# Browsing by Subject "physics, atomic, molecular & chemical"

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Item Open Access Analysis of femtosecond stimulated Raman spectroscopy of excited-state evolution in bacteriorhodopsin(2010) Niu, Kai; Zhao, Bin; Sun, Zhigang; Lee, Soo-YThe dispersive lines observed in time-resolved femtosecond stimulated Raman spectroscopy (FSRS), using a pair of 809 nm, 3 ps Raman pump, and 840-960 nm ultrashort probe pulse, for the first 500 fs photoisomerization dynamics in the excited state of bacteriorhodopsin, BR* (S-1), created by a prior 500 nm, 35 fs actinic pump pulse, have previously been attributed to Raman initiated by nonlinear emission (RINE). We used four-wave mixing energy level diagrams to describe the FSRS process, which include RINE as a subset, and a 29-mode harmonic oscillator model for BR568 in the calculations. Our calculations showed that FSRS of BR* effectively occurs from the ground vibrational state of each of the observed 800-1800 cm(-1) modes of S-1. The lifetime on S-1 determines the linewidth and decay of the dispersive lines, and is estimated to be similar to 600 fs, comparable to the stimulated emission decay time. The FSRS dipole couplings are from the ground vibrational state of S-1 to high energy vibrational states on BR (S-0), and we place a fast decay lifetime of similar to 100 fs on S-0 which can be attributed to the correlation function from the many unobserved low frequency modes. The FSRS dispersive lines are shown to be due to the inverse Raman scattering term with vertical bar 0 >< 1 vertical bar vibrational coherence on the S-1 surface, and are not due to RINE with vibrational coherence on the S-0 surface. Our calculations show that the RINE process gives rise to broad featureless spectra. (C) 2010 American Institute of Physics. [doi: 10.1063/1.3330818]Item Open Access Extraction of state-to-state reactive scattering attributes from wave packet in reactant Jacobi coordinates(2010) Sun, Zhigang; Guo, Hua; Zhang, Dong HThe S-matrix for a scattering system provides the most detailed information about the dynamics. In this work, we discuss the calculation of S-matrix elements for the A+BC -> AB+C, AC+B type reaction. Two methods for extracting S-matrix elements from a single wave packet in reactant Jacobi coordinates are reviewed and compared. Both methods are capable of extracting the state-to-state attributes for both product channels from a single wave packet propagation. It is shown through the examples of H+HD, Cl+H-2, and H+HCl reactions that such reactant coordinate based methods are easy to implement, numerically efficient, and accurate. Additional efficiency can be gained by the use of a L-shaped grid with two-dimensional fast Fourier transform. (C) 2010 American Institute of Physics. [doi:10.1063/1.3328109]Item Open Access Time-dependent wavepacket investigation of state-to-state reactive scattering of Cl with para-H-2 including the open-shell character of the Cl atom(2010) Sun, Z; Zhang, DH; Alexander, MHWe describe a time-dependent wavepacket based method for the calculation of the state-to-state cross sections for the Cl+H-2 reaction including all couplings arising from the nonzero spin and electronic orbital angular momenta of the Cl atom. Reactant-product decoupling allows us to use a physically correct basis in both the reactant and the product arrangements. Our calculated results agree well with the experimental results of Yang and co-workers. We also describe a model with two coupled potential energy surfaces, which includes the spin-orbit coupling, which is responsible for the largest non-Born-Oppenheimer effects in the Cl+H-2 reaction but neglects the off-diagonal electronically diabatic coupling and all Coriolis couplings due to the electronic spin and orbital angular momenta. The comparison of the results of the full six-state and two-state models with an electronically adiabatic (one-state) description reveals that the latter describes well the reaction out of the ground spin-orbit state, while the two-state model, which is computationally much faster than the full six-state model, describes well the reaction from both the ground and excited spin-orbit states.Item Open Access Ultraviolet Absorption Coefficients of Melanosomes Containing Eumelanin As Related to the Relative Content of DHI and DHICA(2010) Peles, Dana N; Lin, Erica; Wakamatsu, Kazumasa; Ito, Shosuke; Simon, John DCentral to understanding the photochemical function(s) of melanosomes is the determination of their absorption properties and an understanding of how the absorption varies with the molecular composition of melanin. Herein, the absorption coefficients for melanosomes containing predominantly eumelanin, a polymeric pigment derived from the molecular precursors 5,6-dihydroxyindole (DHI) and 5,6-dihydroxyindole-2-carboxylic acid (DHICA), are reported for) lambda = 244 nm. The absorption coefficient varies with the DHICA/DHI ratio, determined from chemical degradation analyses. With increasing DHICA content, the absorption coefficient of the melanosome increases. This observation is consistent with reported extinction coefficients, which reveal that at 244 nm, the extinction coefficient of DHICA is a factor of similar to 2.1 greater than that of DHI. The melanosome absorption coefficients are compared to predicted values based on a linear combination of the absorption of the constituent monomers.