Best Practices for Foundations in Molecular Simulations [Article v1.0].

This document provides a starting point for approaching molecular simulations, guiding beginning practitioners to what issues they need to know about before and while starting their first simulations, and why those issues are so critical. This document makes no claims to provide an adequate introduction to the subject on its own. Instead, our goal is to help people know what issues are before beginning, and to provide references to good resources on those topics.

Generating carbon schwarzites via zeolite-templating.

Zeolite-templated carbons (ZTCs) comprise a relatively recent material class synthesized via the chemical vapor deposition of a carbon-containing precursor on a zeolite template, followed by the removal of the template. We have developed a theoretical framework to generate a ZTC model from any given zeolite structure, which we show can successfully predict the structure of known ZTCs. We use our method to generate a library of ZTCs from all known zeolites, to establish criteria for which zeolites can produce experimentally accessible ZTCs, and to identify over 10 ZTCs that have never before been synthesized.

Anomalous Effects of Velocity Rescaling Algorithms: The Flying Ice Cube Effect Revisited.

The flying ice cube effect is a molecular dynamics simulation artifact in which the use of velocity rescaling thermostats sometimes causes violation of the equipartition theorem, affecting both structural and dynamic properties. The reason for this artifact and the conditions under which it occurs have not been fully understood. Since the flying ice cube effect was first demonstrated, a new velocity rescaling algorithm (the CSVR thermostat) has been developed and become popular without its effects on the equipartition theorem being truly known.

Effect of ring rotation upon gas adsorption in SIFSIX-3-M (M = Fe, Ni) pillared square grid networks.

Dynamic and flexible metal-organic frameworks (MOFs) that respond to external stimuli, such as stress, light, heat, and the presence of guest molecules, hold promise for applications in chemical sensing, drug delivery, gas separations, and catalysis. A greater understanding of the relationship between flexible constituents in MOFs and gas adsorption may enable the rational design of MOFs with dynamic moieties and stimuli-responsive behavior. Here, we detail the effect of subtle structural changes upon the gas sorption behavior of two "SIFSIX" pillared square grid frameworks, namely SIFSIX-3-M (M = Ni, Fe).

Adsorbate-induced lattice deformation in IRMOF-74 series.

IRMOF-74 analogues are among the most widely studied metal-organic frameworks (MOFs) for adsorption applications because of their one-dimensional channels and high metal density. Most studies involving the IRMOF-74 series assume that the crystal lattice is rigid. This assumption guides the interpretation of experimental data, as changes in the crystal symmetry have so far been ignored as a possibility in the literature.

Statistical mechanical model of gas adsorption in porous crystals with dynamic moieties.

Some nanoporous, crystalline materials possess dynamic constituents, for example, rotatable moieties. These moieties can undergo a conformation change in response to the adsorption of guest molecules, which qualitatively impacts adsorption behavior. We pose and solve a statistical mechanical model of gas adsorption in a porous crystal whose cages share a common ligand that can adopt two distinct rotational conformations.

Nanoporous Materials Can Tune the Critical Point of a Pure Substance.

Molecular simulations and NMR relaxometry experiments demonstrate that pure benzene or xylene confined in isoreticular metal-organic frameworks (IRMOFs) exhibit true vapor-liquid phase equilibria where the effective critical point may be reduced by tuning the structure of the MOF. Our results are consistent with vapor and liquid phases extending over many MOF unit cells. These results are counterintuitive since the MOF pore diameters are approximately the same length scale as the adsorbate molecules.