Computational Aspects of Single-Molecule Kinetics for Coupled Catalytic Cycles: A Spectral Analysis.

Catalysis from single active sites is analyzed using methods developed from single-molecule kinetics. Using a stochastic Markov-state description, the observable properties of general catalytic networks of reactions are expressed using an eigenvalue decomposition of the transition matrix for the Markov process. By the use of a sensitivity analysis, the necessary eigenvalues and eigenvectors are related to the energies of controlling barriers and wells located along the reaction routes. A generalization of the energetic span theory allows the eigenvalues to be computed from several activation energies corresponding to distinct barrier-well pairings. The formalism is demonstrated for model problems and for a physically realistic mechanism for an alkene hydrogenation reaction on a single-atom catalyst. The spectral analysis permits a hierarchy of timescales to be identified from the single-molecule signal, which correspond to specific relaxation modes in the network.

The role of the three body photodissociation channel of water in the evolution of dioxygen in astrophysical applications.

A recent experiment at the Dalian Coherent Light Source (DCLS) has provided measurements of the partial cross sections for the photodissociation of water vapor over an unprecedented range of wavelengths in the vacuum ultraviolet (VUV) region. It was found that the three body dissociation channel, H + H + O(3P/1D), becomes prominent at wavelengths shorter than the Lyman α-line at 121.6 nm. The present work explores the kinetic consequences of this discovery for several astrophysically motivated examples. The irradiation of a dilute low-temperature gas by unscreened solar radiation, similar to early stage photochemical processing in a comet coma, shows significant increase in the production of O2-molecules at shorter times, <1 day, that might physically correspond to the photochemical reaction zone of the coma. Several examples of planetary atmospheres show increased O-atom production at high altitudes but relatively little modification of the equilibrium O2 concentrations predicted by conventional models.

Kinetic Study of Gas-Phase Reactions of Pyruvic Acid with HO2.

Gas-phase reactions between pyruvic acid (PA) and HO2 radicals were examined using ab initio quantum chemistry and transition state theory. The rate coefficients were determined over a temperature range of 200-400 K including tunneling contributions. Six potential reaction pathways were identified. The two hydrogen abstraction reactions yielding the H2O2 product were found to have high barriers. The HO2 radical was also found to have a catalytic effect on the intramolecular hydrogen transfer reactions occurring by three distinct routes. These hydrogen-shift reactions are very interesting mechanistically although they are highly endothermic. The only reaction that contributes significantly to the consumption of PA is a multistep pathway involving a peroxy-radical intermediate, PA + HO2 → CH3COOH + OH + CO2. This exothermic process has potential atmospheric relevance because it produces an OH radical as a product. Atmospheric models currently have difficulty predicting accurate OH concentrations for certain atmospheric conditions, such as environments free of NOx and the nocturnal boundary layer. Reactions of this sort, although not necessary with PA, may account for a portion of this deficit. The present study helps settle the issue of the relative roles of reaction and photolysis in consumption of PA in the troposphere.

Gas-Phase Reaction Kinetics of Pyruvic Acid with OH Radicals: The Role of Tunneling, Complex Formation, and Conformational Structure.

The gas-phase reaction of pyruvic acid (PA) with the OH radical is studied theoretically using accurate quantum chemistry and transition state theory. Two chemically distinct H-atom abstraction reactions and two distinct OH addition reactions have been identified. The rate coefficients for these four processes were calculated. Quantum tunneling was included in each rate using the small curvature tunneling method. The influence of the conformational structure of PA was found to be particularly intriguing. While the trans-cis structure was found to dominantly react by H-atom abstraction from the methyl site, the trans-trans conformer was found to react mostly through H-atom abstraction from the acid site. A general formalism was developed to model the kinetics of the reactions that involve multiple conformers, interconverting prereactive complexes, and multiple transition states. Comparison of the results obtained with available experimental rate observations reveals agreement with the trans-trans conformer of PA but disagreement with the results obtained for a full statistical mixture of reagents. The role of these reactions in the atmospheric processing of PA is discussed.

Double Hydrogen-Atom Exchange Reactions of HX (X = F, Cl, Br, I) with HO2.

A novel double hydrogen atom exchange process, HX + H'O2 → H'X + HO2 for the halogen series X = F, Cl, Br, and I, is identified using theoretical methods. These concerted reactions are mediated through a stabilized five-membered planar ring transition state structure. The transition state barrier for the double exchange process is found to be significantly lower than that for the abstraction reaction of a single hydrogen atom. Density functional theory employing the M11 exchange functional is used to compute parameters of the potential energy surface and the rate coefficients are obtained using transition state theory with small curvature tunneling. For low temperatures, the exchange reaction proceeds at a rate several orders of magnitude faster than the abstraction channel, which is also calculated. The exchange process may be observed using isotope scrambling reactions; such reactions may contribute to observed isotope abundances in the atmosphere. The rate coefficients for the isotopically labeled reactions are computed. It is found that the trends in reactivity within the series of halogen reactions can be quantitatively understood using the degree of electron delocalization at the transition state. The barriers are found to fall as the electronegativity of the halogen atom decreases.

Reaction Kinetics of HBr with HO2: A New Channel for Isotope Scrambling Reactions.

The gas phase reaction kinetics of HBr with the HO2 radical are investigated over the temperature range of T = 200-1500 K using a theoretical approach based on transition state theory. The parameters for the potential energy surface are computed using density functional theory with the M11 exchange functional. The rate coefficient for the HBr + HO2 → Br + H2O2 abstraction channel is found to be somewhat larger than previous estimates at low temperatures due to quantum tunneling. The present study reveals the existence of a novel exchange pathway, HBr + H'O2 → H'Br + HO2, which exhibits a much lower reaction barrier than does the abstraction route. The transition state for this process is a symmetrical planar five-membered-ring-shaped structure. At low temperatures, this concerted double hydrogen transfer reaction is several orders of magnitude faster than the abstraction channel. The exchange process may be observed using isotope scrambling reactions; such reactions may contribute to observed isotope abundances in the atmosphere. The rate coefficients for the isotopically labeled reactions are computed.

Sum over Histories Representation for Kinetic Sensitivity Analysis: How Chemical Pathways Change When Reaction Rate Coefficients Are Varied.

The sensitivity of kinetic observables is analyzed using a newly developed sum over histories representation of chemical kinetics. In the sum over histories representation, the concentrations of the chemical species are decomposed into the sum of probabilities for chemical pathways that follow molecules from reactants to products or intermediates. Unlike static flux methods for reaction path analysis, the sum over histories approach includes the explicit time dependence of the pathway probabilities. Using the sum over histories representation, the sensitivity of an observable with respect to a kinetic parameter such as a rate coefficient is then analyzed in terms of how that parameter affects the chemical pathway probabilities. The method is illustrated for species concentration target functions in H2 combustion where the rate coefficients are allowed to vary over their associated uncertainty ranges. It is found that large sensitivities are often associated with rate limiting steps along important chemical pathways or by reactions that control the branching of reactive flux.

Multitarget global sensitivity analysis of n-butanol combustion.

A model for the combustion of butanol is studied using a recently developed theoretical method for the systematic improvement of the kinetic mechanism. The butanol mechanism includes 1446 reactions, and we demonstrate that it is straightforward and computationally feasible to implement a full global sensitivity analysis incorporating all the reactions. In addition, we extend our previous analysis of ignition-delay targets to include species targets. The combination of species and ignition targets leads to multitarget global sensitivity analysis, which allows for a more complete mechanism validation procedure than we previously implemented. The inclusion of species sensitivity analysis allows for a direct comparison between reaction pathway analysis and global sensitivity analysis.

A study of resonance progressions in the F + HCl → Cl + HF reaction: a lifetime matrix analysis of pre-reactive and post-reactive collision complexes.

Quantum scattering calculations were performed for the F + HCl → Cl + HF reaction for total angular momentum J = 0-6 using an ab initio potential energy surface. Employing a time-independent algorithm on a very fine energy grid allowed the resolution of hundreds of narrow resonances with lifetimes in the picosecond range. The resonances were assigned to rotationally excited van der Waals complexes lying in the entrance and exit channels. Resonance peaks observed in the J = 0 calculation broke into multiplets for J > 0 corresponding to the range of allowed helicity states. The Smith lifetime matrix, Q(E), was used to efficiently extract the resonance properties. The largest eigenvalue of Q(E) was used for the position and total width, while the corresponding eigenvector was used to obtain the partial widths. A simple model based on the conventional treatment of rotationally excited van der Waals triatomics was used to predict the resonance spectrum to an accuracy of ~0.02 kcal∕mol. The model predicts the density of resonance states in good agreement with the exact scattering results.

Theoretical determination of the rate coefficient for the HO2 + HO2 → H2O2+O2 reaction: adiabatic treatment of anharmonic torsional effects.

The HO(2) + HO(2) → H(2)O(2) + O(2) chemical reaction is studied using statistical rate theory in conjunction with high level ab initio electronic structure calculations. A new theoretical rate coefficient is generated that is appropriate for both high and low temperature regimes. The transition state region for the ground triplet potential energy surface is characterized using the CASPT2/CBS/aug-cc-pVTZ method with 14 active electrons and 10 active orbitals. The reaction is found to proceed through an intermediate complex bound by approximately 9.79 kcal/mol. There is no potential barrier in the entrance channel, although the free energy barrier was determined using a large Monte Carlo sampling of the HO(2) orientations. The inner (tight) transition state lies below the entrance threshold. It is found that this inner transition state exhibits two saddle points corresponding to torsional conformations of the complex. A unified treatment based on vibrational adiabatic theory is presented that permits the reaction to occur on an equal footing for any value of the torsional angle. The quantum tunneling is also reformulated based on this new approach. The rate coefficient obtained is in good agreement with low temperature experimental results but is significantly lower than the results of shock tube experiments for high temperatures.

A six-dimensional wave packet study of the vibrational overtone induced decomposition of hydrogen peroxide.

A converged quantum wave packet study is presented for the unimolecular reaction HOOH → OH+OH induced by the fifth OH-overtone excitation employing an ab initio potential energy surface. All six internal vibrational degrees of freedom are explicitly represented in this simulation for total angular momentum zero. It is found that the decay of the survival probability and of the autocorrelation function is non-exponential and that the long time dynamics is likely due to the superposition of a number of resonance states. The simulated overtone spectrum and rotational product distribution is in good agreement with experimental measurements. It is concluded that: (1) the reaction dynamics is non-statistical on a 30 ps timescale, (2) the observed line width is roughly a factor of 1.7 larger than implied by the reactive lifetimes suggesting that a significant portion of the linewidth is due to intramolecular vibrational energy relaxation, and (3) the quantum reaction rate is suppressed by about a factor of two relative to its classical counterpart.

Will water act as a photocatalyst for cluster phase chemical reactions? Vibrational overtone-induced dehydration reaction of methanediol.

The possibility of water catalysis in the vibrational overtone-induced dehydration reaction of methanediol is investigated using ab initio dynamical simulations of small methanediol-water clusters. Quantum chemistry calculations employing clusters with one or two water molecules reveal that the barrier to dehydration is lowered by over 20 kcal/mol because of hydrogen-bonding at the transition state. Nevertheless, the simulations of the reaction dynamics following OH-stretch excitation show little catalytic effect of water and, in some cases, even show an anticatalytic effect. The quantum yield for the dehydration reaction exhibits a delayed threshold effect where reaction does not occur until the photon energy is far above the barrier energy. Unlike thermally induced reactions, it is argued that competition between reaction and the irreversible dissipation of photon energy may be expected to raise the dynamical threshold for the reaction above the transition state energy. It is concluded that quantum chemistry calculations showing barrier lowering are not sufficient to infer water catalysis in photochemical reactions, which instead require dynamical modeling.

Global sensitivity analysis of chemical-kinetic reaction mechanisms: construction and deconstruction of the probability density function.

This paper investigates global sensitivity analysis as applied to reaction mechanisms. It uses the HDMR (high-dimensional model representation) expansion and the features of the sensitivity indices to explore the probability density function (pdf) of predicted target outputs that results from the uncertainties in the rate coefficients. We study the autoignition of H(2)/O(2) mixtures, where the pdf describes the uncertainty in ignition delay times due to the uncertainties in the rate coefficients. The global sensitivity analysis in conjunction with the HDMR expansion allows for the deconstruction of the pdf in several different ways. These deconstructions allow the features of the pdf to be understood in terms of the constitute reactions in much finer detail than the study of a variance decomposition alone.

Water catalysis and anticatalysis in photochemical reactions: observation of a delayed threshold effect in the reaction quantum yield.

The possible catalysis of photochemical reactions by water molecules is considered. Using theoretical simulations, we investigate the HF-elimination reaction of fluoromethanol in small water clusters initiated by the overtone excitation of the hydroxyl group. The reaction occurs in competition with the process of water evaporation that dissipates the excitation and quenches the reaction. Although the transition state barrier is stabilized by over 20 kcal/mol through hydrogen bonding with water, the quantum yield versus energy shows a pronounced delayed threshold that effectively eliminates the catalytic effect. It is concluded that the quantum chemistry calculations of barrier lowering are not sufficient to infer water catalysis in some photochemical reactions, which instead require dynamical modeling.

Theoretical validation of chemical kinetic mechanisms: combustion of methanol.

A new technique is proposed that uses theoretical methods to systematically improve the performance of chemical kinetic mechanisms. Using a screening method, the chemical reaction steps that most strongly influence a given kinetic observable are identified. The associated rate coefficients are then improved by high-level quantum chemistry and transition-state-theory calculations, which leads to new values for the coefficients and smaller uncertainty ranges. This updating process is continued as new reactions emerge as the most important steps in the target observable. The screening process employed is a global sensitivity analysis that involves Monte Carlo sampling of the full N-dimensional uncertainty space of rate coefficients, where N is the number of reaction steps. The method is applied to the methanol combustion mechanism of Li et al. (Int. J. Chem. Kinet. 2007, 39, 109.). It was found that the CH(3)OH + HO(2) and CH(3)OH + O(2) reactions were the most important steps in setting the ignition delay time, and the rate coefficients for these reactions were updated. The ignition time is significantly changed for a broad range of high-concentration methanol/oxygen mixtures in the updated mechanism.

Dynamics and spectroscopy of vibrational overtone excited glyoxylic acid and 2,2-dihydroxyacetic acid in the gas-phase.

The early time dynamics of vibrationally excited glyoxylic acid and of its monohydrate 2,2-dihydroxyacetic acid are investigated by theoretical and spectroscopic methods. A combination of "on-the-fly" dynamical simulations and cavity ring-down spectroscopy on the excited O-H stretching vibrational levels of these molecules observed that conformers that possess the correct structure and orientation react upon excitation of Deltaupsilon(OH)=4,5, while the structurally different but near isoenergetic conformers do not undergo unimolecular decay by the same direct and fast process. Experiment and theory give a femtosecond time scale for hydrogen atom chattering in the vibrationally excited glyoxylic acid. This process is the precursor for the concerted decarboxylation of the ketoacid. We extrapolate the results obtained here to suggest a rapid subpicosecond overall reaction. In these light-initiated reactions, relatively cold hydroxycarbenes, stable against further unimolecular decay, are expected products since most of the excitation energy is consumed by the endothermicity of the reaction. Glyoxylic acid and its monohydrate are atmospherically relevant ketoacids. The vibrational overtone initiated reactions of glyoxylic acid leading to di- and monohydroxycarbenes on subpicosecond time scales are potentially of importance in atmospheric chemistry since the reaction is sufficiently rapid to avoid collisional dissipation.

Fundamental and overtone vibrational spectra of gas-phase pyruvic acid.

Pyruvic acid (CH(3)COCOOH) is an important keto acid present in the atmosphere. In this study, the vibrational spectroscopy of gas-phase pyruvic acid has been investigated with special emphasis on the overtone transitions of the OH-stretch, with Delta v(OH) = 2, 4, 5. Assignments were made to fundamental and combination bands in the mid-IR. The two lowest energy rotational conformers of pyruvic acid are clearly observed in the spectrum. The lowest energy conformer possesses an intramolecular hydrogen bond, while the next lowest rotational conformer does not. This difference is clearly seen in the spectra of the OH vibrational overtone transitions, and it is reflected in the anharmonicities of the OH-stretching modes for each conformer. The spectra of the OH-stretching vibration for both conformers were investigated to establish the effect of the hydrogen bond on frequency, intensity, and line width.

Infrared spectra of SF6(-) x HCOOH x Ar(n) (n = 0-2): infrared triggered reaction and Ar-induced reactive inhibition.

We present the infrared spectra of SF(6)(-) x HCOOH x Ar(m) (m=0-2) complexes. We find that the binding motif involves a single hydrogen bond between the SF(6)(-) anion and the OH group of the formic acid, with the CH group weakly tethered to a neighboring F atom. Similar to the case of hydrated SF(6)(-), the SF bond involved in the (OH-F) bond is significantly stretched and weakened by the attachment of the HCOOH ligand. The bare complex undergoes reaction upon infrared absorption in the CH/OH stretching region of the formic acid moiety, leading predominantly to the formation of SF(4)(-) + 2HF + CO(2). The reaction can be inhibited by attachment of two Ar atoms. We discuss a likely reaction mechanism in the framework of ab initio calculations, suggesting that reaction proceeds via tunneling through the potential barrier.

Experimental and theoretical study of the OH vibrational spectra and overtone chemistry of gas-phase vinylacetic acid.

In this study we present the gas-phase vibrational spectrum of vinylacetic acid with a focus on the nu = 1-5 vibrational states of the OH stretching transitions. Cross sections for nu = 1, 2, 4 and 5 of the OH stretching vibrational transitions are derived on the basis of the vapor pressure data obtained for vinylacetic acid. Ab initio calculations are used to assist in the band assignments of the experimental spectra, and to determine the threshold for the decarboxylation of vinylacetic acid. When compared to the theoretical energy barrier to decarboxylation, it is found that the nu OH = 4 transition with thermal excitation of low frequency modes or rotational motion and nu OH = 5 transitions have sufficient energy for the reaction to proceed following overtone excitation.

Dynamics of vibrational overtone excited pyruvic acid in the gas phase: line broadening through hydrogen-atom chattering.

The dynamics of overtone-excited pyruvic acid (PA) is studied using a combination of experimental and theoretical methods. It is experimentally observed that high overtone excitation of the OH-stretching mode of PA in the gas phase leads to a unimolecular decarboxylation reaction. An RRKM analysis of the rate is consistent with previous experiments for the thermal reaction but is inconsistent with the present overtone chemistry; from this it is concluded that the overtone-induced reaction is likely to be a direct reaction. Using a Fourier transform infrared spectrometer and a cavity ring-down spectrometer, the spectrum for the OH-stretch fundamental and overtone transitions is measured. We assign two conformers of PA in the spectrum, the Tc and Tt, corresponding to distinct orientations of the OH-group. The spectral peaks for the Tc-conformer broaden dramatically at the third and fourth overtones while those of the Tt-conformer remain relatively narrow. Using a three-mode quantum mechanical model for the vibrational states, the line positions and intensities are well reproduced by theory. The line widths, and the associated dynamical interpretation, are provided by a direct dynamics calculation, where the potential is computed "on-the-fly" and all degrees of freedom are included. It is found that the line broadening is due to the onset of H-atom chattering between the two O-atoms, an effect that occurs for the Tc-conformer but not the Tt-conformer. This H-atom-transfer process is the first step of the decarboxylation reaction mechanism, which subsequently involves breaking the C-C bond. The theoretical and experimental line widths agree but do not correspond to the full reaction time which is much longer than the initial chattering step.