Inspired by the success of the ring-polymer molecular dynamics (RPMD) method, we derive a transition-state-theory version (RPTST) with a dividing surface which is, in general, conical in ring-polymer space. It is explained why this conical form is a good approximation to the optimal dividing surface and therefore why centroid-based quantum transition-state theories are inaccurate for asymmetric barriers at low temperatures. The geometry of the ring-polymer transition state is found to describe a finite-difference approximation to the semi-classical instanton trajectory (a classical periodic orbit of length βħ on the inverted potential). Based on this, a new practical method for locating multidimensional instantons is proposed, by computing saddle points on the ring-polymer surface, and a derivation for the reaction rate constant based on the "ImF" premise using the ring-polymer formalism is shown to be far simpler than in previous instanton approaches based on functional determinants. The resulting expression is based only on the ring-polymer potential at the transition-state and its Hessian, and is applied to evaluate the rate in a number of polyatomic systems. We show that a free-energy version of the ImF instanton theory is related to RPTST and thereby provide an explanation for why RPMD produces accurate results for thermal reaction rates in the deep-tunnelling regime and demonstrate how it can be made more efficient and systematically improved. From this, we also explain why RPMD is seen to underestimate the rates of symmetric reactions and overestimate the rates of asymmetric reactions. We also present a ring-polymer instanton derivation of a theory for calculating tunnelling splittings leading to another new practical method, which owing to its simple form, is easily extended to determine the entire tunnelling-splitting pattern of molecular clusters with two or more degenerate wells. This method is applied to the water dimer, trimer, and octamer, and shown to be in good overall agreement with experiment and to provide a deeper understanding of the tunnelling pathways.

This thesis presents an implementation of path integral molecular dynamics (PIMD) for sampling equilibrium and dynamical properties within the molecular modelling toolkit (MMTK) [J. Comp. Chem. 21, 79 (2000)], an open source Python package. Rigorous simulation using this code serves to benchmark this implementation as well as the robust- ness of the path integral Langevin equation as a thermostat [J. Chem. Phys. 133, 124104 (2010)]. PIMD is used to calculate equilibrium properties for clusters of HeN-CO2 at low- temperatures, with comparison to experimental and exact results. We characterize the convergence of structural and energetic properties as a function of path-integral discretiza- tion error. The radial and angular distribution of these clusters is studied as a function of size in the absence of rotation and bosonic exchange. These distributions are subsequently used to calculate vibrational shifts of CO2. This result is compared to high-accuracy path integral Monte Carlo simulations which include rotational and exchange effects. These sim- ulations indicate that the neglect of rotational degrees of freedom leads to an unphysical localization of helium atoms and incorrect vibrational shifts when compared to experiment. Approximate real-time quantum dynamics is presented for doped helium clusters using the ring-polymer molecular dynamics (RPMD) method. The accuracy of RPMD is tested iii for low-temperature simulations and compared to exact results. Preliminary calculation of the dynamics of the helium solvated CO2 dopant with respect to the center of mass of the cluster is presented. The effect of a cartesian integrator versus a normal-mode integrator for quantum dynamics is addressed. The path integral ground-state method is applied in order to calculate T = 0 properties. A convergence study of the ground-state energy of the quantum harmonic oscillator with respect to sampling time and path discretization is shown. As a final application of this implementation, a sugar in a periodic water box is simulated at T = 300K. The calculation of rotamer populations and a dipole autocorrelation indicate negligible change with the inclusion of quantum effects. This work offers a comprehensive foundation from which to base future PIMD centered research.

This thesis presents an implementation of path integral molecular dynamics (PIMD) for sampling equilibrium and dynamical properties within the molecular modelling toolkit (MMTK) [J. Comp. Chem. 21, 79 (2000)], an open source Python package. Rigorous simulation using this code serves to benchmark this implementation as well as the robust- ness of the path integral Langevin equation as a thermostat [J. Chem. Phys. 133, 124104 (2010)]. PIMD is used to calculate equilibrium properties for clusters of HeN-CO2 at low- temperatures, with comparison to experimental and exact results. We characterize the convergence of structural and energetic properties as a function of path-integral discretiza- tion error. The radial and angular distribution of these clusters is studied as a function of size in the absence of rotation and bosonic exchange. These distributions are subsequently used to calculate vibrational shifts of CO2. This result is compared to high-accuracy path integral Monte Carlo simulations which include rotational and exchange effects. These sim- ulations indicate that the neglect of rotational degrees of freedom leads to an unphysical localization of helium atoms and incorrect vibrational shifts when compared to experiment. Approximate real-time quantum dynamics is presented for doped helium clusters using the ring-polymer molecular dynamics (RPMD) method. The accuracy of RPMD is tested iii for low-temperature simulations and compared to exact results. Preliminary calculation of the dynamics of the helium solvated CO2 dopant with respect to the center of mass of the cluster is presented. The effect of a cartesian integrator versus a normal-mode integrator for quantum dynamics is addressed. The path integral ground-state method is applied in order to calculate T = 0 properties. A convergence study of the ground-state energy of the quantum harmonic oscillator with respect to sampling time and path discretization is shown. As a final application of this implementation, a sugar in a periodic water box is simulated at T = 300K. The calculation of rotamer populations and a dipole autocorrelation indicate negligible change with the inclusion of quantum effects. This work offers a comprehensive foundation from which to base future PIMD centered research.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第20066号 / 農博第2195号 / 新制||農||1045(附属図書館) / 学位論文||H28||N5022(農学部図書室) / 京都大学大学院農学研究科地域環境科学専攻 / (主査)教授 髙橋 千太郎, 教授 近藤 直, 教授 飯田 訓久 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

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