Binary phase behavior of select organosulfur compounds in supercritical carbon dioxide: A Monte Carlo molecular simulation study.

Pressure-composition binary phase diagrams were determined for methanethiol, dimethyl sulfide, thiophene, benzothiophene, or dibenzothiophene with carbon dioxide at temperatures from 363 to 453 K and pressures from 2 to 20 MPa. Utilizing Gibbs ensemble Monte Carlo molecular simulation, phase coexistence compositions were determined, along with the impact of 4% water cosolvent on select results. Solution structure as a function of pressure and temperature is characterized via radial distribution functions.

Monte Carlo molecular simulation of solution and surface-bound DNA hybridization of short oligomers at varying surface densities.

DNA microarrays utilize surface bound sequences to probe for target sequences in samples of interest, and density of surface coverage plays an important role in any duplex formation and subsequent detection. Here, Monte Carlo molecular simulations utilize a modified coarse-grained DNA model to calculate the impact of binding density and arrangement as well as temperature on duplex structure and hydrogen bonding patterns for two different undecamer sequences. Results indicate a modest, sequence-dependent increase in dissociation related to the proximity of neighboring duplexes but little impact on duplex structure or hydrogen bonding pattern.

Conformational analysis of 6α- and 6β-naltrexol and derivatives and relationship to opioid receptor affinity.

Naltrexol and its C₆ α and β desoxy, iodo, mesyl, tosyl, trifyl, dimethylcarbamyl, and diphenylcarbamyl derivatives were studied in their energy-minimized C ring chair-like and boat-like conformations using B3LYP/6-31G** and SM5.4/A to estimate aqueous solvation free energy. The results were compared to experimental opioid receptor binding affinities.

Effect of surface binding on heterogeneous DNA melting equilibria: a Monte Carlo simulation study.

Deoxyribonucleic acid (DNA) microarrays are constructed with a surface-immobilized single-stranded probe sequence that hydrogen bonds with its complementary target strand from solution and is subsequently detected, making their hybridization equilibrium of central importance. Unexpectedly, the effect of surface immobilization is that if the sequences of probe and target are exchanged, the hybridization equilibrium shifts. Here, configurational-bias Monte Carlo simulations using a coarse-grained model for DNA were carried out for an undecamer double helix both in solution and bound to a surface to determine dissociation equilibria.

Partial molar volume and solvation structure of naphthalene in supercritical carbon dioxide: a Monte Carlo simulation study.

Monte Carlo simulations were used to investigate the solvation of naphthalene in supercritical carbon dioxide at a temperature of 308.38 K just above the solvent's critical temperature and at pressures of 74.6, 79.

Transferable potentials for phase equilibria. 7. Primary, secondary, and tertiary amines, nitroalkanes and nitrobenzene, nitriles, amides, pyridine, and pyrimidine.

The transferable potentials for phase equilibria (TraPPE) force fields are extended to amine, nitro, nitrile, and amide functionalities and to pyridine and pyrimidine. In many cases, the same parameters for a functional group are used for both united-atom and explicit-hydrogen representations of alkyl tails. Following the TraPPE philosophy, the nonbonded interaction parameters were fitted to the vapor-liquid coexistence curves for selected one-component systems.

Effects of conformational distributions on sigma profiles in COSMO theories.

The charge density or sigma profile of a solute molecule is an essential component in COSMO (conductor-like screen model) based solvation theories, and its generation depends on the molecular conformation used. The usual procedure is to determine the conformation of an isolated molecule, and assume that this is unchanged when the molecule is placed in solution. In this paper, the conformations of 1-hexanol and 2-methoxy-ethanol in both the liquid and vapor phases obtained from Gibbs ensemble simulation and from an isolated-molecule quantum DFT optimization are used to determine the effect of realistic conformation differences on COSMO-based properties predictions.

Elucidating the vibrational spectra of hydrogen-bonded aggregates in solution: electronic structure calculations with implicit solvent and first-principles molecular dynamics simulations with explicit solvent for 1-hexanol in n-hexane.

Fourier transform infrared spectroscopy is a popular method for the experimental investigation of hydrogen-bonded aggregates, but linking spectral information to microscopic information on aggregate size distribution and aggregate architecture is an arduous task. Static electronic structure calculations with an implicit solvent model, Car-Parrinello molecular dynamics (CPMD) using the Becke-Lee-Yang-Parr (BLYP) exchange and correlation energy functionals and classical molecular dynamics simulations for the all-atom version of the optimized parameters for liquid simulations (OPLS-AA) force field were carried out for an ensemble of 1-hexanol aggregates solvated in n-hexane. The initial configurations for these calculations were size-selected from a distribution of aggregates obtained from a large-scale Monte Carlo simulation.

Aspects of glycosidic bond formation in aqueous solution: chemical bonding and the role of water.

A model of the specific acid-catalyzed glycosidic bond formation in liquid water at ambient conditions is studied based on constrained Car-Parrinello ab initio molecular dynamics. Specifically the reaction of alpha-D-glucopyranose and methanol is found to proceed by a D(N)A(N) mechanism. The D(N) step consists of a concerted protonation of the O(1) hydroxyl leaving group; this process results in the breaking of the C(1)-O(1) bond, and oxocarbenium ion formation involving C(1)=O(5).

Binary phase behavior and aggregation of dilute methanol in supercritical carbon dioxide: a Monte Carlo simulation study.

Configurational-bias Monte Carlo simulations in the Gibbs and isobaric-isothermal ensembles using the transferable potentials for phase equilibria force field were carried out to investigate the thermophysical properties of mixtures containing supercritical carbon dioxide and methanol. The binary vapor-liquid coexistence curves were calculated at 333.15 and 353.

Glycosidic bond formation in aqueous solution: on the oxocarbenium intermediate.

The mechanism of specific acid-catalyzed glycosidic bond formation between methanol and alpha-d-glucopyranoside in aqueous solution at 300 K was studied using Car-Parrinello molecular dynamics. The reaction was found to proceed through a non-solvent equilibrated oxocarbenium cation intermediate characterized by the loss of a hydrogen-bonding interaction between the ring oxygen and solvating water. The mechanism, which was found to be D(N)A(N) in nature, is discussed in detail.