21 research outputs found

    Direct-Coupling O<sub>2</sub> Bond Forming a Pathway in Cobalt Oxide Water Oxidation Catalysts

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    We report a catalytic mechanism for water oxidation in a cobalt oxide cubane model compound, in which the crucial O–O bond formation step takes place by direct coupling between two Co<sup>IV</sup>(O) metal oxo groups. Our results are based upon density functional theory (DFT) calculations and are consistent with experimental studies of the CoPi water oxidation catalyst. The computation of energetics and barriers for the steps leading up to and including the O–O bond formation uses an explicit solvent model within a hybrid quantum mechanics/molecular mechanics (QM/MM) framework, and captures the essential hydrogen-bonding effects and dynamical flexibility of this system

    Building Force Fields: An Automatic, Systematic, and Reproducible Approach

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    The development of accurate molecular mechanics force fields is a significant challenge that must be addressed for the continued success of molecular simulation. We developed the ForceBalance method to automatically derive accurate force field parameters using flexible combinations of experimental and theoretical reference data. The method is demonstrated in the parametrization of two rigid water models, yielding new parameter sets (TIP3P-FB and TIP4P-FB) that accurately describe many physical properties of water

    Training and Validation of a Liquid-Crystalline Phospholipid Bilayer Force Field

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    We present a united-atom model (gb-fb15) for the molecular dynamics simulation of hydrated liquid-crystalline dipalmitoylphosphatidylcholine (DPPC) phospholipid bilayers. This model was constructed through the parameter-space minimization of a regularized least-squares objective function via the ForceBalance method. The objective function was computed using a training set of experimental bilayer area per lipid and deuterium order parameter. This model was validated by comparison to experimental volume per lipid, X-ray scattering form factor, thermal area expansivity, area compressibility modulus, and lipid lateral diffusion coefficient. These comparisons demonstrate that gb-fb15 is robust to temperature variation and an improvement over the original model for both the training and validation properties

    Polarizable Molecular Simulations Reveal How Silicon-Containing Functional Groups Govern the Desalination Mechanism in Nanoporous Graphene

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    We report a molecular dynamics (MD) simulation study of reverse osmosis desalination using nanoporous monolayer graphene passivated by SiH<sub>2</sub> and Si­(OH)<sub>2</sub> functional groups. A highly accurate and detailed polarizable molecular mechanics force field model was developed for simulating graphene nanopores of various sizes and geometries. The simulated water fluxes and ion rejection percentages are explained using detailed atomistic mechanisms derived from analysis of the simulation trajectories. Our main findings are as follows: (1) The Si­(OH)<sub>2</sub> pores possess superior ion rejection rates due to selective electrostatic repulsion of Cl<sup>–</sup> ions, but Na<sup>+</sup> ions are attracted to the pore and block water transfer. (2) By contrast, the SiH<sub>2</sub> pores operate via a steric mechanism that excludes ions based on the size and flexibility of their hydration layers. (3) In the absence of ions, water flux is directly proportional to the solvent accessible area within the pore; however, simulated fluxes are lower than those inferred from recent experimental work. We also provide some hypotheses that could resolve the differences between simulation and experiment

    Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data

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    We introduce ForceBalance, a method and free software package for systematic force field optimization with the ability to parametrize a wide variety of functional forms using flexible combinations of reference data. We outline several important challenges in force field development and how they are addressed in ForceBalance, and present an example calculation where these methods are applied to develop a highly accurate polarizable water model. ForceBalance is available for free download at https://simtk.org/home/forcebalance

    Calculations of the Electric Fields in Liquid Solutions

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    The electric field created by a condensed-phase environment is a powerful and convenient descriptor for intermolecular interactions. Not only does it provide a unifying language to compare many different types of interactions, but it also possesses clear connections to experimental observables, such as vibrational Stark effects. We calculate here the electric fields experienced by a vibrational chromophore (the carbonyl group of acetophenone) in an array of solvents of diverse polarities using molecular dynamics simulations with the AMOEBA polarizable force field. The mean and variance of the calculated electric fields correlate well with solvent-induced frequency shifts and band broadening, suggesting Stark effects as the underlying mechanism of these key solution-phase spectral effects. Compared to fixed-charge and continuum models, AMOEBA was the only model examined that could describe nonpolar, polar, and hydrogen bonding environments in a consistent fashion. Nevertheless, we found that fixed-charge force fields and continuum models were able to replicate <i>some</i> results of the polarizable simulations accurately, allowing us to clearly identify which properties and situations require explicit polarization and/or atomistic representations to be modeled properly, and to identify for which properties and situations simpler models are sufficient. We also discuss the ramifications of these results for modeling electrostatics in complex environments, such as proteins

    What Can Density Functional Theory Tell Us about Artificial Catalytic Water Splitting?

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    Water splitting by artificial catalysts is a critical process in the production of hydrogen gas as an alternative fuel. In this paper, we examine the essential role of theoretical calculations, with particular focus on density functional theory (DFT), in understanding the water-splitting reaction on these catalysts. First, we present an overview of DFT thermochemical calculations on water-splitting catalysts, addressing how these calculations are adapted to condensed phases and room temperature. We show how DFT-derived chemical descriptors of reactivity can be surprisingly good estimators for reactive trends in water-splitting catalysts. Using this concept, we recover trends for bulk catalysts using simple model complexes for at least the first-row transition-metal oxides. Then, using the CoPi cobalt oxide catalyst as a case study, we examine the usefulness of simulation for predicting the kinetics of water splitting. We demonstrate that the appropriate treatment of solvent effects is critical for computing accurate redox potentials with DFT, which, in turn, determine the rate-limiting steps and electrochemical overpotentials. Finally, we examine the ability of DFT to predict mechanism, using ruthenium complexes as a focal point for discussion. Our discussion is intended to provide an overview of the current strengths and weaknesses of the state-of-the-art DFT methodologies for condensed-phase molecular simulation involving transition metals and also to guide future experiments and computations toward the understanding and development of novel water-splitting catalysts

    Tensor Hypercontraction Second-Order Møller–Plesset Perturbation Theory: Grid Optimization and Reaction Energies

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    We have recently introduced the tensor hypercontraction (THC) method for electronic structure, including MP2. Here, we present an algorithm for THC-MP2 that lowers the memory requirements as well as the prefactor while maintaining the formal quartic scaling that we demonstrated previously. We also describe a procedure to optimize quadrature grids used in grid-based least-squares (LS) THC-MP2. We apply this algorithm to generate grids for first-row atoms with less than 100 points/atom while incurring negligible errors in the computed energies. We benchmark the LS-THC-MP2 method using optimized grids for a wide variety of tests sets including conformational energies and reaction barriers in both the cc-pVDZ and cc-pVTZ basis sets. These tests demonstrate that the THC methodology is not limited to small basis sets and that it incurs negligible errors in both absolute and relative energies

    Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

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    The increasing availability of high-quality experimental data and first-principles calculations creates opportunities for developing more accurate empirical force fields for simulation of proteins. We developed the AMBER-FB15 protein force field by building a high-quality quantum chemical data set consisting of comprehensive potential energy scans and employing the ForceBalance software package for parameter optimization. The optimized potential surface allows for more significant thermodynamic fluctuations away from local minima. In validation studies where simulation results are compared to experimental measurements, AMBER-FB15 in combination with the updated TIP3P-FB water model predicts equilibrium properties with equivalent accuracy, and temperature dependent properties with significantly improved accuracy, in comparison with published models. We also discuss the effect of changing the protein force field and water model on the simulation results
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