Publications by authors named "Douglas Doren"

Density functional theory electronic structure calculations were used to explore the mechanism for the Diels-Alder reaction between 2,5-dimethylfuran and maleic anhydride (MA). Reaction paths are reported for uncatalyzed and Lewis and Brønsted acid-catalyzed reactions in vacuum and in a broad range of solvents. The calculations show that, while the uncatalyzed Diels-Alder reaction is thermally feasible in vacuum, a Lewis acid (modeled as Na(+)) lowers the activation barrier by interacting with the dienophile (MA) and decreasing the HOMO-LUMO gap of the reactants.

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The structures and thermochemistry of molecular clusters containing sulfuric acid, water, ammonia, and/or dimethylamine ((CH3)2NH or DMA) are explored using a combination of Monte Carlo configuration sampling, semiempirical calculations, and density functional theory (DFT) calculations. Clusters are of the general form [(BH(+))n(HSO4(-))n(H2O)y], where B = NH3 or DMA, 2 ≤ n ≤ 8, and 0 ≤ y ≤ 10. Cluster formulas are written based on the computed structures, which uniformly show proton transfer from each sulfuric acid molecule to a base molecule while the water molecules remain un-ionized.

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The structures of positively and negatively charged clusters of sulfuric acid with ammonia and/or dimethylamine ((CH(3))(2)NH or DMA) are investigated using a combination of Monte Carlo configuration sampling, semiempirical calculations, and density functional theory (DFT) calculations. Positively charged clusters of the formula [(NH(4)(+))(x)(HSO(4)(-))(y)](+), where x = y + 1, are studied for 1 ≤ y ≤ 10. These clusters exhibit strong cation-anion interactions, with no contribution to the hydrogen-bonding network from the bisulfate ion protons.

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This report describes a detailed structural, electronic, and catalytic characterization of zinc gallium oxonitride photocatalysts with a spinel crystal structure. The bandgap decreases to less than 3 eV with increasing nitrogen content (<3 wt%) and these photocatalysts are active in visible light (λ>420 nm) for the degradation of cresol and rhodamine B. Density functional theory calculations show that this bandgap reduction is in part associated with hybridization between the dopant N 2p states and Zn 3d orbitals at the top of the valence band.

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The performances of several two-step scoring approaches for molecular docking were assessed for their ability to predict binding geometries and free energies. Two new scoring functions designed for "step 2 discrimination" were proposed and compared to our CHARMM implementation of the linear interaction energy (LIE) approach using the Generalized-Born with Molecular Volume (GBMV) implicit solvation model. A scoring function S1 was proposed by considering only "interacting" ligand atoms as the "effective size" of the ligand and extended to an empirical regression-based pair potential S2.

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Tautomerization of amino acids between the neutral form (NF) and the zwitterionic form (ZW) in water has been extensively studied, often using glycine as a model to understand this fundamental process. In spite of many advanced studies, the tautomerization reaction remains poorly understood because of the intrinsic complexities of the system, including multiple accessible reaction pathways, charge transfer, and variations of solvation structure. To establish an accurate model that can be used for molecular dynamics simulations, a ReaxFF reactive force field has been developed for glycine.

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To enable large-scale reactive dynamic simulations of copper oxide/water and copper ion/water interactions we have extended the ReaxFF reactive force field framework to Cu/O/H interactions. To this end, we employed a multistage force field development strategy, where the initial training set (containing metal/metal oxide/metal hydroxide condensed phase data and [Cu(H(2)O)(n)](2+) cluster structures and energies) is augmented by single-point quantum mechanices (QM) energies from [Cu(H(2)O)(n)](2+) clusters abstracted from a ReaxFF molecular dynamics simulation. This provides a convenient strategy to both enrich the training set and to validate the final force field.

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Copper ions play crucial roles in many enzymatic and aqueous processes. A critical analysis of the fundamental properties of copper complexes is essential to understand their impact on a wide range of chemical interactions. However the study of copper complexes is complicated by the presence of strong polarization and charge transfer effects, multiple oxidation states, and quantum effects like Jahn-Teller distortions.

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The structure of an accurate ab initio model of aqueous sodium ion was calculated at two high temperature state points (573 K, 0.72 g/cm(3) and 723 K, 0.0098 g/cm(3)) by a two-step procedure.

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Statistical error distributions for enthalpies of formation as predicted by 18 different density functionals have been analyzed using a test set of 675 molecules. Systematic errors, dependent on the number of valence electrons, have been identified for some functionals. A simple empirical correction makes a significant improvement in the prediction error for these single functionals.

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The potential of mean force (PMF) of sodium chloride in water has been calculated by using the ab initio classical free-energy perturbation method at five state points: at 973 K with densities of 0.2796, 0.0935, and 0.

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Hybrid density functional theory/molecular mechanics (DFT/MM) methods have been used to investigate the effects of vanadium substitution in ETS-10. Models have been developed to contain varying concentrations of V(IV) and V(V) within the O-M-O (M = Ti, V) chain. Most of the V-substituted models have a localized mid-gap state.

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The structure of an accurate ab initio model of aqueous chloride ion was calculated at two high-temperature state points (573 K, 0.725 g/cm(3) and 723 K, 0.0098 g/cm(3)) by a two-step procedure.

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Hybrid DFT/MM methods have been used to investigate the electronic and geometric properties of the microporous titanosilicate ETS-10. A comparison of finite length and periodic models demonstrates that band gap energies for ETS-10 can be well represented with relatively small cluster models. Optimization of finite clusters leads to different local geometries for bulk and end sites, where the local bulk TiO6 geometry is in good agreement with recent experimental results.

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Neural networks can be used generate potential energy hypersurfaces by fitting to a data set of energies at discrete geometries, as might be obtained from ab initio calculations. Prior work has shown that this method can generate accurate fits in complex systems of several dimensions. The present paper explores fundamental properties of neural network potential representations in some simple prototypes of one, two, and three dimensions.

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An efficient approach is described for using accurate ab initio calculations to determine the rates of elementary condensation and evaporation processes that lead to nucleation of aqueous aerosols. The feasibility of the method is demonstrated in an application to evaporation rates of water dimer at 230 K. The method, known as ABC-FEP (ab initio/classical free energy perturbation), begins with a calculation of the potential of mean force for the dissociation (evaporation) of small water clusters using a molecular dynamics (MD) simulation with a model potential.

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[CpCr(mu-Cl)Cl](2) reacted with dioxygen (O(2)) to produce CpCr(O)Cl(2) (1), which has been structurally characterized. Although 1 oxidized PPh(3) and 1,4-cyclohexadiene catalytically, it did not epoxidize olefins. DFT calculations have been performed on the system to characterize the potential energy surface for the epoxidation of ethylene and, in particular, the consequences of the crossing from the doublet surface of the starting materials to the quartet surface of the product (i.

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