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Richard A Mathies - One of the best experts on this subject based on the ideXlab platform.
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Femtosecond Stimulated Raman Spectroscopy
Chemphyschem : a European journal of chemical physics and physical chemistry, 2016Co-Authors: D. Dietze, Richard A MathiesAbstract:Femtosecond Stimulated Raman Spectroscopy (FSRS) is an ultrafast nonlinear optical technique that provides vibrational structural information with high temporal (sub-50 fs) precision and high spectral (10 cm(-1) ) resolution. Since the first full demonstration of its capabilities ≈15 years ago, FSRS has evolved into a mature technique, giving deep insights into chemical and biochemical reaction dynamics that would be inaccessible with any other technique. It is now being routinely applied to virtually all possible photochemical reactions and systems spanning from single molecules in solution to thin films, bulk crystals and macromolecular proteins. This review starts with an historic overview and discusses the theoretical and experimental concepts behind this technology. Emphasis is put on the current state-of-the-art experimental realization and several variations of FSRS that have been developed. The unique capabilities of FSRS are illustrated through a comprehensive presentation of experiments to date followed by prospects.
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Chromophore dynamics in the PYP photocycle from femtosecond Stimulated Raman Spectroscopy.
The journal of physical chemistry. B, 2014Co-Authors: Mark Creelman, Masato Kumauchi, Wouter D. Hoff, Richard A MathiesAbstract:Femtosecond Stimulated Raman Spectroscopy (FSRS) is used to examine the structural dynamics of the para-hydroxycinnamic acid (HCA) chromophore during the first 300 ps of the photoactive yellow protein (PYP) photocycle, as the system transitions from its vertically excited state to the early ground state cis intermediate, I0. A downshift in both the C7═C8 and C1═O stretches upon photoexcitation reveals that the chromophore has shifted to an increasingly quinonic form in the excited state, indicating a charge shift from the phenolate moiety toward the C9═O carbonyl, which continues to increase for 170 fs. In addition, there is a downshift in the C9═O carbonyl out-of-plane vibration on an 800 fs time scale as PYP transitions from its excited state to I0, indicating that weakening of the hydrogen bond with Cys69 and out-of-plane rotation of the C9═O carbonyl are key steps leading to photoproduct formation. HOOP intensity increases on a 3 ps time scale during the formation of I0, signifying distortion about th...
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Optimally shaped narrowband picosecond pulses for femtosecond Stimulated Raman Spectroscopy
Optics express, 2013Co-Authors: David P. Hoffman, Mark Creelman, David T. Valley, Scott R. Ellis, Richard A MathiesAbstract:A comparison between a Fabry-Perot etalon filter and a conventional grating filter for producing the picosecond (ps) Raman pump pulses for femtosecond Stimulated Raman Spectroscopy (FSRS) is presented. It is shown that for pulses of equal energy the etalon filter produces Raman signals twice as large as that of the grating filter while suppressing the electronically resonant background signal. The time asymmetric profile of the etalon-generated pulse is shown to be responsible for both of these observations. A theoretical discussion is presented which quantitatively supports this hypothesis. It is concluded that etalons are the ideal method for the generation of narrowband ps pulses for FSRS because of the optical simplicity, efficiency, improved FSRS intensity and reduced backgrounds.
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structural dynamics of a noncovalent charge transfer complex from femtosecond Stimulated Raman Spectroscopy
Journal of Physical Chemistry B, 2012Co-Authors: Tomotsumi Fujisawa, Mark Creelman, Richard A MathiesAbstract:Femtosecond Stimulated Raman Spectroscopy is used to examine the structural dynamics of photoinduced charge transfer within a noncovalent electron acceptor/donor complex of pyromellitic dianhydride (PMDA, electron acceptor) and hexamethylbenzene (HMB, electron donor) in ethylacetate and acetonitrile. The evolution of the vibrational spectrum reveals the ultrafast structural changes that occur during the charge separation (Franck–Condon excited state complex → contact ion pair) and the subsequent charge recombination (contact ion pair → ground state complex). The Franck–Condon excited state is shown to have significant charge-separated character because its vibrational spectrum is similar to that of the ion pair. The charge separation rate (2.5 ps in ethylacetate and ∼0.5 ps in acetonitrile) is comparable to solvation dynamics and is unaffected by the perdeuteration of HMB, supporting the dominant role of solvent rearrangement in charge separation. On the other hand, the charge recombination slows by a fac...
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Probing structural evolution along multidimensional reaction coordinates with femtosecond Stimulated Raman Spectroscopy
Physical chemistry chemical physics : PCCP, 2011Co-Authors: Renee R. Frontiera, Jyotishman Dasgupta, Chong Fang, Richard A MathiesAbstract:Mapping out multidimensional potential energy surfaces has been a goal of physical chemistry for decades in the quest to both predict and control chemical reactivity. Recently a new spectroscopic approach called Femtosecond Stimulated Raman Spectroscopy or FSRS was introduced that can structurally interrogate multiple dimensions of a reactive potential energy surface. FSRS is an ultrafast laser technique which provides complete time-resolved, background-free Raman spectra in a few laser shots. The FSRS technique provides simultaneous ultrafast time (∼50 fs) and spectral (∼8 cm−1) resolution, thus enabling one to follow reactive structural evolutions as they occur. In this perspective we summarize how FSRS has been used to follow structural dynamics and provide mechanistic detail on three classical chemical reactions: a structural isomerization, an electron transfer reaction, and a proton transfer reaction.
David W. Mccamant - One of the best experts on this subject based on the ideXlab platform.
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ultraviolet light makes dgmp floppy femtosecond Stimulated Raman Spectroscopy of 2 deoxyguanosine 5 monophosphate
Journal of Physical Chemistry B, 2017Co-Authors: Joohyun Lee, Reddy J Challa, David W. MccamantAbstract:The ultrafast dynamics of 2′-deoxyguanosine 5′-monophosphate after excitation with ultraviolet light has been studied with femtosecond transient absorption (TA) and femtosecond Stimulated Raman Spectroscopy (FSRS). TA kinetics and transient anisotropy spectra reveal a rapid relaxation from the Franck–Condon region, producing an extremely red-shifted Stimulated emission band at ∼440 nm that is formed after 200 fs and subsequent relaxation for 0.8–1.5 ps, consistent with prior studies. Viscosity dependence shows that the initial relaxation, before 0.5 ps, is the same in water or viscous glycerol/water mixtures, but after 0.5 ps the dynamics significantly slow down in a viscous solution. This indicates that large amplitude structural changes occur after 0.5 ps following photoexcitation. FSRS obtained with both 480 and 600 nm Raman pump pulses observe very broad Raman peaks at 509 and 1530 cm–1, as well as a narrower peak at 1179 cm–1. All of the Raman peaks decay with 0.7–1.3 ps time constants. The 1530 cm–1...
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Femtosecond Stimulated Raman Spectroscopy
Encyclopedia of Spectroscopy and Spectrometry, 2017Co-Authors: David W. MccamantAbstract:Femtosecond Stimulated Raman Spectroscopy is a method of time-resolved vibrational Spectroscopy that has been developed since 1994. The method requires three ultrafast laser pulses: a 20–150 femtosecond (fs) actinic pump that excites a sample to an excited electronic state, a 1–3 picosecond (ps) Raman pump pulse that initiates the Stimulated Raman transition, and a 20–150 fs broad-bandwidth probe pulse. In femtosecond Stimulated Raman Spectroscopy, the probe experiences amplification at Raman resonances, that is, at wavelengths whose optical frequency differs from that of the Raman pump by an amount that matches a Raman-active molecular vibration in the sample.
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Stimulated Raman Spectroscopy using chirped pulses
Journal of Raman Spectroscopy, 2014Co-Authors: Barbara Dunlap, Peter Richter, David W. MccamantAbstract:We present a detailed theoretical and experimental characterization of a new methodology for Stimulated Raman Spectroscopy using two duplicates of a chirped, broadband laser pulse. Because of the linear variation of laser frequency with time (‘chirp’), when the pulses are delayed relative to one another, there exists a narrow bandwidth, instantaneous frequency difference between them, which, when resonant with a Raman-active vibration in the sample, generates Stimulated Raman gain in one pulse and inverse Raman loss in the other. This method has previously been used for coherent Raman imaging and termed ‘spectral focusing’. Here, gain and loss signals are spectrally resolved, and the spectrally integrated signals are used to determine the spectral resolution of the measured Raman spectrum. Material dispersion is used to generate a range of pulse durations, and it is shown that there is only a small change in the magnitude of the signal and the spectral resolution as the pulse is stretched from 800 to 1800 fs in duration. A quantitative theory of the technique is developed, which reproduces both the magnitude and linewidth of the experimental signals when third-order dispersion and phase-matching efficiency are included. The theoretical calculations show that both spectral resolution and signal magnitude are severely hampered by the third-order dispersion in the laser pulse, and hence, a minimal amount of chirp produces the most signal with only a slight loss of spectral resolution. Copyright © 2014 John Wiley & Sons, Ltd.
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pump power dependence in resonance femtosecond Stimulated Raman Spectroscopy
Journal of Raman Spectroscopy, 2013Co-Authors: Reddy J Challa, David W. MccamantAbstract:Femtosecond Stimulated Raman Spectroscopy (FSRS) has emerged as a powerful new technique that is capable of obtaining resonance Raman spectra of fluorescent species and transient photochemical intermediates. Unlike related transient infrared absorption techniques, the FSRS signal is quite sensitive to the laser power utilized in the vibrational probing event. In particular, FSRS spectra are highly sensitive to the intensity of the picosecond Raman-pump pulse. We have measured the power dependence of the FSRS signal using pulse energies from ~10−9 to ~10−5 J and molecules with a range of molar absorptivities at the Raman-pump wavelength of 400 nm, including β-carotene (e400 = 58 300 M−1 cm−1), para-nitroaniline (17 800 M−1 cm−1), nitronaphthalene (247 M−1 cm−1) and ferrocene (57 M−1 cm−1). We show that for strongly absorbing molecular systems, such as β-carotene and para-nitroaniline, the ground-state (GS) FSRS signal actually decreases with increasing pump power at pump fluences above ~10−2 J cm−2, due to depletion of the GS population. However, for weakly absorbing species like nitronaphthalene and ferrocene, the signal increases linearly with increasing pump fluence until ~0.5 J cm−2, at which point two-photon absorption by the solute induces nonlinear absorption of the pump pulse and attenuation of the FSRS signal. The data are quantitatively simulated with a photophysical kinetic model, and the results are analyzed to provide simple guidelines for acceptable Raman-pump powers in resonance FSRS experiments. The acceptable Raman-pump power is proportional to the focused beam area and depends inversely on the sample's molar absorptivity. Copyright © 2013 John Wiley & Sons, Ltd.
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Phase-matching and dilution effects in two-dimensional femtosecond Stimulated Raman Spectroscopy.
The journal of physical chemistry. A, 2013Co-Authors: Barbara Dunlap, Kristina C. Wilson, David W. MccamantAbstract:We present theoretical and experimental data for the attenuation of the cascade signal in two-dimensional femtosecond Stimulated Raman Spectroscopy (2D-FSRS). In previous studies, the cascade signal, caused by two third-order interactions, was found to overwhelm the desired fifth-order signal that would measure vibrational anharmonic coupling. Theoretically, it is found that changing the phase-matching conditions and sample concentration would attenuate the cascade signal, while only slightly decreasing the fifth-order signal. By increasing the crossing angle between the Raman pump and probe and the impulsive pump and probe, the phase-matching efficiency of the cascade signal is significantly attenuated, while the fifth-order efficiency remains constant. The dilution experiments take advantage of the difference in the concentration dependence for the fifth-order and cascade signal, in which the fifth-order signal is proportional to concentration and the cascade signal is proportional to concentration squa...
Philipp Kukura - One of the best experts on this subject based on the ideXlab platform.
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femtosecond Stimulated Raman Spectroscopy
Annual Review of Physical Chemistry, 2007Co-Authors: Philipp Kukura, David W. Mccamant, Richard A MathiesAbstract:Femtosecond Stimulated Raman Spectroscopy (FSRS) is a new ultrafast spectroscopic technique that provides vibrational structural information with high temporal (50-fs) and spectral (10-cm -1 ) resolution. As a result ofthese unique capabilities, FSRS studies of chemical and biochemical reaction dynamics are expected to grow rapidly giving previously unattainable insight into the structural dynamics of reactively evolving systems with atomic spatial and femtosecond temporal resolution. This review discusses the experimental and theoretical concepts behind FSRS, with an emphasis on the origins of its unique temporal and spectral capabilities. We illustrate these capabilities with vibrational studies of ultrafast electronic dynamics, as well as the direct structural observation of nonstationary vibrational wave-packet motion in small molecules and in complex biochemical reaction dynamics.
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Femtosecond broadband Stimulated Raman Spectroscopy: Apparatus and methods
Review of Scientific Instruments, 2004Co-Authors: David W. Mccamant, Sangwoon Yoon, Philipp Kukura, Richard A MathiesAbstract:The laser, detection system, and methods that enable femtosecond broadband Stimulated Raman Spectroscopy (FSRS) are presented in detail. FSRS is a unique tool for obtaining high time resolution (
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femtosecond broadband Stimulated Raman Spectroscopy apparatus and methods
Review of Scientific Instruments, 2004Co-Authors: David W. Mccamant, Sangwoon Yoon, Philipp Kukura, Richard A MathiesAbstract:The laser, detection system, and methods that enable femtosecond broadband Stimulated Raman Spectroscopy (FSRS) are presented in detail. FSRS is a unique tool for obtaining high time resolution (<100 fs) vibrational spectra with an instrument response limited frequency resolution of <10 cm(-1). A titanium:Sapphire-based laser system produces the three different pulses needed for FSRS: (1) A femtosecond visible actinic pump that initiates the photochemistry, (2) a narrow bandwidth picosecond Raman pump that provides the energy reservoir for amplification of the probe, and (3) a femtosecond continuum probe that is amplified at Raman resonances shifted from the Raman pump. The dependence of the Stimulated Raman signal on experimental parameters is explored, demonstrating the expected exponential increase in Raman intensity with concentration, pathlength, and Raman pump power. Raman spectra collected under different electronic resonance conditions using highly fluorescent samples highlight the fluorescence rejection capabilities of FSRS. Data are also presented illustrating our ability: (i) To obtain spectra when there is a large transient absorption change by using a shifted excitation difference technique and (ii) to obtain high time resolution vibrational spectra of transient electronic states.
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Theory of femtosecond Stimulated Raman Spectroscopy.
The Journal of chemical physics, 2004Co-Authors: Soo-y. Lee, David W. Mccamant, Philipp Kukura, Dong-hui Zhang, Richard A MathiesAbstract:Femtosecond broadband Stimulated Raman Spectroscopy (FSRS) is a new technique that produces high-resolution (time-resolved) vibrational spectra from either the ground or excited electronic states of molecules, free from background fluorescence. FSRS uses simultaneously a narrow bandwidth approximately 1-3 ps Raman pump pulse with a continuum approximately 30-50 fs Stokes probe pulse to produce sharp Raman gains, at positions corresponding to vibrational transitions in the sample, riding on top of the continuum Stokes probe spectrum. When FSRS is preceded by a femtosecond actinic pump pulse that initiates the photochemistry of interest, time-resolved Raman Spectroscopy can be carried out. We present two theoretical approaches to FSRS: one is based on a coupling of Raman pump and probe light waves with the vibrations in the medium, and another is a quantum-mechanical description. The latter approach is used to discuss the conditions of applicability and limitations of the coupled-wave description. Extension of the quantum-mechanical description to the case where the Raman pump beam is on resonance with an excited electronic state, as well as when FSRS is used to probe a nonstationary vibrational wave packet prepared by an actinic pump pulse, is also discussed.
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Femtosecond Time-Resolved Stimulated Raman Spectroscopy of the S2(1Bu+) Excited State of β-Carotene
The journal of physical chemistry. A, 2004Co-Authors: Philipp Kukura, David W. Mccamant, Richard A MathiesAbstract:The electronic and vibrational structure of β-carotene's early excited states are examined using femtosecond time-resolved Stimulated Raman Spectroscopy. The vibrational spectrum of the short-lived (∼160 fs) second excited singlet state (S2, 1Bu+) of β-carotene is obtained. Broad, resonantly enhanced vibrational features are observed at ∼1100, 1300, and 1650 cm-1 that decay with a time constant corresponding to the electronic lifetime of S2. The temporal evolution of the vibrational spectra are consistent with significant population of only two low-lying excited electronic states (1Bu+ and 2Ag-) in the ultrafast relaxation pathway of β-carotene.
Renee R. Frontiera - One of the best experts on this subject based on the ideXlab platform.
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Probing structural evolution along multidimensional reaction coordinates with femtosecond Stimulated Raman Spectroscopy
Physical chemistry chemical physics : PCCP, 2011Co-Authors: Renee R. Frontiera, Jyotishman Dasgupta, Chong Fang, Richard A MathiesAbstract:Mapping out multidimensional potential energy surfaces has been a goal of physical chemistry for decades in the quest to both predict and control chemical reactivity. Recently a new spectroscopic approach called Femtosecond Stimulated Raman Spectroscopy or FSRS was introduced that can structurally interrogate multiple dimensions of a reactive potential energy surface. FSRS is an ultrafast laser technique which provides complete time-resolved, background-free Raman spectra in a few laser shots. The FSRS technique provides simultaneous ultrafast time (∼50 fs) and spectral (∼8 cm−1) resolution, thus enabling one to follow reactive structural evolutions as they occur. In this perspective we summarize how FSRS has been used to follow structural dynamics and provide mechanistic detail on three classical chemical reactions: a structural isomerization, an electron transfer reaction, and a proton transfer reaction.
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Surface-Enhanced Femtosecond Stimulated Raman Spectroscopy.
The journal of physical chemistry letters, 2011Co-Authors: Renee R. Frontiera, Natalie L. Gruenke, Anne Isabelle Henry, Richard P. Van DuyneAbstract:Surface-enhanced Raman Spectroscopy (SERS) and femtosecond Stimulated Raman Spectroscopy (FSRS) have revolutionized the Raman Spectroscopy field. SERS provides spectroscopicdetectionofsinglemolecules,andFSRSenablestheacquisitionofRamanspectraon the ultrafast time scale of molecular motion. Here, we present the first successful combination of these two techniques, demonstrating surface-enhanced femtosecond Stimulated Raman spectros- copy(SE-FSRS)usinggoldnanoantennaswithembeddedreportermolecules.Usingapicosecond Raman and femtosecond probe pulse, the time- and ensemble-averaged enhancement factor is estimated to be in the range of 10 4 10 6 . We report the line shapes, power dependence, and magnitude of the SE-FSRS signal and discuss contributions to sample degradation on the minute time scale. With these first successful proof-of-principle experiments, time-resolved SE-FSRS techniques can now be rationally attempted with the goals of investigating the dynamics of plasmonic materials as well as examining the contributions of environmental heterogeneities by probing more homogeneous molecular subsets. SECTION: Nanoparticles and Nanostructures
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femtosecond Stimulated Raman Spectroscopy
Laser & Photonics Reviews, 2011Co-Authors: Renee R. Frontiera, Richard A MathiesAbstract:Advances in the field of Femtosecond Stimulated Raman Spectroscopy (FSRS), a new time-resolved structural technique that provides complete vibrational spectra on the ultrafast timescale, are reviewed. When coupled with a femtosecond optical trigger, the time evolution of a reacting species can be monitored with unprecedented <25 femtosecond temporal and 5 cm-1 spectral resolution. New technological and theoretical advances including the development of tunable FSRS and a background-free FSRS format are discussed. The most recent experimental studies focus on ultrafast reaction dynamics in electronically excited states: isomerization in cyanobacterial phytochrome, ultrafast spin flipping in a solar cell sensitizer, and excited state proton transfer in green fluorescent protein. The use of FSRS to directly map multidimensional reactive potential energy surfaces and to probe the mechanism of reactive internal conversion is prospectively discussed.
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Femtosecond Stimulated Raman Spectroscopy
Laser & Photonics Reviews, 2010Co-Authors: Renee R. Frontiera, Richard A MathiesAbstract:Advances in the field of Femtosecond Stimulated Raman Spectroscopy (FSRS), a new time-resolved structural technique that provides complete vibrational spectra on the ultrafast timescale, are reviewed. When coupled with a femtosecond optical trigger, the time evolution of a reacting species can be monitored with unprecedented
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ultrafast excited state isomerization in phytochrome revealed by femtosecond Stimulated Raman Spectroscopy
Proceedings of the National Academy of Sciences of the United States of America, 2009Co-Authors: Jyotishman Dasgupta, Renee R. Frontiera, Keenan C Taylor, Clark J Lagarias, Richard A MathiesAbstract:Photochemical interconversion between the red-absorbing (Pr) and the far-red-absorbing (Pfr) forms of the photosensory protein phytochrome initiates signal transduction in bacteria and higher plants. The Pr-to-Pfr transition commences with a rapid Z-to-E photoisomerization at the C15C16 methine bridge of the bilin prosthetic group. Here, we use femtosecond Stimulated Raman Spectroscopy to probe the structural changes of the phycocyanobilin chromophore within phytochrome Cph1 on the ultrafast time scale. The enhanced intensity of the C15–H hydrogen out-of-plane (HOOP) mode, together with the appearance of red-shifted CC stretch and NH in-plane rocking modes within 500 fs, reveal that initial distortion of the C15C16 bond occurs in the electronically excited I* intermediate. From I*, 85% of the excited population relaxes back to Pr in 3 ps, whereas the rest goes on to the Lumi-R photoproduct consistent with the 15% photochemical quantum yield. The C15–H HOOP and skeletal modes evolve to a Lumi-R-like pattern after 3 ps, thereby indicating that the C15C16 Z-to-E isomerization occurs on the excited-state surface.
Shaul Mukamel - One of the best experts on this subject based on the ideXlab platform.
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Manipulating Impulsive Stimulated Raman Spectroscopy with a Chirped Probe Pulse
The journal of physical chemistry letters, 2017Co-Authors: Lorenzo Monacelli, Shaul Mukamel, Giovanni Batignani, Giuseppe Fumero, Carino Ferrante, Tullio ScopignoAbstract:Photophysical and photochemical processes are often dominated by molecular vibrations in various electronic states. Dissecting the corresponding, often overlapping, spectroscopic signals from different electronic states is a challenge hampering their interpretation. Here we address impulsive Stimulated Raman Spectroscopy (ISRS), a powerful technique able to coherently stimulate and record Raman-active modes using broadband pulses. Using a quantum-mechanical treatment of the ISRS process, we show the mode-specific way the various spectral components of the broadband probe contribute to the signal generated at a given wavelength. We experimentally demonstrate how to manipulate the signal by varying the probe chirp and the phase-matching across the sample, thereby affecting the relative phase between the various contributions to the signal. These novel control knobs allow us to selectively enhance desired vibrational features and distinguish spectral components arising from different excited states.
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Energy flow between spectral components in 2D broadband Stimulated Raman Spectroscopy
Physical chemistry chemical physics : PCCP, 2015Co-Authors: Giovanni Batignani, Shaul Mukamel, Giuseppe Fumero, Tullio ScopignoAbstract:We introduce a general theoretical description of non resonant impulsive femtosecond Stimulated Raman Spectroscopy in a multimode harmonic model. In this technique an ultrashort actinic pulse creates coherences of low frequency modes and is followed by a paired narrowband Raman pulse and a broadband probe pulse. Using closed-time-path-loop (CTPL) diagrams, the response on both the red and the blue sides of the broadband pulse with respect to the narrowband Raman pulse is calculated, the process couples high and low frequency modes, which share the same ground state. The transmitted intensity oscillates between the red and the blue side, while the total number of photons is conserved. The total energy of the probe signal is periodically modulated in time by the coherence created in the low frequency modes.
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stochastic liouville equations for femtosecond Stimulated Raman Spectroscopy
arXiv: Quantum Physics, 2015Co-Authors: Bijay Kumar Agarwalla, Konstantin E. Dorfman, Hideo Ando, Shaul MukamelAbstract:Electron and vibrational dynamics of molecules are commonly studied by subjecting them to two interactions with a fast actinic pulse that prepares them in a nonstationary state and after a variable delay period $T$, probing them with a Raman process induced by a combination of a broadband and a narrowband pulse. This technique known as femtosecond Stimulated Raman Spectroscopy (FSRS) can effectively probe time resolved vibrational resonances. We show how FSRS signals can be modeled and interpreted using the stochastic Liouville equations (SLE) originally developed for NMR lineshapes. The SLE provides a convenient simulation protocol that can describe complex dynamics due to coupling to collective coordinates at much lower cost that a full dynamical simulation. The origin of the dispersive features which appear when there is no separation of timescales between vibrational variations and dephasing is clarified.
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stochastic liouville equations for femtosecond Stimulated Raman Spectroscopy
Journal of Chemical Physics, 2015Co-Authors: Bijay Kumar Agarwalla, Konstantin E. Dorfman, Hideo Ando, Shaul MukamelAbstract:Electron and vibrational dynamics of molecules are commonly studied by subjecting them to two interactions with a fast actinic pulse that prepares them in a nonstationary state and after a variable delay period T, probing them with a Raman process induced by a combination of a broadband and a narrowband pulse. This technique, known as femtosecond Stimulated Raman Spectroscopy (FSRS), can effectively probe time resolved vibrational resonances. We show how FSRS signals can be modeled and interpreted using the stochastic Liouville equations (SLE), originally developed for NMR lineshapes. The SLE provide a convenient simulation protocol that can describe complex dynamics caused by coupling to collective bath coordinates at much lower cost than a full dynamical simulation. The origin of the dispersive features that appear when there is no separation of timescales between vibrational variations and the dephasing time is clarified.
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femtosecond Stimulated Raman Spectroscopy of the cyclobutane thymine dimer repair mechanism a computational study
Journal of the American Chemical Society, 2014Co-Authors: Hideo Ando, Konstantin E. Dorfman, Benjamin P. Fingerhut, Jason D Biggs, Shaul MukamelAbstract:Cyclobutane thymine dimer, one of the major lesions in DNA formed by exposure to UV sunlight, is repaired in a photoreactivation process, which is essential to maintain life. The molecular mechanism of the central step, i.e., intradimer C—C bond splitting, still remains an open question. In a simulation study, we demonstrate how the time evolution of characteristic marker bands (C═O and C═C/C—C stretch vibrations) of cyclobutane thymine dimer and thymine dinucleotide radical anion, thymidylyl(3′→5′)thymidine, can be directly probed with femtosecond Stimulated Raman Spectroscopy (FSRS). We construct a DFT(M05-2X) potential energy surface with two minor barriers for the intradimer C5—C5′ splitting and a main barrier for the C6—C6′ splitting, and identify the appearance of two C5═C6 stretch vibrations due to the C6—C6′ splitting as a spectroscopic signature of the underlying bond splitting mechanism. The sequential mechanism shows only absorptive features in the simulated FSRS signals, whereas the fast conce...
