Finishing_a_Structure

Bruker SMART APEX II Diffractometer

PRINTING THE RESULTS AND PREPARING THE FILES

FOR SUBMISSION AND PUBLICATION

Software version APEX2 v2.1-0

J. Tanski 2/15/06; rev. S. MacMillan 1/14/07

This guide is useful for completing a crystal structure and preparing the

necessary files for submission and publication.

After data collection is complete, finish the data reduction according to Steps 1.9-1.13 described in the Routine Data Collection section of this Quick Start Guide. Once the structure has been solved and preliminarily refined on the APEX2 computer, move to the IBM PC to finish the structure and print the results.

3.1 The rest of the process must be done in SHELXTL. Double click on

the SHELXTL icon at the top of the desktop. Select PROJECT-NEW. Browse to the directory on the APEX2 computer that contains the structure file (filename.hkl):

/frames on Bruker-3b-server/guest/APEXUsers/…/Filename/work/… Name the project, highlight filename.hkl, and click OPEN.

Note: If you rename the structure file in XPREP after this point, you must create a new project using the newly created structure file.

3.2 To finish the structure model, it is best to first refine the structure

anisotropically, label and sort the atoms sensibly, then add hydrogen atoms and refine. There are also a number of things that need to be added to or edited in the instruction file (filename.ins) and the result file (filename.res). Access these files by using the EDIT menu in SHELXTL.

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i. To refine the structure anisotropically, add ANIS to the instruction file. Type this command on its own line, after the line containing BOND. Also enter the crystal size and collection temperature (in degrees Celsius) if these are not present in the instructions file. Use the SIZE and TEMP commands, each on their own line. Save and Refine.

So for JT373V, the instruction file would look similar to the following (before refinement):

TITL JT373V in P21

CELL 0.71073 9.5129 10.8084 14.3731 90 103.632 90 ZERR 4.00 0.0007 0.0007 0.0010 0.001 0.001 0.001 LATT 1

SFAC C CL N O V UNIT 80 16 8 16 1 TEMP -148

SIZE 0.030 0.100 0.160 L.S. 4 BOND ANIS FMAP 2 PLAN 20

ii. Label the atoms sensibly in XP and then sort them using the commands: sort/n (enter) sort $A1 $A2 $A3 … (enter), where A is an element in the structure. Type info to check that the atom list has been sorted and then save the information by typing file and then quit. Refine.

So for JT373V, the process for sorting would look similar to the following:

XP>> sort/n

XP>> sort $V $O $N $Cl $C

iii. Once finished, open the result file and type EXTI 0.00001 to refine the extinction coefficient. This command should be on its own line, 系数

after the line containing BOND. Save this file, select EDIT-COPY .RES -> .INS, and refine. If the extinction coefficient refines to zero, enter REM in front of EXTI and save.

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iv. For polar and non-centrosymmetric space groups, verify that the correct orientation of the polar axes has been chosen. This is done by typing TWIN and BASF 0.5 into the instruction file, each on their own line. Type these commands after the line containing BOND. If the correct orientation has been chosen, the value of the BASF will refine to approximately zero. If the value refines to approximately one, type MOVE 1 1 1 -1 into the instruction file, after the line containing the BASF value. Repeat the refinement. Certain space groups require special values; see p. 11-3 in the SHELX Manual.

v. Hydrogen atoms can be added in XP by typing the command hadd. Verify that the hydrogen atoms are in the correct positions and that there are the correct number of hydrogen atoms at each position. Hydrogen atoms are labeled automatically based on the labeling scheme made in Step ii; there is no need to rename them. After adding hydrogens and saving, exit XP and refine. In the results file, replace all methyl hydrogen tags as 137 and save.

The weighting scheme should be repeatedly updated until it remains constant. Sometimes the suggested weighting scheme leads to a GooF value <1. The GooF value should be >1; if there is a discrepancy here, adjust the weighting scheme appropriately until the GooF is just above 1. When the refinement has converged, the max shift is ~0.00.

vi. Check that all thermal parameters are reasonable; they should be approximately 0.04. Delete any disagreeable reflections (see JMT). Use SQUEEZE, as described in Appendix IV, for any horribly disordered solvent or counterions. Check suspicious space groups with Platon, as described in Appendix III.

Insert any miscellaneous commands into the instruction file, such as CONF (torsional angles) or BIND (distance between specified atoms). Insert ACTA into the instruction file to create the filename.cif file. This command will also alert you to a discrepancy in the UNIT instruction. If there is a problem, see the filename.lst file. Modify the UNIT instruction in the instruction file, save and run the final XL refinement.

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3.3 The parameter file (filename.pcf) must be modified so that the

completed structure (contained in the .cif) is acceptable for submission to the Cambridge Structure Database and for publication.

Select EDIT-EDIT to open a notepad window. Select FILE-OPEN and under “Files of Type” select “All Files”. Browse to find filename.pcf.

Modify the .pcf file to resolve the important fields as shown below. Type the correct information into the fields; do not remove the quotation marks surrounding the field.

Note: Remember to put quotation marks around the ? in the exptl_crystal_density_meas field.

data_bisws

_symmetry_cell_setting 'Triclinic' _symmetry_space_group_name_H-M 'P-1 ' Correct to 125 _cell_measurement_temperature 153(2) _cell_measurement_reflns_used ? _cell_measurement_theta_min ? See JMT if not present _cell_measurement_theta_max ?

_exptl_crystal_description '?' Input description, e.g. block, plate... _exptl_crystal_colour '?' _exptl_crystal_size_max ?

_exptl_crystal_size_mid ? Input crystal color _exptl_crystal_size_min ? _exptl_crystal_density_meas '?' Input crystal size _exptl_crystal_density_method '?' _exptl_absorpt_correction_type 'none' _exptl_absorpt_correction_T_min ? Correct to empirical _exptl_absorpt_correction_T_max ?

_diffrn_ambient_temperature 153(2) Correct to 125 _diffrn_radiation_type 'MoK\\a' _diffrn_radiation_source 'sealed tube' _diffrn_radiation_monochromator 'graphite'

_diffrn_measurement_device_type 'CCD area detector' _diffrn_measurement_method 'phi and omega scans' _diffrn_detector_area_resol_mean ? _diffrn_standards_number ? _diffrn_standards_interval_count ? _diffrn_standards_decay_% ?

_computing_data_collection 'Bruker SMART' _computing_cell_refinement 'Bruker SMART' _computing_data_reduction 'Bruker SAINT' _computing_structure_solution 'Bruker SHELXTL' _computing_structure_refinement 'Bruker SHELXTL' _computing_molecular_graphics 'Bruker SHELXTL' _computing_publication_material 'Bruker SHELXTL'

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3.4 Generate a report by running XCIF. This should be done twice; the

first time will be to print out tables that will go into the binder log book. The second time will be to generate the report such that it can be opened and modified in Microsoft Word. If XL is run after this step, XCIF must be run again. Select XCIF; hit ENTER to proceed through the options.

Choose OPTION R (“Use another CIF file to resolve ? items”) and hit ENTER four times to complete the option with the default settings.

OPTION C (“Set compound name for tables”) and enter a compound name after the “Input new name” prompt. Do not simply accept the sample filename for this.

OPTION N (“Set next table number”) and type 1 if starting from the beginning, or another number as appropriate (see below).

OPTION T (“Crystal/atom table for .cif”) and hit ENTER twice until the “Filename for tables” prompt appears. Enter filename.tex.

For the first run of XCIF, select the default [ang] definition file, and type Y for the first prompt only and N for the rest. For the second run of XCIF, type def and then Y or N as indicated below.

Crystal data table? – Y (Table 1)

Atom coordinates table? – Y (Table 2)

Selected bond lengths and angles table? – N

Full bond lengths and angles table? – Y (Table 3) Anisotropic displacement params table? – Y (Table 4) Hydrogen atom coordinates table? – Y (Table 5)

Selected torsion angles table? – N (Only Y is CONF is in .ins file) Full torsion angles table? – N

Hydrogen bond table? – N (Only Y if HTAB completed)

OPTION F (“Structure factor tables from .fcf”) and hit ENTER twice until the “Filename for tables” prompt appears. Enter filename.sft and accept the next two defaults.

Select OPTION X and enter filename.tex to print. Make sure there is no missing data; select OPTION Q to quit.

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3.5 After running XCIF, some information may still be missing from the

generated .cif file. These must be edited manually. Select EDIT-EDIT .CIF to open the file.

. . .

_cell_length_a 9.8190(3) _cell_length_b 14.0298(4) _cell_length_c 11.5874(3) _cell_angle_alpha 90.00

_cell_angle_beta 110.244(2) _cell_angle_gamma 90.00

_cell_volume 1497.66(7) _cell_formula_units_Z 2

_cell_measurement_temperature 388(2) _cell_measurement_reflns_used 2026 _cell_measurement_theta_min 2.37 _cell_measurement_theta_max 23.07 . . .

_exptl_absorpt_coefficient_mu 3.051

_exptl_absorpt_correction_type ‘empirical’ _exptl_absorpt_correction_T_min 0.5806 _exptl_absorpt_correction_T_max 0.7501 _exptl_absorpt_process_details ‘?’ . . .

_diffrn_ambient_temperature 388(2) _diffrn_radiation_wavelength 0.71073 _diffrn_radiation_type MoK\\a

Correct to 125 Type sadabs Correct to 125

In most structures some of the hydrogen atoms are refined (Q peaks are assigned as H’s and then refined when running XL), and the rest of them are located in calculated positions through Add Hydrogen in XShell (or the command HADD in XP). If all the hydrogen atoms in the structure are in calculated positions (none of them was located and refined), scroll down to the section after the _refine_special_details paragraph and change the corresponding line:

_atom_sites_solution_hydrogens geom

_refine_ls_hydrogen_treatment mixed _refine_ls_extinction_method SHELXL Change to constr

Note: If XL was run after running XCIF, XCIF must be redone and the .cif file manually edited.

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3.6 It is easiest to print ORTEP diagrams from XP.

i. Open the structure in XP. Type “fmol/n” and then “proj” to see and rotate the structure. After exiting, type “kill $q” to remove the Q peaks. If desired, type “kill $h” to remove the hydrogens. If you want to save certain hydrogens, type “pick $h” to delete (enter), skip (space bar), and assign atoms (type label, return). Type “/” to get out of pick. If hydrogens will be present in the plot, enter the command “ATYP $H 1” (correct shading) and “LABL 4 500” (correct labeling).

ii. Type “PROJ” and orient the structure in a reasonable manner. The command “MPLN atom1 atom2 atom3” will orient the molecule such that the named atoms are in the plane of the screen.

iii. -bonded ligands (i.e: Cp rings, centroids) should be created using the “CENT/X” command. The centroid should be joined to the metal (“JOIN X1A M”, for example) and the bonds from the ring to the metal deleted (“UNDO C1 M”, for example). To save it for later, type “SAVE name”. This creates a file called name.sav, which can be read in again with the “NEXT name” command.

iv. To create the ORTEP diagram, type “TELP 0 -20 0.04”. Hit ENTER until prompted for the plot file. Type a name.

v. The ORTEP drawing should appear on the screen. A small

rectangle will appear next to the first atom in the list; move it to a good location and click the left mouse button to label that atom. Hit ENTER if you want to skip a label. Type “b” to get out of the labeling screen.

vi. Type “DRAW filename” to print the diagram. Use this command to create .pdf files of the diagram also.

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3.7 Submit the .cif file to the CHECKCIF/PATON service. Upload the file

at http://journals.iucr.org/services/cif/checkcif.html.

After selecting SEND CIF FOR CHECKING, a series of alerts will be given. Special attention must be given to alerts category A and B.

3.8 In both log books, record that the structure was completed. From the

APEX2 computer, transfer the entire sample folder to the external hard drive. Place the print out of Table 1 and an ORTEP diagram of the structure in the binder log book.

3.9 When the structure is submitted for publication, the .cif file must be

submitted to the Cambridge Structural Database. See the instructions at http://www.ccdc.cam.ac.uk/products/csd/deposit/.

Any available information on the journal, authors and title of the publication must be added at the top of the .cif file. Copy the contents of the file CifPubTemplate.pcf (IBM PC) into the beginning of the .cif file, and enter the journal, author, and title information.

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