Accelerated direct semiclassical molecular dynamics using a compact finite difference Hessian scheme

This paper shows how a compact finite difference Hessian approximation scheme can be proficiently implemented into semiclassical initial value representation molecular dynamics. Effects of the approximation on the monodromy matrix calculation are tested by propagating initial sampling distributions to determine power spectra for analytic potential energy surfaces and for \u201con the fly\u201d carbon dioxide direct dynamics. With the approximation scheme the computational cost is significantly reduced, making ab initio direct semiclassical dynamics computationally more feasible and, at the same time, properly reproducing important quantum effects inherent in the monodromy matrix and the pre-exponential factor of the semiclassical propagator

Semiclassical molecular vibrational spectroscopy of the pre-reaction complex for the Cl - + CH 3 Cl S N 2 reaction

Semiclassical (SC) molecular dynamics theory provides a general and well-defined tool for including all quantum effects in classical mechanics.Particularly, the semiclassical initial value representation (SC-IVR) theory has been developed as a powerful and accurate tool for calculating molecular vibrational spectral densities, which exclusively relies on the classical trajectories. The pre-reaction complex Cl - ---CH 3 Cl of S N 2 reaction Cl - + CH 3 Cl is of interest to investigate the molecular vibrational power spectrum by SC-IVR methods. An analytic potential energy surface (J. Phys.Chem. 1990, 94, 2778) is used to perform molecular dynamics simulations with 10,000 ~ 500,000 trajectories. Among all semiclassical molecular dynamics trajectories, no dissociation to Cl - + CH 3 Cl or isomerization barrier crossing occurs. From the SC-IVR calculation, quantitative fundamental frequencies (vibrational quantum level 0-1 transition) are obtained with harmonic and anharmonic molecular zero-point vibrational energies (ZPE) of 24.34 and 24.12 kcal/mol respectively. The SC-IVR spectroscopy also shows qualitative overtone frequencies and vibrational modes coupling. The frequencies are further compared with second order vibrational perturbation theory (VPT2) calculations and molecular dynamics classical power spectrum. The weak coupling between vibrational modes agrees with the intrinsic non-RRKM behaviors of Cl - + CH 3 Cl S N 2 reaction

Evaluating the accuracy of Hessian approximations for direct dynamics simulations

Direct dynamics simulations are a very useful and general approach for studying the atomistic properties of complex chemical systems, since an electronic structure theory representation of a system\u2019s potential energy surface is possible without the need for fitting an analytic potential energy function. In this paper, recently introduced compact finite difference (CFD) schemes for approximating the Hessian [J. Chem. Phys.2010, 133, 074101] are tested by employing the monodromy matrix equations of motion. Several systems, including carbon dioxide and benzene, are simulated, using both analytic potential energy surfaces and on-the-fly direct dynamics. The results show, depending on the molecular system, that electronic structure theory Hessian direct dynamics can be accelerated up to 2 orders of magnitude. The CFD approximation is found to be robust enough to deal with chaotic motion, concomitant with floppy and stiff mode dynamics, Fermi resonances, and other kinds of molecular couplings. Finally, the CFD approximations allow parametrical tuning of different CFD parameters to attain the best possible accuracy for different molecular systems. Thus, a direct dynamics simulation requiring the Hessian at every integration step may be replaced with an approximate Hessian updating by tuning the appropriate accuracy

Strikingly Different Effects of Hydrogen Bonding on the Photodynamics of Individual Nucleobases in DNA: Comparison of Guanine and Cytosine

Ab initio surface hopping dynamics calculations were performed to study the photophysical behavior of cytosine and guanine embedded in DNA using a quantum mechanical/molecular mechanics (QM/MM) approach. It was found that the decay rates of photo excited cytosine and guanine were affected in a completely different way by the hydrogen bonding to the DNA environment. In case of cytosine, the geometrical restrictions exerted by the hydrogen bonds did not influence the relaxation time of cytosine significantly due to the generally small cytosine ring puckering required to access the crossing region between excited and ground state. On the contrary, the presence of hydrogen bonds significantly altered the photodynamics of guanine. The analysis of the dynamics indicates that the major contribution to the lifetime changes comes from the interstrand hydrogen bonds. These bonds considerably restricted the out-of-plane motions of the NH(2) group of guanine which are necessary for the ultrafast decay to the ground state. As a result, only a negligible amount of trajectories decayed into the ground state for guanine embedded in DNA within the simulation time of 0.5 ps, while for comparison, the isolated guanine relaxed to the ground state with a lifetime of about 0.22 ps. These examples show that, in addition to phenomena related to electronic interactions between nucleobases, there also exist relatively simple mechanisms in DNA by which the lifetime of a nucleobase is significantly enhanced as compared to the gas phase

Indirect dynamics in a highly exoergic substitution reaction

The highly exoergic nucleophilic substitution reaction F- + CH3I shows reaction dynamics strikingly different from that of substitution reactions of larger halogen anions. Over a wide range of collision energies, a large fraction of indirect scattering via a long-lived hydrogen-bonded complex is found both in crossed-beam imaging experiments and in direct chemical dynamics simulations. Our measured differential scattering cross sections show large-angle scattering and low product velocities for all collision energies, resulting from efficient transfer of the collision energy to internal energy of the CH3F reaction product. Both findings are in strong contrast to the previously studied substitution reaction of Cl - + CH3I [ Science2008, 319, 183-186] at all but the lowest collision energies, a discrepancy that was not captured in a subsequent study at only a low collision energy [ J. Phys. Chem. Lett.2010, 1, 2747-2752]. Our direct chemical dynamics simulations at the DFT/B97-1 level of theory show that the reaction is dominated by three atomic-level mechanisms, an indirect reaction proceeding via an F--HCH2I hydrogen-bonded complex, a direct rebound, and a direct stripping reaction. The indirect mechanism is found to contribute about one-half of the overall substitution reaction rate at both low and high collision energies. This large fraction of indirect scattering at high collision energy is particularly surprising, because the barrier for the F--HCH2I complex to form products is only 0.10 eV. Overall, experiment and simulation agree very favorably in both the scattering angle and the product internal energy distributions. \ua9 2013 American Chemical Society.Peer reviewed: YesNRC publication: Ye