Capturing Crystal Shape Evolution from Molecular Simulations.

A simple and efficient algorithm for tracking shape evolution of small-molecule organic crystals during molecular simulations is described. It is based on the reconstruction of a crystal surface from molecular coordinates using an alpha-shape triangulation algorithm followed by the DBSCAN clustering of neighboring triangles with similar normal vectors to crystal faces. No information except the unit cell parameters is needed beforehand, enabling the user to automatically detect not only existing but also new forming crystal faces and edges, which is valuable for prediction of growth and dissolution kinetics. The results are demonstrated for aspirin and paracetamol crystals.

Insights into pharmaceutical nanocrystal dissolution: a molecular dynamics simulation study on aspirin.

The presented molecular dynamics simulations are the first simulations to reveal dynamic dissolution of a pharmaceutical crystal in its experimentally determined shape. Continuous dissolution at constant undersaturation of the surrounding medium is ensured by introducing a plane of sticky dummy atoms into the water slab. These atoms have a strong interaction potential with dissolved aspirin molecules, but interactions with water are excluded from the calculations. Thus, the number of aspirin molecules diffusing freely in solution is kept at a low value and continuous dissolution of the aspirin crystal is monitored. Further insight into face-specific dissolution is drawn. The dissolution mechanism of receding edges is found for the (001) plane. These findings are in good agreement with experimental results. While the proposed dissolution mechanism for the (100) plane is terrace sinking on a rough surface, no pronounced dissolution of the perfectly flat face is seen in the present work. Molecular simulations of pharmaceuticals in their experimentally obtained structure therefore have shown to be especially suited for the investigation of dissolving faces, where the edges have a pronounced effect. In contrast to previous studies a propagation of the dissolution front into the crystal face is reported, and the crystal bulk is stable over the whole simulation time of 150 ns.

Influence of Monovalent Salts on α-Glycine Crystal Growth from Aqueous Solution: Molecular Dynamics Simulations at Constant Supersaturation Conditions.

The growth of α-glycine crystals from aqueous solution is investigated at constant supersaturations by utilizing the constant chemical potential molecular dynamics method. The study considers two faces (010) and (011) that predominantly determine the α-glycine crystal morphology. The general Amber force field (GAFF) with two different charge sets derived from semi-empirical calculations using the complete neglect of differential overlap method (CNDO) and from density functional calculations using the double-numerical plus d- and p-polarization basis set (DNP) is applied to describe α-glycine. The extended simple point charge model is used to simulate water. It is observed that the GAFF/DNP set leads to a much slower integration of glycine molecules into the crystal structure than the GAFF/CNDO set. The GAFF/CNDO set, however, causes the growth even at concentrations well below the experimental solubility. For the GAFF/DNP set, the influence of potassium chloride (KCl) and sodium chloride (NaCl) on the face growth rates is investigated. The parameters recently proposed by Yagasaki et al. [J. Chem. Theory Comput. 2020, 16, 2460-2473] are used to describe salt ions, as standard GAFF parameters lead to the unexpected formation of salt clusters at a concentration lower than the experimental solubility value. According to our simulation results, both salts suppress the growth of the (011) and (010) faces. The inhibiting effect of NaCl is much stronger than that of KCl for the (011) face, while both salts have a similar inhibiting effect on the (010) face. The results are in line with the experimental observations of the impact of salt ions on the α-glycine growth rates for the (011) face reported in literature.

Data Filtering for Effective Analysis of Crystal-Solution Interface Molecular Dynamics Simulations.

Analysis of processes occurring at the solid-solution interface during crystal growth and dissolution simulations requires an effective way to detect rare, uncorrelated transitions from the liquid to the solid state or vice versa. Because of the oscillatory behavior of molecules, this is not a trivial problem. Usually, to take the thermal vibration and rotational flexibility of the molecules into account, the data (e.g., orientation, center of mass position) needed to determine the molecular state are averaged over some time interval. Then they are evaluated using some order parameters to classify the individual molecules as being either crystalline or in solution. In this case, the results can be very sensitive to the time interval, which is mostly chosen in some heuristic way. To suppress the problem of fast non-Markovian dynamics and to make the identification of the molecular state more reliable and robust, the application of a Kalman filter, optionally combined with a hysteretic approach, is proposed in this contribution. A scheme to estimate the filter parameters is introduced. To demonstrate the approach, simple and widely used order parameters based on the structural features of molecules are taken. The obtained results are clearly superior to those based on the data averaging technique and are important for the effective transition rates calculation as well as for the general analysis of the time evolution of interfaces.