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1.
In this and the following paper, we describe the ultrafast structural fluctuations and rearrangements of the hydrogen bonding network of water using two-dimensional (2D) infrared spectroscopy. 2D IR spectra covering all the relevant time scales of molecular dynamics of the hydrogen bonding network of water were studied for the OH stretching absorption of HOD in D2O. Time-dependent evolution of the 2D IR line shape serves as a spectroscopic observable that tracks how different hydrogen bonding environments interconvert while changes in spectral intensity result from vibrational relaxation and molecular reorientation of the OH dipole. For waiting times up to the vibrational lifetime of 700 fs, changes in the 2D line shape reflect the spectral evolution of OH oscillators induced by hydrogen bond dynamics. These dynamics, characterized through a set of 2D line shape analysis metrics, show a rapid 60 fs decay, an underdamped oscillation on a 130 fs time scale induced by hydrogen bond stretching, and a long time decay constant of 1.4 ps. 2D surfaces for waiting times larger than 700 fs are dominated by the effects of vibrational relaxation and the thermalization of this excess energy by the solvent bath. Our modeling based on fluctuations with Gaussian statistics is able to reproduce the changes in dispersed pump-probe and 2D IR spectra induced by these relaxation processes, but misses the asymmetry resulting from frequency-dependent spectral diffusion. The dynamical origin of this asymmetry is discussed in the companion paper.  相似文献   

2.
The vibrational Stokes shift of the OH stretching transition nu(OH) of water is the shift between the ground-state absorption and the excited-state (v=1) emission. A recent measurement on HOD in D(2)O solvent [S. Woutersen and H. J. Bakker, Phys. Rev. Lett. 83, 2077 (1999)] of a 70 cm(-1) redshift, and a subsequent calculation of a 57 cm(-1) redshift using equilibrium molecular dynamics simulations [C. P. Lawrence and J. L. Skinner, J. Chem. Phys. 117, 8847 (2002)] were in good agreement. We now report extensive measurements of the vibrational Stokes shift in HOD/D(2)O using an ultrafast IR pump, Raman probe method. The vibrational Stokes shift is seen to depend on the pump pulse frequency and on time delay; by varying these parameters it can be made to range from 112 to -32 cm(-1) (negative values indicate a blueshift in the excited state). The equilibrium vibrational Stokes shift is actually a negative rather than a positive quantity. Possible reasons for the disagreement between experiment and theory are briefly discussed.  相似文献   

3.
Water dynamics as reflected by the spectral diffusion of the water hydroxyl stretch were measured in w(0) = 2 (1.7 nm diameter) Aerosol-OT (AOT)/water reverse micelles in carbon tetrachloride and in isooctane solvents using ultrafast 2D IR vibrational echo spectroscopy. Orientational relaxation and population relaxation are observed for w(0) = 2, 4, and 7.5 in both solvents using IR pump-probe measurements. It is found that the pump-probe observables are sensitive to w(0), but not to the solvent. However, initial analysis of the vibrational echo data from the water nanopool in the reverse micelles in the isooctane solvent seems to yield different dynamics than the CCl(4) system in spite of the fact that the spectra, vibrational lifetimes, and orientational relaxation are the same in the two systems. It is found that there are beat patterns in the interferograms with isooctane as the solvent. The beats are observed from a signal generated by the AOT/isooctane system even when there is no water in the system. A beat subtraction data processing procedure does a reasonable job of removing the distortions in the isooctane data, showing that the reverse micelle dynamics are the same within experimental error regardless of whether isooctane or carbon tetrachloride is used as the organic phase. Two time scales are observed in the vibrational echo data, ~1 and ~10 ps. The slower component contains a significant amount of the total inhomogeneous broadening. Physical arguments indicate that there is a much slower component of spectral diffusion that is too slow to observe within the experimental window, which is limited by the OD stretch vibrational lifetime.  相似文献   

4.
Two-dimensional infrared (2D IR) spectroscopy of the symmetric and asymmetric C[Triple Bond]O stretching vibrations of Rh(CO)(2)acac in hexane has been used to investigate vibrational coherence transfer, dephasing, and population relaxation in a multilevel vibrational system. The transfer of coherence between close-lying vibrational frequencies results in extra relaxation-induced peaks in the 2D IR spectrum, whose amplitude depends on the coherence transfer rate. Coherence transfer arises from the mutual interaction of the bright CO stretches with dark states, which in this case reflects the mutual d-pi(*) back bonding of the Rh center to both the terminal carbonyls and the acetylacenonate ligand. For 2D IR relaxation experiments with variable waiting times, coherent dynamics lead to the modulation of peak amplitudes, while incoherent population relaxation and exchange results in the growth of the relaxation-induced peaks. We have modeled the data by propagating the density matrix with the Redfield equation, incorporating all vibrational relaxation processes during all three experimental time periods and including excitation reorientation effects arising from relaxation. Coherence and population transfer time scales from the symmetric to the asymmetric stretch were found to be 350 fs and 3 ps, respectively. We also discuss a diagrammatic approach to incorporating all vibrational relaxation processes into the nonlinear response function, and show how coherence transfer influences the analysis of structural variables from 2D IR spectroscopy.  相似文献   

5.
The signatures of nanosolvation on the one‐ and two‐dimensional (1D and 2D) IR spectra of a proton‐transfer mode in a hydrogen‐bonded complex dissolved in polar solvent molecule nanoclusters of varying size are elucidated by using mixed quantum–classical molecular dynamics simulations. For this particular system, increasing the number of solvent molecules successively from N=7 to N=9 initiates the transition of the system from a cluster state to a bulk‐like state. Both the 1D and 2D IR spectra reflect this transition through pronounced changes in their peak intensities and numbers, but the time‐resolved 2D IR spectra also manifest spectral features that uniquely identify the onset of the cluster‐to‐bulk transition. In particular, it is observed that in the 1D IR spectra, the relative intensities of the peaks change such that the number of peaks decreases from three to two as the size of the cluster increases from N=7 to N=9. In the 2D IR spectra, off‐diagonal peaks are observed in the N=7 and N=8 cases at zero waiting time, but not in the N=9 case. It is known that there are no off‐diagonal peaks in the 2D IR spectrum of the bulk version of this system at zero waiting time, so the disappearance of these peaks is a unique signature of the onset of bulk‐like behavior. Through an examination of the trajectories of various properties of the complex and solvent, it is possible to relate the emergence of these off‐diagonal peaks to an interplay between the vibrations of the complex and the solvent polarization dynamics.  相似文献   

6.
Dual-frequency 2D IR heterodyne photon-echo spectroscopy of C[triple bond]N and C=O stretching vibrational modes in 2-cyanocoumarin is reported. We have shown that the interaction among these modes provides convenient and useful structural constraints for molecules. Implementation of two pulse sequences, 4, 4, and 6 microm and 6, 6, and 4 microm, allowed the clear determination of contributions caused by vibrational relaxation. Positive correlation between C[triple bond]N and C=O frequency distributions was observed in 2-cyanocoumarin. Because C[triple bond]N modes are highly localized and have frequencies in a spectral region with minimal water absorption, the C[triple bond]N/C=O interactions have a strong potential for use as structural reporters in proteins. In addition to CN/CO peaks, the cross-peaks responsible for the C[triple bond]N/C=C interaction are also observed in the 2D IR spectra, where C=C is a coumarin ring stretching mode. We have demonstrated that 2D IR spectroscopy can utilize interactions of strong IR modes with weak local modes as structural reporters.  相似文献   

7.
An ensemble of exciton Hamiltonians for the amide-I band of the folded and unfolded states of a helical beta-heptapeptide is generated using a molecular dynamics (MD) simulation. The correlated fluctuations of its parameters and their signatures in two-dimensional (2D) vibrational echo spectroscopy are computed. This technique uses infrared pulse sequences to provide ultrafast snapshots of molecular structural fluctuations, in analogy with multidimensional NMR. The present study demonstrates that, by combining a method of calculating the vibrational Hamiltonian from MD snapshots and the nonlinear exciton equations (NEE), it may be possible to simulate realistic multidimensional IR spectra of chemically and biologically interesting systems.  相似文献   

8.
Vibrational cooling by 9-methyladenine was studied in a series of solvents by femtosecond transient absorption spectroscopy. Signals at UV and near-UV probe wavelengths were assigned to hot ground state population created by ultrafast internal conversion following electronic excitation by a 267 nm pump pulse. A characteristic time for vibrational cooling was determined from bleach recovery signals at 250 nm. This time increases progressively in H2O (2.4 ps), D2O (4.2 ps), methanol (4.5 ps), and acetonitrile (13.1 ps), revealing a pronounced solvent effect on the dissipation of excess vibrational energy. The trend also indicates that the rate of cooling is enhanced in solvents with a dense network of hydrogen bonds. The faster rate of cooling seen in H2O vs D2O is noteworthy in view of the similar hydrogen bonding and macroscopic thermal properties of both liquids. We propose that the solvent isotope effect arises from differences in the rates of solute-solvent vibrational energy transfer. Given the similarities of the vibrational friction spectra of H2O and D2O at low frequencies, the solvent isotope effect may indicate that a considerable portion of the excess energy decays by exciting relatively high frequency (>/=700 cm-1) solvent modes.  相似文献   

9.
Femtosecond two-dimensional infrared (2D IR) spectroscopy has been applied to study the conformations of a model dipeptide, N-acetyl-L-prolinamide (AcProNH2) in deuterated chloroform (CDCl3). Spectral features in the amide-I and -II regions are obtained by rephasing (R), nonrephasing (NR), and reverse photon echo (RPE) pulse sequences with two polarization conditions. The 2D spectra obtained by the RPE and NR sequences with (0, 0, 0, 0) polarization reveal new spectral features associated with the multiple conformers of AcProNH2 that are difficult to discern using R sequence and linear-IR spectroscopy. The high resolving power of the RPE sequence comes from destructive interference between the positive and negative peaks of nearby vibrators, similar to the NR sequence. The RPE response functions that are useful for 2D spectral simulations are evaluated, including the effects of vibrational frequency correlations. The 2D spectra obtained with (45, -45, 90, 0) polarization exhibit clear cross-peak patterns in the off-diagonal region for the R and RPE sequences but in the diagonal region for the NR sequence. These patterns, free from strong diagonal contributions, are crucial for structure determination. DFT calculations, normal-mode analysis, Hessian matrix reconstruction, and vibrational exciton Hamiltonian diagonalization yield molecular parameters needed for quantitative simulations of 2D spectra: angles between transition dipoles, coupling constants, and off-diagonal anharmonicities of the amide-I and -II modes are obtained for solvated trans-C7 and cis structures and for gas-phase trans conformers in the region of phi = -120 degrees to 0 degrees and psi = -100 degrees to 180 degrees in the Ramachandran space. Systematic simulations based on a 4:1 population ratio of the solvated trans-C7 and cis structures reproduce well the 2D spectral features obtained at both polarization conditions. However, better agreement between the experimental and simulated cross-peak patterns can be reached if the dihedral angles of the major trans conformer are close to (phi, psi) = (-80 degrees , 100 degrees ). Our results suggest that the major conformer of AcProNH2 in CDCl3 deviates from the gas-phase global minimum, the trans-C7 form, to an extended intermediate between the C7 and polyproline-II structure. These results are discussed in relationship with earlier findings obtained by NMR, transient IR studies, and MD simulations.  相似文献   

10.
Quantum chemical computations, molecular dynamics simulations, and linear and nonlinear infrared spectral simulations are carried out for four representative biomolecules: cellobiose, alanine tripeptide, L ‐α‐glycerylphosphorylethanolamine, and the DNA base monomer guanine. Anharmonic transition frequencies and anharmonicities for the molecules in vacuum are evaluated. Instantaneous normal‐mode analysis is performed and the vibrational frequency distribution correlations are examined for the molecules solvated in TIP3P water. Many local and regional motions of the biomolecules are predicted to be anharmonically coupled and their vibrational frequencies are predicted to be largely correlated. These coupled and correlated vibrational motions can be easily visualized by pairwise cross peaks in the femtosecond broadband two‐dimensional infrared (2D IR) spectra, which are simulated using time‐domain third‐order nonlinear response functions. A network of distinctive spectral profiles of the 2D IR cross peaks, including peak orientations and positive and negative signal patterns, are shown to be intimately connected with the couplings and correlations. The results show that the vibrational couplings and correlations, driven by solvent interactions and also by intrinsic vibrational interactions, are vibrational mode dependent and thus chemical group dependent, and form the structural and dynamical basis of the anharmonic vibrators that are ubiquitous in biomolecules.  相似文献   

11.
12.
The vibrational relaxation dynamics of pseudo-halide anions XCN- (X = O, S, Se) in polar solvents were studied to understand the effect of charge on solute-to-solvent intermolecular energy transfer (IET) and solvent assisted intramolecular vibrational relaxation (IVR) pathways. The T1 relaxation times of the CN stretch in these anions were measured by IR pump/IR probe spectroscopy, in which the 0-1 transition was excited, and the 0-1 and 1-2 transitions were monitored to follow the recovery of the ground state and decay of the excited state. For these anions in five solvents, H2O, D2O, CH3OH, CH3CN, and (CH3)2SO, relaxation rates followed the trend of OCN- > SCN- > SeCN-. For these anions and isotopes of SCN-, the relaxation rate was a factor of a few (2.5-10) higher in H2O than in D2O. To further probe the solvent isotope effect, the relaxation rates of S12C14N-, S13C14N-, and S12C15N- in deuterated methanols (CH3OH, CH3OD, CH3OH, CD3OD) were compared. Relaxation rate was found to be affected by the change of solvent vibrational band at the CN- stretching mode (CD3 symmetric stretch) and lower frequency regions, suggesting the presence of both direct IET and solvent assisted IVR relaxation pathways. The possible relaxation pathways and mechanisms for the observed trends in solute and solvent dependence were discussed.  相似文献   

13.
Vibrational modes are excited by ultrashort tunable IR pulses and the time dependence of the excitation is measured by a second (visible) pulse. Spectra taken at a time delay of several picoseconds give evidence for the population lifetimes of CH-stretching modes of aromatic hydrogen, CH2 and CH3 vibrations. Relaxation times between 6 and 8 ps were found. Results are presented for two coumarins in different solvents.  相似文献   

14.
Infrared absorption and vibrational circular dichroism (IR and VCD) spectra of model fragments of TrpZip-style beta-hairpin structures are simulated using density functional theory (DFT) methods to estimate the influence of fragment size, end effects, conformational irregularities, peptide side chains, and solvent. Different fragmentation schemes, computing the strands and turn segments separately, were tested by varying the sizes of each and their respective overlaps. For suitably overlapping fragments, atomic property tensors were found to be reliably transferable, as tested by their ability to generate simulated spectra in good agreement with results from ab initio DFT computations for the entire peptide. This fragment approach significantly reduces computational times and opens up a wider range of systems that can be studied with a DFT-based approach as compared to previous methods based on uniform repeating sequences. However, vacuum calculations do not adequately represent the frequency dispersion of solvated molecules, and thus, some alternate strategies for solvation correction are explored for improving the simulation accuracy. Unlike for regular periodic secondary structure, the solvent significantly impacts the spectral shapes of hairpins, due to the different degrees of hydration of individual amide groups, which can be exposed to or shielded from water due to external vs internal hydrogen bonding. This is amplified by the shielding of selected amides from the solvent due to bulky side chains. The peptide plus solvent was structurally modeled with molecular dynamics methods, and then an electrostatic field-based parametrization correction was added to the force field and intensity tensors to compensate for the solvent dipolar field. The effect of the shielding and subsequent reordering of modes has a larger impact on VCD than IR band shapes.  相似文献   

15.
The dynamics of reactions of CN radicals with cyclohexane, d(12)-cyclohexane, and tetramethylsilane have been studied in solutions of chloroform, dichloromethane, and the deuterated variants of these solvents using ultraviolet photolysis of ICN to initiate a reaction. The H(D)-atom abstraction reactions produce HCN (DCN) that is probed in absorption with sub-picosecond time resolution using ~500 cm(-1) bandwidth infrared (IR) pulses in the spectral regions corresponding to C-H (or C-D) and C≡N stretching mode fundamental and hot bands. Equivalent IR spectra were obtained for the reactions of CN radicals with the pure solvents. In all cases, the reaction products are formed at early times with a strong propensity for vibrational excitation of the C-H (or C-D) stretching (v(3)) and H-C-N (D-C-N) bending (v(2)) modes, and for DCN products there is also evidence of vibrational excitation of the v(1) mode, which involves stretching of the C≡N bond. The vibrationally excited products relax to the ground vibrational level of HCN (DCN) with time constants of ~130-270 ps (depending on molecule and solvent), and the majority of the HCN (DCN) in this ground level is formed by vibrational relaxation, instead of directly from the chemical reaction. The time-dependence of reactive production of HCN (DCN) and vibrational relaxation is analysed using a vibrationally quantum-state specific kinetic model. The experimental outcomes are indicative of dynamics of exothermic reactions over an energy surface with an early transition state. Although the presence of the chlorinated solvent may reduce the extent of vibrational excitation of the nascent products, the early-time chemical reaction dynamics in these liquid solvents are deduced to be very similar to those for isolated collisions in the gas phase. The transient IR spectra show additional spectroscopic absorption features centered at 2037 cm(-1) and 2065 cm(-1) (in CHCl(3)) that are assigned, respectively, to CN-solvent complexes and recombination of I atoms with CN radicals to form INC molecules. These products build up rapidly, with respective time constants of 8-26 and 11-22 ps. A further, slower rise in the INC absorption signal (with time constant >500 ps) is attributed to diffusive recombination after escape from the initial solvent cage and accounts for more than 2/3 of the observed INC.  相似文献   

16.
The in vivo formation of beta-pleated protein aggregates underlies a number of fatal neurodegenerative disorders, such as Alzheimer disease. Since molecular mechanisms of protein misfolding and aggregation remain poorly understood, this has been calling for many diverse biophysical tools capable of addressing different dynamic and conformational aspects of the phenomenon. The two model polypeptides used in this study are poly(l-tyrosine) and insulin. According to FT-IR spectra, poly(l-tyrosine) produced two distinct types of films with dominant either disordered or antiparallel beta-sheet conformations depending on carrier solvent used for film's deposition. Electrochemical analysis of both the types of polypeptide films by the means of cyclic voltammetry and differential pulse voltammetry proved that different electrochemical behaviour of the tyrosine residues is determined by the conformation of polypeptide chains. We have rationalized this difference in terms of varying electrochemical accessibility of Tyr residues in each structure. We have also carried out spectral and electrochemical characterization of insulin beta-sheet-rich amyloid fibrils. It appears that the detectable electrochemical response of the protein stems from the presence of four tyrosine residues per insulin monomer. Since hydrophobic residues, among them tyrosines play an important role in the formation of protein amyloid fibrils, but, on a molecular level, may be also critical in explaining neurotoxic properties of aggregates, their electrochemical properties may become a very valuable complementary tool in biophysical studies on protein misfolding.  相似文献   

17.
The center line slope (CLS) method is often used to extract the frequency-frequency correlation function (FFCF) from 2D IR spectra to delineate dynamics and to identify homogeneous and inhomogeneous contributions to the absorption line shape of a system. While the CLS method is extremely efficient, quite accurate, and immune to many experimental artifacts, it has only been developed and properly applied to systems that have a single vibrational band, or to systems of two species that have spectrally resolved absorption bands. In many cases, the constituent spectra of multiple component systems overlap and cannot be distinguished from each other. This situation creates ambiguity when analyzing 2D IR spectra because dynamics for different species cannot be separated. Here a mathematical formulation is presented that extends the CLS method for a system consisting of two components (chemically distinct uncoupled oscillators). In a single component system, the CLS corresponds to the time-dependent portion of the normalized FFCF. This is not the case for a two component system, as a much more complicated expression arises. The CLS method yields a series of peak locations originating from slices taken through the 2D spectra. The slope through these peak locations yields the CLS value for the 2D spectra at a given T(w). We derive analytically that for two component systems, the peak location of the system can be decomposed into a weighted combination of the peak locations of the constituent spectra. The weighting depends upon the fractional contribution of each species at each wavelength and also on the vibrational lifetimes of both components. It is found that an unknown FFCF for one species can be determined as long as the peak locations (referred to as center line data) of one of the components are known, as well as the vibrational lifetimes, absorption spectra, and other spectral information for both components. This situation can arise when a second species is introduced into a well characterized single species system. An example is a system in which water exists in bulk form and also as water interacting with an interface. An algorithm is presented for back-calculating the unknown FFCF of the second component. The accuracy of the algorithm is tested with a variety of model cases in which all components are initially known. The algorithm successfully reproduces the FFCF for the second component within a reasonable degree of error.  相似文献   

18.
We report the first spectroscopic observation of and vibrational predissociation dynamics for ArBr(2). Measurements are reported for the linear and T-shaped isomers with time and frequency resolution near the Fourier limit of a 15 ps pulse. For the T-shaped isomer, the Ar-Br(2) bond energy D(0) for the B state, nu(')=19, is found to be 200 cm(-1), yielding a D(0)(X) value of 213 cm(-1). Product appearance rates are determined for nu(')=16-25 of the B state of ArBr(2). While the rate generally increases with increasing vibrational quantum number, the trend is not monotonic. Also, obtaining reproducible rates for any given vibrational level requires very careful control of the experimental conditions. The data suggest that ArBr(2) undergoes vibrational predissociation (VP) in the sparse intramolecular vibrational relaxation regime. These observations are consistent with theoretical calculations that show that T-shaped ArBr(2) undergoes VP in the sparse regime, such that lifetimes are strongly dependent on both the vibrational and rotational quantum numbers. As for ArI(2), a linear isomer of ArBr(2) is found to contribute a quasicontinuous background to the excitation spectra. Direct excitation of this continuum results in a very broad product vibrational distribution.  相似文献   

19.
Ultrafast two-dimensional infrared (2DIR) spectroscopy has been proven to be an exceptionally useful method to study chemical exchange processes between different vibrational chromophores under thermal equilibria. Here, we present experimental results on the thermal equilibrium ion pairing dynamics of Li(+) and SCN(-) ions in N,N-dimethylformamide. Li(+) and SCN(-) ions can form a contact ion pair (CIP). Varying the relative concentration of Li(+) in solution, we could control the equilibrium CIP and free SCN(-) concentrations. Since the CN stretch frequency of Li-SCN CIP is blue-shifted by about 16 cm(-1) from that of free SCN(-) ion, the CN stretch IR spectrum is a doublet. The temperature-dependent IR absorption spectra reveal that the CIP formation is an endothermic (0.57 kJ∕mol) process and the CIP state has larger entropy by 3.12 J∕(K?mol) than the free ion states. Since the two ionic configurations are spectrally distinguishable, this salt solution is ideally suited for nonlinear IR spectroscopic investigations to study ion pair association and dissociation dynamics. Using polarization-controlled IR pump-probe methods, we first measured the lifetimes and orientational relaxation times of these two forms of ionic configurations. The vibrational population relaxation times of both the free ion and CIP are about 32 ps. However, the orientational relaxation time of the CIP, which is ~47 ps, is significantly longer than that of the free SCN(-), which is ~7.7 ps. This clearly indicates that the effective moment of inertia of the CIP is much larger than that of the free SCN(-). Then, using chemical exchange 2DIR spectroscopy and analyzing the diagonal peak and cross-peak amplitude changes with increasing the waiting time, we determined the contact ion pair association and dissociation time constants that are found to be 165 and 190 ps, respectively. The results presented and discussed in this paper are believed to be important, not only because the ion-pairing dynamics is one of the most fundamental physical chemistry problems but also because such molecular ion-ion interactions are of critical importance in understanding Hofmeister effects on protein stability.  相似文献   

20.
The dynamics of the IR emission induced by excitation of the acetylene molecule at the 3(2) Ka2, A1Au<--4(1) la1, X1Sigmag+ transition was investigated. Vibrationally resolved IR emission spectra were recorded at different delay times after the laser excitation pulse. The observed IR emission was assigned to transitions between vibrational levels of the acetylene molecule in the ground state. Values of the relaxation parameters of different vibrational levels of the ground state were obtained. The Ti-->Tj transition was detected by cavity ring-down spectroscopy in the 455 nm spectral range after excitation of the acetylene molecule at the same transition. Rotationally resolved spectra of the respective transition were obtained and analyzed at different delay times after the laser excitation pulse. The dynamics of the S1-->Tx-->T1-->S0 transitions was investigated, and the relaxation parameter values were estimated for the T1 state.  相似文献   

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