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Information card for entry 7102378
Preview
| Coordinates | 7102378.cif |
|---|---|
| Original paper (by DOI) | HTML |
| Formula | C40 H28 Cu4 F24 N12 O4 P4 |
|---|---|
| Calculated formula | C40 H28 Cu4 F24 N12 O4 P4 |
| SMILES | c1ccc[n]2c1c1cc[n]3c[n]1[Cu@]2(C#[O])[n]1c[n]2c(cc1)c1cccc[n]1[Cu@]2([n]1c[n]2c(cc1)c1cccc[n]1[Cu@]2([n]1c[n]2c(cc1)c1cccc[n]1[Cu@@]32C#[O])C#[O])C#[O].[P](F)(F)(F)(F)(F)[F-].[P](F)(F)(F)(F)(F)[F-].[P](F)(F)(F)(F)(F)[F-].[P](F)(F)(F)(F)(F)[F-].c1ccc[n]2c1c1cc[n]3c[n]1[Cu@@]2(C#[O])[n]1c[n]2c(cc1)c1cccc[n]1[Cu@@]2([n]1c[n]2c(cc1)c1cccc[n]1[Cu@@]2([n]1c[n]2c(cc1)c1cccc[n]1[Cu@]32C#[O])C#[O])C#[O].[P](F)(F)(F)(F)(F)[F-].[P](F)(F)(F)(F)(F)[F-].[P](F)(F)(F)(F)(F)[F-].[P](F)(F)(F)(F)(F)[F-] |
| Title of publication | Bowl-shaped Cu(I) metallamacrocyclic ethylene and carbonyl adducts as structural analogues of organic calixarenes. |
| Authors of publication | Maekawa, Masahiko; Konaka, Hisashi; Minematsu, Toshie; Kuroda-Sowa, Takayoshi; Munakata, Megumu; Kitagawa, Susumu |
| Journal of publication | Chemical communications (Cambridge, England) |
| Year of publication | 2007 |
| Journal issue | 48 |
| Pages of publication | 5179 - 5181 |
| a | 14.8455 ± 0.0008 Å |
| b | 14.8455 ± 0.0008 Å |
| c | 12.2984 ± 0.0009 Å |
| α | 90° |
| β | 90° |
| γ | 90° |
| Cell volume | 2710.4 ± 0.3 Å3 |
| Cell temperature | 150.2 K |
| Number of distinct elements | 7 |
| Space group number | 85 |
| Hermann-Mauguin space group symbol | P 4/n :2 |
| Hall space group symbol | -P 4a |
| Residual factor for significantly intense reflections | 0.0511 |
| Weighted residual factors for all reflections included in the refinement | 0.0928 |
| Goodness-of-fit parameter for all reflections included in the refinement | 1.19 |
| Diffraction radiation wavelength | 0.7107 Å |
| Diffraction radiation type | MoKα |
| Has coordinates | Yes |
| Has disorder | No |
| Has Fobs | No |
| Revision | Date | Message | Files |
|---|---|---|---|
| 176432 (current) | 2016-02-14 | cif/ (antanas@kurmis) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries. |
7102378.cif |
| 106525 | 2014-03-15 | cif/ (saulius@koala.ibt.lt) Adding DOIs to those Chem. Comm. structure descriptions that did not have it before and that could be matched unambiguously. Unambiguously means: a) journal name is "like 'Chem%Com%'" in SQl parlour b) first author's last name is the same in COD and in PubMed b) publication year and first page are the same in COD and in PubMed database. The commands to change these files where: awk '{print $1, $2}' outputs/join-dois.tab \ | xargs -i sh -c ' CODID=$(echo {} | awk "{print \$1}"); DOI=$(echo {} | awk "{print \$2}"); CODFILE=$(echo $CODID | codid2file); if ! grep -q _journal_paper_doi $CODFILE; then ( set -x; echo _journal_paper_doi $DOI >> $CODFILE ); else echo $CODID already has DOI; fi' Some files that did not had new-line at the end had to be fixed afterwards (in the ~/struct/cod/cif/7 directory, a COD working copy): svn st \ | awk '{print $2}' \ | xargs cifparse -q 2> /dev/null \ | awk -F"'" '{print $2}' \ | xargs perl -i -pe 's/_journal_paper_doi/\n_journal_paper_doi/' The working copy containing 'outputs/join-dois.tab' was: Path: /home/saulius/struct/xyz-extraction/dois/chem-comm-refetched-from-pubmed URL: svn+ssh://pitonas.ibt.lt/home/xray/svn-repositories/xyz-extraction/dois/chem-comm-refetched-from-pubmed Repository Root: svn+ssh://pitonas.ibt.lt/home/xray/svn-repositories/xyz-extraction Repository UUID: 9acf3947-1f02-0410-ae2a-984b57ad209b Revision: 2871 Node Kind: directory Schedule: normal Last Changed Author: saulius Last Changed Rev: 2871 Last Changed Date: 2014-03-15 11:18:46 +0200 (Sat, 15 Mar 2014) Three conflicts in files 10/81/7108128.cif, 10/81/7108130.cif and 10/99/7109903.cif were resolved manually. |
7102378.cif |
| 35909 | 2012-02-26 | cif/7/: reorganising range 7 into a prefix-directory tree. | 7102378.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. |
7102378.cif |
| 907 | 2009-11-23 | cif/ Correcting unquoted string values starting with '['. The list of such COD entries was obtained from the PyCifRW parser error log: grep === ~/tests/pycifrw/all-cod-parse-errors.log \ | awk '{print $2}' \ | xargs perl -i -lpe "s/^(\s*)_(.*)(\s+)\[(.*)\$/\$1_\$2\$3'[\$4'/" The resulting entries were checked with 'vcif', 'cif_filter' (uses our CIFParser) and PyCifRW: svn st | grep ^M | awk '{print $NF}' | sort | xargs -n1 vcif -l 2048 svn st | grep ^M | awk '{print $NF}' | sort | xargs -n1 cif_filter > /dev/null svn st $(pwd) \ | grep ^M \ | awk '{print $NF}' \ | sort \ | xargs -n1 -iX sh -c 'cd ~/tests/pycifrw/; set -x; ./cif_reader.py X' No errors were found. |
7102378.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 |
7102378.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. |
7102378.cif |
| 403 | 2008-06-25 | Comitting the Chem-Comm-2007/ CIF files with extracted structural data. |
7102378.cif |
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