Theoretical Determination of the Standard Reduction Potentials of Pheophytin-ainN,N-Dimethyl Formamide and Membrane

Mehta, Nital; Datta, Sambhu N.

doi:10.1021/jp067383t

Cited by 12 publications

(8 citation statements)

References 41 publications

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“…Firstly, we consider the values computed in the absence of a proton source. 29 In agreement with the experimental studies, addition of the first electron requires a strongly cathodic potential. The computed E RED values are somewhat different for the two solvents, with reduction being easier in CH 3 CN.…”

Section: Calculation Of Reduction Potentialssupporting

confidence: 85%

Accessing molecular memoryvia a disulfide switch

et al. 2009

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Herein we describe the results of a combined theoretical and spectroscopic investigation into the design of a simple molecular system intended to act as a memory storage bank. The main operating principle revolves around the two-electron reduction of an aryl disulfide bond. Addition of the first electron leads to elongation of the S-S bond but it breaks only if there is accompanying protonation. Adding a second electron causes S-S bond cleavage, with or without protonation. The structural changes have been assessed by way of quantum chemical calculations and molecular dynamics simulations. Electrochemical studies show that the two-electron reduced product can be re-oxidised at mildly anodic potentials and the cycle can be repeated many times. Both theory and experiment point towards pronounced potential inversion whereby the second reduction potential lies at a significantly more positive potential than that for the first step. Computer simulations of the cyclic voltammograms give rise to numerical values for the reduction potentials that are in quite good agreement with the computed values and also allow determination of the electrochemical rate constants and transfer coefficients. Accurate simulation of the experimental data can be realised only if one proton accompanies the second reduction step. The possibility to design an effective molecular-scale memory device around this system is discussed briefly.

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Section: Calculation Of Reduction Potentialssupporting

confidence: 85%

Accessing molecular memoryvia a disulfide switch

et al. 2009

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“…11,27,28,[69][70][71][72][73][74] In particular, for larger and complex biomolecules, calculation of absolute redox potentials are very successful using hybrid quantum mechanical and molecular mechanical (QM/MM) methods such as SCC-DFTB 11,27,28 and ONIOM calculation methods. 65,66,[75][76][77][78] The latter method has been used by Datta et al in a series of calculations to determine the absolute redox potentials of a number of biomolecules 61,65,66 while SCC-DFTB has recently been used for similar studies on various flavoenzymes. 11,27,28 3.2.…”

Section: Resultsmentioning

confidence: 99%

Theoretical Determination of the Redox Potentials of NRH:Quinone Oxidoreductase 2 Using Quantum Mechanical/Molecular Mechanical Simulations

Rauschnot

Yang

et al. 2009

J. Phys. Chem. B

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NRH:quinone oxidoreductase 2 (NQO2) is a flavoenzyme that catalyzes a one-step two-electron reduction of quinones. During this enzyme catalysis, the 7,8-dimethyl isoalloxazine (flavin) ring of the enzyme-bound cofactor, flavin adenine dinucleotide (FAD), shuttles between reduced and oxidized states as the enzyme passes through multiple cycles of binding/release of alternate substrates. These redox changes in NQO2, however, lead to unequal charge separation between the flavin ring and the active site, which must be stabilized by reorganization of the surrounding protein matrix. In this study, we have used a combined quantum mechanical/molecular mechanical method to simulate the electron and proton addition reactions of the flavin-bound NQO2. We have computed the redox potentials and pK(a)'s of the enzyme-bound flavin. The present work demonstrates that upon reduction, the NQO2 active site stabilizes the flavin anionic hydroquinone state. Simulation data has also allowed quantitative estimation of the electrostatic contributions of active site residues. Their significance in oscillatory redox transition of this flavoenzyme is discussed.

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“…For further discussion of the use of explicit-solvent simulations to compute reduction potentials, we refer readers to the relevant primary literature. 261,[266][267][268][269][270][271][272][273][274] The free energy problem in regard to MC and MD simulations is reviewed elsewhere. 262,275 Standard liquid-phase computer simulations usually utilize either a canonical ensemble, also called an NVT ensemble, 276,277 in which the number of particles (N), volume (V) and temperature (T) are conserved, or an isothermal-isobaric ensemble, also called an NPT ensemble, in which the pressure (P) rather than the volume is fixed.…”

Section: Theoretical Backgroundmentioning

confidence: 99%

“…450 The authors demonstrated that the method could be an efficient approach to free energy simulations of complex electron transfer reactions. 450 Several other enzymatic redox reactions have also been studied recently using the tools of computational electrochemistry, in particular for the following enzymes: photosystem II, 270,[451][452][453] ribonuclease reductase, 454,455 rubredoxin, 456 green fluorescent protein, 457,458 adenosine-5 0 -phosphosulfate reductase, 459 methyltransferases, 460 monoamine oxidase B, 461 and methionine synthase. 462 Billiet et al 463 have studied the thermodynamics of thiol sulfenylation in the sulfenic acid-forming protein human Prx.…”

Section: Applicationsmentioning

confidence: 99%

Computational electrochemistry: prediction of liquid-phase reduction potentials

Marenich

Coote

et al. 2014

Phys. Chem. Chem. Phys.

444

546

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This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.

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Theoretical Determination of the Standard Reduction Potentials of Pheophytin-ainN,N-Dimethyl Formamide and Membrane

Abstract: A physicochemical interpretation of a recently formulated temperature-dependent, steady-state rate expression for the production of glucose equivalent in C(4) plants is given here. We show that the rate equation is applicable to a wide range of C(4) plants.

Cited by 12 publications

References 41 publications

Accessing molecular memoryvia a disulfide switch

Accessing molecular memoryvia a disulfide switch

Theoretical Determination of the Redox Potentials of NRH:Quinone Oxidoreductase 2 Using Quantum Mechanical/Molecular Mechanical Simulations

Computational electrochemistry: prediction of liquid-phase reduction potentials

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