scholarly journals Isotope effect analyses provide evidence for an altered transition state for RNA 2′-O-transphosphorylation catalyzed by Zn2+

2016 ◽  
Vol 52 (24) ◽  
pp. 4462-4465 ◽  
Author(s):  
Shuming Zhang ◽  
Hong Gu ◽  
Haoyuan Chen ◽  
Emily Strong ◽  
Edward W. Ollie ◽  
...  
Keyword(s):  
Transition State ◽  
Isotope Effect ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
Base Catalysis ◽  
Kinetic Isotope

Solvent D2O and18O kinetic isotope effects on RNA 2′-O-transphosphorylation catalyzed by Zn2+demonstrate an altered transition state relative to specific base catalysis.

Unequal primary kinetic isotope effects in the base-catalysed H–D exchange of diastereotopic protons

1980 ◽  
Vol 58 (1) ◽  
pp. 72-78 ◽  
Author(s):  
Robert R. Fraser ◽  
Philippe J. Champagne
Keyword(s):  
Transition State ◽  
Exchange Reaction ◽  
Isotope Effect ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
Deuterium Isotope Effect ◽  
Kinetic Isotope

Primary kinetic isotope effects have been measured for the base-catalyzed exchange reaction of 4′,1″-dimethyl-1,2,3,4-dibenzcyclohepta-1,3-diene-6-one, 1. It was found that the isotope effects kH/kT and kD/kT for the faster exchanging protons (13.6 and 3.8 respectively) are significantly larger than the corresponding values for the slower exchanging protons (4.6 and 1.6 respectively). These differences could result from truly unequal isotope effects due to transition state differences or intrusion of a second pathway for exchange of the less reactive proton in the dedeuteration reaction. The data appear to support the latter interpretation. The secondary deuterium isotope effect was found to be 1.18.

Kinetic evidence for the importance of solvent-separated ion pairs during the solvolyses of adamantylideneadamantyl derivatives

2004 ◽  
Vol 82 (9) ◽  
pp. 1336-1340
Author(s):  
Xicai Huang ◽  
Andrew J Bennet
Keyword(s):  
Ionic Strength ◽  
Transition State ◽  
Isotope Effect ◽  
Kinetic Isotope Effect ◽  
Isotope Effects ◽  
Ion Pairs ◽  
Kinetic Isotope Effects ◽  
Ion Pair ◽  
Salt Effects ◽  
Kinetic Isotope

The aqueous ethanolysis reactions of adamantylideneadamantyl tosylate, -bromide, and -iodide (1-OTs, 1-Br and 1-I) were monitored as a function of ionic strength. Special salt effects are observed during the solvolyses of both homoallylic halides, but not in the case of the tosylate 1-OTs. The measured α-secondary deuterium kinetic isotope effects for the solvolysis of 1-Br in 80:20 and 60:40 v/v ethanol–water mixtures at 25 °C are 1.110 ± 0.018 and 1.146 ± 0.009, respectively. The above results are consistent with the homoallylic halides reacting via a virtual transition state in which both formation and dissociation of a solvent-separated ion pair are partially rate-determining. While the corresponding transition state for adamantylideneadamantyl tosylate involves formation of the solvent-separated ion pair.Key words: salt effects, kinetic isotope effect, internal return, solvolysis, ion pairs.

Isotope Effect Studies on Elimination Reactions. IX. The Nature of the Transition State for the E2 Reaction of 2-Arylethylammonium Ions with Ethoxide in Ethanol

1974 ◽  
Vol 52 (5) ◽  
pp. 749-760 ◽  
Author(s):  
P. J. Smith ◽  
A. N. Bourns
Keyword(s):  
Transition State ◽  
Isotope Effect ◽  
Isotope Effects ◽  
Nitrogen Isotope ◽  
Kinetic Isotope Effects ◽  
Ammonium Ions ◽  
Nitrogen Effect ◽  
Kinetic Isotope ◽  
Leaving Group ◽  
Hydrogen Deuterium

Kinetic isotope effects have been determined for the E2 reaction of some 2-arylethyltrimethyl-ammonium ions with ethoxide in ethanol at 40°. The nitrogen effect, (k14/k15 − 1)100, decreased with increasing electron-withdrawing ability of the para substituent; i.e. 1.37, 1.33, 1.14, and 0.88 for p-OCH3, p-H, p-Cl, and p-CF3, respectively. Furthermore, the primary hydrogen–deuterium isotope effects increased for the same substituents, respectively; i.e. kH/kD = 2.64, 3.23, 3.48, and 4.16. A large positive ρ value of 3.66 was found as well as a small secondary α-deuterium effect of 1.02 for p-H. In addition, the nitrogen isotope effect decreased with increasing strength of the abstracting base for the reaction of ethyltrimethylammonium ion; i.e. 1.86 and 1.41 at 60° for reaction with EtO−–EtOH and t-BuO−–t-BuOH, respectively. The results are discussed in terms of recent theoretical treatments of the effect of base, substituents, and nature of the leaving group on the nature of the transition state for an E2 process. The conclusion is reached that any structural change which causes one bond (C—H) to be weakened more at the transition state will have a corresponding effect on the other bond [Formula: see text]

CALCULATIONS OF KINETIC ISOTOPE EFFECTS FOR THE IODIDE EXCHANGE AND FOR THE SOLVOLYSIS OF METHYL IODIDE

1966 ◽  
Vol 44 (16) ◽  
pp. 1889-1897 ◽  
Author(s):  
Alfred V. Willi
Keyword(s):  
Transition State ◽  
Exchange Reaction ◽  
Isotope Effect ◽  
Secular Equation ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
Force Constants ◽  
Kinetic Isotope ◽  
Experimental Temperature Dependence ◽  
State Formula

Kinetic deuterium and carbon-13 isotope effects are calculated for the SN2 exchange reaction of CH3I with *I−(131) and for the CH3I solvolysis in water. The normal vibrational frequencies of CH3I and of the transition state [Formula: see text] (X = I or OH2) are evaluated from force constants by solving the secular equation with an IBM 7094 computer. Values for force constants of the planar CH3 moiety (with an sp2 C atom) in the transition state are obtained by comparison with suitable stable molecules. For the iodide exchange reaction, there is not much dependence of the calculated D isotope effect on the particular choice of ƒCI and ƒ12 (interaction between CI stretches) if these force constants are within reasonable limits. The bending force constantƒHCI (≠) may then be adj usted to reproduce the experimental D isotope effect.Based on the simple transition state model [Formula: see text] it is not possible to obtain agreement with the experimental D effect in the solvolysis reaction without assuming an extremely high value of ƒHCI. If must be concluded that a water molecule is probably involved in the transition state. On the basis of the model [Formula: see text] the experimental D effect may be reproduced with a suitable choice of ƒHCI and ƒHCO. It is shown that, under favorable circumstances, experimental temperature dependence data may be applied for a distinction between different sets of, ƒCH, ƒHCH, and ƒHCI (or ƒHCO) which reproduce the experimental isotope effect at one temperature.

Isotope Effect Studies on Elimination Reactions. X. The Nature of The Transition State for the ECO2 Reaction of Para- substituted Benzyl Nitrates with Base in 90% by Volume Ethanol–Water

1975 ◽  
Vol 53 (9) ◽  
pp. 1319-1326 ◽  
Author(s):  
Peter James Smith ◽  
Carol Audrey Pollock ◽  
Arthur Newcombe Bourns
Keyword(s):  
Transition State ◽  
Isotope Effect ◽  
Isotope Effects ◽  
Nitrogen Isotope ◽  
Kinetic Isotope Effects ◽  
The Other ◽  
Theoretical Treatment ◽  
Kinetic Isotope ◽  
Hydrogen Deuterium ◽  
Deuterium Isotope Effects

Kinetic isotope effects have been determined for the Eco2 reaction of para-substituted benzyl nitrates with ethoxide in 90 vol.% ethanol–water at 20°. The nitrogen isotope effect, (k14/k15−1)100 decreased with increasing electron-withdrawing ability of the para-substituent; i.e. 2.26, 1.95, 1.60, and 0.84 for p-CH3, p-H, p-CF3, and p-NO2, respectively. Furthermore, the primary hydrogen–deuterium isotope effects increased also for electron-withdrawing substituents; i.e. kH/kD = 5.78, 6.06, 6.40, 6.67, and 7.05 for p-CH3, p-H, p-Br, p-CF3, and p-NO2, respectively. The results are discussed in terms of a recent theoretical treatment dealing with the effect of substituents on the nature of the transition state for a concerted E2 process. The conclusion is reached that any structural change which causes one bond (carbon–hydrogen) to be weakened more at the transition state will have a corresponding effect on the other bond (oxygen–nitrogen).

13C kinetic isotope effects and reaction coordinate motions in transition states for SN2 displacement reactions

1976 ◽  
Vol 54 (7) ◽  
pp. 1146-1161 ◽  
Author(s):  
Warren Edward Buddenbaum ◽  
Vernon Jack Shiner Jr.
Keyword(s):  
Transition State ◽  
Isotope Effect ◽  
Methyl Iodide ◽  
Isotope Effects ◽  
Transition States ◽  
Kinetic Isotope Effects ◽  
Chloride Ions ◽  
Reaction Coordinate ◽  
Kinetic Isotope ◽  
State Models

Reaction coordinate motions and 13C kinetic isotope effects at 25 °C have been calculated for the SN2 reactions of methyl iodide with iodide, cyanide, and chloride ions and for the SN2 reaction of benzyl bromide with hydroxide ion using transition state models characterized by single interaction force constant, F12, between the bond being formed and the bond being broken. The isotope effect calculations show that the dependence of calculated 13C isotope effects on transition state symmetry found by Willi and Sims etal. holds true for reaction barriers corresponding to small values of νL, while the symmetry dependence observed by Bron holds true for barriers corresponding to large values of νL.νL was also found to have a strong influence on the reaction coordinate motions of the transition states. In particular, for the methyl iodide reactions an increase in νL increases the distortion of the methyl group in the direction expected for a classical SN2 reaction. Finally, reaction coordinate motions were used to show that the model proposed by Bron for the borderline region between SN1 and SN2 reaction mechanisms predicts an increase in the 13C kinetic isotope effect with decreasing total bond order and not the decrease suggested by Bron.

Isotope effects in nucleophilic substitution reactions. II. Secondary α-deuterium kinetic isotope effects: a criterion of mechanism?

1979 ◽  
Vol 57 (9) ◽  
pp. 1089-1097 ◽  
Author(s):  
Kenneth Charles Westaway ◽  
Syed Fasahat Ali
Keyword(s):  
Transition State ◽  
Nucleophilic Substitution ◽  
Isotope Effect ◽  
Kinetic Isotope Effect ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
Substitution Reactions ◽  
Nucleophilic Substitution Reactions ◽  
Kinetic Isotope ◽  
Steric Crowding

A very large secondary α-deuterium kinetic isotope effect of 1.179 ± 0.007 (1.086 ± 0.003 per α-deuterium) has been observed for the SN2 reaction of thiophenoxide ion with benzyldimethylphenylammonium ion in DMF at 0°C. This large isotope effect which is far outside the range reported for SN2 reactions, is attributed to the fact that the extraordinarily large steric crowding around the Cα—H bonds in the substrate is reduced in the SN2 transition state. The structure of the transition state is shown to be consistent with this hypothesis.

The Importance of Anharmonicity of The Vibrational Excited States in Chemical Kinetics

1975 ◽  
Vol 53 (20) ◽  
pp. 3069-3074 ◽  
Author(s):  
Jan Bron
Keyword(s):  
Transition State ◽  
Excited States ◽  
Isotope Effects ◽  
Kinetic Isotope Effects ◽  
Vibrational States ◽  
Vibrational Anharmonicity ◽  
Kinetic Isotope ◽  
Large Correction ◽  
Lower Temperature ◽  
Lower Temperature Region

The corrections to rate constants for an harmonicity of vibrational excited states have been evaluated over the temperature range of 200–1100 K. The reaction O2 + X, where X is H or D, has been chosen as the model system. Only the influence of vibrational anharmonicity of the triatomic transition state has been determined. Two geometric shapes for the transition state, bent and isosceles configurations, have been investigated in detail by the bond order method.It is found that the correction can be large, depending upon the geometry and force field of the transition state and the temperature. The magnitude of the correction for anharmonicity of the vibrational excited states depends mainly, at a particular temperature, on the strength of the O—X bond in the transition state. In the case of a large correction, anharmonicity may lead to a nonlinear Arrhenius plot.Because of cancellation effects, the correction for anharmonicity of the excited vibrational states in kinetic isotope effects can be ignored in the lower temperature region. It has also been found that anharmonicity of the vibrational groundstate can explain unexpected large isotope effects.

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