OU Crystallography Lab

Department of Chemistry & Biochemistry
Chemical Crystallography Laboratory

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Steps in Structure Reporting

When preparing a crystal structure report for publication, be sure to check the Notes for Authors section of the selected journal. Authors unfamiliar with preparing crystal structure reports should look through recent issues of the target journal to find articles with similar crystal structures. Emulating the format of the crystal structure reports in these articles will greatly reduce the effort needed. A general outline of information usually required in a crystal structure report is given below.

Most journals require authors to prepare a Crystallographic Information File or CIF to accompany each manuscript that contains one or more crystal structures. Complete information describing the format and content of CIFs can be found at the International Union of Crystallographyweb site. A summary of the cif syntax rules is listed below.

Nearly all discussions of crystal structures include comparisons of the compound in question with previously determined similar compounds. Finding literature examples of compounds with similar functional groups has been made much simpler with the advent of crystal structure databases. In particular manuscripts with compounds having similar organic functional groups are easily located using the Cambridge Structural Database. This database is available to all members of the University of Oklahoma. A review of stereochemistry has been prepared by the University of Chicago.

Outline of a Typical Crystal Structure Report

Summary of CIF Syntax

The Crystallographic Information Framework or CIF format for crystal structure data exchange between individual laboratories, journals, and databases was formally proposed in 19911. This format has been adopted by the International Union of Crystallography as well as all major journals. The file consists of data blocks that contain pairs of data names and data items. A loop facility for handling repeated data items has also been included. The self-descriptive data names are constructed hierarchically from data categories. A sorted list of data names together with their precise definitions are assembled into the CIF Core Dictionaries. The following brief description applies only to the original DDL (dictionary description language) format. A new DDL2 format has also been developed to describe additional categories and category groups that are used in macromolecular crystallography.

A CIF can contain information for more than one crystal structure. One CIF should be prepared for each manuscript. Each CIF should be prepared in plain text(ASCII) characters with records(lines) no longer than 80 characters. The following table shows the overall CIF syntax.

data block

collection of data names and items that pertain to one subject. Each data block begins with a data_ record. Information for each crystal structure in a manuscript is described in a separate data block. The CIF will usually also contain an additional data block that contains author information, references, and other manuscript data items. The block codes must be unique within a single data file.

data name

a character string starting with the underline ( _ ) character. The specific data names, definitions, and accepted values for data items are given in the CIF CORE Dictionaries.

data item

a text string not starting with an underline character, but preceded by an identifying data name. Text strings are strings of characters bounded by blank characters, by single quotes ( ' ), by double quotes ( " ), or by semi-colons ( ; ) as the first character of a line.

data loop

a list of data names, preceded by loop_ and followed by a repeated list of data items. The loop is ended with a blank line. Loops should always be used to describe repeated data items because only the last occurence of a data name is accepted within each data block.

Comments may be included on a line with a pound ( # ) symbol as the first character of the line.

Details of the CIF syntax are best shown by examples.

Data blocks for crystal structure information are usually identified by the block header data_compound_name, where name is some identifier for the compound. The data block with general information such as author names, etc, is usually begun with the header data_common or data_manuscript, where manuscript is some short (< 32 characters) description of the manuscript.

Data items may be listed as numbers or text strings. Numbers must begin with one of the characters 0 through 9, +, -, or .. Numbers may be shown as integer or real values; the real values may be in standard decimal format or in scientific notation preceding the exponent with e. Estimated standard deviations, now called standard uncertainties, are concatenated to a number as an integer in parentheses. For example the number 34.5±1.2 would be written 34.5(12). Standard uncertainties should generally have values in the range of 2 to 19.

   _cell_volume               2435.2(2) 

   _chemical_formula_moiety   "C23 H36 O7"

   loop_ 
       _publ_author_name 
       _publ_author_address 

     'Lastname1, Firstname1' 
   ;  
      Department of Chemistry and Biochemistry
      University of Oklahoma 
      101 Stephenson Parkway 
      Norman, OK  73019-5251  USA 
   ; 
     'Lastname2, Firstname2' 
   ;  
      Department of Chemistry and Biochemistry
      University of Oklahoma 
      101 Stephenson Parkway 
      Norman, OK  73019-5251  USA 
   ; 
   

Because of the rather limited range of the ASCII character set, special characters such as Greek letters are included using the following representations:

\a α \A Α alpha
\b β \B Β beta
\c χ \C Χ chi
\d δ \D Δ delta
\e ε \E Ε epsilon
\f φ \F Φ phi
\g γ \G Γ gamma
\h η \H Η eta
\i ι \I Ι iota
\k κ \K Κ kappa
\l λ \L Λ lambda
\m μ \M Μ mu
\n ν \N Ν nu
\o ο \O Ο omicron
\p π \P Π pi
\q θ \Q Θ theta
\r ρ \R Ρ rho
\s σ \S Σ sigma
\t τ \T Τ tau
\u υ \U Υ upsilon
\w ω \W Ω omega
\x ξ \X Ξ xi
\y ψ \Y Ψ psi
\z ζ \Z Ζ zeta

Selected special characters are shown as they should be presented in the cif and the typographic results.


superscripts Csp^3^ Csp3
subscripts U~eq~ Ueq
acute accent \'e é
grave accent \`a à
circumflex \^e ê
cedilla \,c ç
umlaut \"u ü
degree 120\% 120°
Ångström 1.54\%A 1.54 Å

Reference

  1. S. R. Hall, F. H. Allen, and I. D. Brown, Acta Cryst., 1991, A47, 655-685.
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