Molecular dynamics simulations of structure and dynamics of organic molecular crystals

Abstract

A set of model compounds covering a range of polarity and flexibility have been simulated using GAFF, CHARMM22, OPLS and MM3 force fields to examine how well classical molecular dynamics simulations can reproduce structural and dynamic aspects of organic molecular crystals. Molecular structure, crystal structure and thermal motion, including molecular reorientations and internal rotations, found from the simulations have been compared between force fields and with experimental data. The MM3 force field does not perform well in condensed phase simulations, while GAFF, CHARMM and OPLS perform very similarly. Generally molecular and crystal structure are reproduced well, with a few exceptions. The atomic displacement parameters (ADPs) are mostly underestimated in the simulations with a relative error of up to 70%. Examples of molecular reorientation and internal rotation, observed in the simulations, include in-plane reorientations of benzene, methyl rotations in alanine, decane, isopropylcyclohexane, pyramidal inversion of nitrogen in amino group and rotation of the whole group around the C-N bond. Frequencies of such dynamic processes were calculated, as well as thermodynamic properties for reorientations in benzene and alanine. We conclude that MD simulations can be used for qualitative analysis, while quantitative results should be taken with caution. It is important to compare the outcomes from simulations with as many experimental quantities as available before using them to study or quantify crystal properties not available from experiment.

Anisotropic displacement parameters for molecular crystals from periodic Hartree–Fock and density functional theory calculations

“…Based on their calculations, they suggest new models of anharmonic motion that will reduce the number of parameters typically used for these models (the Gram-Charlier). Nemkevich et al (2010) used traditional force-field-based MD simulations to obtain isotropic harmonic motion. Comparing their results with experimental results, they generally observe that the computed MSDs are much smaller than the experimentally observed ones.…”

Ab Initio and Molecular Dynamics-Based Pair Potentials for Lanthanum Hexaboride

“…Departure from ab initio calculated displacements occurs naturally at the lower temperature regime, producing the expected linear behavior with respect to temperature for classical MD simulations. 50,51 However, the lanthanum displacements are accurate well into the low temperature regime, showing very good predictions for both DFT and experimental data.…”

Crystallographic and Dynamic Aspects of Solid‐State NMR Calibration Compounds: Towards ab Initio NMR Crystallography

“…Ab initio MD simulations are inadequate for MD simulations with large supercells due to the computational cost; in most cases, ab initio MD simulations with the constant number–volume–temperature (NVT) ensemble for 1×1×1 unit cells were used—this is not always physically realistic and can give problems for certain systems. Classical mechanics is the most likely option for simulating the behavior of a large supercell with the unit cell parameters allowed to vary, however, the accuracy of classical MD simulations relies on the quality of the force field used for the MD; force fields are unsuitable for certain crystal structures . MD simulations must be used for adamantane and hexamethylbenzene because these two crystals have dynamic phases at room temperature.…”

“…Classical mechanics is the most likely option for simulating the behavior of al arge supercell with the unit cell parameters allowedt ov ary,h owever,t he accuracyo fc lassical MD simulations relies on the quality of the force field used for the MD;f orce fields are unsuitable for certain crystal structures. [27] MD simulations must be used for adamantane and hexamethylbenzeneb ecause these two crystals have dynamic phases at room temperature. MD was also utilized for the study of 3-methylglutaric acid.…”