Rex T. Skodje

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Name: Skodje, Rex
Organization: University of Colorado , USA
Department: Department of Chemistry and Biochemistry
Title: Professor(PhD)

TOPICS

Co-reporter:Jonathan R. Church and Rex T. Skodje
The Journal of Physical Chemistry A 2016 Volume 120(Issue 43) pp:8503-8511
Publication Date(Web):October 10, 2016
DOI:10.1021/acs.jpca.6b07215
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.
Co-reporter:Shirong Bai; Dingyu Zhou; Michael J. Davis
The Journal of Physical Chemistry Letters 2015 Volume 6(Issue 1) pp:183-188
Publication Date(Web):December 18, 2014
DOI:10.1021/jz502239v
A new representation for chemical kinetics is introduced that is based on a sum over histories formulation that employs chemical pathways defined at a molecular level. The time evolution of a chemically reactive system is described by enumerating the most important pathways followed by a chemical moiety. An explicit formula for the pathway probabilities is derived and takes the form of an integral over a time-ordered product. When evaluating long pathways, the time-ordered product has a simple Monte Carlo representation that is computationally efficient. A small numerical stochastic simulation was used to identify the most important paths to include in the representation. The method was applied to a realistic H2/O2 combustion problem and is shown to yield accurate results.
Co-reporter:Zeb C. Kramer ; Xiang-Kui Gu ; Dingyu D. Y. Zhou ; Wei-Xue Li
The Journal of Physical Chemistry C 2014 Volume 118(Issue 23) pp:12364-12383
Publication Date(Web):May 20, 2014
DOI:10.1021/jp503056u
We present a model of the surface kinetics of the dehydrogenation reaction of methanol on the Pd(111), Pt(111), and Ni(111) metal surfaces. The mechanism consists of 10 reversible dehydrogenation reactions that lead to the final products of CO and H2. The rate coefficients for each step are calculated using ab initio transition state theory that employs a new approach to obtain the symmetry factors. The potential energies and frequencies of the reagents and transition states are computed using plane wave DFT with the PW91 exchange correlation functional. The mechanism is investigated for low coverages using a global sensitivity analysis that monitors the response of a target function of the kinetics to the value of the rate coefficients. On Pd(111) and Ni(111), the reaction COH → CO + H is found to be rate limiting, and overall rates are highly dependent upon the decomposition time of the COH intermediate. Reactions at branches in the reaction network are also particularly important in the kinetics. A stochastic atom-following approach to pathway analysis is used to elucidate both the pathway probabilities in the kinetics and the dependence of the pathways on the values of the key rate coefficients of the mechanisms. On Pd(111) and Ni(111) there exists significant competition between the pathway containing the slow step and faster pathways that bypass the slow step. A discussion is given of the dependence of the model target’s probability density function on the chemical pathways.
Co-reporter:Dingyu D. Y. Zhou, Keli Han, Peiyu Zhang, Lawrence B. Harding, Michael J. Davis, and Rex T. Skodje
The Journal of Physical Chemistry A 2012 Volume 116(Issue 9) pp:2089-2100
Publication Date(Web):February 3, 2012
DOI:10.1021/jp209684s
The HO2 + HO2 → H2O2 + O2 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 HO2 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.
Co-reporter:Zeb C. Kramer ; Kaito Takahashi
Journal of the American Chemical Society 2010 Volume 132(Issue 43) pp:15154-15157
Publication Date(Web):October 13, 2010
DOI:10.1021/ja107335t
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.
Co-reporter:Rex T. Skodje, Alison S. Tomlin, Stephen J. Klippenstein, Lawrence B. Harding and Michael J. Davis
The Journal of Physical Chemistry A 2010 Volume 114(Issue 32) pp:8286-8301
Publication Date(Web):July 23, 2010
DOI:10.1021/jp1047002
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 CH3OH + HO2 and CH3OH + O2 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.
Co-reporter:Kathryn L. Plath, Kaito Takahashi, Rex T. Skodje and Veronica Vaida
The Journal of Physical Chemistry A 2009 Volume 113(Issue 26) pp:7294-7303
Publication Date(Web):March 4, 2009
DOI:10.1021/jp810687t
Pyruvic acid (CH3COCOOH) 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 ΔvOH = 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.
Co-reporter:Kaito Takahashi, Kathryn L. Plath, Rex T. Skodje and Veronica Vaida
The Journal of Physical Chemistry A 2008 Volume 112(Issue 32) pp:7321-7331
Publication Date(Web):July 19, 2008
DOI:10.1021/jp803225c
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.
Hydroxyl
protium
Formyl radical
Methanediol(6CI,7CI,8CI,9CI)
Methanol, fluoro-(8CI,9CI)