Three-pulse Photon Echo Peak Shift Research Articles

Slow solvation dynamics beyond dielectric relaxation by three-pulse photon echo peak shift.

The dynamics of a liquid and its coupling to a solute are crucial for a better understanding of chemical processes in the liquid phase. In isotropic and homogeneous solutions, the time-correlation function of a solute is expected to vanish over time due to the translational and diffusive motions of the solvent. The three-pulse photon echo peak shift (3PEPS) is a third-order nonlinear spectroscopy technique that records the time-correlation function of a solute molecule in a solution, including an offset (inhomogeneity). In this work, we utilized a diffractive optics-based 3PEPS apparatus to fully resolve the dynamics in liquids from femtoseconds to nanoseconds while varying the temperature in the range of 80-298K and the probe solute molecules. Our observations reveal dynamics slower than the dielectric relaxation of n-alcohols, even at room temperature, consisting of a ∼0.5ns time constant that persists below the melting points and a static component (offset) on a nanosecond timescale. Based on the experiments, we suggest that locally formed glass-like clusters in liquids can be responsible for the slow dynamics. Our results may provide new insights into the dynamics of liquids and related phenomena such as liquid-glass and liquid-liquid phase transitions.

Structure and Dynamics of Stacking Interactions in an Antibody Binding Site.

For years, antibodies (Abs) have been used as a paradigm for understanding how protein structure contributes to molecular recognition. However, with the ability to evolve Abs that recognize specific chromophores, they also have great potential as models for how protein dynamics contribute to molecular recognition. We previously raised murine Abs to different chromophores and, with the use of three-pulse photon echo peak shift spectroscopy, demonstrated that the immune system is capable of producing Abs with widely varying flexibility. We now report the characterization of the complexes formed between two Abs, 5D11 and 10A6, and the chromophoric ligand that they were evolved to recognize, 8-methoxypyrene-1,3,6-trisulfonic acid (MPTS). The sequences of the Ab genes indicate that they evolved from a common precursor. We also used a variety of spectroscopic methods to probe the photophysics and dynamics of the Ab-MPTS complexes and found that they are similar to each other but distinct from previously characterized anti-MPTS Abs. Structural studies revealed that this difference likely results from a unique mode of binding in which MPTS is sandwiched between the side chain of PheH98, which interacts with the chromophore via T-stacking, and the side chain of TrpL91, which interacts with the chromophore via parallel stacking. The T-stacking interaction appears to mediate relaxation on the picosecond time scale, while the parallel stacking appears to mediate relaxation on an ultrafast, femtosecond time scale, which dominates the response. The anti-MPTS Abs thus not only demonstrate the simultaneous use of the two limiting modes of stacking for molecular recognition, but also provide a unique opportunity to characterize how dynamics might contribute to molecular recognition. Both types of stacking are common in proteins and protein complexes where they may similarly contribute to dynamics and molecular recognition.

Adaptive mutations alter antibody structure and dynamics during affinity maturation.

While adaptive mutations can bestow new functions on proteins via the introduction or optimization of reactive centers, or other structural changes, a role for the optimization of protein dynamics also seems likely but has been more difficult to evaluate. Antibody (Ab) affinity maturation is an example of adaptive evolution wherein the adaptive mutations may be identified and Abs may be raised to specific targets that facilitate the characterization of protein dynamics. Here, we report the characterization of three affinity matured Abs that evolved from a common germline precursor to bind the chromophoric antigen (Ag), 8-methoxypyrene-1,3,6-trisulfonate (MPTS). In addition to characterizing the sequence, molecular recognition, and structure of each Ab, we characterized the dynamics of each complex by determining their mechanical response to an applied force via three-pulse photon echo peak shift (3PEPS) spectroscopy and deconvoluting the response into elastic, anelastic, and plastic components. We find that for one Ab, affinity maturation was accomplished via the introduction of a single functional group that mediates a direct contact with MPTS and results in a complex with little anelasticity or plasticity. In the other two cases, more mutations were introduced but none directly contact MPTS, and while their effects on structure are subtle, their effects on anelasticity and plasticity are significant, with the level of plasticity correlated with specificity, suggesting that the optimization of protein dynamics may have contributed to affinity maturation. A similar optimization of structure and dynamics may contribute to the evolution of other proteins.

Pseudo-Rephasing and Pseudo-Free-Induction-Decay Mechanism in Two-Color Three-Pulse Photon Echo of a Binary System

We investigate the two-color three-pulse photon echo peak shift in a (left-right) binary system, where each component consists of a heterodimer. On the basis of the model, we find that the effect of the excitonic asymmetry between two components leads to an additional factor in the peak shift. A pseudo-rephasing and pseudo-free-induction-decay mechanism is proposed to explain the resultant negative peak shift, when the differences between the two left/right components have the opposite sign. In such a case, estimates of the electronic coupling strength via two- and one-color peak shift experiments lead to an underestimate of the coupling magnitude.

Proton Disorder in Ice Ih and Inhomogeneous Broadening in Two-Dimensional Infrared Spectroscopy

It is well-known that in ice Ih the oxygen atoms form a regular hexagonal lattice while the positions of the hydrogen atoms are disordered, called proton disorder in the literature. Various OH (OD) stretch vibrational spectroscopies (e.g., IR, Raman, two-dimensional IR (2DIR), and hole burning) have been used to probe this proton disorder in the past several decades. However, the presence and the magnitude of the inhomogeneous broadening due to this proton disorder in the vibrational spectroscopy is still controversial. In this work, we calculate 2DIR spectroscopy for HOD in D2O ice Ih at 80 K with a mixed quantum/classical approach, and make comparison to a recent 2DIR experiment on the same system. Fair agreement is achieved between theory and experiment, although the calculated 2DIR line shape shows inhomogeneous broadening that was not observed in the experiment. However, the theory reproduces the linear IR for the same system fairly well, and the inhomogeneous broadening from the calculation is consistent with the extrapolation of the experimental IR line-widths in the literature. The effect of this proton disorder on the 2DIR line shape is explored in detail. We also calculate the vibrational three-pulse photon echo peak shift signal, which shows signatures of both low-frequency dynamics and inhomogeneous broadening.

Ultrafast solvation response in room temperature ionic liquids: Possible origin and importance of the collective and the nearest neighbour solvent modes

Recent three-pulse photon echo peak shift (3PEPS) measurements [M. Muramatsu, Y. Nagasawa, and H. Miyasaka, J. Phys. Chem. A 115, 3886 (2011)] with several room temperature ionic liquids (RTILs) have revealed multi-exponential dynamics with ultrafast solvation timescale in the range, 20 < τ(1)∕fs < 250, for both imidazolium and phosphonium RTILs. This is striking for two reasons: (i) the timescale is much faster than those reported by the dynamic Stokes shift (DSS) experiments [S. Arzhantsev, H. Jin, G. A. Baker, and M. Maroncelli, J. Phys. Chem. B 111, 4978 (2007)] and (ii) sub-hundered femtosecond solvation response in phosphonium ionic liquids is reported for the first time. Here, we present a mode coupling theory based calculation where such ultrafast solvation in 3PEPS measurements has been visualized to originate from the nearest neighbour solute-solvent interaction. Consideration of Lennard-Jones interaction for the nearest neighbour solute-solvent non-dipolar interaction leads to biphasic dynamics with a predicted ultrafast time constant in the ∼100-250 fs range, followed by a slower one similar to that reported by the 3PEPS measurements. In addition, the calculated fast time constants and amplitudes are found to be in general agreement with those from computer simulations. Different microscopic mechanisms for ultrafast solvation response measured by the 3PEPS and DSS experiments have been proposed and relative contributions of the collective and nearest neighbour solvent modes investigated. Relation between the single particle rotation and ultrafast polar solvation in these RTILs has been explored. Our analyses suggest 3PEPS and DSS experiments are probably sensitive to different components of the total solvation energy relaxation of a laser-excited dye in a given ionic liquid. Several predictions have also been made, which may be re-examined via suitable experiments.

Protein Dynamics and the Diversity of an Antibody Response

The immune system is remarkable in its ability to produce antibodies (Abs) with virtually any specificity from a limited repertoire of germ line precursors. Although the contribution of sequence diversity to this molecular recognition has been studied for decades, recent models suggest that protein dynamics may also broaden the range of targets recognized. To characterize the contribution of protein dynamics to immunological molecular recognition, we report the sequence, thermodynamic, and time-resolved spectroscopic characterization of a panel of eight Abs elicited to the chromophoric antigen 8-methoxypyrene-1,3,6-trisulfonate (MPTS). Based on the sequence data, three of the Abs arose from unique germ line Abs, whereas the remaining five comprise two sets of siblings that arose by somatic mutation of a common precursor. The thermodynamic data indicate that the Abs recognize MPTS via a variety of mechanisms. Although the spectroscopic data reveal small differences in protein dynamics, the anti-MPTS Abs generally show similar levels of flexibility and conformational heterogeneity, possibly representing the convergent evolution of the dynamics necessary for function. However, one Ab is significantly more rigid and conformationally homogeneous than the others, including a sibling Ab from which it differs by only five somatic mutations. This example of divergent evolution demonstrates that point mutations are capable of fixing significant differences in protein dynamics. The results provide unique insight into how high affinity Abs may be produced that bind virtually any target and possibly, from a more general perspective, how new protein functions are evolved.

Bimodal dynamics of mechanically constrained hydrogen bonds revealed by vibrational photon echoes

We have investigated the dynamics of the hydrogen bonds that connect the components of a [2]rotaxane in solution. In this rotaxane, the amide groups in the benzylic-amide macrocycle and the succinamide thread are connected by four equivalent N-H⋅⋅⋅O=C hydrogen bonds. The fluctuations of these hydrogen bonds are mirrored by the frequency fluctuations of the NH-stretch modes, which are probed by means of three-pulse photon-echo peak shift spectroscopy. The hydrogen-bond fluctuations occur on three different time scales, with time constants of 0.1, 0.6, and ≥200 ps. Comparing these three time scales to the ones found in liquid formamide, which contains the same hydrogen-bonded amide motif but without mechanical constraints, we find that the faster two components, which are associated with small-amplitude fluctuations in the strength of the N-H⋅⋅⋅O=C hydrogen bonds, are very similar in the liquid and the rotaxane. However, the third component, which is associated with the breaking and subsequent reformation of hydrogen bonds, is found to be much slower in the rotaxane than in the liquid. It can be concluded that the mechanical bonding in a rotaxane does not influence the amplitude and time scale of the small-amplitude fluctuations of the hydrogen bonds, but strongly slows down the complete dissociation of these hydrogen bonds. This is probably because in a rotaxane breaking of the macrocycle-axle contacts is severely hindered by the mechanical constraints. The hydrogen-bond dynamics in rotaxane-based molecular machines can therefore be regarded as liquidlike on a time scale 1 ps and less, but structurally frozen on longer (up to at least 200 ps) time scales.

Ultrafast Solvation Dynamics in Room Temperature Ionic Liquids Observed by Three-Pulse Photon Echo Peak Shift Measurements

Three-pulse photon echo peak shift (3PEPS) measurement was applied to the investigation of the primary part (<100 ps) of the solvation dynamics in a series of imidazolium ionic liquids (IL) with an organic dye, oxazine 4 (Ox4), utilized as a probe. The ultrafast solvent response in the range of ≤300 fs exhibited dependence on the square root of the anion mass, indicating its relation with the inertial motion of anion. The inertial response of ILs with chloride anion was the fastest among other ILs with heavier and larger anions. Because Ox4 is a cationic dye, it holds a stronger interaction with the anion of IL, thus the ultrafast part of the solvation is strongly affected by the inertial motion of anions. The second solvation component in the range of ≤3.5 ps had better correlation with the reduced mass and the size of both ions included, indicating the beginning of a more global solvation process.

Probing Coherence in Synthetic Cyclic Light-Harvesting Pigments

A series of π-extended cyclic thiophene oligomers of 12, 18, 24, and 30 repeat units have been studied using methods of ultrafast time-resolved absorption, fluorescence upconversion, and three-pulse photon echo. These measurements were conducted in order to examine the structure-function relationships that may affect the coherence between chromophores within the organic macrocycles. Our results indicate that an initial delocalized state can be seen upon excitation of the cyclic thiophenes. Anisotropy measurements show that this delocalized state decays on an ultrafast time scale and is followed by the presence of incoherent hopping. From the use of a phenomenological model, we conclude that our ultrafast anisotropy decay measurements suggest that the system does not reside in the Förster regime and coherence within the system must be considered. Three-pulse photon echo peak shift experiments reveal a clear dependence of initial peak shift with ring size, indicating a weaker coupling to the bath (and stronger intramolecular interactions) as the ring size is increased. Our results suggest that the initial delocalized state increases with ring size to distances (and number of chromophores) comparable to the natural light-harvesting system.

Pure optical dephasing dynamics in semiconducting single-walled carbon nanotubes

We report a detailed study of ultrafast exciton dephasing processes in semiconducting single-walled carbon nanotubes employing a sample highly enriched in a single tube species, the (6,5) tube. Systematic measurements of femtosecond pump-probe, two-pulse photon echo, and three-pulse photon echo peak shift over a broad range of excitation intensities and lattice temperature (from 4.4 to 292 K) enable us to quantify the timescales of pure optical dephasing (T(2)(*)), along with exciton-exciton and exciton-phonon scattering, environmental effects as well as spectral diffusion. While the exciton dephasing time (T(2)) increases from 205 fs at room temperature to 320 fs at 70 K, we found that further decrease of the lattice temperature leads to a shortening of the T(2) times. This complex temperature dependence was found to arise from an enhanced relaxation of exciton population at lattice temperatures below 80 K. By quantitatively accounting the contribution from the population relaxation, the corresponding pure optical dephasing times increase monotonically from 225 fs at room temperature to 508 fs at 4.4 K. We further found that below 180 K, the pure dephasing rate (1/T(2)(*)) scales linearly with temperature with a slope of 6.7 ± 0.6 μeV/K, which suggests dephasing arising from one-phonon scattering (i.e., acoustic phonons). In view of the large dynamic disorder of the surrounding environment, the origin of the long room temperature pure dephasing time is proposed to result from reduced strength of exciton-phonon coupling by motional narrowing over nuclear fluctuations. This consideration further suggests the occurrence of remarkable initial exciton delocalization and makes nanotubes ideal to study many-body effects in spatially confined systems.

Three‐Pulse Photon‐Echo Peak Shift Spectroscopy and Its Application for the Study of Solvation and Nanoscale Excitons

An understanding of chemical reactivity begins with an understanding of the dynamics involved regarding system-bath interactions. Spectroscopic studies of these interactions in condensed-phase multichromophoric systems are intricate and contain much information. Photon-echo spectroscopy has proven to be a useful tool for probing these interactions. A description of three-pulse photon-echo peak shift spectroscopy (3PEPS)--theory, experiment, and application--for the study of solvation and dynamics of nanoscale excitons is presented. Also, we discuss how two-dimensional photon-echo spectroscopy (2DPE) relates to 3PEPS and show how 3PEPS data can be extracted from 2D photon-echo data.

Electronic photon echo spectroscopy and vibrations

Coupling between electronic and nuclear degrees of freedom in Rhodamine 800 has been studied using fluorescence line narrowing (FLN) and three-pulse photon echo peak shift (3PEPS). From the FLN measurement we extract the Huang-Rhys S-factors and frequencies of 16 Franck-Condon active vibrations clustered in two groups centred around 350 cm −1 and 1400 cm −1. The five modes below 500 cm −1 covered by the excitation pulse spectral band create a complex beating pattern in the 3PEPS measurements. After determining the reorganisation energy of the modes involved in the peak shift measurement we are able to obtain the S-factors of the modes. The S-factors from two different experiments are in good agreement. The dephasing rates of these vibrations deviate significantly from the band-gap law. We propose that the main channel for the dephasing of the modes above 225 cm −1 is a second order process involving one phonon and a molecular vibration.

Three-Pulse Photon Echo Peak Shift Measurements of Capped CdSe Quantum Dots

In this article, the results of femtosecond three-pulse photon echo peak shift (3-PEPS) measurements are reported for a series of cadmium selenide core−shell semiconductor nanocrystals. The peak shift data were found to be highly dependent on the shell compositions and particle morphologies. The static inhomogeneity parameter was found to vary from 10 cm−1 for highly isotropic particles to 170 cm−1 for particles with a broad size distribution. We also discuss the high-frequency (≈212 cm−1) longitudinal optical (LO) phonon and the low-frequency (≈13−19 cm−1) longitudinal acoustic (LA) phonon modes (ω00) and how the damping times and frequencies also depend on the choice of capping material.

Diffractive optics based three-pulse photon echo peak shift studies of spectral diffusion in polar liquids: Evidence for long lived frequency correlations

We report a three-pulse photon echo peak shift (3PEPS) apparatus adopting a diffractive beam splitter to generate triplets of femtosecond pulses with tilted wave front, which enhances the overlap over the entire aperture in a noncollinear geometry while preserving femtosecond pulse duration. The apparatus provides highly reproducible 3PEPS data including the long time peak shift, a critical parameter to recognize the spectral inhomogeneity in condensed phases. To demonstrate the high performance of our setup and to examine the inhomogeneous line broadening in liquids, we measured 3PEPS of a carbocyanine dye IR125 in several solvents. The solvation dynamics becomes slower for IR125 compared to the typical values reported previously probably due to the multipolar nature of the excitation in this large and flexible probe molecule. More importantly, inhomogeneity was observed unambiguously in all solvents, and it is excitation energy dependent. It was speculated that slow dielectric relaxation and conformational heterogeneity may be responsible for the inhomogeneity.

Ultrafast energy relaxation and anisotropy decay of the librational motion in liquid water: A molecular dynamics study

We theoretically investigate intermolecular motions in liquid water in terms of third-order infrared (IR) spectroscopy. We calculate two-dimensional (2D) IR spectra, pump-probe signals, and three-pulse stimulated photon echo signals from the combination of equilibrium and nonequilibrium molecular dynamics simulations. The 2D IR spectra and the three-pulse photon echo peak shift exhibit that the frequency correlation of the librational motion decays with a time scale of 100 fs. The two-color 2D IR spectra and the pump-probe signals reveal that the energy transfer from the librational motion at 700 cm(-1) to the low frequency motion below 300 cm(-1) occurs with a time scale of 60 fs and the subsequent relaxation to the hot ground state takes place on a 500 fs time scale. The time scale of the anisotropy decay of the librational motion is found to be approximately 115 fs. The energy dissipation processes are investigated in detail by using the nonequilibrium molecular dynamics simulation, in which an electric field pulse is applied. We show that the fast energy transfer from the librational motion to the low frequency motion is mainly due to the librational-librational energy transfer. We also show that the fast anisotropy decay mainly arises from the rapid intermolecular energy transfer.

Molecular Dynamics Simulation of Nonlinear Spectroscopies of Intermolecular Motions in Liquid Water

Water is the most extensively studied of liquids because of both its ubiquity and its anomalous thermodynamic and dynamic properties. The properties of water are dominated by hydrogen bonds and hydrogen bond network rearrangements. Fundamental information on the dynamics of liquid water has been provided by linear infrared (IR), Raman, and neutron-scattering experiments; molecular dynamics simulations have also provided insights. Recently developed higher-order nonlinear spectroscopies open new windows into the study of the hydrogen bond dynamics of liquid water. For example, the vibrational lifetimes of stretches and a bend, intramolecular features of water dynamics, can be accurately measured and are found to be on the femtosecond time scale at room temperature. Higher-order nonlinear spectroscopy is expressed by a multitime correlation function, whereas traditional linear spectroscopy is given by a one-time correlation function. Thus, nonlinear spectroscopy yields more detailed information on the dynamics of condensed media than linear spectroscopy. In this Account, we describe the theoretical background and methods for calculating higher order nonlinear spectroscopy; equilibrium and nonequilibrium molecular dynamics simulations, and a combination of both, are used. We also present the intermolecular dynamics of liquid water revealed by fifth-order two-dimensional (2D) Raman spectroscopy and third-order IR spectroscopy. 2D Raman spectroscopy is sensitive to couplings between modes; the calculated 2D Raman signal of liquid water shows large anharmonicity in the translational motion and strong coupling between the translational and librational motions. Third-order IR spectroscopy makes it possible to examine the time-dependent couplings. The 2D IR spectra and three-pulse photon echo peak shift show the fast frequency modulation of the librational motion. A significant effect of the translational motion on the fast frequency modulation of the librational motion is elucidated by introducing the "translation-free" molecular dynamics simulation. The isotropic pump-probe signal and the polarization anisotropy decay show fast transfer of the librational energy to the surrounding water molecules, followed by relaxation to the hot ground state. These theoretical methods do not require frequently used assumptions and can thus be called ab initio methods; together with multidimensional nonlinear spectroscopies, they provide powerful methods for examining the inter- and intramolecular details of water dynamics.

Three-pulse photon echo peak shift spectroscopy as a probe of flexibility and conformational heterogeneity in protein folding

We investigate the equilibrium unfolding of Zn-cytochrome c in guanidine hydrochloride by three-pulse photon echo peak shift (3PEPS) spectroscopy. Unexpectedly, the measurements reveal that inhomogeneous broadening of the sample at the midpoint of the denaturation is larger than that of either native or unfolded states. To interpret this finding, we present simulations of the peak shift for both two-state and three-state unfolding models. Both the denaturant concentration dependence of the asymptotic peak shift (APS) and the wavelength dependence of the APS at the midpoint of the denaturation are different for the two models. Our data are consistent with two-state unfolding.

Probe of flexibility and conformational heterogeneity in Zn-cytochrome c (Zn-cyt c) folding by Three-Pulse Photon Echo Peak Shift (3PEPS) Spectroscopy

We investigated the dynamics and conformational heterogeneity of Zn-cyt c with 3PEPS, a type of femtosecond nonlinear spectroscopy that is used to quantify the spectrum of sub-nanosecond protein motions and the inhomogeneous broadening of the system. Wavelength-dependent measurements were performed on the Soret transitions of the folded state, the guanidine hydrochloride unfolded state (4.5 M), and the state at the midpoint (2.5 M) of the denaturant titration. The measurements resolve a substantial increase in the inhomogeneous broadening of the Soret band upon unfolding, as expected due to an increase in conformational diversity upon unfolding.

Solute specific polar solvation studied by photon echo spectroscopy

Polar solvation dynamics of two solute molecules in a series of 1-alcohols has been studied using the three-pulse photon echo peak shift technique. The inertial dynamics, on sub-200 fs timescale, is essentially independent of solvent in the 1-alcohol series. For a given solute, the solvent dependence is mainly manifested in the diffusive solvation dynamics. The solute dependence appears as a significantly stronger inertial component in one of the molecules. We ascribe this solute dependence to the differences in charge redistribution upon excitation. A detailed investigation of oscillations of the peak shift reveals a solvent dependent beating that can be connected to solvation of the vibrational mode in the excited state. The solvent dependence of the dephasing dynamics of the excited state mode can be explained by the electronic transition frequency correlation function and the beating pattern of the echo signal originates from interference between ground and excited state Feynman pathways.