scholarly journals Hydrogen tunnelling in enzyme-catalysed H-transfer reactions: flavoprotein and quinoprotein systems

2006 ◽  
Vol 361 (1472) ◽  
pp. 1375-1386 ◽  
Author(s):  
Michael J Sutcliffe ◽  
Laura Masgrau ◽  
Anna Roujeinikova ◽  
Linus O Johannissen ◽  
Parvinder Hothi ◽  
...  
Keyword(s):  
Temperature Dependence ◽  
Variable Temperature ◽  
Isotope Effects ◽  
Experimental Studies ◽  
Zero Point ◽  
Reaction Rates ◽  
State Theory ◽  
Strong Temperature Dependence ◽  
Methylamine Dehydrogenase ◽  
Point Energy

It is now widely accepted that enzyme-catalysed C–H bond breakage occurs by quantum mechanical tunnelling. This paradigm shift in the conceptual framework for these reactions away from semi-classical transition state theory (TST, i.e. including zero-point energy, but with no tunnelling correction) has been driven over the recent years by experimental studies of the temperature dependence of kinetic isotope effects (KIEs) for these reactions in a range of enzymes, including the tryptophan tryptophylquinone-dependent enzymes such as methylamine dehydrogenase and aromatic amine dehydrogenase, and the flavoenzymes such as morphinone reductase and pentaerythritol tetranitrate reductase, which produced observations that are also inconsistent with the simple Bell-correction model of tunnelling. However, these data—especially, the strong temperature dependence of reaction rates and the variable temperature dependence of KIEs—are consistent with other tunnelling models (termed full tunnelling models), in which protein and/or substrate fluctuations generate a configuration compatible with tunnelling. These models accommodate substrate/protein (environment) fluctuations required to attain a configuration with degenerate nuclear quantum states and, when necessary, motion required to increase the probability of tunnelling in these states. Furthermore, tunnelling mechanisms in enzymes are supported by atomistic computational studies performed within the framework of modern TST, which incorporates quantum nuclear effects.

DEUTERIUM KINETIC ISOTOPE EFFECTS: V TEMPERATURE DEPENDENCE OF β-DEUTERIUM EFFECTS IN WATER SOLVOLYSIS OF ISOPROPYL COMPOUNDS

1961 ◽  
Vol 39 (10) ◽  
pp. 1989-1994 ◽  
Author(s):  
K. T. Leffek ◽  
R. E. Robertson ◽  
S. E. Sugamori
Keyword(s):  
Temperature Dependence ◽  
Isotope Effect ◽  
Isotope Effects ◽  
Zero Point ◽  
Kinetic Isotope Effects ◽  
Methyl Groups ◽  
Deuterium Isotope Effect ◽  
Point Energy ◽  
Kinetic Isotope ◽  
Enthalpy Of Activation

The secondary β-deuterium isotope effect (kH/kD) has been measured over a range of temperature for the water solvolysis reactions of isopropyl methanesulphonate, p-toluenesulphonate, and bromide. In these cases the isotope effect is due to a difference in entropies of activation of the isotopic analogues rather than a difference in the enthalpies of activation. It is suggested that the observed isotope effect is due to internal rotational effects of the methyl groups in the isopropyl radical, and the lack of an isotope effect on the enthalpy of activation is accounted for by a cancellation of an effect from this source and one from zero-point energy.

scholarly journals Photolysis-induced scrambling of PAHs as a mechanism for deuterium storage

2020 ◽  
Vol 635 ◽  
pp. A9 ◽  
Author(s):  
Sandra D. Wiersma ◽  
Alessandra Candian ◽  
Joost M. Bakker ◽  
Jonathan Martens ◽  
Giel Berden ◽  
...  
Keyword(s):  
Transition State ◽  
Ir Spectra ◽  
Density Functional ◽  
Zero Point ◽  
Reaction Rates ◽  
Ion Cyclotron Resonance ◽  
Point Energy ◽  
Polycyclic Aromatic ◽  
Atom Loss ◽  
Ground State Structures

Aims. We investigate the possible role of polycyclic aromatic hydrocarbons (PAHs) as a sink for deuterium in the interstellar medium (ISM) and study UV photolysis as a potential underlying chemical process in the variations of the deuterium fractionation in the ISM. Methods. The UV photo-induced fragmentation of various isotopologs of deuterium-enriched, protonated anthracene and phenanthrene ions (both C14H10 isomers) was recorded in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer. Infrared multiple photon dissociation spectroscopy using the Free-Electron Laser for Infrared eXperiments was applied to provide IR spectra. Infrared spectra calculated using density functional theory were compared to the experimental data to identify the isomers present in the experiment. Transition-state energies and reaction rates were also calculated and related to the experimentally observed fragmentation product abundances. Results. The photofragmentation mass spectra for both UV and IRMPD photolysis only show the loss of atomic hydrogen from [D − C14H10]+, whereas [H − C14D10]+ shows a strong preference for the elimination of deuterium. Transition state calculations reveal facile 1,2-H and -D shift reactions, with associated energy barriers lower than the energy supplied by the photo-excitation process. Together with confirmation of the ground-state structures via the IR spectra, we determined that the photolytic processes of the two different PAHs are largely governed by scrambling where the H and the D atoms relocate between different peripheral C atoms. The ∼0.1 eV difference in zero-point energy between C–H and C–D bonds ultimately leads to faster H scrambling than D scrambling, and increased H atom loss compared to D atom loss. Conclusions. We conclude that scrambling is common in PAH cations under UV radiation. Upon photoexcitation of deuterium-enriched PAHs, the scrambling results in a higher probability for the aliphatic D atom to migrate to a strongly bound aromatic site, protecting it from elimination. We speculate that this could lead to increased deuteration as a PAH moves towards more exposed interstellar environments. Also, large, compact PAHs with an aliphatic C–HD group on solo sites might be responsible for the majority of aliphatic C–D stretching bands seen in astronomical spectra. An accurate photochemical model of PAHs that considers deuterium scrambling is needed to study this further.

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.

scholarly journals Reconciling Imbalanced Transition State Effects with Nonadiabatic CPET Reactions

2021 ◽  
Author(s):  
Joseph Schneider ◽  
McKenna Goetz ◽  
John Anderson
Keyword(s):  
Transition State ◽  
Potential Energy Surfaces ◽  
Variable Temperature ◽  
Reaction Rates ◽  
State Theory ◽  
Energy Relation ◽  
Linear Free Energy ◽  
Proton Potential ◽  
Classical Models ◽  
Free Energy Relation

Recently there have been several experimental demonstrations of how concerted proton electron transfer (CPET) reaction rates are affected by off-main-diagonal energies, namely the stepwise thermodynamic parameters ΔG°PT and ΔG°ET. Semi-classical structure-activity relationships have been invoked to rationalize these asynchronous linear free energy relation-ships despite the widely acknowledged importance of quantum effects such as nonadiabaticity and tunneling in CPET reactions. Here we report variable temperature kinetic isotope effect data for the asynchronous reactivity of a terminal Co-oxo complex with C–H bonds and find evidence of substantial quantum tunneling which is inconsistent with semi-classical models even when including tunneling corrections. This indicates substantial nonadiabatic tunneling in the CPET reactivity of this Co-oxo complex and further motivates the need for a quantum mechanical justification for the in-fluence of ΔG°PT and ΔG°ET on reactivity. To reconcile this dichotomy, we include ΔG°PT and ΔG°ET in nonadiabatic models of CPET by having them influence the anharmonicity and depth of the proton potential energy surfaces, which we approximate as Morse potentials. With this model we independently reproduce the dominant trend with ΔG°PT + ΔG°ET as well as the subtle effect of ΔG°PT − ΔG°ET (or η) in a nonadiabatic framework. The primary route through which these off-diagonal energies influence rates is through vibronic coupling. Our results reconcile predictions from semiclassical transition state theory with models that treat proton transfer quantum mechanically in CPET reactivity and suggest that similar treatments may be possible for other nonadiabatic processes.

The Calculation of Zero-Point Energies of Molecules by Perturbation Methods

1963 ◽  
Vol 18 (2) ◽  
pp. 216-224 ◽  
Author(s):  
Max Wolfsberg
Keyword(s):  
Perturbation Methods ◽  
Secular Equation ◽  
Isotope Effects ◽  
Normal Modes ◽  
Zero Point ◽  
Perturbation Series ◽  
Quantum Mechanical ◽  
Perturbation Scheme ◽  
Point Energy ◽  
The Mean

Two methods are proposed for calculating zero-point energies of molecules. The first makes use of the fact that one can easily write down the quantum mechanical HAMILTONian for a vibrating system. The zero-point energy can then be obtained by a perturbation scheme without solving the secular equation. The second method requires a knowledge of the normal modes and frequencies of a reference molecule, but then enables one to calculate isotope effects by a perturbation scheme. The methods are applied to some examples and the convergence of the perturbation series is investigated. The approximate validity of the law of the mean for the isotope effect on zero-point energies is explored within the framework of the methods.

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