1
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Blanco-Gonzalez A, Manathunga M, Yang X, Olivucci M. Comparative quantum-classical dynamics of natural and synthetic molecular rotors show how vibrational synchronization modulates the photoisomerization quantum efficiency. Nat Commun 2024; 15:3499. [PMID: 38664371 PMCID: PMC11045841 DOI: 10.1038/s41467-024-47477-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
We use quantum-classical trajectories to investigate the origin of the different photoisomerization quantum efficiency observed in the dim-light visual pigment Rhodopsin and in the light-driven biomimetic molecular rotor para-methoxy N-methyl indanylidene-pyrrolinium (MeO-NAIP) in methanol. Our results reveal that effective light-energy conversion requires, in general, an auxiliary molecular vibration (called promoter) that does not correspond to the rotary motion but synchronizes with it at specific times. They also reveal that Nature has designed Rhodopsin to exploit two mechanisms working in a vibrationally coherent regime. The first uses a wag promoter to ensure that ca. 75% of the absorbed photons lead to unidirectional rotations. The second mechanism ensures that the same process is fast enough to avoid directional randomization. It is found that MeO-NAIP in methanol is incapable of exploiting the above mechanisms resulting into a 50% quantum efficiency loss. However, when the solvent is removed, MeO-NAIP rotation is predicted to synchronize with a ring-inversion promoter leading to a 30% increase in quantum efficiency and, therefore, biomimetic behavior.
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Affiliation(s)
- Alejandro Blanco-Gonzalez
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Madushanka Manathunga
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Xuchun Yang
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Massimo Olivucci
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100, Siena, Italy.
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2
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Palombo R, Barneschi L, Pedraza-González L, Yang X, Olivucci M. Picosecond quantum-classical dynamics reveals that the coexistence of light-induced microbial and animal chromophore rotary motion modulates the isomerization quantum yield of heliorhodopsin. Phys Chem Chem Phys 2024; 26:10343-10356. [PMID: 38501246 DOI: 10.1039/d4cp00193a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Rhodopsins are light-responsive proteins forming two vast and evolutionary distinct superfamilies whose functions are invariably triggered by the photoisomerization of a single retinal chromophore. In 2018 a third widespread superfamily of rhodopsins called heliorhodopsins was discovered using functional metagenomics. Heliorhodopsins, with their markedly different structural features with respect to the animal and microbial superfamilies, offer an opportunity to study how evolution has manipulated the chromophore photoisomerization to achieve adaptation. One question is related to the mechanism of such a reaction and how it differs from that of animal and microbial rhodopsins. To address this question, we use hundreds of quantum-classical trajectories to simulate the spectroscopically documented picosecond light-induced dynamics of a heliorhodopsin from the archaea thermoplasmatales archaeon (TaHeR). We show that, consistently with the observations, the trajectories reveal two excited state decay channels. However, inconsistently with previous hypotheses, only one channel is associated with the -C13C14- rotation of microbial rhodopsins while the second channel is characterized by the -C11C12- rotation typical of animal rhodopsins. The fact that such -C11C12- rotation is aborted upon decay and ground state relaxation, explains why illumination of TaHeR only produces the 13-cis isomer with a low quantum efficiency. We argue that the documented lack of regioselectivity in double-bond excited state twisting motion is the result of an "adaptation" that could be completely lost via specific residue substitutions modulating the steric hindrance experienced along the isomerization motion.
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Affiliation(s)
- Riccardo Palombo
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Siena, Italy.
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA.
| | - Leonardo Barneschi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Siena, Italy.
| | - Laura Pedraza-González
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, I-56124 Pisa, Italy
| | - Xuchun Yang
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA.
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Siena, Italy.
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA.
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3
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Francis WJC, Grewal H, Wainwright AAC, Yang X, Olivucci M, Miller RJD. Resonant multiphoton processes and excitation limits to structural dynamics. Struct Dyn 2024; 11:024301. [PMID: 38433875 PMCID: PMC10908556 DOI: 10.1063/4.0000239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/13/2024] [Indexed: 03/05/2024]
Abstract
Understanding the chemical reactions that give rise to functional biological systems is at the core of structural biology. As techniques are developed to study the chemical reactions that drive biological processes, it must be ensured that the reaction occurring is indeed a biologically relevant pathway. There is mounting evidence indicating that there has been a propagation of systematic error in the study of photoactive biological processes; the optical methods used to probe the structural dynamics of light activated protein functions have failed to ensure that the photoexcitation prepares a well-defined initial state relevant to the biological process of interest. Photoexcitation in nature occurs in the linear (one-photon per chromophore) regime; however, the extreme excitation conditions used experimentally give rise to biologically irrelevant multiphoton absorption. To evaluate and ensure the biological relevance of past and future experiments, a theoretical framework has been developed to determine the excitation conditions, which lead to resonant multiphoton absorption (RMPA) and thus define the excitation limit in general for the study of structural dynamics within the 1-photon excitation regime. Here, we apply the theoretical model to bacteriorhodopsin (bR) and show that RMPA occurs when excitation conditions exceed the linear saturation threshold, well below typical excitation conditions used in this class of experiments. This work provides the guidelines to ensure excitation in the linear 1-photon regime is relevant to biological and chemical processes.
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Affiliation(s)
- William J C Francis
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada and Department of Physics, University of Toronto, 60 St. George Street, Toronto, Ontario M5S 3J1, Canada
| | - Harmanjot Grewal
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada and Department of Physics, University of Toronto, 60 St. George Street, Toronto, Ontario M5S 3J1, Canada
| | - Alexander A C Wainwright
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada and Department of Physics, University of Toronto, 60 St. George Street, Toronto, Ontario M5S 3J1, Canada
| | | | | | - R J Dwayne Miller
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada and Department of Physics, University of Toronto, 60 St. George Street, Toronto, Ontario M5S 3J1, Canada
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4
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Bezabih MS, Kaliakin DS, Blanco-González A, Barneschi L, Tarnovsky AN, Olivucci M. Comparative Study of Uracil Excited-State Photophysics in Water and Acetonitrile via RMS-CASPT2-Driven Quantum-Classical Trajectories. J Phys Chem B 2023; 127:10871-10879. [PMID: 38055701 DOI: 10.1021/acs.jpcb.3c06433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
We present a nonadiabatic molecular dynamics study of the ultrafast processes occurring in uracil upon UV light absorption, leading to electronic excitation and subsequent nonradiative decay. Previous studies have indicated that the mechanistic details of this process are drastically different depending on whether the process takes place in the gas phase, acetonitrile, or water. However, such results have been produced using quantum chemical methods that did not incorporate both static and dynamic electron correlation. In order to assess the previously proposed mechanisms, we simulate the photodynamics of uracil in the three environments mentioned above using quantum-classical trajectories and, for solvated uracil, hybrid quantum mechanics/molecular mechanics (QM/MM) models driven by the rotated multistate complete active space second-order perturbation (RMS-CASPT2) method. To do so, we exploit the gradient recently made available in OpenMolcas and compare the results to those obtained using the complete active space self-consistent field (CASSCF) method only accounting for static electron correlation. We show that RMS-CASPT2 produces, in general, a mechanistic picture different from the one obtained at the CASSCF level but confirms the hypothesis advanced on the basis of previous ROKS and TDDFT studies thus highlighting the importance of incorporating dynamic electron correlation in the investigation of ultrafast electronic deactivation processes.
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Affiliation(s)
- Meseret Simachew Bezabih
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Danil S Kaliakin
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | | | - Leonardo Barneschi
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
| | - Alexander N Tarnovsky
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
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5
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Barneschi L, Kaliakin D, Huix-Rotllant M, Ferré N, Filatov Gulak M, Olivucci M. Assessment of the Electron Correlation Treatment on the Quantum-Classical Dynamics of Retinal Protonated Schiff Base Models: XMS-CASPT2, RMS-CASPT2, and REKS Methods. J Chem Theory Comput 2023; 19:8189-8200. [PMID: 37937990 DOI: 10.1021/acs.jctc.3c00879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
We compare the performance of three different multiconfigurational wave function-based electronic structure methods and two implementations of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method. The study is characterized by three features: (i) it uses a small set of quantum-classical trajectories rather than potential energy surface mapping, (ii) it focuses, exclusively, on the photoisomerization of retinal protonated Schiff base models, and (iii) it probes the effect of both methyl substitution and the increase in length of the conjugate π-system. For each tested method, the corresponding analytical gradients are used to drive the quantum-classical (Tully's FSSH method) trajectory propagation, including the recent multistate XMS-CASPT2 and RMS-CASPT2 gradients. It is shown that while CASSCF, XMS-CASPT2, and RMS-CASPT2 yield consistent photoisomerization dynamics descriptions, REKS produces, in some of these systems, qualitatively different behavior that is attributed to a flatter and topographically different excited state potential energy surface. The origin of this behavior can be traced back to the effect of the employed density functional approximation. The above studies are further expanded by benchmarking, at the CASSCF and REKS levels, the electronic structure methods using a QM/MM model of the visual pigment rhodopsin.
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Affiliation(s)
- Leonardo Barneschi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
| | - Danil Kaliakin
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Miquel Huix-Rotllant
- Aix-Marseille Université, CNRS, Institut Chimie Radicalaire, 13013 Marseille, France
| | - Nicolas Ferré
- Aix-Marseille Université, CNRS, Institut Chimie Radicalaire, 13013 Marseille, France
| | - Michael Filatov Gulak
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
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6
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Cárdenas G, Ledentu V, Huix-Rotllant M, Olivucci M, Ferré N. Automatic Rhodopsin Modeling with Multiple Protonation Microstates. J Phys Chem A 2023; 127:9365-9380. [PMID: 37877699 DOI: 10.1021/acs.jpca.3c05413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Automatic Rhodopsin Modeling (ARM) is a simulation protocol providing QM/MM models of rhodopsins capable of reproducing experimental electronic absorption and emission trends. Currently, ARM is restricted to a single protonation microstate for each rhodopsin model. Herein, we incorporate an extension of the minimal electrostatic model (MEM) into the ARM protocol to account for all relevant protonation microstates at a given pH. The new ARM+MEM protocol determines the most important microstates contributing to the description of the absorption spectrum. As a test case, we have applied this methodology to simulate the pH-dependent absorption spectrum of a toy model, showing that the single-microstate picture breaks down at certain pH values. Subsequently, we applied ARM+MEM toAnabaenasensory rhodopsin, confirming an improved description of its absorption spectrum when the titration of several key residues is considered.
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Affiliation(s)
| | | | | | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, 53100 Siena, Italy
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, ICR, 13013 Marseille, France
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7
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Li Manni G, Fdez. Galván I, Alavi A, Aleotti F, Aquilante F, Autschbach J, Avagliano D, Baiardi A, Bao JJ, Battaglia S, Birnoschi L, Blanco-González A, Bokarev SI, Broer R, Cacciari R, Calio PB, Carlson RK, Carvalho Couto R, Cerdán L, Chibotaru LF, Chilton NF, Church JR, Conti I, Coriani S, Cuéllar-Zuquin J, Daoud RE, Dattani N, Decleva P, de Graaf C, Delcey M, De Vico L, Dobrautz W, Dong SS, Feng R, Ferré N, Filatov(Gulak) M, Gagliardi L, Garavelli M, González L, Guan Y, Guo M, Hennefarth MR, Hermes MR, Hoyer CE, Huix-Rotllant M, Jaiswal VK, Kaiser A, Kaliakin DS, Khamesian M, King DS, Kochetov V, Krośnicki M, Kumaar AA, Larsson ED, Lehtola S, Lepetit MB, Lischka H, López Ríos P, Lundberg M, Ma D, Mai S, Marquetand P, Merritt ICD, Montorsi F, Mörchen M, Nenov A, Nguyen VHA, Nishimoto Y, Oakley MS, Olivucci M, Oppel M, Padula D, Pandharkar R, Phung QM, Plasser F, Raggi G, Rebolini E, Reiher M, Rivalta I, Roca-Sanjuán D, Romig T, Safari AA, Sánchez-Mansilla A, Sand AM, Schapiro I, Scott TR, Segarra-Martí J, Segatta F, Sergentu DC, Sharma P, Shepard R, Shu Y, Staab JK, Straatsma TP, Sørensen LK, Tenorio BNC, Truhlar DG, Ungur L, Vacher M, Veryazov V, Voß TA, Weser O, Wu D, Yang X, Yarkony D, Zhou C, Zobel JP, Lindh R. The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry. J Chem Theory Comput 2023; 19:6933-6991. [PMID: 37216210 PMCID: PMC10601490 DOI: 10.1021/acs.jctc.3c00182] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Indexed: 05/24/2023]
Abstract
The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.
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Affiliation(s)
- Giovanni Li Manni
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Ignacio Fdez. Galván
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Ali Alavi
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
- Yusuf Hamied
Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Flavia Aleotti
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Francesco Aquilante
- Theory and
Simulation of Materials (THEOS) and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jochen Autschbach
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
| | - Davide Avagliano
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Alberto Baiardi
- ETH Zurich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Jie J. Bao
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Stefano Battaglia
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Letitia Birnoschi
- The Department
of Chemistry, The University of Manchester, M13 9PL, Manchester, U.K.
| | - Alejandro Blanco-González
- Chemistry
Department, Bowling Green State University, Overmann Hall, Bowling Green, Ohio 43403, United States
| | - Sergey I. Bokarev
- Institut
für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
- Chemistry
Department, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Ria Broer
- Theoretical
Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Roberto Cacciari
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Paul B. Calio
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Rebecca K. Carlson
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Rafael Carvalho Couto
- Division
of Theoretical Chemistry and Biology, School of Engineering Sciences
in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Luis Cerdán
- Instituto
de Ciencia Molecular, Universitat de València, Catedrático José Beltrán
Martínez n. 2, 46980 Paterna, Spain
- Instituto
de Óptica (IO−CSIC), Consejo
Superior de Investigaciones Científicas, 28006, Madrid, Spain
| | - Liviu F. Chibotaru
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Nicholas F. Chilton
- The Department
of Chemistry, The University of Manchester, M13 9PL, Manchester, U.K.
| | | | - Irene Conti
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Sonia Coriani
- Department
of Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, 2800 Kongens Lyngby, Denmark
| | - Juliana Cuéllar-Zuquin
- Instituto
de Ciencia Molecular, Universitat de València, Catedrático José Beltrán
Martínez n. 2, 46980 Paterna, Spain
| | - Razan E. Daoud
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Nike Dattani
- HPQC Labs, Waterloo, N2T 2K9 Ontario Canada
- HPQC College, Waterloo, N2T 2K9 Ontario Canada
| | - Piero Decleva
- Istituto
Officina dei Materiali IOM-CNR and Dipartimento di Scienze Chimiche
e Farmaceutiche, Università degli
Studi di Trieste, I-34121 Trieste, Italy
| | - Coen de Graaf
- Department
of Physical and Inorganic Chemistry, Universitat
Rovira i Virgili, Tarragona 43007, Spain
- ICREA, Pg. Lluís
Companys 23, 08010 Barcelona, Spain
| | - Mickaël
G. Delcey
- Division
of Theoretical Chemistry and Biology, School of Engineering Sciences
in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Luca De Vico
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Werner Dobrautz
- Chalmers
University of Technology, Department of Chemistry
and Chemical Engineering, 41296 Gothenburg, Sweden
| | - Sijia S. Dong
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry and Chemical Biology, Department of Physics, and Department
of Chemical Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Rulin Feng
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
- Department
of Chemistry, Fudan University, Shanghai 200433, China
| | - Nicolas Ferré
- Institut
de Chimie Radicalaire (UMR-7273), Aix-Marseille
Univ, CNRS, ICR 13013 Marseille, France
| | | | - Laura Gagliardi
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Marco Garavelli
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Yafu Guan
- State Key
Laboratory of Molecular Reaction Dynamics and Center for Theoretical
Computational Chemistry, Dalian Institute
of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, People’s Republic of China
| | - Meiyuan Guo
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Matthew R. Hennefarth
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Matthew R. Hermes
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Chad E. Hoyer
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Miquel Huix-Rotllant
- Institut
de Chimie Radicalaire (UMR-7273), Aix-Marseille
Univ, CNRS, ICR 13013 Marseille, France
| | - Vishal Kumar Jaiswal
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Andy Kaiser
- Institut
für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Danil S. Kaliakin
- Chemistry
Department, Bowling Green State University, Overmann Hall, Bowling Green, Ohio 43403, United States
| | - Marjan Khamesian
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Daniel S. King
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Vladislav Kochetov
- Institut
für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Marek Krośnicki
- Institute
of Theoretical Physics and Astrophysics, Faculty of Mathematics, Physics
and Informatics, University of Gdańsk, ul Wita Stwosza 57, 80-952, Gdańsk, Poland
| | | | - Ernst D. Larsson
- Division
of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
| | - Susi Lehtola
- Molecular
Sciences Software Institute, Blacksburg, Virginia 24061, United States
- Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 University of Helsinki, Finland
| | - Marie-Bernadette Lepetit
- Condensed
Matter Theory Group, Institut Néel, CNRS UPR 2940, 38042 Grenoble, France
- Theory
Group, Institut Laue Langevin, 38042 Grenoble, France
| | - Hans Lischka
- Department
of Chemistry and Biochemistry, Texas Tech
University, Lubbock, Texas 79409-1061, United States
| | - Pablo López Ríos
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Marcus Lundberg
- Department
of Chemistry − Ångström Laboratory, Uppsala University, SE-75120 Uppsala, Sweden
| | - Dongxia Ma
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Philipp Marquetand
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | | | - Francesco Montorsi
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Maximilian Mörchen
- ETH Zurich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Artur Nenov
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Vu Ha Anh Nguyen
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore
| | - Yoshio Nishimoto
- Graduate
School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Meagan S. Oakley
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overmann Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Markus Oppel
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Daniele Padula
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università
di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Riddhish Pandharkar
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Quan Manh Phung
- Department
of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Institute
of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Felix Plasser
- Department
of Chemistry, Loughborough University, Loughborough, LE11 3TU, U.K.
| | - Gerardo Raggi
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
- Quantum
Materials and Software LTD, 128 City Road, London, EC1V 2NX, United Kingdom
| | - Elisa Rebolini
- Scientific
Computing Group, Institut Laue Langevin, 38042 Grenoble, France
| | - Markus Reiher
- ETH Zurich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Ivan Rivalta
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Daniel Roca-Sanjuán
- Instituto
de Ciencia Molecular, Universitat de València, Catedrático José Beltrán
Martínez n. 2, 46980 Paterna, Spain
| | - Thies Romig
- Institut
für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Arta Anushirwan Safari
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Aitor Sánchez-Mansilla
- Department
of Physical and Inorganic Chemistry, Universitat
Rovira i Virgili, Tarragona 43007, Spain
| | - Andrew M. Sand
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana 46208, United States
| | - Igor Schapiro
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Thais R. Scott
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
- Department
of Chemistry, Pritzker School of Molecular Engineering, James Franck
Institute, Chicago Center for Theoretical Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Javier Segarra-Martí
- Instituto
de Ciencia Molecular, Universitat de València, Catedrático José Beltrán
Martínez n. 2, 46980 Paterna, Spain
| | - Francesco Segatta
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, 40136 Bologna, Italy
| | - Dumitru-Claudiu Sergentu
- Department
of Chemistry, University at Buffalo, State
University of New York, Buffalo, New York 14260-3000, United States
- Laboratory
RA-03, RECENT AIR, A. I. Cuza University of Iaşi, RA-03 Laboratory (RECENT AIR), Iaşi 700506, Romania
| | - Prachi Sharma
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Ron Shepard
- Chemical
Sciences and Engineering Division, Argonne
National Laboratory, Lemont, Illinois 60439, USA
| | - Yinan Shu
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Jakob K. Staab
- The Department
of Chemistry, The University of Manchester, M13 9PL, Manchester, U.K.
| | - Tjerk P. Straatsma
- National
Center for Computational Sciences, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831-6373, United States
- Department
of Chemistry and Biochemistry, University
of Alabama, Tuscaloosa, Alabama 35487-0336, United States
| | | | - Bruno Nunes Cabral Tenorio
- Department
of Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, 2800 Kongens Lyngby, Denmark
| | - Donald G. Truhlar
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Liviu Ungur
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore
| | - Morgane Vacher
- Nantes
Université, CNRS, CEISAM, UMR 6230, F-44000 Nantes, France
| | - Valera Veryazov
- Division
of Theoretical Chemistry, Chemical Centre, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
| | - Torben Arne Voß
- Institut
für Physik, Universität Rostock, Albert-Einstein-Str. 23-24, 18059 Rostock, Germany
| | - Oskar Weser
- Electronic
Structure Theory Department, Max Planck
Institute for Solid State Research, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Dihua Wu
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - Xuchun Yang
- Chemistry
Department, Bowling Green State University, Overmann Hall, Bowling Green, Ohio 43403, United States
| | - David Yarkony
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Chen Zhou
- Department
of Chemistry, Chemical Theory Center, and Minnesota Supercomputing
Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United
States
| | - J. Patrick Zobel
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Roland Lindh
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
- Uppsala
Center for Computational Chemistry (UC3), Uppsala University, PO Box 576, SE-751 23 Uppsala. Sweden
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8
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Broser M, Andruniów T, Kraskov A, Palombo R, Katz S, Kloz M, Dostál J, Bernardo C, Kennis JTM, Hegemann P, Olivucci M, Hildebrandt P. Experimental Assessment of the Electronic and Geometrical Structure of a Near-Infrared Absorbing and Highly Fluorescent Microbial Rhodopsin. J Phys Chem Lett 2023; 14:9291-9295. [PMID: 37815402 DOI: 10.1021/acs.jpclett.3c02167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
The recently discovered Neorhodopsin (NeoR) exhibits absorption and emission maxima in the near-infrared spectral region, which together with the high fluorescence quantum yield makes it an attractive retinal protein for optogenetic applications. The unique optical properties can be rationalized by a theoretical model that predicts a high charge transfer character in the electronic ground state (S0) which is otherwise typical of the excited state S1 in canonical retinal proteins. The present study sets out to assess the electronic structure of the NeoR chromophore by resonance Raman (RR) spectroscopy since frequencies and relative intensities of RR bands are controlled by the ground and excited state's properties. The RR spectra of NeoR differ dramatically from those of canonical rhodopsins but can be reliably reproduced by the calculations carried out within two different structural models. The remarkable agreement between the experimental and calculated spectra confirms the consistency and robustness of the theoretical approach.
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Affiliation(s)
- Matthias Broser
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
| | - Tadeusz Andruniów
- Department of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Anastasia Kraskov
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Riccardo Palombo
- Dipartimento di Biotecnologie, Chimica e Farmacia, Universitâ di Siena, via A. Moro 2, 53100 Siena, Italy
| | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Miroslav Kloz
- ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, 25241 Dolní Břežany, Czech Republic
| | - Jakub Dostál
- ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, 25241 Dolní Břežany, Czech Republic
| | - César Bernardo
- ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, 25241 Dolní Břežany, Czech Republic
| | - John T M Kennis
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Peter Hegemann
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Universitâ di Siena, via A. Moro 2, 53100 Siena, Italy
- Department of Chemistry, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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9
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Ikonnikov E, Paolino M, Garcia-Alvarez JC, Orozco-Gonzalez Y, Granados C, Röder A, Léonard J, Olivucci M, Haacke S, Kornilov O, Gozem S. Photoelectron Spectroscopy of Oppositely Charged Molecular Switches in the Aqueous Phase: Theory and Experiment. J Phys Chem Lett 2023:6061-6070. [PMID: 37358397 DOI: 10.1021/acs.jpclett.3c00828] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
XUV photoelectron spectroscopy (XPS) is a powerful method for investigating the electronic structures of molecules. However, the correct interpretation of results in the condensed phase requires theoretical models that account for solvation. Here we present experimental aqueous-phase XPS of two organic biomimetic molecular switches, NAIP and p-HDIOP. These switches are structurally similar, but have opposite charges and thus present a stringent benchmark for solvation models which need to reproduce the observed ΔeBE = 1.1 eV difference in electron binding energy compared to the 8 eV difference predicted in the gas phase. We present calculations using implicit and explicit solvent models. The latter employs the average solvent electrostatic configuration and free energy gradient (ASEC-FEG) approach. Both nonequilibrium polarizable continuum models and ASEC-FEG calculations give vertical binding energies in good agreement with the experiment for three different computational protocols. Counterions, explicitly accounted for in ASEC-FEG, contribute to the stabilization of molecular states and reduction of ΔeBE upon solvation.
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Affiliation(s)
- E Ikonnikov
- Max Born Institute, Max-Born-Straße 2A, 12489 Berlin, Germany
| | - M Paolino
- Department of Biotechnology, Chemistry and PharmacyUniversity of Siena, Via A. Moro 2, I-53100 Siena, Italy
| | | | | | - C Granados
- Max Born Institute, Max-Born-Straße 2A, 12489 Berlin, Germany
| | - A Röder
- Max Born Institute, Max-Born-Straße 2A, 12489 Berlin, Germany
| | - J Léonard
- Strasbourg Institute of Material Physics and Chemistry, University of Strasbourg - CNRS, 23 Rue du Loess, 67000 Strasbourg, France
| | - M Olivucci
- Department of Biotechnology, Chemistry and PharmacyUniversity of Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - S Haacke
- Strasbourg Institute of Material Physics and Chemistry, University of Strasbourg - CNRS, 23 Rue du Loess, 67000 Strasbourg, France
| | - O Kornilov
- Max Born Institute, Max-Born-Straße 2A, 12489 Berlin, Germany
| | - S Gozem
- Georgia State University, Atlanta, Georgia 30303, United States
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10
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Boeije Y, Olivucci M. Correction: From a one-mode to a multi-mode understanding of conical intersection mediated ultrafast organic photochemical reactions. Chem Soc Rev 2023. [PMID: 37350322 DOI: 10.1039/d3cs90055j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Abstract
Correction for 'From a one-mode to a multi-mode understanding of conical intersection mediated ultrafast organic photochemical reactions' by Yorrick Boeije et al., Chem. Soc. Rev., 2023, 52, 2643-2687, https://doi.org/10.1039/D2CS00719C.
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Affiliation(s)
- Yorrick Boeije
- Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Massimo Olivucci
- Chemistry Department, University of Siena, Via Aldo Moro n. 2, 53100 Siena, Italy
- Chemistry Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, USA
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11
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Pedraza-González L, Barneschi L, Marszałek M, Padula D, De Vico L, Olivucci M. Automated QM/MM Screening of Rhodopsin Variants with Enhanced Fluorescence. J Chem Theory Comput 2023; 19:293-310. [PMID: 36516450 DOI: 10.1021/acs.jctc.2c00928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present a computational protocol for the fast and automated screening of excited-state hybrid quantum mechanics/molecular mechanics (QM/MM) models of rhodopsins to be used as fluorescent probes based on the automatic rhodopsin modeling protocol (a-ARM). Such "a-ARM fluorescence screening protocol" is implemented through a general Python-based driver, PyARM, that is also proposed here. The implementation and performance of the protocol are benchmarked using different sets of rhodopsin variants whose absorption and, more relevantly, emission spectra have been experimentally measured. We show that, despite important limitations that make unsafe to use it as a black-box tool, the protocol reproduces the observed trends in fluorescence and it is capable of selecting novel potentially fluorescent rhodopsins. We also show that the protocol can be used in mechanistic investigations to discern fluorescence enhancement effects associated with a near degeneracy of the S1/S2 states or, alternatively, with a barrier generated via coupling of the S0/S1 wave functions.
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Affiliation(s)
- Laura Pedraza-González
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Leonardo Barneschi
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Michał Marszałek
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy.,Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiaǹskiego 27, 50-370 Wrocław, Poland
| | - Daniele Padula
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Luca De Vico
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy.,Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
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12
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Boeije Y, Olivucci M. From a one-mode to a multi-mode understanding of conical intersection mediated ultrafast organic photochemical reactions. Chem Soc Rev 2023; 52:2643-2687. [PMID: 36970950 DOI: 10.1039/d2cs00719c] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
This review discusses how ultrafast organic photochemical reactions are controlled by conical intersections, highlighting that decay to the ground-state at multiple points of the intersection space results in their multi-mode character.
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Affiliation(s)
- Yorrick Boeije
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Massimo Olivucci
- Chemistry Department, University of Siena, Via Aldo Moro n. 2, 53100 Siena, Italy
- Chemistry Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, USA
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13
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Barneschi L, Marsili E, Pedraza-González L, Padula D, De Vico L, Kaliakin D, Blanco-González A, Ferré N, Huix-Rotllant M, Filatov M, Olivucci M. On the fluorescence enhancement of arch neuronal optogenetic reporters. Nat Commun 2022; 13:6432. [PMID: 36307417 PMCID: PMC9616920 DOI: 10.1038/s41467-022-33993-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
The lack of a theory capable of connecting the amino acid sequence of a light-absorbing protein with its fluorescence brightness is hampering the development of tools for understanding neuronal communications. Here we demonstrate that a theory can be established by constructing quantum chemical models of a set of Archaerhodopsin reporters in their electronically excited state. We found that the experimentally observed increase in fluorescence quantum yield is proportional to the computed decrease in energy difference between the fluorescent state and a nearby photoisomerization channel leading to an exotic diradical of the protein chromophore. This finding will ultimately support the development of technologies for searching novel fluorescent rhodopsin variants and unveil electrostatic changes that make light emission brighter and brighter.
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Affiliation(s)
- Leonardo Barneschi
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Emanuele Marsili
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy ,grid.8250.f0000 0000 8700 0572University of Durham, Department of Chemistry, South Road, Durham, DH1 3LE United Kingdom ,grid.5337.20000 0004 1936 7603Present Address: Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Laura Pedraza-González
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy ,grid.5395.a0000 0004 1757 3729Present Address: Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe Moruzzi, 13, I-56124 Pisa, Italy
| | - Daniele Padula
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Luca De Vico
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Danil Kaliakin
- grid.253248.a0000 0001 0661 0035Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403 USA
| | - Alejandro Blanco-González
- grid.253248.a0000 0001 0661 0035Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403 USA
| | - Nicolas Ferré
- grid.462456.70000 0004 4902 8637Institut de Chimie Radicalaire (UMR-7273), Aix-Marseille Université, CNRS, 13397 Marseille, Cedex 20 France
| | - Miquel Huix-Rotllant
- grid.462456.70000 0004 4902 8637Institut de Chimie Radicalaire (UMR-7273), Aix-Marseille Université, CNRS, 13397 Marseille, Cedex 20 France
| | - Michael Filatov
- grid.258803.40000 0001 0661 1556Department of Chemistry, Kyungpook National University, Daegu, 702-701 South Korea
| | - Massimo Olivucci
- grid.9024.f0000 0004 1757 4641Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy ,grid.253248.a0000 0001 0661 0035Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403 USA ,grid.11843.3f0000 0001 2157 9291University of Strasbourg Institute for Advanced Studies, 5, alleé duGeń eŕ al Rouvillois, F-67083 Strasbourg, France
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14
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Paolino M, Saletti M, Reale A, Licciardi M, Varvarà P, Marquette A, Léonard J, Bonechi C, Donati A, Giorgi G, Giuliani G, Carlotti B, Ortica F, Latterini L, Gentile M, Paccagnini E, Olivucci M, Cappelli A. Design, Synthesis and Characterization of a Visible‐Light‐Sensitive Molecular Switch and Its PEGylation Towards a Self‐Assembling Molecule. Chemistry 2022; 28:e202201477. [PMID: 35695822 PMCID: PMC9541190 DOI: 10.1002/chem.202201477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Marco Paolino
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Mario Saletti
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Annalisa Reale
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Mariano Licciardi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF) Università degli Studi di Palermo Via Archirafi 32 90123 Palermo Italy
| | - Paola Varvarà
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF) Università degli Studi di Palermo Via Archirafi 32 90123 Palermo Italy
| | - Arnaud Marquette
- Institut de Physique et Chimie des Matériaux de Strasbourg Université de Strasbourg CNRS UMR 7504 Strasbourg France
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg Université de Strasbourg CNRS UMR 7504 Strasbourg France
| | - Claudia Bonechi
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Alessandro Donati
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Gianluca Giorgi
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Germano Giuliani
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Benedetta Carlotti
- Dipartimento di Chimica, Biologia e Biotecnologie Università di Perugia Via Elce di Sotto, 8 06123 Perugia Italy
| | - Fausto Ortica
- Dipartimento di Chimica, Biologia e Biotecnologie Università di Perugia Via Elce di Sotto, 8 06123 Perugia Italy
| | - Loredana Latterini
- Dipartimento di Chimica, Biologia e Biotecnologie Università di Perugia Via Elce di Sotto, 8 06123 Perugia Italy
| | - Mariangela Gentile
- Dipartimento di Scienze della Vita Università degli Studi di Siena Via A. Moro 53100 Siena Italy
| | - Eugenio Paccagnini
- Dipartimento di Scienze della Vita Università degli Studi di Siena Via A. Moro 53100 Siena Italy
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
- Chemistry Department Bowling Green State University 43403 Bowling Green OH USA) ok
| | - Andrea Cappelli
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
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15
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Paolino M, Rullo M, Maramai S, de Candia M, Pisani L, Catto M, Mugnaini C, Brizzi A, Cappelli A, Olivucci M, Corelli F, Altomare CD. Design, synthesis and biological evaluation of light-driven on-off multitarget AChE and MAO-B inhibitors. RSC Med Chem 2022; 13:873-883. [PMID: 35923722 PMCID: PMC9298480 DOI: 10.1039/d2md00042c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/19/2022] [Indexed: 08/13/2023] Open
Abstract
Neurodegenerative diseases are multifactorial disorders characterized by protein misfolding, oxidative stress, and neuroinflammation, finally resulting in neuronal loss and cognitive dysfunctions. Nowadays, an attractive strategy to improve the classical treatments is the development of multitarget-directed molecules able to synergistically interact with different enzymes and/or receptors. In addition, an interesting tool to refine personalized therapies may arise from the use of bioactive species able to modify their activity as a result of light irradiation. To this aim, we designed and synthesized a small library of cinnamic acid-inspired isomeric compounds with light modulated activity able to inhibit acetylcholinesterase (AChE) and monoamine oxidase B (MAO-B), with remarkable selectivity over butyrylcholinesterase (BChE) and MAO-A, which have been investigated as the enzyme targets related to Alzheimer's disease (AD). The inhibitory activities were evaluated for the pure E-diastereomers and the E/Z-diastereomer mixtures, obtained upon UV irradiation. Molecular docking studies were carried out to rationalize the differences in the inhibition potency of the E and Z diastereomers of the best performing analogue 1c. Our preliminary findings may open-up the way for developing innovative multitarget photo-switch drugs against neurodegenerative diseases.
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Affiliation(s)
- Marco Paolino
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Mariagrazia Rullo
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro Via E. Orabona 4 70125 Bari Italy
| | - Samuele Maramai
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Modesto de Candia
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro Via E. Orabona 4 70125 Bari Italy
| | - Leonardo Pisani
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro Via E. Orabona 4 70125 Bari Italy
| | - Marco Catto
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro Via E. Orabona 4 70125 Bari Italy
| | - Claudia Mugnaini
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Antonella Brizzi
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Andrea Cappelli
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
- Chemistry Department, Bowling Green State University USA
| | - Federico Corelli
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Cosimo D Altomare
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro Via E. Orabona 4 70125 Bari Italy
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16
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Pedraza-González L, Barneschi L, Padula D, De Vico L, Olivucci M. Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol. Top Curr Chem (Cham) 2022; 380:21. [PMID: 35291019 PMCID: PMC8924150 DOI: 10.1007/s41061-022-00374-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/29/2022] [Indexed: 10/27/2022]
Abstract
In recent years, photoactive proteins such as rhodopsins have become a common target for cutting-edge research in the field of optogenetics. Alongside wet-lab research, computational methods are also developing rapidly to provide the necessary tools to analyze and rationalize experimental results and, most of all, drive the design of novel systems. The Automatic Rhodopsin Modeling (ARM) protocol is focused on providing exactly the necessary computational tools to study rhodopsins, those being either natural or resulting from mutations. The code has evolved along the years to finally provide results that are reproducible by any user, accurate and reliable so as to replicate experimental trends. Furthermore, the code is efficient in terms of necessary computing resources and time, and scalable in terms of both number of concurrent calculations as well as features. In this review, we will show how the code underlying ARM achieved each of these properties.
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Affiliation(s)
- Laura Pedraza-González
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy. .,Department of Chemistry and Industrial Chemistry, University of Pisa, Via Moruzzi 13, 56124, Pisa, Italy.
| | - Leonardo Barneschi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Daniele Padula
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Luca De Vico
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy.
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy. .,Department of Chemistry, Bowling Green State University, Bowling Green, OH, 43403, USA.
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17
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Tassone G, Paolino M, Pozzi C, Reale A, Salvini L, Giorgi G, Orlandini M, Galvagni F, Mangani S, Yang X, Carlotti B, Ortica F, Latterini L, Olivucci M, Cappelli A. Xanthopsin-Like Systems via Site-Specific Click-Functionalization of a Retinoic Acid Binding Protein. Chembiochem 2022; 23:e202100449. [PMID: 34647400 PMCID: PMC8934143 DOI: 10.1002/cbic.202100449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/12/2021] [Indexed: 01/07/2023]
Abstract
The use of light-responsive proteins to control both living or synthetic cells, is at the core of the expanding fields of optogenetics and synthetic biology. It is thus apparent that a richer reaction toolbox for the preparation of such systems is of fundamental importance. Here, we provide a proof-of-principle demonstration that Morita-Baylis-Hillman adducts can be employed to perform a facile site-specific, irreversible and diastereoselective click-functionalization of a lysine residue buried into a lipophilic binding pocket and yielding an unnatural chromophore with an extended π-system. In doing so we effectively open the path to the in vitro preparation of a library of synthetic proteins structurally reminiscent of xanthopsin eubacterial photoreceptors. We argue that such a library, made of variable unnatural chromophores inserted in an easy-to-mutate and crystallize retinoic acid transporter, significantly expand the scope of the recently introduced rhodopsin mimics as both optogenetic and "lab-on-a-molecule" tools.
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Affiliation(s)
| | - Marco Paolino
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Cecilia Pozzi
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Annalisa Reale
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Laura Salvini
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100 Siena, Italy
| | - Gianluca Giorgi
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Maurizio Orlandini
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Federico Galvagni
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Stefano Mangani
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Xuchun Yang
- Chemistry Department, Bowling Green State University, Overman Hall, Bowling Green, OH 43403, USA
| | - Benedetta Carlotti
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Fausto Ortica
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Loredana Latterini
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy,Chemistry Department, Bowling Green State University, Overman Hall, Bowling Green, OH 43403, USA
| | - Andrea Cappelli
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
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18
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Chatterjee G, Jha A, Blanco-Gonzalez A, Tiwari V, Manathunga M, Duan HG, Tellkamp F, Prokhorenko VI, Ferré N, Dasgupta J, Olivucci M, Miller RJD. Torsionally broken symmetry assists infrared excitation of biomimetic charge-coupled nuclear motions in the electronic ground state. Chem Sci 2022; 13:9392-9400. [PMID: 36093002 PMCID: PMC9384489 DOI: 10.1039/d2sc02133a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/19/2022] [Indexed: 11/21/2022] Open
Abstract
The concerted interplay between reactive nuclear and electronic motions in molecules actuates chemistry. Here, we demonstrate that out-of-plane torsional deformation and vibrational excitation of stretching motions in the electronic ground...
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Affiliation(s)
- Gourab Chatterjee
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
| | - Ajay Jha
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
| | | | - Vandana Tiwari
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
- Department of Chemistry, University of Hamburg Martin-Luther-King Platz 6 20146 Hamburg Germany
| | | | - Hong-Guang Duan
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
| | - Friedjof Tellkamp
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
| | - Valentyn I Prokhorenko
- Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 22761 Hamburg Germany
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, ICR 13013 Marseille France
| | - Jyotishman Dasgupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research Mumbai 400005 India
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University Bowling Green OH 43403 USA
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena I-53100 Siena Italy
| | - R J Dwayne Miller
- Departments of Chemistry and Physics, University of Toronto 80 St. George Street Toronto M5S 3H6 Canada
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19
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Nikolaev DM, Manathunga M, Orozco-Gonzalez Y, Shtyrov AA, Guerrero Martínez YO, Gozem S, Ryazantsev MN, Coutinho K, Canuto S, Olivucci M. Free Energy Computation for an Isomerizing Chromophore in a Molecular Cavity via the Average Solvent Electrostatic Configuration Model: Applications in Rhodopsin and Rhodopsin-Mimicking Systems. J Chem Theory Comput 2021; 17:5885-5895. [PMID: 34379429 DOI: 10.1021/acs.jctc.1c00221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a novel technique for computing the free energy differences between two chromophore "isomers" hosted in a molecular environment (a generalized solvent). Such an environment may range from a relatively rigid protein cavity to a flexible solvent environment. The technique is characterized by the application of the previously reported "average electrostatic solvent configuration" method, and it is based on the idea of using the free energy perturbation theory along with a chromophore annihilation procedure in thermodynamic cycle calculations. The method is benchmarked by computing the ground-state room-temperature relative stabilities between (i) the cis and trans isomers of prototypal animal and microbial rhodopsins and (ii) the analogue isomers of a rhodopsin-like light-driven molecular switch in methanol. Furthermore, we show that the same technology can be used to estimate the activation free energy for the thermal isomerization of systems i-ii by replacing one isomer with a transition state. The results show that the computed relative stability and isomerization barrier magnitudes for the selected systems are in line with the available experimental observation in spite of their widely diverse complexity.
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Affiliation(s)
- Dmitrii M Nikolaev
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | - Madushanka Manathunga
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Yoelvis Orozco-Gonzalez
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States.,Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Andrey A Shtyrov
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | | | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Mikhail N Ryazantsev
- Saint Petersburg State University, 7/9 Universitetskaya nab., St. Petersburg 199034, Russia.,Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 195251, Russia
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, São Paulo 05508-090, Brazil
| | - Sylvio Canuto
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, São Paulo 05508-090, Brazil
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States.,Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy.,Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg-CNRS, UMR 7504, F-67034 Strasbourg, France
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20
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Abstract
The primary event occurring during the E-to-Z photoisomerization reaction of retinal protonated Schiff base (rPSB) is single-to-double bond inversion. In this work we examine the nuclear dynamics that occurs when the initial excited state is a superposition of the S1 and S2 electronic excited states that might be created in a laser experiment. The nuclear dynamics is dominated by double bond inversion that is parallel to the derivative coupling vector of S1 and S2. Thus, the molecule behaves as if it were at a conical intersection even if the states are nondegenerate.
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Affiliation(s)
- Massimo Olivucci
- Chemistry Deparment, University of Siena, Via Aldo Moro n. 2, 53100 Siena, Italy
- Chemistry Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Thierry Tran
- Department of Chemistry, University College London, 20 Gordon Street, WC1H 0AJ London, United Kingdom
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College, London SW7 2AZ, United Kingdom
| | - Graham A Worth
- Department of Chemistry, University College London, 20 Gordon Street, WC1H 0AJ London, United Kingdom
| | - Michael A Robb
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College, London SW7 2AZ, United Kingdom
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21
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Pooler DRS, Pierron R, Crespi S, Costil R, Pfeifer L, Léonard J, Olivucci M, Feringa BL. Effect of charge-transfer enhancement on the efficiency and rotary mechanism of an oxindole-based molecular motor. Chem Sci 2021; 12:7486-7497. [PMID: 34163839 PMCID: PMC8171491 DOI: 10.1039/d1sc01105g] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/25/2021] [Indexed: 01/04/2023] Open
Abstract
Harvesting energy and converting it into mechanical motion forms the basis for both natural and artificial molecular motors. Overcrowded alkene-based light-driven rotary motors are powered through sequential photochemical and thermal steps. The thermal helix inversion steps are well characterised and can be manipulated through adjustment of the chemical structure, however, the insights into the photochemical isomerisation steps still remain elusive. Here we report a novel oxindole-based molecular motor featuring pronounced electronic push-pull character and a four-fold increase of the photoisomerization quantum yield in comparison to previous motors of its class. A multidisciplinary approach including synthesis, steady-state and transient absorption spectroscopies, and electronic structure modelling was implemented to elucidate the excited state dynamics and rotary mechanism. We conclude that the charge-transfer character of the excited state diminishes the degree of pyramidalisation at the alkene bond during isomerisation, such that the rotational properties of this oxindole-based motor stand in between the precessional motion of fluorene-based molecular motors and the axial motion of biomimetic photoswitches.
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Affiliation(s)
- Daisy R S Pooler
- Stratingh Institute for Chemistry, Zernike Institute for Advanced Materials, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Robin Pierron
- Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg, CNRS, UMR 7504 F-67034 Strasbourg France
| | - Stefano Crespi
- Stratingh Institute for Chemistry, Zernike Institute for Advanced Materials, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Romain Costil
- Stratingh Institute for Chemistry, Zernike Institute for Advanced Materials, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Lukas Pfeifer
- Stratingh Institute for Chemistry, Zernike Institute for Advanced Materials, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg, CNRS, UMR 7504 F-67034 Strasbourg France
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena 53100 Siena Italy
- Chemistry Department, Bowling Green State University Bowling Green Ohio 43403 USA
| | - Ben L Feringa
- Stratingh Institute for Chemistry, Zernike Institute for Advanced Materials, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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22
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Paolino M, Giovannini T, Manathunga M, Latterini L, Zampini G, Pierron R, Léonard J, Fusi S, Giorgi G, Giuliani G, Cappelli A, Cappelli C, Olivucci M. On the Transition from a Biomimetic Molecular Switch to a Rotary Molecular Motor. J Phys Chem Lett 2021; 12:3875-3884. [PMID: 33856801 DOI: 10.1021/acs.jpclett.1c00526] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The experimental investigation of the unidirectional motion characterizing the photoisomerization of single-molecule rotary motors requires accessible lab prototypes featuring an electronic circular dichroism (ECD) signal that is sensitive to the geometrical and electronic changes occurring during an ultrafast reactive process. Here we report a combined experimental/computational study of a candidate obtained via the asymmetrization of a light-driven biomimetic molecular switch. We show that the achieved motor has an ECD band that is remarkably sensitive to the isomerization motion, and it is therefore suitable for time-resolved ECD studies. However, we also find that, unexpectedly, the synthesized motor isomerizes on a time scale longer than the subpicosecond time measured for the achiral parent, a result that points to alternative candidates conserving a high reaction speed.
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Affiliation(s)
- Marco Paolino
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | | | - Madushanka Manathunga
- Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403-0001, United States
| | - Loredana Latterini
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Giulia Zampini
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Robin Pierron
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67000 Strasbourg, France
| | - Jérémie Léonard
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67000 Strasbourg, France
| | - Stefania Fusi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Gianluca Giorgi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Germano Giuliani
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Andrea Cappelli
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
- Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403-0001, United States
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23
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Mroginski MA, Adam S, Amoyal GS, Barnoy A, Bondar AN, Borin VA, Church JR, Domratcheva T, Ensing B, Fanelli F, Ferré N, Filiba O, Pedraza-González L, González R, González-Espinoza CE, Kar RK, Kemmler L, Kim SS, Kongsted J, Krylov AI, Lahav Y, Lazaratos M, NasserEddin Q, Navizet I, Nemukhin A, Olivucci M, Olsen JMH, Pérez de Alba Ortíz A, Pieri E, Rao AG, Rhee YM, Ricardi N, Sen S, Solov'yov IA, De Vico L, Wesolowski TA, Wiebeler C, Yang X, Schapiro I. Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochem Photobiol 2021; 97:243-269. [PMID: 33369749 DOI: 10.1111/php.13372] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/01/2020] [Indexed: 02/06/2023]
Abstract
This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.
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Affiliation(s)
| | - Suliman Adam
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gil S Amoyal
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avishai Barnoy
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Veniamin A Borin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jonathan R Church
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tatiana Domratcheva
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Department Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Bernd Ensing
- Van 't Hoff Institute for Molecular Science and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam, The Netherlands
| | - Francesca Fanelli
- Department of Life Sciences, Center for Neuroscience and Neurotechnology, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | | | - Ofer Filiba
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Laura Pedraza-González
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy
| | - Ronald González
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | - Rajiv K Kar
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lukas Kemmler
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Seung Soo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Yigal Lahav
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.,MIGAL - Galilee Research Institute, S. Industrial Zone, Kiryat Shmona, Israel
| | - Michalis Lazaratos
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Berlin, Germany
| | - Qays NasserEddin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isabelle Navizet
- MSME, Univ Gustave Eiffel, CNRS UMR 8208, Univ Paris Est Creteil, Marne-la-Vallée, France
| | - Alexander Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy.,Chemistry Department, Bowling Green State University, Bowling Green, OH, USA
| | - Jógvan Magnus Haugaard Olsen
- Department of Chemistry, Aarhus University, Aarhus, Denmark.,Department of Chemistry, Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Alberto Pérez de Alba Ortíz
- Van 't Hoff Institute for Molecular Science and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Amsterdam, The Netherlands
| | - Elisa Pieri
- Aix-Marseille Univ, CNRS, ICR, Marseille, France
| | - Aditya G Rao
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Young Min Rhee
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Niccolò Ricardi
- Département de Chimie Physique, Université de Genève, Genève, Switzerland
| | - Saumik Sen
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Luca De Vico
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Siena, Italy
| | | | - Christian Wiebeler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Xuchun Yang
- Chemistry Department, Bowling Green State University, Bowling Green, OH, USA
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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24
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Giuliani G, Melaccio F, Gozem S, Cappelli A, Olivucci M. QM/MM Investigation of the Spectroscopic Properties of the Fluorophore of Bacterial Luciferase. J Chem Theory Comput 2021; 17:605-613. [PMID: 33449693 DOI: 10.1021/acs.jctc.0c01078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We employ replica-exchange molecular dynamics (REMD) and a hybrid ab initio multiconfigurational quantum mechanics/molecular mechanics (QM/MM) approach to model the absorption and fluorescence properties of bacterial luciferin-luciferase. Specifically, we employ complete active space perturbation theory (CASPT2) and study the effect of active space, basis set, and IPEA shift on the computed energies. We discuss the effect of the protein environment on the fluorophore's excited-state potential energy surface and the role that the protein plays in enhancing the fluorescence quantum yield in bacterial bioluminescence.
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Affiliation(s)
- Germano Giuliani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Federico Melaccio
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Andrea Cappelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy.,Department of Chemistry, Bowling Green State University, Bowing Green, Ohio 43403, United States
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25
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Marsili E, Olivucci M, Lauvergnat D, Agostini F. Quantum and Quantum-Classical Studies of the Photoisomerization of a Retinal Chromophore Model. J Chem Theory Comput 2020; 16:6032-6048. [PMID: 32931266 DOI: 10.1021/acs.jctc.0c00679] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report an in-depth analysis of the photo-induced isomerization of the 2-cis-penta-2,4-dieniminium cation: a minimal model of the 11-cis retinal protonated Schiff base chromophore of the dim-light photoreceptor rhodopsin. Based on recently developed three-dimensional potentials parametrized on ab initio multi-state multi-configurational second-order perturbation theory data, we perform quantum-dynamical studies. In addition, simulations based on various quantum-classical methods, among which Tully surface hopping and the coupled-trajectory approach derived from the exact factorization, allow us to validate their performance against vibronic wavepacket propagation and, therefore, a purely quantum treatment. Quantum-dynamics results uncover qualitative differences with respect to the two-dimensional Hahn-Stock potentials, widely used as model potentials for the isomerization of the same chromophore, due to the increased dimensionality and three-mode correlation. Quantum-classical simulations show, instead, that three-dimensional model potentials are capable of capturing a number of features revealed by atomistic simulations and experimental observations. In particular, a recently reported vibrational phase relationship between double-bond torsion and hydrogen-out-of-plane modes critical for rhodopsin isomerization efficiency is correctly reproduced.
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Affiliation(s)
- Emanuele Marsili
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France.,Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy.,Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - David Lauvergnat
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France
| | - Federica Agostini
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France
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26
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Aquilante F, Autschbach J, Baiardi A, Battaglia S, Borin VA, Chibotaru LF, Conti I, De Vico L, Delcey M, Fdez Galván I, Ferré N, Freitag L, Garavelli M, Gong X, Knecht S, Larsson ED, Lindh R, Lundberg M, Malmqvist PÅ, Nenov A, Norell J, Odelius M, Olivucci M, Pedersen TB, Pedraza-González L, Phung QM, Pierloot K, Reiher M, Schapiro I, Segarra-Martí J, Segatta F, Seijo L, Sen S, Sergentu DC, Stein CJ, Ungur L, Vacher M, Valentini A, Veryazov V. Modern quantum chemistry with [Open]Molcas. J Chem Phys 2020; 152:214117. [PMID: 32505150 DOI: 10.1063/5.0004835] [Citation(s) in RCA: 218] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.
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Affiliation(s)
- Francesco Aquilante
- Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, Buffalo, New York 14260-3000, USA
| | - Alberto Baiardi
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Stefano Battaglia
- Department of Chemistry - BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
| | - Veniamin A Borin
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Liviu F Chibotaru
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Irene Conti
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Luca De Vico
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Mickaël Delcey
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Ignacio Fdez Galván
- Department of Chemistry - BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
| | - Nicolas Ferré
- Aix-Marseille University, CNRS, Institut Chimie Radicalaire, Marseille, France
| | - Leon Freitag
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Xuejun Gong
- Department of Chemistry, University of Singapore, 3 Science Drive 3, 117543 Singapore
| | - Stefan Knecht
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Ernst D Larsson
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, Lund 22100, Sweden
| | - Roland Lindh
- Department of Chemistry - BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
| | - Marcus Lundberg
- Department of Chemistry - Ångström Laboratory, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Per Åke Malmqvist
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, Lund 22100, Sweden
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Jesper Norell
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Michael Odelius
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Thomas B Pedersen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
| | - Laura Pedraza-González
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Quan M Phung
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Kristine Pierloot
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Javier Segarra-Martí
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, United Kingdom
| | - Francesco Segatta
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, Bologna I-40136, Italy
| | - Luis Seijo
- Departamento de Química, Instituto Universitario de Ciencia de Materiales Nicolás Cabrera, and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Saumik Sen
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | | | - Christopher J Stein
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Liviu Ungur
- Department of Chemistry, University of Singapore, 3 Science Drive 3, 117543 Singapore
| | - Morgane Vacher
- Laboratoire CEISAM - UMR CNRS 6230, Université de Nantes, 44300 Nantes, France
| | - Alessio Valentini
- Theoretical Physical Chemistry, Research Unit MolSys, Université de Liège, Allée du 6 Août, 11, 4000 Liège, Belgium
| | - Valera Veryazov
- Division of Theoretical Chemistry, Lund University, P.O. Box 124, Lund 22100, Sweden
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27
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Manathunga M, Jenkins AJ, Orozco-Gonzalez Y, Ghanbarpour A, Borhan B, Geiger JH, Larsen DS, Olivucci M. Computational and Spectroscopic Characterization of the Photocycle of an Artificial Rhodopsin. J Phys Chem Lett 2020; 11:4245-4252. [PMID: 32374610 PMCID: PMC9272672 DOI: 10.1021/acs.jpclett.0c00751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The photocycle of a reversible photoisomerizing rhodopsin mimic (M2) is investigated. This system, based on the cellular retinoic acid binding protein, is structurally different from natural rhodopsin systems, but exhibits a similar isomerization upon light irradiation. More specifically, M2 displays a 15-cis to all-trans conversion of retinal protonated Schiff base (rPSB) and all-trans to 15-cis isomerization of unprotonated Schiff base (rUSB). Here we use hybrid quantum mechanics/molecular mechanics (QM/MM) tools coupled with transient absorption and cryokinetic UV-vis spectroscopies to investigate these isomerization processes. The results suggest that primary rPSB photoisomerization of M2 occurs around the C13═C14 double bond within 2 ps following an aborted-bicycle pedal (ABP) isomerization mechanism similar to natural microbial rhodopsins. The rUSB isomerization is much slower and occurs within 48 ps around the C15═N double bond. Our findings reveal the possibility to engineer naturally occurring mechanistic features into artificial rhodopsins and also constitute a step toward understanding the photoisomerization of UV pigments. We conclude by reinforcing the idea that the presence of the retinal chromophore inside a tight protein cavity is not mandatory to exhibit ABP mechanism.
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Affiliation(s)
- Madushanka Manathunga
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Adam J Jenkins
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Yoelvis Orozco-Gonzalez
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Alireza Ghanbarpour
- Department of Chemistry, Michigan State University, Lansing, Michigan 48824, United States
| | - Babak Borhan
- Department of Chemistry, Michigan State University, Lansing, Michigan 48824, United States
| | - James H Geiger
- Department of Chemistry, Michigan State University, Lansing, Michigan 48824, United States
| | - Delmar S Larsen
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
- Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 Université de Strasbourg-CNRS, F-67034 Strasbourg, France
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28
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Gozem S, Johnson PJM, Halpin A, Luk HL, Morizumi T, Prokhorenko VI, Ernst OP, Olivucci M, Miller RJD. Excited-State Vibronic Dynamics of Bacteriorhodopsin from Two-Dimensional Electronic Photon Echo Spectroscopy and Multiconfigurational Quantum Chemistry. J Phys Chem Lett 2020; 11:3889-3896. [PMID: 32330041 PMCID: PMC9198827 DOI: 10.1021/acs.jpclett.0c01063] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Owing to the ultrafast time scale of the photoinduced reaction and high degree of spectral overlap among the reactant, product, and excited electronic states in bacteriorhodopsin (bR), it has been a challenge for traditional spectroscopies to resolve the interplay between vibrational dynamics and electronic processes occurring in the retinal chromophore of bR. Here, we employ ultrafast two-dimensional electronic photon echo spectroscopy to follow the early excited-state dynamics of bR preceding the isomerization. We detect an early periodic photoinduced absorptive signal that, employing a hybrid multiconfigurational quantum/molecular mechanical model of bR, we attribute to periodic mixing of the first and second electronic excited states (S1 and S2, respectively). This recurrent interaction between S1 and S2, induced by a bond length alternation of the retinal chromohore, supports the hypothesis that the ultrafast photoisomerization in bR is initiated by a process involving coupled nuclear and electronic motion on three different electronic states.
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Affiliation(s)
- Samer Gozem
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Philip J M Johnson
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - Alexei Halpin
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - Hoi Ling Luk
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Valentyn I Prokhorenko
- Max Planck Institute for the Structure and Dynamics of Matter, Atomically Resolved Dynamics Division, Building 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Department of Biotechnology, Chemistry and Pharmacology, Universitá di Siena, via De Gasperi 2, I-53100Siena, Italy
| | - R J Dwayne Miller
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
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29
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Pedraza-González L, Marín MDC, Jorge AN, Ruck TD, Yang X, Valentini A, Olivucci M, De Vico L. Web-ARM: A Web-Based Interface for the Automatic Construction of QM/MM Models of Rhodopsins. J Chem Inf Model 2020; 60:1481-1493. [PMID: 31909998 PMCID: PMC7101466 DOI: 10.1021/acs.jcim.9b00615] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This article introduces Web-ARM, a specialized tool, online available, designed to build quantum mechanical/molecular mechanical models of rhodopsins, a widely spread family of light-responsive proteins. Web-ARM allows the rapidly building of models of rhodopsins with a documented quality and the prediction of trends in UV-vis absorption maximum wavelengths, based on their excitation energies computed at the CASPT2//CASSCF/Amber level of theory. Web-ARM builds upon the recently reported, python-based a-ARM protocol [J. Chem. Theory Comput., 2019, 15, 3134-3152] and, as such, necessitates only a crystallographic structure or a comparative model in PDB format and a very basic knowledge of the studied rhodopsin system. The user-friendly web interface uses such input to generate congruous, gas-phase models of rhodopsins and, if requested, their mutants. We present two possible applications of Web-ARM, which showcase how the interface can be employed to assist both research and educational activities in fields at the interface between chemistry and biology. The first application shows how, through Web-ARM, research projects (e.g., rhodopsin and rhodopsin mutant screening) can be carried out in significantly less time with respect to using the required computational photochemistry tools via a command line. The second application documents the use of Web-ARM in a real-life educational/training activity, through a hands-on experience illustrating the concepts of rhodopsin color tuning.
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Affiliation(s)
- Laura Pedraza-González
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - María Del Carmen Marín
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Alejandro N Jorge
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States of America
| | - Tyler D Ruck
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States of America
| | - Xuchun Yang
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States of America
| | - Alessio Valentini
- Theoretical Physical Chemistry, Research Unit MolSys, Université de Liège, Allée du 6 Août, 11, 4000 Liège, Belgium
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States of America
| | - Luca De Vico
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
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30
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Gueye M, Paolino M, Gindensperger E, Haacke S, Olivucci M, Léonard J. Vibrational coherence and quantum yield of retinal-chromophore-inspired molecular switches. Faraday Discuss 2020; 221:299-321. [DOI: 10.1039/c9fd00062c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
UV-Vis transient absorption (TA) spectroscopy is used to carry out a systematic investigation of the ultrafast CC double photoisomerization dynamics and quantum yield of each isomer of a set of six chromophores based on the same retinal-inspired, indanylidene pyrrolinium (IP) molecular framework.
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Affiliation(s)
- Moussa Gueye
- Université de Strasbourg
- CNRS
- Institut de Physique et Chimie des Matériaux de Strasbourg
- UMR 7504
- F-67034 Strasbourg
| | - Marco Paolino
- Dipartimento di Biotechnologie
- Chimica e Farmacia
- Università di Siena
- I-53100 Siena
- Italy
| | - Etienne Gindensperger
- Université de Strasbourg
- CNRS
- Laboratoire de Chimie Quantique
- Institut de Chimie
- UMR 7177
| | - Stefan Haacke
- Université de Strasbourg
- CNRS
- Institut de Physique et Chimie des Matériaux de Strasbourg
- UMR 7504
- F-67034 Strasbourg
| | - Massimo Olivucci
- Dipartimento di Biotechnologie
- Chimica e Farmacia
- Università di Siena
- I-53100 Siena
- Italy
| | - Jérémie Léonard
- Université de Strasbourg
- CNRS
- Institut de Physique et Chimie des Matériaux de Strasbourg
- UMR 7504
- F-67034 Strasbourg
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31
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Gholami S, Pedraza-González L, Yang X, Granovsky AA, Ioffe IN, Olivucci M. Multistate Multiconfiguration Quantum Chemical Computation of the Two-Photon Absorption Spectra of Bovine Rhodopsin. J Phys Chem Lett 2019; 10:6293-6300. [PMID: 31545053 PMCID: PMC7141604 DOI: 10.1021/acs.jpclett.9b02291] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Recently, progress in IR sources has led to the discovery that humans can detect infrared (IR) light. This is hypothesized to be due to the two-photon absorption (TPA) events promoting the retina dim-light rod photoreceptor rhodopsin to the same excited state populated via one-photon absorption (OPA). Here, we combine quantum mechanics/molecular mechanics and extended multiconfiguration quasi-degenerate perturbation theory calculations to simulate the TPA spectrum of bovine rhodopsin (Rh) as a model for the human photoreceptor. The results show that the TPA spectrum of Rh has an intense S0 → S1 band but shows also S0 → S2 and S0 → S3 transitions whose intensities, relative to the S0 → S1 band, are significantly increased when compared to the corresponding bands of the OPA spectrum. In conclusion, we show that IR light in the 950 nm region can be perceived by rod photoreceptors, thus supporting the two-photon origin of the IR perception. We also found that the same photoreceptor can perceive red (i.e., close to 680 nm) light provided that TPA induces population of S2.
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Affiliation(s)
- Samira Gholami
- Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States
| | - Laura Pedraza-González
- Department of Biotechnology, Chemistry and Pharmacy , Università di Siena , via A. Moro 2 , I-53100 Siena , Siena , Italy
| | - Xuchun Yang
- Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States
| | | | - Ilya N Ioffe
- Department of Chemistry , Lomonosov Moscow State University , 119991 Moscow , Russia
| | - Massimo Olivucci
- Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States
- Department of Biotechnology, Chemistry and Pharmacy , Università di Siena , via A. Moro 2 , I-53100 Siena , Siena , Italy
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32
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Fdez. Galván I, Vacher M, Alavi A, Angeli C, Aquilante F, Autschbach J, Bao JJ, Bokarev SI, Bogdanov NA, Carlson RK, Chibotaru LF, Creutzberg J, Dattani N, Delcey MG, Dong SS, Dreuw A, Freitag L, Frutos LM, Gagliardi L, Gendron F, Giussani A, González L, Grell G, Guo M, Hoyer CE, Johansson M, Keller S, Knecht S, Kovačević G, Källman E, Li Manni G, Lundberg M, Ma Y, Mai S, Malhado JP, Malmqvist PÅ, Marquetand P, Mewes SA, Norell J, Olivucci M, Oppel M, Phung QM, Pierloot K, Plasser F, Reiher M, Sand AM, Schapiro I, Sharma P, Stein CJ, Sørensen LK, Truhlar DG, Ugandi M, Ungur L, Valentini A, Vancoillie S, Veryazov V, Weser O, Wesołowski TA, Widmark PO, Wouters S, Zech A, Zobel JP, Lindh R. OpenMolcas: From Source Code to Insight. J Chem Theory Comput 2019; 15:5925-5964. [DOI: 10.1021/acs.jctc.9b00532] [Citation(s) in RCA: 399] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ignacio Fdez. Galván
- Department of Chemistry − Ångström Laboratory, Uppsala University, P.O. Box 538, SE-751 21 Uppsala, Sweden
- Department of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
| | - Morgane Vacher
- Department of Chemistry − Ångström Laboratory, Uppsala University, P.O. Box 538, SE-751 21 Uppsala, Sweden
| | - Ali Alavi
- Max Planck Institut für Festkörperforschung, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Celestino Angeli
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Francesco Aquilante
- Département de Chimie Physique, Université de Genève, 30 quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Jie J. Bao
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Sergey I. Bokarev
- Institut für Physik, Universität Rostock, Albert-Einstein-Straße 23-24, 18059 Rostock, Germany
| | - Nikolay A. Bogdanov
- Max Planck Institut für Festkörperforschung, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Rebecca K. Carlson
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Liviu F. Chibotaru
- Theory of Nanomaterials Group, University of Leuven, Celestijnenlaan 200F, Leuven 3001, Belgium
| | - Joel Creutzberg
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91 Stockholm, Sweden
- Division of Theoretical Chemistry, Kemicentrum, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Nike Dattani
- Harvard Smithsonian Center for Astrophysics, Cambridge, Massachusetts 02138, United States
| | - Mickaël G. Delcey
- Department of Chemistry − Ångström Laboratory, Uppsala University, P.O. Box 538, SE-751 21 Uppsala, Sweden
| | - Sijia S. Dong
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205 A, 69120 Heidelberg, Germany
| | - Leon Freitag
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Luis Manuel Frutos
- Departamento de Química Analítica, Química Física e Ingeniería Química, and Instituto de Investigación Química “Andrés M. del Río”, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Laura Gagliardi
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Frédéric Gendron
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260-3000, United States
| | - Angelo Giussani
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
- Instituto de Ciencia Molecular, Universitat de València, Apartado 22085, ES-46071 Valencia, Spain
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Gilbert Grell
- Institut für Physik, Universität Rostock, Albert-Einstein-Straße 23-24, 18059 Rostock, Germany
| | - Meiyuan Guo
- Department of Chemistry − Ångström Laboratory, Uppsala University, P.O. Box 538, SE-751 21 Uppsala, Sweden
| | - Chad E. Hoyer
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Marcus Johansson
- Division of Theoretical Chemistry, Kemicentrum, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Sebastian Keller
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Stefan Knecht
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Goran Kovačević
- Division of Materials Physics, Ruđer Bošković Institute, P.O.B. 180, Bijenička 54, HR-10002 Zagreb, Croatia
| | - Erik Källman
- Department of Chemistry − Ångström Laboratory, Uppsala University, P.O. Box 538, SE-751 21 Uppsala, Sweden
| | - Giovanni Li Manni
- Max Planck Institut für Festkörperforschung, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Marcus Lundberg
- Department of Chemistry − Ångström Laboratory, Uppsala University, P.O. Box 538, SE-751 21 Uppsala, Sweden
| | - Yingjin Ma
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - João Pedro Malhado
- Department of Chemistry, Imperial College London, London SW7 2AZ, United Kingdom
| | - Per Åke Malmqvist
- Division of Theoretical Chemistry, Kemicentrum, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Stefanie A. Mewes
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205 A, 69120 Heidelberg, Germany
- Centre for Theoretical Chemistry and Physics, The New Zealand Institute for Advanced Study (NZIAS), Massey University Albany, Private Bag
102904, Auckland 0632, New Zealand
| | - Jesper Norell
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Moro 2, 53100 Siena, Italy
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- USIAS and Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg-CNRS, 67034 Strasbourg, France
| | - Markus Oppel
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Quan Manh Phung
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven 3001, Belgium
| | - Kristine Pierloot
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven 3001, Belgium
| | - Felix Plasser
- Department of Chemistry, Loughborough University, Loughborough LE11 3TU, United Kingdom
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Andrew M. Sand
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Prachi Sharma
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Christopher J. Stein
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Lasse Kragh Sørensen
- Department of Chemistry − Ångström Laboratory, Uppsala University, P.O. Box 538, SE-751 21 Uppsala, Sweden
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Mihkel Ugandi
- Department of Chemistry − Ångström Laboratory, Uppsala University, P.O. Box 538, SE-751 21 Uppsala, Sweden
| | - Liviu Ungur
- Department of Chemistry, National University of Singapore, 117543 Singapore
| | - Alessio Valentini
- Theoretical Physical Chemistry, Research Unit MolSys, Allée du 6 Août, 11, 4000 Liège, Belgium
| | - Steven Vancoillie
- Division of Theoretical Chemistry, Kemicentrum, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Valera Veryazov
- Division of Theoretical Chemistry, Kemicentrum, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Oskar Weser
- Max Planck Institut für Festkörperforschung, Heisenbergstraße 1, 70569 Stuttgart, Germany
| | - Tomasz A. Wesołowski
- Département de Chimie Physique, Université de Genève, 30 quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
| | - Per-Olof Widmark
- Division of Theoretical Chemistry, Kemicentrum, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Sebastian Wouters
- Brantsandpatents, Pauline van Pottelsberghelaan 24, 9051 Sint-Denijs-Westrem, Belgium
| | - Alexander Zech
- Département de Chimie Physique, Université de Genève, 30 quai Ernest-Ansermet, CH-1211 Genève 4, Switzerland
| | - J. Patrick Zobel
- Division of Theoretical Chemistry, Kemicentrum, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Roland Lindh
- Department of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-751 23 Uppsala, Sweden
- Uppsala Center for Computational Chemistry (UC3), Uppsala University, P.O. Box 596, SE-751 24 Uppsala, Sweden
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33
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Schapiro I, Gueye M, Paolino M, Fusi S, Marchand G, Haacke S, Martin ME, Huntress M, Vysotskiy VP, Veryazov V, Léonard J, Olivucci M. Synthesis, spectroscopy and QM/MM simulations of a biomimetic ultrafast light-driven molecular motor. Photochem Photobiol Sci 2019; 18:2259-2269. [PMID: 31347633 DOI: 10.1039/c9pp00223e] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A molecular motor potentially performing a continuous unidirectional rotation is studied by a multidisciplinary approach including organic synthesis, transient spectroscopy and excited state trajectory calculations. A stereogenic center was introduced in the N-alkylated indanylidene-pyrroline Schiff base framework of a previously investigated light-driven molecular switch in order to achieve the unidirectional C[double bond, length as m-dash]C rotary motion typical of Feringa's motor. Here we report that the specific substitution pattern of the designed chiral molecule must critically determine the unidirectional efficiency of the light-induced rotary motion. More specifically, we find that a stereogenic center containing a methyl group and a hydrogen atom as substituents does not create a differential steric effect large enough to fully direct the motion in either the clockwise or counterclockwise direction especially along the E→Z coordinate. However, due to the documented ultrafast character and electronic circular dichroism activity of the investigated system, we find that it provides the basis for development of a novel generation of rotary motors with a biomimetic framework and operating on a picosecond time scale.
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Affiliation(s)
- Igor Schapiro
- Université de Strasbourg, CNRS, UMR 7504, Institut de Physique et Chimie des Matériaux de Strasbourg, 23 du Loess, 67034 Strasbourg, France
| | - Moussa Gueye
- Université de Strasbourg, CNRS, UMR 7504, Institut de Physique et Chimie des Matériaux de Strasbourg, 23 du Loess, 67034 Strasbourg, France
| | - Marco Paolino
- Dipartimento di Biotecnologia, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, via Aldo Moro 2, I-53100 Siena, Italy.
| | - Stefania Fusi
- Dipartimento di Biotecnologia, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, via Aldo Moro 2, I-53100 Siena, Italy.
| | - Gabriel Marchand
- Université de Strasbourg, CNRS, UMR 7504, Institut de Physique et Chimie des Matériaux de Strasbourg, 23 du Loess, 67034 Strasbourg, France
| | - Stefan Haacke
- Université de Strasbourg, CNRS, UMR 7504, Institut de Physique et Chimie des Matériaux de Strasbourg, 23 du Loess, 67034 Strasbourg, France
| | - M Elena Martin
- Area de Química Física, Universidad de Extremadura, Avenida de Elvas sn, E-06071, Badajoz, Spain
| | - Mark Huntress
- Chemistry Department, Bowling Green State University, Bowling Green Ohio 43403, USA
| | - Victor P Vysotskiy
- Division of Theoretical Chemistry, Kemicentrum, Lund University, P.O. Box 124, Lund, SE-221 00, Sweden
| | - Valera Veryazov
- Division of Theoretical Chemistry, Kemicentrum, Lund University, P.O. Box 124, Lund, SE-221 00, Sweden
| | - Jérémie Léonard
- Université de Strasbourg, CNRS, UMR 7504, Institut de Physique et Chimie des Matériaux de Strasbourg, 23 du Loess, 67034 Strasbourg, France
| | - Massimo Olivucci
- Dipartimento di Biotecnologia, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, via Aldo Moro 2, I-53100 Siena, Italy. and Chemistry Department, Bowling Green State University, Bowling Green Ohio 43403, USA
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34
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Pieri E, Ledentu V, Sahlin M, Dehez F, Olivucci M, Ferré N. CpHMD-Then-QM/MM Identification of the Amino Acids Responsible for the Anabaena Sensory Rhodopsin pH-Dependent Electronic Absorption Spectrum. J Chem Theory Comput 2019; 15:4535-4546. [PMID: 31264415 DOI: 10.1021/acs.jctc.9b00221] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Anabaena Sensory Rhodopsin (ASR), a microbial photoactive protein featuring the retinal chromophore in two different conformations, exhibits a pH-dependent electronic absorption spectrum. Using the recently developed CpHMD-then-QM/MM multiscale protocol applied to ASR embedded in a membrane model, the pH-induced changes in its maximum absorption wavelength have been reproduced and analyzed. While the acidic tiny red-shift is essentially correlated with the deprotonation of an aspartic acid located on the ASR extracellular side, the larger blue-shift experimentally reported at pH values larger than 5 involves a cluster of titrating residues sitting on the cytoplasmic side. The ASR pH-dependent spectrum is the consequence of the competitive stabilization of retinal ground and excited states by the protein electrostatic potential.
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Affiliation(s)
- Elisa Pieri
- Aix-Marseille Univ , CNRS, ICR , 13013 Marseille , France
| | | | - Michael Sahlin
- Aix-Marseille Univ , CNRS, ICR , 13013 Marseille , France
| | - François Dehez
- Laboratoire de Physique et Chimie Théorique , UMR 7019, Faculté des Sciences et Technique , Campus Aiguillettes , 54506 Vandoeuvre-les-Nancy , France
| | - Massimo Olivucci
- Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States.,Dipartimento di Biotecnologie, Chimica e Farmacia , Università degli Studi di Siena , via A. Moro 2 , 53100 Siena , Italy
| | - Nicolas Ferré
- Aix-Marseille Univ , CNRS, ICR , 13013 Marseille , France
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35
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Agathangelou D, Orozco-Gonzalez Y, Del Carmen Marín M, Roy PP, Brazard J, Kandori H, Jung KH, Léonard J, Buckup T, Ferré N, Olivucci M, Haacke S. Effect of point mutations on the ultrafast photo-isomerization of Anabaena sensory rhodopsin. Faraday Discuss 2019; 207:55-75. [PMID: 29388996 DOI: 10.1039/c7fd00200a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anabaena sensory rhodopsin (ASR) is a particular microbial retinal protein for which light-adaptation leads to the ability to bind both the all-trans, 15-anti (AT) and the 13-cis, 15-syn (13C) isomers of the protonated Schiff base of retinal (PSBR). In the context of obtaining insight into the mechanisms by which retinal proteins catalyse the PSBR photo-isomerization reaction, ASR is a model system allowing to study, within the same protein, the protein-PSBR interactions for two different PSBR conformers at the same time. A detailed analysis of the vibrational spectra of AT and 13C, and their photo-products in wild-type ASR obtained through femtosecond (pump-) four-wave-mixing is reported for the first time, and compared to bacterio- and channelrhodopsin. As part of an extensive study of ASR mutants with blue-shifted absorption spectra, we present here a detailed computational analysis of the origin of the mutation-induced blue-shift of the absorption spectra, and identify electrostatic interactions as dominating steric effects that would entail a red-shift. The excited state lifetimes and isomerization reaction times (IRT) for the three mutants V112N, W76F, and L83Q are studied experimentally by femtosecond broadband transient absorption spectroscopy. Interestingly, in all three mutants, isomerization is accelerated for AT with respect to wild-type ASR, and this the more, the shorter the wavelength of maximum absorption. On the contrary, the 13C photo-reaction is slightly slowed down, leading to an inversion of the ESLs of AT and 13C, with respect to wt-ASR, in the blue-most absorbing mutant L83Q. Possible mechanisms for these mutation effects, and their steric and electrostatic origins are discussed.
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Affiliation(s)
- D Agathangelou
- University of Strasbourg, CNRS, Inst. de Physique et Chimie des Matériaux de Strasbourg, 67034 Strasbourg, France.
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36
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Pedraza-González L, De Vico L, del Carmen Marín M, Fanelli F, Olivucci M. a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement. J Chem Theory Comput 2019; 15:3134-3152. [PMID: 30916955 PMCID: PMC7141608 DOI: 10.1021/acs.jctc.9b00061] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Automatic Rhodopsin Modeling (ARM) protocol has recently been proposed as a tool for the fast and parallel generation of basic hybrid quantum mechanics/molecular mechanics (QM/MM) models of wild type and mutant rhodopsins. However, in its present version, input preparation requires a few hours long user's manipulation of the template protein structure, which also impairs the reproducibility of the generated models. This limitation, which makes model building semiautomatic rather than fully automatic, comprises four tasks: definition of the retinal chromophore cavity, assignment of protonation states of the ionizable residues, neutralization of the protein with external counterions, and finally congruous generation of single or multiple mutations. In this work, we show that the automation of the original ARM protocol can be extended to a level suitable for performing the above tasks without user's manipulation and with an input preparation time of minutes. The new protocol, called a-ARM, delivers fully reproducible (i.e., user independent) rhodopsin QM/MM models as well as an improved model quality. More specifically, we show that the trend in vertical excitation energies observed for a set of 25 wild type and 14 mutant rhodopsins is predicted by the new protocol better than when using the original. Such an agreement is reflected by an estimated (relative to the probed set) trend deviation of 0.7 ± 0.5 kcal mol-1 (0.03 ± 0.02 eV) and mean absolute error of 1.0 kcal mol-1 (0.04 eV).
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Affiliation(s)
- Laura Pedraza-González
- Department of Biotechnologies, Chemistry and Pharmacy, Università degli Studi di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Luca De Vico
- Department of Biotechnologies, Chemistry and Pharmacy, Università degli Studi di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - María del Carmen Marín
- Department of Biotechnologies, Chemistry and Pharmacy, Università degli Studi di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Francesca Fanelli
- Department of Life Sciences, Center for Neuroscience and Neurotechnology, Università degli Studi di Modena e Reggio Emilia, I-41125 Modena, Italy
| | - Massimo Olivucci
- Department of Biotechnologies, Chemistry and Pharmacy, Università degli Studi di Siena, via A. Moro 2, I-53100 Siena, Italy
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
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Pagano K, Paolino M, Fusi S, Zanirato V, Trapella C, Giuliani G, Cappelli A, Zanzoni S, Molinari H, Ragona L, Olivucci M. Bile Acid Binding Protein Functionalization Leads to a Fully Synthetic Rhodopsin Mimic. J Phys Chem Lett 2019; 10:2235-2243. [PMID: 30995409 DOI: 10.1021/acs.jpclett.9b00210] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Rhodopsins are photoreceptive proteins using light to drive a plethora of biological functions such as vision, proton and ion pumping, cation and anion channeling, and gene and enzyme regulation. Here we combine organic synthesis, NMR structural studies, and photochemical characterization to show that it is possible to prepare a fully synthetic mimic of rhodopsin photoreceptors. More specifically, we conjugate a bile acid binding protein with a synthetic mimic of the rhodopsin protonated Schiff base chromophore to achieve a covalent complex featuring an unnatural protein host, photoswitch, and photoswitch-protein linkage with a reverse orientation. We show that, in spite of its molecular-level diversity, light irradiation of the prepared mimic fuels a photochromic cycle driven by sequential photochemical and thermal Z/E isomerizations reminiscent of the photocycles of microbial rhodopsins.
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Affiliation(s)
- Katiuscia Pagano
- Istituto per lo Studio delle Macromolecole, CNR , Via A. Corti 12 , 20133 Milano , Italy
| | - Marco Paolino
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022) , Università degli Studi di Siena , Via Aldo Moro 2 , 53100 Siena , Italy
| | - Stefania Fusi
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022) , Università degli Studi di Siena , Via Aldo Moro 2 , 53100 Siena , Italy
| | | | | | - Germano Giuliani
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022) , Università degli Studi di Siena , Via Aldo Moro 2 , 53100 Siena , Italy
| | - Andrea Cappelli
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022) , Università degli Studi di Siena , Via Aldo Moro 2 , 53100 Siena , Italy
| | - Serena Zanzoni
- Centro Piattaforme Tecnologiche , Università di Verona , Strada Le Grazie , 37134 Verona , Italy
| | - Henriette Molinari
- Istituto per lo Studio delle Macromolecole, CNR , Via A. Corti 12 , 20133 Milano , Italy
| | - Laura Ragona
- Istituto per lo Studio delle Macromolecole, CNR , Via A. Corti 12 , 20133 Milano , Italy
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018-2022) , Università degli Studi di Siena , Via Aldo Moro 2 , 53100 Siena , Italy
- Chemistry Department , Bowling Green State University , Bowling Green , Ohio 43403 , United States
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38
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Marín MDC, De Vico L, Dong SS, Gagliardi L, Truhlar DG, Olivucci M. Assessment of MC-PDFT Excitation Energies for a Set of QM/MM Models of Rhodopsins. J Chem Theory Comput 2019; 15:1915-1923. [PMID: 30721054 PMCID: PMC7096677 DOI: 10.1021/acs.jctc.8b01069] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A methodology for the automatic production of quantum mechanical/molecular mechanical (QM/MM) models of retinal-binding rhodopsin proteins and subsequent prediction of their spectroscopic properties has been proposed recently by some of the authors. The technology employed for the evaluation of the excitation energies is called Automatic Rhodopsin Modeling (ARM), and it involves the use of the complete active space self-consistent field (CASSCF) method followed by a multiconfiguration second-order perturbation theory (in particular, CASPT2) calculation of external correlation energies. Although it was shown that ARM is capable of successfully reproducing and predicting spectroscopic property trends in chromophore-embedding protein sets, practical applications of such technology are limited by the high computational costs of the multiconfiguration perturbation theory calculations. In the present work we benchmark the more affordable multiconfiguration pair-density functional theory (MC-PDFT) method whose accuracy has been recently validated for retinal chromophores in the gas phase, indicating that MC-PDFT could potentially be used to analyze large (e.g., few hundreds) sets of rhodopsin proteins. Here, we test this theory for a set of rhodopsin QM/MM models whose experimental absorption maxima (λ a max) have been measured. The results indicate that MC-PDFT may be employed to calculate λ a max values for this important class of photoresponsive proteins.
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Affiliation(s)
- María Del Carmen Marín
- Department of Biotechnologies, Chemistry and Pharmacy , University of Siena , 53100 Siena , Italy
- Chemistry Department , Bowling Green State University , Bowling Green , 43403 Ohio , United States
| | - Luca De Vico
- Department of Biotechnologies, Chemistry and Pharmacy , University of Siena , 53100 Siena , Italy
| | - Sijia S Dong
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , United States
| | - Laura Gagliardi
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , Minneapolis , Minnesota 55455-0431 , United States
| | - Massimo Olivucci
- Department of Biotechnologies, Chemistry and Pharmacy , University of Siena , 53100 Siena , Italy
- Chemistry Department , Bowling Green State University , Bowling Green , 43403 Ohio , United States
- USIAS Institut d'Études Avanceés , Université de Strasbourg , 67083 Strasbourg , France
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39
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Marsili E, Farag MH, Yang X, De Vico L, Olivucci M. Two-State, Three-Mode Parametrization of the Force Field of a Retinal Chromophore Model. J Phys Chem A 2019; 123:1710-1719. [PMID: 30753077 DOI: 10.1021/acs.jpca.8b10010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, the potential energy surfaces of the penta-2,4-dieniminium cation have been investigated using several electronic structure methods. The resulting pool of geometrical, electronic, and energy data provides a suitable basis for the construction of a topographically correct analytical model of the molecule force field and, therefore, for a better understanding of this class of molecules, which includes the chromophore of visual pigments. In the present contribution, we report the construction of such a model for regions of the force field that drive the photochemical and thermal isomerization of the central double bound of the cation. While previous models included only two modes, it is here shown that the proposed three-mode model and corresponding set of parameters are able to reproduce the complex topographical and electronic structure features seen in electronically correlated data obtained at the XMCQDPT2//CASSCF/6-31G* level of theory.
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Affiliation(s)
- Emanuele Marsili
- Dipartimento di Biotecnologie, Chimica e Farmacia , Università di Siena , via A. Moro 2 , I-53100 Siena , Italy
| | - Marwa H Farag
- Department of Chemistry , University of Southern California , Los Angeles , California 90089-0482 , United States
| | - Xuchun Yang
- Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States and
| | - Luca De Vico
- Dipartimento di Biotecnologie, Chimica e Farmacia , Università di Siena , via A. Moro 2 , I-53100 Siena , Italy
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia , Università di Siena , via A. Moro 2 , I-53100 Siena , Italy.,Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States and.,Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 , Université de Strasbourg-CNRS , F-67034 Strasbourg , France
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40
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Agathangelou D, Orozco-Gonzalez Y, del Carmen Marin Pérez M, Brazard J, Kandori H, Jung KH, Léonard J, Ferré N, Olivucci M, S. H. Anabaena Sensory Rhodopsin: Effect of point mutations on PSBR photo-isomerization speed. EPJ Web Conf 2019. [DOI: 10.1051/epjconf/201920510004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report new experimental results on the ultrafast photo-isomerization of ASR - PSBR where, unlike other retinal proteins, point mutations lead to a 2-fold increase of the photo-isomerization speed for the all-trans isomer. Prominent low-frequency vibrational coherences are reported for both the excited and photo-product ground states.
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41
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Marín MDC, Agathangelou D, Orozco-Gonzalez Y, Valentini A, Kato Y, Abe-Yoshizumi R, Kandori H, Choi A, Jung KH, Haacke S, Olivucci M. Fluorescence Enhancement of a Microbial Rhodopsin via Electronic Reprogramming. J Am Chem Soc 2018; 141:262-271. [PMID: 30532962 DOI: 10.1021/jacs.8b09311] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The engineering of microbial rhodopsins with enhanced fluorescence is of great importance in the expanding field of optogenetics. Here we report the discovery of two mutants (W76S/Y179F and L83Q) of a sensory rhodopsin from the cyanobacterium Anabaena PCC7120 with opposite fluorescence behavior. In fact, while W76S/Y179F displays, with respect to the wild-type protein, a nearly 10-fold increase in red-light emission, the second is not emissive. Thus, the W76S/Y179F, L83Q pair offers an unprecedented opportunity for the investigation of fluorescence enhancement in microbial rhodopsins, which is pursued by combining transient absorption spectroscopy and multiconfigurational quantum chemistry. The results of such an investigation point to an isomerization-blocking electronic effect as the direct cause of instantaneous (subpicosecond) fluorescence enhancement.
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Affiliation(s)
- María Del Carmen Marín
- Biotechnology, Pharmacy and Chemistry Department , University of Siena , Siena 53100 , Italy.,Chemistry Department , Bowling Green State University , Bowling Green , Ohio 43403 , United States
| | - Damianos Agathangelou
- University of Strasbourg-CNRS , Institute of Physics and Chemistry of Materials of Strasbourg , 67034 Strasbourg , France
| | - Yoelvis Orozco-Gonzalez
- Chemistry Department , Bowling Green State University , Bowling Green , Ohio 43403 , United States.,Université de Strasbourg , USIAS Institut d'Études Avanceés , 67083 Strasbourg , France
| | - Alessio Valentini
- Theoretical Physical Chemistry , UR Molsys, University of Liège , Liège , Belgium
| | - Yoshitaka Kato
- Department of Life Science and Applied Chemistry , Nagoya Institute of Technology , Showa-ku , Nagoya 466-8555 , Japan
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry , Nagoya Institute of Technology , Showa-ku , Nagoya 466-8555 , Japan.,OptoBioTechnology Research Center , Nagoya Institute of Technology , Showa-ku , Nagoya 466-8555 , Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry , Nagoya Institute of Technology , Showa-ku , Nagoya 466-8555 , Japan.,OptoBioTechnology Research Center , Nagoya Institute of Technology , Showa-ku , Nagoya 466-8555 , Japan
| | - Ahreum Choi
- Department of Life Science and Institute of Biological Interfaces , Sogang University , Sogang 04107 , South Korea
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces , Sogang University , Sogang 04107 , South Korea
| | - Stefan Haacke
- University of Strasbourg-CNRS , Institute of Physics and Chemistry of Materials of Strasbourg , 67034 Strasbourg , France
| | - Massimo Olivucci
- Biotechnology, Pharmacy and Chemistry Department , University of Siena , Siena 53100 , Italy.,Chemistry Department , Bowling Green State University , Bowling Green , Ohio 43403 , United States.,Université de Strasbourg , USIAS Institut d'Études Avanceés , 67083 Strasbourg , France
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42
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Manathunga M, Yang X, Olivucci M. Electronic State Mixing Controls the Photoreactivity of a Rhodopsin with all- trans Chromophore Analogues. J Phys Chem Lett 2018; 9:6350-6355. [PMID: 30336038 PMCID: PMC6261349 DOI: 10.1021/acs.jpclett.8b02550] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Rhodopsins hosting synthetic retinal protonated Schiff base analogues are important for developing tools for optogenetics and high-resolution imaging. The ideal spectroscopic properties of such analogues include long-wavelength absorption/emission and fast/hindered photoisomerization. While the former may be achieved, for instance, by elongating the chromophore π-system, the latter requires a detailed understanding of the substituent effects (i.e., steric or electronic) on the chromophore light-induced dynamics. In the present letter we compare the results of quantum mechanics/molecular mechanics excited-state trajectories of native and analogue-hosting microbial rhodopsins from the eubacterium Anabaena. The results uncover a relationship between the nature of the substituent on the analogue (i.e., electron-donating (a Me group) or electron-withdrawing (a CF3 group)) and rhodopsin excited-state lifetime. Most importantly, we show that electron-donating or -withdrawing substituents cause a decrease or an increase in the electronic mixing of the first two excited states which, in turn, controls the photoisomerization speed.
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Affiliation(s)
- Madushanka Manathunga
- Department of Chemistry, Bowling Green State
University, Bowling Green, OH 43403, USA
| | - Xuchun Yang
- Department of Chemistry, Bowling Green State
University, Bowling Green, OH 43403, USA
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State
University, Bowling Green, OH 43403, USA
- Dipartimento di Biotecnologie, Chimica e Farmacia,
Università di Siena, via A. Moro 2, I-53100 Siena, Italy
- Institut de Physique et Chimie des Matériaux
de Strasbourg, UMR 7504 Université de Strasbourg-CNRS, F-67034 Strasbourg,
France
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43
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Nikolaev D, Shtyrov AA, Panov MS, Jamal A, Chakchir OB, Kochemirovsky VA, Olivucci M, Ryazantsev MN. A Comparative Study of Modern Homology Modeling Algorithms for Rhodopsin Structure Prediction. ACS Omega 2018; 3:7555-7566. [PMID: 30087916 PMCID: PMC6068592 DOI: 10.1021/acsomega.8b00721] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/21/2018] [Indexed: 06/08/2023]
Abstract
Rhodopsins are seven α-helical membrane proteins that are of great importance in chemistry, biology, and modern biotechnology. Any in silico study on rhodopsin properties and functioning requires a high-quality three-dimensional structure. Due to particular difficulties with obtaining membrane protein structures from the experiment, in silico prediction of the three-dimensional rhodopsin structure based only on its primary sequence is an especially important task. For the last few years, significant progress was made in the field of protein structure prediction, especially for methods based on comparative modeling. However, the majority of this progress was made for soluble proteins and further investigations are needed to achieve similar progress for membrane proteins. In this paper, we evaluate the performance of modern protein structure prediction methodologies (implemented in the Medeller, I-TASSER, and Rosetta packages) for their ability to predict rhodopsin structures. Three widely used methodologies were considered: two general methodologies that are commonly applied to soluble proteins and a methodology that uses constraints that are specific for membrane proteins. The test pool consisted of 36 target-template pairs with different sequence similarities that was constructed on the basis of 24 experimental rhodopsin structures taken from the RCSB database. As a result, we showed that all three considered methodologies allow obtaining rhodopsin structures with the quality that is close to the crystallographic one (root mean square deviation (RMSD) of the predicted structure from the corresponding X-ray structure up to 1.5 Å) if the target-template sequence identity is higher than 40%. Moreover, all considered methodologies provided structures of average quality (RMSD < 4.0 Å) if the target-template sequence identity is higher than 20%. Such structures can be subsequently used for further investigation of molecular mechanisms of protein functioning and for the development of modern protein-based biotechnologies.
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Affiliation(s)
- Dmitrii
M. Nikolaev
- Nanotechnology
Research and Education Centre RAS, Saint-Petersburg
Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | - Andrey A. Shtyrov
- Nanotechnology
Research and Education Centre RAS, Saint-Petersburg
Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | - Maxim S. Panov
- Institute
of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya emb., St. Petersburg 199034, Russia
| | - Adeel Jamal
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Oleg B. Chakchir
- Nanotechnology
Research and Education Centre RAS, Saint-Petersburg
Academic University, 8/3 Khlopina Street, St. Petersburg 194021, Russia
| | - Vladimir A. Kochemirovsky
- Institute
of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya emb., St. Petersburg 199034, Russia
| | - Massimo Olivucci
- Department
of Biotechnology, Chemistry and Pharmacy, Università di Siena, via A. Moro 2, Siena I-53100, Italy
| | - Mikhail N. Ryazantsev
- Institute
of Chemistry, Saint Petersburg State University, 7/9 Universitetskaya emb., St. Petersburg 199034, Russia
- Institute
of Macromolecular Compounds of the Russian Academy of Sciences, 31 Bolshoy pr., St. Petersburg 199004, Russia
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44
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El-Tahawy MMT, Nenov A, Weingart O, Olivucci M, Garavelli M. Relationship between Excited State Lifetime and Isomerization Quantum Yield in Animal Rhodopsins: Beyond the One-Dimensional Landau-Zener Model. J Phys Chem Lett 2018; 9:3315-3322. [PMID: 29791163 PMCID: PMC6650607 DOI: 10.1021/acs.jpclett.8b01062] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We show that the speed of the chromophore photoisomerization of animal rhodopsins is not a relevant control knob for their light sensitivity. This result is at odds with the momentum-driven tunnelling rationale (i.e., assuming a one-dimensional Landau-Zener model for the decay: Zener, C. Non-Adiabatic Crossing of Energy Levels. Proc. R. Soc. London, Ser. A 1932, 137 (833), 696-702) holding that a faster nuclear motion through the conical intersection translates into a higher quantum yield and, thus, light sensitivity. Instead, a model based on the phase-matching of specific excited state vibrational modes should be considered. Using extensive semiclassical hybrid quantum mechanics/molecular mechanics trajectory computations to simulate the photoisomerization of three animal rhodopsin models (visual rhodopsin, squid rhodopsin and human melanopsin), we also demonstrate that phase-matching between three different modes (the reactive carbon and hydrogen twisting coordinates and the bond length alternation mode) is required to achieve high quantum yields. In fact, such "phase-matching" mechanism explains the computational results and provides a tool for the prediction of the photoisomerization outcome in retinal proteins.
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Affiliation(s)
- Mohsen M. T. El-Tahawy
- Dipartimento di Chimica Industriale “Toso Montanari″, Università degli Studi di Bologna, Viale del Risorgimento, 4I -40136 Bologna, Italy
- Chemistry Department, Faculty of Science, Damanhour University, Damanhour 22511, Egypt
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari″, Università degli Studi di Bologna, Viale del Risorgimento, 4I -40136 Bologna, Italy
| | - Oliver Weingart
- Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
- Chemistry Department, Bowling Green State University, Bowling Green, OH 43403
- Corresponding Author; (M.O.): ; Phone: +39 051 20 9 9476. Fax: +39 051 20 9 9456 (M.G.)
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari″, Università degli Studi di Bologna, Viale del Risorgimento, 4I -40136 Bologna, Italy
- Corresponding Author; (M.O.): ; Phone: +39 051 20 9 9476. Fax: +39 051 20 9 9456 (M.G.)
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45
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Smyrnova D, Marín MDC, Olivucci M, Ceulemans A. Systematic Excited State Studies of Reversibly Switchable Fluorescent Proteins. J Chem Theory Comput 2018; 14:3163-3172. [PMID: 29772175 DOI: 10.1021/acs.jctc.8b00050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The reversibly switchable fluorescent proteins Dronpa, rsFastLime, rsKame, Padron, and bsDronpa feature the same chromophore but display a 40 nm variation in absorption maxima and an only 18 nm variation in emission maxima. In the present contribution, we employ QM/MM models to investigate the mechanism of such remarkably different spectral variations, which are caused by just a few amino acid replacements. We show that the models, which are based on CASPT2//CASSCF level of QM theory, reproduce the observed trends in absorption maxima, with only a 3.5 kcal/mol blue-shift, and in emission maxima, with an even smaller 1.5 kcal/mol blue-shift with respect to the observed quantities. In order to explain the variations across the series, we look at the chromophore's electronic structure change during absorption and emission. Such analysis indicates that a change in charge-transfer character, which is more pronounced during absorption, triggers a cascade of hydrogen-bond-network rearrangements, suggesting preparation to an isomerization event. We also show how the contribution of Arg 89 and Arg 64 residues to the chromophore conformational changes correlate with the spectral variations in absorption and emission. Furthermore, we describe how the conical intersection stability is related to the protein's photophysical properties. While for the Dronpa, rsFastLime, and rsKame triad, the stability correlates with the photoswitching speed, this does not happen for bsDronpa and Padron, suggesting a less obvious photoisomerization mechanism.
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Affiliation(s)
- Daryna Smyrnova
- Quantum Chemistry and Physical Chemistry Division, Department of Chemistry , KU Leuven , Celestijnenlaan 200F , B-3001 Heverlee , Belgium
| | - María Del Carmen Marín
- Department of Biotechnology, Chemistry, and Pharmacy , Universitá di Siena , via A. Moro 2 , I-53100 Siena , Italy.,Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry, and Pharmacy , Universitá di Siena , via A. Moro 2 , I-53100 Siena , Italy.,Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States
| | - Arnout Ceulemans
- Quantum Chemistry and Physical Chemistry Division, Department of Chemistry , KU Leuven , Celestijnenlaan 200F , B-3001 Heverlee , Belgium
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46
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Gueye M, Manathunga M, Agathangelou D, Orozco Y, Paolino M, Fusi S, Haacke S, Olivucci M, Léonard J. Engineering the vibrational coherence of vision into a synthetic molecular device. Nat Commun 2018; 9:313. [PMID: 29358689 PMCID: PMC5778125 DOI: 10.1038/s41467-017-02668-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 12/15/2017] [Indexed: 11/09/2022] Open
Abstract
The light-induced double-bond isomerization of the visual pigment rhodopsin operates a molecular-level optomechanical energy transduction, which triggers a crucial protein structure change. In fact, rhodopsin isomerization occurs according to a unique, ultrafast mechanism that preserves mode-specific vibrational coherence all the way from the reactant excited state to the primary photoproduct ground state. The engineering of such an energy-funnelling function in synthetic compounds would pave the way towards biomimetic molecular machines capable of achieving optimum light-to-mechanical energy conversion. Here we use resonance and off-resonance vibrational coherence spectroscopy to demonstrate that a rhodopsin-like isomerization operates in a biomimetic molecular switch in solution. Furthermore, by using quantum chemical simulations, we show why the observed coherent nuclear motion critically depends on minor chemical modifications capable to induce specific geometric and electronic effects. This finding provides a strategy for engineering vibrationally coherent motions in other synthetic systems. The ultrafast, vibrationally coherent photoisomerization of rhodopsin is a model of efficient photomechanical energy conversion at the molecular scale. Here, the authors demonstrate a similar photoreaction in synthetic compounds, unraveling the underlying mechanism and discussing its implications.
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Affiliation(s)
- Moussa Gueye
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67034, Strasbourg, France
| | - Madushanka Manathunga
- Department of Chemistry, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Damianos Agathangelou
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67034, Strasbourg, France
| | - Yoelvis Orozco
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67034, Strasbourg, France
| | - Marco Paolino
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100, Siena, Italy
| | - Stefania Fusi
- Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100, Siena, Italy
| | - Stefan Haacke
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67034, Strasbourg, France
| | - Massimo Olivucci
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67034, Strasbourg, France. .,Department of Chemistry, Bowling Green State University, Bowling Green, OH, 43403, USA. .,Dipartimento di Biotechnologie, Chimica e Farmacia, Università di Siena, I-53100, Siena, Italy.
| | - Jérémie Léonard
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, F-67034, Strasbourg, France.
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47
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Orozco-Gonzalez Y, Manathunga M, Marín MDC, Agathangelou D, Jung KH, Melaccio F, Ferré N, Haacke S, Coutinho K, Canuto S, Olivucci M. An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and Application to Rhodopsin Systems. J Chem Theory Comput 2017; 13:6391-6404. [DOI: 10.1021/acs.jctc.7b00860] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yoelvis Orozco-Gonzalez
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
- USIAS Institut d’É;tudes Avanceés, Université de Strasbourg, 5 alleé
du Geńeŕal Rouvillois, F-67083 Strasbourg, France
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Madushanka Manathunga
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - María del Carmen Marín
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Damianos Agathangelou
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
| | - Kwang-Hwan Jung
- Department
of Life Science and Institute of Biological Interfaces, Sogang University 35 Baekbeom-Ro, Mapo-Gu, Seoul 04107, Korea
| | - Federico Melaccio
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, ICR, 13013 Marseille, France
| | - Stefan Haacke
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, 05508-090 Cidade Universitária, São Paulo/SP, Brazil
| | - Sylvio Canuto
- Instituto de Física, Universidade de São Paulo, 05508-090 Cidade Universitária, São Paulo/SP, Brazil
| | - Massimo Olivucci
- Université de Strasbourg-CNRS, UMR 7504, Institut de Physique et Chimie des Mateŕiaux de Strasbourg, F-67034 Strasbourg, France
- USIAS Institut d’É;tudes Avanceés, Université de Strasbourg, 5 alleé
du Geńeŕal Rouvillois, F-67083 Strasbourg, France
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Department
of Biotechnology, Chemistry e Pharmacy, Università di Siena, via A. Moro 2, I-53100 Siena, Italy
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48
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Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
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49
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Manathunga M, Yang X, Orozco-Gonzalez Y, Olivucci M. Impact of Electronic State Mixing on the Photoisomerization Time Scale of the Retinal Chromophore. J Phys Chem Lett 2017; 8:5222-5227. [PMID: 28981285 DOI: 10.1021/acs.jpclett.7b02344] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Spectral data show that the photoisomerization of retinal protonated Schiff base (rPSB) chromophores occurs on a 100 fs time scale or less in vertebrate rhodopsins, it is several times slower in microbial rhodopsins and it is between one and 2 orders of magnitude slower in solution. These time scale variations have been attributed to specific modifications of the topography of the first excited state potential energy surface of the chromophore. However, it is presently not clear which specific environment effects (e.g., electrostatic, electronic, or steric) are responsible for changing the surface topography. Here, we use QM/MM models and excited state trajectory computations to provide evidence for an increase in electronic mixing between the first and the second excited state of the chromophore when going from vertebrate rhodopsin to the solution environments. Ultimately, we argue that a correlation between the lifetime of the first excited state and electronic mixing between such state and its higher neighbor, may have been exploited to evolve rhodopsins toward faster isomerization and, possibly, light-sensitivity.
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Affiliation(s)
- Madushanka Manathunga
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Xuchun Yang
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
| | - Yoelvis Orozco-Gonzalez
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
- Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 Université de Strasbourg-CNRS, F-67034 Strasbourg, France
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena , via A. Moro 2, I-53100 Siena, Italy
- Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 Université de Strasbourg-CNRS, F-67034 Strasbourg, France
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Valentini A, Rivero D, Zapata F, García-Iriepa C, Marazzi M, Palmeiro R, Fdez. Galván I, Sampedro D, Olivucci M, Frutos LM. Optomechanical Control of Quantum Yield in Trans
-Cis
Ultrafast Photoisomerization of a Retinal Chromophore Model. Angew Chem Int Ed Engl 2017; 56:3842-3846. [DOI: 10.1002/anie.201611265] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 01/12/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Alessio Valentini
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
- Department of Biotechnology; Chemistry and Pharmacy; University of Siena; via A. Moro 2 53100 Siena Italy
| | - Daniel Rivero
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
| | - Felipe Zapata
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
| | - Cristina García-Iriepa
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
- Departamento de Química; Centro de Investigación en Síntesis Química (CISQ); University of La Rioja; Madre de Dios, 53 26006 Logroño Spain
| | - Marco Marazzi
- Theory-Modeling-Simulation SRSMC; Université de Lorraine-Nancy; Vandoeuvre-lès-Nancy, Nancy France
- Theory-Modeling-Simulation SRSMC; CNRS; SRSMC Boulevard des Aiguillettes Vandoeuvre-lès-Nancy France
| | - Raúl Palmeiro
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
| | - Ignacio Fdez. Galván
- Department of Chemistry-Ångström; Uppsala Center for Computational Chemistry-UC 3; Uppsala University; Box 518 75120 Uppsala Sweden
| | - Diego Sampedro
- Departamento de Química; Centro de Investigación en Síntesis Química (CISQ); University of La Rioja; Madre de Dios, 53 26006 Logroño Spain
| | - Massimo Olivucci
- Department of Biotechnology; Chemistry and Pharmacy; University of Siena; via A. Moro 2 53100 Siena Italy
- Department of Chemistry; Bowling Green State University; Bowling Green OH 43403 USA
- USIAS and Institut de Physique et Chimie des Matériaux de Strasbourg; Université de Strasbourg-CNRS; 67034 Strasbourg France
| | - Luis Manuel Frutos
- Department of Analytical Chemistry; Physical Chemistry and Chemical Engineering; University of Alcalá; Ctra. A2 Km 33,6 28871 Alcalá de Henares Spain
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