Finite temperature string by K-means clustering sampling with order parameters as collective variables for molecular crystals: application to polymorphic transformation between β-CL-20 and ε-CL-20

Abstract

Polymorphic transformation of molecular crystals is a fundamental phase transition process, and it is important practically in the chemical, material, biopharmaceutical, and energy storage industries. However, understanding of the transformation...

Experimental and Theoretical Investigation of External Electric-Field-Induced Crystallization of TKX-50 from Solution by Finite-Temperature String with Order Parameters as Collective Variables for Ionic Crystals

“…Moreover, the differences in PMF between the transition state and TKX-50 are close to each other, and those between the transition state and the supersaturated formic acid solution are also close to each other. This indicates that the difference is not related to the type of OPs or whether it is K-means clustering, as is in agreement with our previous investigation [56].…”

“…Moreover, the differences in PMF between the transition state and TKX-50 are close to each other, and those between the transition state and the supersaturated formic acid solution are also close to each other. This indicates that the difference is not related to the type of OPs or whether it is K-means clustering, as is in agreement with our previous investigation [56]. In order to gain further mechanistic insights into the crystallization of TKX-50 from the supersaturated formic acid solution, the local OPs of TKX-50 were shown for the key snapshots at the points of the PFM curve along the trajectory going from crystal to solution (see Figure 7).…”

“…In most cases, OPs show a central region with the TKX-50 structure surrounded by molecules with intermediate values of OPs corresponding to the surface of the crystal. This indicates that similar to the polymorphic transformation [ 56 , 72 ], the crystallization from solution is also an interface-induced and locally initiated development process.…”

“…Therefore, the theoretical investigation of the phase transformation mechanism by the finite-temperature string method with order parameters as collective variables and the K-means clustering algorithm has been feasible. Recently, to improve the convergence rate of FTS with OP as collective variables for molecular crystal, we used a K-means clustering algorithm based on the Euclidean distance and sample weights to smooth the initial FTS and the minimum-free-energy path connecting between β -CL-20 and ε -CL-20 was sketched, and the free-energy profile along the path was obtained [ 56 ]. The crystallization of ionic crystals from solution is a common phase transition phenomenon, and this technique has been used abundantly in industry, with practical applications in pharmaceutical, chemical, petrochemical, food industries, and biotechnology, making it a multitrillion-dollar business [ 22 , 57 , 58 , 59 , 60 , 61 ].…”

Finite Temperature String with Order Parameter as Collective Variables for Molecular Crystal: A Case of Polymorphic Transformation of TNT under External Electric Field

“…(3) Determining the MFEP using SMCV method The MFEPs can be determined with the SMCV method, as detailed in our previous investigations [47,48]. It consists of five steps:…”