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 Kitakawa,Shusuke Yamanaka,Yuki Mitsuta,Mitsutaka Okumura,Kizashi Yamaguchi,Tomohiro Maruyama,Takashi Kawakami,Jinta Oonari

doi:10.3390/molecules24040821

Colin Kitakawa, Shusuke Yamanaka + Show 6 more

Open Access

https://doi.org/10.3390/molecules24040821

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Journal: Molecules (Basel, Switzerland)	Publication Date: Feb 25, 2019
Citations: 3	License type: CC BY 4.0

Affiliation: Osaka University

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.

Highlights

The quantum mechanics/molecular mechanics (QM/MM) approach, which was first proposed in the 1970s [1,2], is widely applied to biochemical reactions and molecular materials [3,4,5,6].The essential idea of this approach is that the entire system can be divided into the QM region, that is described by quantum mechanics and the MM region, that is described by using classical point charges and force fields
This “electric embedding” type of QM/MM treatment usually leads to an improved modeling of the target system as desired, but sometimes it leads to over-polarization of the QM region near the QM/MM boundaries [4], resulting in less accuracy
The validity of the QM description critically depends on the appropriate choices of important residues, lipids, and water molecules that are included in the QM region [5]

Summary

Introduction

The quantum mechanics/molecular mechanics (QM/MM) approach, which was first proposed in the 1970s [1,2], is widely applied to biochemical reactions and molecular materials [3,4,5,6].The essential idea of this approach is that the entire system can be divided into the QM region, that is described by quantum mechanics and the MM region, that is described by using classical point charges and force fields. The MM region is, important, because the surrounding environment, such as proteins, lipids, and solvents often strongly affect the electronic structure of the QM region For this reason, in most contemporary QM/MM methods, the electronic structure of the QM region is calculated in the presence of the MM point charges. In most contemporary QM/MM methods, the electronic structure of the QM region is calculated in the presence of the MM point charges This “electric embedding” type of QM/MM treatment usually leads to an improved modeling of the target system as desired, but sometimes it leads to over-polarization of the QM region near the QM/MM boundaries [4], resulting in less accuracy.

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Conclusion