1
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Hutchison CM, Perrett S, van Thor JJ. XFEL Beamline Optical Instrumentation for Ultrafast Science. J Phys Chem B 2024; 128:8855-8868. [PMID: 39087627 PMCID: PMC11421085 DOI: 10.1021/acs.jpcb.4c01492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024]
Abstract
Free electron lasers operating in the soft and hard X-ray regime provide capabilities for ultrafast science in many areas, including X-ray spectroscopy, diffractive imaging, solution and material scattering, and X-ray crystallography. Ultrafast time-resolved applications in the picosecond, femtosecond, and attosecond regimes are often possible using single-shot experimental configurations. Aside from X-ray pump and X-ray probe measurements, all other types of ultrafast experiments require the synchronized operation of pulsed laser excitation for resonant or nonresonant pumping. This Perspective focuses on the opportunities for the optical control of structural dynamics by applying techniques from nonlinear spectroscopy to ultrafast X-ray experiments. This typically requires the synthesis of two or more optical pulses with full control of pulse and interpulse parameters. To this end, full characterization of the femtosecond optical pulses is also highly desirable. It has recently been shown that two-color and two-pulse femtosecond excitation of fluorescent protein crystals allowed a Tannor-Rice coherent control experiment, performed under characterized conditions. Pulse shaping and the ability to synthesize multicolor and multipulse conditions are highly desirable and would enable XFEL facilities to offer capabilities for structural dynamics. This Perspective will give a summary of examples of the types of experiments that could be achieved, and it will additionally summarize the laser, pulse shaping, and characterization that would be recommended as standard equipment for time-resolved XFEL beamlines, with an emphasis on ultrafast time-resolved serial femtosecond crystallography.
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Affiliation(s)
- Christopher
D. M. Hutchison
- Department
of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United
Kingdom
| | - Samuel Perrett
- Department
of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United
Kingdom
| | - Jasper J. van Thor
- Department
of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, United
Kingdom
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2
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Braun J, Powell AK, Unterreiner AN. Gaining Insights into the Interplay between Optical and Magnetic Properties in Photoexcited Coordination Compounds. Chemistry 2024; 30:e202400977. [PMID: 38693865 DOI: 10.1002/chem.202400977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/19/2024] [Accepted: 04/30/2024] [Indexed: 05/03/2024]
Abstract
We describe early and recent advances in the fascinating field of combined magnetic and optical properties of inorganic coordination compounds and in particular of 3d-4f single molecule magnets. We cover various applied techniques which allow for the correlation of results obtained in the frequency and time domain in order to highlight the specific properties of these compounds and the future challenges towards multidimensional spectroscopic tools. An important point is to understand the details of the interplay of magnetic and optical properties through performing time-resolved studies in the presence of external fields especially magnetic ones. This will enable further exploration of this fundamental interactions i. e. the two components of electromagnetic radiation influencing optical properties.
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Affiliation(s)
- Jonas Braun
- Institute of Inorganic Chemistry (AOC), Karlsruhe Institute of Technology (KIT), Kaiserstr. 12, 76131, Karlsruhe, Germany
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Kaiserstr. 12, 76131, Karlsruhe, Germany
- Institute for Quantum Materials and Technologies (IQMT), Karlsruhe Institute of Technology (KIT), Kaiserstr. 12, 76131, Karlsruhe, Germany
| | - Annie K Powell
- Institute of Inorganic Chemistry (AOC), Karlsruhe Institute of Technology (KIT), Kaiserstr. 12, 76131, Karlsruhe, Germany
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Kaiserstr. 12, 76131, Karlsruhe, Germany
- Institute for Quantum Materials and Technologies (IQMT), Karlsruhe Institute of Technology (KIT), Kaiserstr. 12, 76131, Karlsruhe, Germany
| | - Andreas-Neil Unterreiner
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology (KIT), Kaiserstr. 12, 76131, Karlsruhe, Germany
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3
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Phelps R, Agapaki E, Brechin EK, Johansson JO. Tracking the conical intersection dynamics for the photoinduced Jahn-Teller switch of a Mn(iii) complex. Chem Sci 2024; 15:11956-11964. [PMID: 39092124 PMCID: PMC11290422 DOI: 10.1039/d4sc00145a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/24/2024] [Indexed: 08/04/2024] Open
Abstract
Octahedral Mn(iii) ions predominantly exhibit an axially elongated Jahn-Teller (JT) distortion, which is responsible for their large uniaxial magnetic anisotropy. As a result, they are often used in the synthesis of single-molecule magnets (SMMs). Modulation of the JT distortion using femtosecond laser pulses could offer a route to controlling the magnetisation direction, and therefore is promising for the development of data storage devices that work on ultrafast timescales. Photoinduced switching of the distortion from an axially elongated to an axially compressed structure has been demonstrated for various Mn(iii) complexes. However, the dynamics around the region of the conical intersection for the photoinduced JT switch remains unclear. Here, ultrafast transient absorption spectra were recorded for solutions of tris(2,2,6,6-tetramethyl-3,5-heptanedionato)manganese(iii) (Mn(dpm)3) in ethanol to further explore the dynamics of the photoinduced JT switch. We observe the generation of a vibrational wavepacket on the excited state surface, which has a frequency of approximately 155 cm-1 and encompasses a JT-active vibrational mode. This coherent motion is maintained after passage through the conical intersection back to the ground state, which launches wavepackets along the ground state potential energy surface (PES) with frequencies of approximately 180 and 110 cm-1 that we assign to the elongated and compressed state, respectively. Inspection of the relative phases of the frequencies reveals phase shifts that are consistent with a one-mode reaction coordinate, and passes through the conical intersection at 1/4 and 3/4 of the excited state vibrational period. Our results provide direct insights into the non-adiabatic dynamics of Mn(iii) complexes, which can be used to guide the synthesis of optically controlled SMMs.
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Affiliation(s)
- Ryan Phelps
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road EH9 3FJ Edinburgh UK
| | - Eleftheria Agapaki
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road EH9 3FJ Edinburgh UK
| | - Euan K Brechin
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road EH9 3FJ Edinburgh UK
| | - J Olof Johansson
- EaStCHEM School of Chemistry, University of Edinburgh David Brewster Road EH9 3FJ Edinburgh UK
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4
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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] [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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5
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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] [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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6
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Kuntze K, Pooler DRS, Di Donato M, Hilbers MF, van der Meulen P, Buma WJ, Priimagi A, Feringa BL, Crespi S. A visible-light-driven molecular motor based on barbituric acid. Chem Sci 2023; 14:8458-8465. [PMID: 37592992 PMCID: PMC10430646 DOI: 10.1039/d3sc03090c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
We present a class of visible-light-driven molecular motors based on barbituric acid. Due to a serendipitous reactivity we observed during their synthesis, these motors possess a tertiary stereogenic centre on the upper half, characterised by a hydroxy group. Using a combination of femto- and nanosecond transient absorption spectroscopy, molecular dynamics simulations and low-temperature 1H NMR experiments we found that these motors operate similarly to push-pull second-generation overcrowded alkene-based molecular motors. Interestingly, the hydroxy group at the stereocentre enables a hydrogen bond with the carbonyl groups of the barbituric acid lower half, which drives a sub-picosecond excited-state isomerisation, as observed spectroscopically. Computational simulations predict an excited state "lasso" mechanism where the intramolecular hydrogen bond pulls the molecule towards the formation of the metastable state, with a high predicted quantum yield of isomerisation (68%) in gas phase.
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Affiliation(s)
- Kim Kuntze
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 4 9746 AG Groningen The Netherlands
- Faculty of Engineering and Natural Sciences, Tampere University FI-33101 Tampere Finland
| | - Daisy R S Pooler
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 4 9746 AG Groningen The Netherlands
| | - Mariangela Di Donato
- European Laboratory for Non Linear Spectroscopy (LENS) via N. Carrara 1 50019 Sesto Fiorentino Italy
- ICCOM-CNR via Madonna del Piano 10 50019 Sesto Fiorentino FI Italy
| | - Michiel F Hilbers
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Pieter van der Meulen
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 4 9746 AG Groningen The Netherlands
| | - Wybren Jan Buma
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University Toernooiveld 7c 6525 ED Nijmegen The Netherlands
| | - Arri Priimagi
- Faculty of Engineering and Natural Sciences, Tampere University FI-33101 Tampere Finland
| | - Ben L Feringa
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 4 9746 AG Groningen The Netherlands
| | - Stefano Crespi
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 4 9746 AG Groningen The Netherlands
- Department of Chemistry, Ångström Laboratory, Uppsala University Box 523 751 20 Uppsala Sweden
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7
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Paolino M, de Candia M, Purgatorio R, Catto M, Saletti M, Tondo AR, Nicolotti O, Cappelli A, Brizzi A, Mugnaini C, Corelli F, Altomare CD. Investigation on Novel E/Z 2-Benzylideneindan-1-One-Based Photoswitches with AChE and MAO-B Dual Inhibitory Activity. Molecules 2023; 28:5857. [PMID: 37570828 PMCID: PMC10421270 DOI: 10.3390/molecules28155857] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
The multitarget therapeutic strategy, as opposed to the more traditional 'one disease-one target-one drug', may hold promise in treating multifactorial neurodegenerative syndromes, such as Alzheimer's disease (AD) and related dementias. Recently, combining a photopharmacology approach with the multitarget-directed ligand (MTDL) design strategy, we disclosed a novel donepezil-like compound, namely 2-(4-((diethylamino)methyl)benzylidene)-5-methoxy-2,3-dihydro-1H-inden-1-one (1a), which in the E isomeric form (and about tenfold less in the UV-B photo-induced isomer Z) showed the best activity as dual inhibitor of the AD-related targets acetylcholinesterase (AChE) and monoamine oxidase B (MAO-B). Herein, we investigated further photoisomerizable 2-benzylideneindan-1-one analogs 1b-h with the unconjugated tertiary amino moiety bearing alkyls of different bulkiness and lipophilicity. For each compound, the thermal stable E geometric isomer, along with the E/Z mixture as produced by UV-B light irradiation in the photostationary state (PSS, 75% Z), was investigated for the inhibition of human ChEs and MAOs. The pure E-isomer of the N-benzyl(ethyl)amino analog 1h achieved low nanomolar AChE and high nanomolar MAO-B inhibition potencies (IC50s 39 and 355 nM, respectively), whereas photoisomerization to the Z isomer (75% Z in the PSS mixture) resulted in a decrease (about 30%) of AChE inhibitory potency, and not in the MAO-B one. Molecular docking studies were performed to rationalize the different E/Z selectivity of 1h toward the two target enzymes.
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Affiliation(s)
- Marco Paolino
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, I-53100 Siena, Italy; (M.P.); (M.S.); (A.C.); (A.B.); (C.M.); (F.C.)
| | - Modesto de Candia
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, I-70125 Bari, Italy; (M.d.C.); (R.P.); (M.C.); (A.R.T.); (O.N.)
| | - Rosa Purgatorio
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, I-70125 Bari, Italy; (M.d.C.); (R.P.); (M.C.); (A.R.T.); (O.N.)
| | - Marco Catto
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, I-70125 Bari, Italy; (M.d.C.); (R.P.); (M.C.); (A.R.T.); (O.N.)
| | - Mario Saletti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, I-53100 Siena, Italy; (M.P.); (M.S.); (A.C.); (A.B.); (C.M.); (F.C.)
| | - Anna Rita Tondo
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, I-70125 Bari, Italy; (M.d.C.); (R.P.); (M.C.); (A.R.T.); (O.N.)
| | - Orazio Nicolotti
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, I-70125 Bari, Italy; (M.d.C.); (R.P.); (M.C.); (A.R.T.); (O.N.)
| | - Andrea Cappelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, I-53100 Siena, Italy; (M.P.); (M.S.); (A.C.); (A.B.); (C.M.); (F.C.)
| | - Antonella Brizzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, I-53100 Siena, Italy; (M.P.); (M.S.); (A.C.); (A.B.); (C.M.); (F.C.)
| | - Claudia Mugnaini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, I-53100 Siena, Italy; (M.P.); (M.S.); (A.C.); (A.B.); (C.M.); (F.C.)
| | - Federico Corelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, I-53100 Siena, Italy; (M.P.); (M.S.); (A.C.); (A.B.); (C.M.); (F.C.)
| | - Cosimo D. Altomare
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, I-70125 Bari, Italy; (M.d.C.); (R.P.); (M.C.); (A.R.T.); (O.N.)
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8
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Liu L, Fang WH, Martinez TJ. A Nitrogen Out-of-Plane (NOOP) Mechanism for Imine-Based Light-Driven Molecular Motors. J Am Chem Soc 2023; 145:6888-6898. [PMID: 36920260 DOI: 10.1021/jacs.3c00275] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Light-driven molecular motors have generated considerable interest due to their potential applications in material and biological systems. Recently, Greb and Lehn reported a new class of molecular motors, chiral N-alkyl imines, which undergo unidirectional rotation induced by light and heat. The mechanism of unidirectional motion in molecular motors containing a C═N group has been assumed to consist of photoinduced torsion about the double bond. In this work, we present a computational study of the photoisomerization dynamics of a chiral N-alkyl imine motor. We find that the location and energetics of minimal energy conical intersections (MECIs) alone are insufficient to understand the mechanism of the motor. Furthermore, a key part of the mechanism consists of out-of-plane distortions of the N atom (followed by isomerization about the double bond). Dynamic effects and out-of-plane distortions are critical to understand the observed (rather low) quantum yield for photoisomerization. Our results provide hints as to how the photoisomerization quantum yield might be increased, improving the efficiency of this class of molecular motors.
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Affiliation(s)
- Lihong Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.,Department of Chemistry and PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Todd J Martinez
- Department of Chemistry and PULSE Institute, Stanford University, Stanford, California 94305, United States.,SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
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9
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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] [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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10
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Abiola TT, Toldo JM, do Casal MT, Flourat AL, Rioux B, Woolley JM, Murdock D, Allais F, Barbatti M, Stavros VG. Direct structural observation of ultrafast photoisomerization dynamics in sinapate esters. Commun Chem 2022; 5:141. [PMID: 36697608 PMCID: PMC9814104 DOI: 10.1038/s42004-022-00757-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/13/2022] [Indexed: 01/27/2023] Open
Abstract
Sinapate esters have been extensively studied for their potential application in 'nature-inspired' photoprotection. There is general consensus that the relaxation mechanism of sinapate esters following photoexcitation with ultraviolet radiation is mediated by geometric isomerization. This has been largely inferred through indirect studies involving transient electronic absorption spectroscopy in conjunction with steady-state spectroscopies. However, to-date, there is no direct experimental evidence tracking the formation of the photoisomer in real-time. Using transient vibrational absorption spectroscopy, we report on the direct structural changes that occur upon photoexcitation, resulting in the photoisomer formation. Our mechanistic analysis predicts that, from the photoprepared ππ* state, internal conversion takes place through a conical intersection (CI) near the geometry of the initial isomer. Our calculations suggest that different CI topographies at relevant points on the seam of intersection may influence the isomerization yield. Altogether, we provide compelling evidence suggesting that a sinapate ester's geometric isomerization can be a more complex dynamical process than originally thought.
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Affiliation(s)
- Temitope T. Abiola
- grid.7372.10000 0000 8809 1613Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL UK
| | - Josene M. Toldo
- grid.462456.70000 0004 4902 8637Aix Marseille Université, CNRS, ICR, Marseille, France
| | - Mariana T. do Casal
- grid.462456.70000 0004 4902 8637Aix Marseille Université, CNRS, ICR, Marseille, France
| | - Amandine L. Flourat
- grid.417885.70000 0001 2185 8223URD Agro-Biotechnologies (ABI), CEBB, AgroParisTech, 51110 Pomacle, France
| | - Benjamin Rioux
- grid.417885.70000 0001 2185 8223URD Agro-Biotechnologies (ABI), CEBB, AgroParisTech, 51110 Pomacle, France
| | - Jack M. Woolley
- grid.7372.10000 0000 8809 1613Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL UK
| | - Daniel Murdock
- grid.7372.10000 0000 8809 1613Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL UK
| | - Florent Allais
- grid.417885.70000 0001 2185 8223URD Agro-Biotechnologies (ABI), CEBB, AgroParisTech, 51110 Pomacle, France
| | - Mario Barbatti
- grid.462456.70000 0004 4902 8637Aix Marseille Université, CNRS, ICR, Marseille, France ,grid.440891.00000 0001 1931 4817Institut Universitaire de France, 75231 Paris, France
| | - Vasilios G. Stavros
- grid.7372.10000 0000 8809 1613Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL UK
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11
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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] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Indexed: 11/07/2022]
Abstract
HBDI-like chromophores represent a novel set of biomimetic switches mimicking the fluorophore of the green fluorescent protein that are currently studied with the hope to expand the molecular switch/motor toolbox. However, until now members capable of absorbing visible light in their neutral (i. e. non-anionic) form have not been reported. In this contribution we report the preparation of an HBDI-like chromophore based on a 3-phenylbenzofulvene scaffold capable of absorbing blue light and photoisomerizing on the picosecond timescale. More specifically, we show that double-bond photoisomerization occurs in both the E-to-Z and Z-to-E directions and that these can be controlled by irradiating with blue and UV light, respectively. Finally, as a preliminary applicative result, we report the incorporation of the chromophore in an amphiphilic molecule and demonstrate the formation of a visible-light-sensitive nanoaggregated state in water.
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Affiliation(s)
- Marco Paolino
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
| | - Mario Saletti
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
| | - Annalisa Reale
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
| | - Mariano Licciardi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF)Università degli Studi di PalermoVia Archirafi 3290123PalermoItaly
| | - Paola Varvarà
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF)Università degli Studi di PalermoVia Archirafi 3290123PalermoItaly
| | - Arnaud Marquette
- Institut de Physique et Chimie des Matériaux de StrasbourgUniversité de StrasbourgCNRS UMR7504StrasbourgFrance
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de StrasbourgUniversité de StrasbourgCNRS UMR7504StrasbourgFrance
| | - Claudia Bonechi
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
| | - Alessandro Donati
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
| | - Gianluca Giorgi
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
| | - Germano Giuliani
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
| | - Benedetta Carlotti
- Dipartimento di Chimica, Biologia e BiotecnologieUniversità di PerugiaVia Elce di Sotto, 806123PerugiaItaly
| | - Fausto Ortica
- Dipartimento di Chimica, Biologia e BiotecnologieUniversità di PerugiaVia Elce di Sotto, 806123PerugiaItaly
| | - Loredana Latterini
- Dipartimento di Chimica, Biologia e BiotecnologieUniversità di PerugiaVia Elce di Sotto, 806123PerugiaItaly
| | - Mariangela Gentile
- Dipartimento di Scienze della VitaUniversità degli Studi di SienaVia A. Moro53100SienaItaly
| | - Eugenio Paccagnini
- Dipartimento di Scienze della VitaUniversità degli Studi di SienaVia A. Moro53100SienaItaly
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
- Chemistry DepartmentBowling Green State University43403Bowling GreenOHUSA) ok
| | - Andrea Cappelli
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022)Università degli Studi di SienaVia A. Moro 253100SienaItaly
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12
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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] [Abstract] [Key Words] [MESH Headings] [Grants] [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)
- Giusy Tassone
- Dipartimento di Biotecnologie, Chimica e Farmacia, Dipartimento di Eccellenza 2018-2022), Università degli Studi di Siena, Via A. Moro 2, 53100, Siena, Italy
| | - 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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13
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Demoulin B, Maiuri M, Berbasova T, Geiger JH, Borhan B, Garavelli M, Cerullo G, Rivalta I. Control of Protonated Schiff Base Excited State Decay within Visual Protein Mimics: A Unified Model for Retinal Chromophores. Chemistry 2021; 27:16389-16400. [PMID: 34653286 DOI: 10.1002/chem.202102383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 11/07/2022]
Abstract
Artificial biomimetic chromophore-protein complexes inspired by natural visual pigments can feature color tunability across the full visible spectrum. However, control of excited state dynamics of the retinal chromophore, which is of paramount importance for technological applications, is lacking due to its complex and subtle photophysics/photochemistry. Here, ultrafast transient absorption spectroscopy and quantum mechanics/molecular mechanics simulations are combined for the study of highly tunable rhodopsin mimics, as compared to retinal chromophores in solution. Conical intersections and transient fluorescent intermediates are identified with atomistic resolution, providing unambiguous assignment of their ultrafast excited state absorption features. The results point out that the electrostatic environment of the chromophore, modified by protein point mutations, affects its excited state properties allowing control of its photophysics with same power of chemical modifications of the chromophore. The complex nature of such fine control is a fundamental knowledge for the design of bio-mimetic opto-electronic and photonic devices.
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Affiliation(s)
- Baptiste Demoulin
- Laboratoire de Chimie, Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, 69342, Lyon, France
| | - Margherita Maiuri
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133, Milano, Italy
| | - Tetyana Berbasova
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - James H Geiger
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Babak Borhan
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133, Milano, Italy
| | - Ivan Rivalta
- Laboratoire de Chimie, Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, 69342, Lyon, France.,Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
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14
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Pooler DRS, Lubbe AS, Crespi S, Feringa BL. Designing light-driven rotary molecular motors. Chem Sci 2021; 12:14964-14986. [PMID: 34909140 PMCID: PMC8612399 DOI: 10.1039/d1sc04781g] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/14/2021] [Indexed: 01/04/2023] Open
Abstract
The ability to induce and amplify motion at the molecular scale has seen tremendous progress ranging from simple molecular rotors to responsive materials. In the two decades since the discovery of light-driven rotary molecular motors, the development of these molecules has been extensive; moving from the realm of molecular chemistry to integration into dynamic molecular systems. They have been identified as actuators holding great potential to precisely control the dynamics of nanoscale devices, but integrating molecular motors effectively into evermore complex artificial molecular machinery is not trivial. Maximising efficiency without compromising function requires conscious and judicious selection of the structures used. In this perspective, we focus on the key aspects of motor design and discuss how to manipulate these properties without impeding motor integrity. Herein, we describe these principles in the context of molecular rotary motors featuring a central double bond axle and emphasise the strengths and weaknesses of each design, providing a comprehensive evaluation of all artificial light-driven rotary motor scaffolds currently present in the literature. Based on this discussion, we will explore the trajectory of research into the field of molecular motors in the coming years, including challenges to be addressed, potential applications, and future prospects.
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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
| | - Anouk S Lubbe
- Stratingh Institute for Chemistry, Zernike Institute for Advanced Materials, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Stefano Crespi
- Stratingh Institute for Chemistry, Zernike Institute for Advanced Materials, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - 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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15
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Karak P, Ruud K, Chakrabarti S. Demystifying the Origin of Vibrational Coherence Transfer Between the S 1 and T 1 States of the Pt-pop Complex. J Phys Chem Lett 2021; 12:9768-9773. [PMID: 34595923 DOI: 10.1021/acs.jpclett.1c02789] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We demonstrate that spin-vibronic coupling is the most significant mechanism in vibrational coherence transfer (VCT) from the singlet (S1) to the triplet (T1) state of the [Pt2(P2O5H2)4]4- complex. Our time-dependent correlation function-based study shows that the rate of intersystem crossing (kISC) through direct spin-orbit coupling is negligibly small, making VCT vanishingly small due to the ultrashort decoherence time (2.5 ps). However, the inclusion of the spin-vibronic contribution to the net kISC in selective normal modes along the Pt-Pt axis increases the kISC to such an extent that VCT becomes feasible. Our results suggest that kISC for the S1 →T2 (τISC = 1.084 ps) is much faster than the S1 → T1 (τISC = 763.4 ps) and S1 → T3 (τISC = 13.38 ps) in CH3CN solvent, indicating that VCT is possible from the low-lying excited singlet (S1) to the triplet (T1) state through the intermediate T2 state. This is the first example where VCT occurs solely due to spin-vibronic interactions. This finding can pave the way for new types of photocatalysis.
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Affiliation(s)
- Pijush Karak
- Department of Chemistry, University of Calcutta, 92 A. P. C. Road, Kolkata 700009, West Bengal, India
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø - The Arctic University of Norway, 9037 Tromsø, Norway
| | - Swapan Chakrabarti
- Department of Chemistry, University of Calcutta, 92 A. P. C. Road, Kolkata 700009, West Bengal, India
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16
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Hervé M, Boyer A, Brédy R, Compagnon I, Allouche AR, Lépine F. Controlled ultrafast ππ*-πσ* dynamics in tryptophan-based peptides with tailored micro-environment. Commun Chem 2021; 4:124. [PMID: 36697624 PMCID: PMC9814788 DOI: 10.1038/s42004-021-00557-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/26/2021] [Indexed: 01/28/2023] Open
Abstract
Ultrafast charge, energy and structural dynamics in molecules are driven by the topology of the multidimensional potential energy surfaces that determines the coordinated electronic and nuclear motion. These processes are also strongly influenced by the interaction with the molecular environment, making very challenging a general understanding of these dynamics on a microscopic level. Here we use electrospray and mass spectrometry technologies to produce isolated molecular ions with a controlled micro-environment. We measure ultrafast photo-induced ππ*-πσ* dynamics in tryptophan species in the presence of a single, charged adduct. A striking increase of the timescale by more than one order of magnitude is observed when changing the added adduct atom. A model is proposed to rationalize the results, based on the localized and delocalized effects of the adduct on the electronic structure of the molecule. These results offer perspectives to control ultrafast molecular processes by designing the micro-environment on the Angström length scale.
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Affiliation(s)
- Marius Hervé
- grid.436142.60000 0004 0384 4911Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, Villeurbanne, France
| | - Alexie Boyer
- grid.436142.60000 0004 0384 4911Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, Villeurbanne, France
| | - Richard Brédy
- grid.436142.60000 0004 0384 4911Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, Villeurbanne, France
| | - Isabelle Compagnon
- grid.436142.60000 0004 0384 4911Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, Villeurbanne, France
| | - Abdul-Rahman Allouche
- grid.436142.60000 0004 0384 4911Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, Villeurbanne, France
| | - Franck Lépine
- grid.436142.60000 0004 0384 4911Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, Villeurbanne, France
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17
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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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18
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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] [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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19
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Aster A, Bornhof AB, Sakai N, Matile S, Vauthey E. Lifetime Broadening and Impulsive Generation of Vibrational Coherence Triggered by Ultrafast Electron Transfer. J Phys Chem Lett 2021; 12:1052-1057. [PMID: 33470820 DOI: 10.1021/acs.jpclett.0c03641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The absorption band shape of chromophores in liquid solution at room temperature is usually dominated by pure electronic dephasing dynamics, which occurs on the sub-100 fs time scale. Herein, we report on a series of dyads consisting of a naphthalenediimide (NDI) electron acceptor with one or two phenyl-based donors for which photoinduced intramolecular electron transfer is fast enough to be competitive with pure electronic dephasing. As a consequence, the absorption band of the π-π* transition of these dyads is broader than that of the NDI alone to an extent that scales with the electron transfer rate. Additionally, this reaction is so fast that it leads to the impulsive excitation of a low-frequency vibrational mode of the charge-separated product. Quantum-chemical calculations suggest that this vibration involves the C-N donor-acceptor bond, which shortens considerably upon electron transfer.
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Affiliation(s)
- Alexander Aster
- Department of Physical Chemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | - Anna-Bea Bornhof
- Department of Organic Chemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | - Eric Vauthey
- Department of Physical Chemistry, University of Geneva, CH-1211 Geneva, Switzerland
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20
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De Sio A, Sommer E, Nguyen XT, Groß L, Popović D, Nebgen BT, Fernandez-Alberti S, Pittalis S, Rozzi CA, Molinari E, Mena-Osteritz E, Bäuerle P, Frauenheim T, Tretiak S, Lienau C. Intermolecular conical intersections in molecular aggregates. NATURE NANOTECHNOLOGY 2021; 16:63-68. [PMID: 33199882 DOI: 10.1038/s41565-020-00791-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
Conical intersections (CoIns) of multidimensional potential energy surfaces are ubiquitous in nature and control pathways and yields of many photo-initiated intramolecular processes. Such topologies can be potentially involved in the energy transport in aggregated molecules or polymers but are yet to be uncovered. Here, using ultrafast two-dimensional electronic spectroscopy (2DES), we reveal the existence of intermolecular CoIns in molecular aggregates relevant for photovoltaics. Ultrafast, sub-10-fs 2DES tracks the coherent motion of a vibrational wave packet on an optically bright state and its abrupt transition into a dark state via a CoIn after only 40 fs. Non-adiabatic dynamics simulations identify an intermolecular CoIn as the source of these unusual dynamics. Our results indicate that intermolecular CoIns may effectively steer energy pathways in functional nanostructures for optoelectronics.
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Affiliation(s)
- Antonietta De Sio
- Institut für Physik and Center of Interface Science, Carl von Ossietzky Universität, Oldenburg, Germany.
| | - Ephraim Sommer
- Institut für Physik and Center of Interface Science, Carl von Ossietzky Universität, Oldenburg, Germany
| | - Xuan Trung Nguyen
- Institut für Physik and Center of Interface Science, Carl von Ossietzky Universität, Oldenburg, Germany
| | - Lynn Groß
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | - Duško Popović
- Institut für Organische Chemie II und Neue Materialien, Universität Ulm, Ulm, Germany
| | | | - Sebastian Fernandez-Alberti
- National University of Quilmes/CONICET, Department of Science and Technology, Bernal (B1876BXD), Buenos Aires Province, Argentina
| | | | | | - Elisa Molinari
- Istituto Nanoscienze-CNR, Modena, Italy
- Università di Modena e Reggio Emilia, Dipartimento di Scienze Fisiche, Informatiche e Matematiche, Modena, Italy
| | - Elena Mena-Osteritz
- Institut für Organische Chemie II und Neue Materialien, Universität Ulm, Ulm, Germany
| | - Peter Bäuerle
- Institut für Organische Chemie II und Neue Materialien, Universität Ulm, Ulm, Germany
| | - Thomas Frauenheim
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
- Computational Science Research Center, Beijing and Computational Science and Applied Research Institute Shenzhen, Shenzhen, China
| | - Sergei Tretiak
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Christoph Lienau
- Institut für Physik and Center of Interface Science, Carl von Ossietzky Universität, Oldenburg, Germany
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21
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Hu Y, Xu C, Ye L, Gu FL, Zhu C. Nonadiabatic molecular dynamics simulation for the ultrafast photoisomerization of dMe-OMe-NAIP based on TDDFT on-the-fly potential energy surfaces. Phys Chem Chem Phys 2021; 23:5236-5243. [PMID: 33629668 DOI: 10.1039/d0cp06104b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Global switching on-the-fly trajectory surface hopping molecular dynamics simulation was performed on the accurate TD-B3LYP/6-31G* potential energy surfaces for E-to-Z and Z-to-E photoisomerization of dMe-OMe-NAIP up to S1(ππ*) excitation. The present TD(DFT) simulation provides accurate calculation for conical intersections between the first-excited and ground states. Thus, simulated quantum yield and lifetime of 0.23 and 620 fs (0.15 and 600 fs) for E-to-Z (Z-to-E) isomerization are in good (relatively good) agreement with experimental observation of 0.25 and 480 fs (0.24 and 430 fs), respectively. Simulated results reveal that photoisomerization pathways are initially uphill to conical intersection zones on the S1 potential energy surface and then downhill to product zones. Three types of representative conical intersections are found for determining photoisomerization mechanisms: one is the rotation type responsible for reactive isomerization and the other two are close to E and Z configurations, respectively, only for nonreactive isomerization. The present conclusions can be held in general for similar large NAIP systems of photoinduced isomerization based on E and Z configurations.
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Affiliation(s)
- Ying Hu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment of South China Normal University, Guangzhou 51006, P. R. China.
| | - Chao Xu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment of South China Normal University, Guangzhou 51006, P. R. China.
| | - Linfeng Ye
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment of South China Normal University, Guangzhou 51006, P. R. China. and Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao 266237, P. R. China
| | - Feng Long Gu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment of South China Normal University, Guangzhou 51006, P. R. China.
| | - Chaoyuan Zhu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, School of Chemistry & Environment of South China Normal University, Guangzhou 51006, P. R. China. and Department of Applied Chemistry and Institute of Molecular Science, National Chiao-Tung University, Hsinchu 30010, Taiwan. and Department of Applied Chemistry and Center for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
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22
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Hart SM, Banal JL, Bathe M, Schlau-Cohen GS. Identification of Nonradiative Decay Pathways in Cy3. J Phys Chem Lett 2020; 11:5000-5007. [PMID: 32484350 DOI: 10.1021/acs.jpclett.0c01201] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Photoexcited fluorescent markers are extensively used in spectroscopy, imaging, and analysis of biological systems. The performance of fluorescent markers depends on high levels of emission, which are limited by competing nonradiative decay pathways. Small-molecule fluorescent dyes have been increasingly used as markers due to their high and stable emission. Despite their prevalence, the nonradiative decay pathways of these dyes have not been determined. Here, we investigate these pathways for a widely used indocarbocyanine dye, Cy3, using transient grating spectroscopy. We identify a nonradiative decay pathway via a previously unknown dark state formed within ∼1 ps of photoexcitation. Our experiments, in combination with electronic structure calculations, suggest that the generation of the dark state is mediated by picosecond vibrational mode coupling, likely via a conical intersection. We further identify the vibrational modes, and thus structural elements, responsible for the formation and dynamics of the dark state, providing insight into suppressing nonradiative decay pathways in fluorescent markers such as Cy3.
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Affiliation(s)
- Stephanie M Hart
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - James L Banal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Gabriela S Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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23
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Leveraging excited-state coherence for synthetic control of ultrafast dynamics. Nature 2020; 582:214-218. [DOI: 10.1038/s41586-020-2353-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 03/13/2020] [Indexed: 11/08/2022]
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24
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Bonafé FP, Aradi B, Hourahine B, Medrano CR, Hernández FJ, Frauenheim T, Sánchez CG. A Real-Time Time-Dependent Density Functional Tight-Binding Implementation for Semiclassical Excited State Electron–Nuclear Dynamics and Pump–Probe Spectroscopy Simulations. J Chem Theory Comput 2020; 16:4454-4469. [DOI: 10.1021/acs.jctc.9b01217] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Franco P. Bonafé
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Teórica y Computacional, Córdoba, Argentina
- Instituto de Investigaciones en Fisicoquímica de Córdoba, INFIQC (CONICET - Universidad Nacional de Córdoba), Córdoba, Argentina
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, Universitát Bremen, Bremen, Germany
| | - Ben Hourahine
- SUPA, Department of Physics, John Anderson Building, The University of Strathclyde, 107 Rottenrow, Glasgow G15 6QN, United Kingdom
| | - Carlos R. Medrano
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Teórica y Computacional, Córdoba, Argentina
- Instituto de Investigaciones en Fisicoquímica de Córdoba, INFIQC (CONICET - Universidad Nacional de Córdoba), Córdoba, Argentina
| | - Federico J. Hernández
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Teórica y Computacional, Córdoba, Argentina
- Instituto de Investigaciones en Fisicoquímica de Córdoba, INFIQC (CONICET - Universidad Nacional de Córdoba), Córdoba, Argentina
- Department of Physics, Universidad de Santiago de Chile, Av. Ecuador 3493, Santiago, Chile
| | - Thomas Frauenheim
- Bremen Center for Computational Materials Science, Universitát Bremen, Bremen, Germany
- Computational Science Research Center (CSRC) Beijing and Computational Science and Applied Research (CSAR) Institute, Shenzhen, China
| | - Cristián G. Sánchez
- Instituto Interdisciplinario de Ciencias Básicas, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Exactas y Naturales, Mendoza, Argentina
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25
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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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26
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Beckwith JS, Rumble CA, Vauthey E. Data analysis in transient electronic spectroscopy – an experimentalist's view. INT REV PHYS CHEM 2020. [DOI: 10.1080/0144235x.2020.1757942] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Joseph S. Beckwith
- Department of Physical Chemistry, University of Geneva, Geneva, Switzerland
| | | | - Eric Vauthey
- Department of Physical Chemistry, University of Geneva, Geneva, Switzerland
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27
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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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28
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Schnedermann C, Alvertis AM, Wende T, Lukman S, Feng J, Schröder FAYN, Turban DHP, Wu J, Hine NDM, Greenham NC, Chin AW, Rao A, Kukura P, Musser AJ. A molecular movie of ultrafast singlet fission. Nat Commun 2019; 10:4207. [PMID: 31527736 PMCID: PMC6746807 DOI: 10.1038/s41467-019-12220-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/26/2019] [Indexed: 11/09/2022] Open
Abstract
The complex dynamics of ultrafast photoinduced reactions are governed by their evolution along vibronically coupled potential energy surfaces. It is now often possible to identify such processes, but a detailed depiction of the crucial nuclear degrees of freedom involved typically remains elusive. Here, combining excited-state time-domain Raman spectroscopy and tree-tensor network state simulations, we construct the full 108-atom molecular movie of ultrafast singlet fission in a pentacene dimer, explicitly treating 252 vibrational modes on 5 electronic states. We assign the tuning and coupling modes, quantifying their relative intensities and contributions, and demonstrate how these modes coherently synchronise to drive the reaction. Our combined experimental and theoretical approach reveals the atomic-scale singlet fission mechanism and can be generalized to other ultrafast photoinduced reactions in complex systems. This will enable mechanistic insight on a detailed structural level, with the ultimate aim to rationally design molecules to maximise the efficiency of photoinduced reactions.
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Affiliation(s)
- Christoph Schnedermann
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK.
- Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford, OX1 3QZ, UK.
| | - Antonios M Alvertis
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Torsten Wende
- Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford, OX1 3QZ, UK
| | - Steven Lukman
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
- Institute of Materials Research and Engineering, Agency for Science Technology and Research (A*STAR), 2 Fusionopolis Way, Singapore, 138634, Singapore
| | - Jiaqi Feng
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Florian A Y N Schröder
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - David H P Turban
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Jishan Wu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Nicholas D M Hine
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Neil C Greenham
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Alex W Chin
- Centre National de la Recherce Scientifique, Institute des Nanosciences de Paris, Sorbonne Universite, Paris, France
| | - Akshay Rao
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Philipp Kukura
- Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford, OX1 3QZ, UK
| | - Andrew J Musser
- Department of Physics and Astronomy, University of Sheffield, Hounsfield Road, Sheffield, S3 7RH, UK.
- Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, NY, 14853, USA.
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29
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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] [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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30
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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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31
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Bizimana LA, Farfan CA, Brazard J, Turner DB. E to Z Photoisomerization of Phytochrome Cph1Δ Exceeds the Born-Oppenheimer Adiabatic Limit. J Phys Chem Lett 2019; 10:3550-3556. [PMID: 31181167 DOI: 10.1021/acs.jpclett.9b01137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The Born-Oppenheimer adiabatic limit applies broadly in chemistry because most reactions occur on the ground electronic state. Photochemical reactions involve two or more electronic states and need not be subject to this adiabatic limit. The spectroscopic signatures of nonadiabatic processes are subtle, and therefore, experimental investigations have been limited to the few systems dominated by single photochemical outcomes. Systems with branched excited-state pathways have been neglected, despite their potential to reveal insights into photochemical reactivity. Here we present experimental evidence from coherent three-dimensional electronic spectroscopy that the E to Z photoisomerization of phytochrome Cph1 is strongly nonadiabatic, and the simulations reproduce the measured features only when the photoisomerization proceeds nonadiabatically near, but not through, a conical intersection. The results broaden the general understanding of photoisomerization mechanisms and motivate future studies of nonadiabatic processes with multiple outcomes arising from branching on excited-state potential energy surfaces.
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Affiliation(s)
- Laurie A Bizimana
- Department of Chemistry , New York University , 100 Washington Square East , New York , New York 10003 , United States
| | - Camille A Farfan
- Department of Chemistry , New York University , 100 Washington Square East , New York , New York 10003 , United States
| | - Johanna Brazard
- Department of Chemistry , New York University , 100 Washington Square East , New York , New York 10003 , United States
| | - Daniel B Turner
- Department of Chemistry , New York University , 100 Washington Square East , New York , New York 10003 , United States
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32
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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] [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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33
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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] [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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34
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Hernández FJ, Bonafé FP, Aradi B, Frauenheim T, Sánchez CG. Simulation of Impulsive Vibrational Spectroscopy. J Phys Chem A 2019; 123:2065-2072. [DOI: 10.1021/acs.jpca.9b00307] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Federico J. Hernández
- Universidad Nacional de Córdoba. Facultad de Ciencias Quı́micas, Departamento de Quı́mica Teórica y Computacional, Córdoba Argentina
- Instituto de Investigaciones en Fisicoquímica de Córdoba, INFIQC (CONICET-Universidad Nacional de Córdoba), Córdoba 5000, Argentina
| | - Franco P. Bonafé
- Universidad Nacional de Córdoba. Facultad de Ciencias Quı́micas, Departamento de Quı́mica Teórica y Computacional, Córdoba Argentina
- Instituto de Investigaciones en Fisicoquímica de Córdoba, INFIQC (CONICET-Universidad Nacional de Córdoba), Córdoba 5000, Argentina
| | - Bálint Aradi
- Bremen Center for Computational Materials Science, Universität Bremen, Bremen 28359, Germany
| | - Thomas Frauenheim
- Bremen Center for Computational Materials Science, Universität Bremen, Bremen 28359, Germany
| | - Cristián G. Sánchez
- Universidad Nacional de Córdoba. Facultad de Ciencias Quı́micas, Departamento de Quı́mica Teórica y Computacional, Córdoba Argentina
- Instituto de Investigaciones en Fisicoquímica de Córdoba, INFIQC (CONICET-Universidad Nacional de Córdoba), Córdoba 5000, Argentina
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35
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Multidimensional Vibrational Coherence Spectroscopy. Top Curr Chem (Cham) 2018; 376:35. [DOI: 10.1007/s41061-018-0213-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/31/2018] [Indexed: 10/28/2022]
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36
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van Grondelle R. Photoinduced processes in nucleic acids and proteins: concluding remarks. Faraday Discuss 2018; 207:513-521. [PMID: 29564457 DOI: 10.1039/c8fd00049b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Light induced charge and energy transport in nucleic acids and proteins is the basis of fundamental biological processes such as photosynthesis, vision, DNA-photostability, DNA-photodamage and photosensing. This article summarises the concluding remarks given at the Faraday Discussions meeting on this topic. The specific themes arising from the meeting that are discussed herein include charge transfer in nucleic acids and proteins, excited state dynamics and topology, vibrations and dynamic disorder, proteins and charge transfer states, nanobiophotonics coupled to biomedical applications and photosynthesis.
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Affiliation(s)
- Rienk van Grondelle
- Faculty of Science, Department of Physics and Astronomy, Vrije Universiteit Amsterdam, The Netherlands
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