Cargando…

Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing

A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called ‘PDF-Global-Fit’ and is implemented by extension of the program FI...

Descripción completa

Detalles Bibliográficos
Autores principales: Schlesinger, Carina, Habermehl, Stefan, Prill, Dragica
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8202035/
https://www.ncbi.nlm.nih.gov/pubmed/34188612
http://dx.doi.org/10.1107/S1600576721002569
_version_ 1783707904299237376
author Schlesinger, Carina
Habermehl, Stefan
Prill, Dragica
author_facet Schlesinger, Carina
Habermehl, Stefan
Prill, Dragica
author_sort Schlesinger, Carina
collection PubMed
description A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called ‘PDF-Global-Fit’ and is implemented by extension of the program FIDEL (fit with deviating lattice parameters). The structure solution is based on a global optimization approach starting from random structural models in selected space groups. No prior indexing of the powder data is needed. The new method requires only the molecular geometry and a carefully determined PDF. The generated random structures are compared with the experimental PDF and ranked by a similarity measure based on cross-correlation functions. The most promising structure candidates are fitted to the experimental PDF data using a restricted simulated annealing structure solution approach within the program TOPAS, followed by a structure refinement against the PDF to identify the correct crystal structure. With the PDF-Global-Fit it is possible to determine the local structure of crystalline and disordered organic materials, as well as to determine the local structure of unindexable powder patterns, such as nanocrystalline samples, by a fit to the PDF. The success of the method is demonstrated using barbituric acid as an example. The crystal structure of barbituric acid form IV solved and refined by the PDF-Global-Fit is in excellent agreement with the published crystal structure data.
format Online
Article
Text
id pubmed-8202035
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher International Union of Crystallography
record_format MEDLINE/PubMed
spelling pubmed-82020352021-06-28 Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing Schlesinger, Carina Habermehl, Stefan Prill, Dragica J Appl Crystallogr Research Papers A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called ‘PDF-Global-Fit’ and is implemented by extension of the program FIDEL (fit with deviating lattice parameters). The structure solution is based on a global optimization approach starting from random structural models in selected space groups. No prior indexing of the powder data is needed. The new method requires only the molecular geometry and a carefully determined PDF. The generated random structures are compared with the experimental PDF and ranked by a similarity measure based on cross-correlation functions. The most promising structure candidates are fitted to the experimental PDF data using a restricted simulated annealing structure solution approach within the program TOPAS, followed by a structure refinement against the PDF to identify the correct crystal structure. With the PDF-Global-Fit it is possible to determine the local structure of crystalline and disordered organic materials, as well as to determine the local structure of unindexable powder patterns, such as nanocrystalline samples, by a fit to the PDF. The success of the method is demonstrated using barbituric acid as an example. The crystal structure of barbituric acid form IV solved and refined by the PDF-Global-Fit is in excellent agreement with the published crystal structure data. International Union of Crystallography 2021-05-09 /pmc/articles/PMC8202035/ /pubmed/34188612 http://dx.doi.org/10.1107/S1600576721002569 Text en © Carina Schlesinger et al. 2021 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
Schlesinger, Carina
Habermehl, Stefan
Prill, Dragica
Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing
title Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing
title_full Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing
title_fullStr Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing
title_full_unstemmed Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing
title_short Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing
title_sort structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8202035/
https://www.ncbi.nlm.nih.gov/pubmed/34188612
http://dx.doi.org/10.1107/S1600576721002569
work_keys_str_mv AT schlesingercarina structuredeterminationoforganiccompoundsbyafittothepairdistributionfunctionfromscratchwithoutpriorindexing
AT habermehlstefan structuredeterminationoforganiccompoundsbyafittothepairdistributionfunctionfromscratchwithoutpriorindexing
AT prilldragica structuredeterminationoforganiccompoundsbyafittothepairdistributionfunctionfromscratchwithoutpriorindexing