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WIREs Comput Mol Sci
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The ONIOM method: its foundation and applications to metalloenzymes and photobiology

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Abstract The ONIOM (our Own N‐layer Integrated molecular Orbital molecular Mechanics) method is one of the most popular, successful, and easily‐to‐implement hybrid quantum mechanics/molecular mechanics (QM/MM) methods to treat complex molecular systems. Hybrid QM/MM methods take advantage of the high accuracy of QM methods and the low computational cost of MM methods. One key feature of the ONIOM method is a simple linear extrapolation procedure, which allows the ONIOM method to be further extended to two‐layer ONIOM(QM1:QM2), three‐layer ONIOM(QM1:QM2:MM), and, in principle, any n‐layer n‐level‐of‐theory methods. Such hierarchical features of the ONIOM method are unique among the hybrid QM/MM methods. This review article provides an overview of the theoretical foundation and recent development of the ONIOM method. Some of its recent applications to metalloenzymes and photobiology will also be highlighted. Prospective ONIOM development for more realistic simulations on the complex systems will be discussed finally. © 2011 John Wiley & Sons, Ltd. This article is categorized under: Electronic Structure Theory > Combined QM/MM Methods

Possible mechanisms for the UV‐induced peptide backbone cleavage and green‐to‐red conversion.

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Schematic changes of the electronic structures of the chromophores and the protein environments for different models at crossings.

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Dynamic changes of the bridge torsion angle (τH in degree) against bond distance (R5 in Å) for the Ntrans chromophore in the off‐state protein, evolving from Frank–Condon (FC) point in S1 (blue) hopping to S0 (pink) via nonadiabatic crossing (NC).

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Possible reaction mechanisms in Dronpa.

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The ONIOM‐optimized structures: the CoC bond cleavage (step 1: left) and the hydrogen transfer (step 2: intermediate in the middle and transition state in the right). Some important distances are also shown in Å.

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Proposed mechanisms for the radical formation and hydrogen transfer from the substrate to the Ado radial in methylmalonyl‐CoA mutase and gas phase.

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Our proposed new mechanism for bacterial tryptophan 2,3‐dioxygenase (xcTDO) (solid arrows). The previously proposed feasible dioxetane route is also shown (dash lines).

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Calculated and experimental circular dichroism spectra.

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Two conformers of soybean lipoxygenase‐1found in this study.

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(a) Two quantum mechanical (QM) models used for the ONIOM calculations. Wavy lines represent quantum mechanics/molecular mechanics (QM/MM) boundaries. The residue numbering is based on the Protein Data Bank (PDB) file 1F8N. (b) Two water conformations considered in the ONIOM calculations.

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Acceptance of a proton by the bridging hydroxide ligand.

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The hydrogen abstraction step in the myo‐inositol oxygenase catalyzed reaction.

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Models for calculations. Model‐AS and Model‐ALL contain 91 and 4617 atoms [with 91 quantum mechanical (QM) atoms including the link atoms], respectively.

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myo‐Inositol oxygenase catalyzed reaction.

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Optimized butane by full quantum mechanical (QM) and generalized ONIOM(QM:HF/3‐21G) with three units (QM: B3LYP/6‐31G* for first and second rows; MP2/6‐31G for third and fourth rows). The distances and bond angles are in plane and italic fonts, respectively.

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A schematic diagram for the ONIOM‐CT method.

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The our Own N‐layer Integrated molecular Orbital molecular Mechanics (ONIOM) extrapolative scheme and definition for two‐, three‐, and n‐layer systems. The definition of atom sets around the boundary are shown [Q1: link atom connection (LAC), H: link atom (LA), and M1: link atom host (LAH)].

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