Revisiting ground-state and transition-state effects, the split-site model, and the "fundamentalist position" of enzyme catalysis

Biochemistry ◽  
1995 ◽  
Vol 34 (14) ◽  
pp. 4507-4510 ◽  
Author(s):  
Dennis J. Murphy
Keyword(s):  
Transition State ◽  
Ground State ◽  
Enzyme Catalysis ◽  
Site Model

scholarly journals An alternative view of enzyme catalysis

2005 ◽  
Vol 77 (11) ◽  
pp. 1873-1886 ◽  
Author(s):  
Fredric M. Menger
Keyword(s):  
Transition State ◽  
Enzyme Catalysis ◽  
Alternative View ◽  
Spatiotemporal Model ◽  
Substrate Complex ◽  
Site Model ◽  
Enzyme Substrate ◽  
Transition State Stabilization ◽  
Computational Data ◽  
The Many

This paper begins with a brief review of theories and concepts that have influenced today's view of enzyme catalysis: transition-state stabilization, entropy, orbital steering, proximity, and intramolecularity. The discussion then launches into the "spatiotemporal" model of enzyme catalysis in which fast intramolecular and enzymatic rates are ascribed to short distances that are imposed rigidly upon the reacting entities. An equation relating rate and distance is set forth, as are experimental and computational data supporting this relationship. Finally, enzyme systems themselves are analyzed in terms of the distance parameter and the so-called "split-site" model in which ground-state geometries play a crucial role. Among the many surprising conclusions is a transition-state stabilization by noncovalent forces (e.g., hydrogen-bonding) that are positioned far away from the actual transition-state chemistry. The model also confronts and dismisses the claim in classical enzymology that the ubiquitous enzyme-substrate complex is either inconsequential or inhibitory to the overall reaction rate.

Effect of Medium on Reactivity for Alkaline Hydrolysis of p-Nitrophenyl Acetate and S-p-Nitrophenyl Thioacetate in DMSO-H2O Mixtures of Varying Compositions: Ground State and Transition State Contributions

2021 ◽  
Author(s):  
Ik-Hwan Um ◽  
Seungjae Kim
Keyword(s):  
Transition State ◽  
Alkaline Hydrolysis ◽  
Ground State ◽  
Rate Constants ◽  
Kinetic Data ◽  
Reaction Medium ◽  
Stepwise Mechanism ◽  
Rate Determining Step ◽  
Leaving Group ◽  
Hydrolysis Of

Second-order rate constants (kN) for reactions of p-nitrophenyl acetate (1) and S-p-nitrophenyl thioacetate (2) with OH‒ have been measured spectrophotometrically in DMSO-H2O mixtures of varying compositions at 25.0 ± 0.1 oC. The kN value increases from 11.6 to 32,800 M‒1s‒1 for the reactions of 1 and from 5.90 to 190,000 M‒1s‒1 for those of 2 as the reaction medium changes from H2O to 80 mol % DMSO, indicating that the effect of medium on reactivity is more remarkable for the reactions of 2 than for those of 1. Although 2 possesses a better leaving group than 1, the former is less reactive than the latter by a factor of 2 in H2O. This implies that expulsion of the leaving group is not advanced in the rate-determining transition state (TS), i.e., the reactions of 1 and 2 with OH‒ proceed through a stepwise mechanism, in which expulsion of the leaving group from the addition intermediate occurs after the rate-determining step (RDS). Addition of DMSO to H2O would destabilize OH‒ through electronic repulsion between the anion and the negative-dipole end in DMSO. However, destabilization of OH‒ in the ground state (GS) is not solely responsible for the remarkably enhanced reactivity upon addition of DMSO to the medium. The effect of medium on reactivity has been dissected into the GS and TS contributions through combination of the kinetic data with the transfer enthalpies (ΔΔHtr) from H2O to DMSO-H2O mixtures for OH‒ ion.

Communication: Photodissociation of CH3CHO at 308 nm: Observation of H-roaming, CH3-roaming, and transition state pathways together along the ground state surface

2015 ◽  
Vol 142 (4) ◽  
pp. 041101 ◽  
Author(s):  
Hou-Kuan Li ◽  
Po-Yu Tsai ◽  
Kai-Chan Hung ◽  
Toshio Kasai ◽  
King-Chuen Lin
Keyword(s):  
Transition State ◽  
Ground State

scholarly journals SN2 regioselectivity in the esterification of 5- and 7-membered azacycloalkane quaternary salts: a DFT study to reveal the transition state ring conformation prevailing over the ground state ring strain

2014 ◽  
Vol 12 (34) ◽  
pp. 6717-6724 ◽  
Author(s):  
Akihiro Kimura ◽  
Susumu Kawauchi ◽  
Takuya Yamamoto ◽  
Yasuyuki Tezuka
Keyword(s):  
Transition State ◽  
Ground State ◽  
Dft Study ◽  
Ring Conformation ◽  
Ring Strain ◽  
Quaternary Salts

SN2 regioselectivity in 5- and 7-membered azacycloalkanes quaternary salts is directed by the transition state ring conformation.

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.

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