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Hirshfeld atom refinement

Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR met...

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Autores principales: Capelli, Silvia C., Bürgi, Hans-Beat, Dittrich, Birger, Grabowsky, Simon, Jayatilaka, Dylan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4174878/
https://www.ncbi.nlm.nih.gov/pubmed/25295177
http://dx.doi.org/10.1107/S2052252514014845
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author Capelli, Silvia C.
Bürgi, Hans-Beat
Dittrich, Birger
Grabowsky, Simon
Jayatilaka, Dylan
author_facet Capelli, Silvia C.
Bürgi, Hans-Beat
Dittrich, Birger
Grabowsky, Simon
Jayatilaka, Dylan
author_sort Capelli, Silvia C.
collection PubMed
description Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly–l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree–Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints – even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu’s), all other structural parameters agree within less than 2 csu’s. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å(2) as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements – an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.
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spelling pubmed-41748782014-10-07 Hirshfeld atom refinement Capelli, Silvia C. Bürgi, Hans-Beat Dittrich, Birger Grabowsky, Simon Jayatilaka, Dylan IUCrJ Research Papers Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly–l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree–Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints – even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu’s), all other structural parameters agree within less than 2 csu’s. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å(2) as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements – an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å. International Union of Crystallography 2014-08-29 /pmc/articles/PMC4174878/ /pubmed/25295177 http://dx.doi.org/10.1107/S2052252514014845 Text en © Silvia C. Capelli 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
Capelli, Silvia C.
Bürgi, Hans-Beat
Dittrich, Birger
Grabowsky, Simon
Jayatilaka, Dylan
Hirshfeld atom refinement
title Hirshfeld atom refinement
title_full Hirshfeld atom refinement
title_fullStr Hirshfeld atom refinement
title_full_unstemmed Hirshfeld atom refinement
title_short Hirshfeld atom refinement
title_sort hirshfeld atom refinement
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4174878/
https://www.ncbi.nlm.nih.gov/pubmed/25295177
http://dx.doi.org/10.1107/S2052252514014845
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