Chan Eric J, Tuckerman Mark E
Chemistry Department, Curtin University, Bentley, WA, 6102, Australia.
Department of Chemistry, New York University, New York City, NY, 10003, USA.
Acta Crystallogr B Struct Sci Cryst Eng Mater. 2024 Dec 1;80(Pt 6):575-94. doi: 10.1107/S205252062400132X.
A novel approach to computationally enhance the sampling of molecular crystal structures is proposed and tested. This method is based on the use of extended variables coupled to a Monte Carlo based crystal polymorph generator. Inspired by the established technique of quasi-random sampling of polymorphs using the rigid molecule constraint, this approach represents molecular clusters as extended variables within a thermal reservoir. Polymorph unit-cell variables are generated using pseudo-random sampling. Within this framework, a harmonic coupling between the extended variables and polymorph configurations is established. The extended variables remain fixed during the inner loop dedicated to polymorph sampling, enforcing a stepwise propagation of the extended variables to maintain system exploration. The final processing step results in a polymorph energy landscape, where the raw structures sampled to create the extended variable trajectory are re-optimized without the thermal coupling term. The foundational principles of this approach are described and its effectiveness using both a Metropolis Monte Carlo type algorithm and modifications that incorporate replica exchange is demonstrated. A comparison is provided with pseudo-random sampling of polymorphs for the molecule coumarin. The choice to test a design of this algorithm as relevant for enhanced sampling of crystal structures was due to the obvious relation between molecular structure variables and corresponding crystal polymorphs as representative of the inherent vapor to crystal transitions that exist in nature. Additionally, it is shown that the trajectories of extended variables can be harnessed to extract fluctuation properties that can lead to valuable insights. A novel thermodynamic variable is introduced: the free energy difference between ensembles of Z' = 1 and Z' = 2 crystal polymorphs.
提出并测试了一种通过计算增强分子晶体结构采样的新方法。该方法基于使用与基于蒙特卡罗的晶体多晶型生成器耦合的扩展变量。受使用刚性分子约束进行多晶型准随机采样的既定技术启发，此方法将分子簇表示为热库中的扩展变量。使用伪随机采样生成多晶型晶胞变量。在此框架内，建立了扩展变量与多晶型构型之间的谐波耦合。在专用于多晶型采样的内循环中，扩展变量保持固定，强制扩展变量逐步传播以维持系统探索。最终处理步骤产生多晶型能量景观，其中为创建扩展变量轨迹而采样的原始结构在没有热耦合项的情况下重新优化。描述了该方法的基本原理，并展示了其使用 metropolis 蒙特卡罗类型算法以及结合副本交换的修改的有效性。对分子香豆素的多晶型伪随机采样进行了比较。选择测试与增强晶体结构采样相关的该算法设计是由于分子结构变量与相应晶体多晶型之间存在明显关系，这些多晶型代表了自然界中存在的从蒸汽到晶体的固有转变。此外，结果表明，可以利用扩展变量的轨迹来提取波动特性，从而获得有价值的见解。引入了一个新的热力学变量：Z' = 1 和 Z' = 2 晶体多晶型系综之间的自由能差。
