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Coburger P, Masero F, Bösken J, Mougel V, Grützmacher H. A Germapyramidane Switches Between 3D Cluster and 2D Cyclic Structures in Single-Electron Steps. Angew Chem Int Ed Engl 2022; 61:e202211749. [PMID: 36152009 PMCID: PMC9828763 DOI: 10.1002/anie.202211749] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Indexed: 01/12/2023]
Abstract
Reaction of the imidazolium-substituted iphosphate-diide, (Ipr)2 C2 P2 (IDP), with GeCl2 ⋅ dioxane and KBArF24 [(BarF24 )- =tetrakis[(3,5-trifluoromethyl)phenyl]borate)] afforded the dicationic spherical-aromatic nido-cluster [Ge(η4 -IDP)]2+ ([1]2+ ) (Ipr=1,3-bis(2,6-diisopropylphenyl)imidazolium-2-ylidene). This complex is a rare heavy analogue of the elusive pyramidane [C(η4 -C4 H4 )]. [1]2+ undergoes two reversible one-electron reductions, which yield the radical cation [2]⋅+ and the neutral GeII species 3. Both [2]⋅+ and 3 rearrange in solution forming the 2D aromatic and planar imidazolium-substituted digermolide [4]2+ and germole-diide 5, respectively. Both planar species can be oxidized back to [1]2+ using AgSbF6 . These redox-isomerizations correspond to the fundamental transformation of a 3D aromatic cluster into a 2D aromatic ring compound upon reduction and vice versa. The mechanism of these reactions was elucidated using DFT calculations and cyclic voltammetry experiments.
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Affiliation(s)
- Peter Coburger
- Department of Chemistry and Applied BiosciencesETH ZürichVladimir-Prelog-Weg 1–5/108093ZürichSwitzerland
| | - Fabio Masero
- Department of Chemistry and Applied BiosciencesETH ZürichVladimir-Prelog-Weg 1–5/108093ZürichSwitzerland
| | - Jonas Bösken
- Department of Chemistry and Applied BiosciencesETH ZürichVladimir-Prelog-Weg 1–5/108093ZürichSwitzerland
| | - Victor Mougel
- Department of Chemistry and Applied BiosciencesETH ZürichVladimir-Prelog-Weg 1–5/108093ZürichSwitzerland
| | - Hansjörg Grützmacher
- Department of Chemistry and Applied BiosciencesETH ZürichVladimir-Prelog-Weg 1–5/108093ZürichSwitzerland
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2
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UV-induced -OCH 3 rotamerization in a matrix-isolated methoxy-substituted ortho-hydroxyaryl Schiff base. Photochem Photobiol Sci 2022; 21:835-847. [PMID: 35076900 DOI: 10.1007/s43630-021-00166-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/27/2021] [Indexed: 10/19/2022]
Abstract
A new methoxy-substituted ortho-hydroxyaryl Schiff base, 4-(3-methoxy-2-hydroxybenzylidene-amino) phenol was synthesized from 4-aminophenol and 2-hydroxy-3-methoxybenzaldehyde in methanol solution and characterized by 1H-NMR, 13C-NMR and infrared spectroscopies and elemental analysis. The compound was isolated in a cryogenic (10 K) argon matrix, and the analysis of the infrared spectrum of the matrix-isolated compound revealed that it corresponds to the E-enol-imine isomeric form, with 3 different conformers being present in the matrix. These conformers share as common structural features the conformation of the free hydroxyl group (trans relatively to the para-substituent of the ring) and the presence of an OH…N intramolecular H-bond involving the methoxy-substituted phenol ring and the azomethine bridge, while they differ in the orientation of the methoxy-substituent group. The structures and relative energies of the conformers of the molecule, and relevant barriers for their interconversion were obtained through quantum chemical calculations, which were also used to calculate the infrared spectra of the different forms. Calculations were also carried out for the higher-energy Z-enol-imine and keto-amine forms of the compound. Upon UV (230 nm) irradiation, -OCH3 rotamerization was observed, leading to conversion of the lowest energy conformer, where the methoxy group is aligned with the plane of the ring, into the other two conformers initially present in the matrix, in which the OCH3 group is out-of-the-plane of the ring. As for other phenolic compounds previously studied, spontaneous quantum mechanical tunneling conversion of the cis-OH conformers present in the gas-phase into the three observed conformers was found to take place during matrix deposition.
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3
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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] [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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4
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Structural Relevance of Intramolecular H-Bonding in Ortho-Hydroxyaryl Schiff Bases: The Case of 3-(5-bromo-2-hydroxybenzylideneamino) Phenol. Molecules 2021; 26:molecules26092814. [PMID: 34068634 PMCID: PMC8126046 DOI: 10.3390/molecules26092814] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 12/22/2022] Open
Abstract
A new Schiff base compound, 3-(5-bromo-2-hydroxybenzylideneamino)phenol (abbreviated as BHAP) was synthesized and characterized by 1H- and 13C- nuclear magnetic resonance and infrared spectroscopies. DFT/B3LYP/6-311++G(d,p) calculations were undertaken in order to explore the conformational space of both the E- and Z- geometrical isomers of the enol-imine and keto-amine tautomers of the compound. Optimized geometries and relative energies were obtained, and it was shown that the most stable species is the E-enol-imine form, which may exist in four low-energy intramolecularly hydrogen-bonded forms (I, II, V, and VI) that are almost isoenergetic. These conformers were concluded to exist in the gas phase equilibrium with nearly equal populations. On the other hand, the infrared spectra of the compound isolated in a cryogenic argon matrix (10 K) are compatible with the presence in the matrix of only two of these conformers (conformers II and V), while conformers I and VI convert to these ones by quantum mechanical tunneling through the barrier associated with the rotation of the OH phenolic group around the C–O bond. The matrix isolation infrared spectrum was then assigned and interpreted with help of the DFT(B3LYP)/6-311++G(d,p) calculated infrared spectra for conformers II and V. In addition, natural bond orbital (NBO) analysis was performed on the most stable conformer of the experimentally relevant isomeric form (E-enol-imino conformer V) to shed light on details of its electronic structure. This investigation stresses the fundamental structural relevance of the O–H···N intramolecular H-bond in o-hydroxyaryl Schiff base compounds.
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5
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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: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [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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6
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7
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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] [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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8
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Smolobochkin AV, Gazizov AS, Urgenishbay NM, Melyashova AS, Burilov AR, Pudovik MA. Synthesis of (E)-4-(4-chlorobenzylidene)-3,4-dihydro-2H-pyrrole-based pyrrolinium salts. Russ Chem Bull 2020. [DOI: 10.1007/s11172-020-2771-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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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] [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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10
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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] [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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11
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A new ICT based Schiff-base chemosensor for colorimetric selective detection of copper and its copper complex for both colorimetric and fluorometric detection of Cysteine. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2018.08.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Abstract
Two groups of coumarin derivatives, 4-methyl-2-oxo-2H-chromen-7-yl 4-alkoxybenzoates (coumarin esters), In, and 4-methyl-2-oxo-2H-chromen-7-yl 4-(2-(4-alkoxyphenyl)diazenyl) benzoates (coumarin azoesters), IIn, were synthesized and investigated for their mesophase behavior and stability. Each group constitutes five series that differ from each other by length of the mesogenic part. Within each homologous series, the length of the terminal alkoxy group varies between 6, 8, 10, 12 and 16 carbons. Mesophase behavior was investigated by differential scanning calorimetry (DSC) and identified by polarized light microscopy (PLM). Density functional theory (DFT) calculations for coumarin derivatives were discussed. The results revealed that the incorporation of azo group incorporated in the mesogenic core decreases the energy differences, increases the dipole moments and stabilities of coumarin azoesters series more than coumarin esters.
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13
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Cameron D, Eisler S. Photoswitchable double bonds: Synthetic strategies for tunability and versatility. J PHYS ORG CHEM 2018. [DOI: 10.1002/poc.3858] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- David Cameron
- Department of Chemistry; University of New Brunswick; Fredericton New Brunswick Canada
| | - Sara Eisler
- Department of Chemistry; University of New Brunswick; Fredericton New Brunswick Canada
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14
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Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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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15
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Wang C, Zhang Q, Wang X, Chang H, Zhang S, Tang Y, Xu J, Qi R, Cheng Y. Dynamic Modulation of Enzyme Activity by Near-Infrared Light. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700968] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Changping Wang
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
| | - Qiang Zhang
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
| | - Xinyu Wang
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
| | - Hong Chang
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy; East China Normal University; Shanghai China
| | - Yuankai Tang
- State Key Laboratory of Precision Spectroscopy; East China Normal University; Shanghai China
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy; East China Normal University; Shanghai China
| | - Ruijuan Qi
- Key Laboratory of Polar Materials and Devices; East China Normal University; Shanghai China
| | - Yiyun Cheng
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
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16
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Wang C, Zhang Q, Wang X, Chang H, Zhang S, Tang Y, Xu J, Qi R, Cheng Y. Dynamic Modulation of Enzyme Activity by Near-Infrared Light. Angew Chem Int Ed Engl 2017; 56:6767-6772. [DOI: 10.1002/anie.201700968] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/04/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Changping Wang
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
| | - Qiang Zhang
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
| | - Xinyu Wang
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
| | - Hong Chang
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy; East China Normal University; Shanghai China
| | - Yuankai Tang
- State Key Laboratory of Precision Spectroscopy; East China Normal University; Shanghai China
| | - Jianhua Xu
- State Key Laboratory of Precision Spectroscopy; East China Normal University; Shanghai China
| | - Ruijuan Qi
- Key Laboratory of Polar Materials and Devices; East China Normal University; Shanghai China
| | - Yiyun Cheng
- Shanghai Key Laboratory of Regulatory Biology; School of Life Sciences; East China Normal University; Shanghai China
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17
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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] [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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18
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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. [DOI: 10.1002/ange.201611265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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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19
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Nikolaev DM, Emelyanov A, Boitsov VM, Panov MS, Ryazantsev MN. A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling. F1000Res 2017; 6:33. [PMID: 28435665 PMCID: PMC5381632 DOI: 10.12688/f1000research.10541.3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/23/2017] [Indexed: 12/25/2022] Open
Abstract
It was demonstrated in recent studies that some rhodopsins can be used in optogenetics as fluorescent indicators of membrane voltage. One of the promising candidates for these applications is archaerhodopsin-3. While it has already shown encouraging results, there is still a large room for improvement. One of possible directions is increasing the intensity of the protein's fluorescent signal. Rational design of mutants with an improved signal is an important task, which requires both experimental and theoretical studies. Herein, we used a homology-based computational approach to predict the three-dimensional structure of archaerhodopsin-3, and a Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid approach with high-level multireference ab initio methodology (SORCI+Q/AMBER) to model optical properties of this protein. We demonstrated that this methodology allows for reliable prediction of structure and spectral properties of archaerhodopsin-3. The results of this study can be utilized for computational molecular design of efficient fluorescent indicators of membrane voltage for modern optogenetics on the basis of archaerhodopsin-3.
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Affiliation(s)
- Dmitrii M Nikolaev
- Saint-Petersburg National Research Academic University of the Russian Academy of Science, St. Petersburg, Russian Federation
| | - Anton Emelyanov
- Saint-Petersburg National Research Academic University of the Russian Academy of Science, St. Petersburg, Russian Federation
| | - Vitaly M Boitsov
- Saint-Petersburg National Research Academic University of the Russian Academy of Science, St. Petersburg, Russian Federation
| | - Maxim S Panov
- Saint-Petersburg State University, St. Petersburg, Russian Federation
| | - Mikhail N Ryazantsev
- Saint-Petersburg State University, St. Petersburg, Russian Federation.,Saint-Petersburg Scientific Center of the Russian Academy of Sciences, St. Petersburg, Russian Federation
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20
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Paolino M, Gueye M, Pieri E, Manathunga M, Fusi S, Cappelli A, Latterini L, Pannacci D, Filatov M, Léonard J, Olivucci M. Design, Synthesis, and Dynamics of a Green Fluorescent Protein Fluorophore Mimic with an Ultrafast Switching Function. J Am Chem Soc 2016; 138:9807-25. [DOI: 10.1021/jacs.5b10812] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Marco Paolino
- Dipartimento di Biotecnologie, Chimica
e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Moussa Gueye
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, Université de Strasbourg, CNRS UMR 7504, Strasbourg, France
| | - Elisa Pieri
- 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, United States
| | - Stefania Fusi
- 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
| | - Loredana Latterini
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Danilo Pannacci
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, 06123 Perugia, Italy
| | - Michael Filatov
- Department of Chemistry,
School of Natural Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798, Korea
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, Université de Strasbourg, CNRS UMR 7504, Strasbourg, France
| | - 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, United States
- University of Strasbourg Institute for Advanced Studies, 5, allée du Général
Rouvillois F-67083 Strasbourg, France
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21
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Jiménez-Sánchez A, Santillan R. A photochromic-acidochromic HCl fluorescent probe. An unexpected chloride-directed recognition. Analyst 2016; 141:4108-20. [PMID: 27156709 DOI: 10.1039/c6an00509h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Non-classical protomerism of Schiff bases offers several advantages; for example, specific interactions in the -C[double bond, length as m-dash]N- linkage can be controlled and differentiated because the interactions are not governed by keto-enol tautomerism. Herein, the pH sensing properties of a new protomeric Schiff base probe () are reported. In particular, among several acids, the probe displays significant optical responses upon interaction with hydrochloric acid (HCl). X-ray structural analysis confirmed the existence of an intermolecular interaction with HCl through a -C[double bond, length as m-dash]NH-ClO- linkage. Moreover, an optical response via a second channel is manifested as photochromic fluorescence behavior. The properties of were investigated by UV-vis and fluorescence spectroscopy in a solution and the solid state. Its strong acidofluorochromic behavior was analyzed and its pKa and values were determined, which revealed a photobasic character. Positive solvatochromism that resulted from specific interactions taking place in was studied using four different solvent scales, namely, Lippert-Mataga, Kamlet-Taft, Catalán and the recently proposed scale of Laurence et al., which yielded consistent results. Finally, theoretical calculations were conducted to analyze the mechanism of the probe in terms of natural transition orbitals (NTOs) and the spatial extent of charge transfer excitations.
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Affiliation(s)
- Arturo Jiménez-Sánchez
- Facultad de Química, Universidad Nacional Autónoma de México, México, D. F. 04510, México.
| | - Rosa Santillan
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del IPN, CINVESTAV, Apdo. Postal 14-740, México, D. F. 07000, México
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22
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Schapiro I. The Origin of Bond Selectivity and Excited-State Reactivity in Retinal Analogues. J Phys Chem A 2016; 120:3353-65. [DOI: 10.1021/acs.jpca.6b00701] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Igor Schapiro
- Fritz Haber
Center for Molecular
Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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23
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Hu D, Huang J, Xie Y, Yue L, Zhuang X, Lan Z. Nonadiabatic dynamics and photoisomerization of biomimetic photoswitches. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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24
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Martínez-López D, Yu ML, García-Iriepa C, Campos PJ, Frutos LM, Golen JA, Rasapalli S, Sampedro D. Hydantoin-based molecular photoswitches. J Org Chem 2015; 80:3929-39. [PMID: 25806596 DOI: 10.1021/acs.joc.5b00244] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A new family of molecular photoswitches based on arylidenehydantoins is described together with their synthesis and photochemical and photophysical studies. A series of hydantoin derivatives have been prepared as single isomers using simple and versatile chemistry in good yields. Our studies show that the photostationary states of these compounds can be easily controlled by means of external factors, such as the light source or filters. Moreover, the detailed investigations proved that these switches are efficient (i.e., they make efficient use of the light energy, are high fatigue resistant, and are very photostable). In some cases, the switches can be completely turned on/off, a desirable feature for specific applications. A series of theoretical calculations have also been carried out to understand the photoisomerization mechanism at the molecular level.
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Affiliation(s)
- David Martínez-López
- †Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química (CISQ), Madre de Dios, 51, 26006 Logroño, Spain
| | - Meng-Long Yu
- ‡Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Darmouth 02747, United States
| | - Cristina García-Iriepa
- †Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química (CISQ), Madre de Dios, 51, 26006 Logroño, Spain.,§Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Alcalá de Henares, 28871 Madrid, Spain
| | - Pedro J Campos
- †Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química (CISQ), Madre de Dios, 51, 26006 Logroño, Spain
| | - Luis Manuel Frutos
- §Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Alcalá de Henares, 28871 Madrid, Spain
| | - James A Golen
- ‡Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Darmouth 02747, United States
| | - Sivappa Rasapalli
- ‡Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, North Darmouth 02747, United States
| | - Diego Sampedro
- †Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química (CISQ), Madre de Dios, 51, 26006 Logroño, Spain
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25
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26
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Gozem S, Melaccio F, Luk HL, Rinaldi S, Olivucci M. Learning from photobiology how to design molecular devices using a computer. Chem Soc Rev 2014; 43:4019-36. [DOI: 10.1039/c4cs00037d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Learning how to model photo-responsive proteins may open the way to the design of lightpowered biomimetic molecular devices.
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Affiliation(s)
- S. Gozem
- Department of Chemistry
- Bowling Green State University
- Bowling Green, USA
| | - F. Melaccio
- Dipartimento di Chimica
- Università di Siena
- Siena, Italy
| | - H. L. Luk
- Department of Chemistry
- Bowling Green State University
- Bowling Green, USA
| | - S. Rinaldi
- Dipartimento di Chimica
- Università di Siena
- Siena, Italy
| | - M. Olivucci
- Department of Chemistry
- Bowling Green State University
- Bowling Green, USA
- Dipartimento di Chimica
- Università di Siena
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27
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García-Iriepa C, Marazzi M, Frutos LM, Sampedro D. E/Z Photochemical switches: syntheses, properties and applications. RSC Adv 2013. [DOI: 10.1039/c2ra22363e] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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28
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Léonard J, Schapiro I, Briand J, Fusi S, Paccani RR, Olivucci M, Haacke S. Mechanistic Origin of the Vibrational Coherence Accompanying the Photoreaction of Biomimetic Molecular Switches. Chemistry 2012; 18:15296-304. [DOI: 10.1002/chem.201201430] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 08/29/2012] [Indexed: 11/08/2022]
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29
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Liu YJ, Roca-Sanjuán D, Lindh R. Computational Photochemistry and Photophysics: the state of the art. PHOTOCHEMISTRY 2012. [DOI: 10.1039/9781849734882-00042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This review starts with the most basic concepts in photochemistry and photophysics, followed by a chronological introduction of theoretical methods and relevant applications in the history of computational photochemistry, along with the authors’ comments on the methodologies currently available for photochemical studies. Recent advances in the field are next summarized and discussed, focusing separately on methodology and computational techniques and some highlighted applied works carried out during the last two years on the topics of photodissociations, photostability, photodimerizations, photoisomerizations, proton/hydrogen transfer, photodecarboxylations, charge transport, bioexcimers, chemiluminescence and bioluminescence. We finish this review by conclusions and an outlook of the future.
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Affiliation(s)
- Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry Beijing Normal University Beijing China
| | - Daniel Roca-Sanjuán
- Department of Chemistry - Ångström, Theoretical Chemistry Programme Uppsala University Uppsala Sweden
| | - Roland Lindh
- Department of Chemistry - Ångström, Theoretical Chemistry Programme Uppsala University Uppsala Sweden
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30
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Blanco-Lomas M, Campos PJ, Sampedro D. Synthesis and Photoisomerization of Rhodopsin-Based Molecular Switches. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200870] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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31
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Blanco-Lomas M, Campos PJ, Sampedro D. Benzylidene-oxazolones as molecular photoswitches. Org Lett 2012; 14:4334-7. [PMID: 22877084 DOI: 10.1021/ol301741g] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The synthesis and photochemical study of a family of molecular switches inspired by the green fluorescent protein (GFP) chromophore is presented. These compounds can be easily synthesized, and their photophysical properties may be tuned. Due to their efficient photoisomerization and high stability, these compounds can be switched on/off by using light and heat or light with different wavelengths.
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Affiliation(s)
- Marina Blanco-Lomas
- Departamento de Química, Centro de Investigación en Síntesis Química (CISQ), Universidad de La Rioja, Madre de Dios, 51, E-26006, Logroño, La Rioja, Spain
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32
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Fuß W. Hula-twist cis–trans isomerization: The role of internal forces and the origin of regioselectivity. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.01.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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33
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Blanco-Lomas M, Samanta S, Campos PJ, Woolley GA, Sampedro D. Reversible photocontrol of peptide conformation with a rhodopsin-like photoswitch. J Am Chem Soc 2012; 134:6960-3. [PMID: 22482865 DOI: 10.1021/ja301868p] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reversible photocontrol of biomolecules requires chromophores that can efficiently undergo large conformational changes upon exposure to wavelengths of light that are compatible with living systems. We designed a benzylidene-pyrroline chromophore that mimics the Schiff base of rhodopsin and can be used to introduce light-switchable intramolecular cross-links in peptides and proteins. This new class of photoswitch undergoes an ~10 Å change in end-to-end distance upon isomerization and can be used to control the conformation of a target peptide efficiently and reversibly using, alternately, violet (400 nm) and blue (446 nm) light.
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Affiliation(s)
- Marina Blanco-Lomas
- Departamento de Química, Unidad Asociada al C.S.I.C., Universidad de La Rioja, Madre de Dios 51, E-26006 Logroño, La Rioja, Spain
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34
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Dunkelberger AD, Kieda RD, Shin JY, Rossi Paccani R, Fusi S, Olivucci M, Fleming Crim F. Photoisomerization and Relaxation Dynamics of a Structurally Modified Biomimetic Photoswitch. J Phys Chem A 2012; 116:3527-33. [DOI: 10.1021/jp300153a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Adam D. Dunkelberger
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
| | - Ryan D. Kieda
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
| | - Jae Yoon Shin
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
| | | | - Stefania Fusi
- Department
of Chemistry, Università di Siena, Siena I-53100, Italy
| | - Massimo Olivucci
- Department
of Chemistry, Università di Siena, Siena I-53100, Italy
- Department
of Chemistry, Bowling Green State University, Bowling Green, Ohio
43403, United States
| | - F. Fleming Crim
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
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35
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Rossi Paccani R, Donati D, Fusi S, Latterini L, Farina G, Zanirato V, Olivucci M. Toward a stable α-cycloalkyl amino acid with a photoswitchable cationic side chain. J Org Chem 2012; 77:1738-48. [PMID: 22239068 DOI: 10.1021/jo2022263] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The N-alkylated indanylidenepyrroline (NAIP) Schiff base 3 is an unnatural α-amino acid precursor potentially useful for the preparation of semisynthetic peptides and proteins incorporating charged side chains whose structure can be modulated via Z/E photoisomerization. Here we report that the heteroallylic protons of 3 led to partial loss of ethanol accompanied by formation of the novel heterocyclic system 4 during attempted deprotection. We also show that the same protons catalyze the thermal isomerization of 3, making the light-driven conformational control concept ineffective for times longer than a few hours. These problems are not present in the previously unreported compound 5 where the acidic methyl group is replaced by an H atom. Therefore, 5, rather than 3, constitutes a promising prototype for the design of building blocks capable to modulate the electrostatic potential of a protein in specific locations via light irradiation.
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36
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Melaccio F, Ferré N, Olivucci M. Quantum chemical modeling of rhodopsin mutants displaying switchable colors. Phys Chem Chem Phys 2012; 14:12485-95. [DOI: 10.1039/c2cp40940b] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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37
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Filatov M. Theoretical Study of the Photochemistry of a Reversible Three-State Bis-Thiaxanthylidene Molecular Switch. Chemphyschem 2011; 12:3348-53. [DOI: 10.1002/cphc.201100444] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Indexed: 11/11/2022]
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38
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Schapiro I, Melaccio F, Laricheva EN, Olivucci M. Using the computer to understand the chemistry of conical intersections. Photochem Photobiol Sci 2011; 10:867-86. [DOI: 10.1039/c0pp00290a] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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