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The multiscale coarse-graining (MS-CG) method is a method for constructing a coarse-grained (CG) model of a system using data obtained from molecular dynamics simulations of the corresponding atomically detailed model. The formal statistical mechanical derivation of the method shows that the potential energy function extracted from an MS-CG calculation is a variational approximation for the true potential of mean force of the CG sites, one that becomes exact in the limit that a complete basis set is used in the variational calculation if enough data are obtained from the atomistic simulations. Most applications of the MS-CG method have employed a representation for the nonbonded part of the CG potential that is a sum of all possible pair interactions. This approach, despite being quite successful for some CG models, is inadequate for some others. Here we propose a systematic method for including three body terms as well as two body terms in the nonbonded part of the CG potential energy. The current method is more general than a previous version presented in a recent paper of this series [L. Larini, L. Lu, and G. A. Voth, J. Chem. Phys. 132, 164107 (2010)], in the sense that it does not make any restrictive choices for the functional form of the three body potential. We use hierarchical multiresolution functions that are similar to wavelets to develop very flexible basis function expansions with both two and three body basis functions. The variational problem is solved by a numerical technique that is capable of automatically selecting an appropriate subset of basis functions from a large initial set. We apply the method to two very different coarse-grained models: a solvent free model of a two component solution made of identical Lennard-Jones particles and a one site model of SPC/E water where a site is placed at the center of mass of each water molecule. These calculations show that the inclusion of three body terms in the nonbonded CG potential can lead to significant improvement in the accuracy of CG potentials and hence of CG simulations. [ABSTRACT FROM AUTHOR]

The dynamics of complex systems often involve thermally activated barrier crossing events that allow these systems to move from one basin of attraction on the high dimensional energy surface to another. Such events are ubiquitous, but challenging to simulate using conventional simulation tools, such as molecular dynamics. Recently, E and Zhou [Nonlinearity 24(6), 1831 (2011)] proposed a set of dynamic equations, the gentlest ascent dynamics (GAD), to describe the escape of a system from a basin of attraction and proved that solutions of GAD converge to index-1 saddle points of the underlying energy. In this paper, we extend GAD to enable finite temperature simulations in which the system hops between different saddle points on the energy surface. An effective strategy to use GAD to sample an ensemble of low barrier saddle points located in the vicinity of a locally stable configuration on the high dimensional energy surface is proposed. The utility of the method is demonstrated by studying the low barrier saddle points associated with point defect activity on a surface. This is done for two representative systems, namely, (a) a surface vacancy and ad-atom pair and (b) a heptamer island on the (111) surface of copper. [ABSTRACT FROM AUTHOR]

Markov state models of molecular kinetics (MSMs), in which the long-time statistical dynamics of a molecule is approximated by a Markov chain on a discrete partition of configuration space, have seen widespread use in recent years. This approach has many appealing characteristics compared to straightforward molecular dynamics simulation and analysis, including the potential to mitigate the sampling problem by extracting long-time kinetic information from short trajectories and the ability to straightforwardly calculate expectation values and statistical uncertainties of various stationary and dynamical molecular observables. In this paper, we summarize the current state of the art in generation and validation of MSMs and give some important new results. We describe an upper bound for the approximation error made by modeling molecular dynamics with a MSM and we show that this error can be made arbitrarily small with surprisingly little effort. In contrast to previous practice, it becomes clear that the best MSM is not obtained by the most metastable discretization, but the MSM can be much improved if non-metastable states are introduced near the transition states. Moreover, we show that it is not necessary to resolve all slow processes by the state space partitioning, but individual dynamical processes of interest can be resolved separately. We also present an efficient estimator for reversible transition matrices and a robust test to validate that a MSM reproduces the kinetics of the molecular dynamics data. [ABSTRACT FROM AUTHOR]

An algorithm is derived for computer simulation of geodesics on the constant-potential-energy hypersurface of a system of N classical particles. First, a basic time-reversible geodesic algorithm is derived by discretizing the geodesic stationarity condition and implementing the constant-potential-energy constraint via standard Lagrangian multipliers. The basic NVU algorithm is tested by single-precision computer simulations of the Lennard-Jones liquid. Excellent numerical stability is obtained if the force cutoff is smoothed and the two initial configurations have identical potential energy within machine precision. Nevertheless, just as for NVE algorithms, stabilizers are needed for very long runs in order to compensate for the accumulation of numerical errors that eventually lead to 'entropic drift' of the potential energy towards higher values. A modification of the basic NVU algorithm is introduced that ensures potential-energy and step-length conservation; center-of-mass drift is also eliminated. Analytical arguments confirmed by simulations demonstrate that the modified NVU algorithm is absolutely stable. Finally, we present simulations showing that the NVU algorithm and the standard leap-frog NVE algorithm have identical radial distribution functions for the Lennard-Jones liquid. [ABSTRACT FROM AUTHOR]

Extended Lagrangian Born–Oppenheimer molecular dynamics (XL-BOMD) [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for orbital-free Hohenberg–Kohn density-functional theory and for charge equilibration and polarizable force-field models that can be derived from the same orbital-free framework. The purpose is to introduce the most recent features of orbital-based XL-BOMD to molecular dynamics simulations based on charge equilibration and polarizable force-field models. These features include a metric tensor generalization of the extended harmonic potential, preconditioners, and the ability to use only a single Coulomb summation to determine the fully equilibrated charges and the interatomic forces in each time step for the shadow Born–Oppenheimer potential energy surface. The orbital-free formulation has a charge-dependent, short-range energy term that is separate from long-range Coulomb interactions. This enables local parameterizations of the short-range energy term, while the long-range electrostatic interactions can be treated separately. The theory is illustrated for molecular dynamics simulations of an atomistic system described by a charge equilibration model with periodic boundary conditions. The system of linear equations that determines the equilibrated charges and the forces is diagonal, and only a single Ewald summation is needed in each time step. The simulations exhibit the same features in accuracy, convergence, and stability as are expected from orbital-based XL-BOMD. [ABSTRACT FROM AUTHOR]

In this paper, we describe implementation of the semiclassical Liouville method for simulating molecular dynamics on coupled electronic surfaces in the electronic adiabatic representation. We cast the formalism in terms of semiclassical motion on Born-Oppenheimer potential energy surfaces with nonadiabatic coupling arising from the coordinate dependence of the adiabatic electronic eigenstates. Using perturbation theory and asymptotic evaluation of the resulting time integrals, we derive an expression for the probability of transition between adiabatic states which agrees with the result given previously by Miller and George [W. H. Miller and T. F. George, J. Chem. Phys. 56, 5637 (1972)]. We also demonstrate numerically the equivalence of semiclassical trajectory-based calculations in the adiabatic and diabatic representations by performing molecular dynamics simulations on a model two-state system and comparing with exact quantum mechanical results. Excellent agreement between the exact and semiclassical treatments is obtained in both representations. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Molecular structures that permit intramolecular rotational motion have the potential to function as molecular rotors. We have employed density functional theory and vibrational frequency analysis to study the characteristic structure and vibrational behavior of the molecule (4′,4″″-(bicyclo[2,2,2]octane-1,4-diyldi-4,1-phenylene)-bis-2,2′:6′,2″-terpyridine. IR active vibrational modes were found that favor intramolecular rotation. To demonstrate the rotor behavior of the isolated single molecule, ab initio molecular dynamics simulations at various temperatures were carried out. This molecular rotor is expected to be thermally triggered via excitation of specific vibrational modes, which implies randomness in its direction of rotation. [ABSTRACT FROM AUTHOR]

Using molecular dynamics simulations, it is demonstrated that monovalent counterions can induce aggregation of similarly charged rod-like polyelectrolyte chains. The critical value of the linear charge density for aggregation is shown to be close to the critical value for the extended-collapsed transition of a single flexible polyelectrolyte chain, and decreases with increasing valency of the counterions. The potential of mean force along the center of mass reaction coordinate between two similarly charged rod-like polyelectrolytes is shown to develop an attractive well for large linear charge densities. In the attractive regime, the angular distribution of the condensed counterions is no longer isotropic. [ABSTRACT FROM AUTHOR]

The multiscale coarse-graining (MS-CG) method is a method for determining the effective potential energy function for a coarse-grained (CG) model of a molecular system using data obtained from molecular dynamics simulation of the corresponding atomically detailed model. The coarse-grained potential obtained using the MS-CG method is a variational approximation for the exact many-body potential of mean force for the coarse-grained sites. Here we propose a new numerical algorithm with noise suppression capabilities and enhanced numerical stability for the solution of the MS-CG variational problem. The new method, which is a variant of the elastic net method [Friedman et al., Ann. Appl. Stat. 1, 302 (2007)], allows us to construct a large basis set, and for each value of a so-called 'penalty parameter' the method automatically chooses a subset of the basis that is most important for representing the MS-CG potential. The size of the subset increases as the penalty parameter is decreased. The appropriate value to choose for the penalty parameter is the one that gives a basis set that is large enough to fit the data in the simulation data set without fitting the noise. This procedure provides regularization to mitigate potential numerical problems in the associated linear least squares calculation, and it provides a way to avoid fitting statistical error. We also develop new basis functions that are similar to multiresolution Haar functions and that have the differentiability properties that are appropriate for representing CG potentials. We demonstrate the feasibility of the combined use of the elastic net method and the multiresolution basis functions by performing a variational calculation of the CG potential for a relatively simple system. We develop a method to choose the appropriate value of the penalty parameter to give the optimal basis set. The combined effect of the new basis functions and the regularization provided by the elastic net method opens the possibility of using very large basis sets for complicated CG systems with many interaction potentials without encountering numerical problems in the variational calculation. [ABSTRACT FROM AUTHOR]

A simple model electronic Hamiltonian to describe the potential energy surfaces of several low-lying d-d states of the [Fe(bpy)3]2+ complex is developed for use in molecular dynamics (MD) simulation studies. On the basis of a method proposed previously for first-row transition metal ions in aqueous solution, the model Hamiltonian is constructed using density functional theory calculations for the lowest singlet and quintet states. MD simulations are then carried out for the two spin states in aqueous solution in order to examine the performance of the model Hamiltonian. The simulation results indicate that the present model electronic Hamiltonian reasonably describes the potential energy surfaces of the two spin states of the aqueous [Fe(bpy)3]2+ system, while retaining sufficient simplicity for application in simulation studies on excited state dynamics. [ABSTRACT FROM AUTHOR]

Simulation of non-adiabatic molecular dynamics requires the description of multiple electronic state potential energy surfaces and their couplings. Ab initio molecular dynamics approaches provide an attractive avenue to accomplish this, but at great computational expense. Interpolation approaches provide a possible route to achieve flexible descriptions of the potential energy surfaces and their couplings at reduced expense. A previously developed approach based on modified Shepard interpolation required global diabatization, which can be problematic. Here, we extensively revise this previous approach, avoiding the need for global diabatization. The resulting interpolated potentials provide only adiabatic energies, gradients, and derivative couplings. This new interpolation approach has been integrated with the ab initio multiple spawning method and it has been rigorously validated against direct dynamics. It is shown that, at least for small molecules, constructing an interpolated PES can be more efficient than performing direct dynamics as measured by the total number of ab initio calculations that are required for a given accuracy. [ABSTRACT FROM AUTHOR]

The electric field dependence of the structure and dynamics of water at 77 K, i.e., below the glass transition temperature (136 K), is investigated using molecular dynamics simulations. Transitions are found at two critical field strengths, denoted E1 and E2. The transition around E1≈3.5 V/nm is characterized by the onset of significant structural disorder, a rapid increase in the orientational polarization, and a maximum in the dynamical fluctuations. At E2≈40 V/nm, the system crystallizes in discrete steps into a body-centered-cubic unit cell that minimizes the potential energy by simultaneous superpolarization of the water molecular dipoles and maximization of the intermolecular hydrogen bonds. The stepwise and discontinuous increase of the orientational polarization with the increasing electric field indicates that the dipole relaxation in the electric field is highly cooperative. [ABSTRACT FROM AUTHOR]

Atomistic non-equilibrium molecular dynamics simulations of shock wave compression of quartz have been performed using the so-called BKS semi-empirical potential of van Beest, Kramer, and van Santen [Phys. Rev. B 43, 5068 (1991)] to construct the Hugoniot of quartz. Our scheme mimics the real world experimental set up by using a flyer-plate impactor to initiate the shock wave and is the first shock wave simulation that uses a geometry optimised system of a polar slab in a three-dimensional system employing periodic boundary conditions. Our scheme also includes the relaxation of the surface dipole in the polar quartz slab which is an essential pre-requisite to a stable simulation. The original BKS potential is unsuited to shock wave calculations and so we propose a simple modification. With this modification, we find that our calculated Hugoniot is in good agreement with experimental shock wave data up to 25 GPa, but significantly diverges beyond this point. We conclude that our modified BKS potential is suitable for quartz under representative pressure conditions of the Earth core, but unsuitable for high-pressure shock wave simulations. We also find that the BKS potential incorrectly prefers the β-quartz phase over the α-quartz phase at zero-temperature, and that there is a β → α phase-transition at 6 GPa. [ABSTRACT FROM AUTHOR]

Analysis of surface fluctuation spectra is performed for a large cluster of particles interacting via a sum of the short-range Lennard-Jones potential and long-range ±1/r potential, where the positive sign corresponds to the gravity, and negative corresponds to the electrostatic interaction. The spectral amplitudes of thermally driven capillary modes in a self-consistent field induced by cluster particles including the modes with no axial symmetry are derived in the approximation of small amplitudes. It is demonstrated that within used approximation, the surface tension is independent of the field strength. The low wave vector amplitudes are damped by attracting field that compresses the cluster and magnified by repulsing field leading to cluster fission. The fission threshold is found to be different from that found by Bohr and Wheeler and Frenkel due to the replacement of the ordinary surface tension by the bare one. Molecular dynamics study of a cluster with the long-range interaction in the vapor environment is performed using a novel integrator for a multiscale system. Simulation scheme implies rotation of the long-range components of forces acting on cluster particles thus vanishing an artificial torque. Simulation results justify theoretical conclusion of modes damping and independence of the surface tension of the field strength. Fission threshold evaluated from simulation data is in a good agreement with theory. [ABSTRACT FROM AUTHOR]

The dynamic heat capacity of a simple polymeric, model glassformer was computed using molecular dynamics simulations by sinusoidally driving the temperature and recording the resultant energy. The underlying potential energy landscape of the system was probed by taking a time series of particle positions and quenching them. The resulting dynamic heat capacity demonstrates that the long time relaxation is the direct result of dynamics resulting from the potential energy landscape. Moreover, the equilibrium (low frequency) portion of the potential energy landscape contribution to the heat capacity is found to increase rapidly at low temperatures and at high packing fractions. This increase in the heat capacity is explained by a statistical mechanical model based on the distribution of minima in the potential energy landscape. [ABSTRACT FROM AUTHOR]

A biased potential molecular dynamics simulation approach, accelerated molecular dynamics (AMD), has been implemented in the framework of ab initio molecular dynamics for the study of chemical reactions. Using two examples, the double proton transfer reaction in formic acid dimer and the hypothetical adiabatic ring opening and subsequent rearrangement reactions in methylenecyclopropane, it is demonstrated that ab initio AMD can be readily employed to efficiently explore the reactive potential energy surface, allowing the prediction of chemical reactions and the identification of metastable states. An adaptive variant of the AMD method is developed, which additionally affords an accurate representation of both the free-energy surface and the mechanism associated with the chemical reaction of interest and can also provide an estimate of the reaction rate. [ABSTRACT FROM AUTHOR]

All the channels of the reaction dynamics of gas-phase H (or D) atoms with D (or H) atoms adsorbed onto a Cu(111) surface have been studied by quasiclassical constant energy molecular dynamics simulations. The surface is flexible and is prepared at different temperature values, such as 30 K, 94 K, and 160 K. The adsorbates were distributed randomly on the surface to create 0.18 ML, 0.28 ML, and 0.50 ML of coverages. The multi-layer slab is mimicked by a many-body embedded-atom potential energy function. The slab atoms can move according to the exerted external forces. Treating the slab atoms non-rigid has an important effect on the dynamics of the projectile atom and adsorbates. Significant energy transfer from the projectile atom to the surface lattice atoms takes place especially during the first impact that modifies significantly the details of the dynamics of the collisions. Effects of the different temperatures of the slab are investigated in this study. Interaction between the surface atoms and the adsorbates is modeled by a modified London-Eyring-Polanyi-Sato (LEPS) function. The LEPS parameters are determined by using the total energy values which were calculated by a density functional theory and a generalized gradient approximation for an exchange-correlation energy for many different orientations, and locations of one- and two-hydrogen atoms on the Cu(111) surface. The rms value of the fitting procedure is about 0.16 eV. Many different channels of the processes on the surface have been examined, such as inelastic reflection of the incident hydrogen, subsurface penetration of the incident projectile and adsorbates, sticking of the incident atom on the surface. In addition, hot-atom and Eley-Rideal direct processes are investigated. The hot-atom process is found to be more significant than the Eley-Rideal process. Furthermore, the rate of subsurface penetration is larger than the sticking rate on the surface. In addition, these results are compared and analyzed as a function of the surface temperatures. [ABSTRACT FROM AUTHOR]

Classical molecular dynamics simulations have been carried out for gaseous CO2 starting from various anisotropic intermolecular potential energy surfaces. Through calculations for a large number of molecules treated as rigid rotors, the time evolution of the interaction-induced electric dipole vector is obtained and the Laplace transform of its autocorrelation function gives the collision-induced absorption rototranslational spectrum. The results are successfully compared with those of previous similar calculations before studies of the influences of the intermolecular potential and induced-dipole components are made. The calculated spectra show a significant sensitivity to anisotropic forces consistently with previous analyses limited to the spectral moments. The present results also demonstrate the importance of vibrational and back-induction contributions to the induced dipole. Comparisons between measured far infrared (0-250 cm-1) spectra at different temperatures and results calculated without the use of any adjustable parameter are made. When the best and more complete input data are used, the quality of our predictions is similar to that obtained by Gruszka et al. [Mol. Phys. 93, 1007 (1998)] after the introduction of ad hoc short-range overlap contributions. Our results thus largely obviate the need for such contributions the magnitudes of which remain questioned. Nevertheless, problems remain since, whereas good agreements with measurements are obtained above 50 cm-1, the calculations significantly underestimate the absorption below, a problem which is discussed in terms of various possible error sources. [ABSTRACT FROM AUTHOR]

Mass tensor molecular dynamics method was first introduced by Bennett [J. Comput. Phys. 19, 267 (1975)] for efficient sampling of phase space through the use of generalized atomic masses. Here, we show how to apply this method to ab initio molecular dynamics simulations with minimal computational overhead. Test calculations on liquid water show a threefold reduction in computational effort without making the fixed geometry approximation. We also present a simple recipe for estimating the optimal atomic masses using only the first derivatives of the potential energy. [ABSTRACT FROM AUTHOR]

Polarizable continuum models (PCMs) are a widely used family of implicit solvent models based on reaction-field theory and boundary-element discretization of the solute/continuum interface. An often overlooked aspect of these theories is that discretization of the interface typically does not afford a continuous potential energy surface for the solute. In addition, we show that discretization can lead to numerical singularities and violations of exact variational conditions. To fix these problems, we introduce the switching/Gaussian (SWIG) method, a discretization scheme that overcomes several longstanding problems with PCMs. Our approach generalizes a procedure introduced by York and Karplus [J. Phys. Chem. A 103, 11060 (1999)], extending it beyond the conductor-like screening model. Comparison to other purportedly smooth PCM implementations reveals certain artifacts in these alternative approaches, which are avoided using the SWIG methodology. The versatility of our approach is demonstrated via geometry optimizations, vibrational frequency calculations, and molecular dynamics simulations, for solutes described using quantum mechanics and molecular mechanics. [ABSTRACT FROM AUTHOR]

The molecular dynamics technique with the ab initio based classical reactive force field ReaxFF is used to study the adsorption dynamics of O2 on Pt(111) for both normal and oblique impacts. Overall, good quantitative agreement with the experimental data is found at low incident energies. Specifically, our simulations reproduce the characteristic minimum of the trapping probability at kinetic incident energies around 0.1 eV. This feature is determined by the presence of a physisorption well in the ReaxFF potential energy surface (PES) and the progressive suppression of a steering mechanism when increasing the translational kinetic energy (or the molecule’s rotational energy) because of steric hindrance. In the energy range between 0.1 and 0.4 eV, the sticking probability increases, similar to molecular beam sticking data. For very energetic impacts (above 0.4 eV), ReaxFF predicts sticking probabilities lower than experimental sticking data by almost a factor of 3 due to an overall less attractive ReaxFF PES compared to experiments and density functional theory. For oblique impacts, the trapping probability is reduced by the nonzero parallel momentum because of the PES corrugation and does not scale with the total incident kinetic energy. Furthermore, our simulations predict quasispecular (slightly supraspecular) distributions of angles of reflection, in accordance with molecular beam experiments. Increasing the beam energy (between 1.2 and 1.7 eV) causes the angular distributions to broaden and to exhibit a tail toward the surface normal because molecules have enough momentum to get very near the surface and thus probe more corrugated repulsive regions of the PES. [ABSTRACT FROM AUTHOR]

The ring polymer molecular dynamics (RPMD) and partially adiabatic centroid molecular dynamics (PA-CMD) methods are compared and contrasted in an application to the infrared absorption spectrum of a recently parametrized flexible, polarizable, Thole-type potential energy model for liquid water. Both methods predict very similar spectra in the low-frequency librational and intramolecular bending region at wavenumbers below 2500 cm-1. However, the RPMD spectrum is contaminated in the high-frequency O–H stretching region by contributions from the internal vibrational modes of the ring polymer. This problem is avoided in the PA-CMD method, which adjusts the elements of the Parrinello–Rahman mass matrix so as to shift the frequencies of these vibrational modes beyond the spectral range of interest. PA-CMD does not require any more computational effort than RPMD and it is clearly the better of the two methods for simulating vibrational spectra. [ABSTRACT FROM AUTHOR]

The dissociation dynamics of the excited Xe3+ molecular ion through the Π(1/2)u and Π(1/2)g conical intersection was interrogated by computational simulation in which no adjustable parameters were used. The electronic ground and excited state potential energy surfaces were generated by the diatomics-in-molecules method, and the Ehrenfest mean-field and Tully surface-hopping approaches treated the nonadiabatic interactions. Reproduction of the experimental spectrum of the symmetric photofragmentation as a function of excitation energy was obtained within the region of interest (2.5–3.75 eV), with the exception of a 0.25 eV width on the red side of the spectral apex. Good agreement was obtained with the experimental dissociated photofragment kinetic energy spectra. It was determined that the greatest contribution to the nonadiabatic coupling between the two states originated from the bending vibrational mode of the molecule in the Σ(1/2)u, ground electronic state before excitation. [ABSTRACT FROM AUTHOR]

The authors report a global potential energy surface for the ground electronic state of HO2(X 2A″), which improves upon the XXZLG potential [Xu and et al., J. Chem. Phys. 122, 244305 (2005)] with additional high-level ab initio points for the long-range interaction potential in the O+OH channel. Exact J=0 quantum mechanical reaction probabilities were calculated on the new potential and the rate constant for the title reaction was obtained using a J-shifting method. The calculated rate constant is in good agreement with available experimental values and our results predict a significantly lower rate at temperature range below 30 K, offering a possible explanation for the “interstellar oxygen problem.” [ABSTRACT FROM AUTHOR]

An efficient method for the calculation of minimum free energy pathways and free energy profiles for conformational transitions is presented. Short restricted perturbation-targeted molecular dynamics trajectories are used to generate an approximate free energy surface. Approximate reaction pathways for the conformational change are constructed from one-dimensional line segments on this surface using a Monte Carlo optimization. Accurate free energy profiles are then determined along the pathways by means of one-dimensional adaptive umbrella sampling simulations. The method is illustrated by its application to the alanine “dipeptide.” Due to the low computational cost and memory demands, the method is expected to be useful for the treatment of large biomolecular systems. [ABSTRACT FROM AUTHOR]

Time-reversible ab initio molecular dynamics based on a lossless multichannel decomposition for the integration of the electronic degrees of freedom [Phys. Rev. Lett. 97, 123001 (2006)] is explored. The authors present a lossless time-reversible density matrix molecular dynamics scheme. This approach often allows for stable Hartree-Fock simulations using only one single self-consistent field cycle per time step. They also present a generalization, introducing an additional “forcing” term, that in a special case includes a hybrid Lagrangian, i.e., Car-Parrinello-type, method, which can systematically be constrained to the Born-Oppenheimer potential energy surface by using an increasing number of self-consistency cycles in the nuclear force calculations. Furthermore, in analog to the reversible and symplectic leapfrog or velocity Verlet schemes, where not only the position but also the velocity is propagated, the authors propose a Verlet-type density velocity formalism for time-reversible Born-Oppenheimer molecular dynamics. [ABSTRACT FROM AUTHOR]

Parallel replica dynamics simulation methods appropriate for the simulation of chemical reactions in molecular systems with many conformational degrees of freedom have been developed and applied to study the microsecond-scale pyrolysis of n-hexadecane in the temperature range of 2100–2500 K. The algorithm uses a transition detection scheme that is based on molecular topology, rather than energetic basins. This algorithm allows efficient parallelization of small systems even when using more processors than particles (in contrast to more traditional parallelization algorithms), and even when there are frequent conformational transitions (in contrast to previous implementations of the parallel replica algorithm). The parallel efficiency for pyrolysis initiation reactions was over 90% on 61 processors for this 50-atom system. The parallel replica dynamics technique results in reaction probabilities that are statistically indistinguishable from those obtained from direct molecular dynamics, under conditions where both are feasible, but allows simulations at temperatures as much as 1000 K lower than direct molecular dynamics simulations. The rate of initiation displayed Arrhenius behavior over the entire temperature range, with an activation energy and frequency factor of Ea=79.7 kcal/mol and log A/s-1=14.8, respectively, in reasonable agreement with experiment and empirical kinetic models. Several interesting unimolecular reaction mechanisms were observed in simulations of the chain propagation reactions above 2000 K, which are not included in most coarse-grained kinetic models. More studies are needed in order to determine whether these mechanisms are experimentally relevant, or specific to the potential energy surface used. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We present results from kinetic Monte Carlo (KMC) simulations of diffusion in a model glass former. We find that the diffusion constants obtained from KMC simulations have Arrhenius temperature dependence, while the correct behavior, obtained from molecular dynamics simulations, can be super-Arrhenius. We conclude that the discrepancy is due to undersampling of higher-lying local minima in the KMC runs. We suggest that the relevant connectivity of minima on the potential energy surface is proportional to the energy density of the local minima, which determines the “inherent structure entropy.” The changing connectivity with potential energy may produce a correlation between dynamics and thermodynamics. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A potential energy surface for H[sub 5][sup +] has been constructed by a modified Shepard interpolation on a sparse set of data points, using second order Möller–Plesset perturbation theory. An improved version of the surface was also obtained by substituting the energy values at the data points with values evaluated using a coupled cluster treatment (with single and double excitations, and perturbative treatment of triple excitations). Classical simulations for the collisions between H[sub 3][sup +]+HD and H[sub 3][sup +]+D[sub 2] were carried out in order to calculate the total integral cross sections and rate coefficients for these systems. There is good agreement with earlier experimental data for rate coefficients at temperatures between 80 and 300 K, but the predicted rate coefficient for the reaction of H[sub 3][sup +]+HD at 10 K deviates from the most recent experimental measurement, suggesting that quantum rather than classical reaction dynamics are necessary. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Investigates the change in structure with size in (CO[sub 2])[sub N] clusters in the crossover regime from icosahedral to cubic morphology by molecular dynamics simulation. Characterization of the minima in the potential energy surface visited by the solid clusters at finite temperature.

Studies the distribution of vibrational potential energy in molecular systems. Extent of coupling between the vibrational degrees of freedom; Relationship between molecular structure and internal energy distribution; Possible use as a diagnostic aid in molecular dynamic simulations.

FN.-

The adiabatic approximation, typically assumed when performing standard Born-Oppenheimer (BO) molecular dynamics, can become unreliable at finite temperature, and specifically when the temperature is larger than the electronic energy gap between the ground state and the low-lying excited states. In this regime, relevant for many important chemical processes, the non-adiabatic couplings between the electronic energy states can produce finite temperature effects in several molecular properties, such as the geometry, the vibrational frequencies, the binding energy, and several chemical reactions. In this work, we introduce a novel finite-temperature non-adiabatic molecular dynamics based on a novel covariant formulation of the electronic partition function. In this framework, the nuclei are not constrained to move in a specific electronic potential energy surface. Then, by using a rigorous variational upper bound to the free energy, we are led to an approximate partition function that can be evaluated numerically. The method can be applied to any technique capable to provide an energy value over a given wave function ansatz depending on several variational parameters and atomic positions. In this work, we have applied the proposed method within a quantum Monte Carlo (QMC) scheme. In particular, we consider in this first application only classical ions, but we explicitly include an electronic correlation (Jastrow) term in the wave function, by extending in this way the standard variational QMC method, from ground state to finite temperature properties. We show that our approximation reduces correctly to the standard ground-state Born-Oppenheimer (gsBO) at zero temperature and to the correct high temperature limit. Moreover, at temperatures large enough, this method improves the upper bound of the free energy obtained with a single BO energy surface, since within our approach it is possible to estimate the electron entropy of a correlated ansatz in an efficient way. We test this new method on the simple hydrogen molecule, where at low temperature we recover the correct gsBO low temperature limit. Moreover, we show that the dissociation of the molecule is possible at a temperature much smaller than the one corresponding to the gsBO energy surface, in good agreement with experimental evidence. Several extensions of the proposed technique are also discussed, as for instance the inclusion of quantum effects for ions and the calculation of critical (magnetic, superconducting) temperatures. [ABSTRACT FROM AUTHOR]