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Information card for entry 9012736
Preview
| Coordinates | 9012736.cif |
|---|---|
| Original paper (by DOI) | HTML |
| External links | AMCSD; ChemSpider |
| Common name | Tetrahydrofuran deuterate |
|---|---|
| Formula | D2 O |
| Calculated formula | D2 O |
| SMILES | [2H]O[2H] |
| Title of publication | Structure and thermal expansivity of tetrahydrofuran deuterate determined by neutron powder diffraction Sample: T = 205 K, host lattice |
| Authors of publication | Jones, C. Y.; Marshall, S. L.; Chakoumakos, B. C.; Rawn, C. J.; Ishii, Y. |
| Journal of publication | Journal of Physical Chemistry B |
| Year of publication | 2003 |
| Journal volume | 107 |
| Pages of publication | 6026 - 6031 |
| a | 17.198 Å |
| b | 17.198 Å |
| c | 17.198 Å |
| α | 90° |
| β | 90° |
| γ | 90° |
| Cell volume | 5086.67 Å3 |
| Ambient diffraction temperature | 205 K |
| Number of distinct elements | 2 |
| Space group number | 227 |
| Hermann-Mauguin space group symbol | F d -3 m :2 |
| Hall space group symbol | -F 4vw 2vw 3 |
| Has coordinates | Yes |
| Has disorder | No |
| Has Fobs | No |
| Revision | Date | Message | Files |
|---|---|---|---|
| 291877 (current) | 2024-05-16 | Inserting missing Z values in most entries in the 9 range |
9012736.cif |
| 287555 | 2023-11-12 | cod/ (saulius@tasmanijos-velnias) Linking AMCSD entries to those COD records that had identical cell parameters, formula and bibliography, and identical atomic coordinates *after* determining atom types in AMCSD records using the 'cif_guess_AMCSD_atom_types' script from the r9700 of the ^/trunk in 'cod-tools' package repository [1]. Some COD entries matched several AMCSD entries; for those multiple related AMCSD entries were noted using the COD_RELATDE_ENTRY category, and multiple mineral names were inserted using the '_[local]_alternative_name_[]' datanames in a loop. Ref.: [1] Working Copy Root Path: /home/saulius/src/cod-tools URL: svn+ssh://www.crystallography.net/home/coder/svn-repositories/cod-tools/trunk Relative URL: ^/trunk Repository Root: svn+ssh://www.crystallography.net/home/coder/svn-repositories/cod-tools Repository UUID: 04be6746-3802-0410-999d-98508da1e98c Revision: 9701 Node Kind: directory Schedule: normal Last Changed Author: saulius Last Changed Rev: 9701 Last Changed Date: 2023-11-12 11:14:50 +0200 (Sun, 12 Nov 2023) |
9012736.cif |
| 202019 | 2017-10-14 | cif/ Marking COD entries in range 9 that are known to be related to ChemSpider entries using the _cod_related_entry data loop. |
9012736.cif |
| 176465 | 2016-02-16 | cif/ (antanas@kurmis) Replacing _[local]_cod_* tags with their equivalents from the COD CIF dictionary in multiple entries in range 9. |
9012736.cif |
| 120115 | 2014-07-12 | Adding DOIs to range 9 structures. | 9012736.cif |
| 85285 | 2013-05-05 | cod/ (saulius@koala.ibt.lt) Removing outdated _amcsd_database_code data items from all series 9 CIFs. |
9012736.cif |
| 77877 | 2013-03-29 | cod/ (saulius@koala.ibt.lt) Removing mineral names from those crystal structures that do not actually describe minerals (e.g. synthetic entries; data source: file COD-minerals.xlsx from my 2012-08-24 15:47 e-mail). |
9012736.cif |
| 77586 | 2013-03-28 | cod/cif/ (saulius@koala.ibt.lt) Merging mineral data updates (_chemical_name_mineral, _chemical_name_common, structural formulae) sent to me by T.D. in his e-mail. The merge was done by the command: for i in split/*.cif do ( B=$(basename $i); C=$(echo $B|awk '{print "/home/saulius/struct/cod/cif/"substr($0,1,1)"/"substr($0,2,2)"/"substr($0,4,2)"/"$0}'); ( set -x; cif_merge --over \ _chemical_name_mineral,_chemical_name_structure_type,_chemical_name_common,_chemical_name_systematic,_chemical_formula_structural,_chemical_formula_sum \ $C $i ) \ | cif_filter --add-cif-header $C \ | sponge $C ) done in the working copy of the following repository: URL: svn+ssh://pitonas.ibt.lt/home/xray/svn-repositories/xyz-extraction/contributions Repository Root: svn+ssh://pitonas.ibt.lt/home/xray/svn-repositories/xyz-extraction Repository UUID: 9acf3947-1f02-0410-ae2a-984b57ad209b Revision: 2625 Node Kind: directory Schedule: normal Last Changed Author: saulius Last Changed Rev: 2625 Last Changed Date: 2013-03-28 15:13:00 +0200 (Thu, 28 Mar 2013) |
9012736.cif |
| 35913 | 2012-02-28 | cif/9/ Reorganising range 9 into a prefix-directory tree. Range 9 is the last range to be reorganised. |
9012736.cif |
| 22768 | 2011-07-16 | cif/9 A few more fixed formulae. |
9012736.cif |
| 1210 | 2010-06-10 | cif/9/ Updating 13213 AMCSD CIFs, taking new data from the AMCSD database and adding the assigned AMCSD numbers. |
9012736.cif |
| 1071 | 2010-04-10 | cif/9/ Updating COD entries from AMCSD, processed in the AMCSD-resynchronisation-2009.06.24/ directory. Entries are updated if they could be unambiguously mapped to a unique COD number by automatic search scripts in AMCSD-resynchronisation-2009.06.24/. |
9012736.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. |
9012736.cif |
| 903 | 2009-11-23 | cif/ Setting svn:keywords property on those CIFs that did not have them. |
9012736.cif |
| 893 | 2009-11-20 | cif/ Generating _diffrn_ambient_temperature and _diffrn_ambient_pressure tags from the CIF file comments like "T = 100K" (using the 975 revision of cif_create_AMCSD_pressure_temp_tags). Mostly, series 9 CIFs (obtained AMCSD) have such comments. Only files that did not had these tags originally were changed. The tags were generated using the following command: ( \ set -x; \ find $(/bin/ls -rd ?) -name \*.cif \ | xargs -n1 -iX \ bash -c 'awk "/^#/,/^data_/{print}/^data_/{exit}" X \ | grep -v "^data_" > tmp-$$; \ cif_create_AMCSD_pressure_temp_tags X >> tmp-$$; \ if (grep -q _diffrn_ambient_temperature tmp-$$ >& /dev/null && \ ! grep -q _diffrn_ambient_temperature X >& /dev/null) || \ (grep -q _diffrn_ambient_pressure tmp-$$ >& /dev/null && \ ! grep -q _diffrn_ambient_pressure X >& /dev/null); \ then \ mv -v tmp-$$ X; \ fi; \ rm -f tmp-$$' \ ) >& make-temp-pressure-tags.log After this, the modified files were checked using 'vcif': svn st | grep ^M | awk '{print $NF}' | xargs -n1 vcif -l 2048 It was checked that for the other tags, only tag order and value formatting has changed in the modifed files, if at all: ( \ set -x; \ svn st ? \ | awk '/^M/{print $NF}' \ | sort \ | xargs -n1 -iX \ bash -c 'echo -e "\n"=== X ===; \ diff -b \ <(svn cat X | sort) \ <(sort X)' \ ) 2>&1 | tee diff-sorted.log tdbgrep === diff-sorted.log \ | grep -v ^=== \ | grep -v '^> _diffrn_' \ | grep . \ | grep -vE '^[0-9]+a[0-9]+' \ | less and the changed files were validated against the cif_core.dic (thus checking, among others checks, that the values of the inserted tags have correct types): ( \ set -x; \ svn st ? \ | awk '/^M/{print $NF}' \ | sort \ | xargs -n1 -iX \ bash -c 'echo === X ===; \ cif_validate \ --dic ~/struct/CIF-dictionaries/cif_core.dic \ X \ --check-all \ --do-not-check-tag-exists-local' \ ) >& validate-pressure-temperature.log |
9012736.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. |
9012736.cif |
| 649 | 2009-04-18 | Depositing new CIFs from AMCSD-resynchronisation-2009.03.27/. |
9012736.cif |
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