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Donald G Truhlar - One of the best experts on this subject based on the ideXlab platform.
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multistructural anharmonicity controls the radical generation process in biofuel combustion
Journal of the American Chemical Society, 2019Co-Authors: Zhandong Wang, Lili Xing, Donald G TruhlarAbstract:The OH radical plays an important role in combustion, and isopentanol (3-methylbutan-1-ol) is a promising sustainable fuel additive and second-generation biofuel. The abstractions of H atoms from fuel molecules are key initiation steps for chain branching in combustion chemistry. In comparison with the more frequently studied ethanol, isopentanol has a longer carbon chain that allows a greater number of products, and experimental work is unavailable for the branching fractions to the various products. However, the site-dependent kinetics of isopentanol with OH radicals are usually experimentally unavailable. Alcohol oxidation by OH is also important in the atmosphere, and in the present study we calculate the rate constants and branching fractions of the hydrogen abstraction reaction of isopentanol by OH radical in a broad temperature range of 298-2400 K, covering temperatures important for atmospheric chemistry and those important for combustion. The calculations are done by multipath variational transition state theory (MP-VTST). With a combination of electronic structure calculations, we determine previously missing thermochemical data. With MP-VTST, a multidimensional tunneling approximation, multiple-structure anharmonicity, and Torsional Potential anharmonicity, we carried out more realistic rate constant calculations than can be computed by conventional single-structure harmonic transition state theory or by the empirical relations that are currently used in atmospheric and combustion modeling. The roles of various factors in determining the rates are elucidated, and we show that recrossing, tunneling, and multiple structures are all essential for accurate work. We conclude that the multiple structure anharmonicity is the most important correction to conventional transition state theory for this reaction, although recrossing effects and tunneling are by no means insignificant and the tunneling depends significantly on the path. The thermodynamic and kinetics data determined in this work are indispensable for the gas-phase degradation of alcohols in the atmosphere and for the detailed understanding and prediction of ignition mechanisms of biofuels in combustion.
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improved Potential energy surfaces of thioanisole and the effect of upper surface variations on the product distribution upon photodissociation
Principles and Practice of Constraint Programming, 2018Co-Authors: Yinan Shu, Donald G TruhlarAbstract:Abstract Electronically nonadiabatic photodissociation can be investigated in detail by experiments. This provides an opportunity to validate the current theory of electronically nonadiabatic processes, but is great challenge because the time scale of photodissociation processes can be long compared to the current capability for accurate direct dynamics simulations. To circumvent this difficulty, we have been using analytic diabatic Potential energy matrices, such that the simulation time scale can be extended to the nanosecond region without neglecting the effects of external electron correlation. In previous work, we have developed full-dimensional three-state Potential energy matrices for thioanisole photodissociation. In the current work, we extend this work in two main ways: (i) we improve the treatment of the initial Torsional Potential, and (ii) we shift the Potential energy surfaces to investigate the quantitative effect on the dissociation lifetimes and product branching ratios of changing the energy and location of the S1–S2 conical intersection.
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hydrogen shift isomerizations in the kinetics of the second oxidation mechanism of alkane combustion reactions of the hydroperoxypentylperoxy ooqooh radical
Combustion and Flame, 2018Co-Authors: Junwei Lucas Bao, Lili Xing, Zhandong Wang, Xuetao Wang, Donald G TruhlarAbstract:Abstract Hydroperoxyalkylperoxy species are important intermediates that are generated during the autoignition of transport fuels. In combustion, the fate of hydroperoxyalkylperoxy is important for the performance of advanced combustion engines, especially for autoignition. A key fate of the hydroperoxyalkylperoxy is a 1,5 H-shift, for which kinetics data are experimentally unavailable. In the present work, we study 1-hydroperoxypentan-3-yl)dioxidanyl (CH3CH2CH(OO)CH2CH2OOH) as a model compound to clarify the kinetics of 1,5 H-shift of hydroperoxyalkylperoxy species, in particular α-H isomerization and alternative competitive pathways. With a combination of electronic structure calculations, we determine previously missing thermochemical data, and with multipath variational transition state theory (MP-VTST), a multidimensional tunneling (MT) approximation, multiple-structure anharmonicity, and Torsional Potential anharmonicity, we obtained much more accurate rate constants than the ones that can computed by conventional single-structure harmonic transition state theory (TST) and than the empirically estimated rate constants that are currently used in combustion modeling. The roles of various factors in determining the rates are elucidated. The pressure-dependent rate constants for these competitive reactions are computed using system-specific quantum RRK theory. The calculated temperature range is 298–1500 K, and the pressure range is 0.01–100 atm. The accurate thermodynamic and kinetics data determined in this work are indispensable in the detailed understanding and prediction of ignition properties of hydrocarbons and alternative fuels.
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kinetics and branching fractions of the hydrogen abstraction reaction from methyl butenoates by h atoms
Physical Chemistry Chemical Physics, 2017Co-Authors: Xiaoqing You, Chung King Law, Donald G TruhlarAbstract:In order to explore the hydrogen abstraction reaction kinetics of unsaturated methyl esters by hydrogen atoms, we selected two molecules for study, in particular methyl 3-butenoate and methyl 2-butenoate, whose CC double bonds are at different locations. We first determined an accurate and efficient electronic structure method for the investigation by considering eight hydrogen abstraction reactions and comparing their barrier heights and reaction energies computed using several exchange–correlation density functionals to those obtained from CCSD(T)-F12a/jun-cc-pVTZ coupled cluster calculations. In this way, we found the M06-2X/ma-TZVP method to have the best performance with a mean unsigned deviation from the CCSD(T) calculations of 0.51 kcal mol−1. Based on quantum-chemical calculations by using the M06-2X/ma-TZVP method, we then computed rate constants for 298–2500 K by direct dynamics calculations using multi-structural canonical variational transition state theory including tunneling by the multi-dimensional small-curvature tunneling approximation (MS-CVT/SCT). The computed transmission coefficients were compared with those obtained using the zero-curvature tunneling (ZCT) and one-dimensional Eckart tunneling (ET) approximations. We employed the multi-structural Torsional method (MS-T) to include the multiple-structure and Torsional Potential anharmonic effects. The results show that the variational recrossing transmission coefficients range from 0.6 to 1.0, and the multi-structural Torsional anharmonicity introduces a factor of 0.5–2.5 into the rate constant, while the tunneling transmission coefficients obtained by SCT can be as large as 17.4 and differ considerably from those determined by the less accurate ZCT and ET approximations. In addition, independent of the location of the CC double bond, the dominant hydrogen abstraction reactions occur at the allylic sites.
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Degradation of Carbonyl Hydroperoxides in the Atmosphere and in Combustion
2017Co-Authors: Lili Xing, Feng Zhang, Junwei Lucas Bao, Zhandong Wang, Donald G TruhlarAbstract:Oxygenates with carbonyl and hydroperoxy functional groups are important intermediates that are generated during the autoxidation of organic compounds in the atmosphere and during the autoignition of transport fuels. In the troposphere, the degradation of carbonyl hydroperoxides leads to low-vapor-pressure polyfunctional species that may precipitate in clouds and fog droplets or to the formation of secondary organic aerosols (SOAs). In combustion, the fate of carbonyl hydroperoxides is important for the performance of advanced combustion engines, especially for autoignition. A key fate of the carbonyl hydroperoxides is reaction with OH radicals, for which kinetics data are experimentally unavailable. Here, we study 4-hydroperoxy-2-pentanone (CH3C(O)CH2CH(OOH)CH3) as a model compound to clarify the kinetics of OH reactions with carbonyl hydroperoxides, in particular H atom abstraction and OH addition reactions. With a combination of electronic structure calculations, we determine previously missing thermochemical data, and with multipath variational transition state theory (MP-VTST), a multidimensional tunneling (MT) approximation, multiple-structure anharmonicity, and Torsional Potential anharmonicity, we obtained much more accurate rate constants than the ones that can computed by conventional single-structure harmonic transition state theory (TST) and than the empirically estimated rate constants that are currently used in atmospheric and combustion modeling. The roles of various factors in determining the rates are elucidated. The pressure-dependent rate constants for the addition reaction are computed using system-specific quantum RRK theory. The calculated temperature range is 298–2400 K, and the pressure range is 0.01–100 atm. The accurate thermodynamic and kinetics data determined in this work are indispensable in the global modeling of SOAs in atmospheric science and in the detailed understanding and prediction of ignition properties of hydrocarbons and alternative fuels
E. M. Terentjev - One of the best experts on this subject based on the ideXlab platform.
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flii6 flij molecular motor assists with unfolding in the type iii secretion export apparatus
Scientific Reports, 2020Co-Authors: Jiri Kucera, E. M. TerentjevAbstract:: The role of rotational molecular motors of the ATP synthase class is integral to the metabolism of cells. Yet the function of FliI6-FliJ complex, a homolog of the F1 ATPase motor, within the flagellar export apparatus remains unclear. We use a simple two-state model adapted from studies of linear molecular motors to identify key features of this motor. The two states are the 'locked' ground state where the FliJ coiled coil filament experiences angular fluctuations in an asymmetric Torsional Potential, and a 'free' excited state in which FliJ undergoes rotational diffusion. Michaelis-Menten kinetics was used to treat transitions between these two states, and obtain the average angular velocity of the unloaded FliJ filament within the FliI6 stator: ωmax ≈ 9.0 rps. The motor was then studied under external counter torque conditions in order to ascertain its maximal power output: Pmax ≈ 42 kBT/s (or 102 kW/mol), and the stall torque: Gstall ≈ 3 kBT/rad (or 0.01 nN·nm/rad). Two modes of action within the flagellar export apparatus are proposed, in which the motor performs useful work either by continuously 'grinding' through the resistive environment of the export gate, or by exerting equal and opposite stall force on it. In both cases, the resistance is provided by flagellin subunits entering the flagellar export channel prior to their unfolding. We therefore propose that the function of the FliI6-FliJ complex is to lower the energy barrier, and therefore assist in unfolding of the flagellar proteins before feeding them into the transport channel.
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flii6 flij molecular motor assists with unfolding in the type iii secretion export apparatus
bioRxiv, 2020Co-Authors: Jiri Kucera, E. M. TerentjevAbstract:The role of rotational molecular motors of the ATPase class is integral to the metabolism of cells. Yet the function of FliI6-FliJ complex - a homolog of the F1 ATPase motor - within the flagellar export apparatus remains unclear. We use a simple two-state model adapted from studies of linear molecular motors to identify key features of this motor. The two states are the 9locked9 ground state where the FliJ coiled coil filament experiences fluctuations in an asymmetric Torsional Potential, and a 9free9 excited state in which FliJ undergoes rotational diffusion. Michaelis-Menten kinetics was used to treat transitions between these two states, and obtain the average angular velocity of the FliJ filament within the FliI6 stator: Wmax = 9 rps. The motor was then studied under external counter-torque conditions in order to ascertain its maximal power output: Pmax = 42 kT/s, and the stall torque: Gstall = 3 kT/rad. Two modes of action within the flagellar export apparatus are proposed, in which the motor performs useful work either by continuously 9grinding9 through the resistive environment, or by exerting equal and opposite stall force on it. In both cases, the resistance is provided by flagellin subunits entering the flagellar export channel prior to their unfolding. We therefore propose that the function of the FliI6-FliJ complex is to lower the energy barrier and therefore assist in unfolding of the flagellar proteins before feeding them into the transport channel.
Jingjing Zheng - One of the best experts on this subject based on the ideXlab platform.
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quantum thermochemistry multistructural method with Torsional anharmonicity based on a coupled Torsional Potential
Journal of Chemical Theory and Computation, 2013Co-Authors: Jingjing Zheng, Donald G TruhlarAbstract:We present a new approximation for calculating partition functions and thermodynamic functions by the multistructural method with Torsional anharmonicity (MS-T). The new approximation is based on a reference Potential with Torsional barriers obtained from a calculation that includes local Torsional coupling. By comparing to a fully coupled classical rotational-Torsional partition function evaluated as a numerical phase space integral, the method is shown to provide improved accuracy in the classical limit. Quantum effects, which are most important at low temperatures, are included based on the harmonic approximation (which can be upgraded to a quasiharmonic approximation, that is, harmonic formulas with effective frequencies). Calculations were performed for six molecules (ethanol, 1-butanol, hexane, isohexane, heptane, and isoheptane), one radical (1-pentyl radical), and the saddle point structures of a hydrogen abstraction reaction (hydroxyl plus ethanol) to illustrate the difference between the new cou...
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quantum thermochemistry multistructural method with Torsional anharmonicity based on a coupled Torsional Potential
Journal of Chemical Theory and Computation, 2013Co-Authors: Jingjing Zheng, Donald G TruhlarAbstract:We present a new approximation for calculating partition functions and thermodynamic functions by the multistructural method with Torsional anharmonicity (MS-T). The new approximation is based on a reference Potential with Torsional barriers obtained from a calculation that includes local Torsional coupling. By comparing to a fully coupled classical rotational-Torsional partition function evaluated as a numerical phase space integral, the method is shown to provide improved accuracy in the classical limit. Quantum effects, which are most important at low temperatures, are included based on the harmonic approximation (which can be upgraded to a quasiharmonic approximation, that is, harmonic formulas with effective frequencies). Calculations were performed for six molecules (ethanol, 1-butanol, hexane, isohexane, heptane, and isoheptane), one radical (1-pentyl radical), and the saddle point structures of a hydrogen abstraction reaction (hydroxyl plus ethanol) to illustrate the difference between the new coupled-Potential MS-T approximation and the original uncoupled-Potential MS-T approximation. The new method improves the agreement with experimental results of calcuated thermodynamic functions for 1-butanol, hexane, isohexane, and heptane.
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biofuel combustion energetics and kinetics of hydrogen abstraction from carbon 1 in n butanol by the hydroperoxyl radical calculated by coupled cluster and density functional theories and multistructural variational transition state theory with multidimensional tunneling
Journal of Physical Chemistry A, 2012Co-Authors: I M Alecu, Jingjing Zheng, Ewa Papajak, Donald G TruhlarAbstract:Multistructural canonical variational transition-state theory with small-curvature multidimensional tunneling (MS-CVT/SCT) is employed to calculate thermal rate constants for hydrogen-atom abstraction from carbon-1 of n-butanol by the hydroperoxyl radical over the temperature range 250-2000 K. The M08-SO hybrid meta-GGA density functional was validated against CCSD(T)-F12a explicitly correlated wave function calculations with the jul-cc-pVTZ basis set. It was then used to compute the properties of all stationary points and the energies and Hessians of a few nonstationary points along the reaction path, which were then used to generate a Potential energy surface by the multiconfiguration Shepard interpolation (MCSI) method. The internal rotations in the transition state for this reaction (like those in the reactant alcohol) are strongly coupled to each other and generate multiple stable conformations, which make important contributions to the partition functions. It is shown that neglecting to account for the multiple-structure effects and Torsional Potential anharmonicity effects that arise from the Torsional modes would lead to order-of-magnitude errors in the calculated rate constants at temperatures of interest in combustion.
Jiri Kucera - One of the best experts on this subject based on the ideXlab platform.
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flii6 flij molecular motor assists with unfolding in the type iii secretion export apparatus
Scientific Reports, 2020Co-Authors: Jiri Kucera, E. M. TerentjevAbstract:: The role of rotational molecular motors of the ATP synthase class is integral to the metabolism of cells. Yet the function of FliI6-FliJ complex, a homolog of the F1 ATPase motor, within the flagellar export apparatus remains unclear. We use a simple two-state model adapted from studies of linear molecular motors to identify key features of this motor. The two states are the 'locked' ground state where the FliJ coiled coil filament experiences angular fluctuations in an asymmetric Torsional Potential, and a 'free' excited state in which FliJ undergoes rotational diffusion. Michaelis-Menten kinetics was used to treat transitions between these two states, and obtain the average angular velocity of the unloaded FliJ filament within the FliI6 stator: ωmax ≈ 9.0 rps. The motor was then studied under external counter torque conditions in order to ascertain its maximal power output: Pmax ≈ 42 kBT/s (or 102 kW/mol), and the stall torque: Gstall ≈ 3 kBT/rad (or 0.01 nN·nm/rad). Two modes of action within the flagellar export apparatus are proposed, in which the motor performs useful work either by continuously 'grinding' through the resistive environment of the export gate, or by exerting equal and opposite stall force on it. In both cases, the resistance is provided by flagellin subunits entering the flagellar export channel prior to their unfolding. We therefore propose that the function of the FliI6-FliJ complex is to lower the energy barrier, and therefore assist in unfolding of the flagellar proteins before feeding them into the transport channel.
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flii6 flij molecular motor assists with unfolding in the type iii secretion export apparatus
bioRxiv, 2020Co-Authors: Jiri Kucera, E. M. TerentjevAbstract:The role of rotational molecular motors of the ATPase class is integral to the metabolism of cells. Yet the function of FliI6-FliJ complex - a homolog of the F1 ATPase motor - within the flagellar export apparatus remains unclear. We use a simple two-state model adapted from studies of linear molecular motors to identify key features of this motor. The two states are the 9locked9 ground state where the FliJ coiled coil filament experiences fluctuations in an asymmetric Torsional Potential, and a 9free9 excited state in which FliJ undergoes rotational diffusion. Michaelis-Menten kinetics was used to treat transitions between these two states, and obtain the average angular velocity of the FliJ filament within the FliI6 stator: Wmax = 9 rps. The motor was then studied under external counter-torque conditions in order to ascertain its maximal power output: Pmax = 42 kT/s, and the stall torque: Gstall = 3 kT/rad. Two modes of action within the flagellar export apparatus are proposed, in which the motor performs useful work either by continuously 9grinding9 through the resistive environment, or by exerting equal and opposite stall force on it. In both cases, the resistance is provided by flagellin subunits entering the flagellar export channel prior to their unfolding. We therefore propose that the function of the FliI6-FliJ complex is to lower the energy barrier and therefore assist in unfolding of the flagellar proteins before feeding them into the transport channel.
Anne B Mccoy - One of the best experts on this subject based on the ideXlab platform.
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coupling of torsion and oh stretching in tert butyl hydroperoxide i the cold and warm first oh stretching overtone spectrum
Journal of Chemical Physics, 2021Co-Authors: Anne S Hansen, Rachel M Huchmala, Emil Vogt, Mark A Boyer, Trisha Bhagde, Michael F Vansco, Casper V Jensen, Alexander Kjaersgaard, Henrik G Kjaergaard, Anne B MccoyAbstract:The infrared (IR) spectrum of tert-butyl hydroperoxide (TBHP) in the region of the first OH-stretching overtone has been observed under jet-cooled and thermal (300 K, 3 Torr) conditions at ∼7017 cm−1. The jet-cooled spectrum is recorded by IR multiphoton excitation with UV laser-induced fluorescence detection of OH radical products, while direct IR absorption is utilized under thermal conditions. Prior spectroscopic studies of TBHP and other hydroperoxides have shown that the OH-stretch and XOOH (X = H or C) torsion vibrations are strongly coupled, resulting in a double well Potential associated with the Torsional motion about the OO bond that is different for each of the OH-stretching vibrational states. A low barrier between the wells on the Torsional Potential results in tunneling split energy levels, which leads to four distinct transitions associated with excitation of the coupled OH-stretch-torsion states. In order to interpret the experimental results, two theoretical models are used that include the OH-stretch-torsion coupling in TBHP. Both methods are utilized to compute the vibrational transitions associated with the coupled OH-stretch-torsion states of TBHP, revealing the underlying transitions that compose the experimentally observed features. A comparison between theory and experiment illustrates the necessity for treatments that include OH-stretch and COOH torsion in order to unravel the spectral features observed in the first OH-stretching overtone region of TBHP.
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role of oh stretch torsion coupling and quantum yield effects in the first oh overtone spectrum of cis cis hoono
Journal of Chemical Physics, 2005Co-Authors: Anne B Mccoy, Andrew K Mollner, Joseph S Francisco, Mitchio OkumuraAbstract: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 ~90°, 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 2nuOH region. These differences are attributed to the fact that several of the experimentally accessible states do not have sufficient energy to dissociate to OH+NO2 and therefore are not detectable in an action spectrum. Scaling of the intensities of transitions to these states, assuming D0=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 Delta n=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 Delta n=+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.