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Information card for entry 4021457
Preview
| Coordinates | 4021457.cif |
|---|---|
| Original paper (by DOI) | HTML |
| Chemical name | (1R*, 5R*, 7S*)-7-ethyl-5-hydroxymethyl-7-vinyl-6- oxabicyclo[3.2.1]octane-1-carboxylic acid |
|---|---|
| Formula | C13 H14 O4 |
| Calculated formula | C13 H20 O4 |
| SMILES | O1[C@@]2(CCC[C@](C2)(C(=O)O)[C@@]1(C=C)CC)CO.O1[C@]2(CCC[C@@](C2)(C(=O)O)[C@]1(C=C)CC)CO |
| Title of publication | Synthesis and Structure of Hydroxyl Acids of General Structure 7,7-Alkenyl/alkynyl-5-hydroxymethyl-6-oxabicyclo[3.2.1]octane- 1-carboxylic Acid |
| Authors of publication | Natalia Pérez-Hernández; Martín Febles; Cirilo Pérez; Matías L. Rodríguez; Concepción Foces-Foces; Julio D. Martín |
| Journal of publication | Journal of Organic Chemistry |
| Year of publication | 2006 |
| Journal volume | 71 |
| Pages of publication | 1139 - 1151 |
| a | 7.686 ± 0.003 Å |
| b | 7.823 ± 0.002 Å |
| c | 12.384 ± 0.002 Å |
| α | 108.9 ± 0.014° |
| β | 89.388 ± 0.016° |
| γ | 108.722 ± 0.013° |
| Cell volume | 663.6 ± 0.3 Å3 |
| Cell temperature | 170 ± 2 K |
| Ambient diffraction temperature | 170 ± 2 K |
| Number of distinct elements | 3 |
| Space group number | 2 |
| Hermann-Mauguin space group symbol | P -1 |
| Hall space group symbol | -P 1 |
| Residual factor for all reflections | 0.1063 |
| Residual factor for significantly intense reflections | 0.1026 |
| Weighted residual factors for significantly intense reflections | 0.2394 |
| Weighted residual factors for all reflections included in the refinement | 0.2417 |
| Goodness-of-fit parameter for all reflections included in the refinement | 1.063 |
| Diffraction radiation wavelength | 0.71073 Å |
| Diffraction radiation type | MoKα |
| Has coordinates | Yes |
| Has disorder | Yes |
| Has Fobs | No |
| Revision | Date | Message | Files |
|---|---|---|---|
| 176467 (current) | 2016-02-16 | cif/ (antanas@kurmis) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries in range 4. |
4021457.cif |
| 130149 | 2015-01-27 | cod/ (saulius@kolibris) Deriving Hall space group symbols for 12003 CIFs using the 'cif_filter --estimate-spacegroup' command. |
4021457.cif |
| 120074 | 2014-07-11 | Adding DOIs to range 4/02 structures. | 4021457.cif |
| 34330 | 2012-02-24 | cif/4/ Reorganising CIF range 4 into a prefix tree. |
4021457.cif |
| 5312 | 2011-01-03 | cif/ Adding files, updated with the 'cif_fix_enum' program and the cif_core.dic dictionary. The enumerator values were fixed, mostly incorrect case, but also some values that had extra underscores, dashes or spaces. Unfortunately, 22 had non-ASCII characters with the 8-th bit set, and these got incorrectly interpreted as latin1 characters and converted to their UTF8 equivalents by Perl. To fix the structures, however, they need to be redeposited from the original files with the new CIFParser/cif_filter version. |
4021457.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. |
4021457.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 |
4021457.cif |
| 111 | 2008-02-10 | Adding processed CIF files with datat from the J-Org-Chem-2006/. |
4021457.cif |
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