Scott Habershon

Ring-Polymer Molecular Dynamics: Quantum Effects in Chemical Dynamics from Classical Trajectories in an Extended Phase Space

This article reviews the ring-polymer molecular dynamics model for condensed-phase quantum dynamics. This model, which involves classical evolution in an extended ring-polymer phase space, provides a practical approach to approximating the effects of quantum fluctuations on the dynamics of condensed-phase systems. The review covers the theory, implementation, applications, and limitations of the approximation.

Competing quantum effects in the dynamics of a flexible water model

Numerous studies have identified large quantum mechanical effects in the dynamics of liquid water. In this paper, we suggest that these effects may have been overestimated due to the use of rigid water models and flexible models in which the intramolecular interactions were described using simple harmonic functions. To demonstrate this, we introduce a new simple point charge model for liquid water, q-TIP4P/F, in which the O-H stretches are described by Morse-type functions. We have parametrized this model to give the correct liquid structure, diffusion coefficient, and infrared absorption frequencies in quantum (path integral-based) simulations. The model also reproduces the experimental temperature variation of the liquid density and affords reasonable agreement with the experimental melting temperature of hexagonal ice at atmospheric pressure. By comparing classical and quantum simulations of the liquid, we find that quantum mechanical fluctuations increase the rates of translational diffusion and orientational relaxation in our model by a factor of around 1.15. This effect is much smaller than that observed in all previous simulations of empirical water models, which have found a quantum effect of at least 1.4 regardless of the quantum simulation method or the water model employed. The small quantum effect in our model is a result of two competing phenomena. Intermolecular zero point energy and tunneling effects destabilize the hydrogen-bonding network, leading to a less viscous liquid with a larger diffusion coefficient. However, this is offset by intramolecular zero point motion, which changes the average water monomer geometry resulting in a larger dipole moment, stronger intermolecular interactions, and a slower diffusion. We end by suggesting, on the basis of simulations of other potential energy models, that the small quantum effect we find in the diffusion coefficient is associated with the ability of our model to produce a single broad O-H stretching band in the infrared absorption spectrum.

Comparison of path integral molecular dynamics methods for the infrared absorption spectrum of liquid water

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.

Zero point energy leakage in condensed phase dynamics: An assessment of quantum simulation methods for liquid water

The approximate quantum mechanical ring polymer molecular dynamics (RPMD) and linearized semiclassical initial value representation (LSC-IVR) methods are compared and contrasted in a study of the dynamics of the flexible q-TIP4P/F water model at room temperature. For this water model, a RPMD simulation gives a diffusion coefficient that is only a few percent larger than the classical diffusion coefficient, whereas a LSC-IVR simulation gives a diffusion coefficient that is three times larger. We attribute this discrepancy to the unphysical leakage of initially quantized zero point energy (ZPE) from the intramolecular to the intermolecular modes of the liquid as the LSC-IVR simulation progresses. In spite of this problem, which is avoided by construction in RPMD, the LSC-IVR may still provide a useful approximation to certain short-time dynamical properties which are not so strongly affected by the ZPE leakage. We illustrate this with an application to the liquid water dipole absorption spectrum, for which the RPMD approximation breaks down at frequencies in the O-H stretching region owing to contamination from the internal modes of the ring polymer. The LSC-IVR does not suffer from this difficulty and it appears to provide quite a promising way to calculate condensed phase vibrational spectra.

Quantum diffusion of hydrogen and muonium atoms in liquid water and hexagonal ice.

We have used the ring polymer molecular dynamics method to study the diffusion of muonium, hydrogen, and deuterium atoms in liquid water and hexagonal ice over a wide temperature range (8-361 K). Quantum effects are found to dramatically reduce the diffusion of muonium in water relative to that predicted by classical simulation. This leads to a simple explanation for the lack of any significant isotope effect in the observed diffusion coefficients of these species in the room temperature liquid. Our results indicate that the mechanism of the diffusion in liquid water is similar to the intercavity hopping mechanism observed in ice, supplemented by the diffusion of the cavities in the liquid. Within the same model, we have also been able to simulate the observed crossover in the c-axis diffusion coefficients of hydrogen and deuterium in hexagonal ice. Finally, we have been able to obtain good agreement with experimental data on the diffusion of muonium in hexagonal ice at 8 K, where the process is entirely quantum mechanical.

Developments in genetic algorithm techniques for structure solution from powder diffraction data

Abstract This paper presents an overview of developments that have taken place in recent years in the genetic algorithm technique for structure solution from powder diffraction data. After a brief resumé, of the essential features of the genetic algorithm technique for structure solution, the paper highlights recent developments in fundamental aspects of the technique, including the development of parallel computing concepts, the analysis of the evolutionary history in genetic algorithm structure solution calculations and the combination of energy information together with the powder diffraction data in structure solution. Several examples are also given to illustrate the application of the genetic algorithm technique to solve crystal structures of different types of organic molecular materials, including oligopeptides and multi-component co-crystals.

Development of a multipopulation parallel genetic algorithm for structure solution from powder diffraction data

Previously, the genetic algorithm (GA) approach for direct‐space crystal structure solution from powder diffraction data has been applied successfully in the structure determination of a range of organic molecular materials. In this article, we present a further development of our approach, namely a multipopulation parallel GA (PGA), which is shown to give rise to increased speed, efficiency, and reliability of structure solution calculations, as well as providing new opportunities for further optimizing our GA methodology. The multipopulation PGA is based on the independent evolution of different subpopulations, with occasional interaction (e.g., transfer of structures) allowed to occur between the different subpopulations. Different strategies for carrying out this interpopulation communication are considered in this article, and comparisons are made to the conventional single‐population GA. The increased power offered by the PGA approach creates the opportunity for structure determination of molecular crystals of increasing complexity.

Ultrafast Photoprotecting Sunscreens in Natural Plants

We explore the ultrafast photoprotective properties of a series of sinapic acid derivatives in a range of solvents, utilizing femtosecond transient electronic absorption spectroscopy. We find that a primary relaxation mechanism displayed by the plant sunscreen sinapoyl malate and other related molecular species may be understood as a multistep process involving internal conversion of the initially photoexcited 1(1)ππ* state along a trans-cis photoisomerization coordinate, leading to the repopulation of the original trans ground-state isomer or the formation of a stable cis isomer.

Free energy calculations for a flexible water model

In this work, we consider the problem of calculating the classical free energies of liquids and solids for molecular models with intramolecular flexibility. We show that thermodynamic integration from the fully-interacting solid of interest to a Debye crystal reference state, with anisotropic harmonic interactions derived from the Hessian of the original crystal, provides a straightforward route to calculating the Gibbs free energy of the solid. To calculate the molecular liquid free energy, it is essential to correctly account for contributions from both intermolecular and intramolecular motion; we employ thermodynamic integration to a Lennard-Jones reference fluid, coupled with direct evaluation of the molecular ro-vibrational partition function. These approaches are used to study the low-pressure classical phase diagram of the flexible q-TIP4P/F water model. We find that, while the experimental ice-I/liquid and ice-III/liquid coexistence lines are described reasonably well by this model, the ice-II phase is predicted to be metastable. In light of this finding, we go on to examine how the coupling between intramolecular flexibility and intermolecular interactions influences the computed phase diagram by comparing our results with those of the underlying rigid-body water model.

Thermodynamic integration from classical to quantum mechanics

We present a new method for calculating quantum mechanical corrections to classical free energies, based on thermodynamic integration from classical to quantum mechanics. In contrast to previous methods, our method is numerically stable even in the presence of strong quantum delocalization. We first illustrate the method and its relationship to a well-established method with an analysis of a one-dimensional harmonic oscillator. We then show that our method can be used to calculate the quantum mechanical contributions to the free energies of ice and water for a flexible water model, a problem for which the established method is unstable.