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Halogen bonding has emerged as an important noncovalent interaction in a myriad of applications, including drug design, supramolecular assembly, and catalysis. Current understanding of the halogen bond is informed by electronic structure calculations on isolated molecules and/or crystal structures that are not readily transferable to liquids and disordered phases. To address this issue, we present a first-principles simulation-based approach for quantifying halogen bonds in molecular systems rooted in an understanding of nuclei-nuclei and electron-nuclei spatial correlations. We then demonstrate how this approach can be used to quantify the structure and dynamics of halogen bonds in condensed phases, using solid and liquid molecular chlorine as prototypical examples with high concentrations of halogen bonds. We close with a discussion of how the knowledge generated by our first-principles approach may inform the development of classical empirical models, with a consistent representation of halogen bonding.
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Many atomic liquids can form transient covalent bonds reminiscent of those in the corresponding solid states. These directional interactions dictate many important properties of the liquid state, necessitating a quantitative, atomic-scale understanding of bonding in these complex systems. A prototypical example is liquid silicon, wherein transient covalent bonds give rise to local tetrahedral order and consequent non-trivial effects on liquid state thermodynamics and dynamics. To further understand covalent bonding in liquid silicon, and similar liquids, we present an ab initio simulation-based approach for quantifying the structure and dynamics of covalent bonds in condensed phases. Through the examination of structural correlations among silicon nuclei and maximally localized Wannier function centers, we develop a geometric criterion for covalent bonds in liquid Si. We use this to monitor the dynamics of transient covalent bonding in the liquid state and estimate a covalent bond lifetime. We compare covalent bond dynamics to other processes in liquid Si and similar liquids and suggest experiments to measure the covalent bond lifetime.
The dynamics of desorption from a submonolayer of adsorbed atoms or ions are significantly influenced by the absence or presence of lateral diffusion of the adsorbed particles. When diffusion is present, the adsorbate configuration is simultaneously changed by two distinct processes, proceeding in parallel: adsorption/desorption, which changes the total adsorbate coverage, and lateral diffusion, which is coverage conserving. Inspired by experimental results, we here study the effects of these competing processes by kinetic Monte Carlo simulations of a simple lattice-gas model. In order to untangle the various effects, we perform large-scale simulations, in which we monitor coverage, correlation length, and cluster-size distributions, as well as the behavior of representative individual clusters, during desorption. For each initial adsorbate configuration, we perform multiple, independent simulations, without and with diffusion, respectively. We find that, compared to desorption without diffusion, the coverage-conserving diffusion process produces two competing effects: a retardation of the desorption rate, which is associated with a coarsening of the adsorbate configuration, and an acceleration due to desorption of monomers evaporated from the cluster perimeters. The balance between these two effects is governed by the structure of the adsorbate layer at the beginning of the desorption process. Deceleration and coarsening are predominant for configurations dominated by monomers and small clusters, while acceleration is predominant for configurations dominated by large clusters.
Traditional classifications of crystalline phases focus on nuclear degrees of freedom. Through examination of both electronic and nuclear structure, we introduce the concept of an electronic plastic crystal. Such a material is classified by crystalline nuclear structure, while localized electronic degrees of freedom - here lone pairs - exhibit orientational motion at finite temperatures. This orientational motion is an emergent phenomenon arising from the coupling between electronic structure and polarization fluctuations generated by collective motions, such as phonons. Using ab initio molecular dynamics simulations, we predict the existence of electronic plastic crystal motion in halogen crystals and halide perovskites, and suggest that such motion may be found in a broad range of solids with lone pair electrons. Such fluctuations in the charge density should be observable, in principle via synchrotron scattering.
One of the most promising applications in nanoscience is the design of new materials to improve water permeability and selectivity of nanoporous membranes. Understanding the molecular architecture behind these fascinating structures and how it impacts the water flow is an intricate but necessary task. We studied here, the water flux through multi-layered nanoporous molybdenum disulfide (MLNMoS$_2$) membranes with different nanopore sizes and length. Molecular dynamics simulations show that the permeability do not increase with the inverse of the membrane thickness, violating the classical hydrodynamic behavior. The data also reveals that the water dynamics is slower than that observed in frictionless carbon nanotubes and multi-layer graphene membranes, which we explain in terms of an anchor mechanism observed in between layers. We show that the membrane permeability is critically dependent on the nanopore architecture, bringing important insights into the manufacture of new desalination membranes.
We used molecular dynamics simulations to predict the steady state crystal shape of naphthalene grown from ethanol solution. The simulations were performed at constant supersaturation by utilizing a recently proposed algorithm [Perego et al., J. Chem. Phys., 142, 2015, 144113]. To bring the crystal growth within the timescale of a molecular dynamics simulation we applied Well-Tempered Metadynamics with a spatially constrained collective variable, which focuses the sampling on the growing layer. We estimated that the resulting steady state crystal shape corresponds to a rhombic prism, which is in line with experiments. Further, we observed that at the investigated supersaturations, the ${00bar{1}}$ face grows in a two step two dimensional nucleation mechanism while the considerably faster growing faces ${1bar{1}0}$ and ${20bar{1}}$ grow new layers with a one step two dimensional nucleation mechanism.
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