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.

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.

The development of synthetic biology: a patent analysis.

In the past decades, synthetic biology has gained interest regarding research and development efforts within the biotechnology domain. However, it is unclear to what extent synthetic biology has matured already into being commercially exploitable. By means of a patent analysis, this study shows that there is an increasing trend regarding synthetic biology related patent applications.

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.

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.

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.

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.

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.

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.

The diagnostic reliability of sexual sadism.

Previous studies have reported low diagnostic agreement on the paraphilias, especially sexual sadism. In the present study, 34 evaluators throughout the United States reviewed summaries of 12 committed sex offenders. The evaluators agreed more than 90% of the time on whether offenders met criteria for any paraphilia in general and sexual sadism in particular.

Diagnostic and risk profiles of men detained under Wisconsin's sexually violent person law.

Previous studies described the characteristics of individuals committed under sexual offender civil commitment laws in Arizona, Florida, and Washington. This study describes the diagnostic and risk profiles of 331 sexual offenders held under Wisconsin's sexual offender statute and compares them to the people held in those other states. Persons detained under Wisconsin's law substantially differ from those in the other states.

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.

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.

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.

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.

Influence of shunt surgery on healthcare expenditures of elderly fee-for-service Medicare beneficiaries with hydrocephalus.

Object: The goal in this study was to determine the percentage of patients with hydrocephalus who were treated with shunt surgery and to assess Medicare expenditures for those with and without shunt surgery.

Methods: Retrospective cost analyses were performed using the Standard Analytic Files of paid claims for beneficiaries enrolled in both Parts A (Inpatient) and B (Outpatient) of the Medicare program for 1997 through 2001. The main outcome measures were 5-year total payments and 5-year payments for separate types of service; for example, acute hospital (inpatient and outpatient), skilled nursing facility, home health, and physician/supplier services.

Effectiveness of sex offender treatment for psychopathic sexual offenders.

Meta-analyses have suggested that sexual offender treatment (SOT) completion is associated with lowered sexual recidivism rates for convicted sexual offenders. The paucity of properly designed studies allows for the alternative explanation of less recidivism among treated samples as reflecting that lower risk offenders disproportionately self-select into treatment. A test of the "self-selection explanation" can occur by investigating treatment effect on known high-risk offenders.

Structure of an accurate ab initio model of the aqueous Cl- ion at high temperatures.

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.

What do we know about the effect of aging on recidivism risk for sexual offenders?

Meta-analytic and multiple sample study findings indicate there is an overall inverse relationship between sexual offenders' age at the time of their release from incarceration and their sexual recidivism risk (Hanson, 2002; Hanson & Bussière, 1998). Very recent studies, however, document limits to the generalizability of that finding. This article attempts to integrate the new empirical results into a coherent picture concerning the relationship between aging and recidivism risk for sexual offenders.

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.

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.

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.

Toward a multidimensional model for sexual recidivism risk.

The paradigm underlying current sexual offender recidivism risk assessment procedures conceptualizes such risk in a linear fashion, ranging on a single continuum from 0% to 100%. Each risk and protective characteristic thought of relevance in an evaluation is used as an indicator of increased or decreased risk, respectively, along that same continuum. This conceptualization of risk was useful as a starting place for the application of empirically supported risk and protective factors.