Crystallography Open Database

Information card for entry 2004578

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Coordinates	2004578.cif
Original IUCr paper	HTML

Structure parameters

Chemical name	aqua(2,2'-bipyrimidine-N,N')(4,5-dihydroxy-1,2-benzoquinonate-O,O')copper(II) pentahydrate
Formula	C14 H20 Cu N4 O10
Calculated formula	C14 H20 Cu N4 O10
SMILES	[Cu]12(OC3=CC(=O)C(=O)C=C3O1)([n]1cccnc1c1[n]2cccn1)[OH2].O.O.O.O.O
Title of publication	Two 2,5-Dihydroxy-1,4-benzoquinonate-<i>O</i>,<i>O</i>'-Containing Mononuclear Complexes: [Cu(C~6~H~2~O~4~)(C~8~H~6~N~4~)(H~2~O)].5H~2~O and [Ni(C~6~H~2~O~4~)(C~12~H~12~N~2~)~2~].H~2~O (C~8~H~6~N~4~ = 2,2'-Bipyrimidine, C~12~H~12~N~2~ = 4,4'-Dimethyl-2,2'-bipyridine)
Authors of publication	Decurtins, S.; Schmalle, H. W.; Schneuwly, P.; Zheng, L.-M.
Journal of publication	Acta Crystallographica Section C
Year of publication	1996
Journal volume	52
Journal issue	3
Pages of publication	561 - 566
a	18.326 ± 0.004 Å
b	16.953 ± 0.003 Å
c	13.516 ± 0.003 Å
α	90°
β	111.25 ± 0.03°
γ	90°
Cell volume	3913.7 ± 1.6 Å³
Cell temperature	295 ± 2 K
Ambient diffraction temperature	295 ± 2 K
Number of distinct elements	5
Space group number	15
Hermann-Mauguin space group symbol	C 1 2/c 1
Hall space group symbol	-C 2yc
Residual factor for all reflections	0.1518
Residual factor for significantly intense reflections	0.0481
Weighted residual factors for all reflections	0.1468
Weighted residual factors for significantly intense reflections	0.1055
Goodness-of-fit parameter for all reflections	1.039
Goodness-of-fit parameter for significantly intense reflections	1.091
Diffraction radiation wavelength	0.71073 Å
Diffraction radiation type	MoKα
Has coordinates	Yes
Has disorder	No
Has F_obs	No

Version history

Revision	Date	Message	Files
176759 (current)	2016-02-19	cif/2/ (antanas@echidna.ibt.lt) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries in subrange 2/00.	2004578.cif
134621	2015-04-02	The 'cif_fix_values' script with an option '--fix-only-weighting-scheme' and 'cif_filter' script were run over CIF files which included an incorrect value of the data item '_refine_ls_weighting_scheme'. Read the log for more details. There were more than 18k CIF files with values to modify. Usually these incorrect values include comment with formulas, but values of this data item must be an enumerator. The script creates new data item '_refine_ls_weighting_details' to store these comments with formulas, and writes the enumerator 'calc' as a value of data item '_refine_ls_weighting_scheme'. There exists some exceptions in the script.	2004578.cif
91933	2013-12-28	cif/ (saulius@koala.ibt.lt) Adding DOIs that could be assigned unambiguously to the range 2x CIFs.	2004578.cif
32112	2012-02-03	cif/: committing an update of 45+ thous files, with information appended from the originals.	2004578.cif
26848	2011-09-28	cif/2/, hkl/2/, html/ Reorganising CIFs of the range 2* into the "prefix-directory" tree.	2004578.cif
26029	2011-09-17	cif/2/ Reverting changes of revision 25271: ( cd cif/2/; svn merge -r25271:25270 . ) The problem was that the reprocessed files from IUCr, although were more complete, "resurrected" data errors that were corrected in the previous recisions. The additional data that have been extracted during the reprocessing will have to be merged without overwriting the existing values in COD files, except some explicit and controlled cases (such as publication titles and chemical names).	2004578.cif
25271	2011-09-10	cif/2/ Adding reporocessed IUCr CIFs for the years 1980-2010. The CIFs now contain more complete bibliography, substance names, correctly unfolded text fields (using the CIF line unfolding protocol), explicitely set cell angles, and _cod_data_source_block fields.	2004578.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.	2004578.cif
853	2009-11-16	cif/ Reconstructing spacegroup designators from the symmetry operators were possible. The comands used can be found in the log file reformat-spacegroups-2009.11.14.log committed with the current revision. Only lines that contained spacegroup designators were changed, and all files pass vcif test after the conversion.	2004578.cif
846	2009-11-14	cif/ Fixing _journal_volume values that had series letters prepended to them. Now the series letters are appended to the _journal_name_full, if needed, and the _journal_volume is purely numeric. To mimimise textual changes to CIFs this was done in several stages. First of all, a list of _journal_volume was compiled from the COD CIF collection: bash -xc 'find ? -name \*.cif \ \| xargs cif_values \ --file \ --tag _journal_volume' \ >& cod-journal-volumes-`-date`.log & giving us a cod-journal-volumes-2009.11.13.log file (committed for reference as well). Then a list of volume names with letters was extracted and most of them transformed automatically into a correct form: awk '$3~/^[A-Z][0-9]/' cod-journal-volumes-2009.11.13.log \ \| awk '{print $1}' \ \| xargs -n1 -iI \ bash -c 'echo === I ===;\ awk "/^#/,/^data_/{print}/^data_/{exit}" I > tmp-$$; \ cif_adjust_journal_name_volume I \ \| grep -E "_journal_name_full\|_journal_volume" >> tmp-$$; \ awk "/^data_/,/\$eof/" I \ \| grep -vE "^(data_\|_journal_name_full\|_journal_volume)" >> tmp-$$;\ mv -v tmp-$$ I' Note that this procedure assumes that all tags are at the beginning of the line, each value follows its tag on the same line, and there is only one tag per line. This procedure is not suitable for general CIFs, but fortunately, only very few CIFs in COD do not conform these rules. After the automatic conversion, a syntax check was run: svn st ? \ \| awk '{print $NF}' \ \| xargs -n1 -iI sh -c 'echo -n I"\r"; vcif -l 2048 I \|\| echo "!!! I !!!\n"' Entries that were found to have errors (very few, less than 10) were reverted and fixed manually. The entries that had letters embedded into them were grepped separately: awk '$3~/[A-Z][0-9]/' cod-journal-volumes-2009.11.13.log \ \| awk '$3~/^[^A-Z]/' and fixed manually. After all fixes, the previous 'vcif' test was rerun, yielding no syntax errors, and in addition a 'cif_filter' roundtrip test was run: svn st ? \ \| awk '{print $NF}' \ \| xargs -n1 -iI \ bash -c ' \ echo -en I "\r"; \ diff \ <(cif_filter I >& /dev/null) \ <(cif_filter I \| cif_filter >& /dev/null) \ \|\| echo "!!! I !!!\n"' This last test discovered one misspelled '_journal_yrae' tag in the 2/2003193.cif entry that was fixed by hand.	2004578.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/'	2004578.cif
14	2008-01-14	Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files.	2004578.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.	2004578.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)	2004578.cif