Cif File Entries for the Diffractometer

Cif File Entries for the Purdue Quest Diffractometer (June 2020) A CIF (Crystallographic Information File) is written by the refinement program, but it is usually incomplete, and some required items need to be added by hand before the CIF file will pass checking. Checking, done online via the web page https://checkcif.iucr.org/, is required if you want to publish crystallographic data in a peer reviewed journal. This document contains general data collection items for all data sets collect on the two Purdue Bruker Quest diffractometer. The CIF format uses text only (ASCII characters). This means, if it is not on the key board, don’t use it. Each basic entry consists of two items: The identifier, and the value. The identifier usually starts with an underscore, and might consist of several words connected by underscores (e.g. _diffrn_radiation_monochromator). It is followed by the value, which, depending on the item, is a number or text. It has to be either a single number or word, or it has to be marked as a single item with single parentheses (e.g. 'fine focus sealed tube'). Each line should not exceed 80 characters (that’s legacy from times when e-mails could not handle longer lines). If an entry is longer than 80 characters, you should use semicolons instead of the single parentheses. It may then stretch over several lines. Values have to be in the cif “library”. Numbers have to be in an acceptable range, words have to be one of a list of allowed entries in the “CIF Dictionary” (e.g. at http://www.iucr.org/resources/cif/dictionaries/cif_core). Tables in a cif file are following a more complicated procedure. For a complete description of the CIF file format for reporting crystal structures, and on current developments regarding cif files, see http://www.iucr.org/resources/cif. The CIF code allows to express some non-ASCII characters (such as Greek letters or Umlauts). H\"ubschle, for example, will be printed as Hübschle when converted to text using “printcif” or making tables. Beware of typos!! With a CIF file based on a dataset from one of the Purdue Bruker Quest instruments and refined with Shelxle and Shelxl2014, usually the following items have to be added or edited. They are listed in the order in which they will appear in the cif file, and are given in blocks similar as in the cif file. Items in black can be copied directly. Items in red need a second look and a value looked up or a decision made. Edits can be made using a simple text editor such as Notepad or programs like Encifer or FinalCif. Do not use advanced text editors such as MS Word. You may also try out FinalCif to automatically extract missing items from the raw data files and to create tables and reports (read the FinalCif software documentation first!). 1. Cell measurement details _cell_measurement_reflns_used _cell_measurement_theta_min _cell_measurement_theta_max from p4p file, 1st value of SAINGL line from p4p file, 2nd value of SAINGL line from p4p file, 3rd value of SAINGL line 2. Crystal colour and shape _exptl_crystal_description _exptl_crystal_colour from p4p file, MORPH entry from p4p file, CCOLOR entry _exptl_crystal_size_max _exptl_crystal_size_mid _exptl_crystal_size_min from p4p file, CSIZE entry from p4p file, CSIZE entry from p4p file, CSIZE entry 3. Absorption correction details _exptl_absorpt_correction_type 'multi-scan' _exptl_absorpt_correction_T_min obtain value from “abs” file, 3rd last line _exptl_absorpt_correction_T_max obtain value from “abs” file, 3rd last line _exptl_absorpt_process_details ; SADABS 2016/2: Krause, L., Herbst-Irmer, R., Sheldrick G.M. & Stalke D. (2015). J. Appl. Cryst. 48, 3-10. ; (These four entries might be already added if the original hkl file has been used rather than the one processed in XPREP). 4. Instrument details Quest instrument with molybdenum source: _diffrn_source _diffrn_source_current _diffrn_source_voltage _diffrn_radiation_monochromator _diffrn_measurement_device _diffrn_measurement_device_type _diffrn_detector_type _diffrn_measurement_method _diffrn_detector_area_resol_mean 'fine focus sealed tube X-ray source' '30 mA' '50 kV' 'Triumph curved graphite crystal' 'three circle diffractometer' 'Bruker AXS D8 Quest' 'PhotonII charge-integrating pixel array (CPAD)' 'omega and phi scans' 7.4074 Quest instrument with copper source: 'I-mu-S microsource X-ray tube' _diffrn_source_current _diffrn_source_voltage _diffrn_radiation_monochromator _diffrn_measurement_device _diffrn_measurement_device_type _diffrn_detector_type counting pixel array' _diffrn_measurement_method _diffrn_detector_area_resol_mean '1.0 mA' '50 kV' 'laterally graded multilayer (Goebel) mirror' 'four circle diffractometer' 'Bruker AXS D8 Quest' 'PhotonIII_C14 charge-integrating and photon 'omega and phi scans' 7.4074 The entries _diffrn_radiation_monochromator, _diffrn_measurement_device, _diffrn_detector_type, _diffrn_source_current and _diffrn_source_voltage are not automatically added to the cif file. Add them anyway (it also helps to populate all entries in reports you might create using FinalCIF). 5. Software details: _computing_data_collection _computing_cell_refinement _computing_data_reduction _computing_structure_solution ' Apex4 v2022.10-0 (Bruker, 2022) ' ' SAINT V8.40B (Bruker, 2020)' ' SAINT V8.40B (Bruker, 2020)' 'SHELXS-97 (Sheldrick, 2008)' or 'SHELXM (Sheldrick, 2008)' or 'SHELXT (Sheldrick, 2015b)' _computing_structure_refinement ; SHELXL-2018/3 (Sheldrick, 2015a, 2018), SHELXLE Rev1428 (H\"ubschle et al., 2011) ; 6. Structure solution methods _atom_sites_solution_primary _atom_sites_solution_secondary 'direct', 'patt', 'dual space' or 'isomor' 'difmap' or 'none' Use 'direct' if you used TREF in XS or XM to solve the structure (direct methods). Use 'patt' if you used PATT in XS to solve the structure. Use 'dual space' if you used ShelXT to solve the structure. Use 'isomor' if you solved the structure by isomorphous replacement. Use difmap if you assigned Q-peaks as atoms. Use none if no atoms needed to be added during refinement. 7. Absolute Configuration: _chemical_absolute_configuration 'ad' or 'syn' or 'unk' This entry only applies for chiral and non-centrosymmetric structures. Use 'ad' (anomalous dispersion) if you refined a Flack parameter and got a reliable value close to zero with a small esd. Use 'syn' (synthesis) if you assigned the absolute structure based on a known chiral center, e.g. from the starting material that did not change during synthesis. Use 'unk' (unkown) if you don’t know 8. Authors, software cited above and acknowledgements. Add below the data_ line at the top and above the remainder of the cif text. Repeat the author loop (below _publ_author_address) as often as needed to include all authors (you, advisor, etc). Delete any software you did not use. _publ_contact_author_name _publ_contact_author_address ; Your Department Purdue University Your Street Address West Lafayette IN Your ZIP-code USA ; _publ_contact_author_email _publ_contact_author_fax _publ_contact_author_phone 'Last Name, First Name(s)' 'your e-mail' 'your department fax number' 'your department phone number' loop_ _publ_author_name _publ_author_address ; ; 'Last Name, First Name(s)' Department University or Company Street Address City State, ZIP-code Country _publ_section_references ; Bruker (2022). Apex4 2022.1-1, SAINT V8.40B, Bruker AXS Inc.: Madison (WI), USA, 2022. H\"ubschle, C. B., Sheldrick, G. M. and Dittrich, B. (2011). J. Appl. Cryst. 44, 1281--1284. Sheldrick, G.M. (2008). Acta Cryst. A64, 112--122. Sheldrick, G. M. (2008). CELL_NOW. Version 2008/4. University of G\"ottingen, Germany. Sheldrick, G. M. (2018). SHELXL2018. University of G\"ottingen, Germany. Sheldrick, G. M. (2015a). Crystal structure refinement with SHELXL, Acta Cryst. C71, 3--8. Sheldrick, G. M. (2015b). SHELXT--Integrated space-group and crystal-structure determination, Acta Cryst. A71 3--8. _publ_section_acknowledgements ; This material is based upon work supported by the National Science Foundation through the Major Research Instrumentation Program under Grant No. CHE 1625543. (Funding for the single crystal X-ray diffractometer). ;