Vibrational relaxation pathways of amide I and amide II modes in N-methylacetamide

We studied the vibrational energy relaxation mechanisms of the amide I and amide II modes of N-methylacetamide (NMA) monomers dissolved in bromoform using polarization-resolved femtosecond two-color vibrational spectroscopy. The results show that the excited amide I vibration transfers its excitation energy to the amide II vibration with a time constant of 8.3 ± 1 ps. In addition to this energy exchange process, we observe that the excited amide I and amide II vibrations both relax to a final thermal state. For the amide I mode this latter process dominates the vibrational relaxation of this mode. We find that the vibrational relaxation of the amide I mode depends on frequency which can be well explained from the presence of two subbands with different vibrational lifetimes (~1.1 ps on the low frequency side and ~2.7 ps on the high frequency side) in the amide I absorption spectrum.     

The anharmonic vibrational potential and relaxation pathways of the amide I and II modes of N-methylacetamide

We investigate the influence of isotopic substitution and solvation of N-methylacetamide (NMA) on anharmonic vibrational coupling and vibrational relaxation of the amide I and amide II modes. Differences in the anharmonic potential of isotopic derivatives of NMA in D2O and DMSO-d6 are quantified by extraction of the anharmonic parameters and the transition dipole moment angles from cross-peaks in the two-dimensional infrared (2D-IR) spectra. To interpret the effects of isotopic substitution and solvent interaction on the anharmonic potential, density functional theory and potential energy distribution calculations are performed. It is shown that the origin of anharmonic variation arises from differing local mode contributions to the normal modes of the NMA isotopologues, particularly in amide II. The time domain manifestation of the coupling is the coherent exchange of excitation between amide modes seen as the quantum beats in femtosecond pump-probes. The biphasic behavior of population relaxation of the pump-probe and 2D-IR experiments can be understood by the rapid exchange of strongly coupled modes within the peptide backbone, followed by picosecond dissipation into weakly coupled modes of the bath.     

Vibrational energy relaxation of isotopically labeled amide I modes in cytochrome c: theoretical investigation of vibrational energy relaxation rates and pathways

With use of a time-dependent perturbation theory, vibrational energy relaxation (VER) of isotopically labeled amide I modes in cytochrome c solvated with water is investigated. Contributions to the VER are decomposed into two contributions from the protein and water. The VER pathways are visualized by using radial and angular excitation functions for resonant normal modes. Key differences of VER among different amide I modes are demonstrated, leading to a detailed picture of the spatial anisotropy of the VER. The results support the experimental observation that amide I modes in proteins relax with subpicosecond time scales, while the relaxation mechanism turns out to be sensitive to the environment of the amide I mode.     

Vibrational relaxation in simulated two-dimensional infrared spectra of two amide modes in solution

Two-dimensional infrared spectroscopy is capable of following the transfer of vibrational energy between modes in real time. We develop a method to include vibrational relaxation in simulations of two-dimensional infrared spectra at finite temperature. The method takes into account the correlated fluctuations that occur in the frequencies of the vibrational states and in the coupling between them as a result of interaction with the environment. The fluctuations influence the two-dimensional infrared line shape and cause vibrational relaxation during the waiting time, which is included using second-order perturbation theory. The method is demonstrated by applying it to the amide-I and amide-II modes in N-methylacetamide in heavy water. Stochastic information on the fluctuations is obtained from a molecular dynamics trajectory, which is converted to time dependent frequencies and couplings with a map from a density functional calculation. Solvent dynamics with the same frequency as the energy gap between the two amide modes lead to efficient relaxation between amide-I and amide-II on a 560 fs time scale. We show that the cross peak intensity in the two-dimensional infrared spectrum provides a good measure for the vibrational relaxation.     

Vibrational relaxation in liquid nitrogen

The time constant for the collisional deactivation of the υ = 1 vibrational level of N₂ is found to be 1.5 ± 0.5 s in liquid nitrogen of 99.9995% purity of 78 K. This result is consistent with a simple binary collision theory of vibrational relaxation for liquids.     

Vibrational relaxation in liquid diethylamine

Two types of time resolved experiments have been performed on the intermediate sized polyatomic molecule diethylamine, in the liquid phase, in order to elucidate the pathway for vibrational relaxation of the ν = 3 level of the NH stretching mode, which has 9420 cm^?1 of energy. Both techniques had calibrated absolute sensitivities and were specific for vibrational modes of ca. 3000 cm^?1, yet with neither were transient populations in such modes observable. It is inferred that population relaxation in this highly excited room temperature system proceeds on the subpicosecond time scale to lower lying levels. The importance of intramolecular channels for this decay is suggested.     

Vibrational frequencies of sodium clusters

The vibrational frequencies of Na_N clusters (2 ? N ? 72) are calculated by direct diagonalization of the dynamical matrix. Density functional theory with a spherically averaged pseudopotential is used to compute the total energy. The geometry is optimized by the simulated annealing technique. Contributions to the Hessian matrix due to electron relaxation following the ionic displacements are calculated in linear response theory. The frequencies are in the range 0-220 cm^?1 and the electron relaxation strongly modifies those of the modes dominated by radial oscillations, particularly the breathing mode frequencies that are proportional to N?1/3 . The filling of atomic shells produces a stepwise behavior of the highest frequencies. The giant dipole resonance energies are obtained as a byproduct of the calculation. © 1995 John Wiley & Sons, Inc.     

Vibrational modes and force constants ofp-bromotoluene

The characteristic features of the normal vibrational modes ofp-bromotoluene were calculated; the assignments of spectral bands reported previously were corrected. The force constants of the molecule were estimated in terms of the model of the unified valence and force field.     

Vibrational relaxation in the condensed phase

A modified Landau-Teller equation for vibrational relaxation in the condensed phase is proposed. This equation differs from previous approaches by accounting for the fluctuations of the energies of the vibrational levels that result from the interactions with the surroundings (bath). In the conventional approach the effects of the bath are only included in the coupling between the relaxing and accepting vibrational modes. It is shown that the additional inclusion of the fluctuations of the energy levels can lead to a dramatic change of the vibrational relaxation rate.     

Vibrational relaxation and intermediate strong coupling

In this paper the effect of collisions with inert gas molecules upon the intermediate strong coupling situation, found in the fluorescence of isolated pyrene molecules after pulse laser excitation in the S₀ → S₃ absorption band, is studied.     

Vibrational relaxation of deuterium in argon fluid

Experimental measurements on vibrational population relaxation in deuterium/argon fluid mixtures over a wide range of density and temperature are compa     

Vibrational dynamics of DNA. I. Vibrational basis modes and couplings

Carrying out density functional theory calculations of four DNA bases, base derivatives, Watson-Crick (WC) base pairs, and multiple-layer base pair stacks, we studied vibrational dynamics of delocalized modes with frequency ranging from 1400 to 1800 cm(-1). These modes have been found to be highly sensitive to structure fluctuation and base pair conformation of DNA. By identifying eight fundamental basis modes, it is shown that the normal modes of base pairs and multilayer base pair stacks can be described by linear combinations of these vibrational basis modes. By using the Hessian matrix reconstruction method, vibrational coupling constants between the basis modes are determined for WC base pairs and multilayer systems and are found to be most strongly affected by the hydrogen bonding interaction between bases. It is also found that the propeller twist and buckle motions do not strongly affect vibrational couplings and basis mode frequencies. Numerically simulated IR spectra of guanine-cytosine and adenine-thymine bases pairs as well as of multilayer base pair stacks are presented and described in terms of coupled basis modes. It turns out that, due to the small interlayer base-base vibrational interactions, the IR absorption spectrum of multilayer base pair system does not strongly depend on the number of base pairs.     

Vibrational modes in partially optimized molecular systems

In this paper the authors develop a method to accurately calculate localized vibrational modes for partially optimized molecular structures or for structures containing link atoms. The method avoids artificially introduced imaginary frequencies and keeps track of the invariance under global translations and rotations. Only a subblock of the Hessian matrix has to be constructed and diagonalized, leading to a serious reduction of the computational time for the frequency analysis. The mobile block Hessian approach (MBH) proposed in this work can be regarded as an extension of the partial Hessian vibrational analysis approach proposed by Head [Int. J. Quantum Chem. 65, 827 (1997)]. Instead of giving the nonoptimized region of the system an infinite mass, it is allowed to move as a rigid body with respect to the optimized region of the system. The MBH approach is then extended to the case where several parts of the molecule can move as independent multiple rigid blocks in combination with single atoms. The merits of both models are extensively tested on ethanol and di-n-octyl-ether.     

Vibrational and rotational relaxation of 1-hexyne in solution

The IR and isotropic Raman bandwidths of the ν(CH) and ν(CC) stretching modes of 1-hexyne have been measured in dilute solutions in n C₇H₁₆ and CCl₄ as a function of T. The deduced vibrational and rotational bandwidths are interpreted in terms of different models.     

Vibrational relaxation by collision in polyatomic molecules

A model of a harmonic oscillator with friction is used to discuss the conversion of translational energy to vibrational by collision of an atom with a polyatomic molecule. It is shown that adiabatic conversion implies that E ² may substantially exceed the value calculated, neglecting the interaction of the bond with the rest of the molecule.     

Vibrational relaxation of phenol in benzonitrile and benzene solutions

The Raman bandwidths and the frequency shifts of the ν₁₂(A₁) mode and the IR ν₃(OH) stretching mode of phenol and phenol-OD have been measured as a function of concentration in benzonitrile and benzene solutions. Opposite isotope effects of deuterium substitution in the hydroxyl group of phenol on the bandwidths of the ν₁₂ and the ν₃(OH) modes have been found. The experimental bandwidths are discussed in terms of available theoretical models for dephasing and other mechanisms of broadening. The isolated binary collision dephasing model of Fischer-Laubereau, the Knapp-Fischer concentration-fluctuation model and the Robertson-Yarwood model have been tested. It has been stated that the purely repulsive potential is responsible for vibrational dephasing of the ν₁₂ mode of phenol in benzene while the concentration-fluctuation model reproduces the experimental data for that mode in benzonitrile. The coupling between the ν₃(OH) and ν₂(OH…N) modes is the dominant mechanism for broadening of the ν₃(OH) mode of phenol in benzonitrile.     

Structural relaxation in the hydrogen-bonding liquids N-methylacetamide and water studied by optical Kerr effect spectroscopy

Structural relaxation in the peptide model N-methylacetamide (NMA) is studied experimentally by ultrafast optical Kerr effect spectroscopy over the normal-liquid temperature range and compared to the relaxation measured in water at room temperature. It is seen that in both hydrogen-bonding liquids, beta relaxation is present, and in each case, it is found that this can be described by the Cole-Cole function. For NMA in this temperature range, the alpha and beta relaxations are each found to have an Arrhenius temperature dependence with indistinguishable activation energies. It is known that the variations on the Debye function, including the Cole-Cole function, are unphysical, and we introduce two general modifications: One allows for the initial rise of the function, determined by the librational frequencies, and the second allows the function to be terminated in the alpha relaxation.     

Vibrational relaxation of azide ions in liquid-to-supercritical water

The dynamics of vibrational energy relaxation (VER) of the aqueous azide anion was studied over a wide temperature (300 K ≤ T ≤ 663 K) and density (0.6 g cm(-3) ≤ ρ ≤ 1.0 g cm(-3)) range thereby covering the liquid and the supercritical phase of the water solvent. Femtosecond mid-infrared spectroscopy on the ν(3) band associated with the asymmetric stretching vibration of the azide anion was used to monitor the relaxation dynamics in a time-resolved fashion. The variation of the vibrational relaxation rate constant with temperature and density was found to be rather small. Surprisingly, the simple isolated binary collision model is able to fully reproduce the experimentally observed temperature and density dependence of the relaxation rate provided a local density correction around the vibrationally excited solute based on classical molecular dynamics simulations is used. The simulations further suggest that head-on collisions of the solvent with the terminal nitrogen atoms rather than side-on collisions with the central nitrogen atom of the azide govern the vibrational energy relaxation of this system. Finally, the importance of hydrogen bonding for the VER dynamics in this system is briefly discussed.