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Multiscale Molecular Dynamics Simulations of an Active Self-Assembling Material
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Transport Properties of Liquid Pentaerythritol Tetranitrate (PETN) from Molecular Dynamics Simulations
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Revealing Surface Waters on an Antifreeze Protein by Fusion Protein Crystallography Combined with Molecular Dynamic Simulations
Antifreeze proteins (AFPs) adsorb to ice through an extensive, flat, relatively hydrophobic surface. It has been suggested that this ice-binding site (IBS) organizes surface waters into an ice-like clathrate arrangement that matches and fuses to the quasi-liquid layer on the ice surface. On cooling, these waters join the ice lattice and freeze the AFP to its ligand. Evidence for the generality of this binding mechanism is limited because AFPs tend to crystallize with their IBS as a preferred protein–protein contact surface, which displaces some bound waters. Type III AFP is a 7 kDa globular protein with an IBS made up two adjacent surfaces. In the crystal structure of the most active isoform (QAE1), the part of the IBS that docks to the primary prism plane of ice is partially exposed to solvent and has clathrate waters present that match this plane of ice. The adjacent IBS, which matches the pyramidal plane of ice, is involved in protein–protein crystal contacts with few surface waters. Here we have changed the protein–protein contacts in the ice-binding region by crystallizing a fusion of QAE1 to maltose-binding protein. In this 1.9 Å structure, the IBS that fits the pyramidal plane of ice is exposed to solvent. By combining crystallography data with MD simulations, the surface waters on both sides of the IBS were revealed and match well with the target ice planes. Here, the waters on the pyramidal plane IBS were loosely constrained, which might explain why other isoforms of type III AFP that lack the prism plane IBS are less active than QAE1. The AFP fusion crystallization method can potentially be used to force the exposure to solvent of the IBS on other AFPs to reveal the locations of key surface waters.
Molecular Dynamics Simulations of Reverse Osmosis in Silica Nanopores
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An Ab Initio -Derived Force Field for Amorphous Silica Interfaces for Use in Molecular Dynamics Simulations
Here, we present a classical interatomic force field, silica-DDEC, to describe the interactions of amorphous and crystalline silica surfaces, parametrized using density functional theory-based charges. Charge schemes for silica surfaces were developed using the density-derived electrostatic and chemical (DDEC) method, which reproduces atomic charges of the periodic models as well as the electrostatic potential away from the atom sites. Lennard–Jones parameters were determined by requiring the correct description of (i) the amorphous silica density, coordination defects, and local coordination geometry, relative to experimental measurements, and (ii) water-silica interatomic distances compared with ab initio results. Deprotonated surface silanol sites are also described within the model based on DDEC charges. The result is a general electronic structure-derived model for describing fully flexible amorphous and crystalline silica surfaces and interactions of liquids with silica surfaces of varying structure and protonation state.
Properties of Erythritol Tetranitrate from Molecular Dynamics Simulation
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Sum Frequency Generation Spectroscopy and Molecular Dynamics Simulations Reveal a Rotationally Fluid Adsorption State of α-Pinene on Silica
A rotationally fluid state of α-pinene at fused silica/vapor interfaces is revealed by computational and experimental vibrational sum frequency generation (SFG) studies. We report the first assignment of the vibrational modes in the notoriously congested C-H stretching region of α-pinene and identify its bridge methylene group on the four-membered ring ("βCH2") as the origin of its dominant spectral feature. We find that the spectra are perfused with Fermi resonances that need to be accounted for explicitly in the computation of vibrational spectra of strained hydrocarbons such α-pinene. The preferred orientations of α-pinene are consistent with optimization of van der Waals contacts with the silica surface that results in a bimodal distribution of highly fluxional orientations in which the βCH2 group points "towards" or "away from” the surface. The reported findings are particularly relevant to the exposure of α-pinene to primary oxidants in heterogeneous catalytic pathways that exploit α-pinene as a sustainable feedstock for fine chemicals and polymers.
Competitive B2 and B33 Nucleation during Solidification of Ni 50 Zr 50 Alloy: Molecular Dynamics Simulation and Classical Nucleation Theory
We studied the homogenous nucleation of the stoichiometric B2 and B33 phases in the Ni 50 Zr 50 alloy using the persistent embryo method and the classical nucleation theory. The two phases become very close competitors at large supercoolings, which is consistent with the experimental observations. In the case of the B2 phase, the linear temperature dependence of the solid–liquid interface (SLI) free energy extrapolated to the melting temperature leads to the same value as the one obtained from the capillarity fluctuation method (CFM). In the case of the B33 phases, the SLI free energy is also a linear function of temperature at large supercoolings, but the extrapolation to the melting temperature leads to a value which is considerably different from the CFM value. This is persistent with the large anisotropy of the SLI properties of the B33 phase nearby the melting temperature observed in the simulation of the nominally flat interface migration.