Glenn V. Lo

Bonded exciplex formation from stacked thymine and adenine: semiclassical simulations

The nonradiative decay of a π-stacked adenine and thymine, following excitation of thymine by an ultrafast laser pulse, was studied by semiclassical dynamics simulations. The simulation found that a bonded exciplex is formed after excitation due to strong interaction between the stacked bases. The strong interaction significantly lowers the energy gap between the LUMO and HOMO and consequently facilitates the deactivation of the electronically excited molecule. It also restricts the deformation vibration of the excited thymine molecule, which slows down the coupling between the HOMO and LUMO energy levels and delays the deactivation of the excited adenine molecule to the electronic ground state.

Dynamics of laser-excited stacked adenines: Semiclassical simulations

The nonradiative decay of a π-stacked pair of adenine molecules, following laser excitation, was studied by semiclassical dynamics simulations. Two deactivation pathways were characterized. One pathway involves an ultrafast internal conversion within ~600 fs induced by an out-of-plane vibration of the H atom and deformation of the pyrimidine ring at the C(2) site. A slower process (~2400 fs) involves covalent bond formation between the stacked molecules, which lowers the excimer state energy and inhibits the deformation of the pyrimidine ring; the decay is also induced by an out-of-plane vibration of the H atom at the C(2) site of the pyrimidine ring.

A semiclassical dynamics study of the photoisomerization of methyl-substituted azobenzene

A semiclassical dynamics simulation study is reported for a trans–cis photoisomerization cycle of four azo compounds, including azobenzene, 2-methylazobenzene, 2,6-dimethylazobenzene, and 2,2′-dimethylazobenzene. For both trans → cis and cis → trans isomerization processes, each compound is excited by a 50 fs (fwhm) laser pulse with a photon energy leading to a ππ* excitation. It is found that the compound in both cases follows a rotational path from reactant to product and that the isomerization dynamics is significantly affected by substitution. The relative times for completing a trans–cis isomerization cycle for four compounds, 2,6-dimethylazobenzene > 2,2-dimethylazobenzene and 2,6-dimethylazobenzene > 2-methylazobenzene> azobenzene, follow the same order as for the photoinduced formation of the surface relief grating of polymers based on these four compounds. The simulation results provide a basis for understanding the surface relief grating formation of azobenzene-based materials upon irradiation with laser beams.

Competing Deactivation Channels for Excited π-Stacked Cytosines

The deactivation of π-stacked cytosine molecules following excitation by ultrashort laser pulses was studied using semiclassical dynamics simulations. Another deactivation channel was found to compete with a previously reported path that led to dimerization. For both pathways, the initial excited state was found to form a charge-separated neutral exciton state, which forms an excimer state by charge transfer. When the interbase distance becomes less than 3 A, charge recombination occurs due to strong intermolecular interaction, ultimately leading to an avoided crossing. Results indicate that the C2–N1–C6–C5 and ––– dihedral angles play a significant role in the vibronic coupling between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). Vibrational energy distribution determines the fate of the excimer at the avoided crossing. Higher-amplitude vibration of C5 or C6 atoms leads to a nonadiabatic transition to the electronic ground state (a photophysical pathway); otherwise, a chemical reaction leading to the formation of cyclobutane type dimer occurs as found in earlier studies. The S1 and S0 potential energy surfaces calculated at TD-DFT level and the simulated trajectories were found to be consistent with CASPT2 results.

Mechanisms of Laser-Induced Reactions of Stacked Benzene Molecules: A Semiclassical Dynamics Simulation and CASSCF Calculation

The response to ultrashort laser pulses of two stacked benzene molecules has been studied by semiclassical dynamics simulation; two typical pathways were found following excitation of one of the benzene molecules by a 25 fs (FWHM), 4.7 eV photon. With a fluence of 40.49 J/m2, the stacked molecules form a cyclobutane benzene dimer; the formation of the two covalent bonds linking two benzenes occurs asynchronously after the excimer decays to electronic ground state. With a fluence of 43.26 J/m2, only one bond is formed, which breaks about 50 fs after formation, followed by separation into the two molecules. The deformation of benzene ring is found to play an important role in the bond cleavage.

Effect of Initial Orientation on the Laser-Induced Cycloaddition Reaction of Benzene and Ethylene

The [2 + 2] photocycloaddition reaction of benzene and ethylene was investigated by semiclassical dynamics simulation and complete active space self-consistent field (CASSCF) ab initio calculations. Following laser excitation of the benzene molecule, two mechanisms were observed depending on the location of the second C of ethylene in relation to the hexagonal prism space defined by the first C and the plane of the benzene ring. Synchronous formation of two bonds was observed when the second C is outside the prism space; an asynchronous mechanism is observed otherwise. Charge transfer was observed only in the asynchronous mechanism; CASSCF calculations suggest that the asynchronous mechanism involves a barrierless path from the Frank-Condon point to a conical intersection, while the synchronous mechanism involves 0.8 eV barrier. These results are consistent with a higher quantum yield observed in the simulations for the asynchronous pathway.

An SPMD-Like Algorithm for Parallelizing Molecular Dynamics Using OpenMP

The efficiency and scalability of early efforts to parallelize molecular dynamics calculations on shared-memory systems using OpenMP have been limited by attempts to avoid data race. Recent work has produced better performance, but involves significant revisions to the serial code. A new algorithm addresses these limitations.

Two-level parallelization of Ehrenfest force calculations in ab initio molecular dynamics simulation

A two-level parallel code for Ehrenfest force calculations in ab initio molecular dynamics simulations was developed for a shared memory multiprocessor cluster. Coarse-grain parallelism was implemented by atomic decomposition and a fine-grained parallelism was exploited to perform matrix multiplications. This two-level parallelism efficiently enhances the speed of computations.