Understanding solid–solid polymorphic transitions within molecular crystals on the molecular scale is a challenging task. It is, however, crucial for the understanding of transitions that are thought to occur through cooperative motion, which offer an interesting perspective for future applications. In this paper, we study the energy barriers and mechanisms involved in the β → α DL-norleucine transition at the molecular scale by applying different computational techniques. We conclude that the mechanism of the transition is a cooperative movement of bilayers through an intermediate state. The results indicate that local fluctuations in the conformations of the aliphatic chains play a crucial role in keeping the cooperative mechanism sustainable at large length scales. We have characterized the intermediate state.

Here we present a comprehensive evaluation of a set of well-known all-atom force fields with the scope to model dynamic phenomena in molecular crystals composed of polyaromatic hydrocarbons. The capability of the force fields to reproduce experimentally and computationally available data is thoroughly scrutinized against anthracene molecular crystals that serve as a model system. First, the properties of the solid crystalline phase are investigated by employing geometry optimization using molecular mechanics. Because any inaccuracies can be easily overlooked in the constrained solid crystalline phase, the interaction energy of a variety of dimer conformations is obtained by employing an extensive local minima search algorithm. The larger configurational freedom in the dimer conformations better reflects the incorporation of molecules at the surface during crystal growth. The results are compared to known ab initio calculations as very little experimental data concerning the anthracene dimer are available. Finally, for three force fields with different performance in other tests, a polymorph prediction is carried out. Overall, we show that some of the selected all-atom force fields (BMM2, BMM3, W99, and isoPAHAP) perform remarkably well, whereas others (Amber, Bordat, Dreiding, DRESP, MM2, and MM3) fail to reproduce known computational data for a variety of reasons.

The enantiotropically related α and β polymorphs of dl-norleucine are an interesting probe for polymorphism in molecular crystals. We present the results of quantitative molecular dynamics simulations of these two polymorphs at both stable and metastable temperatures. Because of a fully flexible force field, we can judge the differences in crystal and molecular properties between the polymorphs. In simulations of the β polymorph at 350 K, we observe partial phase transitions which we could follow with the help of specifically designed order parameters. The transitions are exclusively occurring along b′. This indicates a possible transformation mechanism in which first shifts of bilayers occur in this direction, followed by shifts along a′. The transformed lattice parameters and molecular properties behave identically with temperature for the two polymorphs. Consequently, the polymorphs only differ in the orientation of the molecular bilayers, which explains the ease of transitions between them. The partial transitions consist of different types which differ in the number of interfaces involved and in the amount of distortion of the crystal. At the time scale of the simulations, we did not observe a full polymorphic phase transition.

To determine the stabilizing effect of different promoter molecules on the clathrate, the Gibbs free energy of fully occupied binary sH hydrogen clathrates with secondary guest molecules in the large cages is calculated with Monte Carlo simulations. The small and medium cages of sH are occupied by one H2 guest molecule. Various promoter molecules enclathrated in the large cages are considered. Simulations are conducted in the pressure range of 250–1000 atm for temperatures ranging from 233 to 273 K. We investigate the effect of dipole moment and molecular size on the thermodynamic stability of sH hydrogen clathrate hydrate.

Kinetic processes play a crucial role in the formation and evolution of molecular layers. In this perspective we argue that adaptive kinetic Monte Carlo is a powerful simulation technique for determining key kinetic processes in molecular solids. The applicability of the method is demonstrated by simulating the diffusion of a CO admolecule on a water ice surface, which is an important process for the formation of organic compounds on interstellar dust grains. CO diffusion is found to follow Arrhenius behavior and the corresponding effective activation energy for diffusion is determined to be 50 ± 1 meV. A coarse graining algorithm is applied which greatly enhances the efficiency of the simulations at low temperatures, down to 10 K, without altering the underlying physical processes. Eventually, we argue that a combination of both on- and off-lattice kinetic Monte Carlo techniques is a good way for simulating large-scale processes in molecular solids over long time spans.

Kinetic processes play a crucial role in the formation and evolution of molecular layers. In this perspective we argue that adaptive kinetic Monte Carlo is a powerful simulation technique for determining key kinetic processes in molecular solids. The applicability of the method is demonstrated by simulating the diffusion of a CO admolecule on a water ice surface, which is an important process for the formation of organic compounds on interstellar dust grains. CO diffusion is found to follow Arrhenius behavior and the corresponding effective activation energy for diffusion is determined to be 50 ± 1 meV. A coarse graining algorithm is applied which greatly enhances the efficiency of the simulations at low temperatures, down to 10 K, without altering the underlying physical processes. Eventually, we argue that a combination of both on- and off-lattice kinetic Monte Carlo techniques is a good way for simulating large-scale processes in molecular solids over long time spans.