DFT Study of Solvent Effects in Acid-Catalyzed Diels-Alder Cycloadditions of 2,5-Dimethylfuran and Maleic Anhydride.

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. A Brønsted acid (modeled as a proton) can bind to a carbonyl oxygen in MA, changing the reaction mechanism from concerted to stepwise and eliminating the activation barrier. Solvation effects were studied with the SMD model. Electrostatic effects play the largest role in determining the solvation energy of the transition state, which tracks the net dipole moment at the transition state. For the uncatalyzed reaction, the dipole moment is largely determined by charge transfer between the reactants, but in the reactions with ionic catalysts, there is no simple relationship between solvation of the transition state and charge transfer between the reactants. Nonelectrostatic contributions to solvation of the reactants and transition state also make significant contributions to the activation energy.

Formation and growth of molecular clusters containing sulfuric acid, water, ammonia, and dimethylamine.

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. Cluster formation is energetically favorable, owing to strong electrostatic attraction among the ions. Water has a minor effect on the energetics of cluster formation, lowering the free energy of formation by ∼ 10% depending on the cluster size and number of water molecules. Cluster growth (addition of one base molecule and one sulfuric acid molecule to a pre-existing cluster) and base substitution (substituting DMA for ammonia) are also energetically favorable processes for both anhydrous and hydrated clusters. However, the effect of water is different for different bases. Hydrated ammonium bisulfate clusters have a more favorable free energy for growth (i.e., incrementing n with fixed y) than anhydrous clusters, while the reverse is observed for dimethylammonium bisulfate clusters, where the free energy for growth is more favorable for anhydrous clusters. The substitution of DMA for ammonia in bisulfate clusters is favorable but exhibits a complex water dependence. Base substitution in smaller bisulfate clusters is enhanced by the presence of water, while base substitution in larger bisulfate clusters is less favorable for hydrated clusters than that for anhydrous clusters. While DMA substitution can stabilize small clusters containing one or a few sulfuric acid molecules, the free energy advantage of forming amine clusters relative to ammonia clusters becomes less pronounced at larger sizes, especially when the effect of water is considered.

Structure and energetics of nanometer size clusters of sulfuric acid with ammonia and dimethylamine.

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. A similar hydrogen-bonding network is found for the [(DMAH(+))(5)(HSO(4)(-))(4)](-) cluster. Negatively charged clusters derived from the reaction of DMA with [(H(2)SO(4))(3)(NH(4)(+))(HSO(4)(-))(2)](-) are also studied, up to the fully reacted cluster [(DMAH(+))(4)(HSO(4)(-))(5)](-). These clusters exhibit anion-anion and ion-molecule interactions in addition to cation-anion interactions. While the hydrogen-bonding network is extensive for both positively and negatively charged clusters, the binding energies of ions and molecules in these clusters are determined mostly by electrostatic interactions. The thermodynamics of amine substitution is explored and compared to experimental thermodynamic and kinetic data. Ammonia binds more strongly than DMA to sulfuric acid due to its greater participation in hydrogen bonding and its ability to form a more compact structure that increases electrostatic attraction between oppositely charged ions. However, the greater gas-phase basicity of DMA is sufficient to overcome the stronger binding of ammonia, making substitution of DMA for ammonia thermodynamically favorable. For small clusters of both polarities, substitutions of surface ammonium ions are facile. As the cluster size increases, an ammonium ion becomes encapsulated in the center of the cluster, making it inaccessible to substitution.

Structure analysis and photocatalytic properties of spinel zinc gallium oxonitrides.

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. X-ray photoelectron measurements indicate that nitrogen is indeed interacting with the oxide precursor through the formation of both nitride- and oxonitride-type species. The incorporation of nitrogen reduces the uniformity of the local structure of the spinel Zn-Ga-O-N (ZGON) species, as reflected in X-ray absorption spectra and Raman measurements relative to zinc gallate, which suggests the presence of defects. The oxonitrides exhibit faster photocatalytic rates of reaction than the oxide precursor. The degradation mechanisms were determined to be via the attack by hydroxyl radicals and holes for rhodamine B and cresol, respectively. Addition of Pt as a co-catalyst increased the rate of photodegradation, a result attributed to better charge separation.

Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy.

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. The S1 and S2 scoring schemes were trained and 5-fold cross-validated on a diverse set of 259 protein-ligand complexes from the Ligand Protein Database (LPDB). The regression-based parameters for S1 and S2 also demonstrated reasonable transferability in the CSARdock 2010 benchmark using a new data set (NRC HiQ) of diverse protein-ligand complexes. The ability of the scoring functions to accurately predict ligand geometry was evaluated by calculating the discriminative power (DP) of the scoring functions to identify native poses. The parameters for the LIE scoring function with the optimal discriminative power (DP) for geometry (step 1 discrimination) were found to be very similar to the best-fit parameters for binding free energy over a large number of protein-ligand complexes (step 2 discrimination). Reasonable performance of the scoring functions in enrichment of active compounds in four different protein target classes established that the parameters for S1 and S2 provided reasonable accuracy and transferability. Additional analysis was performed to definitively separate scoring function performance from molecular weight effects. This analysis included the prediction of ligand binding efficiencies for a subset of the CSARdock NRC HiQ data set where the number of ligand heavy atoms ranged from 17 to 35. This range of ligand heavy atoms is where improved accuracy of predicted ligand efficiencies is most relevant to real-world drug design efforts.

Development of a ReaxFF reactive force field for glycine and application to solvent effect and tautomerization.

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. A training set for the ReaxFF hydrocarbon potential was augmented with several glycine conformers and glycine-water complexes. The force field parameters were optimized to reproduce the quantum mechanically derived energies of the species in the training set. The optimized potential could accurately describe the properties of gas-phase glycine. It was applied to investigate the effect of solvation on the conformational distribution of glycine. Molecular dynamics simulations indicated significant differences in the dominant conformers in the gas phase and in water. This suggests that the tautomerization of glycine occurs through a conformational isomerization followed by the proton transfer event. The direct reaction mechanism of the NF → ZW proton transfer reaction in water, as well as mechanisms mediated by one or two water molecules, were investigated using molecular dynamics simulations. The results suggest that the proton transfer reaction is most likely mediated by a single water molecule. The ReaxFF potential developed in this work provides an accurate description of proton transfer in glycine and thus provides a useful methodology for simulating proton transfer reactions in organic molecules in the aqueous environment.

Development and validation of a ReaxFF reactive force field for Cu cation/water interactions and copper metal/metal oxide/metal hydroxide condensed phases.

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. To further validate the force field description we performed molecular dynamics simulations on Cu(2+)/water systems. We found good agreement between our results and earlier experimental and QM-based molecular dynamics work for the average Cu/water coordination, Jahn-Teller distortion, and inversion in [Cu(H(2)O)(6)](2+) clusters and first- and second-shell O-Cu-O angular distributions, indicating that this force field gives a satisfactory description of the Cu-cation/water interactions. We believe that this force field provides a computationally convenient method for studying the solution and surface chemistry of metal cations and metal oxides and, as such, has applications for studying protein/metal cation complexes, pH-dependent crystal growth/dissolution, and surface catalysis.

Development of a ReaxFF reactive force field for aqueous chloride and copper chloride.

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. These complications make the experimental observations difficult to interpret. In order to provide a computationally inexpensive yet reliable method for simulation of aqueous-phase copper chemistry, ReaxFF reactive force field parameters have been developed. The force field parameters have been trained against a large set of DFT-derived energies for condensed-phase copper-chloride clusters as well as chloride/water and copper-chloride/water clusters sampled from molecular dynamics (MD) simulations. The parameters were optimized by iteratively training them against configurations generated from ReaxFF MD simulations that are performed multiple times with improved sets of parameters. This cycle was repeated until the ReaxFF results were in accordance with the DFT-derived values. We have performed MD simulations on chloride/water and copper-chloride/water systems to validate the optimized force field. The structural properties of the chloride/water system are in accord with previous experimental and computational studies. The properties of copper-chloride/water agreed with the experimental observations including evidence of the Jahn-Teller distortion. The results of this study demonstrate the applicability of ReaxFF for the precise characterization of aqueous copper chloride. This force field provides a base for the design of a computationally inexpensive tool for the investigation of various properties and functions of metal ions in industrial, environmental, and biological environments.

Polyfunctional methodology for improved DFT thermochemical predictions.

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. Linear combinations of enthalpy estimates from different density functionals are identified that exploit the error correlations among the functionals and allow for further improvements in the accuracy of thermodynamic predictions. A good compromise between accuracy and computational efforts is achieved by the BLUE (best linear unbiased estimator) combination of three functionals, B3LYP, BLYP, and VSXC (polyfunctional 3 or PF3). The PF3 method has a mean absolute deviation (MAD) from experiment of 2.4 kcal/mol on the G3 set of 271 molecules. This can be compared to the MAD of 4.9 kcal/mol for B3LYP and 1.2 kcal/mol for the more costly G3 method. On the larger set of 675 molecules, the MAD for PF3 is 3.0 kcal/mol. Opportunities for further improvements in the accuracy of this method are discussed.

Structure of an accurate ab initio model of the aqueous Na+ ion at high temperatures.

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. First, the structure of an approximate model (the TIP4-FQ model for water and Na-H2O interactions from Liu et al.) was calculated from a molecular dynamics simulation of the model. Then the difference between the structure of the ab initio model and the approximate model was calculated by non-Boltzmann weighting of a sample of 500 configurations taken from the approximate model simulation. Radial distribution functions, average coordination numbers, the distribution of coordination numbers, and an analysis of orientations of water in the first coordination shell are reported for both state points. The average oxygen coordination number (calculated up to the inflection point in the running coordination number) was 4.71 at 573 K and 3.48 at 723 K. Most configurations have four or five coordinated waters at 573 K and three or four at 723 K. At 723 K, waters with their dipole moments pointed at the sodium ion were most common. A wider variety of orientations was found at 573 K and higher density. The difference in structure between the approximate and quantum models was small but significant.

Sodium chloride in supercritical water as a function of density: potentials of mean force and an equation for the dissociation constant from 723 to 1073 K and from 0 to 0.9 g/cm(3).

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 0.0101 g/cm (3) and at 723 K with densities of 0.0897 and 0.0098 g/cm (3). The method is based on a QM-MM model in which Na-H 2O, Cl-H 2O, and Na-Cl interactions are calculated by ab initio methods. The water-water interactions are from the polarizable TIP4P-FQ model. The logarithm of the dissociation constant (log K c) has been calculated from the PMF. These predictions, together with experimental measurements, were used to derive an equation for log K c at densities from 0 to 0.9 g/cm (3) and temperatures from 723 to 1073 K, as well as from 600 to 1073 K for densities from 0.29 g/cm (3) to 0.9 g/cm (3). Extrapolation of the present equation below 723 K for densities less than 0.29 g/cm (3) does not fit the experimental results. This is attributed to long-range changes in the local dielectric constant due to the high compressibility. Comparisons with previous predictions and simulations are presented.

A visible light photocatalyst: effects of vanadium substitution on ETS-10.

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. The occupation of this localized state depends upon the dopant oxidation state, leading to the addition of multiple low energy transitions. A linear correlation has been identified between band gap energies estimated using ground state orbital energies and those calculated using the more accurate and computationally demanding time-dependent DFT (TDDFT) method for a variety of transition metal substituted models of ETS-10. Consistent with experimental data for V substitution, our models predict a decrease in the optical band gap with increasing [V], due to a lowering of the delocalized d-orbital states at the bottom of the conduction band with increasing V d-orbital character. This effect is more pronounced in the case of V(V) substitution than V(IV). Excitation energies for the V-doped models, calculated with TDDFT methods correlate well with experimental data, allowing for the assignment of specific optical transitions to experimental UV-Vis spectra. The electronic structure of V-substituted ETS-10 at high V concentration demonstrates band gap energies within the visible range of the spectrum. Additionally, at high [V] the band gap energy and presence of low energy electron traps can be controlled by the relative concentration of V(IV) and V(V) along the O-M-O chain, establishing V-substituted ETS-10 as a promising visible light photocatalyst.

Electronic and geometric properties of ETS-10: QM/MM studies of cluster models.

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. Geometry optimizations reveal that any asymmetry within the axial O-Ti-O chain is negligible. The band gap in the optimized model corresponds to a O(2p) --> Tibulk(3d) transition. The results suggest that the three Ti atom, single chain, symmetric, finite cluster is an effective model for the geometric and electronic properties of bulk and end TiO6 groups in ETS-10.

Neural Network Models of Potential Energy Surfaces: Prototypical Examples.

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. Optimal fits to the data are achieved by adjusting the network parameters using an extended Kalman filtering algorithm, which is described in detail. The examples provide insight into the relationships between the form of the function being fit, the amount of data needed for an adequate fit, and the optimal network configuration and number of neurons needed. The quality of the network interpolation is substantially improved if gradients as well as the energy are available for fitting. The fitting algorithm is effective in providing an accurate interpolation of the underlying potential function even when random noise is added to the data used in the fit.

Free energy perturbation study of water dimer dissociation kinetics.

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. The free energy perturbation is used to calculate how changing from the model potential to a potential calculated from ab initio methods would alter the potential of mean force. The difference in free energy is the Boltzmann-weighted average of the difference between the ab initio and classical potential energies, with the average taken over a sample of configurations from the MD simulation. In principle, the method does not require a highly accurate model potential, though more accurate potentials require fewer configurations to achieve a small sampling error in the free energy perturbation step. To test the feasibility of obtaining accurate potentials of mean force from ab initio calculations at a modest number of configurations, the free energy perturbation method has been used to correct the errors when some standard models for bulk water (SPC, TIP4P, and TIP4PFQ) are applied to water dimer. To allow a thorough exploration of sampling issues, a highly accurate fit to results of accurate ab initio calculations, known as SAPT-5s, as been used a proxy for the ab initio calculations. It is shown that accurate values for a point on the potential of mean force can be obtained from any of the water models using ab initio calculations at only 50 configurations. Thus, this method allows accurate simulations of small clusters without the need to develop water models specifically for clusters.

Spin surface crossing in chromium-mediated olefin epoxidation with O(2).

[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.e. a chromium(III) epoxide adduct). These calculations suggested that "spin-blocking" was not a significant problem and that the reaction of CpCr(O)Cl(2) (3) with ethylene should have a lower activation barrier. On the basis of this computational prediction, 3 was prepared; it was found to epoxidize olefins stoichiometrically.