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使用盆地跳跃全局优化方法对苯进行晶体结构预测。

Crystal Structure Prediction for Benzene Using Basin-Hopping Global Optimization.

作者信息

Banerjee Atreyee, Jasrasaria Dipti, Niblett Samuel P, Wales David J

机构信息

Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

Max Planck Institute for Polymer Research, 55128 Mainz, Germany.

出版信息

J Phys Chem A. 2021 May 6;125(17):3776-3784. doi: 10.1021/acs.jpca.1c00903. Epub 2021 Apr 21.

DOI:10.1021/acs.jpca.1c00903
PMID:33881850
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8279651/
Abstract

Organic molecules can be stable in distinct crystalline forms, known as polymorphs, which have significant consequences for industrial applications. Here, we predict the polymorphs of crystalline benzene computationally for an accurate anisotropic model parametrized to reproduce electronic structure calculations. We adapt the basin-hopping global optimization procedure to the case of crystalline unit cells, simultaneously optimizing the molecular coordinates and unit cell parameters to locate multiple low-energy structures from a variety of crystal space groups. We rapidly locate all the well-established experimental polymorphs of benzene, each of which corresponds to a single local energy minimum of the model. Our results show that basin-hopping can be both an efficient and effective tool for polymorphic crystal structure prediction, requiring no experimental knowledge of cell parameters or symmetry.

摘要

有机分子可以以不同的晶体形式稳定存在,即多晶型物,这对工业应用具有重大影响。在此,我们通过计算预测结晶苯的多晶型物,以获得一个精确的各向异性模型参数化,用于重现电子结构计算。我们将盆地跳跃全局优化程序应用于晶体晶胞的情况,同时优化分子坐标和晶胞参数,以便从各种晶体空间群中定位多个低能量结构。我们快速定位了苯所有已确定的实验多晶型物,每一种都对应于该模型的一个局部能量最小值。我们的结果表明,盆地跳跃可以成为多晶型晶体结构预测的一种高效且有效的工具,无需关于晶胞参数或对称性的实验知识。

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本文引用的文献

1
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J Chem Theory Comput. 2021 Mar 9;17(3):1988-1999. doi: 10.1021/acs.jctc.0c01101. Epub 2021 Feb 2.
2
: from visualization to analysis, design and prediction.从可视化到分析、设计与预测。
J Appl Crystallogr. 2020 Feb 1;53(Pt 1):226-235. doi: 10.1107/S1600576719014092.
3
Crystal Structure Prediction via Basin-Hopping Global Optimization Employing Tiny Periodic Simulation Cells, with Application to Water-Ice.
通过采用微小周期性模拟单元的盆地跳跃全局优化进行晶体结构预测,并应用于水冰
J Chem Theory Comput. 2019 Jun 11;15(6):3889-3900. doi: 10.1021/acs.jctc.9b00073. Epub 2019 May 14.
4
GAtor: A First-Principles Genetic Algorithm for Molecular Crystal Structure Prediction.GAtor:用于分子晶体结构预测的第一性原理遗传算法。
J Chem Theory Comput. 2018 Apr 10;14(4):2246-2264. doi: 10.1021/acs.jctc.7b01152. Epub 2018 Mar 7.
5
Stochastic Neural Network Approach for Learning High-Dimensional Free Energy Surfaces.用于学习高维自由能面的随机神经网络方法。
Phys Rev Lett. 2017 Oct 13;119(15):150601. doi: 10.1103/PhysRevLett.119.150601. Epub 2017 Oct 11.
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Optimal Alignment of Structures for Finite and Periodic Systems.有限和周期性系统结构的最优对齐
J Chem Theory Comput. 2017 Oct 10;13(10):4914-4931. doi: 10.1021/acs.jctc.7b00543. Epub 2017 Sep 14.
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Energy landscapes for machine learning.机器学习的能量景观
Phys Chem Chem Phys. 2017 May 24;19(20):12585-12603. doi: 10.1039/c7cp01108c.
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9
Report on the sixth blind test of organic crystal structure prediction methods.有机晶体结构预测方法第六次盲测报告。
Acta Crystallogr B Struct Sci Cryst Eng Mater. 2016 Aug 1;72(Pt 4):439-59. doi: 10.1107/S2052520616007447.
10
Modeling Polymorphic Molecular Crystals with Electronic Structure Theory.用电子结构理论对多晶分子晶体建模。
Chem Rev. 2016 May 11;116(9):5567-613. doi: 10.1021/acs.chemrev.5b00648. Epub 2016 Mar 23.