Crystallography Open Database
- COD Home
- Accessing COD Data
- Add Your Data
- Documentation
Information card for entry 2004672
Preview
| Coordinates | 2004672.cif |
|---|---|
| Original IUCr paper | HTML |
| Chemical name | (2,2'-bipyridyl)(methyl)(phenyl)palladium(II) |
|---|---|
| Formula | C17 H16 N2 Pd |
| Calculated formula | C17 H16 N2 Pd |
| SMILES | [Pd]1([n]2c(c3[n]1cccc3)cccc2)(c1ccccc1)C |
| Title of publication | A Second Polymorph of 2,2'-Bipyridyl(methyl)(phenyl)palladium(II) |
| Authors of publication | Spek, A. L.; Janssen, M. D.; Markies, B. A.; van Koten, G. |
| Journal of publication | Acta Crystallographica Section C |
| Year of publication | 1996 |
| Journal volume | 52 |
| Journal issue | 4 |
| Pages of publication | 868 - 871 |
| a | 25.303 ± 0.003 Å |
| b | 9.953 ± 0.004 Å |
| c | 25.071 ± 0.003 Å |
| α | 90° |
| β | 112.08 ± 0.01° |
| γ | 90° |
| Cell volume | 5851 ± 3 Å3 |
| Cell temperature | 300 K |
| Ambient diffraction temperature | 300 K |
| Number of distinct elements | 4 |
| Space group number | 14 |
| Hermann-Mauguin space group symbol | P 1 21/c 1 |
| Hall space group symbol | -P 2ybc |
| Residual factor for significantly intense reflections | 0.069 |
| Weighted residual factors for significantly intense reflections | 0.19 |
| Goodness-of-fit parameter for significantly intense reflections | 1.023 |
| Diffraction radiation wavelength | 0.71073 Å |
| Diffraction radiation type | MoKα |
| Has coordinates | Yes |
| Has disorder | No |
| Has Fobs | No |
| Revision | Date | Message | Files |
|---|---|---|---|
| 176435 (current) | 2016-02-14 | cif/ (antanas@kurmis) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries from ranges 1, 2. |
2004672.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. |
2004672.cif |
| 91933 | 2013-12-28 | cif/ (saulius@koala.ibt.lt) Adding DOIs that could be assigned unambiguously to the range 2x CIFs. |
2004672.cif |
| 32112 | 2012-02-03 | cif/: committing an update of 45+ thous files, with information appended from the originals. | 2004672.cif |
| 26848 | 2011-09-28 | cif/2/, hkl/2/, html/ Reorganising CIFs of the range 2* into the "prefix-directory" tree. |
2004672.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). |
2004672.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. |
2004672.cif |
| 5310 | 2011-01-02 | cif/ Running cif_fix_enum with the core CIF dictionary on COD ranges 2, 8 and 9. Range 9 remained unchanged, and in ranges 2 and 8 there were 17309 modified files, most changes were fixes enumerator case. |
2004672.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. |
2004672.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 |
2004672.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. |
2004672.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. |
2004672.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/' |
2004672.cif |
| 14 | 2008-01-14 | Appending a header with SVN keywords, COD URL and copying policy to all COD CIF files. |
2004672.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. |
2004672.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) |
2004672.cif |
All data in the COD and the database itself are dedicated to the
public domain and licensed under the
CC0
License
.
Users of the data should acknowledge the original authors of the
structural data.