Crystallography Open Database

Information card for entry 8000000

7719462 << 8000000 >> 8000001

Preview

Coordinates	8000000.cif
Original paper (by DOI)	HTML

Structure parameters

Formula	C6 H22 Cd0.5 Cl3 Co N5 O4 S
Calculated formula	C6 H22 Cd0.5 Cl3 Co N5 O4 S
SMILES	[Cd](Cl)(Cl)[S]1[Co]23([NH2]CC1)([NH2]CC[NH2]2)[NH2]CC[NH2]3.Cl(=O)(=O)(=O)[O-]
Title of publication	The First S-Bridged CoIIICdIICoIII and CoIIICdII2CoIII Structures Controlled by Chirality of Mono(thiolato)-Type Cobalt(III) Units
Authors of publication	Takashi Aridomi; Tatsuya Kawamoto; Asako Igashira-Kamiyama; Takumi Konno
Journal of publication	Chemistry Letters
Year of publication	2005
Journal volume	34
Journal issue	3
Pages of publication	292
a	8.5547 ± 0.0014 Å
b	13.8816 ± 0.0014 Å
c	13.5666 ± 0.0013 Å
α	90°
β	96.041 ± 0.01°
γ	90°
Cell volume	1602.1 ± 0.3 Å³
Cell temperature	296 ± 2 K
Ambient diffraction temperature	296 ± 2 K
Number of distinct elements	8
Space group number	14
Hermann-Mauguin space group symbol	P 1 21/n 1
Hall space group symbol	-P 2yn
Residual factor for all reflections	0.153
Residual factor for significantly intense reflections	0.0435
Weighted residual factors for significantly intense reflections	0.0956
Weighted residual factors for all reflections included in the refinement	0.123
Goodness-of-fit parameter for all reflections included in the refinement	0.969
Diffraction radiation wavelength	0.71069 Å
Diffraction radiation type	MoKα
Has coordinates	Yes
Has disorder	No
Has F_obs	No

Version history

Revision	Date	Message	Files
211175 (current)	2018-09-26	cif/ Removing _chemical_name_systematic and _chemical_name_common data items with placeholder values from 513 entries in range 8.	8000000.cif
176466	2016-02-16	cif/ (antanas@kurmis) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries in range 8.	8000000.cif
130149	2015-01-27	cod/ (saulius@kolibris) Deriving Hall space group symbols for 12003 CIFs using the 'cif_filter --estimate-spacegroup' command.	8000000.cif
120070	2014-07-11	cif/ (saulius@koala.ibt.lt) Adding DOIs for structures in ranges 5, 6 and 8.	8000000.cif
35911	2012-02-28	cif/ Reorganising ranges 1, 3, 5, 6 and 8 into a prefix-directory tree.	8000000.cif
17004	2011-03-31	cif/ Commiting CIFs, that were updated with the 'cif_fix_values' script, using options '--fix-misspelled replacement_values.lst', '--fix-temperature' and '--fix-enums' with built-in table of enum values. The following cmd was used: > (set -x; find ? -name \*.cif \| sort \| xargs -i sh -c 'if !( > cif_fix_values --fix-misspelled ~/../inputs/replacament_values.lst {} \| > cif_filter --add-cif-header {} \| > sponge {} ) 2>&1 \| grep NOTE; then svn revert {}; > fi' ) &	8000000.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.	8000000.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	8000000.cif
725	2009-05-14	cif/: Fixing the misspelled _atom_site_symetry_multiplicity tag: saulius@delfinas checks/ > pwd /home/saulius/struct/cod/cif/checks saulius@delfinas checks/ > find ../[2-9]/ -name \*.cif \ \| xargs grep -l _atom_site_symetry_multiplicity \ \| xargs -n1 -t \ perl -i -pe 's/_atom_site_symetry_multiplicity/_atom_site_symmetry_multiplicity/'	8000000.cif
21	2008-01-26	Replacing all my collected files in COD with a newly regenerated CIF files that now have correct syntax.	8000000.cif
19	2008-01-26	Changing all end-of-line codes from DOS style to UNIX style in all COD CIF files, for more convenient processing: In the cod/cif/ directory: ff \*.cif \| xargs perl -i -pe 's/\r\n/\n/'	8000000.cif
14	2008-01-14	Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files.	8000000.cif
13	2008-01-13	Setting the svn:keywords property to "Author Date Revision URL Id" for all CIF files in the cod/cif directory.	8000000.cif
1	2007-11-30	Adding all .cif files from the COD, downloaded in a Cod.zip file on 2007.02.07 (and the same Cod.zip is downloadable today, on 2007.11.29)	8000000.cif