Structural Observation of the Primary Isomerization in Vision with Femtosecond-Stimulated Raman

Kukura, Philipp; McCamant, David W.; Yoon, Sangwoon; Wandschneider, Daniel B.; Mathies, Richard A.

doi:10.1126/science.1118379

Cited by 614 publications

(764 citation statements)

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“…Experimental work 50 with femtosecond stimulated Raman spectroscopy has shown that there are significant changes in the retinal spectra during the transition from the dark-adapted state to the stable bathorhodopsin intermediate. 51 The experimental work suggests that the full transition from dark-adapted to bathorhodopsin state is about 1 ps in length and that the efficiency of the process, as well as the capture of the energy for large-scale conformational change is very high.…”

Section: Time-scale For Isomerizationmentioning

confidence: 99%

How a small change in retinal leads to G‐protein activation: Initial events suggested by molecular dynamics calculations

Stevens

Woolf

2006

Proteins

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Rhodopsin is the prototypical G-protein coupled receptor, coupling light activation with high efficiency to signaling molecules. The dark-state X-ray structures of the protein provide a starting point for consideration of the relaxation from initial light activation to conformational changes that may lead to signaling. In this study we create an energetically unstable retinal in the light activated state and then use molecular dynamics simulations to examine the types of compensation, relaxation, and conformational changes that occur following the cis-trans light activation. The results suggest that changes occur throughout the protein, with changes in the orientation of Helices 5 and 6, a closer interaction between Ala 169 on Helix 4 and retinal, and a shift in the Schiff base counterion that also reflects changes in sidechain interactions with the retinal. Taken together, the simulation is suggestive of the types of changes that lead from local conformational change to light-activated signaling in this prototypical system.

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Section: Time-scale For Isomerizationmentioning

confidence: 99%

How a small change in retinal leads to G‐protein activation: Initial events suggested by molecular dynamics calculations

Stevens

Woolf

2006

Proteins

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“…During photochemical reactions in protein environment, one often faces the problem that large amounts of energy are dissipated on very short length and timescales [1][2][3]. A similar situation arises in molecular electronic devices [4].…”

Section: Introductionmentioning

confidence: 99%

Vibrational energy transport in the presence of intrasite vibrational energy redistribution

Schade

Hamm

2009

The Journal of Chemical Physics

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Vibrational energy transport in the presence of intrasite vibrational energy redistribution AbstractThe mechanism of vibrational energy flow is studied in a regime where a diffusion equation is likely to break down, i.e., on length scales of a few chemical bonds and time scales of a few picoseconds. This situation occurs, for example, during photochemical reactions in protein environment. To that end, a toy model is introduced that on the one hand mimics the vibrational normal mode distribution of proteins, and on the other hand is small enough to numerically time propagate the system fully quantum mechanically. Comparing classical and quantum-mechanical results, the question is addressed to what extent the classical nature of the molecular dynamics simulations (which would be the only choice for the modeling of a real molecular system) affects the vibrational energy flow mechanism. Small differences are found which are due to the different ways classical and quantum mechanics distribute thermal energy over vibrational modes. In either case, a ballistic and a diffusive phase can be identified. For these small length and time scales, the latter is governed by intrasite vibrational energy redistribution, since vibrational energy does not necessarily thermalize completely within individual peptide units. Overall, the model suggests a picture that unifies many of the observations made recently in experiments.Vibrational energy transport in the presence of intra-site vibrational energy redistribution Marco Schade and Peter HammPhysikalisch-Chemisches Institut, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland (Dated: September 16, 2009) The mechanism of vibrational energy flow is studied in a regime where a diffusion equation is likely to break down, i.e. on length scales of a few chemical bonds and timescales of a few picoseconds. This situation occurs for example during photochemical reactions in protein environment. To that end, a toy model is introduced that on the one hand mimics the vibrational normal mode distribution of proteins, and on the other hand is small enough to numerically time-propagate the system fully quantum-mechanically. Comparing classical and quantum-mechanical results, the question is addressed to what extent the classical nature of the molecular dynamics simulations (which would be the only choice for the modelling of a real molecular system) affects the vibrational energy flow mechanism. Small differences are found which are due to the different ways how classical and quantum mechanics distribute thermal energy over vibrational modes. In either case, a ballistic and a diffusive phase can be identified. For these small length and timescales, the latter is governed by intra-site vibrational energy redistribution, since vibrational energy does not necessarily thermalize completely within individual peptide units. Overall, the model suggests a picture that unifies many of the observations made recently in experiments.

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“…Nonlinear spectroscopies [1,2] such as multidimensional [3] and fs stimulated Raman spectroscopy [4] have become standard techniques in the field of chemical reaction dynamics, combining high energy with high temporal resolution. X-ray free electron lasers (XFELs) [5][6][7] with pulse durations in the fs range and unprecedented high intensities, hold the potential for transferring these techniques to the x-ray domain, to ultimately study the coherent interplay of electronic and vibrational degrees of freedom with high temporal and spatial resolution [8][9][10].…”

mentioning

confidence: 99%

Stimulated Electronic X-Ray Raman Scattering

Weninger

Purvis²,

Ryan³

et al. 2013

Phys. Rev. Lett.

132

111

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We demonstrate strong stimulated inelastic x-ray scattering by resonantly exciting a dense gas target of neon with femtosecond, high-intensity x-ray pulses from an x-ray free-electron laser (XFEL). A small number of lower energy XFEL seed photons drive an avalanche of stimulated resonant inelastic x-ray scattering processes that amplify the Raman scattering signal by several orders of magnitude until it reaches saturation. Despite the large overall spectral width, the internal spiky structure of the XFEL spectrum determines the energy resolution of the scattering process in a statistical sense. This is demonstrated by observing a stochastic line shift of the inelastically scattered x-ray radiation. In conjunction with statistical methods, XFELs can be used for stimulated resonant inelastic x-ray scattering, with spectral resolution smaller than the natural width of the core-excited, intermediate state. [5][6][7] with pulse durations in the fs range and unprecedented high intensities, hold the potential for transferring these techniques to the x-ray domain, to ultimately study the coherent interplay of electronic and vibrational degrees of freedom with high temporal and spatial resolution [8][9][10]. The high penetration depth of x rays, combined with the element and chemical sensitivity of inelastic x-ray scattering [11][12][13] could open pathways to temporally resolve complex dynamical processes such as energy transfer in light harvesting complexes or reaction dynamics of catalytic processes [14,15]. However, the cross section for x-ray Raman scattering is small compared to that in the visible spectral domain. Therefore, even at XFELs, single shot measurements are challenging, especially in dilute samples in the gas or liquid phase.This difficulty could be overcome by stimulating the Raman scattering process to produce a strong coherent amplification of the signal. We present the first demonstration of stimulated resonant electronic x-ray Raman scattering (SRXRS) in an atomic gas. Resonant x-ray Raman scattering, also referred to as resonant inelastic x-ray scattering [12], was discovered in 1974 [11] and since then has developed into a standard tool to study electronic and vibrational excitations in solids [16][17][18], liquids [19], gases [20], and on surfaces and interfaces [21,22]. Although several theoretical feasibility studies of SRXRS have been presented [23][24][25][26], no experiment has yet demonstrated this effect.SRXRS would ideally be realized by a narrow-band, tuneable two-color x-ray source: one frequency to excite an electronic inner-shell transition and the other, lower frequency to dump an electron into the short-lived core hole. Although the production of narrow-band x rays has been realized [27,28], and schemes for two-color self seeded sources have been proposed [29], there are currently no tunable, two-color, coherent sources available to perform such an experiment. Instead of this ideal, presently unrealizable approach, we report the demonstration of SRXRS in neon with a self-amplified...

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Structural Observation of the Primary Isomerization in Vision with Femtosecond-Stimulated Raman

Cited by 614 publications

References 23 publications

How a small change in retinal leads to G‐protein activation: Initial events suggested by molecular dynamics calculations

How a small change in retinal leads to G‐protein activation: Initial events suggested by molecular dynamics calculations

Vibrational energy transport in the presence of intrasite vibrational energy redistribution

Stimulated Electronic X-Ray Raman Scattering

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