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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...

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Autores principales: Chodkiewicz, Michał, Pawlędzio, Sylwia, Woińska, Magdalena, Woźniak, Krzysztof
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2022
Materias:
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.
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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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