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A mixed phosphine sulfide/selenide structure as an instructional example for how to evaluate the quality of a model
This paper compares variations on a structure model derived from an X-ray diffraction data set from a solid solution of chalcogenide derivatives of cis-1,2-bis(diphenylphosphanyl)ethylene, namely, 1,2-(ethene-1,2-diyl)bis(diphenylphoshpine sulfide/selenide), C(26)H(22)P(2)S(1.13)Se(0.87). A...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10088320/ https://www.ncbi.nlm.nih.gov/pubmed/37057016 http://dx.doi.org/10.1107/S2056989023002700 |
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author | Parkin, Sean Cunningham, Jeremy Rawls, Brian Bender, John E. Staples, Richard J. Biros, Shannon M. |
author_facet | Parkin, Sean Cunningham, Jeremy Rawls, Brian Bender, John E. Staples, Richard J. Biros, Shannon M. |
author_sort | Parkin, Sean |
collection | PubMed |
description | This paper compares variations on a structure model derived from an X-ray diffraction data set from a solid solution of chalcogenide derivatives of cis-1,2-bis(diphenylphosphanyl)ethylene, namely, 1,2-(ethene-1,2-diyl)bis(diphenylphoshpine sulfide/selenide), C(26)H(22)P(2)S(1.13)Se(0.87). A sequence of processes are presented to ascertain the composition of the crystal, along with strategies for which aspects of the model to inspect to ensure a chemically and crystallographically realistic structure. Criteria include mis-matches between F (obs) (2) and F (calc) (2), plots of |F (obs)| vs |F (calc)|, residual electron density, checkCIF alerts, pitfalls of the OMIT command used to suppress ill-fitting data, comparative size of displacement ellipsoids, and critical inspection of interatomic distances. Since the structure is quite small, solves easily, and presents a number of readily expressible refinement concepts, we feel that it would make a straightforward and concise instructional piece for students learning how to determine if their model provides the best fit for the data and show students how to critically assess their structures. |
format | Online Article Text |
id | pubmed-10088320 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-100883202023-04-12 A mixed phosphine sulfide/selenide structure as an instructional example for how to evaluate the quality of a model Parkin, Sean Cunningham, Jeremy Rawls, Brian Bender, John E. Staples, Richard J. Biros, Shannon M. Acta Crystallogr E Crystallogr Commun Modern Approaches and Tools for Teaching Crystallography This paper compares variations on a structure model derived from an X-ray diffraction data set from a solid solution of chalcogenide derivatives of cis-1,2-bis(diphenylphosphanyl)ethylene, namely, 1,2-(ethene-1,2-diyl)bis(diphenylphoshpine sulfide/selenide), C(26)H(22)P(2)S(1.13)Se(0.87). A sequence of processes are presented to ascertain the composition of the crystal, along with strategies for which aspects of the model to inspect to ensure a chemically and crystallographically realistic structure. Criteria include mis-matches between F (obs) (2) and F (calc) (2), plots of |F (obs)| vs |F (calc)|, residual electron density, checkCIF alerts, pitfalls of the OMIT command used to suppress ill-fitting data, comparative size of displacement ellipsoids, and critical inspection of interatomic distances. Since the structure is quite small, solves easily, and presents a number of readily expressible refinement concepts, we feel that it would make a straightforward and concise instructional piece for students learning how to determine if their model provides the best fit for the data and show students how to critically assess their structures. International Union of Crystallography 2023-03-28 /pmc/articles/PMC10088320/ /pubmed/37057016 http://dx.doi.org/10.1107/S2056989023002700 Text en © Parkin 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 | Modern Approaches and Tools for Teaching Crystallography Parkin, Sean Cunningham, Jeremy Rawls, Brian Bender, John E. Staples, Richard J. Biros, Shannon M. A mixed phosphine sulfide/selenide structure as an instructional example for how to evaluate the quality of a model |
title | A mixed phosphine sulfide/selenide structure as an instructional example for how to evaluate the quality of a model |
title_full | A mixed phosphine sulfide/selenide structure as an instructional example for how to evaluate the quality of a model |
title_fullStr | A mixed phosphine sulfide/selenide structure as an instructional example for how to evaluate the quality of a model |
title_full_unstemmed | A mixed phosphine sulfide/selenide structure as an instructional example for how to evaluate the quality of a model |
title_short | A mixed phosphine sulfide/selenide structure as an instructional example for how to evaluate the quality of a model |
title_sort | mixed phosphine sulfide/selenide structure as an instructional example for how to evaluate the quality of a model |
topic | Modern Approaches and Tools for Teaching Crystallography |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10088320/ https://www.ncbi.nlm.nih.gov/pubmed/37057016 http://dx.doi.org/10.1107/S2056989023002700 |
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