Index k saddles and dividing surfaces in phase space, with applications to isomerization dynamics

In this paper we continue our studies of the phase space geometry and dynamics associated with index k saddles (k > 1) of the potential energy surface. Using normal form theory, we give an explicit formula for a "dividing surface" in phase space, i.e. a co-dimension one surface (within the energy shell) through which all trajectories that "cross" the region of the index k saddle must pass. With a generic non-resonance assumption, the normal form provides k (approximate) integrals that describe the saddle dynamics in a neighborhood of the index k saddle. These integrals provide a symbolic description of all trajectories that pass through a neighborhood of the saddle. We give a parametrization of the dividing surface which is used as the basis for a numerical method to sample the dividing surface. Our techniques are applied to isomerization dynamics on a potential energy surface having 4 minima; two symmetry related pairs of minima are connected by low energy index one saddles, with the pairs themselves connected via higher energy index one saddles and an index two saddle at the origin. We compute and sample the dividing surface and show that our approach enables us to distinguish between concerted crossing ("hilltop crossing") isomerizing trajectories and those trajectories that are not concerted crossing (potentially sequentially isomerizing trajectories). We then consider the effect of additional "bath modes" on the dynamics, which is a four degree-of-freedom system. For this system we show that the normal form and dividing surface can be realized and sampled and that, using the approximate integrals of motion and our symbolic description of trajectories, we are able to choose initial conditions corresponding to concerted crossing isomerizing trajectories and (potentially) sequentially isomerizing trajectories.Comment: 49 pages, 12 figure

Roaming at Constant Kinetic Energy:Chesnavich's Model and the Hamiltonian Isokinetic Thermostat

We consider the roaming mechanism for chemical reactions under the nonholonomic constraint of constant kinetic energy. Our study is carried out in the context of the Hamiltonian isokinetic thermostat applied to Chesnavich's model for an ion-molecule reaction. Through an analysis of phase space structures we show that imposing the nonholonomic constraint does not prevent the system from exhibiting roaming dynamics, and that the origin of the roaming mechanism turns out to be analogous to that found in the previously studied Hamiltonian case.Comment: arXiv admin note: text overlap with arXiv:1909.0555

Multiple Transition States and Roaming in Ion-Molecule Reactions: a Phase Space Perspective

We provide a dynamical interpretation of the recently identified `roaming' mechanism for molecular dissociation reactions in terms of geometrical structures in phase space. These are NHIMs (Normally Hyperbolic Invariant Manifolds) and their stable/unstable manifolds that define transition states for ion-molecule association or dissociation reactions. The associated dividing surfaces rigorously define a roaming region of phase space, in which both reactive and nonreactive trajectories can be trapped for arbitrarily long times.Comment: 20 pages, 6 figure

Bulgac-Kusnezov-Nos\'e-Hoover thermostats

In this paper we formulate Bulgac-Kusnezov constant temperature dynamics in phase space by means of non-Hamiltonian brackets. Two generalized versions of the dynamics are similarly defined: one where the Bulgac-Kusnezov demons are globally controlled by means of a single additional Nos\'e variable, and another where each demon is coupled to an independent Nos\'e-Hoover thermostat. Numerically stable and efficient measure-preserving time-reversible algorithms are derived in a systematic way for each case. The chaotic properties of the different phase space flows are numerically illustrated through the paradigmatic example of the one-dimensional harmonic oscillator. It is found that, while the simple Bulgac-Kusnezov thermostat is apparently not ergodic, both of the Nos\'e-Hoover controlled dynamics sample the canonical distribution correctly