Iron Complex as a Water-Oxidizing Catalyst: Free-Energy Barriers, Proton-Coupled Electron Transfer, Spin Dynamics, and Role of Water Molecules in the Reaction Mechanism

2019 ◽  
Vol 124 (1) ◽  
pp. 205-218 ◽  
Author(s):  
Koteswara Rao Gorantla ◽  
Bhabani S. Mallik
Keyword(s):  
Electron Transfer ◽  
Free Energy ◽  
Reaction Mechanism ◽  
Spin Dynamics ◽  
Iron Complex ◽  
Water Molecules ◽  
Energy Barriers ◽  
Catalyst Free ◽  
Proton Coupled Electron Transfer

scholarly journals Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome c oxidase

2015 ◽  
Vol 112 (7) ◽  
pp. 2040-2045 ◽  
Author(s):  
Vivek Sharma ◽  
Giray Enkavi ◽  
Ilpo Vattulainen ◽  
Tomasz Róg ◽  
Mårten Wikström
Keyword(s):  
Electron Transfer ◽  
Free Energy ◽  
Proton Transfer ◽  
Short Circuit ◽  
Proton Pumping ◽  
Free Energy Calculations ◽  
Water Molecules ◽  
Transfer Event ◽  
Proton Coupled Electron Transfer ◽  
Dynamics Simulations

Molecular oxygen acts as the terminal electron sink in the respiratory chains of aerobic organisms. Cytochrome c oxidase in the inner membrane of mitochondria and the plasma membrane of bacteria catalyzes the reduction of oxygen to water, and couples the free energy of the reaction to proton pumping across the membrane. The proton-pumping activity contributes to the proton electrochemical gradient, which drives the synthesis of ATP. Based on kinetic experiments on the O–O bond splitting transition of the catalytic cycle (A → PR), it has been proposed that the electron transfer to the binuclear iron–copper center of O2 reduction initiates the proton pump mechanism. This key electron transfer event is coupled to an internal proton transfer from a conserved glutamic acid to the proton-loading site of the pump. However, the proton may instead be transferred to the binuclear center to complete the oxygen reduction chemistry, which would constitute a short-circuit. Based on atomistic molecular dynamics simulations of cytochrome c oxidase in an explicit membrane–solvent environment, complemented by related free-energy calculations, we propose that this short-circuit is effectively prevented by a redox-state–dependent organization of water molecules within the protein structure that gates the proton transfer pathway.

scholarly journals The Reaction Mechanism with Free Energy Barriers for Electrochemical Dihydrogen Evolution on MoS2

2015 ◽  
Vol 137 (20) ◽  
pp. 6692-6698 ◽  
Author(s):  
Yufeng Huang ◽  
Robert J. Nielsen ◽  
William A. Goddard ◽  
Manuel P. Soriaga
Keyword(s):  
Free Energy ◽  
Reaction Mechanism ◽  
Energy Barriers

The role of proton coupled electron transfer in water oxidation

2012 ◽  
Vol 5 (7) ◽  
pp. 7704 ◽  
Author(s):  
Christopher J. Gagliardi ◽  
Aaron K. Vannucci ◽  
Javier J. Concepcion ◽  
Zuofeng Chen ◽  
Thomas J. Meyer
Keyword(s):  
Electron Transfer ◽  
Water Oxidation ◽  
Proton Coupled Electron Transfer

The Role of Free Energy in Interligand Electron Transfer

1989 ◽  
pp. 253-266 ◽  
Author(s):  
L. K. Orman ◽  
D. R. Anderson ◽  
T. Yabe ◽  
J. B. Hopkins
Keyword(s):  
Electron Transfer ◽  
Free Energy

Role of Proton-Coupled Electron Transfer in the Redox Interconversion between Benzoquinone and Hydroquinone

2012 ◽  
Vol 134 (45) ◽  
pp. 18538-18541 ◽  
Author(s):  
Na Song ◽  
Christopher J. Gagliardi ◽  
Robert A. Binstead ◽  
Ming-Tian Zhang ◽  
Holden Thorp ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Proton Coupled Electron Transfer ◽  
Redox Interconversion

scholarly journals Intriguing Role of Water in Plant Hormone Perception

2021 ◽  
Author(s):  
Chuankai Zhao ◽  
Diego Eduardo Kleiman ◽  
Diwakar Shukla
Keyword(s):  
Free Energy ◽  
Plant Growth ◽  
Binding Site ◽  
Plant Hormones ◽  
Plant Hormone ◽  
Water Molecules ◽  
Water Displacement ◽  
Dynamics Simulations ◽  
Free Energy Of Binding

Plant hormones are small molecules that regulate plant growth, development, and responses to biotic and abiotic stresses. Plant hormones are specifically recognized by the binding site of their receptors. In this work, we investigated the role of water displacement and reorganization at the binding site of plant receptors on the binding of eight classes of phytohormones (auxin, jasmonate, gibberellin, strigolactone, brassinosteroid, cytokinin, salicylic acid, and abscisic acid) using extensive molecular dynamics simulations and inhomogeneous solvation theory. Our findings demonstrated that displacement of water molecules by phytohormones contributes to free energy of binding via entropy gain and is associated with free energy barriers. Also, our results have shown that displacement of unfavorable water molecules in the binding site can be exploited in rational agrochemical design. Overall, this study uncov- ers the role of water molecules in plant hormone perception, which creates new avenues for agrochemical design to target plant growth and development.

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