Biomedical subjects
Publications and source records attributed to James A Miller.
In this article, we discuss the application of master equation methods to problems in gas phase chemical kinetics. The focus is on reactions that take place over multiple, interconnected potential wells and on the dissociation of weakly bound free radicals. These problems are of paramount importance in combustion chemistry. To illustrate specific points, we draw on our experience with reactions we have studied previously.
Ab initio calculations of portions of the C2H5O potential energy surface critical to the title reaction are presented. These calculations are based on QCISD geometries and frequencies and RQCISD(T) energies extrapolated to the complete-basis-set limit. Rate coefficients for the reaction of C2H4 with OH are calculated using this surface and the two transition-state model of Greenwald and co-workers [J. Phys. Chem. A 2005, 109, 6031] for the association of OH with C2H4. The present calculations reproduce most of the experimental data, including the temperature and pressure dependence of the rate coefficients, with only a small (0.4 kcal/mol) adjustment to the energy barrier for direct hydrogen abstraction. We confirm the importance of this channel above 800 K and find that a significant fraction of the total rate coefficient (approximately 10%) is due to the formation of vinyl alcohol above this temperature. Calculations of the vinyl alcohol channel are consistent with the recent observation of this molecule in low-pressure flames [Taatjes, C. A.; Hansen, N.; McIlroy, A.; Miller, J. A.; Senosiain, J. P.; Klippenstein, S. J.; Qi, F.; Sheng, L.; Zhang, Y.; Cool, T. A.; Wang, J.; Westmoreland, P. R.; Law, M. E.; Kasper, T.; Kohse-Höinghaus, K. Science 2005, 308, 1887] and suggest that this reaction should be included in hydrocarbon oxidation mechanisms.
The potential in the vicinity of the stationary points on the surface for the decomposition of ground-state vinoxy and acetyl radicals has been calculated using the RQCISD(T) method extrapolated to the infinite-basis set limit. Rate coefficients for the decomposition pathways of these two radicals were computed using the master equation and variational transition state theory. Agreement between our calculated rate coefficients for H + CH(2)CO <--> CH(3) + CO and experimental data is very good, without the need for empirical adjustments to the ab initio energy barriers. Multireference configuration-interaction calculations indicate two competitive channels for vinoxy decomposition, with the channel leading to H + CH(2)CO being preferred at photodissociation energies. However, at typical combustion conditions, vinoxy decomposes primarily to CO and methyl. In contrast, decomposition of acetyl shows only one decomposition channel, leading to CO and methyl. The implications of a low-lying exit channel for the calculation of theoretical rate coefficients are discussed briefly.
The isomeric composition of C(5)H(x) (x = 2-6, 8) flame species is analyzed for rich flames fueled by allene, propyne, cyclopentene, or benzene. Different isomers are identified by their known ionization energies and/or by comparison of the observed photoionization efficiencies with theoretical simulations based on calculated ionization energies and Franck-Condon factors. The experiments combine flame-sampling molecular-beam mass spectrometry with photoionization by tunable vacuum-UV synchrotron radiation. The theoretical simulations employ the rovibrational properties obtained with B3LYP/6-311++G(d,p) density functional theory and electronic energies obtained from QCISD(T) electronic structure calculations extrapolated to the complete basis set limit. For C(5)H(3), the comparison reveals the presence of both the H(2)CCCCCH (i-C(5)H(3)) and the HCCCHCCH (n-C(5)H(3)) isomer. The simulations also suggest a modest amount of cyclo-CCHCHCCH-, which is consistent with a minor signal for C(5)H(2) that is apparently due to cyclo-CCHCCCH-. For C(5)H(4), contributions from the CH(2)CCCCH(2) (1,2,3,4-pentatetraene), CH(2)CCHCCH, and CH(3)CCCCH (1,3-pentadiyne) isomers are evident, as is some contribution from CHCCH(2)CCH (1,4-pentadiyne) in the cyclopentene and benzene flames. Signal at m/z = 65 originates mainly from the cyclopentadienyl radical. For C(5)H(6), contributions from cyclopentadiene, CH(3)CCCHCH(2), CH(3)CHCHCCH, and CH(2)CHCH(2)CCH are observed. No signal is observed for C(5)H(7) species. Cyclopentene, CH(2)CHCHCHCH(3) (1,3-pentadiene), CH(3)CCCH(2)CH(3) (2-pentyne), and CH(2)CHCH(2)CHCH(2) (1,4-pentadiene) contribute to the signal at m/z = 68. Newly derived ionization energies for i- and n-C(5)H(3) (8.20 +/- 0.05 and 8.31 +/- 0.05 eV, respectively), CH(2)CCHCCH (9.22 +/- 0.05 eV), and CH(2)CHCH(2)CCH (9.95 +/- 0.05 eV) are within the error bars of the QCISD(T) calculations. The combustion chemistry of the observed C(5)H(x) intermediates and the impact on flame chemistry models are discussed.
Quantitative identification of isomers of hydrocarbon radicals in flames is critical to understanding soot formation. Isomers of C4H3 and C4H5 in flames fueled by allene, propyne, cyclopentene, or benzene are identified by comparison of the observed photoionization efficiencies with theoretical simulations based on calculated ionization energies and Franck-Condon factors. The experiments combine molecular-beam mass spectrometry (MBMS) with photoionization by tunable vacuum-ultraviolet synchrotron radiation. The theoretical simulations employ the rovibrational properties obtained with B3LYP/6-311++G(d,p) density functional theory and electronic energies obtained from QCISD(T) ab initio calculations extrapolated to the complete basis set limit. For C4H3, the comparisons reveal the presence of the resonantly stabilized CH2CCCH isomer (i-C4H3). For C4H5, contributions from the CH2CHCCH2 (i-C4H5) and some combination of the CH3CCCH2 and CH3CHCCH isomers are evident. Quantitative concentration estimates for these species are made for allene, cyclopentene, and benzene flames. Because of low Franck-Condon factors, sensitivity to n-isomers of both C4H3 and C4H5 is limited. Adiabatic ionization energies, as obtained from fits of the theoretical predictions to the experimental photoionization efficiency curves, are within the error bars of the QCISD(T) calculations. For i-C4H3 and i-C4H5, these fitted adiabatic ionization energies are (8.06 +/- 0.05) eV and (7.60 +/- 0.05) eV, respectively. The good agreement between the fitted and theoretical ionization thresholds suggests that the corresponding theoretically predicted radical heats of formation (119.1, 76.3, 78.7, and 79.1 kcal/mol at 0 K for i-C4H3, i-C4H5, CH3CCCH2, and CH3CHCCH, respectively) are also quite accurate.
Before the recent discovery that enols are intermediates in many flames, they appeared in no combustion models. Furthermore, little is known about enols' flame chemistry. Enol formation in low-pressure flames takes place in the preheat zone, and its precursors are most likely fuel species or the early products of fuel decomposition. The OH + ethene reaction has been shown to dominate ethenol production in ethene flames although this reaction has appeared insufficient to describe ethenol formation in all hydrocarbon oxidation systems. In this work, the mole fraction profiles of ethenol in several representative low-pressure flames are correlated with those of possible precursor species as a means for judging likely formation pathways in flames. These correlations and modeling suggest that the reaction of OH with ethene is in fact the dominant source of ethenol in many hydrocarbon flames, and that addition-elimination reactions of OH with other alkenes are also likely to be responsible for enol formation in flames. On this basis, enols are predicted to be minor intermediates in most flames and should be most prevalent in olefinic flames where reactions of the fuel with OH can produce enols directly.
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The nitroimidazole radiosensitizer CI-1010 ((R)-alpha-[[(2-bromoethyl)-amino]methyl]-2-nitro-1H-imidazole-1-ethanol monohydrobromide) causes selective, irreversible, retinal photoreceptor apoptosis in vivo. The mouse 661 W photoreceptor cell line was used as a neuronotypic model of CI-1010-mediated retinal degeneration. Exposure to CI-1010 for 24 h induced apoptosis in 661 W cells, as determined by ultrastructural analysis, agarose electrophoresis and analysis of TUNEL-positive nuclei. CI-1010 caused a loss of viability in 661 W cells, as measured by the reduction of MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide). A clear link was established between the onset of apoptosis and activity of caspase-3 and caspase-8, prior to poly[ADP-ribose]polymerase (PARP) cleavage. Pretreatment with caspase inhibitors, ZVAD.fmk or DEVD-CHO, prevented morphological changes in most CI-1010-treated cells. Evaluation of mitochondrial inner membrane potential (Deltapsi(m)) in live 661 W cells using the fluorescent dye, tetramethylrhodamine methyl ester revealed retention of (Deltapsi(m)) until after caspase activation. Absence of cytochrome c in the cytoplasm in treated cells further supports the hypothesis of a mitochondrial-independent mechanism of cell death. Significant increase in DNA crosslinks observed in 661 W cells correlates with induction and phosphorylation of p53 at multiple serine sites. Cell cycle analysis of 661 W cells reveals a G(2) arrest in response to CI-1010-induced DNA damage and neuronal cell death. Increased protein expression of Bax, Fas, and FasL, concomitant to the loss of Bcl-xL in treated 661 W cells may be modulated by p53. This study evaluates in vitro mechanisms of CI-1010-induced cell death in photoreceptors and provides evidence in support of a p53-linked activation of caspase-3 in response to DNA damage caused by CI-1010.
The potential energy surface for the reaction between OH and acetylene has been calculated using the RQCISD(T) method and extrapolated to the complete basis-set limit. Rate coefficients were determined for a wide range of temperatures and pressures, based on this surface and the solution of the one-dimensional and two-dimensional master equations. With a small adjustment to the association energy barrier (1.1 kcal/mol), agreement with experiments is good, considering the discrepancies in such data. The rate coefficient for direct hydrogen abstraction is significantly smaller than that commonly used in combustion models. Also in contrast to previous models, ketene + H is found to be the main product at normal combustion conditions. At low temperatures and high pressures, stabilization of the C2H2OH adduct is the dominant process. Rate coefficient expressions for use in modeling are provided.
In this article, we discuss in detail the addition of hydrogen atoms to diacetylene and the reverse dissociation reactions, H + C(4)H(2)<==>i-C(4)H(3) (R1) and H + C(4)H(2)<==>n-C(4)H(3) (R2). The theory utilizes high-level electronic structure methodology to characterize the potential energy surface, Rice-Ramsperger-Kassel-Marcus (RRKM) theory to calculate microcanonical/J-resolved rate coefficients, and a two-dimensional master-equation approach to extract phenomenological (thermal) rate coefficients. Comparison is made with experimental results where they are available. The rate coefficients k1(T, p) and k2(T, p) are cast in forms that can be used in chemical kinetic modeling. In addition, we predict values of the heats of formation of i-C(4)H(3) and n-C(4)H(3) and discuss their importance in flame chemistry. Our basis-set extrapolated, quadratic-configuration-interaction with single and double excitations (and triple excitations added perturbatively), QCISD(T), predictions of these heats of formation at 298 K are 130.8 kcal/mol for n-C(4)H(3) and 119.3 kcal/mol for the i-isomer; multireference CI calculations with a nine-electron, nine-orbital, complete-active-space (CAS) reference wavefunction give just slightly larger values for these parameters. Our results are in good agreement with the recent focal-point analysis of Wheeler et al. (J. Chem. Phys. 2004, 121, 8800-8813), but they differ substantially for DeltaH0(f 298)(n-C(4)H(3)) with the earlier diffusion Monte Carlo predictions of Krokidis et al. (Int. J. Chem. Kinet.2001, 33, 808-820).
Models for chemical mechanisms of hydrocarbon oxidation rely on spectrometric identification of molecular structures in flames. Carbonyl (keto) compounds are well-established combustion intermediates. However, their less-stable enol tautomers, bearing OH groups adjacent to carbon-carbon double bonds, are not included in standard models. We observed substantial quantities of two-, three-, and four-carbon enols by photoionization mass spectrometry of flames burning representative compounds from modern fuel blends. Concentration profiles demonstrate that enol flame chemistry cannot be accounted for purely by keto-enol tautomerization. Currently accepted hydrocarbon oxidation mechanisms will likely require revision to explain the formation and reactivity of these unexpected compounds.
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