Crystallography Open Database

Information card for entry 4021403

Preview

Coordinates	4021403.cif
Original paper (by DOI)	HTML
External links	PubChem

Structure parameters

Common name	(R)-sec-butylammonium_(Rp)-O-ethyl phenylphosphonothioate
Formula	C12 H22 N O2 P S
Calculated formula	C12 H22 N O2 P S
SMILES	S=[P@]([O-])(OCC)c1ccccc1.[NH3+][C@@H](CC)C
Title of publication	Enantiopure O-Substituted Phenylphosphonothioic Acids: Chiral Recognition Ability during Salt Crystallization and Chiral Recognition Mechanism
Authors of publication	Yuka Kobayashi; Fumi Morisawa; Kazuhiko Saigo
Journal of publication	Journal of Organic Chemistry
Year of publication	2006
Journal volume	71
Pages of publication	606 - 615
a	6.577 ± 0.0005 Å
b	14.56 ± 0.0012 Å
c	16.131 ± 0.002 Å
α	90°
β	90°
γ	90°
Cell volume	1544.7 ± 0.2 Å³
Cell temperature	296.1 K
Number of distinct elements	6
Space group number	19
Hermann-Mauguin space group symbol	P 21 21 21
Hall space group symbol	P 2ac 2ab
Residual factor for significantly intense reflections	0.057
Weighted residual factors for all reflections included in the refinement	0.083
Goodness-of-fit parameter for all reflections included in the refinement	0.788
Diffraction radiation wavelength	0.7107 Å
Diffraction radiation type	MoKα
Has coordinates	Yes
Has disorder	No
Has F_obs	No

Version history

Revision	Date	Message	Files
301812 (current)	2025-08-19	Add cross-references to PubChem compounds in COD range 4/02/ Each referenced PubChem compound corresponds to the full crystal structure.	4021403.cif
295947	2024-11-16	Replaced the '\/Y' character sequence with the backslash character ('\') in multiple data values.	4021403.cif
277840	2022-09-14	cif/ Added space group information derived from the space group operation list using the 'cif_filter' program.	4021403.cif
176467	2016-02-16	cif/ (antanas@kurmis) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries in range 4.	4021403.cif
120074	2014-07-11	Adding DOIs to range 4/02 structures.	4021403.cif
34330	2012-02-24	cif/4/ Reorganising CIF range 4 into a prefix tree.	4021403.cif
966	2010-01-30	cif/ Adding _cod_database_code tags to all COD entries. Adding tag description to the cif_cod.dic dictionary so that COD entries can be validated.	4021403.cif
858	2009-11-18	cod/cif/ Changing all _chemical_formula_sum values, were necessary, to conform IUCr recommended syntax and sorting order. After this operation, it will be easier to search for structures using the _chemical_formula_sum values. Only those files and thos lines that really needed to be changed were changed; otehrwise the CIFs were not reformatted. The procedure was as follows: first, all files were passed through a 'cif_filter --parse-formula-sum' command, and the lines containing _cif_formula_sum matching tags were extracted. The extracted tags were "spliced" into the CIF files using the ./bin/{un,}grepciftag commands and awk to filter out old tags and add new tags in their place; the replacement was only done if the new tags contained "_cod_" tags ('grep -q _cod_ tmp-$$'), indicating that cif_filter has altered the formula, or the original file did not contain the _chemical_formula_sum tag ('! grep -q _chemical_formula_sum X'), indicating that cif_filter has guessed the chemical_formula_sum from the file (which should not have happened, actually). If the file was different, disregarding spaces, from the original one ('if ! diff -wb X tmp2-$$'), the original was replaced by the new file, to be committed to the repository. The full command for this step was: ( \ set -x; \ find ? -name \.cif \ \| xargs -n1 -iX \ sh -c 'cif_filter --parse-formula-sum X \ \| ./bin/grepciftag _chemical_formula_sum > tmp-$$; \ if grep -q _cod_ tmp-$$ \|\| ! grep -q _chemical_formula_sum X; \ then \ awk "/^#/,/_chemical_formula_sum/{print} /_chemical_formula_sum/{exit}" X \ \| ./bin/ungrepciftag _chemical_formula_sum > tmp2-$$; \ cat tmp-$$ >> tmp2-$$; \ awk "/_chemical_formula_sum/,/\$eof/" X \ \| ./bin/ungrepciftag _chemical_formula_sum >> tmp2-$$; \ if ! diff -wb X tmp2-$$; \ then \ mv -fv tmp2-$$ X; \ fi; \ fi; \ rm -f tmp-$$ tmp2-$$' \ ) >& sort-chemical-formulae-2009.11.16.log Next, the files were searched that differ from their originals only by the order of CIF tags: svn st \ \| awk '/^M/{print $NF}' \ \| sort \| xargs -n1 -iX \ bash -c 'if diff -q <(svn cat X\|sort) <(sort X) >& /dev/null; \ then echo X; \ fi' \ >& only-reordered.lst These files, after manual inspection ('cat only-reordered.lst \| xargs svn diff \| less'), were reverted to the originals: cat only-reordered.lst \| xargs svn revert Finally, a syntax check was performed using 'vcif': svn st \| awk '/^M/{print $NF}' \ \| sort \| xargs -n1 -iX \ sh -c 'echo -n X"\r"; vcif -l 2048 X \|\| { echo == X == ; echo X >&2; }' \ 2> vcif-check-2009.11.18.err A check on the whole COD archive showed the same files as recorded in vcif-check-2009.11.18.err: find ? -name \.cif \ \| sort \ \| xargs -n1 -iX \ sh -c 'echo -n X"\r"; \ vcif -l 2048 X \|\| { echo == X == ; echo X >&2; }' \ 2> vcif-all-check-`-date`.err diff vcif-check-2009.11.18.err vcif-all-check-2009.11.18.err Since no differences were detected in between vcif-check-2009.11.18.err and vcif-all-check-2009.11.18.err, the latter was deleted and is not committed. The check reveled two broken files, 2/2000267.cif and 2/2001000.cif; these were corrected manually. Afther this, one more 'vcif' check showed no syntax errors, and the changes are committed into the COD repository. 19798 files have modifications in this commit, according to svn st \| grep '^M' \| wc -l	4021403.cif
111	2008-02-10	Adding processed CIF files with datat from the J-Org-Chem-2006/.	4021403.cif