Intra- and intermolecular effects on the Compton profile of the ionic liquid 1,3-dimethylimidazolium chloride.

We present a comprehensive simulation study on the solid-liquid phase transition of the ionic liquid 1,3-dimethylimidazolium chloride in terms of the changes in the atomic structure and their effect on the Compton profile. The structures were obtained by using ab initio molecular dynamics simulations. Chosen radial distribution functions of the liquid structure are presented and found generally to be in good agreement with previous ab initio molecular dynamics and neutron scattering studies. The main contributions to the predicted difference Compton profile are found to arise from intermolecular changes in the phase transition. This prediction can be used for interpreting future experiments.

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.

Understanding the solubility of triamino-trinitrobenzene in hydrous tetramethylammonium fluoride: a first principles molecular dynamics simulation study.

With the aim to understand the relatively high solubility of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), an important energetic material with a high degree of inter- and intra-molecular hydrogen bonding, in fluoride anion containing ionic liquids (ILs), first principles molecular dynamics simulations in the isobaric-isothermal ensemble were carried out for a system using hydrous tetramethylammonium fluoride as the prototypical solvent. Simulations initiated from both molecular TATB and its Meisenheimer complex (i.e., a σ-complex of the fluoride and the electrophilic ring of TATB) yield a Zundel-type complex where a proton is shared between an amino group and an F(-) ion, whereas the Meisenheimer complex is found to be only transiently stable. An analysis of the electronic structure probing the Wannier function centers supports the finding of a proton-sharing complex with a three-center four-electron like bond. The Zundel-type complex also yields an electronic absorption spectrum consistent with the experimentally observed color change. This study provides evidence that the remarkable solubility of otherwise hard-to-dissolve molecular crystals in ILs can be aided by chemical modification of the solute.

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.

Synthesis of glycine-containing complexes in impacts of comets on early Earth.

Delivery of prebiotic compounds to early Earth from an impacting comet is thought to be an unlikely mechanism for the origins of life because of unfavourable chemical conditions on the planet and the high heat from impact. In contrast, we find that impact-induced shock compression of cometary ices followed by expansion to ambient conditions can produce complexes that resemble the amino acid glycine. Our ab initio molecular dynamics simulations show that shock waves drive the synthesis of transient C-N bonded oligomers at extreme pressures and temperatures. On post impact quenching to lower pressures, the oligomers break apart to form a metastable glycine-containing complex. We show that impact from cometary ice could possibly yield amino acids by a synthetic route independent of the pre-existing atmospheric conditions and materials on the planet.

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.

Isobaric-isothermal molecular dynamics simulations utilizing density functional theory: an assessment of the structure and density of water at near-ambient conditions.

We present herein a comprehensive density functional theory study toward assessing the accuracy of two popular gradient-corrected exchange correlation functionals on the structure and density of liquid water at near ambient conditions in the isobaric-isothermal ensemble. Our results indicate that both PBE and BLYP functionals under predict the density and over structure the liquid. Adding the dispersion correction due to Grimme (1, 2) improves the predicted densities for both BLYP and PBE in a significant manner. Moreover, the addition of the dispersion correction for BLYP yields an oxygen-oxygen radial distribution function in excellent agreement with experiment. Thus, we conclude that one can obtain a very satisfactory model for water using BLYP and a correction for dispersion.

Ab initio simulation of the equation of state and kinetics of shocked water.

We report herein first principles simulations of water under shock loading and the chemical reactivity under these hot, compressed conditions. Using a recently developed simulation technique for shock compression, we observe that water achieves chemical equilibrium in less than 2 ps for all shock conditions studied. We make comparison to the experimental results for the Hugoniot pressure and density final states. Our simulations show that decomposition occurs through the reversible reaction H(2)O <--> H(+) + OH(-), in agreement with experiment. Near the approximate intersection of the Hugoniot and the Neptune isentrope, we observe high concentrations of charged species that contribute electronic states near the band gap.

Bulk and interfacial aqueous fluoride: an investigation via first principles molecular dynamics.

Using first principles molecular dynamics simulation, we have studied a fluoride anion embedded in a periodically replicated water slab composed of 215 water molecules to mimic both bulk and interfacial solvation. In contrast to some recent experiments, our findings suggest that there are only small structural changes for fluoride and its first solvation shell in the bulk. Moreover, the presence of fluoride does not significantly alter the rotational dynamics of nearby water. In addition, we have computed the molecular dipole moments using Wannier centers. At the interface, the presence of fluoride increases the molecular dipole moments of nearby water molecules, whereas in the bulk, the dipole moments for water appear to be essentially invariant to the presence of fluoride in the vicinity. Previous studies of the air-water interface have showed interfacial water to have higher average HOMO energies and, thus, likely to be more prone to electrophilic attack. With the addition of fluoride, the most likely reactive site for electrophilic reactions shifts to the anion. This finding could explain the known large increase in reaction rates for heterogeneous process of interest in atmospheric science. The reactive properties of other anions near the air-water interface are of general interest in heterogeneous chemistry and can be elucidated using a similar type of analysis, as performed here for the fluoride anion.

Ion spatial distributions at the liquid-vapor interface of aqueous potassium fluoride solutions.

X-Ray photoemission spectroscopy operating under ambient pressure conditions is used to probe ion distributions throughout the interfacial region of a free-flowing aqueous liquid micro-jet of 6 M potassium fluoride. Varying the energy of the ejected photoelectrons by carrying out experiments as a function of X-ray wavelength measures the composition of the aqueous-vapor interfacial region at various depths. The F(-) to K(+) atomic ratio is equal to unity throughout the interfacial region to a depth of 2 nm. The experimental ion profiles are compared with the results of a classical molecular dynamics simulation of a 6 M aqueous KF solution employing polarizable potentials. The experimental results are in qualitative agreement with the simulations when integrated over an exponentially decaying probe depth characteristic of an APPES experiment. First principles molecular dynamics simulations have been used to calculate the potential of mean force for moving a fluoride anion across the air-water interface. The results show that the fluoride anion is repelled from the interface, consistent with the depletion of F(-) at the interface revealed by the APPES experiment and polarizable force field-based molecular dynamics simulation. Together, the APPES and MD simulation data provide a detailed description of the aqueous-vapor interface of alkali fluoride systems. This work offers the first direct observation of the ion distribution at an aqueous potassium fluoride solution interface. The current experimental results are compared to those previously obtained for saturated solutions of KBr and KI to underscore the strong difference in surface propensity between soft/large and hard/small halide ions in aqueous solution.

Ultrafast transformation of graphite to diamond: an ab initio study of graphite under shock compression.

We report herein ab initio molecular dynamics simulations of graphite under shock compression in conjunction with the multiscale shock technique. Our simulations reveal that a novel short-lived layered diamond intermediate is formed within a few hundred of femtoseconds upon shock loading at a shock velocity of 12 kms (longitudinal stress>130 GPa), followed by formation of cubic diamond. The layered diamond state differs from the experimentally observed hexagonal diamond intermediate found at lower pressures and previous hydrostatic calculations in that a rapid buckling of the graphitic planes produces a mixture of hexagonal and cubic diamond (layered diamond). Direct calculation of the x-ray absorption spectra in our simulations reveals that the electronic structure of the final state closely resembles that of compressed cubic diamond.

Ab initio molecular dynamics study of the solvated OHCl- complex: implications for the atmospheric oxidation of chloride anion to molecular chlorine.

We have studied the OHCl(-) complex in a six-water cluster and in bulk liquid water by means of Born−Oppenheimer molecular dynamics based on generalized gradient-corrected BLYP density functional theory. Self-interaction-corrected results, which predict a hydrogen-bonded OH···Cl(-) complex, are compared to the uncorrected results, which predict a hemibonded (HO-Cl)(-). A second-order Møller−Plesset potential energy landscape of the gas-phase complex in its ground-state was computed to determine which of the two configurations represents the true nature of the complex. Because no evidence of a local minimum was found in the vicinity of the geometry corresponding to (HO-Cl)(-), we conclude that the self-interaction-corrected results are more accurate and, therefore, that the complex is held together by a hydrogen-bond-like interaction in both an asymmetric solvation environment, as represented by the cluster, and a symmetric solvation environment, as represented by the bulk system. We postulate that the mechanism that governs the atmospheric oxidation of Cl(-)(aq) to Cl(2)(g) on the surface of marine aerosols is initiated by the formation of a H-bonded OH···Cl(-) complex. Furthermore, because no evidence of charge transfer from Cl(-) to OH was found, in either the liquid or the cluster environment, we propose that the second step of the oxidation of Cl(-) is the reaction of the complex with a second Cl(-), resulting in the formation of the species Cl(2)(-) and OH(-). Cl(2)(g) could then be formed via an electron-transfer reaction with an impinging OH molecule.

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.

Evidence for alterations in circulating low-molecular-weight antioxidants and increased lipid peroxidation in smokers on hemodialysis.

BACKGROUND/AIM: Cardiovascular disease is the major cause of mortality in dialysis patients, accounting for about 40% of deaths in most large registries. Oxidative stress has been strongly implicated in the pathogenesis of these events. As end-stage renal disease is a state of elevated free radical activity, the aim of the present study was to investigate the negative impact of smoking in 57 male hemodialysis patients. METHODS: The patients, who were 20-85 years of age (mean age 51.0 +/- 14 years), had been on hemodialysis for at least 6 months before participating in this study. Fasting blood sampling for serum lipid, albumin, urate and lipophilic antioxidants such as tocopherols, carotenes, ascorbate and lipid peroxides was performed. RESULTS: The plasma malondialdehyde (MDA) concentration was significantly higher in hemodialysis patients who smoked compared to hemodialysis patients who were nonsmokers (1.92 +/- 0.52 vs. 1.59 +/- 0.42 nmol/ml, p = 0.006). No association was found between levels of MDA in smokers and parameters such as body mass index, serum cholesterol, serum triglycerides and smoking index. There were no significant differences in the plasma levels of uric acid, alpha-tocopherol, gamma-tocopherol, delta-tocopherol, alpha-carotene, beta-carotene and retinol between the two groups. A significantly lower level of plasma ascorbate was observed in hemodialysis patients who smoked compared to the nonsmoking hemodialysis patients or healthy controls (4.59 +/- 4.0 vs. 9.57 +/- 4.0 and 10.16 +/- 4.6 microg/ml, p < 0.05). Moreover, in smokers, the plasma levels of ascorbate were negatively correlated with the levels of plasma MDA (r = -0.43, p < 0.001) of each patient. Partial correlation analysis of the plasma levels of the measured antioxidants and the smoking index revealed a negative correlation between the plasma levels of lipid-normalized lycopene and the smoking index (r = -0.53, p < 0.05). CONCLUSION: Our data suggest that cigarette smoking further increases plasma-circulating products of lipid peroxidation, which are already increased in nonsmoking hemodialysis patients as compared to matched healthy controls. The lower plasma levels of ascorbate in hemodialysis patients who smoke suggest that these patients may be more susceptible to oxidative tissue damage caused by smoking.