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Quantum crystallographic charge density of urea
Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using hi...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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International Union of Crystallography
2016
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937779/ https://www.ncbi.nlm.nih.gov/pubmed/27437111 http://dx.doi.org/10.1107/S2052252516006242 |
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author | Wall, Michael E. |
author_facet | Wall, Michael E. |
author_sort | Wall, Michael E. |
collection | PubMed |
description | Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the data is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. The results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement. |
format | Online Article Text |
id | pubmed-4937779 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-49377792016-07-19 Quantum crystallographic charge density of urea Wall, Michael E. IUCrJ Research Papers Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the data is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. The results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement. International Union of Crystallography 2016-06-08 /pmc/articles/PMC4937779/ /pubmed/27437111 http://dx.doi.org/10.1107/S2052252516006242 Text en © Michael E. Wall 2016 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 Wall, Michael E. Quantum crystallographic charge density of urea |
title | Quantum crystallographic charge density of urea |
title_full | Quantum crystallographic charge density of urea |
title_fullStr | Quantum crystallographic charge density of urea |
title_full_unstemmed | Quantum crystallographic charge density of urea |
title_short | Quantum crystallographic charge density of urea |
title_sort | quantum crystallographic charge density of urea |
topic | Research Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937779/ https://www.ncbi.nlm.nih.gov/pubmed/27437111 http://dx.doi.org/10.1107/S2052252516006242 |
work_keys_str_mv | AT wallmichaele quantumcrystallographicchargedensityofurea |