1
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Shi W, Ma J, Jiang C, Taketsugu T. Advanced theoretical design of light-driven molecular rotary motors: enhancing thermal helix inversion and visible-light activation. Phys Chem Chem Phys 2024; 26:15672-15680. [PMID: 38766713 DOI: 10.1039/d4cp00037d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
In this study, we have advanced the field of light-driven molecular rotary motors (LDMRMs) by achieving two pivotal goals: lowering the thermal helix inversion (THI) barrier and extending the absorption wavelength into the visible spectrum. This study involves the structural reengineering of a second-generation visible LDMRM, resulting in the synthesis of a novel class, specifically, 2-((2S)-5-methoxy-2-methyl-2,3-dihydro-1H-cyclopenta[a]naphthalen-1-yl)-3-oxo-2,3-dihydro-1H-dibenzo[e,g]indole-6,9-dicarbonitrile. This redesigned motor stands out with its two photoisomerization stages and two thermal helix inversions, featuring exceptionally low THI barriers (4.00 and 2.05 kcal mol-1 at the OM2/MRCI level for the EM → EP and ZM → ZP processes, respectively). Moreover, it displays absorption wavelengths in the visible light range (482.98 and 465.76 nm for the EP and ZP isomers, respectively, at the TD-PBE0-D3/6-31G(d,p) level), surpassing its predecessors in efficiency, as indicated by the narrow HOMO-LUMO energy gap. Ultrafast photoisomerization kinetics (approximately 0.8-1.6 ps) and high quantum yields (around 0.3-0.6) were observed through trajectory surface hopping simulations. Additionally, the simulated time-resolved fluorescence emission spectrum indicates a significantly reduced "dark state" duration (0.09-0.26 ps) in these newly designed LDMRMs compared to the original ones, marking a substantial leap forward in the design and efficiency of LDMRMs.
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Affiliation(s)
- Weiliang Shi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Jianzheng Ma
- Ministry of Education Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Shaanxi Province Key Laboratory of Quantum Information and Quantum Optoelectronic Devices, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Chenwei Jiang
- Ministry of Education Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Shaanxi Province Key Laboratory of Quantum Information and Quantum Optoelectronic Devices, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
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2
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Lee IS, Filatov M, Min SK. Formulation of transition dipole gradients for non-adiabatic dynamics with polaritonic states. J Chem Phys 2024; 160:154103. [PMID: 38624116 DOI: 10.1063/5.0202095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/31/2024] [Indexed: 04/17/2024] Open
Abstract
A general formulation of the strong coupling between photons confined in a cavity and molecular electronic states is developed for the state-interaction state-average spin-restricted ensemble-referenced Kohn-Sham method. The light-matter interaction is included in the Jaynes-Cummings model, which requires the derivation and implementation of the analytical derivatives of the transition dipole moments between the molecular electronic states. The developed formalism is tested in the simulations of the nonadiabatic dynamics in the polaritonic states resulting from the strong coupling between the cavity photon mode and the ground and excited states of the penta-2,4-dieniminium cation, also known as PSB3. Comparison with the field-free simulations of the excited-state decay dynamics in PSB3 reveals that the light-matter coupling can considerably alter the decay dynamics by increasing the excited state lifetime and hindering photochemically induced torsion about the C=C double bonds of PSB3. The necessity of obtaining analytical transition dipole gradients for the accurate propagation of the dynamics is underlined.
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Affiliation(s)
- In Seong Lee
- Center for Multidimensional Carbon Materials (CMCM), Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Michael Filatov
- Center for Multidimensional Carbon Materials (CMCM), Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Seung Kyu Min
- Center for Multidimensional Carbon Materials (CMCM), Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan 44919, Republic of Korea
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3
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Dupuy L, Rikus A, Maitra NT. Exact-Factorization-Based Surface Hopping without Velocity Adjustment. J Phys Chem Lett 2024:2643-2649. [PMID: 38422391 DOI: 10.1021/acs.jpclett.4c00115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
While surface hopping has emerged as a powerful method for simulating non-adiabatic dynamics in large molecules, the ad hoc nature of the necessary velocity adjustments and decoherence corrections in the algorithm somewhat reduces its reliability. Here we propose a new scheme that eliminates these aspects by combining the nuclear equation from the quantum-trajectory surface-hopping approach with the electronic equation derived from the exact-factorization approach. The resulting method, denoted QTSH-XF, yields a surface-hopping method on firmer ground than previous and is shown to successfully capture dynamics in Tully models and in a linear vibronic coupling model of the photoexcited uracil cation.
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Affiliation(s)
- Lucien Dupuy
- Department of Physics, Rutgers University, Newark, New Jersey 07102, United States
| | - Anton Rikus
- Department of Physics, Rutgers University, Newark, New Jersey 07102, United States
- University of Münster, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, 48149 Münster, Germany
| | - Neepa T Maitra
- Department of Physics, Rutgers University, Newark, New Jersey 07102, United States
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4
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Wasowicz TJ, Dąbkowska I, Kivimäki A, Richter R. Two-body dissociation of isoxazole following double photoionization - an experimental PEPIPICO and theoretical DFT and MP2 study. Phys Chem Chem Phys 2023; 25:31655-31666. [PMID: 37964643 DOI: 10.1039/d3cp03760f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
The dissociative double photoionization of isoxazole molecules has been investigated experimentally and theoretically. The experiment has been carried out in the 27.5-36 eV photon energy range using vacuum ultraviolet (VUV) synchrotron radiation excitation combined with ion time-of-flight (TOF) spectrometry and photoelectron-photoion-photoion coincidence (PEPIPICO) technique. Five well-resolved two-body dissociation channels have been identified in the isoxazole's coincidence maps, and their appearance energies have been determined. The coincidence yield curves of these dissociation channels have been obtained in the photon energy ranges from their appearance energies up to 36 eV. The double photoionization of isoxazole produces a C3H3NO2+ transient dication, which decomposes into fragments differing from previously reported photofragmentation products of isoxazole. We have found no evidence of pathways leading to the C3H2NO+, HCN+, C2H2O+, C3HN+, or C2H2+ fragments or their neutral counterparts that have been observed in previous neutral photodissociation and single photoionization studies. Instead, the dissociation of isoxazole after the ejection of two electrons is bond-selective and is governed by two reactions, HCO+ + H2CCN+ and H2CO+ + HCCN+, whose appearance energies are 28.6 (±0.3) and 29.4 (±0.3) eV, respectively. A third dissociation channel turns out to be a variant of the most intense channel (HCO+ + H2CCN+), where one of the fragment ions contains a heavy isotope. Two minor dissociation channels occurring at higher energies, CO+ + CH3CN+ and CN+ + H3CCO+, are also identified. The density functional and ab initio quantum chemical calculations have been performed to elucidate the dissociative charge-separating mechanisms and determine the energies of the observed photoproducts. The present work unravels hitherto unexplored photodissociation mechanisms of isoxazole and thus provides deeper insight into the photophysics of five-membered heterocyclic molecules containing two heteroatoms.
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Affiliation(s)
- Tomasz J Wasowicz
- Division of Complex Systems Spectroscopy, Institute of Physics and Computer Science, Gdansk University of Technology, ul. G. Narutowicza 11/12, 80-233 Gdansk, Poland.
| | - Iwona Dąbkowska
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63, 80-308 Gdansk, Poland
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5
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Wen J, Mai S, González L. Excited-State Dynamics Simulations of a Light-Driven Molecular Motor in Solution. J Phys Chem A 2023; 127:9520-9529. [PMID: 37917883 PMCID: PMC10658450 DOI: 10.1021/acs.jpca.3c05841] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/14/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
Molecular motors, where light can be transformed into motion, are promising in the design of nanomechanical devices. For applications, however, finding relationships between molecular motion and the environment is important. Here, we report the study of excited-state dynamics of an overcrowded alkene in solution using a hybrid quantum mechanics/molecular mechanics (QM/MM) approach combined with excited-state molecular dynamics simulations. Using QM/MM surface-hopping trajectories, we calculated time-resolved emission and transient absorption spectra. These show the rise of a short-lived Franck-Condon state, followed by the formation of a dark state in the first 150 fs before the molecular motor relaxes to the ground state in about 1 ps. From the analysis of radial distribution functions, we infer that the orientation of the solvent with respect to the molecular motor in the electronic excited state is similar to that in the ground state during the photoisomerization.
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Affiliation(s)
- Jin Wen
- State
Key Laboratory for Modification of Chemical Fibers and Polymer Materials,
College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, Vienna 1090, Austria
| | - Sebastian Mai
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, Vienna 1090, Austria
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, Vienna 1090, Austria
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6
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Villaseco Arribas E, Vindel-Zandbergen P, Roy S, Maitra NT. Different flavors of exact-factorization-based mixed quantum-classical methods for multistate dynamics. Phys Chem Chem Phys 2023; 25:26380-26395. [PMID: 37750820 DOI: 10.1039/d3cp03464j] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
The exact factorization approach has led to the development of new mixed quantum-classical methods for simulating coupled electron-ion dynamics. We compare their performance for dynamics when more than two electronic states are occupied at a given time, and analyze: (1) the use of coupled versus auxiliary trajectories in evaluating the electron-nuclear correlation terms, (2) the approximation of using these terms within surface-hopping and Ehrenfest frameworks, and (3) the relevance of the exact conditions of zero population transfer away from nonadiabatic coupling regions and total energy conservation. Dynamics through the three-state conical intersection in the uracil radical cation as well as polaritonic models in one dimension are studied.
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Affiliation(s)
| | - Patricia Vindel-Zandbergen
- Department of Physics, Rutgers University, Newark 07102, New Jersey, USA.
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Saswata Roy
- Department of Physics, Rutgers University, Newark 07102, New Jersey, USA.
| | - Neepa T Maitra
- Department of Physics, Rutgers University, Newark 07102, New Jersey, USA.
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7
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Regen-Pregizer BL, Ozcelik A, Mayer P, Hampel F, Dube H. A photochemical method to evidence directional molecular motions. Nat Commun 2023; 14:4595. [PMID: 37524701 PMCID: PMC10390485 DOI: 10.1038/s41467-023-40190-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 07/17/2023] [Indexed: 08/02/2023] Open
Abstract
Light driven synthetic molecular motors represent crucial building blocks for advanced molecular machines and their applications. A standing challenge is the development of very fast molecular motors able to perform rotations with kHz, MHz or even faster frequencies. Central to this challenge is the direct experimental evidence of directionality because analytical methods able to follow very fast motions rarely deliver precise geometrical insights. Here, a general photochemical method for elucidation of directional motions is presented. In a macrocyclization approach the molecular motor rotations are restricted and forced to proceed in two separate ~180° rotation-photoequilibria. Therefore, all four possible photoinduced rotation steps (clockwise and counterclockwise directions) can be quantified. Comparison of the corresponding quantum yields to the unrestricted motor delivers direct evidence for unidirectionality. This method can be used for any ultrafast molecular motor even in cases where no high energy intermediates are present during the rotation cycle.
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Affiliation(s)
- Benjamin Lukas Regen-Pregizer
- Friedrich-Alexander Universität Erlangen-Nürnberg, Department of Chemistry and Pharmacy, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Ani Ozcelik
- Friedrich-Alexander Universität Erlangen-Nürnberg, Department of Chemistry and Pharmacy, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Peter Mayer
- Ludwig-Maximilians Universität München, Department of Chemistry and Center for Integrated Protein Science CIPSM, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Frank Hampel
- Friedrich-Alexander Universität Erlangen-Nürnberg, Department of Chemistry and Pharmacy, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Henry Dube
- Friedrich-Alexander Universität Erlangen-Nürnberg, Department of Chemistry and Pharmacy, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany.
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8
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Singhania A, Kalita S, Chettri P, Ghosh S. Accounts of applied molecular rotors and rotary motors: recent advances. NANOSCALE ADVANCES 2023; 5:3177-3208. [PMID: 37325522 PMCID: PMC10262963 DOI: 10.1039/d3na00010a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Molecular machines are nanoscale devices capable of performing mechanical works at molecular level. These systems could be a single molecule or a collection of component molecules that interrelate with one another to produce nanomechanical movements and resulting performances. The design of the components of molecular machine with bioinspired traits results in various nanomechanical motions. Some known molecular machines are rotors, motors, nanocars, gears, elevators, and so on based on their nanomechanical motion. The conversion of these individual nanomechanical motions to collective motions via integration into suitable platforms yields impressive macroscopic output at varied sizes. Instead of limited experimental acquaintances, the researchers demonstrated several applications of molecular machines in chemical transformation, energy conversion, gas/liquid separation, biomedical use, and soft material fabrication. As a result, the development of new molecular machines and their applications has accelerated over the previous two decades. This review highlights the design principles and application scopes of several rotors and rotary motor systems because these machines are used in real applications. This review also offers a systematic and thorough overview of current advancements in rotary motors, providing in-depth knowledge and predicting future problems and goals in this area.
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Affiliation(s)
- Anup Singhania
- Natural Product Chemistry Group, Chemical Sciences & Technology Division, CSIR-North East Institute of Science & Technology Jorhat 785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Sudeshna Kalita
- Natural Product Chemistry Group, Chemical Sciences & Technology Division, CSIR-North East Institute of Science & Technology Jorhat 785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Prerna Chettri
- Natural Product Chemistry Group, Chemical Sciences & Technology Division, CSIR-North East Institute of Science & Technology Jorhat 785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
| | - Subrata Ghosh
- Natural Product Chemistry Group, Chemical Sciences & Technology Division, CSIR-North East Institute of Science & Technology Jorhat 785006 Assam India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201002 India
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9
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Ma J, Zhao D, Yu L, Jiang C, Lan Z, Li F. Simultaneously improving the efficiencies of photo- and thermal isomerization of an oxindole-based light-driven molecular rotary motor by a structural redesign. Phys Chem Chem Phys 2023; 25:12800-12809. [PMID: 37129050 DOI: 10.1039/d3cp00559c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We designed a novel highly efficient light-driven molecular rotary motor theoretically by using electronic structure calculations and nonadiabatic dynamics simulations, and it showed excellent performance for both photo- and thermal isomerization processes simultaneously. By the small structural modification based on 3-(2,7-dimethyl-2,3-dihydro-1H-inden-1-ylidene)-1-methylindolin-2-one (DDIYM) synthesized by Feringa et al. recently, an oxindole-based light-driven molecular rotary motor, 3-(1,5-dimethyl-4,5-dihydrocyclopenta[b]pyrrol-6(1H)-ylidene)-1-methylindolin-2-one (DDPYM), is proposed, which displays a significant electronic push-pull character and weak steric hindrance for double-bond isomerization. The newly designed motor DDPYM shows a remarkable improvement of the quantum yield for both EP → ZM and ZP → EM photoisomerization processes, compared to the original motor DDIYM. Furthermore, the rotary motion in photoisomerization processes of DDPYM behaves more like a pure axial rotational motion approximately, while that of DDIYM is an obvious precessional motion. The weakness of the steric hindrance reduces the energy barriers of the thermal helix EM → EP and ZM → ZP inversion steps, and would accelerate two ground-state isomerization steps significantly. Our results confirm the feasibility of simultaneously improving the efficiencies of photo- and thermal isomerization of oxindole-based light-driven molecular rotary motors and this design idea sheds light on the future development of more efficient molecular motors.
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Affiliation(s)
- Jianzheng Ma
- Ministry of Education Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Shaanxi Province Key Laboratory of Quantum Information and Quantum Optoelectronic Devices, School of Physics, Xi'an Jiaotong University, Xian 710049, China.
| | - Di Zhao
- Ministry of Education Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Shaanxi Province Key Laboratory of Quantum Information and Quantum Optoelectronic Devices, School of Physics, Xi'an Jiaotong University, Xian 710049, China.
| | - Le Yu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Shaanxi Key Laboratory of Physico-Inorganic Chemistry, Northwest University, Xi'an 710127, China
| | - Chenwei Jiang
- Ministry of Education Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Shaanxi Province Key Laboratory of Quantum Information and Quantum Optoelectronic Devices, School of Physics, Xi'an Jiaotong University, Xian 710049, China.
| | - Zhenggang Lan
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China.
| | - Fuli Li
- Ministry of Education Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Shaanxi Province Key Laboratory of Quantum Information and Quantum Optoelectronic Devices, School of Physics, Xi'an Jiaotong University, Xian 710049, China.
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10
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Towards the engineering of a photon-only two-stroke rotary molecular motor. Nat Commun 2022; 13:6433. [PMID: 36307476 PMCID: PMC9616945 DOI: 10.1038/s41467-022-33695-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 09/27/2022] [Indexed: 12/25/2022] Open
Abstract
The rational engineering of photoresponsive materials, e.g., light-driven molecular motors, is a challenging task. Here, we use structure-related design rules to prepare a prototype molecular rotary motor capable of completing an entire revolution using, exclusively, the sequential absorption of two photons; i.e., a photon-only two-stroke motor. The mechanism of rotation is then characterised using a combination of non-adiabatic dynamics simulations and transient absorption spectroscopy measurements. The results show that the rotor moiety rotates axially relative to the stator and produces, within a few picoseconds at ambient T, an intermediate with the same helicity as the starting structure. We discuss how such properties, that include a 0.25 quantum efficiency, can help overcome the operational limitations of the classical overcrowded alkene designs.
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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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Marco Paolino
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Mario Saletti
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Annalisa Reale
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Mariano Licciardi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF) Università degli Studi di Palermo Via Archirafi 32 90123 Palermo Italy
| | - Paola Varvarà
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF) Università degli Studi di Palermo Via Archirafi 32 90123 Palermo Italy
| | - Arnaud Marquette
- Institut de Physique et Chimie des Matériaux de Strasbourg Université de Strasbourg CNRS UMR 7504 Strasbourg France
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg Université de Strasbourg CNRS UMR 7504 Strasbourg France
| | - Claudia Bonechi
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Alessandro Donati
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Gianluca Giorgi
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Germano Giuliani
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
| | - Benedetta Carlotti
- Dipartimento di Chimica, Biologia e Biotecnologie Università di Perugia Via Elce di Sotto, 8 06123 Perugia Italy
| | - Fausto Ortica
- Dipartimento di Chimica, Biologia e Biotecnologie Università di Perugia Via Elce di Sotto, 8 06123 Perugia Italy
| | - Loredana Latterini
- Dipartimento di Chimica, Biologia e Biotecnologie Università di Perugia Via Elce di Sotto, 8 06123 Perugia Italy
| | - Mariangela Gentile
- Dipartimento di Scienze della Vita Università degli Studi di Siena Via A. Moro 53100 Siena Italy
| | - Eugenio Paccagnini
- Dipartimento di Scienze della Vita Università degli Studi di Siena Via A. Moro 53100 Siena Italy
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
- Chemistry Department Bowling Green State University 43403 Bowling Green OH USA) ok
| | - Andrea Cappelli
- Dipartimento di Biotecnologie, Chimica e Farmacia (Dipartimento di Eccellenza 2018–2022) Università degli Studi di Siena Via A. Moro 2 53100 Siena Italy
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12
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Ma J, Zhao D, Jiang C, Lan Z, Li F. Effect of Temperature on Photoisomerization Dynamics of a Newly Designed Two-Stroke Light-Driven Molecular Rotary Motor. Int J Mol Sci 2022; 23:ijms23179694. [PMID: 36077091 PMCID: PMC9456002 DOI: 10.3390/ijms23179694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
The working mechanism of conventional light-driven molecular rotary motors, especially Feringa-type motors, contains two photoisomerization steps and two thermal helix inversion steps. Due to the existence of a thermal helix inversion step, both the ability to work at lower temperatures and the rotation speed are limited. In this work, a two-stroke light-driven molecular rotary motor, 2-(1,5-dimethyl-4,5-dihydrocyclopenta[b]pyrrol-6(1H)-ylidene)-1,2-dihydro-3H-pyrrol-3-one (DDPY), is proposed, which is capable of performing unidirectional and repetitive rotation by only two photoisomerization (EP→ZP and ZP→EP) steps. With trajectory surface-hopping simulation at the semi-empirical OM2/MRCI level, the EP→ZP and ZP→EP nonadiabatic dynamics of DDPY were systematically studied at different temperatures. Both EP→ZP and ZP→EP photoisomerizations are on an ultrafast timescale (ca. 200–300 fs). The decay mode of EP→ZP photoisomerization is approximately bi-exponential, while that of ZP→EP photoisomerization is found to be periodic. For EP and ZP isomers of DDPY, after the S0→S1 excitation, the dynamical processes of nonadiabatic decay are both followed by twisting about the central C=C double bond and the pyramidalization of the C atom at the stator-axle linkage. The effect of temperature on the nonadiabatic dynamics of EP→ZP and ZP→EP photoisomerizations of DDPY has been systematically investigated. The average lifetimes of the S1 excited state and quantum yields for both EP→ZP and ZP→EP photoisomerization are almost temperature-independent, while the corresponding unidirectionality of rotation is significantly increased (e.g., 74% for EP→ZP and 72% for ZP→EP at 300 K vs 100% for EP→ZP and 94% for ZP→EP at 50 K) with lowering the temperature.
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Affiliation(s)
- Jianzheng Ma
- Ministry of Education Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Shaanxi Province Key Laboratory of Quantum Information and Quantum Optoelectronic Devices, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Di Zhao
- Ministry of Education Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Shaanxi Province Key Laboratory of Quantum Information and Quantum Optoelectronic Devices, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Chenwei Jiang
- Ministry of Education Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Shaanxi Province Key Laboratory of Quantum Information and Quantum Optoelectronic Devices, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
- Correspondence: (C.J.); (Z.L.)
| | - Zhenggang Lan
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
- Correspondence: (C.J.); (Z.L.)
| | - Fuli Li
- Ministry of Education Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Shaanxi Province Key Laboratory of Quantum Information and Quantum Optoelectronic Devices, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
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13
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Kochman MA, Gryber T, Durbeej B, Kubas A. Simulation and analysis of the relaxation dynamics of a photochromic furylfulgide. Phys Chem Chem Phys 2022; 24:18103-18118. [PMID: 35880631 DOI: 10.1039/d2cp02143a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Furylfulgides, a class of photochromic organic compounds, show a complex system of photoinduced reactions. In the present study, the excited-state dynamics of the Eα and Eβ isomers of a representative furylfulgide is modelled with the use of nonadiabatic molecular dynamics simulations. Moreover, a pattern recognition algorithm is employed in order to automatically identify relaxation pathways, and to quantify the photoproduct distributions. The simulation results indicate that, despite differing only in the orientation of the furyl group, the two isomers show markedly different photochemical behaviour. The predominant Eα isomer undergoes photocyclisation with a quantum yield (QY) of 0.27 ± 0.10. For this isomer, the undesired E → Z photoisomerisation around the central double bond represents a minor side reaction, with a QY of 0.09 ± 0.07. In contrast, the minority Eβ isomer, which is incapable of photocyclisation, undergoes efficient E → Z photoisomerisation, with a QY as high as 0.56 ± 0.14. The relaxation kinetics and the photoproduct distributions are interpreted in the light of the available experimental data.
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Affiliation(s)
- Michał Andrzej Kochman
- Institute of Physical Chemistry, Polish Academy of Sciences, Marcina Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Tomasz Gryber
- Institute of Physical Chemistry, Polish Academy of Sciences, Marcina Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Bo Durbeej
- Division of Theoretical Chemistry, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden
| | - Adam Kubas
- Institute of Physical Chemistry, Polish Academy of Sciences, Marcina Kasprzaka 44/52, 01-224 Warsaw, Poland.
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14
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Villaseco Arribas E, Agostini F, Maitra NT. Exact Factorization Adventures: A Promising Approach for Non-Bound States. Molecules 2022; 27:molecules27134002. [PMID: 35807246 PMCID: PMC9267945 DOI: 10.3390/molecules27134002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022] Open
Abstract
Modeling the dynamics of non-bound states in molecules requires an accurate description of how electronic motion affects nuclear motion and vice-versa. The exact factorization (XF) approach offers a unique perspective, in that it provides potentials that act on the nuclear subsystem or electronic subsystem, which contain the effects of the coupling to the other subsystem in an exact way. We briefly review the various applications of the XF idea in different realms, and how features of these potentials aid in the interpretation of two different laser-driven dissociation mechanisms. We present a detailed study of the different ways the coupling terms in recently-developed XF-based mixed quantum-classical approximations are evaluated, where either truly coupled trajectories, or auxiliary trajectories that mimic the coupling are used, and discuss their effect in both a surface-hopping framework as well as the rigorously-derived coupled-trajectory mixed quantum-classical approach.
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Affiliation(s)
| | - Federica Agostini
- Institut de Chimie Physique UMR8000, Université Paris-Saclay, CNRS, 91405 Orsay, France;
| | - Neepa T. Maitra
- Department of Physics, Rutgers University, Newark, NJ 07102, USA;
- Correspondence:
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15
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Ha JK, Min SK. Independent Trajectory Mixed Quantum-Classical Approaches Based on the Exact Factorization. J Chem Phys 2022; 156:174109. [DOI: 10.1063/5.0084493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mixed quantum-classical dynamics based on the exact factorization exploits the "derived" electron-nuclear correlation (ENC) term aiming for the description of quantum coherences. The ENC contains interactions between the phase of electronic states and nuclear quantum momenta which depend on the spatial shape of the nuclear density.The original surface hopping based on the exact factorization (SHXF) [\textit{J. Phys. Chem. Lett.} \textbf{2018}, \textit{9}, 1097] exploits frozen Gaussian functions to construct the nuclear density in the ENC term while the phase of electronic states is approximated as a fictitious nuclear momentum change.However, in reality, the width of nuclear wave packets varies in time depending on the shape of potential energy surfaces.In this work, we present a modified SHXF approach and a newly-developed Ehrenfest dynamics based on the exact factorization (EhXF) with time-dependent Gaussian functions and phases by enforcing total energy conservation.We perform numerical tests for various one-dimensional two-state model Hamiltonians.Overall, the time-dependent width of Gaussian functions and the energy conserving phase show a reliable decoherence compared to the original frozen Gaussian-based SHXF and the exact quantum mechanical calculation.Especially, the energy conserving phase is crucial for EhXF to reproduce the correct quantum dynamics.
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Affiliation(s)
- Jong-Kwon Ha
- Chemistry, Ulsan National Institute of Science and Technology, Korea, Republic of (South Korea)
| | - Seung Kyu Min
- Ulsan National Institute of Science and Technology, Korea, Republic of (South Korea)
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16
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Design and Nonadiabatic Photoisomerization Dynamics Study of a Three-Stroke Light-Driven Molecular Rotary Motor. Int J Mol Sci 2022; 23:ijms23073908. [PMID: 35409268 PMCID: PMC8999534 DOI: 10.3390/ijms23073908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 01/01/2023] Open
Abstract
Working cycle of conventional light-driven molecular rotary motors (LDMRMs), especially Feringa-type motors, usually have four steps, two photoisomerization steps, and two thermal helix inversion (THI) steps. THI steps hinder the ability of the motor to operate at lower temperatures and limit the rotation speed of LDMRMs. A three-stroke LDMRM, 2-(2,7-dimethyl-2,3-dihydro-1H-inden-1-ylidene)-1,2-dihydro-3H-pyrrol-3-one (DDIY), is proposed, which is capable of completing an unidirectional rotation by two photoisomerization steps and one thermal helix inversion step at room temperature. On the basis of trajectory surface-hopping simulation at the semi-empirical OM2/MRCI level, the EP→ZP and ZP→EM nonadiabatic photoisomerization dynamics of DDIY were systematically analyzed. Quantum yields of EP→ZP and ZP→EM photoisomerization of DDIY are ca. 34% and 18%, respectively. Both EP→ZP and ZP→EM photoisomerization processes occur on an ultrafast time scale (ca. 100-300 fs). This three-stroke LDMRM may stimulate further research for the development of new families of more efficient LDMRMs.
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17
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Solvation Effects on the Thermal Helix Inversion of Molecular Motors from QM/MM Calculations. CHEMISTRY 2022. [DOI: 10.3390/chemistry4010016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Molecular motors convert light and thermal energies into mechanical work, offering good opportunities to design novel molecular devices. Among them, molecular motors alternate a photoisomerization and a thermal helix inversion to achieve unidirectional rotation. The rotational speed is limited by the helix inversion step, which in turn is governed by a barrier in the electronic ground state. In this work, we systematically study the solvation effect on the thermal process of selected molecular motors, comparing reaction barriers obtained from both density functional theory (DFT) in the isolated system and umbrella sampling within a hybrid quantum mechanics/molecular mechanics (QM/MM) model in solution. We find more prominent solvation effects on those molecular motors with larger dipole moments. The results could provide insight into how to functionalize molecular motors to speed up their rotation.
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18
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Vindel-Zandbergen P, Matsika S, Maitra NT. Exact-Factorization-Based Surface Hopping for Multistate Dynamics. J Phys Chem Lett 2022; 13:1785-1790. [PMID: 35170972 DOI: 10.1021/acs.jpclett.1c04132] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A surface-hopping algorithm recently derived from the exact factorization approach, SHXF [Ha et al. J. Phys. Chem. Lett. 2018, 9, 1097], introduces an additional term in the electronic equation of surface hopping that couples electronic states through the quantum momentum. This term not only provides a first-principles description of decoherence, but here we show it is crucial to accurately capture nonadiabatic dynamics when more than two states are occupied at any given time. Using a vibronic coupling model of the uracil cation, we show that the lack of this term in traditional surface-hopping methods, including those with decoherence corrections, leads to failure to predict the dynamics through a three-state intersection, while SHXF performs similarly to the multiconfiguration time-dependent Hartree quantum dynamics benchmark.
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Affiliation(s)
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Neepa T Maitra
- Department of Physics, Rutgers University, Newark, New Jersey 07102, United States
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19
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Coupled- and Independent-Trajectory Approaches Based on the Exact Factorization Using the PyUNIxMD Package. Top Curr Chem (Cham) 2022; 380:8. [PMID: 35083549 DOI: 10.1007/s41061-021-00361-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/11/2021] [Indexed: 10/19/2022]
Abstract
We present mixed quantum-classical approaches based on the exact factorization framework. The electron-nuclear correlation term in the exact factorization enables us to deal with quantum coherences by accounting for electronic and nuclear nonadiabatic couplings effectively within classical nuclei approximation. We compare coupled- and independent-trajectory approximations with each other to understand algorithms in description of the bifurcation of nuclear wave packets and the correct spatial distribution of electronic wave functions along with nuclear trajectories. Finally, we show numerical results for comparisons of coupled- and independent-trajectory approaches for the photoisomerization of a protonated Schiff base from excited state molecular dynamics (ESMD) simulations with the recently developed Python-based ESMD code, namely, the PyUNIxMD program.
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20
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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: 72] [Impact Index Per Article: 24.0] [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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21
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Lee S, Park W, Nakata H, Filatov M, Choi CH. Recent advances in ensemble density functional theory and linear response theory for strong correlation. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Seunghoon Lee
- Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena California USA
| | - Woojin Park
- Department of Chemistry Kyungpook National University Daegu South Korea
| | - Hiroya Nakata
- Department of Chemistry Kyungpook National University Daegu South Korea
| | - Michael Filatov
- Department of Chemistry Kyungpook National University Daegu South Korea
| | - Cheol Ho Choi
- Department of Chemistry Kyungpook National University Daegu South Korea
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22
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Abstract
In this paper, we discuss coupled-trajectory schemes for molecular-dynamics simulations of excited-state processes. New coupled-trajectory strategies to capture decoherence effects, revival of coherence and nonadiabatic interferences in long-time dynamics are proposed, and compared to independent-trajectory schemes. The working framework is provided by the exact factorization of the electron-nuclear wave function, and it exploits ideas emanating from various surface-hopping schemes. The new coupled-trajectory algorithms are tested on a one-dimensional two-state system using different model parameters which allow one to induce different dynamics. The benchmark is provided by the numerically exact solution of the time-dependent Schrödinger equation.
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Affiliation(s)
- Carlotta Pieroni
- CNRS, Institut de Chimie Physique UMR8000, Université Paris-Saclay, 91405 Orsay, France.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Federica Agostini
- CNRS, Institut de Chimie Physique UMR8000, Université Paris-Saclay, 91405 Orsay, France
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23
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Vindel-Zandbergen P, Ibele LM, Ha JK, Min SK, Curchod BFE, Maitra NT. Study of the Decoherence Correction Derived from the Exact Factorization Approach for Nonadiabatic Dynamics. J Chem Theory Comput 2021; 17:3852-3862. [PMID: 34138553 PMCID: PMC8280698 DOI: 10.1021/acs.jctc.1c00346] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
![]()
We present a detailed
study of the decoherence correction to surface
hopping that was recently derived from the exact factorization approach.
Ab initio multiple spawning calculations that use the same initial
conditions and the same electronic structure method are used as a
reference for three molecules: ethylene, the methaniminium cation,
and fulvene, for which nonadiabatic dynamics follows a photoexcitation.
A comparison with the Granucci–Persico energy-based decoherence
correction and the augmented fewest-switches surface-hopping scheme
shows that the three decoherence-corrected methods operate on individual
trajectories in a qualitatively different way, but the results averaged
over trajectories are similar for these systems.
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Affiliation(s)
| | - Lea M Ibele
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Jong-Kwon Ha
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Seung Kyu Min
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Basile F E Curchod
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Neepa T Maitra
- Department of Physics, Rutgers University, Newark, New Jersey 07102, United States
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24
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Lee IS, Ha JK, Han D, Kim TI, Moon SW, Min SK. PyUNIxMD: A Python-based excited state molecular dynamics package. J Comput Chem 2021; 42:1755-1766. [PMID: 34197646 PMCID: PMC8362049 DOI: 10.1002/jcc.26711] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 01/17/2023]
Abstract
Theoretical/computational description of excited state molecular dynamics is nowadays a crucial tool for understanding light-matter interactions in many materials. Here we present an open-source Python-based nonadiabatic molecular dynamics program package, namely PyUNIxMD, to deal with mixed quantum-classical dynamics for correlated electron-nuclear propagation. The PyUNIxMD provides many interfaces for quantum chemical calculation methods with commercial and noncommercial ab initio and semiempirical quantum chemistry programs. In addition, the PyUNIxMD offers many nonadiabatic molecular dynamics algorithms such as fewest-switch surface hopping and its derivatives as well as decoherence-induced surface hopping based on the exact factorization (DISH-XF) and coupled-trajectory mixed quantum-classical dynamics (CTMQC) for general purposes. Detailed structures and flows of PyUNIxMD are explained for the further implementations by developers. We perform a nonadiabatic molecular dynamics simulation for a molecular motor system as a simple demonstration.
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Affiliation(s)
- In Seong Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Jong-Kwon Ha
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Daeho Han
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Tae In Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Sung Wook Moon
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Seung Kyu Min
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
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25
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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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26
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Wang Y, Gu Z, Deng X, Zhang B. Ultraviolet-light-triggered isomerization of Rydberg-excited propanal: Real-time capture of ultrafast structural evolution and dynamics investigation. J Chem Phys 2021; 154:054301. [PMID: 33557549 DOI: 10.1063/5.0039802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Structure rearrangement processes, such as isomerization, are attracting extensive interest as a potential carrier in molecular scale electronics design. UV-light-triggered isomerization of Rydberg-excited propanal with two UV photons has been investigated with time-resolved photoelectron spectroscopy. By following the photoionization from 3s Rydberg states in the time domain, the ultrafast structural evolution and the corresponding photoisomerization dynamics are observed and tracked in real-time. The conversion barrier for isomerization from cis-propanal to gauche isomer is estimated to be about 1500 ± 100 cm-1 experimentally. Both the photoisomerization yield and the conversion rate have shown strong dependence on the excitation energy. It is observed that whether vibration modes are selectively excited or not, cis-to-gauche photoisomerization of propanal in 3s Rydberg state occurs once the excitation energy is higher than the conversion barrier without any vibrational excitation specificity. This yields a powerful approach to studying structural evolution dynamics in large molecules, which may have applications in molecular devices.
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Affiliation(s)
- Yanmei Wang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Zhenfei Gu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Xulan Deng
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Bing Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
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27
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Martinez P, Rosenzweig B, Hoffmann NM, Lacombe L, Maitra NT. Case studies of the time-dependent potential energy surface for dynamics in cavities. J Chem Phys 2021; 154:014102. [PMID: 33412864 PMCID: PMC7968936 DOI: 10.1063/5.0033386] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/10/2020] [Indexed: 11/14/2022] Open
Abstract
The exact time-dependent potential energy surface driving the nuclear dynamics was recently shown to be a useful tool to understand and interpret the coupling of nuclei, electrons, and photons in cavity settings. Here, we provide a detailed analysis of its structure for exactly solvable systems that model two phenomena: cavity-induced suppression of proton-coupled electron-transfer and its dependence on the initial state, and cavity-induced electronic excitation. We demonstrate the inadequacy of simply using a weighted average of polaritonic surfaces to determine the dynamics. Such a weighted average misses a crucial term that redistributes energy between the nuclear and the polaritonic systems, and this term can in fact become a predominant term in determining the nuclear dynamics when several polaritonic surfaces are involved. Evolving an ensemble of classical trajectories on the exact potential energy surface reproduces the nuclear wavepacket quite accurately, while evolving on the weighted polaritonic surface fails after a short period of time. The implications and prospects for application of mixed quantum-classical methods based on this surface are discussed.
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Affiliation(s)
- Phillip Martinez
- Department of Physics and Astronomy, Hunter College of the City University of New York, 695 Park Avenue, New York, New York 10065, USA
| | | | - Norah M. Hoffmann
- Department of Physics, Rutgers University, Newark, New Jersey 07102, USA
| | - Lionel Lacombe
- Department of Physics, Rutgers University, Newark, New Jersey 07102, USA
| | - Neepa T. Maitra
- Department of Physics, Rutgers University, Newark, New Jersey 07102, USA
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28
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Kolodzeiski E, Amirjalayer S. Elucidating the Impact of Molecular Motors on Their Solvation Environment. J Phys Chem B 2020; 124:10879-10888. [DOI: 10.1021/acs.jpcb.0c06343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Elena Kolodzeiski
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Straße 10, Münster 48149, Germany
- Center for Nanotechnology, Heisenbergstraße 11, Münster 48149, Germany
- Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Straße 10, Münster 48149, Germany
| | - Saeed Amirjalayer
- Physikalisches Institut, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Straße 10, Münster 48149, Germany
- Center for Nanotechnology, Heisenbergstraße 11, Münster 48149, Germany
- Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Wilhelm-Klemm-Straße 10, Münster 48149, Germany
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29
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Filatov M, Lee S, Choi CH. Computation of Molecular Ionization Energies Using an Ensemble Density Functional Theory Method. J Chem Theory Comput 2020; 16:4489-4504. [PMID: 32421323 DOI: 10.1021/acs.jctc.0c00218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Computation of the ionization energies and of the respective Dyson orbitals based on the use of the extended Koopmans theorem (EKT) is implemented in connection with an ensemble density functional theory (eDFT) method, the state-interaction state-averaged spin-restricted ensemble-referenced Kohn-Sham (SI-SA-REKS or SSR) method. The new methodology enables fast computation of the ionization energies and evaluation of the respective Dyson orbitals, the square norms of which are related with the ionization probabilities, in the ground and excited electronic states of molecules. As the application of EKT recycles the intermediate quantities from the SSR analytical energy gradient, evaluation of the ionization energies and probabilities can be carried out on-the-fly during the nonadiabatic molecular dynamics simulations. This opens up a perspective for fast theoretical simulation of the time-resolved photoelectron spectroscopy observations. In the present work, the new methodology is tested in the computation of the ionization energies and Dyson orbitals of several molecules in the ground and excited electronic states, including strongly correlated species, such as the ozone molecule, dissociating chemical bonds, and conical intersections.
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Affiliation(s)
- Michael Filatov
- Department of Chemistry, Kyungpook National University, Daegu 702-701, South Korea
| | - Seunghoon Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 702-701, South Korea
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30
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Lacombe L, Maitra NT. Embedding via the Exact Factorization Approach. PHYSICAL REVIEW LETTERS 2020; 124:206401. [PMID: 32501082 DOI: 10.1103/physrevlett.124.206401] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
We present a quantum electronic embedding method derived from the exact factorization approach to calculate static properties of a many-electron system. The method is exact in principle but the practical power lies in utilizing input from a low-level calculation on the entire system in a high-level method computed on a small fragment, as in other embedding methods. Here, the exact factorization approach defines an embedding Hamiltonian on the fragment. Various Hubbard models demonstrate that remarkably accurate ground-state energies are obtained over the full range of weak to strongly correlated systems.
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Affiliation(s)
- Lionel Lacombe
- Department of Physics, Rutgers University, Newark, New Jersey 07102, USA
| | - Neepa T Maitra
- Department of Physics, Rutgers University, Newark, New Jersey 07102, USA
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31
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Lacombe L, Hoffmann NM, Maitra NT. Exact Potential Energy Surface for Molecules in Cavities. PHYSICAL REVIEW LETTERS 2019; 123:083201. [PMID: 31491208 DOI: 10.1103/physrevlett.123.083201] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Indexed: 06/10/2023]
Abstract
We find and analyze the exact time-dependent potential energy surface driving the proton motion for a model of cavity-induced suppression of proton-coupled electron transfer. We show how, in contrast to the polaritonic surfaces, its features directly correlate to the proton dynamics and we discuss cavity modifications of its structure responsible for the suppression. The results highlight the interplay between nonadiabatic effects from coupling to photons and coupling to electrons and suggest caution is needed when applying traditional dynamics methods based on polaritonic surfaces.
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Affiliation(s)
- Lionel Lacombe
- Department of Physics and Astronomy, Hunter College of the City University of New York, 695 Park Avenue, New York, New York 10065, USA
| | - Norah M Hoffmann
- Department of Physics and Astronomy, Hunter College of the City University of New York, 695 Park Avenue, New York, New York 10065, USA
- Max Planck Institute for the Structure and Dynamics of Matter and Center for Free-Electron Laser Science and Department of Physics, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Neepa T Maitra
- Department of Physics and Astronomy, Hunter College of the City University of New York, 695 Park Avenue, New York, New York 10065, USA
- Physics Program and Chemistry Program, Graduate Center of the City University of New York, New York 10016, USA
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32
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Abstract
Directed motion at the nanoscale is a central attribute of life, and chemically driven motor proteins are nature's choice to accomplish it. Motivated and inspired by such bionanodevices, in the past few decades chemists have developed artificial prototypes of molecular motors, namely, multicomponent synthetic species that exhibit directionally controlled, stimuli-induced movements of their parts. In this context, photonic and redox stimuli represent highly appealing modes of activation, particularly from a technological viewpoint. Here we describe the evolution of the field of photo- and redox-driven artificial molecular motors, and we provide a comprehensive review of the work published in the past 5 years. After an analysis of the general principles that govern controlled and directed movement at the molecular scale, we describe the fundamental photochemical and redox processes that can enable its realization. The main classes of light- and redox-driven molecular motors are illustrated, with a particular focus on recent designs, and a thorough description of the functions performed by these kinds of devices according to literature reports is presented. Limitations, challenges, and future perspectives of the field are critically discussed.
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Affiliation(s)
- Massimo Baroncini
- CLAN-Center for Light Activated Nanostructures , Istituto ISOF-CNR , via Gobetti 101 , 40129 Bologna , Italy.,Dipartimento di Scienze e Tecnologie Agro-alimentari , Università di Bologna , viale Fanin 44 , 40127 Bologna , Italy
| | - Serena Silvi
- CLAN-Center for Light Activated Nanostructures , Istituto ISOF-CNR , via Gobetti 101 , 40129 Bologna , Italy.,Dipartimento di Chimica "G. Ciamician" , Università di Bologna , via Selmi 2 , 40126 Bologna , Italy
| | - Alberto Credi
- CLAN-Center for Light Activated Nanostructures , Istituto ISOF-CNR , via Gobetti 101 , 40129 Bologna , Italy.,Dipartimento di Scienze e Tecnologie Agro-alimentari , Università di Bologna , viale Fanin 44 , 40127 Bologna , Italy
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