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.     

Frequency-domain time-resolved four wave mixing spectroscopy of vibrational coherence transfer with single-color excitation

Triply vibrationally enhanced four-wave mixing spectroscopy is employed to observe vibrational coherence transfer between the asymmetric and symmetric CO-stretching modes of rhodium(I) dicarbonyl acetylacetonate (RDC). Coherence transfer is a nonradiative transition of a coherent superposition of quantum states to a different coherent superposition due to coupling of the vibrational modes through the bath. All three excitation pulses in the experiment are resonant with a single quantum coherence, but coherence transfer results in new coherences with different frequencies. The new output frequency is observed with a monochromator that resolves it from the stronger peak at the original excitation frequency. This technique spectrally resolves pathways that include coherence transfer, discriminates against spectral features created solely by radiative transitions, and temporally resolves modulations created by interference between different coherence transfer pathways. Redfield theory simulates the temporal modulations in the impulsive limit, but it is also clear that coherence transfer violates the secular approximation invoked in most Redfield theories. Instead, it requires non-Markovian and bath memory effects. RDC may provide a simple model for the development of theories that incorporate these effects.     

Two-dimensional infrared spectroscopy of antiparallel beta-sheet secondary structure

We investigate the sensitivity of femtosecond Fourier transform two-dimensional infrared spectroscopy to protein secondary structure with a study of antiparallel beta-sheets. The results show that 2D IR spectroscopy is more sensitive to structural differences between proteins than traditional infrared spectroscopy, providing an observable that allows comparison to quantitative models of protein vibrational spectroscopy. 2D IR correlation spectra of the amide I region of poly-l-lysine, concanavalin A, ribonuclease A, and lysozyme show cross-peaks between the IR-active transitions that are characteristic of amide I couplings for polypeptides in antiparallel hydrogen-bonding registry. For poly-l-lysine, the 2D IR spectrum contains the eight-peak structure expected for two dominant vibrations of an extended, ordered antiparallel beta-sheet. In the proteins with antiparallel beta-sheets, interference effects between the diagonal and cross-peaks arising from the sheets, combined with diagonally elongated resonances from additional amide transitions, lead to a characteristic "Z"-shaped pattern for the amide I region in the 2D IR spectrum. We discuss in detail how the number of strands in the sheet, the local configurational disorder in the sheet, the delocalization of the vibrational excitation, and the angle between transition dipole moments affect the position, splitting, amplitude, and line shape of the cross-peaks and diagonal peaks.     

Effects of hydrogen bonding on the ring stretching modes of pyridine

The effects of hydrogen bonding on the ring stretching modes (both ring breathing and triangle) of pyridine are experimentally investigated using noisy light based coherent Raman scattering spectroscopy. Three systems, pyridine/formamide, pyridine/water, and pyridine/acetic acid, provide varying degrees of strength for the diluent-pyridine hydrogen bond complex. Formamide forms a relatively weaker hydrogen bond, while acetic acid essentially fully transfers a proton to pyridine. Both dilution studies and temperature studies are performed on the three systems. Together, these provide a broad context in which a very simple model for the electronic behavior of pyridine is formulated. This model is based on a molecular orbital picture and electrostatic arguments, and it well explains the observed experimental results. Additionally, a new mechanism for the line broadening of the ring breathing mode for the pyridine-water hydrogen bonded complex is proposed.     

Frequency- and time-resolved coherence transfer spectroscopy

Frequency-domain two-color triply vibrational enhanced four-wave mixing using a new phase-matching geometry discriminates against coherent multidimensional spectral features created solely by radiative transitions, spectrally resolves pathways with different numbers of coherence transfer steps, and temporally resolves modulations created by interference between coherence transfer pathways. Coherence transfer is a nonradiative transition where a superposition of quantum states evolves to a different superposition. The asymmetric and symmetric C[triple bond]O stretching modes of rhodium(I) dicarbonyl acetylacetonate are used as a model system for coherence transfer. A simplified theoretical model based on Redfield theory is used to describe the experimental results.     

Interferometric coherence transfer modulations in triply vibrationally enhanced four-wave mixing

Triply vibrationally enhanced (TRIVE) four-wave mixing (FWM) spectroscopy in a mixed frequency/time domain experiment contains new output coherences that isolate nonlinear pathways that involve coherence transfer. Coherence transfer occurs when a thermal bath induces coupling between two states so a quantum mechanical entanglement of a pair of quantum states evolves to entangle a new pair of quantum states. The FWM includes several equivalent coherence pathways that interfere and create a temporal modulation of the output coherence that is a signature of coherence transfer. The transfer shifts the output coherence frequency and isolates coherence transfer pathways from the stronger FWM processes that form the basis of coherent multidimensional spectroscopy. The use of coherence transfer offers the opportunity for another form of coherent multidimensional spectroscopy where cross-peaks appear because of the coherence transfer between quantum states. Since this approach is based on frequency domain methods, it requires only short-term phase coherence during the excitation process so the method is not constrained to accessing the quantum states lying within the excitation pulse bandwidth.     

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.     

The photodissociation dynamics of O2 at 193 nm: an O3PJ angular momentum polarization study

In the following paper we present translational anisotropy and angular momentum polarization data for O((3)P(1)) and O((3)P(2)) products of the photodissociation of molecular oxygen at 193 nm. The data were obtained using polarized laser photodissociation coupled with resonantly enhanced multiphoton ionization and velocity-map ion imaging. Under the jet-cooled conditions employed, absorption is believed to be dominated by excitation into the Herzberg continuum. The experimental data are compared with previous experiments and theoretical calculations at this and other wavelengths. Semi-classical calculations performed by Groenenboom and van Vroonhoven [J. Chem. Phys, 2002, 116, 1965] are used to estimate the alignment parameters arising from incoherent excitation and dissociation and these are shown to agree qualitatively well with the available experimental data. Following the work of Alexander et al. [J. Chem. Phys, 2003, 118, 10566], orientation and alignment parameters arising from coherent excitation and dissociation are modelled more approximately by estimating phase differences generated subsequent to dissociation via competing adiabatic pathways leading to the same asymptotic products. These calculations lend support to the view that large values of the coherent alignment moments, but small values of the corresponding orientation moments, could arise from coherent excitation of (and subsequent dissociation via) parallel and perpendicular components of the Herzberg I, II and III transitions.     

Ion-pair interaction in pyridinium carboxylate solutions

Ion-pair interactions between pyridinium cations and various carboxylate anions are explored using noisy light based coherent anti-Stokes Raman scattering (I(2)CARS). Binary mixtures of pyridine and various carboxylic acids (including halo-acetic acids, straight-chain carboxylic acids, and pivalic acid) are prepared. A Br?nsted type acid-base reaction occurs in these mixtures to create pyridinium and carboxylate ions. Both pyridine, itself, and pyridinium have strong I(2)CARS signals originating from their ring breathing modes. The vibrational frequency of the ring breathing mode for pyridine is blue-shifted by hydrogen bonding, and that same mode for pyridinium is red-shifted by ion-pair interaction. Frequency shift data for the ring breathing mode of pyridine and pyridinium are presented. These data are discussed in terms of a simplistic model for the electronic behavior of these compounds.     

Two-dimensional infrared spectra of the 13C=18O isotopomers of alanine residues in an alpha-helix

The parameters needed to describe the two-dimensional infrared (2D IR) spectra of the isotopically labeled alpha-helix are presented. The 2D IR spectra in the amide-I' spectral region of a series of singly 13C=18O-labeled 25-residue alpha-helices were measured by three-pulse heterodyned spectral interferometry. The dependence of the spectra on the population time was measured. Individual isotopomer levels (residues 11-14) were clearly identified in 2D IR, downshifted by approximately 61 cm(-1) from the main helical band. By analyzing the line shapes of the 13C=18O diagonal peaks that appeared at approximately 1571.3 +/- 0.8 cm(-1) for all four labeled samples, we observed wider structural distributions for residues 14 and 11 than those for 12 and 13. A small fast component in the correlation function was used to estimate the dynamics of these distributions. In all cases, the v = 1 --> 2 transition showed a more Lorentzian-like line shape and also decayed faster than the v = 0 --> 1 transition, indicating that the population relaxation time of the v = 2 state was significantly faster than the v = 1 state. The amide transitions with naturally abundant 13C=16O appeared at approximately 1594 cm(-1), forming very weak and blurred cross-peaks with 13C=18O isotopomer modes. The effects of spectral interferences on the coherence time dependence of the detection frequency spectrum were also investigated. The methods of first moments and Wigner analysis were developed to circumvent the interference effects on the weak isotopomer transitions. The structural origin of the distributions for individual isotopomers was proposed to be an effect of nearby lysine residues on the intrahelical hydrogen-bond network.     

Mechanism of the organocatalyzed decarboxylative Knoevenagel-Doebner reaction. A theoretical study

We have investigated important intermediates and key transition states of the organocatalyzed Knoevenagel condensation using density functional theory and two different basis sets (6-31 G(d,p) and 6-311++G(2df,2pd)), both in gas phase and simulating the bulk solvent (pyridine) using the PCM method. Calculated structures for reactants, intermediates, and key transition states suggest that the secondary amine catalyst is essential, both for activating the aldehyde for nucleophilic attack, and in the possible decarboxylation pathways. The calculated results are shown to agree with available experimental information. On the basis of the results obtained, the studied mechanism may be important in the understanding of vinylphenol production during malting and brewing of wheat and barley grains.     

Dehydrogenation of aromatic molecules under a scanning tunneling microscope: pathways and inelastic spectroscopy simulations

We have performed a theoretical study on the dehydrogenation of benzene and pyridine molecules on Cu(100) induced by a scanning tunneling microscope (STM). Density functional theory calculations have been used to characterize benzene, pyridine, and different dehydrogenation products. The adiabatic pathways for single and double dehydrogenation have been evaluated with the nudge elastic band method. After identification of the transition states, the analysis of the electronic structure along the reaction pathway yields interesting information on the electronic process that leads to H-scission. The adiabatic barriers show that the formation of double dehydrogenated fragments is difficult and probably beyond reach under the actual experimental conditions. However, nonadiabatic processes cannot be ruled out. Hence, in order to identify the final dehydrogenation products, the inelastic spectra are simulated and compared with the experimental ones. We can then assign phenyl (C6H5) and alpha-pyridil (alpha-C5H4N) as the STM-induced dehydrogenation products of benzene and pyridine, respectively. Our simulations permit us to understand why phenyl, pyridine, and alpha-pyridil present tunneling-active C-H stretch modes in opposition to benzene.     

Phonon-driven exciton dissociation at donor-acceptor polymer heterojunctions: direct versus bridge-mediated vibronic coupling pathways

We present a molecular-level, quantum dynamical analysis of phonon-driven exciton dissociation at polymer heterojunctions, using a linear vibronic coupling model parametrized for 3 electronic states and 24 vibrational modes. Quantum dynamical simulations were carried out using the multiconfiguration time-dependent Hartree method. In this study, which significantly extends the two-state model of Tamura et al. (Tamura, H.; Bittner, E. R.; Burghardt, I. J. Chem. Phys. 2007, 126, 021103), we focus on the role of bridge states, which can mediate the decay of the photogenerated exciton and possibly interfere with the direct transition toward an interfacial charge-separated state. Both the direct and bridge-mediated pathways are found to depend critically on the dynamical interplay of high-frequency C=C stretch modes and low-frequency ring-torsional modes. The dynamical mechanism is interpreted in terms of a hierarchical electron-phonon model, leading to the identification of generalized reaction coordinates for the nonadiabatic process. Variation of the vibronic coupling model parameters in a realistic range provides evidence that the direct exciton decay pathway is not dynamically robust, and bridge-mediated pathways can become dominant. The ultrafast, coherent dynamics is of pronounced nonequilibrium character and cannot be modeled by conventional kinetic equations. The predicted femtosecond to picosecond decay times are consistent with time-resolved spectroscopic observations.     

Electronic transition dipole moment directions of reduced anionic flavin in stretched poly(vinyl alcohol) films

The IR and UV/vis linear dichroic spectra of reduced anionic flavin mononucleotide (FMNH-) partially oriented in poly(vinyl alcohol) (PVA) films have been measured to determine the direction of the major electronic transition dipole moments. The IR linear dichroism (LD) was measured in the 1750-1350 cm(-1) region to provide the overall molecular orientation of the FMNH- in the stretched films. Time-dependent density functional theory using the B3LYP functional was used to calculate the normal modes and the transition dipole moments of reduced lumiflavin. The calculated normal modes assisted in IR band assignments and in the determination of the IR transition dipole moment directions which were required for the determination of the orientation parameters for FMNH- in PVA films. The UV/vis LD spectrum was measured over the 200-700 nm region and was resolved into contributions from three pi-->pi* transitions. The directions of the transitions are 90 degrees+/-4 degrees at 440 nm, 79 degrees+/-4 degrees at 350 nm, and 93 degrees+/-4 degrees at 290 nm with counterclockwise rotations with respect to the N5-N10 axis. Comparison of the calculated and experimentally determined transition dipole moments allowed for refined assignment of the transition dipole moment directions. To our knowledge, this is the first experimental evidence that the 350-450 nm absorption arises from two unique transitions. Remarkably, the two lowest energy transition dipole moments for FMNH- are nearly parallel to those obtained in prior studies for both oxidized and semiquinone flavin.     

Vibrational relaxation pathways of AI and AII modes in N-methylacetamide clusters

We studied the pathways of vibrational energy relaxation of the amide I (~1660 cm?1) and amide II (~1560 cm?1) vibrational modes of N-methylacetamide (NMA) in CCl? solution using two-color femtosecond vibrational spectroscopy. We measured the transient spectral dynamics upon excitation of each of these amide modes. The results show that there is no energy transfer between the amide I (AI) and amide II (AII) modes. Instead we find that the vibrational energy is transferred on a picosecond time scale to a common combination tone of lower-frequency modes. By use of polarization-resolved femtosecond pump-probe measurements we also study the reorientation dynamics of the NMA molecules and the relative angle between the transition dipole moments of the AI and AII vibrations. The spectral dynamics at later times after the excitation (>40 ps) reveal the presence of a dissociation process of the NMA aggregates, trimers, and higher order structures into dimers and monomers. By measuring the dissociation kinetics at different temperatures, we determined the activation energy of this dissociation E(a) = 35 ± 3 kJ mol?1.     

Influence of velocity effects on the shape of N(2) (and air) broadened H(2)O lines revisited with classical molecular dynamics simulations

The modeling of the shape of H(2)O lines perturbed by N(2) (and air) using the Keilson-Storer (KS) kernel for collision-induced velocity changes is revisited with classical molecular dynamics simulations (CMDS). The latter have been performed for a large number of molecules starting from intermolecular-potential surfaces. Contrary to the assumption made in a previous study [H. Tran, D. Bermejo, J.-L. Domenech, P. Joubert, R. R. Gamache, and J.-M. Hartmann, J. Quant. Spectrosc. Radiat. Transf. 108, 126 (2007)], the results of these CMDS show that the velocity-orientation and -modulus changes statistically occur at the same time scale. This validates the use of a single memory parameter in the Keilson-Storer kernel to describe both the velocity-orientation and -modulus changes. The CMDS results also show that velocity- and rotational state-changing collisions are statistically partially correlated. A partially correlated speed-dependent Keilson-Storer model has thus been used to describe the line-shape. For this, the velocity changes KS kernel parameters have been directly determined from CMDS, while the speed-dependent broadening and shifting coefficients have been calculated with a semi-classical approach. Comparisons between calculated spectra and measurements of several lines of H(2)O broadened by N(2) (and air) in the ν(3) and 2ν(1) + ν(2) + ν(3) bands for a wide range of pressure show very satisfactory agreement. The evolution of non-Voigt effects from Doppler to collisional regimes is also presented and discussed.     

Restoration of coherence effects in high-power excitation of an intramolecular quasicontinuum

Three theoretical models were advanced for the dynamics of molecular multiphoton excitation: (i) The zero-order optically active mode connected by intramolecular random anharmonic couplings to a background manifold. (ii) Molecular eigenstates coupled by random radiative transition dipole moments. (iii) The kinetic master equation approach. It is demonstrated that in the Markoffian limit, as long as the intramolecular vibrational relaxation width is small relative to the Rabi frequency, these three approaches are equivalent. In the case of high-field excitation, coherent quantum effects are exhibited even in a randomly coupled system. Resurrection of the quantum oscillations and coherent pumping can be exhibited in intense field excitation on the time scale of intramolecular vibrational relaxation.     

给、吸电子基团对吡嗪衍生物电子结构影响的DFT研究

采用B3LYP方法在6—31G^#基组水平上优化了对位取代吡嗪衍生物的几何构型，利用TD—DFT方法计算了它们的前线分子轨道能级和电子光谱．结果表明，带有给、吸电子基团对吡嗪衍生物与苯、吡啶相比，也具有很好的共轭性；随着分子共轭链的增长，分子的偶极矩增大，前线分子轨道能级差减小，最大吸收波长发生红移．对于具有相同共轭链的同分异构体，推电子基团与具有给电子性质的共轭链相连，则分子的电荷转移明显，导致偶极矩增大，前线分子轨道能级间的电子跃迁更容易；吸电子基团与具有给电子性质的共轭链相连，情况正好相反，这些结果对分子设计有重要意义。     

Adiabatic states derived from a spin-coupled diabatic transformation: semiclassical trajectory study of photodissociation of HBr and the construction of potential curves for LiBr+

The development of spin-coupled diabatic representations for theoretical semiclassical treatments of photodissociation dynamics is an important practical goal, and some of the assumptions required to carry this out may be validated by applications to simple systems. With this objective, we report here a study of the photodissociation dynamics of the prototypical HBr system using semiclassical trajectory methods. The valence (spin-free) potential energy curves and the permanent and transition dipole moments were computed using high-level ab initio methods and were transformed to a spin-coupled diabatic representation. The spin-orbit coupling used in the transformation was taken as that of atomic bromine at all internuclear distances. Adiabatic potential energy curves, nonadiabatic couplings and transition dipole moments were then obtained from the diabatic ones and were used in all the dynamics calculations. Nonadiabatic photodissociation probabilities were computed using three semiclassical trajectory methods, namely, coherent switching with decay of mixing (CSDM), fewest switches with time uncertainty (FSTU), and its recently developed variant with stochastic decoherence (FTSU/SD), each combined with semiclassical sampling of the initial vibrational state. The calculated branching fraction to the higher fine-structure level of the bromine atom is in good agreement with experiment and with more complete theoretical treatments. The present study, by comparing our new calculations to wave packet calculations with distance-dependent ab initio spin-orbit coupling, validates the semiclassical trajectory methods, the semiclassical initial state sample scheme, and the use of a distance-independent spin-orbit coupling for future applications to polyatomic photodissociation. Finally, using LiBr(+) as a model system, it is shown that accurate spin-coupled potential curves can also be constructed for odd-electron systems using the same strategy as for HBr.