Calculation of kinetic rate constants from thermodynamic data

NASA Technical Reports Server (NTRS)

Marek, C. John

1995-01-01

A new scheme for relating the absolute value for the kinetic rate constant k to the thermodynamic constant Kp is developed for gases. In this report the forward and reverse rate constants are individually related to the thermodynamic data. The kinetic rate constants computed from thermodynamics compare well with the current kinetic rate constants. This method is self consistent and does not have extensive rules. It is first demonstrated and calibrated by computing the HBr reaction from H2 and Br2. This method then is used on other reactions.

Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water

PubMed Central

Juraszek, Jarek; Bolhuis, Peter G.

2008-01-01

We report rate constant calculations and a reaction coordinate analysis of the rate-limiting folding and unfolding process of the Trp-cage mini-protein in explicit solvent using transition interface sampling. Previous transition path sampling simulations revealed that in this (un)folding process the protein maintains its compact configuration, while a (de)increase of secondary structure is observed. The calculated folding rate agrees reasonably with experiment, while the unfolding rate is 10 times higher. We discuss possible origins for this mismatch. We recomputed the rates with the forward flux sampling method, and found a discrepancy of four orders of magnitude, probably caused by the method's higher sensitivity to the choice of order parameter with respect to transition interface sampling. Finally, we used the previously computed transition path-sampling ensemble to screen combinations of many order parameters for the best model of the reaction coordinate by employing likelihood maximization. We found that a combination of the root mean-square deviation of the helix and of the entire protein was, of the set of tried order parameters, the one that best describes the reaction coordination. PMID:18676648

Rate constant for reaction of vitamin C with protein radicals in γ-irradiated aqueous albumin solution at 295 K

NASA Astrophysics Data System (ADS)

Miyazaki, Tetsuo; Yoshimura, Toru; Mita, Kazuya; Suzuki, Keiji; Watanabe, Masami

1995-02-01

When an aqueous solution of albumin (0.1 kg dm -3) is irradiated by γ-rays at 295 K, albumin radicals with a long lifetime are observed by ESR. The reaction of vitamin C with the albumin radicals has been studied at 295 K in the albumin solution, which is considered as a model of cells. The rate constant for the reaction of vitamin C with the albumin radicals was measured as 0.014 dm 3 mol -1 s -1, which is much smaller than the reported rate constants (10 6-10 10 dm 3 mol -1 s -1) for the reaction of vitamin C with radicals in a dilute aqueous solution. The small rate constant for the reaction of vitamin C is ascribed to the reaction in polymer coils in the albumin solution, since vitamin C and albumin radicals diffuse very slowly in the coils.

Application of an Artificial Neural Network to the Prediction of OH Radical Reaction Rate Constants for Evaluating Global Warming Potential.

PubMed

Allison, Thomas C

2016-03-03

Rate constants for reactions of chemical compounds with hydroxyl radical are a key quantity used in evaluating the global warming potential of a substance. Experimental determination of these rate constants is essential, but it can also be difficult and time-consuming to produce. High-level quantum chemistry predictions of the rate constant can suffer from the same issues. Therefore, it is valuable to devise estimation schemes that can give reasonable results on a variety of chemical compounds. In this article, the construction and training of an artificial neural network (ANN) for the prediction of rate constants at 298 K for reactions of hydroxyl radical with a diverse set of molecules is described. Input to the ANN consists of counts of the chemical bonds and bends present in the target molecule. The ANN is trained using 792 (•)OH reaction rate constants taken from the NIST Chemical Kinetics Database. The mean unsigned percent error (MUPE) for the training set is 12%, and the MUPE of the testing set is 51%. It is shown that the present methodology yields rate constants of reasonable accuracy for a diverse set of inputs. The results are compared to high-quality literature values and to another estimation scheme. This ANN methodology is expected to be of use in a wide range of applications for which (•)OH reaction rate constants are required. The model uses only information that can be gathered from a 2D representation of the molecule, making the present approach particularly appealing, especially for screening applications.

Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials

NASA Astrophysics Data System (ADS)

Cannon, William R.; Baker, Scott E.

2017-10-01

Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in scope and application by the fact that the determination of enzyme rate constants is laborious and low throughput. We present a statistical thermodynamic formulation of the law of mass action for coupled reactions at both steady states and non-stationary states. The formulation uses chemical potentials instead of rate constants. When used to model deterministic systems, the method corresponds to a rescaling of the time dependent reactions in such a way that steady states can be reached on the same time scale but with significantly fewer computational steps. The relationships between reaction affinities, free energy changes and generalized detailed balance are central to the discussion. The significance for applications in systems biology are discussed as is the concept and assumption of maximum entropy production rate as a biological principle that links thermodynamics to natural selection.

Kinetic Analysis for the Multistep Profiles of Organic Reactions: Significance of the Conformational Entropy on the Rate Constants of the Claisen Rearrangement.

PubMed

Sumiya, Yosuke; Nagahata, Yutaka; Komatsuzaki, Tamiki; Taketsugu, Tetsuya; Maeda, Satoshi

2015-12-03

The significance of kinetic analysis as a tool for understanding the reactivity and selectivity of organic reactions has recently been recognized. However, conventional simulation approaches that solve rate equations numerically are not amenable to multistep reaction profiles consisting of fast and slow elementary steps. Herein, we present an efficient and robust approach for evaluating the overall rate constants of multistep reactions via the recursive contraction of the rate equations to give the overall rate constants for the products and byproducts. This new method was applied to the Claisen rearrangement of allyl vinyl ether, as well as a substituted allyl vinyl ether. Notably, the profiles of these reactions contained 23 and 84 local minima, and 66 and 278 transition states, respectively. The overall rate constant for the Claisen rearrangement of allyl vinyl ether was consistent with the experimental value. The selectivity of the Claisen rearrangement reaction has also been assessed using a substituted allyl vinyl ether. The results of this study showed that the conformational entropy in these flexible chain molecules had a substantial impact on the overall rate constants. This new method could therefore be used to estimate the overall rate constants of various other organic reactions involving flexible molecules.

Rate constants for the reactions of OH with CH3Cl, CH2Cl2, CHCl3, and CH3Br

NASA Technical Reports Server (NTRS)

Hsu, K.-J.; Demore, W. B.

1994-01-01

Rate constants for the reactions of OH with CH3Cl, CH2Cl2, CHCl3, and CH3Br have been measured by a relative rate technique in which the reaction rate of each compound was compared to that of HFC-152a (CH3CHF2) and (for CH2Cl2) HFC-161 (CH3CH2F). Using absolute rate constants for HFC-152a and HFC-161, which we have determined relative to those for CH4, CH3CCl3, and C2H6, temperature dependent rate constants of both compounds were derived. The derived rate constant for CH3Br is in good agreement with recent absolute measurements. However, for the chloromethanes all the rate constants are lower at atmospheric temperatures than previously reported, especially for CH2Cl2 where the present rate constant is about a factor of 1.6 below the JPL 92-20 value. The new rate constant appears to resolve a discrepancy between the observed atmospheric concentrations and those calculated from the previous rate constant and estimated release rates.

Absolute rate constants for the reaction of OH with cyclopentane and cycloheptane from 233 to 351 K.

PubMed

Gennaco, Michael A; Huang, Yi-wen; Hannun, Reem A; Dransfield, Timothy J

2012-12-27

Absolute rate constant measurements for the reactions of OH with cyclopentane and cycloheptane in the gas phase in 6-8 Torr of nitrogen from 233 to 351 K in the Harvard University High-Pressure Flow System (HPFS) are reported. Hydroxyl concentrations were measured using laser-induced fluorescence, and alkane concentrations were measured using Fourier transform infrared spectroscopy. Results were fit to a modified Arrhenius equation based on transition state theory (ignoring tunneling): k(T) = B e(-E(a)/T)/T(1 - e(-1.44ν(1)/T))(2)(1 - e(-1.44ν(2)/T)), with ν(1) and ν(2) bending frequencies set to 280 and 500 cm(-1) . Results were as follows for E(a) (K) and k (298) (10(-12) cm(3) s(-1)): cyclopentane, 460 ± 32, 4.85; cycloheptane, 319 ± 36, 9.84. This work represents the second absolute temperature-dependent rate constant measurement reported for cycloheptane, and the third absolute temperature-dependent rate constant measurement reported near room temperature for the reaction of OH and cyclopentane. For the title reactions, the reaction barriers reported here are in agreement with the reaction barrier previously reported for cyclohexane and considerably higher than the barrier previously reported for cyclo-octane, a result that is not predicted by our current understanding of hydrocarbon reactivity.

A simple method relating specific rate constants k(E,J) and Thermally averaged rate constants k(infinity)(T) of unimolecular bond fission and the reverse barrierless association reactions.

PubMed

Troe, J; Ushakov, V G

2006-06-01

This work describes a simple method linking specific rate constants k(E,J) of bond fission reactions AB --> A + B with thermally averaged capture rate constants k(cap)(T) of the reverse barrierless combination reactions A + B --> AB (or the corresponding high-pressure dissociation or recombination rate constants k(infinity)(T)). Practical applications are given for ionic and neutral reaction systems. The method, in the first stage, requires a phase-space theoretical treatment with the most realistic minimum energy path potential available, either from reduced dimensionality ab initio or from model calculations of the potential, providing the centrifugal barriers E(0)(J). The effects of the anisotropy of the potential afterward are expressed in terms of specific and thermal rigidity factors f(rigid)(E,J) and f(rigid)(T), respectively. Simple relationships provide a link between f(rigid)(E,J) and f(rigid)(T) where J is an average value of J related to J(max)(E), i.e., the maximum J value compatible with E > or = E0(J), and f(rigid)(E,J) applies to the transitional modes. Methods for constructing f(rigid)(E,J) from f(rigid)(E,J) are also described. The derived relationships are adaptable and can be used on that level of information which is available either from more detailed theoretical calculations or from limited experimental information on specific or thermally averaged rate constants. The examples used for illustration are the systems C6H6+ <==> C6H5+ + H, C8H10+ --> C7H7+ + CH3, n-C9H12+ <==> C7H7+ + C2H5, n-C10H14+ <==> C7H7+ + C3H7, HO2 <==> H + O2, HO2 <==> HO + O, and H2O2 <==> 2HO.

Variational RRKM theory calculation of thermal rate constant for carbon—hydrogen bond fission reaction of nitro benzene

NASA Astrophysics Data System (ADS)

Manesh, Afshin Taghva; Heidarnezhad, Zabi alah; Masnabadi, Nasrin

2013-07-01

The present work provides quantitative results for the rate of unimolecular carbon-hydrogen bond fission reaction of benzene and nitro benzene at elevated temperatures up to 2000 K. The potential energy surface for each C-H (in the ortho, meta, and para sites) bond fission reaction of nitro benzene was investigated by ab initio calculations. The geometry and vibrational frequencies of the species involved in this process were optimized at the MP2 level of theory, using the cc-pvdz basis set. Since C-H bond fission channel is barrier less reaction, we have used variational RRKM theory to predict rate constants. By means of calculated rate constant at the different temperatures, the activation energy and exponential factor were determined. The Arrhenius expression for C-H bond fission reaction of nitro benzene on the ortho, meta and para sites are k( T) = 2.1 × 1017exp(-56575.98/ T), k( T) = 2.1 × 1017exp(-57587.45/ T), and k( T) = 3.3 × 1016exp(-57594.79/ T) respectively. The Arrhenius expression for C-H bond fission reaction of benzene is k( T) = 2 × 1018exp(-59343.48.18/ T). The effect of NO2 group, location of hydrogen atoms on the substituted benzene ring, reaction degeneracy, benzene ring resonance and tunneling effect on the rate expression have been discussed.

Rate Constants and Activation Energies for Gas-Phase Reactions of Three Cyclic Volatile Methyl Siloxanes with the Hydroxyl Radical.

PubMed

Safron, Andreas; Strandell, Michael; Kierkegaard, Amelie; Macleod, Matthew

2015-07-01

Reaction with hydroxyl radicals (OH) is the major pathway for removal of cyclic volatile methyl siloxanes (cVMS) from air. We present new measurements of second-order rate constants for reactions of the cVMS octamethylcyclotetrasiloxane (D 4 ), decamethylcyclopentasiloxane (D 5 ), and dodecamethylcyclohexasiloxane (D 6 ) with OH determined at temperatures between 313 and 353 K. Our measurements were made using the method of relative rates with cyclohexane as a reference substance and were conducted in a 140-mL gas-phase reaction chamber with online mass spectrometry analysis. When extrapolated to 298 K, our measured reaction rate constants of D 4 and D 5 with the OH radical are 1.9 × 10 -12 (95% confidence interval (CI): (1.7-2.2) × 10 -12 ) and 2.6 × 10 -12 (CI: (2.3-2.9) × 10 -12 ) cm 3 molecule -1 s -1 , respectively, which are 1.9× and 1.7× faster than previous measurements. Our measured rate constant for D 6 is 2.8 × 10 -12 (CI: (2.5-3.2) × 10 -12 ) cm 3 molecule -1 s -1 and to our knowledge there are no comparable laboratory measurements in the literature. Reaction rates for D 5 were 33% higher than for D 4 (CI: 30-37%), whereas the rates for D 6 were only 8% higher than for D 5 (CI: 5-10%). The activation energies of the reactions of D 4 , D 5 , and D 6 with OH were not statistically different and had a value of 4300 ± 2800 J/mol.

Applying constraints on model-based methods: Estimation of rate constants in a second order consecutive reaction

NASA Astrophysics Data System (ADS)

Kompany-Zareh, Mohsen; Khoshkam, Maryam

2013-02-01

This paper describes estimation of reaction rate constants and pure ultraviolet/visible (UV-vis) spectra of the component involved in a second order consecutive reaction between Ortho-Amino benzoeic acid (o-ABA) and Diazoniom ions (DIAZO), with one intermediate. In the described system, o-ABA was not absorbing in the visible region of interest and thus, closure rank deficiency problem did not exist. Concentration profiles were determined by solving differential equations of the corresponding kinetic model. In that sense, three types of model-based procedures were applied to estimate the rate constants of the kinetic system, according to Levenberg/Marquardt (NGL/M) algorithm. Original data-based, Score-based and concentration-based objective functions were included in these nonlinear fitting procedures. Results showed that when there is error in initial concentrations, accuracy of estimated rate constants strongly depends on the type of applied objective function in fitting procedure. Moreover, flexibility in application of different constraints and optimization of the initial concentrations estimation during the fitting procedure were investigated. Results showed a considerable decrease in ambiguity of obtained parameters by applying appropriate constraints and adjustable initial concentrations of reagents.

Perturbation theory in the catalytic rate constant of the Henri-Michaelis-Menten enzymatic reaction.

PubMed

Bakalis, Evangelos; Kosmas, Marios; Papamichael, Emmanouel M

2012-11-01

The Henry-Michaelis-Menten (HMM) mechanism of enzymatic reaction is studied by means of perturbation theory in the reaction rate constant k (2) of product formation. We present analytical solutions that provide the concentrations of the enzyme (E), the substrate (S), as well as those of the enzyme-substrate complex (C), and the product (P) as functions of time. For k (2) small compared to k (-1), we properly describe the entire enzymatic activity from the beginning of the reaction up to longer times without imposing extra conditions on the initial concentrations E ( o ) and S ( o ), which can be comparable or much different.

Effects of Water Molecule on CO Oxidation by OH: Reaction Pathways, Kinetic Barriers, and Rate Constants.

PubMed

Zhang, Linyao; Yang, Li; Zhao, Yijun; Zhang, Jiaxu; Feng, Dongdong; Sun, Shaozeng

2017-07-06

The water dilute oxy-fuel combustion is a clean combustion technology for near-zero emission power; and the presence of water molecule could have both kinetic and dynamic effects on combustion reactions. The reaction OH + CO → CO 2 + H, one of the most important elementary reactions, has been investigated by extensive electronic structure calculations. And the effects of a single water molecule on CO oxidation have been studied by considering the preformed OH(H 2 O) complex reacts with CO. The results show little change in the reaction pathways, but the additional water molecule actually increases the vibrationally adiabatic energy barriers (V a G ). Further thermal rate constant calculations in the temperature range of 200 to 2000 K demonstrate that the total low-pressure limit rate constant for the water assisted OH(H 2 O) + CO → CO 2 + H 2 O + H reaction is 1-2 orders lower than that of the water unassisted one, which is consistent with the change of V a G . Therefore, the hydrated radical OH(H 2 O) would actually slow down the oxidation of CO. Meanwhile, comparisons show that the M06-2X/aug-cc-pVDZ method gives a much better estimation in energy and thus is recommended to be employed for direct dynamics simulations.

Rate Constants and Activation Energies for Gas‐Phase Reactions of Three Cyclic Volatile Methyl Siloxanes with the Hydroxyl Radical

PubMed Central

Safron, Andreas; Strandell, Michael; Kierkegaard, Amelie

2015-01-01

ABSTRACT Reaction with hydroxyl radicals (OH) is the major pathway for removal of cyclic volatile methyl siloxanes (cVMS) from air. We present new measurements of second‐order rate constants for reactions of the cVMS octamethylcyclotetrasiloxane (D4), decamethylcyclopentasiloxane (D5), and dodecamethylcyclohexasiloxane (D6) with OH determined at temperatures between 313 and 353 K. Our measurements were made using the method of relative rates with cyclohexane as a reference substance and were conducted in a 140‐mL gas‐phase reaction chamber with online mass spectrometry analysis. When extrapolated to 298 K, our measured reaction rate constants of D4 and D5 with the OH radical are 1.9 × 10−12 (95% confidence interval (CI): (1.7–2.2) × 10−12) and 2.6 × 10−12 (CI: (2.3–2.9) × 10−12) cm3 molecule−1 s−1, respectively, which are 1.9× and 1.7× faster than previous measurements. Our measured rate constant for D6 is 2.8 × 10−12 (CI: (2.5–3.2) × 10−12) cm3 molecule−1 s−1 and to our knowledge there are no comparable laboratory measurements in the literature. Reaction rates for D5 were 33% higher than for D4 (CI: 30–37%), whereas the rates for D6 were only 8% higher than for D5 (CI: 5–10%). The activation energies of the reactions of D4, D5, and D6 with OH were not statistically different and had a value of 4300 ± 2800 J/mol. PMID:27708500

HO + CO reaction rates and H/D kinetic isotope effects: master equation models with ab initio SCTST rate constants.

PubMed

Weston, Ralph E; Nguyen, Thanh Lam; Stanton, John F; Barker, John R

2013-02-07

Ab initio microcanonical rate constants were computed using Semi-Classical Transition State Theory (SCTST) and used in two master equation formulations (1D, depending on active energy with centrifugal corrections, and 2D, depending on total energy and angular momentum) to compute temperature-dependent rate constants for the title reactions using a potential energy surface obtained by sophisticated ab initio calculations. The 2D master equation was used at the P = 0 and P = ∞ limits, while the 1D master equation with centrifugal corrections and an empirical energy transfer parameter could be used over the entire pressure range. Rate constants were computed for 75 K ≤ T ≤ 2500 K and 0 ≤ [He] ≤ 10(23) cm(-3). For all temperatures and pressures important for combustion and for the terrestrial atmosphere, the agreement with the experimental rate constants is very good, but at very high pressures and T ≤ 200 K, the theoretical rate constants are significantly smaller than the experimental values. This effect is possibly due to the presence in the experiments of dimers and prereactive complexes, which were not included in the model calculations. The computed H/D kinetic isotope effects are in acceptable agreement with experimental data, which show considerable scatter. Overall, the agreement between experimental and theoretical H/D kinetic isotope effects is much better than in previous work, and an assumption of non-RRKM behavior does not appear to be needed to reproduce experimental observations.

Photochemical parameters of atmospheric source gases: accurate determination of OH reaction rate constants over atmospheric temperatures, UV and IR absorption spectra

NASA Astrophysics Data System (ADS)

Orkin, V. L.; Khamaganov, V. G.; Martynova, L. E.; Kurylo, M. J.

2012-12-01

The emissions of halogenated (Cl, Br containing) organics of both natural and anthropogenic origin contribute to the balance of and changes in the stratospheric ozone concentration. The associated chemical cycles are initiated by the photochemical decomposition of the portion of source gases that reaches the stratosphere. Reactions with hydroxyl radicals and photolysis are the main processes dictating the compound lifetime in the troposphere and release of active halogen in the stratosphere for a majority of halogen source gases. Therefore, the accuracy of photochemical data is of primary importance for the purpose of comprehensive atmospheric modeling and for simplified kinetic estimations of global impacts on the atmosphere, such as in ozone depletion (i.e., the Ozone Depletion Potential, ODP) and climate change (i.e., the Global Warming Potential, GWP). The sources of critically evaluated photochemical data for atmospheric modeling, NASA/JPL Publications and IUPAC Publications, recommend uncertainties within 10%-60% for the majority of OH reaction rate constants with only a few cases where uncertainties lie at the low end of this range. These uncertainties can be somewhat conservative because evaluations are based on the data from various laboratories obtained during the last few decades. Nevertheless, even the authors of the original experimental works rarely estimate the total combined uncertainties of the published OH reaction rate constants to be less than ca. 10%. Thus, uncertainties in the photochemical properties of potential and current atmospheric trace gases obtained under controlled laboratory conditions still may constitute a major source of uncertainty in estimating the compound's environmental impact. One of the purposes of the presentation is to illustrate the potential for obtaining accurate laboratory measurements of the OH reaction rate constant over the temperature range of atmospheric interest. A detailed inventory of accountable sources of

Discovery of a Significant Acetone•Hydroperoxy Adduct Chaperone Effect and Its Impact on the Determination of Room Temperature Rate Constants for Acetonylperoxy/Hydroperoxy Self-Reactions and Cross Reaction Via Infrared Kinetic Spectroscopy.

NASA Astrophysics Data System (ADS)

Grieman, F. J.; Hui, A. O.; Okumura, M.; Sander, S. P.

2017-12-01

In order to model the upper troposphere/lower stratosphere in regions containing acetone properly, the kinetics of the acetonylperoxy/hydroperoxy self-reactions and cross reaction have been studied over a wide temperature range using Infrared Kinetic Spectroscopy. We report here the determination of different rate constants for the acetonylperoxy chemistry that we obtained at 298 K compared to currently accepted values. A considerable increase in the observed HO2 self-reaction rate constant due to rate enhancement via the chaperone effect from the reaction between HO2 and the (CH3)2CO•HO2 hydrogen-bonded adduct, even at room temperature, was discovered that was previously ignored. Correct determination of the acetonylperoxy and hydroperoxy kinetics must include this dependence of the HO2 self-reaction rate on acetone concentration. Via excimer laser flash photolysis to create the radical reactants, HO2 absorption was monitored in the infrared by diode laser wavelength modulation detection simultaneously with CH3C(O)CH2O2absorption monitored in the ultraviolet at 300 nm as a function of time. Resulting decay curves were fit concurrently first over a short time scale to obtain the rate constants minimizing subsequent product reactions. Modeling/fitting with a complete reaction scheme was then performed to refine the rate constants and test their veracity. Experiments were carried out over a variety of concentrations of acetone and methanol. Although no effect due to methanol concentration was found at room temperature, the rate constant for the hydroperoxy self-reaction was found to increase linearly with acetone concentration which is interpreted as the adduct being formed and resulting in a chaperone mechanism that enhances the self-reaction rate: (CH3)2CO·HO2 + HO2 → H2O2 + O2 + (CH3)2CO Including this effect, the resulting room temperature rate constants for the cross reaction and the acetonylperoxy self-reaction were found to be 2-3 times smaller than

Absolute rate constant for the reaction of atomic chlorine with hydrogen peroxide vapor over the temperature range 265-400 K

NASA Technical Reports Server (NTRS)

Michael, J. V.; Whytock, D. A.; Lee, J. H.; Payne, W. A.; Stief, L. J.

1977-01-01

Rate constants for the reaction of atomic chlorine with hydrogen peroxide were measured from 265-400 K using the flash photolysis-resonance fluorescence technique. Analytical techniques were developed to measure H2O2 under reaction conditions. Due to ambiguity in the interpretation of the analytical results, the data combine to give two equally acceptable representations of the temperature dependence. The results are compared to previous work at 298 K and are theoretically discussed in terms of the mechanism of the reaction. Additional experiments on the H + H2O2 reaction at 298 and 359 K are compared with earlier results from this laboratory and give a slightly revised bimolecular rate constant.

The reaction H + C4H2 - Absolute rate constant measurement and implication for atmospheric modeling of Titan

NASA Technical Reports Server (NTRS)

Nava, D. F.; Mitchell, M. B.; Stief, L. J.

1986-01-01

The absolute rate constant for the reaction H + C4H2 has been measured over the temperature (T) interval 210-423 K, using the technique of flash photolysis-resonance fluorescence. At each of the five temperatures employed, the results were independent of variations in C4H2 concentration, total pressure of Ar or N2, and flash intensity (i.e., the initial H concentration). The rate constant, k, was found to be equal to 1.39 x 10 to the -10th exp (-1184/T) cu cm/s, with an error of one standard deviation. The Arrhenius parameters at the high pressure limit determined here for the H + C4H2 reaction are consistent with those for the corresponding reactions of H with C2H2 and C3H4. Implications of the kinetic carbon chemistry results, particularly those at low temperature, are considered for models of the atmospheric carbon chemistry of Titan. The rate of this reaction, relative to that of the analogous, but slower, reaction of H + C2H2, appears to make H + C4H2 a very feasible reaction pathway for effective conversion of H atoms to molecular hydrogen in the stratosphere of Titan.

Rate constants of chemical reactions from semiclassical transition state theory in full and one dimension.

PubMed

Greene, Samuel M; Shan, Xiao; Clary, David C

2016-06-28

Semiclassical Transition State Theory (SCTST), a method for calculating rate constants of chemical reactions, offers gains in computational efficiency relative to more accurate quantum scattering methods. In full-dimensional (FD) SCTST, reaction probabilities are calculated from third and fourth potential derivatives along all vibrational degrees of freedom. However, the computational cost of FD SCTST scales unfavorably with system size, which prohibits its application to larger systems. In this study, the accuracy and efficiency of 1-D SCTST, in which only third and fourth derivatives along the reaction mode are used, are investigated in comparison to those of FD SCTST. Potential derivatives are obtained from numerical ab initio Hessian matrix calculations at the MP2/cc-pVTZ level of theory, and Richardson extrapolation is applied to improve the accuracy of these derivatives. Reaction barriers are calculated at the CCSD(T)/cc-pVTZ level. Results from FD SCTST agree with results from previous theoretical and experimental studies when Richardson extrapolation is applied. Results from our implementation of 1-D SCTST, which uses only 4 single-point MP2/cc-pVTZ energy calculations in addition to those for conventional TST, agree with FD results to within a factor of 5 at 250 K. This degree of agreement and the efficiency of the 1-D method suggest its potential as a means of approximating rate constants for systems too large for existing quantum scattering methods.

The chemistry of bromine in the stratosphere: Influence of a new rate constant for the reaction BrO + HO2

NASA Technical Reports Server (NTRS)

Pirre, Michel; Marceau, Francois J.; Lebras, Georges; Maguin, Francoise; Poulet, Gille; Ramaroson, Radiela

1994-01-01

The impact of new laboratory data for the reaction BrO + HO2 yields HOBr + O2 in the depletion of global stratospheric ozone has been estimated using a one-dimensional photochemical model taking into account the heterogeneous reaction on sulphate aerosols which converts N2O5 into HNO3. Assuring an aerosol loading 2 times as large as the 'background' and a reaction probability of 0.1 for the above heterogeneous reaction, the 6 fold increase in the measured rate constant for the reaction of BrO with HO2 increases the computed depletion of global ozone produced by 20 ppt of total bromine from 2.01 percent to 2.36 percent. The use of the higher rate constant increases the HOBr mixing ratio and makes the bromine partitioning and the ozone depletion very sensitive to the branching ratio of the potential channel forming HBr in the BrO + HO2 reaction.

Temperature-Dependent Rate Constants and Substituent Effects for the Reactions of Hydroxyl Radicals With Three Partially Fluorinated Ethers

NASA Technical Reports Server (NTRS)

Hsu, K.-J.; DeMore, W. B.

1995-01-01

Rate constants and temperature dependencies for the reactions of OH with CF3OCH3 (HFOC-143a), CF2HOCF2H (HFOC-134), and CF3OCF2H (HFOC-125) were studied using a relative rate technique in the temperature range 298-393 K. The following absolute rate constants were derived: HFOC-143a, 1.9E-12 exp(-1555/T); HFOC-134, 1.9E-12 exp(-2006/T); HFOC-125, 4.7E-13 exp(-2095/T). Units are cm(exp 3)molecule(exp -1) s(exp -1). Substituent effects on OH abstraction rate constants are discussed, and it is shown that the CF3O group has an effect on the OH rate constants similar to that of a fluorine atom. The effects are related to changes in the C-H bond energies of the reactants (and thereby the activation energies) rather than changes in the preexponential factors. On the basis of a correlation of rate constants with bond energies, the respective D(C-H) bond strengths in the three ethers are found to be 102, 104, and 106 kcal/mol, with an uncertainty of about 1 kcal/mol.

Quantum calculations of the rate constant for the O(3P)+HCl reaction on new ab initio 3A″ and 3A' surfaces

NASA Astrophysics Data System (ADS)

Xie, Tiao; Bowman, Joel M.; Peterson, K. A.; Ramachandran, B.

2003-11-01

We report the thermal rate constant of the O(3P)+HCl→OH+Cl reaction calculated from 200 to 3200 K, using new fits to extensive ab initio calculations [B. Ramachandran and K. A. Peterson, J. Chem. Phys. 119, 9590 (2003), preceding paper]. The rate constants are obtained for both the 3A″ and 3A' surfaces using exact quantum reactive scattering calculations for selected values of the total angular momentum and the J-shifting approximation for both the 3A″ and 3A' surfaces. The results are compared with the ICVT/μOMT rate constants calculated by the POLYRATE program and all available experimental data. Other related high-energy reaction channels are also studied qualitatively for their contribution to the total thermal rate constant at high temperature.

Rate constants and temperature dependences for the reactions of hydroxyl radical with several halogenated methanes, ethanes, and propanes by relative rate measurements

NASA Technical Reports Server (NTRS)

Hsu, K.-J.; DeMore, W. B.

1995-01-01

Rate constants of 15 OH reactions with halogen-substituted alkanes, C1 to C3, were studied using a relative rate technique in the temperature range 283-403 K. Compounds studied were CHF2Cl (22), CHF2Br (22B), CH3F (41), CH2F2 (32), CHF3 (23), CHClFCCl2F (122a), CHCl2CF3 (123), CHClFCF3 (124), CH3CF3 (143a), CH3CH2F (161), CF3CHFCF3 (227ea), CF3CH2CF3 (236fa), CF3CHFCHF2 (236ea), and CHF2CF2CH2F (245ca). Using CH4, CH3CCl3, CF3CF2H, and C2H6 as primary reference standards (JPL 92-20 rate constants), absolute rate constants are derived. Results are in good agreement with previous experimental results for six of the compounds studied, including CHF2Cl, CHF2Br, CH2F2, CH3CF3, CHFClCFCl2, and CF3CHFCF3. For the remainder the relative rate constants are lower than those derived from experiments in which OH loss was used to measure the reaction rate. Comparisons of the derived Arrhenius A factors with previous literature transition-state calculations show order of magnitude agreement in most cases. However, the experimental A factors show a much closer proportionality to the number of H atoms in the molecule than is evident from the transition state calculations. For most of the compounds studied, an A factor of (8 +/- 3)E-13 cm(exp 3)/(molecule s) per C-H bond is observed. A new measurement of the ratio k(CH3CCl3)/k(CH4) is reported that is in good agreement with previous data.

Pulsed EPR measurements on reaction rate constants for addition of photo-generated radicals to double bonds of diethyl fumarate and diethyl maleate

NASA Astrophysics Data System (ADS)

Takahashi, Hirona; Hagiwara, Kenta; Kawai, Akio

2016-11-01

Addition reaction of photo-generated radicals to double bonds of diethyl fumarate (deF) and diethyl maleate (deM), which are geometrical isomers, was studied by means of time-resolved- (TR-) and pulsed-electron paramagnetic resonance (EPR). Analysis of TR-EPR spectra indicates that adduct radicals from deF and deM should have the same structure. The double bonds of these monomers are converted to single ones by addition reaction, which allows hindered internal rotation to give the same structure of adduct radical. The rate constants for addition reaction of photo-generated radicals were determined by Stern-Volmer analysis of the decay time of electron spin-echo intensity of these radicals measured by the pulsed EPR method. Rate constants for deF were found to be larger than those for deM. This relation is in good consistent with efficiency of polymerisation of deF and deM. Experimentally determined rate constants were evaluated by introducing the addition reaction model on the basis of two important factors enthalpy and polar effects.

Rate constant for the H˙ + H2O → ˙OH + H2 reaction at elevated temperatures measured by pulse radiolysis.

PubMed

Muroya, Y; Yamashita, S; Lertnaisat, P; Sanguanmith, S; Meesungnoen, J; Jay-Gerin, J-P; Katsumura, Y

2017-11-22

Maintaining the structural integrity of materials in nuclear power plants is an essential issue associated with safe operation. Hydrogen (H 2 ) addition or injection to coolants is a powerful technique that has been widely applied such that the reducing conditions in the coolant water avoid corrosion and stress corrosion cracking (SCC). Because the radiation-induced reaction of ˙OH + H 2 → H˙ + H 2 O plays a crucial role in these systems, the rate constant has been measured at operation temperatures of the reactors (285-300 °C) by pulse radiolysis, generating sufficient data for analysis. The reverse reaction H˙ + H 2 O → ˙OH + H 2 is negligibly slow at ambient temperature; however, it accelerates considerably quickly at elevated temperatures. Although the reverse reaction reduces the effectiveness of H 2 addition, reliable rate constants have not yet been measured. In this study, the rate constants have been determined in a temperature range of 250-350 °C by pulse radiolysis in an aqueous I - solution.

Computational study of the reactions of methanol with the hydroperoxyl and methyl radicals. 2. Accurate thermal rate constants.

PubMed

Alecu, I M; Truhlar, Donald G

2011-12-29

Multistructural canonical variational-transition-state theory with multidimensional tunneling (MS-CVT/MT) is employed to calculate thermal rate constants for the abstraction of hydrogen atoms from both positions of methanol by the hydroperoxyl and methyl radicals over the temperature range 100-3000 K. The M08-HX hybrid meta-generalized gradient approximation density functional and M08-HX with specific reaction parameters, both with the maug-cc-pVTZ basis set, were validated in part 1 of this study (Alecu, I. M.; Truhlar, D. G. J. Phys. Chem. A2011, 115, 2811) against highly accurate CCSDT(2)(Q)/CBS calculations for the energetics of these reactions, and they are used here to compute the properties of all stationary points and the energies, gradients, and Hessians of nonstationary points along each considered reaction path. The internal rotations in some of the transition states are found to be highly anharmonic and strongly coupled to each other, and they generate multiple structures (conformations) whose contributions are included in the partition function. It is shown that the previous estimates for these rate constants used to build kinetic models for the combustion of methanol, some of which were based on transition state theory calculations with one-dimensional tunneling corrections and harmonic-oscillator approximations or separable one-dimensional hindered rotor treatments of torsions, are appreciably different than the ones presently calculated using MS-CVT/MT. The rate constants obtained from the best MS-CVT/MT calculations carried out in this study, in which the important effects of corner cutting due to small and large reaction path curvature are captured via a microcanonical optimized multidimensional tunneling (μOMT) treatment, are recommended for future refinement of the kinetic model for methanol combustion. © 2011 American Chemical Society

Reaction rate constants and mean population percentage for nitrifiers in an alternating oxidation ditch system.

PubMed

Mantziaras, I D; Katsiri, A

2011-01-01

This paper presents a methodology for the determination of reaction rate constants for nitrifying bacteria and their mean population percentage in biomass in an alternating oxidation ditch system. The method used is based on the growth rate equations of the ASM1 model (IWA) (Henze et al. in Activated sludge models ASM1, ASM2, ASM2d, and ASM3. IWA Scientific and Technical Report no. 9, IWA Publishing, London, UK, 2000) and the application of mass balance equations for nitrifiers and ammonium nitrogen in an operational cycle of the ditch system. The system consists of two ditches operating in four phases. Data from a large-scale oxidation ditch pilot plant with a total volume of 120 m(3) within an experimental period of 8 months was used. Maximum specific growth rate for autotrophs (μ(A)) and the half-saturation constant for ammonium nitrogen (K(NH)) were found to be 0.36 day(-1) and 0.65 mgNH(4)-N/l, respectively. Additionally, the average population percentage of the nitrifiers in the biomass was estimated to be around 3%.

The effect of addition of primary positive salts, complex salt, on the ionic strength and rate constant at various temperatures by reaction kinetics

NASA Astrophysics Data System (ADS)

Kurade, S. S.; Ramteke, A. A.

2018-05-01

In this work, we have investigated the rate of reaction by using ionic strength at different temperatures. The main goal of this experiment is to determine the relation between ionic strength with reaction rate, reaction time and rate constant with temperature. It is observed that the addition of positive salt indicate the increasing ionic strength with increase in run time at various temperatures. Thus the temperature affects the speed of reaction and mechanism by which chemical reaction occurs and time variable plays vital role in the progress of reaction at different temperatures.

Instanton rate constant calculations close to and above the crossover temperature.

PubMed

McConnell, Sean; Kästner, Johannes

2017-11-15

Canonical instanton theory is known to overestimate the rate constant close to a system-dependent crossover temperature and is inapplicable above that temperature. We compare the accuracy of the reaction rate constants calculated using recent semi-classical rate expressions to those from canonical instanton theory. We show that rate constants calculated purely from solving the stability matrix for the action in degrees of freedom orthogonal to the instanton path is not applicable at arbitrarily low temperatures and use two methods to overcome this. Furthermore, as a by-product of the developed methods, we derive a simple correction to canonical instanton theory that can alleviate this known overestimation of rate constants close to the crossover temperature. The combined methods accurately reproduce the rate constants of the canonical theory along the whole temperature range without the spurious overestimation near the crossover temperature. We calculate and compare rate constants on three different reactions: H in the Müller-Brown potential, methylhydroxycarbene → acetaldehyde and H 2  + OH → H + H 2 O. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

High-level theoretical study of the reaction between hydroxyl and ammonia: Accurate rate constants from 200 to 2500 K

NASA Astrophysics Data System (ADS)

Nguyen, Thanh Lam; Stanton, John F.

2017-10-01

Hydrogen abstraction from NH3 by OH to produce H2O and NH2—an important reaction in combustion of NH3 fuel—was studied with a theoretical approach that combines high level quantum chemistry and advanced chemical kinetics methods. Thermal rate constants calculated from first principles agree well (within 5%-20%) with available experimental data over a temperature range that extends from 200 to 2500 K. Quantum mechanical tunneling effects were found to be important; they lead to a decided curvature and non-Arrhenius behavior for the rate constant.

High-level theoretical study of the reaction between hydroxyl and ammonia: Accurate rate constants from 200 to 2500 K.

PubMed

Nguyen, Thanh Lam; Stanton, John F

2017-10-21

Hydrogen abstraction from NH 3 by OH to produce H 2 O and NH 2 -an important reaction in combustion of NH 3 fuel-was studied with a theoretical approach that combines high level quantum chemistry and advanced chemical kinetics methods. Thermal rate constants calculated from first principles agree well (within 5%-20%) with available experimental data over a temperature range that extends from 200 to 2500 K. Quantum mechanical tunneling effects were found to be important; they lead to a decided curvature and non-Arrhenius behavior for the rate constant.

High-level theoretical study of the reaction between hydroxyl and ammonia: Accurate rate constants from 200 to 2500 K

DOE PAGES

Nguyen, Thanh Lam; Stanton, John F.

2017-06-02

Hydrogen abstraction from NH 3 by OH to produce H 2O and NH 2 — an important reaction in combustion of NH 3 fuel — was studied with a theoretical approach that combines high level quantum chemistry and advanced chemical kinetics methods. Thermal rate constants calculated from first principles agree well (within 5 to 20%) with available experimental data over a temperature range that extends from 200 to 2500 K. Here, quantum mechanical tunneling effects were found to be important; they lead to a decided curvature and non-Arrhenius behavior for the rate constant.

Determination of Bimolecular Rate Constants for Reactions of Hydroxyl Radical with Pharmaceutical and Cosmetics Chemicals - Implications to the Fate in the Aquatic Environment

NASA Astrophysics Data System (ADS)

Nakajima, H.; Arakaki, T.; Anastasio, C.

2008-12-01

Large organic compounds such as hyaluronic acid and chondroitin sulfate are often used in pharmaceutical and cosmetics products, but their chemical degradation pathways are not well understood. To better elucidate their fate in the aquatic environment, we initiated a study to determine bimolecular rate constants between these organic compounds and hydroxyl radical (OH), which is a potent oxidant in the environment. The lifetimes of many organic compounds are determined by reactions with OH radicals, and the lifetime of OH is often controlled by reactions with organic compounds. To determine these bimolecular rate constants we used a competition kinetics technique with either hydrogen peroxide or nitrate as a source of OH and benzoate as the competing sink. Since the molecular weights of some of the large organic compounds we studied were not known, we used dissolved organic carbon (DOC) concentrations to determine mole-carbon based bimolecular rate constants, instead of the commonly used molar-based bimolecular rate constants. We will report the mole-carbon based bimolecular rate constants of OH, determined at room temperature, with hyaluronic acid, chondroitin sulfate and some other large organic compounds.

EXPERIMENTAL PROTOCOL FOR DETERMINING PROTOLYSIS REACTION RATE CONSTANTS

EPA Science Inventory

An experimental protocol to determine photolysis rates of chemicals which photolyze relatively rapidly in the gas phase has been developed. This procedure provides a basis for evaluating the relative importance of one atmospheric reaction pathway (i.e., photolysis) for organic su...

Estimation of rate constants of PCB dechlorination reactions using an anaerobic dehalogenation model.

PubMed

Karakas, Filiz; Imamoglu, Ipek

2017-02-15

This study aims to estimate anaerobic dechlorination rate constants (k m ) of reactions of individual PCB congeners using data from four laboratory microcosms set up using sediment from Baltimore Harbor. Pathway k m values are estimated by modifying a previously developed model as Anaerobic Dehalogenation Model (ADM) which can be applied to any halogenated hydrophobic organic (HOC). Improvements such as handling multiple dechlorination activities (DAs) and co-elution of congeners, incorporating constraints, using new goodness of fit evaluation led to an increase in accuracy, speed and flexibility of ADM. DAs published in the literature in terms of chlorine substitutions as well as specific microorganisms and their combinations are used for identification of pathways. The best fit explaining the congener pattern changes was found for pathways of Phylotype DEH10, which has the ability to remove doubly flanked chlorines in meta and para positions, para flanked chlorines in meta position. The range of estimated k m values is between 0.0001-0.133d -1 , the median of which is found to be comparable to the few available published biologically confirmed rate constants. Compound specific modelling studies such as that performed by ADM can enable monitoring and prediction of concentration changes as well as toxicity during bioremediation. Copyright © 2016 Elsevier B.V. All rights reserved.

Room-temperature and temperature-dependent QSRR modelling for predicting the nitrate radical reaction rate constants of organic chemicals using ensemble learning methods.

PubMed

Gupta, S; Basant, N; Mohan, D; Singh, K P

2016-07-01

Experimental determinations of the rate constants of the reaction of NO3 with a large number of organic chemicals are tedious, and time and resource intensive; and the development of computational methods has widely been advocated. In this study, we have developed room-temperature (298 K) and temperature-dependent quantitative structure-reactivity relationship (QSRR) models based on the ensemble learning approaches (decision tree forest (DTF) and decision treeboost (DTB)) for predicting the rate constant of the reaction of NO3 radicals with diverse organic chemicals, under OECD guidelines. Predictive powers of the developed models were established in terms of statistical coefficients. In the test phase, the QSRR models yielded a correlation (r(2)) of >0.94 between experimental and predicted rate constants. The applicability domains of the constructed models were determined. An attempt has been made to provide the mechanistic interpretation of the selected features for QSRR development. The proposed QSRR models outperformed the previous reports, and the temperature-dependent models offered a much wider applicability domain. This is the first report presenting a temperature-dependent QSRR model for predicting the nitrate radical reaction rate constant at different temperatures. The proposed models can be useful tools in predicting the reactivities of chemicals towards NO3 radicals in the atmosphere, hence, their persistence and exposure risk assessment.

Direct Dynamics Simulation of the Thermal 3CH2 + 3O2 Reaction. Rate Constant and Product Branching Ratios.

PubMed

Lakshmanan, Sandhiya; Pratihar, Subha; Machado, Francisco B C; Hase, William L

2018-05-31

The reaction of 3 CH 2 with 3 O 2 is of fundamental importance in combustion, and the reaction is complex as a result of multiple extremely exothermic product channels. In the present study, direct dynamics simulations were performed to study the reaction on both the singlet and triplet potential energy surfaces (PESs). The simulations were performed at the UM06/6-311++G(d,p) level of theory. Trajectories were calculated at a temperature of 300 K, and all reactive trajectories proceeded through the carbonyl oxide Criegee intermediate, CH 2 OO, on both the singlet and triplet PESs. The triplet surface leads to only one product channel, H 2 CO + O( 3 P), while the singlet surface leads to eight product channels with their relative importance as CO + H 2 O > CO + OH + H ∼ H 2 CO + O( 1 D) > HCO + OH ∼ CO 2 + H 2 ∼ CO + H 2 + O( 1 D) > CO 2 + H + H > HCO + O( 1 D) + H. The reaction on the singlet PES is barrierless, consistent with experiment, and the total rate constant on the singlet surface is (0.93 ± 0.22) × 10 -12 cm 3 molecule -1 s -1 in comparison to the recommended experimental rate constant of 3.3 × 10 -12 cm 3 molecule -1 s -1 . The simulation product yields for the singlet PES are compared with experiment, and the most significant differences are for H, CO 2 , and H 2 O. The reaction on the triplet surface is also barrierless, inconsistent with experiment. A discussion is given of the need for future calculations to address (1) the barrier on the triplet PES for 3 CH 2 + 3 O 2 → 3 CH 2 OO, (2) the temperature dependence of the 3 CH 2 + 3 O 2 reaction rate constant and product branching ratios, and (3) the possible non-RRKM dynamics of the 1 CH 2 OO Criegee intermediate.

Recovering a full dimensional quantum rate constant from a reduced dimensionality calculation: Application to the OH+CO{r_arrow}H+CO{sub 2} reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dzegilenko, F.N.; Bowman, J.M.

1996-08-01

Two reduced dimensionality theories are used to calculate the thermal rate constant for the OH+CO{r_arrow}H+CO{sub 2} reaction. The standard theory employs energy-shift approximations to extract the full six degree-of-freedom quantum rate constant for this reaction from the previous two degree-of-freedom (2-DOF) quantum calculations of Hernandez and Clary [M.I. Hernandez and D.C. Clary, J. Chem. Phys. {bold 101}, 2779 (1994)]. Three extra bending modes and one extra {open_quote}{open_quote}spectator{close_quote}{close_quote} CO stretch mode are treated adiabatically in the harmonic fashion. The parameters of the exit channel transition state are used to evaluate the frequencies of those additional modes. A new reduced dimensionality theorymore » is also applied to this reaction. This theory explicitly addresses the finding from the 2-DOF calculations that the reaction proceeds mainly via complex formation. A J-shifting approximation has been used to take into account the initial states with non-zero values of total angular momentum in both reduced dimensionality theories. Cumulative reaction probabilities and thermal rate constants are calculated and compared with the previous quasiclassical and reduced dimensionality quantum calculations and with experiment. The rate constant from the new reduced dimensionality theory is between a factor of 5 and 100 times smaller than the statistical transition state theory result, and is in much better agreement with experiment. {copyright} {ital 1996 American Institute of Physics.}« less

Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soudackov, Alexander V.; Hammes-Schiffer, Sharon

2015-11-21

Rate constant expressions for vibronically nonadiabatic proton transfer and proton-coupled electron transfer reactions are presented and analyzed. The regimes covered include electronically adiabatic and nonadiabatic reactions, as well as high-frequency and low-frequency proton donor-acceptor vibrational modes. These rate constants differ from previous rate constants derived with the cumulant expansion approach in that the logarithmic expansion of the vibronic coupling in terms of the proton donor-acceptor distance includes a quadratic as well as a linear term. The analysis illustrates that inclusion of this quadratic term in the framework of the cumulant expansion framework may significantly impact the rate constants at highmore » temperatures for proton transfer interfaces with soft proton donor-acceptor modes that are associated with small force constants and weak hydrogen bonds. The effects of the quadratic term may also become significant in these regimes when using the vibronic coupling expansion in conjunction with a thermal averaging procedure for calculating the rate constant. In this case, however, the expansion of the coupling can be avoided entirely by calculating the couplings explicitly for the range of proton donor-acceptor distances sampled. The effects of the quadratic term for weak hydrogen-bonding systems are less significant for more physically realistic models that prevent the sampling of unphysical short proton donor-acceptor distances. Additionally, the rigorous relation between the cumulant expansion and thermal averaging approaches is clarified. In particular, the cumulant expansion rate constant includes effects from dynamical interference between the proton donor-acceptor and solvent motions and becomes equivalent to the thermally averaged rate constant when these dynamical effects are neglected. This analysis identifies the regimes in which each rate constant expression is valid and thus will be important for future applications to

Rate constants for the slow Mu + propane abstraction reaction at 300 K by diamagnetic RF resonance.

PubMed

Fleming, Donald G; Cottrell, Stephen P; McKenzie, Iain; Ghandi, Khashayar

2015-08-14

The study of kinetic isotope effects for H-atom abstraction rates by incident H-atoms from the homologous series of lower mass alkanes (CH4, C2H6 and, here, C3H8) provides important tests of reaction rate theory on polyatomic systems. With a mass of only 0.114 amu, the most sensitive test is provided by the rates of the Mu atom. Abstraction of H by Mu can be highly endoergic, due to the large zero-point energy shift in the MuH bond formed, which also gives rise to high activation energies from similar zero-point energy corrections at the transition state. Rates are then far too slow near 300 K to be measured by conventional TF-μSR techniques that follow the disappearance of the spin-polarised Mu atom with time. Reported here is the first measurement of a slow Mu reaction rate in the gas phase by the technique of diamagnetic radio frequency (RF) resonance, where the amplitude of the MuH product formed in the Mu + C3H8 reaction is followed with time. The measured rate constant, kMu = (6.8 ± 0.5) × 10(-16) cm(3) s(-1) at 300 K, is surprisingly only about a factor of three slower than that expected for H + C3H8, indicating a dominant contribution from quantum tunneling in the Mu reaction, consistent with elementary transition state theory calculations of the kMu/kH kinetic isotope effect.

Rate constants for the thermal decomposition of ethanol and its bimolecular reactions with OH and D : reflected shock tube and theoretical studies.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sivaramakrishnan, R.; Su, M.-C.; Michael, J. V.

2010-09-09

The thermal decomposition of ethanol and its reactions with OH and D have been studied with both shock tube experiments and ab initio transition state theory-based master equation calculations. Dissociation rate constants for ethanol have been measured at high T in reflected shock waves using OH optical absorption and high-sensitivity H-atom ARAS detection. The three dissociation processes that are dominant at high T are: C{sub 2}H{sub 5}OH {yields} C{sub 2}H{sub 4} + H{sub 2}O; C{sub 2}H{sub 5}OH {yields} CH{sub 3} + CH{sub 2}OH; C{sub 2}H{sub 5}OH {yields} C{sub 2}H{sub 5} + OH. The rate coefficient for reaction C was measuredmore » directly with high sensitivity at 308 nm using a multipass optical White cell. Meanwhile, H-atom ARAS measurements yield the overall rate coefficient and that for the sum of reactions B and C, since H-atoms are instantaneously formed from the decompositions of CH{sub 2}OH and C{sub 2}H{sub 5} into CH{sub 2}O + H and C{sub 2}H{sub 4} + H, respectively. By difference, rate constants for reaction 1 could be obtained. One potential complication is the scavenging of OH by unreacted ethanol in the OH experiments, and therefore, rate constants for OH + C{sub 2}H{sub 5}OH {yields} products were measured using tert-butyl hydroperoxide (tBH) as the thermal source for OH. The present experiments can be represented by the Arrhenius expression k = (2.5 {+-} 0.43) x 10{sup -11} exp(- 911 {+-} 191 K/T) cm{sup 3} molecule{sup -1} s{sup -1} over the T range 857-1297 K. For completeness, we have also measured the rate coefficient for the reaction of D atoms with ethanol D + C{sub 2}H{sub 5}OH {yields} products whose H analogue is another key reaction in the combustion of ethanol. Over the T range 1054-1359 K, the rate constants from the present experiments can be represented by the Arrhenius expression, k = (3.98 {+-} 0.76) x 10{sup -10} exp(- 4494 {+-} 235 K/T) cm{sup 3} molecule{sup -1} s{sup -1}. The high-pressure rate coefficients for reactions B

An Analysis of Descriptors of Volatile Organic Compounds and Their Impact on Rate Constant for Reaction with Hydroxyl Radicals

DTIC Science & Technology

2018-05-01

the descriptors were correlated to experimental rate constants. The five descriptors fell into one of two categories: whole molecule descriptors or...model based on these correlations . Although that goal was not achieved in full, considerable progress has been made, and there is potential for a...readme.txt) and compiled. We then searched for correlations between the calculated properties from theory and the experimental measurements of reaction rate

Arrhenius Rate: constant volume burn

DOE Office of Scientific and Technical Information (OSTI.GOV)

Menikoff, Ralph

A constant volume burn occurs for an idealized initial state in which a large volume of reactants at rest is suddenly raised to a high temperature and begins to burn. Due to the uniform spatial state, there is no fluid motion and no heat conduction. This reduces the time evolu tion to an ODE for the reaction progress variable. With an Arrhenius reaction rate, two characteristics of thermal ignition are illustrated: induction time and thermal runaway. The Frank-Kamenetskii approximation then leads to a simple expression for the adiabatic induction time. For a first order reaction, the analytic solution is derivedmore » and used to illustrate the effect of varying the activation temperature; in particular, on the induction time. In general, the ODE can be solved numerically. This is used to illustrate the effect of varying the reaction order. We note that for a first order reaction, the time evolution of the reaction progress variable has an exponential tail. In contrast, for a reaction order less than one, the reaction completes in a nite time. The reaction order also affects the induction time.« less

Representing Rate Equations for Enzyme-Catalyzed Reactions

ERIC Educational Resources Information Center

Ault, Addison

2011-01-01

Rate equations for enzyme-catalyzed reactions are derived and presented in a way that makes it easier for the nonspecialist to see how the rate of an enzyme-catalyzed reaction depends upon kinetic constants and concentrations. This is done with distribution equations that show how the rate of the reaction depends upon the relative quantities of…

Theoretical investigation on H abstraction reaction mechanisms and rate constants of sevoflurane with the OH radical

NASA Astrophysics Data System (ADS)

Ren, Hongjiang; Li, Xiaojun; Qu, Yingjuan; Li, Feng

2018-01-01

The H abstraction reaction mechanism for sevoflurane with an ·OH radical was investigated theoretically using dual levels B3LYP/6-311++G(d, p)//QCISD(T)/6-311G(d, p). Thermochemistry properties at 298.15-2000 K were analyzed with the standard statistical thermodynamics method. Three pathways P(1), P(2) and P(3) were found and corresponded to the H13, H14 and H15 abstractions reactions with the Gibbs free barriers of 54.86, 55.05 and 54.86 kJ mol-1, respectively. The corresponding rate constants for three pathways over a wide temperature range of 298.15-2000 K were calculated and the results are in good agreement with the experimental data.

Multivariate curve resolution-alternating least squares and kinetic modeling applied to near-infrared data from curing reactions of epoxy resins: mechanistic approach and estimation of kinetic rate constants.

PubMed

Garrido, M; Larrechi, M S; Rius, F X

2006-02-01

This study describes the combination of multivariate curve resolution-alternating least squares with a kinetic modeling strategy for obtaining the kinetic rate constants of a curing reaction of epoxy resins. The reaction between phenyl glycidyl ether and aniline is monitored by near-infrared spectroscopy under isothermal conditions for several initial molar ratios of the reagents. The data for all experiments, arranged in a column-wise augmented data matrix, are analyzed using multivariate curve resolution-alternating least squares. The concentration profiles recovered are fitted to a chemical model proposed for the reaction. The selection of the kinetic model is assisted by the information contained in the recovered concentration profiles. The nonlinear fitting provides the kinetic rate constants. The optimized rate constants are in agreement with values reported in the literature.

Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soudackov, Alexander; Hammes-Schiffer, Sharon

2015-11-17

Rate constant expressions for vibronically nonadiabatic proton transfer and proton-coupled electron transfer reactions are presented and analyzed. The regimes covered include electronically adiabatic and nonadiabatic reactions, as well as high-frequency and low-frequency regimes for the proton donor-acceptor vibrational mode. These rate constants differ from previous rate constants derived with the cumulant expansion approach in that the logarithmic expansion of the vibronic coupling in terms of the proton donor-acceptor distance includes a quadratic as well as a linear term. The analysis illustrates that inclusion of this quadratic term does not significantly impact the rate constants derived using the cumulant expansion approachmore » in any of the regimes studied. The effects of the quadratic term may become significant when using the vibronic coupling expansion in conjunction with a thermal averaging procedure for calculating the rate constant, however, particularly at high temperatures and for proton transfer interfaces with extremely soft proton donor-acceptor modes that are associated with extraordinarily weak hydrogen bonds. Even with the thermal averaging procedure, the effects of the quadratic term for weak hydrogen-bonding systems are less significant for more physically realistic models that prevent the sampling of unphysical short proton donor-acceptor distances, and the expansion of the coupling can be avoided entirely by calculating the couplings explicitly for the range of proton donor-acceptor distances. This analysis identifies the regimes in which each rate constant expression is valid and thus will be important for future applications to proton transfer and proton-coupled electron transfer in chemical and biological processes. We are grateful for support from National Institutes of Health Grant GM056207 (applications to enzymes) and the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of

The Br+HO 2 reaction revisited: Absolute determination of the rate constant at 298 K

NASA Astrophysics Data System (ADS)

Laverdet, G.; Le Bras, G.; Mellouki, A.; Poulet, G.

1990-09-01

The absolute determination of the rate constant for the reaction Br+HO 2→HBr+O 2 has been done at 298 K using the discharge-flor EPR method. The value k1 = (1.5±0.2) × 10 -12 cm 3 molecule -1 s -1 was obtained. Previous indirect measurements of k1 from a discharge-flow, LIF/mass spectrometric study of the Br/H 2CO/O 2 system have been reinterpreted, leading to values for k1 ranging from 1.0 × 10 -12 to 2.2 × 10 -12 cm 3 molecule -1 s -1 at 298 K. These results are discussed and compared with other literature values.

Quantum instanton calculation of rate constant for CH4 + OH → CH3 + H2O reaction: Torsional anharmonicity and kinetic isotope effect

NASA Astrophysics Data System (ADS)

Wang, Wenji; Zhao, Yi

2012-12-01

Thermal rate constants for the title reaction are calculated by using the quantum instanton approximation within the full dimensional Cartesian coordinates. The results reveal that the quantum effect is remarkable for the reaction at both low and high temperatures, and the obtained rates are in good agreement with experimental measurements at high temperatures. Compared to the harmonic approximation, the torsional anharmonic effect of the internal rotation has a little influence on the rates at low temperatures, however, it enhances the rate by about 20% at 1000 K. In addition, the free energy barriers for the isotopic reactions and the temperature dependence of kinetic isotope effects are also investigated. Generally speaking, for the title reaction, the replacement of OH with OD will reduce the free energy barrier, while substituting D for H (connected to C) will increase the free energy barrier.

The reaction of peroxy radicals with OH: rate constants and HO2 yields

NASA Astrophysics Data System (ADS)

Fittschen, C. M.; Assaf, E.; Schoemaecker, C.; Vereecken, L.

2017-12-01

Peroxy radicals, RO2, are key species in the atmosphere. They are formed from a reaction of OH radicals with hydrocarbon: RH + OH + O2 → RO2 + H2O In polluted environments, RO2 radicals react predominantly with NO, leading to formation of NO2 and eventually through photolysis of NO2 to formation of O3. At low NOx concentrations such as in the marine boundary layer or the background troposphere, the lifetime of RO2 radicals increases and other reaction pathways become competitive. Atmospheric chemistry models have considered until recently only the self- and cross reaction with other RO2 radicals or with HO2 radicals as the major fate for RO2 radicals under low NOx conditions. Recently, the rate constants for the reaction of peroxy radicals with OH radicals RO2 + OH → products has been measured for CH3O2 [1, 2] and C2H5O2 [3] and it was shown to become competitive to other sinks [4]. However, in order to evaluate the impact of this so far neglected sink for peroxy radicals on the composition of remote atmospheres, the reaction products must be known. A recently improved experimental set-up combining laser photolysis with two simultaneous cw-CRDS detections in the near IR allowing for a time resolved, absolute quantification of OH and RO2 radicals has been used for a further investigation of this class of reactions. High-repetition rate LIF is used for determining relative OH profiles. For CH3O2 radicals, HO2 has been determined as major product recently [5]. Currently, we study the next larger perxoy, C2H5O2, using different radical precursors (C2H5I, (COCl)2/C2H6, XeF2/C2H6) and also deuterated C2D5I in order to elucidate the product yield. Preliminary results show a much lower HO2 yield for C2H5O2 compared to CH3O2. The most recent results will be presented at the conference. [1] A. Bossolasco, E. Faragó, C. Schoemaecker, and C. Fittschen, CPL, 593, 7, (2014). [2] E. Assaf, B. Song, A. Tomas, C. Schoemaecker, C. Fittschen, JPC A, 120, 8923 (2016) [3] Eszter

Direct rate constant measurements for the reaction of ground-state atomic oxygen with ethylene, 244-1052 K

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klemm, R.B.; Nesbitt, F.L.; Skolnik, E.G.

The rate constant for the reaction of ground-state atomic oxygen with ethylene was determined by using two techniques: flash photolysis-resonance fluorescence (FP-RF, 244-1052 K) and discharge flow-resonance fluorescence (DF-RF, 298-1017 K). Kinetic complications due to the presence of molecular oxygen in the FP-RF experiments at high temperatures (T > 800 K) were overcome by using NO as the photolytic source of the O atoms. The rate constant, k/sub 1/ (T), derived in this study exhibits extreme non-Arrhenius behavior, but it can be successfully fit to the sum of exponentials expression, 244-1052 K, k/sub 1/(T) = (1.02 +/- 0.06) x 10/supmore » -11/ exp(-753 +/- 17 K/T) + (2.75 +/- 0.26) x 10/sup -10/ exp(-4220 +/- 550 K/T), in units of cm/sup 3/ molecule/sup -1/ s/sup -1/. Additionally, a fit of the results of this work to a simple transition-state theory expression and the comparison of these results with those of other workers are discussed.« less

Rate of reaction of OH with HNO3

NASA Technical Reports Server (NTRS)

Wine, P. H.; Ravishankara, A. R.; Kreutter, N. M.; Shah, R. C.; Nicovich, J. M.; Thompson, R. L.; Wuebbles, D. J.

1981-01-01

Measurements of the kinetics of the reaction of OH with HNO3, and mechanisms of HNO3 removal from the stratosphere, are reported. Bimolecular rate constants were determined at temperatures between 224 and 366 K by monitoring the concentrations of OH radicals produced by HNO3 photolysis and HNO3 according to their resonance fluorescence and 184.9-nm absorption, respectively. The rate constant measured at 298 K is found to be somewhat faster than previously accepted values, with a negative temperature dependence. Calculations of a one-dimensional transport-kinetic atmospheric model on the basis of the new rate constant indicate reductions in O3 depletion due to chlorofluoromethane release and NOx injection, of magnitudes dependent on the nature of the reaction products.

Calculated rate constants for the reaction ClO + O yields Cl + O2 between 220 and 1000 deg K. [molecular trajectories and stratospheric ozone

NASA Technical Reports Server (NTRS)

Jaffee, R. L.

1978-01-01

Classical trajectory calculations are presented for the reaction ClO + O yields Cl + O2, a reaction which is an important step in the chlorine-catalyzed destruction of ozone which is thought to occur in the 220 and 1000 K. The calculated rate constant is 4.36 x 10 to the minus 11th power exp (-191/T)cu cm molecule (-1)s(-1) and its value at 300 K is 2.3 plus or minus 10 to the 11th power cu cm molecule (-1)s(-1), about a factor of 2 lower than recent experimental data. The empirical potential energy surface used in the calculations was constructed to fit experimental data for ClO, O2 and ClOO molecules. Other important features of this potential surface, such as the barrier to reaction, were varied systematically and calculations were performed for a range of conditions to determine the best theoretical rate constants. Results demonstrate the utility of classical trajectory methods for determining activation energies and other kinetic data for important atmospheric reactions.

Effects of reactant rotational excitation on H + O2--> OH + O reaction rate constant: quantum wave packet, quasi-classical trajectory and phase space theory calculations.

PubMed

Lin, Shi Ying; Guo, Hua; Lendvay, György; Xie, Daiqian

2009-06-21

We examine the impact of initial rotational excitation on the reactivity of the H + O(2)--> OH + O reaction. Accurate Chebyshev wave packet calculations have been carried out for the upsilon(i) = 0, j(i) = 9 initial state of O(2) and the J = 50 partial wave. In addition, we present Gaussian-weighted quasi-classical trajectory and phase space theory calculations of the integral cross section and thermal rate constant for the title reaction. These theoretical results suggest that the initial rotational excitation significantly enhances reactivity with an amount comparable to the effect of initial vibrational state excitation. The inclusion of internally excited reactants is shown to improve the agreement with experimental rate constant.

Atmospheric reaction of Cl + methacrolein: a theoretical study on the mechanism, and pressure- and temperature-dependent rate constants.

PubMed

Sun, Cuihong; Xu, Baoen; Zhang, Shaowen

2014-05-22

Methacrolein is a major degradation product of isoprene, the reaction of methacrolein with Cl atoms may play some roles in the degradation of isoprene where these species are relatively abundant. However, the energetics and kinetics of this reaction, which govern the reaction branching, are still not well understood so far. In the present study, two-dimensional potential energy surfaces were constructed to analyze the minimum energy path of the barrierless addition process between Cl and the C═C double bond of methacrolein, which reveals that the terminal addition intermediate is directly formed from the addition reaction. The terminal addition intermediate can further yield different products among which the reaction paths abstracting the aldehyde hydrogen atom and the methyl hydrogen atom are dominant reaction exits. The minimum reaction path for the direct aldehydic hydrogen atom abstraction is also obtained. The reaction kinetics was calculated by the variational transition state theory in conjunction with the master equation method. From the theoretical model we predicted that the overall rate constant of the Cl + methacrolein reaction at 297 K and atmospheric pressure is koverall = 2.3× 10(-10) cm(3) molecule(-1) s(-1), and the branching ratio of the aldehydic hydrogen abstraction is about 12%. The reaction is pressure dependent at P < 10 Torr with the high pressure limit at about 100 Torr. The calculated results could well account for the experimental observations.

Pressure dependence of the absolute rate constant for the reaction OH + C2H2 from 228 to 413K

NASA Technical Reports Server (NTRS)

Michael, J. V.; Nava, D. F.; Borokowski, R. P.; Payne, W. A.; Stief, L. J.

1980-01-01

The pressure dependence of absolute rate constants for the reaction of OH + C2H2 yields products has been examined at five temperatures ranging from 228 to 413 K. The experimental techniques which was used is flash photolysis-resonance fluoresence. OH was produced by water photolysis and hydroxyl resonance fluorescent photons were measured by multiscaling techniques. The results indicate that the low pressure bimolecular rate constant is 4 x 10 the the minus 13th power cu cm molecule (-1) s(-1) over the temperature range studied. A substantial increase in the bimolecular rate constant with an increase in pressure was observed at all temperatures except 228 K. This indicates the importance of initial adduct formation and subsequent stablization. The high pressure results are well represented by the Arrhenius expression (k sub bi) sub infinity = (6.83 + or - 1.19) x 10 to the minus 12th power exp(-646 + or - 47/T)cu cm molecule (-1) s(-1). The results are compared to previous investigated and are theoretically discussed. The implications of these results on modeling of terrestrial and planetary atmospheres and also in combustion chemistry are discussed.

Flame Chemiluminescence Rate Constants for Quantitative Microgravity Combustion Diagnostics

NASA Technical Reports Server (NTRS)

Luque, Jorge; Smith, Gregory P.; Jeffries, Jay B.; Crosley, David R.; Weiland, Karen (Technical Monitor)

2001-01-01

Absolute excited state concentrations of OH(A), CH(A), and C2(d) were determined in three low pressure premixed methane-air flames. Two dimensional images of chemiluminescence from these states were recorded by a filtered CCD camera, processed by Abel inversion, and calibrated against Rayleigh scattering, Using a previously validated 1-D flame model with known chemistry and excited state quenching rate constants, rate constants are extracted for the reactions CH + O2 (goes to) OH(A) + CO and C2H + O (goes to) CH(A) + CO at flame temperatures. Variations of flame emission intensities with stoichiometry agree well with model predictions.

Rate Constants for the Reactions of OH with CH(sub 3)Cl, CH(sub 2) C1(sub 2), CHC1(sub 3)and CH(sub 3)Br

NASA Technical Reports Server (NTRS)

Hsu, H-J.; DeMore, W.

1994-01-01

Rate constants for the reactions of OH with CH3C1, CH2Cl2, CHCl3 and CH3Br have been measured by a relative rate technique in which the reaction rate of each compound was compared to that of HFC-152a (CH3CHF2)and for CH2Cl2, HFC-161 (CH3CH2F).

Non-equilibrium reaction rates in chemical kinetic equations

NASA Astrophysics Data System (ADS)

Gorbachev, Yuriy

2018-05-01

Within the recently proposed asymptotic method for solving the Boltzmann equation for chemically reacting gas mixture, the chemical kinetic equations has been derived. Corresponding one-temperature non-equilibrium reaction rates are expressed in terms of specific heat capacities of the species participate in the chemical reactions, bracket integrals connected with the internal energy transfer in inelastic non-reactive collisions and energy transfer coefficients. Reactions of dissociation/recombination of homonuclear and heteronuclear diatomic molecules are considered. It is shown that all reaction rates are the complex functions of the species densities, similarly to the unimolecular reaction rates. For determining the rate coefficients it is recommended to tabulate corresponding bracket integrals, additionally to the equilibrium rate constants. Correlation of the obtained results with the irreversible thermodynamics is established.

The Kinetic Rate Law for Autocatalytic Reactions.

ERIC Educational Resources Information Center

Mata-Perez, Fernando; Perez-Benito, Joaquin F.

1987-01-01

Presented is a method of obtaining accurate rate constants for autocatalytic reactions. The autocatalytic oxidation of dimethylamine by permanganate ion in aqueous solution is used as an example. (RH)

Calculation of individual isotope equilibrium constants for geochemical reactions

USGS Publications Warehouse

Thorstenson, D.C.; Parkhurst, D.L.

2004-01-01

Theory is derived from the work of Urey (Urey H. C. [1947] The thermodynamic properties of isotopic substances. J. Chem. Soc. 562-581) to calculate equilibrium constants commonly used in geochemical equilibrium and reaction-transport models for reactions of individual isotopic species. Urey showed that equilibrium constants of isotope exchange reactions for molecules that contain two or more atoms of the same element in equivalent positions are related to isotope fractionation factors by ?? = (Kex)1/n, where n is the number of atoms exchanged. This relation is extended to include species containing multiple isotopes, for example 13C16O18O and 1H2H18O. The equilibrium constants of the isotope exchange reactions can be expressed as ratios of individual isotope equilibrium constants for geochemical reactions. Knowledge of the equilibrium constant for the dominant isotopic species can then be used to calculate the individual isotope equilibrium constants. Individual isotope equilibrium constants are calculated for the reaction CO2g = CO2aq for all species that can be formed from 12C, 13C, 16O, and 18O; for the reaction between 12C18 O2aq and 1H218Ol; and among the various 1H, 2H, 16O, and 18O species of H2O. This is a subset of a larger number of equilibrium constants calculated elsewhere (Thorstenson D. C. and Parkhurst D. L. [2002] Calculation of individual isotope equilibrium constants for implementation in geochemical models. Water-Resources Investigation Report 02-4172. U.S. Geological Survey). Activity coefficients, activity-concentration conventions for the isotopic variants of H2O in the solvent 1H216Ol, and salt effects on isotope fractionation have been included in the derivations. The effects of nonideality are small because of the chemical similarity of different isotopic species of the same molecule or ion. The temperature dependence of the individual isotope equilibrium constants can be calculated from the temperature dependence of the fractionation

Elongational flow of polymer melts at constant strain rate, constant stress and constant force

NASA Astrophysics Data System (ADS)

Wagner, Manfred H.; Rolón-Garrido, Víctor H.

2013-04-01

Characterization of polymer melts in elongational flow is typically performed at constant elongational rate or rarely at constant tensile stress conditions. One of the disadvantages of these deformation modes is that they are hampered by the onset of "necking" instabilities according to the Considère criterion. Experiments at constant tensile force have been performed even more rarely, in spite of the fact that this deformation mode is free from necking instabilities and is of considerable industrial relevance as it is the correct analogue of steady fiber spinning. It is the objective of the present contribution to present for the first time a full experimental characterization of a long-chain branched polyethylene melt in elongational flow. Experiments were performed at constant elongation rate, constant tensile stress and constant tensile force by use of a Sentmanat Extensional Rheometer (SER) in combination with an Anton Paar MCR301 rotational rheometer. The accessible experimental window and experimental limitations are discussed. The experimental data are modelled by using the Wagner I model. Predictions of the steady-start elongational viscosity in constant strain rate and creep experiments are found to be identical, albeit only by extrapolation of the experimental data to Hencky strains of the order of 6. For constant stress experiments, a minimum in the strain rate and a corresponding maximum in the elongational viscosity is found at a Hencky strain of the order of 3, which, although larger than the steady-state value, follows roughly the general trend of the steady-state elongational viscosity. The constitutive analysis also reveals that constant tensile force experiments indicate a larger strain hardening potential than seen in constant elongation rate or constant tensile stress experiments. This may be indicative of the effect of necking under constant elongation rate or constant tensile stress conditions according to the Considère criterion.

Three Rate-Constant Kinetic Model for Permanganate Reactions Autocatalyzed by Colloidal Manganese Dioxide: The Oxidation of L-Phenylalanine.

PubMed

Perez-Benito, Joaquin F; Ferrando, Jordi

2014-12-26

The reduction of permanganate ion to MnO(2)-Mn(2)O(3) soluble colloidal mixed oxide by l-phenylalanine in aqueous phosphate-buffered neutral solutions has been followed by a spectrophotometric method, monitoring the decay of permanganate ion at 525 nm and the formation of the colloidal oxide at 420 nm. The reaction is autocatalyzed by the manganese product, and three rate constants have been required to fit the experimental absorbance-time kinetic data. The reaction shows base catalysis, and the values of the activation parameters at different pHs have been determined. A mechanism including both the nonautocatalytic and the autocatalytic reaction pathways, and in agreement with the available experimental data, has been proposed. Some key features of this mechanism are the following: (i) of the two predominant forms of the amino acid, the anionic form exhibits a stronger reducing power than the zwitterionic form; (ii) the nonautocatalytic reaction pathway starts with the transfer of the hydrogen atom in the α position of the amino acid to permanganate ion; and (iii) the autocatalytic reaction pathway involves the reduction of Mn(IV) to Mn(II) by the amino acid and the posterior reoxidation of Mn(II) to Mn(IV) by permanganate ion.

Geraniol (2,6-dimethyl-2,6-octadien-8-ol) reactions with ozone and OH radical: Rate constants and gas-phase products

NASA Astrophysics Data System (ADS)

Forester, Crystal D.; Ham, Jason E.; Wells, J. R.

The bimolecular rate constants, kOH+geraniol, (231±58)×10 -12 cm 3 molecule -1 s -1 and k+geraniol, (9.3±2.3)×10 -16 cm 3 molecule -1 s -1, were measured using the relative rate technique for the reaction of the hydroxyl radical (OH) and ozone (O 3) with 2,6-dimethyl-2,6-octadien-8-ol (geraniol) at (297±3) K and 1 atmosphere total pressure. To more clearly define part of geraniol's indoor environment degradation mechanism, the products of the geraniol+OH and geraniol+O 3 reactions were also investigated. The identified geraniol+OH and geraniol+O 3 reaction products were: acetone, hydroxyacetaldehyde (glycolaldehyde, HC( dbnd O)CH 2OH), ethanedial (glyoxal, HC( dbnd O)C( dbnd O)H), and 2-oxopropanal (methylglyoxal, CH 3C( dbnd O)C( dbnd O)H). The use of derivatizing agents O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine (PFBHA) and N,O-bis(trimethylsilyl) trifluoroacetamide (BSTFA) were used to propose 4-oxopentanal as the other major geraniol+OH and geraniol+O 3 reaction product. The elucidation of this other reaction product was facilitated by mass spectrometry of the derivatized reaction products coupled with plausible geraniol+OH and geraniol+O 3 reaction mechanisms based on previously published volatile organic compound+OH and volatile organic compound+O 3 gas-phase reaction mechanisms.

Weak Acid Ionization Constants and the Determination of Weak Acid-Weak Base Reaction Equilibrium Constants in the General Chemistry Laboratory

ERIC Educational Resources Information Center

Nyasulu, Frazier; McMills, Lauren; Barlag, Rebecca

2013-01-01

A laboratory to determine the equilibrium constants of weak acid negative weak base reactions is described. The equilibrium constants of component reactions when multiplied together equal the numerical value of the equilibrium constant of the summative reaction. The component reactions are weak acid ionization reactions, weak base hydrolysis…

Upper limits for the rate constant for the reaction Br + H2O2 yields HB2 + HO2

NASA Technical Reports Server (NTRS)

Leu, M.-T.

1980-01-01

Upper limits for the rate constant for the reaction Br + H2O2 yields HBr + HO2 have been measured over the temperature range 298 to 417 K in a discharge flow system using a mass spectrometer as a detector. Results are k sub 1 less than 1.5 x 10 to the -15th power cu cm/s at 298 K and k sub 1 less than 3.0 x 10 to the -15th power cu cm/s at 417 K, respectively. The implication to stratospheric chemistry is discussed.

The vibrational dependence of dissociative recombination: Rate constants for N{sub 2}{sup +}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guberman, Steven L., E-mail: slg@sci.org

Dissociative recombination rate constants are reported with electron temperature dependent uncertainties for the lowest 5 vibrational levels of the N{sub 2}{sup +} ground state. The rate constants are determined from ab initio calculations of potential curves, electronic widths, quantum defects, and cross sections. At 100 K electron temperature, the rate constants overlap with the exception of the third vibrational level. At and above 300 K, the rate constants for excited vibrational levels are significantly smaller than that for the ground level. It is shown that any experimentally determined total rate constant at 300 K electron temperature that is smaller thanmore » 2.0 × 10{sup −7} cm{sup 3}/s is likely to be for ions that have a substantially excited vibrational population. Using the vibrational level specific rate constants, the total rate constant is in very good agreement with that for an excited vibrational distribution found in a storage ring experiment. It is also shown that a prior analysis of a laser induced fluorescence experiment is quantitatively flawed due to the need to account for reactions with unknown rate constants. Two prior calculations of the dissociative recombination rate constant are shown to be inconsistent with the cross sections upon which they are based. The rate constants calculated here contribute to the resolution of a 30 year old disagreement between modeled and observed N{sub 2}{sup +} ionospheric densities.« less

Reaction of atomic bromine with acetylene and loss rate of atmospheric acetylene due to reaction with OH, Cl, O, and Br

NASA Technical Reports Server (NTRS)

Payne, W. A.; Nava, D. F.; Brunning, J.; Stief, L. J.

1986-01-01

The first-order, diffusion, and bimolecular rate constants for the reaction Br + C2H2 yields C2H3Br are evaluated. The rate constants are measured at 210, 248, 298, and 393 K and at pressures between 15-100 torr Ar using flash photolysis combined with time-resolved detection of atomic bromine via Br resonance radiation. It is observed that the reaction is not affected by pressure or temperature and the bimolecular constant = (4.0 + or - 0.8) x 10 to the -15th cu cm/sec with an error of two standard deviations. The C2H2 + Br reaction rates are compared with reactions of C2H2 with Cl, OH, NH2, and H. The loss rates for atmospheric C2H2 for reactions with OH, Cl, O, and Br are calculated as a function of altitude.

Calculated rate constants of the chemical reactions involving the main byproducts SO2F, SOF2, SO2F2 of SF6 decomposition in power equipment

NASA Astrophysics Data System (ADS)

Fu, Yuwei; Rong, Mingzhe; Yang, Kang; Yang, Aijun; Wang, Xiaohua; Gao, Qingqing; Liu, Dingxin; Murphy, Anthony B.

2016-04-01

SF6 is widely used in electrical equipment as an insulating gas. In the presence of an electric arc, partial discharge (PD) or spark, SF6 dissociation products (such as SF2, SF3 and SF4) react with the unavoidable gas impurities (such as water vapor and oxygen), electrodes and surrounding solid insulation materials, forming several toxic and corrosive byproducts. The main stable decomposition products are SO2F, SO2F2 and SOF2, which have been confirmed experimentally to have a direct relationship with discharge faults, and are thus expected to be useful in the fault diagnosis of power equipment. Various studies have been performed of the main SF6 decomposition species and their concentrations under different types of faults. However, most of the experiments focused on the qualitative analysis of the relationship between the stable products and discharge faults. Although some theoretical research on the formation of main SF6 derivatives have been carried out using chemical kinetics models, the basic data (chemical reactions and their rate constants) adopted in the model are inaccurate and incomplete. The complex chemical reactions of SF6 with the impurities are ignored in most cases. The rate constants of some reactions obtained at ambient temperature or in a narrow temperature range are adopted in the models over a far greater range, for example up to 12 000 K, due to the difficulty in the experimental measurement and theoretical estimation of rate coefficients, particularly at high temperatures. Therefore, improved theoretical models require not only the consideration of additional SF6 decomposition reactions in the presence of impurities but also on improved values of rate constants. This paper is devoted to determining the rate constants of the chemical reactions relating to the main byproducts of SF6 decomposition in SF6 gas-insulated power equipment: SO2F, SOF2 and SO2F2. Quantum chemistry calculations with density functional theory, conventional

Rate Constant and RRKM Product Study for the Reaction Between CH3 and C2H3 at T = 298K

NASA Technical Reports Server (NTRS)

Thorn, R. Peyton, Jr.; Payne, Walter A., Jr.; Chillier, Xavier D. F.; Stief, Louis J.; Nesbitt, Fred L.; Tardy, D. C.

2000-01-01

The total rate constant k1 has been determined at P = 1 Torr nominal pressure (He) and at T = 298 K for the vinyl-methyl cross-radical reaction CH3 + C2H3 yields products. The measurements were performed in a discharge flow system coupled with collision-free sampling to a mass spectrometer operated at low electron energies. Vinyl and methyl radicals were generated by the reactions of F with C2H4 and CH4, respectively. The kinetic studies were performed by monitoring the decay of C2H3 with methyl in excess, 6 < |CH3|(sub 0)/|C2H3|(sub 0) < 21. The overall rate coefficient was determined to be k1(298 K) = (1.02 +/- 0.53)x10(exp -10) cubic cm/molecule/s with the quoted uncertainty representing total errors. Numerical modeling was required to correct for secondary vinyl consumption by reactions such as C2H3 + H and C2H3 + C2H3. The present result for k1 at T = 298 K is compared to two previous studies at high pressure (100-300 Torr He) and to a very recent study at low pressure (0.9-3.7 Torr He). Comparison is also made with the rate constant for the similar reaction CH3 + C2H5 and with a value for k1 estimated by the geometric mean rule employing values for k(CH3 + CH3) and k(C2H3 + C2H3). Qualitative product studies at T = 298 K and 200 K indicated formation of C3H6, C2H2, and C2H5 as products of the combination-stabilization, disproportionation, and combination-decomposition channels, respectively, of the CH3 + C2H3 reaction. We also observed the secondary C4H8 product of the subsequent reaction of C3H5 with excess CH3; this observation provides convincing evidence for the combination-decomposition channel yielding C3H5 + H. RRKM calculations with helium as the deactivator support the present and very recent experimental observations that allylic C-H bond rupture is an important path in the combination reaction. The pressure and temperature dependencies of the branching fractions are also predicted.

Combined valence bond-molecular mechanics potential-energy surface and direct dynamics study of rate constants and kinetic isotope effects for the H + C2H6 reaction.

PubMed

Chakraborty, Arindam; Zhao, Yan; Lin, Hai; Truhlar, Donald G

2006-01-28

This article presents a multifaceted study of the reaction H+C(2)H(6)-->H(2)+C(2)H(5) and three of its deuterium-substituted isotopologs. First we present high-level electronic structure calculations by the W1, G3SX, MCG3-MPWB, CBS-APNO, and MC-QCISD/3 methods that lead to a best estimate of the barrier height of 11.8+/-0.5 kcal/mol. Then we obtain a specific reaction parameter for the MPW density functional in order that it reproduces the best estimate of the barrier height; this yields the MPW54 functional. The MPW54 functional, as well as the MPW60 functional that was previously parametrized for the H+CH(4) reaction, is used with canonical variational theory with small-curvature tunneling to calculate the rate constants for all four ethane reactions from 200 to 2000 K. The final MPW54 calculations are based on curvilinear-coordinate generalized-normal-mode analysis along the reaction path, and they include scaled frequencies and an anharmonic C-C bond torsion. They agree with experiment within 31% for 467-826 K except for a 38% deviation at 748 K; the results for the isotopologs are predictions since these rate constants have never been measured. The kinetic isotope effects (KIEs) are analyzed to reveal the contributions from subsets of vibrational partition functions and from tunneling, which conspire to yield a nonmonotonic temperature dependence for one of the KIEs. The stationary points and reaction-path potential of the MPW54 potential-energy surface are then used to parametrize a new kind of analytical potential-energy surface that combines a semiempirical valence bond formalism for the reactive part of the molecule with a standard molecular mechanics force field for the rest; this may be considered to be either an extension of molecular mechanics to treat a reactive potential-energy surface or a new kind of combined quantum-mechanical/molecular mechanical (QM/MM) method in which the QM part is semiempirical valence bond theory; that is, the new potential

Determination of the rate constant for the NH2(X(2)B1) + NH2(X(2)B1) reaction at low pressure and 293 K.

PubMed

Bahng, Mi-Kyung; Macdonald, R Glen

2008-12-25

The rate constant for the reaction NH(2)(X(2)B(1)) + NH(2)(X(2)B(1)) --> products was measured in CF(4), N(2) and Ar carrier gases at 293 +/- 2 K over a pressure range from 2 to 10 Torr. The NH(2) radical was produced by the 193 nm photolysis of NH(3) dilute in the carrier gas. Both the loss of NH(3) and its subsequent recovery and the production of NH(2) and subsequent reaction were monitored simultaneously following the photolysis laser pulse. Both species were detected using quantitative time-resolved high-resolution absorption spectroscopy. The NH(3) molecule was monitored in the NIR using a rotation transition of the nu(1) + nu(3) first combination band near 1500 nm, and the NH(2) radical was monitored using the (1)2(21) <-- (1)3(31) rotational transition of the (0,7,0)A(2)A(1) <-- (0,0,0) X(2)B(1) band near 675 nm. The low-pressure rate constant showed a linear dependence on pressure. The slope of the pressure dependence was dominated by a recombination rate constant for NH(2) + NH(2) given by (8.0 +/- 0.5) x 10(-29), (5.7 +/- 0.7) x 10(-29), and (3.9 +/- 0.4) x 10(-29) cm(6) molecule(-2) s(-1) in CF(4), N(2), and Ar bath gases, respectively, where the uncertainties are +/-2sigma in the scatter of the measurements. The average of the three independent measurements of the sum of the disproportionation rate constants (the zero pressure rate constant) was (3.4 +/- 6) x 10(-13) cm(3) molecule(-1) s(-1), where the uncertainty is +/-2sigma in the scatter of the measurements.

Virtual Instrument for Determining Rate Constant of Second-Order Reaction by pX Based on LabVIEW 8.0

PubMed Central

Meng, Hu; Li, Jiang-Yuan; Tang, Yong-Huai

2009-01-01

The virtual instrument system based on LabVIEW 8.0 for ion analyzer which can measure and analyze ion concentrations in solution is developed and comprises homemade conditioning circuit, data acquiring board, and computer. It can calibrate slope, temperature, and positioning automatically. When applied to determine the reaction rate constant by pX, it achieved live acquiring, real-time displaying, automatical processing of testing data, generating the report of results; and other functions. This method simplifies the experimental operation greatly, avoids complicated procedures of manual processing data and personal error, and improves veracity and repeatability of the experiment results. PMID:19730752

Virtual Instrument for Determining Rate Constant of Second-Order Reaction by pX Based on LabVIEW 8.0.

PubMed

Meng, Hu; Li, Jiang-Yuan; Tang, Yong-Huai

2009-01-01

The virtual instrument system based on LabVIEW 8.0 for ion analyzer which can measure and analyze ion concentrations in solution is developed and comprises homemade conditioning circuit, data acquiring board, and computer. It can calibrate slope, temperature, and positioning automatically. When applied to determine the reaction rate constant by pX, it achieved live acquiring, real-time displaying, automatical processing of testing data, generating the report of results; and other functions. This method simplifies the experimental operation greatly, avoids complicated procedures of manual processing data and personal error, and improves veracity and repeatability of the experiment results.

Scale-Dependent Rates of Uranyl Surface Complexation Reaction in Sediments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Chongxuan; Shang, Jianying; Kerisit, Sebastien N.

Scale-dependency of uranyl[U(VI)] surface complexation rates was investigated in stirred flow-cell and column systems using a U(VI)-contaminated sediment from the US Department of Energy, Hanford site, WA. The experimental results were used to estimate the apparent rate of U(VI) surface complexation at the grain-scale and in porous media. Numerical simulations using molecular, pore-scale, and continuum models were performed to provide insights into and to estimate the rate constants of U(VI) surface complexation at the different scales. The results showed that the grain-scale rate constant of U(VI) surface complexation was over 3 to 10 orders of magnitude smaller, dependent on themore » temporal scale, than the rate constant calculated using the molecular simulations. The grain-scale rate was faster initially and slower with time, showing the temporal scale-dependency. The largest rate constant at the grain-scale decreased additional 2 orders of magnitude when the rate was scaled to the porous media in the column. The scaling effect from the grain-scale to the porous media became less important for the slower sorption sites. Pore-scale simulations revealed the importance of coupled mass transport and reactions in both intragranular and inter-granular domains, which caused both spatial and temporal dependence of U(VI) surface complexation rates in the sediment. Pore-scale simulations also revealed a new rate-limiting mechanism in the intragranular porous domains that the rate of coupled diffusion and surface complexation reaction was slower than either process alone. The results provided important implications for developing models to scale geochemical/biogeochemical reactions.« less

Laser Measurements of the H Atom + Ozone Rate Constant at Atmospheric Temperatures

NASA Astrophysics Data System (ADS)

Liu, Y.; Smith, G. P.; Peng, J.; Reppert, K. J.; Callahan, S. L.

2015-12-01

The exothermic H + O3 reaction produces OH(v) Meinel band emissions, used to derive mesospheric H concentrations and chemical heating rates. We have remeasured its rate constant to reduce resulting uncertainties and the measurement extend to lower mesospheric temperatures using modern laser techniques. H atoms are produced by pulsed ultraviolet laser trace photolysis of O3, followed by reaction of O(D) with added H2. A second, delayed, frequency-mixed dye laser measures the reaction decay rate with the remaining ozone by laser induced fluorescence. We monitor either the H atom decay by 2 photon excitation at 205 nm and detection of red fluorescence, or the OH(v=9) product time evolution with excitation of the B-X (0,9) band at 237 nm and emission in blue B-A bands. By cooling the enclosed low pressure flow cell we obtained measurements from 146-305 K. Small kinetic modeling corrections are made for secondary regeneration of H atoms. The results fully confirm the current NASA JPL recommendation for this rate constant, and establish its extrapolation down to the lower temperatures of the mesosphere. This work was supported by the NSF Aeronomy Program and an NSF Physics summer REU student grant.

Modeling the pH and temperature dependence of aqueousphase hydroxyl radical reaction rate constants of organic micropollutants using QSPR approach.

PubMed

Gupta, Shikha; Basant, Nikita

2017-11-01

Designing of advanced oxidation process (AOP) requires knowledge of the aqueous phase hydroxyl radical ( ● OH) reactions rate constants (k OH ), which are strictly dependent upon the pH and temperature of the medium. In this study, pH- and temperature-dependent quantitative structure-property relationship (QSPR) models based on the decision tree boost (DTB) approach were developed for the prediction of k OH of diverse organic contaminants following the OECD guidelines. Experimental datasets (n = 958) pertaining to the k OH values of aqueous phase reactions at different pH (n = 470; 1.4 × 10 6 to 3.8 × 10 10  M -1  s -1 ) and temperature (n = 171; 1.0 × 10 7 to 2.6 × 10 10  M -1  s -1 ) were considered and molecular descriptors of the compounds were derived. The Sanderson scale electronegativity, topological polar surface area, number of double bonds, and halogen atoms in the molecule, in addition to the pH and temperature, were found to be the relevant predictors. The models were validated and their external predictivity was evaluated in terms of most stringent criteria parameters derived on the test data. High values of the coefficient of determination (R 2 ) and small root mean squared error (RMSE) in respective training (> 0.972, ≤ 0.12) and test (≥ 0.936, ≤ 0.16) sets indicated high generalization and predictivity of the developed QSPR model. Other statistical parameters derived from the training and test data also supported the robustness of the models and their suitability for screening new chemicals within the defined chemical space. The developed QSPR models provide a valuable tool for predicting the ● OH reaction rate constants of emerging new water contaminants for their susceptibility to AOPs.

RELATIVE RATE CONSTANTS OF CONTAMINANT CANDIDATE LIST PESTICIDES WITH HYDROXYL RADICALS

EPA Science Inventory

The objective of this study was to establish the rate constants for the reactions of selected pesticides listed on the US EPA Contaminant Candidate List, with UV and hydroxyl radicals (·OH). Batch experiments were conducted in phosphate buffered solution at pH 7. All pestici...

Rate constant for the fraction of atomic chlorine with formaldehyde from 200 to 500K

NASA Technical Reports Server (NTRS)

Michael, J. V.; Nava, D. F.; Payne, W. A.; Stief, L. J.

1978-01-01

A flash photolysis - resonance fluorescence technique was used to measure rate constant. The results were independent of substantial variations in H2CO, total pressure (Ar), and flash intensity (i.e., initial Cl). The rate constant was shown to be invariant with temperature, the best representation for this temperature range being K = (7.48 + or - 0.50) x 10 to the minus 11 power cu cm molecule-1 s-1 where the error is one standard deviation. The rate constant is theoretically discussed and the potential importance of the reaction in stratospheric chemistry is considered.

Nonadiabatic effects on the charge transfer rate constant: A numerical study of a simple model system

NASA Astrophysics Data System (ADS)

Shin, Seokmin; Metiu, Horia

1995-06-01

We use a minimal model to study the effects of the upper electronic states on the rate of a charge transfer reaction. The model consists of three ions and an electron, all strung on a line. The two ions at the ends of the structure are held fixed, but the middle ion and the electron are allowed to move in one dimension, along the line joining them. The system has two bound states, one in which the electron ties the movable ion to the fixed ion at the left, and the other in which the binding takes place to the fixed ion at the right. The transition between these bound states is a charge transfer reaction. We use the flux-flux correlation function theory to perform two calculations of the rate constant for this reaction. In one we obtain numerically the exact rate constant. In the other we calculate the exact rate constant for the case when the reaction proceeds exclusively on the ground adiabatic state. The difference between these calculations gives the magnitude of the nonadiabatic effects. We find that the nonadiabatic effects are fairly large even when the gap between the ground and the excited adiabatic state substantially exceeds the thermal energy. The rate in the nonadiabatic theory is always smaller than that of the adiabatic one. Both rate constants satisfy the Arrhenius formula. Their activation energies are very close but the nonadiabatic one is always higher. The nonadiabatic preexponential is smaller, due to the fact that the upper electronic state causes an early recrossing of the reactive flux. The description of this reaction in terms of two diabatic states, one for reactants and one for products, is not always adequate. In the limit when nonadiabaticity is small, we need to use a third diabatic state, in which the electron binds to the moving ion as the latter passes through the transition state; this is an atom transfer process. The reaction changes from an atom transfer to an electron transfer, as nonadiabaticity is increased.

Radiosensitization of DNA by Cisplatin Adducts Results from an Increase in the Rate Constant for the Reaction with Hydrated Electrons and Formation of Pt(I).

PubMed

Behmand, B; Marignier, J-L; Mostafavi, M; Wagner, J R; Hunting, D J; Sanche, L

2015-07-30

Pulse radiolysis measurements of the decay of hydrated electrons in solutions containing different concentrations of the oligonucleotide GTG with and without a cisplatin adduct show that the presence of a cisplatin moiety accelerates the reaction between hydrated electrons and the oligonucleotide. The rate constant of the reaction is found to be 2.23 × 10(10) mol(-1) L s(-1), which indicates that it is diffusion controlled. In addition, we show for the first time the formation of a Pt(I) intermediate as a result of the reaction of hydrated electrons with GTG-cisplatin. A putative reaction mechanism is proposed, which may form the basis of the radiosensitization of cancer cells in concomitant chemoradiation therapy with cisplatin.

Radiosensitization of DNA by Cisplatin Adducts Results from an Increase in the Rate Constant for the Reaction with Hydrated Electrons and Formation of PtI

PubMed Central

Behmand, B.; Marignier, J.-L.; Mostafavi, M.; Wagner, J. R.; Hunting, D. J.; Sanche, L.

2015-01-01

Pulse radiolysis measurements of the decay of hydrated electrons in solutions containing different concentrations of the oligonucleotide GTG with and without a cisplatin adduct show that the presence of a cisplatin moiety accelerates the reaction between hydrated electrons and the oligonucleotide. The rate constant of the reaction is found to be 2.23 × 1010 mol−1 L s−1, which indicates that it is diffusion controlled. In addition, we show for the first time the formation of a PtI intermediate as a result of the reaction of hydrated electrons with GTG-cisplatin. A putative reaction mechanism is proposed, which may form the basis of the radiosensitization of cancer cells in concomitant chemoradiation therapy with cisplatin. PMID:26098937

Free Radical Chemistry of Disinfection Byproducts 2: Rate Constants and Degradation Mechanism of Trichloronitromethane (Chloropicrin)

DOE Office of Scientific and Technical Information (OSTI.GOV)

B. J. Mincher; S. K. Cole; W. J. Cooper

2007-02-01

Absolute rate constants for the free-radical-induced degradation of trichloronitromethane (TCNM, chloropicrin) were determined using electron pulse radiolysis and transient absorption spectroscopy. Rate constants for hydroxyl radical, OH, and hydrated electron, eaq-, reactions were (4.97 ± 0.28) × 107 M-1 s-1 and (2.13 ± 0.03) × 1010 M-1 s-1, respectively. It appears that the OH adds to the nitro-group, while the eaq- reacts via dissociative electron attachment to give two carbon centered radicals. The mechanisms of these free radical reactions with TCNM were investigated, using 60Co gamma irradiation at various absorbed doses, measuring the disappearance of TCNM and the appearance ofmore » the product nitrate and chloride ions. The rate constants and mechanistic data were combined in a kinetic computer model that was used to describe the major free radical pathways for the destruction of TCNM in solution. These data are applicable to other advanced oxidation/reduction processes.« less

Predicting the Rate Constant of Electron Tunneling Reactions at the CdSe-TiO2 Interface.

PubMed

Hines, Douglas A; Forrest, Ryan P; Corcelli, Steven A; Kamat, Prashant V

2015-06-18

Current interest in quantum dot solar cells (QDSCs) motivates an understanding of the electron transfer dynamics at the quantum dot (QD)-metal oxide (MO) interface. Employing transient absorption spectroscopy, we have monitored the electron transfer rate (ket) at this interface as a function of the bridge molecules that link QDs to TiO2. Using mercaptoacetic acid, 3-mercaptopropionic acid, 8-mercaptooctanoic acid, and 16-mercaptohexadecanoic acid, we observe an exponential attenuation of ket with increasing linker length, and attribute this to the tunneling of the electron through the insulating linker molecule. We model the electron transfer reaction using both rectangular and trapezoidal barrier models that have been discussed in the literature. The one-electron reduction potential (equivalent to the lowest unoccupied molecular orbital) of each molecule as determined by cyclic voltammetry (CV) was used to estimate the effective barrier height presented by each ligand at the CdSe-TiO2 interface. The electron transfer rate (ket) calculated for each CdSe-ligand-TiO2 interface using both models showed the results in agreement with the experimentally determined trend. This demonstrates that electron transfer between CdSe and TiO2 can be viewed as electron tunneling through a layer of linking molecules and provides a useful method for predicting electron transfer rate constants.

Rate constants for proteins binding to substrates with multiple binding sites using a generalized forward flux sampling expression

NASA Astrophysics Data System (ADS)

Vijaykumar, Adithya; ten Wolde, Pieter Rein; Bolhuis, Peter G.

2018-03-01

To predict the response of a biochemical system, knowledge of the intrinsic and effective rate constants of proteins is crucial. The experimentally accessible effective rate constant for association can be decomposed in a diffusion-limited rate at which proteins come into contact and an intrinsic association rate at which the proteins in contact truly bind. Reversely, when dissociating, bound proteins first separate into a contact pair with an intrinsic dissociation rate, before moving away by diffusion. While microscopic expressions exist that enable the calculation of the intrinsic and effective rate constants by conducting a single rare event simulation of the protein dissociation reaction, these expressions are only valid when the substrate has just one binding site. If the substrate has multiple binding sites, a bound enzyme can, besides dissociating into the bulk, also hop to another binding site. Calculating transition rate constants between multiple states with forward flux sampling requires a generalized rate expression. We present this expression here and use it to derive explicit expressions for all intrinsic and effective rate constants involving binding to multiple states, including rebinding. We illustrate our approach by computing the intrinsic and effective association, dissociation, and hopping rate constants for a system in which a patchy particle model enzyme binds to a substrate with two binding sites. We find that these rate constants increase as a function of the rotational diffusion constant of the particles. The hopping rate constant decreases as a function of the distance between the binding sites. Finally, we find that blocking one of the binding sites enhances both association and dissociation rate constants. Our approach and results are important for understanding and modeling association reactions in enzyme-substrate systems and other patchy particle systems and open the way for large multiscale simulations of such systems.

RATE CONSTANTS FOR THE REACTIONS OF OH RADICALS AND CL ATOMS WITH DI-N-PROPYL ETHER AND DI-N-BUTYL ETHER AND THEIR DEUTERATED ANALOGS. (R825252)

EPA Science Inventory

Using relative rate methods, rate constants for the gas-phase reactions of OH radicals and Cl atoms with di-n-propyl ether, di-n-propyl ether-d₁₄, di-n-butyl ether and di-n-butyl ether-d₁₈ have been measured at 296 ? 2 K and atmos...

The gaseous explosive reaction at constant pressure : the reaction order and reaction rate

NASA Technical Reports Server (NTRS)

Stevens, F W

1931-01-01

The data given in this report covers the explosive limits of hydrocarbon fuels. Incidental to the purpose of the investigation here reported, the explosive limits will be found to be expressed for the condition of constant pressure, in the fundamental terms of concentrations (partial pressures) of fuel and oxygen.

Falloff curve and specific rate constants for the reaction NO/sub 2/ + NO/sub 2/ /r reversible/ N/sub 2/O/sub 4/

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borrell, P.; Cobos, C.J.; Luther, K.

1988-07-28

The rate of association of NO/sub 2/ to N/sub 2/O/sub 4/ was measured in N/sub 2/ at pressures from 1 to 207 bar. This way the reaction was observed in a large section of its falloff range. The relaxation of NO/sub 2//N/sub 2/O/sub 4/ mixtures was followed after laser flash photolysis of N/sub 2/O/sub 4/ at 248 nm. From the results the falloff curve was constructed, which gives the high- and low-pressure rate constants at 298 K (in cm/sup 3/ molecule/sup /minus/1/ s/sup /minus/1/): k/sub ass//sup infinity/ = (8.3 /plus minus/ 1.0) /times/ 10/sup /minus/13/ and k/sub ass//sup 0/ =more » (1.4 /plus minus/ 0.2) /times/ 10/sup /minus/33/(N/sub 2/). Earlier measurements believed to be in the low-pressure regime, have not been free from falloff effects. The low value of k/sup infinity/ was analyzed with the statistic adiabatic channel model, and specific rate constants, k(E,J), were calculated. They increase very steeply with energy just above the reaction threshold and go through maxima at low excess energies. These unusual effects are analyzed theoretically and the strong contributions are pointed out of the low-frequency vibrations which disappear during the dissociation of N/sub 2/O/sub 4/.« less

Theory for rates, equilibrium constants, and Brønsted slopes in F1-ATPase single molecule imaging experiments

PubMed Central

Volkán-Kacsó, Sándor; Marcus, Rudolph A.

2015-01-01

A theoretical model of elastically coupled reactions is proposed for single molecule imaging and rotor manipulation experiments on F1-ATPase. Stalling experiments are considered in which rates of individual ligand binding, ligand release, and chemical reaction steps have an exponential dependence on rotor angle. These data are treated in terms of the effect of thermodynamic driving forces on reaction rates, and lead to equations relating rate constants and free energies to the stalling angle. These relations, in turn, are modeled using a formalism originally developed to treat electron and other transfer reactions. During stalling the free energy profile of the enzymatic steps is altered by a work term due to elastic structural twisting. Using biochemical and single molecule data, the dependence of the rate constant and equilibrium constant on the stall angle, as well as the Børnsted slope are predicted and compared with experiment. Reasonable agreement is found with stalling experiments for ATP and GTP binding. The model can be applied to other torque-generating steps of reversible ligand binding, such as ADP and Pi release, when sufficient data become available. PMID:26483483

Single-shot characterization of enzymatic reaction constants Km and kcat by an acoustic-driven, bubble-based fast micromixer.

PubMed

Xie, Yuliang; Ahmed, Daniel; Lapsley, Michael Ian; Lin, Sz-Chin Steven; Nawaz, Ahmad Ahsan; Wang, Lin; Huang, Tony Jun

2012-09-04

In this work we present an acoustofluidic approach for rapid, single-shot characterization of enzymatic reaction constants K(m) and k(cat). The acoustofluidic design involves a bubble anchored in a horseshoe structure which can be stimulated by a piezoelectric transducer to generate vortices in the fluid. The enzyme and substrate can thus be mixed rapidly, within 100 ms, by the vortices to yield the product. Enzymatic reaction constants K(m) and k(cat) can then be obtained from the reaction rate curves for different concentrations of substrate while holding the enzyme concentration constant. We studied the enzymatic reaction for β-galactosidase and its substrate (resorufin-β-D-galactopyranoside) and found K(m) and k(cat) to be 333 ± 130 μM and 64 ± 8 s(-1), respectively, which are in agreement with published data. Our approach is valuable for studying the kinetics of high-speed enzymatic reactions and other chemical reactions.

Absolute rate of the reaction of Cl(p-2) with molecular hydrogen from 200 - 500 K

NASA Technical Reports Server (NTRS)

Whytock, D. A.; Lee, J. H.; Michael, J. V.; Payne, W. A.; Stief, L. J.

1976-01-01

Rate constants for the reaction of atomic chlorine with hydrogen are measured from 200 - 500 K using the flash photolysis-resonance fluorescence technique. The results are compared with previous work and are discussed with particular reference to the equilibrium constant for the reaction and to relative rate data for chlorine atom reactions. Theoretical calculations, using the BEBO method with tunneling, give excellent agreement with experiment.

On the Theory of Oxidation-Reduction Reactions Involving Electron Transfer. V. Comparison and Properties of Electrochemical and Chemical Rate Constants

DOE R&D Accomplishments Database

Marcus, R. A.

1962-01-01

Using a theory of electron transfers which takes cognizance of reorganization of the medium outside the inner coordination shell and of changes of bond lengths inside it, relations between electrochemical and related chemical rate constants are deduced and compared with the experimental data. A correlation is found, without the use of arbitrary parameters. Effects of weak complexes with added electrolytes are included under specified conditions. The deductions offer a way of coordinating a variety of data in the two fields, internally as well as with each those in another. For example, the rate of oxidation or reduction of a series of related reactants by one reagent is correlated with that of another and with that of the corresponding electrochemical oxidation-reduction reaction, under certain specified conditions. These correlations may also provide a test for distinguishing an electron from an atom transfer mechanism. (auth)

Efficient quantum-classical method for computing thermal rate constant of recombination: application to ozone formation.

PubMed

Ivanov, Mikhail V; Babikov, Dmitri

2012-05-14

Efficient method is proposed for computing thermal rate constant of recombination reaction that proceeds according to the energy transfer mechanism, when an energized molecule is formed from reactants first, and is stabilized later by collision with quencher. The mixed quantum-classical theory for the collisional energy transfer and the ro-vibrational energy flow [M. Ivanov and D. Babikov, J. Chem. Phys. 134, 144107 (2011)] is employed to treat the dynamics of molecule + quencher collision. Efficiency is achieved by sampling simultaneously (i) the thermal collision energy, (ii) the impact parameter, and (iii) the incident direction of quencher, as well as (iv) the rotational state of energized molecule. This approach is applied to calculate third-order rate constant of the recombination reaction that forms the (16)O(18)O(16)O isotopomer of ozone. Comparison of the predicted rate vs. experimental result is presented.

Eight-dimensional quantum reaction rate calculations for the H+CH{sub 4} and H{sub 2}+CH{sub 3} reactions on recent potential energy surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Yong; Zhang, Dong H., E-mail: zhangdh@dicp.ac.cn

2014-11-21

Eight-dimensional (8D) transition-state wave packet simulations have been performed on two latest potential energy surfaces (PES), the Zhou-Fu-Wang-Collins-Zhang (ZFWCZ) PES [Y. Zhou, B. Fu, C. Wang, M. A. Collins, and D. H. Zhang, J. Chem. Phys. 134, 064323 (2011)] and the Xu-Chen-Zhang (XCZ)-neural networks (NN) PES [X. Xu, J. Chen, and D. H. Zhang, Chin. J. Chem. Phys. 27, 373 (2014)]. Reaction rate constants for both the H+CH{sub 4} reaction and the H{sub 2}+CH{sub 3} reaction are calculated. Simulations of the H+CH{sub 4} reaction based on the XCZ-NN PES show that the ZFWCZ PES predicts rate constants with reasonable highmore » accuracy for low temperatures while leads to slightly lower results for high temperatures, in line with the distribution of interpolation error associated with the ZFWCZ PES. The 8D H+CH{sub 4} rate constants derived on the ZFWCZ PES compare well with full-dimensional 12D results based on the equivalent m-ZFWCZ PES, with a maximum relative difference of no more than 20%. Additionally, very good agreement is shown by comparing the 8D XCZ-NN rate constants with the 12D results obtained on the ZFWCZ-WM PES, after considering the difference in static barrier height between these two PESs. The reaction rate constants calculated for the H{sub 2}+CH{sub 3} reaction are found to be in good consistency with experimental observations.« less

Tunneling Rate Constants for H2CO+H on Amorphous Solid Water Surfaces

NASA Astrophysics Data System (ADS)

Song, Lei; Kästner, Johannes

2017-12-01

Formaldehyde (H2CO) is one of the most abundant molecules observed in the icy mantle covering interstellar grains. Studying its evolution can contribute to our understanding of the formation of complex organic molecules in various interstellar environments. In this work, we investigated the hydrogenation reactions of H2CO yielding CH3O, CH2OH, and the hydrogen abstraction resulting in H2+HCO on an amorphous solid water (ASW) surface using a quantum mechanics/molecular mechanics (QM/MM) model. The binding energies of H2CO on the ASW surface vary broadly, from 1000 to 9370 K. No correlation was found between binding energies and activation energies of hydrogenation reactions. Combining instanton theory with QM/MM modeling, we calculated rate constants for the Langmuir-Hinshelwood and the Eley-Rideal mechanisms for the three product channels of H+H2CO surface reactions down to 59 K. We found that the channel producing CH2OH can be ignored, owing to its high activation barrier leading to significantly lower rates than the other two channels. The ASW surface influences the reactivity in favor of formation of CH3O (branching ratio ˜80%) and hinders the H2CO dissociation into H2+HCO. In addition, kinetic isotope effects are strong in all reaction channels and vary strongly between the channels. Finally, we provide fits of the rate constants to be used in astrochemical models.

Inflation with a constant rate of roll

NASA Astrophysics Data System (ADS)

Motohashi, Hayato; Starobinsky, Alexei A.; Yokoyama, Jun'ichi

2015-09-01

We consider an inflationary scenario where the rate of inflaton roll defined by ̈phi/H dot phi remains constant. The rate of roll is small for slow-roll inflation, while a generic rate of roll leads to the interesting case of 'constant-roll' inflation. We find a general exact solution for the inflaton potential required for such inflaton behaviour. In this model, due to non-slow evolution of background, the would-be decaying mode of linear scalar (curvature) perturbations may not be neglected. It can even grow for some values of the model parameter, while the other mode always remains constant. However, this always occurs for unstable solutions which are not attractors for the given potential. The most interesting particular cases of constant-roll inflation remaining viable with the most recent observational data are quadratic hilltop inflation (with cutoff) and natural inflation (with an additional negative cosmological constant). In these cases even-order slow-roll parameters approach non-negligible constants while the odd ones are asymptotically vanishing in the quasi-de Sitter regime.

Inflation with a constant rate of roll

DOE Office of Scientific and Technical Information (OSTI.GOV)

Motohashi, Hayato; Starobinsky, Alexei A.; Yokoyama, Jun'ichi, E-mail: motohashi@kicp.uchicago.edu, E-mail: alstar@landau.ac.ru, E-mail: yokoyama@resceu.s.u-tokyo.ac.jp

2015-09-01

We consider an inflationary scenario where the rate of inflaton roll defined by {sup ··}φ/H φ-dot remains constant. The rate of roll is small for slow-roll inflation, while a generic rate of roll leads to the interesting case of 'constant-roll' inflation. We find a general exact solution for the inflaton potential required for such inflaton behaviour. In this model, due to non-slow evolution of background, the would-be decaying mode of linear scalar (curvature) perturbations may not be neglected. It can even grow for some values of the model parameter, while the other mode always remains constant. However, this always occurs formore » unstable solutions which are not attractors for the given potential. The most interesting particular cases of constant-roll inflation remaining viable with the most recent observational data are quadratic hilltop inflation (with cutoff) and natural inflation (with an additional negative cosmological constant). In these cases even-order slow-roll parameters approach non-negligible constants while the odd ones are asymptotically vanishing in the quasi-de Sitter regime.« less

Association rate constants for reactions between resonance-stabilized radicals: C 3H 3 + C 3H 3, C 3H 3 + C 3H 5, and C 3H 5 + C 3H 5

DOE PAGES

Georgievskii, Yuri; Miller, James A.; Klippenstein, Stephen J.

2007-05-18

Reactions between resonance-stabilized radicals play an important role in combustion chemistry. The theoretical prediction of rate coefficients and product distributions for such reactions is complicated by the fact that the initial complex-formation steps and some dissociation steps are barrierless. In this work, direct variable reaction coordinate transition state theory (VRC-TST) is used to predict accurately the association rate constants for the self and cross reactions of propargyl and allyl radicals. For each reaction, a set of multifaceted dividing surfaces is used to account for the multiple possible addition channels. Because of their resonant nature the geometric relaxation of the radicalsmore » is important. Here, the effect of this relaxation is explicitly calculated with the UB3LYP/cc-pvdz method for each mutual orientation encountered in the configurational integrals over the transition state dividing surfaces. The final energies are obtained from CASPT2/cc-pvdz calculations with all π-orbitals in the active space. Evaluations along the minimum energy path suggest that basis set corrections are negligible. The VRC-TST approach was also used to calculate the association rate constant and the corresponding number of states for the C 6H 5 + H → C 6H 6 exit channel of the C 3H 3 + C 3H 3 reaction, which is also barrierless. For this reaction, the interaction energies were evaluated with the CASPT2(2e,2o)/cc-pvdz method and a 1-D correction is included on the basis of CAS+1+2+QC/aug-cc-pvtz calculations for the CH 3 + H reference system. For the C 3H 3 + C 3H 3 reaction, the VRC-TST results for the energy and angular momentum resolved numbers of states in the entrance channels and in the C 6H 5 + H exit channel are incorporated in a master equation simulation to determine the temperature and pressure dependence of the phenomenological rate coefficients. The rate constants for the C 3H 3 + C 3H 3 and C 3H 5 + C 3H 5 self-reactions compare favorably

Correcting reaction rates measured by saturation-transfer magnetic resonance spectroscopy

NASA Astrophysics Data System (ADS)

Gabr, Refaat E.; Weiss, Robert G.; Bottomley, Paul A.

2008-04-01

Off-resonance or spillover irradiation and incomplete saturation can introduce significant errors in the estimates of chemical rate constants measured by saturation-transfer magnetic resonance spectroscopy (MRS). Existing methods of correction are effective only over a limited parameter range. Here, a general approach of numerically solving the Bloch-McConnell equations to calculate exchange rates, relaxation times and concentrations for the saturation-transfer experiment is investigated, but found to require more measurements and higher signal-to-noise ratios than in vivo studies can practically afford. As an alternative, correction formulae for the reaction rate are provided which account for the expected parameter ranges and limited measurements available in vivo. The correction term is a quadratic function of experimental measurements. In computer simulations, the new formulae showed negligible bias and reduced the maximum error in the rate constants by about 3-fold compared to traditional formulae, and the error scatter by about 4-fold, over a wide range of parameters for conventional saturation transfer employing progressive saturation, and for the four-angle saturation-transfer method applied to the creatine kinase (CK) reaction in the human heart at 1.5 T. In normal in vivo spectra affected by spillover, the correction increases the mean calculated forward CK reaction rate by 6-16% over traditional and prior correction formulae.

Rate Constants and Mechanisms of Protein–Ligand Binding

PubMed Central

Pang, Xiaodong; Zhou, Huan-Xiang

2017-01-01

Whereas protein–ligand binding affinities have long-established prominence, binding rate constants and binding mechanisms have gained increasing attention in recent years. Both new computational methods and new experimental techniques have been developed to characterize the latter properties. It is now realized that binding mechanisms, like binding rate constants, can and should be quantitatively determined. In this review, we summarize studies and synthesize ideas on several topics in the hope of providing a coherent picture of and physical insight into binding kinetics. The topics include microscopic formulation of the kinetic problem and its reduction to simple rate equations; computation of binding rate constants; quantitative determination of binding mechanisms; and elucidation of physical factors that control binding rate constants and mechanisms. PMID:28375732

USE OF ROUGH SETS AND SPECTRAL DATA FOR BUILDING PREDICTIVE MODELS OF REACTION RATE CONSTANTS

EPA Science Inventory

A model for predicting the log of the rate constants for alkaline hydrolysis of organic esters has been developed with the use of gas-phase min-infrared library spectra and a rule-building software system based on the mathematical theory of rough sets. A diverse set of 41 esters ...

A comprehensive model to determine the effects of temperature and species fluctuations on reaction rates in turbulent reacting flows

NASA Technical Reports Server (NTRS)

Foy, E.; Ronan, G.; Chinitz, W.

1982-01-01

A principal element to be derived from modeling turbulent reacting flows is an expression for the reaction rates of the various species involved in any particular combustion process under consideration. A temperature-derived most-likely probability density function (pdf) was used to describe the effects of temperature fluctuations on the Arrhenius reaction rate constant. A most-likely bivariate pdf described the effects of temperature and species concentrations fluctuations on the reaction rate. A criterion is developed for the use of an "appropriate" temperature pdf. The formulation of models to calculate the mean turbulent Arrhenius reaction rate constant and the mean turbulent reaction rate is considered and the results of calculations using these models are presented.

On determining dose rate constants spectroscopically.

PubMed

Rodriguez, M; Rogers, D W O

2013-01-01

To investigate several aspects of the Chen and Nath spectroscopic method of determining the dose rate constants of (125)I and (103)Pd seeds [Z. Chen and R. Nath, Phys. Med. Biol. 55, 6089-6104 (2010)] including the accuracy of using a line or dual-point source approximation as done in their method, and the accuracy of ignoring the effects of the scattered photons in the spectra. Additionally, the authors investigate the accuracy of the literature's many different spectra for bare, i.e., unencapsulated (125)I and (103)Pd sources. Spectra generated by 14 (125)I and 6 (103)Pd seeds were calculated in vacuo at 10 cm from the source in a 2.7 × 2.7 × 0.05 cm(3) voxel using the EGSnrc BrachyDose Monte Carlo code. Calculated spectra used the initial photon spectra recommended by AAPM's TG-43U1 and NCRP (National Council of Radiation Protection and Measurements) Report 58 for the (125)I seeds, or TG-43U1 and NNDC(2000) (National Nuclear Data Center, 2000) for (103)Pd seeds. The emitted spectra were treated as coming from a line or dual-point source in a Monte Carlo simulation to calculate the dose rate constant. The TG-43U1 definition of the dose rate constant was used. These calculations were performed using the full spectrum including scattered photons or using only the main peaks in the spectrum as done experimentally. Statistical uncertainties on the air kerma/history and the dose rate/history were ≤0.2%. The dose rate constants were also calculated using Monte Carlo simulations of the full seed model. The ratio of the intensity of the 31 keV line relative to that of the main peak in (125)I spectra is, on average, 6.8% higher when calculated with the NCRP Report 58 initial spectrum vs that calculated with TG-43U1 initial spectrum. The (103)Pd spectra exhibit an average 6.2% decrease in the 22.9 keV line relative to the main peak when calculated with the TG-43U1 rather than the NNDC(2000) initial spectrum. The measured values from three different investigations are

Oxidation of CO by N/sub 2/O between 1076 and 1228 K: determination of the rate constant of the exchange reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loirat, H.; Caralp, F.; Destriau, M.

New measurements of the rate constant of the direct reaction of CO with N/sub 2/O are reported with the principal purpose of removing some of the remaining discrepancies on its value. Experiments were performed at lower temperatures (1076-1228 K) and lower pressure (approx. 15 Torr) than those prevailing in most of previous works, by using a static reactor. It is shown that, under these experimental conditions, the reaction proceeds essentially according to the direct reaction CO + N/sub 2/O ..-->.. CO/sub 2/ + N/sub 2/ (1). The previously proposed wet mechanism is not significant under our experimental conditions. It hasmore » to be taken into account, however, to describe the observed production and consumption of molecular oxygen. The Arrhenius expression derived from these experiments is k/sub 1/ = 10/sup 14.4 +/- 0.3 exp(-(46 +- 2) kcal mol/sup -1/RT) cm/sup 3/ mol/sup -1/ s/sup -1/. A detailed analysis of the results shows that the uncertainties in side reactions do not greatly influence the value of k/sub 1/. A critical discussion of the data reported in the literature is presented. In spite of remaining uncertainties in the reaction mechanism, the present results, obtained in a low-temperature range, show that the low activation energy values of reaction 1, reported in several works performed at higher temperatures, are highly unlikely« less

Hybrid Quantum Mechanical and Molecular Mechanics Study of the SN2 Reaction of CCl4 + OH- in Aqueous Solution: The Potential of Mean Force, Reaction Energetics, and Rate Constants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Ting; Yin, Hongyun; Wang, Dunyou

2012-02-16

The bimolecular nucleophilic substitution reaction of CCl{sub 4} and OH{sup -} in aqueous solution was investigated on the basis of a combined quantum mechanical and molecular mechanics method. A multilayered representation approach is employed to achieve high accuracy results at the CCSD(T) level of theory. The potential of mean force calculations at the DFT level and CCSD(T) level of theory yield reaction barrier heights of 22.7 and 27.9 kcal/mol, respectively. Both the solvation effects and the solvent-induced polarization effect have significant contributions to the reaction energetics, for example, the solvation effect raises the saddle point by 10.6 kcal/mol. The calculatedmore » rate constant coefficient is 8.6 x 10{sup -28} cm{sup 3} molecule{sup -1} s{sup -1} at the standard state condition, which is about 17 orders magnitude smaller than that in the gas phase. Among the four chloromethanes (CH{sub 3}Cl, CH{sub 2}Cl{sub 2}, CHCl{sub 3}, and CCl{sub 4}), CCl{sub 4} has the lowest free energy activation barrier for the reaction with OH{sup -1} in aqueous solution, confirming the trend that substitution of Cl by H in chloromethanes diminishes the reactivity.« less

Rate and Equilibrium Constants for the Addition of N-Heterocyclic Carbenes into Benzaldehydes: A Remarkable 2-Substituent Effect**

PubMed Central

Collett, Christopher J; Massey, Richard S; Taylor, James E; Maguire, Oliver R; O'Donoghue, AnnMarie C; Smith, Andrew D

2015-01-01

Rate and equilibrium constants for the reaction between N-aryl triazolium N-heterocyclic carbene (NHC) precatalysts and substituted benzaldehyde derivatives to form 3-(hydroxybenzyl)azolium adducts under both catalytic and stoichiometric conditions have been measured. Kinetic analysis and reaction profile fitting of both the forward and reverse reactions, plus onwards reaction to the Breslow intermediate, demonstrate the remarkable effect of the benzaldehyde 2-substituent in these reactions and provide insight into the chemoselectivity of cross-benzoin reactions. PMID:25908493

Determination of equilibrium and rate constants for complex formation by fluorescence correlation spectroscopy supplemented by dynamic light scattering and Taylor dispersion analysis.

PubMed

Zhang, Xuzhu; Poniewierski, Andrzej; Jelińska, Aldona; Zagożdżon, Anna; Wisniewska, Agnieszka; Hou, Sen; Hołyst, Robert

2016-10-04

The equilibrium and rate constants of molecular complex formation are of great interest both in the field of chemistry and biology. Here, we use fluorescence correlation spectroscopy (FCS), supplemented by dynamic light scattering (DLS) and Taylor dispersion analysis (TDA), to study the complex formation in model systems of dye-micelle interactions. In our case, dyes rhodamine 110 and ATTO-488 interact with three differently charged surfactant micelles: octaethylene glycol monododecyl ether C 12 E 8 (neutral), cetyltrimethylammonium chloride CTAC (positive) and sodium dodecyl sulfate SDS (negative). To determine the rate constants for the dye-micelle complex formation we fit the experimental data obtained by FCS with a new form of the autocorrelation function, derived in the accompanying paper. Our results show that the association rate constants for the model systems are roughly two orders of magnitude smaller than those in the case of the diffusion-controlled limit. Because the complex stability is determined by the dissociation rate constant, a two-step reaction mechanism, including the diffusion-controlled and reaction-controlled rates, is used to explain the dye-micelle interaction. In the limit of fast reaction, we apply FCS to determine the equilibrium constant from the effective diffusion coefficient of the fluorescent components. Depending on the value of the equilibrium constant, we distinguish three types of interaction in the studied systems: weak, intermediate and strong. The values of the equilibrium constant obtained from the FCS and TDA experiments are very close to each other, which supports the theoretical model used to interpret the FCS data.

Theoretical rate constants of super-exchange hole transfer and thermally induced hopping in DNA.

PubMed

Shimazaki, Tomomi; Asai, Yoshihiro; Yamashita, Koichi

2005-01-27

Recently, the electronic properties of DNA have been extensively studied, because its conductivity is important not only to the study of fundamental biological problems, but also in the development of molecular-sized electronics and biosensors. We have studied theoretically the reorganization energies, the activation energies, the electronic coupling matrix elements, and the rate constants of hole transfer in B-form double-helix DNA in water. To accommodate the effects of DNA nuclear motions, a subset of reaction coordinates for hole transfer was extracted from classical molecular dynamics (MD) trajectories of DNA in water and then used for ab initio quantum chemical calculations of electron coupling constants based on the generalized Mulliken-Hush model. A molecular mechanics (MM) method was used to determine the nuclear Franck-Condon factor. The rate constants for two types of mechanisms of hole transfer-the thermally induced hopping (TIH) and the super-exchange mechanisms-were determined based on Marcus theory. We found that the calculated matrix elements are strongly dependent on the conformations of the nucleobase pairs of hole-transferable DNA and extend over a wide range of values for the "rise" base-step parameter but cluster around a particular value for the "twist" parameter. The calculated activation energies are in good agreement with experimental results. Whereas the rate constant for the TIH mechanism is not dependent on the number of A-T nucleobase pairs that act as a bridge, the rate constant for the super-exchange process rapidly decreases when the length of the bridge increases. These characteristic trends in the calculated rate constants effectively reproduce those in the experimental data of Giese et al. [Nature 2001, 412, 318]. The calculated rate constants were also compared with the experimental results of Lewis et al. [Nature 2000, 406, 51].

Rate constant for the reaction NH2 + NO from 216 to 480 K

NASA Technical Reports Server (NTRS)

Stief, L. J.; Brobst, W. D.; Nava, D. F.; Borkowski, R. P.; Michael, J. V.

1982-01-01

The absolute rate constant was measured by the technique of flash photolysis-laser induced fluorescence (FP-LIF). NH2 radicals were produced by the flash photolysis of ammonia and the fluorescent NH2 photons were measured by multiscaling techniques. At each temperature, the results were independent of variations in total pressure, and flash intensity. The results are compared with previous determinations using the techniques of mass spectrometry, absorption spectroscopy, laser absorption spectroscopy, and laser induced fluorescence. The implications of the results are discussed with regard to combustion, post combustion, and atmospheric chemistry. The results are also discussed theoretically.

Theoretical derivation for reaction rate constants of H abstraction from thiophenol by the H/O radical pool

PubMed Central

Batiha, Marwan; Altarawneh, Mohammednoor; Al-Harahsheh, Mohammad; Altarawneh, Ibrahem; Rawadieh, Saleh

2011-01-01

Reaction and activation energy barriers are calculated for the H abstraction reactions (C6H5SH + X• → C6H5S + XH, X = H, OH and HO2) at the BB1K/GTLarge level of theory. The corresponding reactions with H2S and CH3SH are also investigated using the G3B3 and CBS-QB3 methods in order to demonstrate the accuracy of BB1K functional in finding activation barriers for hydrogen atom transfer reactions. Arrhenius parameters for the title reactions are fitted in the temperature range of 300 K–2000 K. The calculated reaction enthalpies are in good agreement with their corresponding experimental reaction enthalpies. It is found that H abstraction by OH radicals from the thiophenol molecule proceed in a much slower rate in reference to the analogous phenol molecule. ΔfH298o of thiophenoxy radical is calculated to be 63.3 kcal/mol. Kinetic parameters presented herein should be useful in describing the decomposition rate of thiophenol; i.e., one of the major aromatic sulfur carriers, at high temperatures. PMID:22485200

Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation.

PubMed

Liebermeister, Wolfram; Uhlendorf, Jannis; Klipp, Edda

2010-06-15

Standard rate laws are a key requisite for systematically turning metabolic networks into kinetic models. They should provide simple, general and biochemically plausible formulae for reaction velocities and reaction elasticities. At the same time, they need to respect thermodynamic relations between the kinetic constants and the metabolic fluxes and concentrations. We present a family of reversible rate laws for reactions with arbitrary stoichiometries and various types of regulation, including mass-action, Michaelis-Menten and uni-uni reversible Hill kinetics as special cases. With a thermodynamically safe parameterization of these rate laws, parameter sets obtained by model fitting, sampling or optimization are guaranteed to lead to consistent chemical equilibrium states. A reformulation using saturation values yields simple formulae for rates and elasticities, which can be easily adjusted to the given stationary flux distributions. Furthermore, this formulation highlights the role of chemical potential differences as thermodynamic driving forces. We compare the modular rate laws to the thermodynamic-kinetic modelling formalism and discuss a simplified rate law in which the reaction rate directly depends on the reaction affinity. For automatic handling of modular rate laws, we propose a standard syntax and semantic annotations for the Systems Biology Markup Language. An online tool for inserting the rate laws into SBML models is freely available at www.semanticsbml.org. Supplementary data are available at Bioinformatics online.

Comparison of TID Effects in Space-Like Variable Dose Rates and Constant Dose Rates

NASA Technical Reports Server (NTRS)

Harris, Richard D.; McClure, Steven S.; Rax, Bernard G.; Evans, Robin W.; Jun, Insoo

2008-01-01

The degradation of the LM193 dual voltage comparator has been studied at different TID dose rate profiles, including several different constant dose rates and a variable dose rate that simulates the behavior of a solar flare. A comparison of results following constant dose rate vs. variable dose rates is made to explore how well the constant dose rates used for typical part testing predict the performance during a simulated space-like mission. Testing at a constant dose rate equal to the lowest dose rate seen during the simulated flare provides an extremely conservative estimate of the overall amount of degradation. A constant dose rate equal to the average dose rate is also more conservative than the variable rate. It appears that, for this part, weighting the dose rates by the amount of total dose received at each rate (rather than the amount of time at each dose rate) results in an average rate that produces an amount of degradation that is a reasonable approximation to that received by the variable rate.

Channel specific rate constants for reactions of O(1D) with HCl and HBr

NASA Technical Reports Server (NTRS)

Wine, P. H.; Wells, J. R.; Ravishankara, A. R.

1986-01-01

The absolute rate coefficients and product yields for reactions of O(1D) with HCl(1) and HBr(2) at 287 K are presently determined by means of the time-resolved resonance fluorescence detection of O(3P) and H(2S) in conjunction with pulsed laser photolysis of O3/HX/He mixtures. Total rate coefficients for O(1D) removal are found to be, in units of 10 to the -10th cu cm/molecule per sec, k(1) = 1.50 + or - 0.18 and k(2) 1.48 + or - 0.16; the absolute accuracy of these rate coefficients is estimated to be + or - 20 percent.

Reversible Hydrogen Transfer Reactions in Thiyl Radicals From Cysteine and Related Molecules: Absolute Kinetics and Equilibrium Constants Determined by Pulse Radiolysis

PubMed Central

Koppenol, Willem H.

2013-01-01

The mercapto group of cysteine (Cys) is a predominant target for oxidative modification, where one-electron oxidation leads to the formation of Cys thiyl radicals, CysS•. These Cys thiyl radicals enter 1,2- and 1,3-hydrogen transfer reactions, for which rate constants are reported in this paper. The products of these 1,2- and 1,3-hydrogen transfer reactions are carbon-centered radicals at position C3 (α-mercaptoalkyl radicals) and C2 (•Cα radicals) of Cys, respectively. Both processes can be monitored separately in Cys analogues such as cysteamine (CyaSH) and penicillamine (PenSH). At acidic pH, thiyl radicals from CyaSH permit only the 1,2-hydrogen transfer according to equilibrium 12, +H3NCH2CH2S• ⇌ +H3NCH2 •CH–SH, where rate constants for forward and reverse reaction are k12 ≈ 105 s−1 and k−12 ≈ 1.5 × 105s−1, respectively. In contrast, only the 1,3-hydrogen transfer is possible for thiyl radicals from PenSH according to equilibrium 14, (+H3N/CO2H)Cα–C(CH3)2–S• ⇌ (+H3N/CO2H)•Cα–C(CH3)2–SH, where rate constants for the forward and the reverse reaction are k14 = 8 × 104 s−1 and k−14 = 1.4 × 106 s−1. The •Cα radicals from PenSH and Cys have the additional opportunity for β-elimination of HS•/S•−, which proceeds with k39 ≈ (3 ± 1) × 104 s−1 from •Cα radicals from PenSH and k−34 ≈ 5 × 103 s−1 from •Cα radicals from Cys. The rate constants quantified for the 1,2- and 1,3-hydrogen transfer reactions can be used as a basis to calculate similar processes for Cys thiyl radicals in proteins, where hydrogen transfer reactions, followed by the addition of oxygen, may lead to the irreversible modification of target proteins. PMID:22483034

Atmospheric fate of a series of carbonyl nitrates: photolysis frequencies and OH-oxidation rate constants.

PubMed

Suarez-Bertoa, R; Picquet-Varrault, B; Tamas, W; Pangui, E; Doussin, J-F

2012-11-20

Multifunctional organic nitrates are potential NO(x) reservoirs whose atmospheric chemistry is somewhat little known. They could play an important role in the spatial distribution of reactive nitrogen species and consequently in ozone formation and distribution in remote areas. In this work, the rate constants for the reaction with OH radical and the photolysis frequencies of α-nitrooxyacetone, 3-nitrooxy-2-butanone, and 3-methyl-3-nitrooxy-2-butanone have been determined at room temperature at 1000 mbar total pressure of synthetic air. The rate constants for the OH oxidation were measured using the relative rate technique, with methanol as reference compound. The following rate constants were obtained for the reaction with OH: k(OH) = (6.7 ± 2.5) × 10(-13) cm(3) molecule(-1) s(-1) for α-nitrooxyacetone, (10.6 ± 4.1) × 10(-13) cm(3) molecule(-1) s(-1) for 3-nitrooxy-2-butanone, and (2.6 ± 0.9) × 10(-13) cm(3) molecule(-1) s(-1) for 3-methyl-3-nitrooxy-2-butanone. The corresponding photolysis frequencies extrapolated to typical atmospheric conditions for July first at noon at 40° latitude North were (4.8 ± 0.3) × 10(-5) s(-1), (5.7 ± 0.3) × 10(-5) s(-1), and (7.4 ± 0.2) × 10(-5) s(-1), respectively. The data show that photolysis is a major atmospheric sink for these organic nitrates.

On determining dose rate constants spectroscopically

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodriguez, M.; Rogers, D. W. O.

2013-01-15

Purpose: To investigate several aspects of the Chen and Nath spectroscopic method of determining the dose rate constants of {sup 125}I and {sup 103}Pd seeds [Z. Chen and R. Nath, Phys. Med. Biol. 55, 6089-6104 (2010)] including the accuracy of using a line or dual-point source approximation as done in their method, and the accuracy of ignoring the effects of the scattered photons in the spectra. Additionally, the authors investigate the accuracy of the literature's many different spectra for bare, i.e., unencapsulated {sup 125}I and {sup 103}Pd sources. Methods: Spectra generated by 14 {sup 125}I and 6 {sup 103}Pd seedsmore » were calculated in vacuo at 10 cm from the source in a 2.7 Multiplication-Sign 2.7 Multiplication-Sign 0.05 cm{sup 3} voxel using the EGSnrc BrachyDose Monte Carlo code. Calculated spectra used the initial photon spectra recommended by AAPM's TG-43U1 and NCRP (National Council of Radiation Protection and Measurements) Report 58 for the {sup 125}I seeds, or TG-43U1 and NNDC(2000) (National Nuclear Data Center, 2000) for {sup 103}Pd seeds. The emitted spectra were treated as coming from a line or dual-point source in a Monte Carlo simulation to calculate the dose rate constant. The TG-43U1 definition of the dose rate constant was used. These calculations were performed using the full spectrum including scattered photons or using only the main peaks in the spectrum as done experimentally. Statistical uncertainties on the air kerma/history and the dose rate/history were Less-Than-Or-Slanted-Equal-To 0.2%. The dose rate constants were also calculated using Monte Carlo simulations of the full seed model. Results: The ratio of the intensity of the 31 keV line relative to that of the main peak in {sup 125}I spectra is, on average, 6.8% higher when calculated with the NCRP Report 58 initial spectrum vs that calculated with TG-43U1 initial spectrum. The {sup 103}Pd spectra exhibit an average 6.2% decrease in the 22.9 keV line relative to the main peak

Rapid estimation of glucosinolate thermal degradation rate constants in leaves of Chinese kale and broccoli (Brassica oleracea) in two seasons.

PubMed

Hennig, Kristin; Verkerk, Ruud; Bonnema, Guusje; Dekker, Matthijs

2012-08-15

Kinetic modeling was used as a tool to quantitatively estimate glucosinolate thermal degradation rate constants. Literature shows that thermal degradation rates differ in different vegetables. Well-characterized plant material, leaves of broccoli and Chinese kale plants grown in two seasons, was used in the study. It was shown that a first-order reaction is appropriate to model glucosinolate degradation independent from the season. No difference in degradation rate constants of structurally identical glucosinolates was found between broccoli and Chinese kale leaves when grown in the same season. However, glucosinolate degradation rate constants were highly affected by the season (20-80% increase in spring compared to autumn). These results suggest that differences in glucosinolate degradation rate constants can be due to variation in environmental as well as genetic factors. Furthermore, a methodology to estimate rate constants rapidly is provided to enable the analysis of high sample numbers for future studies.

Rate variations of a hetero-Diels--Alder reaction in supercritical fluid CO{sub 2}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, R.L.; Glaeser, R.; Bush, D.

1999-11-01

The hetero-Diels-Alder reaction between anthracene and excess 4-phenyl-1,2,4-triazoline-3,5-dione has been investigated in supercritical CO{sub 2} at 40 C and pressures between 75 and 216 bar. Biomolecular reaction rate constants have been measured via fluorescence spectroscopy by following the decrease in anthracene concentration with reaction time. The reaction rate is elevated in the vicinity of the critical pressure. This difference is consistent with local composition enhancement and can be modeled with the Peng-Robinson equation of state.

Relationship between reaction rate constants of organic pollutants and their molecular descriptors during Fenton oxidation and in situ formed ferric-oxyhydroxides.

PubMed

Jia, Lijuan; Shen, Zhemin; Su, Pingru

2016-05-01

Fenton oxidation is a promising water treatment method to degrade organic pollutants. In this study, 30 different organic compounds were selected and their reaction rate constants (k) were determined for the Fenton oxidation process. Gaussian09 and Material Studio software sets were used to carry out calculations and obtain values of 10 different molecular descriptors for each studied compound. Ferric-oxyhydroxide coagulation experiments were conducted to determine the coagulation percentage. Based upon the adsorption capacity, all of the investigated organic compounds were divided into two groups (Group A and Group B). The percentage adsorption of organic compounds in Group A was less than 15% (wt./wt.) and that in the Group B was higher than 15% (wt./wt.). For Group A, removal of the compounds by oxidation was the dominant process while for Group B, removal by both oxidation and coagulation (as a synergistic process) took place. Results showed that the relationship between the rate constants (k values) and the molecular descriptors of Group A was more pronounced than for Group B compounds. For the oxidation-dominated process, EHOMO and Fukui indices (f(0)x, f(-)x, f(+)x) were the most significant factors. The influence of bond order was more significant for the synergistic process of oxidation and coagulation than for the oxidation-dominated process. The influences of all other molecular descriptors on the synergistic process were weaker than on the oxidation-dominated process. Copyright © 2015. Published by Elsevier B.V.

Estimating reaction rate coefficients within a travel-time modeling framework.

PubMed

Gong, R; Lu, C; Wu, W-M; Cheng, H; Gu, B; Watson, D; Jardine, P M; Brooks, S C; Criddle, C S; Kitanidis, P K; Luo, J

2011-01-01

A generalized, efficient, and practical approach based on the travel-time modeling framework is developed to estimate in situ reaction rate coefficients for groundwater remediation in heterogeneous aquifers. The required information for this approach can be obtained by conducting tracer tests with injection of a mixture of conservative and reactive tracers and measurements of both breakthrough curves (BTCs). The conservative BTC is used to infer the travel-time distribution from the injection point to the observation point. For advection-dominant reactive transport with well-mixed reactive species and a constant travel-time distribution, the reactive BTC is obtained by integrating the solutions to advective-reactive transport over the entire travel-time distribution, and then is used in optimization to determine the in situ reaction rate coefficients. By directly working on the conservative and reactive BTCs, this approach avoids costly aquifer characterization and improves the estimation for transport in heterogeneous aquifers which may not be sufficiently described by traditional mechanistic transport models with constant transport parameters. Simplified schemes are proposed for reactive transport with zero-, first-, nth-order, and Michaelis-Menten reactions. The proposed approach is validated by a reactive transport case in a two-dimensional synthetic heterogeneous aquifer and a field-scale bioremediation experiment conducted at Oak Ridge, Tennessee. The field application indicates that ethanol degradation for U(VI)-bioremediation is better approximated by zero-order reaction kinetics than first-order reaction kinetics. Copyright © 2010 The Author(s). Journal compilation © 2010 National Ground Water Association.

Estimating Reaction Rate Coefficients Within a Travel-Time Modeling Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gong, R; Lu, C; Luo, Jian

A generalized, efficient, and practical approach based on the travel-time modeling framework is developed to estimate in situ reaction rate coefficients for groundwater remediation in heterogeneous aquifers. The required information for this approach can be obtained by conducting tracer tests with injection of a mixture of conservative and reactive tracers and measurements of both breakthrough curves (BTCs). The conservative BTC is used to infer the travel-time distribution from the injection point to the observation point. For advection-dominant reactive transport with well-mixed reactive species and a constant travel-time distribution, the reactive BTC is obtained by integrating the solutions to advective-reactive transportmore » over the entire travel-time distribution, and then is used in optimization to determine the in situ reaction rate coefficients. By directly working on the conservative and reactive BTCs, this approach avoids costly aquifer characterization and improves the estimation for transport in heterogeneous aquifers which may not be sufficiently described by traditional mechanistic transport models with constant transport parameters. Simplified schemes are proposed for reactive transport with zero-, first-, nth-order, and Michaelis-Menten reactions. The proposed approach is validated by a reactive transport case in a two-dimensional synthetic heterogeneous aquifer and a field-scale bioremediation experiment conducted at Oak Ridge, Tennessee. The field application indicates that ethanol degradation for U(VI)-bioremediation is better approximated by zero-order reaction kinetics than first-order reaction kinetics.« less

Rate and Equilibrium Constants for the Addition of N‐Heterocyclic Carbenes into Benzaldehydes: A Remarkable 2‐Substituent Effect†

PubMed Central

Collett, Christopher J.; Massey, Richard S.; Taylor, James E.; Maguire, Oliver R.

2015-01-01

Abstract Rate and equilibrium constants for the reaction between N‐aryl triazolium N‐heterocyclic carbene (NHC) precatalysts and substituted benzaldehyde derivatives to form 3‐(hydroxybenzyl)azolium adducts under both catalytic and stoichiometric conditions have been measured. Kinetic analysis and reaction profile fitting of both the forward and reverse reactions, plus onwards reaction to the Breslow intermediate, demonstrate the remarkable effect of the benzaldehyde 2‐substituent in these reactions and provide insight into the chemoselectivity of cross‐benzoin reactions. PMID:27478264

Constant growth rate can be supported by decreasing energy flux and increasing aerobic glycolysis.

PubMed

Slavov, Nikolai; Budnik, Bogdan A; Schwab, David; Airoldi, Edoardo M; van Oudenaarden, Alexander

2014-05-08

Fermenting glucose in the presence of enough oxygen to support respiration, known as aerobic glycolysis, is believed to maximize growth rate. We observed increasing aerobic glycolysis during exponential growth, suggesting additional physiological roles for aerobic glycolysis. We investigated such roles in yeast batch cultures by quantifying O2 consumption, CO2 production, amino acids, mRNAs, proteins, posttranslational modifications, and stress sensitivity in the course of nine doublings at constant rate. During this course, the cells support a constant biomass-production rate with decreasing rates of respiration and ATP production but also decrease their stress resistance. As the respiration rate decreases, so do the levels of enzymes catalyzing rate-determining reactions of the tricarboxylic-acid cycle (providing NADH for respiration) and of mitochondrial folate-mediated NADPH production (required for oxidative defense). The findings demonstrate that exponential growth can represent not a single metabolic/physiological state but a continuum of changing states and that aerobic glycolysis can reduce the energy demands associated with respiratory metabolism and stress survival. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Ab initio rate constants from hyperspherical quantum scattering: Application to H+C2H6 and H+CH3OH

NASA Astrophysics Data System (ADS)

Kerkeni, Boutheïna; Clary, David C.

2004-10-01

The dynamics and kinetics of the abstraction reactions of H atoms with ethane and methanol have been studied using a quantum mechanical procedure. Bonds being broken and formed are treated with explicit hyperspherical quantum dynamics. The ab initio potential energy surfaces for these reactions have been developed from a minimal number of grid points (average of 48 points) and are given by analytical functionals. All the degrees of freedom except the breaking and forming bonds are optimized using the second order perturbation theory method with a correlation consistent polarized valence triple zeta basis set. Single point energies are calculated on the optimized geometries with the coupled cluster theory and the same basis set. The reaction of H with C2H6 is endothermic by 1.5 kcal/mol and has a vibrationally adiabatic barrier of 12 kcal/mol. The reaction of H with CH3OH presents two reactive channels: the methoxy and the hydroxymethyl channels. The former is endothermic by 0.24 kcal/mol and has a vibrationally adiabatic barrier of 13.29 kcal/mol, the latter reaction is exothermic by 7.87 kcal/mol and has a vibrationally adiabatic barrier of 8.56 kcal/mol. We report state-to-state and state-selected cross sections together with state-to-state rate constants for the title reactions. Thermal rate constants for these reactions exhibit large quantum tunneling effects when compared to conventional transition state theory results. For H+CH3OH, it is found that the CH2OH product is the dominant channel, and that the CH3O channel contributes just 2% at 500 K. For both reactions, rate constants are in good agreement with some measurements.

Development of a QSAR model for predicting aqueous reaction rate constants of organic chemicals with hydroxyl radicals.

PubMed

Luo, Xiang; Yang, Xianhai; Qiao, Xianliang; Wang, Ya; Chen, Jingwen; Wei, Xiaoxuan; Peijnenburg, Willie J G M

2017-03-22

Reaction with hydroxyl radicals (˙OH) is an important removal pathway for organic pollutants in the aquatic environment. The aqueous reaction rate constant (k OH ) is therefore an important parameter for fate assessment of aquatic pollutants. Since experimental determination fails to meet the requirement of being able to efficiently handle numerous organic chemicals at limited cost and within a relatively short period of time, in silico methods such as quantitative structure-activity relationship (QSAR) models are needed to predict k OH . In this study, a QSAR model with a larger and wider applicability domain as compared with existing models was developed. Following the guidelines for the development and validation of QSAR models proposed by the Organization for Economic Co-operation and Development (OECD), the model shows satisfactory performance. The applicability domain of the model has been extended and contained chemicals that have rarely been covered in most previous studies. The chemicals covered in the current model contain functional groups including [double bond splayed left]C[double bond, length as m-dash]C[double bond splayed right], -C[triple bond, length as m-dash]C-, -C 6 H 5 , -OH, -CHO, -O-, [double bond splayed left]C[double bond, length as m-dash]O, -C[double bond, length as m-dash]O(O)-, -COOH, -C[triple bond, length as m-dash]N, [double bond splayed left]N-, -NH 2 , -NH-C(O)-, -NO 2 , -N[double bond, length as m-dash]C-N[double bond splayed right], [double bond splayed left]N-N[double bond splayed right], -N[double bond, length as m-dash]N-, -S-, -S-S-, -SH, -SO 3 , -SO 4 , -PO 4 , and -X (F, Cl, Br, and I).

Multi-target QSPR modeling for simultaneous prediction of multiple gas-phase kinetic rate constants of diverse chemicals

NASA Astrophysics Data System (ADS)

Basant, Nikita; Gupta, Shikha

2018-03-01

The reactions of molecular ozone (O3), hydroxyl (•OH) and nitrate (NO3) radicals are among the major pathways of removal of volatile organic compounds (VOCs) in the atmospheric environment. The gas-phase kinetic rate constants (kO3, kOH, kNO3) are thus, important in assessing the ultimate fate and exposure risk of atmospheric VOCs. Experimental data for rate constants are not available for many emerging VOCs and the computational methods reported so far address a single target modeling only. In this study, we have developed a multi-target (mt) QSPR model for simultaneous prediction of multiple kinetic rate constants (kO3, kOH, kNO3) of diverse organic chemicals considering an experimental data set of VOCs for which values of all the three rate constants are available. The mt-QSPR model identified and used five descriptors related to the molecular size, degree of saturation and electron density in a molecule, which were mechanistically interpretable. These descriptors successfully predicted three rate constants simultaneously. The model yielded high correlations (R2 = 0.874-0.924) between the experimental and simultaneously predicted endpoint rate constant (kO3, kOH, kNO3) values in test arrays for all the three systems. The model also passed all the stringent statistical validation tests for external predictivity. The proposed multi-target QSPR model can be successfully used for predicting reactivity of new VOCs simultaneously for their exposure risk assessment.

Rate constants for CF{sub 3} + H{sub 2} {r_arrow} CF{sub 3}H + H and CF{sub 3}H + H {r_arrow} CF{sub 3} + H{sub 2} reactions in the temperature range 1100--1600 K

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hranisavljevic, J.; Michael, J.V.

1998-09-24

The shock tube technique coupled with H-atom atomic resonance absorption spectrometry has been used to study the reactions (1) CF{sub 3} + H{sub 2} {r_arrow} CF{sub 3}H + H and (2) CF{sub 3}H + H {r_arrow} CF{sub 3} + H{sub 2} over the temperature ranges 1168--1673 K and 1111--1550 K, respectively. The results can be represented by the Arrhenius expressions k{sub 1} = 2.56 {times} 10{sup {minus}11} exp({minus}8549K/T) and k{sub 2} = 6.13 {times} 10{sup {minus}11} exp({minus}7364K/T), both in cm{sup 3} molecule{sup {minus}1} s{sup {minus}1}. Equilibrium constants were calculated from the two Arrhenius expressions in the overlapping temperature range, andmore » good agreement was obtained with the literature values. The rate constants for reaction 2 were converted into rate constants for reaction 1 using literature equilibrium constants. These data are indistinguishable from direct k{sub 1} measurements, and an Arrhenius fit for the joint set is k{sub 1} = 1.88 {times} 10{sup {minus}11} exp({minus}8185K/T) cm{sup 3} molecule{sup {minus}1} s{sup {minus}1}. The CF{sub 3} + H{sub 2} {r_arrow} CF{sub 3}H + H reaction was further modeled using conventional transition-state theory, which included ab initio electronic structure determinations of reactants, transition state, and products.« less

Impact of uncertainties in inorganic chemical rate constants on tropospheric composition and ozone radiative forcing

NASA Astrophysics Data System (ADS)

Newsome, Ben; Evans, Mat

2017-12-01

Chemical rate constants determine the composition of the atmosphere and how this composition has changed over time. They are central to our understanding of climate change and air quality degradation. Atmospheric chemistry models, whether online or offline, box, regional or global, use these rate constants. Expert panels evaluate laboratory measurements, making recommendations for the rate constants that should be used. This results in very similar or identical rate constants being used by all models. The inherent uncertainties in these recommendations are, in general, therefore ignored. We explore the impact of these uncertainties on the composition of the troposphere using the GEOS-Chem chemistry transport model. Based on the Jet Propulsion Laboratory (JPL) and International Union of Pure and Applied Chemistry (IUPAC) evaluations we assess the influence of 50 mainly inorganic rate constants and 10 photolysis rates on tropospheric composition through the use of the GEOS-Chem chemistry transport model. We assess the impact on four standard metrics: annual mean tropospheric ozone burden, surface ozone and tropospheric OH concentrations, and tropospheric methane lifetime. Uncertainty in the rate constants for NO2 + OH →M HNO3 and O3 + NO → NO2 + O2 are the two largest sources of uncertainty in these metrics. The absolute magnitude of the change in the metrics is similar if rate constants are increased or decreased by their σ values. We investigate two methods of assessing these uncertainties, addition in quadrature and a Monte Carlo approach, and conclude they give similar outcomes. Combining the uncertainties across the 60 reactions gives overall uncertainties on the annual mean tropospheric ozone burden, surface ozone and tropospheric OH concentrations, and tropospheric methane lifetime of 10, 11, 16 and 16 %, respectively. These are larger than the spread between models

Calculating constants of the rates of the reactions of excitation, ionization, and atomic exchange: A model of a shock oscillator with a change of the Hamiltonian of the system

NASA Astrophysics Data System (ADS)

Tsyganov, D. L.

2017-11-01

A new model for calculating the rates of reactions of excitation, ionization, and atomic exchange is proposed. Diatomic molecule AB is an unstructured particle M upon the exchange of elastic-vibrational (VT) energy, i.e., a model of a shock forceful oscillator with a change in Hamiltonian (SFOH). The SFOH model is based on the quantum theory of strong perturbations. The SFOH model allows generalization in simulating the rates of the reactions of excitation, ionization, and atomic exchange in the vibrational-vibrational (VV) energy exchange of diatomic molecules, and the exchange of VV- and VT-energy of polyatomic molecules. The rate constants of the excitation of metastables A 3Σ u +, B 3Π g , W 3Δ u , B'3Σ u -, a'3Σ u -, and the ionization of a nitrogen molecules from ground state X2Σ g + upon a collision with a heavy structureless particle (a nitrogen molecule), are found as examples.

The Rate Constant for Fluorescence Quenching

ERIC Educational Resources Information Center

Legenza, Michael W.; Marzzacco, Charles J.

1977-01-01

Describes an experiment that utilizes fluorescence intensity measurements from a Spectronic 20 to determine the rate constant for the fluorescence quenching of various aromatic hydrocarbons by carbon tetrachloride in an ethanol solvent. (MLH)

Title: Elucidation of Environmental Fate of Artificial Sweeteners (Aspartame, Acesulfame K and Saccharin) by Determining Bimolecular Rate Constants with Hydroxyl Radical at Various pH and Temperature Conditions and Possible Reaction By-Products

NASA Astrophysics Data System (ADS)

Teraji, T.; Arakaki, T.; Suzuka, T.

2012-12-01

Use of artificial sweeteners in beverages and food has been rapidly increasing because of their non-calorie nature. In Japan, aspartame, acesulfame K and sucralose are among the most widely used artificial sweeteners. Because the artificial sweeteners are not metabolized in human bodies, they are directly excreted into the environment without chemical transformations. We initiated a study to better understand the fate of artificial sweeteners in the marine environment. The hydroxyl radical (OH), the most potent reactive oxygen species, reacts with various compounds and determines the environmental oxidation capacity and the life-time of many compounds. The steady-state OH concentration and the reaction rate constants between the compound and OH are used to estimate the life-time of the compound. In this study, we determine the bimolecular rate constants between aspartame, acefulfame K and saccharin and OH at various pH and temperature conditions using a competition kinetics technique. We use hydrogen peroxide as a photochemical source of OH. Bimolecular rate constant we obtained so far for aspartame was (2.6±1.2)×109 M-1 s-1 at pH = 3.0 and (4.9±2.3)×109 M-1 s-1 at pH = 5.5. Little effect was seen by changing the temperatures between 15 and 40 oC. Activation energy (Ea) was calculated to be -1.0 kJ mol-1 at pH = 3.0, +8.5 kJ mol-1 at pH = 5.5, which could be regarded as zero. We will report bimolecular rate constants at different pHs and temperatures for acesulfame K and saccharin, as well. Possible reaction by-products for aspartame will be also reported. We will further discuss the fate of aspartame in the coastal environment.

Evaluated rate constants for selected HCFC's and HFC's with OH and O((sup)1D)

NASA Technical Reports Server (NTRS)

Hampson, Robert F.; Kurylo, Michael J.; Sander, Stanley P.

1990-01-01

The chemistry of HCFC's and HFC's in the troposphere is controlled by reactions with OH in which a hydrogen atom is abstracted from the halocarbon to form water and a halo-alkyl radical. The halo-alkyl radical subsequently reacts with molecular oxygen to form a peroxy radical. The reactions of HCFC's and HFC's with O(exp1D) atoms are unimportant in the troposphere, but may be important in producing active chlorine of OH in the stratosphere. Here, the rate constants for the reactions of OH and O(exp1D) with many HFC's and HCFC's are evaluated. Recommendations are given for the five HCFC's and three HFC's specified by AFEAS as primary alternatives as well as for all other isomers of C1 and C2 HCFC's and HFC's where rate data exist. In addition, recommendations are included for CH3CCl3, CH2Cl2, and CH4.

Estimation of hydrolysis rate constants for carbamates ...

EPA Pesticide Factsheets

Cheminformatics based tools, such as the Chemical Transformation Simulator under development in EPA’s Office of Research and Development, are being increasingly used to evaluate chemicals for their potential to degrade in the environment or be transformed through metabolism. Hydrolysis represents a major environmental degradation pathway; unfortunately, only a small fraction of hydrolysis rates for about 85,000 chemicals on the Toxic Substances Control Act (TSCA) inventory are in public domain, making it critical to develop in silico approaches to estimate hydrolysis rate constants. In this presentation, we compare three complementary approaches to estimate hydrolysis rates for carbamates, an important chemical class widely used in agriculture as pesticides, herbicides and fungicides. Fragment-based Quantitative Structure Activity Relationships (QSARs) using Hammett-Taft sigma constants are widely published and implemented for relatively simple functional groups such as carboxylic acid esters, phthalate esters, and organophosphate esters, and we extend these to carbamates. We also develop a pKa based model and a quantitative structure property relationship (QSPR) model, and evaluate them against measured rate constants using R square and root mean square (RMS) error. Our work shows that for our relatively small sample size of carbamates, a Hammett-Taft based fragment model performs best, followed by a pKa and a QSPR model. This presentation compares three comp

Determination of rate constants and branching ratios for TCE degradation by zero-valent iron using a chain decay multispecies model.

PubMed

Hwang, Hyoun-Tae; Jeen, Sung-Wook; Sudicky, Edward A; Illman, Walter A

2015-01-01

The applicability of a newly-developed chain-decay multispecies model (CMM) was validated by obtaining kinetic rate constants and branching ratios along the reaction pathways of trichloroethene (TCE) reduction by zero-valent iron (ZVI) from column experiments. Changes in rate constants and branching ratios for individual reactions for degradation products over time for two columns under different geochemical conditions were examined to provide ranges of those parameters expected over the long-term. As compared to the column receiving deionized water, the column receiving dissolved CaCO3 showed higher mean degradation rates for TCE and all of its degradation products. However, the column experienced faster reactivity loss toward TCE degradation due to precipitation of secondary carbonate minerals, as indicated by a higher value for the ratio of maximum to minimum TCE degradation rate observed over time. From the calculated branching ratios, it was found that TCE and cis-dichloroethene (cis-DCE) were dominantly dechlorinated to chloroacetylene and acetylene, respectively, through reductive elimination for both columns. The CMM model, validated by the column test data in this study, provides a convenient tool to determine simultaneously the critical design parameters for permeable reactive barriers and natural attenuation such as rate constants and branching ratios. Copyright © 2015 Elsevier B.V. All rights reserved.

The reaction mechanism with free energy barriers at constant potentials for the oxygen evolution reaction at the IrO 2 (110) surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ping, Yuan; Nielsen, Robert J.; Goddard, William A.

How to efficiently oxidize H 2O to O 2 (oxygen evolution reaction, OER) in photoelectrochemical cells (PEC) is a great challenge due to its complex charge transfer process, high overpotential, and corrosion. So far no OER mechanism has been fully explained atomistically with both thermodynamic and kinetics. IrO 2 is the only known OER catalyst with both high catalytic activity and stability in acidic conditions. This is important because PEC experiments often operate at extreme pH conditions. In this work, we performed first-principles calculations integrated with implicit solvation at constant potentials to examine the detailed atomistic reaction mechanism of OERmore » at the IrO 2 (110) surface. We determined the surface phase diagram, explored the possible reaction pathways including kinetic barriers, and computed reaction rates based on the microkinetic models. Furthermore, this allowed us to resolve several long-standing puzzles about the atomistic OER mechanism.« less

The reaction mechanism with free energy barriers at constant potentials for the oxygen evolution reaction at the IrO 2 (110) surface

DOE PAGES

Ping, Yuan; Nielsen, Robert J.; Goddard, William A.

2016-12-09

How to efficiently oxidize H 2O to O 2 (oxygen evolution reaction, OER) in photoelectrochemical cells (PEC) is a great challenge due to its complex charge transfer process, high overpotential, and corrosion. So far no OER mechanism has been fully explained atomistically with both thermodynamic and kinetics. IrO 2 is the only known OER catalyst with both high catalytic activity and stability in acidic conditions. This is important because PEC experiments often operate at extreme pH conditions. In this work, we performed first-principles calculations integrated with implicit solvation at constant potentials to examine the detailed atomistic reaction mechanism of OERmore » at the IrO 2 (110) surface. We determined the surface phase diagram, explored the possible reaction pathways including kinetic barriers, and computed reaction rates based on the microkinetic models. Furthermore, this allowed us to resolve several long-standing puzzles about the atomistic OER mechanism.« less

Determination of Chemical Kinetic Rate Constants of a Model for Carbothermal Processing of Lunar Regolith Simulant Using Methane

NASA Technical Reports Server (NTRS)

Balasubramaniam, R; Gokoglu, S.; Hegde, U.

2009-01-01

We have previously developed a chemical conversion model of the carbothermal processing of lunar regolith using methane to predict the rate of production of carbon monoxide. In this carbothermal process, gaseous methane is pyrolyzed as it flows over the hot surface of a molten zone of lunar regolith and is converted to carbon and hydrogen. Hydrogen is carried away by the exiting stream of gases and carbon is deposited on the melt surface. The deposited carbon mixes with the melt and reacts with the metal oxides in it to produce carbon monoxide that bubbles out of the melt. In our model, we assume that the flux of carbon deposited is equal to the product of the surface reaction rate constant gamma and the concentration of methane adjacent to the melt surface. Similarly, the rate of consumption of carbon per unit volume in the melt is equal to the product of the melt reaction rate constant k and the concentrations of carbon and metal oxide in the melt. In this paper, we describe our effort to determine gamma and k by comparison of the predictions from our model with test data obtained by ORBITEC (Orbital Technologies Corporation). The concentration of methane adjacent to the melt surface is a necessary input to the model. It is inferred from the test data by a mass balance of methane, adopting the usual assumptions of the continuously-stirred-tank-reactor model, whereby the average concentration of a given gaseous species equals its exit concentration. The reaction rates gamma and k have been determined by a non-linear least-squares fit to the test data for the production of carbon monoxide and the fraction of the incoming methane that is converted. The comparison of test data with our model predictions using the determined chemical kinetic rate constants provides a consistent interpretation of the process over the full range of temperatures, pressures, and methane flow rates used in the tests, thereby increasing our confidence to use the model for scale-up purposes.

Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association.

PubMed

Frembgen-Kesner, Tamara; Elcock, Adrian H

2010-11-03

Theory and computation have long been used to rationalize the experimental association rate constants of protein-protein complexes, and Brownian dynamics (BD) simulations, in particular, have been successful in reproducing the relative rate constants of wild-type and mutant protein pairs. Missing from previous BD studies of association kinetics, however, has been the description of hydrodynamic interactions (HIs) between, and within, the diffusing proteins. Here we address this issue by rigorously including HIs in BD simulations of the barnase-barstar association reaction. We first show that even very simplified representations of the proteins--involving approximately one pseudoatom for every three residues in the protein--can provide excellent reproduction of the absolute association rate constants of wild-type and mutant protein pairs. We then show that simulations that include intermolecular HIs also produce excellent estimates of association rate constants, but, for a given reaction criterion, yield values that are decreased by ∼35-80% relative to those obtained in the absence of intermolecular HIs. The neglect of intermolecular HIs in previous BD simulation studies, therefore, is likely to have contributed to the somewhat overestimated absolute rate constants previously obtained. Consequently, intermolecular HIs could be an important component to include in accurate modeling of the kinetics of macromolecular association events. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Co-solvent effects on reaction rate and reaction equilibrium of an enzymatic peptide hydrolysis.

PubMed

Wangler, A; Canales, R; Held, C; Luong, T Q; Winter, R; Zaitsau, D H; Verevkin, S P; Sadowski, G

2018-04-25

This work presents an approach that expresses the Michaelis constant KaM and the equilibrium constant Kth of an enzymatic peptide hydrolysis based on thermodynamic activities instead of concentrations. This provides KaM and Kth values that are independent of any co-solvent. To this end, the hydrolysis reaction of N-succinyl-l-phenylalanine-p-nitroanilide catalysed by the enzyme α-chymotrypsin was studied in pure buffer and in the presence of the co-solvents dimethyl sulfoxide, trimethylamine-N-oxide, urea, and two salts. A strong influence of the co-solvents on the measured Michaelis constant (KM) and equilibrium constant (Kx) was observed, which was found to be caused by molecular interactions expressed as activity coefficients. Substrate and product activity coefficients were used to calculate the activity-based values KaM and Kth for the co-solvent free reaction. Based on these constants, the co-solvent effect on KM and Kx was predicted in almost quantitative agreement with the experimental data. The approach presented here does not only reveal the importance of understanding the thermodynamic non-ideality of reactions taking place in biological solutions and in many technological applications, it also provides a framework for interpreting and quantifying the multifaceted co-solvent effects on enzyme-catalysed reactions that are known and have been observed experimentally for a long time.

Determining Role of the Chain Mechanism in the Temperature Dependence of the Gas-Phase Rate of Combustion Reactions

NASA Astrophysics Data System (ADS)

Azatyan, V. V.; Bolod'yan, I. A.; Kopylov, N. P.; Kopylov, S. N.; Prokopenko, V. M.; Shebeko, Yu. N.

2018-05-01

It is shown that the strong dependence of the rate of gas-phase combustion reactions on temperature is determined by the high values of the reaction rate constants of free atoms and radicals. It is established that with a branched chain mechanism, a special role in the reaction rate temperature dependence is played by positive feedback between the concentrations of active intermediate species and the rate of their change. The role of the chemical mechanism in the temperature dependence of the process rate with and without inhibitors is considered.

Multi-path variational transition state theory for chemical reaction rates of complex polyatomic species: ethanol + OH reactions.

PubMed

Zheng, Jingjing; Truhlar, Donald G

2012-01-01

Complex molecules often have many structures (conformations) of the reactants and the transition states, and these structures may be connected by coupled-mode torsions and pseudorotations; some but not all structures may have hydrogen bonds in the transition state or reagents. A quantitative theory of the reaction rates of complex molecules must take account of these structures, their coupled-mode nature, their qualitatively different character, and the possibility of merging reaction paths at high temperature. We have recently developed a coupled-mode theory called multi-structural variational transition state theory (MS-VTST) and an extension, called multi-path variational transition state theory (MP-VTST), that includes a treatment of the differences in the multi-dimensional tunneling paths and their contributions to the reaction rate. The MP-VTST method was presented for unimolecular reactions in the original paper and has now been extended to bimolecular reactions. The MS-VTST and MP-VTST formulations of variational transition state theory include multi-faceted configuration-space dividing surfaces to define the variational transition state. They occupy an intermediate position between single-conformation variational transition state theory (VTST), which has been used successfully for small molecules, and ensemble-averaged variational transition state theory (EA-VTST), which has been used successfully for enzyme kinetics. The theories are illustrated and compared here by application to three thermal rate constants for reactions of ethanol with hydroxyl radical--reactions with 4, 6, and 14 saddle points.

Development of a model for predicting reaction rate constants of organic chemicals with ozone at different temperatures.

PubMed

Li, Xuehua; Zhao, Wenxing; Li, Jing; Jiang, Jingqiu; Chen, Jianji; Chen, Jingwen

2013-08-01

To assess the persistence and fate of volatile organic compounds in the troposphere, the rate constants for the reaction with ozone (kO3) are needed. As kO3 values are only available for hundreds of compounds, and experimental determination of kO3 is costly and time-consuming, it is of importance to develop predictive models on kO3. In this study, a total of 379 logkO3 values at different temperatures were used to develop and validate a model for the prediction of kO3, based on quantum chemical descriptors, Dragon descriptors and structural fragments. Molecular descriptors were screened by stepwise multiple linear regression, and the model was constructed by partial least-squares regression. The cross validation coefficient QCUM(2) of the model is 0.836, and the external validation coefficient Qext(2) is 0.811, indicating that the model has high robustness and good predictive performance. The most significant descriptor explaining logkO3 is the BELm2 descriptor with connectivity information weighted atomic masses. kO3 increases with increasing BELm2, and decreases with increasing ionization potential. The applicability domain of the proposed model was visualized by the Williams plot. The developed model can be used to predict kO3 at different temperatures for a wide range of organic chemicals, including alkenes, cycloalkenes, haloalkenes, alkynes, oxygen-containing compounds, nitrogen-containing compounds (except primary amines) and aromatic compounds. Copyright © 2013 Elsevier Ltd. All rights reserved.

Simulation of weak polyelectrolytes: a comparison between the constant pH and the reaction ensemble method

NASA Astrophysics Data System (ADS)

Landsgesell, Jonas; Holm, Christian; Smiatek, Jens

2017-03-01

The reaction ensemble and the constant pH method are well-known chemical equilibrium approaches to simulate protonation and deprotonation reactions in classical molecular dynamics and Monte Carlo simulations. In this article, we demonstrate the similarity between both methods under certain conditions. We perform molecular dynamics simulations of a weak polyelectrolyte in order to compare the titration curves obtained by both approaches. Our findings reveal a good agreement between the methods when the reaction ensemble is used to sweep the reaction constant. Pronounced differences between the reaction ensemble and the constant pH method can be observed for stronger acids and bases in terms of adaptive pH values. These deviations are due to the presence of explicit protons in the reaction ensemble method which induce a screening of electrostatic interactions between the charged titrable groups of the polyelectrolyte. The outcomes of our simulation hint to a better applicability of the reaction ensemble method for systems in confined geometries and titrable groups in polyelectrolytes with different pKa values.

What Is a Reaction Rate?

ERIC Educational Resources Information Center

Schmitz, Guy

2005-01-01

The definition of reaction rate is derived and demonstrations are made for the care to be taken while using the term. Reaction rate can be in terms of a reaction property, the extent of reaction and thus it is possible to give a definition applicable in open and closed systems.

Decomposition reaction rate of BCl3-C3H6(propene)-H2 in the gas phase.

PubMed

Xiao, Jun; Su, Kehe; Liu, Yan; Ren, Hongjiang; Zeng, Qingfeng; Cheng, Laifei; Zhang, Litong

2012-07-05

The decomposition reaction rate in the BCl(3)-C(3)H(6)-H(2) gas phase reaction system in preparing boron carbides was investigated based on the most favorable reaction pathways proposed by Jiang et al. [Theor. Chem. Accs. 2010, 127, 519] and Yang et al. [J. Theor. Comput. Chem. 2012, 11, 53]. The rate constants of all the elementary reactions were evaluated with the variational transition state theory. The vibrational frequencies for the stationary points as well as the selected points along the minimum energy paths (MEPs) were calculated with density functional theory at the B3PW91/6-311G(d,p) level and the energies were refined with the accurate model chemistry method G3(MP2). For the elementary reaction associated with a transition state, the MEP was obtained with the intrinsic reaction coordinates, while for the elementary reaction without transition state, the relaxed potential energy surface scan was employed to obtain the MEP. The rate constants were calculated for temperatures within 200-2000 K and fitted into three-parameter Arrhenius expressions. The reaction rates were investigated by using the COMSOL software to solve numerically the coupled differential rate equations. The results show that the reactions are, consistent with the experiments, appropriate at 1100-1500 K with the reaction time of 30 s for 1100 K, 1.5 s for 1200 K, 0.12 s for 1300 K, 0.011 s for 1400 K, or 0.001 s for 1500 K, for propene being almost completely consumed. The completely dissociated species, boron carbides C(3)B, C(2)B, and CB, have very low concentrations, and C(3)B is the main product at higher temperatures, while C(2)B is the main product at lower temperatures. For the reaction time 1 s, all these concentrations approach into a nearly constant. The maximum value (in mol/m(3)) is for the highest temperature 1500 K with the orders of -13, -17, and -23 for C(3)B, C(2)B, and CB, respectively. It was also found that the logarithm of the overall reaction rate and reciprocal

Rate Coefficient for the (4)Heμ + CH4 Reaction at 500 K: Comparison between Theory and Experiment.

PubMed

Arseneau, Donald J; Fleming, Donald G; Li, Yongle; Li, Jun; Suleimanov, Yury V; Guo, Hua

2016-03-03

The rate constant for the H atom abstraction reaction from methane by the muonic helium atom, Heμ + CH4 → HeμH + CH3, is reported at 500 K and compared with theory, providing an important test of both the potential energy surface (PES) and reaction rate theory for the prototypical polyatomic CH5 reaction system. The theory used to characterize this reaction includes both variational transition-state (CVT/μOMT) theory (VTST) and ring polymer molecular dynamics (RPMD) calculations on a recently developed PES, which are compared as well with earlier calculations on different PESs for the H, D, and Mu + CH4 reactions, the latter, in particular, providing for a variation in atomic mass by a factor of 36. Though rigorous quantum calculations have been carried out for the H + CH4 reaction, these have not yet been extended to the isotopologues of this reaction (in contrast to H3), so it is important to provide tests of less rigorous theories in comparison with kinetic isotope effects measured by experiment. In this regard, the agreement between the VTST and RPMD calculations and experiment for the rate constant of the Heμ + CH4 reaction at 500 K is excellent, within 10% in both cases, which overlaps with experimental error.

The Hydroxyl Radical Reaction Rate Constant and Products of Cyclohexanol

DTIC Science & Technology

2007-10-01

Analysis Samples from kinetic studies were quantitativelymon- itored using a Hewlett-Packard (HP) gas chromato- graph (GC) 5890 with a flame ionization...excluded from the reaction mixture and the COL concentration was approximately doubled (4.9–9 ppm). Product Study Analysis Reactant mixtures and standards...from product identi- fication experiments were sampled by exposing a 100% polydimethylsiloxane solid phase microextrac- tion fiber (SPME) in the

Reaction rates and kinetic isotope effects of H{sub 2} + OH → H{sub 2}O + H

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meisner, Jan; Kästner, Johannes, E-mail: kaestner@theochem.uni-stuttgart.de

2016-05-07

We calculated reaction rate constants including atom tunneling of the reaction of dihydrogen with the hydroxy radical down to a temperature of 50 K. Instanton theory and canonical variational theory with microcanonical optimized multidimensional tunneling were applied using a fitted potential energy surface [J. Chen et al., J. Chem. Phys. 138, 154301 (2013)]. All possible protium/deuterium isotopologues were considered. Atom tunneling increases at about 250 K (200 K for deuterium transfer). Even at 50 K the rate constants of all isotopologues remain in the interval 4 ⋅ 10{sup −20} to 4 ⋅ 10{sup −17} cm{sup 3} s{sup −1}, demonstrating thatmore » even deuterated versions of the title reaction are possibly relevant to astrochemical processes in molecular clouds. The transferred hydrogen atom dominates the kinetic isotope effect at all temperatures.« less

The Unimolecular Reactions of CF3CHF2 Studied by Chemical Activation: Assignment of Rate Constants and Threshold Energies to the 1,2-H Atom Transfer, 1,1-HF and 1,2-HF Elimination Reactions, and the Dependence of Threshold Energies on the Number of F-Atom Substituents in the Fluoroethane Molecules.

PubMed

Smith, Caleb A; Gillespie, Blanton R; Heard, George L; Setser, D W; Holmes, Bert E

2017-11-22

The recombination of CF 3 and CHF 2 radicals in a room-temperature bath gas was used to prepare vibrationally excited CF 3 CHF 2 * molecules with 101 kcal mol -1 of vibrational energy. The subsequent 1,2-H atom transfer and 1,1-HF and 1,2-HF elimination reactions were observed as a function of bath gas pressure by following the CHF 3 , CF 3 (F)C: and C 2 F 4 product concentrations by gas chromatography using a mass spectrometer as the detector. The singlet CF 3 (F)C: concentration was measured by trapping the carbene with trans-2-butene. The experimental rate constants are 3.6 × 10 4 , 4.7 × 10 4 , and 1.1 × 10 4 s -1 for the 1,2-H atom transfer and 1,1-HF and 1,2-HF elimination reactions, respectively. These experimental rate constants were matched to statistical RRKM calculated rate constants to assign threshold energies (E 0 ) of 88 ± 2, 88 ± 2, and 87 ± 2 kcal mol -1 to the three reactions. Pentafluoroethane is the only fluoroethane that has a competitive H atom transfer decomposition reaction, and it is the only example with 1,1-HF elimination being more important than 1,2-HF elimination. The trend of increasing threshold energies for both 1,1-HF and 1,2-HF processes with the number of F atoms in the fluoroethane molecule is summarized and investigated with electronic-structure calculations. Examination of the intrinsic reaction coordinate associated with the 1,1-HF elimination reaction found an adduct between CF 3 (F)C: and HF in the exit channel with a dissociation energy of ∼5 kcal mol -1 . Hydrogen-bonded complexes between HF and the H atom migration transition state of CH 3 (F)C: and the F atom migration transition state of CF 3 (F)C: also were found by the calculations. The role that these carbene-HF complexes could play in 1,1-HF elimination reactions is discussed.

Reduction of Iron-Oxide-Carbon Composites: Part I. Estimation of the Rate Constants

NASA Astrophysics Data System (ADS)

Halder, S.; Fruehan, R. J.

2008-12-01

A new ironmaking concept using iron-oxide-carbon composite pellets has been proposed, which involves the combination of a rotary hearth furnace (RHF) and an iron bath smelter. This part of the research focuses on studying the two primary chemical kinetic steps. Efforts have been made to experimentally measure the kinetics of the carbon gasification by CO2 and wüstite reduction by CO by isolating them from the influence of heat- and mass-transport steps. A combined reaction model was used to interpret the experimental data and determine the rate constants. Results showed that the reduction is likely to be influenced by the chemical kinetics of both carbon oxidation and wüstite reduction at the temperatures of interest. Devolatilized wood-charcoal was observed to be a far more reactive form of carbon in comparison to coal-char. Sintering of the iron-oxide at the high temperatures of interest was found to exert a considerable influence on the reactivity of wüstite by virtue of altering the internal pore surface area available for the reaction. Sintering was found to be predominant for highly porous oxides and less of an influence on the denser ores. It was found using an indirect measurement technique that the rate constants for wüstite reduction were higher for the porous iron-oxide than dense hematite ore at higher temperatures (>1423 K). Such an indirect mode of measurement was used to minimize the influence of sintering of the porous oxide at these temperatures.

Ab initio thermal rate calculations of HO + HO = O(3P) + H2O reaction and isotopologues.

PubMed

Nguyen, Thanh Lam; Stanton, John F

2013-04-04

The forward and reverse reactions, HO + HO ⇌ O((3)P) + H2O, which play roles in both combustion and laboratory studies, were theoretically characterized with a master equation approach to compute thermal reaction rate constants at both the low and high pressure limits. Our ab initio k(T) results for the title reaction and two isotopic variants agree very well with experiments (within 15%) over a wide temperature range. The calculated reaction rate shows a distinctly non-Arrhenius behavior and a strong curvature consistent with the experiment. This characteristic behavior is due to effects of positive barrier height and quantum mechanical tunneling. Tunneling is very important and contributes more than 70% of total reaction rate at room temperature. A prereactive complex is also important in the overall reaction scheme.

Precisely and Accurately Inferring Single-Molecule Rate Constants

PubMed Central

Kinz-Thompson, Colin D.; Bailey, Nevette A.; Gonzalez, Ruben L.

2017-01-01

The kinetics of biomolecular systems can be quantified by calculating the stochastic rate constants that govern the biomolecular state versus time trajectories (i.e., state trajectories) of individual biomolecules. To do so, the experimental signal versus time trajectories (i.e., signal trajectories) obtained from observing individual biomolecules are often idealized to generate state trajectories by methods such as thresholding or hidden Markov modeling. Here, we discuss approaches for idealizing signal trajectories and calculating stochastic rate constants from the resulting state trajectories. Importantly, we provide an analysis of how the finite length of signal trajectories restrict the precision of these approaches, and demonstrate how Bayesian inference-based versions of these approaches allow rigorous determination of this precision. Similarly, we provide an analysis of how the finite lengths and limited time resolutions of signal trajectories restrict the accuracy of these approaches, and describe methods that, by accounting for the effects of the finite length and limited time resolution of signal trajectories, substantially improve this accuracy. Collectively, therefore, the methods we consider here enable a rigorous assessment of the precision, and a significant enhancement of the accuracy, with which stochastic rate constants can be calculated from single-molecule signal trajectories. PMID:27793280

Density functional theory study of hydrogen atom abstraction from a series of para-substituted phenols: why is the Hammett σ(p)+ constant able to represent radical reaction rates?

PubMed

Yoshida, Tatsusada; Hirozumi, Koji; Harada, Masataka; Hitaoka, Seiji; Chuman, Hiroshi

2011-06-03

The rate of hydrogen atom abstraction from phenolic compounds by a radical is known to be often linear with the Hammett substitution constant σ(+), defined using the S(N)1 solvolysis rates of substituted cumyl chlorides. Nevertheless, a physicochemical reason for the above "empirical fact" has not been fully revealed. The transition states of complexes between the 2,2-diphenyl-1-picrylhydrazyl radical (dpph·) and a series of para-substituted phenols were determined by DFT (Density Functional Theory) calculations, and then the activation energy as well as the homolytic bond dissociation energy of the O-H bond and charge distribution in the transition state were calculated. The heterolytic bond dissociation energy of the C-Cl bond and charge distribution in the corresponding para-substituted cumyl chlorides were calculated in parallel. Excellent correlations among σ(+), charge distribution, and activation and bond dissociation energies revealed quantitatively that there is a strong similarity between the two reactions, showing that the electron-deficiency of the π-electron system conjugated with a substituent plays a crucial role in determining rates of the two reactions. The results provide a new insight into and physicochemical understanding of σ(+) in the hydrogen abstraction from substituted phenols by a radical.

Shock tube measurements of specific reaction rates in branched chain CH4-CO-O2 system

NASA Technical Reports Server (NTRS)

Brabbs, T. A.; Brokaw, R. S.

1974-01-01

Rate constants of two elementary bimolecular reactions involved in the oxidation of methane were determined by monitoring the exponential growth of CO flame band emission behind incident shocks in three suitably chosen gas mixtures.

Loss Process for the C2H5 Radical in the Atmospheres of Jupiter and Saturn: First Direct, Absolute Measurement of the Rate Constant for the Reaction H + C2H5 at Low Pressure and Temperature

NASA Astrophysics Data System (ADS)

Stief, L. J.; Pimentel, A. S.; Payne, W. A.; Nesbitt, F. L.; Cody, R. J.

2003-05-01

Photochemical models of the atmospheres of Jupiter and Saturn predict the reaction H + C2H5 to be the most important loss process for C2H5 in these atmospheres. In addition, the reaction channel H + C2H5 -> 2 CH3 is a significant source of the methyl radical. There are only two relatively modern studies of the H + C2H5 reaction, both of which depend on extensive modeling involving eight elementary reactions. The motivation for the present study is the lack of direct, absolute measurements of the rate constant for the H + C2H5 reaction at low pressures and temperatures appropriate for outer planet models. In the present experiments the reactants H and C2H5 are rapidly and simultaneously generated by reaction of F with appropriate mixtures of H2 and C2H6. Using the technique of discharge-flow with collision-free sampling to a mass spectrometer, we monitor the decay of C2H5 in excess H. In contrast to previous studies of this reaction, the primary H + C2H5 reaction is isolated and the radical decays only by reaction with H and by loss at the wall. Secondary reactions such as the self-reaction of C2H5 are negligible. At P = 1 Torr He we measure k (298K) = 1.13 x 10-10 cm3 molecule-1 s-1 and k (202K) = 1.18 x 10-10 cm3 molecule-1 s-1. Experiments at T = 155 K are in progress. The reaction is temperature independent as expected based on studies of other atom-radical reactions. Our result at T = 298 K lies between those of the two relatively modern but complex studies of this reaction. The present total rate constant data and planned product yield studies at low pressures and temperatures will then be available for use in future photochemical models of the atmospheres of the outer planets. The Planetary Atmospheres Program of NASA Headquarters is supporting this research.

Acceleration and sensitivity analysis of lattice kinetic Monte Carlo simulations using parallel processing and rate constant rescaling

NASA Astrophysics Data System (ADS)

Núñez, M.; Robie, T.; Vlachos, D. G.

2017-10-01

Kinetic Monte Carlo (KMC) simulation provides insights into catalytic reactions unobtainable with either experiments or mean-field microkinetic models. Sensitivity analysis of KMC models assesses the robustness of the predictions to parametric perturbations and identifies rate determining steps in a chemical reaction network. Stiffness in the chemical reaction network, a ubiquitous feature, demands lengthy run times for KMC models and renders efficient sensitivity analysis based on the likelihood ratio method unusable. We address the challenge of efficiently conducting KMC simulations and performing accurate sensitivity analysis in systems with unknown time scales by employing two acceleration techniques: rate constant rescaling and parallel processing. We develop statistical criteria that ensure sufficient sampling of non-equilibrium steady state conditions. Our approach provides the twofold benefit of accelerating the simulation itself and enabling likelihood ratio sensitivity analysis, which provides further speedup relative to finite difference sensitivity analysis. As a result, the likelihood ratio method can be applied to real chemistry. We apply our methodology to the water-gas shift reaction on Pt(111).

High-Temperature Slow Crack Growth of Silicon Carbide Determined by Constant-Stress-Rate and Constant-Stress Testing

NASA Technical Reports Server (NTRS)

Choi, Sung H.; Salem, J. A.; Nemeth, N. N.

1998-01-01

High-temperature slow-crack-growth behaviour of hot-pressed silicon carbide was determined using both constant-stress-rate ("dynamic fatigue") and constant-stress ("static fatigue") testing in flexure at 1300 C in air. Slow crack growth was found to be a governing mechanism associated with failure of the material. Four estimation methods such as the individual data, the Weibull median, the arithmetic mean and the median deviation methods were used to determine the slow crack growth parameters. The four estimation methods were in good agreement for the constant-stress-rate testing with a small variation in the slow-crack-growth parameter, n, ranging from 28 to 36. By contrast, the variation in n between the four estimation methods was significant in the constant-stress testing with a somewhat wide range of n= 16 to 32.

The Hydroxyl Radical Reaction Rate Constant and Products of Dimethyl Succinate

DTIC Science & Technology

2008-03-01

phase reaction of OH + DMS, 10 liters of chamber content were flowed over 2,4- dinitrophenylhydrazine (DNPH) impregnated cartridges. Hydrazones formed... dinitrophenylhydrazine (DNPH) derivatization (method described in experimental methods), and GC/MS/MS (where samples were directly introduced into the mass

Pressure-dependent rate constants for PAH growth: formation of indene and its conversion to naphthalene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mebel, Alexander M.; Georgievskii, Yuri; Jasper, Ahren W.

2016-01-01

Unraveling the mechanisms for growth of polycyclic aromatic hydrocarbons (PAHs) requires accurate temperature- and pressure-dependent rate coefficients for a great variety of feasible pathways. Even the pathways for the formation of the simplest PAHs, indene and naphthalene, are fairly complex. These pathways provide important prototypes for modeling larger PAH growth. In this work we employ the ab initio RRKM theory-based master equation approach to predict the rate constants involved in the formation of indene and its conversion to naphthalene. The reactions eventually leading to indene involve C9Hx (x = 8–11) potential energy surfaces (PESs) and include C6H5 + C3H4 (allenemore » and propyne), C6H6 + C3H3, benzyl + C2H2, C6H5 + C3H6, C6H6 + C3H5 and C6H5 + C3H5. These predictions allow us to make a number of valuable observations on the role of various mechanisms. For instance, we demonstrate that reactions which can significantly contribute to the formation of indene include phenyl + allene and H-assisted isomerization to indene of its major product, 3-phenylpropyne, benzyl + acetylene, and the reactions of the phenyl radical with propene and the allyl radical, both proceeding via the 3-phenylpropene intermediate. 3-Phenylpropene can be activated to a 1-phenylallyl radical, which in turn rapidly decomposes to indene. Next, indene can be converted to benzofulvene or naphthalene under typical combustion conditions, via its activation by H atom abstraction and methyl substitution on the five-membered ring followed by isomerization and decomposition of the resulting 1-methylindenyl radical, C10H9 → C10H8 + H. Alternatively, the same region of the C10H9 PES can be accessed through the reaction of benzyl with propargyl, C7H7 + C3H3 → C10H10 → C10H9 + H, which therefore can also contribute to the formation of benzofulvene or naphthalene. Benzofulvene easily transforms to naphthalene by H-assisted isomerization. An analysis of the effect of pressure on the

Reflected shock tube studies of high-temperature rate constants for OH + CH4 --> CH3 + H2O and CH3 + NO2 --> CH3O + NO.

PubMed

Srinivasan, N K; Su, M-C; Sutherland, J W; Michael, J V

2005-03-10

The reflected shock tube technique with multipass absorption spectrometric detection of OH radicals at 308 nm has been used to study the reactions OH + CH(4) --> CH(3) + H(2)O and CH(3) + NO(2) --> CH(3)O + NO. Over the temperature range 840-2025 K, the rate constants for the first reaction can be represented by the Arrhenius expression k = (9.52 +/- 1.62) x 10(-11) exp[(-4134 +/- 222 K)/T] cm(3) molecule(-1) s(-1). Since this reaction is important in both combustion and atmospheric chemistry, there have been many prior investigations with a variety of techniques. The present results extend the temperature range by 500 K and have been combined with the most accurate earlier studies to derive an evaluation over the extended temperature range 195-2025 K. A three-parameter expression describes the rate behavior over this temperature range, k = (1.66 x 10(-18))T(2.182) exp[(-1231 K)/T] cm(3) molecule(-1) s(-1). Previous theoretical studies are discussed, and the present evaluation is compared to earlier theoretical estimates. Since CH(3) radicals are a product of the reaction and could cause secondary perturbations in rate constant determinations, the second reaction was studied by OH radical production from the fast reactions CH(3)O --> CH(2)O + H and H + NO(2) --> OH + NO. The measured rate constant is 2.26 x 10(-11) cm(3) molecule(-1) s(-1) and is not dependent on temperature from 233 to 1700 K within experimental error.

Computer Calculation of First-Order Rate Constants

ERIC Educational Resources Information Center

Williams, Robert C.; Taylor, James W.

1970-01-01

Discusses the computer program used to calculate first-order rate constants. Discussion includes data preparation, weighting options, comparison techniques, infinity point adjustment, least-square fit, Guggenheim calculation, and printed outputs. Exemplifies the utility of the computer program by two experiments: (1) the thermal decomposition of…

Determining the folding and unfolding rate constants of nucleic acids by biosensor. Application to telomere G-quadruplex.

PubMed

Zhao, Yong; Kan, Zhong-yuan; Zeng, Zhi-xiong; Hao, Yu-hua; Chen, Hua; Tan, Zheng

2004-10-20

Nucleic acid molecules may fold into secondary structures, and the formation of such structures is involved in many biological processes and technical applications. The folding and unfolding rate constants define the kinetics of conformation interconversion and the stability of these structures and is important in realizing their functions. We developed a method to determine these kinetic parameters using an optical biosensor based on surface plasmon resonance. The folding and unfolding of a nucleic acid is coupled with a hybridization reaction by immobilization of the target nucleic acid on a sensor chip surface and injection of a complementary probe nucleic acid over the sensor chip surface. By monitoring the time course of duplex formation, both the folding and unfolding rate constants for the target nucleic acid and the association and dissociation rate constants for the target-probe duplex can all be derived from the same measurement. We applied this method to determine the folding and unfolding rate constants of the G-quadruplex of human telomere sequence (TTAGGG)(4) and its association and dissociation rate constants with the complementary strand (CCCTAA)(4). The results show that both the folding and unfolding occur on the time scale of minutes at physiological concentration of K(+). We speculate that this property might be important for telomere elongation. A complete set of the kinetic parameters for both of the structures allows us to study the competition between the formation of the quadruplex and the duplex. Calculations indicate that the formation of both the quadruplex and the duplex is strand concentration-dependent, and the quadruplex can be efficiently formed at low strand concentration. This property may provide the basis for the formation of the quadruplex in vivo in the presence of a complementary strand.

Uncertainty quantification of reaction mechanisms accounting for correlations introduced by rate rules and fitted Arrhenius parameters

DOE PAGES

Prager, Jens; Najm, Habib N.; Sargsyan, Khachik; ...

2013-02-23

We study correlations among uncertain Arrhenius rate parameters in a chemical model for hydrocarbon fuel-air combustion. We consider correlations induced by the use of rate rules for modeling reaction rate constants, as well as those resulting from fitting rate expressions to empirical measurements arriving at a joint probability density for all Arrhenius parameters. We focus on homogeneous ignition in a fuel-air mixture at constant-pressure. We also outline a general methodology for this analysis using polynomial chaos and Bayesian inference methods. Finally, we examine the uncertainties in both the Arrhenius parameters and in predicted ignition time, outlining the role of correlations,more » and considering both accuracy and computational efficiency.« less

Stochastic theory of large-scale enzyme-reaction networks: Finite copy number corrections to rate equation models

NASA Astrophysics Data System (ADS)

Thomas, Philipp; Straube, Arthur V.; Grima, Ramon

2010-11-01

Chemical reactions inside cells occur in compartment volumes in the range of atto- to femtoliters. Physiological concentrations realized in such small volumes imply low copy numbers of interacting molecules with the consequence of considerable fluctuations in the concentrations. In contrast, rate equation models are based on the implicit assumption of infinitely large numbers of interacting molecules, or equivalently, that reactions occur in infinite volumes at constant macroscopic concentrations. In this article we compute the finite-volume corrections (or equivalently the finite copy number corrections) to the solutions of the rate equations for chemical reaction networks composed of arbitrarily large numbers of enzyme-catalyzed reactions which are confined inside a small subcellular compartment. This is achieved by applying a mesoscopic version of the quasisteady-state assumption to the exact Fokker-Planck equation associated with the Poisson representation of the chemical master equation. The procedure yields impressively simple and compact expressions for the finite-volume corrections. We prove that the predictions of the rate equations will always underestimate the actual steady-state substrate concentrations for an enzyme-reaction network confined in a small volume. In particular we show that the finite-volume corrections increase with decreasing subcellular volume, decreasing Michaelis-Menten constants, and increasing enzyme saturation. The magnitude of the corrections depends sensitively on the topology of the network. The predictions of the theory are shown to be in excellent agreement with stochastic simulations for two types of networks typically associated with protein methylation and metabolism.

Calculated third order rate constants for interpreting the mechanisms of hydrolyses of chloroformates, carboxylic Acid halides, sulfonyl chlorides and phosphorochloridates.

PubMed

Bentley, T William

2015-05-08

Hydrolyses of acid derivatives (e.g., carboxylic acid chlorides and fluorides, fluoro- and chloroformates, sulfonyl chlorides, phosphorochloridates, anhydrides) exhibit pseudo-first order kinetics. Reaction mechanisms vary from those involving a cationic intermediate (SN1) to concerted SN2 processes, and further to third order reactions, in which one solvent molecule acts as the attacking nucleophile and a second molecule acts as a general base catalyst. A unified framework is discussed, in which there are two reaction channels-an SN1-SN2 spectrum and an SN2-SN3 spectrum. Third order rate constants (k3) are calculated for solvolytic reactions in a wide range of compositions of acetone-water mixtures, and are shown to be either approximately constant or correlated with the Grunwald-Winstein Y parameter. These data and kinetic solvent isotope effects, provide the experimental evidence for the SN2-SN3 spectrum (e.g., for chloro- and fluoroformates, chloroacetyl chloride, p-nitrobenzoyl p-toluenesulfonate, sulfonyl chlorides). Deviations from linearity lead to U- or V-shaped plots, which assist in the identification of the point at which the reaction channel changes from SN2-SN3 to SN1-SN2 (e.g., for benzoyl chloride).

Influences of brain tissue poroelastic constants on intracranial pressure (ICP) during constant-rate infusion.

PubMed

Li, Xiaogai; von Holst, Hans; Kleiven, Svein

2013-01-01

A 3D finite element (FE) model has been developed to study the mean intracranial pressure (ICP) response during constant-rate infusion using linear poroelasticity. Due to the uncertainties in the poroelastic constants for brain tissue, the influence of each of the main parameters on the transient ICP infusion curve was studied. As a prerequisite for transient analysis, steady-state simulations were performed first. The simulated steady-state pressure distribution in the brain tissue for a normal cerebrospinal fluid (CSF) circulation system showed good correlation with experiments from the literature. Furthermore, steady-state ICP closely followed the infusion experiments at different infusion rates. The verified steady-state models then served as a baseline for the subsequent transient models. For transient analysis, the simulated ICP shows a similar tendency to that found in the experiments, however, different values of the poroelastic constants have a significant effect on the infusion curve. The influence of the main poroelastic parameters including the Biot coefficient α, Skempton coefficient B, drained Young's modulus E, Poisson's ratio ν, permeability κ, CSF absorption conductance C(b) and external venous pressure p(b) was studied to investigate the influence on the pressure response. It was found that the value of the specific storage term S(ε) is the dominant factor that influences the infusion curve, and the drained Young's modulus E was identified as the dominant parameter second to S(ε). Based on the simulated infusion curves from the FE model, artificial neural network (ANN) was used to find an optimised parameter set that best fit the experimental curve. The infusion curves from both the FE simulation and using ANN confirmed the limitation of linear poroelasticity in modelling the transient constant-rate infusion.

Competition kinetics using the UV/H2O2 process: a structure reactivity correlation for the rate constants of hydroxyl radicals toward nitroaromatic compounds.

PubMed

García Einschlag, Fernando S; Carlos, Luciano; Capparelli, Alberto L

2003-10-01

The rate constants for hydroxyl radical reaction toward a set of nitroaromatic substrates kS, have been measured at 25 degrees C using competition experiments in the UV/H2O2 process. For a given pair of substrates S1 and S2, the relative reactivity beta (defined as kS1/kS2) was calculated from the slope of the corresponding double logarithmic plot, i.e., of ln[S1] vs. ln[S2]. This method is more accurate and remained linear for larger conversions in comparison with the plots of ln[S1] and ln[S2] against time. The rate constants measured ranged from 0.33 to 8.6 x 10(9) M(-1)s(-1). A quantitative structure-reactivity relationship was found using the Hammett equation. Assuming sigma values to be additive, a value of -0.60 was obtained for the reaction constant rho. This value agrees with the high reactivity and the electrophilic nature of HO* radical.

Rate constants for OH with selected large alkanes : shock-tube measurements and an improved group scheme.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sivaramakrishnan, R.; Michael, J. V.; Chemical Sciences and Engineering Division

High-temperature rate constant experiments on OH with the five large (C{sub 5}-C{sub 8}) saturated hydrocarbons n-heptane, 2,2,3,3-tetramethylbutane (2,2,3,3-TMB), n-pentane, n-hexane, and 2,3-dimethylbutane (2,3-DMB) were performed with the reflected-shock-tube technique using multipass absorption spectrometric detection of OH radicals at 308 nm. Single-point determinations at {approx}1200 K on n-heptane, 2,2,3,3-TMB, n-hexane, and 2,3-DMB were previously reported by Cohen and co-workers; however, the present work substantially extends the database to both lower and higher temperature. The present experiments span a wide temperature range, 789-1308 K, and represent the first direct measurements of rate constants at T > 800 K for n-pentane. The presentmore » work utilized 48 optical passes corresponding to a total path length of {approx}4.2 m. As a result of this increased path length, the high OH concentration detection sensitivity permitted pseudo-first-order analyses for unambiguously measuring rate constants. The experimental results can be expressed in Arrhenius form in units of cm{sup 3} molecule{sup -1} s{sup -1} as follows: K{sub OH+n-heptane} = (2.48 {+-} 0.17) x 10{sup -10} exp[(-1927 {+-} 69 K)/T] (838-1287 K); k{sub OH+2,2,3,3-TMB} = (8.26 {+-} 0.89) x 10{sup -11} exp[(-1337 {+-} 94 K)/T] (789-1061 K); K{sub OH+n-pentane} = (1.60 {+-} 0.25) x 10{sup -10} exp[(-1903 {+-} 146 K)/T] (823-1308 K); K{sub OH+n-hexane} = (2.79 {+-} 0.39) x 10{sup -10} exp[(-2301 {+-} 134 K)/T] (798-1299 K); and k{sub OH+2,3-DMB} = (1.27 {+-} 0.16) x 10{sup -10} exp[(-1617 {+-} 118 K)/T] (843-1292 K). The available experimental data, along with lower-T determinations, were used to obtain evaluations of the experimental rate constants over the temperature range from {approx}230 to 1300 K for most of the title reactions. These extended-temperature-range evaluations, given as three-parameter fits, are as follows: k{sub OH+n-heptane} = 2.059 x 10{sup -5}T{sup 1.401} exp(33 K

Rate constants for the quenching of metastable O2 (1Sigma g +) molecules

NASA Technical Reports Server (NTRS)

Kwang, Y. C.; Leu, M.-T.

1985-01-01

The O2 (1Sigma g +) rates for CO2, H2, N2, Cl2, CO, O3, and 2,3 DMB-2 are determined by monitoring the 762-nm emission in a fast-flow-discharge chemiluminescence detection system (Leu, 1984; Leu and Smith, 1981). The results are presented in tables and graphs and briefly characterized. The rate constants (in cu cm/s x 10 to the -16th) are 4600 + or - 500 for CO2, 7000 + or - 300 for H2, 17 + or - 1 for N2, 4.5 + or - 0.8 for Cl2, 45 + or - 5 for CO, 220,000 + or - 30,000 for O3, and 6000 + or - 100 for 2,3 DMB-2. The temperature dependence of the CO2 and O3 quenching reactions at 245-362 K is found to be negligible.

18 CFR 806.12 - Constant-rate aquifer testing.

Code of Federal Regulations, 2014 CFR

2014-04-01

... withdraw or increase a withdrawal of groundwater shall perform a constant-rate aquifer test in accordance... groundwater availability analysis to determine the availability of water during a 1-in-10-year recurrence...

18 CFR 806.12 - Constant-rate aquifer testing.

Code of Federal Regulations, 2012 CFR

2012-04-01

... withdraw or increase a withdrawal of groundwater shall perform a constant-rate aquifer test in accordance... groundwater availability analysis to determine the availability of water during a 1-in-10-year recurrence...

18 CFR 806.12 - Constant-rate aquifer testing.

Code of Federal Regulations, 2011 CFR

2011-04-01

... withdraw or increase a withdrawal of groundwater shall perform a constant-rate aquifer test in accordance... groundwater availability analysis to determine the availability of water during a 1-in-10-year recurrence...

18 CFR 806.12 - Constant-rate aquifer testing.

Code of Federal Regulations, 2013 CFR

2013-04-01

... withdraw or increase a withdrawal of groundwater shall perform a constant-rate aquifer test in accordance... groundwater availability analysis to determine the availability of water during a 1-in-10-year recurrence...

Biodegradation testing of chemicals with high Henry's constants - Separating mass and effective concentration reveals higher rate constants.

PubMed

Birch, Heidi; Andersen, Henrik R; Comber, Mike; Mayer, Philipp

2017-05-01

During simulation-type biodegradation tests, volatile chemicals will continuously partition between water phase and headspace. This study addressed how (1) this partitioning affects test results and (2) can be accounted for by combining equilibrium partition and dynamic biodegradation models. An aqueous mixture of 9 (semi)volatile chemicals was first generated using passive dosing and then diluted with environmental surface water producing concentrations in the ng/L to μg/L range. After incubation for 2 h to 4 weeks, automated Headspace Solid Phase Microextraction (HS-SPME) was applied directly on the test systems to measure substrate depletion by biodegradation relatively to abiotic controls. HS-SPME was also applied to determine air to water partitioning ratios. Biodegradation rate constants relating to the chemical in the water phase, k water , were generally a factor 1 to 11 times higher than biodegradation rate constants relating to the total mass of chemical in the test system, k system , with one exceptional factor of 72 times for a long chain alkane. True water phase degradation rate constants were found (i) more appropriate for risk assessment than test system rate constants, (ii) to facilitate extrapolation to other air-water systems and (iii) to be better defined input parameters for aquatic exposure and fate models. Copyright © 2017 Elsevier Ltd. All rights reserved.

Calculation of the rate constant for state-selected recombination of H+O2(v) as a function of temperature and pressure

NASA Astrophysics Data System (ADS)

Teitelbaum, Heshel; Caridade, Pedro J. S. B.; Varandas, António J. C.

2004-06-01

Classical trajectory calculations using the MERCURY/VENUS code have been carried out on the H+O2 reactive system using the DMBE-IV potential energy surface. The vibrational quantum number and the temperature were selected over the ranges v=0 to 15, and T=300 to 10 000 K, respectively. All other variables were averaged. Rate constants were determined for the energy transfer process, H+O2(v)-->H+O2(v''), for the bimolecular exchange process, H+O2(v)-->OH(v')+O, and for the dissociative process, H+O2(v)-->H+O+O. The dissociative process appears to be a mere extension of the process of transferring large amounts of energy. State-to-state rate constants are given for the exchange reaction, and they are in reasonable agreement with previous results, while the energy transfer and dissociative rate constants have never been reported previously. The lifetime distributions of the HO2 complex, calculated as a function of v and temperature, were used as a basis for determining the relative contributions of various vibrational states of O2 to the thermal rate coefficients for recombination at various pressures. This novel approach, based on the complex's ability to survive until it collides in a secondary process with an inert gas, is used here for the first time. Complete falloff curves for the recombination of H+O2 are also calculated over a wide range of temperatures and pressures. The combination of the two separate studies results in pressure- and temperature-dependent rate constants for H+O2(v)(+Ar)⇄HO2(+Ar). It is found that, unlike the exchange reaction, vibrational and rotational-translational energy are liabilities in promoting recombination.

ESTIMATION OF PHOSPHATE ESTER HYDROLYSIS RATE CONSTANTS - ALKALINE HYDROLYSIS

EPA Science Inventory

SPARC (SPARC Performs Automated Reasoning in Chemistry) chemical reactivity models were extended to allow the calculation of alkaline hydrolysis rate constants of phosphate esters in water. The rate is calculated from the energy difference between the initial and transition state...

Rate constant for the reaction of OH with CH3CCl2F (HCFC-141b) determined by relative rate measurements with CH4 and CH3CCl3

NASA Technical Reports Server (NTRS)

Huder, Karin; Demore, William B.

1993-01-01

Determination of accurate rate constants for OH abstraction is of great importance for the calculation of lifetimes for HCFCs and their impact on the atmosphere. For HCFC-141b there has been some disagreement in the literature for absolute measurements of this rate constant. In the present work rate constant ratios for HCFC-141b were measured at atmospheric pressure in the temperature range of 298-358 K, with CH4 and CH3CCl3 as reference gases. Ozone was photolyzed at 254 nm in the presence of water vapor to produce OH radicals. Relative depletions of 141b and the reference gases were measured by FTIR. Arrhenius expressions for 141b were derived from each reference gas and found to be in good agreement with each other. The combined expression for HCFC-141b which we recommend is 1.4 x 10 exp -12 exp(-1630/T) with k at 298 K being 5.9 x 10 exp -15 cu cm/molec-s. This value is in excellent agreement with the JPL 92-20 recommendation.

Cheap but accurate calculation of chemical reaction rate constants from ab initio data, via system-specific, black-box force fields

NASA Astrophysics Data System (ADS)

Steffen, Julien; Hartke, Bernd

2017-10-01

Building on the recently published quantum-mechanically derived force field (QMDFF) and its empirical valence bond extension, EVB-QMDFF, it is now possible to generate a reliable potential energy surface for any given elementary reaction step in an essentially black box manner. This requires a limited and pre-defined set of reference data near the reaction path and generates an accurate approximation of the reference potential energy surface, on and off the reaction path. This intermediate representation can be used to generate reaction rate data, with far better accuracy and reliability than with traditional approaches based on transition state theory (TST) or variational extensions thereof (VTST), even if those include sophisticated tunneling corrections. However, the additional expense at the reference level remains very modest. We demonstrate all this for three arbitrarily chosen example reactions.

Comparison of rate constants for (PO3-) transfer by the Mg(II), Cd(II), and Li(I) forms of phosphoglucomutase.

PubMed

Ray, W J; Post, C B; Puvathingal, J M

1989-01-24

Net rate constants that define the steady-state rate through a sequence of steps and the corresponding effective energy barriers for two (PO3-)-transfer steps in the phosphoglucomutase reaction were compared as a function of metal ion, M, where M = Mg2+ and Cd2+. These steps involve the reaction of either the 1-phosphate or the 6-phosphate of glucose 1,6-bisphosphate (Glc-P2) bound to the dephosphoenzyme (ED) to produce the phosphoenzyme (EP) and the free monophosphates, glucose 1-phosphate (Glc-1-P) or glucose 6-phosphate (Glc-6-P): EP.M + Glc-1-P----ED.M.Glc-P2----EP.M.Glc-6-P6. Before this comparison was made, net rate constants for the Cd2+ enzyme, obtained at high enzyme concentration via 31P NMR saturation-transfer studies [Post, C. B., Ray, W. J., Jr., & Gorenstein, D. G. (1989) Biochemistry (preceding paper in this issue)], were appropriately scaled by using the observed constants to calculate both the expected isotope-transfer rate at equilibrium and the steady-state rate under initial velocity conditions and comparing the calculated values with those measured in dilute solution. For the Mg2+ enzyme, narrow limits on possible values of the corresponding net rate constants were imposed on the basis of initial velocity rate constants for the forward and reverse directions plus values for the equilibrium distribution of central complexes, since direct measurement is not feasible. The effective energy barriers for both the Mg2+ and Cd2+ enzymes, calculated from the respective net rate constants, together with previously values for the equilibrium distribution of complexes in both enzymic systems [Ray, W. J., Jr., & Long, J. W. (1976) Biochemistry 15, 4018-4025], show that the 100-fold decrease in the kappa cat for the Cd2+ relative to the Mg2+ enzyme is caused by two factors: the increased stability of the intermediate bisphosphate complex and the decreased ability to cope with the phosphate ester involving the 1-hydroxyl group of the glucose ring. In fact, it

Reflected shock tube studies of high-temperature rate constants for OH + NO2 --> HO2 + NO and OH + HO2 --> H2O + O2.

PubMed

Srinivasan, Nanda K; Su, Meng-Chih; Sutherland, James W; Michael, Joe V; Ruscic, Branko

2006-06-01

The motivation for the present study comes from the preceding paper where it is suggested that accepted rate constants for OH + NO2 --> NO + HO2 are high by approximately 2. This conclusion was based on a reevaluation of heats of formation for HO2, OH, NO, and NO2 using the Active Thermochemical Table (ATcT) approach. The present experiments were performed in C2H5I/NO2 mixtures, using the reflected shock tube technique and OH-radical electronic absorption detection (at 308 nm) and using a multipass optical system. Time-dependent profile decays were fitted with a 23-step mechanism, but only OH + NO2, OH + HO2, both HO2 and NO2 dissociations, and the atom molecule reactions, O + NO2 and O + C2H4, contributed to the decay profile. Since all of the reactions except the first two are known with good accuracy, the profiles were fitted by varying only OH + NO2 and OH + HO2. The new ATcT approach was used to evaluate equilibrium constants so that back reactions were accurately taken into account. The combined rate constant from the present work and earlier work by Glaenzer and Troe (GT) is k(OH+NO2) = 2.25 x 10(-11) exp(-3831 K/T) cm3 molecule(-1) s(-1), which is a factor of 2 lower than the extrapolated direct value from Howard but agrees well with NO + HO2 --> OH + NO2 transformed with the updated equilibrium constants. Also, the rate constant for OH + HO2 suitable for combustion modeling applications over the T range (1200-1700 K) is (5 +/- 3) x 10(-11) cm3 molecule(-1) s(-1). Finally, simulating previous experimental results of GT using our updated mechanism, we suggest a constant rate for k(HO2+NO2) = (2.2 +/- 0.7) x 10(-11) cm3 molecule(-1) s(-1) over the T range 1350-1760 K.

(In)validity of the constant field and constant currents assumptions in theories of ion transport.

PubMed Central

Syganow, A; von Kitzing, E

1999-01-01

Constant electric fields and constant ion currents are often considered in theories of ion transport. Therefore, it is important to understand the validity of these helpful concepts. The constant field assumption requires that the charge density of permeant ions and flexible polar groups is virtually voltage independent. We present analytic relations that indicate the conditions under which the constant field approximation applies. Barrier models are frequently fitted to experimental current-voltage curves to describe ion transport. These models are based on three fundamental characteristics: a constant electric field, negligible concerted motions of ions inside the channel (an ion can enter only an empty site), and concentration-independent energy profiles. An analysis of those fundamental assumptions of barrier models shows that those approximations require large barriers because the electrostatic interaction is strong and has a long range. In the constant currents assumption, the current of each permeating ion species is considered to be constant throughout the channel; thus ion pairing is explicitly ignored. In inhomogeneous steady-state systems, the association rate constant determines the strength of ion pairing. Among permeable ions, however, the ion association rate constants are not small, according to modern diffusion-limited reaction rate theories. A mathematical formulation of a constant currents condition indicates that ion pairing very likely has an effect but does not dominate ion transport. PMID:9929480

Inverse problem analysis for identification of reaction kinetics constants in microreactors for biodiesel synthesis

NASA Astrophysics Data System (ADS)

Pontes, P. C.; Naveira-Cotta, C. P.

2016-09-01

The theoretical analysis for the design of microreactors in biodiesel production is a complicated task due to the complex liquid-liquid flow and mass transfer processes, and the transesterification reaction that takes place within these microsystems. Thus, computational simulation is an important tool that aids in understanding the physical-chemical phenomenon and, consequently, in determining the suitable conditions that maximize the conversion of triglycerides during the biodiesel synthesis. A diffusive-convective-reactive coupled nonlinear mathematical model, that governs the mass transfer process during the transesterification reaction in parallel plates microreactors, under isothermal conditions, is here described. A hybrid numerical-analytical solution via the Generalized Integral Transform Technique (GITT) for this partial differential system is developed and the eigenfunction expansions convergence rates are extensively analyzed and illustrated. The heuristic method of Particle Swarm Optimization (PSO) is applied in the inverse analysis of the proposed direct problem, to estimate the reaction kinetics constants, which is a critical step in the design of such microsystems. The results present a good agreement with the limited experimental data in the literature, but indicate that the GITT methodology combined with the PSO approach provide a reliable computational algorithm for direct-inverse analysis in such reactive mass transfer problems.

A Simple Approach to Evaluate the Kinetic Rate Constant for ATP Synthesis in Resting Human Skeletal Muscle at 7 T

PubMed Central

Ren, Jimin; Sherry, A. Dean; Malloy, Craig R.

2015-01-01

Inversion transfer (IT) is a well-established technique with multiple attractive features for analysis of kinetics. However, its application in measurement of ATP synthesis rate in vivo has lagged behind the more common ST techniques. One well-recognized issue with IT is the complexity of data analysis in comparison to much simpler analysis by ST. This complexity arises, in part, because the γ-ATP spin is involved in multiple chemical reactions and magnetization exchanges, whereas Pi is involved in a single reaction, Pi → γ-ATP. By considering the reactions involving γ-ATP only as a lumped constant, the rate constant for the reaction of physiological interest, kPi→γATP, can be determined. Here, we present a new IT data analysis method to evaluate kPi→γATP using data collected from resting human skeletal muscle at 7T. The method is based on the basic Bloch-McConnell equation, which relates kPi→γATP with ṁPi, the rate of Pi magnetization change. The kPi→γATP value is accessed from ṁPi data by more familiar linear correlation approaches. For a group of human subjects (n = 15), the kPi→γATP value derived for resting calf muscle was 0.066 ± 0.017 s−1, in agreement with literature reported values. In this study we also explored possible time-saving strategies to speed up data acquisition for kPi→γATP evaluation using simulations. The analysis indicates that it is feasible to carry out a 31P inversion transfer experiment in ~10 minutes or shorter at 7T with reasonable outcome in kPi→γATP variance for measurement of ATP synthesis in resting human skeletal muscle. We believe that this new IT data analysis approach will facilitate the wide acceptance of IT to evaluate ATP synthesis rate in vivo. PMID:25943328

Reaction rates for mesoscopic reaction-diffusion kinetics

DOE PAGES

Hellander, Stefan; Hellander, Andreas; Petzold, Linda

2015-02-23

The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical properties of the system, and it may produce unphysical results for models where those assumptions fail. In that case, other more comprehensive models are better suited, such as hard-sphere Brownian dynamics (BD). Although the RDME is a model in its own right, and not inferred from any specific microscale model, it proves useful to attempt to approximate a microscale model by a specific choice of mesoscopic reaction rates. In thismore » paper we derive mesoscopic scale-dependent reaction rates by matching certain statistics of the RDME solution to statistics of the solution of a widely used microscopic BD model: the Smoluchowski model with a Robin boundary condition at the reaction radius of two molecules. We also establish fundamental limits on the range of mesh resolutions for which this approach yields accurate results and show both theoretically and in numerical examples that as we approach the lower fundamental limit, the mesoscopic dynamics approach the microscopic dynamics. Finally, we show that for mesh sizes below the fundamental lower limit, results are less accurate. Thus, the lower limit determines the mesh size for which we obtain the most accurate results.« less

Reaction rates for mesoscopic reaction-diffusion kinetics

PubMed Central

Hellander, Stefan; Hellander, Andreas; Petzold, Linda

2016-01-01

The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical properties of the system, and it may produce unphysical results for models where those assumptions fail. In that case, other more comprehensive models are better suited, such as hard-sphere Brownian dynamics (BD). Although the RDME is a model in its own right, and not inferred from any specific microscale model, it proves useful to attempt to approximate a microscale model by a specific choice of mesoscopic reaction rates. In this paper we derive mesoscopic scale-dependent reaction rates by matching certain statistics of the RDME solution to statistics of the solution of a widely used microscopic BD model: the Smoluchowski model with a Robin boundary condition at the reaction radius of two molecules. We also establish fundamental limits on the range of mesh resolutions for which this approach yields accurate results and show both theoretically and in numerical examples that as we approach the lower fundamental limit, the mesoscopic dynamics approach the microscopic dynamics. We show that for mesh sizes below the fundamental lower limit, results are less accurate. Thus, the lower limit determines the mesh size for which we obtain the most accurate results. PMID:25768640

High-level direct-dynamics variational transition state theory calculations including multidimensional tunneling of the thermal rate constants, branching ratios, and kinetic isotope effects of the hydrogen abstraction reactions from methanol by atomic hydrogen.

PubMed

Meana-Pañeda, Rubén; Truhlar, Donald G; Fernández-Ramos, Antonio

2011-03-07

We report a detailed theoretical study of the hydrogen abstraction reaction from methanol by atomic hydrogen. The study includes the analysis of thermal rate constants, branching ratios, and kinetic isotope effects. Specifically, we have performed high-level computations at the MC3BB level together with direct dynamics calculations by canonical variational transition state theory (CVT) with the microcanonically optimized multidimensional tunneling (μOMT) transmission coefficient (CVT/μOMT) to study both the CH(3)OH+H→CH(2)OH+H(2) (R1) reaction and the CH(3)OH+H→CH(3)O+H(2) (R2) reaction. The CVT/μOMT calculations show that reaction R1 dominates in the whole range 298≤T (K)≤2500 and that anharmonic effects on the torsional mode about the C-O bond are important, mainly at high temperatures. The activation energy for the total reaction sum of R1 and R2 reactions changes substantially with temperature and, therefore, the use of straight-line Arrhenius plots is not valid. We recommend the use of new expressions for the total R1 + R2 reaction and for the R1 and R2 individual reactions. © 2011 American Institute of Physics.

Probabilistic models and uncertainty quantification for the ionization reaction rate of atomic Nitrogen

NASA Astrophysics Data System (ADS)

Miki, K.; Panesi, M.; Prudencio, E. E.; Prudhomme, S.

2012-05-01

The objective in this paper is to analyze some stochastic models for estimating the ionization reaction rate constant of atomic Nitrogen (N + e- → N+ + 2e-). Parameters of the models are identified by means of Bayesian inference using spatially resolved absolute radiance data obtained from the Electric Arc Shock Tube (EAST) wind-tunnel. The proposed methodology accounts for uncertainties in the model parameters as well as physical model inadequacies, providing estimates of the rate constant that reflect both types of uncertainties. We present four different probabilistic models by varying the error structure (either additive or multiplicative) and by choosing different descriptions of the statistical correlation among data points. In order to assess the validity of our methodology, we first present some calibration results obtained with manufactured data and then proceed by using experimental data collected at EAST experimental facility. In order to simulate the radiative signature emitted in the shock-heated air plasma, we use a one-dimensional flow solver with Park's two-temperature model that simulates non-equilibrium effects. We also discuss the implications of the choice of the stochastic model on the estimation of the reaction rate and its uncertainties. Our analysis shows that the stochastic models based on correlated multiplicative errors are the most plausible models among the four models proposed in this study. The rate of the atomic Nitrogen ionization is found to be (6.2 ± 3.3) × 1011 cm3 mol-1 s-1 at 10,000 K.

ESTIMATION OF CARBOXYLIC ACID ESTER HYDROLYSIS RATE CONSTANTS

EPA Science Inventory

SPARC chemical reactivity models were extended to calculate hydrolysis rate constants for carboxylic acid esters from molecular structure. The energy differences between the initial state and the transition state for a molecule of interest are factored into internal and external...

Calculated Third Order Rate Constants for Interpreting the Mechanisms of Hydrolyses of Chloroformates, Carboxylic Acid Halides, Sulfonyl Chlorides and Phosphorochloridates

PubMed Central

Bentley, T. William

2015-01-01

Hydrolyses of acid derivatives (e.g., carboxylic acid chlorides and fluorides, fluoro- and chloroformates, sulfonyl chlorides, phosphorochloridates, anhydrides) exhibit pseudo-first order kinetics. Reaction mechanisms vary from those involving a cationic intermediate (SN1) to concerted SN2 processes, and further to third order reactions, in which one solvent molecule acts as the attacking nucleophile and a second molecule acts as a general base catalyst. A unified framework is discussed, in which there are two reaction channels—an SN1-SN2 spectrum and an SN2-SN3 spectrum. Third order rate constants (k3) are calculated for solvolytic reactions in a wide range of compositions of acetone-water mixtures, and are shown to be either approximately constant or correlated with the Grunwald-Winstein Y parameter. These data and kinetic solvent isotope effects, provide the experimental evidence for the SN2-SN3 spectrum (e.g., for chloro- and fluoroformates, chloroacetyl chloride, p-nitrobenzoyl p-toluenesulfonate, sulfonyl chlorides). Deviations from linearity lead to U- or V-shaped plots, which assist in the identification of the point at which the reaction channel changes from SN2-SN3 to SN1-SN2 (e.g., for benzoyl chloride). PMID:26006228

Reactions of cisplatin with cysteine and methionine at constant pH; a computational study.

PubMed

Zimmermann, Tomás; Burda, Jaroslav V

2010-02-07

Interactions of hydrated cisplatin complexes cis-[Pt(NH(3))(2)Cl(H(2)O)](+) and cis-[Pt(NH(3))(2)(OH)(H(2)O)](+) with cysteine and methionine in an aqueous solution at constant pH were explored using computational methods. Thermodynamic parameters of considered reactions were studied in a broad pH range, taking up to 4 protonation states of each molecule into account. Reaction free energies at constant pH were obtained from standard Gibbs free energies using the Legendre transformation. Solvation free energies and pK(a) values were calculated using the PCM model with UAHF cavities, recently adapted by us for transition metal complexes. The root mean square error of pK(a) values on a set of model platinum complexes and amino acids was equal to 0.74. At pH 7, the transformed Gibbs free energies differ by up to 15 kcal mol(-1) from the Gibbs free energies of model reactions with a constant number of protons. As for cysteine, calculations confirmed a strong preference for kappaS monodenate bonding in a broad pH range. The most stable product of the second reaction step, which proceeds from monodentate to chelate complex, is the kappa(2)S,N coordinated chelate. The reaction with methionine is more complex. In the first step all three considered methionine donor atoms (N, S and O) are thermodynamically preferred products depending on the platinum complex and the pH. This is in accordance with the experimental observation of a pH dependent migration between N and S donor atoms in a chemically related system. The most stable chelates of platinum with methionine are kappa(2)S,N and kappa(2)N,O bonded complexes. The comparison of reaction free energies of both amino acids suggests, that the bidentate methionine ligand can be displaced even by the monodentate cysteine ligand under certain conditions.

Global Kinetic Constants for Thermal Oxidative Degradation of a Cellulosic Paper

NASA Technical Reports Server (NTRS)

Kashiwagi, Takashi; Nambu, Hidesaburo

1992-01-01

Values of global kinetic constants for pyrolysis, thermal oxidative degradation, and char oxidation of a cellulosic paper were determined by a derivative thermal gravimetric study. The study was conducted at heating rates of 0.5, 1, 1.5, 3, and 5 C/min in ambient atmospheres of nitrogen, 0.28, 1.08, 5.2 percent oxygen concentrations, and air. Sample weight loss rate, concentrations of CO, CO2, and H2O in the degradation products, and oxygen consumption were continuously measured during the experiment. Values of activation energy, preexponential factor, orders of reaction, and yields of CO, CO2, H2O, total hydrocarbons, and char for each degradation reaction were derived from the results. Heat of reaction for each reaction was determined by differential scanning calorimetry. A comparison of the calculated CO, CO2, H2O, total hydrocarbons, sample weight loss rate, and oxygen consumption was made with the measured results using the derived kinetic constants, and the accuracy of the values of kinetic constants was discussed.

Method of controlling fusion reaction rates

DOEpatents

Kulsrud, Russell M.; Furth, Harold P.; Valeo, Ernest J.; Goldhaber, Maurice

1988-01-01

A method of controlling the reaction rates of the fuel atoms in a fusion reactor comprises the step of polarizing the nuclei of the fuel atoms in a particular direction relative to the plasma confining magnetic field. Fusion reaction rates can be increased or decreased, and the direction of emission of the reaction products can be controlled, depending on the choice of polarization direction.

Method of controlling fusion reaction rates

DOEpatents

Kulsrud, Russell M.; Furth, Harold P.; Valeo, Ernest J.; Goldhaber, Maurice

1988-03-01

A method of controlling the reaction rates of the fuel atoms in a fusion reactor comprises the step of polarizing the nuclei of the fuel atoms in a particular direction relative to the plasma confining magnetic field. Fusion reaction rates can be increased or decreased, and the direction of emission of the reaction products can be controlled, depending on the choice of polarization direction.

The lowest-lying electronic singlet and triplet potential energy surfaces for the HNO-NOH system: energetics, unimolecular rate constants, tunneling and kinetic isotope effects for the isomerization and dissociation reactions.

PubMed

Bozkaya, Uğur; Turney, Justin M; Yamaguchi, Yukio; Schaefer, Henry F

2012-04-28

The lowest-lying electronic singlet and triplet potential energy surfaces (PES) for the HNO-NOH system have been investigated employing high level ab initio quantum chemical methods. The reaction energies and barriers have been predicted for two isomerization and four dissociation reactions. Total energies are extrapolated to the complete basis set limit applying focal point analyses. Anharmonic zero-point vibrational energies, diagonal Born-Oppenheimer corrections, relativistic effects, and core correlation corrections are also taken into account. On the singlet PES, the (1)HNO → (1)NOH endothermicity including all corrections is predicted to be 42.23 ± 0.2 kcal mol(-1). For the barrierless decomposition of (1)HNO to H + NO, the dissociation energy is estimated to be 47.48 ± 0.2 kcal mol(-1). For (1)NOH → H + NO, the reaction endothermicity and barrier are 5.25 ± 0.2 and 7.88 ± 0.2 kcal mol(-1). On the triplet PES the reaction energy and barrier including all corrections are predicted to be 7.73 ± 0.2 and 39.31 ± 0.2 kcal mol(-1) for the isomerization reaction (3)HNO → (3)NOH. For the triplet dissociation reaction (to H + NO) the corresponding results are 29.03 ± 0.2 and 32.41 ± 0.2 kcal mol(-1). Analogous results are 21.30 ± 0.2 and 33.67 ± 0.2 kcal mol(-1) for the dissociation reaction of (3)NOH (to H + NO). Unimolecular rate constants for the isomerization and dissociation reactions were obtained utilizing kinetic modeling methods. The tunneling and kinetic isotope effects are also investigated for these reactions. The adiabatic singlet-triplet energy splittings are predicted to be 18.45 ± 0.2 and 16.05 ± 0.2 kcal mol(-1) for HNO and NOH, respectively. Kinetic analyses based on solution of simultaneous first-order ordinary-differential rate equations demonstrate that the singlet NOH molecule will be difficult to prepare at room temperature, while the triplet NOH molecule is viable with respect to isomerization and dissociation reactions up to

Potential Energy Surface for Large Barrierless Reaction Systems: Application to the Kinetic Calculations of the Dissociation of Alkanes and the Reverse Recombination Reactions.

PubMed

Yao, Qian; Cao, Xiao-Mei; Zong, Wen-Gang; Sun, Xiao-Hui; Li, Ze-Rong; Li, Xiang-Yuan

2018-05-31

The isodesmic reaction method is applied to calculate the potential energy surface (PES) along the reaction coordinates and the rate constants of the barrierless reactions for unimolecular dissociation reactions of alkanes to form two alkyl radicals and their reverse recombination reactions. The reaction class is divided into 10 subclasses depending upon the type of carbon atoms in the reaction centers. A correction scheme based on isodesmic reaction theory is proposed to correct the PESs at UB3LYP/6-31+G(d,p) level. To validate the accuracy of this scheme, a comparison of the PESs at B3LYP level and the corrected PESs with the PESs at CASPT2/aug-cc-pVTZ level is performed for 13 representative reactions, and it is found that the deviations of the PESs at B3LYP level are up to 35.18 kcal/mol and are reduced to within 2 kcal/mol after correction, indicating that the PESs for barrierless reactions in a subclass can be calculated meaningfully accurately at a low level of ab initio method using our correction scheme. High-pressure limit rate constants and pressure dependent rate constants of these reactions are calculated based on their corrected PESs and the results show the pressure dependence of the rate constants cannot be ignored, especially at high temperatures. Furthermore, the impact of molecular size on the pressure-dependent rate constants of decomposition reactions of alkanes and their reverse reactions has been studied. The present work provides an effective method to generate meaningfully accurate PESs for large molecular system.

Kinetics of the creatine kinase reaction in neonatal rabbit heart: An empirical analysis of the rate equation

DOE Office of Scientific and Technical Information (OSTI.GOV)

McAuliffe, J.J.; Perry, S.B.; Brooks, E.E.

1991-03-12

Here the authors define the kinetics of the creatine kinase (CK) reaction in an intact mammalian heart containing the full rnage of CK isoenzymes. Previously derived kinetic constants were refit for the reaction occurring at 37C. Steady-state metabolite concentrations from {sup 31}P NMR and standard biochemical techniques were determined. {sup 31}P magnetization transfer data were obtained to determine unidirectional creatine kinase fluxes in hearts with differing total creatine contents and differing mitochondrial CK activities during KCl arrest and isovolumic work for both the forward reaction (MgATP synthesis) and reverse reaction (phosphocreatine synthesis). The NMR kinetic data and substrate concentrations datamore » were used in conjunction with a kinetic model based on MM-CK in solution to determine the applicability of the solution-based kinetic models to the CK kinetics of the intact heart. The results indicated that no single set of rate equation constants could describe both the KCl-arrested and working hearts. Analysis of the results indicated that the CK reaction is rate limited in the direction of ATP synthesis, the size of the guanidino substrate pool drives the measured CK flux in the intact heart, and during isovolumic work, the CK reaction operates under saturating conditions; that is, the substrate concentrations are at least 2-fold greater than the K{sub m} or K{sub im} for each substrate. However, during KCl arrest the reaction does not operate under saturating conditions and the CK reaction velocity is strongly influenced by the guanidino substrate pool size.« less

Rate Coefficients for Reactions of Ethynyl Radical (C2H) With HCN and CH3CN: Implications for the Formation of Comples Nitriles on Titan

NASA Technical Reports Server (NTRS)

Hoobler, Ray J.; Leone, Stephen R.

1997-01-01

Rate coefficients for the reactions of C2H + HCN yields products and C2H + CH3CN yields products have been measured over the temperature range 262-360 K. These experiments represent an ongoing effort to accurately measure reaction rate coefficients of the ethynyl radical, C2H, relevant to planetary atmospheres such as those of Jupiter and Saturn and its satellite Titan. Laser photolysis of C2H2 is used to produce C2H, and transient infrared laser absorption is employed to measure the decay of C2H to obtain the subsequent reaction rates in a transverse flow cell. Rate constants for the reaction C2H + HCN yields products are found to increase significantly with increasing temperature and are measured to be (3.9-6.2) x 10(exp 13) cm(exp 3) molecules(exp -1) s(exp -1) over the temperature range of 297-360 K. The rate constants for the reaction C2H + CH3CN yields products are also found to increase substantially with increasing temperature and are measured to be (1.0-2.1) x 10(exp -12) cm(exp 3) molecules(exp -1) s(exp -1) over the temperature range of 262-360 K. For the reaction C2H + HCN yields products, ab initio calculations of transition state structures are used to infer that the major products form via an addition/elimination pathway. The measured rate constants for the reaction of C2H + HCN yields products are significantly smaller than values currently employed in photochemical models of Titan, which will affect the HC3N distribution.

Effect of hydrostatic pressure, temperature, and solvent on the rate of the Diels-Alder reaction between 9,10-anthracenedimethanol and maleic anhydride

NASA Astrophysics Data System (ADS)

Kiselev, V. D.; Kornilov, D. A.; Anikin, O. V.; Latypova, L. I.; Konovalov, A. I.

2017-03-01

The rate of the reaction between 9,10-anthracenedimethanol and maleic anhydride in 1,4-dioxane, acetonitrile, trichloromethane, and toluene is studied at 25, 35, 45°C in the pressure range of 1-1772 bar. The rate constants, enthalpies, entropies and activation volumes are determined. It is shown that the rate of reaction with 9,10-anthracenedimethanol is approximately one order of magnitude higher than with 9-anthracenemethanol.

Transition state theory thermal rate constants and RRKM-based branching ratios for the N((2)D) + CH(4) reaction based on multi-state and multi-reference ab initio calculations of interest for the Titan's chemistry.

PubMed

Ouk, Chanda-Malis; Zvereva-Loëte, Natalia; Scribano, Yohann; Bussery-Honvault, Béatrice

2012-10-30

Multireference single and double configuration interaction (MRCI) calculations including Davidson (+Q) or Pople (+P) corrections have been conducted in this work for the reactants, products, and extrema of the doublet ground state potential energy surface involved in the N((2)D) + CH(4) reaction. Such highly correlated ab initio calculations are then compared with previous PMP4, CCSD(T), W1, and DFT/B3LYP studies. Large relative differences are observed in particular for the transition state in the entrance channel resolving the disagreement between previous ab initio calculations. We confirm the existence of a small but positive potential barrier (3.86 ± 0.84 kJ mol(-1) (MR-AQCC) and 3.89 kJ mol(-1) (MRCI+P)) in the entrance channel of the title reaction. The correlation is seen to change significantly the energetic position of the two minima and five saddle points of this system together with the dissociation channels but not their relative order. The influence of the electronic correlation into the energetic of the system is clearly demonstrated by the thermal rate constant evaluation and it temperature dependance by means of the transition state theory. Indeed, only MRCI values are able to reproduce the experimental rate constant of the title reaction and its behavior with temperature. Similarly, product branching ratios, evaluated by means of unimolecular RRKM theory, confirm the NH production of Umemoto et al., whereas previous works based on less accurate ab initio calculations failed. We confirm the previous findings that the N((2)D) + CH(4) reaction proceeds via an insertion-dissociation mechanism and that the dominant product channels are CH(2)NH + H and CH(3) + NH. Copyright © 2012 Wiley Periodicals, Inc.

Rationalizing 5000-Fold Differences in Receptor-Binding Rate Constants of Four Cytokines

PubMed Central

Pang, Xiaodong; Qin, Sanbo; Zhou, Huan-Xiang

2011-01-01

The four cytokines erythropoietin (EPO), interleukin-4 (IL4), human growth hormone (hGH), and prolactin (PRL) all form four-helix bundles and bind to type I cytokine receptors. However, their receptor-binding rate constants span a 5000-fold range. Here, we quantitatively rationalize these vast differences in rate constants by our transient-complex theory for protein-protein association. In the transient complex, the two proteins have near-native separation and relative orientation, but have yet to form the short-range specific interactions of the native complex. The theory predicts the association rate constant as ka=ka0exp(−ΔGel∗/kBT) where ka0 is the basal rate constant for reaching the transient complex by random diffusion, and the Boltzmann factor captures the rate enhancement due to electrostatic attraction. We found that the vast differences in receptor-binding rate constants of the four cytokines arise mostly from the differences in charge complementarity among the four cytokine-receptor complexes. The basal rate constants (ka0) of EPO, IL4, hGH, and PRL were similar (5.2 × 105 M−1s−1, 2.4 × 105 M−1s−1, 1.7 × 105 M−1s−1, and 1.7 × 105 M−1s−1, respectively). However, the average electrostatic free energies (ΔGe1∗) were very different (−4.2 kcal/mol, −2.4 kcal/mol, −0.1 kcal/mol, and −0.5 kcal/mol, respectively, at ionic strength = 160 mM). The receptor-binding rate constants predicted without adjusting any parameters, 6.2 × 108 M−1s−1, 1.3 × 107 M−1s−1, 2.0 × 105 M−1s−1, and 7.6 × 104 M−1s−1, respectively, for EPO, IL4, hGH, and PRL agree well with experimental results. We uncover that these diverse rate constants are anticorrelated with the circulation concentrations of the cytokines, with the resulting cytokine-receptor binding rates very close to the limits set by the half-lives of the receptors, suggesting that these binding rates are functionally relevant and perhaps evolutionarily

Theoretical Evaluation of the Transient Response of Constant Head and Constant Flow-Rate Permeability Tests

USGS Publications Warehouse

Zhang, M.; Takahashi, M.; Morin, R.H.; Esaki, T.

1998-01-01

A theoretical analysis is presented that compares the response characteristics of the constant head and the constant flowrate (flow pump) laboratory techniques for quantifying the hydraulic properties of geologic materials having permeabilities less than 10-10 m/s. Rigorous analytical solutions that describe the transient distributions of hydraulic gradient within a specimen are developed, and equations are derived for each method. Expressions simulating the inflow and outflow rates across the specimen boundaries during a constant-head permeability test are also presented. These solutions illustrate the advantages and disadvantages of each method, including insights into measurement accuracy and the validity of using Darcy's law under certain conditions. The resulting observations offer practical considerations in the selection of an appropriate laboratory test method for the reliable measurement of permeability in low-permeability geologic materials.

Explanation of the unusual temperature dependence of the atmospherically important OH + H(2)S --> H(2)O + HS reaction and prediction of the rate constant at combustion temperatures.

PubMed

Ellingson, Benjamin A; Truhlar, Donald G

2007-10-24

Rate constants for the OH + H2S --> H2O + HS reaction, which is important for both atmospheric chemistry and combustion, are calculated by direct dynamics with the M06-2X density functional using the MG3S basis set. Energetics are compared to high-level MCG3/3//MC-QCISD/3 wave function theory and to results obtained by other density functionals. We employ canonical variational transition-state theory with multidimensional tunneling contributions and scaled generalized normal-mode frequencies evaluated in redundant curvilinear coordinates with anharmonicity included in the torsion. The transition state has a quantum mechanically distinguishable, nonsuperimposable mirror image that corresponds to a separate classical reaction path; the effect of the multiple paths is examined through use of a symmetry number and by torsional methods. Calculations with the reference-potential Pitzer-Gwinn treatment of the torsional mode agree with experiment, within experimental scatter, and predict a striking temperature dependence of the activation energy, increasing from -0.1 kcal/mol at 200 K to 0.2, 1.0, 3.4, and 9.8 kcal/mol at 300, 500, 1000, and 2400 K. The unusual temperature dependence arises from a dynamical bottleneck at an energy below reactants, following an addition complex on the reaction path with a classical binding energy of 4.4 kcal/mol. As a way to check the mechanism, kinetic isotope effects of the OH + D2S and OD + D2S reactions have been predicted.

Reaction of SO2 with OH in the atmosphere.

PubMed

Long, Bo; Bao, Junwei Lucas; Truhlar, Donald G

2017-03-15

The OH + SO 2 reaction plays a critical role in understanding the oxidation of SO 2 in the atmosphere, and its rate constant is critical for clarifying the fate of SO 2 in the atmosphere. The rate constant of the OH + SO 2 reaction is calculated here by using beyond-CCSDT correlation energy calculations for a benchmark, validated density functional methods for direct dynamics, canonical variational transition state theory with anharmonicity and multidimensional tunneling for the high-pressure rate constant, and system-specific quantum RRK theory for pressure effects; the combination of these methods can compete in accuracy with experiments. There has been a long-term debate in the literature about whether the OH + SO 2 reaction is barrierless, but our calculations indicate a positive barrier with an transition structure that has an enthalpy of activation of 0.27 kcal mol -1 at 0 K. Our results show that the high-pressure limiting rate constant of the OH + SO 2 reaction has a positive temperature dependence, but the rate constant at low pressures has a negative temperature dependence. The computed high-pressure limiting rate constant at 298 K is 1.25 × 10 -12 cm 3 molecule -1 s -1 , which agrees excellently with the value (1.3 × 10 -12 cm 3 molecule -1 s -1 ) recommended in the most recent comprehensive evaluation for atmospheric chemistry. We show that the atmospheric lifetime of SO 2 with respect to oxidation by OH depends strongly on altitude (in the range 0-50 km) due to the falloff effect. We introduce a new interpolation procedure for fitting the combined temperature and pressure dependence of the rate constant, and it fits the calculated rate constants over the whole range with a mean unsigned error of only 7%. The present results provide reliable kinetics data for this specific reaction, and also they demonstrate convenient theoretical methods that can be reliable for predicting rate constants of other gas-phase reactions.

Hydrolysis rate constants and activation parameters for phosphate- and phosphonate-bridged phthalonitrile monomers under acid, neutral and alkali conditions.

PubMed

Belsky, Kirill S; Sulimov, Artem V; Bulgakov, Boris A; Babkin, Alexandr V; Kepman, Alexey V

2017-08-01

Hydrolysis data for Bis(3-(3,4-dicyanophenoxy)phenyl) phenyl phosphate and Bis(3-(3,4-dicyanophenoxy)phenyl) phenylphosphonate under pH 4, 7 and 10 are presented. Conversion/time plots collected by HPLC analysis, typical chromatograms and NMR spectra of the reactions products are given. Pseudo-first order rate constants are determined for both substrates at 25, 50 and 80 °C. Activation parameters were calculated from Arrhenius equation.

18 CFR 806.12 - Constant-rate aquifer testing.

Code of Federal Regulations, 2010 CFR

2010-04-01

... groundwater availability analysis to determine the availability of water during a 1-in-10-year recurrence... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false Constant-rate aquifer testing. 806.12 Section 806.12 Conservation of Power and Water Resources SUSQUEHANNA RIVER BASIN...

ESTIMATION OF PHOSPHATE ESTER HYDROLYSIS RATE CONSTANTS. I. ALKALINE HYDROLYSIS

EPA Science Inventory

SPARC (SPARC Performs Automated Reasoning in Chemistry) chemical reactivity models were extended to allow the calculation of alkaline hydrolysis rate constants of phosphate esters in water. The rate is calculated from the energy difference between the initial and transition state...

MICROBIAL TRANSFORMATION RATE CONSTANTS OF STRUCTURALLY DIVERSE MAN-MADE CHEMICALS

EPA Science Inventory

To assist in estimating microbially mediated transformation rates of man-made chemicals from their chemical structures, all second order rate constants that have been measured under conditions that make the values comparable have been extracted from the literature and combined wi...

Higher success rate with transcranial electrical stimulation of motor-evoked potentials using constant-voltage stimulation compared with constant-current stimulation in patients undergoing spinal surgery.

PubMed

Shigematsu, Hideki; Kawaguchi, Masahiko; Hayashi, Hironobu; Takatani, Tsunenori; Iwata, Eiichiro; Tanaka, Masato; Okuda, Akinori; Morimoto, Yasuhiko; Masuda, Keisuke; Tanaka, Yuu; Tanaka, Yasuhito

2017-10-01

During spine surgery, the spinal cord is electrophysiologically monitored via transcranial electrical stimulation of motor-evoked potentials (TES-MEPs) to prevent injury. Transcranial electrical stimulation of motor-evoked potential involves the use of either constant-current or constant-voltage stimulation; however, there are few comparative data available regarding their ability to adequately elicit compound motor action potentials. We hypothesized that the success rates of TES-MEP recordings would be similar between constant-current and constant-voltage stimulations in patients undergoing spine surgery. The objective of this study was to compare the success rates of TES-MEP recordings between constant-current and constant-voltage stimulation. This is a prospective, within-subject study. Data from 100 patients undergoing spinal surgery at the cervical, thoracic, or lumbar level were analyzed. The success rates of the TES-MEP recordings from each muscle were examined. Transcranial electrical stimulation with constant-current and constant-voltage stimulations at the C3 and C4 electrode positions (international "10-20" system) was applied to each patient. Compound muscle action potentials were bilaterally recorded from the abductor pollicis brevis (APB), deltoid (Del), abductor hallucis (AH), tibialis anterior (TA), gastrocnemius (GC), and quadriceps (Quad) muscles. The success rates of the TES-MEP recordings from the right Del, right APB, bilateral Quad, right TA, right GC, and bilateral AH muscles were significantly higher using constant-voltage stimulation than those using constant-current stimulation. The overall success rates with constant-voltage and constant-current stimulations were 86.3% and 68.8%, respectively (risk ratio 1.25 [95% confidence interval: 1.20-1.31]). The success rates of TES-MEP recordings were higher using constant-voltage stimulation compared with constant-current stimulation in patients undergoing spinal surgery. Copyright © 2017

Rate constants and mechanisms for the crystallization of Al nano-goethite under environmentally relevant conditions

NASA Astrophysics Data System (ADS)

Bazilevskaya, Ekaterina; Archibald, Douglas D.; Martínez, Carmen Enid

2012-07-01

Mobile inorganic and organic nanocolloidal particles originate-from and interact-with bulk solid phases in soil and sediment environments, and as such, they contribute to the dynamic properties of environmental systems. In particular, ferrihydrite and (nano)goethite are the most abundant of nanocolloidal Fe oxy(hydr)oxides in these environments. We therefore investigated the ferrihydrite to goethite phase transformation using experimental reaction conditions that mimicked environmental conditions where the formation of nanocolloidal Fe oxy(hydr)oxides may occur: slow titration of dilute solutions to pH 5 at 25 °C with and without 2 mol% Al. Subsequently, the rate constants from 54-d nano-goethite aging/crystallization experiments at 50 °C were determined using aliquots pulled for vibrational spectroscopy (including multivariate curve resolution, MCR, analyses of infrared spectra) and synchrotron-based X-ray diffraction (XRD). We also present a mechanistic model that accounts for the nano-goethite crystallization observed by the aforementioned techniques, and particle structural characteristics observed by dynamic light scattering (DLS) and transmission electron microscopy (TEM). In contrast to the common assumption that metastable ferrihydrite precipitates first, before it transforms to goethite, the presence of characteristic infrared bands in freshly synthesized nanoparticle suspensions indicate goethite can precipitate directly from solution under environmentally relevant conditions: low Fe concentration, ambient temperature, and pH maintained at 5. However, the presence of 2 mol% Al prevented direct goethite precipitation. Rate constants obtained by fitting the contributions from the MCR-derived goethite-like component to the OH-stretching region were (7.4 ± 1.1) × 10-7 s-1 for 0% Al and (4.2 ± 0.4) × 10-7 s-1 for 2 mol% Al suspensions. Rate constants derived from intensities of OH-bending infrared vibrations (795 and 895 cm-1) showed similar values

Typewriting rate as a function of reaction time.

PubMed

Hayes, V; Wilson, G D; Schafer, R L

1977-12-01

This study was designed to determine the relationship between reaction time and typewriting rate. Subjects were 24 typists ranging in age from 19 to 39 yr. Reaction times (.001 sec) to a light were recorded for each finger and to each alphabetic character and three punctuation marks. Analysis of variance yielded significant differences in reaction time among subjects and fingers. Correlation between typewriting rate and average reaction time to the alphabetic characters and three punctuation marks was --.75. Correlation between typewriting rate and the difference between the reaction time of the hands was --.42. Factors influencing typewriting rate may include reaction time of the fingers, difference between the reaction time of the hands, and reaction time to individual keys on the typewriter. Implications exist for instructional methodology and further research.

A comprehensive model to determine the effects of temperature and species fluctuations on reaction rates in turbulent reacting flows

NASA Technical Reports Server (NTRS)

Chinitz, W.; Foy, E.; Rowan, G.; Goldstein, D.

1982-01-01

The use of probability theory to determine the effects of turbulent fluctuations on reaction rates in turbulent combustion systems is briefly reviewed. Results are presented for the effect of species fluctuations in particular. It is found that turbulent fluctuations of species act to reduce the reaction rates, in contrast with the temperature fluctuations previously determined to increase Arrhenius reaction rate constants. For the temperature fluctuations, a criterion is set forth for determining if, in a given region of a turbulent flow field, the temperature can be expected to exhibit ramp like fluctuations. Using the above results, along with results previously obtained, a model is described for testing the effects of turbulent fluctuations of temperature and species on reaction rates in computer programs dealing with turbulent reacting flows. An alternative model which employs three variable probability density functions (temperature and two species) and is currently being formulated is discussed as well.

pH & Rate of Enzymatic Reactions.

ERIC Educational Resources Information Center

Clariana, Roy B.

1991-01-01

A quantitative and inexpensive way to measure the rate of enzymatic reaction is provided. The effects of different pH levels on the reaction rate of an enzyme from yeast are investigated and the results graphed. Background information, a list of needed materials, directions for preparing solutions, procedure, and results and discussion are…

A simple approach to evaluate the kinetic rate constant for ATP synthesis in resting human skeletal muscle at 7 T.

PubMed

Ren, Jimin; Sherry, A Dean; Malloy, Craig R

2016-09-01

Inversion transfer (IT) is a well-established technique with multiple attractive features for analysis of kinetics. However, its application in measurement of ATP synthesis rate in vivo has lagged behind the more common saturation transfer (ST) techniques. One well-recognized issue with IT is the complexity of data analysis in comparison with much simpler analysis by ST. This complexity arises, in part, because the γ-ATP spin is involved in multiple chemical reactions and magnetization exchanges, whereas Pi is involved in a single reaction, Pi → γ-ATP. By considering the reactions involving γ-ATP only as a lumped constant, the rate constant for the reaction of physiological interest, kPi→γATP , can be determined. Here, we present a new IT data analysis method to evaluate kPi→γATP using data collected from resting human skeletal muscle at 7 T. The method is based on the basic Bloch-McConnell equation, which relates kPi→γATP to m˙Pi, the rate of Pi magnetization change. The kPi→γATP value is accessed from m˙Pi data by more familiar linear correlation approaches. For a group of human subjects (n = 15), the kPi→γATP value derived for resting calf muscle was 0.066 ± 0.017 s(-1) , in agreement with literature-reported values. In this study we also explored possible time-saving strategies to speed up data acquisition for kPi→γATP evaluation using simulations. The analysis indicates that it is feasible to carry out a (31) P IT experiment in about 10 min or less at 7 T with reasonable outcome in kPi→γATP variance for measurement of ATP synthesis in resting human skeletal muscle. We believe that this new IT data analysis approach will facilitate the wide acceptance of IT to evaluate ATP synthesis rate in vivo. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Absolute rate of the reaction of C l(2P) with methane from 200-500 K

NASA Technical Reports Server (NTRS)

Whytock, D. A.; Lee, J. H.; Michael, J. V.; Payne, W. A.; Stief, L. J.

1976-01-01

Rate constants for the reaction of atomic chlorine with methane have been measured from 200-500K using the flash photolysis-resonance fluorescence technique. When the results from fourteen equally spaced experimental determinations are plotted in Arrhenius form a definite curvature is noted. The results are compared to previous work and are theoretically discussed.

On the validity of specific rate constants (kSA) in Fe0/H2O systems.

PubMed

Noubactep, C

2009-05-30

The validity of the specific reaction rate constants (k(SA)) in modelling contaminant removal in Fe(0)/H(2)O systems is questioned. It is shown that the current k(SA)-model does not consider the large reactive surface area provided by the in-situ formed oxide film, and thus the adsorptive interactions between contaminants and film materials. Furthermore, neither the dynamic nature of film formation nor the fact that the Fe(0) surface is shielded by the film is considered. Suggestions are made how the k(SA)-model could be further developed to meet its original goal.

Steady-State Computation of Constant Rotational Rate Dynamic Stability Derivatives

NASA Technical Reports Server (NTRS)

Park, Michael A.; Green, Lawrence L.

2000-01-01

Dynamic stability derivatives are essential to predicting the open and closed loop performance, stability, and controllability of aircraft. Computational determination of constant-rate dynamic stability derivatives (derivatives of aircraft forces and moments with respect to constant rotational rates) is currently performed indirectly with finite differencing of multiple time-accurate computational fluid dynamics solutions. Typical time-accurate solutions require excessive amounts of computational time to complete. Formulating Navier-Stokes (N-S) equations in a rotating noninertial reference frame and applying an automatic differentiation tool to the modified code has the potential for directly computing these derivatives with a single, much faster steady-state calculation. The ability to rapidly determine static and dynamic stability derivatives by computational methods can benefit multidisciplinary design methodologies and reduce dependency on wind tunnel measurements. The CFL3D thin-layer N-S computational fluid dynamics code was modified for this study to allow calculations on complex three-dimensional configurations with constant rotation rate components in all three axes. These CFL3D modifications also have direct application to rotorcraft and turbomachinery analyses. The modified CFL3D steady-state calculation is a new capability that showed excellent agreement with results calculated by a similar formulation. The application of automatic differentiation to CFL3D allows the static stability and body-axis rate derivatives to be calculated quickly and exactly.

A new approach using coagulation rate constant for evaluation of turbidity removal

NASA Astrophysics Data System (ADS)

Al-Sameraiy, Mukheled

2017-06-01

Coagulation-flocculation-sedimentation processes for treating three levels of bentonite synthetic turbid water using date seeds (DS) and alum (A) coagulants were investigated in the previous research work. In the current research, the same experimental results were used to adopt a new approach on a basis of using coagulation rate constant as an investigating parameter to identify optimum doses of these coagulants. Moreover, the performance of these coagulants to meet (WHO) turbidity standard was assessed by introducing a new evaluating criterion in terms of critical coagulation rate constant (kc). Coagulation rate constants (k2) were mathematically calculated in second order form of coagulation process for each coagulant. The maximum (k2) values corresponded to doses, which were obviously to be considered as optimum doses. The proposed criterion to assess the performance of coagulation process of these coagulants was based on the mathematical representation of (WHO) turbidity guidelines in second order form of coagulation process stated that (k2) for each coagulant should be ≥ (kc) for each level of synthetic turbid water. For all tested turbid water, DS coagulant could not satisfy it. While, A coagulant could satisfy it. The results obtained in the present research are exactly in agreement with the previous published results in terms of finding optimum doses for each coagulant and assessing their performances. On the whole, it is recommended considering coagulation rate constant to be a new approach as an indicator for investigating optimum doses and critical coagulation rate constant to be a new evaluating criterion to assess coagulants' performance.

Full-dimensional analytical potential energy surface describing the gas-phase Cl + C2H6 reaction and kinetics study of rate constants and kinetic isotope effects.

PubMed

Rangel, Cipriano; Espinosa-Garcia, Joaquin

2018-02-07

Within the Born-Oppenheimer approximation a full-dimensional analytical potential energy surface, PES-2017, was developed for the gas-phase hydrogen abstraction reaction between the chlorine atom and ethane, which is a nine body system. This surface presents a valence-bond/molecular mechanics functional form dependent on 60 parameters and is fitted to high-level ab initio calculations. This reaction presents little exothermicity, -2.30 kcal mol -1 , with a low height barrier, 2.44 kcal mol -1 , and intermediate complexes in the entrance and exit channels. We found that the energetic description was strongly dependent on the ab initio level used and it presented a very flat topology in the entrance channel, which represents a theoretical challenge in the fitting process. In general, PES-2017 reproduces the ab initio information used as input, which is merely a test of self-consistency. As a first test of the quality of the PES-2017, a theoretical kinetics study was performed in the temperature range 200-1400 K using two approaches, i.e. the variational transition-state theory and quasi-classical trajectory calculations, with spin-orbit effects. The rate constants show reasonable agreement with experiments in the whole temperature range, with the largest differences at the lowest temperatures, and this behaviour agrees with previous theoretical studies, thus indicating the inherent difficulties in the theoretical simulation of the kinetics of the title reaction. Different sources of error were analysed, such as the limitations of the PES and theoretical methods, recrossing effects, and the tunnelling effect, which is negligible in this reaction, and the manner in which the spin-orbit effects were included in this non-relativistic study. We found that the variation of spin-orbit coupling along the reaction path, and the influence of the reactivity of the excited Cl( 2 P 1/2 ) state, have relative importance, but do not explain the whole discrepancy. Finally, the

Determination of the rate coefficient for the N2/+/ + O reaction in the ionosphere

NASA Technical Reports Server (NTRS)

Torr, D. G.; Torr, M. R.; Orsini, N.; Hanson, W. B.; Hoffman, J. H.; Walker, J. C. G.

1977-01-01

Using approximately 400 simultaneous measurements of ion and neutral densities and temperatures, and the spectrum of the solar flux measured by the Atmosphere Explorer C satellite, we have determined the rate constant k1 for the reaction between N2(+) and O in the ionosphere for ion temperatures between 600 and 700 K. We find that k1 = 1.1 x 10 to the minus 10th power cu cm per sec, with a standard deviation of + or - 15%. If we use the temperature dependence for this reaction determined in the laboratory then at 300 K we find excellent agreement with the recommended laboratory value.

Direct Measurement of Equilibrium Constants for High-Affinity Hemoglobins

PubMed Central

Kundu, Suman; Premer, Scott A.; Hoy, Julie A.; Trent, James T.; Hargrove, Mark S.

2003-01-01

The biological functions of heme proteins are linked to their rate and affinity constants for ligand binding. Kinetic experiments are commonly used to measure equilibrium constants for traditional hemoglobins comprised of pentacoordinate ligand binding sites and simple bimolecular reaction schemes. However, kinetic methods do not always yield reliable equilibrium constants with more complex hemoglobins for which reaction mechanisms are not clearly understood. Furthermore, even where reaction mechanisms are clearly understood, it is very difficult to directly measure equilibrium constants for oxygen and carbon monoxide binding to high-affinity (KD ≪ 1 μM) hemoglobins. This work presents a method for direct measurement of equilibrium constants for high-affinity hemoglobins that utilizes a competition for ligands between the "target" protein and an array of "scavenger" hemoglobins with known affinities. This method is described for oxygen and carbon monoxide binding to two hexacoordinate hemoglobins: rice nonsymbiotic hemoglobin and Synechocystis hemoglobin. Our results demonstrate that although these proteins have different mechanisms for ligand binding, their affinities for oxygen and carbon monoxide are similar. Their large affinity constants for oxygen, 285 and ∼100 μM−1 respectively, indicate that they are not capable of facilitating oxygen transport. PMID:12770899

Correlated uncertainties in Monte Carlo reaction rate calculations

NASA Astrophysics Data System (ADS)

Longland, Richard

2017-07-01

Context. Monte Carlo methods have enabled nuclear reaction rates from uncertain inputs to be presented in a statistically meaningful manner. However, these uncertainties are currently computed assuming no correlations between the physical quantities that enter those calculations. This is not always an appropriate assumption. Astrophysically important reactions are often dominated by resonances, whose properties are normalized to a well-known reference resonance. This insight provides a basis from which to develop a flexible framework for including correlations in Monte Carlo reaction rate calculations. Aims: The aim of this work is to develop and test a method for including correlations in Monte Carlo reaction rate calculations when the input has been normalized to a common reference. Methods: A mathematical framework is developed for including correlations between input parameters in Monte Carlo reaction rate calculations. The magnitude of those correlations is calculated from the uncertainties typically reported in experimental papers, where full correlation information is not available. The method is applied to four illustrative examples: a fictional 3-resonance reaction, 27Al(p, γ)28Si, 23Na(p, α)20Ne, and 23Na(α, p)26Mg. Results: Reaction rates at low temperatures that are dominated by a few isolated resonances are found to minimally impacted by correlation effects. However, reaction rates determined from many overlapping resonances can be significantly affected. Uncertainties in the 23Na(α, p)26Mg reaction, for example, increase by up to a factor of 5. This highlights the need to take correlation effects into account in reaction rate calculations, and provides insight into which cases are expected to be most affected by them. The impact of correlation effects on nucleosynthesis is also investigated.

Absolute rate constants for O + NO + M /= He, Ne, Ar, Kr/ yields NO2 + M from 217-500 K

NASA Technical Reports Server (NTRS)

Michael, J. V.; Payne, W. A.; Whytock, D. A.

1976-01-01

Rate constants for the reaction O + NO + M yields NO2 + M have been obtained at temperatures from 217-500 K in four different rare gases by a method combining flash photolysis with time resolved detection of O(3-P) by resonance fluorescence. The measured rate constants in Arrhenius form are (10.8 plus or minus 1.2) x 10 to the -33rd exp(1040 plus or minus 60/1.987 T) for helium; (9.01 plus or minus 1.16) x 10 to the -33rd exp(1180 plus or minus 70/1.987 T) for argon; (9.33 plus or minus 1.10) x 10 to the -33rd exp(1030 plus or minus 60/1.987 T) for neon; and (9.52 plus or minus 1.10) x 10 to the -33rd exp(1140 plus or minus 70/1.987 T) for krypton in units of cm to the 6th/sq molecule/s.

Mixing effects on apparent reaction rates and isotope fractionation during denitrification in a heterogeneous aquifer

USGS Publications Warehouse

Green, Christopher T.; Böhlke, John Karl; Bekins, Barbara A.; Phillips, Steven P.

2010-01-01

Gradients in contaminant concentrations and isotopic compositions commonly are used to derive reaction parameters for natural attenuation in aquifers. Differences between field‐scale (apparent) estimated reaction rates and isotopic fractionations and local‐scale (intrinsic) effects are poorly understood for complex natural systems. For a heterogeneous alluvial fan aquifer, numerical models and field observations were used to study the effects of physical heterogeneity on reaction parameter estimates. Field measurements included major ions, age tracers, stable isotopes, and dissolved gases. Parameters were estimated for the O2 reduction rate, denitrification rate, O2 threshold for denitrification, and stable N isotope fractionation during denitrification. For multiple geostatistical realizations of the aquifer, inverse modeling was used to establish reactive transport simulations that were consistent with field observations and served as a basis for numerical experiments to compare sample‐based estimates of “apparent” parameters with “true“ (intrinsic) values. For this aquifer, non‐Gaussian dispersion reduced the magnitudes of apparent reaction rates and isotope fractionations to a greater extent than Gaussian mixing alone. Apparent and true rate constants and fractionation parameters can differ by an order of magnitude or more, especially for samples subject to slow transport, long travel times, or rapid reactions. The effect of mixing on apparent N isotope fractionation potentially explains differences between previous laboratory and field estimates. Similarly, predicted effects on apparent O2threshold values for denitrification are consistent with previous reports of higher values in aquifers than in the laboratory. These results show that hydrogeological complexity substantially influences the interpretation and prediction of reactive transport.

An Unusual Salt Effect in an Interfacial Nucleophilic Substitution Reaction.

PubMed

Li, Shuheng; Mrksich, Milan

2018-06-12

This paper reports a kinetic characterization of the interfacial reaction of N-methylpyrrolidine with a self-assembled monolayer presenting an iodoalkyl group. SAMDI (self-assembled monolayers for matrix-assisted laser desorption/ionization) mass spectrometry was used to determine the extent of reaction for monolayers that were treated with a range of concentrations of the nucleophile for a range of times. These data revealed a second-order rate constant for the reaction that was approximately 100-fold greater than that for the analogous solution-phase reaction. However, addition of sodium iodide to the reaction mixture resulted in a 7-fold decrease in the reaction rate. Addition of bromide and chloride salts also gave slower rate constants for the reaction, but only at 100- and 1000-fold higher concentrations than was observed with iodide, respectively. The corresponding solution-phase reactions, by contrast, had rate constants that were unaffected by the concentration of halide salts. This work provides a well-characterized example illustrating the extent to which the kinetics and properties of an interfacial reaction can depart substantially from their better-understood solution-phase counterparts.

Reaction rate kinetics for in situ combustion retorting of Michigan Antrim oil shale

USGS Publications Warehouse

Rostam-Abadi, M.; Mickelson, R.W.

1984-01-01

The intrinsic reaction rate kinetics for the pyrolysis of Michigan Antrim oil shale and the oxidation of the carbonaceous residue of this shale have been determined using a thermogravimetric analysis method. The kinetics of the pyrolysis reaction were evaluated from both isothermal and nonisothermal rate data. The reaction was found to be second-order with an activation energy of 252.2 kJ/mole, and with a frequency factor of 9.25 ?? 1015 sec-1. Pyrolysis kinetics were not affected by heating rates between 0.01 to 0.67??K/s. No evidence of any reactions among the oil shale mineral constituents was observed at temperatures below 1173??K. However, it was found that the presence of pyrite in oil shale reduces the primary devolatilization rate of kerogen and increases the amount of residual char in the spent shale. Carbonaceous residues which were prepared by heating the oil shale at a rate of 0.166??K/s to temperatures between 923??K and 1073??K, had the highest reactivities when oxidized at 0.166??K/s in a gas having 21 volume percent oxygen. Oxygen chemisorption was found to be the initial precursor to the oxidation process. The kinetics governing oxygen chemisorption is (Equation Presented) where X is the fractional coverage. The oxidation of the carbonaceous residue was found also to be second-order. The activation energy and the frequency factor determined from isothermal experiments were 147 kJ/mole and 9.18??107 sec-1 respectively, while the values of these parameters obtained from a nonisothermal experiment were 212 kJ/mole and 1.5??1013 sec-1. The variation in the rate constants is attributed to the fact that isothermal and nonisothermal analyses represent two different aspects of the combustion process.

The Kinetic Mechanism of Phenylalanine Hydroxylase: Intrinsic Binding and Rate Constants from Single Turnover Experiments†

PubMed Central

Roberts, Kenneth M.; Pavon, Jorge Alex; Fitzpatrick, Paul F.

2013-01-01

Phenylalanine hydroxylase (PheH) catalyzes the key step in the catabolism of dietary phenylalanine, its hydroxylation to tyrosine using tetrahydrobiopterin (BH4) and O2. A complete kinetic mechanism for PheH was determined by global analysis of single turnover data in the reaction of PheHΔ117, a truncated form of the enzyme lacking the N-terminal regulatory domain. Formation of the productive PheHΔ117-BH4-phenylalanine complex begins with the rapid binding of BH4 (Kd = 65 µM). Subsequent addition of phenylalanine to the binary complex to form the productive ternary complex (Kd = 130 µM) is approximately ten-fold slower. Both substrates can also bind to the free enzyme to form inhibitory binary complexes. O2 rapidly binds to the productive ternary complex; this is followed by formation of an unidentified intermediate, detectable as a decrease in absorbance at 340 nm, with a rate constant of 140 s−1. Formation of the 4a-hydroxypterin and Fe(IV)O intermediates is ten-fold slower and is followed by the rapid hydroxylation of the amino acid. Product release is the rate-determining step and largely determines kcat. Similar reactions using 6-methyltetrahydropterin indicate a preference for the physiological pterin during hydroxylation. PMID:23327364

On rates and mechanisms of OH and O3 reactions with isoprene-derived hydroxy nitrates.

PubMed

Lee, Lance; Teng, Alex P; Wennberg, Paul O; Crounse, John D; Cohen, Ronald C

2014-03-06

Eight distinct hydroxy nitrates are stable products of the first step in the atmospheric oxidation of isoprene by OH. The subsequent chemical fate of these molecules affects global and regional production of ozone and aerosol as well as the location of nitrogen deposition. We synthesized and purified 3 of the 8 isoprene hydroxy nitrate isomers: (E/Z)-2-methyl-4-nitrooxybut-2-ene-1-ol and 3-methyl-2-nitrooxybut-3-ene-1-ol. Oxidation of these molecules by OH and ozone was studied using both chemical ionization mass spectrometry and thermo-dissociation laser induced fluorescence. The OH reaction rate constants at 300 K measured relative to propene at 745 Torr are (1.1 ± 0.2) × 10(-10) cm(3) molecule(-1) s(-1) for both the E and Z isomers and (4.2 ± 0.7) × 10(-11) cm(3) molecule(-1) s(-1) for the third isomer. The ozone reaction rate constants for (E/Z)-2-methyl-4-nitrooxybut-2-ene-1-ol are (2.7 ± 0.5) × 10(-17) and (2.9 ± 0.5) × 10(-17) cm(3) molecule(-1) s(-1), respectively. 3-Methyl-2-nitrooxybut-3-ene-1-ol reacts with ozone very slowly, within the range of (2.5-5) × 10(-19) cm(3) molecule(-1) s(-1). Reaction pathways, product yields, and implications for atmospheric chemistry are discussed. A condensed mechanism suitable for use in atmospheric chemistry models is presented.

Bayesian Estimation of Thermonuclear Reaction Rates for Deuterium+Deuterium Reactions

NASA Astrophysics Data System (ADS)

Gómez Iñesta, Á.; Iliadis, C.; Coc, A.

2017-11-01

The study of d+d reactions is of major interest since their reaction rates affect the predicted abundances of D, 3He, and 7Li. In particular, recent measurements of primordial D/H ratios call for reduced uncertainties in the theoretical abundances predicted by Big Bang nucleosynthesis (BBN). Different authors have studied reactions involved in BBN by incorporating new experimental data and a careful treatment of systematic and probabilistic uncertainties. To analyze the experimental data, Coc et al. used results of ab initio models for the theoretical calculation of the energy dependence of S-factors in conjunction with traditional statistical methods based on χ 2 minimization. Bayesian methods have now spread to many scientific fields and provide numerous advantages in data analysis. Astrophysical S-factors and reaction rates using Bayesian statistics were calculated by Iliadis et al. Here we present a similar analysis for two d+d reactions, d(d, n)3He and d(d, p)3H, that has been translated into a total decrease of the predicted D/H value by 0.16%.

Effective rate constants for nanostructured heterogeneous catalysts

NASA Astrophysics Data System (ADS)

Hendy, Shaun; Gaston, Nicola; Zhang, Philip; Lund, Nat

2012-02-01

There is currently a high level of interest in the use of nanostructured materials for catalysis. For instance, gold, which is largely inert in the bulk, can exhibit strong catalytic activity when in nanoparticle form. With precious metal catalysts such as Pt and Pd in high demand, the use of these materials in nanoparticle form can also substantially reduce costs by exposure of more surface area for the same volume of material. When reactants are plentiful, the effective activity of a nanoparticulate catalyst will increase roughly with its surface area. However, under diffusion-limited conditions, the reactant must diffuse to active sites on the catalyst, so a high surface area and a high density of active sites may bring diminishing returns if reactant is consumed faster than it arrives. Here we apply a mathematical homogenisation approach to derive simple expressions for the effective reactivity of a nanostructured catalyst under diffusion limited conditions that relate the intrinsic rate constants of the surfaces presented by the catalyst to an effective rate constant. When highly active catalytic sites, such as step edges or other defects are present, we show that distinct limiting cases emerge depending on the degree of overlap of the reactant depletion zone about each site. In gases, the size of this depletion zone is approximately the mean free path, so the effective reactivity will depend on the structure of the catalyst on that scale. We discuss implications for the optimal design of nanoparticle catalysts.

Kinetic rate constant prediction supports the conformational selection mechanism of protein binding.

PubMed

Moal, Iain H; Bates, Paul A

2012-01-01

The prediction of protein-protein kinetic rate constants provides a fundamental test of our understanding of molecular recognition, and will play an important role in the modeling of complex biological systems. In this paper, a feature selection and regression algorithm is applied to mine a large set of molecular descriptors and construct simple models for association and dissociation rate constants using empirical data. Using separate test data for validation, the predicted rate constants can be combined to calculate binding affinity with accuracy matching that of state of the art empirical free energy functions. The models show that the rate of association is linearly related to the proportion of unbound proteins in the bound conformational ensemble relative to the unbound conformational ensemble, indicating that the binding partners must adopt a geometry near to that of the bound prior to binding. Mirroring the conformational selection and population shift mechanism of protein binding, the models provide a strong separate line of evidence for the preponderance of this mechanism in protein-protein binding, complementing structural and theoretical studies.

Ozone-Induced Dissociation of Conjugated Lipids Reveals Significant Reaction Rate Enhancements and Characteristic Odd-Electron Product Ions

NASA Astrophysics Data System (ADS)

Pham, Huong T.; Maccarone, Alan T.; Campbell, J. Larry; Mitchell, Todd W.; Blanksby, Stephen J.

2013-02-01

Ozone-induced dissociation (OzID) is an alternative ion activation method that relies on the gas phase ion-molecule reaction between a mass-selected target ion and ozone in an ion trap mass spectrometer. Herein, we evaluated the performance of OzID for both the structural elucidation and selective detection of conjugated carbon-carbon double bond motifs within lipids. The relative reactivity trends for [M + X]+ ions (where X = Li, Na, K) formed via electrospray ionization (ESI) of conjugated versus nonconjugated fatty acid methyl esters (FAMEs) were examined using two different OzID-enabled linear ion-trap mass spectrometers. Compared with nonconjugated analogues, FAMEs derived from conjugated linoleic acids were found to react up to 200 times faster and to yield characteristic radical cations. The significantly enhanced reactivity of conjugated isomers means that OzID product ions can be observed without invoking a reaction delay in the experimental sequence (i.e., trapping of ions in the presence of ozone is not required). This possibility has been exploited to undertake neutral-loss scans on a triple quadrupole mass spectrometer targeting characteristic OzID transitions. Such analyses reveal the presence of conjugated double bonds in lipids extracted from selected foodstuffs. Finally, by benchmarking of the absolute ozone concentration inside the ion trap, second order rate constants for the gas phase reactions between unsaturated organic ions and ozone were obtained. These results demonstrate a significant influence of the adducting metal on reaction rate constants in the fashion Li > Na > K.

Bimolecular Rate Constants for FAD-Dependent Glucose Dehydrogenase from Aspergillus terreus and Organic Electron Acceptors.

PubMed

Tsuruoka, Nozomu; Sadakane, Takuya; Hayashi, Rika; Tsujimura, Seiya

2017-03-10

The flavin adenine dinucleotide-dependent glucose dehydrogenase (FAD-GDH) from Aspergillus species require suitable redox mediators to transfer electrons from the enzyme to the electrode surface for the application of bioelectrical devices. Although several mediators for FAD-GDH are already in use, they are still far from optimum in view of potential, kinetics, sustainability, and cost-effectiveness. Herein, we investigated the efficiency of various phenothiazines and quinones in the electrochemical oxidation of FAD-GDH from Aspergillus terreus . At pH 7.0, the logarithm of the bimolecular oxidation rate constants appeared to depend on the redox potentials of all the mediators tested. Notably, the rate constant of each molecule for FAD-GDH was approximately 2.5 orders of magnitude higher than that for glucose oxidase from Aspergillus sp. The results suggest that the electron transfer kinetics is mainly determined by the formal potential of the mediator, the driving force of electron transfer, and the electron transfer distance between the redox active site of the mediator and the FAD, affected by the steric or chemical interactions. Higher k ₂ values were found for ortho-quinones than for para-quinones in the reactions with FAD-GDH and glucose oxidase, which was likely due to less steric hindrance in the active site in the case of the ortho-quinones.

Phototransformation rate constants of PAHs associated with soot particles.

PubMed

Kim, Daekyun; Young, Thomas M; Anastasio, Cort

2013-01-15

Photodegradation is a key process governing the residence time and fate of polycyclic aromatic hydrocarbons (PAHs) in particles, both in the atmosphere and after deposition. We have measured photodegradation rate constants of PAHs in bulk deposits of soot particles illuminated with simulated sunlight. The photodegradation rate constants at the surface (k(p)(0)), the effective diffusion coefficients (D(eff)), and the light penetration depths (z(0.5)) for PAHs on soot layers of variable thickness were determined by fitting experimental data with a model of coupled photolysis and diffusion. The overall disappearance rates of irradiated low molecular weight PAHs (with 2-3 rings) on soot particles were influenced by fast photodegradation and fast diffusion kinetics, while those of high molecular weight PAHs (with 4 or more rings) were apparently controlled by either the combination of slow photodegradation and slow diffusion kinetics or by very slow diffusion kinetics alone. The value of z(0.5) is more sensitive to the soot layer thickness than the k(p)(0) value. As the thickness of the soot layer increases, the z(0.5) values increase, but the k(p)(0) values are almost constant. The effective diffusion coefficients calculated from dark experiments are generally higher than those from the model fitting method for illumination experiments. Due to the correlation between k(p)(0) and z(0.5) in thinner layers, D(eff) should be estimated by an independent method for better accuracy. Despite some limitations of the model used in this study, the fitted parameters were useful for describing empirical results of photodegradation of soot-associated PAHs. Copyright © 2012 Elsevier B.V. All rights reserved.

Phototransformation Rate Constants of PAHs Associated with Soot Particles

PubMed Central

Kim, Daekyun; Young, Thomas M.; Anastasio, Cort

2013-01-01

Photodegradation is a key process governing the residence time and fate of polycyclic aromatic hydrocarbons (PAHs) in particles, both in the atmosphere and after deposition. We have measured photodegradation rate constants of PAHs in bulk deposits of soot particles illuminated with simulated sunlight. The photodegradation rate constants at the surface (k0p), the effective diffusion coefficients (Deff), and the light penetration depths (z0.5) for PAHs on soot layers of variable thickness were determined by fitting experimental data with a model of coupled photolysis and diffusion. The overall disappearance rates of irradiated low molecular weight PAHs (with 2-3 rings) on soot particles were influenced by fast photodegradation and fast diffusion kinetics, while those of high molecular weight PAHs (with 4 or more rings) were apparently controlled by either the combination of slow photodegradation and slow diffusion kinetics or by very slow diffusion kinetics alone. The value of z0.5 is more sensitive to the soot layer thickness than the k0p value. As the thickness of the soot layer increases, the z0.5 values increase, but the k0p values are almost constant. The effective diffusion coefficients calculated from dark experiments are generally higher than those from the model fitting method for illumination experiments. Due to the correlation between k0p and z0.5 in thinner layers, Deff should be estimated by an independent method for better accuracy. Despite some limitations of the model used in this study, the fitted parameters were useful for describing empirical results of photodegradation of soot-associated PAHs. PMID:23247292

Hydrogen transfer reactions of interstellar Complex Organic Molecules

NASA Astrophysics Data System (ADS)

Álvarez-Barcia, S.; Russ, P.; Kästner, J.; Lamberts, T.

2018-06-01

Radical recombination has been proposed to lead to the formation of complex organic molecules (COMs) in CO-rich ices in the early stages of star formation. These COMs can then undergo hydrogen addition and abstraction reactions leading to a higher or lower degree of saturation. Here, we have studied 14 hydrogen transfer reactions for the molecules glyoxal, glycoaldehyde, ethylene glycol, and methylformate and an additional three reactions where CHnO fragments are involved. Over-the-barrier reactions are possible only if tunneling is invoked in the description at low temperature. Therefore the rate constants for the studied reactions are calculated using instanton theory that takes quantum effects into account inherently. The reactions were characterized in the gas phase, but this is expected to yield meaningful results for CO-rich ices due to the minimal alteration of reaction landscapes by the CO molecules. We found that rate constants should not be extrapolated based on the height of the barrier alone, since the shape of the barrier plays an increasingly larger role at decreasing temperature. It is neither possible to predict rate constants based only on considering the type of reaction, the specific reactants and functional groups play a crucial role. Within a single molecule, though, hydrogen abstraction from an aldehyde group seems to be always faster than hydrogen addition to the same carbon atom. Reactions that involve heavy-atom tunneling, e.g., breaking or forming a C-C or C-O bond, have rate constants that are much lower than those where H transfer is involved.

Using a Family of Dividing Surfaces Normal to the Minimum EnergyPath for Quantum Instanton Rate Constants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Yimin; Miller, Wlliam H.

2006-02-22

One of the outstanding issues in the quantum instanton (QI) theory (or any transition state-type theory) for thermal rate constants of chemical reactions is the choice of an appropriate ''dividing surface'' (DS) that separates reactants and products. (In the general version of the QI theory, there are actually two dividing surfaces involved.) This paper shows one simple and general way for choosing DS's for use in QI Theory, namely using the family of (hyper) planes normal to the minimum energy path (MEP) on the potential energy surface at various distances s along it. Here the reaction coordinate is not onemore » of the dynamical coordinates of the system (which will in general be the Cartesian coordinates of the atoms), but rather simply a parameter which specifies the DS. It is also shown how this idea can be implemented for an N-atom system in 3d space in a way that preserves overall translational and rotational invariance. Numerical application to a simple system (the colliner H + H{sub 2} reaction) is presented to illustrate the procedure.« less

Impact of transverse and longitudinal dispersion on first-order degradation rate constant estimation

NASA Astrophysics Data System (ADS)

Stenback, Greg A.; Ong, Say Kee; Rogers, Shane W.; Kjartanson, Bruce H.

2004-09-01

A two-dimensional analytical model is employed for estimating the first-order degradation rate constant of hydrophobic organic compounds (HOCs) in contaminated groundwater under steady-state conditions. The model may utilize all aqueous concentration data collected downgradient of a source area, but does not require that any data be collected along the plume centerline. Using a least squares fit of the model to aqueous concentrations measured in monitoring wells, degradation rate constants were estimated at a former manufactured gas plant (FMGP) site in the Midwest U.S. The estimated degradation rate constants are 0.0014, 0.0034, 0.0031, 0.0019, and 0.0053 day -1 for acenaphthene, naphthalene, benzene, ethylbenzene, and toluene, respectively. These estimated rate constants were as low as one-half those estimated with the one-dimensional (centerline) approach of Buscheck and Alcantar [Buscheck, T.E., Alcantar, C.M., 1995. Regression techniques and analytical solutions to demonstrate intrinsic bioremediation. In: Hinchee, R.E., Wilson, J.T., Downey, D.C. (Eds.), Intrinsic Bioremediation, Battelle Press, Columbus, OH, pp. 109-116] which does not account for transverse dispersivity. Varying the transverse and longitudinal dispersivity values over one order of magnitude for toluene data obtained from the FMGP site resulted in nearly a threefold variation in the estimated degradation rate constant—highlighting the importance of reliable estimates of the dispersion coefficients for obtaining reasonable estimates of the degradation rate constants. These results have significant implications for decision making and site management where overestimation of a degradation rate may result in remediation times and bioconversion factors that exceed expectations. For a complex source area or non-steady-state plume, a superposition of analytical models that incorporate longitudinal and transverse dispersion and time may be used at sites where the centerline method would not be

Charring rate of wood exposed to a constant heat flux

Treesearch

R. H. White; H. C. Tran

1996-01-01

A critical factor in the fire endurance of a wood member is its rate of charring. Most available charring rate data have been obtained using the time-temperature curves of the standard fire resistance tests (ASTM E 119 and ISO 834) to define the fire exposure. The increased use of heat release calorimeters using exposures of constant heat flux levels has broadened the...

Study on improving the turbidity measurement of the absolute coagulation rate constant.

PubMed

Sun, Zhiwei; Liu, Jie; Xu, Shenghua

2006-05-23

The existing theories dealing with the evaluation of the absolute coagulation rate constant by turbidity measurement were experimentally tested for different particle-sized (radius = a) suspensions at incident wavelengths (lambda) ranging from near-infrared to ultraviolet light. When the size parameter alpha = 2pi a/lambda > 3, the rate constant data from previous theories for fixed-sized particles show significant inconsistencies at different light wavelengths. We attribute this problem to the imperfection of these theories in describing the light scattering from doublets through their evaluation of the extinction cross section. The evaluations of the rate constants by all previous theories become untenable as the size parameter increases and therefore hampers the applicable range of the turbidity measurement. By using the T-matrix method, we present a robust solution for evaluating the extinction cross section of doublets formed in the aggregation. Our experiments show that this new approach is effective in extending the applicability range of the turbidity methodology and increasing measurement accuracy.

Relationship of compressive stress-strain response of engineering materials obtained at constant engineering and true strain rates

DOE PAGES

Song, Bo; Sanborn, Brett

2018-05-07

In this paper, a Johnson–Cook model was used as an example to analyze the relationship of compressive stress-strain response of engineering materials experimentally obtained at constant engineering and true strain rates. There was a minimal deviation between the stress-strain curves obtained at the same constant engineering and true strain rates. The stress-strain curves obtained at either constant engineering or true strain rates could be converted from one to the other, which both represented the intrinsic material response. There is no need to specify the testing requirement of constant engineering or true strain rates for material property characterization, provided that eithermore » constant engineering or constant true strain rate is attained during the experiment.« less

Relationship of compressive stress-strain response of engineering materials obtained at constant engineering and true strain rates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Bo; Sanborn, Brett

In this paper, a Johnson–Cook model was used as an example to analyze the relationship of compressive stress-strain response of engineering materials experimentally obtained at constant engineering and true strain rates. There was a minimal deviation between the stress-strain curves obtained at the same constant engineering and true strain rates. The stress-strain curves obtained at either constant engineering or true strain rates could be converted from one to the other, which both represented the intrinsic material response. There is no need to specify the testing requirement of constant engineering or true strain rates for material property characterization, provided that eithermore » constant engineering or constant true strain rate is attained during the experiment.« less

Communication: Prediction of the rate constant of bimolecular hydrogen exchange in the water dimer using an ab initio potential energy surface.

PubMed

Wang, Yimin; Bowman, Joel M; Huang, Xinchuan

2010-09-21

We report the properties of two novel transition states of the bimolecular hydrogen exchange reaction in the water dimer, based on an ab initio water dimer potential [A. Shank et al., J. Chem. Phys. 130, 144314 (2009)]. The realism of the two transition states is assessed by comparing structures, energies, and harmonic frequencies obtained from the potential energy surface and new high-level ab initio calculations. The rate constant for the exchange is obtained using conventional transition state theory with a tunneling correction. We employ a one-dimensional approach for the tunneling calculations using a relaxed potential from the full-dimensional potential in the imaginary-frequency normal mode of the saddle point, Q(im). The accuracy of this one-dimensional approach has been shown for the ground-state tunneling splittings for H and D-transfer in malonaldehyde and for the D+H(2) reaction [Y. Wang and J. M. Bowman, J. Chem. Phys. 129, 121103 (2008)]. This approach is applied to calculate the rate constant for the H(2)O+H(2)O exchange and also for H(2)O+D(2)O→2HOD. The local zero-point energy is also obtained using diffusion Monte Carlo calculations in the space of real-frequency-saddle-point normal modes, as a function of Q(im).

Extension of a Kinetic-Theory Approach for Computing Chemical-Reaction Rates to Reactions with Charged Particles

NASA Technical Reports Server (NTRS)

Liechty, Derek S.; Lewis, Mark J.

2010-01-01

Recently introduced molecular-level chemistry models that predict equilibrium and nonequilibrium reaction rates using only kinetic theory and fundamental molecular properties (i.e., no macroscopic reaction rate information) are extended to include reactions involving charged particles and electronic energy levels. The proposed extensions include ionization reactions, exothermic associative ionization reactions, endothermic and exothermic charge exchange reactions, and other exchange reactions involving ionized species. The extensions are shown to agree favorably with the measured Arrhenius rates for near-equilibrium conditions.

Evaluation of the rate constants of sugar transport through maltoporin (LamB) of Escherichia coli from the sugar-induced current noise

PubMed Central

1995-01-01

LamB (maltoporin) of Escherichia coli outer membrane was reconstituted into artificial lipid bilayer membranes. The channel contains a binding site for sugars and is blocked for ions when the site is occupied by a sugar. The on and off reactions of sugar binding cause an increase of the noise of the current through the channel. The sugar-induced current noise of maltoporin was used for the evaluation of the sugar-binding kinetics for different sugars of the maltooligosaccharide series and for sucrose. The on rate constant for sugar binding was between 10(6) and 10(7) M-1.s-1 for the maltooligosaccharides and corresponds to the movement of the sugars from the aqueous phase to the central binding site. The off rate (corresponding to the release of the sugars from the channel) decreased with increasing number of glucose residues in the maltooligosaccharides from approximately 2,000 s-1 for maltotriose to 180 s-1 for maltoheptaose. The kinetics for sucrose movement was considerably slower. The activation energies of the stability constant and of the rate constants for sugar binding were evaluated from noise experiments at different temperatures. The role of LamB in the transport of maltooligosaccharides across the outer membrane is discussed. PMID:7539481

Unimolecular reaction of acetone oxide and its reaction with water in the atmosphere.

PubMed

Long, Bo; Bao, Junwei Lucas; Truhlar, Donald G

2018-05-29

Criegee intermediates (i.e., carbonyl oxides with two radical sites) are known to be important atmospheric reagents; however, our knowledge of their reaction kinetics is still limited. Although experimental methods have been developed to directly measure the reaction rate constants of stabilized Criegee intermediates, the experimental results cover limited temperature ranges and do not completely agree well with one another. Here we investigate the unimolecular reaction of acetone oxide [(CH 3 ) 2 COO] and its bimolecular reaction with H 2 O to obtain rate constants with quantitative accuracy comparable to experimental accuracy. We do this by using CCSDT(Q)/CBS//CCSD(T)-F12a/DZ-F12 benchmark results to select and validate exchange-correlation functionals, which are then used for direct dynamics calculations by variational transition state theory with small-curvature tunneling and torsional and high-frequency anharmonicity. We find that tunneling is very significant in the unimolecular reaction of (CH 3 ) 2 COO and its bimolecular reaction with H 2 O. We show that the atmospheric lifetimes of (CH 3 ) 2 COO depend on temperature and that the unimolecular reaction of (CH 3 ) 2 COO is the dominant decay mode above 240 K, while the (CH 3 ) 2 COO + SO 2 reaction can compete with the corresponding unimolecular reaction below 240 K when the SO 2 concentration is 9 × 10 10 molecules per cubic centimeter. We also find that experimental results may not be sufficiently accurate for the unimolecular reaction of (CH 3 ) 2 COO above 310 K. Not only does the present investigation provide insights into the decay of (CH 3 ) 2 COO in the atmosphere, but it also provides an illustration of how to use theoretical methods to predict quantitative rate constants of medium-sized Criegee intermediates.

Quantitative Prediction of Rate Constants for Aqueous Racemization To Avoid Pointless Stereoselective Syntheses

PubMed Central

Ballard, Andrew; Ahmad, Hiwa O.; Narduolo, Stefania; Rosa, Lucy; Chand, Nikki; Cosgrove, David A.; Varkonyi, Peter; Asaad, Nabil; Tomasi, Simone

2017-01-01

Abstract Racemization has a large impact upon the biological properties of molecules but the chemical scope of compounds with known rate constants for racemization in aqueous conditions was hitherto limited. To address this remarkable blind spot, we have measured the kinetics for racemization of 28 compounds using circular dichroism and 1H NMR spectroscopy. We show that rate constants for racemization (measured by ourselves and others) correlate well with deprotonation energies from quantum mechanical (QM) and group contribution calculations. Such calculations thus provide predictions of the second‐order rate constants for general‐base‐catalyzed racemization that are usefully accurate. When applied to recent publications describing the stereoselective synthesis of compounds of purported biological value, the calculations reveal that racemization would be sufficiently fast to render these expensive syntheses pointless. PMID:29072355

Kinetics of the benzyl + O(3P) reaction: a quantum chemical/statistical reaction rate theory study.

PubMed

da Silva, Gabriel; Bozzelli, Joseph W

2012-12-14

The resonance stabilized benzyl radical is an important intermediate in the combustion of aromatic hydrocarbons and in polycyclic aromatic hydrocarbon (PAH) formation in flames. Despite being a free radical, benzyl is relatively stable in thermal, oxidizing environments, and is predominantly removed through bimolecular reactions with open-shell species other than O(2). In this study the reaction of benzyl with ground-state atomic oxygen, O((3)P), is examined using quantum chemistry and statistical reaction rate theory. C(7)H(7)O energy surfaces are generated at the G3SX level, and include several novel pathways. Transition state theory is used to describe elementary reaction kinetics, with canonical variational transition state theory applied for barrierless O atom association with benzyl. Apparent rate constants and branching ratios to different product sets are obtained as a function of temperature and pressure from solving the time-dependent master equation, with RRKM theory for microcanonical k(E). These simulations indicate that the benzyl + O reaction predominantly forms the phenyl radical (C(6)H(5)) plus formaldehyde (HCHO), with lesser quantities of the C(7)H(6)O products benzaldehyde, ortho-quinone methide, and para-quinone methide (+H), along with minor amounts of the formyl radical (HCO) + benzene. Addition of O((3)P) to the methylene site in benzyl produces a highly vibrationally excited C(7)H(7)O* adduct, the benzoxyl radical, which can β-scission to benzaldehyde + H and phenyl + HCHO. In order to account for the experimental observation of benzene as the major reaction product, a roaming radical mechanism is proposed that converts the nascent products phenyl and HCHO to benzene + HCO. Oxygen atom addition at the ortho and para ring sites in benzyl, which has not been previously considered, is shown to lead to the quinone methides + H; these species are less-stable isomers of benzaldehyde that are proposed as important combustion intermediates, but

A first-passage scheme for determination of overall rate constants for non-diffusion-limited suspensions

NASA Astrophysics Data System (ADS)

Lu, Shih-Yuan; Yen, Yi-Ming

2002-02-01

A first-passage scheme is devised to determine the overall rate constant of suspensions under the non-diffusion-limited condition. The original first-passage scheme developed for diffusion-limited processes is modified to account for the finite incorporation rate at the inclusion surface by using a concept of the nonzero survival probability of the diffusing entity at entity-inclusion encounters. This nonzero survival probability is obtained from solving a relevant boundary value problem. The new first-passage scheme is validated by an excellent agreement between overall rate constant results from the present development and from an accurate boundary collocation calculation for the three common spherical arrays [J. Chem. Phys. 109, 4985 (1998)], namely simple cubic, body-centered cubic, and face-centered cubic arrays, for a wide range of P and f. Here, P is a dimensionless quantity characterizing the relative rate of diffusion versus surface incorporation, and f is the volume fraction of the inclusion. The scheme is further applied to random spherical suspensions and to investigate the effect of inclusion coagulation on overall rate constants. It is found that randomness in inclusion arrangement tends to lower the overall rate constant for f up to the near close-packing value of the regular arrays because of the inclusion screening effect. This screening effect turns stronger for regular arrays when f is near and above the close-packing value of the regular arrays, and consequently the overall rate constant of the random array exceeds that of the regular array. Inclusion coagulation too induces the inclusion screening effect, and leads to lower overall rate constants.

Quantification of in Situ Biodegradation Rate Constants Using a Novel Combined Isotope Approach

NASA Astrophysics Data System (ADS)

Blum, P.; Sültenfuß, J.; Martus, P.

2014-12-01

Numerous studies have shown the enormous potential of the compound-specific isotope analysis (CSIA) for studying the biodegradation of organic compounds such as monoaromatic hydrocarbons (BTEX), polyaromatic hydrocarbons (PAH), chlorinated solvents and other organic contaminants and environmental transformation mechanisms in groundwater. In addition, two-dimensional isotope analysis such as carbon and hydrogen have been successfully studied indicating the potential to also investigate site-specific reaction mechanisms. The main objective of the current study however is to quantify real effective in situ biodegradation rate constants in a coal-tar contaminated aquifer by combining compound-specific isotope analysis (CSIA) and tracer-based (3H-3He) ground-water dating (TGD). Hence, groundwater samples are used to determine groundwater residence times, and carbon and hydrogen stable isotopes are analyzed for selected BTEX and PAH. The results of the hydrogen stable isotopes surprisingly indicate no isotope fractionation and therefore no biodegradation. In contrast, for stable carbon isotopes of selected BTEX such as o-xylene and toluene, isotope shifts are detected indicating active biodegradation under sulfate-reducing conditions. These and previous results of stable carbon isotopes show that only for o-xylene a clear evidence for biodegradation is possible for the studied site. Nevertheless, in combining these results with the groundwater residence times, which range between 1 year for the shallow wells (20 m below surface) and 41 years for the deeper wells (40 m below surface), it is feasible to effectively determine in situ biodegradation rate constants for o-xylene. Conversely, the outcome also evidently demonstrate the major limitations of the novel combined isotope approach for a successful implementation of monitored natural attenuation (MNA) at such field sites.

A simple reaction-rate model for turbulent diffusion flames

NASA Technical Reports Server (NTRS)

Bangert, L. H.

1975-01-01

A simple reaction rate model is proposed for turbulent diffusion flames in which the reaction rate is proportional to the turbulence mixing rate. The reaction rate is also dependent on the mean mass fraction and the mean square fluctuation of mass fraction of each reactant. Calculations are compared with experimental data and are generally successful in predicting the measured quantities.

Diffusional falsification of kinetic constants on Lineweaver-Burk plots.

PubMed

Ghim, Y S; Chang, H N

1983-11-07

The effect of mass transfer resistances on the Lineweaver-Burk plots in immobilized enzyme systems has been investigated numerically and with analytical approximate solutions. While Hamilton, Gardner & Colton (1974) studied the effect of internal diffusion resistances in planar geometry, our study was extended to the combined effect of internal and external diffusion in cylindrical and spherical geometries as well. The variation of Lineweaver-Burk plots with respect to the geometries was minimized by modifying the Thiele modulus and the Biot number with the shape factor. Especially for a small Biot number all the three Lineweaver-Burk plots fell on a single line. As was discussed by Hamilton et al. (1974), the curvature of the line for large external diffusion resistances was small enough to be assumed linear, which was confirmed from the two approximate solutions for large and small substrate concentrations. Two methods for obtaining intrinsic kinetic constants were proposed: First, we obtained both maximum reaction rate and Michaelis constant by fitting experimental data to a straight line where external diffusion resistance was relatively large, and second, we obtained Michaelis constant from apparent Michaelis constant from the figure in case we knew maximum reaction rate a priori.

Electron-ion dissociative recombination rate constants relevant to the Titan atmosphere and the Interstellar Medium

NASA Astrophysics Data System (ADS)

Osborne, David; Lawson, Patrick; Adams, Nigel

2014-01-01

Following the arrival of Cassini at Titan in 2004, the Titan atmosphere has been shown to contain large complex polycyclic-aromatic hydrocarbons. Since Cassini has provided a great deal of data, there exists a need for kinetic rate data to help with modeling this atmosphere. One type of kinetic data needed is electron-ion dissociative recombination (e-IDR) rate constants. These data are not readily available for larger compounds, such as naphthalene, or oxygen containing compounds, such as 1,4 dioxane or furan. Here, the rate constants for naphthalene, 1,4 dioxane, and furan have been measured and their temperature dependencies are determined when possible, using the University of Georgia's Variable Temperature Flowing Afterglow. The rate constants are compared with those previously published for other compounds; these show trends which illustrate the effects which multi-rings and oxygen heteroatoms substitutions have upon e-IDR rate constants.

Methodologies for extracting kinetic constants for multiphase reacting flow simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, S.L.; Lottes, S.A.; Golchert, B.

1997-03-01

Flows in industrial reactors often involve complex reactions of many species. A computational fluid dynamics (CFD) computer code, ICRKFLO, was developed to simulate multiphase, multi-species reacting flows. The ICRKFLO uses a hybrid technique to calculate species concentration and reaction for a large number of species in a reacting flow. This technique includes a hydrodynamic and reacting flow simulation with a small but sufficient number of lumped reactions to compute flow field properties followed by a calculation of local reaction kinetics and transport of many subspecies (order of 10 to 100). Kinetic rate constants of the numerous subspecies chemical reactions aremore » difficult to determine. A methodology has been developed to extract kinetic constants from experimental data efficiently. A flow simulation of a fluid catalytic cracking (FCC) riser was successfully used to demonstrate this methodology.« less

QSPR prediction of the hydroxyl radical rate constant of water contaminants.

PubMed

Borhani, Tohid Nejad Ghaffar; Saniedanesh, Mohammadhossein; Bagheri, Mehdi; Lim, Jeng Shiun

2016-07-01

In advanced oxidation processes (AOPs), the aqueous hydroxyl radical (HO) acts as a strong oxidant to react with organic contaminants. The hydroxyl radical rate constant (kHO) is important for evaluating and modelling of the AOPs. In this study, quantitative structure-property relationship (QSPR) method is applied to model the hydroxyl radical rate constant for a diverse dataset of 457 water contaminants from 27 various chemical classes. The constricted binary particle swarm optimization and multiple-linear regression (BPSO-MLR) are used to obtain the best model with eight theoretical descriptors. An optimized feed forward neural network (FFNN) is developed to investigate the complex performance of the selected molecular parameters with kHO. Although the FFNN prediction results are more accurate than those obtained using BPSO-MLR, the application of the latter is much more convenient. Various internal and external validation techniques indicate that the obtained models could predict the logarithmic hydroxyl radical rate constants of a large number of water contaminants with less than 4% absolute relative error. Finally, the above-mentioned proposed models are compared to those reported earlier and the structural factors contributing to the AOP degradation efficiency are discussed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Electron-ion dissociative recombination rate constants relevant to the Titan atmosphere and the Interstellar Medium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Osborne, David; Lawson, Patrick; Adams, Nigel, E-mail: ngadams@uga.edu

Following the arrival of Cassini at Titan in 2004, the Titan atmosphere has been shown to contain large complex polycyclic-aromatic hydrocarbons. Since Cassini has provided a great deal of data, there exists a need for kinetic rate data to help with modeling this atmosphere. One type of kinetic data needed is electron-ion dissociative recombination (e-IDR) rate constants. These data are not readily available for larger compounds, such as naphthalene, or oxygen containing compounds, such as 1,4 dioxane or furan. Here, the rate constants for naphthalene, 1,4 dioxane, and furan have been measured and their temperature dependencies are determined when possible,more » using the University of Georgia's Variable Temperature Flowing Afterglow. The rate constants are compared with those previously published for other compounds; these show trends which illustrate the effects which multi-rings and oxygen heteroatoms substitutions have upon e-IDR rate constants.« less

Reaction kinetics of resveratrol with tert-butoxyl radicals

NASA Astrophysics Data System (ADS)

Džeba, Iva; Pedzinski, Tomasz; Mihaljević, Branka

2012-09-01

The rate constant for the reaction of t-butoxyl radicals with resveratrol was studied under pseudo-first order conditions. The rate constant was determined by measuring the phenoxyl radical formation rate at 390 nm as function of resveratrol concentration in acetonitrile. The rate constant was determined to be 6.5×108 M-1s-1. This high value indicates the high reactivity consistent with the strong antioxidant activity of resveratrol.

Statistical methods for thermonuclear reaction rates and nucleosynthesis simulations

NASA Astrophysics Data System (ADS)

Iliadis, Christian; Longland, Richard; Coc, Alain; Timmes, F. X.; Champagne, Art E.

2015-03-01

Rigorous statistical methods for estimating thermonuclear reaction rates and nucleosynthesis are becoming increasingly established in nuclear astrophysics. The main challenge being faced is that experimental reaction rates are highly complex quantities derived from a multitude of different measured nuclear parameters (e.g., astrophysical S-factors, resonance energies and strengths, particle and γ-ray partial widths). We discuss the application of the Monte Carlo method to two distinct, but related, questions. First, given a set of measured nuclear parameters, how can one best estimate the resulting thermonuclear reaction rates and associated uncertainties? Second, given a set of appropriate reaction rates, how can one best estimate the abundances from nucleosynthesis (i.e., reaction network) calculations? The techniques described here provide probability density functions that can be used to derive statistically meaningful reaction rates and final abundances for any desired coverage probability. Examples are given for applications to s-process neutron sources, core-collapse supernovae, classical novae, and Big Bang nucleosynthesis.

Reaction Rate Theory in Coordination Number Space: An Application to Ion Solvation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roy, Santanu; Baer, Marcel D.; Mundy, Christopher J.

2016-04-14

Understanding reaction mechanisms in many chemical and biological processes require application of rare event theories. In these theories, an effective choice of a reaction coordinate to describe a reaction pathway is essential. To this end, we study ion solvation in water using molecular dynamics simulations and explore the utility of coordination number (n = number of water molecules in the first solvation shell) as the reaction coordinate. Here we compute the potential of mean force (W(n)) using umbrella sampling, predicting multiple metastable n-states for both cations and anions. We find with increasing ionic size, these states become more stable andmore » structured for cations when compared to anions. We have extended transition state theory (TST) to calculate transition rates between n-states. TST overestimates the rate constant due to solvent-induced barrier recrossings that are not accounted for. We correct the TST rates by calculating transmission coefficients using the reactive flux method. This approach enables a new way of understanding rare events involving coordination complexes. We gratefully acknowledge Liem Dang and Panos Stinis for useful discussion. This research used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. SR, CJM, and GKS were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative, a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy.« less

Energy conservation and maximal entropy production in enzyme reactions.

PubMed

Dobovišek, Andrej; Vitas, Marko; Brumen, Milan; Fajmut, Aleš

2017-08-01

A procedure for maximization of the density of entropy production in a single stationary two-step enzyme reaction is developed. Under the constraints of mass conservation, fixed equilibrium constant of a reaction and fixed products of forward and backward enzyme rate constants the existence of maximum in the density of entropy production is demonstrated. In the state with maximal density of entropy production the optimal enzyme rate constants, the stationary concentrations of the substrate and the product, the stationary product yield as well as the stationary reaction flux are calculated. The test, whether these calculated values of the reaction parameters are consistent with their corresponding measured values, is performed for the enzyme Glucose Isomerase. It is found that calculated and measured rate constants agree within an order of magnitude, whereas the calculated reaction flux and the product yield differ from their corresponding measured values for less than 20 % and 5 %, respectively. This indicates that the enzyme Glucose Isomerase, considered in a non-equilibrium stationary state, as found in experiments using the continuous stirred tank reactors, possibly operates close to the state with the maximum in the density of entropy production. Copyright © 2017 Elsevier B.V. All rights reserved.

Raman Spectral Determination of Chemical Reaction Rate Characteristics

NASA Astrophysics Data System (ADS)

Balakhnina, I. A.; Brandt, N. N.; Mankova, A. A.; Chikishev, A. Yu.; Shpachenko, I. G.

2017-09-01

The feasibility of using Raman spectroscopy to determine chemical reaction rates and activation energies has been demonstrated for the saponification of ethyl acetate. The temperature dependence of the reaction rate was found in the range from 15 to 45°C.

Calibrating reaction rates for the CREST model

NASA Astrophysics Data System (ADS)

Handley, Caroline A.; Christie, Michael A.

2017-01-01

The CREST reactive-burn model uses entropy-dependent reaction rates that, until now, have been manually tuned to fit shock-initiation and detonation data in hydrocode simulations. This paper describes the initial development of an automatic method for calibrating CREST reaction-rate coefficients, using particle swarm optimisation. The automatic method is applied to EDC32, to help develop the first CREST model for this conventional high explosive.

Effect of surface curvature on diffusion-limited reactions on a curved surface

NASA Astrophysics Data System (ADS)

Eun, Changsun

2017-11-01

To investigate how the curvature of a reactive surface can affect reaction kinetics, we use a simple model in which a diffusion-limited bimolecular reaction occurs on a curved surface that is hollowed inward, flat, or extended outward while keeping the reactive area on the surface constant. By numerically solving the diffusion equation for this model using the finite element method, we find that the rate constant is a non-linear function of the surface curvature and that there is an optimal curvature providing the maximum value of the rate constant, which indicates that a spherical reactant whose entire surface is reactive (a uniformly reactive sphere) is not the most reactive species for a given reactive surface area. We discuss how this result arises from the interplay between two opposing effects: the exposedness of the reactive area to its partner reactants, which causes the rate constant to increase as the curvature increases, and the competition occurring on the reactive surface, which decreases the rate constant. This study helps us to understand the role of curvature in surface reactions and allows us to rationally design reactants that provide a high reaction rate.

Reaction Order Ambiguity in Integrated Rate Plots

ERIC Educational Resources Information Center

Lee, Joe

2008-01-01

Integrated rate plots are frequently used in reaction kinetics to determine orders of reactions. It is often emphasised, when using this methodology in practice, that it is necessary to monitor the reaction to a substantial fraction of completion for these plots to yield unambiguous orders. The present article gives a theoretical and statistical…

A Transition in the Cumulative Reaction Rate of Two Species Diffusion with Bimolecular Reaction

NASA Astrophysics Data System (ADS)

Rajaram, Harihar; Arshadi, Masoud

2015-04-01

Diffusion and bimolecular reaction between two initially separated reacting species is a prototypical small-scale description of reaction induced by transverse mixing. It is also relevant to diffusion controlled transport regimes as encountered in low-permeability matrix blocks in fractured media. In previous work, the reaction-diffusion problem has been analyzed as a Stefan problem involving a distinct moving boundary (reaction front), which predicts that front motion scales as √t, and the cumulative reaction rate scales as 1/√t-. We present a general non-dimensionalization of the problem and a perturbation analysis to show that there is an early time regime where the cumulative reaction rate scales as √t- rather than 1/√t. The duration of this early time regime (where the cumulative rate is kinetically rather than diffusion controlled) depends on the rate parameter, in a manner that is consistently predicted by our non-dimensionalization. We also present results on the scaling of the reaction front width. We present numerical simulations in homogeneous and heterogeneous porous media to demonstrate the limited influence of heterogeneity on the behavior of the reaction-diffusion system. We illustrate applications to the practical problem of in-situ chemical oxidation of TCE and PCE by permanganate, which is employed to remediate contaminated sites where the DNAPLs are largely dissolved in the rock matrix.

Reaction rates of α-tocopheroxyl radicals confined in micelles and in human plasma lipoproteins.

PubMed

Vanzani, Paola; Rigo, Adelio; Zennaro, Lucio; Di Paolo, Maria Luisa; Scarpa, Marina; Rossetto, Monica

2014-08-01

α-Tocopherol, the main component of vitamin E, traps highly reactive radicals which otherwise might react with lipids present in plasmatic lipoproteins or in cell membranes. The α-tocopheroxyl radicals generated by this process have also a pro-oxidant action which is contrasted by their reaction with ascorbate or by bimolecular self-reaction (dismutation). The kinetics of this bimolecular self-reaction were explored in solution such as ethanol, and in heterogeneous systems such as deoxycholic acid micelles and in human plasma. According to ESR measurements, the kinetic rate constant (2k(d)) of the bimolecular self-reaction of α-tocopheroxyl radicals in micelles and in human plasma was calculated to be of the order of 10(5) M(-1) s(-1) at 37 °C. This value was obtained considering that the reactive radicals are confined into the micellar pseudophase and is one to two orders of magnitude higher than the value we found in homogeneous phase. The physiological significance of this high value is discussed considering the competition between bimolecular self-reaction and the α-tocopheroxyl radical recycling by ascorbate. Copyright © 2014 Elsevier B.V. All rights reserved.

Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation Using Maximum Entropy-Based Simulations with Application to Central Metabolism of Neurospora crassa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cannon, William; Zucker, Jeremy; Baxter, Douglas

We report the application of a recently proposed approach for modeling biological systems using a maximum entropy production rate principle in lieu of having in vivo rate constants. The method is applied in four steps: (1) a new ODE-based optimization approach based on Marcelin’s 1910 mass action equation is used to obtain the maximum entropy distribution, (2) the predicted metabolite concentrations are compared to those generally expected from experiment using a loss function from which post-translational regulation of enzymes is inferred, (3) the system is re-optimized with the inferred regulation from which rate constants are determined from the metabolite concentrationsmore » and reaction fluxes, and finally (4) a full ODE-based, mass action simulation with rate parameters and allosteric regulation is obtained. From the last step, the power characteristics and resistance of each reaction can be determined. The method is applied to the central metabolism of Neurospora crassa and the flow of material through the three competing pathways of upper glycolysis, the non-oxidative pentose phosphate pathway, and the oxidative pentose phosphate pathway are evaluated as a function of the NADP/NADPH ratio. It is predicted that regulation of phosphofructokinase (PFK) and flow through the pentose phosphate pathway are essential for preventing an extreme level of fructose 1, 6-bisphophate accumulation. Such an extreme level of fructose 1,6-bisphophate would otherwise result in a glassy cytoplasm with limited diffusion, dramatically decreasing the entropy and energy production rate and, consequently, biological competitiveness.« less

Pulsed laser photolysis and quantum chemical-statistical rate study of the reaction of the ethynyl radical with water vapor

NASA Astrophysics Data System (ADS)

Carl, Shaun A.; Minh Thi Nguyen, Hue; Elsamra, Rehab M. I.; Tho Nguyen, Minh; Peeters, Jozef

2005-03-01

The rate coefficient of the gas-phase reaction C2H+H2O→products has been experimentally determined over the temperature range 500-825K using a pulsed laser photolysis-chemiluminescence (PLP-CL) technique. Ethynyl radicals (C2H) were generated by pulsed 193nm photolysis of C2H2 in the presence of H2O vapor and buffer gas N2 at 15Torr. The relative concentration of C2H radicals was monitored as a function of time using a CH * chemiluminescence method. The rate constant determinations for C2H+H2O were k1(550K)=(2.3±1.3)×10-13cm3s-1, k1(770cm3s-1, and k1(825cm3s-1. The error in the only other measurement of this rate constant is also discussed. We have also characterized the reaction theoretically using quantum chemical computations. The relevant portion of the potential energy surface of C2H3O in its doublet electronic ground state has been investigated using density functional theory B3LYP /6-311++G(3df,2p) and molecular orbital computations at the unrestricted coupled-cluster level of theory that incorporates all single and double excitations plus perturbative corrections for the triple excitations, along with the 6-311++G(3df,2p) basis set [(U)CCSD(T)/6-311++G(3df,2p)] and using UCCSD(T )/6-31G(d,p) optimized geometries. Five isomers, six dissociation products, and sixteen transition structures were characterized. The results confirm that the hydrogen abstraction producing C2H2+OH is the most facile reaction channel. For this channel, refined computations using (U)CCSD(T)/6-311++G(3df,2p)//(U)CCSD(T)/6-311++G(d,p) and complete-active-space second-order perturbation theory/complete-active-space self-consistent-field theory (CASPT2/CASSCF) [B. O. Roos, Adv. Chem. Phys. 69, 399 (1987)] using the contracted atomic natural orbitals basis set (ANO-L) [J. Almlöf and P. R. Taylor, J. Chem. Phys.86, 4070 (1987)] were performed, yielding zero-point energy-corrected potential energy barriers of 17kJmol-1 and 15kJmol-1, respectively. Transition-state theory rate constant

Dissociation constants, neutralization enthalpies and reactions of 3-styryl-2-mercaptopropenoic and 3-(1-naphthyl)-2-mercaptopropenoic acids.

PubMed

Izquierdo, A; Bosch, E; Beltran, J L

1984-06-01

Dissociation constants (pK(a1) and pK(a2) in water-ethanol medium for 3-styryl-2-mercaptopropenoic and 3-(1-naphthyl)-2-mercaptopropenoic acid have been determined potentiometrically, and pK(a2) for both in aqueous medium, spectrophotometrically. Neutralization enthalpies in water-ethanol medium have been determined by thermometric titration. The reactions with metal ions have been studied, and the main reactions are described. The most sensitive reactions are with titanium(IV) (pD = 7.00) and nickel(II) (pD = 6.50).

Propagation rate constants for the peroxidation of sterols on the biosynthetic pathway to cholesterol.

PubMed

Lamberson, Connor R; Muchalski, Hubert; McDuffee, Kari B; Tallman, Keri A; Xu, Libin; Porter, Ned A

2017-10-01

The free radical chain autoxidation of cholesterol and the oxidation products formed, i.e. oxysterols, have been the focus of intensive study for decades. The peroxidation of sterol precursors to cholesterol such as 7-dehydrocholesterol (7-DHC) and desmosterol as well as their oxysterols has received less attention. The peroxidation of these sterol precursors can become important under circumstances in which genetic conditions or exposures to small molecules leads to an increase of these biosynthetic intermediates in tissues and fluids. 7-DHC, for example, has a propagation rate constant for peroxidation some 200 times that of cholesterol and this sterol is found at elevated levels in a devastating human genetic condition, Smith-Lemli-Opitz syndrome (SLOS). The propagation rate constants for peroxidation of sterol intermediates on the biosynthetic pathway to cholesterol were determined by a competition kinetic method, i.e. a peroxyl radical clock. In this work, propagation rate constants for lathosterol, zymostenol, desmosterol, 7-dehydrodesmosterol and other sterols in the Bloch and Kandutsch-Russell pathways are assigned and these rate constants are related to sterol structural features. Furthermore, potential oxysterols products are proposed for sterols whose oxysterol products have not been determined. Copyright © 2017 Elsevier B.V. All rights reserved.

Reaction rates for a generalized reaction-diffusion master equation

DOE PAGES

Hellander, Stefan; Petzold, Linda

2016-01-19

It has been established that there is an inherent limit to the accuracy of the reaction-diffusion master equation. Specifically, there exists a fundamental lower bound on the mesh size, below which the accuracy deteriorates as the mesh is refined further. In this paper we extend the standard reaction-diffusion master equation to allow molecules occupying neighboring voxels to react, in contrast to the traditional approach in which molecules react only when occupying the same voxel. We derive reaction rates, in two dimensions as well as three dimensions, to obtain an optimal match to the more fine-grained Smoluchowski model, and show inmore » two numerical examples that the extended algorithm is accurate for a wide range of mesh sizes, allowing us to simulate systems that are intractable with the standard reaction-diffusion master equation. In addition, we show that for mesh sizes above the fundamental lower limit of the standard algorithm, the generalized algorithm reduces to the standard algorithm. We derive a lower limit for the generalized algorithm which, in both two dimensions and three dimensions, is on the order of the reaction radius of a reacting pair of molecules.« less

Reaction rates for a generalized reaction-diffusion master equation

PubMed Central

Hellander, Stefan; Petzold, Linda

2016-01-01

It has been established that there is an inherent limit to the accuracy of the reaction-diffusion master equation. Specifically, there exists a fundamental lower bound on the mesh size, below which the accuracy deteriorates as the mesh is refined further. In this paper we extend the standard reaction-diffusion master equation to allow molecules occupying neighboring voxels to react, in contrast to the traditional approach in which molecules react only when occupying the same voxel. We derive reaction rates, in two dimensions as well as three dimensions, to obtain an optimal match to the more fine-grained Smoluchowski model, and show in two numerical examples that the extended algorithm is accurate for a wide range of mesh sizes, allowing us to simulate systems that are intractable with the standard reaction-diffusion master equation. In addition, we show that for mesh sizes above the fundamental lower limit of the standard algorithm, the generalized algorithm reduces to the standard algorithm. We derive a lower limit for the generalized algorithm which, in both two dimensions and three dimensions, is on the order of the reaction radius of a reacting pair of molecules. PMID:26871190

Soliton solutions, stability analysis and conservation laws for the brusselator reaction diffusion model with time- and constant-dependent coefficients

NASA Astrophysics Data System (ADS)

Inc, Mustafa; Yusuf, Abdullahi; Isa Aliyu, Aliyu; Hashemi, M. S.

2018-05-01

This paper studies the brusselator reaction diffusion model (BRDM) with time- and constant-dependent coefficients. The soliton solutions for BRDM with time-dependent coefficients are obtained via first integral (FIM), ansatz, and sine-Gordon expansion (SGEM) methods. Moreover, it is well known that stability analysis (SA), symmetry analysis and conservation laws (CLs) give several information for modelling a system of differential equations (SDE). This is because they can be used for investigating the internal properties, existence, uniqueness and integrability of different SDE. For this reason, we investigate the SA via linear stability technique, symmetry analysis and CLs for BRDM with constant-dependent coefficients in order to extract more physics and information on the governing equation. The constraint conditions for the existence of the solutions are also examined. The new solutions obtained in this paper can be useful for describing the concentrations of diffusion problems of the BRDM. It is shown that the examined dependent coefficients are some of the factors that are affecting the diffusion rate. So, the present paper provides much motivational information in comparison to the existing results in the literature.

GROUND WATER ISSUE - CALCULATION AND USE OF FIRST-ORDER RATE CONSTANTS FOR MONITORED NATURAL ATTENUATION STUDIES

EPA Science Inventory

This issue paper explains when and how to apply first-order attenuation rate constant calculations in monitored natural attenuation (MNA) studies. First-order attenuation rate constant calculations can be an important tool for evaluating natural attenuation processes at ground-wa...

Binding Rate Constants Reveal Distinct Features of Disordered Protein Domains.

PubMed

Dogan, Jakob; Jonasson, Josefin; Andersson, Eva; Jemth, Per

2015-08-04

Intrinsically disordered proteins (IDPs) are abundant in the proteome and involved in key cellular functions. However, experimental data about the binding kinetics of IDPs as a function of different environmental conditions are scarce. We have performed an extensive characterization of the ionic strength dependence of the interaction between the molten globular nuclear co-activator binding domain (NCBD) of CREB binding protein and five different protein ligands, including the intrinsically disordered activation domain of p160 transcriptional co-activators (SRC1, TIF2, ACTR), the p53 transactivation domain, and the folded pointed domain (PNT) of transcription factor ETS-2. Direct comparisons of the binding rate constants under identical conditions show that the association rate constant, kon, for interactions between NCBD and disordered protein domains is high at low salt concentrations (90-350 × 10(6) M(-1) s(-1) at 4 °C) but is reduced significantly (10-30-fold) with an increasing ionic strength and reaches a plateau around physiological ionic strength. In contrast, the kon for the interaction between NCBD and the folded PNT domain is only 7 × 10(6) M(-1) s(-1) (4 °C and low salt) and displays weak ionic strength dependence, which could reflect a distinctly different association that relies less on electrostatic interactions. Furthermore, the basal rate constant (in the absence of electrostatic interactions) is high for the NCBD interactions, exceeding those typically observed for folded proteins. One likely interpretation is that disordered proteins have a large number of possible collisions leading to a productive on-pathway encounter complex, while folded proteins are more restricted in terms of orientation. Our results highlight the importance of electrostatic interactions in binding involving IDPs and emphasize the significance of including ionic strength as a factor in studies that compare the binding properties of IDPs to those of ordered proteins.

The role of reaction affinity and secondary minerals in regulating chemical weathering rates at the Santa Cruz Soil Chronosequence, California

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maher, K.; Steefel, C. I.; White, A.F.

2009-02-25

In order to explore the reasons for the apparent discrepancy between laboratory and field weathering rates and to determine the extent to which weathering rates are controlled by the approach to thermodynamic equilibrium, secondary mineral precipitation and flow rates, a multicomponent reactive transport model (CrunchFlow) was used to interpret soil profile development and mineral precipitation and dissolution rates at the 226 ka marine terrace chronosequence near Santa Cruz, CA. Aqueous compositions, fluid chemistry, transport, and mineral abundances are well characterized (White et al., 2008, GCA) and were used to constrain the reaction rates for the weathering and precipitating minerals inmore » the reactive transport modeling. When primary mineral weathering rates are calculated with either of two experimentally determined rate constants, the nonlinear, parallel rate law formulation of Hellmann and Tisser and [2006] or the aluminum inhibition model proposed by Oelkers et al. [1994], modeling results are consistent with field-scale observations when independently constrained clay precipitation rates are accounted for. Experimental and field rates, therefore, can be reconciled at the Santa Cruz site. Observed maximum clay abundances in the argillic horizons occur at the depth and time where the reaction fronts of the primary minerals overlap. The modeling indicates that the argillic horizon at Santa Cruz can be explained almost entirely by weathering of primary minerals and in situ clay precipitation accompanied by undersaturation of kaolinite at the top of the profile. The rate constant for kaolinite precipitation was also determined based on model simulations of mineral abundances and dissolved Al, SiO{sub 2}(aq) and pH in pore waters. Changes in the rate of kaolinite precipitation or the flow rate do not affect the gradient of the primary mineral weathering profiles, but instead control the rate of propagation of the primary mineral weathering fronts and

[Study of Reaction Dynamics between Bovine Serum Albumin and Folic Acid by Stopped-Flow/Fluorescence].

PubMed

Ye, San-xian; Luo, Yun-jing; Qiao, Shu-liang; Li, Li; Liu, Cai-hong; Shi, Jian-long; An, Xue-jing

2016-01-01

As a kind of coenzyme of one-carbon enzymes in vivo, folic acid belongs to B vitamins, which can interact with other vitamins and has great significance for converting among amino acids, dividing growth of cells and protein synthesis reactions. Half-life, concentration and reaction rate constant of drugs are important parameters in pharmacokinetic study. In this paper, by utilizing fluorescence spectrophotometer and stopped-flow spectrum analyzer, reaction kinetic parameters between bovine serum albumin(BSA) and folic acid in a bionic system have been investigated, which provide references for parameters of drug metabolism related to folic acid. By using Stern-Volmer equation dealing with fluorescence quenching experiments data, we concluded that under 25, 30, and 37 degrees C, the static quenching constants of folic acid to intrinsic fluorescence from bovine serum albumin were 2.455 x 10(10), 4.900 x 10(10) and 6.427 x 10(10) L x mol(-1) x s(-1) respectively; The results of kinetic reaction rate have shown that the reaction rate of BSA and folic acid are greater than 100 mol x L(-1) x s(-1) at different temperatures, pH and buffering media, illustrating that the quenching mechanism between BSA and folic acid is to form composite static quenching process. Reaction concentration of bovine serum albumin and its initial concentration were equal to the secondary reaction formula, and the correlation coefficient was 0.998 7, while the half-life (t1/2) was 0.059 s at physiological temperature. With the increase of folic acid concentration, the apparent rate constant of this reaction had a linear increasing trend, the BSA fluorescence quenching rate constant catalyzed by folic acid was 3.174 x 10(5) mol x L(-1) x s(-1). Furthermore, with different buffer, the apparent rate constant and reaction rate constant of BSA interacting with folic acid were detected to explore the influence on the reaction under physiological medium, which is of great significance to determine the

Likelihood inference of non-constant diversification rates with incomplete taxon sampling.

PubMed

Höhna, Sebastian

2014-01-01

Large-scale phylogenies provide a valuable source to study background diversification rates and investigate if the rates have changed over time. Unfortunately most large-scale, dated phylogenies are sparsely sampled (fewer than 5% of the described species) and taxon sampling is not uniform. Instead, taxa are frequently sampled to obtain at least one representative per subgroup (e.g. family) and thus to maximize diversity (diversified sampling). So far, such complications have been ignored, potentially biasing the conclusions that have been reached. In this study I derive the likelihood of a birth-death process with non-constant (time-dependent) diversification rates and diversified taxon sampling. Using simulations I test if the true parameters and the sampling method can be recovered when the trees are small or medium sized (fewer than 200 taxa). The results show that the diversification rates can be inferred and the estimates are unbiased for large trees but are biased for small trees (fewer than 50 taxa). Furthermore, model selection by means of Akaike's Information Criterion favors the true model if the true rates differ sufficiently from alternative models (e.g. the birth-death model is recovered if the extinction rate is large and compared to a pure-birth model). Finally, I applied six different diversification rate models--ranging from a constant-rate pure birth process to a decreasing speciation rate birth-death process but excluding any rate shift models--on three large-scale empirical phylogenies (ants, mammals and snakes with respectively 149, 164 and 41 sampled species). All three phylogenies were constructed by diversified taxon sampling, as stated by the authors. However only the snake phylogeny supported diversified taxon sampling. Moreover, a parametric bootstrap test revealed that none of the tested models provided a good fit to the observed data. The model assumptions, such as homogeneous rates across species or no rate shifts, appear to be

A review of reaction rates in high temperature air

NASA Technical Reports Server (NTRS)

Park, Chul

1989-01-01

The existing experimental data on the rate coefficients for the chemical reactions in nonequilibrium high temperature air are reviewed and collated, and a selected set of such values is recommended for use in hypersonic flow calculations. For the reactions of neutral species, the recommended values are chosen from the experimental data that existed mostly prior to 1970, and are slightly different from those used previously. For the reactions involving ions, the recommended rate coefficients are newly chosen from the experimental data obtained more recently. The reacting environment is assumed to lack thermal equilibrium, and the rate coefficients are expressed as a function of the controlling temperature, incorporating the recent multitemperature reaction concept.

Frost heave susceptibility of saturated soil under constant rate of freezing

NASA Astrophysics Data System (ADS)

Ryokai, K.; Iguro, M.; Yoneyama, K.

Introduced are the results of experiments carried out to quantitatively obtain the frost heave pressure and displacement of soil subjected to artificial freezing or freezing around in-ground liquefied natural gas storage tanks. This experiment is conducted to evaluate the frost heave susceptibility of saturated soil under overconsolidation. In other words, this experiment was carried out to obtain the relation of the over-burden pressure and freezing rate to the frost heave ratio by observing the frost heave displacement and freezing time of specimens by freezing the specimens at a constant freezing rate under a constant overburden pressure, while letting water freely flow in and out of the system. Introduced are the procedures for frost heave test required to quantitatively obtain the frost heave displacement and pressure of soil. Furthermore, the relation between the frost heave susceptibility and physical properties of soil obtained by this test is reported.

Evaluating free vs bound oxygen on ignition of nano-aluminum based energetics leads to a critical reaction rate criterion

NASA Astrophysics Data System (ADS)

Zhou, Wenbo; DeLisio, Jeffery B.; Wang, Xizheng; Egan, Garth C.; Zachariah, Michael R.

2015-09-01

This study investigates the ignition of nano-aluminum (n-Al) and n-Al based energetic materials (nanothermites) at varying O2 pressures (1-18 atm), aiming to differentiate the effects of free and bound oxygen on ignition and to assess if it is possible to identify a critical reaction condition for ignition independent of oxygen source. Ignition experiments were conducted by rapidly heating the samples on a fine Pt wire at a heating rate of ˜105 °C s-1 to determine the ignition time and temperature. The ignition temperature of n-Al was found to reduce as the O2 pressure increased, whereas the ignition temperatures of nanothermites (n-Al/Fe2O3, n-Al/Bi2O3, n-Al/K2SO4, and n-Al/K2S2O8) had different sensitivities to O2 pressure depending on the formulations. A phenomenological kinetic/transport model was evaluated to correlate the concentrations of oxygen both in condensed and gaseous phases, with the initiation rate of Al-O at ignition temperature. We found that a constant critical reaction rate (5 × 10-2 mol m-2 s-1) for ignition exists which is independent to ignition temperature, heating rate, and free vs bound oxygen. Since for both the thermite and the free O2 reaction the critical reaction rate for ignition is the same, the various ignition temperatures are simply reflecting the conditions when the critical reaction rate for thermal runaway is achieved.

Rate constants of nine C6-C9 alkanes with OH from 230 to 379 K: chemical tracers for [OH].

PubMed

Sprengnether, Michele M; Demerjian, Kenneth L; Dransfield, Timothy J; Clarke, James S; Anderson, James G; Donahue, Neil M

2009-04-30

We report absolute rate-constant measurements for the reactions of nine C(6)-C(9) alkanes with OH in 8-10 torr of nitrogen from 230 to 379 K in the Harvard University High-Pressure Flow System. Hydroxyl concentrations were measured using laser-induced fluorescence, and alkane concentrations were measured using Fourier transform infrared Spectroscopy. Ethane's reactivity was simultaneously measured as a test of experimental performance. Results were fit to a modified Arrhenius equation based on transition state theory (ignoring tunneling), k(T) = Be(-E(a)/T)/(T(1 - e(- 1.44nu(1)/T))(2)(1 - e(- 1.44nu(2)/T)), with nu(1) and nu(2) bending frequencies, set to 280 and 500 cm(-1). Results were as follows for B (10(-9) K cm(3) s(-1)), E(a) (K), and k(298) (10(-12) cm(3) s(-1)): cyclohexane, 3.24 +/- 0.14, 332 +/- 12, 7.13; cyclo-octane, 3.47 +/- 0.30, 149 +/- 26, 14.1; 2-methylhexane, 1.45 +/- 0.08, 110 +/- 15, 6.72; 3-methylhexane, 1.50 +/- 0.08, 128 +/- 16, 6.54; methylcyclopentane, 1.65 +/- 0.07, 109 +/- 13, 7.65; methylcyclohexane, 1.86 +/- 0.09, 83 +/- 14, 9.43; methylcycloheptane, 3.45 +/- 0.45, 142 +/- 36, 14.4; n-propylcyclohexane, 2.83 +/- 0.14, 112 +/- 15, 13.0; isopropylcyclohexane, 1.79 +/- 0.11, -44 +/- 34, 13.9. Uncertainties are one sigma results from linear regression fits and are likely underestimated. Room temperature rate coefficients of reaction are accurate to within 10% at two sigma. A comprehensive fit to 17 separate studies including the present work for cyclohexane gives good agreement with the present results: terms as above, 3.09 +/- 0.12, 326 +/- 12, 6.96. Five of these compounds are routinely measured in urban air within a suite of atmospheric nonmethane hydrocarbons and reach parts per billion levels. The remaining four are C8-C9 cycloalkanes with low anthropogenic emissions. Because of their high, specific reactivity with OH, their concentration decays may be used as an indirect measurement of [OH] in the atmosphere or laboratory. This data

Constant-load versus heart rate-targeted exercise - Responses of systolic intervals

NASA Technical Reports Server (NTRS)

Lance, V. Q.; Spodick, D. H.

1975-01-01

Various systolic intervals were measured prior to and during heart rate-targeted bicycle ergometer exercise. There were striking similarities within each matched exercise set for Q-Im, isovolumetric contraction time, preejection period (PEP), and PEP/left ventricular ejection time (LVET). LVET was significantly shorter for rate-targeted exercise. It is concluded that either constant-load or rate-targeted bicycle ergometry may be used with the choice of method determined by the purpose of the protocol, and that systolic intervals (except LVET) should not be much altered owing to the method chosen.

Origin of the Non-Arrhenius Behavior of the Rates of Enzymatic Reactions.

PubMed

Roy, Subhendu; Schopf, Patrick; Warshel, Arieh

2017-07-13

The origin of the non-Arrhenius behavior of the rate constant for hydride transfer enzymatic reactions has been a puzzling problem since its initial observation. This effect has been used originally to support the idea that enzymes work by dynamical effects and more recently to suggest an entropy funnel model. Our analysis, however, has advanced the idea that the reason for the non-Arrhenius trend reflects the temperature dependence of the rearrangements of the protein polar groups in response to the change in the charge distribution of the reacting system during the transition from the ground state (GS) to the transition state (TS). Here we examine the validity of our early proposal by simulating the catalytic reaction of alcohol dehydrogenase (ADH) and determine the microscopic origin of the entropic and enthalpic contributions to the activation barrier. The corresponding analysis establishes the origin of the non-Arrhenius behaviors and quantifies our original suggestion that the classical effect is due to the entropic contributions of the environment. We also find that the quantum effects reflect in part the temperature dependence of the donor-acceptor distance.

Minimum reaction network necessary to describe Ar/CF4 plasma etch

NASA Astrophysics Data System (ADS)

Helpert, Sofia; Chopra, Meghali; Bonnecaze, Roger T.

2018-03-01

Predicting the etch and deposition profiles created using plasma processes is challenging due to the complexity of plasma discharges and plasma-surface interactions. Volume-averaged global models allow for efficient prediction of important processing parameters and provide a means to quickly determine the effect of a variety of process inputs on the plasma discharge. However, global models are limited based on simplifying assumptions to describe the chemical reaction network. Here a database of 128 reactions is compiled and their corresponding rate constants collected from 24 sources for an Ar/CF4 plasma using the platform RODEo (Recipe Optimization for Deposition and Etching). Six different reaction sets were tested which employed anywhere from 12 to all 128 reactions to evaluate the impact of the reaction database on particle species densities and electron temperature. Because many the reactions used in our database had conflicting rate constants as reported in literature, we also present a method to deal with those uncertainties when constructing the model which includes weighting each reaction rate and filtering outliers. By analyzing the link between a reaction's rate constant and its impact on the predicted plasma densities and electron temperatures, we determine the conditions at which a reaction is deemed necessary to the plasma model. The results of this study provide a foundation for determining which minimal set of reactions must be included in the reaction set of the plasma model.

BAYESIAN ESTIMATION OF THERMONUCLEAR REACTION RATES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Iliadis, C.; Anderson, K. S.; Coc, A.

The problem of estimating non-resonant astrophysical S -factors and thermonuclear reaction rates, based on measured nuclear cross sections, is of major interest for nuclear energy generation, neutrino physics, and element synthesis. Many different methods have been applied to this problem in the past, almost all of them based on traditional statistics. Bayesian methods, on the other hand, are now in widespread use in the physical sciences. In astronomy, for example, Bayesian statistics is applied to the observation of extrasolar planets, gravitational waves, and Type Ia supernovae. However, nuclear physics, in particular, has been slow to adopt Bayesian methods. We presentmore » astrophysical S -factors and reaction rates based on Bayesian statistics. We develop a framework that incorporates robust parameter estimation, systematic effects, and non-Gaussian uncertainties in a consistent manner. The method is applied to the reactions d(p, γ ){sup 3}He, {sup 3}He({sup 3}He,2p){sup 4}He, and {sup 3}He( α , γ ){sup 7}Be, important for deuterium burning, solar neutrinos, and Big Bang nucleosynthesis.« less

Structure dependence of the rate coefficients of hydroxyl radical+aromatic molecule reaction

NASA Astrophysics Data System (ADS)

Wojnárovits, László; Takács, Erzsébet

2013-06-01

The rate coefficients of hydroxyl radical addition to the rings of simple aromatic molecules (kOH) were evaluated based on the literature data. By analyzing the methods of kOH determination and the data obtained the most probable values were selected for the kOH's of individual compounds and thereby the most reliable dataset was created for monosubstituted aromatics and p-substituted phenols. For these compounds the rate coefficients fall in a narrow range between 2×109 mol-1 dm3 s-1 and 1×1010 mol-1 dm3 s-1. Although the values show some regular trend with the electron donating/withdrawing nature of the substituent, the log kOH-σp Hammett substituent constant plots do not give straight lines because these high kOH's are controlled by both, the chemical reactivity and the diffusion. However, the logarithms of the rate coefficients of the chemical reactivity controlled reactions (kchem), are calculated by the equation 1/kOH=1/kchem+1/kdiff, and accepting for the diffusion controlled rate coefficient kdiff=1.1×1010 mol-1 dm3 s-1, show good linear correlation with σp.

Determination of thermodynamics and kinetics of RNA reactions by force

PubMed Central

Tinoco, Ignacio; Li, Pan T. X.; Bustamante, Carlos

2008-01-01

Single-molecule methods have made it possible to apply force to an individual RNA molecule. Two beads are attached to the RNA; one is on a micropipette, the other is in a laser trap. The force on the RNA and the distance between the beads are measured. Force can change the equilibrium and the rate of any reaction in which the product has a different extension from the reactant. This review describes use of laser tweezers to measure thermodynamics and kinetics of unfolding/refolding RNA. For a reversible reaction the work directly provides the free energy; for irreversible reactions the free energy is obtained from the distribution of work values. The rate constants for the folding and unfolding reactions can be measured by several methods. The effect of pulling rate on the distribution of force-unfolding values leads to rate constants for unfolding. Hopping of the RNA between folded and unfolded states at constant force provides both unfolding and folding rates. Force-jumps and force-drops, similar to the temperature jump method, provide direct measurement of reaction rates over a wide range of forces. The advantages of applying force and using single-molecule methods are discussed. These methods, for example, allow reactions to be studied in non-denaturing solvents at physiological temperatures; they also simplify analysis of kinetic mechanisms because only one intermediate at a time is present. Unfolding of RNA in biological cells by helicases, or ribosomes, has similarities to unfolding by force. PMID:17040613

Real-time association rate constant measurement using combination tapered fiber-optic biosensor (CTFOB) dip-probes

NASA Astrophysics Data System (ADS)

Simmonds, Boris; Wang, Chun-Wei; Kapoor, Rakesh

2010-02-01

This document reports a novel method of measuring association rate constant (ka) for antibody-antigen interaction using evanescent wave-based combination tapered fiber-optic biosensor (CTFOB) dip-probes. The method was demonstrated by measuring association rate constant for bovine serum albumin (BSA) and anti-BSA antibody interaction. "Direct method" was used for detection; goat anti-BSA "capture" antibodies were immobilized on the probe surfaces while the antigen (BSA) was directly labeled with Alexa 488 dye. The probes were subsequently submerged in 3nM Labeled BSA in egg albumin (1 mg/ml). The fluorescence signal recorded was proportional to BSA anti-BSA conjugates and continuous signal was acquired suing a fiber optic spectrometer (Ocean Optics, Inc.). A 476 nm diode laser was use as an excitation source. Association constant was estimated from a plot of signal as a function of time. Measured association rate constant ka for the binding of BSA with anti-BSA at room temperature is (8.33 +/- 0.01) x 104 M-1s-1.

A new analytical method for estimating lumped parameter constants of linear viscoelastic models from strain rate tests

NASA Astrophysics Data System (ADS)

Mattei, G.; Ahluwalia, A.

2018-04-01

We introduce a new function, the apparent elastic modulus strain-rate spectrum, E_{app} ( \\dot{ɛ} ), for the derivation of lumped parameter constants for Generalized Maxwell (GM) linear viscoelastic models from stress-strain data obtained at various compressive strain rates ( \\dot{ɛ}). The E_{app} ( \\dot{ɛ} ) function was derived using the tangent modulus function obtained from the GM model stress-strain response to a constant \\dot{ɛ} input. Material viscoelastic parameters can be rapidly derived by fitting experimental E_{app} data obtained at different strain rates to the E_{app} ( \\dot{ɛ} ) function. This single-curve fitting returns similar viscoelastic constants as the original epsilon dot method based on a multi-curve global fitting procedure with shared parameters. Its low computational cost permits quick and robust identification of viscoelastic constants even when a large number of strain rates or replicates per strain rate are considered. This method is particularly suited for the analysis of bulk compression and nano-indentation data of soft (bio)materials.

Determination of the rate constant for the NH2(X2B1) + NH2(X2B1) recombination reaction with collision partners He, Ne, Ar, and N2 at low pressures and 296 K. Part 1.

PubMed

Altinay, Gokhan; Macdonald, R Glen

2012-02-09

The recombination rate constant for the NH(2)(X(2)B(1)) + NH(2)(X(2)B(1)) → N(2)H(4)(X(1)A(1)) reaction in He, Ne, Ar, and N(2) was measured over the pressure range 1-20 Torr at a temperature of 296 K. The NH(2) radical was produced by 193 nm laser photolysis of NH(3) dilute in the third-body gas. The production of NH(2) and the loss of NH(3) were monitored by high-resolution continuous-wave absorption spectroscopy: NH(2) on the (1)2(21) ← (1)3(31) rotational transition of the (0,7,0)A(2)A(1) ← (0,0,0) X(2)B(1) vibronic band and NH(3) on either inversion doublet of the (q)Q(3)(3) rotational transition of the ν(1) fundamental. Both species were detected simultaneously following the photolysis laser pulse. The broader Doppler width of the NH(2) spectral transition allowed temporal concentration measurements to be extended up to 20 Torr before pressure broadening effects became significant. Fall-off behavior was identified and the bimolecular rate constants for each collision partner were fit to a simple Troe form defined by the parameters, k(0), k(inf), and F(cent). This work is the first part of a two part series in which part 2 will discuss the measurements with more efficient energy transfer collision partners CH(4), C(2)H(6), CO(2), CF(4), and SF(6). The pressure range was too limited to extract any new information on k(inf), and k(inf) was taken from the theoretical calculations of Klippenstein et al. (J. Phys. Chem A 2009, 113, 10241) as k(inf) = 7.9 × 10(-11) cm(3) molecule(-1) s(-1) at 296 K. The individual Troe parameters were: He, k(0) = 2.8 × 10(-29) and F(cent) = 0.47; Ne, k(0) = 2.7 × 10(-29) and F(cent) = 0.34; Ar, k(0) = 4.4 × 10(-29) and F(cent) = 0.41; N(2), k(0) = 5.7 × 10(-29) and F(cent) = 0.61, with units cm(6) molecule(-2) s(-1) for k(0). In the case of N(2) as the third body, it was possible to measure the recombination rate constant for the NH(2) + H reaction near 20 Torr total pressure. The pure three-body recombination rate

The Gaseous Explosive Reaction : The Effect of Inert Gases

NASA Technical Reports Server (NTRS)

Stevens, F W

1928-01-01

Attention is called in this report to previous investigations of gaseous explosive reactions carried out under constant volume conditions, where the effect of inert gases on the thermodynamic equilibrium was determined. The advantage of constant pressure methods over those of constant volume as applied to studies of the gaseous explosive reaction is pointed out and the possibility of realizing for this purpose a constant pressure bomb mentioned. The application of constant pressure methods to the study of gaseous explosive reactions, made possible by the use of a constant pressure bomb, led to the discovery of an important kinetic relation connecting the rate of propagation of the zone of explosive reaction within the active gases, with the initial concentrations of those gases: s = K(sub 1)(A)(sup n1)(B)(sup n2)(C)(sup n3)------. By a method analogous to that followed in determining the effect of inert gases on the equilibrium constant K, the present paper records an attempt to determine their kinetic effect upon the expression given above.

Determination of the Rate Constants for the NH 2 (X 2 B 1 ) + NH 2 (X 2 B 1 ) and NH 2 (X 2 B 1 ) + H Recombination Reactions in N 2 as a Function of Temperature and Pressure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Altinay, Gokhan; Macdonald, R. Glen

2015-07-16

The recombination rate constants for the reactions NH2 + NH2 → N2H4 (reaction k1b) and NH2 + H → NH3 (reaction k2b) with N2 as a third-body have been measured as a function of temperature and pressure. The temperature range was from 292 to 533 K and the pressure range from a few Torr up to 300–400 Torr, well within the pressure falloff region. The NH2 radical was produced by 193 nm pulsed-laser photolysis of NH3 in a temperature controlled flow chamber. High-resolution time-resolved laser absorption spectroscopy was used to follow the temporal concentration profiles of both NH2 and NH3, simultaneously. The NH2 radical was monitored at 14800.65 cm–1 using the 1231 (0,7,0)Ã2A1 ← 1331 (0,0,0)more » $$\\tilde{X}$$2B1 ro-vibronic transition, and NH3 monitored at 3336.39 cm–1 on the qQ3(3)s (1,0,0,0) ← (0,0,0,0) ro-vibrational transition. The necessary collisional broadening parameters for each molecule were measured in separate experiments. The pressure and temperature dependence of k1b can be represented by the Troe parameters: k0, the low-pressure three-body recombination rate constant, k0(T) = (1.14 ± 0.59) × 10–19T–(3.41±0.28) cm6 molecule–2 s–1, and Fcent, the pressure broadening parameter, Fcent = 0.15 ± 0.12, independent of temperature. The data could not be fit by three-independent parameters, and the high-pressure limiting rate constant k∞(T) = 9.33 × 10–10T–0.414 e33/T cm3 molecule–1 s–1 was taken from the high-quality theoretical calculations of Klippenstein et al. (J. Phys. Chem A 2009, 113, 10241). The pressure and temperature dependence of k2b, can be represented by the Troe parameters: k0(T) = (9.95 ± 0.58) × 10–26T(-1.76±0.092) cm6 molecule–2 s–1, Fcent = 0.5 ± 0.2, k∞ = 2.6 × 10–10 cm3 molecule–1 s–1. Again, the data could not be fit with three independent parameters, and k2b∞ was chosen to be 2.6 × 10–10 cm3 molecule–1 s–1 and fixed in the analysis.« less

Development of linear free energy relationships for aqueous phase radical-involved chemical reactions.

PubMed

Minakata, Daisuke; Mezyk, Stephen P; Jones, Jace W; Daws, Brittany R; Crittenden, John C

2014-12-02

Aqueous phase advanced oxidation processes (AOPs) produce hydroxyl radicals (HO•) which can completely oxidize electron rich organic compounds. The proper design and operation of AOPs require that we predict the formation and fate of the byproducts and their associated toxicity. Accordingly, there is a need to develop a first-principles kinetic model that can predict the dominant reaction pathways that potentially produce toxic byproducts. We have published some of our efforts on predicting the elementary reaction pathways and the HO• rate constants. Here we develop linear free energy relationships (LFERs) that predict the rate constants for aqueous phase radical reactions. The LFERs relate experimentally obtained kinetic rate constants to quantum mechanically calculated aqueous phase free energies of activation. The LFERs have been applied to 101 reactions, including (1) HO• addition to 15 aromatic compounds; (2) addition of molecular oxygen to 65 carbon-centered aliphatic and cyclohexadienyl radicals; (3) disproportionation of 10 peroxyl radicals, and (4) unimolecular decay of nine peroxyl radicals. The LFERs correlations predict the rate constants within a factor of 2 from the experimental values for HO• reactions and molecular oxygen addition, and a factor of 5 for peroxyl radical reactions. The LFERs and the elementary reaction pathways will enable us to predict the formation and initial fate of the byproducts in AOPs. Furthermore, our methodology can be applied to other environmental processes in which aqueous phase radical-involved reactions occur.

Theoretical study of thermodynamic properties and reaction rates of importance in the high-speed research program

NASA Technical Reports Server (NTRS)

Langhoff, Stephen; Bauschlicher, Charles; Jaffe, Richard

1992-01-01

One of the primary goals of NASA's high-speed research program is to determine the feasibility of designing an environmentally safe commercial supersonic transport airplane. The largest environmental concern is focused on the amount of ozone destroying nitrogen oxides (NO(x)) that would be injected into the lower stratosphere during the cruise portion of the flight. The limitations placed on NO(x) emission require more than an order of magnitude reduction over current engine designs. To develop strategies to meet this goal requires first gaining a fundamental understanding of the combustion chemistry. To accurately model the combustor requires a computational fluid dynamics approach that includes both turbulence and chemistry. Since many of the important chemical processes in this regime involve highly reactive radicals, an experimental determination of the required thermodynamic data and rate constants is often very difficult. Unlike experimental approaches, theoretical methods are as applicable to highly reactive species as stable ones. Also our approximation of treating the dynamics classically becomes more accurate with increasing temperature. In this article we review recent progress in generating thermodynamic properties and rate constants that are required to understand NO(x) formation in the combustion process. We also describe our one-dimensional modeling efforts to validate an NH3 combustion reaction mechanism. We have been working in collaboration with researchers at LeRC, to ensure that our theoretical work is focused on the most important thermodynamic quantities and rate constants required in the chemical data base.

A novel solution for hydroxylated PAHs removal by oxidative coupling reaction using Mn oxide.

PubMed

Kang, Ki-Hoon; Lim, Dong-Min; Shin, Hyun-Sang

2008-01-01

In this study, removals of 1-naphthol by oxidative-coupling reaction using birnessite, one of the natural Mn oxides present in soil, was investigated in various experimental conditions (reaction time, Mn oxide loadings, pH). The removal efficiency of 1-naphthol by birnessite was high in all the experimental conditions, and UV-visible and mass spectrometric analyses on the supernatant after reaction confirmed that the reaction products were oligomers formed by oxidative-coupling reaction. Pseudo-first order rate constants, k, for the oxidative transformation of 1-naphthol by birnessite was derived from the kinetic experiments under various amounts of birnessite loadings, and using the observed pseudo-first order rate constants with respect to birnessite loadings, the surface area normalised specific rate constant, k(surf), was also determined to be 9.3 x 10(-4) (L/m(2).min) for 1-naphthol. In addition, the oxidative transformation of 1-naphthol was found to be dependent on solution pH, and the pseudo-first order rate constants were increased from 0.129 at pH 10 to 0.187 at pH 4. (c) IWA Publishing 2008.

On the possibility of negative activation energies in bimolecular reactions

NASA Technical Reports Server (NTRS)

Jaffe, R. L.

1978-01-01

The temperature dependence of the rate constants for model reacting systems was studied to understand some recent experimental measurements which imply the existence of negative activation energies. A collision theory model and classical trajectory calculations are used to demonstrate that the reaction probability can vary inversely with collision energy for bimolecular reactions occurring on attractive potential energy surfaces. However, this is not a sufficient condition to ensure that the rate constant has a negative temperature dependence. On the basis of these calculations, it seems unlikely that a true bimolecular reaction between neutral molecules will have a negative activation energy.

Bioluminescent Reaction by Immobilized Luciferase

NASA Astrophysics Data System (ADS)

Tanaka, Ryuta; Takahama, Eriko; Iinuma, Masataka; Ikeda, Takeshi; Kadoya, Yutaka; Kuroda, Akio

We have investigated an effect of immobilization of luciferase molecules at the optical fiber end on a bioluminescent reaction. The time dependence of measured count rates of emitted photons has been analyzed by fitting with numerical solution of differential equations including the effect of the product-inhibitor and the deactivation of the luciferase. Through the analysis, we have successfully extracted kinetic constants such as, reaction rate, number of active luciferase molecules, etc. Ratio of active molecules to total luciferase molecules in immobilization was one order of magnitude lower than that in solution. The reaction rate of the bioluminescent process was also different from the one of free luciferase in solution.

Analysis of reaction schemes using maximum rates of constituent steps

PubMed Central

Motagamwala, Ali Hussain; Dumesic, James A.

2016-01-01

We show that the steady-state kinetics of a chemical reaction can be analyzed analytically in terms of proposed reaction schemes composed of series of steps with stoichiometric numbers equal to unity by calculating the maximum rates of the constituent steps, rmax,i, assuming that all of the remaining steps are quasi-equilibrated. Analytical expressions can be derived in terms of rmax,i to calculate degrees of rate control for each step to determine the extent to which each step controls the rate of the overall stoichiometric reaction. The values of rmax,i can be used to predict the rate of the overall stoichiometric reaction, making it possible to estimate the observed reaction kinetics. This approach can be used for catalytic reactions to identify transition states and adsorbed species that are important in controlling catalyst performance, such that detailed calculations using electronic structure calculations (e.g., density functional theory) can be carried out for these species, whereas more approximate methods (e.g., scaling relations) are used for the remaining species. This approach to assess the feasibility of proposed reaction schemes is exact for reaction schemes where the stoichiometric coefficients of the constituent steps are equal to unity and the most abundant adsorbed species are in quasi-equilibrium with the gas phase and can be used in an approximate manner to probe the performance of more general reaction schemes, followed by more detailed analyses using full microkinetic models to determine the surface coverages by adsorbed species and the degrees of rate control of the elementary steps. PMID:27162366

Temperature Dependence of the Rate Constant for the CH3 Recombination Reaction: A Loss Process in Outer Planet Atmospheres

NASA Technical Reports Server (NTRS)

Cody, R. J.; Payne, W. A.; Thorn, R. P., Jr.; Romani, P. N.; Stief, L. J.; Nesbitt, F. L.; Iannone, M. A.; Tardy, D. C.

2002-01-01

The methyl free radical (CH3) has been observed in the atmospheres of Saturn and Neptune by the ISO satellite. There are discrepancies between the column densities for the CH3 radical derived from the ISO observations and the column densities derived from atmospheric photochemical models. For Neptune the model column density is 1.5 times that derived from ISO. For Saturn the model is 6 times that from ISO. The recombination of methyl radicals is the major loss process for methyl in these atmospheres. The serious disagreement between observed and calculated levels of CH3 has led to suggestions that the atmospheric models greatly underestimated the loss of CH3 due to poor knowledge of the rate of the reaction (1) CH3 + CH3 + M goes to C2H6 + M at the low temperatures and pressures of these atmospheric systems. Although the reaction CH3 + CH3 + M goes to C2H6 + M has been extensively studied both theoretically and experimentally, the laboratory conditions have been, with only a few exceptions, higher temperatures (T greater than 298K), higher pressures (P greater than or equal to 10 Torr - 13.3 mbar) or M=Ar rather than H2 or He as the bath gas.

Rates and equilibrium constants of the ligand-induced conformational transition of an HCN ion channel protein domain determined by DEER spectroscopy.

PubMed

Collauto, Alberto; DeBerg, Hannah A; Kaufmann, Royi; Zagotta, William N; Stoll, Stefan; Goldfarb, Daniella

2017-06-14

Ligand binding can induce significant conformational changes in proteins. The mechanism of this process couples equilibria associated with the ligand binding event and the conformational change. Here we show that by combining the application of W-band double electron-electron resonance (DEER) spectroscopy with microfluidic rapid freeze quench (μRFQ) it is possible to resolve these processes and obtain both equilibrium constants and reaction rates. We studied the conformational transition of the nitroxide labeled, isolated carboxy-terminal cyclic-nucleotide binding domain (CNBD) of the HCN2 ion channel upon binding of the ligand 3',5'-cyclic adenosine monophosphate (cAMP). Using model-based global analysis, the time-resolved data of the μRFQ DEER experiments directly provide fractional populations of the open and closed conformations as a function of time. We modeled the ligand-induced conformational change in the protein using a four-state model: apo/open (AO), apo/closed (AC), bound/open (BO), bound/closed (BC). These species interconvert according to AC + L ⇌ AO + L ⇌ BO ⇌ BC. By analyzing the concentration dependence of the relative contributions of the closed and open conformations at equilibrium, we estimated the equilibrium constants for the two conformational equilibria and the open-state ligand dissociation constant. Analysis of the time-resolved μRFQ DEER data gave estimates for the intrinsic rates of ligand binding and unbinding as well as the rates of the conformational change. This demonstrates that DEER can quantitatively resolve both the thermodynamics and the kinetics of ligand binding and the associated conformational change.

A Study of Interactions between Mixing and Chemical Reaction Using the Rate-Controlled Constrained-Equilibrium Method

NASA Astrophysics Data System (ADS)

Hadi, Fatemeh; Janbozorgi, Mohammad; Sheikhi, M. Reza H.; Metghalchi, Hameed

2016-10-01

The rate-controlled constrained-equilibrium (RCCE) method is employed to study the interactions between mixing and chemical reaction. Considering that mixing can influence the RCCE state, the key objective is to assess the accuracy and numerical performance of the method in simulations involving both reaction and mixing. The RCCE formulation includes rate equations for constraint potentials, density and temperature, which allows taking account of mixing alongside chemical reaction without splitting. The RCCE is a dimension reduction method for chemical kinetics based on thermodynamics laws. It describes the time evolution of reacting systems using a series of constrained-equilibrium states determined by RCCE constraints. The full chemical composition at each state is obtained by maximizing the entropy subject to the instantaneous values of the constraints. The RCCE is applied to a spatially homogeneous constant pressure partially stirred reactor (PaSR) involving methane combustion in oxygen. Simulations are carried out over a wide range of initial temperatures and equivalence ratios. The chemical kinetics, comprised of 29 species and 133 reaction steps, is represented by 12 RCCE constraints. The RCCE predictions are compared with those obtained by direct integration of the same kinetics, termed detailed kinetics model (DKM). The RCCE shows accurate prediction of combustion in PaSR with different mixing intensities. The method also demonstrates reduced numerical stiffness and overall computational cost compared to DKM.

Annealed importance sampling with constant cooling rate

NASA Astrophysics Data System (ADS)

Giovannelli, Edoardo; Cardini, Gianni; Gellini, Cristina; Pietraperzia, Giangaetano; Chelli, Riccardo

2015-02-01

Annealed importance sampling is a simulation method devised by Neal [Stat. Comput. 11, 125 (2001)] to assign weights to configurations generated by simulated annealing trajectories. In particular, the equilibrium average of a generic physical quantity can be computed by a weighted average exploiting weights and estimates of this quantity associated to the final configurations of the annealed trajectories. Here, we review annealed importance sampling from the perspective of nonequilibrium path-ensemble averages [G. E. Crooks, Phys. Rev. E 61, 2361 (2000)]. The equivalence of Neal's and Crooks' treatments highlights the generality of the method, which goes beyond the mere thermal-based protocols. Furthermore, we show that a temperature schedule based on a constant cooling rate outperforms stepwise cooling schedules and that, for a given elapsed computer time, performances of annealed importance sampling are, in general, improved by increasing the number of intermediate temperatures.

Astrophysical Nuclear Reaction Rates in the Dense Metallic Environments

NASA Astrophysics Data System (ADS)

Kilic, Ali Ihsan

2017-09-01

Nuclear reaction rates can be enhanced by many orders of magnitude in dense and relatively cold astrophysical plasmas such as in white dwarfs, brown dwarfs, and giant planets. Similar conditions are also present in supernova explosions where the ignition conditions are vital for cosmological models. White dwarfs are compact objects that have both extremely high interior densities and very strong local magnetic fields. For the first time, a new formula has been developed to explain cross section and reaction rate quantities for light elements that includes not only the nuclear component but also the material dependence, magnetic field, and crystal structure dependency in dense metallic environments. I will present the impact of the developed formula on the cross section and reaction rates for light elements. This could have possible technological applications in energy production using nuclear fusion reactions.

Reaction rate for carbon burning in massive stars

NASA Astrophysics Data System (ADS)

Jiang, C. L.; Santiago-Gonzalez, D.; Almaraz-Calderon, S.; Rehm, K. E.; Back, B. B.; Auranen, K.; Avila, M. L.; Ayangeakaa, A. D.; Bottoni, S.; Carpenter, M. P.; Dickerson, C.; DiGiovine, B.; Greene, J. P.; Hoffman, C. R.; Janssens, R. V. F.; Kay, B. P.; Kuvin, S. A.; Lauritsen, T.; Pardo, R. C.; Sethi, J.; Seweryniak, D.; Talwar, R.; Ugalde, C.; Zhu, S.; Bourgin, D.; Courtin, S.; Haas, F.; Heine, M.; Fruet, G.; Montanari, D.; Jenkins, D. G.; Morris, L.; Lefebvre-Schuhl, A.; Alcorta, M.; Fang, X.; Tang, X. D.; Bucher, B.; Deibel, C. M.; Marley, S. T.

2018-01-01

Carbon burning is a critical phase for nucleosynthesis in massive stars. The conditions for igniting this burning stage, and the subsequent isotope composition of the resulting ashes, depend strongly on the reaction rate for 12C+12C fusion at very low energies. Results for the cross sections for this reaction are influenced by various backgrounds encountered in measurements at such energies. In this paper, we report on a new measurement of 12C+12C fusion cross sections where these backgrounds have been minimized. It is found that the astrophysical S factor exhibits a maximum around Ecm=3.5 -4.0 MeV, which leads to a reduction of the previously predicted astrophysical reaction rate.

Analysis of reaction schemes using maximum rates of constituent steps

DOE PAGES

Motagamwala, Ali Hussain; Dumesic, James A.

2016-05-09

In this paper, we show that the steady-state kinetics of a chemical reaction can be analyzed analytically in terms of proposed reaction schemes composed of series of steps with stoichiometric numbers equal to unity by calculating the maximum rates of the constituent steps, r max,i, assuming that all of the remaining steps are quasi-equilibrated. Analytical expressions can be derived in terms of r max,i to calculate degrees of rate control for each step to determine the extent to which each step controls the rate of the overall stoichiometric reaction. The values of r max,i can be used to predict themore » rate of the overall stoichiometric reaction, making it possible to estimate the observed reaction kinetics. This approach can be used for catalytic reactions to identify transition states and adsorbed species that are important in controlling catalyst performance, such that detailed calculations using electronic structure calculations (e.g., density functional theory) can be carried out for these species, whereas more approximate methods (e.g., scaling relations) are used for the remaining species. Finally, this approach to assess the feasibility of proposed reaction schemes is exact for reaction schemes where the stoichiometric coefficients of the constituent steps are equal to unity and the most abundant adsorbed species are in quasi-equilibrium with the gas phase and can be used in an approximate manner to probe the performance of more general reaction schemes, followed by more detailed analyses using full microkinetic models to determine the surface coverages by adsorbed species and the degrees of rate control of the elementary steps.« less

Does phenomenological kinetics provide an adequate description of heterogeneous catalytic reactions?

PubMed

Temel, Burcin; Meskine, Hakim; Reuter, Karsten; Scheffler, Matthias; Metiu, Horia

2007-05-28

Phenomenological kinetics (PK) is widely used in the study of the reaction rates in heterogeneous catalysis, and it is an important aid in reactor design. PK makes simplifying assumptions: It neglects the role of fluctuations, assumes that there is no correlation between the locations of the reactants on the surface, and considers the reacting mixture to be an ideal solution. In this article we test to what extent these assumptions damage the theory. In practice the PK rate equations are used by adjusting the rate constants to fit the results of the experiments. However, there are numerous examples where a mechanism fitted the data and was shown later to be erroneous or where two mutually exclusive mechanisms fitted well the same set of data. Because of this, we compare the PK equations to "computer experiments" that use kinetic Monte Carlo (kMC) simulations. Unlike in real experiments, in kMC the structure of the surface, the reaction mechanism, and the rate constants are known. Therefore, any discrepancy between PK and kMC must be attributed to an intrinsic failure of PK. We find that the results obtained by solving the PK equations and those obtained from kMC, while using the same rate constants and the same reactions, do not agree. Moreover, when we vary the rate constants in the PK model to fit the turnover frequencies produced by kMC, we find that the fit is not adequate and that the rate constants that give the best fit are very different from the rate constants used in kMC. The discrepancy between PK and kMC for the model of CO oxidation used here is surprising since the kMC model contains no lateral interactions that would make the coverage of the reactants spatially inhomogeneous. Nevertheless, such inhomogeneities are created by the interplay between the rate of adsorption, of desorption, and of vacancy creation by the chemical reactions.

The role of reaction affinity and secondary minerals in regulating chemical weathering rates at the Santa Cruz Soil Chronosequence, California

USGS Publications Warehouse

Maher, K.; Steefel, Carl; White, A.F.; Stonestrom, David A.

2009-01-01

In order to explore the reasons for the apparent discrepancy between laboratory and field weathering rates and to determine the extent to which weathering rates are controlled by the approach to thermodynamic equilibrium, secondary mineral precipitation, and flow rates, a multicomponent reactive transport model (CrunchFlow) was used to interpret soil profile development and mineral precipitation and dissolution rates at the 226 ka Marine Terrace Chronosequence near Santa Cruz, CA. Aqueous compositions, fluid chemistry, transport, and mineral abundances are well characterized [White A. F., Schulz M. S., Vivit D. V., Blum A., Stonestrom D. A. and Anderson S. P. (2008) Chemical weathering of a Marine Terrace Chronosequence, Santa Cruz, California. I: interpreting the long-term controls on chemical weathering based on spatial and temporal element and mineral distributions. Geochim. Cosmochim. Acta 72 (1), 36-68] and were used to constrain the reaction rates for the weathering and precipitating minerals in the reactive transport modeling. When primary mineral weathering rates are calculated with either of two experimentally determined rate constants, the nonlinear, parallel rate law formulation of Hellmann and Tisserand [Hellmann R. and Tisserand D. (2006) Dissolution kinetics as a function of the Gibbs free energy of reaction: An experimental study based on albite feldspar. Geochim. Cosmochim. Acta 70 (2), 364-383] or the aluminum inhibition model proposed by Oelkers et al. [Oelkers E. H., Schott J. and Devidal J. L. (1994) The effect of aluminum, pH, and chemical affinity on the rates of aluminosilicate dissolution reactions. Geochim. Cosmochim. Acta 58 (9), 2011-2024], modeling results are consistent with field-scale observations when independently constrained clay precipitation rates are accounted for. Experimental and field rates, therefore, can be reconciled at the Santa Cruz site. Additionally, observed maximum clay abundances in the argillic horizons occur at

Modeling crystal growth from solution with molecular dynamics simulations: approaches to transition rate constants.

PubMed

Reilly, Anthony M; Briesen, Heiko

2012-01-21

The feasibility of using the molecular dynamics (MD) simulation technique to study crystal growth from solution quantitatively, as well as to obtain transition rate constants, has been studied. The dynamics of an interface between a solution of Lennard-Jones particles and the (100) face of an fcc lattice comprised of solute particles have been studied using MD simulations, showing that MD is, in principle, capable of following growth behavior over large supersaturation and temperature ranges. Using transition state theory, and a nearest-neighbor approximation growth and dissolution rate constants have been extracted from equilibrium MD simulations at a variety of temperatures. The temperature dependence of the rates agrees well with the expected transition state theory behavior. © 2012 American Institute of Physics

Characterization of shock-dependent reaction rates in an aluminum/perfluoropolyether pyrolant

NASA Astrophysics Data System (ADS)

Wilson, Dennis; Granier, John; Johnson, Richard; Littrell, Donald

2017-01-01

Energetic formulations of perfluoropolyether (PFPE) and aluminum are highly non-ideal. They release energy via a fast self-oxidized combustion wave rather than a true self-sustaining detonation. Unlike high explosives, the reactions are shock dependent and can be overdriven to control energy release rate. Reaction rate experiments show that the velocity can vary from 1.25 to 3 km/s. This paper examines the effect of the initial shock conditions upon the reaction rate of the explosive. The following conditions were varied in a series of reaction rate experiments: the high explosive booster mass and geometry; shock attenuation; confinement; and rate stick diameter and length. Several experiments designed to isolate and quantify these dependencies are described and summarized.

ESTIMATION OF PHOSPHATE ESTER HYDROLYSIS RATE CONSTANTS. II. ACID AND GENERAL BASE CATALYZED HYDROLYSIS

EPA Science Inventory

SPARC (SPARC Performs Automated Reasoning in Chemistry) chemical reactivity models were extended to calculate acid and neutral hydrolysis rate constants of phosphate esters in water. The rate is calculated from the energy difference between the initial and transition states of a ...

Isoprene/methyl acrylate Diels-Alder reaction in supercritical carbon dioxide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, B.; Akgerman, A.

1999-12-01

The Diels-Alder reaction between isoprene and methyl acrylate was carried out in supercritical carbon dioxide in the temperature range 110--140 C and the pressure range 95.2--176.9 atm in a 300 cm{sup 3} autoclave. The high-pressure phase behavior of the reaction mixture in the vicinity of its critical region was determined in a mixed vessel with a sight window to ensure that all the experiments were performed in the supercritical single-phase region. Kinetic data were obtained at different temperatures, pressures, and reaction times. It was observed that in the vicinity of the critical point the reaction rate constant decreases with increasingmore » pressure. It was also determined that the reaction selectivity does not change with operating conditions. Transition-state theory was used to explain the effect of pressure on reaction rate and product selectivity. Additional experiments were conducted at constant temperature but different phase behaviors (two-phase region, liquid phase, supercritical phase) by adjusting the initial composition and pressure. It was shown that the highest reaction rate is in the supercritical region.« less

Reaction rate for carbon burning in massive stars

DOE PAGES

Jiang, C. L.; Santiago-Gonzalez, D.; Almaraz-Calderon, S.; ...

2018-01-10

Carbon burning is a critical phase for nucleosynthesis in massive stars. The conditions for igniting this burning stage, and the subsequent isotope composition of the resulting ashes, depend strongly on the reaction rate for 12C+ 12C fusion at very low energies. Results for the cross sections for this reaction are influenced by various backgrounds encountered in measurements at such energies. In this paper, we report on a new measurement of 12C+ 12C fusion cross sections where these backgrounds have been minimized. In conclusion, it is found that the astrophysical S factor exhibits a maximum around E cm=3.5–4.0 MeV, which leadsmore » to a reduction of the previously predicted astrophysical reaction rate.« less

Unsteady flow past an airfoil pitched at constant rate

NASA Technical Reports Server (NTRS)

Lourenco, L.; Vandommelen, L.; Shib, C.; Krothapalli, A.

1992-01-01

The unsteady flow past a NACA 0012 airfoil that is undertaking a constant-rate pitching up motion is investigated experimentally by the PIDV technique in a water towing tank. The Reynolds number is 5000, based upon the airfoil's chord and the free-stream velocity. The airfoil is pitching impulsively from 0 to 30 deg. with a dimensionless pitch rate alpha of 0.131. Instantaneous velocity and associated vorticity data have been acquired over the entire flow field. The primary vortex dominates the flow behavior after it separates from the leading edge of the airfoil. Complete stall emerges after this vortex detaches from the airfoil and triggers the shedding of a counter-rotating vortex near the trailing edge. A parallel computational study using the discrete vortex, random walk approximation has also been conducted. In general, the computational results agree very well with the experiment.

Microfabricated microengine with constant rotation rate

DOEpatents

Romero, Louis A.; Dickey, Fred M.

1999-01-01

A microengine uses two synchronized linear actuators as a power source and converts oscillatory motion from the actuators into constant rotational motion via direct linkage connection to an output gear or wheel. The microengine provides output in the form of a continuously rotating output gear that is capable of delivering drive torque at a constant rotation to a micromechanism. The output gear can have gear teeth on its outer perimeter for directly contacting a micromechanism requiring mechanical power. The gear is retained by a retaining means which allows said gear to rotate freely. The microengine is microfabricated of polysilicon on one wafer using surface micromachining batch fabrication.

The Elementary Mass Action Rate Constants of P-gp Transport for a Confluent Monolayer of MDCKII-hMDR1 Cells

PubMed Central

Tran, Thuy Thanh; Mittal, Aditya; Aldinger, Tanya; Polli, Joseph W.; Ayrton, Andrew; Ellens, Harma; Bentz, Joe

2005-01-01

The human multi-drug resistance membrane transporter, P-glycoprotein, or P-gp, has been extensively studied due to its importance to human health and disease. Thus far, the kinetic analysis of P-gp transport has been limited to steady-state Michaelis-Menten approaches or to compartmental models, neither of which can prove molecular mechanisms. Determination of the elementary kinetic rate constants of transport will be essential to understanding how P-gp works. The experimental system we use is a confluent monolayer of MDCKII-hMDR1 cells that overexpress P-gp. It is a physiologically relevant model system, and transport is measured without biochemical manipulations of P-gp. The Michaelis-Menten mass action reaction is used to model P-gp transport. Without imposing the steady-state assumptions, this reaction depends upon several parameters that must be simultaneously fitted. An exhaustive fitting of transport data to find all possible parameter vectors that best fit the data was accomplished with a reasonable computation time using a hierarchical algorithm. For three P-gp substrates (amprenavir, loperamide, and quinidine), we have successfully fitted the elementary rate constants, i.e., drug association to P-gp from the apical membrane inner monolayer, drug dissociation back into the apical membrane inner monolayer, and drug efflux from P-gp into the apical chamber, as well as the density of efflux active P-gp. All three drugs had overlapping ranges for the efflux active P-gp, which was a benchmark for the validity of the fitting process. One novel finding was that the association to P-gp appears to be rate-limited solely by drug lateral diffusion within the inner monolayer of the plasma membrane for all three drugs. This would be expected if P-gp structure were open to the lipids of the apical membrane inner monolayer, as has been suggested by recent structural studies. The fitted kinetic parameters show how P-gp efflux of a wide range of xenobiotics has been

Reactions and reaction rates in the regional aquifer beneath the Pajarito Plateau, north-central New Mexico, USA

NASA Astrophysics Data System (ADS)

Hereford, Anne G.; Keating, Elizabeth H.; Guthrie, George D.; Zhu, Chen

2007-05-01

Reactions and reaction rates within aquifers are fundamental components of critical hydrological processes. However, reactions simulated in laboratory experiments typically demonstrate rates that are much faster than those observed in the field. Therefore, it is necessary to conduct more reaction rate analyses in natural settings. This study of geochemical reactions in the regional aquifer in the Pajarito Plateau near Los Alamos, New Mexico combines modeling with petrographic assessment to further knowledge and understanding of complex natural hydrologic systems. Groundwater geochemistry shows marked evolution along assumed flow paths. The flow path chosen for this study was evaluated using inverse mass balance modeling to calculate the mass transfer. X-ray diffraction and field emission gun scanning electron microscopy were used to identify possible reactants and products. Considering the mineralogy of the aquifer and saturation indices for the regional water refined initial interpretations. Calculations yielded dissolution rates for plagioclase on the order of 10-15 mol s-1 m-2 and for K-feldspar on the order of 10-17 mol s-1 m-2, orders of magnitude slower than laboratory rates. While these rates agree with other aquifer studies, they must be considered in the light of the uncertainty associated with geometric surface area estimates, 14C ages, and aquifer properties.

Determination of the Rate Coefficients of the SO2 plus O plus M yields SO3 plus M Reaction

NASA Technical Reports Server (NTRS)

Hwang, S. M.; Cooke, J. A.; De Witt, K. J.; Rabinowitz, M. J.

2010-01-01

Rate coefficients of the title reaction R(sub 31) (SO2 +O+M yields SO3 +M) and R(sub 56) (SO2 + HO2 yields SO3 +OH), important in the conversion of S(IV) to S(VI),were obtained at T =970-1150 K and rho (sub ave) = 16.2 micro mol/cubic cm behind reflected shock waves by a perturbation method. Shock-heated H2/ O2/Ar mixtures were perturbed by adding small amounts of SO2 (1%, 2%, and 3%) and the OH temporal profiles were then measured using laser absorption spectroscopy. Reaction rate coefficients were elucidated by matching the characteristic reaction times acquired from the individual experimental absorption profiles via simultaneous optimization of k(sub 31) and k(sub 56) values in the reaction modeling (for satisfactory matches to the observed characteristic times, it was necessary to take into account R(sub 56)). In the experimental conditions of this study, R(sub 31) is in the low-pressure limit. The rate coefficient expressions fitted using the combined data of this study and the previous experimental results are k(sub 31,0)/[Ar] = 2.9 10(exp 35) T(exp ?6.0) exp(?4780 K/T ) + 6.1 10(exp 24) T(exp ?3.0) exp(?1980 K/T ) cm(sup 6) mol(exp ?2)/ s at T = 300-2500 K; k(sub 56) = 1.36 10(exp 11) exp(?3420 K/T ) cm(exp 3)/mol/s at T = 970-1150 K. Computer simulations of typical aircraft engine environments, using the reaction mechanism with the above k(sub 31,0) and k(sub 56) expressions, gave the maximum S(IV) to S(VI) conversion yield of ca. 3.5% and 2.5% for the constant density and constant pressure flow condition, respectively. Moreover, maximum conversions occur at rather higher temperatures (?1200 K) than that where the maximum k(sub 31,0) value is located (approximately 800 K). This is because the conversion yield is dependent upon not only the k(sup 31,0) and k(sup 56) values (production flux) but also the availability of H, O, and HO2 in the system (consumption flux).

Anomalous diffusion with linear reaction dynamics: from continuous time random walks to fractional reaction-diffusion equations.

PubMed

Henry, B I; Langlands, T A M; Wearne, S L

2006-09-01

We have revisited the problem of anomalously diffusing species, modeled at the mesoscopic level using continuous time random walks, to include linear reaction dynamics. If a constant proportion of walkers are added or removed instantaneously at the start of each step then the long time asymptotic limit yields a fractional reaction-diffusion equation with a fractional order temporal derivative operating on both the standard diffusion term and a linear reaction kinetics term. If the walkers are added or removed at a constant per capita rate during the waiting time between steps then the long time asymptotic limit has a standard linear reaction kinetics term but a fractional order temporal derivative operating on a nonstandard diffusion term. Results from the above two models are compared with a phenomenological model with standard linear reaction kinetics and a fractional order temporal derivative operating on a standard diffusion term. We have also developed further extensions of the CTRW model to include more general reaction dynamics.

Control of serpentinisation rate by reaction-induced cracking

NASA Astrophysics Data System (ADS)

Malvoisin, Benjamin; Brantut, Nicolas; Kaczmarek, Mary-Alix

2017-10-01

Serpentinisation of mantle rocks requires the generation and maintenance of transport pathways for water. The solid volume increase during serpentinisation can lead to stress build-up and trigger cracking, which ease fluid penetration into the rock. The quantitative effect of this reaction-induced cracking mechanism on reactive surface generation is poorly constrained, thus hampering our ability to predict serpentinisation rate in geological environments. Here we use a combined approach with numerical modelling and observations in natural samples to provide estimates of serpentinisation rate at mid-ocean ridges. We develop a micromechanical model to quantify the propagation of serpentinisation-induced cracks in olivine. The maximum crystallisation pressure deduced from thermodynamic calculations reaches several hundreds of megapascals but does not necessary lead to crack propagation if the olivine grain is subjected to high compressive stresses. The micromechanical model is then coupled to a simple geometrical model to predict reactive surface area formation during grain splitting, and thus bulk reaction rate. Our model reproduces quantitatively experimental kinetic data and the typical mesh texture formed during serpentinisation. We also compare the model results with olivine grain size distribution data obtained on natural serpentinised peridotites from the Marum ophiolite and the Papuan ultramafic belt (Papua New Guinea). The natural serpentinised peridotites show an increase of the number of olivine grains for a decrease of the mean grain size by one order of magnitude as reaction progresses from 5 to 40%. These results are in agreement with our model predictions, suggesting that reaction-induced cracking controls the serpentinisation rate. We use our model to estimate that, at mid-ocean ridges, serpentinisation occurs up to 12 km depth and reaction-induced cracking reduces the characteristic time of serpentinisation by one order of magnitude, down to values

Absolute rate constant for the O plus NO chemiluminescence in the near infrared

NASA Technical Reports Server (NTRS)

Golde, M. F.; Roche, A. E.; Kaufman, F.

1973-01-01

Infrared chemiluminescence from the process O + NO (+M) NO2 + hv (+M) has been studied between 1.3 and 4.1 micrometer. The wavelength dependence of the continuum between 1.3 and 3.3 micrometer is in fair agreement with previous studies and the measured radiative rate constant at 1.51 micrometer establishes the NO-O glow in this spectral range as a secondary emission standard. Comparison with previous studies of the visible region of the glow implies that the overall radiative rate constant lies in the range (9.4 to 11.2) x 10 to the minus 17 power cu cm sec/1. In the region 3.3 to 4.1 micrometer, the previously observed broad band, peaking at 3.7 micrometer, shows a complex kinetic dependence on O and M.

The Multicenter Aerobic Iron Respiratory Chain of Acidithiobacillus ferrooxidans Functions as an Ensemble with a Single Macroscopic Rate Constant

DOE PAGES

Li, Ting-Feng; Painter, Richard G.; Ban, Bhupal; ...

2015-06-03

Electron transfer reactions among three prominent colored proteins in intact cells of Acidithiobacillus ferrooxidans were monitored using an integrating cavity absorption meter that permitted the acquisition of accurate absorbance data in suspensions of cells that scattered light. The concentrations of proteins in the periplasmic space were estimated to be 350 and 25 mg/ml for rusticyanin and cytochrome c, respectively; cytochrome a was present as one molecule for every 91 nm2 in the cytoplasmic membrane. All three proteins were rapidly reduced to the same relative extent when suspensions of live bacteria were mixed with different concentrations of ferrous ions at pHmore » 1.5. The subsequent molecular oxygen-dependent oxidation of the multicenter respiratory chain occurred with a single macroscopic rate constant, regardless of the proteins' in vitro redox potentials or their putative positions in the aerobic iron respiratory chain. The crowded electron transport proteins in the periplasm of the organism constituted an electron conductive medium where the network of protein interactions functioned in a concerted fashion as a single ensemble with a standard reduction potential of 650 mV. The appearance of product ferric ions was correlated with the reduction levels of the periplasmic electron transfer proteins; the limiting first-order catalytic rate constant for aerobic respiration on iron was 7,400 s -1. The ability to conduct direct spectrophotometric studies under noninvasive physiological conditions represents a new and powerful approach to examine the extent and rates of biological events in situ without disrupting the complexity of the live cellular environment.« less

Theory and simulation of the time-dependent rate coefficients of diffusion-influenced reactions.

PubMed Central

Zhou, H X; Szabo, A

1996-01-01

A general formalism is developed for calculating the time-dependent rate coefficient k(t) of an irreversible diffusion-influenced reaction. This formalism allows one to treat most factors that affect k(t), including rotational Brownian motion and conformational gating of reactant molecules and orientation constraint for product formation. At long times k(t) is shown to have the asymptotic expansion k(infinity)[1 + k(infinity) (pie Dt)-1/2 /4 pie D + ...], where D is the relative translational diffusion constant. An approximate analytical method for calculating k(t) is presented. This is based on the approximation that the probability density of the reactant pair in the reactive region keeps the equilibrium distribution but with a decreasing amplitude. The rate coefficient then is determined by the Green function in the absence of chemical reaction. Within the framework of this approximation, two general relations are obtained. The first relation allows the rate coefficient for an arbitrary amplitude of the reactivity to be found if the rate coefficient for one amplitude of the reactivity is known. The second relation allows the rate coefficient in the presence of conformational gating to be found from that in the absence of conformational gating. The ratio k(t)/k(0) is shown to be the survival probability of the reactant pair at time t starting from an initial distribution that is localized in the reactive region. This relation forms the basis of the calculation of k(t) through Brownian dynamics simulations. Two simulation procedures involving the propagation of nonreactive trajectories initiated only from the reactive region are described and illustrated on a model system. Both analytical and simulation results demonstrate the accuracy of the equilibrium-distribution approximation method. PMID:8913584

Incorporating reaction-rate dependence in reaction-front models of wellbore-cement/carbonated-brine systems

DOE PAGES

Iyer, Jaisree; Walsh, Stuart D. C.; Hao, Yue; ...

2017-03-08

Contact between wellbore cement and carbonated brine produces reaction zones that alter the cement's chemical composition and its mechanical properties. The reaction zones have profound implications on the ability of wellbore cement to serve as a seal to prevent the flow of carbonated brine. Under certain circumstances, the reactions may cause resealing of leakage pathways within the cement or at cement-interfaces; either due to fracture closure in response to mechanical weakening or due to the precipitation of calcium carbonate within the fracture. In prior work, we showed how mechanical sealing can be simulated using a diffusion-controlled reaction-front model that linksmore » the growth of the cement reaction zones to the mechanical response of the fracture. Here, we describe how such models may be extended to account for the effects of the calcite reaction-rate. We discuss how the relative rates of reaction and diffusion within the cement affect the precipitation of calcium carbonate within narrow leakage pathways, and how such behavior relates to the formation of characteristic reaction modes in the direction of flow. In addition, we compare the relative impact of precipitation and mechanical deformation on fracture sealing for a range of flow conditions and fracture apertures. Here, we conclude by considering how the prior leaching of calcium from cement may influence the sealing behavior of fractures, and the implication of prior leaching on the ability of laboratory tests to predict long-term sealing.« less

Incorporating reaction-rate dependence in reaction-front models of wellbore-cement/carbonated-brine systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Iyer, Jaisree; Walsh, Stuart D. C.; Hao, Yue

Contact between wellbore cement and carbonated brine produces reaction zones that alter the cement's chemical composition and its mechanical properties. The reaction zones have profound implications on the ability of wellbore cement to serve as a seal to prevent the flow of carbonated brine. Under certain circumstances, the reactions may cause resealing of leakage pathways within the cement or at cement-interfaces; either due to fracture closure in response to mechanical weakening or due to the precipitation of calcium carbonate within the fracture. In prior work, we showed how mechanical sealing can be simulated using a diffusion-controlled reaction-front model that linksmore » the growth of the cement reaction zones to the mechanical response of the fracture. Here, we describe how such models may be extended to account for the effects of the calcite reaction-rate. We discuss how the relative rates of reaction and diffusion within the cement affect the precipitation of calcium carbonate within narrow leakage pathways, and how such behavior relates to the formation of characteristic reaction modes in the direction of flow. In addition, we compare the relative impact of precipitation and mechanical deformation on fracture sealing for a range of flow conditions and fracture apertures. Here, we conclude by considering how the prior leaching of calcium from cement may influence the sealing behavior of fractures, and the implication of prior leaching on the ability of laboratory tests to predict long-term sealing.« less

Singlet oxygen reactions with flavonoids. A theoretical-experimental study.

PubMed

Morales, Javier; Günther, Germán; Zanocco, Antonio L; Lemp, Else

2012-01-01

Detection of singlet oxygen emission, λ(max) = 1270 nm, following laser excitation and steady-state methods were employed to measure the total reaction rate constant, k(T), and the reactive reaction rate constant, k(r), for the reaction between singlet oxygen and several flavonoids. Values of k(T) determined in deuterated water, ranging from 2.4×10(7) M(-1) s(-1) to 13.4×10(7) M(-1) s(-1), for rutin and morin, respectively, and the values measured for k(r), ranging from 2.8×10(5) M(-1) s(-1) to 65.7×10(5) M(-1) s(-1) for kaempferol and morin, respectively, being epicatechin and catechin chemically unreactive. These results indicate that all the studied flavonoids are good quenchers of singlet oxygen and could be valuable antioxidants in systems under oxidative stress, in particular if a flavonoid-rich diet was previously consumed. Analysis of the dependence of rate constant values with molecular structure in terms of global descriptors and condensed Fukui functions, resulting from electronic structure calculations, supports the formation of a charge transfer exciplex in all studied reactions. The fraction of exciplex giving reaction products evolves through a hydroperoxide and/or an endoperoxide intermediate produced by singlet oxygen attack on the double bond of the ring C of the flavonoid.

Determination of acidity constants of curcumin in aqueous solution and apparent rate constant of its decomposition

NASA Astrophysics Data System (ADS)

Bernabé-Pineda, Margarita; Ramírez-Silva, María. Teresa; Romero-Romo, Mario; González-Vergara, Enrique; Rojas-Hernández, Alberto

2004-04-01

The stability of curcumin (H 3Cur) in aqueous media is improved when the systems in which it is present are at high pH values (higher than 11.7), fitting a model describable by a pseudo-zero order with a rate constant k' for the disappearance of the Cur 3- species of 1.39 (10 -9) M min -1. There were three acidity constants measured for the curcumin as follows: p KA3=10.51±0.01 corresponding to the equilibrium HCur 2-=Cur 3-+H +, a p KA2=9.88±0.02 corresponding to the equilibrium H 2Cur -=HCur -2+H +. These p KA values were attributed to the hydrogen of the phenol part of the curcumin, while the p KA1=8.38±0.04 corresponds to the equilibrium H 3Cur=H 2Cur -+H + and is attributed the acetylacetone type group. Formation of quinoid structures play an important role in the tautomeric forms of the curcumin in aqueous media, which makes the experimental values differ from the theoretically calculated ones, depending on the conditions adopted in the study.

Toward an understanding of the turbidity measurement of heterocoagulation rate constants of dispersions containing particles of different sizes.

PubMed

Liu, Jie; Xu, Shenghua; Sun, Zhiwei

2007-11-06

Our previous studies have shown that the determination of coagulation rate constants by turbidity measurement becomes impossible for a certain operating wavelength (that is, its blind point) because at this wavelength the change in the turbidity of a dispersion completely loses its response to the coagulation process. Therefore, performing the turbidity measurement in the wavelength range near the blind point should be avoided. In this article, we demonstrate that the turbidity measurement of the rate constant for coagulation of a binary dispersion containing particles of two different sizes (heterocoagulation) presents special difficulties because the blind point shifts with not only particle size but also with the component fraction. Some important aspects of the turbidity measurement for the heterocoagulation rate constant are discussed and experimentally tested. It is emphasized that the T-matrix method can be used to correctly evaluate extinction cross sections of doublets formed during the heterocoagulation process, which is the key data determining the rate constant from the turbidity measurement, and choosing the appropriate operating wavelength and component fraction are important to achieving a more accurate rate constant. Finally, a simple scheme in experimentally determining the sensitivity of the turbidity changes with coagulation over a wavelength range is proposed.

Influence of reaction-induced fracturing on serpentinisation rate

NASA Astrophysics Data System (ADS)

Malvoisin, B.; Brantut, N.; Kaczmarek, M. A.

2017-12-01

The alteration of mantle rocks at mid-ocean ridges (i.e. serpentinisation) can lead to a solid volume increase responsible for stress build-up and cracking during reaction (reaction-induced fracturing). This mechanism has been proposed to play a key role for maintaining fluid pathways during reaction. However, its impact on the reaction rate is not yet quantified. We propose here a micromechanical model to quantify the influence of the crystallisation pressure generated during serpentine precipitation on crack propagation in olivine. This model is then coupled to a simple geometrical model to calculate the generation of reactive surface area during grain splitting, and thus bulk reaction rate. The model is able to reproduce experimental kinetic data as well as the mesh texture observed in natural samples. The model results are compared to olivine grain size distribution in serpentinised peridotites from the Marum ophiolite and the Papuan ultramafic belt (Papuan New Guinea). The observations and the model both indicate a decrease of the mean grain size by one order of magnitude as the reaction progresses from 5 to 40 %. Based on this good agreement, we use our model to predict that cracking reduces the characteristic time of serpentinisation by one order of magnitude, down to values comprised between 10 and 1,000 yr. The peak serpentinisation is also shifted 4 km above the previous predictions due to effective pressure increase with depth.

Influence of a reaction medium on the oxidation of aromatic nitrogen-containing compounds by peroxyacids

NASA Astrophysics Data System (ADS)

Dutka, V. S.; Matsyuk, N. V.; Dutka, Yu. V.

2011-01-01

The influence of different solvents on the oxidation reaction rate of pyridine (Py), quinoline (QN), acridine (AN), α-oxyquinoline (OQN) and α-picolinic acid (APA) by peroxydecanoic acid (PDA) was studied. It was found that the oxidation rate grows in the series Py < QN < AN, and the rate of the oxidation reaction of compounds containing a substituent in the α position from a reactive center is significantly lower than for unsubstituted analogues. The effective energies of activation of the oxidation reaction were found. It was shown that in the first stage, the reaction mechanism includes the rapid formation of an intermediate complex nitrogen-containing compound, peroxyacid, which forms products upon decomposing in the second stage. A kinetic equation that describes the studied process is offered. The constants of equilibrium of the intermediate complex formation ( K eq) and its decomposition constant ( k 2) in acetone and benzene were calculated. It was shown that the nature of the solvent influences the numerical values of both K p and k 2. It was established that introduction of acetic acid (which is able to form compounds with Py) into the reaction medium slows the rate of the oxidation process drastically. Correlation equations linking the polarity, polarizability, electrophilicity, and basicity of solvents with the constant of the PDA oxidation reaction rate for Py were found. It was concluded that the basicity and polarity of the solvent have a decisive influence on the oxidation reaction rate, while the polarizability and electrophilicity of the reaction medium do not influence the oxidation reaction rate.

Prediction of Rate Constant for Supramolecular Systems with Multiconfigurations.

PubMed

Guo, Tao; Li, Haiyan; Wu, Li; Guo, Zhen; Yin, Xianzhen; Wang, Caifen; Sun, Lixin; Shao, Qun; Gu, Jingkai; York, Peter; Zhang, Jiwen

2016-02-25

The control of supramolecular systems requires a thorough understanding of their dynamics, especially on a molecular level. It is extremely difficult to determine the thermokinetic parameters of supramolecular systems, such as drug-cyclodextrin complexes with fast association/dissociation processes by experimental techniques. In this paper, molecular modeling combined with novel mathematical relationships integrating the thermodynamic/thermokinetic parameters of a series of isomeric multiconfigurations to predict the overall parameters in a range of pH values have been employed to study supramolecular dynamics at the molecular level. A suitable form of Eyring's equation was derived and a two-stage model was introduced. The new approach enabled accurate prediction of the apparent dissociation/association (k(off)/k(on)) and unbinding/binding (k-r/kr) rate constants of the ubiquitous multiconfiguration complexes of the supramolecular system. The pyronine Y (PY) was used as a model system for the validation of the presented method. Interestingly, the predicted k(off) value ((40 ± 1) × 10(5) s(-1), 298 K) of PY is largely in agreement with that previously determined by fluorescence correlation spectroscopy ((5 ± 3) × 10(5) s(-1), 298 K). Moreover, the k(off)/k(on) and k-r/kr for flurbiprofen-β-cylcodextrin and ibuprofen-β-cyclodextrin systems were also predicted and suggested that the association processes are diffusion-controlled. The methodology is considered to be especially useful in the design and selection of excipients for a supramolecular system with preferred association and dissociation rate constants and understanding their mechanisms. It is believed that this new approach could be applicable to a wide range of ligand-receptor supramolecular systems and will surely help in understanding their complex mechanism.

Scalar dissipation rates in non-conservative transport systems

PubMed Central

Engdahl, Nicholas B.; Ginn, Timothy R.; Fogg, Graham E.

2014-01-01

This work considers how the inferred mixing state of diffusive and advective-diffusive systems will vary over time when the solute masses are not constant over time. We develop a number of tools that allow the scalar dissipation rate to be used as a mixing measure in these systems without calculating local concentration gradients. The behavior of dissipation rates are investigated for single and multi-component kinetic reactions and a commonly studied equilibrium reaction. The scalar dissipation rate of a tracer experiencing first order decay can be determined exactly from the decay constant and the dissipation rate of a passive tracer, and the mixing rate of a conservative component is not the superposition of the solute specific mixing rates. We then show how the behavior of the scalar dissipation rate can be determined from a limited subset of an infinite domain. Corrections are derived for constant and time dependent limits of integration the latter is used to approximate dissipation rates in advective-diffusive systems. Several of the corrections exhibit similarities to the previous work on mixing, including non-Fickian mixing. This illustrates the importance of accounting for the effects that reaction systems or limited monitoring areas may have on the inferred mixing state. PMID:23584457

DEPENDENCE OF X-RAY BURST MODELS ON NUCLEAR REACTION RATES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cyburt, R. H.; Keek, L.; Schatz, H.

2016-10-20

X-ray bursts are thermonuclear flashes on the surface of accreting neutron stars, and reliable burst models are needed to interpret observations in terms of properties of the neutron star and the binary system. We investigate the dependence of X-ray burst models on uncertainties in (p, γ ), ( α , γ ), and ( α , p) nuclear reaction rates using fully self-consistent burst models that account for the feedbacks between changes in nuclear energy generation and changes in astrophysical conditions. A two-step approach first identified sensitive nuclear reaction rates in a single-zone model with ignition conditions chosen to matchmore » calculations with a state-of-the-art 1D multi-zone model based on the Kepler stellar evolution code. All relevant reaction rates on neutron-deficient isotopes up to mass 106 were individually varied by a factor of 100 up and down. Calculations of the 84 changes in reaction rate with the highest impact were then repeated in the 1D multi-zone model. We find a number of uncertain reaction rates that affect predictions of light curves and burst ashes significantly. The results provide insights into the nuclear processes that shape observables from X-ray bursts, and guidance for future nuclear physics work to reduce nuclear uncertainties in X-ray burst models.« less

Biotransformation of trace organic chemicals during groundwater recharge: How useful are first-order rate constants?

PubMed

Regnery, J; Wing, A D; Alidina, M; Drewes, J E

2015-08-01

This study developed relationships between the attenuation of emerging trace organic chemicals (TOrC) during managed aquifer recharge (MAR) as a function of retention time, system characteristics, and operating conditions using controlled laboratory-scale soil column experiments simulating MAR. The results revealed that MAR performance in terms of TOrC attenuation is primarily determined by key environmental parameters (i.e., redox, primary substrate). Soil columns with suboxic and anoxic conditions performed poorly (i.e., less than 30% attenuation of moderately degradable TOrC) in comparison to oxic conditions (on average between 70-100% attenuation for the same compounds) within a residence time of three days. Given this dependency on redox conditions, it was investigated if key parameter-dependent rate constants are more suitable for contaminant transport modeling to properly capture the dynamic TOrC attenuation under field-scale conditions. Laboratory-derived first-order removal kinetics were determined for 19 TOrC under three different redox conditions and rate constants were applied to MAR field data. Our findings suggest that simplified first-order rate constants will most likely not provide any meaningful results if the target compounds exhibit redox dependent biotransformation behavior or if the intention is to exactly capture the decline in concentration over time and distance at field-scale MAR. However, if the intention is to calculate the percent removal after an extended time period and subsurface travel distance, simplified first-order rate constants seem to be sufficient to provide a first estimate on TOrC attenuation during MAR. Copyright © 2015 Elsevier B.V. All rights reserved.

Kinetics of Al + H2O reaction: theoretical study.

PubMed

Sharipov, Alexander; Titova, Nataliya; Starik, Alexander

2011-05-05

Quantum chemical calculations were carried out to study the reaction of Al atom in the ground electronic state with H(2)O molecule. Examination of the potential energy surface revealed that the Al + H(2)O → AlO + H(2) reaction must be treated as a complex process involving two steps: Al + H(2)O → AlOH + H and AlOH + H → AlO + H(2). Activation barriers for these elementary reaction channels were calculated at B3LYP/6-311+G(3df,2p), CBS-QB3, and G3 levels of theory, and appropriate rate constants were estimated by using a canonical variational theory. Theoretical analysis exhibited that the rate constant for the Al + H(2)O → products reaction measured by McClean et al. must be associated with the Al + H(2)O → AlOH + H reaction path only. The process of direct HAlOH formation was found to be negligible at a pressure smaller than 100 atm.

Accurate acceleration of kinetic Monte Carlo simulations through the modification of rate constants.

PubMed

Chatterjee, Abhijit; Voter, Arthur F

2010-05-21

We present a novel computational algorithm called the accelerated superbasin kinetic Monte Carlo (AS-KMC) method that enables a more efficient study of rare-event dynamics than the standard KMC method while maintaining control over the error. In AS-KMC, the rate constants for processes that are observed many times are lowered during the course of a simulation. As a result, rare processes are observed more frequently than in KMC and the time progresses faster. We first derive error estimates for AS-KMC when the rate constants are modified. These error estimates are next employed to develop a procedure for lowering process rates with control over the maximum error. Finally, numerical calculations are performed to demonstrate that the AS-KMC method captures the correct dynamics, while providing significant CPU savings over KMC in most cases. We show that the AS-KMC method can be employed with any KMC model, even when no time scale separation is present (although in such cases no computational speed-up is observed), without requiring the knowledge of various time scales present in the system.

A laser flash photolysis-resonance fluorescence kinetics study of the reaction Cl/2P/ + CH4 yields CH3 + HCl

NASA Technical Reports Server (NTRS)

Ravishankara, A. R.; Wine, P. H.

1980-01-01

The technique of laser flash photolysis-resonance fluorescence is employed to study the kinetics of the reaction Cl(2P) + CH4 yields CH3 + HCl over the temperature range 221-375 K. At temperatures less than or equal to 241 K the apparent bimolecular rate constant is found to be dependent upon the identity of the chemically inert gases in the reaction mixture. For Cl2/CH4/He reaction mixtures (total pressure = 50 torr) different bimolecular rate constants are measured at low and high methane concentrations. For Cl2/CH4/CCl/He and Cl2/CH4/Ar reaction mixtures, the bimolecular rate constant is independent of methane concentration, being approximately equal to the rate constant measured at low methane concentrations for Cl2/CH4/He mixtures. These rate constants are in good agreement with previous results obtained using the discharge flow-resonance fluorescence and competitive chlorination techniques. At 298 K the measured bimolecular rate constant is independent of the identity of the chemically inert gases in the reaction mixture and in good agreement with all previous investigations. The low-temperature results obtained in this investigation and all previous investigations can be rationalized in terms of a model which assumes that the Cl(2P 1/2) state reacts with CH4 much faster than the Cl(2P 3/2) state. Extrapolation of this model to higher temperatures, however, is not straightforward.

Revisiting the Dielectric Constant Effect on the Nucleophile and Leaving Group of Prototypical Backside Sn2 Reactions: a Reaction Force and Atomic Contribution Analysis.

PubMed

Pedraza-González, Laura Milena; Galindo, Johan Fabian; Gonzalez, Ronald; Reyes, Andrés

2016-10-09

The solvent effect on the nucleophile and leaving group atoms of the prototypical F - + CH 3 Cl → CH 3 F + Cl - backside bimolecular nucleophilic substitution reaction (S N 2) is analyzed employing the reaction force and the atomic contributions methods on the intrinsic reaction coordinate (IRC). Solvent effects were accounted for using the polarizable continuum solvent model. Calculations were performed employing eleven dielectric constants, ε, ranging from 1.0 to 78.5, to cover a wide spectrum of solvents. The reaction force data reveals that the solvent mainly influences the region of the IRC preceding the energy barrier, where the structural rearrangement to reach the transition state occurs. A detailed analysis of the atomic role in the reaction as a function of ε reveals that the nucleophile and the carbon atom are the ones that contribute the most to the energy barrier. In addition, we investigated the effect of the choice of nucleophile and leaving group on the ΔE 0 and ΔE ↕ of Y - + CH 3 X → YCH 3 + X - (X,Y= F, Cl, Br, I) in aqueous solution. Our analysis allowed us to find relationships between the atomic contributions to the activation energy and leaving group ability and nucleophilicity.

Acoustic emission of rock mass under the constant-rate fluid injection

NASA Astrophysics Data System (ADS)