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Fragmentation and transferability in Hirshfeld atom refinement
Hirshfeld atom refinement (HAR) is one of the most effective methods for obtaining accurate structural parameters for hydrogen atoms from X-ray diffraction data. Unfortunately, it is also relatively computationally expensive, especially for larger molecules due to wavefunction calculations. Here, a...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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International Union of Crystallography
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8895009/ https://www.ncbi.nlm.nih.gov/pubmed/35371499 http://dx.doi.org/10.1107/S2052252522000690 |
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author | Chodkiewicz, Michał Pawlędzio, Sylwia Woińska, Magdalena Woźniak, Krzysztof |
author_facet | Chodkiewicz, Michał Pawlędzio, Sylwia Woińska, Magdalena Woźniak, Krzysztof |
author_sort | Chodkiewicz, Michał |
collection | PubMed |
description | Hirshfeld atom refinement (HAR) is one of the most effective methods for obtaining accurate structural parameters for hydrogen atoms from X-ray diffraction data. Unfortunately, it is also relatively computationally expensive, especially for larger molecules due to wavefunction calculations. Here, a fragmentation approach has been tested as a remedy for this problem. It gives an order of magnitude improvement in computation time for larger organic systems and is a few times faster for metal–organic systems at the cost of only minor differences in the calculated structural parameters when compared with the original HAR calculations. Fragmentation was also applied to polymeric and disordered systems where it provides a natural solution to problems that arise when HAR is applied. The concept of fragmentation is closely related to the transferable aspherical atom model (TAAM) and allows insight into possible ways to improve TAAM. Hybrid approaches combining fragmentation with the transfer of atomic densities between chemically similar atoms have been tested. An efficient handling of intermolecular interactions was also introduced for calculations involving fragmentation. When applied in fragHAR (a fragmentation approach for polypeptides) as a replacement for the original approach, it allowed for more efficient calculations. All of the calculations were performed with a locally modified version of Olex2 combined with a development version of discamb2tsc and ORCA. Care was taken to efficiently use the power of multicore processors by simple implementation of load-balancing, which was found to be very important for lowering computational time. |
format | Online Article Text |
id | pubmed-8895009 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-88950092022-03-31 Fragmentation and transferability in Hirshfeld atom refinement Chodkiewicz, Michał Pawlędzio, Sylwia Woińska, Magdalena Woźniak, Krzysztof IUCrJ Research Papers Hirshfeld atom refinement (HAR) is one of the most effective methods for obtaining accurate structural parameters for hydrogen atoms from X-ray diffraction data. Unfortunately, it is also relatively computationally expensive, especially for larger molecules due to wavefunction calculations. Here, a fragmentation approach has been tested as a remedy for this problem. It gives an order of magnitude improvement in computation time for larger organic systems and is a few times faster for metal–organic systems at the cost of only minor differences in the calculated structural parameters when compared with the original HAR calculations. Fragmentation was also applied to polymeric and disordered systems where it provides a natural solution to problems that arise when HAR is applied. The concept of fragmentation is closely related to the transferable aspherical atom model (TAAM) and allows insight into possible ways to improve TAAM. Hybrid approaches combining fragmentation with the transfer of atomic densities between chemically similar atoms have been tested. An efficient handling of intermolecular interactions was also introduced for calculations involving fragmentation. When applied in fragHAR (a fragmentation approach for polypeptides) as a replacement for the original approach, it allowed for more efficient calculations. All of the calculations were performed with a locally modified version of Olex2 combined with a development version of discamb2tsc and ORCA. Care was taken to efficiently use the power of multicore processors by simple implementation of load-balancing, which was found to be very important for lowering computational time. International Union of Crystallography 2022-02-26 /pmc/articles/PMC8895009/ /pubmed/35371499 http://dx.doi.org/10.1107/S2052252522000690 Text en © Michał Chodkiewicz et al. 2022 https://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. |
spellingShingle | Research Papers Chodkiewicz, Michał Pawlędzio, Sylwia Woińska, Magdalena Woźniak, Krzysztof Fragmentation and transferability in Hirshfeld atom refinement |
title | Fragmentation and transferability in Hirshfeld atom refinement |
title_full | Fragmentation and transferability in Hirshfeld atom refinement |
title_fullStr | Fragmentation and transferability in Hirshfeld atom refinement |
title_full_unstemmed | Fragmentation and transferability in Hirshfeld atom refinement |
title_short | Fragmentation and transferability in Hirshfeld atom refinement |
title_sort | fragmentation and transferability in hirshfeld atom refinement |
topic | Research Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8895009/ https://www.ncbi.nlm.nih.gov/pubmed/35371499 http://dx.doi.org/10.1107/S2052252522000690 |
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