Mixed quantum-classical molecular dynamics analysis of the molecular-level mechanisms of vibrational frequency shifts

A detailed analysis of the origins of vibrational frequency shifts of diatomic molecules (I2 and ICl) in a rare gas (Xe) liquid is presented. Specifically, vibrationally adiabatic mixed quantum-classical molecular dynamics simulations are used to obtain the instantaneous frequency shifts and correlate the shifts to solvent configurations. With this approach, important mechanistic questions are addressed, including the following: How many solvent atoms determine the frequency shift? What solvent atom configurations lead to blue shifts, and which lead to red shifts? What is the effect of solute asymmetry? The mechanistic analysis can be generally applied and should be useful in understanding what information is provided by infrared and Raman spectra about the environment of the probed vibrational mode.     

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 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.     

A modified landau-teller model for vibrational relaxation of small molecular ions

We report a new interpretation of vibrational relaxation of molecular ions based on a modified Landau-Teller model. Distorted wave calculations show the relaxation to be dominated by repulsive forces. The ion-induced-dipole forces alter the steepness of the repulsive force and increase the effective collision energy. Incorporating these modifications into the Landau-Teller model correctly predicts the observed dependence of the cross sections on collision energy.     

A study of molecular vibrational relaxation mechanism in condensed phase based upon mixed quantum-classical molecular dynamics. I. A test of IBC model for the relaxation of a nonpolar solute in nonpolar solvent at high density

In order to investigate vibrational relaxation mechanism in condensed phase, a series of mixed quantum-classical molecular dynamics calculations have been executed for nonpolar solute in nonpolar solvent and polar solute in polar solvent. In the first paper (Paper I), relaxation mechanism of I2 in Ar, where Lennard-Jones force is predominant in the interaction, is investigated as a function of density and temperature, focusing our attention on the isolated binary collision (IBC) model. The model was originally established for the relaxation in gas phase. A key question, here, is "can we apply the IBC model to the relaxation in the high-density fluid?" Analyzing the trajectory of solvent molecule as well as its interaction with the solute, we found that collisions between them may be defined clearly even in the high-density fluid. Change of the survival probability of the vibrationally first excited state on collision was traced. The change caused by collisions with a particular solvent molecule was also traced together with the interaction between them. Each collision makes a contribution to the relaxation by a stepwise change in the probability. The analysis clearly shows that the relaxation is caused by collisions even in the high-density fluid. The difference between stepwise relaxation and the continuous one found for the total relaxation in the low-density fluid and in the high-density one, respectively, was clarified to come from just the difference in frequency of the collision. The stronger the intensity of the collision is, the greater the relaxation caused by the collision is. Further, the shorter the collision time is, the greater the resultant relaxation is. The discussion is followed by the succeeding paper (Paper II), where we report that molecular mechanism of the relaxation of a polar molecule in supercritical water is significantly different from that assumed in the IBC model despite that the density dependence of the relaxation rate showed a linear correlation with the local density of water around the solute, the linear correlation being apparently in good accordance with the IBC model. The puzzle will be solved in Paper II.     

Supercritical ammonia: a molecular dynamics simulation and vibrational spectroscopic investigation

Combining infrared spectroscopy and molecular dynamics simulations, we have investigated the structural and dynamical properties of ammonia from liquid state (T = 220 and 303 K) up to the supercritical domain along the isotherm T = 423 K. Infrared spectra show that the N-H stretching and bending modes are significantly perturbed which is interpreted as a signature of the change of the local environment. In order to compare the experimental spectra with those obtained using molecular dynamics simulation, we have used a flexible four sites model which allows to take into account the anharmonicity in all the vibration modes particularly that of the inversion mode of the molecule. A good agreement between our experimental and calculated spectra has been obtained hence validating the intermolecular potential used in this study to simulate supercritical ammonia. The detailed analysis of the molecular dynamics simulation results provides a quantitative insight of the relative importance of hydrogen bonding versus nonhydrogen bonded interactions that governs the structure of fluid ammonia.     

Solvation of calcium ions in methanol-water mixtures: molecular dynamics simulation

Molecular dynamics simulations of CaCl2 solutions in water and methanol-water mixtures, with methanol concentrations of 5, 10, 50, and 90 mol %, at room temperature, have been performed. The methanol and water molecules have been modeled as flexible three-site bodies. Solvation of the calcium ions has been discussed on the basis of the radial and angular distribution functions, the orientation of the solvent molecules, and their geometrical arrangement in the coordination shells. Analysis of the H-bonds of the solvent molecules coordinated by Ca2+ has been done. Residence time of the solvent molecules in the coordination shell has been calculated. The preferential hydration of the calcium ions has been found over the whole range of the mixture composition. The water concentration in the first and second coordination shells of Ca2+ significantly exceeds the water content in the solution, despite the very similar interaction energy of the calcium ion with water and methanol. In aqueous solution and methanol-water mixtures, the first coordination shell of Ca2+ is irregular and long-living. The solvent molecules prefer the anti-dipole arrangement, but, in aqueous solutions and water-rich mixtures, the water molecules in the primary shell have only one H-bonded neighbor.     

Sampling the proton transfer reaction coordinate in mixed quantum-classical molecular dynamics simulations

An umbrella sampling approach based on the vibrational energy gap is presented and examined for exploring the reaction coordinate for a proton transfer (PT) reaction. The technique exploits the fact that for a PT reaction the energy gap between the vibrational ground and excited states of the transferring proton reaches a minimum at the transition state. Umbrella sampling is used within mixed quantum-classical simulations to identify the transition state configurations and explore the reaction free energy curve and vibrationally nonadiabatic coupling. The method is illustrated by application to a model phenol-amine proton transfer reaction complex in a nanoconfined solvent. The results from this new umbrella sampling approach are consistent with those obtained from previous umbrella sampling calculations based on a collective solvent coordinate. This sampling approach further provides insight into the vibrationally nonadiabatic coupling for the proton transfer reaction and has potential for simulating vibrational spectra of PT reaction complexes in solution.     

Applications of quantum-classical and quantum-stochastic molecular dynamics simulations for proton transfer processes

Quantum-classical and quantum-stochastic molecular dynamics models (QCMD/QSMD) are formulated and applied to describe proton transfer processes in three model systems - the proton bound ammonia-ammonia dimer in an external electrostatic field; malonaldehyde, which undergoes a quantum tautomeric rearrangement; and phospholipase A₂, an enzyme which induces a water dissociation process in its active site followed by proton hopping to a histidine imidazole ring. The proton dynamics are described by the time-dependent Schrödinger equation. The dynamics of the classical atoms are described using classical molecular dynamics. Coupling between the quantum proton (s) and the classical atoms is accomplished via conventional or extended Hellmann-Feynman forces, as well as the time-dependence of the potential energy function in the Schrödinger equation. The interaction of the system with its environment is described by stochastic forces. Possible extensions of the models as well as future applications in molecular structure and dynamics analysis will be briefly discussed.     

DNA strand break: structural and electrostatic properties studied by molecular dynamics simulation

Due to their lethal consequences and a relatively high probability of introduction of repair errors and mutations, single and double strand breaks are among the most important and dangerous DNA lesions. However, the mechanisms of their recognition and repair processes are only poorly known at present. This work defines and analyzes a DNA with single strand break as a template study for future complex analyses of biologically serious double strand break damage and its enzymatic repair mechanisms. Besides a non-damaged DNA serving as a reference system with no surprising results, system with open valences of the atoms at the strand break ends as well as a system with filled valences were simulated. In both cases during the first few nanoseconds the broken ends of strand breaks are significantly exposed to the outside of the molecule. However, with increasing time, the system with single strand break with open valences is partially disrupted. On the contrary, the system with filled valences shows stable conformation with newly created hydrogen bond between the two strand break endings. Moreover, these endings are steadily situated in the inner part of the molecule, thus making the recognition and docking process of a repair enzyme more complicated in the case of filled valences.     

Dielectric relaxation in water–cholesterol mixture cluster: molecular dynamics simulation

Molecular dynamics (MD) studies of the cluster composed of cholesterol (C₂₇H₄₅OH) and water molecules are presented. We have investigated several dynamical quantities of cholesterol as a function of its concentration in the mixture cluster and the temperature. The main attention was focused on the temperature and concentration dependence of the calculated total dipole moment autocorrelation function and dielectric loss of the cluster.     

Effect of ions on the vibrational relaxation of liquid water

We study the relaxation of the O-H stretch vibration of water in aqueous salt solutions using femtosecond two-color pump-probe spectroscopy. The vibrational lifetimes are measured for a series of salts consisting of the anions Cl(-), Br(-), and I(-) and the cations Li(+), Na(+), and Mg(2+), for a range of concentrations from 0.5 M up to 6 M (chloride salts), 9 M (bromide salts), and 10 M (iodide salts). In addition to the previously found dependence of the vibrational lifetime on the nature of the anion, the lifetime is found to depend on concentration and is observed to show a small but significant dependence on the nature of the cation. We present a model in which all the effects of ions on the vibrational relaxaton of liquid water are accounted for.     

New all-atom force field for molecular dynamics simulation of an AlPO(4)-34 molecular sieve

A force field of the triclinic framework of AlPO(4)-34, important in methanol-hydrocarbon conversion reactions, was developed using an empirical potential function. Molecular dynamics simulation of an AlPO(4)-34 triclinic framework segment of 1216 atoms, containing the template molecules isopropylamine and water, was performed with explicit consideration of atomic charges. The average RMS difference between instantaneous positions of the framework atoms during 1 ns simulation and their positions in the structure determined from single crystal X-ray diffraction was calculated, and the average structure of the flexible framework was determined. The computed Debye-Waller factors and simulated FTIR spectra are in good agreement with the experimental data. The new force field permits detailed molecular dynamics simulations of flexible, charged aluminophosphate molecular sieves which should lead to a better understanding of the catalytic processes and the crucial role played by templating molecules.     

Microviscosity effects on the vibrational relaxation rates in molecular liquids

The isotropic Raman band of the CO stretching mode of the N,N-dimethylformamide (DMF) molecule has been studied as a function of solvents' hydrodynamic properties. The effect of solvent viscosity on linewidth (Γ_iso) has been studied in detail, particularly using the theory of microviscosity. Modifications have been made in the ƒ(ϱ, η, n) parameter which relates the vibrational relaxation rate with viscosity, density and dispersion energy on the basis of microviscosity.     

Sulfur dioxide in water: structure and dynamics studied by an ab initio quantum mechanical charge field molecular dynamics simulation

An ab initio Quantum Mechanical Charge Field Molecular Dynamics Simulation (QMCF MD) was performed to investigate structure and dynamics behavior of hydrated sulfur dioxide (SO(2)) at the Hartree-Fock level of theory employing Dunning DZP basis sets for solute and solvent molecules. The intramolecular structural characteristics of SO(2), such as S═O bond lengths and O═S═O bond angle, are in good agreement with the data available from a number of different experiments. The structural features of the hydrated SO(2) were primarily evaluated in the form of S-O(wat) and O(SO(2))-H(wat) radial distribution functions (RDFs) which gave mean distances of 2.9 and 2.2 ?, respectively. The dynamical behavior characterizes the solute molecule to have structure making properties in aqueous solution or water aerosols, where the hydrated SO(2) can easily get oxidized to form a number of sulfur(VI) species, which are believed to play an important role in the atmospheric processes.     

Direct dynamics study of ultrafast vibrational energy relaxation in ice Ih

Car-Parrinello molecular dynamics (CPMD) and a previously developed wave packet model are used to study ultrafast relaxation in water clusters. Water clusters of 15 water molecules are used to represent ice Ih. The relaxation is studied by exciting a symmetric or an asymmetric stretch mode of the central water molecule. The CPMD results suggest that relaxation occurs within 100 fs. This is in agreement with experimental work by Woutersen and Bakker and the earlier wave packet calculations. The CPMD results further indicate that the excitation energy is transferred both intramolecularly and intermolecularly on roughly the same time scale. The intramolecular energy transfer occurs predominantly between the symmetric and asymmetric modes while the bend mode is largely left unexcited on the short time scale studied here.