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.     

Electrostatic DFT map for the complete vibrational amide band of NMA

An anharmonic vibrational Hamiltonian for the amide I, II, III, and A modes of N-methyl acetamide (NMA), recast in terms of the 19 components of an external electric field and its first and second derivative tensors (electrostatic DFT map), is calculated at the DFT(BPW91/6-31G(d,p)) level. Strong correlations are found between NMA geometry and the amide frequency fluctuations calculated using this Hamiltonian together with the fluctuating solvent electric field obtained from the MD simulations in TIP3 water. The amide I and A frequencies are strongly positively correlated with the C=O and N-H bond lengths. The C=O and C-N amide bond lengths are negatively correlated, suggesting the solvent-induced fluctuations of the contribution of zwitterionic resonance form. Sampling the global electric field in the entire region of the transition charge densities (TCDs) is required for accurate infrared line shape simulations. Collective electrostatic solvent coordinates which represent the fluctuations of the 10 lowest amide fundamental and overtone states are reported. Normal-mode analysis of an NMA-3H(2)O cluster shows that the 660 cm(-1) to 1100 cm(-1) oscillation found in the frequency autocorrelation functions of the amide modes may be ascribed to the two bending vibrations of intermolecular hydrogen bonds with the amide oxygen of NMA.     

Anharmonic vibrational probe for N-methylacetamide in different micro-environments

In the present study, anharmonic vibrational properties of the amide modes in N-methylacetamide (NMA), a model molecule for peptide vibrational spectroscopy, are examined by DFT calculations. The 3N-6 normal mode frequencies, diagonal and off-diagonal anharmonicities are evaluated by means of the second order vibrational perturbation theory (VPT2). Good performance of B3LYP/6-31+G** is found for predicting vibrational frequencies in comparison with gas phase experimental data. The amide vibrational modes are assigned through potential energy distribution analysis (PED). The solvation effect on the amide vibrational modes is modeled within the PCM method. From gas phase to polar solvents, red shifts are observed for both harmonic and anharmonic vibrational frequency of amide I mode while the CO bond length increases upon the solvent polarity. Cubic and quartic force constants are further calculated to evaluate the origin of the anharmonicity for the amide I mode of NMA in different micro-environments.     

Electronic coherences and vibrational wave-packets in single molecules studied with femtosecond phase-controlled spectroscopy

Employing femtosecond pulse-shaping techniques we investigate ultrafast, coherent and incoherent dynamics in single molecules at room temperature. In first experiments single molecules are excited into their purely electronic 0-0 transition by phase-locked double-pulse sequences with pulse durations of 75 fs and 20 nm spectral band width. Their femtosecond kinetics can then be understood in terms of a 2-level system and modelled with the optical Bloch equations. We find that we observe the coherence decay in single molecules, and the purely electronic dephasing times can be retrieved directly in the time domain. In addition, the Rabi-frequencies and thus the transition dipole moments of single molecules are determined from these data. Upon excitation of single molecules into a vibrational level of the electronically excited state also incoherent intra-molecular vibrational relaxation is recorded. Increasing the spectral band width of the excitation pulses to up to 120 nm (resulting in a transform-limited pulse width of 15 fs) coherent superpositions of excited state vibrational modes, i.e. vibrational wave packets, are excited. The wave-packet oscillations in the excited state potential energy surface are followed in time by a phase-controlled pump-probe scheme, which permits to record wave packet interference, and to determine the energies of vibrational modes and their coupling strengths to the electronic transition.     

Chirp-driven vibrational distribution in transition metal carbonyl complexes

In this theoretical study vibrational ladder climbing in transition metal carbonyl complexes, as a possible means to initialize chemical ground state reactions, and the resulting vibrational population distribution using chirped mid-infrared femtosecond laser pulses is investigated. Our model system is MnBr(CO)(5), a strong IR-absorber within an experimentally easily accessible wavelength region. Special emphasis is put on the perturbation due to additional vibrational modes, especially on one, which allows dissociation at low energies. The related potential energy surface for the three representative modes is calculated, whereon quantum dynamics calculations, including the laser-molecule interaction, are performed. No significant coupling could be detected, neither in the bound, nor in the dissociative region. Contrarily, we found a dynamical barrier even for energies high above the dissociation limit. Different vibrational population distributions after the laser excitation of the CO stretching mode could be generated in dependence of the chirp parameters. Based on these findings we simulated the laser excitation corresponding to an experiment by M. Joffre et al., Proc. Natl. Acad. Ssi. U. S. A., 2004, 101(36), 13216-13220, where coherent vibrational ladder climbing in carboxyhemoglobin was demonstrated and we could offer an explanation for an open question, concerning the interpretation of the spectroscopic data.     

Vibrational dynamics of deoxyguanosine 5'-monophosphate following UV excitation

The relaxation dynamics of the DNA nucleotide deoxyguanosine 5'-monophosphate (dGMP) following 266 nm photoexcitation has been studied by transient IR spectroscopy with femtosecond time resolution. The induced dynamics of the amide I (carbonyl) stretch, the asymmetric guanine ring stretch and the phosphate asymmetric stretch are monitored in the region 1000-1800 cm(-1). Excitation and subsequent rapid internal conversion to a "hot" ground state is reflected by depletion of the vibrational ground states of the amide I stretch and guanine ring stretch. However, the vibrational ground state of the phosphate is left unperturbed, indicating the absence of vibrational coupling between the guanine ring system and the phosphate group. The vibrational ground state of the amide I is repopulated in 2.5 ps (±0.2 ps) while it takes 3.7 ps (±0.5 ps) to repopulate the guanine ring vibration. This article discusses two possible relaxation pathways of dGMP, as well as the implications of the weak phosphate dynamics.     

Development of a tunable femtosecond stimulated raman apparatus and its application to beta-carotene

We have developed a tunable femtosecond stimulated Raman spectroscopy (FSRS) apparatus and used it to perform time-resolved resonance Raman experiments with <100 fs temporal and <35 cm(-1) spectral resolution. The key technical change that facilitates this advance is the use of a tunable narrow-bandwidth optical parametric amplifier (NB-OPA) presented recently by Shim et al. (Shim, S.; Mathies, R. A. Appl. Phys. Lett. 2006, 89, 121124). The practicality of tunable FSRS is demonstrated by examining the photophysical dynamics of beta-carotene. Using 560 nm Raman excitation, the resonant S1 state modes are enhanced by a factor of approximately 200 compared with 800 nm FSRS experiments. The improved signal-to-noise ratios facilitate the measurement of definitive time constants for beta-carotene dynamics including the 180 fs appearance of the S1 vibrational features due to direct internal conversion from S2 and their characteristic 9 ps decay to S0. By tuning the FSRS system to 590 nm Raman excitation, we are able to selectively enhance vibrational features of the hot ground state S hot 0 and monitor its approximately 5 ps cooling dynamics. This tunable FSRS system is valuable because it facilitates the direct observation of structural changes of selected resonantly enhanced states and intermediates during photochemical and photobiological reactions.     

Simulation of vibrational energy transfer in two-dimensional infrared spectroscopy of amide I and amide II modes in solution

Population transfer between vibrational eigenstates is important for many phenomena in chemistry. In solution, this transfer is induced by fluctuations in molecular conformation as well as in the surrounding solvent. We develop a joint electrostatic density functional theory map that allows us to connect the mixing of and thereby the relaxation between the amide I and amide II modes of the peptide building block N-methyl acetamide. This map enables us to extract a fluctuating vibrational Hamiltonian from molecular dynamics trajectories. The linear absorption spectrum, population transfer, and two-dimensional infrared spectra are then obtained from this Hamiltonian by numerical integration of the Schrodinger equation. We show that the amide I/amide II cross peaks in two-dimensional infrared spectra in principle allow one to follow the vibrational population transfer between these two modes. Our simulations of N-methyl acetamide in heavy water predict an efficient relaxation between the two modes with a time scale of 790 fs. This accounts for most of the relaxation of the amide I band in peptides, which has been observed to take place on a time scale of 450 fs in N-methyl acetamide. We therefore conclude that in polypeptides, energy transfer to the amide II mode offers the main relaxation channel for the amide I vibration.     

Excitonic effects in two-dimensional vibrational spectra of liquid formamide

The linear and two-dimensional infrared (2DIR) responses of the amide I vibrational mode in liquid formamide are investigated experimentally and theoretically using molecular dynamics simulations. The recent method based on the numerical integration of the Schr?dinger equation is employed to calculate the 2DIR spectra. Special attention is devoted to the interplay of the structural dynamics and the excitonic nature of the amide I modes in determining the optical response of the studied system. In particular, combining experimental data, simulated spectra and analysis of the simulated atomic trajectory in terms of a transition dipole coupling model, we provide a convincing explanation of the peculiar features of the 2DIR spectra, which show a substantial increase of the antidiagonal bandwidth with increasing frequency. We point out that, at variance with liquid water, the 2DIR spectral profile of formamide is determined more by the excitonic nature of the vibrational states than by the fast structural dynamics responsible for the frequency fluctuations.     

On the temperature dependence of amide I frequencies of peptides in solution

The temperature dependence of the amide I vibrational frequencies of peptides in solution was investigated. In D2O, the amide I' bands of both an alpha-helical oligopeptide, the random-coil poly(L-lysine), and the simplest amide, N-methyl acetamide (NMA), exhibit linear frequency shifts of approximately 0.07 cm(-1)/degrees C with increasing temperature. Similar amide I frequency shifts are also observed for NMA in both polar (acetonitrile and DMSO) and nonpolar (1,4-dioxane) organic solvents, thus ruling out hydrogen-bonding strength as the cause of these effects. The experimental NMA amide I frequencies in the organic solvents can be accurately described by a simple theory based on the Onsager reaction field with temperature-dependent solvent dielectric properties and a solute molecular cavity. DFT-level calculations (BPW91/cc-pVDZ) for NMA with an Onsager reaction field confirm the significant contribution of the molecular cavity to the predicted amide I frequencies. Comparison of the computations to experimental data shows that the frequency-dependent response of the reaction field, taken into account by the index of refraction, is crucial for describing the amide I frequencies in polar solvents. The poor predictions of the model for the NMA amide I band in D2O might be due, in part, to the unknown temperature dependence of the refractive index of D2O in the mid-IR range, which was approximated by the available values in the visible region.     

Femtosecond Time-Resolved Stimulated Raman Spectroscopy: Application to the Ultrafast Internal Conversion in beta-Carotene

We have developed the technique of femtosecond stimulated Raman spectroscopy (FSRS), which allows the rapid collection of high-resolution vibrational spectra on the femtosecond time scale. FSRS combines a sub-50 fs actinic pump pulse with a two-pulse stimulated Raman probe to obtain vibrational spectra whose frequency resolution limits are uncoupled from the time resolution. This allows the acquisition of spectra with <100 fs time resolution and <30 cm(-1) frequency resolution. Additionally, FSRS is unaffected by background fluorescence, provides rapid (100 ms) acquisition times, and exhibits traditional spontaneous Raman line shapes. FSRS is used here to study the relaxation dynamics of beta-carotene. Following optical excitation to S(2) (1B(u) (+)) the molecule relaxes in 160 fs to S(1) (2A(g) (-)) and then undergoes two distinct stages of intramolecular vibrational energy redistribution (IVR) with 200 and 450 fs time constants. These processes are attributed to rapid (200 fs) distribution of the internal conversion energy from the S(1) C=C modes into a restricted bath of anharmonically coupled modes followed by complete IVR in 450 fs. FSRS is a valuable new technique for studying the vibrational structure of chemical reaction intermediates and transition states.     

Coherent Vibrational and Dissociation Dynamics of Polyatomic Radical Cations

The ultrafast dynamics of polyatomic radical cations contribute to important processes including energy transfer in photovoltaics, electron transfer in photocatalysis, radiation-induced DNA damage, and chemical reactions in the upper atmosphere and space. Probing these dynamics in the gas phase is challenging due to the rapid dissociation of polyatomic radical cations following electron removal, which arises from excess electronic excitation of the molecule during the ionization process. This Concept article introduces the reader to how the pump-probe technique of femtosecond time-resolved mass spectrometry (FTRMS) can overcome this challenge to capture coherent vibrational dynamics on the femtosecond timescale in polyatomic radical cations and enable the analysis of their dissociation pathways. Examples of FTRMS applied to three families of polyatomic radical cations are discussed.     

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 spectroscopic determination of local solvent electric field, solute-solvent electrostatic interaction energy, and their fluctuation amplitudes

IR probes have been extensively used to monitor local electrostatic and solvation dynamics. Particularly, their vibrational frequencies are highly sensitive to local solvent electric field around an IR probe. Here, we show that the experimentally measured vibrational frequency shifts can be inversely used to determine local electric potential distribution and solute-solvent electrostatic interaction energy. In addition, the upper limits of their fluctuation amplitudes are estimated by using the vibrational bandwidths. Applying this method to fully deuterated N-methylacetamide (NMA) in D(2)O and examining the solvatochromic effects on the amide I' and II' mode frequencies, we found that the solvent electric potential difference between O(═C) and D(-N) atoms of the peptide bond is about 5.4 V, and thus, the approximate solvent electric field produced by surrounding water molecules on the NMA is 172 MV/cm on average if the molecular geometry is taken into account. The solute-solvent electrostatic interaction energy is estimated to be -137 kJ/mol, by considering electric dipole-electric field interaction. Furthermore, their root-mean-square fluctuation amplitudes are as large as 1.6 V, 52 MV/cm, and 41 kJ/mol, respectively. We found that the water electric potential on a peptide bond is spatially nonhomogeneous and that the fluctuation in the electrostatic peptide-water interaction energy is about 10 times larger than the thermal energy at room temperature. This indicates that the peptide-solvent interactions are indeed important for the activation of chemical reactions in aqueous solution.     

Non-Gaussian statistics of amide I mode frequency fluctuation of N-methylacetamide in methanol solution: linear and nonlinear vibrational spectra

By carrying out molecular dynamics simulations of an N-methylacetamide (NMA) in methanol solution, the amide I mode frequency fluctuation and hydrogen bonding dynamics were theoretically investigated. Combining an extrapolation formula developed from systematic ab initio calculation studies of NMA-(CH3OH)n clusters with a classical molecular dynamics simulation method, we were able to quantitatively describe the solvatochromic vibrational frequency shift induced by the hydrogen-bonding interaction between NMA and solvent methanol. It was found that the fluctuating amide I mode frequency distribution is notably non-Gaussian and it can be decomposed into two Gaussian peaks that are associated with two distinctively different solvation structures. The ensemble-average-calculated linear response function associated with the IR absorption is found to be oscillating, which is in turn related to the doublet amide I band shape. Numerically calculated infrared absorption spectra are directly compared with experiment and the agreement was found to be excellent. By using the Onsager's regression hypothesis, the rate constants of the interconversion process between the two solvation structures were obtained. Then, the nonlinear response functions associated with two-dimensional infrared pump-probe spectroscopy were simulated. The physics behind the two-dimensional line shape and origin of the cross peaks in the time-resolved pump-probe spectra is explained and the result is compared with 2D spectra experimentally measured recently by Woutersen et al.     

Imaging H2O photofragments in the predissociation of the HCl-H2O hydrogen-bonded dimer

The state-to-state vibrational predissociation (VP) dynamics of the hydrogen-bonded HCl-H(2)O dimer was studied following excitation of the dimer's HCl stretch by detecting the H(2)O fragment. Velocity map imaging (VMI) and resonance-enhanced multiphoton ionization (REMPI) were used to determine pair-correlated product energy distributions. Following vibrational excitation of the HCl stretch of the dimer, H(2)O fragments were detected by 2 + 1 REMPI via the C (1)B(1) (000) ← X (1)A(1) (000) transition. REMPI spectra clearly show H(2)O from dissociation produced in the ground vibrational state. The fragments' center-of-mass (c.m.) translational energy distributions were determined from images of selected rotational states of H(2)O and were converted to rotational state distributions of the HCl cofragment. The distributions were consistent with the previously measured dissociation energy of D(0) = 1334 ± 10 cm(-1) and show a clear preference for rotational levels in the HCl fragment that minimize translational energy release. The usefulness of 2 + 1 REMPI detection of water fragments is discussed.     

Nonadiabatic effects on peptide vibrational dynamics induced by conformational changes

Quantum dynamical simulations of vibrational spectroscopy have been carried out for glycine dipeptide (CH(3)-CO-NH-CH(2)-CO-NH-CH(3)). Conformational structure and dynamics are modeled in terms of the two Ramachandran dihedral angles of the molecular backbone. Potential energy surfaces and harmonic frequencies are obtained from electronic structure calculations at the density functional theory (DFT) [B3LYP/6-31+G(d)] level. The ordering of the energetically most stable isomers (C(7) and C(5)) is reversed upon inclusion of the quantum mechanical zero point vibrational energy. Vibrational spectra of various isomers show distinct differences, mainly in the region of the amide modes, thereby relating conformational structures and vibrational spectra. Conformational dynamics is modeled by propagation of quantum mechanical wave packets. Assuming a directed energy transfer to the torsional degrees of freedom, transitions between the C(7) and C(5) minimum energy structures occur on a sub-picosecond time scale (700...800 fs). Vibrationally nonadiabatic effects are investigated for the case of the coupled, fundamentally excited amide I states. Using a two state-two mode model, the resulting wave packet dynamics is found to be strongly nonadiabatic due to the presence of a seam of the two potential energy surfaces. Initially prepared adiabatic vibrational states decay upon conformational change on a time scale of 200...500 fs with population transfer of more than 50% between the coupled amide I states. Also the vibrational energy transport between localized (excitonic) amide I vibrational states is strongly influenced by torsional dynamics of the molecular backbone where both enhanced and reduced decay rates are found. All these observations should allow the detection of conformational changes by means of time-dependent vibrational spectroscopy.     

Overtone-induced dissociation and isomerization dynamics of the hydroxymethyl radical (CH2OH and CD2OH). I. A theoretical study

The dissociation of the hydroxymethyl radical, CH(2)OH, and its isotopolog, CD(2)OH, following the excitation of high OH stretch overtones is studied by quasi-classical molecular dynamics calculations using a global potential energy surface (PES) fitted to ab initio calculations. The PES includes CH(2)OH and CH(3)O minima, dissociation products, and all relevant barriers. Its analysis shows that the transition states for OH bond fission and isomerization are both very close in energy to the excited vibrational levels reached in recent experiments and involve significant geometry changes relative to the CH(2)OH equilibrium structure. The energies of key stationary points are refined using high-level electronic structure calculations. Vibrational energies and wavefunctions are computed by coupled anharmonic vibrational calculations. They show that high OH-stretch overtones are mixed with other modes. Consequently, trajectory calculations carried out at energies about ~3000 cm(-1) above the barriers reveal that despite initial excitation of the OH stretch, the direct OH bond fission is relatively slow (10 ps) and a considerable fraction of the radicals undergoes isomerization to the methoxy radical. The computed dissociation energies are: D(0)(CH(2)OH → CH(2)O + H) = 10,188 cm(-1), D(0)(CD(2)OH → CD(2)O + H) = 10,167 cm(-1), D(0)(CD(2)OH → CHDO + D) = 10,787 cm(-1). All are in excellent agreement with the experimental results. For CH(2)OH, the barriers for the direct OH bond fission and isomerization are: 14,205 and 13,839 cm(-1), respectively.     

Vibrational analysis of excited and ground electronic states of all-trans retinal protonated Schiff-bases

We report on vibrational coherence dynamics in excited and ground electronic states of all-trans retinal protonated Schiff-bases (RPSB), investigated by time-resolved Degenerate Four-Wave-Mixing (DFWM). The results show that wave packet dynamics in the excited state of RPSB consist of only low-frequency (<800 cm(-1)) modes. Such low-frequency wave packet motion is observed over a broad range of detection wavelengths ranging from excited state absorption (～500 nm) to stimulated emission (>600 nm). Our results indicate that low-frequency coherences in the excited state are not activated directly by laser excitation but rather by internal vibrational energy redistribution. This is supported by the observation that similar coherence dynamics are not observed in the electronic ground state. Challenging previous experimental results, we show that the formation of low-frequency coherence dynamics in RPSB does not require significant excess vibrational energy deposition in the excited state vibrational manifolds. Concerning ground state wave packet dynamics, we observe a set of high-frequency (>800 cm(-1)) modes, reflecting mainly single and double bond stretching motion in the retinal polyene-chain. Dephasing of these high-frequency coherences is mode-dependent and partially differs from analogous vibrational dephasing of the all-trans retinal chromophore in a protein environment (bacteriorhodopsin).