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Quantum Chemical and QM/MM Models in Biochemistry

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Biomolecular Simulations

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2022))

Abstract

Quantum chemical (QC) calculations provide a basis for deriving a microscopic understanding of enzymes and photobiological systems. Here we describe how QC models can be used to explore the electronic structure, dynamics, and energetics of biomolecules. We introduce the hybrid quantum mechanics/classical mechanics (QM/MM) approach, where a quantum mechanically described system of interest is embedded in a classically described force field representation of the biochemical surroundings. We also discuss the QM cluster model approach, as well as embedding theories, that provide complementary methodologies to model quantum mechanical effects in biomolecules. The chapter also provides some practical guides for building quantum biochemical models using the quinone reduction catalysis in respiratory complex I and a model reaction in solution as examples.

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Acknowledgments

We thank Dr. Mikael P. Johansson for helpful discussions. Computational resources were provided in part by HPC Europa3 grant 2000831 HPCE3 “Mechanism of long-range electron transfer in respiratory complex I.”

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Authors and Affiliations

  1. Department Chemie, Technische Universität München, Garching, Germany

    Patricia Saura, Michael Röpke, Ana P. Gamiz-Hernandez & Ville R. I. Kaila

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  1. Patricia Saura
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  2. Michael Röpke
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  3. Ana P. Gamiz-Hernandez
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  4. Ville R. I. Kaila
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Correspondence to Ville R. I. Kaila .

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Editors and Affiliations

  1. Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France

    Massimiliano Bonomi

  2. Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy

    Carlo Camilloni

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Saura, P., Röpke, M., Gamiz-Hernandez, A.P., Kaila, V.R.I. (2019). Quantum Chemical and QM/MM Models in Biochemistry. In: Bonomi, M., Camilloni, C. (eds) Biomolecular Simulations. Methods in Molecular Biology, vol 2022. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9608-7_4

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  • DOI: https://doi.org/10.1007/978-1-4939-9608-7_4

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