DOI: 10.1063/1.3638268. Polymorph specific RMSD local order parameters for molecular crystals and nuclei: α-, β-, and γ-glycine

Polymorph specific RMSD local order parameters for molecular crystals and nuclei: α-, β-, and γ-glycine

10.1063/1.3638268

Crossref journal-article

AIP Publishing

The Journal of Chemical Physics (317)

Abstract

Crystal nucleation is important for many processes including pharmaceutical crystallization, biomineralization, and material synthesis. The progression of structural changes which occur during crystal nucleation are often described using order parameters. Polymorph specific order parameters have been developed for crystallization of spherically symmetric particles; however, polymorph specific order parameters for molecular crystals remain a challenge. We introduce template based polymorph specific order parameters for molecular crystals. For each molecule in a simulation, we compute the root mean squared deviation (RMSD) between the local environment around the molecule and a template of the perfect crystal structure for each polymorph. The RMSD order parameters can clearly distinguish the α-, β-, and γ-glycine polymorph crystal structures in the bulk crystal and also in solvated crystallites. Surface melting of glycine crystallites in supersaturated aqueous solution is explored using the newly developed order parameters. The solvated α-glycine crystallite has a thinner surface melted layer than the γ-glycine crystallite. α-glycine forms first out of aqueous solution, so surface melted layer thickness may provide insight into interfacial energy and polymorph selection.

Bibliography

Duff, N., & Peters, B. (2011). Polymorph specific RMSD local order parameters for molecular crystals and nuclei: Î±-, Î²-, and Î³-glycine. The Journal of Chemical Physics, 135(13).

Authors 2

Nathan Duff (first)
Baron Peters (additional)

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See supplementary material at http://dx.doi.org/10.1063/1.3638268 for detailed discussions on the creation of the dummy oxygen atom, the pruning procedure for Bicalutamide, and the local density cutoff to identify solvated glycine clusters.
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Dates

Type	When
Created	13 years, 10 months ago (Oct. 3, 2011, 7:24 p.m.)
Deposited	2 years, 1 month ago (June 26, 2023, 2:18 a.m.)
Indexed	3 weeks, 5 days ago (July 30, 2025, 6:57 a.m.)
Issued	13 years, 10 months ago (Oct. 3, 2011)
Published	13 years, 10 months ago (Oct. 3, 2011)
Published Online	13 years, 10 months ago (Oct. 3, 2011)
Published Print	13 years, 10 months ago (Oct. 7, 2011)

Funders 1

National Science Foundation 10.13039/100000001
Region: Americas
gov (National government)
Labels4
1. U.S. National Science Foundation
2. NSF
3. US NSF
4. USA NSF
Awards1
1. 0955502

BibTeX

@article{Duff_2011, title={Polymorph specific RMSD local order parameters for molecular crystals and nuclei: α-, β-, and γ-glycine}, volume={135}, ISSN={1089-7690}, url={http://dx.doi.org/10.1063/1.3638268}, DOI={10.1063/1.3638268}, number={13}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Duff, Nathan and Peters, Baron}, year={2011}, month=oct }

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