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Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time–accuracy trade-off

Aspherical atom refinement is the key to achieving accurate structure models, displacement parameters, hydrogen-bond lengths and analysis of weak interactions, amongst other examples. There are various quantum crystallographic methods to perform aspherical atom refinement, including Hirshfeld atom r...

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Autores principales: Jha, Kunal Kumar, Kleemiss, Florian, Chodkiewicz, Michał Leszek, Dominiak, Paulina Maria
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9901929/
https://www.ncbi.nlm.nih.gov/pubmed/36777135
http://dx.doi.org/10.1107/S1600576722010883
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author Jha, Kunal Kumar
Kleemiss, Florian
Chodkiewicz, Michał Leszek
Dominiak, Paulina Maria
author_facet Jha, Kunal Kumar
Kleemiss, Florian
Chodkiewicz, Michał Leszek
Dominiak, Paulina Maria
author_sort Jha, Kunal Kumar
collection PubMed
description Aspherical atom refinement is the key to achieving accurate structure models, displacement parameters, hydrogen-bond lengths and analysis of weak interactions, amongst other examples. There are various quantum crystallographic methods to perform aspherical atom refinement, including Hirshfeld atom refinement (HAR) and transferable aspherical atom model (TAAM) refinement. Both HAR and TAAM have their limitations and advantages, the former being more accurate and the latter being faster. With the advent of non-spherical atoms in Olex2 (NoSpherA2), it is now possible to overcome some limitations, like treating disorder, twinning and network structures, in aspherical refinements using HAR, TAAM or both together. TAAM refinement in NoSpherA2 showed significant improvement in refinement statistics compared with independent atom model (IAM) refinements on a diverse set of X-ray diffraction data. The sensitivity of TAAM towards poor data quality and disorder was observed in terms of higher refinement statistics for such structures. A comparison of IAM with TAAM and HAR in NoSpherA2 indicated that the time taken by TAAM refinements was of the same order of magnitude as that taken by IAM, while in HAR the time taken using a minimal basis set was 50 times higher than for IAM and rapidly increased with increasing size of the basis sets used. The displacement parameters for hydrogen and non-hydrogen atoms were very similar in both HAR and TAAM refinements. The hydrogen-bond lengths were slightly closer to neutron reference values in the case of HAR with higher basis sets than in TAAM. To benefit from the advantages of each method, a new hybrid refinement approach has been introduced, allowing a combination of IAM, HAR and TAAM in one structure refinement. Refinement of coordination complexes involving metal–organic compounds and network structures such as covalent organic frameworks and metal–organic frameworks is now possible in a hybrid mode such as IAM–TAAM or HAR–TAAM, where the metal atoms are treated via either the IAM or HAR method and the organic part via TAAM, thus reducing the computational costs without compromising the accuracy. Formal charges on the metal and ligand can also be introduced in hybrid-mode refinement.
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spelling pubmed-99019292023-02-10 Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time–accuracy trade-off Jha, Kunal Kumar Kleemiss, Florian Chodkiewicz, Michał Leszek Dominiak, Paulina Maria J Appl Crystallogr Research Papers Aspherical atom refinement is the key to achieving accurate structure models, displacement parameters, hydrogen-bond lengths and analysis of weak interactions, amongst other examples. There are various quantum crystallographic methods to perform aspherical atom refinement, including Hirshfeld atom refinement (HAR) and transferable aspherical atom model (TAAM) refinement. Both HAR and TAAM have their limitations and advantages, the former being more accurate and the latter being faster. With the advent of non-spherical atoms in Olex2 (NoSpherA2), it is now possible to overcome some limitations, like treating disorder, twinning and network structures, in aspherical refinements using HAR, TAAM or both together. TAAM refinement in NoSpherA2 showed significant improvement in refinement statistics compared with independent atom model (IAM) refinements on a diverse set of X-ray diffraction data. The sensitivity of TAAM towards poor data quality and disorder was observed in terms of higher refinement statistics for such structures. A comparison of IAM with TAAM and HAR in NoSpherA2 indicated that the time taken by TAAM refinements was of the same order of magnitude as that taken by IAM, while in HAR the time taken using a minimal basis set was 50 times higher than for IAM and rapidly increased with increasing size of the basis sets used. The displacement parameters for hydrogen and non-hydrogen atoms were very similar in both HAR and TAAM refinements. The hydrogen-bond lengths were slightly closer to neutron reference values in the case of HAR with higher basis sets than in TAAM. To benefit from the advantages of each method, a new hybrid refinement approach has been introduced, allowing a combination of IAM, HAR and TAAM in one structure refinement. Refinement of coordination complexes involving metal–organic compounds and network structures such as covalent organic frameworks and metal–organic frameworks is now possible in a hybrid mode such as IAM–TAAM or HAR–TAAM, where the metal atoms are treated via either the IAM or HAR method and the organic part via TAAM, thus reducing the computational costs without compromising the accuracy. Formal charges on the metal and ligand can also be introduced in hybrid-mode refinement. International Union of Crystallography 2023-02-01 /pmc/articles/PMC9901929/ /pubmed/36777135 http://dx.doi.org/10.1107/S1600576722010883 Text en © Kunal Kumar Jha et al. 2023 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
Jha, Kunal Kumar
Kleemiss, Florian
Chodkiewicz, Michał Leszek
Dominiak, Paulina Maria
Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time–accuracy trade-off
title Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time–accuracy trade-off
title_full Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time–accuracy trade-off
title_fullStr Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time–accuracy trade-off
title_full_unstemmed Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time–accuracy trade-off
title_short Aspherical atom refinements on X-ray data of diverse structures including disordered and covalent organic framework systems: a time–accuracy trade-off
title_sort aspherical atom refinements on x-ray data of diverse structures including disordered and covalent organic framework systems: a time–accuracy trade-off
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9901929/
https://www.ncbi.nlm.nih.gov/pubmed/36777135
http://dx.doi.org/10.1107/S1600576722010883
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