Tunneling matrix element and tunneling pathways of protein electron transfer calculated with a fragment molecular orbital method

Practical ways to calculate the tunneling matrix elements and analyze the tunneling pathways for protein electron-transfer (ET) reactions with a fragment molecular orbital (FMO) method are presented. The straightforward use of minimal basis sets only for the atoms involved in the covalent bond detac...

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Veröffentlicht in:The Journal of chemical physics 2020-09, Vol.153 (10), p.104104-104104
Hauptverfasser: Kitoh-Nishioka, Hirotaka, Shigeta, Yasuteru, Ando, Koji
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creator Kitoh-Nishioka, Hirotaka
Shigeta, Yasuteru
Ando, Koji
description Practical ways to calculate the tunneling matrix elements and analyze the tunneling pathways for protein electron-transfer (ET) reactions with a fragment molecular orbital (FMO) method are presented. The straightforward use of minimal basis sets only for the atoms involved in the covalent bond detachment in FMO can properly describe the ETs through the protein main-chains with the cost-effective two-body corrections (FMO2) without losing the quality of double-zeta basis sets. The current FMO codes have been interfaced with density functional theory, polarizable continuum model, and model core potentials, with which the FMO-based protein ET calculations can consider the effects of electron correlation, solvation, and transition-metal redox centers. The reasonable performance of the FMO-based ET calculations is demonstrated for three different sets of protein-ET model molecules: (1) hole transfer between two tryptophans covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, (2) ET between two plastoquinones covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, and (3) hole transfer between ruthenium (Ru) and copper (Cu) complexes covalently bridged by a stretch of a polyglycine linker as a model for Ru-modified derivatives of azurin.
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source American Institute of Physics (AIP) Journals; Alma/SFX Local Collection
subjects Computational chemistry
Continuum modeling
Coordination compounds
Copper
Covalence
Covalent bonds
Density functional theory
Electron transfer
Electrons
Molecular orbitals
Physics
Proteins
Ruthenium
Solvation
Transition metals
title Tunneling matrix element and tunneling pathways of protein electron transfer calculated with a fragment molecular orbital method
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