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.     

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.     

Initial excited-state structural dynamics of 2'-deoxyguanosine determined via UV resonance Raman spectroscopy

The resonance Raman spectra of 2'-deoxyguanosine, a DNA nucleoside, were measured in aqueous solution at wavelengths throughout its 260 nm absorption band. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism with two electronic states yielded the initial excited-state structural dynamics in both states. The vibrational modes containing the N(7)═C(8) stretching and C(8)-H bending internal coordinates were found to exhibit significant initial structural dynamics upon photoexcitation to either state and are coincident with the photochemical reaction coordinate involving the formation of the 2'-deoxyguanosine cation radical.     

Unraveling the structure of hydrogen bond stretching mode infrared absorption bands: an anharmonic density functional theory study on 7-azaindole dimers

The structure of the linear infrared absorption spectrum of the N-H stretching mode in 7-azaindole dimers is analyzed by quartic anharmonic vibrational force field calculations based on density functional theory. It is demonstrated that a multiple Fermi resonance model including contributions from 12 fingerprint vibrational modes, most of them containing considerable contributions of N-H bending motions, combined with a single low-frequency mode satisfactorily explains the complex line shape of N-H stretching mode absorption band.     

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.     

High resolution photofragment translational spectroscopy studies of the near ultraviolet photolysis of 2,5-dimethylpyrrole

The photodissociation dynamics of 2,5-dimethylpyrrole (2,5-DMP) has been investigated following excitation at 193.3 nm and at many near ultraviolet (UV) wavelengths in the range 244 < lambda(phot) < 282 nm using H Rydberg atom photofragment translational spectroscopy (PTS). Complementary UV absorption and, at the longest excitation wavelengths, one photon resonant multiphoton ionisation spectra of 2,5-DMP are reported also; analysis of the latter highlights the role of methyl torsional motions in promoting the parent absorption. The deduced fragmentation dynamics show parallels with that reported recently (B. Cronin, M. G. D. Nix, R. H. Qadiri and M. N. R. Ashfold, Phys. Chem. Chem. Phys., 2004, 6, 5031) for the bare pyrrole molecule. Excitation at the longer wavelengths leads to (vibronically induced) population of the 1(1)A(2)(pisigma*) excited state of 2,5-DMP, but once lambda(phot) decreases to approximately 250 nm stronger, dipole allowed transitions start to become apparent in the parent absorption. All total kinetic energy release (TKER) spectra of the H + 2,5-dimethylpyrrolyl (2,5-DMPyl) fragments measured at lambda(phot)> or=244 nm show a structured fast component, many of which are dominated by a peak with TKER approximately 5100 cm(-1); analysis of this structure reveals lambda(phot) dependent population of selected vibrational levels of 2,5-DMPyl, and enables determination of the N-H bond strength in 2,5-DMP: D(0) = 30 530 +/- 100 cm(-1). Two classes of behaviour are proposed to account for details of the observed energy partitioning. Both assume that N-H bond fission involves passage over (or tunnelling through) a small exit channel barrier on the 1(1)A(2) potential energy surface, but differ according to the vibrational energy content of the photo-prepared molecules. Specific parent out-of-plane skeletal modes that promote the 1(1)A(2)-X(1)A(1) absorption appear to evolve adiabatically into the corresponding vibrations of the 2,5-DMPyl products. Methyl torsions can also promote the 1(1)A(2)<-- X(1)A(1) absorption in 2,5-DMP, and provide a means of populating a much higher density of excited vibrational levels than in pyrrole. Such excited levels are deduced to dissociate by redistributing the minimum amount of internal energy necessary to overcome the exit channel barrier in the N-H dissociation coordinate. Coupling with the ground state surface via a conical intersection at extended N-H bond lengths is proposed as a further mechanism for modest translational --> vibrational energy transfer within the separating products. The parent absorption cross-section increases considerably at wavelengths approximately 250 nm, and PTS spectra recorded at lambda(phot)< or = 254 nm display a second, unstructured, peak at lower TKER. As in pyrrole, this slower component is attributed to H atoms from the unimolecular decay of highly vibrationally excited ground state molecules formed via radiationless decay from photo-excited states lying above the 1(1)A(2) state.     

Calculations of intermode coupling constants and simulations of amide I,II, and III vibrational spectra of dipeptides

Amide I, II, and III vibrations of polypeptides are important marker modes whose vibrational spectra can provide critical information on structure and dynamics of proteins in solution. The extent of delocalization and vibrational properties of amide normal mode can be described by the amide local mode frequencies and intermode coupling constants between a pair of amide local modes. To determine these fundamental quantities, the previous Hessian matrix reconstruction method has been generalized here and applied to the density functional theory results for various dipeptide conformers. The calculation results are then used to simulate IR absorption, vibrational circular dichroism, and 2D IR spectra of dipeptides. The relationships between dipeptide backbone conformations and these vibrational spectra are discussed. It is believed that the present computational method and results will be of use to quantitatively simulate vibrational spectra of complicated polypeptides beyond simple dipeptides     

Vibrational dynamics of pyrrole via frequency-domain spectroscopy

The N-H stretch overtones of pyrrole, a key constituent of biologic building blocks, were studied by room temperature photoacoustic and jet-cooled action spectroscopies to unravel their intramolecular dynamics. Contrary to "isolated" states excited with two and three N-H stretch quanta, the one with four quanta shows strong accidental resonances with two other states involving three quanta of N-H stretch and one quantum of C-H stretch. The inhomogeneously reduced features in the action spectra provide the means for getting insight into the intramolecular interactions and the factors controlling energy flow within pyrrole. The time dependence of the survival probability of the 4ν(1) N-H stretch, deduced from the vibrational Hamiltonian, shows an initial decay in ~0.3 ps with ensuing quantum beats from the N-H-C-H resonance and their decay with a time constant of about 5 ps as a result of weaker coupling to bath states.     

Dependence of amide vibrations on hydrogen bonding

The effect of hydrogen bonding on the amide group vibrational spectra has traditionally been rationalized by invoking a resonance model where hydrogen bonding impacts the amide functional group by stabilizing its [(-)O-C=NH (+)] structure over the [O=C-NH] structure. However, Triggs and Valentini's UV-Raman study of solvation and hydrogen bonding effects on epsilon-caprolactum, N, N-dimethylacetamide (DMA), and N-methylacetamide (NMA) ( Triggs, N. E.; Valentini, J. J. J. Phys. Chem. 1992, 96, 6922-6931) casts doubt on the validity of this model by demonstrating that, contrary to the resonance model prediction, carbonyl hydrogen bonding does not impact the AmII' frequency of DMA. In this study, we utilize density functional theory (DFT) calculations to examine the impact of hydrogen bonding on the C=O and N-H functional groups of NMA, which is typically used as a simple model of the peptide bond. Our calculations indicate that, as expected, the hydrogen bonding frequency dependence of the AmI vibration predominantly derives from the C=O group, whereas the hydrogen bonding frequency dependence of the AmII vibration primarily derives from N-H hydrogen bonding. In contrast, the hydrogen bonding dependence of the conformation-sensitive AmIII band derives equally from both C=O and N-H groups and thus, is equally responsive to hydrogen bonding at the C=O or N-H site. Our work shows that a clear understanding of the normal mode composition of the amide vibrations is crucial for an accurate interpretation of the hydrogen bonding dependence of amide vibrational frequencies.     

Full dimensional quantum calculations of vibrational energies of N-methyl acetamide

We report quantum calculations of vibrational states of trans N-methyl acetamide (H3C-HNCO-CH3) in full dimensionality using the code MULTIMODE. In this code, the full potential is represented as a hierarchical sum of n-mode potentials in the normal coordinates. All 30 one- and 435 two-mode potentials are included in the sum, as well as a restricted set of 10 three-mode potentials corresponding to the experimentally probed amide band. The electronic energies on the various n-mode grids are obtained using ab initio M?ller-Plesset perturbation theory with a triple-zeta quality, correlation-consistent basis set. Convergence tests of the low-lying vibrational eigenvalues of the amide band show that this limited three-mode representation of the full potential yields well converged results that are in excellent agreement with experiment. The infrared spectrum in the region of the amide bands is calculated and also agrees well with experiment.     

First-principles simulation of amide and aromatic side chain ultraviolet spectroscopy of a cyclic dipeptide

By combining time-dependent density functional theory (TDDFT) and molecular dynamics (MD) simulations, we calculate the ultraviolet absorption and circular dichroism (CD) of a cyclic dipeptide, cyclo(L-Pro-D-Tyr), in the 185-300 nm region. The absorption is dominated by the phenol chromophore of tyrosine. The CD spectrum shows both phenol and amide units transitions. A crude coherent two-dimensional ultraviolet spectrum (2DUV) calculated by neglecting the two-excitation states shows a cross-peak between two transitions of the phenol in the tyrosine side chain. Additional cross-peaks between the side chain and the backbone are observed when using a chirality-induced pulse polarization configuration.     

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.     

Electron-vibrational dynamics of photoexcited polyfluorenes

The highly polarizable pi-electron system of conjugated molecules forms the basis for their unique electronic and photophysical properties, which play an important role in numerous biological phenomena and make them important materials for technological applications. We present a theoretical investigation of the dynamics and relaxation of photoexcited states in conjugated polyfluorenes, which are promising materials for display applications. Our analysis shows that both fast (approximately 20 fs) and slow (approximately 1 ps) nuclear motions couple to the electronic degrees of freedom during the excited-state dynamics. Delocalized excitations dominate the absorption, whereas emission comes from localized (self-trapped) excitons. This localization is attributed to an inherent nonlinear coupling among vibronic degrees of freedom which leads to lattice and torsional distortions and results in specific signatures in spectroscopic observables. Computed vertical absorption and fluorescence frequencies as well as photoluminescence band shapes show good agreement with experiment. Finally, we demonstrate that dimerization such as spiro-linking does not affect the emission properties of molecules because the excitation becomes confined on a single chain of the composite molecule.     

Primary reaction dynamics of halorhodopsin,observed by sub-picosecond IR – vibrational spectroscopy

The primary all-trans to 13-cis chromophore isomerization of the light driven chloride pump halorhodopsin has been studied by means of transient absorption spectroscopy in the visible and mid-infrared regime at a time resolution of better than 100 and 220 fs, respectively. The picosecond vibrational dynamics are dominated by two time constants, i.e., 2 and 7.7 ps in accordance with the biphasic decay of the retinal excited electronic state and electronic ground state formation with 1.5 and 6.6 ps. The transient vibrational spectra of the participating electronic states strongly suggest the existence of two distinct S₁ populations as a result of an early branching reaction. It is shown that the 13-cis product is formed with the fast time constant, whereas the all-trans educt state is repopulated via both time constants. Concomitant protein dynamics are indicated by spectral changes on a similar time scale in the amide region.     

Vibrational dynamics of N-H, C-D, and C=O modes in formamide

By means of heterodyned two-dimensional IR photon echo experiments on liquid formamide and isotopomers the vibrational frequency dynamics of the N-H stretch mode, the C-D mode, and the C=O mode were obtained. In each case the vibrational frequency correlation function is fitted to three exponentials representing ultrafast (few femtoseconds), intermediate (hundreds of femtoseconds), and slow (many picoseconds) correlation times. In the case of N-H there is a significant underdamped contribution to the correlation decay that was not seen in previous experiments and is attributed to hydrogen-bond librational modes. This underdamped motion is not seen in the C-D or C=O correlation functions. The motions probed by the C-D bond are generally faster than those seen by N-H and C=O, indicating that the environment of C-D interchanges more rapidly, consistent with a weaker C-D...O=C bond. The correlation decays of N-H and C=O are similar, consistent with both being involved in strong H bonding.     

Nonadiabatic quantum dynamics of Br2 in solid Ar: A four-dimensional study of the B to C state predissociation

Quantum dynamics simulations are performed for a diatomics-in-molecules based model of Br₂ in solid Ar which incorporates four nuclear degrees of freedom and four electronic states. The nuclear motions comprise two large amplitude coordinates describing the Br₂ bond distance and an effective symmetry-preserving matrix mode. Two symmetry-lowering harmonic modes are added in the spirit of linear vibronic coupling theory. Initiating the dynamics on the B state by means of an ultrafast laser pulse, nonadiabatic transitions to the two degenerate C states are monitored and the effect of vibrational preexcitation in the electronic ground state is investigated.     

Conformational changes of fibrinogen after adsorption

The adsorption behavior of fibrinogen to two biomedical polyurethanes and a perfluorinated polymer has been investigated. Changes in the secondary structure of adsorbed fibrinogen were monitored using attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) and sum frequency generation vibrational spectroscopy (SFG). SFG measurements were performed in the amide I range as well as in the C-H/N-H stretching range. Amide I signals from SFG demonstrate that fibrinogen has post-adsorption conformational changes that are dependent upon the polymer surface properties. For example, strong attenuation of the amide I and N-H stretching signals with increasing residence time was observed for fibrinogen adsorbed to poly(ether urethane) but not for the other two polymers. This change is not readily observed by ATR-FTIR. Differences in the observed spectral changes for fibrinogen adsorbed to each polymer are explained by different initial binding mechanisms and post-adsorption conformational changes.     

Lattice dynamics of tetrahedrally bonded boron nitride probed by inelastic X-ray scattering

We report experimental results on the lattice dynamics of zincblende and wurtzite boron nitride obtained by inelastic X-ray scattering (IXS) on polycrystalline samples. The generalized vibrational density of states and the orientation averaged longitudinal acoustic phonon dispersion are determined, and the longitudinal and shear sound speeds as well as the Debye temperature are derived. Our results are compared to ab initio lattice dynamics calculations and available elastic and thermodynamic data.