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The biosynthesis of abietadiene is the first biosynthetically relevant process shown to involve a potential energy surface with a bifurcating reaction pathway. Herein, we use gas-phase, enzyme-free direct dynamics simulations to study the behavior of the key reaction (bifurcating) step, which is conversion of the C 20 pimaradienyl cation to the abietadienyl cation. In a previous study (J. Am. Chem. Soc.2011, 133, 8335), a truncated C 10 model was used to investigate this reaction. The current work finds that the complete C 20 pimaradienyl cation gives reaction dynamics similar to that reported for the truncated C 10 model. We find that in the absence of the enzyme, the C 20 abietadienyl cation is generated in almost equal quantity (1.3:1) as an unobserved (in nature) seven-membered ring product. These simulations allude to a need for abietadiene synthase to steer the reaction to avoid generation of the seven-membered ring product. The methodology of post-transition state chemical dynamics simulations is also considered. The trajectories are initiated at the rate-controlling transition state (TS) separating the pimaradienyl and abietadienyl cations. Accurate results are expected for the short-time direct motion from this TS toward the abietadienyl cation. However, the dynamics may be less accurate for describing the unimolecular reactions that occur in moving toward the pimaradienyl cation, due to the unphysical flow of zero-point energy. © 2012 American Chemical Society.

World University root node

Department of Chemistry

Journal of Chemical Theory and Computation

Gas-phase chemical dynamics simulations on the bifurcating pathway of the pimaradienyl cation rearrangement: Role of enzymatic steering in abietic acid biosynthesis

Extensive classical chemical dynamics simulations of gas-phase X - + CH 3Y→ XCH 3 + Y - S N2 nucleophilic substitution reactions are reviewed and discussed and compared with experimental measurements and predictions of theoretical models. The primary emphasis is on reactions for which X and Y are halogen atoms. Both reactions with the traditional potential energy surface (PES), which include pre- and postreaction potential energy minima and a central barrier, and reactions with nontraditional PESs are considered. These S N2 reactions exhibit important nonstatistical atomic-level dynamics. The X - + CH 3Y→ X --CH 3Y association rate constant is less than the capture model as a result of inefficient energy transfer from X -+ CH 3Y relative translation to CH 3Y rotation and vibration. There is weak coupling between the low-frequency intermolecular modes of the X --CH 3Y complex and higher frequency CH 3Y intramolecular modes, resulting in non-RRKM kinetics for X --CH 3Y unimolecular decomposition. Recrossings of the [X - CH 3 - Y] - central barrier is important. As a result of the above dynamics, the relative translational energy and temperature dependencies of the S N2 rate constants are not accurately given by statistical theory. The nonstatistical dynamics results in nonstatistical partitioning of the available energy to XCH 3 +Y - reaction products. Besides the indirect, complex forming atomic-level mechanism for the S N2 reaction, direct mechanisms promoted by X - + CH 3Y relative translational or CH 3Y vibrational excitation are possible, e.g., the roundabout mechanism. © 2012 American Chemical Society.

Journal of Physical Chemistry A

Chemical dynamics simulations of X - + CH 3Y → XCH 3 + Y - gas-phase S N2 nucleophilic substitution reactions. Nonstatistical dynamics and nontraditional reaction mechanisms

Previous studies have shown that classical trajectory simulations often give accurate results for short-time intramolecular and unimolecular dynamics, particularly for initial non-random energy distributions. To obtain such agreement between experiment and simulation, the appropriate distributions must be sampled to choose initial coordinates and momenta for the ensemble of trajectories. If a molecules classical phase space is sampled randomly, its initial decomposition will give the classical anharmonic microcanonical (RRKM) unimolecular rate constant for its decomposition. For the work presented here, classical trajectory simulations of the unimolecular decomposition of quantum and classical microcanonical ensembles, at the same fixed total energy, are compared. In contrast to the classical microcanonical ensemble, the quantum microcanonical ensemble does not sample the phase space randomly. The simulations were performed for CH 4, C 2H 5, and Cl - - -CH 3Br using both analytic potential energy surfaces and direct dynamics methods. Previous studies identified intrinsic RRKM dynamics for CH 4 and C 2H 5, but intrinsic non-RRKM dynamics for Cl - - -CH 3Br. Rate constants calculated from trajectories obtained by the time propagation of the classical and quantum microcanonical ensembles are compared with the corresponding harmonic RRKM estimates to obtain anharmonic corrections to the RRKM rate constants. The relevance and accuracy of the classical trajectory simulation of the quantum microcanonical ensemble, for obtaining the quantum anharmonic RRKM rate constant, is discussed. © 2012 American Institute of Physics.

Fulltext

Journal of Chemical Physics

Comparisons of classical chemical dynamics simulations of the unimolecular decomposition of classical and quantum microcanonical ensembles

The scattering of high kinetic energy (1-6.5 eV) xenon and krypton atoms from ice was experimentally measured and theoretically modeled. The ice efficiently accommodates translational energy, but the extent to which the energy is quenched suggests the mechanism for the highest energies and near-normal incidence angles involves more than interaction with just the molecules at the ice surface. Simulations show that for these conditions the xenon penetrates into the selvedge. This penetration into the solid manifests experimentally in that the postcollision translational energy is essentially independent of the incident translational energy. This observation is in stark contrast with what is usually the situation for scattering from a surface. Finally, postexposure desorption measurements showed that some of the incident gas atoms were trapped in the bulk of the ice at temperatures well above where the absorption is thermodynamically stable. The above evidence leads to the conclusion that under conditions of near-normal angles of incidence and high collision energy, much, if not most, of the rare gas penetrates below the ice surface and into the selvedge. A fraction is stably embedded in the near surface region of the ice, whereas the remaining rare gas escapes with two distinct velocity distributions; the first is a result of a thermal process and the second, faster distribution, is the result of ejection from the solid. © 2012 American Chemical Society.

Journal of Physical Chemistry C

Scattering of high-incident-energy Kr and Xe from ice: Evidence that a major channel involves penetration into the bulk

In a previous article (Phys. Chem. Chem. Phys.2010, 12, 4435), nonequilibrium molecular dynamics (MD) simulations of heat transfer from a hot Au{111} substrate to an alkylthiolate self-assembled monolayer (H-SAM) were presented. The simulations were performed for an H-SAM chain length of eight carbon atoms, and a qualitative agreement with the experiments of Wang et al. (Science2007, 317, 787) was found. Here, simulation results are presented for heat transfer to H-SAM surfaces with carbon chain lengths of 10-20 carbon atoms. Relaxation times for heat transfer are extracted, compared with experiment, and a qualitative agreement is obtained. The same relaxation time is found from either the temperature of the H-SAM or the orientational disorder of the H-SAM versus time. For a simulation model with the Au substrate thermally equilibrated, the relaxation times determined from the simulations are approximately a factor of 4 larger than the experimental values. © 2011 American Chemical Society.

Effect of carbon chain length on the dynamics of heat transfer at a gold/hydrocarbon interface: Comparison of simulation with experiment

Algorithms are presented for sampling quantum microcanonical ensembles for a potential energy minimum and for the conical intersection at the minimum energy crossing point of two coupled electronic states. These ensembles may be used to initialize trajectories for chemical dynamics simulations. The unimolecular dynamics of a microcanonical ensemble about a potential energy minimum may be compared with the dynamics predicted by quantum Rice-Ramsperger-Kassel-Marcus (RRKM) theory. If the dynamics is non-RRKM, it will be of particular interest to determine which states have particularly long lifetimes. Initializing a microcanonical ensemble for the electronically excited state at a conical intersection is a model for electronic nonadiabatic dynamics. The trajectory surface-hopping approach may be used to study the ensuing chemical dynamics. A strength of the model is that zero-point energy conditions are included for the initial nonadiabatic dynamics at the conical intersection. © 2011 American Chemical Society.

Algorithms for sampling a quantum microcanonical ensemble of harmonic oscillators at potential minima and conical intersections

We study the nature of highly excited eigenstates of strongly coupled multimode systems with three degrees of freedom. Attempts to dynamically assign the eigenstates using classical-quantum correspondence techniques poses a considerable challenge, due to both the number of degrees of freedom and the extensive chaos in the underlying classical phase space. Nevertheless, we show that sequences of localized states interspersed between delocalized states can be identified readily by using the parametric variation technique proposed earlier by us. In addition, we introduce a novel method to lift the quantum eigenstates onto the classical resonance web using a wavelet-based local time-frequency approach. It is shown that the lifting procedure provides clear information on the various dominant nonlinear resonances that influence the eigenstates. Analyzing the spectroscopic Hamiltonians for CDBrClF and CF 3CHFI as examples, we illustrate our approach and demonstrate the consistency between state space and phase space perspectives of the eigenstates. Two exemplary cases of highly mixed quantum states are discussed to highlight the difficulties associated with their assignment. In particular, we provide arguments to distinguish between the states in terms of their predominantly classical or quantum nature of the mixing. © 2009 American Chemical Society.

Decoding the dynamical information embedded in highly excited vibrational eigenstates: State space and phase space viewpoints

We study the effect of an internal rotor on the classical and quantum intramolecular vibrational energy redistribution (IVR) dynamics of a model system with three degrees of freedom. The system is based on a Hamiltonian proposed by Martens and Reinhardt [J. Chem. Phys. 93, 5621 (1990)] to study IVR in the excited electronic state of para-fluorotoluene. We explicitly construct the state space and show, confirming the mechanism proposed by Martens and Reinhardt, that an excited high frequency mode relaxes via diffusion along a thick layer of chaos created by the low frequency-rotor interactions. However, the corresponding quantum dynamics exhibits no appreciable relaxation of the high frequency mode. We attribute the quantum suppression of the classical thick-layer diffusion to the rotor selection rules and, possibly, dynamical localization effects. © 2007 American Institute of Physics.

Intramolecular vibrational energy redistribution from a high frequency mode in the presence of an internal rotor: Classical thick-layer diffusion and quantum localization