Taking apart the two-dimensional infrared vibrational echo spectra: More information and elimination of distortions

Kwak, Kyungwon; Rosenfeld, Daniel; Fayer, M. D.

doi:10.1063/1.2927906

Cited by 252 publications

(514 citation statements)

References 41 publications

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“…The FFCF, which is given by hδωðtÞδωð0Þi, quantifies the time scales for the frequency fluctuations that report on the dynamics of the environment around the azide anion. To extract the FFCF from our 2D IR data, we use the center line slope (CLS) method introduced by the Fayer group (45,46). In this method, we take slices through the 2D spectrum at each value of ω 1 and locate the position of the maximum in ω 3 .…”

Section: D Ir Spectroscopy | Enzyme Dynamicsmentioning

confidence: 99%

Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase

Bandaria

Dutta

Nydegger

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

118

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The potential for femtosecond to picosecond time-scale motions to influence the rate of the intrinsic chemical step in enzymecatalyzed reactions is a source of significant controversy. Among the central challenges in resolving this controversy is the difficulty of experimentally characterizing thermally activated motions at this time scale in functionally relevant enzyme complexes. We report a series of measurements to address this problem using twodimensional infrared spectroscopy to characterize the time scales of active-site motions in complexes of formate dehydrogenase with the transition-state-analog inhibitor azide (N − 3 ). We observe that the frequency-frequency time correlation functions (FFCF) for the ternary complexes with NAD þ and NADH decay completely with slow time constants of 3.2 ps and 4.6 ps, respectively. This result suggests that in the vicinity of the transition state, the active-site enzyme structure samples a narrow and relatively rigid conformational distribution indicating that the transition-state structure is well organized for the reaction. In contrast, for the binary complex, we observe a significant static contribution to the FFCF similar to what is seen in other enzymes, indicating the presence of the slow motions that occur on time scales longer than our measurement window. 2D IR spectroscopy | enzyme dynamicsT he functional role of protein motions at the femtosecond to picosecond time scale is a hotly debated topic in enzymology. Although such a role could be general in nature, many experimental (1-10) and theoretical (11-23) studies of enzymecatalyzed hydrogen transfers have invoked protein motions at this time scale to explain anomalous kinetic isotope effects (KIE) and their temperature dependence. These studies result in the development of theoretical models, often referred to as Marcus-like models, in which the environmental reorganization that precedes the hydrogen-tunneling event has evolved to optimize the conformation of the transition state for tunneling (1,7,24). Fig. 1 illustrates the physical picture underlying such models. Heavy atom motions along the reorganization coordinate carry the system to a point where the donor and acceptor wells in the double-well hydrogen atom potential are degenerate and tunneling can proceed. At this position, the donor-acceptor distance and its fluctuations determine the tunneling probability. Mathematically, the rate constant for hydrogen transfer in these models is given by expressions of the form where C is the fraction of reactive complexes, the first exponential, in analogy with the Marcus theory for electron transfer, reflects the reorganization of the heavy atoms that modulates the relative energies of the reactants and the products to minimize the energy defect between the zero-point levels of the donor and acceptor wells. ΔG°is the driving force for the reaction, and λ is the reorganization energy. The second exponential gives the overlap between the donor and acceptor wave functions as a function of the donor-acceptor distan...

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Section: D Ir Spectroscopy | Enzyme Dynamicsmentioning

confidence: 99%

Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase

Bandaria

Dutta

Nydegger

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

118

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“…This trend has been observed previously. 3,33,39 We next consider the k I and k II signals using the XXYY polarization configuration ͑k 1 and k 2 have parallel polarizations which is perpendicular to that of k 3 and k 4 ͒. When the transition dipole magnitude and orientation are fixed, intermolecular couplings neglected and the fluctuations are slow, we expect S XXYY = S XXXX / 3.…”

Section: The K I and K Ii Signalsmentioning

confidence: 99%

Coherent infrared multidimensional spectra of the OH stretching band in liquid water simulated by direct nonlinear exciton propagation

Falvo

Palmieri

Mukamel

2009

The Journal of Chemical Physics

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The two-dimensional vibrational response of the disordered strongly fluctuating OH exciton band in liquid water is investigated using a new simulation protocol. The direct nonlinear exciton propagation generalizes the nonlinear exciton equations to include nonadiabatic time dependent Hamiltonian and transition dipole fluctuations. The excitonic picture is retained and the large cancellation between Liouville pathways is built-in from the outset. The sensitivity of the photon echo and double-quantum-coherence techniques to frequency fluctuations, molecular reorientation, intermolecular coupling, and the two-exciton coherence is investigated. The photon echo is particularly sensitive to the frequency fluctuations and molecular reorientation, whereas the double-quantum coherence provides a unique probe for intermolecular couplings and two-exciton coherence.

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“…We then demonstrate the connection between the nodal line [23][24][25][26][27][28] slope and the correlation strength between electronic and vibrational transition energies by showing the corresponding spectra for different correlation strengths. We also discuss the meaning of "rephasing" and nonrephasing pulses sequences for an experiment involving two different types of optical transitions.…”

Section: Introductionmentioning

confidence: 97%

Determining the static electronic and vibrational energy correlations via two-dimensional electronic-vibrational spectroscopy

Dong

Lewis

Oliver

et al. 2015

The Journal of Chemical Physics

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Changes in the electronic structure of pigments in protein environments and of polar molecules in solution inevitably induces a re-adaption of molecular nuclear structure.Both changes of electronic and vibrational energies can be probed with visible or infrared lasers, such as two-dimensional electronic or vibrational spectroscopies. The extent to which the two changes are correlated remains elusive. The recent demonstration of two-dimensional electronic-vibrational (2DEV) spectroscopy potentially enables a direct measurement of this correlation experimentally. However, it has hitherto been unclear how to characterize the correlation from the spectra. In this paper, we present a theoretical formalism to demonstrate the slope of the nodal line between the excited state absorption and ground state bleach peaks in the spectra as a characterization of the correlation between electronic and vibrational transition energies. We also show the dynamics of the nodal line slope is correlated to the vibrational spectral dynamics. Additionally, we demonstrate the fundamental 2DEV spectral line-shape of a monomer with newly developed response functions. a) Electronic mail: grfleming@lbl.gov 1

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Taking apart the two-dimensional infrared vibrational echo spectra: More information and elimination of distortions

Cited by 252 publications

References 41 publications

Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase

Characterizing the dynamics of functionally relevant complexes of formate dehydrogenase

Coherent infrared multidimensional spectra of the OH stretching band in liquid water simulated by direct nonlinear exciton propagation

Determining the static electronic and vibrational energy correlations via two-dimensional electronic-vibrational spectroscopy

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