Molecular Dynamics Simulation of Molecular Crystals under Anisotropic Compression: Bulk and Directional Effects in Anthracene and Paracetamol

Abstract

Parrinello−Rahman pressure-control algebra with an anisotropic external stress field, coupled with recently developed, accurate atom−atom potentials, has been incorporated into new modules of the Milano Chemistry Molecular Simulation (MiCMoS) computer program package for application in molecular dynamics (MD) simulations for organic crystals. Simulations were carried out for two widely different intermolecular environments, anthracene and paracetamol. The results reproduce quantitatively the anisotropic evolution obtained by pressure-dependent X-ray diffraction experiments in hydrostatic conditions. A less usual application concerns the probing of differently oriented uniaxial stresses, which for anthracene reveal a phase transition triggered by mechanical excitation along a direction parallel to the main molecular axis. For paracetamol, differences in compressibility along different crystal directions are borne out and are explained in molecular terms with reference to the hydrogen bonding scheme. Simulations of tensile stress, that is, negative pressure along different crystal directions, provide an estimate of yield points in a range of 0.2−0.5 GPa (2000−5000 atm) and indicate the weakest directions. On the basis of these results, we strongly suggest that classical MD in the atom−atom formulation, even in the absence of thorough treatment of quantum effects, but endowed with flexible algebra and coupled with carefully calibrated intermolecular potentials, can give reliable results of quantitative and semiquantitative character on the structural dynamics of organic crystals, providing an essential support to downstream studies of mechanical, optical, and electronic properties. Widespread use for further experience and validation is encouraged by the availability of the Fortran source codes.

Quasi-static deformation simulations of molecular crystals

“…While there is a general underestimation of the cell lengths, partly due to the neglect of thermal and zero point effects, there is excellent agreement with the monoclinic angle. The calculated interplanar angle, κ , between the normal vectors to the molecular planes of anthracene molecules in the unit cell of 45° is in excellent agreement with a previous calculation 37 (44.5°), which used a different force field, 38 and relatively similar to experiment (≅ 55.5°). 37…”

“…The calculated interplanar angle, κ , between the normal vectors to the molecular planes of anthracene molecules in the unit cell of 45° is in excellent agreement with a previous calculation 37 (44.5°), which used a different force field, 38 and relatively similar to experiment (≅ 55.5°). 37…”

Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K

“…To shed light on the possible nature of our models’ inability to account for the observed residual features, we performed classical molecular dynamics (MD) simulations on crystalline 1-MUR with the MiCMoS package [ 49 , 50 , 51 , 52 ]. Full details of the procedure are documented in Section S3 Supplementary Materials .…”

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 ).…”