Recent Applications of Hybrid Ab Initio Quantum Mechanics – Molecular Mechanics Simulations to Biological Macromolecules

Kang, Jiyoung; Tateno, Masaru

doi:10.5772/35092

Cited by 2 publications

(1 citation statement)

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“…Great progresses have been achieved up to date for improvement of QM/MM calculation algorithms and their applications to biological systems [8][9][10][11][12][13][14][15][16][17][18][19][20][21]. Importance of the environments has been reported from many QM/MM studies.…”

Section: Hybrid Qm/mm Calculation Schemementioning

confidence: 99%

Recent Progresses in Ab Initio Electronic Structure Calculation toward Understandings of Functional Mechanisms of Biological Macromolecular Systems

Kang¹,

Sumi²,

Tateno³

2019

Panorama of Contemporary Quantum Mechanics - Concepts and Applications

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In this chapter, we present recent advances of theoretical analyses toward understandings of functional mechanisms of biological macromolecular systems, employing ab initio electronic structure calculations. Two distinct types of triggers to invoke dramatic rearrangements of electronic structures in the reaction centers are revealed by full ab initio quantum mechanics (QM) calculations (first example) and hybrid ab initio QM/molecular mechanics (MM) molecular dynamics (MD) calculations (second example). First, we demonstrate dramatic rearrangements of molecular orbitals (MOs) induced by binding of a hydroxyl ion (OH À) to the [4Fe-3S] cluster found in hydrogenases, which catalyzes both dissociation and production of dihydrogen (H 2). This induces the significant delocalization of the LUMO, resulting in formation of electron transfer pathways required for the catalysis. Thus, in organisms, just a tiny species (e.g. OH À ligand) can play a key role for the biological functions. Second, we indicate dynamical rearrangements of MOs occurring in the enzymatic reactions of RNA-protein complexes. As the catalysis proceeds, the reactive MOs, which do not belong to the frontier orbitals in the initial stages of the reaction, are dramatically reconstituted in the hybrid ab initio QM/MM MD simulations, resulting in the frontier orbitals, which is a feature characteristic to biological macromolecular systems.

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