Isomerization and dissociation dynamics of HCN in a picosecond infrared laser field: a full-dimensional classical study

We report a full-dimensional study of the classical dynamics of HCN-->HNC isomerization and of HCN rovibrational dissociation driven by a strong but nonionizing picosecond infrared laser field. The dynamics of the isolated molecule and of the molecule in liquid Ar have both been studied. Our theoretical and numerical results show that when all degrees of freedom are accounted for the field induced molecular dynamics can be totally different from what was found in previous studies, where the HCN molecule is restricted to a plane containing the external field. It is shown that as HCN is driven by an infrared laser field, the rotation of the H atom around the C-N bond provides an important and highly efficient energy absorption mechanism. In the presence of a monochromatic picosecond infrared laser field with an intensity of 10(13) W/cm(2), this energy absorption mechanism generates considerable HCN-->HNC isomerization yield or high rovibrational dissociation yield without molecular preorientation or prealignment. Our study of the field induced isomerization and dissociation dynamics of the same system in liquid Ar shows that the picosecond isomerization dynamics is insignificantly affected by the surrounding atomic liquid whereas the dissociation yield may be greatly suppressed in a high density liquid. The implications of this study for full-dimensional quantum dynamics of multiphoton rovibrational excitation and dissociation of triatomics are briefly discussed.     

Isomerization reaction dynamics and equilibrium at the liquid-vapor interface of water. A molecular-dynamics study

The gauche-trans isomerization reaction of 1,2-dichloroethane at the liquid-vapor interface of water is studied using molecular-dynamics computer simulations. The solvent bulk and surface effects on the torsional potential of mean force and on barrier recrossing dynamics are computed. The isomerization reaction involves a large change in the electric dipole moment, and as a result the trans/gauche ratio is considerably affected by the transition from the bulk solvent to the surface. Reactive flux correlation function calculations of the reaction rate reveal that deviation from the transition-state theory due to barrier recrossing is greater at the surface than in the bulk water. This suggests that the system exhibits non-Rice-Ramsperger-Kassel-Marcus behavior due to the weak solvent-solute coupling at the water liquid-vapor interface.     

Computation of density of perfluoroalkyl methacrylates: a molecular modeling approach

Molecular dynamics simulations have been carried out on different perfluoroalkyl methacrylates to predict their densities. Density calculations on selected perfluoroalkyl methacrylates have been performed using molecular dynamics in the NPT ensemble by employing COMPASS force field. The calculated density values compared quite well with the experimental data reported in the literature.     

Insight into the role of hydration on protein dynamics

The potential energy surface of a protein is rough. This intrinsic energetic roughness affects diffusion, and hence the kinetics. The dynamics of a system undergoing Brownian motion on this surface in an implicit continuum solvent simulation can be tuned via the frictional drag or collision frequency to be comparable to that of experiments or explicit solvent simulations. We show that the kinetic rate constant for a local rotational isomerization in stochastic simulations with continuum solvent and a collision frequency of 2 ps(-1) is about 10(4) times faster than that in explicit water and experiments. A further increase in the collision frequency to 60 ps(-1) slows down the dynamics, but does not fully compensate for the lack of explicit water. We also show that the addition of explicit water does not only slow down the dynamics by increasing the frictional drag, but also increases the local energetic roughness of the energy landscape by as much as 1.0 kcal/mol.     

Application of Fokker-Planck-Kramers equation treatment for short-time dynamics of diffusion-controlled reaction in supercritical Lennard-Jones fluids over a wide density range

The validity of a Fokker-Planck-Kramers equation (FPKE) treatment of the rate of diffusion-controlled reaction at short times [K. Ibuki and M. Ueno, J. Chem. Phys. 119, 7054 (2003)] is tested in a supercritical Lennard-Jones fluid over a wide density range by comparing it with the Langevin dynamics and molecular dynamics simulations and other theories. The density n range studied is 0.323n(c)< or =n< or =2.58n(c) and the temperature 1.52T(c), where n(c) and T(c) are the critical density and temperature, respectively. For the rate of bimolecular reactions, the transition between the collision-limited and diffusion-limited regimes is expected to take place in this density range. The simulations show that the rate constant decays with time extensively at high densities, and that the magnitude of decay decreases gradually with decreasing density. The decay profiles of the rate constants obtained by the simulations are reproduced reasonably well by the FPKE treatment in the whole density range studied if a continuous velocity distribution is used in solving the FPKE approximately. If a discontinuous velocity distribution is used instead of the continuous one, the FPKE treatment leads to a rate constant much larger than the simulation results at medium and low densities. The rate constants calculated from the Smoluchowski-Collins-Kimball (SCK) theory based on the diffusion equation are somewhat smaller than the simulation results in medium and low densities when the intrinsic rate constant is chosen to adjust the steady state rate constant in the low density limit to that derived by the kinetic collision theory. The discrepancy is relatively small, so that the SCK theory provides a useful guideline for a qualitative discussion of the density effect on the rate constant.     

Tumbling dynamics of individual absorbed polymer chains in shear flow

The tumbling dynamics of individual absorbed polymer chains in shear flow is studied by employing multi-particle collision dynamics simulation techniques combined with molecular dynamics simulations.We find that the dependence of tumbling frequencies on shear rate is independent of both adsorption strength and surface corrugate.     

Assessing group-based cutoffs and the Ewald method for electrostatic interactions in clusters and in saturated,superheated, and supersaturated vapor phases of dipolar molecules

Monte Carlo simulations in the canonical, isobaric-isothermal, grand canonical, and Gibbs ensembles were used to assess whether the computationally expensive Ewald summation method for the computation of the first-order electrostatic energy can be replaced with a simpler truncation approach for accurate simulations of the saturated, superheated, and supersaturated vapor phases of dipolar and hydrogen-bonding molecules. Rotationally averaged hydrogen fluoride dimer and trimer energies, thermophysical properties and aggregation in the superheated vapor phase of hydrogen fluoride, nucleation free energy barriers for water, and the vapor–liquid coexistence properties of hydrogen fluoride and water were investigated over a wide range of state points. We find that for densities not too close to the critical density, results obtained from simulations using a spherical potential truncation based on neutral groups (molecules or fragments) for the Coulomb interactions are statistically identical to those obtained using the Ewald summation method. Use of the simpler spherical truncation results in a significant reduction of the computational effort for simulations employing molecular mechanics force fields and also allows for straightforward implementation of many-body expansion methods to compute the potential energy from electronic structure calculations of subsystems of the entire vapor-phase system.     

Femtosecond study on the isomerization dynamics of NK88. I. Ground-state dynamics after photoexcitation

Recently, optimal control of a photoisomerization reaction in the liquid phase was demonstrated for the first time on the system 3,3(')-diethyl-2,2(')-thiacyanine (NK88). Additionally, the class of cyanines to which the molecule NK88 belongs draws a lot of attention in different recent theoretical publications. Therefore, a better understanding of the molecular dynamics of this molecular system is of special interest. Experiments using the femtosecond pump-supercontinuum probe technique with an excitation wavelength of 400 nm and a spectral range from 370 to 620 nm for the probe beam have been performed. In order to analyze the dynamics properly the time window has been chosen to comprise the characteristic times of the contributing processes, additionally we have employed two solvents, methanol and ethylene glycol, and have conducted anisotropy measurements. The spectroscopic data have been assigned to different molecular states with the help of density functional theory and second-order Moller-Plesset perturbation theory calculations. The analysis of the data has revealed in the most likely model that three different isomers exist with different lifetimes. On the basis of experimental and theoretical data, a conclusive scheme of the isomerization reaction is presented.     

Elucidating the vibrational spectra of hydrogen-bonded aggregates in solution: electronic structure calculations with implicit solvent and first-principles molecular dynamics simulations with explicit solvent for 1-hexanol in n-hexane

Fourier transform infrared spectroscopy is a popular method for the experimental investigation of hydrogen-bonded aggregates, but linking spectral information to microscopic information on aggregate size distribution and aggregate architecture is an arduous task. Static electronic structure calculations with an implicit solvent model, Car-Parrinello molecular dynamics (CPMD) using the Becke-Lee-Yang-Parr (BLYP) exchange and correlation energy functionals and classical molecular dynamics simulations for the all-atom version of the optimized parameters for liquid simulations (OPLS-AA) force field were carried out for an ensemble of 1-hexanol aggregates solvated in n-hexane. The initial configurations for these calculations were size-selected from a distribution of aggregates obtained from a large-scale Monte Carlo simulation. The vibrational spectra computed from the static electronic structure calculations for monomers and dimers and from the CPMD simulations for aggregates up to pentamers demonstrate the extent of the contribution of dangling or nondonating hydroxyl groups found in linear and branched aggregates to the "monomeric" peak. Furthermore, the computed spectra show that there is no simple relationship between peak shift and aggregate size nor architecture, but the effect of hydrogen-bond cooperativity is shown to differentiate polymer-like (cooperative) and dimer-like (noncooperative) hydrogen bonds in the vibrational spectrum. In contrast to the static electronic structure calculations and the CPMD simulations, the classical molecular dynamics simulations greatly underestimate the vibrational peak shift due to hydrogen bonding.     

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.     

Molecular dynamics simulations of aqueous solutions of ethanolamines

We report on molecular dynamics simulations performed at constant temperature and pressure to study ethanolamines as pure components and in aqueous solutions. A new geometric integration algorithm that preserves the correct phase space volume is employed to study molecules having up to three ethanol chains. The most stable geometry, rotational barriers, and atomic charges were obtained by ab initio calculations in the gas phase. The calculated dipole moments agree well with available experimental data. The most stable conformation, due to intramolecular hydrogen bonding interactions, has a ringlike structure in one of the ethanol chains, leading to high molecular stability. All molecular dynamics simulations were performed in the liquid phase. The interaction parameters are the same for the atoms in the ethanol chains, reducing the number of variables in the potential model. Intermolecular hydrogen bonding is also analyzed, and it is shown that water associates at low water mole fractions. The force field reproduced (within 1%) the experimental liquid densities at different temperatures of pure components and aqueous solutions at 313 K. The excess and partial molar volumes are analyzed as a function of ethanolamine concentration.     

Interfacial energy exchange and reaction dynamics in collisions of gases on model organic surfaces

Molecular beam scattering experiments and molecular dynamics simulations have been combined to develop an atomic-level understanding of energy transfer, accommodation, and reactions during collisions between gases and model organic surfaces. The work highlighted in this progress report has been motivated by the scientific importance of understanding fundamental interfacial chemical reactions and the relevance of reactions on organic surfaces to many areas of environmental chemistry. The experimental investigations have been accomplished by molecular beam scattering from ω-functionalized self-assembled monolayers (SAMs) on gold. Molecular beams provide a source of reactant molecules with precisely characterized collision energy and flux; SAMs afford control over the order, structure, and chemical nature of the surface. The details of molecular motion that affect energy exchange and scattering have been elucidated through classical-trajectory simulations of the experimental data using potential energy surfaces derived from ab initio calculations. Our investigations began by employing rare-gas scattering to explore how alkanethiol chain length and packing density, terminal group relative mass, orientation, and chemical functionality influence energy transfer and accommodation at organic surfaces. Subsequent studies of small molecule scattering dynamics provided insight into the influence of internal energy, molecular orientation, and gas–surface attractive forces in interfacial energy exchange. Building on the understanding of scattering dynamics in non-reactive systems, our work has recently explored the reaction probabilities and mechanisms for O₃ and atomic fluorine in collisions with a variety of functionalized SAM surfaces. Together, this body of work has helped construct a more comprehensive understanding of reaction dynamics at organic surfaces.     

Local density inhomogeneities and dynamics in supercritical water: A molecular dynamics simulation approach

Molecular dynamics atomistic simulations in the canonical ensemble (NVT-MD) have been used to investigate the "Local Density Inhomogeneities and their Dynamics" in pure supercritical water. The simulations were carried out along a near-critical isotherm (Tr = T/Tc = 1.03) and for a wide range of densities below and above the critical one (0.2 rho(c) - 2.0 rho(c)). The results obtained reveal the existence of significant local density augmentation effects, which are found to be sufficiently larger in comparison to those reported for nonassociated fluids. The time evolution of the local density distribution around each molecule was studied in terms of the appropriate time correlation functions C(Delta)rhol(t). It is found that the shape of these functions changes significantly by increasing the density of the fluid. Finally, the local density reorganization times for the first and second coordination shell derived from these correlations exhibit a decreasing behavior by increasing the density of the system, signifying the density effect upon the dynamics of the local environment around each molecule.     

Vibrational relaxation of azide ions in liquid-to-supercritical water

The dynamics of vibrational energy relaxation (VER) of the aqueous azide anion was studied over a wide temperature (300 K ≤ T ≤ 663 K) and density (0.6 g cm(-3) ≤ ρ ≤ 1.0 g cm(-3)) range thereby covering the liquid and the supercritical phase of the water solvent. Femtosecond mid-infrared spectroscopy on the ν(3) band associated with the asymmetric stretching vibration of the azide anion was used to monitor the relaxation dynamics in a time-resolved fashion. The variation of the vibrational relaxation rate constant with temperature and density was found to be rather small. Surprisingly, the simple isolated binary collision model is able to fully reproduce the experimentally observed temperature and density dependence of the relaxation rate provided a local density correction around the vibrationally excited solute based on classical molecular dynamics simulations is used. The simulations further suggest that head-on collisions of the solvent with the terminal nitrogen atoms rather than side-on collisions with the central nitrogen atom of the azide govern the vibrational energy relaxation of this system. Finally, the importance of hydrogen bonding for the VER dynamics in this system is briefly discussed.     

Absorption and emission lineshapes and solvation dynamics of NO in supercritical Ar

We perform a theoretical study of electronic spectroscopy of dilute NO in supercritical Ar fluid. Absorption and emission lineshapes for the A(2)Sigma(+)<--X(2)Pi Rydberg transition of NO in argon have been previously measured and simulated, which yielded results for the NO/Ar ground- and excited-state pair potentials [Larregaray et al., Chem. Phys. 308, 13 (2005)]. Using these potentials, we have performed molecular dynamics simulations and theoretical statistical mechanical calculations of absorption and emission lineshapes and nonequilibrium solvation correlation functions for a wide range of solvent densities and temperatures. Theory was shown to be in good agreement with simulation. Linear response treatment of solvation dynamics was shown to break down at near-critical temperature due to dramatic change in the solute-solvent microstructure upon solute excitation to the Rydberg state and the concomitant increase of the solute size.     

Ab initio molecular dynamics using hybrid density functionals

Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.     

Discontinuous molecular dynamics for rigid bodies: applications

Event-driven molecular dynamics simulations are carried out on two rigid-body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous potentials are compared with simulations in which the molecules interact through standard continuous Lennard-Jones potentials. It is shown that under similar conditions of temperature and pressure, the rigid discontinuous molecular dynamics method reproduces the essential dynamical and structural features found in continuous-potential simulations at both gas and liquid densities. Moreover, the discontinuous molecular dynamics approach is demonstrated to be between 3 and 100 times more efficient than the standard molecular dynamics method depending on the specific conditions of the simulation. The rigid discontinuous molecular dynamics method is also applied to a discontinuous-potential model of a liquid composed of rigid benzene molecules, and equilibrium and dynamical properties are shown to be in qualitative agreement with more detailed continuous-potential models of benzene. The few qualitative differences in the angular dynamics of the two models are related to the relatively crude treatment of variations in the discontinuous repulsive interactions as one benzene molecule rotates by another.     

Vapor-liquid equilibrium of ethanol by molecular dynamics simulation and Voronoi tessellation

Explicit atom simulations of ethanol were performed by molecular dynamics using the OPLS-AA potential. The phase densities were determined self-consistently by comparing the distribution of Voronoi volumes from two-phase and single-phase simulations. This is the first demonstration of the use of Voronoi tessellation in two-phase molecular dynamics simulation of polyatomic fluids. This technique removes all arbitrary determination of the phase diagram by using single-phase simulations to self-consistently validate the probability distribution of Voronoi volumes of the liquid and vapor phases extracted from the two-phase molecular dynamics simulations. Properties from the two phase simulations include critical temperature, critical density, critical pressure, phase diagram, surface tension, and molecule orientation at the interface. The simulations were performed from 375 to 472 K. Also investigated were the vapor pressure and hydrogen bonding along the two phase envelope. The phase envelope agrees extremely well with literature values from GEMC at lower temperatures. The combined use of two-phase molecular dynamics simulation and Voronoi tessellation allows us to extend the phase diagram toward the critical point.