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The (super 17)O NMR parameters of an amorphous calcium aluminisilicate (CAS) is computed from first-principles. The atomic coordinates of a CAS glass of composition (CaO)0.21(Al2O3)0.12(SiO2)0.67 were obtained by quenching a liquid to room temperature by the means of ab initio molecular-dynamics simulations of the Car-Parrinello type.

A study was conducted to investigate the isothermal-isobaric molecular dynamics methods in system subject to holonomic constraints with the goal of devising equations of motion in which the scaling is performed on atomic positions. The result demonstrates that the Kneller-Mulders equations generate an isothermal-isobaric ensemble distribution only for systems with nonzero total force.

The different methods to calculate the accurate vibrational energy relaxation rates for high-frequency modes from classical molecular dynamics simulations are presented. The features and advantages of Fermi's golden rule, a convenient starting point for calculating the vibrational energy relaxation rate constants, are discussed.

A study was conducted to examine the structural and thermodynamic properties of a water droplet enclosed in a spherical cavity embedded in a hydrophobic material. The results indicate that the structure of water near an impenetrable and purely repulsive surface at standard conditions of temperature and pressure is described as a dry, separated state.

A study was conducted to investigate the thermodynamic and structural properties of a Lennard-Jones liquid at a state very close to the triple point as the radius of a hard sphere solute is varied. The result reveals that the oscillatory profiles arise for small, molecular sized radii, where as for large radii smooth interfaces with a drying layer of low vapor density near the solute are seen.

The numerical calculations of the concentration of interstitials in hard-sphere crystals are presented. In a three-dimensional fcc hard-sphere crystal at the melting pint, the concentration of interstitials is 2.7(4) x 10(super -8).

The various important issues related to the implementation of the nonadiabatic dynamics methods in the situation, where quasi-nonavoided crossings take place and play a crucial role in determining the dynamics, are presented. The important connection between dynamics, local environmental symmetry, and electronic structure in determining nonadiabatic relaxation is discussed.

The method of ab initio molecular dynamics was used to study the structural, dynamical, and electronic properties of ionic defects in liquid ammonia at 260 K created by the addition or removal of a proton. The result reveals that the NH4(super +) exhibits a characteristic cationic solvation pattern, in which it donates four hydrogen bonds to neighboring ammonia molecules, giving it a coordination number of 4.

The molecular dynamics simulations performed at constant temperature and pressure to explore ethanolamines pure components and in aqueous solutions are presented. The excess molar volume is slightly overestimated in diethanolamine (DEA) at all concentrations and in methyldiethanolamine (MDEA) at low concentrations of ethanolamine.

Ab initio molecular dynamics simulations are employed to study the structural and proton transport properties of methanol-water mixtures. Structural characteristics analyzed at two different methanol mole fractions reveal enhanced structuring of water as the methanol mole fraction increases in agreement with recent neutron diffraction experiments.

Adiabatic free-energy dynamics (AFED) are used to generate the Ramachandran free-energy surfaces of the alanine di- and tripeptides in a vacuum and in solution using the CHARMM22 force field. It was found that the AFED method could be a powerful tool for studying multidimensional free-energy surfaces in complex systems.

An ab initio molecular dynamics (MD) study, of concentration effects in an aqueous KOH solution, was conducted to investigate the effect of concentration on a directly measurable quantity named infrared (IR) spectrum, as well as on the proton transport mechanism. The result reveals the mechanisms are due to the mobility of both K(super +) and OD(super -) at higher concentration.

Issues concerning the use of high-speed computers to study microscopic details of chemical processes are presented. The Newtonian or Hamiltonian and the Liouvelle approach are reviewed.

A study was conducted to analyze the structure of linear water wires supporting an excess proton using ab initio path integral molecular dynamics. Electron exchange and correlation were characterized at the generalized gradient approximation level. An equilibrium tetramer complex was utilized to carry out the capped water experiment. Experimental results indicated that nuclear quantum effects support a minor role in small linear clusters.

When only equilibrium thermodynamics or averages of position-dependent functions in classical molecular dynamics calculations are sought, the choice of the atomic masses in the Hamiltonian becomes irrelevant. Consequently, the masses can be used as free parameters to help improve conformational sampling efficiency in the spirit of Bennett's mass-tensor dynamics (Bennett C. H. J. Comput. Phys. 1975 , 19 , 267.). Here we report on the effect of reducing side-chain and solvent masses on the folding behavior of a 9-residue hairpin-forming peptide in solution. A physical motivation for reducing the solvent mass is an effective reduction in solvent viscosity. Side-chain mass scaling is motivated by the idea of solvent potentials of mean force which are employed in select coarse-grained protein models. In the limit of very large mass differences, the mass reduction effectively creates an adiabatic decoupling between solvent, side-chain, and backbone motions, so that both the backbone and side chains move on the instantaneous solvent potential of mean force (PMF) surface, and the backbone additionally moves on the side-chain PMF. Because of the arbitrariness in the choice of masses, this limit only needs to be reached approximately in practice. In particular, we show that a 10-fold reduction in solvent masses and a side-chain mass scale that is intermediate between the scaled solvent and the backbone lead to a quantitative enhancement in conformational sampling. [ABSTRACT FROM AUTHOR]

A range of techniques including physical property measurements, neutron scattering experiments, ab initio molecular dynamics, and classical molecular dynamics simulations are used to probe the structural, thermodynamic, and transport properties of a deep eutectic solvent comprised of a 1:2 molar ratio of choline chloride and ethylene glycol. This mixture, known as Ethaline, has many desirable properties for use in a range of applications, and therefore, understanding its liquid structure and transport properties is of interest. Simulation results are able to capture experimental densities, diffusivities, viscosities, and structure factors extremely well. The solvation environment is dynamic and dominated by different hydrogen bonding interactions. Dynamic heterogeneities resulting from hydrogen bonding interactions are quantified. Rotational dynamics of molecular dipole moments of choline and ethylene glycol are computed and found to exhibit a fast and slow mode.

Free energy surfaces of chemical and physical systems are often generated using a popular class of enhanced sampling methods that target a set of collective variables (CVs) chosen to distinguish the characteristic features of these surfaces. While some of these approaches are typically limited to low (∼1-3)-dimensional CV subspaces, methods such as driven adiabatic free-energy dynamics/temperature-accelerated molecular dynamics have been shown to be capable of generating free energy surfaces of quite high dimension by sampling the associated marginal probability distribution via full sweeps over the CV landscape. These approaches repeatedly visit conformational basins, producing a scattering of points within the basins on each visit. Consequently, they are particularly amenable to synergistic combination with regression machine learning methods for filling in the surfaces between the sampled points and for providing a compact and continuous (or semicontinuous) representation of the surfaces that can be easily stored and used for further computation of observable properties. Given the central role of machine learning techniques in this combined approach, it is timely to provide a detailed comparison of the performance of different machine learning strategies and models, including neural networks, kernel ridge regression, support vector machines, and weighted neighbor schemes, for their ability to learn these high-dimensional surfaces as a function of the amount of sampled training data and, once trained, to subsequently generate accurate ensemble averages corresponding to observable properties of the systems. In this article, we perform such a comparison on a set of oligopeptides, in both gas and aqueous phases, corresponding to CV spaces of 2-10 dimensions and assess their ability to provide a global representation of the free energy surfaces and to generate accurate ensemble averages.

The properties of the hydroperoxide anion, HOO(-), in water play a key role in many biological systems and industrial processes. However the dynamics of HOO(-) and its solvation shell are largely unknown. We have undertaken an ab initio molecular dynamics study of aqueous HOO(-) at ambient temperature in liquid water. Two solvation structures for the hydroperoxide anion account for 90% or more of the configurations in a 25 ps NVT run at 300 K: these have four hydrogen bond donors to the terminal oxygen atom of HOO(-) and either one or two hydrogen bond donors to its middle oxygen atom. The H of HOO(-) is essentially always a donor in an H-bond to a water molecule. Two structures with three donors to the terminal O and either one or two at the middle O are also important. A set of five NVE runs totaling 74 ps found considerable variability in the proportions of time spent in each type of solvation pattern. Mean lifetimes of these patterns ranged from 54 to 109 fs, after which the complexes were observed to transform into different, sometimes less favorable structures. Analysis of the electronic structure associated with different solvation patterns indicates that a traditional Lewis-type picture of hydrogen bonding at the middle oxygen and non-Lewis behavior at the terminal oxygen coexist in aqueous HOO(-). The non-Lewis character of the terminal oxygen is compared to similar observations of the oxygen in the hydrated hydroxide ion from previous ab initio molecular dynamics of OH(-)(aq).

The quality of classical biomolecular simulations is inevitably limited by two problems: the accuracy of the force field used and the comprehensiveness of configuration space sampling. In this work we tackle the sampling problem by carrying out driven adiabatic free energy dynamics to obtain converged free energy surfaces of dipeptides in the gas phase and in solution using selected dihedral angles as collective variables. To calculate populations of conformational macrostates observed in experiment, we introduce a fuzzy clustering algorithm in collective-variable space, which delineates macrostates without prior definition of arbitrary boundaries. With this approach, we calculate the conformational preferences of small peptides with six biomolecular force fields chosen from among the most recent and widely used. We assess the accuracy of each force field against recently published Raman or IR-UV spectroscopy measurements of conformer populations for the dipeptides in solution or in the gas phase.

We have computed the (17)O NMR parameters of an amorphous calcium aluminosilicate (CAS) from first-principles. The atomic coordinates of a CAS glass of composition (CaO)(0.21)(Al(2)O (3))(0.12)(SiO (2))(0.67) were obtained by quenching a liquid to room temperature by the means of ab initio molecular-dynamics simulations of the Car-Parrinello type. The structure of the glass is found to be overall in good agreement with diffraction experiments. Some excess nonbridging O (NBO) atoms are found and are compensated by tricluster O atoms, i.e., by 3-fold coordinated O atoms to 4-fold coordinated Al or Si atoms. The glass coordinates were used to compute the (17)O NMR parameters using GGA-DFT and a correction of the Ca 3d orbital energy. The chemical shifts and the electric field gradients were obtained with the gauge including projector augmented-wave (GIPAW) and the projector augmented-wave (PAW) methods, respectively. The simulated 2D-3QMAS NMR spectrum of the CAS glass is in very good agreement with the available experimental data, notably because it takes into account the disorder present in the glass. This agreement further validates our CAS glass model. We show that the oxygen triclusters are not visible in a 2D-3QMAS NMR (17)O spectrum since their NMR parameters overlap with those of the Al-O-Si, Si-O-Si, or Al-O-Al sites. Finally, correlations between the structural characteristics and the values of the NMR parameters are extracted from the calculation with the aim of helping the interpretation of NMR spectra of glasses of similar compositions.