Biomedical subjects

Anne B McCoy

Publications and source records attributed to Anne B McCoy.

At least 19 recordsLinked to original sources

PubMed2006

Experimental and theoretical investigations of the He...I2 rovibronic spectra in the I2 B-X, 20-0 region.

The laser-induced fluorescence and action spectra of I2 in a helium supersonic expansion have been recorded in the I2 B-X, 20-0 region. Two features are identified within the spectra. The lower-energy feature arises from transitions between states that are localized in a T-shaped conformation on both the X- and B-state potentials. The higher-energy feature reflects transitions from states that are localized in a linear conformation on the X state to states that have energies that are larger than the barrier for free rotation of the rare gas atom about the I2 molecule on the B-state potential. Ground-state binding energies of 16.6(6) and 16.3(6) cm-1 were determined for the T-shaped and linear conformers, respectively. These spectra are compared to those calculated using the experimentally determined rotational temperatures. Based on the agreement between the experimental and calculated spectra, the binding energies of the J'=0 states with 0 and 2-6 quanta of excitation in the He...I2 bending mode on the B state were determined. Several models for the B-state potential were used to investigate the origins of the shape of the contour of the higher-energy feature in the spectra for He...I2 and He...Br2. The shape of the contours was found to be relatively insensitive to the choice of potential. This leads us to believe that the spectra of these systems are relatively insensitive to the parameters of the B-state potential energy surface and are more sensitive to properties of the halogen molecule.

Journal Article↗

PubMed2006

Evolution of structure in CH5 + and its deuterated analogues.

Diffusion Monte Carlo simulations are used to investigate the effects of deuteration on the fluxionality of CH(5)(+) or CD(5)(+), using an ab initio potential surface, developed by Jin, Braams, and Bowman [J. Phys. Chem. 2006, 110, 1569]. We find that partial deuteration quenches the fluxional behavior. The spectral consequences are also investigated. We find that, while CH(5)(+) and CD(5)(+) are nearly spherical tops, partial deuteration breaks the rotational symmetry and the mixed isotopologues are generally better characterized as symmetric tops. In addition, we investigate the effects of deuteration on the low-resolution vibrational spectrum and anticipate that signatures of this delocalization will be observable in the vibrational spectrum.

Journal Article↗

PubMed2006

Time-dependent wave packet studies on the Cl + HCl hydrogen exchange reaction.

The initiation of the hydrogen exchange reaction Cl((2)P)+HCl --> ClH+Cl((2)P) by excitation of the HCl molecular stretch to v=2 is studied for total angular momentum quantum number J=(1)/(2) and both even and odd parity. The calculations were performed using a time-dependent propagation from an initial quasi-bound state and employed all three relevant potential energy surfaces and the nonadiabatic couplings between them. Coriolis and spin-orbit coupling were also taken into account. The electronic and HCl rotational distributions of the products in both dissociation channels are analyzed, and the results are interpreted using features of the potential energy surfaces.

Journal Article↗

PubMed2006

Spectroscopic characterization of peroxynitrous acid in cis-perp configurations.

This paper presents experimental evidence, supported by two-dimensional theoretical calculations, that HOONO can be observed in cis-perp (cp) configurations in a pulsed supersonic expansion. The spectral properties (transition frequency, rotational constants, and transition type) of OH overtone transitions originating from a state with predominately cp character are predicted theoretically and compared with those associated with a weak feature at 6996.2 cm(-1) observed experimentally using infrared action spectroscopy. This spectral feature is attributed to HOONO in cp configurations based on its vibrational frequency, rotational band contour, and resultant OH product state distribution.

Molecular Conformation↗

PubMed2006

Photoelectron spectra of Ar(n).(IHI)- (n = 0-6, 12, 20), a theoretical study.

The effects of the introduction of argon atoms on the photoelectron (PE) spectra of Ar(n).(IHI)- with n = 0-6, 12, and 20 are investigated. Time-independent quantum simulations of the spectra using a rigid cage approximation and allowing the motion of the IHI core are performed. As in our previous classical studies on this system, we find an increase in the confinement of the hydrogen atom motion as the number of argon atoms is increased. Comparison of the quantum and classical descriptions of this confinement provides evidence of the importance of quantum mechanical effects in this system. Three approaches are used to calculate the spectrum of the bare (IHI)- system. Excellent agreement is found between the simulated peaks in the = 2 region using a full three-dimensional quantum simulation of the PE spectrum, those from the corresponding experimental threshold photodetachment spectrum and those obtained by employing an adiabatic separation of the motions of the hydrogen and the iodine atoms. This provides further confirmation that these peaks are the result of motions of the iodine atoms. Simulations of the Ar(n).(IHI)- PE spectra show a shift of the spectra to lower electron kinetic energies as the number of argon atoms is increased. Similar shifts are found in the experimental spectra and in our previous study of this system using classical trajectory simulations. It is also found that the I-I motion mainly affects the spectrum features, whereas the progressions associated with hindered rotor transitions are less affected. Finally, an increase in the intensity of the = 0 peak and an accumulation of transitions in the low-frequency hindered rotor region with increasing number of argon atoms are observed.

Journal Article↗

PubMed2006

Prying apart a water molecule with anionic H-bonding: a comparative spectroscopic study of the X-.H2O (X = OH, O, F, Cl, and Br) binary complexes in the 600-3800 cm(-1) region.

A detailed picture of the structural distortions suffered by a water molecule in direct contact with small inorganic anions (e.g., X = halide) is emerging from a series of recent vibrational spectroscopy studies of the gas-phase X-.H2O binary complexes. The extended spectral coverage (600-3800 cm(-1)) presently available with tabletop laser systems, when combined with versatile argon "messenger" techniques for acquiring action spectra of cold complexes, now provides a comprehensive survey of how the interaction evolves from an ion-solvent configuration into a three-center, two-electron covalent bond as the proton affinity of the anion increases. We focus on the behavior of H2O in the X-.H2O (X = Br, Cl, F, O, and OH) complexes, which all adopt asymmetric structures where one hydrogen atom is H-bonded to the ion while the other is free. The positions and intensities of the bands clearly reveal the mechanical consequences of both (zero-point) vibrationally averaged and infrared photoinduced excess charge delocalization mediated by intracluster proton transfer (X-.H2O --> HX.OH-). The fundamentals of the shared proton stretch become quite intense, for example, and exhibit extreme red-shifts as the intracluster proton-transfer process becomes available, first in the vibrationally excited states (F-.H2O) and then finally at the zero-point level (OH-.H2O). In the latter case, the loss of the water molecule's independent character is confirmed through the disappearance of the approximately 1600 cm(-1) HOH intramolecular bending transition and the dramatic (>3000 cm(-1)) red-shift of the shared proton stretch. An unexpected manifestation of vibrationally mediated charge transfer is also observed in the low frequency region, where the 2 <-- 0 overtones of the out-of-plane frustrated rotation of the water are remarkably intense in the Cl-.H2O and Br-.H2O spectra. This effect is traced to changes in the charge distribution along the X-.O axis as the shared proton is displaced perpendicular to it, reducing the charge transfer character of the H-bonding interaction and giving rise to a large quadratic contribution to the dipole moment component that is parallel to the bond axis. Thus, all of these systems are found to exhibit distinct spectral characteristics that can be directly traced to the crucial role of vibrationally mediated charge redistribution within the complex.

Journal Article↗

PubMed2006

Deuteration effects on the structure and infrared spectrum of CH5(+).

The CH5+ molecular ion is well-known for its large amplitude motions that lead to complete scrambling of the hydrogen atoms, even in the vibrational ground state. Experiments have been reported that probe the consequences of these large amplitude motions. We recently reported that quantum zero-point effects partially quench the scrambling when CH5+ is partially deuterated. Here, the consequences of this quantum localization are investigated through calculations of the low-resolution spectra of CH4D+, CHD4+, and CD5+. The spectra are obtained by convoluting stick spectra, evaluated for individual stationary points on an ab initio potential surface, multiplying them by Diffusion Monte Carlo ground state density at that stationary point, and taking the sum. The CH/D stretch regions of CH4D+ and CD5+ are red-shifted relative to CH5+, while the overall shape of the envelope remains unaffected. In contrast, for CHD4+, the shape of the spectral envelope in the CH/D stretch region differs from the other three isotopologs. These signatures of the quantum localization of the deuterium on the spectra are discussed.

Journal Article↗

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.

Journal Article↗

PubMed2005

Stabilization and rovibronic spectra of the T-shaped and linear ground-state conformers of a weakly bound rare-gas-homonuclear dihalogen complex: He...Br2.

Laser-induced fluorescence spectra of Br(2) entrained in a He supersonic expansion have been recorded in the Br(2) B-X, 8-0, 12-0, and 21-0 spectral regions at varying downstream distances, and thus different temperature regimes. Features associated with transitions of the T-shaped and linear He...Br(2)(X,nu(") = 0) complexes are identified. The changes in the relative intensities of the T-shaped and linear features with cooling in the expansion indicate that the linear conformer is energetically more stable than the T-shaped conformer. A He + Br(2)(X,nu(") = 0) ab initio potential-energy surface, computed at the coupled cluster level of theory with a large, flexible basis set, is used to calculate the binding energies of the two conformers, 15.8 and 16.5 cm(-1) for the T-shaped and linear complexes, respectively. This potential and an excited-state potential [M. P. de Lara-Castells, A. A. Buchachenko, G. Delgado-Barrio, and P. Villareal, J. Chem. Phys. 120, 2182 (2004)] are used to calculate the excitation spectra of He...(79)Br(2)(X,nu(") = 0) in the Br(2) B-X, 12-0 region. The calculated spectra are used to make spectral assignments and to determine the energies of the excited-state intermolecular vibrational levels accessed in the observed transitions. Temperature-dependent laser-induced fluorescence spectra and a simple thermodynamic model [D. S. Boucher, J. P. Darr, M. D. Bradke, R. A. Loomis, and A. B. McCoy, Phys. Chem. Chem. Phys. 6, 5275 (2004)] are used to estimate that the linear conformer is 0.4(2) cm(-1) more strongly bound than the T-shaped conformer. Two-laser action spectroscopy experiments reveal that the binding energy of the linear He...(79)Br(2)(X,nu(") = 0) conformer is 17.0(8) cm(-1), and that of the T-shaped He...(79)Br(2)(X,nu(") = 0) conformer is then 16.6(8) cm(-1), in good agreement with the calculated values.

Journal Article↗

PubMed2005

Quantum studies of the vibrations in H3O2- and D3O2-.

The vibrations of H3O2- and D3O2- are investigated using diffusion Monte Carlo (DMC) and vibrational configuration-interaction approaches, as implemented in the program MULTIMODE. These studies use the potential surface recently developed by Huang et al. [ J. Am. Chem. Soc. 126, 5042 (2004)]. The focus of this work is on the vibrational ground state and fundamentals which occur between 100 and 3700 cm(-1). In most cases, excellent agreement is obtained between the fundamental frequencies calculated by the two approaches. This serves to demonstrate the power of both methods for treating this very anharmonic system. Based on the results of the MULTIMODE and DMC treatments, the extent and nature of the couplings in H3O2- and D3O2- are investigated.

Journal Article↗

PubMed2005

The vibrational predissociation spectra of the H5O2 +RGn(RG = Ar,Ne) clusters: correlation of the solvent perturbations in the free OH and shared proton transitions of the Zundel ion.

Predissociation spectra of the H(5)O(2) (+)RG(n)(RG = Ar,Ne) cluster ions are reported in energy regions corresponding to both the OH stretching (3350-3850 cm(-1)) and shared proton (850-1950 cm(-1)) vibrations. The two free OH stretching bands displayed by the Ne complex are quite close to the band origins identified earlier in bare H(5)O(2) (+) [L. I. Yeh, M. Okumura, J. D. Myers, J. M. Price, and Y. T. Lee, J. Chem. Phys. 91, 7319 (1989)], indicating that the symmetrical H(5)O(2) (+) "Zundel" ion remains largely intact in H(5)O(2) (+)Ne. The low-energy spectrum of the Ne complex is simpler than that observed previously for H(5)O(2) (+)Ar, and is dominated by two sharp transitions at 928 and 1047 cm(-1), with a weaker feature at 1763 cm(-1). The H(5)O(2) (+)Ar(n),n = 1-5 spectra generally exhibit complex band structures reflecting solvent-induced symmetry breaking of the Zundel core ion. The extent of solvent perturbation is evaluated with electronic structure calculations, which predict that the rare gas atoms should attach to the spectator OH groups of H(5)O(2) (+) rather than to the shared proton. In the asymmetric complexes, the shared proton resides closer to the more heavily solvated water molecule, leading to redshifts in the rare gas atom-solvated OH stretches and to blueshifts in the shared proton vibrations. The experimental spectra are compared with recent full-dimensional vibrational calculations (diffusion Monte Carlo and multimode/vibrational configuration interaction) on H(5)O(2) (+). These results are consistent with assignment of the strong low-energy bands in the H(5)O(2) (+)Ne spectrum to the vibration of the shared proton mostly along the O-O axis, with the 1763 cm(-1) band traced primarily to the out-of-phase, intramolecular bending vibrations of the two water molecules.

Journal Article↗

PubMed2005

Reactive scattering dynamics in atom+polyatomic systems: F+C2H6-->HF(v,J)+C2H5.

State-to-state scattering dynamics of F+C2H6-->HF(v,J)+C2H5 have been investigated at Ecom=3.2(6) kcalmol under single-collision conditions, via detection of nascent rovibrationally resolved HF(v,J) product states with high-resolution infrared laser absorption methods. State-resolved Doppler absorption profiles are recorded for multiple HF(v,J) transitions originating in the v=0,1,2,3 manifold, analyzed to yield absolute column-integrated densities via known HF transition moments, and converted into nascent probabilities via density-to-flux analysis. The spectral resolution of the probe laser also permits Doppler study of translational energy release into quantum-state-resolved HF fragments, which reveals a remarkable linear correlation between (i) HF(v,J) translational recoil and (ii) the remaining energy available, Eavail=Etot-E(HF(v,J)). The dynamics are interpreted in the context of a simple impulsive model based on conservation of linearangular momentum that yields predictions in good agreement with experiment. Deviations from the model indicate only minor excitation of ethyl vibrations, in contrast with a picture of extensive intramolecular vibrational energy flow but consistent with Franck-Condon excitation of the methylene CH2 bending mode. The results suggest a relatively simple dynamical picture for exothermic atom+polyatomic scattering, i.e., that of early barrier dynamics in atom+diatom systems but modified by impulsive recoil coupling at the transition state between translationalrotational degrees of freedom.

Journal Article↗

PubMed2005

Role of OH-stretch/torsion coupling and quantum yield effects in the first OH overtone spectrum of cis-cis HOONO.

A joint theoretical and experimental investigation is undertaken to study the effects of OH-stretch/HOON torsion coupling and of quantum yield on the previously reported first overtone action spectrum of cis-cis HOONO (peroxynitrous acid). The minimum energy path along the HOON dihedral angle is computed at the coupled cluster singles and doubles with perturbative triples level with correlation consistent polarized quadruple zeta basis set, at the structure optimized using the triple zeta basis set (CCSD(T)/cc-pVQZ//CCSD(T)/cc-pVTZ). The two-dimensional ab initio potential energy and dipole moment surfaces for cis-cis HOONO are calculated as functions of the HOON torsion and OH bond length about the minimum energy path at the CCSD(T)/cc-pVTZ and QCISD/AUG-cc-pVTZ (QCISD-quadratic configuration interaction with single and double excitation and AUG-augmented with diffuse functions) level of theory/basis, respectively. The OH-stretch vibration depends strongly on the torsional angle, and the torsional potential possesses a broad shelf at approximately 90 degrees , the cis-perp conformation. The calculated electronic energies and dipoles are fit to simple functional forms and absorption spectra in the region of the OH fundamental and first overtone are calculated from these surfaces. While the experimental and calculated spectra of the OH fundamental band are in good agreement, significant differences in the intensity patterns are observed between the calculated absorption spectrum and the measured action spectrum in the 2nu(OH) region. These differences are attributed to the fact that several of the experimentally accessible states do not have sufficient energy to dissociate to OH+NO(2) and therefore are not detectable in an action spectrum. Scaling of the intensities of transitions to these states, assuming D(0)=82.0 kJ/mol, is shown to produce a spectrum that is in good agreement with the measured action spectrum. Based on this agreement, we assign two of the features in the spectrum to Deltan=0 transitions (where n is the HOON torsion quantum number) that are blue shifted relative to the origin band, while the large peak near 7000 cm(-1) is assigned to a series of Deltan=+1 transitions, with predominant contributions from torsionally excited states with substantial cis-perp character. The direct absorption spectrum of cis-cis HOONO (6300-6850 cm(-1)) is recorded by cavity ringdown spectroscopy in a discharge flow cell. A single band of HOONO is observed at 6370 cm(-1) and is assigned as the origin of the first OH overtone of cis-cis HOONO. These results imply that the origin band is suppressed by over an order of magnitude in the action spectrum, due to a reduced quantum yield. The striking differences between absorption and action spectra are correctly predicted by the calculations.

Journal Article↗

PubMed2005

Fundamental excitations of the shared proton in the H3O2- and H5O2+ complexes.

We exploit recent advances in argon predissociation spectroscopy to record the spectroscopic signature of the shared proton oscillations in the H3O2- system and compare the resulting spectrum with that of the H5O2+ ion taken under similar conditions. Very intense 1 <-- 0 transitions are observed below 1100 cm(-1) in both cases and are surprisingly sharp, with the 697 cm(-1) transition in H3O2- being among the lowest in energy of any shared proton system measured to date. The assignments of the three fundamental transitions associated with the three-dimensional confinement of the shared proton in H3O2- are carried out with full-dimensional (DMC) calculations to treat this strongly anharmonic vibrational problem.

Letter↗

PubMed2005

Transition state dynamics of Ar(n).(IHI) (n = 0-20).

Classical trajectory simulations of the dynamics of Ar(n).(IHI) with n = 0-20 are performed to investigate the effects of solvation on the transition state dynamics of the I + HI reaction. Initial conditions for the classical trajectories are sampled from the quantum ground-state phase space distribution for Ar(n).(IHI)-, given by the Wigner distribution function. Neumark and co-workers recently reported a shift of the Ar(n).(IHI)- photoelectron spectra to lower electron kinetic energies when the number of argon atoms was increased from 0 to 15. Analogous shifts are found in the present calculations, and excellent agreement between the experimental and calculated shifts is found. Longer lifetimes of the IHI complex and increasing energy transfer between the hydrogen atom and the argon and iodine atoms are also observed as the number of argon atoms is increased.

Journal Article↗

PubMed2005

Full-dimensional vibrational calculations for H5O2+ using an ab initio potential energy surface.

We report quantum diffusion Monte Carlo (DMC) and variational calculations in full dimensionality for selected vibrational states of H(5)O(2) (+) using a new ab initio potential energy surface [X. Huang, B. Braams, and J. M. Bowman, J. Chem. Phys. 122, 044308 (2005)]. The energy and properties of the zero-point state are focused on in the rigorous DMC calculations. OH-stretch fundamentals are also calculated using "fixed-node" DMC calculations and variationally using two versions of the code MULTIMODE. These results are compared with infrared multiphoton dissociation measurements of Yeh et al. [L. I. Yeh, M. Okumura, J. D. Myers, J. M. Price, and Y. T. Lee, J. Chem. Phys. 91, 7319 (1989)]. Some preliminary results for the energies of several modes of the shared hydrogen are also reported.

Journal Article↗

PubMed2005

Argon predissociation spectroscopy of the OH-.H2O and Cl-.H2O complexes in the 1000-1900 cm(-1) region: intramolecular bending transitions and the search for the shared-proton fundamental in the hydroxide monohydrate.

We present argon predissociation vibrational spectra of the OH(-).H(2)O and Cl(-).H(2)O complexes in the 1000-1900 cm(-1) energy range, far below the OH stretching region reported in previous studies. This extension allows us to explore the fundamental transitions of the intramolecular bending vibrations associated with the water molecule, as well as that of the shared proton inferred from previous assignments of overtones in the higher energy region. Although the water bending fundamental in the Cl(-).H(2)O spectrum is in very good agreement with expectations, the OH(-).H(2)O spectrum is quite different than anticipated, being dominated by a strong feature at 1090 cm(-1). New full-dimensionality calculations of the OH(-).H(2)O vibrational level structure using diffusion Monte Carlo and the VSCF/CI methods indicate this band arises from excitation of the shared proton.

Journal Article↗

PubMed2005

Femtosecond dynamics of Cu(H(2)O)(2).

The ultrafast relaxation dynamics of Cu(H(2)O)(2) is investigated using femtosecond photodetachment-photoionization spectroscopy. In addition, stationary points on the Cu(H(2)O)(2) anion, neutral, and cation potential energy surfaces are characterized by ab initio electronic structure calculations. Electron photodetachment from Cu(-)(H(2)O)(2) initiates the dynamics on the ground-state potential energy surface of neutral Cu(H(2)O)(2). The resulting Cu(H(2)O)(2) complexes experience large-amplitude H(2)O reorientation and dissociation. The time evolution of the Cu(H(2)O)(2) fragmentation products is monitored by time-resolved resonant multiphoton ionization. The parent ion, Cu(+)(H(2)O)(2), is not detected above background levels. The rise to a maximum of the Cu(+) signal from Cu(-)(H(2)O)(2), and the decay of the Cu(+)(H(2)O) signal from Cu(-)(H(2)O)(2) have similar tau approximately 10 ps time dependences to the corresponding signals from Cu(-)(H(2)O), but display clear differences at very short and long times. The experimental observations can be understood in terms of the following picture. Prompt dissociation of H(2)O from nascent Cu(H(2)O)(2) gives rise to a vibrationally excited Cu(H(2)O) complex, which dissociates to Cu+H(2)O due to coupling of H(2)O internal rotation to the dissociation coordinate. This prompt dissociation removes all intra-H(2)O vibrational excitation from the intermediate Cu(H(2)O) fragment, which quenches the long time vibrational predissociation to Cu+H(2)O previously observed in analogous experiments on Cu(-)(H(2)O).

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