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Photo-Active Biological Molecular Materials: From Photoinduced Dynamics to Transient Electronic Spectroscopies

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QM/MM Studies of Light-responsive Biological Systems

Part of the book series: Challenges and Advances in Computational Chemistry and Physics ((COCH,volume 31))

Abstract

We present an overview of a methodology for the simulation of the photo-response of biological (macro)molecules, designed around a Quantum Mechanics / Molecular Mechanics (QM/MM) subtractive scheme. The resulting simulation workflow, that goes from the characterization of the photo-active system to the modeling of (transient) electronic spectroscopies is implemented in the software COBRAMM, but is completely general and can be used in the framework of any specific QM/MM implementation. COBRAMM is a smart interface to existing state-of-the-art theoretical chemistry codes, combining different levels of description and different algorithms to realize tailored problem-driven computations. The power of this approach is illustrated by reviewing the studies of two fundamental problems involving biological light-sensitive molecules. First, we will consider the photodynamics of the retinal molecule, the pigment of rhodopsin, a visual receptor protein contained in the rod cells of the retina. Retinal, with its light-induced isomerization, triggers a cascade of events leading to the production of the nerve impulse. Then, we will review some studies focusing on the interaction of DNA systems with ultraviolet (UV) light, a problem that has become one of the benchmark for the development of nonlinear spectroscopy, because of the ultrashort excited state lifetimes that arise from very efficient radiationless excited state decay and consent self-protection of DNA against UV damage.

I.C., M.B., A.N. and I.R. equally contributed to this work.

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Notes

  1. 1.

    Note that the PES exploration step is omitted as we address solely the ground state conformational freedom of the system.

  2. 2.

    Technically realized by keeping the delay between pump and probe short with respect to the molecular dynamics.

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Acknowledgements

The authors acknowledge support from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 814492. M. G acknowledges the support from the European Research Council Advanced Grant STRATUS (ERC-2011-AdG No. 291198). I.R. acknowledges the use of HPC resources of the Pôle Scientifique de Modélisation Numérique (PSMN) at the École Normale Supérieure de Lyon, France. M.G. and I. R. acknowledge support by the French Agence National de la Recherche (FEMTO-2DNA, ANR-15-CE29-0010). Francesco Segatta and Vishal Kumar Jaiswal are gratefully acknowledged for useful discussions.

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  1. Dipartimento di Chimica Industriale Toso Montanari, Universita di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy

    Irene Conti, Matteo Bonfanti, Artur Nenov, Ivan Rivalta & Marco Garavelli

  2. Univ Lyon, Ens de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie, UMR 5182, 69342, Lyon, France

    Ivan Rivalta

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  1. Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland

    Tadeusz Andruniów

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    Massimo Olivucci

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Conti, I., Bonfanti, M., Nenov, A., Rivalta, I., Garavelli, M. (2021). Photo-Active Biological Molecular Materials: From Photoinduced Dynamics to Transient Electronic Spectroscopies. In: Andruniów, T., Olivucci, M. (eds) QM/MM Studies of Light-responsive Biological Systems. Challenges and Advances in Computational Chemistry and Physics, vol 31. Springer, Cham. https://doi.org/10.1007/978-3-030-57721-6_2

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