Stilbene isomerization dynamics on multidimensional potential energy surface. Molecular dynamics simulation

Molecular dynamics study of early picosecond events in the bacteriorhodopsin photocycle: dielectric response, vibrational cooling and the J, K intermediates

“…With confidence gained from the fact that the simulations reproduce the kinetic time scales, we turned to examining the response of the protein to a sudden change in the charge distribution of the retinal chromophore due to the absorption of a photon. The protein environment responds on a timescale of 100 fs, which is similar to that found both in solution (Vachev et al, 1993;Rosenthal et al, 1994) and in other proteins. For instance, the 100 fs timescale also characterizes the dielectric response of the protein for electron transfer in photosynthetic reaction centers (Nonella and Schulten, 1991;Schulten and Tesch, 1991).…”

“…Note that by changing the excited state energy function and charge distribution instantaneously, the dipole moment of the chromophore changes instantaneously as well, hence, suddenly perturbing the internal electrostatic environment of the protein. Similar nonequilibrium molecular dynamics techniques have been applied to study the solution response to the photoexcitation of a pigment in solvent (Vachev et al, 1993;Rosenthal et al, 1994).…”

“…Despite the obvious structural differences between a solvent and a protein, the similarities between the photoisomerization of retinal in bR and cis-stilbene in solution suggest that protein dynamics may affect biochemical reaction rates in a similar way to how solution affects chemical rates. Because the molecular dynamics simulations and ultrafast experiments agree remarkably well in case of solvent photoprocesses (Frederick et al, 1991;Vachev et al, 1993;Rosenthal et al, 1994;Jimenez et al, 1994), it is most reasonable to use these techniques to study reactions in proteins and, in particular, in the femtosecond response of bR to the photoisomerization of retinal. Previous molecular dynamics simulations examined the photoisomerization of retinal in bR, however, none have examined the inertial response of the protein and its relationship to solution dynamics.…”

“…The primary events in the photocycle of bR resemble the photoisomerization of cis-stilbene and other activationless photoisomerization reactions that have been studied extensively during the past 10 years using both ultrafast spec-C12 C20 ,14 troscopy and molecular dynamics simulations (Frederick et al, 1991;Vachev et al, 1993;Rosenthal et al, 1994;Jimenez et al, 1994). In cis-stilbene the photoexcited electronic state starts decaying in solution within 250 fs, a vibrationally hot photoproduct forms, and the final product thermally relaxes together with the solvent on a picosecond time scale (Waldeck, 1991;Sension et al, 1992Sension et al, , 1993Todd and Fleming, 1993).…”

Conformational isomers of stilbene on Si(100)

“…on opposite sides) conformation around the central bridge, for cis-or trans-stilbene, respectively. This isomerisation around the C=C-double bond can be induced by UV irradiation, as already shown in the gas phase and in solution and described theoretically [6][7][8][9]. The molecule is chemically stable against radiation over a broad wavelength range, and is in fact used as a laser-dye [10][11][12].…”