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.
Clathrates have been proposed for use in a variety of applications including gas storage, mixture separation and catalysis due to the potential for controlled guest diffusion through their porous lattices. Here molecular dynamics simulations are employed to study guest transport in clathrates of hydroquinone (HQ) and Dianin's compound (DC). Systems investigated were HQ with methanol and acetonitrile, and DC with methanol and ethanol. Simulations were set up with one guest in the pore, two guests in the pore and one vacancy in the pore and a filled pore, and free-energy barriers for movement between cavities of the pore were estimated for all cases. Comparison between these simulations indicates that guest transport most likely proceeds by molecules moving from full to empty cavities consecutively, one by one, rather than in a concerted manner. Thus, the presence of empty cavities is very important for guest transport, which becomes more energetically demanding in fully loaded systems. Flexibility of the host can assist guest transport. In the studied DC clathrates transport occurs via an intermediate conformation in which the hydroxyl group of the alcohol guest molecule participates in the hydrogen-bonded ring of the host. We also address the issue of the number of methanol guest molecules that DC accommodates, for which conflicting information exists. We found that this is likely to be temperature dependent and suggest that under some conditions the system is most likely non-stoichiometric.
Molecular dynamics provides a means to examine the mechanism of reorientation of hydrogen bond networks that are present in a range of biological and crystalline materials. Simulations of hydroxyl reorientation in the six-membered hydrogen bonded rings in crystalline clathrates of Dianin's compound (DC) and hydroquinone (HQ) reveal that in the clathrate of Dianin's compound with ethanol (DC:ethanol), hydroxyl groups perform single independent flips, and occasionally all six hydroxyls in a ring reorient following a sequential mechanism with participation of the guest ethanol molecule. The free energy estimated for this process agrees well with experimental results. The simulations suggest that hydroxyl reorientation occurs in the empty DC lattice as well, but at a higher energy cost, from which we conclude that it is the participation of ethanol that lowers the barrier of reorientation. Single independent flips of hydroxyl groups are observed to be more frequent in the hydroquinone clathrate with methanol (HQ:methanol) than in DC:ethanol, but reorientation of all six hydroxyls does not occur. This is attributed to the larger difference in energy between the original and reoriented positions of hydroxyl hydrogen atoms in HQ:methanol compared to DC:ethanol.
We report molecular dynamics simulations of the acetonitrile clathrate of hydroquinone, with a focus on the dynamics of acetonitrile methyl groups. There are three inequivalent acetonitrile molecules in the unit cell, one with its dipole parallel to the c-axis, and the other two antiparallel. Although these three guest molecules have previously been found to exhibit two slightly different frequencies of rotation over a wide range of temperatures, the frequencies could not be assigned to specific methyl groups. Perhaps counterintuitively, our simulations suggest that the molecule with the lower frequency is one of the two molecules oriented the same way, the different dynamical behaviour being due to subtle differences in the environments of the molecules.Hydroquinone (HQ) is well known to form crystalline host-guest systems with small molecules such as SO 2 , H 2 S, HBr, CO, CH 4 , CH 3 OH, acetonitrile and methyl isocyanide.
C520the diffi culty to obtain the structural information of the resulted phase, which is mainly caused by the disintegration of the single crystalline form of the parent phase during the transformations. In such cases, the crystal structure determination from the powder X-ray diffraction data is clearly most powerful technique. Herein, we report several examples of the vapour induced crystalline transformations of organic materials investigated using ab initio powder diffraction analysisOne of the examples is the vapour induced transformations of pyromellitic acid (PA : benzene-1,2,4,5-tetracarboxylic acid). As shown in the scheme (see below), PA exhibits a wide variety of the vapour induced transformations. Eight solvates and one unsolvated phase were found by vapour induced transformations. Single crystals of some solvates could be obtained by alternative crystallise pathway, however, some of the solvates (phase U, 1M, 1E and 1iP) could only be obtained by the vapour induced transformations. Thus, the crystal structures of these phases were determined from the powder X-ray diffraction data. The structural analyses revealed that phase 1M and 1E are the mono-methanol and mono-ethanol phases, respectively. Further vapour exposures on the mono-solvate phases gave di-solvate phases (2M and 2E) and these di-solvate phases were also obtained by recrystallisation from the solutions or from the slurry of PA in these solvents. Therefore, phase 1M and 1E are the metastable phases under the existence of the solvent vapour. These mono-solvate phases are obtainable only by the vapour exposure and it clearly shows that solvent vapour exposures are very useful technique to control pseudo-polymorphs.
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