Flux-correlation approach to characterizing reaction pathways in quantum systems: a study of condensed-phase proton-coupled electron transfer

We introduce a simple method for characterizing reactive pathways in quantum systems. Flux auto-correlation and cross-correlation functions are employed to develop a quantitative measure of dynamical coupling in quantum transition events, such as reactive tunnelling and resonant energy transfer. We utilize the method to study condensed-phase proton-coupled electron transfer (PCET) reactions and to determine the relative importance of competing concerted and sequential reaction pathways. Results presented here include numerically exact quantum dynamics simulations for model condensed-phase PCET reactions. This work demonstrates the applicability of the new method for the analysis of both approximate and exact quantum dynamics simulations

Sampling diffusive transition paths

We address the problem of sampling double-ended diffusive paths. The ensemble of paths is expressed using a symmetric version of the Onsager-Machlup formula, which only requires evaluation of the force field and which, upon direct time discretization, gives rise to a symmetric integrator that is accurate to second order. Efficiently sampling this ensemble requires avoiding the well-known stiffness problem associated with sampling infinitesimal Brownian increments of the path, as well as a different type of stiffness associated with sampling the coarse features of long paths. The fine-feature sampling stiffness is eliminated with the use of the fast sampling algorithm (FSA), and the coarse-feature sampling stiffness is avoided by introducing the sliding and sampling (S&S) algorithm. A key feature of the S&S algorithm is that it enables massively parallel computers to sample diffusive trajectories that are long in time. We use the algorithm to sample the transition path ensemble for the structural interconversion of the 38-atom Lennard-Jones cluster at low temperature.Comment: 13 pages 5 figure

Quantum diffusion in liquid water from ring polymer molecular dynamics

We have used the ring polymer molecular-dynamics method to study the translational and orientational motions in an extended simple point charge model of liquid water under ambient conditions. We find, in agreement with previous studies, that quantum-mechanical effects increase the self-diffusion coefficient D and decrease the relaxation times around the principal axes of the water molecule by a factor of around 1.5. These results are consistent with a simple Stokes-Einstein picture of the molecular motion and suggest that the main effect of the quantum fluctuations is to decrease the viscosity of the liquid by about a third. We then go on to consider the system-size scaling of the calculated self-diffusion coefficient and show that an appropriate extrapolation to the limit of infinite system size increases D by a further factor of around 1.3 over the value obtained from a simulation of a system containing 216 water molecules. These findings are discussed in light of the widespread use of classical molecular-dynamics simulations of this sort of size to model the dynamics of aqueous systems

Torsional path integral Monte Carlo method for calculating the absolute quantum free energy of large molecules

A new technique for evaluating the absolute free energy of large molecules is presented. Quantum-mechanical contributions to the intramolecular torsions are included via the torsional path integral Monte Carlo (TPIMC) technique. Importance sampling schemes based on uncoupled free rotors and harmonic oscillators facilitate the use of the TPIMC technique for the direct evaluation of quantum partition functions. Absolute free energies are calculated for the molecules ethane, n-butane, n-octane, and enkephalin, and quantum contributions are found to be significant. Comparison of the TPIMC technique with the harmonic oscillator approximation and a variational technique is performed for the ethane molecule. For all molecules, the quantum contributions to free energy are found to be significant but slightly smaller than the quantum contributions to internal energy

Quantum free energies of the conformers of glycine on an ab initio potential energy surface

The torsional path integral Monte Carlo (TPIMC) technique is used to study the five lowest-energy conformers of glycine. The theoretical method provides an anharmonic and quantum-mechanical description of conformational free energy and is used for the first time with an ab initio potential energy surface. The 3-dimensional torsional potential energy surface of glycine was obtained at the MP2/6-311++G** level of theory and is optimized with respect to the non-torsional degrees of freedom. Calculated conformer populations compare well with those reported in recent matrix-isolation infrared spectroscopy experiments. An additional conformer, not yet observed, is predicted to be heavily populated in the thermal equilibria probed by experiment, and a new explanation for its elusiveness is provided. Quantum effects, such as zero point energy, are found to substantially alter conformer populations, and an algorithm for estimating the role of non-torsional vibrations in the conformational thermodynamics of a molecule is introduced

Torsional path integral Monte Carlo method for the quantum simulation of large molecules

A molecular application is introduced for calculating quantum statistical mechanical expectation values of large molecules at nonzero temperatures. The Torsional Path Integral Monte Carlo (TPIMC) technique applies an uncoupled winding number formalism to the torsional degrees of freedom in molecular systems. The internal energy of the molecules ethane, n-butane, n-octane, and enkephalin are calculated at standard temperature using the TPIMC technique and compared to the expectation values obtained using the harmonic oscillator approximation and a variational technique. All studied molecules exhibited significant quantum mechanical contributions to their internal energy expectation values according to the TPIMC technique. The harmonic oscillator approximation approach to calculating the internal energy performs well for the molecules presented in this study but is limited by its neglect of both anharmonicity effects and the potential coupling of intramolecular torsion

Quantum diffusion in liquid para-hydrogen from ring-polymer molecular dynamics

We have used the ring-polymer molecular dynamics method to calculate approximate Kubo-transformed velocity autocorrelation functions and self-diffusion coefficients for low-pressure liquid para-hydrogen at temperatures of 25 and 14 K. The resulting diffusion coefficients are shown to be consistent with experimental shear viscosities and the established finite-size relation D(L)~=D([infinity])–2.837kBT/6pietaL, where kB is the Boltzmann constant, T the absolute temperature, eta the shear viscosity, and L the length of the (cubic) simulation cell. The diffusion coefficients D(L) obtained in simulations with finite system sizes are therefore too small. However, the extrapolation to infinite system size corrects this deficiency and leads to excellent agreement with experimental results. This both demonstrates the influence of system-size effects on quantum mechanical diffusion coefficients and provides further evidence that ring-polymer molecular dynamics is an accurate as well as practical way of including quantum effects in condensed phase molecular dynamics

Torsional anharmonicity in the conformational thermodynamics of flexible molecules

We present an algorithm for calculating the conformational thermodynamics of large, flexible molecules that combines ab initio electronic structure theory calculations with a torsional path integral Monte Carlo (TPIMC) simulation. The new algorithm overcomes the previous limitations of the TPIMC method by including the thermodynamic contributions of non-torsional vibrational modes and by affordably incorporating the ab initio calculation of conformer electronic energies, and it improves the conventional ab initio treatment of conformational thermodynamics by accounting for the anharmonicity of the torsional modes. Using previously published ab initio results and new TPIMC calculations, we apply the algorithm to the conformers of the adrenaline molecule

Microcanonical rates from ring-polymer molecular dynamics: Direct-shooting, stationary-phase, and maximum-entropy approaches

We address the calculation of microcanonical reaction rates for processes involving significant nuclear quantum effects using ring-polymer molecular dynamics (RPMD), both with and without electronically non-adiabatic transitions. After illustrating the shortcomings of the naive free-particle direct-shooting method, in which the temperature of the internal ring-polymer modes is set to the translational energy scale, we investigate alternative strategies based on the expression for the microcanonical rate in terms of the inverse Laplace transform of the thermal reaction rate. It is shown that simple application of the stationary-phase approximation (SPA) dramatically improves the performance of the microcanonical rates using RPMD, particularly in the low-energy region where tunneling dominates. Using the SPA as a Bayesian prior, numerically exact RPMD microcanonical rates are then obtained using maximum entropy inversion of the thermal reaction rates for both electronically adiabatic and non-adiabatic model systems. Finally, the direct-shooting method is revisited using the SPA-determined temperature for the internal ring-polymer modes, leading to a simple, direct-simulation method with improved accuracy in the tunneling regime. This work suggests a general strategy for the extraction of microcanonical dynamical quantities from RPMD (or other approximate thermal) simulations