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Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)
In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in a...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4468513/ https://www.ncbi.nlm.nih.gov/pubmed/25449625 http://dx.doi.org/10.1107/S2052520614022902 |
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author | van de Streek, Jacco Neumann, Marcus A. |
author_facet | van de Streek, Jacco Neumann, Marcus A. |
author_sort | van de Streek, Jacco |
collection | PubMed |
description | In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom. |
format | Online Article Text |
id | pubmed-4468513 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-44685132015-06-18 Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D) van de Streek, Jacco Neumann, Marcus A. Acta Crystallogr B Struct Sci Cryst Eng Mater Research Papers In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom. International Union of Crystallography 2014-12-01 /pmc/articles/PMC4468513/ /pubmed/25449625 http://dx.doi.org/10.1107/S2052520614022902 Text en © Jacco van de Streek et al. 2014 http://creativecommons.org/licenses/by/2.0/uk/ This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited. |
spellingShingle | Research Papers van de Streek, Jacco Neumann, Marcus A. Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D) |
title | Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D) |
title_full | Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D) |
title_fullStr | Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D) |
title_full_unstemmed | Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D) |
title_short | Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D) |
title_sort | validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (dft-d) |
topic | Research Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4468513/ https://www.ncbi.nlm.nih.gov/pubmed/25449625 http://dx.doi.org/10.1107/S2052520614022902 |
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