Academic literature on the topic 'Computational photobiology'

In this paper we review the results of a group of computational studies of the spectroscopy and photochemistry of light-responsive proteins. We focus on the use of quantum mechanics/molecular mechanics protocols based on a multiconfigurational quantum chemical treatment. More specifically, we discuss the use, limitations, and application of the ab initio CASPT2//CASSCF protocol that, presently, constitutes the method of choice for the investigation of excited state organic molecules, most notably, biological chromophores and fluorophores. At the end of this Review we will also see how the computational investigation of the visual photoreceptor rhodopsin is providing the basis for the design of light-driven artificial molecular devices.

In this paper, we discuss the results of our recent studies on the molecular mechanism, which stand at the basis of the photochemical processes occurring in photobiological systems. These results are obtained using modern, robust, and fairly accurate high-level quantum chemical methods.

Photochemistry is a mature science. A characteristic hallmark of a consolidated scientific discipline is that it increasingly broadens its scope of interests from an initial central core toward the periphery where it interacts with other areas. Most of the current scientific research is characterized by an enriching multidisciplinarity, focusing on topics that combine backgrounds from different fields. In this way, the largest advances are taking place at the interphase between areas where different fields meet.This multidisciplinarity is, I believe, also a characteristic feature of the current situation for photochemistry. Thus, photochemistry was initially focused on the understanding and rationalization at a molecular level of the events occurring after light absorption by simple organic compounds. Molecular organic photochemistry constituted the core of this discipline, and it largely benefited from advances in the understanding of the electronic states provided by quantum mechanics. Later, photochemistry started to grow toward areas such as photobiology, photoinduced electron transfer, supramolecular photochemistry, and photochemistry in heterogeneous media, always expanding its sphere of interest.This context of increasing diversity in topics and specialization is reflected in this issue of Pure and Applied Chemistry. The contributors correspond to some of the plenary plus two invited lectures of the XXth IUPAC Symposium that was held 17ñ22 July in Granada, Spain. The program included plenary and invited lectures and oral contributions grouped in 13 sections covering femtochemistry, photochemistry of biomacromolecules, single-molecule photochemistry, and computational methods in photochemistry to nanotechnology, among others. These workshop titles give an idea of the breadth of themes that were included in this symposium. While it is obvious that the list of contributions correspond to different subdisciplines in photochemistry, all of them have a common scientific framework to rationalize the facts.The purpose of the symposium was to present an overview of the current status of some research fronts in photochemistry. This issue begins with the 2004 Porter Medal Lecture awarded jointly by the Asian, European, and Interamerican Photochemical Societies that was given to Prof. Graham Fleming (University of California, Berkeley) for his continued advances in photosynthesis. Prof. Flemingís studies have constituted a significant contribution to the understanding of the interplay between the structure of photosynthetic centers of green plants and the mechanism of energy migration toward the photosynthetic centers. These events take place in a very short time scale and are governed by the spatial arrangement of the constituents.Continuing with photobiology, the second article by Prof. Jean Cadet (Grenoble University) describes the type of photochemical damage and photoproducts arising from DNA UV irradiation. Knowledge of these processes is important for a better understanding of skin cancer and the possibilities for DNA repair. Closely related with DNA damage occurring upon irradiation, the article by Prof. Tetsuro Majima (Osaka University) provides an account of his excellent work on photosensitized oneelectron oxidation of DNA.The concept of "conical intersection", developed initially by Robb and Bernardi to rationalize the relaxation of excited states, led to the foundation of computational photochemistry, which has proved to be of general application to photochemical reactions. In this issue, Prof. Massimo Olivucci (University of Siena) shows that quantum chemical calculations can also be applied to photochemical reactions occurring in photobiology and, in particular, to the problem of vision. These calculations are characterized by the large number of atoms that are included and the fact that they have to estimate at a high calculation level and with high accuracy the energy of states differring in a few kcal mol-1.The next article corresponds to one of the two invited lectures included in this issue. The one given by Dr. Virginie Lhiaubet-Vallet (Technical University of Valencia) in the workshop Photophysical and Photochemical Approaches in the Control of Toxic and Therapeutic Activity of Drugs describes the enantioselective quenching of chiral drug excited states by biomolecules. Moving from photobiology to free radical polymerization with application in microlithography, the article by Prof. Tito Scaiano (University of Ottawa) reports among other probes an extremely elegant approach to detect the intermediacy of radicals in photochemical reactions based on a silent fluorescent molecular probe containing a free nitroxyl radical.Solar energy storage is a recurrent topic and a long-desired application of photochemistry. In her comprehensive contribution, Prof. Ana Moore (Arizona State University) summarizes the continued seminal contribution of her group to the achievement of an efficient solar energy storage system based on the photochemical generation of long-lived charge-separated states. Another possibility of solar energy storage consists of water splitting. In his article, Prof. Haruo Inoue (Tokyo Metropolitan University) deals with artificial photosynthetic methods based on the use of ruthenium porphyrins as photosensitizers for the two-electron oxidation of water with formation of dioxygen.Also in applied photochemistry, Prof. Luisa De Cola (University of Amsterdam) reports on intramolecular energy transfer in dinuclear metal complexes having a meta-phenylene linker. The systems described by Prof. De Cola have potential application in the field of light-emitting diodes, since most of the complexes described exhibit electroluminescence. The second invited lecture is by Dr. Alberto Credi (University of Bologna), one of Europeís most promising young photochemists. In his interesting article, the operation upon light excitation of a rotaxane molecular machine is described. A macro-ring acting as electron donor moiety in a charge-transfer complex is threaded in a dumbbell-shaped component having two viologen units with different redox potential. Light absorption produces the cyclic movement of the macro-ring from one viologen station to the other.The last two contributions fall within the more classic organic photochemistry realm. Prof. Axel Griesbeck (University of Cologne) describes the multigram synthesis of antimalarial peroxides using singlet-oxygen photosensitizers adsorbed or bonded to polymer matrices. The last contribution comes from Prof. Heinz Roth (University of Rutgers), who has worked during his entire career in the fields of organic photochemistry and radical ion chemistry. Prof. Roth has summarized his vast knowledge in radical ion chemistry, reviewing the mechanism of triplet formation arising from radical ion pair recombination. This mechanism for triplet formation is currently gaining a renewed interest owing to the potential applicability to the development of phosphors.I hope that the present selection will be appealing and attractive for a broad audience of readers interested in photochemistry and will give readers an idea of the state of the art of some current topics in this area.Hermenegildo GarcíaConference Editor

The mechanisms for the reaction of methyl radical with ethylamine were determined by the density functional theory using the atomic structures of the reactants, transition states and products optimized at the B3LYP/6-311++G(3df,2p) level of theory. Seven transition states were identified for the production of CH3CHNH2 + CH4 (TS1), CH3CH2NH + CH4 (TS2), CH2CH2NH2 + CH4 (TS3), CH3CH2NHCH3 + H (TS4), CH3CH2 + CH3NH2 (TS5), C2H6 + CH2NH2 (TS6) and C3H8 + NH2 (TS7) with the corresponding barriers, 9.34, 9.90, 13.46, 27.70, 39.12, 45.82 and 69.34 kcal/mol. Thermodynamics analysis and potential energy surface showed that H-abstraction pathways take place easier than NH2-, CH3–abstractions, H-substitution of the NH2 group and CH3-substitution in ethylamine. The H-abstraction in methylene group of ethylamine is the most favourable on the PES of this reaction system. 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Michael, High-Temperature Shock Tube and Modeling Studies on the Reactions of Methanol with D-Atoms and CH3-Radicals. The Journal of Physical Chemistry A, 2013. 117(40): p. 10186-10195.[6] Poutsma, M.L., Extension of Structure–Reactivity Correlations for the Hydrogen Abstraction Reaction to the Methyl Radical and Comparison to the Chlorine Atom, Bromine Atom, and Hydroxyl Radical. The Journal of Physical Chemistry A, 2016. 120(26): p. 4447-4454.[7] Shi, J., et al., Kinetic mechanisms of hydrogen abstraction reactions from methanol by methyl, triplet methylene and formyl radicals. Computational and Theoretical Chemistry, 2015. 1074: p. 73-82.[8] Peukert, S.L., et al., Direct Measurements of Rate Constants for the Reactions of CH3 Radicals with C2H6, C2H4, and C2H2 at High Temperatures. The Journal of Physical Chemistry A, 2013. 117(40): p. 10228-10238.[9] Sangwan, M., E.N. Chesnokov, and L.N. 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In recent years, world economy and technological advancement have been transformed by Genomics, which allows us to study, design and build biologically relevant molecules. Genomics is already deeply embedded in industries as diverse as pharmaceutical, food and agricultural, environmental and bio-tech in general. Fast and cheap tools for gene sequencing, protein expression and analysis are commonly used for high-throughput genomic-related studies. However, due to experimental difficulties and long time scales (e.g., protein crystallization), protein structure determination, and thus the fundamental structure function rationalization, cannot presently be performed at the same fast pace: a fact that is slowing down the discovery of proteins with new features, as well as ex novo design. These difficulties are particularly felt in the field of photobiology, where the crystal structure of Bovine rhodopsin (Rh, retina dim-light visual photo-receptor), still remains the only structure of a vertebrate photo-receptor sensor available for photobiological studies since the year 2000. Rhodopsins constitute a class of light-triggered proteins that can be found throughout the whole spectrum of living organisms, and represent the perfect blue-print for building light-activated bio-molecular machines. In principle, the problem of not having a sufficient number of rhodopsins molecular structures could be circumvented and overcome with the construction of accurate atomistic computer models of the set of studied photoreceptors, which would allow: (i) in silico fundamental structure-function characterization, (ii) thorough and detailed screening of mutant series, and even (iii) ex novo design. Nevertheless, such models should also be constructed using a fast, relatively cheap, reliable and standardized protocol, of known accuracy. In this thesis, we refine and test the Automatic Rhodopsin Modeling (ARM) computational protocol, which we demonstrate as being capable of helping to address the above issues. Such protocol has the primary target of generating congruous quantum mechanical/molecular mechanical (QM/MM) models of rhodopsins, with the aim of facilitating systematic rhodopsin-mutants studies. The cornerstone of this thesis is the validation of the ARM protocol as a successful attempt to provide a basis for the standardization and reproducibility of rhodopsin QM/MM models, aimed to study the behaviour of photoactive molecules. First, we validate the ARM protocol, which employs a CASPT2//CASSCF/AMBER scheme, for a benchmark set of rhodopsins from different biological kingdoms. We show that ARM is able to reproduce and predict absorption trends in rhodopsin protein sets, with blue-shifted values not much displaced (a few kcal/mol) from the observed data. Secondly, we present how to use this protocol towards a better design of novel mutations as applications for Optogenetics, an innovative biological tool aimed to visualize and control neuron signals through light. Two different microbial rhodopsins are studied: Krokinobacter eikastus rhodopsin 2 (KR2), a light-driven outward sodium pump, and Anabaena sensory rhodopsin (ASR), a light sensor. In both cases, the qualitative and quantitative information acquired from the ARM-obtained QM/MM models reveal nature (electrostatic or steric) and extent of the mutation-induced changes on the retinal configuration, which, in turn, are the cause of the shift in the absorption wavelength of the relative mutants. Finally, we explore the fluorescence of ASR mutants, particularly useful for the visualization of neuronal activity. The target of this work is to use QM/MM simulations to understand the opposite behaviour observed in two blue-shifted ASR mutants, where one presents a negligible fluorescence, while the other displays one order of magnitude enhanced fluorescence, with respect to the wild type protein. Our QM/MM models show that specific electrostatic and steric interactions control the character mixing of different electronic states, opening a path to the rational engineering of highly fluorescent rhodopsins. In conclusion, within the limits of its automation, the ARM protocol allows the study of ground and excited states of specific photoactive proteins: rhodopsins. This opens the way to an improved molecular-level understanding of rhodopsin photochemistry and photobiology. The results obtained highlight the importance of having a standardized, effective and automatic protocol, which renders this kind of studies more efficient and accessible, by drastically shortening the time required to produce accurate and congruous QM/MM models. For the above reasons the author of the present thesis believes that ARM stands as an important cogwheel in the virtuous cycle between experimental and theoretical work, aimed to prepare the photobiological tools for tomorrow’s needs.