Linear Response Functions of Densities and Spin Densities for Systematic Modeling of the QM/MM Approach for Mono- and Poly-Nuclear Transition Metal Systems

Colin K Kitakawa; Tomohiro Maruyama; Jinta Oonari; Yuki Mitsuta; Takashi Kawakami; Mitsutaka Okumura; Kizashi Yamaguchi; Shusuke Yamanaka

doi:10.3390/molecules24040821

Linear Response Functions of Densities and Spin Densities for Systematic Modeling of the QM/MM Approach for Mono- and Poly-Nuclear Transition Metal Systems

Molecules. 2019 Feb 25;24(4):821. doi: 10.3390/molecules24040821.

Authors

Colin K Kitakawa¹, Tomohiro Maruyama², Jinta Oonari³, Yuki Mitsuta⁴, Takashi Kawakami⁵, Mitsutaka Okumura⁶, Kizashi Yamaguchi⁷, Shusuke Yamanaka^{8

9}

Affiliations

¹ Graduate School of Science, Osaka University, Osaka 565-0871, Japan. kitakawac15@chem.sci.osaka-u.ac.jp.
² Graduate School of Science, Osaka University, Osaka 565-0871, Japan. maruyamat16@chem.sci.osaka-u.ac.jp.
³ Graduate School of Science, Osaka University, Osaka 565-0871, Japan. oonarij16@chem.sci.osaka-u.ac.jp.
⁴ Graduate School of Science, Osaka University, Osaka 565-0871, Japan. mitsutay13@chem.sci.osaka-u.ac.jp.
⁵ Graduate School of Science, Osaka University, Osaka 565-0871, Japan. kawakami@chem.sci.osaka-u.ac.jp.
⁶ Graduate School of Science, Osaka University, Osaka 565-0871, Japan. ok@chem.sci.osaka-u.ac.jp.
⁷ Institute for Nanodesign, Osaka University, Osaka 560-8531, Japan. yama@chem.sci.osaka-u.ac.jp.
⁸ Graduate School of Science, Osaka University, Osaka 565-0871, Japan. syama@chem.sci.osaka-u.ac.jp.
⁹ Quantum information, Quantum Biology division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 560-8531, Japan. syama@chem.sci.osaka-u.ac.jp.

Abstract

We applied our analysis, based on a linear response function of density and spin density, to two typical transition metal complex systems-the reaction centers of P450, and oxygen evolving center in Photosystem II, both of which contain open-shell transition metal ions. We discuss the relationship between LRF of electron density and spin density and the types of units and interactions of the systems. The computational results are discussed in relation to quantum mechanics (QM) cluster and quantum mechanics/molecular mechanics (QM/MM) modeling that are employed to compute the reaction centers of enzymes.

Keywords: QM/MM; enzymes; linear response function; transition metal complexes.

MeSH terms

Catalysis
Coordination Complexes / chemistry*
Electron Transport
Molecular Dynamics Simulation
Molecular Structure
Oxidation-Reduction
Oxygen / chemistry*
Photochemical Processes
Photosystem II Protein Complex / chemistry
Quantum Theory
Transition Elements / chemistry*
Water

Substances

Coordination Complexes
Photosystem II Protein Complex
Transition Elements
Water
Oxygen