title: Analysis of femtosecond stimulated Raman spectroscopy of excited-state evolution in bacteriorhodopsin.
abstract: The 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 BR(568) 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 approximately 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 approximately 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 mid |0><1| 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.
authors.affiliation: Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
authors.forename: Kai
authors.initials: K
authors.lastname: Niu
authors.forename: Bin
authors.initials: B
authors.lastname: Zhao
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Sun
authors.forename: Soo-Y
authors.initials: SY
authors.lastname: Lee
mesh_terms: D001436:Bacteriorhodopsins / Q000737:chemistry*; D019617:Halobacterium salinarum / Q000737:chemistry*; D010777:Photochemistry; D013059:Spectrum Analysis, Raman / Q000379:methods*
chemical_list: D001436:Bacteriorhodopsins