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PubMed2006

Quasi-classical trajectories study of Ne79Br2(B) vibrational predissociation.

A full-dimensional quasi-classical trajectories study on the vibrational predissociation (VP) of the Ne79Br2(B) complex is presented. Following the most recent experiments, the Br2(B) vibrational levels v'=16-29 were explored. The total angular momentum, J, was taken to be zero, and a semiclassical Franck-Condon model to compute initial conditions from quantum distributions was employed. Predissociation lifetimes were extracted from Ne79Br2 population decay by using two different exponential laws. Predicted lifetimes are in excellent agreement with the last experimental results [J. A. Cabrera, C. R. Bieler, B. C. Olbricht, W. E. van der Veer and K. C. Janda, J. Chem. Phys., 2005, 123, 054311]. The Br2 fragment ro-vibrational distributions resulting from the VP of the molecule were obtained from the statistics of classical magnitudes using the standard binning procedure. Computed rotational distributions (for the Deltav'=-1, -2 channels) are also in very good agreement with the experimental results [M. Nejad-Sattari and T. A. Stephenson, J. Chem. Phys., 1997, 106 5454]. The influence of two quantum effects-the closing of the Deltav'=-1 dissociation channel and the intramolecular vibrational relaxation (IVR) mechanism-on the agreement with experimental rotational distributions, is discussed. Due to the classical character of our calculations and the binning procedure we used, the agreement of computed vibrational distributions with experimental and quantum theoretical is qualitative. For instance, for v'=28-for which the Deltav'=-1 channel is experimentally found to be closed-the Deltav'=-2 channel becomes statistically more significant. A discussion on the viability of similar quasi-classical methods to model the VP dynamics of analogous clusters is presented.

Journal Article↗
PubMed2006

Vibrational spectrum of the spin crossover complex [Fe(phen)(2)(NCS)(2)] studied by IR and Raman spectroscopy, nuclear inelastic scattering and DFT calculations.

The vibrational modes of the low-spin and high-spin isomers of the spin crossover complex [Fe(phen)(2)(NCS)(2)] (phen = 1,10-phenanthroline) have been measured by IR and Raman spectroscopy and by nuclear inelastic scattering. The vibrational frequencies and normal modes and the IR and Raman intensities have been calculated by density functional methods. The vibrational entropy difference between the two isomers, DeltaS(vib), which is--together with the electronic entropy difference DeltaS(el)--the driving force for the spin-transition, has been determined from the measured and from the calculated frequencies. The calculated difference (DeltaS(vib) = 57-70 J mol(-1) K(-1), depending on the method) is in qualitative agreement with experimental values (20-36 J mol(-1) K(-1)). Only the low energy vibrational modes (20% of the 147 modes of the free molecule) contribute to the entropy difference and about three quarters of the vibrational entropy difference are due to the 15 modes of the central FeN(6) octahedron.

Ferrous Compounds↗
PubMed2006

Vibrational mode and collision energy effects on reaction of H2CO+ with CO2.

The effects of collision energy (Ecol) and five different modes of H2CO+ vibration on the title reaction have been studied over the center-of-mass Ecol range from 0.1 to 3.2 eV, including measurements of product ion recoil velocity distributions. Electronic structure and Rice-Ramsperger-Kassel-Marcus calculations were used to examine properties of various complexes and transition states that might be important along the reaction coordinate. Two product channels are observed, corresponding to Hydrogen Transfer (HT) and Proton Transfer (PT). Both channels are endothermic with similar onset energies of approximately 0.9 eV; however, HT dominates over the entire Ecol range and accounts for 70-85% of the total reaction cross section. Both HT and PT occur by direct mechanisms over the entire Ecol range, and have similar dependence on reactant vibrational and collision energy. Despite these similarities, and the fact that the two channels are nearly isoenergetic and differ only in which product moiety carries the charge, their dynamics appear quite different. PT occurs primarily in large impact parameter stripping collisions, where most of the available energy is partitioned to product recoil. HT, in contrast, results in internally hot products with little recoil energy and a more forward-backward symmetric product velocity distribution. Vibration is found to affect the reaction differently in different collision energy regimes. The appearance thresholds are found to depend only on total energy, i.e., all modes of vibration are equivalent to Ecol. With increasing Ecol, vibrational energy becomes increasingly effective, relative to Ecol, at driving reaction. For HT, this transition occurs just above threshold, while for PT it begins at roughly twice the threshold energy.

Journal Article↗
PubMed2006

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.

Journal Article↗
PubMed2004

Vibrational coupled cluster theory.

The theory and first implementation of a vibrational coupled cluster (VCC) method for calculations of the vibrational structure of molecules is presented. Different methods for introducing approximate VCC methods are discussed including truncation according to a maximum number of simultaneous mode excitations as well as an interaction space order concept is introduced. The theory is tested on calculation of anharmonic frequencies for a three-mode model system and a formaldehyde quartic force field. The VCC method is compared to vibrational self-consistent-field, vibrational Møller-Plesset perturbation theory, and vibrational configuration interaction (VCI). A VCC calculation typically gives higher accuracy than a corresponding VCI calculation with the same number of parameters and the same formal operation count.

Journal Article↗
PubMed2004

Accurate theoretical prediction of vibrational frequencies in an inhomogeneous dynamic environment: a case study of a glutamate molecule in water solution and in a protein-bound form.

We propose a hierarchical approach to model vibrational frequencies of a ligand in a strongly fluctuating inhomogeneous environment such as a liquid solution or when bound to a macromolecule, e.g., a protein. Vibrational frequencies typically measured experimentally are ensemble averaged quantities which result (in part) from the influence of the strongly fluctuating solvent. Solvent fluctuations can be sampled effectively by a classical molecular simulation, which in our model serves as the first, low level of the hierarchy. At the second high level of the hierarchy a small subset of system coordinates is used to construct a patch of the potential surface (ab initio) relevant to the vibration in question. This subset of coordinates is under the influence of an instantaneous external force exerted by the environment. The force is calculated at the lower level of the hierarchy. The proposed methodology is applied to model vibrational frequencies of a glutamate in water and when bound to the Glutamate receptor protein and its mutant. Our results are in close agreement with the experimental values and frequency shifts measured by the Jayaraman group by the Fourier transform infrared spectroscopy [Q. Cheng et al., Biochem. 41, 1602 (2002)]. Our methodology proved useful in successfully reproducing vibrational frequencies of a ligand in such a soft, flexible, and strongly inhomogeneous protein as the Glutamate receptor.

Computer Simulation↗
PubMed2004

Nuclear and electron spin relaxation in paramagnetic complexes in solution: effects of the quantum nature of molecular vibrations.

A model of the paramagnetic relaxation enhancement is developed in terms of electron-spin relaxation caused by the zero-field splitting (ZFS) fluctuating in time due to a coupling between the electron-spin variables and quantum vibrations. The ZFS interaction provides a coupling between the electron-spin variables and vibrational degrees of freedom, and is represented as a Taylor series expansion in a set of vibrational modes (normal coordinates). A two-level harmonic oscillator subsystem is assumed, and the electron-spin relaxation associated with T2V and T1V vibrational relaxation is considered. The description of vibrationally induced electron-spin dynamics is incorporated into the calculations of the paramagnetic relaxation enhancement by the Solomon-Bloembergen-Morgan approach as well as in the framework of the general slow-motion theory. The theoretical predictions are compared with the experimental paramagnetic relaxation enhancement values for the Ni(H2O)6(2+) complex in aqueous solution. The parameters required by the model are obtained from quantum chemical and molecular dynamics studies. Comparison is made between the current model and its recently published classical counterpart.

Journal Article↗
PubMed2004

Femtosecond pump-probe spectroscopy of I2 in a dense rare gas environment: a mixed quantum/classical study of vibrational decoherence.

The process of decoherence of vibrational states of I2 in a dense helium environment is studied theoretically using the mixed quantum/classical method based on the Bohmian formulation of quantum mechanics [E. Gindensperger, C. Meier, and J. A. Beswick, J. Chem. Phys. 113, 9369 (2000)]. Specifically, the revival of vibrational wave packets is a quantum phenomena which depends sensitively on the coherence between the vibrational states excited by an ultrafast laser pulse. Its detection by a pump-probe setup as a function of rare gas pressure forms a very accurate way of detecting vibrational dephasing. Vibrational revivals of I2 in high pressure rare gas environments have been observed experimentally, and the very good agreement with the simulated spectra confirms that the method can accurately describe decoherence processes of quantum systems in interaction with an environment.

Journal Article↗
PubMed2004

Microcanonical unimolecular rate theory at surfaces. II. Vibrational state resolved dissociative chemisorption of methane on Ni(100).

A three-parameter microcanonical theory of gas-surface reactivity is used to investigate the dissociative chemisorption of methane impinging on a Ni(100) surface. Assuming an apparent threshold energy for dissociative chemisorption of E(0)=65 kJ/mol, contributions to the dissociative sticking coefficient from individual methane vibrational states are calculated: (i) as a function of molecular translational energy to model nonequilibrium molecular beam experiments and (ii) as a function of temperature to model thermal equilibrium mbar pressure bulb experiments. Under fairly typical molecular beam conditions (e.g., E(t)>/=25 kJ mol(-1), T(s)>/=475 K, T(n)</=400 K), sticking from methane in the ground vibrational state dominates the overall sticking. In contrast, under thermal equilibrium conditions at temperatures T>/=100 K the dissociative sticking is dominated by methane in vibrationally excited states, particularly those involving excitation of the nu(4) bending mode. Fractional energy uptakes f(j) defined as the fraction of the mean energy of the reacting gas-surface collision complexes that derives from specific degrees of freedom of the reactants (i.e., molecular translation, rotation, vibration, and surface) are calculated for thermal dissociative chemisorption. At 500 K, the fractional energy uptakes are calculated to be f(t)=14%, f(r)=21%, f(v)=40%, and f(s)=25%. Over the temperature range from 500 K to 1500 K relevant to thermal catalysis, the incident gas-phase molecules supply the preponderance of energy used to surmount the barrier to dissociative chemisorption, f(g)=f(t)+f(r)+f(v) approximately 75%, with the highest energy uptake always coming from the molecular vibrational degrees of freedom. The predictions of the statistical, mode-nonspecific microcanonical theory are compared to those of other dynamical theories and to recent experimental data.

Journal Article↗
PubMed2004

Strong enhancement of vibrational relaxation by Watson-Crick base pairing.

We have studied the ultrafast dynamics of NH-stretch vibrational excitations in Watson-Crick base pairs consisting of adenine and uracil derivatives. To estimate the influence of the A:U hydrogen bonding on the vibrational dynamics, we have also studied the uracil derivative in monomeric form. The vibrational relaxation of the NH-stretching mode is found to occur much faster in the Watson-Crick base pair than in monomeric uracil. From the delay dependence of the transient vibrational spectra, it can be concluded that both in base-paired and monomeric uracil, the energy relaxation takes place in two steps, the first step being a rapid transfer of energy from the NH-stretching mode to an accepting mode, the second step the relaxation of this accepting mode. The transient spectra show evidence that in the base pair the hydrogen bond between the nucleobases acts as the accepting mode, and that the hydrogen bonding between the bases is responsible for the extremely fast vibrational relaxation in this system.

Journal Article↗
PubMed2004

Vibrational energy relaxation of naphthalene in the S(1) state in various gases.

Time-resolved fluorescence spectra of naphthalene in the S(1) state have been measured in various gases below 10(2) kPa. The band shape of the fluorescence changed in an earlier time region after the photoexcitation when an excess energy (3300 cm(-1)) above the 0-0 transition energy was given. The excitation energy dependence of the fluorescence band shape of an isolated naphthalene molecule was measured separately, and the time dependence of the fluorescence band shape in gases was found to be due to the vibrational energy relaxation in the S(1) state. We have succeeded in determining the transient excess vibrational energy by comparing the time-resolved fluorescence band shape with the excitation energy dependence of the fluorescence band shape. The excess vibrational energy decayed almost exponentially. From the slope of the decay rate against the buffer gas pressure, we have determined the collisional decay rate of the excess vibrational energy in various gases. The dependence of the vibrational energy relaxation rate on the buffer gas species was similar to the case of azulene. The comparisons with the results in the low temperature argon and the energy relaxation rate in the S(0) state in nitrogen were also discussed.

Journal Article↗
PubMed2005

Angular distribution of different vibrational components of the X and B states reached after resonant Auger decay of core-excited H2O: experiment and theory.

Vibrationally resolved spectra have been obtained for the lowest-lying cationic states X (2)B(1), A (2)A(1), and B (2)B(2) of the water molecule reached after participator resonant Auger decay of core-excited states. The angular distribution has been measured of the first four vibrational components of the X state in the photon energy regions including the O 1s-->4a(1) and the O 1s-->2b(2) core excitations, and for different portions of the vibrational envelope of the B state in the photon energy region including the O 1s-->2b(2) core excitation. For the X state, a large relative spread in beta values of the different vibrational components is observed across both resonances. For the B state, a very different trend is observed for the high binding energy side and the low binding energy side of the related spectral feature as a function of photon energy. A theoretical method based on the scattering K matrix has been used to calculate both the photoabsorption spectrum and the beta values, by taking both interference between direct and resonant photoemission and vibrational/lifetime interference into account. The numerical results show qualitative agreement with the trends detected in the experimental values and explain the conspicuous variations of the beta values primarily in terms of coupling between direct and resonant photoemission by interaction terms of different sign for different final vibrational states.

Journal Article↗
PubMed2005

Dipole moments of HDO in highly excited vibrational states measured by Stark induced photofragment quantum beat spectroscopy.

We report here a measurement of electric dipole moments in highly vibrationally excited HDO molecules. We use photofragment yield detected quantum beat spectroscopy to determine electric field induced splittings of the J=1 rotational levels of HDO excited with 4, 5, and 8 quanta of vibration in the OH stretching mode. The splittings allow us to deduce mua and mub, the projections of dipole moment onto the molecular rotation inertial axes. We compare the measured HDO dipole moment components with the results of quantitative calculations based on Morse oscillator wave functions and an ab initio dipole moment surface. The vibrational dependence of the dipole moment components reflect both structural and electronic changes in HDO upon vibrational excitation; principally the vibrational dependence of the O-H bond length and bond angle, and the resulting change in orientation of the principal inertial coordinate system. The dipole moment data also provide a sensitive test of theoretical dipole moment and potential energy surfaces, particularly for molecular configurations far from equilibrium.

Journal Article↗
PubMed2005

Amide I vibrational circular dichroism of polypeptides: generalized fragmentation approximation method.

Fragment analyses of vibrational circular dichroic response of dipeptides were carried out recently [Choi and Cho, J. Chem. Phys. 120, 4383 (2004)]. In the present paper, by using a minimal size unit peptide containing two chiral carbons covalently bonded to the peptide group, a generalized fragmentation approximation method is discussed and applied to the calculations of infrared-absorption and vibrational circular dichroism (VCD) intensities of amide I vibrations in various secondary structure polypeptides. Unlike the dipole strength determining IR-absorption intensity, the rotational strength is largely determined by the cross terms that are given by the inner product between the transition electric dipole and the transition magnetic dipole of two different peptides. This explains why the signs and magnitudes of VCD peaks are far more sensitive to the relative orientation and distance between different peptide bonds in a given protein. In order to test the validity of fragmentation approximation, three different segments in a globular protein ubiquitin, i.e., right-handed alpha-helix, beta-sheet, and beta-turn regions, were chosen for density-functional theory (DFT) calculations of amide I vibrational properties and the numerically simulated IR-absorption and VCD spectra by using the fragmentation method are directly compared with DFT results. It is believed that the fragmentation approximation method will be of use in numerically simulating vibrational spectra of proteins in solutions.

Journal Article↗
PubMed2005

Classical and quantum mechanical infrared echoes from resonantly coupled molecular vibrations.

The nonlinear response function associated with the infrared vibrational echo is calculated for a quantum mechanical model of resonantly coupled, anharmonic oscillators at zero temperature. The classical mechanical response function is determined from the quantum response function by setting variant Planck's over 2pi-->0, permitting the comparison of the effects of resonant vibrational coupling among an arbitrary number of anharmonic oscillators on quantum and classical vibrational echoes. The quantum response function displays a time dependence that reflects both anharmonicity and resonant coupling, while the classical response function depends on anharmonicity only through a time-independent amplitude, and shows a time dependence controlled only by the resonant coupling. In addition, the classical response function grows without bound in time, a phenomenon associated with the nonlinearity of classical mechanics, and absent in quantum mechanics. This unbounded growth was previously identified in the response function for a system without resonant vibrational energy transfer, and is observed to persist in the presence of resonant coupling among vibrations. Quantitative agreement between classical and quantum response functions is limited to a time scale of duration inversely proportional to the anharmonicity.

Journal Article↗
PubMed2005

Calculation of the tau dependence of the vibration-internal rotation-overall rotation interactions in CH3OH from molecular structure and molecular dynamics.

The Guan and Quade theory for vibration-large-amplitude internal-motion-rotation interactions has been applied to the internal rotation problem in CH(3)OH. Through the molecular dynamics, the cos 3tau and sin 3tau dependence of the torsional-rotational coefficients in the effective Hamiltonian have been calculated from molecular structure. The internal rotation coordinate tau(') for the vibrationally distorted molecule is shown to have the necessary threefold symmetry for all values of tau('). For the methyl deformation modes, the vibrational dependence of the internal rotation potential energy is shown to have a threefold symmetry. The S(t) and S(t)S(t) dependence of the inertia tensor and Coriolis coupling coefficients has been developed in terms of curvilinear internal coordinates. The T transformation separating rotation from vibrations in zeroth order is then applied, the kinetic-energy tensor inverted to momentum space, and finally the effective torsion-rotation coefficients are calculated by Van Vleck perturbation theory. When compared to the empirical results, the kinetic-energy contributions to the cos 3tau and sin 3tau dependence of the coefficients are as follows: 54% of P(a)(2) is accounted for, 28% of P(a)P(b), 16% of P(a)P(c), and 91% of the asymmetry. The calculation is inadequate to account for the P(b)(2),P(c)(2), and P(b)P(c) coefficients, ranging from factors of 20-70, even with the incorrect sign for some of the terms. Anharmonic force contributions from the vibrations have not been used in the calculation since these forces are not known at this time.

Journal Article↗
PubMed2005

Electronic spectroscopy of toluene-rare-gas clusters: the external heavy atom effect and vibrational predissociation.

Toluene-X van der Waals clusters (where X = Ne, Ne2, Ar, Ar2, Kr, Xe) have been investigated by fluorescence excitation spectroscopy in the region of the S1-S0 transition. With the exception of Xe, for each rare-gas studied, we have assigned cluster transitions in the region of all the strong monomer vibrational bands up to 1000 cm(-1) above the origin band. We have further investigated the S1 relaxation dynamics for each vibrational level of each complex, via their fluorescence decay profiles. Clustering with neon has little appreciable effect on the vibrationless S1 lifetime. By contrast, the clusters with argon and krypton exhibit markedly shorter fluorescence lifetimes compared with the monomer. The effect is so severe in the case of toluene-Xe clusters that no fluorescence signals were observed. We interpret these results in terms of an external heavy atom effect in which the rate of intersystem crossing in toluene is influenced by the cluster partner. For clusters built upon excited S1 vibrational levels, the situation is potentially complicated by intramolecular vibrational redistribution and vibrational predissociation (VP). The majority of the fluorescence decay profiles were satisfactorily modeled using single exponential decays. The emission following pumping of the 37(1) level in the toluene-Kr cluster, however, is an exception. We have modeled the decay of this level with a simple kinetic scheme including VP and determined a predissociation rate of (1.04 +/- 0.54) x 10(7) s(-1).

Journal Article↗
PubMed2005

Vibrational raman optical activity as a mean for revealing the helicity of oligosilanes: a quantum chemical investigation.

Using theoretical simulations based on Hartree-Fock and density-functional theory calculations, the simulated vibrational Raman optical activity spectra of helical conformers of heptasilane are shown to present signatures sensitive to the helicity. These signatures are associated with collective wagging, twisting, and rocking motions. These simulated spectra have been obtained by combining analytical and numerical differentiation procedures to evaluate the geometry derivatives of the optical tensors entering into the expressions of the vibrational Raman optical activity intensities. From an investigation of basis set and electron correlation effects, it is shown that, like for local vibrations, diffuse functions are compulsory for evaluating the vibrational Raman optical activity intensities of collective vibrational motions.

Journal Article↗