Cargando…
Hirshfeld atom like refinement with alternative electron density partitions
Hirshfeld atom refinement is one of the most successful methods for the accurate determination of structural parameters for hydrogen atoms from X-ray diffraction data. This work introduces a generalization of the method [generalized atom refinement (GAR)], consisting of the application of various me...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7642787/ https://www.ncbi.nlm.nih.gov/pubmed/33209330 http://dx.doi.org/10.1107/S2052252520013603 |
_version_ | 1783606151826374656 |
---|---|
author | Chodkiewicz, Michał Leszek Woińska, Magdalena Woźniak, Krzysztof |
author_facet | Chodkiewicz, Michał Leszek Woińska, Magdalena Woźniak, Krzysztof |
author_sort | Chodkiewicz, Michał Leszek |
collection | PubMed |
description | Hirshfeld atom refinement is one of the most successful methods for the accurate determination of structural parameters for hydrogen atoms from X-ray diffraction data. This work introduces a generalization of the method [generalized atom refinement (GAR)], consisting of the application of various methods of partitioning electron density into atomic contributions. These were tested on three organic structures using the following partitions: Hirshfeld, iterative Hirshfeld, iterative stockholder, minimal basis iterative stockholder and Becke. The effects of partition choice were also compared with those caused by other factors such as quantum chemical methodology, basis set, representation of the crystal field and a combination of these factors. The differences between the partitions were small in terms of R factor (e.g. much smaller than for refinements with different quantum chemistry methods, i.e. Hartree–Fock and coupled cluster) and therefore no single partition was clearly the best in terms of experimental data reconstruction. In the case of structural parameters the differences between the partitions are comparable to those related to the choice of other factors. We have observed the systematic effects of the partition choice on bond lengths and ADP values of polar hydrogen atoms. The bond lengths were also systematically influenced by the choice of electron density calculation methodology. This suggests that GAR-derived structural parameters could be systematically improved by selecting an optimal combination of the partition and quantum chemistry method. The results of the refinements were compared with those of neutron diffraction experiments. This allowed a selection of the most promising partition methods for further optimization of GAR settings, namely the Hirshfeld, iterative stockholder and minimal basis iterative stockholder. |
format | Online Article Text |
id | pubmed-7642787 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-76427872020-11-17 Hirshfeld atom like refinement with alternative electron density partitions Chodkiewicz, Michał Leszek Woińska, Magdalena Woźniak, Krzysztof IUCrJ Research Papers Hirshfeld atom refinement is one of the most successful methods for the accurate determination of structural parameters for hydrogen atoms from X-ray diffraction data. This work introduces a generalization of the method [generalized atom refinement (GAR)], consisting of the application of various methods of partitioning electron density into atomic contributions. These were tested on three organic structures using the following partitions: Hirshfeld, iterative Hirshfeld, iterative stockholder, minimal basis iterative stockholder and Becke. The effects of partition choice were also compared with those caused by other factors such as quantum chemical methodology, basis set, representation of the crystal field and a combination of these factors. The differences between the partitions were small in terms of R factor (e.g. much smaller than for refinements with different quantum chemistry methods, i.e. Hartree–Fock and coupled cluster) and therefore no single partition was clearly the best in terms of experimental data reconstruction. In the case of structural parameters the differences between the partitions are comparable to those related to the choice of other factors. We have observed the systematic effects of the partition choice on bond lengths and ADP values of polar hydrogen atoms. The bond lengths were also systematically influenced by the choice of electron density calculation methodology. This suggests that GAR-derived structural parameters could be systematically improved by selecting an optimal combination of the partition and quantum chemistry method. The results of the refinements were compared with those of neutron diffraction experiments. This allowed a selection of the most promising partition methods for further optimization of GAR settings, namely the Hirshfeld, iterative stockholder and minimal basis iterative stockholder. International Union of Crystallography 2020-10-29 /pmc/articles/PMC7642787/ /pubmed/33209330 http://dx.doi.org/10.1107/S2052252520013603 Text en © Chodkiewicz et al. 2020 http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Research Papers Chodkiewicz, Michał Leszek Woińska, Magdalena Woźniak, Krzysztof Hirshfeld atom like refinement with alternative electron density partitions |
title | Hirshfeld atom like refinement with alternative electron density partitions |
title_full | Hirshfeld atom like refinement with alternative electron density partitions |
title_fullStr | Hirshfeld atom like refinement with alternative electron density partitions |
title_full_unstemmed | Hirshfeld atom like refinement with alternative electron density partitions |
title_short | Hirshfeld atom like refinement with alternative electron density partitions |
title_sort | hirshfeld atom like refinement with alternative electron density partitions |
topic | Research Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7642787/ https://www.ncbi.nlm.nih.gov/pubmed/33209330 http://dx.doi.org/10.1107/S2052252520013603 |
work_keys_str_mv | AT chodkiewiczmichałleszek hirshfeldatomlikerefinementwithalternativeelectrondensitypartitions AT woinskamagdalena hirshfeldatomlikerefinementwithalternativeelectrondensitypartitions AT wozniakkrzysztof hirshfeldatomlikerefinementwithalternativeelectrondensitypartitions |