Crystallography Open Database

Information card for entry 8000072

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Coordinates	8000072.cif
Original paper (by DOI)	HTML

Structure parameters

Formula	C26 H38 Cl3 N7 O10 Pd2 Ru S3
Calculated formula	C26 H38 Cl3 N7 O10 Pd2 Ru S3
SMILES	[Pd]123[S]([Ru]45([S]6[Pd](Cl)([S]1CC[NH2]3)[NH2]CC6)([n]1c(cccc1)c1[n]4cccc1)[n]1c(cccc1)c1[n]5cccc1)CC[NH2]2.Cl(=O)(=O)(=O)[O-].Cl(=O)(=O)(=O)[O-].O.O
Title of publication	The First RuIIPdII2S3 Metallochelate Ring Formed on a [Ru(bpy)2]2+ Core
Authors of publication	Takashi Yoshimura; Atsushi Shinohara; Masakazu Hirotsu; Takumi Konno
Journal of publication	Chemistry Letters
Year of publication	2005
Journal volume	34
Journal issue	10
Pages of publication	1310
a	13.71 ± 0.004 Å
b	14.199 ± 0.002 Å
c	11.059 ± 0.002 Å
α	93.93 ± 0.01°
β	108.99 ± 0.02°
γ	84.12 ± 0.02°
Cell volume	2023.6 ± 0.7 Å³
Cell temperature	293.2 K
Number of distinct elements	8
Space group number	2
Hermann-Mauguin space group symbol	P -1
Hall space group symbol	-P 1
Residual factor for significantly intense reflections	0.0578
Weighted residual factors for all reflections included in the refinement	0.196
Goodness-of-fit parameter for all reflections included in the refinement	1.007
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
200399 (current)	2017-09-09	cif/8/00/00/ (antanas@kurmis) Marking attached hydrogen atoms in entry 8000072.	8000072.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.	8000072.cif
130149	2015-01-27	cod/ (saulius@kolibris) Deriving Hall space group symbols for 12003 CIFs using the 'cif_filter --estimate-spacegroup' command.	8000072.cif
120070	2014-07-11	cif/ (saulius@koala.ibt.lt) Adding DOIs for structures in ranges 5, 6 and 8.	8000072.cif
35911	2012-02-28	cif/ Reorganising ranges 1, 3, 5, 6 and 8 into a prefix-directory tree.	8000072.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.	8000072.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	8000072.cif
38	2008-01-28	Adding CIF files from the xyz-extraction/deposit/deposition-2008.01.28/cif/ directory. (Chemistry_Letters-2005-issues10-12 and Organometallics-2006-2007-issue2 )	8000072.cif