1
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Cuéllar-Zuquin J, Pepino AJ, Fdez. Galván I, Rivalta I, Aquilante F, Garavelli M, Lindh R, Segarra-Martí J. Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size. J Chem Theory Comput 2023; 19:8258-8272. [PMID: 37882796 PMCID: PMC10851440 DOI: 10.1021/acs.jctc.3c00577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) algorithms. We benchmark two different basis set contractions and several active spaces for each nucleobase and conical intersection type, measuring for the first time how active space size affects conical intersection topographies in these systems and the potential implications these may have toward their description of photoinduced phenomena. Our results show that conical intersection topographies are highly sensitive to the electron correlation included in the model: by changing the amount (and type) of correlated orbitals, conical intersection topographies vastly change, and the changes observed do not follow any converging pattern toward the topographies obtained with the largest and most correlated active spaces. Comparison across systems shows analogous topographies for almost all intersections mediating population transfer to the dark 1nO/Nπ* states, while no similarities are observed for the "ethylene-like" conical intersection ascribed to mediate the ultrafast decay component to the ground state in all DNA/RNA nucleobases. Basis set size seems to have a minor effect, appearing to be relevant only for purine-based derivatives. We rule out structural changes as a key factor in classifying the different conical intersections, which display almost identical geometries across active space and basis set change, and we highlight instead the importance of correctly describing the electronic states involved at these crossing points. Our work shows that careful active space selection is essential to accurately describe conical intersection topographies and therefore to adequately account for their active role in molecular photochemistry.
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Affiliation(s)
- Juliana Cuéllar-Zuquin
- Instituto
de Ciencia Molecular, Universitat de Valencia, P.O. Box 22085, ES-46071 Valencia, Spain
| | - Ana Julieta Pepino
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Ignacio Fdez. Galván
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Ivan Rivalta
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
- ENSL,
CNRS, Laboratoire de Chimie UMR 5182, 46 Allée d’Italie, 69364 Lyon, France
| | - Francesco Aquilante
- Theory
and Simulation of Materials (THEOS), and National Centre for Computational
Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Marco Garavelli
- Dipartimento
di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Roland Lindh
- Department
of Chemistry − BMC, Uppsala University, P.O. Box 576, SE-75123 Uppsala, Sweden
| | - Javier Segarra-Martí
- Instituto
de Ciencia Molecular, Universitat de Valencia, P.O. Box 22085, ES-46071 Valencia, Spain
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2
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Biswas S, Kim J, Zhang X, Scholes GD. Coherent Two-Dimensional and Broadband Electronic Spectroscopies. Chem Rev 2022; 122:4257-4321. [PMID: 35037757 DOI: 10.1021/acs.chemrev.1c00623] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Over the past few decades, coherent broadband spectroscopy has been widely used to improve our understanding of ultrafast processes (e.g., photoinduced electron transfer, proton transfer, and proton-coupled electron transfer reactions) at femtosecond resolution. The advances in femtosecond laser technology along with the development of nonlinear multidimensional spectroscopy enabled further insights into ultrafast energy transfer and carrier relaxation processes in complex biological and material systems. New discoveries and interpretations have led to improved design principles for optimizing the photophysical properties of various artificial systems. In this review, we first provide a detailed theoretical framework of both coherent broadband and two-dimensional electronic spectroscopy (2DES). We then discuss a selection of experimental approaches and considerations of 2DES along with best practices for data processing and analysis. Finally, we review several examples where coherent broadband and 2DES were employed to reveal mechanisms of photoinitiated ultrafast processes in molecular, biological, and material systems. We end the review with a brief perspective on the future of the experimental techniques themselves and their potential to answer an even greater range of scientific questions.
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Affiliation(s)
- Somnath Biswas
- Department of Chemistry, Princeton University, Princeton, New Jersey 08 544, United States
| | - JunWoo Kim
- Department of Chemistry, Princeton University, Princeton, New Jersey 08 544, United States
| | - Xinzi Zhang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08 544, United States
| | - Gregory D Scholes
- Department of Chemistry, Princeton University, Princeton, New Jersey 08 544, United States
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3
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Segarra‐Martí J, Bearpark MJ. Modelling Photoionisation in Isocytosine: Potential Formation of Longer-Lived Excited State Cations in its Keto Form. Chemphyschem 2021; 22:2172-2181. [PMID: 34370368 PMCID: PMC8597144 DOI: 10.1002/cphc.202100402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/09/2021] [Indexed: 11/24/2022]
Abstract
Studying the effects of UV and VUV radiation on non-canonical DNA/RNA nucleobases allows us to compare how they release excess energy following absorption with respect to their canonical counterparts. This has attracted much research attention in recent years because of its likely influence on the origin of our genetic lexicon in prebiotic times. Here we present a CASSCF and XMS-CASPT2 theoretical study of the photoionisation of non-canonical pyrimidine nucleobase isocytosine in both its keto and enol tautomeric forms. We analyse their lowest energy cationic excited states including 2 π + , 2 n O + and 2 n N + and compare these to the corresponding electronic states in cytosine. Investigating lower-energy decay pathways we find - unexpectedly - that keto-isocytosine+ presents a sizeable energy barrier potentially inhibiting decay to its cationic ground state, whereas enol-isocytosine+ features a barrierless and consequently ultrafast pathway analogous to the one previously found for the canonical (keto) form of cytosine+ . Dynamic electron correlation reduces the energy barrier in the keto form substantially (by ∼1 eV) but it is nevertheless still present. We additionally compute the UV/Vis absorption signals of the structures encountered along these decay channels to provide spectroscopic fingerprints to assist future experiments in monitoring these intricate photo-processes.
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Affiliation(s)
- Javier Segarra‐Martí
- Department of ChemistryMolecular Sciences Research HubImperial College LondonWhite City Campus, 82 Wood LaneLondonW12 0BZUK
- Present address: Instituto de Ciencia MolecularUniversitat de ValenciaP.O. Box 22085ES-46071ValenciaSpain
| | - Michael J. Bearpark
- Department of ChemistryMolecular Sciences Research HubImperial College LondonWhite City Campus, 82 Wood LaneLondonW12 0BZUK
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4
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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: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
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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5
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Yang F, Chu T, Zhang Y, Liu X, Sun G, Chen Z. Quality assessment of licorice (Glycyrrhiza glabra L.) from different sources by multiple fingerprint profiles combined with quantitative analysis, antioxidant activity and chemometric methods. Food Chem 2020; 324:126854. [DOI: 10.1016/j.foodchem.2020.126854] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022]
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6
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Maiuri M, Garavelli M, Cerullo G. Ultrafast Spectroscopy: State of the Art and Open Challenges. J Am Chem Soc 2019; 142:3-15. [DOI: 10.1021/jacs.9b10533] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margherita Maiuri
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale, Università degli Studi di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
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7
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Duchi M, O'Hagan MP, Kumar R, Bennie SJ, Galan MC, Curchod BFE, Oliver TAA. Exploring ultraviolet photoinduced charge-transfer dynamics in a model dinucleotide of guanine and thymine. Phys Chem Chem Phys 2019; 21:14407-14417. [PMID: 30869082 DOI: 10.1039/c8cp07864e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An understanding of the initial photoexcited states of DNA is essential to unravelling deleterious photoinduced chemical reactions and the intrinsic ultrafast photoprotection of the genetic code for all life. In our combined experimental and theoretical study, we have elucidated the primary non-radiative relaxation dynamics of a model nucleotide of guanine and thymine (2'-deoxyguanosine 3'-monophosphate 5'-thymidine, d(GpT)) in buffered aqueous solution. Experimentally, we unequivocally demonstrate that the Franck-Condon excited states of d(GpT) are significantly delocalised across both nucleobases, and mediate d(G+pT-) exciplex product formation on an ultrafast (<350 fs) timescale. Theoretical studies show that the nature of the vertical excited states is very dependent on the specific geometry of the dinucleotide, and dictate the degree of delocalised, charge-transfer or localised character. Our mechanism for prompt exciplex formation involves a rapid change in electronic structure and includes a diabatic surface crossing very close to the Franck-Condon region mediating fast d(G+pT-) formation. Exciplexes are quickly converted back to neutral ground state molecules on a ∼10 ps timescale with a high quantum yield, ensuring the photostability of the nucleotide sequence.
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Affiliation(s)
- Marta Duchi
- School of Chemistry, Cantock's University of Bristol, Bristol, BS8 1TS, UK.
| | - Michael P O'Hagan
- School of Chemistry, Cantock's University of Bristol, Bristol, BS8 1TS, UK.
| | - Rhea Kumar
- School of Chemistry, Cantock's University of Bristol, Bristol, BS8 1TS, UK.
| | - Simon J Bennie
- School of Chemistry, Cantock's University of Bristol, Bristol, BS8 1TS, UK.
| | - M Carmen Galan
- School of Chemistry, Cantock's University of Bristol, Bristol, BS8 1TS, UK.
| | - Basile F E Curchod
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK
| | - Thomas A A Oliver
- School of Chemistry, Cantock's University of Bristol, Bristol, BS8 1TS, UK.
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8
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Abstract
After presenting the basic theoretical models of excitation energy transfer and charge transfer, I describe some of the novel experimental methods used to probe them. Finally, I discuss recent results concerning ultrafast energy and charge transfer in biological systems, in chemical systems and in photovoltaics based on sensitized transition metal oxides.
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Affiliation(s)
- Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC, Lausanne Centre for Ultrafast Science (LACUS), FSB, Station 6, CH-1015 Lausanne, Switzerland.
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9
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Segarra‐Martí J, Tran T, Bearpark MJ. Computing the Ultrafast and Radiationless Electronic Excited State Decay of Cytosine and 5‐methyl‐cytosine Cations: Uncovering the Role of Dynamic Electron Correlation. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Javier Segarra‐Martí
- Department of Chemistry, Molecular Sciences Research HubImperial College London White City Campus, 80 Wood Lane W12 0BZ London UK
| | - Thierry Tran
- Department of Chemistry, Molecular Sciences Research HubImperial College London White City Campus, 80 Wood Lane W12 0BZ London UK
| | - Michael J. Bearpark
- Department of Chemistry, Molecular Sciences Research HubImperial College London White City Campus, 80 Wood Lane W12 0BZ London UK
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10
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Segarra-Martí J, Tran T, Bearpark MJ. Ultrafast and radiationless electronic excited state decay of uracil and thymine cations: computing the effects of dynamic electron correlation. Phys Chem Chem Phys 2019; 21:14322-14330. [PMID: 30698175 DOI: 10.1039/c8cp07189f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In this article we characterise the radiationless decay of the first few electronic excited states of the cations of DNA/RNA nucleobases uracil and thymine, including the effects of dynamic electron correlation on energies and geometries (optimised with XMS-CASPT2). In both systems, we find that one state of 2n and another two of 2π+ character can be populated following photoionisation, and their different minima and interstate crossings are located. We find strong similarities between uracil and thymine cations: with accessible conical intersections suggesting that depopulation of their electronic excited states takes place on ultrafast timescales in both systems, suggesting that they are photostable in agreement with previous theoretical (uracil+) evidence. We find that dynamic electron correlation separates the energy levels of the "3-state" conical intersection (D2/D1/D0)CI previously located with CASSCF for uracil+, which will therefore have a different geometry and higher energy. Simulating the electronic and vibrational absorptions allows us to characterise spectral fingerprints that could be used to monitor these cation photo-processes experimentally.
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Affiliation(s)
- Javier Segarra-Martí
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, W12 0BZ, London, UK.
| | - Thierry Tran
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, W12 0BZ, London, UK.
| | - Michael J Bearpark
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, W12 0BZ, London, UK.
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11
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Borrego-Varillas R, Nenov A, Ganzer L, Oriana A, Manzoni C, Tolomelli A, Rivalta I, Mukamel S, Garavelli M, Cerullo G. Two-dimensional UV spectroscopy: a new insight into the structure and dynamics of biomolecules. Chem Sci 2019. [DOI: 10.1039/c9sc03871j] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Two-dimensional ultraviolet spectroscopy has the potential to deliver rich structural and dynamical information on biomolecules such as DNA and proteins.
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Affiliation(s)
| | - A. Nenov
- Dipartimento di Chimica Industriale
- Universitá degli Studi di Bologna
- I-40136 Bologna
- Italy
| | - L. Ganzer
- IFN-CNR
- Dipartimento di Fisica
- Politecnico di Milano
- I-20133 Milano
- Italy
| | - A. Oriana
- IFN-CNR
- Dipartimento di Fisica
- Politecnico di Milano
- I-20133 Milano
- Italy
| | - C. Manzoni
- IFN-CNR
- Dipartimento di Fisica
- Politecnico di Milano
- I-20133 Milano
- Italy
| | - A. Tolomelli
- Dipartimento di Chimica
- Universitá degli Studi di Bologna
- I-40126 Bologna
- Italy
| | - I. Rivalta
- Dipartimento di Chimica Industriale
- Universitá degli Studi di Bologna
- I-40136 Bologna
- Italy
| | - S. Mukamel
- Department of Chemistry
- Department of Physics and Astronomy
- University of California
- Irvine
- USA
| | - M. Garavelli
- Dipartimento di Chimica Industriale
- Universitá degli Studi di Bologna
- I-40136 Bologna
- Italy
| | - G. Cerullo
- IFN-CNR
- Dipartimento di Fisica
- Politecnico di Milano
- I-20133 Milano
- Italy
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12
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Giussani A, Worth GA. Similar chemical structures, dissimilar triplet quantum yields: a CASPT2 model rationalizing the trend of triplet quantum yields in nitroaromatic systems. Phys Chem Chem Phys 2019; 21:10514-10522. [DOI: 10.1039/c9cp00705a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
S1/S0 accessibility strongly influences the triplet quantum yields of nitronaphthalenes.
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Affiliation(s)
- Angelo Giussani
- Department of Chemistry
- University College London
- London WC1H 0AJ
- UK
| | - Graham A. Worth
- Department of Chemistry
- University College London
- London WC1H 0AJ
- UK
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13
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Pepino AJ, Segarra-Martí J, Nenov A, Rivalta I, Improta R, Garavelli M. UV-induced long-lived decays in solvated pyrimidine nucleosides resolved at the MS-CASPT2/MM level. Phys Chem Chem Phys 2018; 20:6877-6890. [PMID: 29459916 DOI: 10.1039/c7cp08235e] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The most relevant 'dark' electronic excited states in DNA/RNA pyrimidine nucleosides are mapped in water employing hybrid MS-CASPT2/MM optimisations with explicit solvation and including the sugar. Conical intersections (CIs) between initially accessed bright 1ππ* and the lowest energy dark 1nπ* excited states, involving the lone pair localised on the oxygen and/or nitrogen atoms are characterised. They are found in the vicinities of the Franck-Condon (FC) region and are shown to facilitate non-adiabatic population transfer. The excited state population of the 1nOπ* state, localised in the carbonyl moiety on all pyrimidine nucleosides, is predicted to rapidly evolve to its minimum, displaying non-negligible potential energy barriers along its non-radiative decay, and accounting for the ps signal registered in pump-probe experiments as well as for an efficient population of the triplet state. Cytidine displays an additional 1nNπ* state localised in the N3 atom and that leads to its excited state minimum displaying large potential energy barriers in the pathway connecting to the CI with the ground state. Sugar-to-base hydrogen/proton transfer processes are assessed in solution for the first time, displaying a sizable barrier along its decay and thus being competitive with other slow decay channels in the ps and ns timescales. A unified deactivation scheme for the long-lived channels of pyrimidine nucleosides is delivered, where the 1nOπ* state is found to mediate the long-lived decay in the singlet manifold and act as the doorway for triplet population and thus accounting for the recorded phosphorescence and, more generally, for the transient/photoelectron spectral signals registered up to the ns timescale.
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Affiliation(s)
- Ana Julieta Pepino
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy.
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15
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Towards Accurate Simulation of Two-Dimensional Electronic Spectroscopy. Top Curr Chem (Cham) 2018; 376:24. [DOI: 10.1007/s41061-018-0201-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/24/2018] [Indexed: 10/14/2022]
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16
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Segarra-Martí J, Zvereva E, Marazzi M, Brazard J, Dumont E, Assfeld X, Haacke S, Garavelli M, Monari A, Léonard J, Rivalta I. Resolving the Singlet Excited State Manifold of Benzophenone by First-Principles Simulations and Ultrafast Spectroscopy. J Chem Theory Comput 2018; 14:2570-2585. [DOI: 10.1021/acs.jctc.7b01208] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Javier Segarra-Martí
- Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342, Lyon, France
| | - Elena Zvereva
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
- A. E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific CentreRussian Academy of Sciences, Arbuzov str. 8, 420088 Kazan, Russia
| | - Marco Marazzi
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
| | - Johanna Brazard
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg and Labex NIE, UMR 7504, F-67000 Strasbourg, France
| | - Elise Dumont
- Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342, Lyon, France
| | - Xavier Assfeld
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
| | - Stefan Haacke
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg and Labex NIE, UMR 7504, F-67000 Strasbourg, France
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”, Università di Bologna, Viale del Risorgimento 4, I-40136 Bologna, Italy
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
| | - Jérémie Léonard
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg and Labex NIE, UMR 7504, F-67000 Strasbourg, France
| | - Ivan Rivalta
- Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342, Lyon, France
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17
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The highly excited-state manifold of guanine: calibration for nonlinear electronic spectroscopy simulations. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2225-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Zvereva E, Segarra-Martí J, Marazzi M, Brazard J, Nenov A, Weingart O, Léonard J, Garavelli M, Rivalta I, Dumont E, Assfeld X, Haacke S, Monari A. The effect of solvent relaxation in the ultrafast time-resolved spectroscopy of solvated benzophenone. Photochem Photobiol Sci 2018; 17:323-331. [DOI: 10.1039/c7pp00439g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Modeling time-resolved spectra to unravel ultra fast solvent reorganization.
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19
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Segarra-Martí J, Jaiswal VK, Pepino AJ, Giussani A, Nenov A, Mukamel S, Garavelli M, Rivalta I. Two-dimensional electronic spectroscopy as a tool for tracking molecular conformations in DNA/RNA aggregates. Faraday Discuss 2018; 207:233-250. [DOI: 10.1039/c7fd00201g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A computational strategy to simulate two-dimensional electronic spectra (2DES) is introduced, which allows characterising ground state conformations of flexible nucleobase aggregates that play a crucial role in nucleic acid photochemistry.
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Affiliation(s)
- Javier Segarra-Martí
- Univ Lyon, Ens de Lyon, CNRS
- Université Claude Bernard Lyon 1
- Laboratoire de Chimie UMR 5182
- Lyon
- France
| | - Vishal K. Jaiswal
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Italy
| | - Ana Julieta Pepino
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Italy
| | - Angelo Giussani
- Department of Chemistry
- University College London
- London WC1H 0AJ
- UK
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Italy
| | - Shaul Mukamel
- Department of Chemistry
- University of California
- Irvine
- USA
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”
- Università di Bologna
- Italy
| | - Ivan Rivalta
- Univ Lyon, Ens de Lyon, CNRS
- Université Claude Bernard Lyon 1
- Laboratoire de Chimie UMR 5182
- Lyon
- France
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20
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Giussani A, Marcheselli J, Mukamel S, Garavelli M, Nenov A. On the Simulation of Two-dimensional Electronic Spectroscopy of Indole-containing Peptides. Photochem Photobiol 2017; 93:1368-1380. [PMID: 28380692 DOI: 10.1111/php.12770] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/27/2017] [Indexed: 01/27/2023]
Abstract
A benchmark study of low-cost multiconfigurational CASSCF/CASPT2 schemes for computing the electronic structure of indole is presented. This facilitates the simulation of near-ultraviolet (UV) pump visible (VIS) probe (i.e. two-color) two-dimensional electronic spectra (2DES) of homo- and hetero-aggregates as well as for processing of multiple snapshots from molecular dynamics simulations. Fingerprint excited-state absorption signatures of indole are identified in a broad spectral window between 10 and 25 k cm-1 . The 18-24 k cm-1 spectral window which has no absorption of the monomer and noninteracting aggregates is ideally suited to embed charge-transfer signatures in stacked aggregates. The small peptide Trp-cage, containing a tryptophan and a tyrosine amino acids, having indole and phenol as side chains, respectively, serves to prove the concept. Clear charge-transfer signatures are found in the proposed spectral window for an interchromophore distance of 5 Å making near-UV pump VIS probe 2DES a suitable technique for resolving closely packed aggregates. We demonstrate that 2DES utilizing ultra-short pulses has the potential to resolve the nature of the spectroscopically resolved electronic states and that the line shapes of the excited-state absorption signals can be correlated to the polarity of the relevant states.
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Affiliation(s)
- Angelo Giussani
- Dipartimento di Chimica "G. Ciamician", Università degli Studi di Bologna, Bologna, Italy
| | | | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, CA
| | - Marco Garavelli
- Dipartimento di Chimica "G. Ciamician", Università degli Studi di Bologna, Bologna, Italy.,Dipartimento di Chimica Industriale "Toso Montanari", Universita degli Studi di Bologna, Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica "G. Ciamician", Università degli Studi di Bologna, Bologna, Italy.,Dipartimento di Chimica Industriale "Toso Montanari", Universita degli Studi di Bologna, Bologna, Italy
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21
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Giussani A, Worth GA. Insights into the Complex Photophysics and Photochemistry of the Simplest Nitroaromatic Compound: A CASPT2//CASSCF Study on Nitrobenzene. J Chem Theory Comput 2017; 13:2777-2788. [DOI: 10.1021/acs.jctc.6b01149] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Angelo Giussani
- School
of Chemistry, University of Birmingham, Edgbaston B15 2TT, U.K
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Graham A. Worth
- School
of Chemistry, University of Birmingham, Edgbaston B15 2TT, U.K
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
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22
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Pola M, Kochman MA, Picchiotti A, Prokhorenko VI, Miller RJD, Thorwart M. Linear photoabsorption spectra and vertical excitation energies of microsolvated DNA nucleobases in aqueous solution. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2017. [DOI: 10.1142/s0219633617500286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Employing density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations in combination with the semiclassical nuclear ensemble method, we have simulated the photoabsorption spectra of the four canonical DNA nucleobases in aqueous solution. In order to model the effects of solvation, for each nucleobase, a number of solvating water molecules were explicitly included in the simulations, and additionally, the bulk solvent was represented by a continuous polarizable medium. We find that the effect of the solvation shell in general is significant, and its inclusion improves the realism of the spectral simulations. The involvement of lone electron pairs in the hydrogen bonding with the solvating water molecules has the effect of systematically increasing the energies of vertical excitation into the [Formula: see text]-type states. Apart from a systematic blue shift of around [Formula: see text][Formula: see text]eV observed in the absorption peaks, the calculated photoabsorption spectra reproduce the measured ones with good accuracy. The photoabsorption spectra are dominated by excited states with [Formula: see text] and partial [Formula: see text] character. No low-energy charge transfer states are observed with the use of the CAM-B3LYP and M06-2X functionals.
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Affiliation(s)
- Martina Pola
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstraße 9, 20355 Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Michal A. Kochman
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Alessandra Picchiotti
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Valentyn I. Prokhorenko
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R. J. Dwayne Miller
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Michael Thorwart
- I. Institut für Theoretische Physik, Universität Hamburg, Jungiusstraße 9, 20355 Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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23
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Wu WJ, Li QS, Li ZS. Insights into the Thermal Eliminations and Photoeliminations of B,N-Heterocycles: A Theoretical Study. J Phys Chem A 2017; 121:753-761. [PMID: 28045528 DOI: 10.1021/acs.jpca.6b09495] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding the photochemistry of organoboron compounds is essential to expand optoelectronic applications. In this work, the complete active space self-consistent field (CASSCF) and its second-order perturbation (CASPT2) methods combining with density functional theory (DFT) have been employed to investigate the elimination mechanisms of compound 6,7-dihydro-54-benzo[d]pyrido[2,1-f][1,2]azaborininr (B4) on the ground state (S0) and the first excited state (S1). B4 is one of the 1,2-B,N-heterocycles that undergo competitive thermal elimination and photoelimination depending on the substitution groups on the B atom and the chelate backbone, thus providing a high-selectivity synthesis strategy for luminescent compounds. Since the energy barrier from B4 to BH3-pyrido[1,2-a]isoindole (D1) and pyrido[1,2-a]isoindole (A1) on the ground state is lower than that from B4 to 54-benzo[d]pyrido[2,1-f][1,2]azaborininr (C4), the retraction ring reaction is expected to proceed with larger probability than the H2 elimination upon heating. On the contrary, photoelimination of H2 may take place easily due to the almost barrierless pathway on the S1 state. Remarkably, we have located an energetically available conical intersection (S1/S0)X-1, which allows for ultrafast S1 → S0 decay and subsequently generation of C4. Our results not only throw light on the experimental observations of the selectivity of thermal elimination and photoelimination but also provide detailed information on the excited state as instructional implications for further synthesis and application of B,N-embedded aromatics.
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Affiliation(s)
- Wen-Jie Wu
- Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory for Chemical Power Source and Green Catalysis, School of Chemistry and Chemical Engineering, Beijing Institute of Technology , Beijing 100081, China
| | - Quan-Song Li
- Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory for Chemical Power Source and Green Catalysis, School of Chemistry and Chemical Engineering, Beijing Institute of Technology , Beijing 100081, China
| | - Ze-Sheng Li
- Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory for Chemical Power Source and Green Catalysis, School of Chemistry and Chemical Engineering, Beijing Institute of Technology , Beijing 100081, China
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24
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Marquetand P, Nogueira JJ, Mai S, Plasser F, González L. Challenges in Simulating Light-Induced Processes in DNA. Molecules 2016. [PMCID: PMC6155660 DOI: 10.3390/molecules22010049] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i) stationary quantum chemical computations; (ii) the explicit description of the initial excitation of DNA with light; (iii) modeling the nonadiabatic excited state dynamics; (iv) simulation of the detected experimental observable; and (v) the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments.
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25
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Borrego-Varillas R, Oriana A, Ganzer L, Trifonov A, Buchvarov I, Manzoni C, Cerullo G. Two-dimensional electronic spectroscopy in the ultraviolet by a birefringent delay line. OPTICS EXPRESS 2016; 24:28491-28499. [PMID: 27958492 DOI: 10.1364/oe.24.028491] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We introduce a 2D electronic spectroscopy setup in the UV spectral range in the partially collinear pump-probe geometry. The required interferometrically phase-locked few-optical-cycle UV pulse pair is generated by combining a passive birefringent interferometer in the visible and nonlinear phase transfer. This is achieved by sum-frequency generation between the phase-locked visible pulse pair and narrowband infrared pulses. We demonstrate a pair of 16-fs, 330-nm pulses whose delay is interferometrically stable with an accuracy better than λ/450. 2DUV maps of pyrene solution probed in the UV and visible spectral ranges are demonstrated.
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26
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Segarra-Martí J, Francés-Monerris A, Roca-Sanjuán D, Merchán M. Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2. Molecules 2016; 21:molecules21121666. [PMID: 27918489 PMCID: PMC6274573 DOI: 10.3390/molecules21121666] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/30/2016] [Accepted: 12/01/2016] [Indexed: 11/16/2022] Open
Abstract
The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess the accuracy of these different computational strategies under study based on a variety of numerical thresholds and optimization methods. Several basis sets and active spaces have also been calibrated to understand to what extent they can influence the resulting geometries and subsequent interpretation of the photochemical decay channels. The study shows small discrepancies between CASSCF and CASPT2 PEHs, displaying a shallow planar or twisted 1(ππ*) minimum, respectively, and thus featuring a qualitatively similar scenario for supporting the ultrafast bi-exponential deactivation registered in thymine upon UV-light exposure. A deeper knowledge of the PEHs at different levels of theory provides useful insight into its correct characterization and subsequent interpretation of the experimental observations. The discrepancies displayed by the different methods studied here are then discussed and framed within their potential consequences in on-the-fly non-adiabatic molecular dynamics simulations, where qualitatively diverse outcomes are expected.
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Affiliation(s)
- Javier Segarra-Martí
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
- Present Address: Laboratoire de Chimie UMR 5182, École Normale Supérieure de Lyon, CNRS, Université de Lyon, 46 Allée d'Italie, F-69364 Lyon Cedex 07, France.
| | - Antonio Francés-Monerris
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
| | - Manuela Merchán
- Instituto de Ciencia Molecular, Universitat de València, P. O. Box 22085, ES-46071 Valencia, Spain.
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