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 critical before beginning, and to provide references to good resources on those topics. We also provide a checklist of key issues to consider before and while setting up molecular simulations which may serve as a foundation for other best practices documents.

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. We show that ZTCs partition space into two disjoint labyrinths that can be described by a pair of interpenetrating nets. Since such a pair of nets also describes a triply periodic minimal surface (TPMS), our results establish the relationship between ZTCs and schwarzites-carbon materials with negative Gaussian curvature that resemble TPMSs-linking the research topics and demonstrating that schwarzites should no longer be thought of as purely hypothetical materials.

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. Meanwhile, the use of simple velocity rescaling and Berendsen (weak coupling) thermostat algorithms has not abated but has actually continued to grow. Here, we have calculated the partitioning of the kinetic energy between translational, rotational, and vibrational modes in simulations of diatomic molecules to explicitly determine whether the equipartition theorem is violated under different thermostats and while rescaling velocities to different kinetic energy distributions. We have found that the underlying cause of the flying ice cube effect is a violation of balance leading to systematic redistributions of kinetic energy under simple velocity rescaling and the Berendsen thermostat. When velocities are instead rescaled to the canonical ensemble's kinetic energy distribution, as is done with the CSVR thermostat, the equipartition theorem is not violated, and we show that the CSVR thermostat satisfies detailed balance. The critical necessity for molecular dynamics practitioners to abandon the use of popular yet incorrect velocity rescaling algorithms is underscored with an example demonstrating that the main result of a highly cited study is entirely due to artifacts resulting from the study's use of the Berendsen thermostat.

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). We observe a pronounced inflection in the Xe adsorption isotherm in the Ni variant. With evidence from X-ray diffraction studies, density functional theory, and molecular simulations, we attribute the inflection to a disordered to ordered transition of the rotational configurations of the pyrazine rings induced by sorbate-sorbent interactions. We also address the effect of cage size, temperature, and sorbate on the guest-induced ring rotation and the adsorption isotherms. The absence of an inflection in the Xe adsorption isotherm in SIFSIX-3-Fe and in the Kr, N2, and CO2 adsorption isotherms in SIFSIX-3-Ni suggest that the inflection is highly sensitive to the match between the size of the cage and the guest molecule.

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. Guest molecules incentivize the ligands to adopt a different rotational configuration than maintained in the empty host. Our model captures inflections, steps, and hysteresis that can arise in the adsorption isotherm as a signature of the rotating ligands. The insights disclosed by our simple model contribute a more intimate understanding of the response and consequence of rotating ligands integrated into porous materials to harness them for gas storage and separations, chemical sensing, drug delivery, catalysis, and nanoscale devices. Particularly, our model reveals design strategies to exploit these moving constituents and engineer improved adsorbents with intrinsic thermal management for pressure-swing adsorption processes.

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. Here, we report a deformation pattern, induced by the adsorption of argon, for IRMOF-74-V. This work has two main implications. First, we use molecular simulations to demonstrate that the IRMOF-74 series undergoes a deformation that is similar to the mechanism behind breathing MOFs, but is unique because the deformation pattern extends beyond a single unit cell of the original structure. Second, we provide an alternative interpretation of experimental small-angle X-ray scattering profiles of these systems, which changes how we view the fundamentals of adsorption in this MOF series.

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. As applications of these materials in catalysis, separations, and gas storage rely on the ability to tune the properties of adsorbed molecules, we anticipate that the ability to systematically control the critical point, thereby preparing spatially inhomogeneous local adsorbate densities, could add a new design tool for MOF applications.