Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “VIBRATION”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,405 records · Page 78Linked to original sources
PubMed2005

Rotational and vibrational relaxation of methane excited to 2nu3 in CH4/H2 and CH4/He mixtures at 296 and 193 K from double-resonance measurements.

A series of time-resolved IR-IR double-resonance experiments have been conducted where methane molecules are excited into a selected rovibrational level of the 2nu3(F2) vibrational substate of the tetradecad and where the time evolution of the population of the various energy levels is probed by a tunable continuous wave laser. The rotational relaxation and vibrational energy transfer processes occurring in methane upon inelastic CH4-H2 and CH4-He collisions have been investigated by this technique at room temperature and at 193 K. By probing transitions in which either the lower or the upper level is the laser-excited level, rotational depopulation rates in the 2nu3(F2) substate were measured. The rate constants for CH4-H2 collisions were found to be 17.7 +/- 2.0 and 18.9 +/- 2.0 micros(-1) Torr(-1) at 296 and 193 K, respectively, and for CH(4)-He collisions they are 12.1 +/- 1.5 and 16.0 +/- 2.0 micros(-1) Torr(-1) at the same temperatures. The vibrational relaxation was investigated by probing other stretching transitions such as 2nu3(F2) - nu3, nu3 + 2nu4 - 2nu4, and nu3 + nu4 - nu4. A kinetic model, taking into account the main collisional processes connecting energy levels up to 6000 cm(-1), that has been developed to describe the various relaxation pathways allowed us to calculate the temporal evolution of populations in these levels and to simulate double-resonance signals. The different rate coefficients of the vibrational relaxation processes involved in these mixtures were determined by fitting simulated signals to the observed signals corresponding to assigned transitions. For vibration to translation energy transfer processes, hydrogen is a much more efficient collision partner than helium, nitrogen, or methane itself at 193 K as well as at room temperature.

Journal Article↗
PubMed2005

Amide I vibrational dynamics of N-methylacetamide in polar solvents: the role of electrostatic interactions.

The vibrational frequency of the amide I transition of peptides is known to be sensitive to the strength of its hydrogen bonding interactions. In an effort to account for interactions with hydrogen bonding solvents in terms of electrostatics, we study the vibrational dynamics of the amide I coordinate of N-methylacetamide in prototypical polar solvents: D2O, CDCl3, and DMSO-d6. These three solvents have varying hydrogen bonding strengths, and provide three distinct solvent environments for the amide group. The frequency-frequency correlation function, the orientational correlation function, and the vibrational relaxation rate of the amide I vibration in each solvent are retrieved by using three-pulse vibrational photon echoes, two-dimensional infrared spectroscopy, and pump-probe spectroscopy. Direct comparisons are made to molecular dynamics simulations. We find good quantitative agreement between the experimentally retrieved and simulated correlation functions over all time scales when the solute-solvent interactions are determined from the electrostatic potential between the solvent and the atomic sites of the amide group.

Amides↗
PubMed2006

Conformational properties of and a reorientation triggered by sugar-water vibrational resonance in the hydroxymethyl group in hydrated beta-glucopyranose.

In this paper, we discuss the conformational properties of the hydroxymethyl group of beta-glucopyranose in aqueous solution and its reorientation mechanism. First, using the values for the hydroxymethyl torsion (O5-C5-C6-O6) angle obtained by our ab initio simulations, we reestimate the experimental ratio of the hydroxymethyl rotamer populations. The reestimated ratio is found to be in agreement with those previously reported in several computational studies, which probably partly explains the discrepancies between theoretical and experimental studies that have been discussed in the literature. Second, our time-frequency analysis on a reorientation in the hydroxymethyl group in an ab initio molecular dynamics trajectory suggests that, before the reorientation, the O6-H6 stretching mode is vibrationally coupled with a proton-accepting first-hydration-shell water molecule, whereas the C6-O6 stretching mode is vibrationally coupled with a proton-donating one. The amount of the total vibrational energy induced by these vibrational couplings is estimated to be comparable to typical values for the potential barriers between hydroxymethyl rotamers. To elucidate the vibrational couplings, we investigate the hydrogen-bonding properties around the hydroxymethyl group during the pretransition period. The implications, validity, and limitation of a possible reorientation mechanism based on these findings are also discussed.

Carbohydrate Conformation↗
PubMed2006

State-selective preparation of NO2+ and the effects of NO2+ vibrational mode on charge transfer with NO.

Two color resonance-enhanced multiphoton ionization (REMPI) scheme of NO(2) through the E (2)Sigma(u)(+) (3psigma) Rydberg state was used to prepare NO(2)(+) in its ground and (100), (010), (02(0)0), (02(2)0), and (001) vibrational states. Photoelectron spectroscopy was used to verify >96% state selection purity, in good agreement with results of Bell et al. for a similar REMPI scheme. The effects of NO(2)(+) vibrational excitation on charge transfer with NO have been studied over the center-of-mass collision energy (E(col)) range from 0.07 to 2.15 eV. Charge transfer is strongly suppressed by collision energy at E(col) < approximately 0.25 eV but is independent of E(col) at higher energies. Mode-specific vibrational effects are observed for both the integral and differential cross-sections. The NO(2)(+) bending vibration strongly enhances charge transfer, with enhancement proportional to the bending quantum number, and is not dependent on the bending angular momentum. The enhancement results from increased charge transfer probability in large impact parameter collisions that lead to small deflection angles. The symmetric stretch also enhances reaction at low collision energies, albeit less efficiently than the bend. The asymmetric stretch has virtually no effect, despite being the highest-energy mode. A model is proposed to account for both the collision energy and the vibrational state dependence.

Journal Article↗
PubMed2005

Dynamics of bimolecular reactions of vibrationally highly excited molecules: quasiclassical trajectory studies.

Excitation functions from quasiclassical trajectory calculations on the H + H2O --> OH + H2, H + HF --> F + H2, and H + H'F --> H' + HF reactions indicate a different behavior at low and high vibrational excitation of the breaking bond. When the reactant tri- or diatomic molecule is in vibrational ground state or in a low vibrationally excited state, all these reactions are activated; i.e., there is a nonzero threshold energy below which there is no reaction. In contrast, at high-stretch excited-states capture-type behavior is observed; i.e., with decreasing translational energy the reactive cross-section diverges. The latter induces extreme vibrational enhancement of the thermal rate consistent with the experiments. The results indicate that the speed-up observed at high vibrational excitation is beyond the applicability of Polanyi's rules in their common form; instead, it can be interpreted in terms of an attractive potential acting on the attacking H atom when it approaches the reactant with a stretched X-H bond.

Journal Article↗
PubMed2006

Theoretical investigation of doubly resonant IR-UV sum-frequency vibrational spectroscopy of binaphthol chiral solution.

The doubly resonant IR-UV sum-frequency vibrational spectroscopy (SFVS) of 1,1'-bi-2-naphthol (BN) solution and its dispersion spectra are analyzed and computed using the ZINDO//AM1 calculation and the direct approach of Raman scattering tensor calculation, which is based on calculations of Franck-Condon factors and on differentiation of the electronic transition moments with respect to the vibrational normal modes. The calculated results indicate that, for the most intense vibrational bands observed in the SFVS experiment, the calculated frequencies, symmetry, order, intensities, and pattern of the enhanced vibrational modes agree with experiment qualitatively, and due to the Franck-Condon progression, there are the doublet peaks in the corresponding resonant sum-frequency dispersion spectra. The polarization resonance Raman spectra of BN for the vibrational modes appearing in SFVS are also computed and associated with the experiment SFVS of BN. This direct evaluation approach of Raman tensors may provide a way of assigning the doubly resonant IR-UV SFVS.

Journal Article↗
PubMed2006

Theoretical studies of solute vibrational energy relaxation at liquid interfaces.

Recent advances in the theoretical understanding of solute vibrational energy relaxation at liquid interfaces and surfaces are described. Non-equilibrium molecular dynamics simulations of the relaxation of an initially excited solute molecule are combined with equilibrium force autocorrelation calculations to gain insight into the factors that influence the vibrational relaxation rate. Diatomic and triatomic nonpolar, polar, and ionic solute molecules adsorbed at the liquid/vapor interface of several liquids as well as at the water/CCl(4) liquid/liquid interface are considered. In general, the vibrational relaxation rate is significantly slower (a factor of 3 to 4) at the liquid/vapor and liquid/liquid interface than in the bulk due to the reduced density, which gives rise to a reduced contribution of the repulsive solvent-solute forces on the vibrational mode. The surface effects on the ionic solutes are much smaller (50% or less slower relaxation relative to the bulk). This is due to the fact that ionic solutes at the interface are able to keep part of their solvation shell to a degree that depends on their size. Thus, a significant portion of the repulsive forces is maintained. A high degree of correlation is found between the peak height of the solvent-solute radial distribution function and the vibrational relaxation rate. The relaxation rate at the liquid/liquid interface strongly depends on the location of the solute across the interface and correlates with the change in the density and polarity profile of the interface.

Journal Article↗
PubMed2006

Vibrational spectroscopy of the pyridazine cation in the ground state.

Vibrational structure of the pyridazine cation in the ground state has been revealed by a vacuum-ultraviolet mass-analyzed threshold ionization (VUV-MATI) spectroscopy. The adiabatic ionization energy is precisely measured to be 70241 +/- 6 cm(-1) (8.7088 +/- 0.0007 eV). The origin is very weakly observed, while a long progression of the nu9(+) (a1) band of which the fundamental vibrational frequency is 647 cm(-1) is predominantly observed. The nu9(+) (a1) mode progression combined with one quantum of the nu3(+) (a1) band at 1698 cm(-1) is found to be even stronger. Many other weakly observed vibrational features of the pyridazine cation are identified in the vibrational energy of 0-3500 cm(-1). The structural change of pyridazine upon ionization, reflected in the vibrational spectrum obtained by the one-photon direct ionization process, is theoretically predicted by ab initio calculations. Ring distortion including contraction of the N=N bond should be responsible for strong excitations of nu3(+) and nu9(+) modes. Franck-Condon analysis is given for the comparison of the experiment and theory.

Journal Article↗
PubMed2005

Semispectroscopic and quantitative structure-property relationship estimates of the equilibrium and vibrationally averaged structure and dipole moment of 1-buten-3-yne.

Systematic quantum chemical calculations have been performed to obtain precise estimates of the equilibrium and vibrationally averaged molecular structure and electric dipole moment of vinylacetylene (VA, 1-buten-3-yne). Anharmonic (cubic and semi-diagonal quartic) MP2/cc-pVTZ force fields in normal coordinates were computed to account for anharmonic vibrational effects, including zero-point contributions to the rotational constants and the electric dipole moment. A simultaneous weighted least-squares structural refinement was performed, resulting in the best semispectroscopic estimate of the re structure of VA. The refinement was based on experimentally measured ground-state rotational constants of two isotopologs of VA corrected to equilibrium values using MP2/cc-pVTZ vibration-rotation interaction constants and all-electron CCSD(T)/aug-cc-pVTZ structural constraints. The semispectroscopic re structure of VA agrees excellently with the high-level CCSD(T)/aug-cc-pVTZ ab initio structure. The most dependable, CCSD(T)/cc-pVQZ//CCSD(T)/aug-cc-pVTZ equilibrium electric dipole moment of VA, in D, is mua= 0.4088, mub= 0.0004, and muc= 0. The vibrationally corrected a-component of 0.4214 D is in excellent agreement with one of the available experimental values. The present analysis shows that mub is negligible even after vibrational correction. A simple quantitative structure-property relationship (QSPR) model resulted in a highly similar estimate, 0.45 D, for the electric dipole moment of VA.

Journal Article↗
PubMed2005

Ab initio vibrational calculations for H2SO4 and H2SO4 x H2O: spectroscopy and the nature of the anharmonic couplings.

Vibrational frequencies for fundamental, overtone, and combination excitations of sulfuric acid (H2SO4) and of sulfuric acid monohydrate cluster (H2SO4 x H2O) are computed directly from ab initio MP2/TZP potential surface points using the correlation-corrected vibrational self-consistent field (CC-VSCF) method, which includes anharmonic effects. The results are compared with experiment. The computed transitions show in nearly all cases good agreement with experimental data and consistent improvement over the harmonic approximation. The CC-VSCF improvements over the harmonic approximation are largest for the overtone and combination excitations and for the OH stretching fundamental. The agreement between the calculations and experiment also supports the validity of the MP2/TZP potential surfaces. Anharmonic coupling between different vibrational modes is found to significantly affect the vibrational frequencies. Analysis of the mean magnitude of the anharmonic coupling interactions between different pairs of normal modes is carried out. The results suggest possible mechanisms for the internal flow of vibrational energy in H2SO4 and H2SO4 x H2O.

Journal Article↗
PubMed2006

Abnormal inversion splitting in NH2D: rotational analysis of the nu5 bending vibrational band system.

A high-resolution Fourier transform infrared spectrum of the nu(5) bending vibrational band system region of the partially deuterated ammonia molecule NH(2)D has been measured and rotationally analyzed. The spectrum consists of strong a-type transitions between the states of same vibrational symmetry and weaker c-type transitions between the states of different vibrational symmetry. The Hamiltonian model used includes interaction terms between the rotational states of both upper and lower inversion doublets. The vibrational term values for the symmetric and the antisymmetric component of the upper-inversion doublet are 1,605.637 965(620) cm(-1) and 1,590.993 82(100) cm(-1), respectively, where the numbers in parentheses are one-standard deviations in the least significant digit. These figures are close to the corresponding values 1,605.62 cm(-1) and 1,590.72 cm(-1) obtained recently from results based on high-level ab initio calculations. The order of the vibrational term values is abnormal in the ammonia family, as typically the symmetric state is lower in wavenumber than the antisymmetric one.

Journal Article↗
PubMed2006

Quantum tunneling in the midrange vibrational fundamentals of tropolone.

The Fourier transform infrared spectrum of tropolone(OH) vapor in the 1175-1700 cm(-1) region is reported at 0.0025 and 0.10 cm(-1) spectral resolutions. The 12 vibrational fundamentals in this region of rapidly rising vibrational state density are dominated by mixtures of the CC, CO, CCH, and COH internal coordinates. Estimates based on the measurement of sharp Q branch peaks are reported for 11 of the spectral doublet component separations DS(v) = |Delta(v) +/- Delta(0)|. Delta(0) = 0.974 cm(-1) is the known zero-point splitting, and three a(1) modes show tunneling splittings Delta(v) approximately Delta(0), four b(2) modes show splittings Delta(v) approximately 0.90Delta(0), and the remaining four modes show splittings Delta(v) falling 5-14% from Delta(0.) Significantly, the splitting for the nominal COH bending mode nu(8) (a(1)) is small, that is, 10% from Delta(0). Many of the vibrational excited states demonstrate strong anharmonic behavior, but there are only mild perturbations on the tautomerization mechanism driving Delta(0). The data suggest, especially for the higher frequency a(1) fundamentals, the onset of selective intramolecular vibrational energy redistribution processes that are fast on the time scale of the tautomerization process. These appear to delocalize and smooth out the topographical modifications of the zero-point potential energy surface that are anticipated to follow absorption of the nu(v) photon. Further, the spectra show the propensity for the Delta(v) splittings of b(2) and other complex vibrations to be damped relative to Delta(0).

Journal Article↗
PubMed2006

Experimental and theoretical study of the vibrational spectra of 12-crown-4-alkali metal cation complexes.

The vibrational, Raman, and IR, spectra of the five 12-crown-4 (12c4) complexes with Li+, Na+, K+, Rb+, and Cs+ alkali metal cations were measured. Except for a small shift of the position of some bands in the vibrational spectra of the Li+ complex, the vibrational spectra of the five complexes are so similar that it is concluded that the five complexes exist in the same conformation. B3LYP/6-31+G* force fields were calculated for six of the eight predicted conformations in a previous report (J. Phys. Chem. A 2005, 109, 8041) of the 12c4-Li+, Na+, and K+ complexes that are of symmetries higher than the C1 symmetry. These six conformations, in energy order, are of C4, Cs, Cs, C(2v), C(2v), and Cs symmetries. Comparison between the experimental and calculated vibrational frequencies assuming any of the above-mentioned six conformations shows that the five complexes exist in the C4 conformation. This agrees with the fact that the five alkali metal cations are larger than the 12c4 ring cavity. The B3LYP/6-31+G* force fields of the C4 conformation of the Li+, Na+ and K+ complexes were scaled using a set of eight scale factors and the scale factors were varied so as to minimize the difference between the calculated and experimental vibrational frequencies. The root-mean-square (rms) deviations of the calculated frequencies from the experimental frequencies were 7.7, 5.6, and 5.1 cm(-1) for the Li+, Na+, and K+ complexes, respectively. To account for the earlier results of the Li+ complex that the Cs conformation is more stable than the C4 conformation by 0.16 kcal/mol at the MP2/6-31+G* level, optimized geometries of the complex were calculated for the C4 and Cs conformations at the MP2/6-311++G** level. The C4 conformation was calculated to be more stable than the Cs conformation by 0.13 kcal/mol.

Journal Article↗
PubMed2007

Application of density functional theory and vibrational spectroscopy toward the rational design of ionic liquids.

Density functional theory methods in combination with vibrational spectroscopy are used to investigate possible variants of molecular structure of the ion pairs of several imidazolium-based ionic liquids (ILs). Multiple stable structures are determined with the anion positioned (a) near to the C2 atom of the imidazolium ring, (b) between N1 and C5, (c) between N3 and C4, and (d) between C4 and C5. Chloride and bromide anions in vacuum also occupy positions above or below the imidazolium ring, but in the condensed state these positions are destabilized. In comparison with the halides that almost equally occupy the positions (a-d), tetrafluoroborate and hexafluorophosphate anions strongly prefer position (a). The position and the type of the anion influence the conformation of the side chains bound to the imidazolium N1 atom, which are able to adopt in vacuum all usual staggered or eclipsed conformations, although in the liquid state some of the conformations are present only as minor forms if at all. Vibrations of the cations depend both on the conformational changes and on the association with the anion. The formation of the ion pairs influences mainly stretching and out-of-plane vibrations of the imidazolium C-H groups and stretching vibrations of the perfluoroanions. Other modes of the ions retain their individuality and practically do not mix. This allows "interionic" vibrations to be separated and to regard the couple of the ions as an anharmonic oscillator. Such a model correlates the molecular structure of various ILs and their melting points without involving the energy of the interaction between the cations and anions but explains structure-melting point correlations on the grounds of quasy-elastic properties.

Journal Article↗
PubMed1996

Qy-excitation resonance Raman spectra of chlorophyll a and bacteriochlorophyll c/d aggregates. Effects of peripheral substituents on the low-frequency vibrational characteristics.

Low-frequency (80-700 cm-1) Qy-excitation resonance Raman (RR) spectra are reported for thin-solid-film aggregates of several chlorophyll (Chl) a and bacteriochlorophyll (BChl) c/d pigments. The pigments include Chl a, pyrochlorophyll a (PChl a), methylpyrochloropyllide a (MPChl a), methylbacteriochloropyllide d (MBChl d), [E,M] BChl cS, [E,E] BChl cF, and [P,E] BChl cF. The BChl c/d's are the principal constituents of the chlorosomal light-harvesting apparatus of green photosynthetic bacteria. Together, the various Chl a's and BChl c/d's represent a series in which the peripheral substituent groups on the chlorin macrocycle are varied in systematic fashion. All of the Chl a and BChl c/d aggregates exhibit rich low-frequency vibrational patterns. In the case of the BChl c/d's, certain modes in the very low-frequency region (100-200 cm-1) experience exceptionally strong Raman intensity enhancements. The frequencies of these modes are qualitatively similar to those of oscillations observed in femtosecond optical experiments on chlorosomes. The RR data indicate that the low-frequency vibrations are best characterized as intramolecular out-of-plane deformations of the chlorin macrocycle rather than intermolecular modes. The coupling of the out-of-plane modes in turn implies that the Qy electronic transition(s) of the aggregate have out-of-plane character. The RR spectra of the BChl c/d's also reveal that the nature of the alkyl substituents at the 8 and 12 positions of the macrocycle plays an important role in determining the detailed features of the low-frequency vibrational patterns. The frequencies of the modes are particularly sensitive to larger substituent groups whose conformations may be more easily perturbed in the tightly packed aggregates. These factors also make aggregates of pigments containing larger substituents more susceptible to structural, electronic, and vibrational inhomgeneities. Collectively, the RR studies of the various pigments delineate the factors which influence the low-frequency vibrational characteristics of chlorosomal aggregates.

Bacterial Proteins↗
PubMed2005

Conversion of large-amplitude vibration to electron excitation at a metal surface.

Gaining insight into the nature and dynamics of the transition state is the essence of mechanistic investigations of chemical reactions, yet the fleeting configuration when existing chemical bonds dissociate while new ones form is extremely difficult to examine directly. Adiabatic potential-energy surfaces--usually derived using quantum chemical methods that assume mutually independent nuclear and electronic motion--quantify the fundamental forces between atoms involved in reaction and thus provide accurate descriptions of a reacting system as it moves through its transition state. This approach, widely tested for gas-phase reactions, is now also commonly applied to chemical reactions at metal surfaces. There is, however, some evidence calling into question the correctness of this theoretical approach for surface reactions: electronic excitation upon highly exothermic chemisorption has been observed, and indirect evidence suggests that large-amplitude vibrations of reactant molecules can excite electrons at metal surfaces. Here we report the detection of 'hot' electrons leaving a metal surface as vibrationally highly excited NO molecules collide with it. Electron emission only occurs once the vibrational energy exceeds the surface work function, and is at least 10,000 times more efficient than the emissions seen in similar systems where large-amplitude vibrations were not involved. These observations unambiguously demonstrate the direct conversion of vibrational to electronic excitation, thus questioning one of the basic assumptions currently used in theoretical approaches to describing bond-dissociation at metal surfaces.

Journal Article↗
PubMed2001

Size evolution of the vibrational predissociation process in Br2...Nen clusters: simulation and kinetic study.

A hybrid quantum-classical simulation of the vibrational predissociation of Br2...Nen, (n = 2-11) clusters in the B electronic state is carried out. The time-evolution of the reactants, products, and intermediates is analyzed by a kinetic mechanism consisting of three elementary steps: direct vibrational predissociation (VP), intramolecular vibrational redistribution (IVR), and evaporative cooling (EC). The importance of intramolecular vibrational redistribution followed by evaporative cooling relative to direct vibrational predissociation is shown to increase rapidly with increasing cluster size. Final product state distributions reveal that only one or less Br2 stretching quantum per neon atom is required in order to achieve complete dissociation (n quanta for n < or = 9 and n - 1 for n = 10 and 11). The proportion of available energy going into translation is proposed as a parameter to study the statistical behavior of the Van der Waals clusters. It is shown to depend only on the number of remaining degrees of freedom, a characteristic of a statistical behavior, for n > or = 3.

Journal Article↗
PubMed2006

Effect of internal conversion of vibrational quanta in electron tunneling: a scheme for direct experimental observation and current/voltage relationships.

Electron tunneling through bridge molecular groups with a strong coupling to a local quantum vibrational mode is considered. A scheme is suggested for direct experimental observation of the effect of internal conversion of vibrational quanta in inelastic electron tunneling. The effect consists of excitation and re-absorption of vibrational quanta in bridge by tunneling electrons. The tunnel current produced by the absorption of vibrational quanta by the same or another electron can in principle be detected in an experimental setup a scheme of which is suggested. Current/voltage dependences have general spectroscopic features. Possible effects that can take place in the case of additional strong interaction with classical vibrational modes are discussed.

Journal Article↗