Kinetic-Bias Model for the Dynamic Simulation of Molecular Aggregation. The Liquid, Solute, Solvated-Nanodrop, and Solvated-Nanocrystal States of Benzoic Acid

Abstract

A kinetically biased molecular dynamics (KB-MD) algorithm is developed as an addition to the Milano Chemistry Molecular Simulation (MiCMoS) package. Within a condensed medium, the algorithm sorts out molecular pairs coupled by a strong interaction energy and reduces their kinetic energy by a damping factor, redistributing the resulting excess among other partners within the medium. The aim is to enhance in an iterative manner the incipient intermolecular cohesion, on the way to the formation of recognition aggregates. The algorithm is applied to bulk liquid and crystalline benzoic acid, to homogeneous solutions in methanol, and to liquid or crystalline nanoclusters embedded in methanol solvent. Favorable outcomes are observed in liquid media with the formation of large molecular clusters and in the enhancement of the lifetimes of nanocrystals. Homogeneous solutions are found to require extremely long simulation times to show significant aggregation. Organization into a crystalline structure from liquid precursors is still a faraway simulation goal, but the present approach can be a useful tool, along with the introduction of appropriate collective structural variables, for tackling this long-standing problem at the atomic level.

Do metastable polymorphs always grow faster? Measuring and comparing growth kinetics of three polymorphs of tolfenamic acid

“…In addition, growth mechanisms along some crystal directions can be very different than well-established mechanisms commonly used in crystal growth predictions, as we have shown here for the length growth of the TFA needles. Predicting kinetics of nucleation for hundreds of predicted polymorphs is also extremely challenging, and although simulations of nucleation using molecular dynamics have been attempted, [62][63][64][65][66] this task remains computationally expensive. As an alternative, some qualitative correlations using structural rugosity have been proposed.…”

Why Is α-d-Glucose Monomorphic? Insights from Accurate Experimental Charge Density at 90 K

“…Classical simulations were carried out with the MiCMoS 2.0 program suite, exploiting both the Coulomb–London–Pauli (CLP) and Lennard–Jones–Coulomb (LJC) force fields embedded in the source code. − 1.0 ns-long NPT trajectories at time steps of 2 fs were run at 90 K and ambient pressure. The simulation box consisted of 3 × 2 × 7 crystallographic unit cells with 168 α- d -glucose molecules and an approximately cubic shape (31.1 × 29.7 × 34.8 Å 3 ).…”

Molecular dynamics investigation of benzoic acid in confined spaces

“…All the simulations were run in parallel mode, with 4-8 threads each. The same box 34 containing 432 BZA molecules at 350 K was used as a starting point under the same assumptions of local equilibrium and manipulated, when necessary, with MiCMoS service modules to build smaller or larger boxes with the desired shape and dimensions (Section 2.2). It is important to note that liquid BZA at 350 K is not at thermodynamic equilibrium.…”