1
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Lawrence JE, Mannouch JR, Richardson JO. A size-consistent multi-state mapping approach to surface hopping. J Chem Phys 2024; 160:244112. [PMID: 38940540 DOI: 10.1063/5.0208575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 06/05/2024] [Indexed: 06/29/2024] Open
Abstract
We develop a multi-state generalization of the recently proposed mapping approach to surface hopping (MASH) for the simulation of electronically nonadiabatic dynamics. This new approach extends the original MASH method to be able to treat systems with more than two electronic states. It differs from previous approaches in that it is size consistent and rigorously recovers the original two-state MASH in the appropriate limits. We demonstrate the accuracy of the method by applying it to a series of model systems for which exact benchmark results are available, and we find that the method is well suited to the simulation of photochemical relaxation processes.
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Affiliation(s)
- Joseph E Lawrence
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
- Simons Center for Computational Physical Chemistry, New York University, New York, New York 10003, USA
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Jonathan R Mannouch
- Hamburg Center for Ultrafast Imaging, Universität Hamburg and the Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Jeremy O Richardson
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
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2
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Stolar T, Pearce BK, Etter M, Truong KN, Ostojić T, Krajnc A, Mali G, Rossi B, Molčanov K, Lončarić I, Meštrović E, Užarević K, Grisanti L. Base-pairing of uracil and 2,6-diaminopurine: from cocrystals to photoreactivity. iScience 2024; 27:109894. [PMID: 38783999 PMCID: PMC11112615 DOI: 10.1016/j.isci.2024.109894] [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: 07/28/2023] [Revised: 12/18/2023] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
We show that the non-canonical nucleobase 2,6-diaminopurine (D) spontaneously base pairs with uracil (U) in water and the solid state without the need to be attached to the ribose-phosphate backbone. Depending on the reaction conditions, D and U assemble in thermodynamically stable hydrated and anhydrated D-U base-paired cocrystals. Under UV irradiation, an aqueous solution of D-U base-pair undergoes photochemical degradation, while a pure aqueous solution of U does not. Our simulations suggest that D may trigger the U photodimerization and show that complementary base-pairing modifies the photochemical properties of nucleobases, which might have implications for prebiotic chemistry.
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Affiliation(s)
- Tomislav Stolar
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
- Federal Institute for Materials Research and Testing (BAM), Richard-Willstätter-Straße 11, 12489 Berlin, Germany
| | - Ben K.D. Pearce
- Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Martin Etter
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Khai-Nghi Truong
- Rigaku Europe SE, Hugenottenallee 167, 63263 Neu-Isenburg, Germany
| | - Tea Ostojić
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
| | - Andraž Krajnc
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Gregor Mali
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Barbara Rossi
- Elettra Sincrotrone Trieste, Strada Statale 14 km 163.5, 34149 Trieste, Italy
| | | | - Ivor Lončarić
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
| | - Ernest Meštrović
- Faculty of Chemical Engineering and Technology, University of Zagreb, Trg Marka Marulića 19, 10000 Zagreb, Croatia
| | | | - Luca Grisanti
- Ruđer Bošković Institute, Bijenička c. 54, 10000 Zagreb, Croatia
- National Research Council - Materials Foundry Institute (CNR-IOM) c/o SISSA (International School for Advanced Studies), Via Bonomea 265, 34136 Trieste, Italy
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3
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Mannouch JR, Kelly A. Quantum Quality with Classical Cost: Ab Initio Nonadiabatic Dynamics Simulations Using the Mapping Approach to Surface Hopping. J Phys Chem Lett 2024; 15:5814-5823. [PMID: 38781480 PMCID: PMC11163471 DOI: 10.1021/acs.jpclett.4c00535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Nonadiabatic dynamics methods are an essential tool for investigating photochemical processes. In the context of employing first-principles electronic structure techniques, such simulations can be carried out in a practical manner using semiclassical trajectory-based methods or wave packet approaches. While all approaches applicable to first-principles simulations are necessarily approximate, it is commonly thought that wave packet approaches offer inherent advantages over their semiclassical counterparts in terms of accuracy and that this trait simply comes at a higher computational cost. Here we demonstrate that the mapping approach to surface hopping (MASH), a recently introduced trajectory-based nonadiabatic dynamics method, can be efficiently applied in tandem with ab initio electronic structure. Our results even suggest that MASH may provide more accurate results than on-the-fly wave packet techniques, all at a much lower computational cost.
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Affiliation(s)
- Jonathan R. Mannouch
- Hamburg Center for Ultrafast
Imaging, Universität Hamburg and
the Max Planck Institute
for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Aaron Kelly
- Hamburg Center for Ultrafast
Imaging, Universität Hamburg and
the Max Planck Institute
for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
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4
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Mukherjee S, Mattos RS, Toldo JM, Lischka H, Barbatti M. Prediction Challenge: Simulating Rydberg photoexcited cyclobutanone with surface hopping dynamics based on different electronic structure methods. J Chem Phys 2024; 160:154306. [PMID: 38624122 DOI: 10.1063/5.0203636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/28/2024] [Indexed: 04/17/2024] Open
Abstract
This research examines the nonadiabatic dynamics of cyclobutanone after excitation into the n → 3s Rydberg S2 state. It stems from our contribution to the Special Topic of the Journal of Chemical Physics to test the predictive capability of computational chemistry against unseen experimental data. Decoherence-corrected fewest-switches surface hopping was used to simulate nonadiabatic dynamics with full and approximated nonadiabatic couplings. Several simulation sets were computed with different electronic structure methods, including a multiconfigurational wavefunction [multiconfigurational self-consistent field (MCSCF)] specially built to describe dissociative channels, multireference semiempirical approach, time-dependent density functional theory, algebraic diagrammatic construction, and coupled cluster. MCSCF dynamics predicts a slow deactivation of the S2 state (10 ps), followed by an ultrafast population transfer from S1 to S0 (<100 fs). CO elimination (C3 channel) dominates over C2H4 formation (C2 channel). These findings radically differ from the other methods, which predicted S2 lifetimes 10-250 times shorter and C2 channel predominance. These results suggest that routine electronic structure methods may hold low predictive power for the outcome of nonadiabatic dynamics.
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Affiliation(s)
| | - Rafael S Mattos
- Aix Marseille University, CNRS, ICR, Marseille 13397, France
| | - Josene M Toldo
- Aix Marseille University, CNRS, ICR, Marseille 13397, France
| | - Hans Lischka
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, USA
| | - Mario Barbatti
- Aix Marseille University, CNRS, ICR, Marseille 13397, France
- Institut Universitaire de France, Paris 75231, France
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5
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Oliveira LMF, Valverde D, Costa GJ, Borin AC. The copious photochemistry of 2,6-diaminopurine: Luminescence, triplet population, and ground state recovery. Photochem Photobiol 2024; 100:323-338. [PMID: 37403286 DOI: 10.1111/php.13833] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/06/2023]
Abstract
9H- and 7H-2,6-Diaminopurine (26DAP) photoinduced events in vacuum were studied at the MS-CASPT2/cc-pVDZ level of theory. The S1 1 (ππ* La ) state is initially populated evolving barrierless towards its minimum energy structure, from where two photochemical events can take place in both tautomers. The first is the return of the electronic population to the ground state via the C6 conical intersection (CI-C6). The second involves an internal conversion to the ground through the C2 conical intersection (CI-C2). According to our geodesic interpolated paths connecting the critical structures, the second route is less favorable in both tautomers, due to the presence of high energy barriers. Our calculations suggest a competition between fluorescence and ultrafast relaxation to the electronic ground state via internal conversion process. Based on our calculated potential energy surfaces and experimental excited state lifetimes from the literature, we can infer that the 7H- must have a greater fluorescence yield than the 9H-tautomer. We also explored the triplet state population mechanisms on the 7H-26DAP to understand their long-lived components observed experimentally.
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Affiliation(s)
- Leonardo M F Oliveira
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Danillo Valverde
- Unité de Chimie Physique Théorique et Structurale, Namur Institute of Structured Matter, Université de Namur, Namur, Belgium
| | - Gustavo J Costa
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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6
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Gate G, Williams A, Boldissar S, Šponer J, Szabla R, de Vries M. The tautomer-specific excited state dynamics of 2,6-diaminopurine using resonance-enhanced multiphoton ionization and quantum chemical calculations. Photochem Photobiol 2024; 100:404-418. [PMID: 38124372 DOI: 10.1111/php.13897] [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: 06/28/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
2,6-Diaminopurine (2,6-dAP) is an alternative nucleobase that potentially played a role in prebiotic chemistry. We studied its excited state dynamics in the gas phase by REMPI, IR-UV hole burning, and ps pump-probe spectroscopy and performed quantum chemical calculations at the SCS-ADC(2) level of theory to interpret the experimental results. We found the 9H tautomer to have a small barrier to ultrafast relaxation via puckering of its 6-membered ring. The 7H tautomer has a larger barrier to reach a conical intersection and also has a sizable triplet yield. These results are discussed relative to other purines, for which 9H tautomerization appears to be more photostable than 7H and homosubstituted purines appear to be less photostable than heterosubstituted or singly substituted purines.
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Affiliation(s)
- Gregory Gate
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Ann Williams
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Samuel Boldissar
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Olomouc-Holice, Czech Republic
| | - Rafal Szabla
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Mattanjah de Vries
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
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7
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Marsili E, Curchod BFE. A Theoretical Perspective on the Photochemistry of Boron-Nitrogen Lewis Adducts. J Phys Chem A 2024; 128:996-1008. [PMID: 38236050 PMCID: PMC10875676 DOI: 10.1021/acs.jpca.3c07016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 01/19/2024]
Abstract
Boron-Nitrogen (B-N) Lewis adducts form a versatile family of compounds with numerous applications in functional molecules. Despite the growing interest in this family of compounds for optoelectronic applications, little is currently known about their photophysics and photochemistry. Even the electronic absorption spectrum of ammonia borane, the textbook example of a B-N Lewis adduct, is unavailable. Given the versatility of the light-induced processes exhibited by these molecules, we propose in this work a detailed theoretical study of the photochemistry and photophysics of simple B-N Lewis adducts. We used advanced techniques in computational photochemistry to identify and characterize the possible photochemical pathways followed by ammonia borane and extended this knowledge to the substituted B-N Lewis adducts pyridine-borane and pyridine-boric acid. The photochemistry observed for this series of molecules allows us to extract qualitative rules to rationalize the light-induced behavior of more complex B-N-containing molecules.
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Affiliation(s)
- Emanuele Marsili
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Basile F. E. Curchod
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
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8
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Jankowska J, Sobolewski AL. Photo-oxidation of methanol in complexes with pyrido[2,3- b]pyrazine: a nonadiabatic molecular dynamics study. Phys Chem Chem Phys 2024; 26:5296-5302. [PMID: 38265828 DOI: 10.1039/d3cp04148d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Excited-state Proton-Coupled Electron Transfer (PCET) constitutes a key step in the photo-oxidation of small, electron-rich systems possessing acidic hydrogen atoms, such as water or alcohols, which can play a vital role in green hydrogen production. In this contribution, we employ ab initio quantum-chemical methods and on-the-fly nonadiabatic molecular dynamics simulations to study the mechanism and the photodynamics of PCET in 1 : 1 pyrido[2,3-b]pyrazine complexes with methanol. We find the process to be ultrafast and efficient when the intramolecular hydrogen bond is formed with one of the β-positioned nitrogen atoms. The complex exhibiting a hydrogen bond with an isolated nitrogen site, on the contrary, shows much lower reactivity. We explain this effect with the stabilization of the reactive ππ* charge-transfer electronic state in the former case.
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Affiliation(s)
- Joanna Jankowska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland.
| | - Andrzej L Sobolewski
- Institute of Physics, Polish Academy of Sciences, al. Lotników 32/46, Warsaw 02-668, Poland
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9
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Toldo JM, Mattos RS, Pinheiro M, Mukherjee S, Barbatti M. Recommendations for Velocity Adjustment in Surface Hopping. J Chem Theory Comput 2024; 20:614-624. [PMID: 38207213 DOI: 10.1021/acs.jctc.3c01159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
This study investigates velocity adjustment directions after hopping in surface hopping dynamics. Using fulvene and a protonated Schiff base (PSB4) as case studies, we investigate the population decay and reaction yields of different sets of dynamics with the velocity adjusted in either the nonadiabatic coupling, gradient difference, or momentum directions. For the latter, in addition to the conventional algorithm, we investigated the performance of a reduced kinetic energy reservoir approach recently proposed. Our evaluation also considered velocity adjustment in the directions of approximate nonadiabatic coupling vectors. While results for fulvene are susceptible to the adjustment approach, PSB4 is not. We correlated this dependence to the topography near the conical intersections. When nonadiabatic coupling vectors are unavailable, the gradient difference direction is the best adjustment option. If the gradient difference is also unavailable, a semiempirical vector direction or the momentum direction with a reduced kinetic energy reservoir becomes an excellent option to prevent an artificial excess of back hoppings. The precise velocity adjustment direction is less crucial for describing the nonadiabatic dynamics than the kinetic energy reservoir's size.
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Affiliation(s)
- Josene M Toldo
- Aix-Marseille University, CNRS, ICR, Marseille 13397, France
| | - Rafael S Mattos
- Aix-Marseille University, CNRS, ICR, Marseille 13397, France
| | - Max Pinheiro
- Aix-Marseille University, CNRS, ICR, Marseille 13397, France
| | | | - Mario Barbatti
- Aix-Marseille University, CNRS, ICR, Marseille 13397, France
- Institut Universitaire de France, Paris 75231, France
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10
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Papineau TV, Jacquemin D, Vacher M. Which Electronic Structure Method to Choose in Trajectory Surface Hopping Dynamics Simulations? Azomethane as a Case Study. J Phys Chem Lett 2024; 15:636-643. [PMID: 38205955 DOI: 10.1021/acs.jpclett.3c03014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Nonadiabatic dynamics simulations have become a standard approach to explore photochemical reactions. Such simulations require underlying potential energy surfaces and couplings between them, calculated at a chosen level of theory, yet this aspect is rarely assessed. Here, in combination with the popular trajectory surface hopping dynamics method, we use a high-accuracy XMS-CASPT2 electronic structure level as a benchmark for assessing the performances of various post-Hartree-Fock methods (namely, CIS, ADC(2), CC2, and CASSCF) and exchange-correlation functionals (PBE, PBE0, and CAM-B3LYP) in a TD-DFT/TDA context, using the isomerization around a double bond as test case. Different relaxation pathways are identified, and the ability of the different methods to reproduce their relative importance and time scale is discussed. The results show that multireference electronic structure methods should be preferred, when studying nonadiabatic decay between excited and ground states. If not affordable, TD-DFT with TDA and hybrid functionals and ADC(2) are efficient alternatives but overestimate the nonradiative decay yield and thus may miss deexcitation pathways.
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Affiliation(s)
| | - Denis Jacquemin
- Nantes Université, CNRS, CEISAM UMR 6230, Nantes F-44000, France
- Institut Universitaire de France (IUF), Paris F-75005, France
| | - Morgane Vacher
- Nantes Université, CNRS, CEISAM UMR 6230, Nantes F-44000, France
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11
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Taylor JT, Tozer DJ, Curchod BFE. On the description of conical intersections between excited electronic states with LR-TDDFT and ADC(2). J Chem Phys 2023; 159:214115. [PMID: 38059547 DOI: 10.1063/5.0176140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/14/2023] [Indexed: 12/08/2023] Open
Abstract
Conical intersections constitute the conceptual bedrock of our working understanding of ultrafast, nonadiabatic processes within photochemistry (and photophysics). Accurate calculation of potential energy surfaces within the vicinity of conical intersections, however, still poses a serious challenge to many popular electronic structure methods. Multiple works have reported on the deficiency of methods like linear-response time-dependent density functional theory within the adiabatic approximation (AA LR-TDDFT) or algebraic diagrammatic construction to second-order [ADC(2)]-approaches often used in excited-state molecular dynamics simulations-to describe conical intersections between the ground and excited electronic states. In the present study, we focus our attention on conical intersections between excited electronic states and probe the ability of AA LR-TDDFT and ADC(2) to describe their topology and topography, using protonated formaldimine and pyrazine as two exemplar molecules. We also take the opportunity to revisit the performance of these methods in describing conical intersections involving the ground electronic state in protonated formaldimine-highlighting in particular how the intersection ring exhibited by AA LR-TDDFT can be perceived either as a (near-to-linear) seam of intersection or two interpenetrating cones, depending on the magnitude of molecular distortions within the branching space.
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Affiliation(s)
- Jack T Taylor
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - David J Tozer
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Basile F E Curchod
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
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12
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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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13
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Mansour R, Toldo JM, Mukherjee S, Pinheiro M, Barbatti M. Temperature effects on the internal conversion of excited adenine and adenosine. Phys Chem Chem Phys 2023; 25:27083-27093. [PMID: 37801041 PMCID: PMC10583498 DOI: 10.1039/d3cp03234e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 09/09/2023] [Indexed: 10/07/2023]
Abstract
This work aims to elucidate the dependence of the excited-state lifetime of adenine and adenosine on temperature. So far, it has been experimentally shown that while adenine's lifetime is unaffected by temperature, adenosine's lifetime strongly depends on it. However, the non-Arrhenius temperature dependence has posed a challenge in explaining this phenomenon. We used surface hopping to simulate the dynamics of adenine and adenosine in the gas phase at 0 and 400 K. The temperature effects were observed under the initial conditions via Wigner sampling with thermal corrections. Our results confirm that adenine's excited-state lifetime does not depend on temperature, while adenosine's lifetime does. Adenosine's dependency is due to intramolecular vibrational energy transfer from adenine to the ribose group. At 0 K, this transfer reduced the mean kinetic energy of adenine's moiety so much that internal conversion is inhibited, and the lifetime elongated by a factor of 2.3 compared to that at 400 K. The modeling also definitively ruled out the influence of viscosity, which was proposed as an alternative explanation previously.
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Affiliation(s)
- Ritam Mansour
- Aix Marseille University, CNRS, ICR, Marseille, France.
| | | | | | - Max Pinheiro
- Aix Marseille University, CNRS, ICR, Marseille, France.
| | - Mario Barbatti
- Aix Marseille University, CNRS, ICR, Marseille, France.
- Institut Universitaire de France, 75231, Paris, France
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14
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Mukhopadhyay T, Jangid B, Dutta AK. State-specific frozen natural orbital for reduced-cost algebraic diagrammatic construction calculations: The application to ionization problem. J Chem Phys 2023; 159:084113. [PMID: 37638624 DOI: 10.1063/5.0160024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023] Open
Abstract
We have developed a reduced-cost algebraic diagrammatic construction (ADC) method based on state-specific frozen natural orbital and natural auxiliary functions. The newly developed method has been benchmarked on the GW100 test set for the ionization problem. The use of state-specific natural orbitals drastically reduces the size of the virtual space with a systematically controllable accuracy and offers a significant speedup over the standard ionization potential (IP)-ADC(3) method. The accuracy of the method can be controlled by two thresholds and nearly a black box to use. The inclusion of the perturbative correction significantly improves the accuracy of the calculated IP values, and the efficiency of the method has been demonstrated by calculating the IP of a molecule with 60 atoms and more than 2216 basis functions.
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Affiliation(s)
- Tamoghna Mukhopadhyay
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Bhavnesh Jangid
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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15
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Ullah N, Chen S, Zhang R. Excited‐state nonadiabatic dynamics simulations on the heptazine and adenine in a water environment: A mini review. J CHIN CHEM SOC-TAIP 2023. [DOI: 10.1002/jccs.202200445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Naeem Ullah
- Department of Physics City University of Hong Kong Kowloon Hong Kong SAR China
- Department of Physics Government Degree College Dara Adam Khel, Higher Education Department Khyber Pakhtunkhwah Pakistan
| | - Shunwei Chen
- Department of Physics City University of Hong Kong Kowloon Hong Kong SAR China
- School of Materials Science and Engineering Qilu University of Technology (Shandong Academy of Sciences) Jinan China
| | - Ruiqin Zhang
- Department of Physics City University of Hong Kong Kowloon Hong Kong SAR China
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16
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Ovad T, Sapunar M, Sršeň Š, Slavíček P, Mašín Z, Jones NC, Hoffmann SV, Ranković M, Fedor J. Excitation and fragmentation of the dielectric gas C 4F 7N: Electrons vs photons. J Chem Phys 2023; 158:014303. [PMID: 36610949 DOI: 10.1063/5.0130216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
C4F7N is a promising candidate for the replacement of sulfur hexafluoride as an insulating medium, and it is important to understand the chemical changes initiated in the molecule by collision with free electrons, specifically the formation of neutral fragments. The first step of neutral fragmentation is electronic excitation, yet neither the absorption spectrum in the vacuum ultraviolet (VUV) region nor the electron energy loss spectrum have previously been reported. Here, we experimentally probed the excited states by VUV photoabsorption spectroscopy and electron energy loss spectroscopy (EELS). We found that the distribution of states populated upon electron impact with low-energy electrons is significantly different from that following photoabsorption. This difference was confirmed and interpreted with ab initio modeling of both VUV and EELS spectra. We propose here a new computational protocol for the simulation of EELS spectra combining the Born approximation with approximate forms of correlated wave functions, which allows us to calculate the (usually very expensive) scattering cross sections at a cost similar to the calculation of oscillator strengths. Finally, we perform semi-classical non-adiabatic dynamics simulations to investigate the possible neutral fragments of the molecule formed through electron-induced neutral dissociation. We show that the product distribution is highly non-statistical.
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Affiliation(s)
- Tomáš Ovad
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Prague 6, Czech Republic
| | - Marin Sapunar
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Prague 6, Czech Republic
| | - Štěpán Sršeň
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Prague 6, Czech Republic
| | - Petr Slavíček
- Department of Physical Chemistry, University of Chemistry and Technology, Technická 5, Prague 6, Czech Republic
| | - Zdeněk Mašín
- Faculty of Mathematics and Physics, Charles University, Institute of Theoretical Physics, V Holešovičkách 2, 18000 Prague, Czech Republic
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark
| | - Søren Vrønning Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark
| | - Miloš Ranković
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague 8, Czech Republic
| | - Juraj Fedor
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague 8, Czech Republic
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17
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Barbatti M, Bondanza M, Crespo-Otero R, Demoulin B, Dral PO, Granucci G, Kossoski F, Lischka H, Mennucci B, Mukherjee S, Pederzoli M, Persico M, Pinheiro M, Pittner J, Plasser F, Sangiogo Gil E, Stojanovic L. Newton-X Platform: New Software Developments for Surface Hopping and Nuclear Ensembles. J Chem Theory Comput 2022; 18:6851-6865. [PMID: 36194696 PMCID: PMC9648185 DOI: 10.1021/acs.jctc.2c00804] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
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Newton-X is an open-source computational platform to
perform nonadiabatic
molecular dynamics based on surface hopping and spectrum simulations
using the nuclear ensemble approach. Both are among the most common
methodologies in computational chemistry for photophysical and photochemical
investigations. This paper describes the main features of these methods
and how they are implemented in Newton-X. It emphasizes the newest
developments, including zero-point-energy leakage correction, dynamics
on complex-valued potential energy surfaces, dynamics induced by incoherent
light, dynamics based on machine-learning potentials, exciton dynamics
of multiple chromophores, and supervised and unsupervised machine
learning techniques. Newton-X is interfaced with several third-party
quantum-chemistry programs, spanning a broad spectrum of electronic
structure methods.
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Affiliation(s)
- Mario Barbatti
- Aix Marseille University, CNRS, ICR, 13013Marseille, France.,Institut Universitaire de France, 75231Paris, France
| | - Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi 13, 56124Pisa, Italy
| | - Rachel Crespo-Otero
- Department of Chemistry, Queen Mary University of London, Mile End Road, E1 4NSLondon, U.K
| | | | - Pavlo O Dral
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, 361005Xiamen, China
| | - Giovanni Granucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi 13, 56124Pisa, Italy
| | - Fábris Kossoski
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, 31000Toulouse, France
| | - Hans Lischka
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas79409, United States
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi 13, 56124Pisa, Italy
| | | | - Marek Pederzoli
- J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejškova 3, 18223Prague 8, Czech Republic
| | - Maurizio Persico
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi 13, 56124Pisa, Italy
| | - Max Pinheiro
- Aix Marseille University, CNRS, ICR, 13013Marseille, France
| | - Jiří Pittner
- J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejškova 3, 18223Prague 8, Czech Republic
| | - Felix Plasser
- Department of Chemistry, Loughborough University, LE11 3TULoughborough, U.K
| | - Eduarda Sangiogo Gil
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi 13, 56124Pisa, Italy
| | - Ljiljana Stojanovic
- Department of Physics and Astronomy, University College London, Gower Street, WC1E 6BTLondon, U.K
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18
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Hutton L, Curchod BFE. Photodynamics of Gas‐Phase Pyruvic Acid Following Light Absorption in the Actinic Region. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202200151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lewis Hutton
- Centre for Computational Chemistry School of Chemistry University of Bristol Bristol BS8 1TS UK
| | - Basile F. E. Curchod
- Centre for Computational Chemistry School of Chemistry University of Bristol Bristol BS8 1TS UK
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19
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Yue L. Trajectory surface hopping molecular dynamics on Chemiluminescence of cyclic peroxides. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ling Yue
- Key Laboratory for Non‐Equilibrium Synthesis and Modulation of Condensed Matter, Ministry of Education, School of Chemistry Xi'an Jiaotong University Xi'an China
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20
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Mandal S, Srinivasan V. Rationalizing the Unexpected Sensitivity in Excited State Lifetimes of Adenine to Tautomerization by Nonadiabatic Molecular Dynamics. J Phys Chem B 2022; 126:7077-7087. [PMID: 36083211 DOI: 10.1021/acs.jpcb.2c03178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The remarkable photostability of canonical nucleobases makes them ideal building blocks for DNA and RNA. Even minor structural changes are expected to lead to drastic alteration of their subpicosecond excited state lifetimes. However, it is interesting to note that while the 9H- and 7H-amino tautomers of adenine possess drastically different lifetimes, 9H- and 7H-keto guanine possess similar excited state lifetimes. With an aim to explain this unexpected difference in sensitivity of lifetimes to tautomerization, we have investigated the excited state relaxation mechanism of UV-excited adenine and guanine tautomers using surface hopping based nonadiabatic molecular dynamics. We find that internal conversion in both guanine tautomers is almost barrierless while both adenine tautomers encounter significant barriers before they can deactivate. Moreover, the major deactivation channel (C2-puckering) in 9H-amino adenine is overall more efficient than the one (C6-puckering) in the 7H-amino form. We trace this difference to the frequent rotation of the amino group which disrupts its conjugation with the heterocyclic ring thereby reducing the strength of nonadiabatic coupling and, hence, delaying internal conversion.
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Affiliation(s)
- Satyajit Mandal
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal 462 066, India
| | - Varadharajan Srinivasan
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal 462 066, India
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21
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Chakraborty P, Liu Y, McClung S, Weinacht T, Matsika S. Nonadiabatic Excited State Dynamics of Organic Chromophores: Take-Home Messages. J Phys Chem A 2022; 126:6021-6031. [PMID: 36069531 DOI: 10.1021/acs.jpca.2c04671] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonadiabatic excited state dynamics are important in a variety of processes. Theoretical and experimental developments have allowed for a great progress in this area, while combining the two is often necessary and the best approach to obtain insight into the photophysical behavior of molecules. In this Feature Article we use examples of our recent work combining time-resolved photoelectron spectroscopy with theoretical nonadiabatic dynamics to highlight important lessons we learned. We compare the nonadiabatic excited state dynamics of three different organic molecules with the aim of elucidating connections between structure and dynamics. Calculations and measurements are compared for uracil, 1,3-cyclooctadiene, and 1,3-cyclohexadiene. The comparison highlights the role of rigidity in influencing the dynamics and the difficulty of capturing the dynamics accurately with calculations.
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Affiliation(s)
- Pratip Chakraborty
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States.,Division of Theoretical Chemistry and Biology, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Yusong Liu
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States.,Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, California 94025, United States
| | - Samuel McClung
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States
| | - Thomas Weinacht
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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22
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Bertram L, Roberts SJ, Powner MW, Szabla R. Photochemistry of 2-thiooxazole: a plausible prebiotic precursor to RNA nucleotides. Phys Chem Chem Phys 2022; 24:21406-21416. [PMID: 36047336 PMCID: PMC7613695 DOI: 10.1039/d2cp03167a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Potentially prebiotic chemical reactions leading to RNA nucleotides involve periods of UV irradiation, which are necessary to promote selectivity and destroy biologially irrelevant side products. Nevertheless, UV light has only been applied to promote specific stages of prebiotic reactions and its effect on complete prebiotic reaction sequences has not been extensively studied. Here, we report on an experimental and computational investigation of the photostability of 2-thiooxazole (2-TO), a potential precursor of pyrimidine and 8-oxopurine nucleotides on early Earth. Our UV-irradiation experiments resulted in rapid decomposition of 2-TO into unidentified small molecule photoproducts. We further clarify the underlying photochemistry by means of accurate ab initio calculations and surface hopping molecular dynamics simulations. Overall, the computational results show efficient rupture of the aromatic ring upon the photoexcitation of 2-TO via breaking of the C-O bond. Consequently, the initial stage of the divergent prebiotic synthesis of pyrimidine and 8-oxopurine nucleotides would require periodic shielding from UV light either with sun screening chromophores or through a planetary scenario that would protect 2-TO until it is transformed into a more stable intermediate compound, e.g. oxazolidinone thione.
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Affiliation(s)
- Lauren Bertram
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK
| | - Samuel J Roberts
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.,MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Matthew W Powner
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Rafał Szabla
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK.,Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, 50-370 Wrocław, Poland.
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23
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Marsili E, Prlj A, Curchod BFE. A Theoretical Perspective on the Actinic Photochemistry of 2-Hydroperoxypropanal. J Phys Chem A 2022; 126:5420-5433. [PMID: 35900368 PMCID: PMC9393889 DOI: 10.1021/acs.jpca.2c03783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The photochemical reactions triggered by the sunlight
absorption
of transient volatile organic compounds in the troposphere are notoriously
difficult to characterize experimentally due to the unstable and short-lived
nature of these organic molecules. Some members of this family of
compounds are likely to exhibit a rich photochemistry given the diversity
of functional groups they can bear. Even more interesting is the photochemical
fate of volatile organic compounds bearing more than one functional
group that can absorb light—this is the case, for example,
of α-hydroperoxycarbonyls, which are formed during the oxidation
of isoprene. Experimental observables characterizing the photochemistry
of these molecules like photoabsorption cross-sections or photolysis
quantum yields are currently missing, and we propose here to leverage
a recently developed computational protocol to predict in silico the
photochemical fate of 2-hydroperoxypropanal (2-HPP) in the actinic
region. We combine different levels of electronic structure methods—SCS-ADC(2)
and XMS-CASPT2—with the nuclear ensemble approach and trajectory
surface hopping to understand the mechanistic details of the possible
nonradiative processes of 2-HPP. In particular, we predict the photoabsorption
cross-section and the wavelength-dependent quantum yields for the
observed photolytic pathways and combine them to determine in silico
photolysis rate constants. The limitations of our protocol and possible
future improvements are discussed.
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Affiliation(s)
- Emanuele Marsili
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Antonio Prlj
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Basile F E Curchod
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
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24
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Mansour R, Toldo JM, Barbatti M. Role of the Hydrogen Bond on the Internal Conversion of Photoexcited Adenosine. J Phys Chem Lett 2022; 13:6194-6199. [PMID: 35767744 DOI: 10.1021/acs.jpclett.2c01554] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Experiments and theory have revealed that hydrogen bonds modify the excited-state lifetimes of nucleosides compared to nucleobases. Nevertheless, how these bonds impact the internal conversion is still unsettled. This work simulates the non-adiabatic dynamics of adenosine conformers in the gas phase with and without hydrogen bonds between the sugar and adenine moieties. The isomer containing the hydrogen bond (syn) exhibits a significantly shorter excited-state lifetime than the isomer without it (anti). However, internal conversion through electron-driven proton transfer between sugar and adenine plays only a minor (although non-negligible) role in the photophysics of adenosine. Either with or without hydrogen bonds, photodeactivation preferentially occurs following the ring-puckering pathways. The role of the hydrogen bond is to avoid the sugar rotation relative to adenine, shortening the distance to the ring-puckering internal conversion.
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Affiliation(s)
- Ritam Mansour
- Aix Marseille University, CNRS, ICR, Marseille 13397, France
| | - Josene M Toldo
- Aix Marseille University, CNRS, ICR, Marseille 13397, France
| | - Mario Barbatti
- Aix Marseille University, CNRS, ICR, Marseille 13397, France
- Institut Universitaire de France, 75231 Paris, France
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25
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Milovanović B, Novak J, Etinski M, Domcke W, Došlić N. On the propensity of formation of cyclobutane dimers in face-to-face and face-to-back uracil stacks in solution. Phys Chem Chem Phys 2022; 24:14836-14845. [PMID: 35697028 DOI: 10.1039/d2cp00495j] [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
UV irradiation of RNA leads to the formation of intra- and inter-strand crosslinks of cyclobutane type. Despite the importance of this reaction, relatively little is known about how the mutual orientation of the two bases affects the outcome of the reaction. Here we report a comparative nonadiabatic molecular dynamics study of face-to-back (F2B) and face-to-face (F2F) stacked uracil-water clusters. The computations were performed using the second-order algebraic-diagrammatic-construction (ADC(2)) method. We found that F2B stacked uracil-water clusters either relax non-reactively to the ground state by an ethylenic twist around the CC bond or remain in the lowest nπ* state in which the two bases gradually move away from each other. This finding is consistent with the low propensity for the formation of intra-strand cyclobutane dimers between adjacent RNA bases. On the contrary, in F2F stacked uracil-water clusters, in addition to non-reactive deactivation, we found a pro-reactive deactivation pathway, which may lead to the formation of cyclobutane uracil dimers in the electronic ground state. On a qualitative level, the observed photodynamics of F2F stacked uracil-water clusters explains the greater propensity of RNA to form inter-strand cyclobutane-type crosslinks.
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Affiliation(s)
| | - Jurica Novak
- Department of Biotechnology, University of Rijeka, HR-51000 Rijeka, Croatia.,Scientific and Educational Center "Biomedical Technologies" School of Medical Biology, South Ural State University, RU-454080, Chelyabinsk, Russia.,Center for Artificial Intelligence and Cybersecurity, University of Rijeka, 51000 Rijeka, Croatia
| | - Mihajlo Etinski
- University of Belgrade, Faculty of Physical Chemistry, Belgrade, Serbia
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Nađa Došlić
- Department of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.
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26
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Li Y, Aquino AJA, Siddique F, Niehaus TA, Lischka H, Nachtigallová D. Pathways to fluorescence via restriction of intramolecular motion in substituted tetraphenylethylenes. Phys Chem Chem Phys 2022; 24:1722-1735. [PMID: 34984424 DOI: 10.1039/d1cp04848a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design of materials with enhanced luminescence properties is a fast-developing field due to the potential applicability of these materials as light-emitting diodes or for bioimaging. A transparent way to enhance the emission properties of interesting molecular candidates is blocking competing and unproductive non-radiative relaxation pathways by the restriction of intramolecular motions. Rationalized functionalization is an important possibility to achieve such restrictions. Using time-dependent density functional theory (TD-DFT) based on the ωB97XD functional and the semiempirical tight-binding method including long-range corrections (TD-LC-DFTB), this work investigates the effect of functionalization of the paradigmatic tetraphenylethylene (TPE) on achieving restricted access to conical intersections (RACI). Photodynamical surface hopping simulations have been performed on a larger set of compounds including TPE and ten functionalized TPE compounds. Functionalization has been achieved by means of electron-withdrawing groups, bulky groups which block the relaxation channels via steric hindrance and groups capable of forming strong hydrogen bonds, which restrict the motion via the formation of hydrogen bond channels. Most of the investigated functionalized TPE candidates show ultrafast deactivation to the ground state due to their still existing structural flexibility, but two examples, one containing -CN and -CF3 groups and a second characterized by a network of hydrogen bonds, have been identified as interesting candidates for creating efficient luminescence properties in solution.
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Affiliation(s)
- Yingchao Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, P. R. China.
| | - Adélia J A Aquino
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, P. R. China. .,Department of Mechanical Engineering, Texas Tech University, Lubbock, TX, 79409, USA
| | - Farhan Siddique
- Department of Pharmaceutical Chemistry, Bahauddin Zakariya University, 60800 Multan, Pakistan.,Royal Institute of Medical Sciences, Multan, Pakistan
| | - Thomas A Niehaus
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - Hans Lischka
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, P. R. China. .,Department of Chemistry and Biochemistry, Texas Tech University Lubbock, TX 79409-1061, USA
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, 16610 Prague 6, Czech Republic. .,IT4Innovations, VŠB-Technical University of Ostrava, 70800 Ostrava-Poruba, Czech Republic
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27
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Understanding the Photolysis of CH 3ONO 2 with the On-the-fly Nonadiabatic Dynamics Simulation at the ADC(2) Level. CHINESE J CHEM PHYS 2022. [DOI: 10.1063/1674-0068/cjcp2201013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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28
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Shahrokh L, Omidyan R, Azimi G. Excited State Deactivation Mechanisms of Protonated Adenine: a Theoretical study. Phys Chem Chem Phys 2022; 24:14898-14908. [DOI: 10.1039/d2cp00106c] [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
Quantum chemical computational method as well as the adiabatic dynamics simulation have been employed to investigate the non-radiative relaxation mechanism of protonated 9H- and 7H-adenine (AH+). We have located three...
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29
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Uratani H, Nakai H. Scalable Ehrenfest Molecular Dynamics Exploiting the Locality of Density-Functional Tight-Binding Hamiltonian. J Chem Theory Comput 2021; 17:7384-7396. [PMID: 34860019 DOI: 10.1021/acs.jctc.1c00950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
To explore the science behind excited-state dynamics in high-complexity chemical systems, a scalable nonadiabatic molecular dynamics (MD) technique is indispensable. In this study, by treating the electronic degrees of freedom at the density-functional tight-binding level, we developed and implemented a reduced scaling and multinode-parallelizable Ehrenfest MD method. To achieve this goal, we introduced a concept called patchwork approximation (PA), where the effective Hamiltonian for real-time propagation of the electronic density matrix is partitioned into a set of local parts. Numerical results for giant icosahedral fullerenes, which comprise up to 6000 atoms, suggest that the scaling of the present PA-based method is less than quadratic, which yields a significant advantage over the conventional cubic scaling method in terms of computational time. The acceleration by the parallelization on multiple nodes was also assessed. Furthermore, the electronic and structural dynamics resulting from the perturbation by the external electric field were accurately reproduced with the PA, even when the electronic excitation was spatially delocalized.
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Affiliation(s)
- Hiroki Uratani
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Waseda Research Institute for Science and Engineering (WISE), 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8245, Japan
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30
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Huang X, Xie W, Došlić N, Gelin MF, Domcke W. Ab Initio Quasiclassical Simulation of Femtosecond Time-Resolved Two-Dimensional Electronic Spectra of Pyrazine. J Phys Chem Lett 2021; 12:11736-11744. [PMID: 34851116 DOI: 10.1021/acs.jpclett.1c03589] [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
Two-dimensional (2D) electronic spectroscopy is a powerful nonlinear technique which provides spectroscopic information on two frequency axes as well as dynamical information as a function of the so-called waiting time. Herein, an ab initio theoretical framework for the simulation of electronic 2D spectra has been developed. The method is based on the classical approximation to the doorway-window representation of three-pulse photon-echo signals and the description of nuclear motion by classical trajectories. Nonadiabatic effects are taken into account by a trajectory surface-hopping algorithm. 2D electronic spectra were simulated with ab initio on-the-fly trajectory calculations using the ADC(2) electronic-structure method for the pyrazine molecule, which is a benchmark system for ultrafast radiationless decay through conical intersections. It is demonstrated that 2D spectroscopy with subfemtosecond UV pulses can provide unprecedented detailed information on the ultrafast photodynamics of polyatomic molecules.
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Affiliation(s)
- Xiang Huang
- Department of Chemistry, Technical University of Munich, Garching, D-85747, Germany
| | - Weiwei Xie
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, 76131, Germany
| | - Nađa Došlić
- Department of Physical Chemistry, Ruder Boscovic Institute, Zagreb, HR-10000, Croatia
| | - Maxim F Gelin
- School of Sciences, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, Garching, D-85747, Germany
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31
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Ullah N, Chen S, Zhang R. Adenine ultrafast photorelaxation via electron-driven proton transfer. Phys Chem Chem Phys 2021; 23:23090-23095. [PMID: 34617085 DOI: 10.1039/d1cp03162g] [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
Photorelaxation of adenine in water was reported to be ultrafast (within 180 fs) primarily due to radiationless relaxation. However, in the last two decades, several experimental and theoretical investigations on photoexcitation of adenine have revealed diverse types of decay mechanisms. Using time-dependent density functional excited-state nonadiabatic dynamics simulations we show that it is the water to adenine electron-driven proton transfer (EDPT) barrierless reaction responsible for the ultrafast component of the adenine relaxation, which, however, occurred only in the case of the 7H isomer of adenine with five water molecules. This result reveals a known reaction pathway, however not found in previous simulations, with inference for the ultrafast relaxation mechanisms of adenine reported in experiments. The 9H isomer of adenine with six water molecules relaxing in a water cluster followed the previously known structural distortion (C2) decay pathway. The observations of the adenine EDPT reaction with water provide the origin of the experimental ultrafast adenine decay component and present a possible method to tackle future computational challenges in molecular-level biological processes.
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Affiliation(s)
- Naeem Ullah
- Department of Physics, City University of Hong Kong, Hong Kong SAR, China.
| | - Shunwei Chen
- School of Materials Science and Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Ruiqin Zhang
- Department of Physics, City University of Hong Kong, Hong Kong SAR, China. .,Beijing Computational Science Research Center, Beijing 100193, China
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32
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Tsuru S, Sharma B, Nagasaka M, Hättig C. Solvent Effects in the Ultraviolet and X-ray Absorption Spectra of Pyridazine in Aqueous Solution. J Phys Chem A 2021; 125:7198-7206. [PMID: 34379425 DOI: 10.1021/acs.jpca.1c05183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Electrostatic interaction of the solvent with the solute and fluctuations of the solvent configurations may make excitation energies of the solute different from those in the gas phase. These effects may dominate photoinduced or chemical reaction dynamics in solution systems and can be observed as shifts or broadening of peaks in absorption spectra. In this work, the nitrogen K-edge X-ray absorption spectra were measured for pyridazine in the gas phase and in aqueous solution. The ultraviolet and X-ray absorption spectra of pyridazine in aqueous solution, as well as those in the gas phase, were then calculated with models based on the algebraic-diagrammatic construction through second order [ADC(2)] with the resolution-of-identity (RI) approximation and compared with the spectra obtained in experiments. For aqueous solution, explicit local solvation structures were extracted from an ab initio molecular dynamics (AIMD) trajectory of pyridazine in bulk water, and RI-ADC(2) was combined with the conductor-like screening model (COSMO). The experimental absorption spectra of pyridazine in aqueous solution were reproduced with good accuracy by theoretical treatment of an ensemble containing the explicit local solvation structures of pyridazine with relevant water molecules combined with the COSMO solvation model of water for long-range solvation.
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Affiliation(s)
- Shota Tsuru
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Bikramjit Sharma
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Masanari Nagasaka
- Institute for Molecular Science and SOKENDAI (The Graduate University for Advanced Studies), Myodaiji, Okazaki 444-8585, Japan
| | - Christof Hättig
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
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33
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Jankowska J, Sobolewski AL. Modern Theoretical Approaches to Modeling the Excited-State Intramolecular Proton Transfer: An Overview. Molecules 2021; 26:molecules26175140. [PMID: 34500574 PMCID: PMC8434569 DOI: 10.3390/molecules26175140] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 02/02/2023] Open
Abstract
The excited-state intramolecular proton transfer (ESIPT) phenomenon is nowadays widely acknowledged to play a crucial role in many photobiological and photochemical processes. It is an extremely fast transformation, often taking place at sub-100 fs timescales. While its experimental characterization can be highly challenging, a rich manifold of theoretical approaches at different levels is nowadays available to support and guide experimental investigations. In this perspective, we summarize the state-of-the-art quantum-chemical methods, as well as molecular- and quantum-dynamics tools successfully applied in ESIPT process studies, focusing on a critical comparison of their specific properties.
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Affiliation(s)
- Joanna Jankowska
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland
- Correspondence:
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34
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Yu XF, Fu TH, Xiao B, Yu HY, Li Q. A theoretical study on the excited-state deactivation paths for the A-5FU dimer. Phys Chem Chem Phys 2021; 23:16089-16106. [PMID: 34291779 DOI: 10.1039/d1cp00030f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The photostability of DNA plays a key role in the normal function of organisms. A-5FU is a base pair derivative of the A-T dimer where the methyl group is replaced by a F atom. Here, accurate static TDDFT calculations and non-adiabatic dynamic simulations are used to systematically investigate the excited-state decay paths of the A-5FU dimer related to the proton transfer and the out-of-plane twisting deformation motion of A and 5FU in the 1ππ* and 1nπ* states. CC2 is used to check the accuracy of the current TDDFT calculations. Our results show that the deformation of the C[double bond, length as m-dash]C or C[double bond, length as m-dash]N double bond in A and 5FU provides an efficient pathway for the depopulation of the lowest excited states, which can compete with the excited-state proton transfer paths in the dimer. This finding indicates that monomer-like decay paths could be important for the photostability of weakly hydrogen-bonded DNA base pairs and provide a new insight into the excited-state decay paths in base pairs and their analogues.
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Affiliation(s)
- Xue-Fang Yu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
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35
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Matsika S. Electronic Structure Methods for the Description of Nonadiabatic Effects and Conical Intersections. Chem Rev 2021; 121:9407-9449. [PMID: 34156838 DOI: 10.1021/acs.chemrev.1c00074] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonadiabatic effects are ubiquitous in photophysics and photochemistry, and therefore, many theoretical developments have been made to properly describe them. Conical intersections are central in nonadiabatic processes, as they promote efficient and ultrafast nonadiabatic transitions between electronic states. A proper theoretical description requires developments in electronic structure and specifically in methods that describe conical intersections between states and nonadiabatic coupling terms. This review focuses on the electronic structure aspects of nonadiabatic processes. We discuss the requirements of electronic structure methods to describe conical intersections and nonadiabatic couplings, how the most common excited state methods perform in describing these effects, and what the recent developments are in expanding the methodology and implementing nonadiabatic couplings.
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Affiliation(s)
- Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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36
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Janicki M, Kufner CL, Todd ZR, Kim SC, O’Flaherty DK, Szostak JW, Šponer J, Góra RW, Sasselov DD, Szabla R. Ribose Alters the Photochemical Properties of the Nucleobase in Thionated Nucleosides. J Phys Chem Lett 2021; 12:6707-6713. [PMID: 34260253 PMCID: PMC9634911 DOI: 10.1021/acs.jpclett.1c01384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Substitution of exocyclic oxygen with sulfur was shown to substantially influence the properties of RNA/DNA bases, which are crucial for prebiotic chemistry and photodynamic therapies. Upon UV irradiation, thionucleobases were shown to efficiently populate triplet excited states and can be involved in characteristic photochemistry or generation of singlet oxygen. Here, we show that the photochemistry of a thionucleobase can be considerably modified in a nucleoside, that is, by the presence of ribose. Our transient absorption spectroscopy experiments demonstrate that thiocytosine exhibits 5 times longer excited-state lifetime and different excited-state absorption features than thiocytidine. On the basis of accurate quantum chemical simulations, we assign these differences to the dominant population of a shorter-lived triplet nπ* state in the nucleoside and longer-lived triplet ππ* states in the nucleobase. This explains the distinctive photoanomerziation of thiocytidine and indicates that the nucleoside will be a less efficient phototherapeutic agent with regard to singlet oxygen generation.
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Affiliation(s)
- Mikołaj
J. Janicki
- Department
of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego
27, 50-370 Wrocław, Poland
| | - Corinna L. Kufner
- Department
of Astronomy, Harvard-Smithsonian Center
for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, United States
| | - Zoe R. Todd
- Department
of Astronomy, Harvard-Smithsonian Center
for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, United States
| | - Seohyun C. Kim
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Derek K. O’Flaherty
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jiří Šponer
- Institute
of Biophysics, Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech
Republic
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacky
University Olomouc, Slechtitelu
241/27, 783 71 Olomouc-Holice, Czech Republic
| | - Robert W. Góra
- Department
of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego
27, 50-370 Wrocław, Poland
| | - Dimitar D. Sasselov
- Department
of Astronomy, Harvard-Smithsonian Center
for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, United States
| | - Rafał Szabla
- EaStCHEM,
School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, U.K.
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37
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Marsili E, Prlj A, Curchod BFE. Caveat when using ADC(2) for studying the photochemistry of carbonyl-containing molecules. Phys Chem Chem Phys 2021; 23:12945-12949. [PMID: 34085679 PMCID: PMC8207513 DOI: 10.1039/d1cp02185k] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/28/2021] [Indexed: 12/21/2022]
Abstract
Several electronic-structure methods are available to study the photochemistry and photophysics of organic molecules. Among them, ADC(2) stands as a sweet spot between computational efficiency and accuracy. As a result, ADC(2) has recently seen its number of applications booming, in particular to unravel the deactivation pathways and photodynamics of organic molecules. Despite this growing success, we demonstrate here that care has to be taken when studying the nonradiative pathways of carbonyl-containing molecules, as ADC(2) appears to suffer from a systematic flaw.
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Affiliation(s)
| | - Antonio Prlj
- Department of Chemistry, Durham University, Durham DH1 3LE, UK.
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38
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Szabla R, Zdrowowicz M, Spisz P, Green NJ, Stadlbauer P, Kruse H, Šponer J, Rak J. 2,6-diaminopurine promotes repair of DNA lesions under prebiotic conditions. Nat Commun 2021; 12:3018. [PMID: 34021158 PMCID: PMC8139960 DOI: 10.1038/s41467-021-23300-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 04/20/2021] [Indexed: 01/04/2023] Open
Abstract
High-yielding and selective prebiotic syntheses of RNA and DNA nucleotides involve UV irradiation to promote the key reaction steps and eradicate biologically irrelevant isomers. While these syntheses were likely enabled by UV-rich prebiotic environment, UV-induced formation of photodamages in polymeric nucleic acids, such as cyclobutane pyrimidine dimers (CPDs), remains the key unresolved issue for the origins of RNA and DNA on Earth. Here, we demonstrate that substitution of adenine with 2,6-diaminopurine enables repair of CPDs with yields reaching 92%. This substantial self-repairing activity originates from excellent electron donating properties of 2,6-diaminopurine in nucleic acid strands. We also show that the deoxyribonucleosides of 2,6-diaminopurine and adenine can be formed under the same prebiotic conditions. Considering that 2,6-diaminopurine was previously shown to increase the rate of nonenzymatic RNA replication, this nucleobase could have played critical roles in the formation of functional and photostable RNA/DNA oligomers in UV-rich prebiotic environments. UV-induced photodamage that likely occurred during the prebiotic synthesis of DNA and RNA is still an untackled issue for their origin on early Earth. Here, the authors show that substitution of 2,6-diaminopurine for adenine enables repair of cyclobutane pyrimidine dimers with high yields, and demonstrate that both 2,6-diaminopurine and adenine nucleosides can be formed under the same prebiotic conditions.
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Affiliation(s)
- Rafał Szabla
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK. .,Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
| | | | - Paulina Spisz
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | | | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Janusz Rak
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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39
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Pápai M, Li X, Nielsen MM, Møller KB. Trajectory surface-hopping photoinduced dynamics from Rydberg states of trimethylamine. Phys Chem Chem Phys 2021; 23:10964-10977. [PMID: 33913464 DOI: 10.1039/d1cp00771h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We present a computational study on nonadiabatic excited-state dynamics initiated from the 3p Rydberg states of trimethylamine (TMA). We utilise a methodology based on full-dimensional (39 D) trajectory surface-hopping (TSH) simulations, in which propagation is carried out on on-the-fly density functional theory (DFT)/time-dependent DFT (TD-DFT) potentials. Both our electronic structure benchmarks to high-level ab initio methods (EOM-CCSD, CASPT2) and TSH simulations demonstrate high-accuracy of the applied CAM-B3LYP functional for the description of Rydberg excited states. Based on our excited-state simulations, we construct the following mechanistic picture: when pumped resonantly to the 3p Rydberg manifold, TMA coherently vibrates along the planarisation mode with a period of 104 fs and an exponential coherence decay time constant of 240 fs. Nonadiabatic dynamics occur on a faster (∼1 ps) and a slower (∼3 ps) timescale, along the N-C stretching mode by mixing with a dissociative σN-C* state. As a minor relaxation channel, 3p → 3s internal conversion occurs via branching at the σN-C*/3s intersection. We find that photodissociaton is hardly observable within 3 ps (1%), which is a failure of the range-separated hybrid CAM-B3LYP functional, as a consequence of its static electron correlation deficiency at long range. In contrast, pure DFT (GGA-BLYP) provides an accurate long-range description (19% dissociation yield), also supported by comparison to recent ultrafast experiments, even if the Rydberg state energies are significantly underestimated (>1 eV). Finally, we reveal the crucial role of vibrational coherence and energy transfer from the planarisation mode for N-C bond activation and resulting nonadiabatic dynamics. The present work illustrates the importance of nuclear-electronic coupling for excited-state dynamics and branching at conical intersections.
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Affiliation(s)
- Mátyás Pápai
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark.
| | - Xusong Li
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark. and CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Martin M Nielsen
- Department of Physics, Technical University of Denmark, Fysikvej 307, DK-2800 Kongens Lyngby, Denmark
| | - Klaus B Møller
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark.
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40
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Barbatti M. Velocity Adjustment in Surface Hopping: Ethylene as a Case Study of the Maximum Error Caused by Direction Choice. J Chem Theory Comput 2021; 17:3010-3018. [PMID: 33844922 DOI: 10.1021/acs.jctc.1c00012] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The most common surface hopping dynamics algorithms require velocity adjustment after hopping to ensure total-energy conservation. Based on the semiclassical analysis, this adjustment must be made parallel to the nonadiabatic coupling vector's direction. Nevertheless, this direction is not always known, and the common practice has been to adjust the velocity in either the linear momentum or velocity directions. This paper benchmarks surface hopping dynamics of photoexcited ethylene with velocity adjustment in several directions, including those of the nonadiabatic coupling vector, the momentum, and the energy gradient difference. It is shown that differences in time constants and structural evolution fall within the statistical uncertainty of the method considering up to 500 trajectories in each dynamics set, rendering the three approaches statistically equivalent. For larger ensembles beyond 1000 trajectories, significant differences between the results arise, limiting the validity of adjustment in alternative directions. Other possible adjustment directions (velocity, single-state gradients, angular momentum) are evaluated as well. Given the small size of ethylene, the results reported in this paper should be considered an upper limit for the error caused by the choice of the velocity-adjustment direction on surface hopping dynamics.
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41
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Milovanović B, Novak J, Etinski M, Domcke W, Došlić N. Simulation of UV absorption spectra and relaxation dynamics of uracil and uracil-water clusters. Phys Chem Chem Phys 2021; 23:2594-2604. [PMID: 33475644 DOI: 10.1039/d0cp05618a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Despite many studies, the mechanisms of nonradiative relaxation of uracil in the gas phase and in aqueous solution are still not fully resolved. Here we combine theoretical UV absorption spectroscopy with nonadiabatic dynamics simulations to identify the photophysical mechanisms that can give rise to experimentally observed decay time constants. We first compute and theoretically assign the electronic spectra of uracil using the second-order algebraic-diagrammatic-construction (ADC(2)) method. The obtained electronic states, their energy differences and state-specific solvation effects are the prerequisites for understanding the photodynamics. We then use nonadiabatic trajectory-surface-hopping dynamics simulations to investigate the photoinduced dynamics of uracil and uracil-water clusters. In contrast to previous studies, we found that a single mechanism - the ethylenic twist around the C[double bond, length as m-dash]C bond - is responsible for the ultrafast component of the nonradiative decay, both in the gas phase and in solution. Very good agreement with the experimentally determined ultrashort decay time constants is obtained.
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Affiliation(s)
| | - Jurica Novak
- Department of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia. and Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Mihajlo Etinski
- University of Belgrade, Faculty of Physical Chemistry, Belgrade, Serbia
| | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Nađa Došlić
- Department of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.
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42
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Mawa I, Panda AN. Insights into the Excited-State Processes in 1-Hydroxy-2-acetonaphthone at ADC(2) and CASSCF Levels. J Phys Chem A 2021; 125:3015-3024. [PMID: 33818112 DOI: 10.1021/acs.jpca.1c02349] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
1-Hydroxy-2-acetonaphthone (HAN) has been extensively studied both experimentally and computationally to ascertain the existence of the excited-state proton transfer process. However, the process of full photocycle including the nonradiative relaxation pathways is yet to be proposed. Therefore, in the present study, we aim at providing a comprehensive picture of the excited-state processes in HAN including the proton transfer and relaxation processes through electronic structure calculations at second-order algebraic diagrammatic construction (ADC(2)) and complete active space second-order perturbation theory (CASPT2)//complete active space self-consistent field (CASSCF) and dynamics simulations at ADC(2) levels. Our studies show that the proton transfer process in the S1 state is barrierless and produces a stable keto form, which is in accordance with previous experimental and computational studies. Adiabatic dynamics simulations at the ADC(2) level confirmed the ultrafast process with an average proton transfer time of 43 fs. The resultant keto conformer then undergoes torsional rotation, leading to a conical intersection that mediates the internal conversion process to the ground state. Our dynamics simulation predicted that this deactivation process occurs at a time scale beyond 600 fs of simulation time. We also explored nonradiative relaxation from the enol Franck-Condon region, and this process was found to be improbable from the static point of view at both the ADC(2) and CASPT2 levels of theory due to a high energy barrier along the torsional coordinate.
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Affiliation(s)
- Ibanrishisha Mawa
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, India
| | - Aditya N Panda
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, India
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43
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Shahrokh L, Omidyan R, Azimi G. Theoretical insights on the excited-state-deactivation mechanisms of protonated thymine and cytosine. Phys Chem Chem Phys 2021; 23:8916-8925. [PMID: 33876051 DOI: 10.1039/d0cp06673g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Ab initio and surface-hopping nonadiabatic dynamics simulation methods were employed to investigate relaxation mechanisms in protonated thymine (TH+) and cytosine (CH+). A few conical intersections were located between 1ππ* and S0 states for each system with the CASSCF (8,8) theoretical model and relevant contributions to the deactivation mechanism of titled systems were addressed by the determination of potential energy profiles at the CASPT2 (12,10) theoretical level. It was revealed that the relaxation of the 1ππ* state of the most stable conformer of both systems to the ground state is mostly governed by the accessible S1/S0 conical intersection resulting from the barrier-free out-of-plane deformation. Interestingly, it was exhibited that the ring puckering coordinate driven from the C6 position of the heterocycle ring in TH+ and CH+ plays the most prominent role in the deactivation mechanism of considered systems. Our ab initio results are also supported by excited-state nonadiabatic dynamics simulations based on ADC(2), describing the ultrashort S1 lifetime of TH+/CH+ by analyzing trajectories leading excited systems to the ground. It was confirmed that the excited-state population mostly relaxes to the ground via the ring puckering coordinate from the C6 moiety. Overall, the theoretical results of this study shed light on the deactivation mechanism of protonated DNA bases.
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Affiliation(s)
- Leila Shahrokh
- Department of Chemistry, University of Isfahan, 81746-73441, Isfahan, Iran.
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44
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Uratani H, Yoshikawa T, Nakai H. Trajectory Surface Hopping Approach to Condensed-Phase Nonradiative Relaxation Dynamics Using Divide-and-Conquer Spin-Flip Time-Dependent Density-Functional Tight Binding. J Chem Theory Comput 2021; 17:1290-1300. [PMID: 33577323 DOI: 10.1021/acs.jctc.0c01155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nonradiative relaxation of excited molecules is central to many crucial issues in photochemistry. Condensed phases are typical contexts in which such problems are considered, and the nonradiative relaxation dynamics are expected to be significantly affected by interactions with the environment, for example, a solvent. We developed a nonadiabatic molecular dynamics simulation technique that can treat the nonradiative relaxation and explicitly include the environment in the calculations without a heavy computational burden. Specifically, we combined trajectory surface hopping with Tully's fewest-switches algorithm, a tight-binding approximated version of spin-flip time-dependent density-functional theory, and divide-and-conquer (DC) spatial fragmentation scheme. Numerical results showed that this method can treat systems with thousands of atoms within reasonable computational resources, and the error arising from DC fragmentation is negligibly small. Using this method, we obtained molecular insights into the solvent dependence of the photoexcited-state dynamics of trans-azobenzene, which demonstrate the importance of the environment for condensed-phase nonradiative relaxation.
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Affiliation(s)
- Hiroki Uratani
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Takeshi Yoshikawa
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan.,Waseda Research Institute for Science and Engineering (WISE), 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Waseda Research Institute for Science and Engineering (WISE), 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8245, Japan
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45
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Tsuru S, Vidal ML, Pápai M, Krylov AI, Møller KB, Coriani S. An assessment of different electronic structure approaches for modeling time-resolved x-ray absorption spectroscopy. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2021; 8:024101. [PMID: 33786337 PMCID: PMC7986275 DOI: 10.1063/4.0000070] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/11/2021] [Indexed: 05/06/2023]
Abstract
We assess the performance of different protocols for simulating excited-state x-ray absorption spectra. We consider three different protocols based on equation-of-motion coupled-cluster singles and doubles, two of them combined with the maximum overlap method. The three protocols differ in the choice of a reference configuration used to compute target states. Maximum-overlap-method time-dependent density functional theory is also considered. The performance of the different approaches is illustrated using uracil, thymine, and acetylacetone as benchmark systems. The results provide guidance for selecting an electronic structure method for modeling time-resolved x-ray absorption spectroscopy.
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Affiliation(s)
- Shota Tsuru
- DTU Chemistry, Technical University of Denmark, Kemitorvet Building 207, DK-2800 Kgs. Lyngby, Denmark
| | - Marta L. Vidal
- DTU Chemistry, Technical University of Denmark, Kemitorvet Building 207, DK-2800 Kgs. Lyngby, Denmark
| | - Mátyás Pápai
- DTU Chemistry, Technical University of Denmark, Kemitorvet Building 207, DK-2800 Kgs. Lyngby, Denmark
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Klaus B. Møller
- DTU Chemistry, Technical University of Denmark, Kemitorvet Building 207, DK-2800 Kgs. Lyngby, Denmark
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, Kemitorvet Building 207, DK-2800 Kgs. Lyngby, Denmark
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46
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Jankowska J, Góra RW. Ultrafast nonradiative deactivation of photoexcited 8-oxo-hypoxanthine: a nonadiabatic molecular dynamics study. Phys Chem Chem Phys 2021; 23:1234-1241. [PMID: 33355573 DOI: 10.1039/d0cp05271j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In the scientific endeavor to understand the chemical origins of life, the photochemistry of the smallest life building blocks, nucleobases, has been a constant object of focus and intense research. Here, we report the results of the first theoretical study on the photo-properties of an 8-oxo-hypoxanthine molecule, the chromophore of 8-oxo-inosine, which is relevant to the recently proposed, prebiotically plausible synthetic routes to the formation of purine- and pyrimidine-nucleotides. With ab initio and semi-empirical OM2/MRCI quantum-chemistry calculations, we predict a strong photostability of the 8-oxo-hypoxanthine system and see the origin of this effect in ultrafast nonradiative relaxation through puckering of the 6-membered heterocyclic ring.
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Affiliation(s)
- Joanna Jankowska
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland.
| | - Robert W Góra
- Department of Physical and Quantum Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
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47
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Vela S, Corminboeuf C. The Photoisomerization Pathway(s) of Push-Pull Phenylazoheteroarenes*. Chemistry 2020; 26:14724-14729. [PMID: 32692427 PMCID: PMC7756763 DOI: 10.1002/chem.202002321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/17/2020] [Indexed: 12/31/2022]
Abstract
Azoheteroarenes are the most recent derivatives targeted to further improve the properties of azo-based photoswitches. Their light-induced mechanism for trans-cis isomerization is assumed to be very similar to that of the parent azobenzene. As such, they inherited the controversy about the dominant isomerization pathway (rotation vs. inversion) depending on the excited state (nπ* vs. ππ*). Although the controversy seems settled in azobenzene, the extent to which the same conclusions apply to the more structurally diverse family of azoheteroarenes is unclear. Here, by means of non-adiabatic molecular dynamics, the photoisomerization mechanism of three prototypical phenyl-azoheteroarenes with increasing push-pull character is unraveled. The evolution of the rotational and inversion conical intersection energies, the preferred pathway, and the associated kinetics upon both nπ* and ππ* excitations can be linked directly with the push-pull substitution effects. Overall, the working conditions of this family of azo-dyes is clarified and a possibility to exploit push-pull substituents to tune their photoisomerization mechanism is identified, with potential impact on their quantum yield.
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Affiliation(s)
- Sergi Vela
- Institute of Chemical Sciences and EngineeringLaboratory for Computational Molecular DesignÉcole Polytechnique Fédérale de Lausanne (EPFL)1015LausanneSwitzerland
| | - Clémence Corminboeuf
- Institute of Chemical Sciences and EngineeringLaboratory for Computational Molecular DesignÉcole Polytechnique Fédérale de Lausanne (EPFL)1015LausanneSwitzerland
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48
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Uratani H, Morioka T, Yoshikawa T, Nakai H. Fast Nonadiabatic Molecular Dynamics via Spin-Flip Time-Dependent Density-Functional Tight-Binding Approach: Application to Nonradiative Relaxation of Tetraphenylethylene with Locked Aromatic Rings. J Chem Theory Comput 2020; 16:7299-7313. [PMID: 33197192 DOI: 10.1021/acs.jctc.0c00936] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Nonadiabatic dynamics around conical intersections between ground and excited states are crucial to understand excited-state phenomena in complex chemical systems. With this background in mind, we present an approach combining fewest-switches trajectory surface hopping and spin-flip (SF) time-dependent (TD) density-functional tight binding (DFTB), which is a simplified version of SF-TD density functional theory (DFT) with semiempirical parametrizations, for computationally efficient nonadiabatic molecular dynamics simulations. The estimated computational time of the SF-TD-DFTB approach is several orders of magnitude lower than that of SF-TD-DFT. In addition, the proposed method reproduces the time scales and quantum yields in photoisomerization reactions of azobenzene at a level comparable with conventional ab initio approaches, demonstrating reasonable accuracy. Finally, we report a practical application of the developed technique to explore the nonradiative relaxation processes of tetraphenylethylene and its derivative with torsionally locked aromatic rings and discuss the effect of locking the rings on the excited-state lifetime.
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Affiliation(s)
- Hiroki Uratani
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Toshiki Morioka
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Takeshi Yoshikawa
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan.,Waseda Research Institute for Science and Engineering (WISE), 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1, Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Waseda Research Institute for Science and Engineering (WISE), 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8245, Japan
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49
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Parker SM, Schiltz CJ. Surface hopping with cumulative probabilities: Even sampling and improved reproducibility. J Chem Phys 2020; 153:174109. [DOI: 10.1063/5.0024372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Shane M. Parker
- Department of Chemistry, Case Western Reserve University, 10800 Euclid Ave., Cleveland, Ohio 44106, USA
| | - Colin J. Schiltz
- Department of Chemistry, Case Western Reserve University, 10800 Euclid Ave., Cleveland, Ohio 44106, USA
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50
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Conti I, Cerullo G, Nenov A, Garavelli M. Ultrafast Spectroscopy of Photoactive Molecular Systems from First Principles: Where We Stand Today and Where We Are Going. J Am Chem Soc 2020; 142:16117-16139. [PMID: 32841559 PMCID: PMC7901644 DOI: 10.1021/jacs.0c04952] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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Computational spectroscopy is becoming a mandatory tool for the interpretation of the
complex, and often congested, spectral maps delivered by modern non-linear multi-pulse
techniques. The fields of Electronic Structure Methods,
Non-Adiabatic Molecular Dynamics, and Theoretical
Spectroscopy represent the three pillars of the virtual ultrafast
optical spectrometer, able to deliver transient spectra in
silico from first principles. A successful simulation strategy requires a
synergistic approach that balances between the three fields, each one having its very
own challenges and bottlenecks. The aim of this Perspective is to demonstrate that,
despite these challenges, an impressive agreement between theory and experiment is
achievable now regarding the modeling of ultrafast photoinduced processes in complex
molecular architectures. Beyond that, some key recent developments in the three fields
are presented that we believe will have major impacts on spectroscopic simulations in
the very near future. Potential directions of development, pending challenges, and
rising opportunities are illustrated.
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Affiliation(s)
- Irene Conti
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Giulio Cerullo
- Dipartimento di Fisica, Politecnico di Milano, IFN-CNR, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
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