Calculation of the Gibbs free energy of solvation and dissociation of HCl in water via Monte Carlo simulations and continuum solvation models.

The Gibbs free energy of solvation and dissociation of hydrogen chloride in water is calculated through a combined molecular simulation/quantum chemical approach at four temperatures between T = 300 and 450 K. The Gibbs free energy is first decomposed into the sum of two components: the Gibbs free energy of transfer of molecular HCl from the vapor to the aqueous liquid phase and the standard-state Gibbs free energy of acid dissociation of HCl in aqueous solution. The former quantity is calculated using Gibbs ensemble Monte Carlo simulations using either Kohn-Sham density functional theory or a molecular mechanics force field to determine the system's potential energy. The latter Gibbs free energy contribution is computed using a continuum solvation model utilizing either experimental reference data or micro-solvated clusters. The predicted combined solvation and dissociation Gibbs free energies agree very well with available experimental data.

Adenosine triphosphate hydrolysis mechanism in kinesin studied by combined quantum-mechanical/molecular-mechanical metadynamics simulations.

Kinesin is a molecular motor that hydrolyzes adenosine triphosphate (ATP) and moves along microtubules against load. While motility and atomic structures have been well-characterized for various members of the kinesin family, not much is known about ATP hydrolysis inside the active site. Here, we study ATP hydrolysis mechanisms in the kinesin-5 protein Eg5 by using combined quantum mechanics/molecular mechanics metadynamics simulations. Approximately 200 atoms at the catalytic site are treated by a dispersion-corrected density functional and, in total, 13 metadynamics simulations are performed with their cumulative time reaching ~0.7 ns. Using the converged runs, we compute free energy surfaces and obtain a few hydrolysis pathways. The pathway with the lowest free energy barrier involves a two-water chain and is initiated by the Pγ-Oß dissociation concerted with approach of the lytic water to PγO3-. This immediately induces a proton transfer from the lytic water to another water, which then gives a proton to the conserved Glu270. Later, the proton is transferred back from Glu270 to HPO(4)2- via another hydrogen-bonded chain. We find that the reaction is favorable when the salt bridge between Glu270 in switch II and Arg234 in switch I is transiently broken, which facilitates the ability of Glu270 to accept a proton. When ATP is placed in the ADP-bound conformation of Eg5, the ATP-Mg moiety is surrounded by many water molecules and Thr107 blocks the water chain, which together make the hydrolysis reaction less favorable. The observed two-water chain mechanisms are rather similar to those suggested in two other motors, myosin and F1-ATPase, raising the possibility of a common mechanism.

Re-examining the properties of the aqueous vapor-liquid interface using dispersion corrected density functional theory.

First-principles molecular dynamics simulations, in which the forces are computed from electronic structure calculations, have great potential to provide unique insight into structure, dynamics, electronic properties, and chemistry of interfacial systems that is not available from empirical force fields. The majority of current first-principles simulations are driven by forces derived from density functional theory with generalized gradient approximations to the exchange-correlation energy, which do not capture dispersion interactions. We have carried out first-principles molecular dynamics simulations of air-water interfaces employing a particular generalized gradient approximation to the exchange-correlation functional (BLYP), with and without empirical dispersion corrections. We assess the utility of the dispersion corrections by comparison of a variety of structural, dynamic, and thermodynamic properties of bulk and interfacial water with experimental data, as well as other first-principles and force field-based simulations.

Vapor-liquid coexistence curves for methanol and methane using dispersion-corrected density functional theory.

First principles Monte Carlo simulations in the Gibbs and isobaric-isothermal ensembles were performed to map the vapor-liquid coexistence curves of methanol and methane described by Kohn-Sham density functional theory using the Becke-Lee-Yang-Parr (BLYP) exchange and correlation functionals with the Grimme correction term for dispersive (D2) interactions. The simulations indicate that the BLYP-D2 description with the TZV2P basis set underpredicts the saturated vapor densities and overpredicts the saturated liquid densities and critical and boiling temperatures for both compounds. Although the deviations are quite large, these results present a significant improvement over the BLYP functional without the correction term, which misses the experimental results by a larger extent in the opposite direction. Simulations at one temperature indicate that use of the larger QZV3P basis set may lead to improved saturated vapor densities, but not to significant changes in the liquid density.

First principles Monte Carlo simulations of aggregation in the vapor phase of hydrogen fluoride.

The aggregation of hydrogen fluoride vapor is explored through the use of Monte Carlo simulations employing Kohn-Sham density functional theory with the exchange/correlation functional of Becke-Lee-Yang-Parr to describe the molecular interactions. Canonical ensemble simulations sampling the classical phase space were carried out for a system consisting of ten molecules at constant density (2700 A(3)/molecule) and at three different temperatures (T = 310, 350, and 390 K). Aggregation-volume-bias and configurational-bias Monte Carlo approaches (along with pre-sampling with an approximate potential) were employed to increase the sampling efficiency of cluster formation and destruction. A hydrogen-bond analysis shows that about two thirds of the HF molecules are part of small aggregates at 310 K, whereas only about 10% of the molecules are clustered at 390 K. As for other hydrogen-bonding systems, the size distribution exhibits some sensitivity to the criteria used to define a hydrogen bond, but the qualitative features are not affected by these differences. From the temperature dependence of the equilibrium constants, the dimer and trimer aggregation energies (not corrected for nuclear quantum effects) are estimated using a simple distance-based hydrogen-bonding criterion as -13 +/- 3 and -65 +/- 16 kJ mol(-1), respectively, whereas these binding energies are found to be somewhat different for a combined distance-angular criterion with values of -17 +/- 6 and -63 +/- 11 kJ mol(-1), respectively. The strictness of the hydrogen-bonding criterion plays a significant role for the assignment of clusters to linear, cyclic, and branched architectures with the fraction of the latter being drastically reduced for the distance-angular criterion. The average molecular dipole moment increases from 1.85 Debye for isolated molecules to about 2.0 D for dimers to about 2.75 D for larger aggregates, and the H-F bond length shows a concomitant, but smaller increase from about 0.94 to 0.98 A.

Structure and dynamics of the aqueous liquid-vapor interface: a comprehensive particle-based simulation study.

This research addresses a comprehensive particle-based simulation study of the structural, dynamic, and electronic properties of the liquid-vapor interface of water utilizing both ab initio (based on density functional theory) and empirical (fixed charge and polarizable) models. Numerous properties such as interfacial width, hydrogen bond populations, dipole moments, and correlation times will be characterized with identical schemes to draw useful conclusions on the strengths and weakness of the proposed models for interfacial water. Our findings indicate that all models considered in this study yield similar results for the radial distribution functions, hydrogen bond populations, and orientational relaxation times. Significant differences in the models appear when examining both the dipole moments and surface relaxation near the aqueous liquid-vapor interface. Here, the ab initio interaction potential predicts a significant decrease in the molecular dipole moment and expansion in the oxygen-oxygen distance as one approaches the interface in accordance with recent experiments. All classical polarizable interaction potentials show a less dramatic drop in the molecular dipole moment, and all empirical interaction potentials studied yield an oxygen-oxygen contraction as the interface is approached.