(3) 0.010(3) 0.008(3) C35 0.037(4) 0.044(4) 0.033(4) 0.007(3) 0.007(3) 0.007(3) C36 0.040(4) 0.051(5) 0.026(3) 0.006(3) 0.006(3) 0.007(4) C37 0.062(6) 0.096(7) 0.069(6) 0.028(5) 0.037(5) 0.021(5) C38 0.081(7) 0.108(9) 0.102(8) 0.045(7) 0.060(6) 0.050(7) C39 0.066(7) 0.096(8) 0.087(7) 0.010(6) 0.037(5) 0.039(6) C40 0.078(7) 0.083(8) 0.125(9) 0.016(6) 0.042(7) 0.026(6) C41 0.057(6) 0.054(6) 0.092(7) -0.006(5) 0.022(5) 0.012(4) C42 0.037(4) 0.044(4) 0.021(3) 0.011(3) 0.003(3) 0.014(3) C43 0.041(4) 0.044(4) 0.039(4) 0.009(3) 0.011(3) 0.001(3) C44 0.068(5) 0.039(4) 0.029(4) 0.003(3) 0.012(4) 0.000(4) C45 0.084(6) 0.040(4) 0.040(4) 0.011(3) 0.035(4) 0.004(4) C46 0.045(4) 0.043(4) 0.051(5) 0.007(4) 0.019(4) -0.007(4) C47 0.047(4) 0.041(4) 0.024(3) 0.003(3) 0.003(3) 0.003(3) C48 0.031(4) 0.044(5) 0.031(4) 0.003(3) 0.009(3) -0.004(3) C49 0.032(4) 0.046(4) 0.047(4) 0.005(3) 0.023(3) -0.002(3) C50 0.028(4) 0.046(4) 0.049(4) 0.006(3) 0.017(3) 0.004(3) C51 0.041(5) 0.071(6) 0.049(5) 0.008(4) 0.014(4) 0.002(4) C52 0.069(6) 0.093(7) 0.053(5) 0.026(5) 0.007(5) -0.030(6) C53 0.053(6) 0.062(7) 0.148(11) 0.050(7) 0.013(7) 0.010(5) C54 0.050(6) 0.072(7) 0.117(9) 0.014(7) 0.022(6) 0.022(5) C55 0.055(5) 0.054(5) 0.092(7) 0.000(5) 0.033(5) -0.002(4) C56 0.023(3) 0.046(4) 0.033(3) 0.005(3) 0.016(3) -0.003(3) C57 0.049(5) 0.053(5) 0.039(4) 0.001(4) 0.022(4) 0.000(4) C58 0.054(5) 0.059(5) 0.053(5) 0.010(4) 0.020(4) -0.006(4) C59 0.050(5) 0.061(5) 0.055(5) 0.023(4) 0.030(4) 0.004(4) C60 0.061(6) 0.101(7) 0.044(5) 0.014(5) 0.020(4) 0.010(5)

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103 C61 0.047(5) 0.061(5) 0.044(4) 0.003(4) 0.016(4) -0.010(4) C62 0.044(4) 0.019(3) 0.025(3) 0.002(3) 0.020(3) 0.004(3) C63 0.040(4) 0.023(3) 0.035(4) 0.002(3) 0.010(3) -0.001(3) C64 0.042(4) 0.026(4) 0.032(3) 0.008(3) 0.018(3) -0.001(3) C65 0.080(6) 0.034(4) 0.043(4) 0.007(3) 0.031(4) -0.004(4) C66 0.118(8) 0.046(5) 0.037(4) 0.012(4) 0.031(5) -0.001(5) C67 0.113(8) 0.079(7) 0.035(4) -0.015(5) 0.030(5) 0.022(6) C68 0.075(6) 0.050(5) 0.054(5) -0.030(4) 0.009(5) 0.002(4) C69 0.053(5) 0.038(4) 0.039(4) 0.012(3) 0.013(3) -0.010(3) C70 0.063(5) 0.023(4) 0.031(4) 0.008(3) 0.013(4) -0.006(3) C71 0.080(6) 0.043(5) 0.042(4) -0.005(4) 0.012(4) 0.001(4) C72 0.119(9) 0.056(6) 0.068(6) 0.003(5) 0.055(7) -0.028(6) C73 0.084(7) 0.084(7) 0.052(5) 0.009(5) 0.025(5) -0.020(5) C74 0.069(6) 0.050(5) 0.048(5) 0.002(4) 0.021(4) -0.010(4) C75 0.127(9) 0.046(5) 0.041(5) 0.015(4) 0.021(6) -0.004(6) C80 0.056(5) 0.120(8) 0.043(5) 0.005(5) 0.025(4) 0.019(5) C81 0.065(7) 0.199(13) 0.033(5) 0.021(7) 0.022(5) 0.018(7) C82 0.065(7) 0.160(12) 0.092(9) 0.081(9) 0.025(6) 0.011(7) C83 0.061(6) 0.074(7) 0.101(8) 0.040(6) 0.019(6) 0.002(5) C84 0.054(6) 0.095(8) 0.090(7) 0.012(6) 0.015(6) -0.030(6) C85 0.053(6) 0.142(10) 0.054(6) -0. 012(6) 0.019(5) -0.038(7) C86 0.038(5) 0.171(11) 0.040(5) 0.016(6) 0.020(4) 0.016(6) N1 0.075(5) 0.047(4) 0.068(4) 0.014(3) 0.040(4) -0.003(4) C87 0.053(5) 0.055(5) 0.042(4) 0.013(4) 0.022(4) -0.002(4) C88 0.096(7) 0.096(7) 0.058(6) 0.021(5) 0.031(5) -0.031(6) N2 0.076(5) 0.029(4) 0.073(5) 0.014(3) 0.022(4) -0.010(3) C89 0.073(6) 0.039(5) 0.054(5) 0.010(4) 0.020(5) -0.005(4) C90 0.105(8) 0.078(7) 0.086(7) 0.017(5) 0.060(6) -0.015(6) N3 0.075(6) 0.121(8) 0.069(5) 0.016(5) 0.021(4) 0.032(5) C91 0.046(5) 0.114(9) 0.038(5) 0.001(5) 0.016(4) 0.030(6) C92 0.064(6) 0.114(8) 0.045(5) -0.002(5) 0.022(4) 0.026(5) _geom_special_details ; All esds (except the esd in the dihe dral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. ; loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance

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104 _geom_bond_site_symmetry_2 _geom_bond_publ_flag Mn1 O1 1.912(3) ? Mn1 O6 1.915(3) 3_756 ? Mn1 O6 1.920(3) ? Mn1 O5 1.921(3) ? Mn1 O4 2.322(4) ? Mn1 O2 2.332(4) ? Mn1 Mn1 2.8566(15) 3_756 ? Mn1 Mn2 3.0991(12) ? Mn1 Mn2 3.1124(11) 3_756 ? Mn1 Mn3 3.1422(12) ? Mn1 Mn5 3.2060(12) ? Mn2 O18 1.913(3) ? Mn2 O3 1.924(3) ? Mn2 O4 1.926(3) ? Mn2 O2 1.941(3) 3_756 ? Mn2 O14 2.152(4) ? Mn2 O6 2.227(4) ? Mn2 Mn1 3.1124(11) 3_756 ? Mn2 Mn6 3.1632(12) ? Mn3 O1 2.083(4) ? Mn3 O10 2.087(4) ? Mn3 O16 2.118(4) ? Mn3 O8 2.132(4) ? Mn3 O18 2.288(4) 3_756 ? Mn3 O6 2.462(3) 3_756 ? Mn3 Mn4 3.2293(12) ? Mn4 O11 2.097(4) ? Mn4 O7 2.131(4) ? Mn4 O10 2.156(4) ? Mn4 O12 2.181(4) ? Mn4 O18 2.264(3) 3_756 ? Mn4 O3 2.309(3) 3_756 ? Mn5 O10 2.064(4) 3_756 ? Mn5 O5 2.074(3) ? Mn5 O20 2.109(4) ? Mn5 O19 2.126(4) ? Mn5 O3 2.302(4) ? Mn6 O13 2.190(4) ? Mn6 O17 2.245(4) ? Mn6 O4 2.247(4) ? Mn6 O16 2.277(4) ? Mn6 O2 2.298(3) 3_756 ? Mn6 O15 2.393(4) ? Mn6 O20 2.422(4) 3_756 ?

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105 O1 C8 1.439(6) ? O2 C7 1.439(6) ? O2 Mn2 1.941(3) 3_756 ? O2 Mn6 2.298(3) 3_756 ? O3 C1 1.443(6) ? O3 Mn4 2.309(3) 3_756 ? O4 C2 1.451(6) ? O5 C3 1.425(6) ? O6 Mn1 1.915(3) 3_756 ? O6 Mn3 2.462(3) 3_756 ? O7 C34 1.249(7) ? O8 C34 1.275(7) ? O10 Mn5 2.064(4) 3_756 ? O11 C48 1.248(7) ? O12 H12A 0.8400 ? O12 H12B 0.94(7) ? O13 C62 1.256(7) ? O14 C62 1.258(7) ? O15 C20 1.242(7) ? O16 C20 1.288(6) ? O17 C13 1.240(7) ? O18 C12 1.452(6) ? O18 Mn4 2.264(3) 3_756 ? O18 Mn3 2.288(4) 3_756 ? O19 C48 1.281(7) 3_756 ? O20 C13 1.278(7) 3_756 ? O20 Mn6 2.422(4) 3_756 ? O21 C10 1.419(6) ? O21 H21A 0.8400 ? O22 C5 1.420(6) ? O22 H22A 0.8400 ? C1 C4 1.520(7) ? C1 H1A 0.9900 ? C1 H1B 0.9900 ? C2 C4 1.536(7) ? C2 H2A 0.9900 ? C2 H2B 0.9900 ? C3 C4 1.537(7) ? C3 H3A 0.9900 ? C3 H3B 0.9900 ? C4 C5 1.562(7) ? C5 H5A 0.9900 ? C5 H5B 0.9900 ? C7 C9 1.536(7) ? C7 H7A 0.9900 ? C7 H7B 0.9900 ?

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106 C8 C9 1.526(7) ? C8 H8A 0.9900 ? C8 H8B 0.9900 ? C9 C12 1.539(7) 3_756 ? C9 C10 1.550(7) ? C10 H10A 0.9900 ? C10 H10B 0.9900 ? C12 C9 1.539(7) 3_756 ? C12 H12D 0.9900 ? C12 H12C 0.9900 ? C13 O20 1.278(7) 3_756 ? C13 C14 1.525(8) ? C14 C16 1.519(8) ? C14 C15 1.529(9) ? C14 H14A 1.0000 ? C15 C80 1.364(10) ? C15 C19 1.382(10) ? C16 C17 1.381(10) ? C16 C18 1.395(10) ? C17 C84 1.356(10) ? C17 H17A 0.9500 ? C18 C86 1.427(11) ? C18 H18A 0.9500 ? C19 C83 1.384(11) ? C19 H19A 0.9500 ? C20 C21 1.530(7) ? C21 C22 1.520(8) ? C21 C28 1.532(8) ? C21 H21B 1.0000 ? C22 C23 1.390(9) ? C22 C27 1.408(9) ? C23 C24 1.381(9) ? C23 H23A 0.9500 ? C24 C25 1.360(12) ? C24 H24A 0.9500 ? C25 C26 1.369(12) ? C25 H25A 0.9500 ? C26 C27 1.404(10) ? C26 H26A 0.9500 ? C27 H27A 0.9500 ? C28 C33 1.401(8) ? C28 C29 1.403(8) ? C29 C30 1.399(9) ? C29 H29A 0.9500 ? C30 C31 1.367(10) ? C30 H30A 0.9500 ?

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107 C31 C32 1.408(10) ? C31 H31A 0.9500 ? C32 C33 1.375(8) ? C32 H32A 0.9500 ? C33 H33A 0.9500 ? C34 C35 1.521(8) ? C35 C36 1.501(9) ? C35 C42 1.521(8) ? C35 H35A 1.0000 ? C36 C41 1.366(10) ? C36 C37 1.369(9) ? C37 C38 1.372(11) ? C37 H37A 0.9500 ? C38 C39 1.368(12) ? C38 H38A 0.9500 ? C39 C40 1.380(12) ? C39 H39A 0.9500 ? C40 C41 1.389(11) ? C40 H40A 0.9500 ? C41 H41A 0.9500 ? C42 C43 1.387(8) ? C42 C47 1.389(9) ? C43 C44 1.370(9) ? C43 H43A 0.9500 ? C44 C45 1.387(9) ? C44 H44A 0.9500 ? C45 C46 1.385(9) ? C45 H45A 0.9500 ? C46 C47 1.391(8) ? C46 H46A 0.9500 ? C47 H47A 0.9500 ? C48 O19 1.281(7) 3_756 ? C48 C49 1.541(8) ? C49 C50 1.501(9) ? C49 C56 1.520(9) ? C49 H49A 1.0000 ? C50 C55 1.401(9) ? C50 C51 1.406(9) ? C51 C52 1.407(10) ? C51 H51A 0.9500 ? C52 C53 1.351(13) ? C52 H52A 0.9500 ? C53 C54 1.360(13) ? C53 H53A 0.9500 ? C54 C55 1.369(11) ? C54 H54A 0.9500 ?

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108 C55 H55A 0.9500 ? C56 C57 1.369(9) ? C56 C61 1.374(8) ? C57 C58 1.389(9) ? C57 H57A 0.9500 ? C58 C59 1.385(9) ? C58 H58A 0.9500 ? C59 C60 1.357(10) ? C59 H59A 0.9500 ? C60 C61 1.424(10) ? C60 H60A 0.9500 ? C61 H61A 0.9500 ? C62 C63 1.534(8) ? C63 C64 1.511(8) ? C63 C70 1.511(9) ? C63 H63A 1.0000 ? C64 C69 1.389(8) ? C64 C65 1.398(8) ? C65 C66 1.365(9) ? C65 H65A 0.9500 ? C66 C67 1.380(11) ? C66 H66A 0.9500 ? C67 C68 1.366(11) ? C67 H67A 0.9500 ? C68 C69 1.384(9) ? C68 H68A 0.9500 ? C69 H69A 0.9500 ? C70 C74 1.357(10) ? C70 C71 1.398(9) ? C71 C75 1.410(11) ? C71 H71A 0.9500 ? C72 C73 1.334(11) ? C72 C75 1.376(12) ? C72 H72A 0.9500 ? C73 C74 1.395(10) ? C73 H73A 0.9500 ? C74 H74A 0.9500 ? C75 H75A 0.9500 ? C80 C81 1.390(11) ? C80 H80A 0.9500 ? C81 C82 1.336(14) ? C81 H81A 0.9500 ? C82 C83 1.360(14) ? C82 H82A 0.9500 ? C83 H83A 0.9500 ? C84 C85 1.326(12) ?

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109 C84 H84A 0.9500 ? C85 C86 1.373(13) ? C85 H85A 0.9500 ? C86 H86A 0.9500 ? N1 C87 1.109(8) ? C87 C88 1.457(10) ? C88 H88A 0.9800 ? C88 H88B 0.9800 ? C88 H88C 0.9800 ? N2 C89 1.132(9) ? C89 C90 1.453(11) ? C90 H90A 0.9800 ? C90 H90B 0.9800 ? C90 H90C 0.9800 ? N3 C91 1.145(11) ? C91 C92 1.483(12) ? C92 H92A 0.9800 ? C92 H92B 0.9800 ? C92 H92C 0.9800 ? loop_ _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_angle _geom_angle_site_symmetry_1 _geom_angle_site_symmetry_3 _geom_angle_publ_flag O1 Mn1 O6 90.91(15) 3_756 ? O1 Mn1 O6 174.58(15) . ? O6 Mn1 O6 83.70(15) 3_756 ? O1 Mn1 O5 93.22(15) . ? O6 Mn1 O5 175.86(15) 3_756 ? O6 Mn1 O5 92.17(15) . ? O1 Mn1 O4 96.04(13) . ? O6 Mn1 O4 91.33(14) 3_756 ? O6 Mn1 O4 83.57(13) . ? O5 Mn1 O4 87.88(14) . ? O1 Mn1 O2 87.61(13) . ? O6 Mn1 O2 83.55(13) 3_756 ? O6 Mn1 O2 92.31(13) . ? O5 Mn1 O2 96.97(14) . ? O4 Mn1 O2 173.77(12) . ? O1 Mn1 Mn1 132.83(11) 3_756 ? O6 Mn1 Mn1 41.92(10) 3_756 3_756 ? O6 Mn1 Mn1 41.78(10) 3_756 ?

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110 O5 Mn1 Mn1 133.95(11) 3_756 ? O4 Mn1 Mn1 86.58(9) 3_756 ? O2 Mn1 Mn1 87.24(9) 3_756 ? O1 Mn1 Mn2 134.39(11) . ? O6 Mn1 Mn2 91.23(11) 3_756 ? O6 Mn1 Mn2 45.56(10) . ? O5 Mn1 Mn2 85.62(11) . ? O4 Mn1 Mn2 38.36(8) . ? O2 Mn1 Mn2 137.85(9) . ? Mn1 Mn1 Mn2 62.86(3) 3_756 ? O1 Mn1 Mn2 85.83(11) 3_756 ? O6 Mn1 Mn2 45.23(10) 3_756 3_756 ? O6 Mn1 Mn2 90.73(11) 3_756 ? O5 Mn1 Mn2 135.48(11) 3_756 ? O4 Mn1 Mn2 136.55(9) 3_756 ? O2 Mn1 Mn2 38.51(9) 3_756 ? Mn1 Mn1 Mn2 62.38(3) 3_756 3_756 ? Mn2 Mn1 Mn2 125.24(3) 3_756 ? O1 Mn1 Mn3 40.11(10) . ? O6 Mn1 Mn3 51.58(10) 3_756 ? O6 Mn1 Mn3 134.49(11) . ? O5 Mn1 Mn3 132.44(10) . ? O4 Mn1 Mn3 88.88(9) . ? O2 Mn1 Mn3 90.71(9) . ? Mn1 Mn1 Mn3 93.13(4) 3_756 ? Mn2 Mn1 Mn3 118.20(3) . ? Mn2 Mn1 Mn3 65.14(3) 3_756 ? O1 Mn1 Mn5 130.76(11) . ? O6 Mn1 Mn5 137.69(10) 3_756 ? O6 Mn1 Mn5 54.66(10) . ? O5 Mn1 Mn5 38.31(10) . ? O4 Mn1 Mn5 91.08(9) . ? O2 Mn1 Mn5 90.33(9) . ? Mn1 Mn1 Mn5 96.13(4) 3_756 ? Mn2 Mn1 Mn5 66.11(3) . ? Mn2 Mn1 Mn5 120.08(3) 3_756 ? Mn3 Mn1 Mn5 170.72(3) . ? O18 Mn2 O3 86.90(14) . ? O18 Mn2 O4 173.64(16) . ? O3 Mn2 O4 94.03(14) . ? O18 Mn2 O2 93.76(14) 3_756 ? O3 Mn2 O2 174.58(15) 3_756 ? O4 Mn2 O2 84.73(14) 3_756 ? O18 Mn2 O14 89.40(14) . ? O3 Mn2 O14 89.38(14) . ? O4 Mn2 O14 96.90(14) . ?

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111 O2 Mn2 O14 96.00(14) 3_756 ? O18 Mn2 O6 87.66(14) . ? O3 Mn2 O6 88.80(14) . ? O4 Mn2 O6 86.07(14) . ? O2 Mn2 O6 85.86(14) 3_756 ? O14 Mn2 O6 176.63(14) . ? O18 Mn2 Mn1 125.43(11) . ? O3 Mn2 Mn1 87.23(11) . ? O4 Mn2 Mn1 48.43(11) . ? O2 Mn2 Mn1 88.02(11) 3_756 ? O14 Mn2 Mn1 144.70(10) . ? O6 Mn2 Mn1 38.00(9) . ? O18 Mn2 Mn1 87.43(10) 3_756 ? O3 Mn2 Mn1 126.30(11) 3_756 ? O4 Mn2 Mn1 86.95(10) 3_756 ? O2 Mn2 Mn1 48.42(10) 3_756 3_756 ? O14 Mn2 Mn1 143.88(10) 3_756 ? O6 Mn2 Mn1 37.62(9) 3_756 ? Mn1 Mn2 Mn1 54.76(3) 3_756 ? O18 Mn2 Mn6 136.42(11) . ? O3 Mn2 Mn6 134.71(10) . ? O4 Mn2 Mn6 44.67(11) . ? O2 Mn2 Mn6 46.25(10) 3_756 ? O14 Mn2 Mn6 80.44(10) . ? O6 Mn2 Mn6 102.84(9) . ? Mn1 Mn2 Mn6 77.27(3) . ? Mn1 Mn2 Mn6 77.36(3) 3_756 ? O1 Mn3 O10 156.49(14) . ? O1 Mn3 O16 94.10(14) . ? O10 Mn3 O16 94.25(15) . ? O1 Mn3 O8 110.72(15) . ? O10 Mn3 O8 87.54(15) . ? O16 Mn3 O8 107.47(15) . ? O1 Mn3 O18 82.78(13) 3_756 ? O10 Mn3 O18 82.73(13) 3_756 ? O16 Mn3 O18 162.69(13) 3_756 ? O8 Mn3 O18 89.47(14) 3_756 ? O1 Mn3 O6 73.22(12) 3_756 ? O10 Mn3 O6 85.10(13) 3_756 ? O16 Mn3 O6 88.37(13) 3_756 ? O8 Mn3 O6 163.00(14) 3_756 ? O18 Mn3 O6 74.41(12) 3_756 3_756 ? O1 Mn3 Mn1 36.26(9) . ? O10 Mn3 Mn1 122.63(10) . ? O16 Mn3 Mn1 86.63(11) . ? O8 Mn3 Mn1 146.27(11) . ?

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112 O18 Mn3 Mn1 80.81(9) 3_756 ? O6 Mn3 Mn1 37.54(8) 3_756 ? O1 Mn3 Mn4 127.28(10) . ? O10 Mn3 Mn4 41.25(10) . ? O16 Mn3 Mn4 135.47(11) . ? O8 Mn3 Mn4 75.51(11) . ? O18 Mn3 Mn4 44.50(9) 3_756 ? O6 Mn3 Mn4 88.93(8) 3_756 ? Mn1 Mn3 Mn4 115.92(3) . ? O11 Mn4 O7 111.37(16) . ? O11 Mn4 O10 91.24(15) . ? O7 Mn4 O10 88.86(15) . ? O11 Mn4 O12 98.40(17) . ? O7 Mn4 O12 98.38(16) . ? O10 Mn4 O12 164.83(16) . ? O11 Mn4 O18 156.18(15) 3_756 ? O7 Mn4 O18 91.35(14) 3_756 ? O10 Mn4 O18 81.82(13) 3_756 ? O12 Mn4 O18 84.69(15) 3_756 ? O11 Mn4 O3 85.93(14) 3_756 ? O7 Mn4 O3 159.92(14) 3_756 ? O10 Mn4 O3 80.36(13) 3_756 ? O12 Mn4 O3 88.63(14) 3_756 ? O18 Mn4 O3 70.48(12) 3_756 3_756 ? O11 Mn4 Mn3 130.82(12) . ? O7 Mn4 Mn3 77.83(11) . ? O10 Mn4 Mn3 39.67(10) . ? O12 Mn4 Mn3 128.95(12) . ? O18 Mn4 Mn3 45.12(9) 3_756 ? O3 Mn4 Mn3 83.12(9) 3_756 ? O10 Mn5 O5 151.72(15) 3_756 ? O10 Mn5 O20 95.01(15) 3_756 ? O5 Mn5 O20 91.17(15) . ? O10 Mn5 O19 90.31(15) 3_756 ? O5 Mn5 O19 112.57(15) . ? O20 Mn5 O19 112.88(17) . ? O10 Mn5 O3 82.47(13) 3_756 ? O5 Mn5 O3 81.64(13) . ? O20 Mn5 O3 158.16(15) . ? O19 Mn5 O3 88.87(14) . ? O10 Mn5 Mn1 118.47(11) 3_756 ? O5 Mn5 Mn1 35.04(9) . ? O20 Mn5 Mn1 83.42(12) . ? O19 Mn5 Mn1 146.34(11) . ? O3 Mn5 Mn1 78.87(9) . ? O13 Mn6 O17 86.55(15) . ?

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113 O13 Mn6 O4 90.18(14) . ? O17 Mn6 O4 173.54(15) . ? O13 Mn6 O16 138.88(14) . ? O17 Mn6 O16 103.71(15) . ? O4 Mn6 O16 82.38(13) . ? O13 Mn6 O2 88.07(13) 3_756 ? O17 Mn6 O2 104.33(14) 3_756 ? O4 Mn6 O2 69.96(12) 3_756 ? O16 Mn6 O2 125.86(13) 3_756 ? O13 Mn6 O15 85.37(14) . ? O17 Mn6 O15 88.42(15) . ? O4 Mn6 O15 96.88(13) . ? O16 Mn6 O15 55.84(13) . ? O2 Mn6 O15 165.29(14) 3_756 ? O13 Mn6 O20 133.51(15) 3_756 ? O17 Mn6 O20 55.25(15) 3_756 ? O4 Mn6 O20 124.73(14) 3_756 ? O16 Mn6 O20 80.99(14) 3_756 ? O2 Mn6 O20 78.49(13) 3_756 3_756 ? O15 Mn6 O20 115.38(14) 3_756 ? O13 Mn6 Mn2 75.00(10) . ? O17 Mn6 Mn2 136.50(12) . ? O4 Mn6 Mn2 37.06(9) . ? O16 Mn6 Mn2 116.17(10) . ? O2 Mn6 Mn2 37.59(9) 3_756 ? O15 Mn6 Mn2 127.74(11) . ? O20 Mn6 Mn2 113.12(10) 3_756 ? C8 O1 Mn1 122.9(3) . ? C8 O1 Mn3 118.1(3) . ? Mn1 O1 Mn3 103.63(15) . ? C7 O2 Mn2 121.3(3) 3_756 ? C7 O2 Mn6 114.1(3) 3_756 ? Mn2 O2 Mn6 96.16(13) 3_756 3_756 ? C7 O2 Mn1 113.9(3) . ? Mn2 O2 Mn1 93.07(14) 3_756 ? Mn6 O2 Mn1 115.81(15) 3_756 ? C1 O3 Mn2 117.9(3) . ? C1 O3 Mn5 111.6(3) . ? Mn2 O3 Mn5 108.69(15) . ? C1 O3 Mn4 124.9(3) 3_756 ? Mn2 O3 Mn4 99.93(14) 3_756 ? Mn5 O3 Mn4 89.81(12) 3_756 ? C2 O4 Mn2 121.9(3) . ? C2 O4 Mn6 111.3(3) . ? Mn2 O4 Mn6 98.27(14) . ? C2 O4 Mn1 113.1(3) . ?

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114 Mn2 O4 Mn1 93.21(13) . ? Mn6 O4 Mn1 117.68(15) . ? C3 O5 Mn1 122.8(3) . ? C3 O5 Mn5 115.9(3) . ? Mn1 O5 Mn5 106.65(15) . ? Mn1 O6 Mn1 96.30(15) 3_756 ? Mn1 O6 Mn2 97.15(14) 3_756 ? Mn1 O6 Mn2 96.44(14) . ? Mn1 O6 Mn3 90.88(13) 3_756 3_756 ? Mn1 O6 Mn3 168.42(18) 3_756 ? Mn2 O6 Mn3 91.65(12) 3_756 ? C34 O7 Mn4 127.6(4) . ? C34 O8 Mn3 130.3(4) . ? Mn5 O10 Mn3 108.58(16) 3_756 ? Mn5 O10 Mn4 100.90(15) 3_756 ? Mn3 O10 Mn4 99.08(15) . ? C48 O11 Mn4 131.6(4) . ? Mn4 O12 H12A 109.5 . ? Mn4 O12 H12B 132(4) . ? H12A O12 H12B 108.4 . ? C62 O13 Mn6 132.1(4) . ? C62 O14 Mn2 126.3(4) . ? C20 O15 Mn6 90.1(3) . ? C20 O16 Mn3 138.7(4) . ? C20 O16 Mn6 94.3(3) . ? Mn3 O16 Mn6 125.54(17) . ? C13 O17 Mn6 97.5(4) . ? C12 O18 Mn2 119.8(3) . ? C12 O18 Mn4 122.9(3) 3_756 ? Mn2 O18 Mn4 101.85(14) 3_756 ? C12 O18 Mn3 111.1(3) 3_756 ? Mn2 O18 Mn3 106.18(15) 3_756 ? Mn4 O18 Mn3 90.37(13) 3_756 3_756 ? C48 O19 Mn5 128.9(4) 3_756 ? C13 O20 Mn5 145.2(4) 3_756 ? C13 O20 Mn6 88.2(4) 3_756 3_756 ? Mn5 O20 Mn6 126.13(19) 3_756 ? C10 O21 H21A 109.5 . ? C5 O22 H22A 109.5 . ? O3 C1 C4 113.9(4) . ? O3 C1 H1A 108.8 . ? C4 C1 H1A 108.8 . ? O3 C1 H1B 108.8 . ? C4 C1 H1B 108.8 . ? H1A C1 H1B 107.7 . ? O4 C2 C4 113.3(4) . ?

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115 O4 C2 H2A 108.9 . ? C4 C2 H2A 108.9 . ? O4 C2 H2B 108.9 . ? C4 C2 H2B 108.9 . ? H2A C2 H2B 107.7 . ? O5 C3 C4 115.7(4) . ? O5 C3 H3A 108.4 . ? C4 C3 H3A 108.4 . ? O5 C3 H3B 108.4 . ? C4 C3 H3B 108.4 . ? H3A C3 H3B 107.4 . ? C1 C4 C2 112.5(4) . ? C1 C4 C3 113.4(5) . ? C2 C4 C3 110.8(4) . ? C1 C4 C5 107.7(4) . ? C2 C4 C5 106.7(4) . ? C3 C4 C5 105.2(4) . ? O22 C5 C4 110.0(4) . ? O22 C5 H5A 109.7 . ? C4 C5 H5A 109.7 . ? O22 C5 H5B 109.7 . ? C4 C5 H5B 109.7 . ? H5A C5 H5B 108.2 . ? O2 C7 C9 114.1(4) . ? O2 C7 H7A 108.7 . ? C9 C7 H7A 108.7 . ? O2 C7 H7B 108.7 . ? C9 C7 H7B 108.7 . ? H7A C7 H7B 107.6 . ? O1 C8 C9 114.9(4) . ? O1 C8 H8A 108.5 . ? C9 C8 H8A 108.5 . ? O1 C8 H8B 108.5 . ? C9 C8 H8B 108.5 . ? H8A C8 H8B 107.5 . ? C8 C9 C7 111.7(4) . ? C8 C9 C12 113.3(5) 3_756 ? C7 C9 C12 111.5(4) 3_756 ? C8 C9 C10 107.6(4) . ? C7 C9 C10 105.8(4) . ? C12 C9 C10 106.4(4) 3_756 ? O21 C10 C9 114.4(4) . ? O21 C10 H10A 108.7 . ? C9 C10 H10A 108.7 . ? O21 C10 H10B 108.7 . ? C9 C10 H10B 108.7 . ?

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116 H10A C10 H10B 107.6 . ? O18 C12 C9 114.2(4) 3_756 ? O18 C12 H12D 108.7 . ? C9 C12 H12D 108.7 3_756 ? O18 C12 H12C 108.7 . ? C9 C12 H12C 108.7 3_756 ? H12D C12 H12C 107.6 . ? O17 C13 O20 119.0(6) 3_756 ? O17 C13 C14 123.5(6) . ? O20 C13 C14 117.5(6) 3_756 ? C16 C14 C13 114.7(5) . ? C16 C14 C15 112.5(6) . ? C13 C14 C15 109.6(5) . ? C16 C14 H14A 106.5 . ? C13 C14 H14A 106.5 . ? C15 C14 H14A 106.5 . ? C80 C15 C19 118.9(8) . ? C80 C15 C14 118.1(7) . ? C19 C15 C14 123.1(7) . ? C17 C16 C18 118.2(7) . ? C17 C16 C14 123.9(7) . ? C18 C16 C14 117.8(7) . ? C84 C17 C16 123.2(9) . ? C84 C17 H17A 118.4 . ? C16 C17 H17A 118.4 . ? C16 C18 C86 118.4(8) . ? C16 C18 H18A 120.8 . ? C86 C18 H18A 120.8 . ? C15 C19 C83 119.9(9) . ? C15 C19 H19A 120.1 . ? C83 C19 H19A 120.1 . ? O15 C20 O16 119.8(5) . ? O15 C20 C21 123.8(5) . ? O16 C20 C21 116.3(5) . ? C22 C21 C20 114.4(5) . ? C22 C21 C28 111.7(4) . ? C20 C21 C28 109.4(4) . ? C22 C21 H21B 107.0 . ? C20 C21 H21B 107.0 . ? C28 C21 H21B 107.0 . ? C23 C22 C27 117.4(6) . ? C23 C22 C21 123.6(6) . ? C27 C22 C21 118.9(6) . ? C24 C23 C22 120.4(8) . ? C24 C23 H23A 119.8 . ? C22 C23 H23A 119.8 . ?

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117 C25 C24 C23 122.6(9) . ? C25 C24 H24A 118.7 . ? C23 C24 H24A 118.7 . ? C24 C25 C26 118.4(8) . ? C24 C25 H25A 120.8 . ? C26 C25 H25A 120.8 . ? C25 C26 C27 120.9(8) . ? C25 C26 H26A 119.5 . ? C27 C26 H26A 119.5 . ? C26 C27 C22 120.2(8) . ? C26 C27 H27A 119.9 . ? C22 C27 H27A 119.9 . ? C33 C28 C29 119.5(6) . ? C33 C28 C21 122.6(5) . ? C29 C28 C21 117.9(5) . ? C30 C29 C28 119.5(6) . ? C30 C29 H29A 120.2 . ? C28 C29 H29A 120.2 . ? C31 C30 C29 120.4(7) . ? C31 C30 H30A 119.8 . ? C29 C30 H30A 119.8 . ? C30 C31 C32 120.4(7) . ? C30 C31 H31A 119.8 . ? C32 C31 H31A 119.8 . ? C33 C32 C31 119.8(7) . ? C33 C32 H32A 120.1 . ? C31 C32 H32A 120.1 . ? C32 C33 C28 120.3(6) . ? C32 C33 H33A 119.8 . ? C28 C33 H33A 119.8 . ? O7 C34 O8 125.8(5) . ? O7 C34 C35 119.8(6) . ? O8 C34 C35 114.3(5) . ? C36 C35 C42 113.7(5) . ? C36 C35 C34 113.4(5) . ? C42 C35 C34 113.1(5) . ? C36 C35 H35A 105.2 . ? C42 C35 H35A 105.2 . ? C34 C35 H35A 105.2 . ? C41 C36 C37 116.9(8) . ? C41 C36 C35 121.4(7) . ? C37 C36 C35 121.7(7) . ? C36 C37 C38 123.2(9) . ? C36 C37 H37A 118.4 . ? C38 C37 H37A 118.4 . ? C39 C38 C37 118.3(9) . ?

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118 C39 C38 H38A 120.8 . ? C37 C38 H38A 120.8 . ? C38 C39 C40 121.0(9) . ? C38 C39 H39A 119.5 . ? C40 C39 H39A 119.5 . ? C39 C40 C41 118.1(10) . ? C39 C40 H40A 121.0 . ? C41 C40 H40A 121.0 . ? C36 C41 C40 122.5(9) . ? C36 C41 H41A 118.8 . ? C40 C41 H41A 118.8 . ? C43 C42 C47 118.8(6) . ? C43 C42 C35 119.0(6) . ? C47 C42 C35 122.1(6) . ? C44 C43 C42 120.7(7) . ? C44 C43 H43A 119.7 . ? C42 C43 H43A 119.7 . ? C43 C44 C45 120.7(7) . ? C43 C44 H44A 119.7 . ? C45 C44 H44A 119.7 . ? C46 C45 C44 119.4(6) . ? C46 C45 H45A 120.3 . ? C44 C45 H45A 120.3 . ? C45 C46 C47 119.7(7) . ? C45 C46 H46A 120.1 . ? C47 C46 H46A 120.1 . ? C42 C47 C46 120.6(6) . ? C42 C47 H47A 119.7 . ? C46 C47 H47A 119.7 . ? O11 C48 O19 126.3(6) 3_756 ? O11 C48 C49 114.9(6) . ? O19 C48 C49 118.7(6) 3_756 ? C50 C49 C56 114.6(5) . ? C50 C49 C48 110.6(5) . ? C56 C49 C48 112.1(5) . ? C50 C49 H49A 106.3 . ? C56 C49 H49A 106.3 . ? C48 C49 H49A 106.3 . ? C55 C50 C51 117.8(7) . ? C55 C50 C49 120.1(7) . ? C51 C50 C49 122.1(6) . ? C50 C51 C52 118.8(8) . ? C50 C51 H51A 120.6 . ? C52 C51 H51A 120.6 . ? C53 C52 C51 120.8(9) . ? C53 C52 H52A 119.6 . ?

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119 C51 C52 H52A 119.6 . ? C52 C53 C54 121.4(10) . ? C52 C53 H53A 119.3 . ? C54 C53 H53A 119.3 . ? C53 C54 C55 119.4(9) . ? C53 C54 H54A 120.3 . ? C55 C54 H54A 120.3 . ? C54 C55 C50 121.8(9) . ? C54 C55 H55A 119.1 . ? C50 C55 H55A 119.1 . ? C57 C56 C61 119.1(6) . ? C57 C56 C49 122.1(6) . ? C61 C56 C49 118.8(6) . ? C56 C57 C58 121.1(7) . ? C56 C57 H57A 119.4 . ? C58 C57 H57A 119.4 . ? C59 C58 C57 120.3(7) . ? C59 C58 H58A 119.9 . ? C57 C58 H58A 119.9 . ? C60 C59 C58 119.2(7) . ? C60 C59 H59A 120.4 . ? C58 C59 H59A 120.4 . ? C59 C60 C61 120.4(7) . ? C59 C60 H60A 119.8 . ? C61 C60 H60A 119.8 . ? C56 C61 C60 119.8(7) . ? C56 C61 H61A 120.1 . ? C60 C61 H61A 120.1 . ? O13 C62 O14 125.9(5) . ? O13 C62 C63 118.4(6) . ? O14 C62 C63 115.6(5) . ? C64 C63 C70 117.1(5) . ? C64 C63 C62 112.7(5) . ? C70 C63 C62 107.0(5) . ? C64 C63 H63A 106.4 . ? C70 C63 H63A 106.4 . ? C62 C63 H63A 106.4 . ? C69 C64 C65 117.0(6) . ? C69 C64 C63 122.6(6) . ? C65 C64 C63 120.1(6) . ? C66 C65 C64 122.3(7) . ? C66 C65 H65A 118.9 . ? C64 C65 H65A 118.9 . ? C65 C66 C67 118.4(7) . ? C65 C66 H66A 120.8 . ? C67 C66 H66A 120.8 . ?

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120 C68 C67 C66 122.0(7) . ? C68 C67 H67A 119.0 . ? C66 C67 H67A 119.0 . ? C67 C68 C69 118.5(8) . ? C67 C68 H68A 120.7 . ? C69 C68 H68A 120.7 . ? C68 C69 C64 121.8(7) . ? C68 C69 H69A 119.1 . ? C64 C69 H69A 119.1 . ? C74 C70 C71 118.2(7) . ? C74 C70 C63 122.9(6) . ? C71 C70 C63 118.7(7) . ? C70 C71 C75 119.8(8) . ? C70 C71 H71A 120.1 . ? C75 C71 H71A 120.1 . ? C73 C72 C75 120.3(8) . ? C73 C72 H72A 119.9 . ? C75 C72 H72A 119.9 . ? C72 C73 C74 120.7(9) . ? C72 C73 H73A 119.7 . ? C74 C73 H73A 119.7 . ? C70 C74 C73 121.4(8) . ? C70 C74 H74A 119.3 . ? C73 C74 H74A 119.3 . ? C72 C75 C71 119.5(8) . ? C72 C75 H75A 120.2 . ? C71 C75 H75A 120.2 . ? C15 C80 C81 119.2(9) . ? C15 C80 H80A 120.4 . ? C81 C80 H80A 120.4 . ? C82 C81 C80 122.7(10) . ? C82 C81 H81A 118.7 . ? C80 C81 H81A 118.7 . ? C81 C82 C83 118.2(10) . ? C81 C82 H82A 120.9 . ? C83 C82 H82A 120.9 . ? C82 C83 C19 121.2(10) . ? C82 C83 H83A 119.4 . ? C19 C83 H83A 119.4 . ? C85 C84 C17 118.5(10) . ? C85 C84 H84A 120.8 . ? C17 C84 H84A 120.8 . ? C84 C85 C86 123.3(9) . ? C84 C85 H85A 118.4 . ? C86 C85 H85A 118.4 . ? C85 C86 C18 118.5(9) . ?

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121 C85 C86 H86A 120.8 . ? C18 C86 H86A 120.8 . ? N1 C87 C88 178.8(9) . ? C87 C88 H88A 109.5 . ? C87 C88 H88B 109.5 . ? H88A C88 H88B 109.5 . ? C87 C88 H88C 109.5 . ? H88A C88 H88C 109.5 . ? H88B C88 H88C 109.5 . ? N2 C89 C90 179.0(9) . ? C89 C90 H90A 109.5 . ? C89 C90 H90B 109.5 . ? H90A C90 H90B 109.5 . ? C89 C90 H90C 109.5 . ? H90A C90 H90C 109.5 . ? H90B C90 H90C 109.5 . ? N3 C91 C92 176.9(10) . ? C91 C92 H92A 109.5 . ? C91 C92 H92B 109.5 . ? H92A C92 H92B 109.5 . ? C91 C92 H92C 109.5 . ? H92A C92 H92C 109.5 . ? H92B C92 H92C 109.5 . ? _diffrn_measured_fraction_theta_max 0.996 _diffrn_reflns_theta_full 27.50 _diffrn_measured_fraction_theta_full 0.996 _refine_diff_density_max 0.609 _refine_diff_density_min -0.659 _refine_diff_density_rms 0.157

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122 APPENDIX C CIF FILE OF STRUCTURE CW10 data_cw10 _audit_creation_method SHELXL-97 _chemical_name_systematic ; ? ; _chemical_name_common ? _chemical_melting_point ? _chemical_formula_moiety ? _chemical_formula_sum 'C15 H31 Cl3 N4 W' _chemical_formula_weight 557.64 loop_ _atom_type_symbol _atom_type_description _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source 'C' 'C' 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'H' 'H' 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'N' 'N' 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'Cl' 'Cl' 0.1484 0.1585 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'W' 'W' -0.8490 6.8722 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' _symmetry_cell_setting Orthorhombic _symmetry_space_group_name_H-M Pna2(1) loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x, -y, z+1/2'

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123 'x+1/2, -y+1/2, z' '-x+1/2, y+1/2, z+1/2' _cell_length_a 15.2755(11) _cell_length_b 15.1852(11) _cell_length_c 9.3285(7) _cell_angle_alpha 90.00 _cell_angle_beta 90.00 _cell_angle_gamma 90.00 _cell_volume 2163.9(3) _cell_formula_units_Z 4 _cell_measurement_temperature 173(2) _cell_measurement_reflns_used 97 _cell_measurement_theta_min 2.0 _cell_measurement_theta_max 28.0 _exptl_crystal_description needles _exptl_crystal_colour red _exptl_crystal_size_max 0.18 _exptl_crystal_size_mid 0.09 _exptl_crystal_size_min 0.06 _exptl_crystal_density_meas ? _exptl_crystal_density_diffrn 1.712 _exptl_crystal_density_method 'not measured' _exptl_crystal_F_000 1096 _exptl_absorpt_coefficient_mu 5.713 _exptl_absorpt_correction_t ype integration _exptl_absorpt_correction_T_min 0.4549 _exptl_absorpt_correction_T_max 0.7259 _exptl_absorpt_process_details 'based on measured indexed crys tal faces, SHELXTL (Bruker 1998)' _exptl_special_details ; ? ; _diffrn_ambient_temperature 193(2) _diffrn_radiation_wavelength 0.71073 _diffrn_radiation_type MoK\a _diffrn_radiation_source 'normal-focus sealed tube' _diffrn_radiation_monochromator graphite _diffrn_measurement_device_type 'SMART CCD area detector' _diffrn_measurement_method '\w scans' _diffrn_detector_area_ resol_mean ? _diffrn_standards_number 0

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124 _diffrn_standards_interval_count ? _diffrn_standards_interval_time ? _diffrn_standards_decay_% none _diffrn_reflns_number 13619 _diffrn_reflns_av_R_equivalents 0.0425 _diffrn_reflns_av_sigmaI/netI 0.0352 _diffrn_reflns_limit_h_min -17 _diffrn_reflns_limit_h_max 19 _diffrn_reflns_limit_k_min -16 _diffrn_reflns_limit_k_max 19 _diffrn_reflns_limit_l_min -11 _diffrn_reflns_limit_l_max 12 _diffrn_reflns_theta_min 1.89 _diffrn_reflns_theta_max 27.49 _reflns_number_total 4767 _reflns_number_gt 4426 _reflns_threshold_expression 'I>2\s(I)' _computing_data_collection 'Bruker SMART (Bruker 1998)' _computing_cell_refinement 'Bruker SMART & SAINT (Bruker 1998)' _computing_data_reduction 'Bruker SHELXTL (Bruker 2000)' _computing_structure_solution 'Bruker SHELXTL' _computing_structure_refinem ent 'Bruker SHELXTL' _computing_molecular_graphics 'Bruker SHELXTL' _computing_publication_material 'Bruker SHELXTL' _refine_special_details ; Refinement of F^2^ against ALL reflect ions. The weighted R-factor wR and goodness of fit S are based on F^2^, c onventional R-factors R are based on F, with F set to zero for negativ e F^2^. The threshold expression of F^2^ > 2sigma(F^2^) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflec tions for refinement. R-factors based on F^2^ are statistically about twice as large as t hose based on F, and Rfactors based on ALL data will be even larger. ; _refine_ls_structure_factor_coef Fsqd _refine_ls_matrix_type full _refine_ls_weighting_scheme calc _refine_ls_weighting_details 'calc w=1/[\s^2^(Fo^2^)+(0.0697P)^2^+20.2234P] where P=(Fo^2^+2Fc^2^)/3' _atom_sites_solution_primary direct _atom_sites_solution_secondary difmap _atom_sites_solution_hydrogens geom

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125 _refine_ls_hydrogen_treatment mixed _refine_ls_extinction_method none _refine_ls_extinction_coef ? _refine_ls_abs_structure_details 'Flack H D (1983), Acta Cryst. A39, 876-881' _refine_ls_abs_structure _Flack 1.010(19) _refine_ls_number_reflns 4767 _refine_ls_number_parameters 214 _refine_ls_number_restraints 1 _refine_ls_R_factor_all 0.0549 _refine_ls_R_factor_gt 0.0501 _refine_ls_wR_factor_ref 0.1319 _refine_ls_wR_factor_gt 0.1292 _refine_ls_goodness_of_fit_ref 1.067 _refine_ls_restrained_S_all 1.067 _refine_ls_shift/su_max 0.000 _refine_ls_shift/su_mean 0.000 loop_ _atom_site_label _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_adp_type _atom_site_occupancy _atom_site_symmetry_multiplicity _atom_site_calc_flag _atom_site_refinement_flags _atom_site_disorder_assembly _atom_site_disorder_group W1 W 0.26495(2) 0.11221(2) 0.33440(9) 0.02623(12) Uani 1 1 d . Cl1 Cl 0.17129(19) 0.0220(2) 0.1952(4) 0.0484(7) Uani 1 1 d . Cl2 Cl 0.3834(2) 0.18013(19) 0.4592(3) 0.0394(6) Uani 1 1 d . Cl3 Cl 0.30930(19) -0.02024(18) 0.4516(3) 0.0414(6) Uani 1 1 d . N1 N 0.3590(6) 0.0937(6) 0.1500(9) 0.0271(17) Uani 1 1 d . N2 N 0.2712(5) 0.2040(6) 0.1885(9) 0.0284(18) Uani 1 1 d . N3 N 0.1822(6) 0.1518(6) 0.4424(10) 0.035(2) Uani 1 1 d . N4 N 0.3657(7) 0.2151(6) -0.0183(10) 0.036(2) Uani 1 1 d . C1 C 0.3377(6) 0.1713(6) 0.0987(10) 0.0254( 19) Uani 1 1 d . C2 C 0.3953(9) 0.1706(9) -0.1491(16) 0.051(3) Uani 1 1 d . H2A H 0.4589 0.1625 -0.1453 0.076 Uiso 1 1 calc R . H2B H 0.3801 0.2064 -0.2328 0.076 Uiso 1 1 calc R . H2C H 0.3667 0.1130 -0.1566 0.076 Uiso 1 1 calc R . C3 C 0.3926(10) 0.3083(8) -0.0079(15) 0.048(3) Uani 1 1 d .

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126 H3A H 0.3769 0.3314 0.0868 0.072 Uiso 1 1 calc R . H3B H 0.3627 0.3427 -0.0822 0.072 Uiso 1 1 calc R . H3C H 0.4561 0.3128 -0.0213 0.072 Uiso 1 1 calc R . C4 C 0.2145(7) 0.2809(7) 0.1512(11) 0.033(2) Uani 1 1 d . H4A H 0.2364 0.3067 0.0593 0.040 Uiso 1 1 calc R . C5 C 0.2247(9) 0.3498(8) 0.2683(14) 0.044(3) Uani 1 1 d . H5A H 0.1992 0.3276 0.3577 0.065 Uiso 1 1 calc R . H5B H 0.1945 0.4040 0.2397 0.065 Uiso 1 1 calc R . H5C H 0.2870 0.3623 0.2829 0.065 Uiso 1 1 calc R . C6 C 0.1205(9) 0.2527(9) 0.1287(14) 0.049(3) Uani 1 1 d . H6A H 0.1188 0.2017 0.0642 0.074 Uiso 1 1 calc R . H6B H 0.0873 0.3013 0.0862 0.074 Uiso 1 1 calc R . H6C H 0.0945 0.2366 0.2211 0.074 Uiso 1 1 calc R . C7 C 0.4330(7) 0.0388(6) 0.1064(11) 0.029(2) Uani 1 1 d . H7A H 0.4616 0.0656 0.0205 0.035 Uiso 1 1 calc R . C8 C 0.4999(8) 0.0331(9) 0.2289(14) 0.045(3) Uani 1 1 d . H8A H 0.5193 0.0926 0.2548 0.067 Uiso 1 1 calc R . H8B H 0.5504 -0.0017 0.1977 0.067 Uiso 1 1 calc R . H8C H 0.4728 0.0050 0.3123 0.067 Uiso 1 1 calc R . C9 C 0.3982(10) -0.0512(8) 0.0669(15) 0.048(3) Uani 1 1 d . H9A H 0.3644 -0.0751 0.1474 0.072 Uiso 1 1 calc R . H9B H 0.4472 -0.0906 0.0453 0.072 Uiso 1 1 calc R . H9C H 0.3603 -0.0462 -0.0174 0.072 Uiso 1 1 calc R . C10 C 0.1109(8) 0.1845(8) 0.5314(13) 0.041(3) Uani 1 1 d . H10A H 0.0899 0.2420 0.4919 0.049 Uiso 1 1 calc R . C11 C 0.0365(10) 0.1180(10) 0.5253(19) 0.057(4) Uani 1 1 d . H11A H -0.0164 0.1438 0.5697 0.068 Uiso 1 1 calc R . H11B H 0.0228 0.1045 0.4239 0.068 Uiso 1 1 calc R . C12 C 0.0603(10) 0.0335(10) 0.603(2) 0.067(5) Uani 1 1 d . H12A H 0.0089 -0.0061 0.6033 0.080 Uiso 1 1 calc R . H12B H 0.1079 0.0036 0.5497 0.080 Uiso 1 1 calc R . C13 C 0.0889(11) 0.0490(11) 0.752(2) 0.076(6) Uani 1 1 d . H13A H 0.1051 -0.0078 0.7964 0.091 Uiso 1 1 calc R . H13B H 0.0399 0.0747 0.8072 0.091 Uiso 1 1 calc R . C14 C 0.1666(13) 0.1109(11) 0.7561(16) 0.070(5) Uani 1 1 d . H14A H 0.2170 0.0833 0.7067 0.083 Uiso 1 1 calc R . H14B H 0.1835 0.1217 0.8570 0.083 Uiso 1 1 calc R . C15 C 0.1448(12) 0.1990(11) 0.6835(16) 0.064(4) Uani 1 1 d . H15A H 0.1000 0.2304 0.7405 0.077 Uiso 1 1 calc R . H15B H 0.1980 0.2362 0.6803 0.077 Uiso 1 1 calc R . loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33

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127 _atom_site_aniso_U_23 _atom_site_aniso_U_13 _atom_site_aniso_U_12 W1 0.02787(19) 0.02665(18) 0.02417(19) 0.0057(2) 0.0059(3) 0.00443(12) Cl1 0.0305(13) 0.0539(18) 0.061(2) 0.0058(15) -0.0032(13) -0.0080(12) Cl2 0.0462(15) 0.0437(15) 0.0282(12) 0.0044(11) -0.0036(11) -0.0012(12) Cl3 0.0404(14) 0.0364(14) 0.0475(16) 0.0178(12) 0.0088(12) 0.0060(11) N1 0.031(4) 0.028(4) 0.022(4) 0.005(3) 0.004(3) 0.001(3) N2 0.030(4) 0.029(4) 0.026(4) 0.003(3) 0.006(3) 0.010(3) N3 0.032(5) 0.038(5) 0.034(5) 0.006(4) 0.010(4) 0.008(4) N4 0.042(5) 0.036(5) 0.031(5) 0.007(4) 0.010(4) 0.003(4) C1 0.028(5) 0.027(5) 0.022(5) -0.001(4) -0.001(4) 0.003(4) C2 0.060(7) 0.057(7) 0.035(7) 0.006(6) 0.012(7) 0.019(6) C3 0.064(8) 0.031(6) 0.049(8) 0.013(5) 0.015(6) 0.003(5) C4 0.038(6) 0.033(5) 0.027(5) 0.014(4) 0.005(4) 0.018(4) C5 0.062(8) 0.029(6) 0.040(6) 0.002(5) 0.001(5) 0.015(5) C6 0.050(7) 0.057(8) 0.041(7) 0.004(6) -0.004(6) 0.023(6) C7 0.036(5) 0.028(5) 0.024(5) 0.004(4) 0.006(4) -0.004(4) C8 0.035(6) 0.053(7) 0.046(7) 0.010(6) 0.003(5) 0.011(5) C9 0.065(8) 0.027(6) 0.052(7) -0.014(5) 0.012(6) 0.006(5) C10 0.045(7) 0.035(6) 0.042(7) 0.000(5) 0.016(5) 0.004(5) C11 0.037(7) 0.068(10) 0.066(10) -0 .002(7) 0.011(7) 0.012(6) C12 0.052(9) 0.051(8) 0.098(14) 0.001(8) 0.036(9) -0.001(7) C13 0.073(11) 0.068(10) 0.086(12) 0.033(9) 0.048(10) 0.028(9) C14 0.085(13) 0.091(13) 0.033(8) 0.002(7) 0.020(8) 0.026(10) C15 0.081(11) 0.071(10) 0.040(8) -0 .023(7) 0.014(7) 0.000(9) _geom_special_details ; All esds (except the esd in the dihe dral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. ; loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance _geom_bond_site_symmetry_2 _geom_bond_publ_flag W1 N3 1.724(9) ? W1 N2 1.951(9) ? W1 N1 2.259(8) ?

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128 W1 Cl1 2.369(3) ? W1 Cl2 2.386(3) ? W1 Cl3 2.387(3) ? W1 C1 2.622(10) ? N1 C1 1.312(12) ? N1 C7 1.462(13) ? N2 C1 1.407(12) ? N2 C4 1.495(12) ? N3 C10 1.457(14) ? N4 C1 1.349(13) ? N4 C2 1.467(16) ? N4 C3 1.477(15) ? C2 H2A 0.9800 ? C2 H2B 0.9800 ? C2 H2C 0.9800 ? C3 H3A 0.9800 ? C3 H3B 0.9800 ? C3 H3C 0.9800 ? C4 C6 1.513(18) ? C4 C5 1.521(17) ? C4 H4A 1.0000 ? C5 H5A 0.9800 ? C5 H5B 0.9800 ? C5 H5C 0.9800 ? C6 H6A 0.9800 ? C6 H6B 0.9800 ? C6 H6C 0.9800 ? C7 C9 1.512(15) ? C7 C8 1.535(16) ? C7 H7A 1.0000 ? C8 H8A 0.9800 ? C8 H8B 0.9800 ? C8 H8C 0.9800 ? C9 H9A 0.9800 ? C9 H9B 0.9800 ? C9 H9C 0.9800 ? C10 C11 1.521(19) ? C10 C15 1.53(2) ? C10 H10A 1.0000 ? C11 C12 1.52(2) ? C11 H11A 0.9900 ? C11 H11B 0.9900 ? C12 C13 1.47(3) ? C12 H12A 0.9900 ? C12 H12B 0.9900 ? C13 C14 1.52(3) ?

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129 C13 H13A 0.9900 ? C13 H13B 0.9900 ? C14 C15 1.54(2) ? C14 H14A 0.9900 ? C14 H14B 0.9900 ? C15 H15A 0.9900 ? C15 H15B 0.9900 ? loop_ _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_angle _geom_angle_site_symmetry_1 _geom_angle_site_symmetry_3 _geom_angle_publ_flag N3 W1 N2 101.2(4) . ? N3 W1 N1 162.6(4) . ? N2 W1 N1 61.7(3) . ? N3 W1 Cl1 94.6(3) . ? N2 W1 Cl1 93.5(3) . ? N1 W1 Cl1 84.0(2) . ? N3 W1 Cl2 96.9(4) . ? N2 W1 Cl2 89.7(3) . ? N1 W1 Cl2 86.7(2) . ? Cl1 W1 Cl2 167.31(11) . ? N3 W1 Cl3 103.6(3) . ? N2 W1 Cl3 155.2(2) . ? N1 W1 Cl3 93.6(2) . ? Cl1 W1 Cl3 86.28(11) . ? Cl2 W1 Cl3 85.73(11) . ? N3 W1 C1 132.9(4) . ? N2 W1 C1 31.8(3) . ? N1 W1 C1 30.0(3) . ? Cl1 W1 C1 89.7(2) . ? Cl2 W1 C1 86.6(2) . ? Cl3 W1 C1 123.5(2) . ? C1 N1 C7 127.1(8) . ? C1 N1 W1 90.4(6) . ? C7 N1 W1 140.7(6) . ? C1 N2 C4 123.8(8) . ? C1 N2 W1 101.4(6) . ? C4 N2 W1 133.8(6) . ? C10 N3 W1 178.7(9) . ? C1 N4 C2 122.9(10) . ? C1 N4 C3 120.5(10) . ?

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130 C2 N4 C3 114.3(10) . ? N1 C1 N4 131.3(9) . ? N1 C1 N2 106.3(8) . ? N4 C1 N2 122.4(9) . ? N1 C1 W1 59.5(5) . ? N4 C1 W1 169.2(7) . ? N2 C1 W1 46.9(5) . ? N4 C2 H2A 109.5 . ? N4 C2 H2B 109.5 . ? H2A C2 H2B 109.5 . ? N4 C2 H2C 109.5 . ? H2A C2 H2C 109.5 . ? H2B C2 H2C 109.5 . ? N4 C3 H3A 109.5 . ? N4 C3 H3B 109.5 . ? H3A C3 H3B 109.5 . ? N4 C3 H3C 109.5 . ? H3A C3 H3C 109.5 . ? H3B C3 H3C 109.5 . ? N2 C4 C6 111.2(9) . ? N2 C4 C5 108.1(9) . ? C6 C4 C5 113.1(10) . ? N2 C4 H4A 108.1 . ? C6 C4 H4A 108.1 . ? C5 C4 H4A 108.1 . ? C4 C5 H5A 109.5 . ? C4 C5 H5B 109.5 . ? H5A C5 H5B 109.5 . ? C4 C5 H5C 109.5 . ? H5A C5 H5C 109.5 . ? H5B C5 H5C 109.5 . ? C4 C6 H6A 109.5 . ? C4 C6 H6B 109.5 . ? H6A C6 H6B 109.5 . ? C4 C6 H6C 109.5 . ? H6A C6 H6C 109.5 . ? H6B C6 H6C 109.5 . ? N1 C7 C9 108.1(9) . ? N1 C7 C8 109.8(9) . ? C9 C7 C8 111.4(10) . ? N1 C7 H7A 109.1 . ? C9 C7 H7A 109.1 . ? C8 C7 H7A 109.1 . ? C7 C8 H8A 109.5 . ? C7 C8 H8B 109.5 . ? H8A C8 H8B 109.5 . ?

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131 C7 C8 H8C 109.5 . ? H8A C8 H8C 109.5 . ? H8B C8 H8C 109.5 . ? C7 C9 H9A 109.5 . ? C7 C9 H9B 109.5 . ? H9A C9 H9B 109.5 . ? C7 C9 H9C 109.5 . ? H9A C9 H9C 109.5 . ? H9B C9 H9C 109.5 . ? N3 C10 C11 108.1(10) . ? N3 C10 C15 108.9(11) . ? C11 C10 C15 112.6(12) . ? N3 C10 H10A 109.1 . ? C11 C10 H10A 109.1 . ? C15 C10 H10A 109.1 . ? C12 C11 C10 111.4(13) . ? C12 C11 H11A 109.3 . ? C10 C11 H11A 109.3 . ? C12 C11 H11B 109.3 . ? C10 C11 H11B 109.3 . ? H11A C11 H11B 108.0 . ? C13 C12 C11 112.6(14) . ? C13 C12 H12A 109.1 . ? C11 C12 H12A 109.1 . ? C13 C12 H12B 109.1 . ? C11 C12 H12B 109.1 . ? H12A C12 H12B 107.8 . ? C12 C13 C14 110.9(12) . ? C12 C13 H13A 109.5 . ? C14 C13 H13A 109.5 . ? C12 C13 H13B 109.5 . ? C14 C13 H13B 109.5 . ? H13A C13 H13B 108.0 . ? C13 C14 C15 111.0(15) . ? C13 C14 H14A 109.4 . ? C15 C14 H14A 109.4 . ? C13 C14 H14B 109.4 . ? C15 C14 H14B 109.4 . ? H14A C14 H14B 108.0 . ? C10 C15 C14 111.0(12) . ? C10 C15 H15A 109.4 . ? C14 C15 H15A 109.4 . ? C10 C15 H15B 109.4 . ? C14 C15 H15B 109.4 . ? H15A C15 H15B 108.0 . ?

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132 _diffrn_measured_fraction_theta_max 0.996 _diffrn_reflns_theta_full 27.49 _diffrn_measured_fraction_theta_full 0.996 _refine_diff_density_max 1.501 _refine_diff_density_min -1.121 _refine_diff_density_rms 0.140

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133 APPENDIX D CIF FILE OF AQUA-CHLORO-( 1,4,8,11-TETRAAZAUNDECANE)NICKEL(II) CHLORIDE data_global #========================== ================== =========== # 1. SUBMISSION DETAILS _publ_contact_author # Name and address of author for correspondence ; Alexandr E. Oblezov Department of Chemistry University of Florida P.O. Box 117200 Gainesville, Florida 32611-7200 ; _publ_contact_author_phone '352 392 5948' _publ_contact_author_fax '352 846 2040' _publ_contact_author_email aoblezov@chem.ufl.edu _publ_requested_journal 'Acta Crystallographica E' _publ_requested_coeditor_name ? _publ_requested_category EM _publ_contact_letter ; Please consider this CIF subm ission for publication as a paper in Acta Crystalographica section E. Relevant files of the figures, schemes and table of structure factor amplitudes will be sent by ftp to the Chester Office as soon as requested. ; #========================== ================== =========== # 2. PROCESSING SUMMARY (IUCr Office Use Only) _journal_date_recd_ele ctronic ? _journal_date_to_coeditor ? _journal_date_from_coeditor ? _journal_date_accepted ?

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134 _journal_date_printers_first ? _journal_date_printers_final ? _journal_date_proofs_out ? _journal_date_proofs_in ? _journal_coeditor_name ? _journal_coeditor_code ? _journal_coeditor_notes ; ? ; _journal_techeditor_code ? _journal_techeditor_notes ; ? ; _journal_coden_ASTM ? _journal_name_full ? _journal_year ? _journal_volume ? _journal_issue ? _journal_page_first ? _journal_page_last ? _journal_suppl_publ_number ? _journal_suppl_publ_pages ? #========================== ================== =========== # 3. TITLE AND AUTHOR LIST _publ_section_title ; Aqua-chloro-1,4,8,11-tetraazaundecanenickel(II) chloride ; _publ_section_title_footnote ; ? ; # The loop structure below should cont ain the names and addresses of all # authors, in the requ ired order of publicati on. Repeat as necessary. loop_ _publ_author_name _publ_author_address 'Oblezov, Alexandr E.' ;

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135 Department of Chemistry University of Florida P.O. Box 117200 Gainesville, Florida 32611-7200, USA ; 'Talham, Daniel R.' ; Department of Chemistry University of Florida P.O. Box 117200 Gainesville, Florida 32611-7200, USA ; 'Abboud, Khalil A.' ; Department of Chemistry University of Florida P.O. Box 117200 Gainesville, Florida 32611-7200, USA ; #========================== ================== =========== # 4. TEXT _publ_section_abstract ; The title compound, [Ni(OH~2~ )Cl(1,4,8,11-tetraazaundecane)]Cl, C~7~H~22~N~4~OCl~2~Ni, has a Nickel atom in a distorted octahedral coordination geometry with the four amino N atoms occupying a square plane while the chloro and aqua ligands occupying the axial positions. The Ni-N bond distances range from 2.079(1) to 2.088(2) \%A. ; _publ_section_comment ; Complexes of transition metals with long alkyl chains are widely used to build Langmuir-Blodgett monolayer s with specific magnetic properties (Culp et al., 2002; Culp et al., 2003). An attempt to accomplish synthesis of Nickel (II) pentaaza m acrocyclic complex with an attached 1-dodecyl chain, the same way as de scribed in (Choi & Suh, 2003), was not successful. The result of this reaction was aqua-chloro-1,4,8,11-tetraazaundecaneNi ckel(II) chloride complex. Lavender prismatic crystals were coll ected and characterized by single crystal X-ray diffraction.

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136 The tetradentate 1,4,8,11-tetraazaundecane ligand is coordinated to the Ni center in a wrap-a round fashion occupying the four square planar positions. The Ni-N bond distances [ave rage bond length is 2.080(2)\%A] are significantly longer than their counterparts in the 1,4,8,11-tetraazaundecaneNickel(II) ca tion [average bond length is 1.923(5)\%A] (Bernard et al., 2001). In the latter, the Ni center is in a square planar coordinati on and with vacant axil positions. The protons of the coordinated wate r and the uncoordinated counterion Cl2 are involved in H-bonding with th eir inversion symmetry equivalents, creating a diamond-shaped interaction. As a result, H-bonding chains are formed along the b-axis. These chai ns are linked together by H-bonds between the amino protons on one hand and both, coordinated and uncoordinated, chlorine ions, thus creating two-dimensional layers in the ab-plane. ; _publ_section_exptl_prep ; To a refluxed solution of NiCl~2 ~.6H~2~O (1.2 g, 5 mmol) in MeOH (50 ml) were added 1,4,8,11-tetraazaundecane (0.8 g, 5 mmol). After 3 hours of refluxing the mixture, th e solvent was evaporated and a light purple product of the reacti on was dissolved in EtOH (20ml). Slow evaporation of the solvent over five days, at room temperature, yielded light purple prismatic crystals. ; _publ_section_exptl_refinement ; The C-H and N-H Hydrogen atoms were placed in idealized positions and were refined riding on their parent atoms. C-H di stance of 0.99 \%A was used for SP^3^ C atoms. N-H distance of 0.93 and 0.92 \%A were used in N-H and N-H~2~ amino groups, respectivately. The H atoms thermal parameters were 1.2U~eq~ of the parent C or N atoms. A hemisphere of frames, 0.3\% in \w, was collected. The first 50 frames were remeasured at the end of data collection to monitor instrument and crystal stability. The water molecule protons were obtained from a difference Fourier map, but did not refine properl y. Thus they were constrained in a riding model on the oxygen atom.

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137 ; _publ_section_references ; Bernard B.R., Haines R.I., Rowley J. E. (2001). Transition Met. Chem. 26 164-169. Bruker (2000). SMART,SAINT & SHELXTL. Data Collection and Processing Software for the SMART System. Bruker-AXS, Madison, Wisconsin, USA. Choi H.J. and Suh M.P. (2003). Inorg. Chem. 42 1151-1157 Culp J.T., Park J.-H., Meisel M.W., and Talham D.R. (2003). Inorg. Chem. 42 2842-2848 Culp J.T., Park J.-H., Stratakis D., Meisel M.W., Talham D.R. (2002). J. Am. Chem. Soc. 124 (34) 10083-10090 ; _publ_section_figure_captions ; Fig. 1: View of an asymmetr ic unit of the title compound. Fig. 2: View of the two dimensional la yer in the crystal structure of the title compound. ; _publ_section_acknowledgements ; We wishes to acknowledge the National Science Foundation and the University of Florida for funding of the purchas e of the X-ray equipment. ; #========================== ================== ============ # If more than one structure is repor ted, sections 5-10 should be filled in # per structure. For each data set, re place the '?' in the data_? line below # by a unique identifier. #========================== ================== ============ # 5. CHEMICAL DATA #========================== ================== ============ # Additional structures (sections 5-10 and associated da ta_? identifiers) # may be added at this point.

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138 #========================== ================== ============ data_ao02 _audit_creation_method SHELXL-97 _chemical_name_systematic ; ? ; _chemical_name_common ? _chemical_melting_point ? _chemical_formula_moiety '(C7 H22 Cl N4 Ni O)+, Cl-' _chemical_formula_sum 'C7 H22 Cl2 N4 Ni O' _chemical_formula_weight 307.90 loop_ _atom_type_symbol _atom_type_description _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source 'C' 'C' 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'H' 'H' 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'N' 'N' 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'O' 'O' 0.0106 0.0060 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'Cl' 'Cl' 0.1484 0.1585 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' 'Ni' 'Ni' 0.3393 1.1124 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' _symmetry_cell_setting Monoclinic _symmetry_space_group_name_H-M 'P 21/n' loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x+1/2, y+1/2, -z+1/2' '-x, -y, -z'

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139 'x-1/2, -y-1/2, z-1/2' _cell_length_a 8.3029(6) _cell_length_b 10.2497(7) _cell_length_c 15.6829(11) _cell_angle_alpha 90.00 _cell_angle_beta 94.470(2) _cell_angle_gamma 90.00 _cell_volume 1330.59(16) _cell_formula_units_Z 4 _cell_measurement_temperature 173(2) _cell_measurement_reflns_used 112 _cell_measurement_theta_min 2.0 _cell_measurement_theta_max 28.0 _exptl_crystal_description plates _exptl_crystal_colour purple _exptl_crystal_size_max 0.26 _exptl_crystal_size_mid 0.24 _exptl_crystal_size_min 0.23 _exptl_crystal_density_meas 'not measured' _exptl_crystal_density_diffrn 1.537 _exptl_crystal_density_method 'not measured' _exptl_crystal_F_000 648 _exptl_absorpt_coefficient_mu 1.843 _exptl_absorpt_correction_t ype integration _exptl_absorpt_correction_T_min 0.5361 _exptl_absorpt_correction_T_max 0.7527 _exptl_absorpt_process_details 'based on measured indexed crys tal faces, SHELXTL (Bruker 1998)' _exptl_special_details ; ? ; _diffrn_ambient_temperature 173(2) _diffrn_radiation_wavelength 0.71073 _diffrn_radiation_type MoK\a _diffrn_radiation_source 'normal-focus sealed tube' _diffrn_radiation_monochromator graphite _diffrn_measurement_device_type 'SMART CCD (1K) area detector' _diffrn_measurement_method '\w scans' _diffrn_detector_area_ resol_mean ? _diffrn_standards_number 0 _diffrn_standards_interval_count ?

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140 _diffrn_standards_interval_time ? _diffrn_standards_decay_% 0 _diffrn_reflns_number 7715 _diffrn_reflns_av_R_equivalents 0.0887 _diffrn_reflns_av_sigmaI/netI 0.0585 _diffrn_reflns_limit_h_min -5 _diffrn_reflns_limit_h_max 10 _diffrn_reflns_limit_k_min -12 _diffrn_reflns_limit_k_max 13 _diffrn_reflns_limit_l_min -20 _diffrn_reflns_limit_l_max 19 _diffrn_reflns_theta_min 2.38 _diffrn_reflns_theta_max 27.50 _reflns_number_total 2944 _reflns_number_gt 2798 _reflns_threshold_expression 'I > 2\s(I)' _computing_data_collection 'Bruker SMART V5.624 (Bruker 1998)' _computing_cell_refinement 'Bruker SMART & SAINT (Bruker 1998)' _computing_data_reduction 'Bruker SAINT V6.22 (Bruker 1998)' _computing_structure_solution 'Bruker SHELXTL V6.1 (Bruker 2000)' _computing_structure_refinem ent 'Bruker SHELXTL' _computing_molecular_graphics 'Bruker SHELXTL' _computing_publication_material 'Bruker SHELXTL' _refine_special_details ; Refinement of F^2^ against ALL reflect ions. The weighted R-factor wR and goodness of fit S are based on F^2^, c onventional R-factors R are based on F, with F set to zero for negativ e F^2^. The threshold expression of F^2^ > 2sigma(F^2^) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflec tions for refinement. R-factors based on F^2^ are statistically about twice as large as t hose based on F, and Rfactors based on ALL data will be even larger. ; _refine_ls_structure_factor_coef Fsqd _refine_ls_matrix_type full _refine_ls_weighting_scheme calc _refine_ls_weighting_details 'calc w=1/[\s^2^(Fo^2^)+(0.0519P)^2^+0.4679P] where P=(Fo^2^+2Fc^2^)/3' _atom_sites_solution_primary direct _atom_sites_solution_secondary difmap _atom_sites_solution_hydrogens geom _refine_ls_hydrogen_treatment constr _refine_ls_extinction_method none

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141 _refine_ls_extinction_coef ? _refine_ls_number_reflns 2944 _refine_ls_number_parameters 136 _refine_ls_number_restraints 0 _refine_ls_R_factor_all 0.0349 _refine_ls_R_factor_gt 0.0339 _refine_ls_wR_factor_ref 0.0899 _refine_ls_wR_factor_gt 0.0889 _refine_ls_goodness_of_fit_ref 1.024 _refine_ls_restrained_S_all 1.024 _refine_ls_shift/su_max 0.000 _refine_ls_shift/su_mean 0.000 loop_ _atom_site_label _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_adp_type _atom_site_occupancy _atom_site_symmetry_multiplicity _atom_site_calc_flag _atom_site_refinement_flags _atom_site_disorder_assembly _atom_site_disorder_group Ni1 Ni 0.78449(2) 0.200477(19) 0.951551(11) 0.01390(10) Uani 1 1 d . Cl1 Cl 0.76001(5) -0.04034(4) 0.94595(2) 0.01992(12) Uani 1 1 d . O1 O 0.80502(17) 0.41211(12) 0.96292(8) 0.0227(3) Uani 1 1 d . H1 H 0.8419 0.4271 1.0219 0.034 Uiso 1 1 d R . H2 H 0.8695 0.4534 0.9214 0.034 Uiso 1 1 d R . N1 N 0.86804(19) 0.18345(15) 1.07950(9) 0.0192(3) Uani 1 1 d . H1C H 0.9422 0.1169 1.0866 0.023 Uiso 1 1 calc R . H1D H 0.9166 0.2598 1.0987 0.023 Uiso 1 1 calc R . C1 C 0.7251(2) 0.1552(2) 1.12727(10) 0.0246(4) Uani 1 1 d . H1A H 0.7499 0.1735 1.1889 0.030 Uiso 1 1 calc R . H1B H 0.6950 0.0620 1.1208 0.030 Uiso 1 1 calc R . N2 N 0.55830(19) 0.21593(14) 0.99917(9) 0.0170(3) Uani 1 1 d . H2C H 0.5102 0.1342 0.9932 0.020 Uiso 1 1 calc R . C2 C 0.5869(2) 0.24066(19) 1.09178(10) 0.0229(3) Uani 1 1 d . H2A H 0.4881 0.2205 1.1208 0.028 Uiso 1 1 calc R . H2B H 0.6141 0.3337 1.1019 0.028 Uiso 1 1 calc R . N3 N 0.68530(19) 0.20861(12) 0.82554(9) 0.0168(3) Uani 1 1 d . H3C H 0.6387 0.1275 0.8135 0.020 Uiso 1 1 calc R . C3 C 0.4440(2) 0.31027(17) 0.95647(11) 0.0219(4) Uani 1 1 d .

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142 H3A H 0.4882 0.3995 0.9643 0.026 Uiso 1 1 calc R . H3B H 0.3404 0.3067 0.9837 0.026 Uiso 1 1 calc R . N4 N 1.00343(19) 0.19338(13) 0.89465(9) 0.0181(3) Uani 1 1 d . H4C H 1.0504 0.2747 0.8950 0.022 Uiso 1 1 calc R . H4D H 1.0736 0.1365 0.9237 0.022 Uiso 1 1 calc R . C4 C 0.4128(2) 0.28200(18) 0.86086(11) 0.0235(4) Uani 1 1 d . H4A H 0.3793 0.1897 0.8536 0.028 Uiso 1 1 calc R . H4B H 0.3215 0.3369 0.8377 0.028 Uiso 1 1 calc R . C5 C 0.5566(2) 0.30616(16) 0.80790(11) 0.0227(4) Uani 1 1 d . H5A H 0.5197 0.3035 0.7464 0.027 Uiso 1 1 calc R . H5B H 0.6008 0.3943 0.8209 0.027 Uiso 1 1 calc R . C6 C 0.8181(2) 0.22318(19) 0.76849(10) 0.0218(3) Uani 1 1 d . H6A H 0.8455 0.3166 0.7629 0.026 Uiso 1 1 calc R . H6B H 0.7835 0.1890 0.7109 0.026 Uiso 1 1 calc R . C7 C 0.9654(2) 0.14816(18) 0.80580(10) 0.0221(3) Uani 1 1 d . H7A H 0.9425 0.0534 0.8052 0.027 Uiso 1 1 calc R . H7B H 1.0584 0.1643 0.7714 0.027 Uiso 1 1 calc R . Cl2 Cl 0.94440(6) 0.48000(4) 1.15627(3) 0.02640(13) Uani 1 1 d . loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_23 _atom_site_aniso_U_13 _atom_site_aniso_U_12 Ni1 0.01377(15) 0.01472(15) 0.01306(14) 0.00 037(6) 0.00004(9) -0.00074(7) Cl1 0.0196(2) 0.0153(2) 0.0246(2) 0 .00160(13) -0.00034(15) -0.00119(14) O1 0.0252(6) 0.0189(6) 0.0239(6) -0.0001( 4) 0.0003(5) -0.0039(5) N1 0.0203(7) 0.0206(6) 0.0162(6) 0.0001( 5) -0.0019(5) -0.0008(6) C1 0.0250(9) 0.0335(9) 0.0151(7) 0.0021( 7) 0.0000(6) -0.0047(8) N2 0.0159(7) 0.0185(6) 0.0166(6) -0.0016( 5) 0.0008(5) -0.0011(5) C2 0.0202(8) 0.0323(9) 0.0166(7) -0.0063( 7) 0.0034(6) -0.0031(7) N3 0.0174(7) 0.0183(7) 0.0145(6) 0.0010( 5) -0.0010(5) -0.0013(5) C3 0.0188(8) 0.0222(8) 0.0246(8) -0 .0025(6) 0.0005(7) 0.0037(6) N4 0.0155(7) 0.0191(7) 0.0196(7) 0.0004( 5) 0.0002(5) -0.0014(5) C4 0.0169(8) 0.0282(8) 0.0246(8) 0.0003( 7) -0.0032(6) 0.0025(7) C5 0.0220(9) 0.0252(9) 0.0201(8) 0.0048( 6) -0.0040(7) 0.0018(7) C6 0.0215(9) 0.0292(8) 0.0147(7) 0.0018( 6) 0.0023(6) -0.0032(7) C7 0.0221(8) 0.0252(8) 0.0196(7) -0.0017( 6) 0.0057(6) -0.0002(7) Cl2 0.0329(3) 0.0203(2) 0.0261(2) 0.00204(15) 0.00343(18) -0.00685(16) _geom_special_details ; All esds (except the esd in the dihe dral angle between two l.s. planes)

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143 are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. ; loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance _geom_bond_site_symmetry_2 _geom_bond_publ_flag Ni1 N1 2.0788(14) yes Ni1 N2 2.0805(16) yes Ni1 N3 2.0825(13) yes Ni1 N4 2.0878(16) yes Ni1 O1 2.1821(13) yes Ni1 Cl1 2.4777(5) yes O1 H1 0.9632 ? O1 H2 0.9721 ? N1 C1 1.481(2) ? N1 H1C 0.9200 ? N1 H1D 0.9200 ? C1 C2 1.515(3) ? C1 H1A 0.9900 ? C1 H1B 0.9900 ? N2 C2 1.475(2) ? N2 C3 1.478(2) ? N2 H2C 0.9300 ? C2 H2A 0.9900 ? C2 H2B 0.9900 ? N3 C5 1.474(2) ? N3 C6 1.480(2) ? N3 H3C 0.9300 ? C3 C4 1.529(2) ? C3 H3A 0.9900 ? C3 H3B 0.9900 ? N4 C7 1.479(2) ? N4 H4C 0.9200 ? N4 H4D 0.9200 ? C4 C5 1.527(3) ? C4 H4A 0.9900 ? C4 H4B 0.9900 ? C5 H5A 0.9900 ? C5 H5B 0.9900 ?

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144 C6 C7 1.523(2) ? C6 H6A 0.9900 ? C6 H6B 0.9900 ? C7 H7A 0.9900 ? C7 H7B 0.9900 ? loop_ _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_angle _geom_angle_site_symmetry_1 _geom_angle_site_symmetry_3 _geom_angle_publ_flag N1 Ni1 N2 84.41(6) . yes N1 Ni1 N3 175.50(6) . yes N2 Ni1 N3 92.08(6) . yes N1 Ni1 N4 99.99(6) . yes N2 Ni1 N4 175.18(5) . yes N3 Ni1 N4 83.62(6) . yes N1 Ni1 O1 89.23(5) . yes N2 Ni1 O1 87.82(5) . yes N3 Ni1 O1 93.46(5) . yes N4 Ni1 O1 90.26(5) . yes N1 Ni1 Cl1 88.33(4) . yes N2 Ni1 Cl1 90.84(4) . yes N3 Ni1 Cl1 88.91(4) . yes N4 Ni1 Cl1 91.25(4) . yes O1 Ni1 Cl1 177.32(3) . yes Ni1 O1 H1 104.7 . ? Ni1 O1 H2 114.9 . ? H1 O1 H2 115.1 . ? C1 N1 Ni1 106.52(10) . ? C1 N1 H1C 110.4 . ? Ni1 N1 H1C 110.4 . ? C1 N1 H1D 110.4 . ? Ni1 N1 H1D 110.4 . ? H1C N1 H1D 108.6 . ? N1 C1 C2 108.36(14) . ? N1 C1 H1A 110.0 . ? C2 C1 H1A 110.0 . ? N1 C1 H1B 110.0 . ? C2 C1 H1B 110.0 . ? H1A C1 H1B 108.4 . ? C2 N2 C3 112.45(14) . ? C2 N2 Ni1 106.62(11) . ?

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145 C3 N2 Ni1 116.94(11) . ? C2 N2 H2C 106.8 . ? C3 N2 H2C 106.8 . ? Ni1 N2 H2C 106.8 . ? N2 C2 C1 108.75(14) . ? N2 C2 H2A 109.9 . ? C1 C2 H2A 109.9 . ? N2 C2 H2B 109.9 . ? C1 C2 H2B 109.9 . ? H2A C2 H2B 108.3 . ? C5 N3 C6 112.40(13) . ? C5 N3 Ni1 115.63(10) . ? C6 N3 Ni1 108.63(11) . ? C5 N3 H3C 106.5 . ? C6 N3 H3C 106.5 . ? Ni1 N3 H3C 106.5 . ? N2 C3 C4 111.95(14) . ? N2 C3 H3A 109.2 . ? C4 C3 H3A 109.2 . ? N2 C3 H3B 109.2 . ? C4 C3 H3B 109.2 . ? H3A C3 H3B 107.9 . ? C7 N4 Ni1 106.55(11) . ? C7 N4 H4C 110.4 . ? Ni1 N4 H4C 110.4 . ? C7 N4 H4D 110.4 . ? Ni1 N4 H4D 110.4 . ? H4C N4 H4D 108.6 . ? C5 C4 C3 115.00(15) . ? C5 C4 H4A 108.5 . ? C3 C4 H4A 108.5 . ? C5 C4 H4B 108.5 . ? C3 C4 H4B 108.5 . ? H4A C4 H4B 107.5 . ? N3 C5 C4 111.97(14) . ? N3 C5 H5A 109.2 . ? C4 C5 H5A 109.2 . ? N3 C5 H5B 109.2 . ? C4 C5 H5B 109.2 . ? H5A C5 H5B 107.9 . ? N3 C6 C7 109.31(13) . ? N3 C6 H6A 109.8 . ? C7 C6 H6A 109.8 . ? N3 C6 H6B 109.8 . ? C7 C6 H6B 109.8 . ? H6A C6 H6B 108.3 . ?

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146 N4 C7 C6 108.04(14) . ? N4 C7 H7A 110.1 . ? C6 C7 H7A 110.1 . ? N4 C7 H7B 110.1 . ? C6 C7 H7B 110.1 . ? H7A C7 H7B 108.4 . ? loop_ _geom_hbond_atom_site_label_D _geom_hbond_atom_site_label_H _geom_hbond_atom_site_label_A _geom_hbond_distance_DH _geom_hbond_distance_HA _geom_hbond_distance_DA _geom_hbond_angle_DHA _geom_hbond_site_symmetry_A O1 H1 Cl2 0.96 2.28 3.2359(13) 174.1 N1 H1D Cl2 0.92 2.44 3.3123(16) 159.4 O1 H2 Cl2 0.97 2.15 3.1066(14) 167.2 3_767 N4 H4C Cl2 0.92 2.64 3.4766(14) 151.3 3_767 N1 H1C Cl1 0.92 2.68 3.4699(17) 144.4 3_757 N4 H4D Cl1 0.92 2.57 3.4356(15) 156.5 3_757 N4 H4C Cl2 0.92 2.64 3.4766(14) 151.3 3_767 _diffrn_measured_fraction_theta_max 0.961 _diffrn_reflns_theta_full 27.50 _diffrn_measured_fraction_theta_full 0.961 _refine_diff_density_max 0.533 _refine_diff_density_min -0.940 _refine_diff_density_rms 0.108

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147 LIST OF REFERENCES 1. Stout G.H. and Jensen L.J. X-ray Stru cture Determination Practical Guide, 1989, John Wiley & Sons, New York, NY USA. 2. SMART Software Reference Manual, Part Number 269-016700, 1996, Siemens Analytical X-ray Instrument s, Inc., Madison, WI USA. 3. SHELXTL Version 5 Reference Manual, Part Number 269-015900, 1994, Siemens Analytical X-ray Instrument s, Inc., Madison, WI USA. 4. SMART CCD System, Service Traini ng Manual, Part Number 269-016601, 1995, Siemens Industrial Automation, Inc., Madison, WI USA. 5. SAINT Version 4 Software Referenc e Manual, Part Number 269-017500, 1995, Siemens Industrial Automation, Inc., Madison, WI USA. 6. International Tables for Crystallogr aphy, Volume A, 1989, Kluwer Academic Publishers, Dordrecht, The Netherlands. 7. Spek A.L., Acta Cryst., 1990, A46, C34. 8. Culp J.T., Park J.-H., Meisel M.W., and Talham D.R., Inorg. Chem., 2003, 42, 2842. 9. Culp J.T., Park J.-H., Stratakis D., Meis el M.W., and Talham D.R., J. Am. Chem. Soc., 2002, 124(34), 10083. 10. Choi H.J. and Suh M.P., Inorg. Chem., 2003, 42, 1151. 11. Oblezov A.E., Talham D.R., and Abboud K.A., Acta Cryst., 2003, E59, m1070. 12. Bernard B.R., Haines R.I., and Rowley J.E., Transition Met. Chem., 2001, 26, 164.

PAGE 159

148 BIOGRAPHICAL SKETCH Alexandr E. Oblezov was born in Ryazan City, Russia, in 1977. He graduated from School #3 of Ryazan City and after successful passing of the entrance exams became a student of M.V. Lomonosov Moscow State University. He obtained his Bachelor and Master of Science degrees in materials science from M.V. Lomonosov Moscow State University. During his underg raduate studies Alexa ndr was awarded and named as a “Soros Student” three times (given for “outst anding achievements in studies and research”). Alexandr ha d two publications before he started his studies at the University of Florida: 1. Andrievski R.A., Kalinnikov G.V., Obl ezov A.E., and Shtansky D.V., Doklady Physics, 2002, 47(5), 353. 2. Tsirlina G.A. and Oblezov A.E., Russ. J. Electrochemistry, 1997, 33(3), 225. After graduation from the University of Fl orida Alexandr is planning to return to Russia and apply his knowledge in industry.


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Table of Contents
    Title Page
        Page i
        Page ii
    Dedication
        Page iii
    Acknowledgement
        Page iv
    Table of Contents
        Page v
        Page vi
    List of Tables
        Page vii
    List of Figures
        Page viii
        Page ix
        Page x
    Abstract
        Page xi
    Introduction
        Page 1
        Page 2
    Experimental work and data collection
        Page 3
        Page 4
        Page 5
        Page 6
        Page 7
        Page 8
        Page 9
        Page 10
        Page 11
        Page 12
        Page 13
        Page 14
        Page 15
    Structure refinement with SHELXTL software package
        Page 16
        Page 17
        Page 18
        Page 19
        Page 20
        Page 21
        Page 22
        Page 23
        Page 24
        Page 25
        Page 26
        Page 27
    Solution and refinement of a structure with a large disorder
        Page 28
        Page 29
        Page 30
        Page 31
        Page 32
        Page 33
        Page 34
        Page 35
        Page 36
        Page 37
        Page 38
        Page 39
        Page 40
        Page 41
        Page 42
    Multimetal cluster structure solution
        Page 43
        Page 44
        Page 45
        Page 46
        Page 47
        Page 48
        Page 49
        Page 50
        Page 51
        Page 52
        Page 53
    Solution of a crystal structure with pseudo symmetry
        Page 54
        Page 55
        Page 56
        Page 57
        Page 58
        Page 59
        Page 60
        Page 61
        Page 62
        Page 63
    Patterson method of structure solution
        Page 64
        Page 65
        Page 66
        Page 67
        Page 68
        Page 69
    Synthesis, crystallization and structure determination of aqua-chloro-(1, 4, 8, 11-tetraazaundecane) nickel (II) chloride
        Page 70
        Page 71
        Page 72
    Appendices
        Page 73
        Page 74
        Page 75
        Page 76
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        Page 146
    References
        Page 147
    Biographical sketch
        Page 148
Full Text












CRYSTAL STRUCTURE DETERMINATION AT THE CENTER FOR X-RAY
CRYSTALLOGRAPHY: A PRACTICAL GUIDE














By

ALEXANDER EVGENIEVICH OBLEZOV


A THESIS PRESENTED TO THE GRADUATE SCHOOL
OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT
OF THE REQUIREMENTS FOR THE DEGREE OF
MASTER OF SCIENCE

UNIVERSITY OF FLORIDA


2003

































Copyright 2003

by

Alexandr Evgenievich Oblezov



























I dedicate this work to my father Evgenii Vasilievich Oblezov

and my mother Gulnara Khazipovna Kharisova.















ACKNOWLEDGMENTS

I thank Dr. Khalil A. Abboud for the opportunity to discover a world of

crystallography under his advisement.

Also I thank everyone who helped and supported me during my studies in the

University of Florida.















TABLE OF CONTENTS


A C K N O W L E D G M E N T S ................................................................................................. iv

LIST OF TABLES ................................................... vii

LIST OF FIGURES ........................................... ............................ viii

ABSTRACT .................................................... ................. xi

CHAPTER

1 IN T R O D U C T IO N ............................................... .. ....................................1.. .. ... 1

2 EXPERIMENTAL WORK AND DATA COLLECTION..................................3...

E q u ip m e n t ............. ......... ..... ... ... .. ................................... .. ..................... 3
Selection and Preparation of Crystal for X-ray Analysis.....................................4...
Examination of the System before Data Collection.............................................6...
Checking of the Cooling System ...................................................6...
C checking of the G oniom eter........................................................ ...............7...
Checking of the X -ray G enerator ................................................ ...............8...
Optical Alignment ......................... ........... .............................8
Single F ram e D iffraction ..................................... ..................... ...............9...
P recise O ptical A lignm ent..................................................... ..... ...............9...
Determination of Cell Parameters (Orientation Matrix) ....................................10
M easuring of F aces ....................................................... .............................. .. 11
D description of the First M ethod.................................................... 12
D description of the Second M ethod .................................................. 12
Full D ata C collection .............................. ............................................ 13
S A IN T .......................................................................................................... 14

3 STRUCTURE REFINEMENT WITH SHELXTL SOFTWARE PACKAGE ........ 16

In tro d u ctio n .......................................................................................................... 1 6
X P R E P .......................................................................................................... 17
In tro d u ctio n ....................................................................................... 1 7
Step by Step Description of Interactive Work with XPREP ....................... 18
X S ..................................................................................................... . 1 9
X P ..................................................................................................... . 2 0
X L ..................................................................................................... . 2 3
W ork w ith nam e.ins File in a Text Editor........................................... ................ 24


v









A applying of A bsorption Correction .................................................... ................ 25
X C IF ..........................................................................................................2 6

4 SOLUTION AND REFINEMENT OF A STRUCTURE WITH A LARGE
D ISO R D E R ....................................................................................................... 28

E xperim ental Section .............. ............................................................ ................ 2 8
Structure Solution and Refinem ent ....................... .......................................... 29

5 MULTIMETAL CLUSTER STRUCTURE SOLUTION ................................... 43

E x p erim en tal S ectio n ...............................................................................................4 3
Structure Solution and Refinem ent ....................... .......................................... 44

6 SOLUTION OF A CRYSTAL STRUCTURE WITH PSEUDO SYMMETRY ..... 54

E x p erim en tal S ectio n ...............................................................................................54
Structure Solution and Refinem ent ....................... .......................................... 55

7 PATTERSON METHOD OF STRUCTURE SOLUTION...............................64

E x p erim mental S section ...............................................................................................64
Structure R efinem ent ... .................................................................. ... ............ 64

8 SYNTHESIS, CRYSTALLIZATION AND STRUCTURE DETERMINATION
OF AQUA-CHLORO-(1,4,8,1 1-TETRAAZAUNDECANE)NICKEL(II)
C H L O R ID E .............................................................................................................. 7 0

In tro d u ctio n .......................................................................................................... 7 0
E xperim ental Section .. ..................................................................... ................ 70
Structure D description .. ...................................................................... ................ 7 1

APPENDIX

A CIF FILE OF STRU CTURE EL06..................................................... ................ 73

B CIF FILE OF STRU CTURE XM 54 ................................................... ................ 93

C CIF FILE OF STRUCTURE CW10 .......... ..........................122

D CIF FILE OF AQUA-CHLORO-(1,4,8,11-TETRAAZAUNDECANE)NICKEL(II)
C H L O R ID E ............................................................................................................ 13 3

LIST O F R EFEREN CE S ... ................................................................... ............... 147

BIOGRAPH ICAL SKETCH .................. .............................................................. 148















LIST OF TABLES


table page

2-1. Parameters of the "Hemisphere" and "Multirun" modes ....................................14

3-1. Sample name.ins file before running XS ............................................................20

3-2. Example of a string of an atom's parameters .....................................................22

3-3. Sam ple of m odify .cif fi le ......................................... ........................ ................ 26

4-1. Results of an orientation matrix collection of el 06. ..........................................29

4 -2 F ile el0 6 .in s .............................................................................................................. 3 3

4-3. Setting of the "part" command in the el06.ins file ..............................................38

5-1. Results of orientation matrix collection for xm 54. ............................................44

5-2. Information revealed with "bang" command .....................................................49

6-1. Results of orientation matrix collection for cw 10 ..............................................55

7-1. Parameters of structure solution with XS............................................................64

8-1. Selected bond lengths (A) for the title compound ..............................................71

8-2. Selected diamond style hydrogen bonds for the title compound [A and ] ..............71















LIST OF FIGURES


figure page

2-1. Scheme of the Siemens SMARTTM/CCD system with 3-circle Siemens
PL A TF O R M TM goniom eter.2 .......................................................... ..................... 4

2-2. The preferred orientation of a crystal on a glass fiber tip of a goniometer head........6

2-3. The low temperature control unit. 1) Cold probe display, 2) "Power" button, 3)
"Liquid nitrogen start filling" button, 4) Level of nitrogen control display ............7...

2-4. The image of the aligned crystal in VIDEO program frame................................9...

2-5. The scheme of the goniometer manual control box. ...........................................10

3-1. Scheme of crystal structure solution with SHELXTL ........................................17

4-1. Scheme of the expected structure provided by the Wagener group (generated by
A CD /Structure D raw ing A pplet) ........................................................ ................ 28

4-2. View of the structure at the start point of the refinement....................................31

4-3. View of the structure after deleting all "noise" q peaks......................................31

4-4. View of the structure after labeling electron density peaks. Color notation: black
for C; dark blue for N; purple for P; light blue for Ru and H; light green for Cl.
The color scheme is used for all figures in this chapter. .....................................32

4-5. View of the structure after the first run of XL. Twenty new electron density peaks
w ere o b tain ed .......................................................................................................... 3 4

4-6. View of the structure during the second run of refinement in XP. ........................35

4-7. View of the structure after the second run of XL new electron density peaks were
d ete rm in e d ............................................................................................................... 3 6

4-8. View of the structure after eliminating "noise" q peaks after the third run of XP...36

4-9. View of the structure after refinement with XL. New twenty electron density peaks
w ere o b tain ed .......................................................................................................... 3 9









4-10. View of the structure after elimination of "noise" q peaks and assigning real
electron density to specific atom types ............................................... ................ 39

4-11. View of the structure including disorder. Thermal ellipsoids of disordered part are
treated in isotropic m ode ........................................ ......................... ................ 4 1

4-12. View of the structure without the minor part of the disorder. Thermal ellipsoids of
disordered part are treated in isotropic m ode ..................................... ................ 41

4-13. Scheme of the structure constructed according to the final result of the structure
solution and refi nem ent .......................................... ......................... ................ 42

5-1. Scheme of the ligands used for the synthesis of the cluster ................................43

5-2. View of the structure as a result of structure solution, completed by program XS.
Color notation: black for C; dark blue for Mn and N; light blue for H; red for 0.
The color scheme is used for all figures in this chapter. .....................................45

5-3. View of the whole cluster at the first step of refinement. ...................................46

5-4. View of the asymmetric unit after elimination of "noise" q electron density peaks.47

5-5. View of the cluster after elimination of "noise" q electron density peaks ............48

5-6. View of the asymmetric unit with labeled electron density peaks........................49

5-7. View of the cluster with electron density peaks assigned to specific atom types as
result of the fi rst run of X P ....................................... ....................... ................ 50

5-8. View of the asymmetric unit after the first run of XL. Twenty new electron density
peaks w ere obtained. ............. ................ .............................................. 50

5-9. View of the asymmetric unit and three identical groups of q peaks .....................51

5-10. View of the cluster at the end of refinem ent. ...................................... ................ 53

5-11. View of the Mn-O core of the cluster at the end of refinement. .............................53

6-1. Scheme of the expected structure provided by the McElwee-White group
(generated by ACD/Structure Drawing Applet)..................................................54

6-2. View of the structure at the first run of XP. ........................................ ................ 56

6-3. Pseudo sym m etry of the structure ....................................................... ................ 57

6-4. View of the structure. A) part of the structure as q peaks, B) part of the structure
after lab elin g ............................................................................................................. 5 7









6-5. View of the structure after the second run of XL refinement. Color notation: black
for C; dark blue for N; light blue for H; light green for Cl and W. The color
schem e is used for all figures in this chapter. ..................................... ................ 58

6-6. View of the structure after eliminating "noise" q peaks. ...................................59

6-7. View of the structure with labeled electron density peaks..................................59

6-8. View of the structure with elements of pseudo symmetry after refinement with XL.
New twenty q electron density peaks were obtained ..........................................60

6-9. View of the structure after deleting "noise" q peaks and relabeling of electron
d en sity p eak s. ........................................................................................................... 6 1

6-10. View of the structure after one more cycle of refinement. Twenty new electron
density peaks q peaks w ere obtained ............................................. ................ 62

6-11. View of the structure after deleting "noise" q peaks and relabeling.....................62

6-12. Final result of the structure solution and refinement...........................................63

7-1. Pseudo sym m etry of the structure ....................................................... ................ 65

7-2. View of the structure after eliminating pseudo symmetry ..................................65

7-3. View of the structure after relabeling atoms. Color notation: black for C; dark blue
for N; light blue for H; light green for Cl and W. The color scheme is used for all
figures in this chapter. ............... ................ .............................................. 66

7-4. View of the structure after the first refinement with XL. Twenty new electron
density peaks w ere obtained ...................................... ...................... ................ 66

7-5. View of the structure after elimination of "noise" q peaks at the second time of
running X P ............. .................................................................................. . 67

7-6. View of the structure after relabeling q peaks..................................... ................ 68

7-7. View of the structure after the second run of refinement....................................68

7-8. View of the structure after elimination of "noise" q peaks (third run of XP). .........69

8-1. View of an asymmetric unit of the title compound.............................................72

8-2. View of the two dimensional layer in the crystal structure of the title compound...72















Abstract of Thesis Presented to the Graduate School
of the University of Florida in Partial Fulfillment of the
Requirements for the Degree of Master of Science

CRYSTAL STRUCTURE DETERMINATION AT THE CENTER FOR X-RAY
CRYSTALLOGRAPHY: A PRACTICAL GUIDE

By

Alexandr Evgenievich Oblezov

December 2003

Chair: Daniel R. Talham
Major Department: Chemistry

Initial steps of working with sophisticated equipment and software of single

structure X-ray determination are not obvious, but confusing. The main idea of this work

is to show to an inexperienced user an operating guideline of Bruker SMART CCD

diffractometer and SHELXTL structure solution and refinement software package.

Detailed description of all operations is provided, as well as examples of step by step

structure refinements of various structures.














CHAPTER 1
INTRODUCTION

Modem chemistry uses many different methods to characterize structures of

organic and inorganic compounds. These techniques can yield information about bonds

and their nature in case of IR spectrometry; presence of specific structural fragments can

be determined with mass-spectroscopy; data about functional groups can be obtained

with NMR, but only single crystal X-ray diffraction can give a detailed picture of a

structure. This method reveals information about position and types of atoms, bond

distances and angles between them, including those of hydrogen bonding and other

significant data.

Knowledge of this method is important to every chemist, especially those working

in synthesis of new materials. Ability to crystallize, to select a good crystal, to collect

data on X-ray diffractometer and then to refine the structure is vital for inorganic

chemists, but because of tremendous development of single crystal X-ray structure

determination technique in last decades, dealing with this method's hardware and

software is neither simple nor easy.1

This work is an attempt to write a practical guide for users of Bruker

diffractometer2 and SHELXTL software,3 used in the Center for X-ray Crystallography of

the University of Florida. Chapter 2 is the detailed description of the process of crystal

preparation and work with the Bruker diffractometer, including SMART software.2

Chapter 3 is a very short manual of SHELXTL software package, describing only the






2


most used commands. The other chapters are thorough examples of step by step structure

solution and refinement of various compounds.














CHAPTER 2
EXPERIMENTAL WORK AND DATA COLLECTION

The purpose of this chapter is to describe the detailed processes of selecting a

crystal, operating an X-ray machine, and working with SMART and SAINT data

collection and reduction programs, respectively.

Equipment

The Bruker SMARTTM/CCD system with Bruker PLATFORMTM goniometer is

used in the Crystallographic X-ray Center of the University of Florida for single crystal

X-ray structure determination (Figure 2-1). X-ray diffraction experiments were

performed on this equipment. The Bruker SMARTTM/CCD system includes:

1. CCD camera (area detector)
2. Camera Electronics Unit (CEU)
3. Frame Buffer computer
4. CCD cooling system with associated cold probe
5. X-ray generator and a sealed tube X-ray source
6. X-ray tube cooling system
7. Video camera, used for optical alignment of crystals.

The X-ray tube is made of molybdenum. A graphite monochromating crystal is

used to isolate X-rays with the wavelength of 0.71073A. Resolution of the CCD detector

is 512 pixels*512 pixels. The distance between the detector and center of the sphere of

reflections, center of crystal, is variable and has a range of 30-200 mm. A personal

computer with Windows operation system is used as a Frame Buffer. SMART is a data

collection program used to operate the system and to collect and analyze crystallographic

data. Leika Stereo Zoom 7 microscope with standard polarizer was used in this work.











Goniornnatr Inidde t Bearm Gar.ne CryniL fRa~dion Saiety
Ha Collimntor MnriOmlomilor Enclosure

Cooing Un., -\ -- -- X-ray Shutmer nd
rennj enc:ioura. Attenuotor Assembly

CCD or ,- .if
Dmactor s .... 1. *X-ray Tube


PLATFOFtM -h
I I




... .1

XMray Generator


LT ee control unit ntou control pnel
Ion ,,iien. a..upped f 1 0 [
wih an Lf dfv.Ce ve i
General GoroOmeter
Control Sysmrn (GGCS)
Crnere Electronics
.Un. i M(CEUW

Figure 2-1. Scheme of the Siemens SMARTTM/CCD system with 3-circle Siemens
PLATFORMTM goniometer.2

Selection and Preparation of Crystal for X-ray Analysis

The first step in X-ray single crystal structure determination is selecting a single

crystal. Readers should be familiar with proper crystallization methods.1 A few

requirements for a suitable crystal are the following:

* it must be single;
* it must be without visible defects;
* it must be of appropriate size-depends on X-ray beam parameters.

A selected single crystal, in theory, could be twinned and its structure could be

determined but the process is complex. Twinned crystals can be identified by using a

microscope with a polarizer. It is recommended to use a microscope with large

magnification and equipped with polarizer for the best result.

Selection of suitable crystals starts with observation of a vial or dish, in which

crystals were grown, under a microscope. At this point a student should judge the quality









of crystals and types of crystals present, according to their shapes and colors. Each

crystal form should be studied as a separate project.

Next step is to select one good single crystal and transfer it into a drop of oil placed

on a microscopy glass slide. When the crystal is in a drop of oil, one can clean it and take

a closer look to confirm that it is single. There are few signs that show a selected crystal

is not single. First, the crystal is not clearly transparent, could indicate that it is a stock of

plates or needles. In this case only one solution is acceptable, choose another crystal. A

second sign is that one or few small crystals are built into large one. This problem could

be fixed by cutting the crystal. The third sign is a presence of hardly visible defects like

fine lines in the body of a crystal, unusual geometry of edges, etc. The solution in this

case is also cutting. When a good single crystal is selected, its size should not exceed

dimensions of 0.5mm*0.5mm*0.5mm (size of the X-ray beam) if so it needs to be cut to

appropriate size.

Special procedures are required for work with air sensitive crystals. Those include

working in glove box and preventing contact of crystals with air by putting an extra

amount of grease or oil on them. Promptness is very important in work with air sensitive

crystals.

The next step is to mount the chosen crystal on a glass fiber tip of a goniometer

head. The optimal orientation of a crystal on this tip can be reached by mounting the

crystal with the largest face along the fiber direction. Fixation of the crystal on the fiber

tip could be made in two ways: by using epoxy and by using oil in case of collecting data

at low temperatures.























Figure 2-2. The preferred orientation of a crystal on a glass fiber tip of a goniometer
head.

Examination of the System before Data Collection

Checking of the Cooling System

It is essential to verify that the cooling system is working properly before mounting

the goniometer head and starting data collection. Inspection of the nitrogen tank is the

first step. A user must be sure that the amount of nitrogen is sufficient to complete data

collection if a low temperature data collection is the goal. The next step is to check the

low temperature (LT) control unit to be sure that liquid nitrogen is flowing (Figure 2-3).

Temperature of -100 C is usually kept on the Siemens machine at the CXC. LT control

panel should display "-100" if all parts of cooling system are working properly (1 on

Figure 2-3). It's possible that flow of liquid nitrogen has been turned off. The turned off

"Power" green button on LT control unit (2 on Figure 2-3) shows that. In this case a user

should turn this button on. "LN2 Start Filling" red button (3 on Figure 2-3) operates the

filling of a small reservoir with liquid nitrogen from the big tank. Three lamps: green,

yellow and red in "Dewar/Cooler" part of LT control unit (4 on Figure 2-3) shows the

level of liquid nitrogen in this reservoir: full, half and empty. After checking the cooling

system the goniometer head with mounted crystal may be installed on the goniometer.









The goniometer head should be installed promptly in order to avoid appearance of ice on

the glass fiber. If the crystal is mounted on the goniometer, the cooling system is

checked, and then a user can proceed to the next step, checking the goniometer. These

operations require work with the SMART software, which is a powerful tool of

collecting, analyzing and solving crystallographic data.2













Figure 2-3. The low temperature control unit. 1) Cold probe display, 2) "Power" button,
3) "Liquid nitrogen start filling" button, 4) Level of nitrogen control display.

Checking of the Goniometer

It is very important to be sure that the goniometer is working properly. Users can

examine it by driving all axes to zero and verifying that all the axes are indeed at zero. To

do that run "GONIOMETER / Zero" in the SMART program. If a user has doubts about

preciseness of the determination of the zero positions at this point he/she can "home"

axes by running "GONIOMETER / Home axis." The values must be 20 = 29.18, co= -

30.77, yp= -157.83. In the case when the marks on axis are too far from home detectors

user can use command "GONIOMETER / Manual" and drive axis "home" manually. It

is highly recommended to start "GONIOMETER / Home axis" again after using

"Manual" command. Successful completion of these operations ensures that the

goniometer works properly. It is important to mention a rare situation when the

goniometer does not respond to commands from SMART program. Reloading of the









goniometer interface must be completed in this case. A user can do it by turning off and

after 5 minutes pause turning back on the "Power" green button of the GGCS block.

Checking of the X-ray Generator

X-ray generator control panel shows the voltage and current used for the X-ray

generation. The standard parameters are 50 kV and 40 mA for the Siemens system in the

CXC. If the X-ray generator control panel displays values of parameters, which differ

from the standard ones, they must be adjusted to the standard (maximum power). This

can be done by using "MODE," ".f," "1" and "EDIT" buttons on the X-ray generator

control panel. Also, these parameters can be modified in the SMART program by

changing values of "GONIOMETER / Generator." In general, maximum power is

recommended, but sometimes it is project dependent. As soon as a user becomes sure

that the system is working properly he/she can start optical alignment of the crystal and

take single frame diffraction frames.

Optical Alignment

Quality of the data and quality of the structure determination depends on the

alignment of a crystal. It must be at the exact center of the X-ray beam and must stay in

this center in spite of any rotation of the goniometer head. To align the crystal, run

"GONIOMETER/Optical" in the SMART and start the video capturing program, Bruker

Advanced X-ray Solution VIDEO for 2000/NT, this depicts single shots and streaming

video from the video camera installed on the goniometer. This video capturing program

has different grid patterns, which are very helpful for precise alignment of crystals. The

video camera is preinstalled so that it is focused on the point, which is the center of the

X-ray beam. The goal of optical alignment is to adjust a crystal so that its center

(geometrical center) falls in the center of the grid pattern, Figure 2-4.


























Figure 2-4. The image of the aligned crystal in VIDEO program frame.

Single Frame Diffraction

Before alignment of the crystal, it is useful to run single frame diffraction with

command "ACQUIRE / Still." It requires that a crystal be placed roughly in the center of

the beam, in other words be visible in the frame of the VIDEO program. The single

frame yields a picture of diffraction, which reveals the quality of crystals. A single

crystal of good quality must produce a diffraction pattern series of bright, not

overlapping, perfectly rounded spots. A user can make a conclusion about singularity of

chosen crystal and its quality at this stage. In case of bad diffraction or absence of

diffraction a new crystal should be tried. If a diffraction picture is acceptable, the user

can proceed to precise optical alignment.

Precise Optical Alignment

A user can start alignment by pushing the "(p" and then the "AXIS PRINT" buttons

on the manual box, Figure 2-5. This command will drive the co and (p axes to the base

position for optical alignment.4 The alignment of a crystal includes the following

operations:








1. According to streaming video, at the VIDEO program frame, adjust the sleds on the
goniometer head to center the crystal in the cross lines the center of a grid pattern.

2. Push the "AXIS PRINT" button again to drive p 180 degrees from its current
position. If the cross lines are not centered on the crystal, move half the error using
the goniometer head screw. Adjust only the screw that moves the pin with the
crystal perpendicular to the axis of the video camera.

3. Repeat 2 until the crystal is centered in the cross lines for both positions of p.

4. Press "Z" button on the manual control box and the "AXIS PRINT." The p spindle
will drive 90 degrees from the previous position.

5. Adjust the crystal in the same way as described in 1-3 for p.

After the optical alignment of the crystal is completed, cell parameters of the

crystal can be determined.

AXIS PRINT
FORWARD

/FSmm
SLOW FAST


m m m REVERSE
A B C D

Figure 2-5. The scheme of the goniometer manual control box.

Determination of Cell Parameters (Orientation Matrix)

The next step in single crystal structure determination is to determine the cell

parameters of the crystal. At this time, the user can set a project name "Crystal Name,"

"Title;" define a directory "Working directory" and "Data Directory" for this project;

describe color and geometry of the crystal in fields "Crystal Color" and "Crystal

Morphology" in "CRYSTAL / Edit Project." Then a dark frame should be defined in

"DETECTOR / Load dark" menu. It means to provide the name of a file with recorded

dark frames (background reading by the CCD detector). These files differ in time of









collecting the dark frame. A file with 10 s. dark frame is usually used at this stage. After

editing the project and loading the dark frame, the data collection of a matrix can be

started. A user must close the safety windows of the diffractometer, push "Reset" button

on the control panel of the machine and start "ACQUIRE / Matrix" in SMART.

After this short data collection, SMART automatically tries to obtain a solution of

cell parameters from this data. A solution includes many parameters and the most

important of them are Bravais lattice type, and a, b, c, a, 0, y. SMART may show more

than one possible solutions. In this case a user can choose one or let SMART do it

automatically, but a user should be aware that if angles are not exact 90, but very close

(e.g. 89.9) SMART may select a lower symmetry Bravais lattice type. At this point,

decision about which solution to follow should be made. If a user decides to choose

another solution than the one picked by SMART, he/she should run "CRYSTAL /

Reduction Cell" and on the final stage choose desired solution. The least-square

refinement of the solution "CRYSTAL / LS" deletes unsuitable peaks from the array and

derives final number of peaks used for cell parameters and an orientation matrix

determination. This number of peaks is usually entered after the name of the project in

the line "Title" of "CRYSTAL / Edit Project" for record keeping.

Measuring of Faces

In order to load face measuring routine, run "CRYSTAL / Faces." Also the

VIDEO program should be started. There are two ways to measure faces which can be

applied separately or simultaneously. The first one is based on driving to specific h k 1

faces and, if found on the crystal, measuring the faces.









Description of the First Method

1. In "CRYSTAL / Faces" mode push "Ctrl + F." In a new window "GONIOMETER
Options" enter h k 1 indexes, usually low ones, and then push "OK."

2. The goniometer rotates the crystal so that the face corresponding to the entered h k
1 indexes become parallel to the direction of video camera and it is seen edge on.

3. Load the face measurement ruler pushing "F 12." Measure size of the face in units
of the ruler of VIDEO program. To convert these units to millimeters multiply
them on 0.019. This coefficient based on magnification of the video camera.

4. Return to SMART window and push "Enter." A new window "GONIOMETER
Options" appears with two parameters, which can be changed. The first parameter
is "Eyepiece Angle" do not change in this method of faces measurement. The
second one "Distance" is the distance of the face from the crystal center. A user
should remember that the real size of the face is a half of the measured crystal
width and the real size should be entered in the second line of the window. Press
"OK" the face is measured.

5. Press "Home" a new window "Crystal Faces" with indexes of already measured
faces and their sizes appears. The opposite face of the measured one with the same
size should be entered here. For example if in step 4 face 1 0 1 was measured with
width 0.05 mm, then enter -1 0 -1 and the same width 0.05mm.

6. Repeat 1-5 so that at least six faces were measured.

The second method of measuring faces is to estimate "Eyepiece Angle" the angle

of rotation of the ruler on VIDEO program frame, and then accept or refuse h k 1 indexes

of faces derived by SMART.

Description of the Second Method

1. Use the goniometer manual control box Figure 2-5 to rotate crystal so that a plane
of a face of the crystal is seen edge on.

2. Switch to VIDEO program window and with command "F 12" load the face
measurement ruler. Push "Ctrl + Z," in a new window "Options" in part "Reticule /
Tilt" enter a tilt angle of the ruler the "Eyepiece Angle," so that the ruler is
perpendicular to an edge of this face. Measure the width of the face "Distance"
in units of the ruler. How to convert it to millimeters is described in the first
method steps 3-5. Remember the "Eyepiece Angle" of the ruler.

3. Return to SMART window, push "AXIS PRINT" button on the manual control
box. This command updates the angles of the goniometer position in the SMART









window. Push "Enter" and in the window "Goniometer Options" enter the
"Eyepiece Angle" and the width of the face "Distance." Then push "OK."

4. SMART shows the calculated h k 1 indexes corresponding to this face. Sometime
calculated indexes are not integers, so a user should decide to accept these indexes
and start to measure a new face, or to refuse proposed by SMART h k 1 indexes and
repeat steps 1-4. The best way is to verify these indexes. To do this proceed
steps 1-5 from the first method using h k 1 indexes derived by SMART. If the
indexes picked by SMART are correct the same face should be visible in VIDEO
window.

5. Same as step 5 in the first method

6. Repeat 1-5 so that at least six faces were measured.

When at least 6 faces were measured, the frame model of the crystal appears in

SMART window. Shape and proportions should be the same as those of the real crystal.

After measuring faces, a user should enter the sizes of the crystal in "CRYSTAL / Edit

Project" window in fields "Maximum Dimension," "Intermediate Dimension,"

"Minimum Dimension." The next step is a full data collection.

Full Data Collection

For collection of full data, a user should decide the exposure time to record every

frame and the corresponding dark frame file in "DETECTOR / Load Dark." Depending

on quality and size of a crystal this time may vary, usually from 20 to 50 seconds.

The next step is to select mode of data collection. There are two: "ACQUIRE /

Hemisphere" and "ACQUIRE / Multirun" (full sphere). If a crystal is high symmetry or

good quality, "Hemisphere" mode should be applied, in other cases "Multirun" regime is

more helpful. The difference between these two modes is in number of collected frames

and angles of the goniometer, at which the frames are collected (Table 2-2).

The last fifty frames in each mode are used to control possible low temperature

alterations of a crystal, and collected at the same position of the goniometer as the first









fifty frames. The time of recording every frame in field "Time" must be the same as

defined in "DETECTOR / Load Dark" menu. These two modes can be edited in

"ACQUIRE / Edit Hemisphere" or "ACQUIRE / Edit Multirun," respectively. At this

point a user can start data collection running "ACQUIRE / Hemisphere" or "ACQUIRE /

Multirun."

Table 2-1. Parameters of the "Hemisphere" and "Multirun" modes.


000q

1 001 -28.00 -28.00 0.00 54.70 2 -0.300 626
3. 2 001 -28.00 -28.00 90.00 54.70 2 -0.300 455
1 4 3 001 -28.00 -28.00 180.00 54.70 2 -0.300 250
4 001 -28.00 -28.00 0.00 54.70 2 -0.300 50_

1 001 -28.00 -28.00 0.00 54.70 2 -0.300 600
2 001 -28.00 -28.00 120.00 54.70 2 -0.300 600
3 001 -28.00 -28.00 240.00 54.70 2 -0.300 600
4 001 -28.00 -28.00 0.00 54.70 2 -0.300 50

SAINT

After the first frame of diffraction data is recorded, a user can start program

SAINT. Purpose of this program is to gather data from each single frame, to integrate

this data and extract the intensity data from the frames.5

1. To start a new project run "PROJECT / New." In a new window "Open a new
Project" define a directory where SMART records *.p4p files of the running data
collection. Pick namel .p4p" and push "OK."

2. Initialize the process of integration of data by clicking "INITIALIZE." This allows
SAINT to read all of the crystal parameters from the "namet.p4p" file (such as,
crystal system, cell dimensions, orientation matrix etc.).

3. Push "EXECUTE" and continue to work in a new window "Basic SAINT menu for
analyzing small molecule area detector frames." Push button "INCREMENT
LAST RUN" three times it increases number of runs up to four. It must be the
same number of runs as in setting of "Hemisphere" or "Multirun" mode, depending









on which one is running. Also the number of frames in every run in this window
must be the same as in running mode of full data collection (Table 2-2).

4. Define waiting time of frame files "Maximum wait for frame file (seconds)." It
must not be less than time of collecting a single frame. Period of 111 seconds is
used in the CXC.

5. In the field "Resolution limit for output" select "20" option and make it 56 deg.

6. Push "INTEGRATE+SORT+GLOBAL" button.

The main outcome of running of program SAINT, which is used in following

structure solution and refinement, is two files, namet.p4p and namet.raw located in

"Work" subdirectory of defined before in SMART "CRYSTAL / Edit Project" working

directory. These files are the result of whole experimental work and are the start point of

structure calculation and refinement in software package SHELXTL.














CHAPTER 3
STRUCTURE REFINEMENT WITH SHELXTL SOFTWARE PACKAGE

Introduction

SHELXTL is the most widely used set of programs for crystal structure solution

and refinement of small molecules. The following is a brief roadmap of using this

package of programs. It is intended to be a quick reference for a crystal structure project.

The complete manual of SHELXTL3 is large and very detailed. In this work, only

programs and commands frequently used for structure solution and refinement are

described.

SHELXTL consists of the following programs:

1. XPREP the main functions of this program are automatic space group
determination, merging of datasets and absorption corrections.

2. XS the program for structure solution by Direct or Patterson methods.

3. XL the least-squares structure refinement.

4. XP the interactive graphic program, which allows visualization of the crystal
structure and editing it.

5. XCIF the program for CIF tables preparation after structure determination and
refinement are completed.

6. XSHELL a program intended for use by the less experienced users for the
determination and refinement of crystal structures.

The step by step process of crystal structure determination and refinement is

depicted on Figure 3-1. The first step work with SMART and SAINT programs as

described in Chapter 2. The result of this work is the raw data file namet.raw and the

parameter file namet.p4p. Step 3 is the start point of working with SHELXTL. Before






17


starting XPREP, a user should define a project in "PROJECT / New" by picking

namet.raw or namet.p4p files and entering "NAMET" as a title of the project.

XPREP

Introduction

XPREP is the first step in structure solution. It is used to determine space groups,

symmetry classes, to define unit-cell contents, to set up SHELXTL files and many others

(step3 on Figure 3-1). XPREP is an interactive program that shows all possible solutions,

proposes the optimal one and waits for user's choice. In most cases, XPREP suggests

correct options, which must always be checked by the user.


RESULT

Figure 3-1. Scheme of crystal structure solution with SHELXTL.









Step by Step Description of Interactive Work with XPREP

1. Push "XPREP." The first action is to determine the lattice type. Possible solutions
are P A B C I F Obv Rev. The correct solution should have "Lattice exceptions"
parameters N(total), N(int/3 sigma), Mean intensity and Mean (int/sigma) equal to
zero or very low value. A user may accept the program's solution or select a
different one and then push "Enter." The main menu of XPREP appears after
determination of lattice type. It contains the following functions:

[D] Read, modify or merge DATASETS
[P] Contour PATTERSON section
[H] Search for HIGHER metric symmetry
[S] Determine or input SPACE GROUP
[A] Absorption, powder, SIR, SAD, MAD etc.
[M] Test for MEROHEDRAL TWINNING
[L] Reset LATTICE type of original cell
[C] Define unit-cell CONTENTS
[F] Set up SHELXTL FILES
[R] RECIPROCAL space displays
[U] UNIT-CELL transformations
[T] Change TOLERANCES
[0] Self-rotation function
[Q] QUIT program

A user can choose a function which to start or can follow XPREP default options
(recommended).

2. In the main menu follow default option "[H] Search for HIGHER metric
symmetry." Push "Enter" and XPREP shows all possible solutions and picks one
of them. A user should pay attention to "R(sym)" parameter for correct solution it
must be the smallest. Select option and push "Enter" XPREP returns to the main
menu.

3. In the main menu follow default option "[S] Determine or input SPACE
GROUP" and push "Enter." In new submenu choose "[I] INPUT known space
group," if space group is known or follow default option "[S] Determine SPACE
GROUP" and push "Enter." New submenu with Bravais lattice types appears. It's
recommended to accept solution determined by the program. Push "Enter" and
program returns to the main menu.

4. In the main, menu follow default option "[D] Read, modify or merge
DATASETS." In this submenu always pick default options until returning to the
main menu.

5. In main menu follow default option "[C] Define unit-cell CONTENTS." In a
new submenu a user can choose "[F] new formula" to enter exact formula of









compound in unit cell or choose "[E] EXIT to main menu" and leave to the main
menu without making any alterations. Usually the exact formula of unit-cell
contents is unknown until final stages of solution and refinement of crystal
structure because synthesis might go unexpected ways and the amount of solvent
molecules in the unit cell is unpredictable. So usually users choose option "[E] -
Exit to main menu."

6. In main menu follow default option "[F] Set up SHELXTL FILES." Enter a
name of files the name of current project, but without "t" "NAME." Answer
"[Y] yes" on question "Do you wish to (over)write the intensity data file
name.hkl?"

7. In main menu follow default option [Q] QUIT program.

At this stage work with XPREP is completed and SHELXTL files are created.

Because the title of new files name.ins and name.hkl (step 5 on Figure 3-1) is different

from one of namet.p4p and namet.raw (step 2 on Figure 3-1) a new project "NAME"

instead of"NAMET" should be started as described before.

XS

XS is a program for structure solution from X-ray diffraction data. It uses files

name.ins and name.hkl (the result of running XPREP) to create structure solution file

name.res which contains crystal data and atom list, as well as listing file name.1st (steps

4-6 on Figure 3-1). Before running program XS, a user should decide what method of

structure solution to use: Direct Methods or Patterson method and enter proper command

in name.ins file as it shown in Table 3-1. If Direct Methods are selected, a user should

watch the parameter "Fourier and peak search RE" during running XS. "RE" should be

less than 0.250 if correct solution was obtained by running XPREP. In case of high value

of "RE" parameter a user should check selected options in XPREP or try Patterson

method of structure solution. The next step of work is XP program (step 7 on Figure 3-

1).









Table 3-1. Sample name.ins file before running XS.

TITL name in R-3
CELL 0.71073 33.8651 33.8651 28.2246 90.000 90.000 120.000
ZERR 15.00 0.0017 0.0017 0.0020 0.000 0.000 0.000
LATT 3
SYMM -Y, X-Y, Z
SYMM -X+Y, -X, Z
SFAC C H 0 S NI SB
UNIT 240 1590 720 120 25.05 60
TEMP -100
TREF < for direct methods > PATT < for Patterson method >
HKLF 4
END


XP

XP is the program with which users work most of the time of crystal structure

determination (step 7 on Figure 3-1). XP is a very powerful program, which has a lot of

functions.3 Only the most useful are described in this chapter. After XP is started, a new

window with black screen and highlighted command line appears. XP is an interactive

program, which is operated with commands, entered on the command line.

To create a connectivity table (start a session) enter command

fmol

It activates the project and shows a list of atoms in the asymmetric unit. XS can

recognize automatically only heavy atoms, like d-metals, so at the first run ofXP a user

may see in the list of atoms heavy metals and a lot of "q" peaks of electron density not

assigned to any atom type. The main idea of work with XP is to assign these peaks of

electron density to specific atom types. Many q electron density peaks are not real. They

are "noise". These "noise" peaks should be eliminated from the structure. Atoms and q

peaks can be deleted with command

kill < name/s of atom/s >









For example "kill ql" to delete only ql peak, "kill $c" to delete all carbon atoms. A

user can use command

pick < name/s of atom/s>

to select atoms, delete them or change their names. Alterations of names of atoms is also

possible with command

name < name of atom before > < name of atom after>

Command

proj

allows users to see wire model of the studied structure. A user can check the number of

bonds of atoms, as well as bond lengths and angles between them, using command

bang < name/s of atom/s >

This is key information for analyzing q peaks. Commands

undo < name of atom 1 > < name of atom 2 >

undo < type of atoms 1 > < type of atoms 2 >

delete bonds or bond between atoms or types of atoms respectively. Examples:

undo c14 o22

undo $mn $n

Commands

link < name of atom 1 > < name of atom 2 >

link < type of atoms 1 > < type of atoms 2 >

create bond or bonds between atoms or types of atoms respectively. Current work can be

saved in XP (step 12 in Figure 3-1) with command

save < name of file >

If a step of refinement is completed a user can save the results and create name.ins file

(step 8 in Figure 3-1) with command









file < name of file >

After running XL (step 9 in Figure 3-1) and starting XP again a user can check whether

electron density peaks are correctly assigned to atom types. Command

info

info < name/s of atom/s >

shows many parameters of atoms (Table 3-2), the most important of which are x, y, z

coordinates, occupation parameter and parameter "Ueq" the thermal parameter or

average displacement, which characterizes conformity of assigned electron density to

measured one.

Table 3-2. Example of a string of an atom's parameters.
Name type X Y Z occupation Ueq.
Cl 1 0.35060 0.66220 0.26130 11.00000 0.05000

Command

uniq < name/s of atom/s>

is used for temporary selection of a separated part of a structure. Command

grow

extends the structure if it has a symmetry element, which splits molecule in two or more

identical parts. Command

hadd

hadd

attaches hydrogen atoms to other target -atoms according to hybridization. Command

telp

creates name.plt file, which is used for generating graphic file name.hgl with command

draw









More specific features and commands of program XP will be discussed in Chapters 4-8

upon consideration of certain problems of structure solution and refinement.

XL

As mentioned before, XL is a least-squares optimization program. It reads file

name.ins created in XP and writes results of calculation into name.res file (step 9 on

Figure 3-1). The full cycle of refinement consists of working with two programs XP

and XL. It is shown on Figure 3-1 as the cycle with steps 6-9.

During running XL, a user should monitor the following parameters:

R1 = (||lFo| Fc||) / |IFo[

wR2 = [I[w(Fo2 Fc2)2] / [w(Fo2)2]]1/2

GooF = S = [Y[w(Fo2 Fc2)2] / (n-p)]1/2

where, w= 1/[C2(Fo2)+(m*p)2+n*p], p = [max(Fo2,0)+ 2* Fc2]/3, m & n constants,

Fo- observed structure factor, Fc calculated structure factor. The exponential form of

the structure factor:

Fhkl 2fni(hxj+kyj+lzj)

Parameters wR2 and RI should decrease with every run of XL if the solution of structure

is correct. XL is the last step in crystal structure refinement. The final outcome of work

of XL is name.cif file (step 10 on Figure 3-1), which contains all information about the

collected data and the structure derived from this data.









Work with name.ins File in a Text Editor

Refinement of a structure includes also editing name.ins and name.res files in a text

editor. There are many commands, which should be included in name.ins for refinement

with a text editor.

Command

anis

entered in a separate string switches refinement to the mode of anisotropic treatment of

thermal vibration ellipsoids. Command

hadd 137 -1.5

adds hydrogen atoms to methyl carbon atoms. Command

omit < h k 1 >

eliminates a specific h k 1 reflection. Command "omit" also used for elimination of

reflections, detected beyond 20=55 deg. reflection sphere, from least square optimization

with XL. Thus separate string

omit -3 55

must be added to the name.ins file before the first run of XL. Commands

cgls

and

L.S.

acta

define which type of least-squares refinement to use. On the first stages of refinement

"cgls" command is more useful, and on the final steps "L.S." and actaa" should be used.

At the final point of structure refinement a user must pay attention to the weighting

scheme in name.res file. A name.ins file has a string before atoms listing with command









WGHT

After a cycle of refinement with XL in the name.res a new string with command

WGHT

appears after line with "end" command. So there are "WGHT" commands in name.res

files and weighting scheme is balanced, when parameters of this command before and

after XL refinement are the same. It can be reached by copying "parameters "after XL"

in place of "parameters before XL." The other commands will be introduced during

consideration of specific cases of structure solution in Chapters 4-8.

Applying of Absorption Correction

At the end of refinement, when the exact formula of unit cell is determined, unit

cell content should be corrected, and then absorption correction should be applied. These

two operations could be completed by running XPREP. For the first one in the main

menu of XPREP a user should follow default option "[C] Define unit-cell

CONTENTS," then in a new submenu he/she can choose "[F] new formula" and enter

exact formula of compound in unit cell. After formula correction XPREP calculates new

Z parameter (number of molecules in unit cell). This number must be equal to Z from

International Crystallographic Tables6 for the space group of this crystal structure.

For absorption correction a user should choose option "[A] Absorption, powder,

SIR, SAD, MAD etc." in the main menu of XPREP, and then in a new submenu follow

option "[F] FACE-indexed absorption correction." In a new submenu a user should

follow options selected by the program until returning to the main menu.

As a result of running XPREP, new name.ins and name.hkl files would be created.

New name.ins file with corrected unit cell contents does not contain information about

atoms there is no atom listing. A user can repeat whole process of refinement of









structure or all information about each already refined atom could be copied from

unmodified name.res file. Parameters RI, wR2, GooF improve (become smaller) after

correction of the unit-cell formula and applying absorption correction, what leads to

better refinement of a crystal structure.

XCIF

The main purpose of program XCIF (step 11 in Figure 3-1) is to create the tables,

which is not a part of structure solution, but it is very important for organization of the

results. Before running XCIF, name.cif file has to be edited in a text editor. The correct

version of parameters, needed to be edited, is saved in a locally created modify.cif file

(Table 3-2) on every computer of the CXC.

Table 3-3. Sample of modify.cif file.

_cell measurement reflns used
cell measurement theta min 2.0
cell measurement theta max 28.0

_exptl_absorpt_correction_type integration to analytical

_exptl_absorpt_process_details
'based on measured indexed crystal faces, SHELXTL (Bruker 1998)'

OR

_exptl_absorpt_process_details
'multiscan (SADABS, Blessing 1995)'

_diffrn_ambienttemperature 173(2)
_diffrn_radiation_wavelength 0.71073
_diffrn_radiation_type MoK\a
diffrn radiation source 'normal-focus sealed tube'
_diffrn_radiation_monochromator graphite
_diffrn_measurement_device_type 'SMART CCD area detector'
diffrn measurement method '\w scans'
diffrn detector area resol mean ?
diffrn standards number 0
diffrn standards interval count ?
diffrn standards interval time ?









_diffrn_standards_decay_% none

_reflns_threshold_expression 'I>2\s(I)'

_computing_data_collection 'Bruker SMART (Bruker 1998)'
_computing_cell_refinement 'Bruker SMART & SAINT (Bruker 1998)'
_computing_data_reduction 'Bruker SHELXTL (Bruker 2000)'
_computing_structure_solution 'Bruker SHELXTL'
_computing_structure_refinement 'Bruker SHELXTL'
_computing_molecular_graphics 'Bruker SHELXTL'
_computing_publication_material 'Bruker SHELXTL'


After file name.cif is modified according to modify.cif, a user can run XCIF. In

new window the main menu contains following options:

1. [S] Change structure code
2. [X] Print from SHELXTL XTEXT format file
3. [R] Use another CIF file to resolve ? items
4. [C] Set compound name for tables (currently 'name')
5. [N] Set next table number (currently 1)
6. [D] Set default directory for format files
7. [T] Crystal/atom tables from .cif
8. [F] Structure factor tables from .fcf
9. [Q] Quit.

A user should go only through commands "[C] Set compound name for tables,"

"[T] Crystal/atom tables from .cif" and "[F] Structure factor tables from .fcf." The result

of work of XCIF is two files name.rtf and name.sft, which need to be formatted in

Microsoft Word by running locally created macros "tbl" and "sft," respectively. These

macros are stored on every computer of the CXC.

The structure refinement is completed. The result of the whole process is table files

name.tbl.doc and name.sft.doc. Graphic files name.hgl should be inserted in Microsoft

Word as pictures and it should be saved as name.drw.doc. The work is done.














CHAPTER 4
SOLUTION AND REFINEMENT OF A STRUCTURE WITH A LARGE DISORDER

This chapter focuses on structure refinement of a structure with a large portion of

disorder over two positions.

Experimental Section

Crystals of structure "el06" were provided by the Wagener group. A scheme of the

expected structure was given in the submission form, Figure 4-1.










N/ \N



Figure 4-1. Scheme of the expected structure provided by the Wagener group (generated
by ACD/Structure Drawing Applet).

Few pale yellow prism-like shaped crystals were selected for the analysis. Using

our polarizing microscope, it was established that the crystals are not twinned. One

crystal with size 0.37*0.19*0.14 mm3 was selected and mounted on the glass fiber of the

goniometer head. The crystal was aligned as described in Chapter 2 and an orientation

matrix was determined using 10 sec/frame exposure time, because the crystal diffracted

well. The results of collecting the matrix after least-squares refinement are shown in

Table 4-1.









Table 4-1. Results of an orientation matrix collection of el 06.

Orientation Matrix:
-0.01094318 0.01455290 0.04128984
0.07639965 0.02656884 0.00842880
-0.03031138 0.06173897 -0.01331213

Lattice parameters & Standard deviations:
12.2226 14.5411 22.9325 90.058 99.354 89.983 4021.59
0.0021 0.0019 0.0052 0.015 0.011 0.013 1.16
Standard deviations corrected for GOF:
0.0017 0.0015 0.0041 0.012 0.009 0.010 0.92

Histograms:
.00 .05 .10 .15 .20 .25 .30 .35 .40 .45 +Inf
H 137 0 0 0 0 0 0 0 0 0
K 137 0 0 0 0 0 0 0 0 0
L 137 0 0 0 0 0 0 0 0 0
Omega 126 11 0 0 0 0 0 0 0 0


The conclusions from the results in Table 4-1 are following:

1. The crystal is single and of good quality, because of all zeros in "Histograms."
2. The number of peaks (137) confirms good diffraction of the crystal.
3. The crystal's lattice is Monoclinic, but SMART recognizes it as Triclinic, because
a=90.058, not exactly 90 deg.
4. Cell parameters are:
a=12.2226 a=90.058
b=14.5411 P=99.354
c=22.9325 y=89.983

A hemisphere of data was collected. The main results of full data collection were

two files el06t.p4p and el06t.raw.

Structure Solution and Refinement

A new project "el06t" was created in SHELXTL and XPREP was started. In all

steps of running XPREP, default options were selected. XPREP determined Monoclinic

crystal system and P21/c space group, because reflections 0 k 0 (k = odd) and h 0 1 (1 =

odd) were unobserved. The results of running XPREP were el06.ins and el06.hkl files.









A new project "el06" was created and program XS was applied to el06.ins file, using

Direct Methods. The RE parameter was 0.275, which is slightly higher than expected for

this good quality crystal.

The solution revealed the Ru and four P positions in addition to a set of q electron

density peaks, as shown in Figure 4-2. At first look, a user can deduce that, according to

the structure provided in the submission form, all P atoms were not correctly assigned.

P2 and P3 should be chlorines and the rest of phosphorous atoms are "noise," but strong

peaks of electron density. From Figure 4-2 it is easy to see phenyl rings in the lower part

of the structure (q peaks of the rings are labeled on the figure) and two "arms" connected

to the Ru atom. All obvious "noise" q peaks were deleted with command "kill." It is

easy to determine "noise" q peaks in the lower part of the structure, because the real

structure is clearly determined. After all obvious "noise" q peaks were deleted the

structure looked more understandable, Figure 4-3. According to the structure description

from the submission form (Figure 4-1) it was known that in Figure 4-3:

1. Q3 and Q4 should be nitrogen atoms

2. P2 and P3 should be chlorine atoms.

3. There should be one iso-pentane ligand connected to Ru atom, but there are
probably two in the figure. It could be a disorder.

4. Initially all disordered atoms should be eliminated. They should be found after
the main part is determined.

5. Q1 more likely should be a phosphorous atom P1.

6. Because of the suspected disorder of the upper part of the structure, Q6 could be
electron density peak of the disordered position of Pl.

7. The rest of the q peaks are carbon atoms.

8. Three cyclopentane ligands should be coordinated to P1 atom. One of these three
ligands is recognizable in the sequence of q peaks Q30-Q54-Q28-Q45.








Atoms were relabeled according to the above mentioned observations, Figure 4-4.












P4

P2 I
^- 1/




\ / 2 //\


Figure 4-2. View of the structure at the start point of the refinement.




I\-


_ P3\P2


II




1<~~~~


Figure 4-3. View of the structure after deleting all "noise" q peaks.











C30


C53 IC50 1C40

C52 C51 C23' C24'


\ ----'C22'

C20 C14 C19 / 13

112

C21 C6 C7
C3 C4 C11


Figure 4-4. View of the structure after labeling electron density peaks. Color notation:
black for C; dark blue for N; purple for P; light blue for Ru and H; light green
for Cl. The color scheme is used for all figures in this chapter.

After the atoms were labeled and sorted, a new file el06.ins was written with

command "file," Table 4-2. This file was edited (added or changed commands

highlighted in bold) in a text editor and then run with XL.

After running XL, the solution with twenty q peaks was obtained, Figure 4-5.

Because of isotropic treatment of the atoms, the four q peaks Q2, Q6, Q17, and Q20 are

obviously "noise," because they are a result of motion of the chlorine atoms. These four

electron density peaks should be removed. The peaks Q4 and Q7 are also the result of

anisotropy of Ru and should be deleted. Q5 is a part of the cyclopentane C50 -C54 and

should be labeled as C54. One more cyclopentane is recognizable already at this stage in

the sequence of peaks C40-Q10O-Q3-Q8-Q12. These atoms are labeled as C40-C41-C42-

C43-C44. Using command "info," high thermal vibration parameter of C24 was

observed and thus deleted, because a more appropriate iso-pentane ligand shape had









sequence of atoms C23-Q9-Q14-Q16 and C25. The other q peaks were deleted as

"noise" and the atoms were labeled as shown on Figure 4-6. The atoms were sorted, filed

and the structure was refined with XL.

Table 4-2. File el06.ins

TITL el06 in P2(1)/c
CELL 0.71073 12.2221 14.5343 22.9264 90.000 99.364 90.000
ZERR 4.00 0.0007 0.0009 0.0014 0.000 0.001 0.000
LATT 1
SYMM -X, 0.5+Y, 0.5-Z
SFAC C H N P CL RU
UNIT 200 250 10 5 10 5
TEMP -100
omit -3 55

cgls 4
BOND
FMAP 2
PLAN 20

FVAR 1.00000
RU1 6 0.26280 0.55940 0.29070 11.00000 0.05000
P1 4 0.13140 0.43830 0.28980 11.00000 0.05000
CL1 5 0.11000 0.66080 0.26670 11.00000 0.05000
CL2 5 0.41810 0.45590 0.31320 11.00000 0.05000
N2 3 0.36790 0.68080 0.20790 11.00000 0.05000
N5 3 0.40300 0.73470 0.29530 11.00000 0.05000
C1 1 0.35060 0.66220 0.26130 11.00000 0.05000
C3 1 0.43410 0.76530 0.19990 11.00000 0.05000
C4 1 0.45330 0.80360 0.26150 11.00000 0.05000
C5 1 0.42610 0.74260 0.35900 11.00000 0.05000
C6 1 0.51940 0.70140 0.39050 11.00000 0.05000
C7 1 0.54530 0.71430 0.45010 11.00000 0.05000
C8 1 0.47880 0.76540 0.48430 11.00000 0.05000
C9 1 0.38460 0.80490 0.44800 11.00000 0.05000
C10 1 0.36120 0.79660 0.38800 11.00000 0.05000
ClI 1 0.59700 0.64620 0.35830 11.00000 0.05000
C12 1 0.50730 0.77130 0.55110 11.00000 0.05000
C13 1 0.25820 0.84860 0.35390 11.00000 0.05000
C14 1 0.34390 0.62310 0.15460 11.00000 0.05000
C14 1 0.25030 0.63840 0.11780 11.00000 0.05000
C15 1 0.23280 0.57990 0.06760 11.00000 0.05000
C16 1 0.31680 0.50320 0.06010 11.00000 0.05000




































C25

/ C24 C \ C30


C12 \ C23 C40 P1


C10 C13



C6 N5 C52

C116
C20




C3 C22 C18 C17
C21


Figure 4-5. View of the structure after the first run of XL. Twenty new electron density
peaks were obtained.


C17 1 0.40780 0.50470 0.10150 11.00000 0.05000
C18 1 0.42950 0.55880 0.14790 11.00000 0.05000
C19 1 0.17360 0.71890 0.12120 11.00000 0.05000
C20 1 0.32160 0.45630 0.00150 11.00000 0.05000
C21 1 0.53450 0.55620 0.19350 11.00000 0.05000
C22 1 0.26760 0.58510 0.37120 11.00000 0.05000
C23 1 0.17460 0.61580 0.42360 11.00000 0.05000
C24 1 0.20100 0.64850 0.48960 11.00000 0.05000
C30 1 -0.03370 0.43460 0.28750 11.00000 0.05000
C50 1 0.10060 0.38040 0.21330 11.00000 0.05000
C51 1 0.20570 0.32570 0.20010 11.00000 0.05000
C52 1 0.16780 0.32930 0.12900 11.00000 0.05000
C53 1 0.05210 0.39370 0.11410 11.00000 0.05000
C40 1 0.19740 0.33190 0.34270 11.00000 0.05000
HKLF 4
END

































Figure 4-6. View of the structure during the second run of refinement in XP.

After one more run of XL, the structure is shown in Figure 4-7. On this figure one

more, in addition to two already existing, cyclopentane rings Q5-Q7-Q9-Q8-Q19

appeared. C30 should be deleted as a wrongly determined carbon atom (it has a high

value of thermal parameter). Strong Q1 electron density peak is the second position of

P1 disordered atom. Peaks Q10O-Q13-Q15-Q17 form the iso-pentane ligand, which is the

second position of original C23-C24-C25-C26 and C27 iso-pentane ligand. It is easer to

work with separate disordered parts during different runs of refinement, so at this run

only disorder of the iso-pentane ligand was considered. Results of eliminating and

relabeling of atoms are shown in Figure 4-8. The list of atoms was sorted and filed.






























012C

C4


Figure 4-7. View of the structure after the second run of XL new electron density peaks
were determined.


Figure 4-8. View of the structure after eliminating "noise" q peaks after the third run of
XP.









In case of disorder, command

part

can be used. Each part requires a "disorder" parameter site occupation factor in the

string with

FVAR part1 and part 2 parameter>

command. This parameter shows the distribution of electron density of disordered atoms.

Initial value of this parameter, entered by user, must be in the range of 0 to 1, usually it is

0.5. The occupation factor of disordered atoms should be changed from 11.00000 to

X1.0 for original atom and -XI.0 for its counter part in the disorder, where X is the

number of "disorder" parameter in the FVAR string.

It is helpful to consider an example with a hypothetical disordered atom AtOl.

Disorder means that the atom AtOl can be found in two (in rare cases three and more)

positions. It is possible because during crystallization same atoms of a structure can

occupy different positions. So there is AtOl' electron density peak, which is the counter

part of disorder of AtOl. In the listing of atoms, peak AtOl should be in "part 1," AtOl'

in "part 2," and the rest of the structure should be in "part 0." The disorder parameter

(initial value 0.5) should be entered in "FVAR" command string. The occupation

parameter should be altered from 11.0000 to 21.0000 for AtOl, and from 11.0000 to

-21.0000 for AtOl'.

Details of setting of "parts" for EL06 structure are shown in Table 4-3. File

el06.ins was edited, saved and the structure was refined with XL one more time. The

results of the refinement and editing in XP of the structure are shown in Figures 4-9 and

Figure 4-10. At this time, refinement was focused on the disorder of phosphorous and its











cyclopentanes, so PI' and C50' atoms were found and set up as members of "part 2." All


atoms with labels containing primes were grouped in "part 2" and their disorder


counterparts in "part 1 ." The whole picture of disorder was recognized as a result of two


fold rotation around the Ru atom, with all coordinated to it ligands, around C 1-Rul bond


with fixed 1,3-di(2,4,6-trimethyl)phenylimidazolidine.


Table 4-3. Setting of the "part" command in the el06.ins file.


File el06.ins before edition.


TITL e106 in P2(1)/c
CELL 0.71073 12.2221 14.5343 22.9264 90.000
99.364 90.000
ZERR 4.00 0.0007 0.0009 0.0014 0.000 0.001
0.000
LATT 1
SYMM -X, 0.5+Y, 0.5-Z
SFAC CH NPCLRU
UNIT 200 250 10 5 10 5
TEMP -100
omit -3 55

cgis 4
BOND
FMAP 2
PLAN 20


WGHT
FVAR
RU1 6


0.100000
0.19969
0.26240 0.55911 0.29028 11.00000 0.03755


0.52790
0.26488
0.32532
0.27831
0.36007
0.21168
0.24040
0.14770
0.12260
0.01350
0.00210


0.54853
0.59514
0.55821
0.59499
0.54663
0.64094
0.48290
0.48740
0.42210
0.43680
0.44730


0.18645
0.36971
0.41939
0.47961
0.51576
0.49176
0.22160
0.17570
0.13350
0.08630
0.32400


11.00000
11.00000
11.00000
11.00000
11.00000
11.00000
11.00000
11.00000
11.00000
11.00000
11.00000


0.07966
0.15289
0.14908
0.19196
0.21120
0.15958
0.05000
0.05000
0.05000
0.05000
0.05000


C54 1 0.07648 0.44929 0.16259 11.00000 0.14476

HKLF 4

END


File el06.ins after edition and setting parts.


TITL e106 in P2(1)/c
CELL 0.71073 12.2221 14.5343
90.000
ZERR 4.00 0.0007 0.0009
0.000
LATT 1
SYMM -X, 0.5+Y, 0.5-Z
SFAC CH NP CL RU
UNIT 200 250 10 5 10 5
TEMP -100
omit -3 55


22.9264 90.000 99.364

0.0014 0.000 0.001


cgls 4
BOND
FMAP 2
PLAN 20


WGHT
FVAR
RU1 6


C22 1
part 1
C23 1
C24 1
C25 1
C26 1
C27 1
part 2
C23' 1
C24' 1
C25' 1
C26' 1
part 0
C30 1


0.100000
0.19969 0.5
0.26240 0.55911 0.29028 11.00000 0.03755


0.52790 0.54853 0.18645 11.00000 0.07966


0.26488
0.32532
0.27831
0.36007
0.21168

0.24040
0.14770
0.12260
0.01350


0.59514
0.55821
0.59499
0.54663
0.64094

0.48290
0.48740
0.42210
0.43680


0.36971 21.00000
0.41939 21.00000
0.47961 21.00000
0.51576 21.00000
0.49176 21.00000

0.22160 -21.00000
0.17570 -21.00000
0.13350 -21.00000
0.08630 -21.00000


0.15289
0.14908
0.19196
0.21120
0.15958

0.05000
0.05000
0.05000
0.05000


0.00210 0.44730 0.32400 11.00000 0.05000


C54 1 0.07648 0.44929 0.16259 11.00000 0.14476
HKLF 4
END





























US U'Ju C19 LU] C21




C20
C4 C3



Figure 4-9. View of the structure after refinement with XL. New twenty electron density
peaks were obtained.



C43
C4C42


C41
C40
SC30 P' C50' C26



C2536 C25 C54 C23' \\/ C23 C27

C2 C24' C7 C12
NC7
C21 7 C19 C22 C1 C
C154 N2 N5 C^ C9


C20

C3 c4


Figure 4-10. View of the structure after elimination of "noise" q peaks and assigning real
electron density to specific atom types.









The next steps of refinement included:

1. changing of isotropic refinement to anisotropic refinement
2. determination the exact cell unit contents
3. applying absorption correction
4. finding or adding hydrogen atoms
5. refining the weighting scheme
6. more detailed consideration of the disordered part and resolution of atoms

All of these procedures, except the last one, are described in the Chapter 3. The

rest of process of refinement of this structure was focused on disordered cyclopentane

ligands. The main difficulty was to find and identify these ligands, because the disorder

parameter was 0.38167. It means that the disordered part in 62% of the time is located in

one position and the rest at the other one, which causes problems locating atoms in the

second position. In order to resolve disordered parts, all cyclopentane ligands were

treated in isotropical mode. The cyclopentane ligands C40-C44 and C30-C34 did not

keep their shapes during refinement with XL, compared to ligand C50-C54. In order to

keep these ligands at constant geometrical shape, command

same C50 > C54

was used and was placed in file el06.ins before lines of the atoms of the C30-C34 and

C40-C44 cyclopentanes. Also four h k 1 peaks (0 4 0, 0 1 1, 0 4 4, 1 0 4) demonstrated

the largest disagreement between Fc2 and Fo2 (from el06.1st file) were omitted with

command "omit." This improved the refinement parameters wR2, RI and GooF. At the

final stage, carbon atoms were relabeled in order to keep number consequence without

skips. The final result of the refinement is depicted in Figures 4-11 and 4-12. The

scheme of the solved structure is shown on Figure 4-13. The CIF file for this structure is

presented in Appendix A.
































Figure 4-11. View of the structure including disorder. Thermal ellipsoids of disordered
part are treated in isotropic mode.


Figure 4-12. View of the structure without the minor part of the disorder. Thermal
ellipsoids of disordered part are treated in isotropic mode.











H2
/C --CH2
H CH2
C CH2


C C \C/CH3

S \ / -CH
CH3 H2C- CH2 H3
Figure 4-13. Scheme of the structure constructed according to the final result of the
structure solution and refinement.













CHAPTER 5
MULTIMETAL CLUSTER STRUCTURE SOLUTION

Large clusters with many metal centers are typical projects for single crystal X-ray

structure determination, but solution of this structure is not trivial. In this Chapter a Mn12

cluster's structure solution is described.

Experimental Section

Brown crystals were provided by the Christou group. A scheme of the ligands

(used for the synthesis of these crystals, as well as Mn(II) ) was given in the submission

form, Figure 5-1. One crystal with dimensions 0.20*0.12*0.05 mm3 was selected for the

structure determination. The crystal was treated according to procedures described in

Chapter 2. The results of collection of orientation matrix with 10 sec/frame dark frame

file are presented in Table 5-1.



H2C \ /OH




H2C I CH2 CH
I CH2

HO OH OH H cOO
OH HO f the cluster
Figure 5-1. Scheme of the ligands used for the synthesis of the cluster









Table 5-1. Results of orientation matrix collection for xm 54.

Orientation Matrix:
0.02926206 0.04185782 0.01827227
0.03962067 -0.01966710 -0.00947578
-0.01726891 0.02561772 -0.03705560

Lattice parameters & Standard deviations:
20.5462 18.9147 25.2994 90.027 111.174 90.053 9168.18
0.0094 0.0128 0.0127 0.053 0.054 0.041 7.47
Standard deviations corrected for GOF:
0.0073 0.0100 0.0099 0.041 0.042 0.032 5.80

Histograms:
.00 .05 .10 .15 .20 .25 .30 .35 .40 .45 +Inf
H 40 0 0 0 0 0 0 0 0 0
K 40 0 0 0 0 0 0 0 0 0
L 40 0 0 0 0 0 0 0 0 0
Omega 35 5 0 0 0 0 0 0 0 0


From Table 5-1 next conclusions could be derived:

1. The selected crystal is single and of good quality, because of all zeros in
"Histograms" section.
2. Number of peaks (40) reveals good diffraction of the crystal.
3. The crystal's lattice is Monoclinic.
4. Cell parameters are:
a=20.5462 a=90.027
b=18.9147 P=111.174
c=25.2994 y=90.053

Full sphere mode was used for full data collection. The result of experimental

work was two files xm54t.p4p and xm54t.raw.

Structure Solution and Refinement

A new project was defined and XPREP was started. All options selected by

XPREP were accepted, except determination of crystal system, which the program

recognized as Triclinic, because of the small value of R parameter for this lattice type

(R=0 for Triclinic; R=0.125 for Monoclinic). The Monoclinic crystal system was









selected and space group P21/c was determined, because reflections 0 k 0 (k = odd) and h

0 1 (1 = odd) were unobserved.

Direct Methods were used for structure solution in program XS. The value of RE

parameter was 0.204, which indicated that solution and refinement could be completed

without problems. View of the structure at the first time of running XP is presented in

Figure 5-2. Manganese atoms were located by the program. Phenyl rings of biphenyl

acetate ligands were easy to recognize in this figure (labeled q electron density peaks).

Command "grow" was applied resulting in the doubling of the structure (Figure 5-3)

showing the complete cluster. Command "fuse" can be used to eliminate all duplicate

atoms and electron density peaks.








__ /

SMn /


\ \_ --

S/ I i





Figure 5-2. View of the structure as a result of structure solution, completed by program
XS. Color notation: black for C; dark blue for Mn and N; light blue for H; red
for 0. The color scheme is used for all figures in this chapter.






46












//
























used many times, in order to determine as many "noise" q peaks as possible, according to
"\.qy, ." K







4\\ \







Figure 5-3. View of the whole cluster at the first step of refinement.

The "noise" electron density peaks were located and deleted, according to the rules

from Chapter 3. The result of the "cleaning" is shown in Figure 5-4. During the process

of eliminating the "noise" q electron density peaks commands "grow" and "fuse" were

used many times, in order to determine as many "noise" q peaks as possible, according to

octahedral coordination of all manganese atoms. The view of the whole cluster at this

stage is presented in Figure 5-5.













I

\ \ o ',7







Mn5

/








Figure 5-4. View of the asymmetric unit after elimination of "noise" q electron density
peaks.

The next step was to assign atom types to the q electron density peaks, according to

the schemes of ligands provided in the submission form. There were only Mn, O, C, and

H atoms in this cluster (hydrogen atoms were not in focus at this stage). The result of

labeling of q peaks is shown in Figure 5-6 (only labels of Mn and 0 atoms are shown for

clear view). The structure of the cluster after the labeling is presented in Figure 5-7. The

list of atoms was sorted and xm54.ins file was saved. This file was edited in a text editor

(commands "omit -3 55" and "cgls" were added) as described in Chapter 3 and Chapter

4. This file was run with XL for the first time. During the least-squires refinement wR2

parameter dropped from 0.37 to 0.33 during 5 cycles, which was a sign that the structure

refinement was on the right track.














Mn4 /

.A \ I\






-,"\ V^6 \

-/ < _





Figure 5-5. View of the cluster after elimination of "noise" q electron density peaks.

The result of the first run of XL is presented in Figure 5-8. Many Q peaks were

recognized as carbon atoms, which were elements of the phenyl rings, Figure 5-9. Using

command "info," it was determined that all atoms of the cluster were successfully located

(except hydrogen atoms). Low values of the q peaks confirmed that. Thus all attention

was focused on the q peaks, which were not elements of the cluster, but solvent

molecules. At the next step the structure refinement focused on three groups of q peaks:

Q14-Q7-Q6, Q16-Q5-Q3, Q10O-Q4-Q2. Command "bang" was used to get information

about bonds and angles in these groups, Table 5-2.









Table 5-2. Information revealed with "bang" command.
Q4 Q2 1.114
Q4 Q10 1.460 174.3
Q2
Q5 Q3 1.088
Q5 Q16 1.480 179.3
Q3
Q7 Q6 1.111
Q7 Q14 1.524 169.0
Q6


Figure 5-6. View of the asymmetric unit with labeled electron density peaks.






























Figure 5-7. View of the cluster with electron density peaks assigned to specific atom
types as result of the first run of XP.


Figure 5-8. View of the asymmetric unit after the first run of XL. Twenty new electron
density peaks were obtained.




































Figure 5-9. View of the asymmetric unit and three identical groups of q peaks.

According to the values of the bond length and the angles from Table 5-2 these

groups of q electron density peaks are three acetonitrile molecules with Q2, Q3, Q6 being

nitrogen atoms. Information provided in the submission form confirms this conclusion.

These groups of q peaks were labeled as acetonitriles and the structure was refined with

XL. As indicated, parameters of XL refinement all atoms (except hydrogen atoms)

were determined correctly at that step. Following stages of refinement included:

1. finding and adding hydrogen atoms
2. changing of isotropic refinement to anisotropic refinement
3. determining the exact unit cell contents
4. applying absorption correction
5. balancing of the weighting scheme.









All of these procedures are described in Chapter 3 and should not cause any

problems in finishing the solution. Finally in asymmetric unit besides a half of cluster,

3 acetonitrile molecules were found, which resulted, according to the space group P21/c

and Z=4, in twelve acetonitrile molecules and two clusters in a unit cell.

One of the acetonitrile molecules was disordered. Program Platon7 for Windows

Taskbar vl.07 was used to eliminate the disordered solvent molecule. Command

"SQUEEZE" was applied to calculate the total number of electrons in voids (volume

where acetonitrile were eliminated). The result of running program Platon were new files

name.ins and name.hkp, which were renamed to xm54.ins and xm54.hkl, respectively.

File xm54.ins should be run through XL refinement one more time. The main idea of

applying program Platon is to find out the exact formula, according to electron count, of

the disordered part and remove its contribution to the intensity data: consequently, to

improve the structural parameters.

The final view of the cluster (without solvent molecules) as result of structure

solution is presented in Figure 5-10. The Mn-O core of this cluster is presented in Figure

5-11. The CIF file for this structure is presented in Appendix B.





































Figure 5-10. View of the cluster at the end of refinement.


013A


Figure 5-11. View of the Mn-O core of the cluster at the end of refinement.














CHAPTER 6
SOLUTION OF A CRYSTAL STRUCTURE WITH PSEUDO SYMMETRY

This chapter focuses on solution of a structure with pseudo symmetry. This type of

symmetry can appear when a very heavy atom, such as tungsten in this project, exists in a

structure. The intensity data of such a crystal is usually dominated by scattering from the

heavy metal. XS treats a heavy atom as sphere and this action results in appearance of

additional pseudo symmetry, e.g. fold of rotation or mirror planes. A user should

recognize and eliminate pseudo symmetry part of a structure during structure refinement.

Experimental Section

Red needles like crystals were provided by the McElwee-White group. A scheme

of the expected structure was drawn in the submission form, Figure 6-1.






w
W- N


1 -

Figure 6-1. Scheme of the expected structure provided by the McElwee-White group
(generated by ACD/Structure Drawing Applet).

A crystal with dimensions 0.18*0.09*0.06 mm3 was selected and mounted on the

goniometer head. The crystal was aligned and an orientation matrix was collected. The

results of determining of the matrix are presented in Table 6-1.









Table 6-1. Results of orientation matrix collection for cw 10.


Orientation Matrix:
0.02881307 -0.05321006 -0.03430764
-0.01663550 -0.03776496 0.05264987
-0.10185793 -0.00892692 -0.01838870

Lattice parameters & Standard deviations:
9.3324 15.1843 15.2727 90.018 90.071
0.0017 0.0025 0.0027 0.018 0.016
Standard deviations corrected for GOF:
0.0017 0.0026 0.0028 0.019 0.016

Histograms:
.00 .05 .10 .15 .20 .25 .30 .35 .4
H 97 0 0 0 0 0 0 0 0
K 97 0 0 0 0 0 0 0 0
L 97 0 0 0 0 0 0 0 0
Omega 85 10 1 1 0 0 0 0


0 .45
0
0
0
0 0


Some conclusions can be derived from Table 6-1:

1. The selected crystal is single and of good quality, because of all zeros in
"Histograms" section.
2. Number of peaks (97) reveals good diffraction of the crystal.
3. The crystal's lattice is Orthorhombic.
4. Cell parameters are:
a=9.3324 a=90.018
b=15.1843 P=90.071
c=15.2727 y=90.035

After measuring the crystal's faces, a hemisphere data collection was completed.

Structure Solution and Refinement

All default options intended by XPREP were correct and were used for

determination of crystallographic parameters. According to systematic absences of

certain h k 1 reflections, space group Pna21 was established by XPREP. Direct Methods

was used for structure solution in XS. It yielded RE=0.189, which was relatively low.

The outcome of the first run of XP is shown in Figure 6-2. The program recognized

heavy atoms WI, C12, and C13, but it seems that C12 and C13 were wrongly determined,


+Inf


90.035
0.018

0.018


2164.23
0.67

0.68









according to the scheme of expected structure. In Figure 6-2, it is impossible to see any

structure motif, because the majority of q electron density peaks forms a sphere

surrounding Wl. All q peaks, C12 and C13 were deleted, and only WI remained in the

atom list, which was saved as cwlO.ins file. Regular corrections were completed, as

described in Chapters 3-5.


Figure 6-2. View of the structure at the first run of XP.

After the first run of XL, the structure presented in Figure 6-3 was obtained.

Except for Q1 1, all peaks seem to have a mirror plane symmetry. This is pseudo

symmetry. The real structure is only a half. Peaks from the right side of the structure

depicted in Figure 6-3 were selected and all q peaks from the left side were deleted.

According to bond length, angles and the scheme of expected structure from the










submission form, two conclusion were made: q electron density peaks Q2, Q6 were

assigned as chlorines; Q9, Q18, Q16, Q15 peaks form a part of the ligand, coordinated to

Wl with two nitrogen atoms (Figure 6-4 A). These peaks were saved and the rest of q

peaks was deleted. Saved q peaks were labeled as shown in Figure 6-4 B. The atoms

were sorted and filed as cwlO.ins file.






















Figure 6-3. Pseudo symmetry of the structure.


N2



N1N


A
Figure 6-4. View of the structure. A) part of the structure as q peaks, B) part of the
structure after labeling.





































Figure 6-5. View of the structure after the second run of XL refinement. Color notation:
black for C; dark blue for N; light blue for H; light green for Cl and W. The
color scheme is used for all figures in this chapter.

After running XL, a structure presented in Figure 6-5 was obtained. No ghost

peaks from pseudo symmetry were observed, but more elements of the ligands appeared.

During refinement, usually, more attention is paid to q peaks with lower numbers, but in

this case some of these peaks were eliminated. For example Q4, because it was not clear

what kind of atom it could be. At the same time q peaks Q6, Q9, Q11 were saved,

because it was obvious that they formed the isopropyl part of the ligand. The structure

with all saved q peaks is presented in Figure 6-6. The q peaks of this structure were

labeled as shown in Figure 6-7. The atom list was sorted and filed. XL was run again

and a structure, depicted on Figure 6-8 was obtained.







59























N3





Figure 6-6. View of the structure after eliminating "noise" q peaks.



N4







CS



CC1 C5

C4


Figure 6-7. View of the structure with labeled electron density peaks.
















C9 V:o. N2








N4








Figure 6-8. View of the structure with elements of pseudo symmetry after refinement
with XL. New twenty q electron density peaks were obtained.

As it can be seen from Figure 6-8, pseudo symmetry of the structure appeared

again. It is obvious that cyclohexane Q9-Q7-Q13-Q14-Q10-Q12 is a mirror image of

real cyclohexane Q2-Q3-Q5-Q6-Q8-Q4. The q peaks of the latter were saved and all

other q peaks were deleted. The saved q peaks were labeled as shown in Figure 6-9. The

list of atoms was sorted, saved, and run with XL. After this run of least-squares

refinement all atoms except hydrogens were found, thus command aniss" was added to

cwlO.ins file, in order to switch refinement of thermal ellipsoids into anisotropic mode.

After one more run of XL a structure, depicted in Figure 6-10, was obtained. At this

point, the important part of structure solution and refinement was finished. To prove it,

all q peaks, except the most intense one Q were eliminated, Figure 6-11. Position of










this Q1 peaks is not a position of a real atom. It is a "noise" peak attributed to the

anisotropy of the heavy WI atom. The rest of refinement was regular and included:

1. finding and adding hydrogen atoms
2. changing of isotropic refinement to anisotropic refinement
3. determining of exact cell unit contents
4. applying absorption correction
5. balancing of the weighting scheme

All these procedures are described in Chapter 3, as well as in Chapters 4 and 5, and

should not cause any problems in finishing the solution. The final result of structure

solution and refinement for this project is presented in Figure 6-12. The CIF file for this

structure is presented in Appendix C.






C3








Cce
C1 9

Cl






N4 0 15





C11


Figure 6-9. View of the structure after deleting "noise" q peaks and relabeling of electron
density peaks.








62





































Figure 6-10. View of the structure after one more cycle of refinement. Twenty new
electron density peaks q peaks were obtained.


N3


C5


C7


C3






4- l


C15


Figure 6-11. View of the structure after deleting "noise" q peaks and relabeling
















C5
t, C6

C4 r


Figure 6-12. Final result of the structure solution and refinement.














CHAPTER 7
PATTERSON METHOD OF STRUCTURE SOLUTION

There are many cases in single crystal structure determination when Direct Method

fails. Thus alternative method of structure solution Patterson Method can be used.

Knowledge of this method is important and helpful. This Chapter is focused on Patterson

the Method of solution of the structure CW10, which was also solved and refined with

Direct Methods in Chapter 6.

Experimental Section

All experimental procedures described in the previous chapter, as well as work with

program XPREP.

Structure Refinement

The result of running XPREP, file cwlO.ins was edited; command "TREF" was

substituted with command "PATT" in order to initiate Patterson method of structure

solution. Modified cwlO.ins file was run with XS. The results of running ofXS are

presented in Table 7-1.

Table 7-1. Parameters of structure solution with XS.
Patterson and peaksearch
Patt. Sup. on vector 1 0.0325 0.5000 0.5000 Height 425. Length 8.92
PATFOM=99.9 Corr. Coeff.=90.2 SYMFOM=99.9 for 9 heavy atoms.

During structure solution with Patterson Method XS established only the heavy

atom positions. In case of this compound it was expected that XS could find out tungsten

atom and may be chlorine atoms. Figure 7-1 proves this forecast. The very heavy atom

Wl caused formation of pseudo symmetry, which is described in Chapter 6.







Refinement of a structure (which starts with running XP at the first time) in case of
Patterson Method is exactly the same, as with Direct Methods of structure solution. All
steps of refinement of CW 10 structure are described in Chapter 6 and only figures and
short descriptions of steps are presented in this Chapter.


Figure 7-1. Pseudo symmetry of the structure.
The result of eliminating pseudo symmetry and labeling presented in Figures 7-2
and Figures 7-3.






I


Figure 7-2. View of the structure after eliminating pseudo symmetry








J

Figure 7-3. View of the structure after relabeling atoms. Color notation: black for C;
dark blue for N; light blue for H; light green for Cl and W. The color scheme
is used for all figures in this chapter.


I


Figure 7-4. View of the structure after the first refinement with XL. Twenty new electron
density peaks were obtained.









After the first run of XL, structure, presented in Figure 7-4, was obtained, then

"noise" q peaks were eliminated, Figure 7-5. Electron density q peaks were assigned to

atoms' types, Figure 7-6. Atoms list was sorted and filed. The structure was refined with

XL and the result of refinement is presented in Figure 7-7. On this figure motif of the

whole molecule is recognizable. Detailed description of finalization of structure

refinement and the final result of the refinement of cwl0O compound is described in

Chapter 6. The CIF file for this structure is presented in Appendix C.







Ni




















Figure 7-5. View of the structure after elimination of "noise" q peaks at the second time
of running XP.












N1


Figure 7-6. View of the structure after relabeling q peaks.






C3

C2

N2

C1

N3





L


Figure 7-7. View of the structure after the second run of refinement.









69

















CS

C4 N3




C1
N4 N2




C2

C3



Figure 7-8. View of the structure after elimination of "noise" q peaks (third run of XP).





C11 C12 C13



C10
C 15


C7 N1


CB

C5





C1


N4

C8


Figure 7-9. View of the structure after relabeling of atoms (third run of XP)














CHAPTER 8
SYNTHESIS, CRYSTALLIZATION AND STRUCTURE DETERMINATION OF
AQUA-CHLORO-(1,4,8,1 1-TETRAAZAUNDECANE)NICKEL(II) CHLORIDE

Introduction

Complexes of transition metals with long alkyl chains are widely used to build

Langmuir-Blodgett monolayers with specific magnetic properties.8'9 The attempt to

accomplish synthesis of nickel (II) pentaaza macrocyclic complex with attached

1-dodecyl chain the same way as described in the paper of H.J. Choi and M.P. Suh10 was

not successful. The result of this reaction was aqua-chloro-(1,4,8,11-tetraazaundecane)

nickel(II) chloride complex. Lavender prismatic crystals were collected and

characterized by single-crystal X-ray diffraction in the same way as described in previous

chapters. The results of this structure determination are published in Acta

Crystallographica Section E11 and the CIF file for this compound is presented in

Appendix D.

Experimental Section

Synthesis of aqua-chloro-(1,4,8,11-tetraazaundecane)nickel (II) chloride was

conducted according to the work ofH.J. Choi and M.P. Suh10 with some modifications.

To a refluxed solution of NiCl2*6H20 (1.2 g, 5 mmol) in MeOH (50 ml) were

added 1,4,8,11-tetraazaundecane (0.8 g, 5 mmol). After 3 hours of refluxing the mixture,

the solvent was evaporated and a light purple product of the reaction was dissolved in

EtOH (20ml). Slow evaporation of the solvent over five days, at room temperature,









yielded light purple prismatic crystals. Structure solution and refinement was completed

according to standard procedures described in Chapters 3 and 4.

Structure Description

In the title compound, nickel has octahedral coordination (Figure 8-1), which

results in elongation of Ni-N bonds compared to those in square planar 1,4,8,11-

tetrazaundecanenickel(II) cation:12 the average Ni-N bond in the title compound is

2.082(2) A, when the average value of the Ni-N bonds in the cation is only 1.922(5) A,

Table 8-1.

Table 8-1. Selected bond lengths (A) for the title compound.
Original data Data for square planar cation12

Nil-Ni 2.0788(14) Nil-Ni 1.907(5)
Nil-N2 2.0805(16) Nil-N2 1.928(5)
Nil-N3 2.0825(13) Nil-N3 1.934(5)
Nil-N4 2.0878(16) Nil-N4 1.916(5)
N1-C1 1.481(2) N1-C1 1.480(9)
N2-C3 1.478(2) N2-C3 1.473(8)
N2-C2 1.475(2) N2-C2 1.476(8)
C1-C2 1.515(3) C1-C2 1.476(11)
C3-C4 1.529(2) C3-C4 1.488(10)
C4-C5 1.527(3) C4-C5 1.508(11)

The protons of the coordinated water and the uncoordinated counterion C12 are

involved in H-bonding with their inversion symmetry equivalents, creating a diamond-

shaped interaction, Table 8-2. As a result, H-bonding chains are formed along the b-axis,

Figure 8-2. These chains are linked together by H-bonds between the amino protons on

one hand and both, coordinated and uncoordinated, chlorine ions, thus creating two-

dimensional layers in the ab-plane.

Table 8-2. Selected diamond style hydrogen bonds for the title compound [A and ]
D-H...A d(D-H) d(H...A) d(D...A) <(DHA)
01-H1...C12 0.96 2.28 3.2359(13) 174.1
01-H2...C12 #1 0.97 2.15 3.1066(14) 167.2






72


Symmetry transformations used to generate equivalent atoms: #1 -x,-y+l,-z


Figure 8-1. View of an asymmetric unit of the title compound.


Figure 8-2. View of the two dimensional layer in the crystal structure of the title
compound.















APPENDIX A
CIF FILE OF STRUCTURE EL06


data el06


audit creation method
chemical name systematic


chemical name common
_chemical_melting_point
_chemical formula_moiety
chemical formula sum
'C41 H61 C12 N2 P Ru'
_chemical formula weight


SHELXL-97


784.86


loop_
_atom_type_symbol


atom_
atom_
atom


type_description
type_scat_dispers
typescat dispers


_atom_type_scat_source
'C' 'C' 0.0033 0.0016
'International Tables Vol
'H' 'H' 0.0000 0.0000
'International Tables Vol
'N' 'N' 0.0061 0.0033
'International Tables Vol
'P' 'P' 0.1023 0.0942
'International Tables Vol


ion_real
ion_imag


C Tables 4.2.6.8 and 6.1.1.4'

C Tables 4.2.6.8 and 6.1.1.4'

C Tables 4.2.6.8 and 6.1.1.4'

C Tables 4.2.6.8 and 6.1.1.4'


'Cl' 'Cl' 0.1484 0.1585
'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
'Ru' 'Ru' -1.2594 0.8363
'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'

_symmetry_cell_setting Monoclinic
_symmetry_space_group_name_H-M P2(1)/c

loop_
symmetry equiv pos as xyz










'x, y, z'
'-x, y+1/2, -z+1/2'
'-x, -y, -z'
'x, -y-1/2, z-1/2'

_cell_length_a
_cell_length b
_cell_length_c
_cell_angle_alpha
_cell_angle beta
_cell_angle_gamma
cell volume
cell formula units
_cell measurement_
cell measurement
cell measurement_
cell measurement


exptl_
exptl_
exptl_
exptl_
exptl_
exptl_
exptl_
exptl_
exptl_


_crystal
_crystal_
_crystal_
_crystal
_crystal
crystal_
crystal_
crystal_
crystal


12.2221(7)
14.5343(9)
22.9264(14)
90.00
99.3640(10)
90.00
4018.4(4)
Z 4
temperature 173(2)
reflns used 137
theta min 2.0
theta max 28.0


_description needles
_colour brown
size_max 0.37
_size_mid 0.19
_size_min 0.14
_density _meas 0
_density_diffrn 1.297
density _method 'not measured'
F 000 1656


_exptl_absorpt_coefficient_mu 0.593
_exptl_absorpt_correction_type integration
_exptl_absorpt_correctionTmin 0.8379
_exptl_absorpt_correctionTmax 0.9310
_exptl_absorpt_process_details
'based on measured indexed crystal faces, SHELXTL (Bruker 1998)'

_exptl_special_details


ambienttemperature 173(2)
radiation_wavelength 0.71073
radiation_type MoK\a
radiation source 'normal-focus sealed tube'
radiation_monochromator graphite
measurement_device_type 'SMART CCD area detector'
measurement method '\w scans'


diffrn_
_diffrn_
_diffrn_
diffrn
diffrn
_diffrn
diffrn









diffrn
diffrn
diffrn
diffrn
_diffrn_
diffrn
diffrn
diffrn
diffrn
diffrn
diffrn
diffrn
diffrn
diffrn
diffrn
diffrn
reflns
reflns_
reflns


detector area resol mean ?
standards number 0
standards interval count ?
standards interval time ?
_standards_decay_% none


reflns
reflns
reflns
reflns
reflns
reflns
reflns
reflns
reflns
reflns
reflns


number 24710
av R equivalents 0.0728
av_sigmal/netl 0.0977
limit h min -11
limit h max 15
limit k min -18
limit k max 18
limit 1 min -24
limit 1 max 29
theta min 1.80
theta max 27.50


number total 9077
number_gt 5056
threshold_expression 'I > 2\s(I)'


_computing_data_collection 'Bruker SMART (Bruker 1998)'
_computing_cell_refinement 'Bruker SMART & SAINT (Bruker 1998)'
_computing_data_reduction 'Bruker SHELXTL (Bruker 2000)'
_computing_structure_solution 'Bruker SHELXTL'
_computing_structure_refinement 'Bruker SHELXTL'
_computing_molecular_graphics 'Bruker SHELXTL'
_computing_publication_material 'Bruker SHELXTL'

refine_special_details

Refinement of F2^ against ALL reflections. The weighted R-factor wR and
goodness of fit S are based on FA2A, conventional R-factors R are based
on F, with F set to zero for negative FA2A. The threshold expression of
FA2A^ > 2sigma(FA2A) is used only for calculating R-factors(gt) etc. and is
not relevant to the choice of reflections for refinement. R-factors based
on FA2A are statistically about twice as large as those based on F, and R-
factors based on ALL data will be even larger.


refinels structure_factor_coef Fsqd
refine ls matrixtype full
_refine ls weighting_scheme calc
_refine ls weighting_details
'calc w=l/[\sA2A(FoA2A)+(0.0849P)A2A+0.0000P] where
P=(Fo^A2A+2FcA2)/3'
atom sites solution primary direct









atom_sites_solution_secondary
atom_sites_solution_hydrogens
refine _s hydrogen treatment
refine ls extinction method
refine ls extinction coef ?
refine ls number reflns 9
refine _lsnumber_parameters
refine ls number restraints
refine ls R factor all 0.1
refine ls R factor_gt 0.C
refine ls wR factor ref 0
refine ls wR_factor_gt 0.
refine_ s_goodness of fit ref
refine ls restrained S all 1.
refine ls shift/su max 0.
refine Is shift/su mean 0.


difmap
geom
mixed
none

077
424
158
310
1648
.1746
1476
1.009
031
)01
000


loop_
atom site label


atom
atom
atom
atom
atom


type_symbol
fract x
fracty
fract z
Uiso_or equiv


_atom_site_adp_type
_atom_site_occupancy
_atom_site_symmetry_multiplicity
_atom_site_calc_flag
_atom_site_refinement_flags
_atom site disorder_assembly
_atomsite disorder_group
Rul Ru 0.26237(3) 0.05905(3) -0.209824(18) 0.04053(15) Uani 1 1 d...
Cll Cl 0.41717(12) -0.04202(9) -0.18789(8) 0.0742(5) Uani 1 1 d. A.
C12 Cl 0.10994(11) 0.16245(10) -0.23346(7) 0.0673(4) Uani 1 1 d. A.
NI N 0.4040(3) 0.2351(3) -0.20368(19) 0.0504(11) Uani 1 1 d...
N2 N 0.3687(3) 0.1818(3) -0.29322(19) 0.0486(10) Uani 1 1 d...
Cl C 0.3568(4) 0.1641(3) -0.2366(2) 0.0421(11) Uani 1 1 d. A.
C2 C 0.4484(6) 0.3069(4) -0.2382(3) 0.0776(19) Uani 1 1 d. A.
H2A H 0.5281 0.3178 -0.2236 0.093 Uiso 1 1 calc R .
H2B H 0.4075 0.3655 -0.2368 0.093 Uiso 1 1 calc R .
C3 C 0.4307(5) 0.2675(4) -0.3001(3) 0.0643(16) Uani 1 1 d. A.
H3A H 0.3868 0.3099 -0.3286 0.077 Uiso 1 1 calc R .
H3B H 0.5022 0.2544 -0.3134 0.077 Uiso 1 1 calc R .
C4 C 0.3438(5) 0.1224(3) -0.3430(3) 0.0533(14) Uani 1 1 d. A.
C5 C 0.2491(5) 0.1368(4) -0.3842(3) 0.0641(16) Uani 1 1 d ...
C6 C 0.2333(7) 0.0795(5) -0.4346(3) 0.089(2) Uani 1 1 d A.









H6A H 0.1686 0.0877 -0.4633 0.107 Uiso 1 1 calc R .
C7 C 0.3063(10) 0.0137(6) -0.4436(4) 0.109(3) Uani 1 1 d...
C8 C 0.4002(9) 0.0029(4) -0.4029(4) 0.102(3) Uani 1 1 d A.
H8A H 0.4515 -0.0435 -0.4096 0.122 Uiso 1 1 calc R..
C9 C 0.4249(6) 0.0568(4) -0.3516(3) 0.0693(18) Uani 1 1 d...
C10 C 0.5321(6) 0.0492(4) -0.3094(3) 0.086(2) Uani 1 1 d. A.
H10AH 0.5826 0.0081 -0.3261 0.129 Uiso 1 1 calc R..
H10B H 0.5178 0.0243 -0.2717 0.129 Uiso 1 1 calc R..
H10C H 0.5660 0.1103 -0.3030 0.129 Uiso 1 1 calc R..
Cll C 0.2890(10) -0.0454(6) -0.4990(4) 0.168(5) Uani 1 1 d. A.
H11A H 0.2758 -0.1093 -0.4884 0.253 Uiso 1 1 calc R .
HI 1B H 0.3553 -0.0425 -0.5179 0.253 Uiso 1 1 calc R..
H11C H 0.2249 -0.0226 -0.5264 0.253 Uiso 1 1 calc R .
C12 C 0.1671(5) 0.2108(5) -0.3761(3) 0.091(2) Uani 1 1 d A.
H12A H 0.1346 0.1978 -0.3406 0.137 Uiso 1 1 calc R..
H12B H 0.1083 0.2123 -0.4107 0.137 Uiso 1 1 calc R..
H12C H 0.2048 0.2704 -0.3718 0.137 Uiso 1 1 calc R..
C13 C 0.4258(4) 0.2418(4) -0.1408(3) 0.0546(14) Uani 1 1 d A.
C14 C 0.3574(4) 0.2950(4) -0.1112(3) 0.0578(14) Uani 1 1 d ..
C15 C 0.3857(5) 0.3035(4) -0.0505(3) 0.0690(17) Uani 1 1 d. A.
H15A H 0.3396 0.3395 -0.0299 0.083 Uiso 1 1 calc R .
C16 C 0.4775(5) 0.2622(5) -0.0188(3) 0.0744(18) Uani 1 1 d ..
C17 C 0.5454(5) 0.2108(4) -0.0497(3) 0.0733(18) Uani 1 1 d. A.
H17AH 0.6094 0.1816 -0.0286 0.088 Uiso 1 1 calc R..
C18 C 0.5216(4) 0.2015(4) -0.1102(3) 0.0589(15) Uani 1 1 d ..
C19 C 0.5989(5) 0.1471(4) -0.1427(3) 0.0781(19) Uani 1 1 d. A.
H19A H 0.6691 0.1361 -0.1162 0.117 Uiso 1 1 calc R..
H19B H 0.6130 0.1820 -0.1773 0.117 Uiso 1 1 calc R..
H19C H 0.5645 0.0880 -0.1555 0.117 Uiso 1 1 calc R..
C20 C 0.5033(6) 0.2707(5) 0.0485(3) 0.101(2) Uani 1 1 d A.
H20A H 0.5484 0.3257 0.0592 0.152 Uiso 1 1 calc R..
H20B H 0.5442 0.2161 0.0651 0.152 Uiso 1 1 calc R .
H20C H 0.4338 0.2756 0.0645 0.152 Uiso 1 1 calc R .
C21 C 0.2573(5) 0.3436(4) -0.1435(3) 0.0749(18) Uani 1 1 d A.
H21AH 0.2809 0.3969 -0.1645 0.112 Uiso 1 1 calc R..
H21B H 0.2105 0.3641 -0.1152 0.112 Uiso 1 1 calc R..
H21C H 0.2151 0.3013 -0.1721 0.112 Uiso 1 1 calc R..
Pl P 0.1705(4) -0.0421(3) -0.15083(19) 0.0684(14) Uani 0.382(3) 1 d P A 1
C22 C 0.2331(11) -0.0143(11) -0.2782(6) 0.063(4) Uiso 0.382(3) 1 d PD A 1
H22A H 0.2906 -0.0564 -0.2826 0.076 Uiso 0.382(3) 1 calc PR A 1
C23 C 0.1449(12) -0.0180(10) -0.3221(6) 0.066(4) Uiso 0.382(3) 1 d PD A 1
H23A H 0.0944 0.0321 -0.3250 0.080 Uiso 0.382(3) 1 calc PR A 1
C24 C 0.1222(14) -0.0850(11) -0.3617(8) 0.080(5) Uiso 0.382(3) 1 d PD A 1
C25 C 0.0171(12) -0.0763(11) -0.4075(7) 0.070(5) Uiso 0.382(3) 1 d PD A 1
H25A H -0.0199 -0.0180 -0.4016 0.105 Uiso 0.382(3) 1 calc PR A 1
H25B H -0.0328 -0.1276 -0.4029 0.105 Uiso 0.382(3) 1 calc PR A 1









H25C H 0.0367 -0.0777 -0.4472 0.105 Uiso 0.382(3) 1 calc PR A 1
C26 C 0.1999(17) -0.1692(14) -0.3731(9) 0.083(6) Uiso 0.382(3) 1 d PD A 1
H26A H 0.2770 -0.1548 -0.3567 0.124 Uiso 0.382(3) 1 calc PR A 1
H26B H 0.1935 -0.1800 -0.4158 0.124 Uiso 0.382(3) 1 calc PR A 1
H26C H 0.1767 -0.2246 -0.3540 0.124 Uiso 0.382(3) 1 calc PR A 1
C27 C 0.0104(11) -0.0425(10) -0.1715(7) 0.060(4) Uiso 0.382(3) 1 d PD A 1
H27A H -0.0182 -0.0975 -0.1526 0.072 Uiso 0.382(3) 1 calc PR A 1
C28 C -0.0768(14) -0.0193(13) -0.2318(6) 0.084(5) Uiso 0.382(3) 1 d PD A 1
H28A H -0.0489 0.0297 -0.2556 0.100 Uiso 0.382(3) 1 calc PR A 1
H28B H -0.0959 -0.0746 -0.2566 0.100 Uiso 0.382(3) 1 calc PR A 1
C29 C -0.1736(13) 0.0134(15) -0.2028(9) 0.104(7) Uiso 0.382(3) 1 d PD A 1
H29A H -0.2327 0.0423 -0.2316 0.125 Uiso 0.382(3) 1 calc PR A 1
H29B H -0.2053 -0.0370 -0.1818 0.125 Uiso 0.382(3) 1 calc PR A 1
C30 C -0.1180(19) 0.0764(17) -0.1646(13) 0.198(15) Uiso 0.382(3) 1 d PD A
1
H30A H -0.1638 0.0922 -0.1342 0.237 Uiso 0.382(3) 1 calc PR A 1
H30B H -0.1066 0.1333 -0.1866 0.237 Uiso 0.382(3) 1 calc PR A 1
C31 C -0.0097(12) 0.0414(10) -0.1354(6) 0.060(4) Uiso 0.382(3) 1 d PD A 1
H31A H -0.0122 0.0243 -0.0939 0.072 Uiso 0.382(3) 1 calc PR A 1
H31B H 0.0491 0.0879 -0.1362 0.072 Uiso 0.382(3) 1 calc PR A 1
C32 C 0.1893(19) -0.1605(11) -0.1532(9) 0.070(7) Uiso 0.382(3) 1 d PD A 1
H32B H 0.2713 -0.1600 -0.1395 0.084 Uiso 0.382(3) 1 calc PR A 1
C33 C 0.162(3) -0.2426(15) -0.1103(10) 0.183(14) Uiso 0.382(3) 1 d PD A 1
H33A H 0.2084 -0.2379 -0.0708 0.220 Uiso 0.382(3) 1 calc PR A 1
H33B H 0.0827 -0.2415 -0.1055 0.220 Uiso 0.382(3) 1 calc PR A 1
C34 C 0.1884(15) -0.3278(10) -0.1415(8) 0.080(5) Uiso 0.382(3) 1 d PD A 1
H34A H 0.2617 -0.3513 -0.1228 0.096 Uiso 0.382(3) 1 calc PR A 1
H34B H 0.1324 -0.3756 -0.1375 0.096 Uiso 0.618(3) 1 calc PR A 1
C35 C 0.190(2) -0.3116(12) -0.1992(8) 0.122(8) Uiso 0.382(3) 1 d PD A 1
H35A H 0.1229 -0.3387 -0.2233 0.146 Uiso 0.382(3) 1 calc PR A 1
H35B H 0.2560 -0.3405 -0.2112 0.146 Uiso 0.382(3) 1 calc PR A 1
C36 C 0.1919(16) -0.2122(11) -0.2092(7) 0.089(6) Uiso 0.382(3) 1 d PD A 1
H36A H 0.1272 -0.1944 -0.2389 0.107 Uiso 0.382(3) 1 calc PR A 1
H36B H 0.2600 -0.1958 -0.2251 0.107 Uiso 0.382(3) 1 calc PR A 1
C37 C 0.212(2) -0.0092(15) -0.0740(11) 0.157(10) Uiso 0.382(3) 1 d PD A 1
H37B H 0.2934 -0.0143 -0.0748 0.189 Uiso 0.382(3) 1 calc PR A 1
C38 C 0.210(2) 0.1040(15) -0.0759(9) 0.139(9) Uiso 0.382(3) 1 d PD A 1
H38C H 0.2705 0.1289 -0.0953 0.167 Uiso 0.382(3) 1 calc PR A 1
H38D H 0.1379 0.1276 -0.0965 0.167 Uiso 0.382(3) 1 calc PR A 1
C39 C 0.228(2) 0.1268(15) -0.0096(9) 0.097(8) Uiso 0.382(3) 1 d PD A 1
H39C H 0.2643 0.1873 -0.0011 0.116 Uiso 0.382(3) 1 calc PR A 1
H39D H 0.1575 0.1255 0.0065 0.116 Uiso 0.382(3) 1 calc PRA 1
C40 C 0.2972(19) 0.0548(16) 0.0117(10) 0.116(8) Uiso 0.382(3) 1 d PD A 1
H40C H 0.3168 0.0564 0.0554 0.139 Uiso 0.382(3) 1 calc PR A 1
H40D H 0.3658 0.0542 -0.0061 0.139 Uiso 0.382(3) 1 calc PR A 1
C41 C 0.222(4) -0.026(2) -0.0093(13) 0.50(5) Uiso 0.382(3) 1 d PD A 1









H41C H 0.2572 -0.0861 0.0025 0.599 Uiso 0.382(3) 1 calc PR A 1
H41D H 0.1494 -0.0221 0.0046 0.599 Uiso 0.382(3) 1 calc PR A 1
Pl' P 0.1333(2) -0.06759(17) -0.20942(12) 0.0609(8) Uani 0.618(3) 1 d P A 2
C22' C 0.2660(8) 0.0868(7) -0.1314(4) 0.065(3) Uiso 0.618(3) 1 d PD A 2
H22B H 0.2135 0.1337 -0.1274 0.078 Uiso 0.618(3) 1 calc PR A 2
C23' C 0.3199(9) 0.0614(7) -0.0776(5) 0.085(3) Uiso 0.618(3) 1 d PD A 2
H23B H 0.3832 0.0233 -0.0773 0.102 Uiso 0.618(3) 1 calc PR A 2
C24' C 0.2948(12) 0.0834(10) -0.0252(7) 0.110(4) Uiso 0.618(3) 1 d PD A 2
C25' C 0.3701(13) 0.0410(11) 0.0264(6) 0.135(6) Uiso 0.618(3) 1 d PD A 2
H25D H 0.4100 -0.0110 0.0125 0.203 Uiso 0.618(3) 1 calc PR A 2
H25E H 0.3258 0.0193 0.0556 0.203 Uiso 0.618(3) 1 calc PR A 2
H25F H 0.4235 0.0872 0.0446 0.203 Uiso 0.618(3) 1 calc PR A 2
C26' C 0.1955(18) 0.1439(17) -0.0058(11) 0.197(12) Uiso 0.618(3) 1 d PD A
2
H26D H 0.2256 0.2016 0.0122 0.295 Uiso 0.618(3) 1 calc PR A 2
H26E H 0.1605 0.1092 0.0229 0.295 Uiso 0.618(3) 1 calc PR A 2
H26F H 0.1401 0.1574 -0.0407 0.295 Uiso 0.618(3) 1 calc PR A 2
C27' C -0.0205(12) -0.0592(10) -0.2032(7) 0.112(5) Uiso 0.618(3) 1 d PD A 2
H27B H -0.0252 -0.1249 -0.1909 0.134 Uiso 0.618(3) 1 calc PR A 2
C28' C -0.0029(12) -0.0205(14) -0.1350(7) 0.151(6) Uiso 0.618(3) 1 d PD A 2
H28C H 0.0116 -0.0718 -0.1064 0.181 Uiso 0.618(3) 1 calc PR A 2
H28D H 0.0599 0.0232 -0.1278 0.181 Uiso 0.618(3) 1 calc PR A 2
C29' C -0.1102(13) 0.0271(11) -0.1294(7) 0.133(5) Uiso 0.618(3) 1 d PD A 2
H29C H -0.1280 0.0211 -0.0890 0.160 Uiso 0.618(3) 1 calc PR A 2
H29D H -0.1079 0.0931 -0.1398 0.160 Uiso 0.618(3) 1 calc PR A 2
C30' C -0.1822(10) -0.0192(11) -0.1687(7) 0.120(5) Uiso 0.618(3) 1 d PD A 2
H30C H -0.2472 0.0207 -0.1818 0.143 Uiso 0.618(3) 1 calc PR A 2
H30D H -0.2084 -0.0734 -0.1488 0.143 Uiso 0.618(3) 1 calc PR A 2
C31' C -0.1383(15) -0.0505(14) -0.2209(7) 0.178(8) Uiso 0.618(3) 1 d PD A 2
H31C H -0.1713 -0.1104 -0.2346 0.214 Uiso 0.618(3) 1 calc PR A 2
H31D H -0.1553 -0.0053 -0.2534 0.214 Uiso 0.618(3) 1 calc PR A 2
C32' C 0.2095(12) -0.1715(8) -0.1633(5) 0.071(4) Uiso 0.618(3) 1 d PD A 2
H32A H 0.2866 -0.1814 -0.1714 0.086 Uiso 0.618(3) 1 calc PR A 2
C33' C 0.1356(9) -0.2616(7) -0.1736(4) 0.084(3) Uiso 0.618(3) 1 d PD A 2
H33C H 0.0557 -0.2464 -0.1832 0.101 Uiso 0.618(3) 1 calc PR A 2
H33D H 0.1570 -0.3003 -0.2055 0.101 Uiso 0.618(3) 1 calc PR A 2
C34' C 0.1627(11) -0.3075(7) -0.1149(5) 0.086(3) Uiso 0.618(3) 1 d PD A 2
H34C H 0.1063 -0.3545 -0.1101 0.104 Uiso 0.618(3) 1 calc PR A 2
H34D H 0.2363 -0.3374 -0.1105 0.104 Uiso 0.618(3) 1 calc PR A 2
C35' C 0.1626(10) -0.2356(7) -0.0725(5) 0.085(3) Uiso 0.618(3) 1 d PD A 2
H35C H 0.2110 -0.2519 -0.0350 0.102 Uiso 0.618(3) 1 calc PR A 2
H35D H 0.0866 -0.2247 -0.0643 0.102 Uiso 0.618(3) 1 calc PR A 2
C36' C 0.2063(10) -0.1508(7) -0.0997(5) 0.089(3) Uiso 0.618(3) 1 d PD A 2
H36C H 0.1571 -0.0976 -0.0963 0.107 Uiso 0.618(3) 1 calc PR A 2
H36D H 0.2815 -0.1357 -0.0788 0.107 Uiso 0.618(3) 1 calc PR A 2
C37' C 0.0987(7) -0.1192(6) -0.2835(4) 0.062(2) Uiso 0.618(3) 1 d PD A 2








H37A H 0.0427 -0.1689 -0.2816 0.074 Uiso 0.618(3) 1 calc PR A 2
C38' C 0.2019(9) -0.1632(8) -0.3070(5) 0.098(4) Uiso 0.618(3) 1 d PD A 2
H38A H 0.2664 -0.1211 -0.3011 0.117 Uiso 0.618(3) 1 calc PR A 2
H38B H 0.2234 -0.2227 -0.2874 0.117 Uiso 0.618(3) 1 calc PR A 2
C39' C 0.1563(12) -0.1762(10) -0.3723(5) 0.098(5) Uiso 0.618(3) 1 d PD A 2
H39A H 0.2149 -0.1635 -0.3963 0.117 Uiso 0.618(3) 1 calc PR A 2
H39B H 0.1308 -0.2404 -0.3798 0.117 Uiso 0.618(3) 1 calc PR A 2
C40' C 0.0686(11) -0.1162(9) -0.3877(5) 0.099(4) Uiso 0.618(3) 1 d PD A 2
H40A H -0.0005 -0.1513 -0.4008 0.118 Uiso 0.618(3) 1 calc PR A 2
H40B H 0.0827 -0.0764 -0.4208 0.118 Uiso 0.618(3) 1 calc PR A 2
C41' C 0.0561(9) -0.0573(7) -0.3342(4) 0.085(3) Uiso 0.618(3) 1 d PD A 2
H41A H 0.1008 -0.0004 -0.3331 0.102 Uiso 0.618(3) 1 calc PR A 2
H41B H -0.0225 -0.0407 -0.3342 0.102 Uiso 0.618(3) 1 calc PR A 2

loop_
atom site aniso label
atom site aniso U 11
atom site aniso U 22
atom site aniso U 33
atom site aniso U 23
atom site aniso U 13
atom site aniso U 12
Rul 0.0413(2) 0.0373(2) 0.0432(2) -0.00019(19) 0.00733(16) -0.00204(18)
Cli 0.0656(9) 0.0490(8) 0.1162(14) 0.0245(8) 0.0390(9) 0.0179(7)
C12 0.0485(8) 0.0663(9) 0.0864(11) 0.0030(8) 0.0086(7) 0.0120(7)
N1 0.059(3) 0.041(2) 0.052(3) -0.006(2) 0.011(2) -0.014(2)
N2 0.061(3) 0.035(2) 0.052(3) -0.001(2) 0.013(2) -0.0067(19)
Cl 0.039(3) 0.038(3) 0.050(3) 0.000(2) 0.009(2) 0.007(2)
C2 0.103(5) 0.060(4) 0.078(5) -0.010(3) 0.038(4) -0.029(3)
C3 0.085(4) 0.043(3) 0.067(4) 0.002(3) 0.018(3) -0.016(3)
C4 0.068(4) 0.036(3) 0.061(4) -0.007(3) 0.026(3) -0.008(3)
C5 0.073(4) 0.067(4) 0.056(4) -0.013(3) 0.022(3) -0.008(3)
C6 0.112(6) 0.093(5) 0.066(5) -0.022(4) 0.020(4) -0.037(5)
C7 0.172(10) 0.084(6) 0.082(6) -0.041(5) 0.056(6) -0.048(6)
C8 0.175(9) 0.045(4) 0.109(7) -0.016(4) 0.091(6) -0.005(5)
C9 0.108(5) 0.037(3) 0.075(4) 0.005(3) 0.050(4) 0.002(3)
C10 0.098(5) 0.077(5) 0.094(5) 0.031(4) 0.048(4) 0.041(4)
C11 0.296(14) 0.122(8) 0.104(7) -0.075(6) 0.087(8) -0.074(8)
C12 0.075(5) 0.129(6) 0.067(4) 0.003(4) 0.004(3) 0.015(4)
C13 0.051(3) 0.050(3) 0.062(4) -0.008(3) 0.007(3) -0.013(3)
C14 0.049(3) 0.061(4) 0.064(4) -0.007(3) 0.012(3) -0.004(3)
C15 0.063(4) 0.078(4) 0.069(4) -0.016(3) 0.018(3) 0.003(3)
C16 0.061(4) 0.099(5) 0.062(4) -0.022(4) 0.005(3) -0.001(4)
C17 0.053(4) 0.091(5) 0.072(4) -0.017(4) -0.001(3) 0.007(3)
C18 0.048(3) 0.064(4) 0.062(4) -0.018(3) 0.000(3) -0.003(3)
C19 0.060(4) 0.086(5) 0.085(5) -0.026(4) 0.001(3) 0.008(3)









C20 0.100(6) 0.139(7) 0.061(5) -0.029(5) 0.004(4) 0.003(5)
C21 0.069(4) 0.070(4) 0.087(5) -0.007(4) 0.017(3) 0.009(3)
P1 0.073(3) 0.074(3) 0.058(3) 0.006(2) 0.011(2) -0.032(2)
P1' 0.0528(15) 0.0672(17) 0.0629(17) 0.0034(13) 0.0101(12) -0.0172(12)

_geom_special_details

All esds (except the esd in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell esds are taken
into account individually in the estimation of esds in distances, angles
and torsion angles; correlations between esds in cell parameters are only
used when they are defined by crystal symmetry. An approximate isotropicc)
treatment of cell esds is used for estimating esds involving l.s. planes.


loop_
_geom bond atom site label 1
_geom bond atom site label_2
_geom bond distance
_geom bond_site_symmetry_2
_geom_bond_publ_flag
Rul C22' 1.836(9). ?
Rul C22 1.882(14). ?
Rul Cl 2.067(5). ?
Rul Cll 2.3835(14). ?
Rul C12 2.3863(14). ?
Rul PI 2.397(4). ?
Rul PI' 2.425(2). ?
N1 CI 1.352(6). ?
N1 C13 1.426(7). ?
N1 C2 1.466(6).?
N2 CI 1.353(6). ?
N2 C4 1.424(6).?
N2 C3 1.481(6). ?
C2 C3 1.513(8). ?
C2 H2A 0.9900. ?
C2 H2B 0.9900. ?
C3 H3A 0.9900. ?
C3 H3B 0.9900. ?
C4 C5 1.384(8). ?
C4 C9 1.412(7).?
C5 C6 1.413(8) .?
C5 C12 1.502(8). ?
C6 C7 1.347(11). ?
C6 H6A 0.9500. ?
C7 C8 1.365(11). ?









C7 C11 1.520(10). ?
C8 C9 1.406(10). ?
C8 H8A 0.9500. ?
C9 C10 1.500(9). ?
C10 H10A 0.9800. ?
C10 H10B 0.9800.?
C10 H10C 0.9800.?
Cll H 11A 0.9800.?
ClI HUB 0.9800.?
Cll H 11C 0.9800.?
C12 H12A 0.9800.?
C12 H12B 0.9800.?
C12 H12C 0.9800.?
C13 C14 1.393(7). ?
C13 C18 1.394(7). ?
C14 C15 1.384(8). ?
C14 C21 1.500(8). ?
C15 C16 1.372(8). ?
C15 H15A 0.9500.?
C16 C17 1.392(8). ?
C16 C20 1.529(8).?
C17 C18 1.376(8). ?
C17 H17A 0.9500.?
C18 C19 1.517(7). ?
C19 H19A 0.9800.?
C19 H19B 0.9800.?
C19 H19C 0.9800.?
C20 H20A 0.9800. ?
C20 H20B 0.9800. ?
C20 H20C 0.9800. ?
C21 H21A 0.9800.?
C21 H21B 0.9800. ?
C21 H21C 0.9800. ?
P1 C32 1.739(16) .?
P1 C37 1.82(2). ?
P1 C27 1.938(14). ?
C22 C23 1.350(15). ?
C22 H22A 0.9500. ?
C23 C24 1.329(17). ?
C23 H23A 0.9500. ?
C24 C25 1.526(18). ?
C24 C26 1.60(2). ?
C25 H25A 0.9800. ?
C25 H25B 0.9800. ?
C25 H25C 0.9800. ?
C26 H26A 0.9800. ?









C26 H26B 0.9800. ?
C26 H26C 0.9800. ?
C27 C31 1.516(15). ?
C27 C28 1.638(15). ?
C27 H27A 1.0000.?
C28 C29 1.523(15). ?
C28 H28A 0.9900. ?
C28 H28B 0.9900. ?
C29 C30 1.368(15). ?
C29 H29A 0.9900. ?
C29 H29B 0.9900. ?
C30 C31 1.474(16). ?
C30 H30A 0.9900. ?
C30 H30B 0.9900. ?
C31 H31A 0.9900.?
C31 H31B 0.9900.?
C32 C36 1.493(16). ?
C32 C33 1.616(16). ?
C32 H32B 1.0000.?
C33 C34 1.492(16). ?
C33 H33A 0.9900. ?
C33 H33B 0.9900. ?
C34 C35 1.347(15). ?
C34 H34A 0.9900. ?
C34 H34B 0.9900. ?
C35 C36 1.464(15). ?
C35 H35A 0.9900.?
C35 H35B 0.9900. ?
C36 H36A 0.9900. ?
C36 H36B 0.9900. ?
C37 C41 1.491(18). ?
C37 C38 1.645(16). ?
C37 H37B 1.0000.?
C38 C39 1.538(16). ?
C38 H38C 0.9900. ?
C38 H38D 0.9900. ?
C39 C40 1.386(16). ?
C39 H39C 0.9900. ?
C39 H39D 0.9900. ?
C40 C41 1.524(18). ?
C40 H40C 0.9900. ?
C40 H40D 0.9900. ?
C41 H41C 0.9900. ?
C41 H41D 0.9900. ?
Pl' C37' 1.841(9). ?
Pl' C27' 1.912(13). ?









P1' C32' 1.986(13). ?
C22' C23' 1.352(12). ?
C22' H22B 0.9500. ?
C23' C24' 1.327(15). ?
C23' H23B 0.9500. ?
C24' C25' 1.507(17). ?
C24' C26' 1.62(2). ?
C25' H25D 0.9800. ?
C25' H25E 0.9800. ?
C25' H25F 0.9800. ?
C26' H26D 0.9800. ?
C26' H26E 0.9800. ?
C26' H26F 0.9800. ?
C27' C31' 1.437(14). ?
C27' C28' 1.643(14). ?
C27' H27B 1.0000.?
C28' C29' 1.505(14). ?
C28' H28C 0.9900. ?
C28' H28D 0.9900. ?
C29' C30' 1.334(12). ?
C29' H29C 0.9900. ?
C29' H29D 0.9900. ?
C30' C31' 1.461(15). ?
C30' H30C 0.9900. ?
C30' H30D 0.9900. ?
C31' H31C 0.9900.?
C31' H31D 0.9900.?
C32' C36' 1.497(13). ?
C32' C33' 1.586(12). ?
C32' H32A 1.0000.?
C33' C34' 1.491(12). ?
C33' H33C 0.9900. ?
C33' H33D 0.9900. ?
C34' C35' 1.426(12). ?
C34' H34C 0.9900. ?
C34' H34D 0.9900. ?
C35' C36' 1.516(12). ?
C35' H35C 0.9900. ?
C35' H35D 0.9900. ?
C36' H36C 0.9900. ?
C36' H36D 0.9900. ?
C37' C41' 1.496(11). ?
C37' C38' 1.584(11). ?
C37' H37A 1.0000.?
C38' C39' 1.522(13). ?
C38' H38A 0.9900. ?









C38' H38B 0.9900. ?
C39' C40' 1.381(13). ?
C39' H39A 0.9900. ?
C39' H39B 0.9900. ?
C40' C41' 1.524(12). ?
C40' H40A 0.9900. ?
C40' H40B 0.9900. ?
C41' H41A 0.9900.?
C41' H41B 0.9900. ?

loop_
_geom_angle_atom_site_label_ 1
_geom_angle_atom_site_label_2
_geom_angle_atom_site_label_3
_geom_angle
_geom_angle_site_symmetry_ 1
_geom_angle_site_symmetry_3
_geom_angle_publ_flag
C22' Rul C22 155.7(5) ?
C22' Rul Cl 101.7(3). ?
C22 Rul Cl 102.2(5). ?
C22' Rul Cll 92.1(3). .?
C22 Rul Cll 82.1(5). .?
Cl Rul Cll 93.18(13). .?
C22' Rul C12 88.7(3). ?
C22 Rul C12 97.6(5). ?
Cl Rul C12 85.43(13) ?
Cll Rul C12 178.50(5) ?
C22' Rul PI 61.4(3).. ?
C22 Rul PI 94.6(4). ?
Cl Rul PI 163.01(17) ?
Cll Rul PI 86.07(12). ?
C12 Rul PI 95.42(12). ?
C22' Rul PI' 94.3(3). ?
C22 Rul PI' 62.4(4).. ?
Cl Rul Pl' 163.11(15). ?
Cll Rul Pl' 91.48(7). ?
C12 Rul Pl' 89.70(7). .?
Pl Rul Pl' 33.66(12). ?
Cl NI C13 127.6(4). ?
C1 N1 C2 113.8(4). .?
C13 NI C2 118.2(4). .?
Cl N2 C4 127.7(4) ?
C1 N2 C3 113.5(4). .?
C4N2C3 118.1(4). .?
N1 Cl N2 106.8(4) .?









N1 Cl Rul 127.3(4) .. ?
N2 Cl Rul 125.3(3). ?
N1 C2 C3 103.2(4). .?
N1 C2H2A 111.1. .?
C3 C2H2A 111.1. .?
N1 C2H2B 111.1. .?
C3 C2H2B 111.1 ..?
H2A C2 H2B 109.1 .. ?
N2 C3 C2 102.5(4). ?
N2 C3 H3A 111.3. .?
C2C3H3A111.3. .?
N2C3H3B 111.3 ..?
C2 C3 H3B 111.3 .?
H3A C3 H3B 109.2. ?
C5 C4 C9 122.4(5). ?
C5 C4N2 120.1(5). .?
C9 C4N2 117.2(5). .?
C4 C5 C6 117.2(6). .?
C4 C5 C12 121.7(5) ?
C6 C5 C12 121.1(7). ?
C7 C6 C5 122.5(8). ?
C7 C6 H6A 118.8.. ?
C5 C6H6A 118.8.. ?
C6 C7 C8 118.8(7). ?
C6 C7 C11 121.5(11) ?
C8 C7 C11 119.5(10) ?
C7 C8 C9 123.4(8). ?
C7 C8 H8A 118.3 ?
C9 C8 H8A 118.3 ?
C8 C9 C4 115.6(7). .?
C8 C9 C10 123.0(7) ?
C4 C9 C10 121.3(6). .?
C9 C10 H10A 109.5 .?
C9 C10H10B 109.5 ?
H10A C10 H10B 109.5 ?
C9 C10 H10C 109.5. ?
H10A C10 H10C 109.5 ?
H10B C10 H10C 109.5 .. ?
C7 C11 H11A 109.5 .?
C7 C11 H11B 109.5 .. ?
H11A C11 H11B 109.5 .?
C7 C11 H11C 109.5 .. ?
H11A C11 H11C 109.5 .?
H11B C11 H11C 109.5 ?
C5 C12 H12A 109.5 .?
C5 C12 H12B 109.5 .. ?









H12A C12 H12B 109.5.. ?
C5 C12 H12C 109.5 ?
H12A C12 H12C 109.5.. ?
H12B C12 H12C 109.5 ?
C14 C13 C18 120.6(5). ?
C14 C13 NI 120.2(5). .?
C18 C13 NI 118.9(5) .?
C15 C14 C13 117.9(5). .?
C15 C14 C21 120.3(5). .?
C13 C14 C21 121.7(5). ?
C16 C15 C14 122.9(6). .?
C16 C15 H15A 118.6. ?
C14 C15 H15A 118.6. .?
C15 C16 C17 117.9(6). .?
C15 C16 C20 121.1(6). .?
C17 C16 C20 121.0(6). .?
C18 C17 C16 121.3(6). .?
C18 C17 H17A 119.3 .?
C16 C17 H17A 119.3 ?
C17 C18 C13 119.2(5). ?
C17 C18 C19 120.0(5). ?
C13 C18 C19 120.7(5). ?
C18 C19 H19A 109.5 ?
C18 C19 H19B 109.5 .?
H19A C19 H19B 109.5 ?
C18 C19 H19C 109.5 .?
H19A C19 H19C 109.5 ?
H19B C19 H19C 109.5 .. ?
C16 C20 H20A 109.5. .?
C16 C20 H20B 109.5 .?
H20A C20 H20B 109.5 ?
C16 C20 H20C 109.5 .?
H20A C20 H20C 109.5 ?
H20B C20 H20C 109.5 .. ?
C14 C21 H21A 109.5 .?
C14 C21 H21B 109.5 .?
H21A C21 H21B 109.5 ?
C14 C21 H21C 109.5 .?
H21A C21 H21C 109.5 ?
H21B C21 H21C 109.5 .. ?
C32 P1 C37 105.9(10). ?
C32 P1 C27 97.0(9).. ?
C37 P1 C27 110.5(10).. ?
C32 P1 Rul 120.9(7).. ?
C37 P1 Rul 107.6(8).. ?
C27 P1 Rul 114.3(5).. ?









C23 C22Rul 131.6(12) ?
C23 C22 H22A 114.2.. ?
Rul C22 H22A 114.2.. ?
C24 C23 C22 126.2(15) ?
C24 C23 H23A 116.9.. ?
C22 C23 H23A 116.9.. ?
C23 C24 C25 117.9(14) ?
C23 C24 C26 127.6(15) ?
C25 C24 C26 114.0(14) ?
C31 C27 C28 98.9(9). ?
C31 C27 P1 96.4(10).. ?
C28 C27 P1 134.4(12). ?
C31 C27 H27A 107.8.. ?
C28 C27 H27A 107.8. ?
P1 C27 H27A 107.8 .?
C29 C28 C27 98.1(11). ?
C29 C28 H28A 112.1. .?
C27 C28 H28A 112.1. .?
C29 C28 H28B 112.1 ..?
C27 C28 H28B 112.1 ..?
H28A C28 H28B 109.8.. ?
C30 C29 C28 98.5(15). .?
C30 C29 H29A 112.1. .?
C28 C29 H29A 112.1. .?
C30 C29H29B 112.1 ..?
C28 C29H29B 112.1 ..?
H29A C29 H29B 109.7. ?
C29 C30 C31 112.0(15) ?
C29 C30 H30A 109.2.. ?
C31 C30 H30A 109.2.. ?
C29 C30 H30B 109.2.. ?
C31 C30 H30B 109.2.. ?
H30A C30 H30B 107.9. ?
C30 C31 C27 104.1(11) .?
C30 C31 H31A 110.9. ?
C27 C31 H31A 110.9 .?
C30 C31 H31B 110.9. ?
C27 C31 H31B 110.9. ?
H31AC31 H31B 109.0. .?
C36 C32 C33 100.9(11) ?
C36 C32P1 123.1(13). ?
C33 C32 P1 132.1(14) .?
C36 C32 H32B 96.5 .. ?
C33 C32 H32B 96.5 .. ?
P1 C32H32B 96.5 ?
C34 C33 C32 103.7(12).. ?









C34 C33 H33A 111.0. .?
C32 C33 H33A 111.0. .?
C34 C33 H33B 111.0. ?
C32 C33 H33B 111.0. ?
H33A C33 H33B 109.0. ?
C35 C34 C33 111.4(13) ?
C35 C34 H34A 109.3 .. ?
C33 C34 H34A 109.3 .. ?
C35 C34 H34B 109.3 ?
C33 C34 H34B 109.3 ?
H34A C34 H34B 108.0. ?
C34 C35 C36 109.3(13) .?
C34 C35 H35A 109.8. ?
C36 C35 H35A 109.8. ?
C34 C35 H35B 109.8 .. ?
C36 C35 H35B 109.8 .. ?
H35A C35 H35B 108.3 ?
C35 C36 C32 111.0(12). ?
C35 C36 H36A 109.4.. ?
C32 C36 H36A 109.4.. ?
C35 C36 H36B 109.4.. ?
C32 C36 H36B 109.4.. ?
H36A C36 H36B 108.0. ?
C41 C37 C38 101.0(14) ?
C41 C37 P1 152.5(18). ?
C38 C37P1 103.7(15). ?
C41 C37 H37B 94.9.. ?
C38 C37 H37B 94.9.. ?
P1 C37 H37B 94.9.. ?
C39 C38 C37 101.0(12) ?
C39C38H38C 111.6. .?
C37C38 H38C 111.6. .?
C39C38H38D 111.6. .?
C37C38 H38D 111.6. .?
H38C C38 H38D 109.4. ?
C40 C39 C38 99.5(15). .?
C40C39H39C 111.9. .?
C38C39H39C 111.9. .?
C40C39H39D 111.9. .?
C38C39H39D 111.9. .?
H39C C39 H39D 109.6. .?
C39 C40 C41 99.7(18). .?
C39C40H40C 111.8 ?
C41 C40H40C 111.8 ?
C39C40H40D 111.8. ?
C41 C40H40D 111.8 ?