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Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design
10.1021/acs.jctc.8b00033 2018-04-20 Hydrogen bond networks play a critical role in determining the stability and specificity of biomolecular complexes, and the ability to design such networks is important for engineering novel structures, interactions, and enzymes. One key feature of hydrogen b... |
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Water Oxidation Catalysis for NiOOH by a Metropolis Monte Carlo Algorithm
10.1021/acs.jctc.7b01214 2018-04-18 Understanding catalytic mechanisms is important for discovering better catalysts, particularly for water splitting reactions that are of great interest to the renewable energy field. One of the best performing catalysts for water oxidation is nickel oxyhydrox... |
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Lifting the Curse of Dimensionality on Enhanced Sampling of Reaction Networks with Parallel Bias Metadynamics
10.1021/acs.jctc.7b01289 2018-04-18 A common challenge to applying metadynamics to the study of complex systems is selecting the proper collective variables to bias. The advent of generic collective variables, specifically social permutation invariant (SPRINT) coordinates, has helped to address... |
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Understanding the Many-Body Basis Set Superposition Error: Beyond Boys and Bernardi
10.1021/acs.jctc.7b01232 2018-04-18 Fragment-based methods promise accurate energetics at a cost that scales linearly with the number of fragments. This promise is founded on the premise that the many-body expansion (or another similar energy decomposition) needs to only consider spatially loca... |
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Hydration Structure and Dynamics of Inhibitor-Bound HIV-1 Protease
10.1021/acs.jctc.8b00097 2018-04-18 Water is essential in many biological processes, and the hydration structure plays a critical role in facilitating protein folding, dynamics, and ligand binding. A variety of biophysical spectroscopic techniques have been used to probe the water solvating pro... |
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A Four-Site Molecular Model for Simulations of Liquid Methanol and Water–Methanol Mixtures: MeOH-4P
10.1021/acs.jctc.7b01265 2018-04-17 In this work, we present a new four-site potential for methanol, MeOH-4P, fitted to reproduce the dielectric constant ε, the surface tension γs, and the liquid density ρ of the pure liquid at T = 298.15 K and p = 1 bar. The partial charges on each site were t... |
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AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms
10.1021/acs.jctc.7b01128 2018-04-16 We report the first parameters of the heme redox cofactors for the polarizable AMOEBA force field in both the ferric and ferrous forms. We consider two types of complexes, one with two histidine side chains as axial ligands and one with a histidine and a meth... |
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One-Dimensional Projection of Collective Variables for Effective Sampling of Complex Chemical Reaction Coordinates
10.1021/acs.jctc.7b01139 2018-04-16 A one-dimensional projection (ODP) technique is introduced to overcome the challenges in multidimensional sampling. With the help of a projected “advancement of reaction (ξ)” control parameter, it was demonstrated that multidimensional samplings could be perf... |
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Parametrization of Molybdenum Cofactors for the AMBER Force Field
10.1021/acs.jctc.8b00137 2018-04-16 Molybdenum-containing enzymes have been receiving significant attention from the scientific community since they participate in important biological processes and in the global biogeochemical cycles of carbon, nitrogen, and sulfur. Molecular modeling studies ... |
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Spatial and Spin Symmetry Breaking in Semidefinite-Programming-Based Hartree–Fock Theory
10.1021/acs.jctc.7b01288 2018-04-16 The Hartree–Fock problem was recently recast as a semidefinite optimization over the space of rank-constrained two-body reduced-density matrices (RDMs) [ Phys. Rev.A 2014, 89, 010502(R)]. This formulation of the problem transfers the nonconvexity of the Hartr... |