A study of molecular vibrational relaxation mechanism in condensed phase based upon mixed quantum-classical molecular dynamics. II. Noncollisional mechanism for the relaxation of a polar solute in supercritical water

Mixed quantum-classical molecular dynamics method has been applied to vibrational relaxation of a hydrophilic model NO in supercritical water at various densities along an isotherm above the critical temperature. The relaxation rate was determined based on Fermi's golden rule at each state point and showed an inverse S-shaped curve as a function of bulk density. The hydration number was also calculated as a function of bulk density based on the calculated radial distribution function, which showed a good correlation with the relaxation rate. Change of the survival probability of the solute vibrational state was analyzed as a function of time together with the trajectory of the solvent water and the interaction with it. We will show that the solvent molecule resides near the solute molecule for a while and the solvent contributes to the relaxation by the random-noiselike Coulombic interaction only when it stays near the solute. After the solvent leaves the solute, it shows no contribution to the relaxation. The relaxation mechanism for this system is significantly different from the collisional one found for a nonpolar solute in nonpolar solvent in Paper I. Then, the relaxation rate is determined, on average, by the hydration number or local density of the solvent. Thus, the density dependence of the relaxation rate for the polar solute in supercritical water is apparently similar to that found for the nonpolar solute in nonpolar solvent, although the molecular process is quite different from each other.     

Umbrella sampling of solute vibrational line shifts in mixed quantum-classical molecular dynamics simulations

An umbrella sampling approach for vibrational frequency line shifts is presented. The technique allows for efficient sampling of the solvent configurations corresponding to frequency shifts of a solute in mixed quantum-classical simulations. The approach is generally applicable and can also be used within traditional perturbation theory calculations of frequency shifts. It is particularly useful in the extraction of detailed mechanistic information about the solute-solvent interactions giving rise to the frequency shifts. The method is illustrated by application to the simple I2 in a liquid Xe system, and the advantages are discussed.     

A comparative study of the properties of polar and nonpolar solvent/solute/polystyrene solutions in microwave fields via molecular dynamics

The influence of an applied microwave field on the dynamics of methylamine-dichloromethane (DCM) mixtures bound within atactic polystyrene (a-PS) over a range of polymer densities from 30 to 94 wt % polymer was examined using atomistic molecular dynamics simulations. This study is an extension of previous studies on methylamine transport in relatively polar polystyrene solutions of methanol and dimethylformamide [M. J. Purdue et al., J. Chem. Phys. 124, 204904 (2006)]. A direct comparison is made across the three types of polystyrene solutions. Consideration is given to both solvent and reagent transport within the polymer solutions under zero-field conditions and in an external electromagnetic field in the canonical ensemble (NVT) at 298.0 K. Various frequencies up to 10(4) GHz and a rms electric field intensity of 0.1 VA were applied. The simulation studies were validated by comparison of the simulated zero-field self-diffusion coefficients of DCM in a-PS with those obtained using pulsed-gradient spin-echo NMR spectrometry. Athermal effects of microwave fields on solute transport behavior within polymer solutions are discussed.     

A vibrational molecular force field of model compounds with biological interest. I. Harmonic dynamics of crystalline urea at 123 K

Normal coordinate calculations have been performed for urea and deuterated urea in the crystalline state. We have used the modified Urey–Bradley–Shimanouchi intramolecular potential energy function and a rather sophisticated intermolecular energy function to reproduce I.R. and Raman frequencies with an average error of 2 cm^–1. The general agreement between the calculation and experiment suggests that intermolecular interactions must be taken into account to determine reliable intramolecular parameters of the potential energy function, mainly the barrier to internal rotation around the C? N bond. The intermolecular energy function, which consists of the Buckingham function and an explicit harmonic function for hydrogen-bonding, then has the merit to reproduce quite well the observed frequencies of lattice vibrations.     

Dependence of diffusivity on density and solute diameter in liquid phase: a molecular dynamics study of Lennard-Jones system

Investigations into the variation of self-diffusivity with solute radius, density, and degree of disorder of the host medium is explored. The system consists of a binary mixture of a relatively smaller sized solute, whose size is varied and a larger sized solvent interacting via Lennard-Jones potential. Calculations have been performed at three different reduced densities of 0.7, 0.8, and 0.933. These simulations show that diffusivity exhibits a maximum for some intermediate size of the solute when the solute diameter is varied. The maximum is found at the same size of the solute at all densities which is at variance with the prediction of the levitation effect. In order to understand this anomaly, additional simulations were carried out in which the degree of disorder has been varied while keeping the density constant. The results show that the diffusivity maximum gradually disappears with increase in disorder. Disorder has been characterized by means of the minimal spanning tree. Simulations have also been carried out in which the degree of disorder is constant and only the density is altered. The results from these simulations show that the maximum in diffusivity now shifts to larger distances with decrease in density. This is in agreement with the changes in void and neck distribution with density of the host medium. These results are in excellent agreement with the predictions of the levitation effect. They suggest that the effect of disorder is to shift the maximum in diffusivity towards smaller solute radius while that of the decrease in density is to shift it towards larger solute radius. Thus, in real systems where the degree of disorder is lower at higher density and vice versa, the effect due to density and disorder have opposing influences. These are confirmed by the changes seen in the velocity autocorrelation function, self part of the intermediate scattering function and activation energy.     

A molecular dynamics study of chirality transfer: The impact of a chiral solute on an achiral solvent

A solvation shell may adapt to the presence of a chiral solute by becoming chiral. The extent of this chirality transfer and its dependence on the solute and solvent characteristics are explored in this article. Molecular dynamics simulations of solvated chiral analytes form the basis of the analysis. The chirality induced in the solvent is assessed based on a series of related chirality indexes originally proposed by Osipov [M. A. Osipov et al., Mol. Phys. 84, 1193 (1995)]. Two solvents are considered: Ethanol and benzyl alcohol. Ethanol provides insight into chirality transfer when the solvent interacts with the solute primarily by a hydrogen bond. Several ethanol models have been considered starting with a nonpolarizable model, progressing to a fluctuating charge model, and finally, to a fully polarizable model. This progression provides some insights into the importance of solvent polarizability in the transfer of chirality. Benzyl alcohol, by virtue of the aromatic ring, increases the number of potential solvent-solute interactions. Thus, with these two solvents, the issue of compatibility between the solvent and solute is also considered. The solvation of three chiral solutes is examined: Styrene oxide, acenaphthenol, and n-(1-(4-bromophenyl)ethyl)pivalamide (PAMD). All three solutes have the possibility of hydrogen bonding with the solvent, the last two may also form ring-ring interactions, and the last also has multiple hydrogen bonding sites. For PAMD, the impact of conformational averaging is examined by comparing the chirality transfer about rigid and flexible solutes.     

Preferential solvation of phenol in binary solvent mixtures. A molecular dynamics study

Molecular dynamics computer simulations were carried out to study the preferential solvation of phenol in equimolar acetonitrile-water and ethanol-water binary mixtures. Two water models were used to investigate the model dependence of preferential solvation. The results are compared to recent intermolecular 1H NOESY experiments reported on the same systems. In the case of acetonitrile-water the local mole fraction obtained from simulations agrees quite well with experiments. In the case of ethanol-water there was a qualitative difference, which was observed for both water models. However, when comparing the degree of preferential solvation of the two cosolvents ethanol and acetonitrile with each of the two water models, the trend obtained from the simulations agrees with experimental data.     

Intramolecular hydrogen bond, molecular structure and vibrational assignment of tetra-acetylethane. A density functional study

The intramolecular hydrogen bond, molecular structure and vibrational frequencies of tetra-acetylethane have been investigated by means of high-level density functional theory (DFT) methods with most popular basis sets. Fourier transform infrared and Fourier transform Raman spectra of this compound and its deuterated analogue were recorded in the regions 400-4000 cm(-1) and 40-4000 cm(-1), respectively. The calculated geometrical parameters of tetra-acetylethane were compared to the experimental results of this compound and its parent molecule (acetylacetone), obtained from X-ray diffraction. The O...O distance in tetra-acetylethane, about 2.424A, suggests that the hydrogen bond in this compound is stronger than acetylacetone. This conclusion is well supported by the NMR proton chemical shifts and O-H stretching mode at 2626 cm(-1). Furthermore, the calculated hydrogen bond energy in the title compound is 17.22 kcal/mol, which is greater than the acetylacetone value. On the other hand, the results of theoretical calculations show that the bulky substitution in alpha-position of acetylacetone results in an increase of the conjugation of pi electrons in the chelate ring. Finally, we applied the atoms in molecules (AIM) theory and natural bond orbital method (NBO) for detail analyzing the hydrogen bond in tetra-acetylethane and acetylacetone. These results are in agreement with the vibrational spectra interpretation and quantum chemical calculation results. Also, the conformations of methyl groups with respect to the plane of the molecule and with respect to each other were investigated.     

A molecular dynamics study on universal properties of polymer chains in different solvent qualities. Part I. A review of linear chain properties

This paper investigates the conformational and scaling properties of long linear polymer chains. These investigations are done with the aid of Monte Carlo (MC) and molecular dynamics (MD) simulations. Chain lengths that comprise several orders of magnitude to reduce errors of finite size scaling, including the effect of solvent quality, ranging from the athermal limit over the theta-transition to the collapsed state of chains are investigated. Also the effect of polydispersity on linear chains is included which is an important issue in the real fabrication of polymers. A detailed account of the hybrid MD and MC simulation model and the exploited numerical methods is given. Many results of chain properties in the extrapolated limit of infinite chain lengths are documented and universal properties of the chains within their universality class are given. An example of the difference between scaling exponents observed in actual solvents and those observed in the extremes of "good solvents" and "theta-solvents" in simulations is provided by comparing simulation results with experimental data on low density polyethylene. This paper is concluded with an outlook on the extension of this study to branched chain systems of many different branching types.     

A quantum equation of motion for chemical reaction systems on an adiabatic double-well potential surface in solution based on the framework of mixed quantum-classical molecular dynamics

We present a quantum equation of motion for chemical reaction systems on an adiabatic double-well potential surface in solution in the framework of mixed quantum-classical molecular dynamics, where the reactant and product states are explicitly defined by dividing the double-well potential into the reactant and product wells. The equation can describe quantum reaction processes such as tunneling and thermal excitation and relaxation assisted by the solvent. Fluctuations of the zero-point energy level, the height of the barrier, and the curvature of the well are all included in the equation. Here, the equation was combined with the surface hopping technique in order to describe the motion of the classical solvent. Applying the present method to model systems, we show two numerical examples in order to demonstrate the potential power of the present method. The first example is a proton transfer by tunneling where the high-energy product state was stabilized very rapidly by solvation. The second example shows a thermal activation mechanism, i.e., the initial vibrational excitation in the reactant well followed by the reacting transition above the barrier and the final vibrational relaxation in the product well.     

Structure and Energetics of model amphiphilic molecules at the water liquid-vapor interface. A molecular dynamics study

A molecular dynamics study of adsorption of p-n-pentylphenol at infinite dilution at the water liquid-vapor interface is reported. The calculated free energy of adsorption is -8.8 +/- 0.7 kcal/mol, in good agreement with the experimental value of -7.3 kcal/mol. The transition between the interfacial region and the bulk solution is sharp and well-defined by energetic, conformational, and orientational criteria. At the water surface, the phenol head group is mostly immersed in aqueous solvent. The most frequent orientation of the hydrocarbon tail is parallel to the interface, due to dispersion interactions with the water surface. This arrangement of the phenol ring and the alkyl chain requires that the chain exhibits a kink. As the polar head group is being moved into the solvent, the chain length increases and the tail becomes increasingly aligned toward the surface normal, such that the nonpolar part of the molecule exposed to water is minimized. The same effect was achieved when phenol was replaced by a more polar head group, phenolate. This result underscores the difference between hydrophobic hydration at the surface and in the bulk solvent, when nonpolar molecular fragments adopt compact conformations.     

Picosecond IR-UV pump-probe spectroscopic study of the dynamics of the vibrational relaxation of jet-cooled phenol. I. Intramolecular vibrational energy redistribution of the OH and CH stretching vibrations of bare phenol

The intramolecular vibrational energy redistribution (IVR) of the OH stretching vibration of jet-cooled phenol-h6 (C6H8OH) and phenol-d8 (C6D8OH) in the electronic ground state has been investigated by picosecond time-resolved IR-UV pump-probe spectroscopy. The OH stretching vibration of phenol was excited with a picosecond IR laser pulse, and the subsequent temporal evolutions of the initially excited level and the redistributed ones due to the IVR were observed by multiphoton ionization detection with a picosecond UV pulse. The IVR lifetime for the OH stretch vibration of phenol-h6 was determined to be 14 ps, while that of the OH stretch for phenol-d8 was found to be 80 ps. This remarkable change of the IVR rate constant upon the dueteration of the CH groups strongly suggests that the "doorway states" for the IVR from the OH level would be the vibrational states involving the CH stretching modes. We also investigated the IVR rate of the CH stretching vibration for phenol-h6. It was found that the IVR lifetime of the CH stretch is less than 5 ps. The fast IVR is described by the strong anharmonic resonance of the CH stretch with many other combinations or overtone bands.     

The structure of the hydrated electron. Part 2. A mixed quantum/classical molecular dynamics embedded cluster density functional theory: single-excitation configuration interaction study

Adiabatic mixed quantum/classical (MQC) molecular dynamics (MD) simulations were used to generate snapshots of the hydrated electron in liquid water at 300 K. Water cluster anions that include two complete solvation shells centered on the hydrated electron were extracted from the MQC MD simulations and embedded in a roughly 18 Ax18 Ax18 A matrix of fractional point charges designed to represent the rest of the solvent. Density functional theory (DFT) with the Becke-Lee-Yang-Parr functional and single-excitation configuration interaction (CIS) methods were then applied to these embedded clusters. The salient feature of these hybrid DFT(CIS)/MQC MD calculations is significant transfer (approximately 18%) of the excess electron's charge density into the 2p orbitals of oxygen atoms in OH groups forming the solvation cavity. We used the results of these calculations to examine the structure of the singly occupied and the lower unoccupied molecular orbitals, the density of states, the absorption spectra in the visible and ultraviolet, the hyperfine coupling (hfcc) tensors, and the infrared (IR) and Raman spectra of these embedded water cluster anions. The calculated hfcc tensors were used to compute electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) spectra for the hydrated electron that compared favorably to the experimental spectra of trapped electrons in alkaline ice. The calculated vibrational spectra of the hydrated electron are consistent with the red-shifted bending and stretching frequencies observed in resonance Raman experiments. In addition to reproducing the visible/near IR absorption spectrum, the hybrid DFT model also accounts for the hydrated electron's 190-nm absorption band in the ultraviolet. Thus, our study suggests that to explain several important experimentally observed properties of the hydrated electron, many-electron effects must be accounted for: one-electron models that do not allow for mixing of the excess electron density with the frontier orbitals of the first-shell solvent molecules cannot explain the observed magnetic, vibrational, and electronic properties of this species. Despite the need for multielectron effects to explain these important properties, the ensemble-averaged radial wavefunctions and energetics of the highest occupied and three lowest unoccupied orbitals of the hydrated electrons in our hybrid model are close to the s- and p-like states obtained in one-electron models. Thus, one-electron models can provide a remarkably good approximation to the multielectron picture of the hydrated electron for many applications; indeed, the two approaches appear to be complementary.     

Solubility of aminotriethylene glycol functionalized single wall carbon nanotubes: A density functional based tight binding molecular dynamics study

Pristine CNTs are exemplary hydrophobic solutes; properly functionalized CNTs can be seen as hydrophilic ones. The solubility of aminotriethylene glycol (ATG) functionalized single walled carbon nanotubes (fSWCNTs) were examined using density functional based tight binding method. According to the dynamics study, the ATG-fSWCNTs interaction energies (IE) and diffusion coefficients (D) are diameter dependent. As the diameter of the (n,0) tube is incrementally increased, a distinguishable pattern is observed, specifically the IE of the ATG-fSWCNT in water is quite higher for n that is an integral multiple of three (n = 9,12,15) while the D is lower due to its π bonding structures. In general, the metallic ATG functionalized nanotube possess a higher IE and a much lower D in aqueous media. © 2019 Wiley Periodicals, Inc.     

Mechanism of water exchange in aqueous uranyl(VI) ion. A density functional molecular dynamics study

Constrained Car-Parrinello molecular dynamics simulations and thermodynamic integration have been performed for an associative pathway of water exchange between aqueous [UO2(OH2)5]2+ and bulk water. The simulated free energy of activation for this process, 6.7 kcal mol(-1), is significantly lower than that computed for a purely dissociative mechanism, 10.8 kcal mol(-1). Because the transient hexahydrate is indicated to have no chemically significant lifetime, the exchange mechanism can be classified as associative interchange.     

A molecular dynamics computer simulation study of room-temperature ionic liquids. I. Equilibrium solvation structure and free energetics

Solvation in 1-ethyl-3-methylmidazolium chloride and in 1-ethyl-3-methylimidazolium hexafluorophosphate near equilibrium is investigated via molecular dynamics computer simulations with diatomic and benzenelike molecules employed as probe solutes. It is found that electrostriction plays an important role in both solvation structure and free energetics. The angular and radial distributions of cations and anions become more structured and their densities near the solute become enhanced as the solute charge separation grows. Due to the enhancement in structural rigidity induced by electrostriction, the force constant associated with solvent configuration fluctuations relevant to charge shift and transfer processes is also found to increase. The effective polarity and reorganization free energies of these ionic liquids are analyzed and compared with those of highly polar acetonitrile. Their screening behavior of electric charges is also investigated.     

Binding of pertechnetate to uranyl(VI) in aqueous solution. A density functional theory molecular dynamics study

According to constrained Car-Parrinello molecular dynamics simulations and thermodynamic integration, the free binding energy between uranyl hydrate and pertechnetate in aqueous solution is significantly lower than that between uranyl and nitrate, namely, by 1.7 kcal mol(-1). This is the first study of the differential binding of these two ligands to uranyl, which can have implications for the separability of uranium and technetium during the reprocessing of nuclear waste.     

Conformational equilibria of terminally blocked single amino acids at the water-hexane interface. A molecular dynamics study

The conformational equilibria of the acetyl and methyl amide terminally blocked L-alanine, L-leucine and L-glutamine amino acids are examined in vacuum, in bulk water, and at the water-hexane interface, using multi-nanosecond molecular dynamics simulations. The two-dimensional probability distribution functions of finding the peptides at different dihedral angles of the backbone, phi and psi, are calculated, and free energy differences between different conformational states are determined. All three peptides are interfacially active, i.e. tend to accumulate at the interface even though they are not amphiphilic. Conformational states stable in both gas phase and water are also stable in the interfacial environment. Their populations, however, cannot be simply predicted from the knowledge of conformational equilibria in the bulk phases, indicating that the interface exerts a unique effect on the peptides. Conformational preferences in the interfacial environment arise from the interplay between electrostatic and hydrophobic effects. As in an aqueous solution, electrostatic solute-solvent interactions lead to the stabilization of more polar peptide conformations. The hydrophobic effect is manifested at the interface by a tendency to segregate polar and nonpolar moieties of the solute into the aqueous and the hexane phases, respectively. For the terminally blocked glutamine, this favors conformations for which such a segregation is compatible with the formation of strong, backbone-side chain intramolecular hydrogen bonds on the hexane side of the interface. The influence of the hydrophobic effect can be also noted in the orientational preferences of the peptides at the interface. The terminally blocked leucine is oriented such that its nonpolar side chain is buried in hexane, whereas the polar side chain of glutamine is immersed in water. The free energies of rotating the peptides along the axis parallel to the interface by more than 90 degrees are substantial. This indicates that peptide folding at interfaces is strong by driven by the tendency to adopt amphiphilic structures.     

A theoretical study of the mechanism of selective fluorination of saturated hydrocarbons by molecular fluorine. Participation of CHCl3 solvent molecules in the ionic process

The fluorination reaction of methane and isobutane by molecular F(2) with and without CHCl(3) solvent was studied with the ab initio and ONIOM theoretical calculations. The electrophilic pathway for the RH + F(2) reaction in general is a two-step process, consisting of hydride abstraction leading to an intermediate of the type R(+)(delta)...HF...F(-)(delta), followed by complicated rearrangement to give the electrophilic substitution product, RF + HF. In the case of methane, the overall barrier for this reaction is too high for the reaction to take place under mild conditions even in the presence of CHCl(3) solvent molecules. In the case of isobutane without CHCl(3), the electrophilic pathway has a high rate-determining barrier of 25 kcal/mol, and is not likely to take place; the radical process forming t-Bu* + HF + F* may be preferred. However, the t-Bu(+)(delta)...HF...F(-)(delta) intermediate and, in particular, the transition state TS2 for rearrangement of the intermediate are highly ionic, and are stabilized dramatically when a few CHCl(3) solvent molecules form a solvation cage. The electrophilic reaction for isobutane + F(2) has a low overall barrier when at least three CHCl(3) molecules are present and can take place under mild conditions with full retention of configuration.