Biomedical subjects

David J Nesbitt

Publications and source records attributed to David J Nesbitt.

At least 19 recordsLinked to original sources

PubMed2006

Imaging nanostructures with scanning photoionization microscopy.

We report detailed studies of local electronic properties in nanostructured thin metallic films using scanning photoionization microscopy. This novel form of microscopy combines the advantages of diffraction-limited optical excitation with the ability to detect both photons and low kinetic energy photoelectrons, permitting sensitive characterization of heterogeneous surfaces under vacuum conditions. Using this technique, correlated measurements of multiphoton photoemission cross section and optical penetration depth are reported for Au films supported on Pt. These results present a first step toward combining confocal fluorescence or Raman microscopy with time-resolved photoelectron imaging spectroscopy in complex metal film environments, which should be ideally suited to investigating local plasmonic effects in nanostructures.

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PubMed2006

Jet cooled spectroscopy of H2DO+: Barrier heights and isotope-dependent tunneling dynamics from H3O+ to D3O+.

The first high resolution spectroscopic data for jet cooled H2DO+ are reported, specifically via infrared laser direct absorption in the OH stretching region with a slit supersonic jet discharge source. Transitions sampling upper (0-) and lower (0+) tunneling states for both symmetric (nu1+ <-- 0+, nu1- <-- 0-, and nu1- <-- 0+) and antisymmetric (nu3+ <-- 0+ and nu3- <-- 0-) OH stretching bands are observed, where +/- refers to wave function reflection symmetry with respect to the planar umbrella mode transition state. The spectra can be well fitted to a Watson asymmetric top Hamiltonian, revealing band origins and rotational constants for benchmark comparison with high-level ab initio theory. Of particular importance are detection and assignment of the relatively weak band (nu1- <-- 0+) that crosses the inversion tunneling gap, which is optically forbidden in H3O+ or D3O+, but weakly allowed in H2DO+ by lowering of the tunneling transition state symmetry from D(3h) to C(2v). In conjunction with other H2DO+ bands, this permits determination of the tunneling splittings to within spectroscopic precision for each of the ground [40.518(10) cm(-1)], nu1 = 1 [32.666(6) cm(-1)], and nu3 = 1 [25.399(11) cm(-1)] states. A one-dimensional zero-point energy corrected potential along the tunneling coordinate is constructed from high-level ab initio CCSD(T) calculations (AVnZ, n = 3,4,5) and extrapolated to the complete basis set limit to extract tunneling splittings via a vibrationally adiabatic treatment. Perturbative scaling of the potential to match splittings for all four isotopomers permits an experimental estimate of DeltaV0 = 652.9(6) cm(-1) for the tunneling barrier, in good agreement with full six-dimensional ab initio results of Rajamaki, Miani, and Halonen (RMH) [J. Chem. Phys. 118, 10929 (2003)]. (DeltaV0 (RMH) = 650 cm(-1)). The 30%-50% decrease in tunneling splitting observed upon nu1 and nu3 vibrational excitations arises from an increase in OH stretch frequencies at the planar transition state, highlighting the transition between sp2 and sp3 hybridizations of the OHD bonds as a function of inversion bending angle.

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PubMed2006

Quantum-state-resolved CO2 scattering dynamics at the gas-liquid interface: incident collision energy and liquid dependence.

Quantum-state-resolved dynamics at the gas-liquid interface are probed by colliding supersonically cooled molecular beams of CO(2) with freshly formed liquid surfaces in a vacuum. Translational, rotational, and vibrational state distributions of both incident and scattered fluxes are measured by high-resolution direct infrared absorption spectroscopy and laser dopplerimetry in the 00(0)0 and 01(1)0 rovibrational manifolds of CO(2) in the asymmetric stretch manifold. The present studies investigate the role of incident molecular beam energy (E(inc) = 1.6(1), 4.7(2), 7.7(2), and 10.6(8) kcal/mol) on these distributions for a series of perfluorinated, hydrocarbon, and hydrogen-bonded liquids. Boltzmann analysis of the internal quantum-state populations provide evidence for nonthermal scattering dynamics, as confirmed by Dopplerimetry on the absorption profiles. The data provide quantum-state-resolved support for a dual channel picture of the scattering process, consisting of either prompt impulsive scattering (IS) or longer duration trapping-desorption (TD) events, with the fraction observed in each channel dependent on incident kinetic energy and the physical properties of the liquid surface. The clear evidence that internal CO(2) rotational populations arising from the IS channel can be adequately described by a Boltzmann temperature (albeit with E(IS) > RT(S)) is consistent with previous gas-solid scattering studies and suggests that even nominally "prompt" IS events reflect both single (i.e. direct) and multiple impulsive interactions with the liquid interface.

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PubMed2006

High-resolution infrared studies in slit supersonic discharges: CH2 stretch excitation of jet-cooled CH2Cl radical.

First high-resolution infrared spectra are presented for jet-cooled CH2 35Cl and CH2 37Cl radicals in the symmetric (nu1) CH2 stretching mode. A detailed spectral assignment yields refined lower and upper state rotational constants, as well as fine structure spin-rotation parameters from least-squares fits to the sub-Doppler line shapes for individual transitions. The rotational constants are consistent with a nearly planar structure, but do not exclude substantial large amplitude bending motion over a small barrier to planarity accessible with zero-point excitation. High level coupled cluster (singles/doubles/triples) calculations, extrapolated to the complete basis set limit, predict a slightly nonplanar equilibrium structure (theta approximately 11 degrees), with a vibrationally adiabatic treatment of the bend coordinate yielding a v = 1<--0 anharmonic frequency (393 cm(-1)) in excellent agreement with matrix studies (nu(bend) approximately 400 cm(-1)). The antisymmetric CH2 stretch vibration is not observed despite high sensitivity detection (signal to noise ratio >20:1) in the symmetric stretch band. This is consistent with density functional theory intensity calculations indicating a >35-fold smaller antisymmetric stretch transition moment for CH2Cl, and yet contrasts dramatically with high-resolution infrared studies of CH2F radical, for which both symmetric and antisymmetric CH2 stretches are observed in a nearly 2:1 intensity ratio. A simple physical model is presented based on a competition between bond-dipole and "charge-sloshing" contributions to the transition moment, which nicely explains the trends in CH2X symmetric versus asymmetric stretch intensities as a function of electron withdrawing group (X = D,Br,Cl,F).

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PubMed2006

Jet-cooled infrared spectroscopy in slit supersonic discharges: symmetric and antisymmetric CH2 stretching modes of fluoromethyl (CH2F) radical.

The combination of shot noise-limited direct absorption spectroscopy with long-path-length slit supersonic discharges has been used to obtain first high-resolution infrared spectra for jet-cooled CH2F radicals in the symmetric (nu1) and antisymmetric (nu5) CH2 stretching modes. Spectral assignment has yielded refined lower- and upper-state rotational constants and fine-structure parameters from least-squares fits to the sub-Doppler line shapes for individual transitions. The rotational constants provide indications of large amplitude vibrational averaging over a low-barrier double minimum inversion-bending potential. This behavior is confirmed by high-level coupled cluster singles/doubles/triples calculations extrapolated to the complete basis set limit and adiabatically corrected for zero point energy. The calculations predict a nonplanar equilibrium structure (theta approximately 29 degrees, where theta is defined to be 180 degrees minus the angle between the C-F bond and the CH2 plane) with a 132 cm(-1) barrier to planarity and a vibrational bend frequency (nu(bend) approximately 276 cm(-1)), in good agreement with previous microwave estimates (nu(bend) = 300 (30) cm(-1)) by Hirota and co-workers [Y. Endo et al., J. Chem. Phys. 79, 1605 (1983)]. The nearly 2:1 ratio of absorption intensities for the symmetric versus antisymmetric bands is in good agreement with density functional theory calculations, but in sixfold contrast with simple local mode CH2 bond dipole predictions of 1:3. This discrepancy arises from a surprisingly strong dependence of the symmetric stretch intensity on the inversion bend angle and provides further experimental support for a nonplanar equilibrium structure.

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PubMed2006

Quantum-state resolved reaction dynamics at the gas-liquid interface: direct absorption detection of HF(v,J) product from F(2P)+squalane.

Exothermic reactive scattering of F atoms at the gas-liquid interface of a liquid hydrocarbon (squalane) surface has been studied under single collision conditions by shot noise limited high-resolution infrared absorption on the nascent HF(v,J) product. The nascent HF(v,J) vibrational distributions are inverted, indicating insufficient time for complete vibrational energy transfer into the surface liquid. The HF(v=2,J) rotational distributions are well fit with a two temperature Boltzmann analysis, with a near room temperature component (T(TD) approximately equal to 290 K) and a second much hotter scattering component (T(HDS) approximately equal to 1040 K). These data provide quantum state level support for microscopic branching in the atom abstraction dynamics corresponding to escape of nascent HF from the liquid surface on time scales both slow and fast with respect to rotational relaxation.

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PubMed2006

Multireference configuration interaction calculations for the F(2P)+HCl-->HF+Cl(2P) reaction: a correlation scaled ground state (1 2A') potential energy surface.

This paper presents a new ground state (1 (2)A(')) electronic potential energy surface for the F((2)P)+HCl-->HF+Cl((2)P) reaction. The ab initio calculations are done at the multireference configuration interaction+Davidson correction (MRCI+Q) level of theory by complete basis set extrapolation of the aug-cc-pVnZ (n=2,3,4) energies. Due to low-lying charge transfer states in the transition state region, the molecular orbitals are obtained by six-state dynamically weighted multichannel self-consistent field methods. Additional perturbative refinement of the energies is achieved by implementing simple one-parameter correlation energy scaling to reproduce the experimental exothermicity (DeltaE=-33.06 kcalmol) for the reaction. Ab initio points are fitted to an analytical function based on sum of two- and three-body contributions, yielding a rms deviation of <0.3 kcalmol for all geometries below 10 kcalmol above the barrier. Of particular relevance to nonadiabatic dynamics, the calculations show significant multireference character in the transition state region, which is located 3.8 kcalmol with respect to F+HCl reactants and features a strongly bent F-H-Cl transition state geometry (theta approximately 123.5 degrees ). Finally, the surface also exhibits two conical intersection seams that are energetically accessible at low collision energies. These seams arise naturally from allowed crossings in the C(infinityv) linear configuration that become avoided in C(s) bent configurations of both the reactant and product, and should be a hallmark of all X-H-Y atom transfer reaction dynamics between ((2)P) halogen atoms.

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PubMed2006

Metal ion dependence, thermodynamics, and kinetics for intramolecular docking of a GAAA tetraloop and receptor connected by a flexible linker.

The GAAA tetraloop-receptor motif is a commonly occurring tertiary interaction in RNA. This motif usually occurs in combination with other tertiary interactions in complex RNA structures. Thus, it is difficult to measure directly the contribution that a single GAAA tetraloop-receptor interaction makes to the folding properties of a RNA. To investigate the kinetics and thermodynamics for the isolated interaction, a GAAA tetraloop domain and receptor domain were connected by a single-stranded A(7) linker. Fluorescence resonance energy transfer (FRET) experiments were used to probe intramolecular docking of the GAAA tetraloop and receptor. Docking was induced using a variety of metal ions, where the charge of the ion was the most important factor in determining the concentration of the ion required to promote docking {[Co(NH(3))(6)(3+)] << [Ca(2+)], [Mg(2+)], [Mn(2+)] << [Na(+)], [K(+)]}. Analysis of metal ion cooperativity yielded Hill coefficients of approximately 2 for Na(+)- or K(+)-dependent docking versus approximately 1 for the divalent ions and Co(NH(3))(6)(3+). Ensemble stopped-flow FRET kinetic measurements yielded an apparent activation energy of 12.7 kcal/mol for GAAA tetraloop-receptor docking. RNA constructs with U(7) and A(14) single-stranded linkers were investigated by single-molecule and ensemble FRET techniques to determine how linker length and composition affect docking. These studies showed that the single-stranded region functions primarily as a flexible tether. Inhibition of docking by oligonucleotides complementary to the linker was also investigated. The influence of flexible versus rigid linkers on GAAA tetraloop-receptor docking is discussed.

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PubMed2006

Slit discharge IR spectroscopy of a jet-cooled cyclopropyl radical: structure and intramolecular tunneling dynamics.

High-resolution infrared spectra of a jet-cooled cyclopropyl radical are reported for the first time, specifically sampling the in-phase antisymmetric CH2 stretch (nu7) vibration. In addition to yielding the first precise gas-phase structural information, the spectra reveal quantum level doubling into lower (+) and upper (-) states due to tunneling of the lone alpha-CH with respect to the CCC plane. The bands clearly reveal intensity alternation due to H atom nuclear spin statistics (6:10 and 10:6 for even:odd Ka+Kc in lower (+) and upper (-) tunneling levels, respectively) consistent with C2v symmetry of the cyclopropyl-tunneling transition state. The two ground-state-tunneling levels fit extremely well to a rigid asymmetric rotor Hamiltonian, but there is clear evidence for both local and global state mixing in the vibrationally excited nu7 tunneling levels. In particular, the upper (-) tunneling component of the nu7 state is split by anharmonic coupling with a nearly isoenergetic dark state, which thereby acquires oscillator strength via intensity sharing with this bright state. From thermal Boltzmann analysis of fractional populations, tunneling splittings for a cyclopropyl radical are estimated to be 3.2 +/- 0.3 cm(-1) and 4.9 +/- 0.3 cm(-1) in the ground and nu7-excited states, respectively. This analysis indicates ground-state stereoracemization of the alpha-CH radical center to be a very fast process [k approximately 2.0(4) x 10(11) s(-1)], with the increase in the tunneling rate upon CH2 in-phase asymmetric stretch excitation consistent with ab initio predictions of equilibrium vs transition-state zero-point energies. Modeling of the ground-state-tunneling splittings with high level ab initio 1D potentials indicates an improved V0 = 1115 +/- 35 cm(-1) barrier height for alpha-CH inversion through the cyclopropyl CCC plane.

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PubMed2006

CH stretch/internal rotor dynamics in ethyl radical: high-resolution spectroscopy in the CH3-stretch manifold.

High-resolution IR absorption spectra of supersonically cooled ethyl radicals (Trot approximately 20 K) have been obtained in a slit supersonic jet discharge expansion, revealing first rotationally resolved data for CH-stretch excitation of the methyl group. Three different vibrational bands are observed, one parallel (k=0<--0) and two perpendicular (/k/1<--0), which for a nearly decoupled methyl rotor framework would correspond to symmetric and (nearly degenerate) asymmetric CH-stretch excitations. However, the splitting between the two asymmetric CH-stretch excitations is anomalously large (approximately 125 cm(-1)), signaling the presence of interactions between the CH2 radical moiety and the opposing CH bond on the methyl group. This suggests an improved zeroth-order vibrational description as an isolated CH stretch, strongly redshifted by hyperconjugation, with localized vibrations in the remaining CH bonds split into symmetric and asymmetric stretches. Such a dynamical picture highlights a remarkably strong coupling between methyl CH-stretch vibrations and C-C torsional geometry and begins to elucidate discrepancies with previous matrix observations.

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PubMed2006

A simple picture for the rotational enhancement of the rate for the F + HCl --> HF + Cl reaction: a dynamical study using a new ab initio potential energy surface.

Quantum scattering calculations for the reaction F + HCl --> HF + Cl are performed on a new ground-state ab initio potential energy surface. The reagent rotation is found to have a dramatic effect on the reaction probability. Furthermore, the exit channel rotational thresholds leave a strong imprint on the reaction probabilities and even on the cumulative reaction probability. A very simple vibrationally adiabatic model is shown to account for most aspects of the reaction dynamics. In this model, the fast vibrational motion is adiabatically eliminated leaving the key reaction dynamics represented by a reduced atom + rotor collision. The shape of the adiabatic potential surface immediately yields to a simple and intuitive interpretation for the rotational enhancement of the rate. The rotational enhancement is shown to be an effect of the entrance channel dynamics of the atom-rotor problem.

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PubMed2006

Quantum deconstruction of the infrared spectrum of CH5+.

We present two quantum calculations of the infrared spectrum of protonated methane (CH5+) using full-dimensional, ab initio-based potential energy and dipole moment surfaces. The calculated spectra compare well with a low-resolution experimental spectrum except below 1000 cm(-1), where the experimental spectrum shows no absorption. The present calculations find substantial absorption features below 1000 cm(-1), in qualitative agreement with earlier classical calculations of the spectrum. The major spectral bands are analyzed in terms of the molecular motions. Of particular interest is an intense feature at 200 cm(-1), which is due to an isomerization mode that connects two equivalent minima. Very recent high-resolution jet-cooled spectra in the CH stretch region (2825 to 3050 cm(-1)) are also reported, and assignments of the band origins are made, based on the present quantum calculations.

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PubMed2005

Direct evidence for nonadiabatic dynamics in atom+polyatom reactions: crossed-jet laser studies of F+D2O-->DF+OD.

Quantum-state-resolved reactive-scattering dynamics of F+D(2)O-->DF+OD have been studied at E(c.m.)=5(1) kcal/mol in low-density crossed supersonic jets, exploiting pulsed discharge sources of F atom and laser-induced fluorescence to detect the nascent OD product under single-collision conditions. The product OD is formed exclusively in the v(OD)=0 state with only modest rotational excitation ( =0.50(1) kcal/mol), consistent with the relatively weak coupling of the 18.1(1) kcal/mol reaction exothermicity into "spectator" bond degrees of freedom. The majority of OD products [68(1)%] are found in the ground ((2)Pi(32) (+/-)) spin-orbit state, which adiabatically correlates with reaction over the lowest and only energetically accessible barrier (DeltaE( not equal) approximately 4 kcal/mol). However, 32(1)% of molecules are produced in the excited spin-orbit state ((2)Pi(12) (+/-)), although from a purely adiabatic perspective, this requires passage over a DeltaE( not equal) approximately 25 kcal/mol barrier energetically inaccessible at these collision energies. This provides unambiguous evidence for nonadiabatic surface hopping in F+D(2)O atom abstraction reactions, indicating that reactive-scattering dynamics even in simple atom+polyatom systems is not always isolated on the ground electronic surface. Additionally, the nascent OD rotational states are well fitted by a two-temperature Boltzmann distribution, suggesting correlated branching of the reaction products into the DF(v=2,3) vibrational manifold.

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PubMed2005

Quantum state-resolved energy transfer dynamics at gas-liquid interfaces: IR laser studies of CO2 scattering from perfluorinated liquids.

An apparatus for detailed study of quantum state-resolved inelastic energy transfer dynamics at the gas-liquid interface is described. The approach relies on supersonic jet-cooled molecular beams impinging on a continuously renewable liquid surface in a vacuum and exploits sub-Doppler high-resolution laser absorption methods to probe rotational, vibrational, and translational distributions in the scattered flux. First results are presented for skimmed beams of jet-cooled CO(2) (T(beam) approximately 15 K) colliding at normal incidence with a liquid perfluoropolyether (PFPE) surface at E(inc) = 10.6(8) kcal/mol. The experiment uses a tunable Pb-salt diode laser for direct absorption on the CO(2) nu(3) asymmetric stretch. Measured rotational distributions in both 00(0)0 and 01(1)0 vibrational manifolds indicate CO(2) inelastically scatters from the liquid surface into a clearly non-Boltzmann distribution, revealing nonequilibrium dynamics with average rotational energies in excess of the liquid (T(s) = 300 K). Furthermore, high-resolution analysis of the absorption profiles reveals that Doppler widths correspond to temperatures significantly warmer than T(s) and increase systematically with the J rotational state. These rotational and translational distributions are consistent with two distinct gas-liquid collision pathways: (i) a T approximately 300 K component due to trapping-desorption (TD) and (ii) a much hotter distribution (T approximately 750 K) due to "prompt" impulsive scattering (IS) from the gas-liquid interface. By way of contrast, vibrational populations in the CO(2) bending mode are inefficiently excited by scattering from the liquid, presumably reflecting much slower T-V collisional energy transfer rates.

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PubMed2005

Large amplitude quantum mechanics in polyatomic hydrides. I. A particles-on-a-sphere model for XH(n).

A framework is presented for converged quantum mechanical calculations on large amplitude dynamics in polyatomic hydrides (XH(n)) based on a relatively simple, but computationally tractable, "particles-on-a-sphere" (POS) model for the intramolecular motion of the light atoms. The model assumes independent two-dimensional (2D) angular motion of H atoms imbedded on the surface of a sphere with an arbitrary interatomic angular potential. This assumption permits systematic evolution from "free rotor" to "tunneling" to "quasi-rigid" polyatomic molecule behavior for small, but finite, values of total angular momentum J. This work focuses on simple triatom (n=2) and tetratom (n=3) systems as a function of interatomic potential stiffness, with explicit consideration of H2O, NH3, and H3O+ as limiting test cases. The POS model also establishes the necessary mathematical groundwork for calculations on dynamically much more challenging XH(n) species with n>3 (e.g., models of CH5+) where such a reduced dimensionality approach offers prospects for being quantum mechanically tractable at low J values (i.e., J=0, 1, 2) characteristic of supersonic jet expansion conditions.

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PubMed2005

Docking kinetics and equilibrium of a GAAA tetraloop-receptor motif probed by single-molecule FRET.

Docking kinetics and equilibrium of fluorescently labeled RNA molecules are studied with single-molecule FRET methods. Time-resolved FRET is used to monitor docking/undocking transitions for RNAs containing a single GAAA tetraloop-receptor tertiary interaction connected by a flexible single-stranded linker. The rate constants for docking and undocking are measured as a function of Mg2+, revealing a complex dependence on metal ion concentration. Despite the simplicity of this model system, conformational heterogeneity similar to that noted in more complex RNA systems is observed; relatively rapid docking/undocking transitions are detected for approximately two-thirds of the RNA molecules, with significant subpopulations exhibiting few or no transitions on the 10- to 30-s time scale for photobleaching. The rate constants are determined from analysis of probability densities, which allows a much wider range of time scales to be analyzed than standard histogram procedures. The data for the GAAA tetraloop receptor are compared with kinetic and equilibrium data for other RNA tertiary interactions.

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PubMed2005

Supersonically cooled hydronium ions in a slit-jet discharge: high-resolution infrared spectroscopy and tunneling dynamics of HD2O+.

Jet-cooled high-resolution infrared spectra of partially deuterated hydronium ion (HD2O+) in the O-H stretch region (nu3 band) are obtained for the first time, exploiting the high ion densities, long absorption path lengths, and concentration modulation capabilities of the slit-jet discharge spectrometer. Least-squares analysis with a Watson asymmetric top Hamiltonian yields rovibrational constants and provides high level tests of ab initio molecular structure predictions. Transitions out of both the lower (nu3(+)<--0(+)) and the upper (nu3(-)<--0(-)) tunneling levels, as well as transitions across the tunneling gap (nu3(-)<--0(+)) are observed. The nu3(-)<--0(+) transitions in HD2O+ acquire oscillator strength by loss of D(3h) symmetry, and permit both ground-state-[27.0318(72) cm(-1)] and excited-state-[17.7612(54) cm(-1)]-tunneling splittings to be determined to spectroscopic precision from a single rovibrational band. The splittings and band origins calculated with recent high level ab initio six-dimensional potential surface predictions for H3O+ and isotopomers [X. C. Huang, S. Carter, and J. M. Bowman, J. Chem. Phys. 118, 5431 (2003); T. Rajamaki, A. Miani, and L. Halonen, J. Chem. Phys. 118, 10929 (2003)] are in very good agreement with the current experimental results.

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PubMed2005

Overtone spectroscopy of H2O clusters in the V(OH) = 2 manifold: infrared-ultraviolet vibrationally mediated dissociation studies.

Spectroscopy and predissociation dynamics of (H2O)2 and Ar-H2O are investigated with vibrationally mediated dissociation (VMD) techniques, wherein upsilon(OH) = 2 overtones of the complexes are selectively prepared with direct infrared pumping, followed by 193 nm photolysis of the excited H2O molecules. As a function of relative laser timing, the photolysis breaks H2O into OH and H fragments either (i) directly inside the complex or (ii) after the complex undergoes vibrational predissociation, with the nascent quantum state distribution of the OH photofragment probed via laser-induced fluorescence. This capability provides the first rotationally resolved spectroscopic analysis of (H2O)2 in the first overtone region and vibrational predissociation dynamics of water dimer and Ar-water clusters. The sensitivity of the VMD approach permits several upsilon(OH) = 2 overtone bands to be observed, the spectroscopic assignment of which is discussed in the context of recent anharmonic theoretical calculations.

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