Rate constant and transmission coefficient in the diffusion theory of reaction rates

1980 ◽  
Vol 72 (12) ◽  
pp. 6606-6613 ◽  
Author(s):  
Marc Mangel
Keyword(s):  
Transmission Coefficient ◽  
Rate Constant ◽  
Diffusion Theory ◽  
Reaction Rates

Dynamics of biochemical and biophysical reactions: insight from computer simulations

2001 ◽  
Vol 34 (4) ◽  
pp. 563-679 ◽  
Author(s):  
Arieh Warshel ◽  
William W. Parson
Keyword(s):  
Electron Transfer ◽  
Transition State ◽  
Transmission Coefficient ◽  
Enzyme Catalysis ◽  
Experimental Studies ◽  
Reaction Rates ◽  
State Theory ◽  
Enzyme Reactions ◽  
Formidable Challenge ◽  
Nuclear Tunneling

1. Introduction 5632. Obtaining rate constants from molecular-dynamics simulations 5642.1 General relationships between quantum electronic structures and reaction rates 5642.2 The transition-state theory (TST) 5692.3 The transmission coefficient 5723. Simulating biological electron-transfer reactions 5753.1 Semi-classical surface-hopping and the Marcus equation 5753.2 Treating quantum mechanical nuclear tunneling by the dispersed-polaron/spin-boson method 5803.3 Density-matrix treatments 5833.4 Charge separation in photosynthetic bacterial reaction centers 5844. Light-induced photoisomerizations in rhodopsin and bacteriorhodopsin 5965. Energetics and dynamics of enzyme reactions 6145.1 The empirical-valence-bond treatment and free-energy perturbation methods 6145.2 Activation energies are decreased in enzymes relative to solution, often by electrostatic effects that stabilize the transition state 6205.3 Entropic effects in enzyme catalysis 6275.4 What is meant by dynamical contributions to catalysis? 6345.5 Transmission coefficients are similar for corresponding reactions in enzymes and water 6365.6 Non-equilibrium solvation effects contribute to catalysis mainly through Δg[Dagger], not the transmission coefficient 6415.7 Vibrationally assisted nuclear tunneling in enzyme catalysis 6485.8 Diffusive processes in enzyme reactions and transmembrane channels 6516. Concluding remarks 6587. Acknowledgements 6588. References 658Obtaining a detailed understanding of the dynamics of a biochemical reaction is a formidable challenge. Indeed, it might appear at first sight that reactions in proteins are too complex to analyze microscopically. At room temperature, even a relatively small protein can have as many as 1034 accessible conformational states (Dill, 1985). In many cases, however, we have detailed structural information about the active site of an enzyme, whereas such information is missing for corresponding chemical systems in solution. The atomic coordinates of the chromophore in bacteriorhodopsin, for example, are known to a resolution of 1–2 Å. In addition, experimental studies of biological processes such as photoisomerization and electron transfer have provided a wealth of detailed information that eventually may make some of these processes classical problems in chemical physics as well as biology.

Bisulfite Degrades Aflatoxin: Effect of Temperature and Concentration of Bisulfite

1978 ◽  
Vol 41 (10) ◽  
pp. 774-780 ◽  
Author(s):  
M. P. DOYLE ◽  
E. H. MARTH
Keyword(s):  
Rate Constant ◽  
Aflatoxin B1 ◽  
Reaction Rate ◽  
Reaction Rates ◽  
Reaction Rate Constant ◽  
Effect Of Temperature ◽  
Kcal Mole ◽  
First Order ◽  
Potassium Acid Phthalate ◽  
Acid Phthalate

Bisulfite reacted with aflatoxin B1 and G1 resulting in their loss of fluorescence. The reaction was first order with rate depending on bisulfite (or the bisulfite and sulfite) concentration(s). Aflatoxin G1 reacted more rapidly with bisulfite than did aflatoxin B1. In the presence of 0.035 M potassium acid phthalate-NaOH buffer (pH 5.5) plus 1.3% (vol/vol) methanol at 25 C, the reaction rate constant for degradation of aflatoxin G1 was 2.23 × 10−2h− and that for aflatoxin B1 was 1.87 × 10−2h− when 50 ml of reaction mixture contained 1.60 g of K2SO3. Besides bisulfite concentrations, temperature influenced reaction rates. The Q10 for the bisulfite-aflatoxin reaction was approximately 2 while activation energies for degrading aflatoxin B1 and aflatoxin G1 were 13.1 and 12.6 kcal/mole, respectively. Data suggest that treating foods with 50 to 500 ppm SO2 probably would not effectively degrade appreciable amounts of aflatoxin. Treating foods with 2000 ppm SO2 or more and increasing the temperature might reduce aflatoxin to an acceptable level.

scholarly journals Impacts of electronically photo-excited NO<sub>2</sub> on air pollution in the South Coast Air Basin of California

2010 ◽  
Vol 10 (3) ◽  
pp. 1171-1181 ◽  
Author(s):  
J. J. Ensberg ◽  
M. Carreras-Sospedra ◽  
D. Dabdub
Keyword(s):  
Particulate Matter ◽  
Rate Constant ◽  
Reaction Rate ◽  
Control Strategies ◽  
Reaction Rates ◽  
Reaction Rate Constant ◽  
South Coast ◽  
Nox Emissions ◽  
The South ◽  
South Coast Air Basin

Abstract. A new path for hydroxyl radical formation via photo-excitation of nitrogen dioxide (NO2) and the reaction of photo-excited NO2 with water is evaluated using the UCI-CIT model for the South Coast Air Basin of California (SoCAB). Two separate studies predict different reaction rates, which differ by nearly an order of magnitude, for the reaction of photo-excited NO2 with water. Impacts of this new chemical mechanism on ozone and particulate matter formation, while utilizing both reaction rates, are quantified by simulating two summer episodes. First, sensitivity simulations are conducted to evaluate the uncertainty in the rate of reaction of photo-excited NO2 with water reported in the literature. Results indicate that the addition of photo-excited NO2 chemistry increases peak 8-h average ozone and particulate matter concentrations. The importance of this new chemistry is then evaluated in the context of pollution control strategies. A series of simulations are conducted to generate isopleths for ozone and particulate matter concentrations, varying baseline nitrogen oxides (NOx) and volatile organic compounds (VOC) emissions. Isopleths are obtained using 1987 emissions, to represent past conditions, and 2005, to represent current conditions in the SoCAB. Results show that the sensitivity of modeled pollutant control strategies due to photoexcitation decreases with the decrease in baseline emissions from 1987 to 2005. Results show that including NO2 photo-excitation, increases the sensitivity of ozone concentration with respect to changes in NOx emissions for both years. In particular, decreasing NOx emissions in 2005 when NO2 photo-excitation is included, while utilizing the higher reaction rate, leads to ozone relative reduction factors that are 15% lower than in a case without photo-excited NO2. This implies that photoexcitation increases the effectiveness in reducing ozone through NOx emissions reductions alone, which has implications for the assessment of future emission control strategies. However, there is still disagreement with respect to the reaction rate constant for the formation of OH. Therefore, further studies are required to reduce the uncertainty in the reaction rate constant before this new mechanism is fully implemented in regulatory applications.

Effects of Solvent Polarity on the Urethane Reaction of 1,2-Propanediol

2012 ◽  
Vol 450-451 ◽  
pp. 38-41
Author(s):  
Peng Fei Yang
Keyword(s):  
Rate Constant ◽  
Solvent Polarity ◽  
Reaction Rates ◽  
Phenyl Isocyanate ◽  
Second Order Reaction ◽  
Polar Solvents ◽  
Initial Stage ◽  
Ft Ir ◽  
Kinetics Of

The urethane reaction kinetics of 1,2-propanediol with phenyl isocyanate are investigated in different solvents, such as xylene, toluene and dimethylformamide. In-situ FT-IR is used to monitor the reaction to work out rate constant. It showsthat the urethane reaction has been found to be a second order reaction, solvents largely affects reaction rates. The reaction is largely accelerated in polar solvents, following the order of dimethylformamide > toluene > xylene. Further more, when dimethylformamide is used as solvent, the rate constants are different between initial stage and final stage, which belongs to different hydroxyls in 1,2-propanediol. However, when toluene or xylene is used as solvent, the rate constant is the same. That is, there is no reactivity difference for hydroxyls in 1,2-propanediol.

Solvent structure effects on solvated electron reactions with ions in 2-butanol/water mixed solvents

1991 ◽  
Vol 69 (5) ◽  
pp. 884-892 ◽  
Author(s):  
Sedigallage A. Peiris ◽  
Gordon R. Freeman
Keyword(s):  
Rate Constant ◽  
Pure Water ◽  
Mixed Solvents ◽  
Reaction Rates ◽  
Bimolecular Reaction ◽  
Activation Energies ◽  
Solvated Electron ◽  
Polar Species ◽  
Water Solvent ◽  
Alcohol Water

The Smoluchowski–Debye–Stokes–Einstein equation for the rate constant k2 of a bimolecular reaction between charged or polar species[Formula: see text]was used to evaluate effects of bulk solvent properties on reaction rates of solvated electrons with [Formula: see text] and [Formula: see text] in 2-butanol/water mixed solvents. To explain detailed effects it was necessary to consider more specific behavior of the solvent. Rate constants k2, activation energies E2, and pre-exponential factors A2 of these reactions vary with the composition of 2-butanol/water mixtures. The values of E2 were in general similar to activation energies of ionic conductance EΛ0 of the solutions, except for much higher values of E2 of [Formula: see text] in alcohol-rich solvents and of [Formula: see text] in pure water solvent. The solvent apparently participates chemically in the [Formula: see text] reaction, and the [Formula: see text] reaction is multistep. Rate constant and conductance measurements of thallium acetate solutions in 2-butanol containing zero and 10 mol% water were complicated by the formation of ion clusters larger than pairs. Key words: alcohol/water mixed solvents, ions, reaction kinetics, solvated kinetics, solvated electron, solvent effects.

Reaction rates of electrons in liquid methanol and ethanol: effects of pressure

1976 ◽  
Vol 54 (8) ◽  
pp. 1177-1188 ◽  
Author(s):  
Gerald L. Bolton ◽  
Maurice G. Robinson ◽  
Gordon R. Freeman
Keyword(s):  
Rate Constant ◽  
Reaction Rates ◽  
Alcohol Molecule ◽  
High Concentration ◽  
Diffusion Controlled ◽  
Pure Alcohol ◽  
Wide Range ◽  
Solvent Density ◽  
Benzene Toluene ◽  
Experimental Values

The value of the rate constant k1 for the reaction e−solv → RO−solv + H, [1], at 295 K and 1 bar is ≤1.4 × 105 s−1 in methanol and ≤8 × 104 s−1 in ethanol. The respective volumes of activation averaged between 1 bar and 2 kbar are ΔV1≠ ≤ −21 and ≤ −22 cm3 mol−1. A high concentration of potassium hydroxide (1 M) or water (5 M) decreases the apparent value of k1 somewhat but has little or no effect on the value of ΔV1≠. The effect of pressure on the rate constant of e−solv + S → product, [2], was also measured for a series of solutes that displays a wide range of reactivity. Experimental values of ΔV2≠ depend on the relative contributions of the effects of solvent density on the reactant diffusion rates, the concentrations of the actual reacting species, and the relative energies of the reactant and intermediate states. For reactions whose rates are near the diffusion controlled limit, k2 ≈ 1010 M−1 s−1 in methanol and ethanol, the values of ΔV2≠ are positive and similar to those for the diffusion of simple ions. ΔV≠(e−solv diffusion) = 4 cm3 mol−1 in methanol and 6 cm3 mol−1 in ethanol. Cadmium chloride is apparently not completely dissociated in alcohols, and k(e−solv + CdCl2) < k(e−solv + CdCl+) < k(e−solv + Cd2+). For a series of compounds with lower rate constants there is a correlation between log k2 and ΔV2≠, the latter being negative for very low values of k2. The products of electron capture by benzene, toluene, ethyl acetate, and possibly acetonitrile appear to be stabilized by protonation: [Formula: see text] S−solv + ROH → SH + RO−slov, [4]. The results indicate that the decomposition of e−solv in a pure alcohol occurs by protonation of the electron site, e−solv + ROH → H + RO−slov, [4′], rather than by electron transfer to an alcohol molecule followed by decomposition of the anion.

scholarly journals The reactivity of the thiol groups of the adenosine triphosphatase of sarcoplasmic reticulum and their location on tryptic fragments of the molecule

1977 ◽  
Vol 167 (3) ◽  
pp. 739-748 ◽  
Author(s):  
David A. Thorley-Lawson ◽  
N. Michael Green
Keyword(s):  
Sarcoplasmic Reticulum ◽  
Rate Constant ◽  
Adenosine Triphosphatase ◽  
Sodium Dodecyl ◽  
Thiol Group ◽  
Order Rate Constant ◽  
Reaction Rates ◽  
Cysteic Acid ◽  
Thiol Groups ◽  
Low Concentrations

The ATPase (adenosine triphosphatase) from sarcoplasmic reticulum contains 20 thiol groups/115000 daltons, measured by using either N-ethyl[14C]maleimide or 5,5′-dithiobis-(2-nitrobenzoate) in sodium dodecyl sulphate. After reduction there were 26 thiol groups, in good agreement with 26.5 residues of cysteic acid found by amino acid analysis. The difference between this and the 20 residues measured before reduction implies the presence of three disulphide residues. The same number of disulphide residues was found by direct measurement. Three to six fewer thiol groups were found in preparations made in the absence of dithiothreitol. The missing residues were accounted for as cysteic acid. The distribution of disulphide bonds and of exposed and buried thiol groups among the tryptic fragments of the molecule was measured after labelling with N-ethyl[14C]-maleimide. The disulphides were confined to fragment B (mol.wt. 55000), whereas several thiol groups were present on each of the fragments (A, B, A1 and A2). The kinetics of the reaction of the ATPase with 5,5′-dithiobis-(2-nitrobenzoate) showed that four or five of the thiol groups were unreactive in the absence of detergent and that 13 of the remainder reacted with a single first-order rate constant. In the presence of ATP and Ca2+ the reaction rate of all but two groups of this class was uniformly decreased. In the presence or absence of ATP and Ca2+ the rate constant for inactivation was close to the rate constant for this class, but was not identical with it. No selective protection of a specific active-site-thiol group was observed. Parallel experiments with sarcoplasmic reticulum gave similar results, except that the reaction rates were a little lower and there were two more buried groups. Solution of ATPase of sarcoplasmic reticulum in detergent greatly increased the reactivity of all thiol groups. The effects of low concentrations of deoxycholate were reversible. EGTA or low concentrations (0.02mm) of Ca2+ of Mg2+ had very little effect on the reactivity.

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