Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function
Abstract
In this study, a method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.
- Authors:
-
- Goethe Univ., Frankfurt am Main (Germany)
- Brookhaven National Lab. (BNL), Upton, NY (United States)
- Brookhaven National Lab. (BNL), Upton, NY (United States); Columbia Univ., New York, NY (United States)
- Publication Date:
- Research Org.:
- Brookhaven National Lab. (BNL), Upton, NY (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1240708
- Report Number(s):
- BNL-111879-2016-JA
Journal ID: ISSN 2053-2733; ACSAD7; R&D Project: PM032; KC0202010
- Grant/Contract Number:
- SC00112704
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Acta Crystallographica. Section A, Foundations and Advances (Online)
- Additional Journal Information:
- Journal Name: Acta Crystallographica. Section A, Foundations and Advances (Online); Journal Volume: 72; Journal Issue: 1; Journal ID: ISSN 2053-2733
- Publisher:
- International Union of Crystallography
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; pair distribution function; organic crystal structures; structure refinement; structure solution
Citation Formats
Prill, Dragica, Juhas, Pavol, Billinge, Simon J. L., and Schmidt, Martin U. Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function. United States: N. p., 2016.
Web. doi:10.1107/S2053273315022457.
Prill, Dragica, Juhas, Pavol, Billinge, Simon J. L., & Schmidt, Martin U. Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function. United States. https://doi.org/10.1107/S2053273315022457
Prill, Dragica, Juhas, Pavol, Billinge, Simon J. L., and Schmidt, Martin U. Fri .
"Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function". United States. https://doi.org/10.1107/S2053273315022457. https://www.osti.gov/servlets/purl/1240708.
@article{osti_1240708,
title = {Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function},
author = {Prill, Dragica and Juhas, Pavol and Billinge, Simon J. L. and Schmidt, Martin U.},
abstractNote = {In this study, a method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.},
doi = {10.1107/S2053273315022457},
journal = {Acta Crystallographica. Section A, Foundations and Advances (Online)},
number = 1,
volume = 72,
place = {United States},
year = {Fri Jan 01 00:00:00 EST 2016},
month = {Fri Jan 01 00:00:00 EST 2016}
}
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Works referencing / citing this record:
Anionic silicate organic frameworks constructed from hexacoordinate silicon centres
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