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Piteša T, Polonius S, González L, Mai S. Excitonic Configuration Interaction: Going Beyond the Frenkel Exciton Model. J Chem Theory Comput 2024; 20:5609-5634. [PMID: 38885637 DOI: 10.1021/acs.jctc.4c00157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
We present the excitonic configuration interaction (ECI) method─a fragment-based analogue of the CI method for electronic structure calculations of multichromophoric systems. It can also be viewed as a generalization of the exciton approach, with the following properties: (i) It constructs the effective Hamiltonian exclusively from monomer calculations. (ii) It employs the strong orthogonality assumption and is exact within McWeeny's group function theory, thus requiring only one-electron density matrices of the monomer states. (iii) It is agnostic of the monomer electronic structure method, allowing us to use/combine different methods. (iv) It includes an embedding point charge scheme (called excitonic Hartree-Fock, EHF) to improve the accuracy of the monomer states, but such that the effective full-system Hamiltonian is not explicitly dependent on the embedding. (v) It is systematically improvable, by expanding the set of monomer states and by including configurations where two or more monomers are excited (defining the ECIS, ECISD, etc., methods). The performance of ECI is assessed by computing the absorption spectrum of two exemplary multichromophoric systems, using CIS as the monomer electronic structure method. The accuracy of ECI significantly depends on the chosen embedding charges and the ECI expansion. The most accurate assessed combinations─ECIS or ECISD with EHF embedding─yield spectra that agree qualitatively and quantitatively with full-system direct calculations, with deviations of the excitation energies below 0.1 eV. We also show that ECISD based on CIS monomer calculations can predict states where two monomers are excited simultaneously (e.g., triplet-triplet double-local excitations) that are inaccessible in a full-system CIS calculation.
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Affiliation(s)
- Tomislav Piteša
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Severin Polonius
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna 1090, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
- Vienna Research Platform Accelerating Photoreaction Discovery, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
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2
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Martínez-Fernández L, Green JA, Esposito L, Jouybari MY, Zhang Y, Santoro F, Kohler B, Improta R. The photoactivated dynamics of dGpdC and dCpdG sequences in DNA: a comprehensive quantum mechanical study. Chem Sci 2024; 15:9676-9693. [PMID: 38939156 PMCID: PMC11206432 DOI: 10.1039/d4sc00910j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/04/2024] [Indexed: 06/29/2024] Open
Abstract
Study of alternating DNA GC sequences by different time-resolved spectroscopies has provided fundamental information on the interaction between UV light and DNA, a process of great biological importance. Multiple decay paths have been identified, but their interplay is still poorly understood. Here, we characterize the photophysics of GC-DNA by integrating different computational approaches, to study molecular models including up to 6 bases described at a full quantum mechanical level. Quantum dynamical simulations, exploiting a nonadiabatic linear vibronic coupling (LVC) model, coupled with molecular dynamics sampling of the initial structures of a (GC)5 DNA duplex, provide new insights into the photophysics in the sub-picosecond time-regime. They indicate a substantial population transfer, within 50 fs, from the spectroscopic states towards G → C charge transfer states involving two stacked bases (CTintra), thus explaining the ultrafast disappearance of fluorescence. This picture is consistent with that provided by quantum mechanical geometry optimizations, using time dependent-density functional theory and a polarizable continuum model, which we use to parametrize the LVC model and to map the main excited state deactivation pathways. For the first time, the infrared and excited state absorption signatures of the various states along these pathways are comprehensively mapped. The computational models suggest that the main deactivation pathways, which, according to experiment, lead to ground state recovery on the 10-50 ps time scale, involve CTintra followed by interstrand proton transfer from the neutral G to C-. Our calculations indicate that CTintra is populated to a larger extent and more rapidly in GC than in CG steps and suggest the likely involvement of monomer-like and interstrand charge transfer decay routes for isolated and less stacked CG steps. These findings underscore the importance of the DNA sequence and thermal fluctuations for the dynamics. They will also aid the interpretation of experimental results on other sequences.
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Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química Física de Materiales, Instituto de Química Física Blas Cabrera, CSIC 28006 Madrid Spain
| | - James Alexander Green
- Institut für Physikalische Theoretische Chemie, Goethe-Universität Frankfurt am Main Frankfurt am Main Germany
| | - Luciana Esposito
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR) Via De Amicis 95 I-80145 Napoli Italy
| | - Martha Yaghoubi Jouybari
- Department of Chemistry and Biomolecular Sciences, University of Ottawa 10 Marie Curie Ottawa Ontario K1N 6N5 Canada
- National Research Council of Canada 100 Sussex Drive Ottawa Ontario K1A 0R6 Canada
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR) Area della Ricerca del CNR, Via Moruzzi 1 I-56124 Pisa Italy
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University 100 West 18th Avenue Columbus Ohio 43210 USA
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR) Area della Ricerca del CNR, Via Moruzzi 1 I-56124 Pisa Italy
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University 100 West 18th Avenue Columbus Ohio 43210 USA
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR) Via De Amicis 95 I-80145 Napoli Italy
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3
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Choudhury A, Santra S, Ghosh D. Understanding the Photoprocesses in Biological Systems: Need for Accurate Multireference Treatment. J Chem Theory Comput 2024; 20:4951-4964. [PMID: 38864715 DOI: 10.1021/acs.jctc.4c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Light-matter interaction is crucial to life itself and revolves around many of the central processes in biology. The need for understanding these photochemical and photophysical processes cannot be overemphasized. Interaction of light with biological systems starts with the absorption of light and subsequent phenomena that occur in the excited states of the system. However, excited states are typically difficult to understand within the mean field approximation of quantum chemical methods. Therefore, suitable multireference methods and methodologies have been developed to understand these phenomena. In this Perspective, we will describe a few methods and methodologies suitable for these descriptions and discuss some persisting difficulties.
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Affiliation(s)
- Arpan Choudhury
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Supriyo Santra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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4
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Myers CA, Lu SY, Shedge S, Pyuskulyan A, Donahoe K, Khanna A, Shi L, Isborn CM. Axial H-Bonding Solvent Controls Inhomogeneous Spectral Broadening, While Peripheral H-Bonding Solvent Controls Vibronic Broadening: Cresyl Violet in Methanol. J Phys Chem B 2024; 128:5685-5699. [PMID: 38832562 DOI: 10.1021/acs.jpcb.4c01401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
The dynamics of the nuclei of both a chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore-solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore-solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both force field and ab initio molecular dynamics trajectories along with the inclusion of only certain solvent molecules in the excited-state calculations, we determine that the methanol molecules axial to the chromophore are responsible for the majority of inhomogeneous broadening, with a single methanol molecule that forms an axial hydrogen bond dominating the response. The strong peripheral hydrogen bonds do not contribute to spectral broadening, as they are very stable throughout the dynamics and do not lead to increased energy-gap fluctuations. We also find that treating the strong peripheral hydrogen bonds as molecular mechanical point charges during the molecular dynamics simulation underestimates the vibronic coupling. Including these peripheral hydrogen bonding methanol molecules in the quantum-mechanical region in a geometry optimization increases the vibronic coupling, suggesting that a more advanced treatment of these strongly interacting solvent molecules during the molecular dynamics trajectory may be necessary to capture the full vibronic spectral broadening.
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Affiliation(s)
- Christopher A Myers
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Shao-Yu Lu
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Sapana Shedge
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Arthur Pyuskulyan
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Katherine Donahoe
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Ajay Khanna
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Liang Shi
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Christine M Isborn
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
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5
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Betti E, Saraceno P, Cignoni E, Cupellini L, Mennucci B. Insights into Energy Transfer in Light-Harvesting Complex II Through Machine-Learning Assisted Simulations. J Phys Chem B 2024; 128:5188-5200. [PMID: 38761151 DOI: 10.1021/acs.jpcb.4c01494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
Light-harvesting complex II (LHCII) is the major antenna of higher plants. Energy transfer processes taking place inside its aggregate of chlorophylls have been experimentally investigated with time-resolved techniques, but a complete understanding of the most relevant energy transfer pathways and relative characteristic times remains elusive. Theoretical models to disentangle experimental data in LHCII have long been challenged by the large size and complex nature of the system. Here, we show that a fully first-principles approach combining molecular dynamics and machine learning can be successfully used to reproduce transient absorption spectra and characterize the EET pathways and the involved times.
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Affiliation(s)
- Elena Betti
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Piermarco Saraceno
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Edoardo Cignoni
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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6
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Runeson JE, Fay TP, Manolopoulos DE. Exciton dynamics from the mapping approach to surface hopping: comparison with Förster and Redfield theories. Phys Chem Chem Phys 2024; 26:4929-4938. [PMID: 38265093 PMCID: PMC10849040 DOI: 10.1039/d3cp05926j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
We compare the recently introduced multi-state mapping approach to surface hopping (MASH) with the Förster and Redfield theories of excitation energy transfer. Whereas Förster theory relies on weak coupling between chromophores, and Redfield theory assumes the electronic excitations to be weakly coupled to fast chromophore vibrations, MASH is free from any perturbative or Markovian approximations. We illustrate this with an example application to the rate of energy transfer in a Frenkel-exciton dimer, showing that MASH interpolates correctly between the opposing regimes in which the Förster and Redfield results are reliable. We then compare the three methods for a realistic model of the Fenna-Matthews-Olson complex with a structured vibrational spectral density and static disorder in the excitation energies. In this case there are no exact results for comparison so we use MASH to assess the validity of Förster and Redfield theories. We find that Förster theory is the more accurate of the two on the picosecond timescale, as has been shown previously for a simpler model of this particular light-harvesting complex. We also explore various ways to sample the initial electronic state in MASH and find that they all give very similar results for exciton dynamics.
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Affiliation(s)
- Johan E Runeson
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, UK.
| | - Thomas P Fay
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - David E Manolopoulos
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, UK.
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7
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Saraceno P, Sláma V, Cupellini L. First-principles simulation of excitation energy transfer and transient absorption spectroscopy in the CP29 light-harvesting complex. J Chem Phys 2023; 159:184112. [PMID: 37962444 DOI: 10.1063/5.0170295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
The dynamics of delocalized excitons in light-harvesting complexes (LHCs) can be investigated using different experimental techniques, and transient absorption (TA) spectroscopy is one of the most valuable methods for this purpose. A careful interpretation of TA spectra is essential for the clarification of excitation energy transfer (EET) processes occurring during light-harvesting. However, even in the simplest LHCs, a physical model is needed to interpret transient spectra as the number of EET processes occurring at the same time is very large to be disentangled from measurements alone. Physical EET models are commonly built by fittings of the microscopic exciton Hamiltonians and exciton-vibrational parameters, an approach that can lead to biases. Here, we present a first-principles strategy to simulate EET and transient absorption spectra in LHCs, combining molecular dynamics and accurate multiscale quantum chemical calculations to obtain an independent estimate of the excitonic structure of the complex. The microscopic parameters thus obtained are then used in EET simulations to obtain the population dynamics and the related spectroscopic signature. We apply this approach to the CP29 minor antenna complex of plants for which we follow the EET dynamics and transient spectra after excitation in the chlorophyll b region. Our calculations reproduce all the main features observed in the transient absorption spectra and provide independent insight on the excited-state dynamics of CP29. The approach presented here lays the groundwork for the accurate simulation of EET and unbiased interpretation of transient spectra in multichromophoric systems.
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Affiliation(s)
- Piermarco Saraceno
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Vladislav Sláma
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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8
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Zubova EA, Strelnikov IA. Experimental detection of conformational transitions between forms of DNA: problems and prospects. Biophys Rev 2023; 15:1053-1078. [PMID: 37974981 PMCID: PMC10643659 DOI: 10.1007/s12551-023-01143-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/06/2023] [Indexed: 11/19/2023] Open
Abstract
Under different conditions, the DNA double helix can take different geometric forms. Of the large number of its conformations, in addition to the "canonical" B form, the A, C, and Z forms are widely known, and the D, Hoogsteen, and X forms are less known. DNA locally takes the A, C, and Z forms in the cell, in complexes with proteins. We compare different methods for detecting non-canonical DNA conformations: X-ray, IR, and Raman spectroscopy, linear and circular dichroism in both the infrared and ultraviolet regions, as well as NMR (measurement of chemical shifts and their anisotropy, scalar and residual dipolar couplings and inter-proton distances from NOESY (nuclear Overhauser effect spectroscopy) data). We discuss the difficulties in applying these methods, the problems of theoretical interpretation of the experimental results, and the prospects for reliable identification of non-canonical DNA conformations.
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Affiliation(s)
- Elena A. Zubova
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin St., Moscow, 119991 Russia
| | - Ivan A. Strelnikov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin St., Moscow, 119991 Russia
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9
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Li J, Zeng T, Zhai Y, Qu Z, Li H. Intermolecular resonance energy transfer between two lutein pigments in light-harvesting complex II studied by frenkel exciton models. Phys Chem Chem Phys 2023; 25:24636-24642. [PMID: 37665609 DOI: 10.1039/d3cp03092j] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The energy transfer pathways in light-harvesting complex II are complicated and the discovery of the energy transfer between the two luteins revealed an unelucidated important role of carotenoids in the energy flow. This energy transfer between the two S2 states of luteins was for the first time investigated using Frenkel exciton models, using a hybrid scheme of molecular mechanics and quantum mechanics. The results show the energy flow between the two luteins under the Förster resonance energy transfer mechanism. The energy transfer caused by energy level resonance occurs in configurations with small energy gaps. This energy transfer pathway is particularly sensitive to conformation. Moreover, according to the statistical characteristics of the data of the energy gaps and coupling values between LUTs, we proposed stochastic exciton Hamiltonian models to facilitate clarification of the energy transfer among pigments in antenna complexes.
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Affiliation(s)
- Jiarui Li
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun, 130023, China.
| | - Tao Zeng
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Yu Zhai
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun, 130023, China.
| | - Zexing Qu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun, 130023, China.
| | - Hui Li
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun, 130023, China.
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10
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Michaelis M, Cupellini L, Mensch C, Perry CC, Delle Piane M, Colombi Ciacchi L. Tidying up the conformational ensemble of a disordered peptide by computational prediction of spectroscopic fingerprints. Chem Sci 2023; 14:8483-8496. [PMID: 37592980 PMCID: PMC10430726 DOI: 10.1039/d3sc02202a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/15/2023] [Indexed: 08/19/2023] Open
Abstract
The most advanced structure prediction methods are powerless in exploring the conformational ensemble of disordered peptides and proteins and for this reason the "protein folding problem" remains unsolved. We present a novel methodology that enables the accurate prediction of spectroscopic fingerprints (circular dichroism, infrared, Raman, and Raman optical activity), and by this allows for "tidying up" the conformational ensembles of disordered peptides and disordered regions in proteins. This concept is elaborated for and applied to a dodecapeptide, whose spectroscopic fingerprint is measured and theoretically predicted by means of enhanced-sampling molecular dynamics coupled with quantum mechanical calculations. Following this approach, we demonstrate that peptides lacking a clear propensity for ordered secondary-structure motifs are not randomly, but only conditionally disordered. This means that their conformational landscape, or phase-space, can be well represented by a basis-set of conformers including about 10 to 100 structures. The implications of this finding have profound consequences both for the interpretation of experimental electronic and vibrational spectral features of peptides in solution and for the theoretical prediction of these features using accurate and computationally expensive techniques. The here-derived methods and conclusions are expected to fundamentally impact the rationalization of so-far elusive structure-spectra relationships for disordered peptides and proteins, towards improved and versatile structure prediction methods.
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Affiliation(s)
- Monika Michaelis
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen Am Fallturm 1 Bremen 28359 Germany
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University Clifton Lane Nottingham NG11 8NS UK
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa Via G. Moruzzi 13 Pisa I-56124 Italy
| | - Carl Mensch
- Molecular Spectroscopy Research Group, Department of Chemistry, University of Antwerp Groenenborgerlaan 171 Antwerp 2020 Belgium
| | - Carole C Perry
- Biomolecular and Materials Interface Research Group, Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University Clifton Lane Nottingham NG11 8NS UK
| | - Massimo Delle Piane
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen Am Fallturm 1 Bremen 28359 Germany
- Department of Applied Science and Technology, Politecnico di Torino Corso Duca degli Abruzzi 24 Torino 10129 Italy
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen Am Fallturm 1 Bremen 28359 Germany
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11
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Improta R. Shedding Light on the Photophysics and Photochemistry of I-Motifs Using Quantum Mechanical Calculations. Int J Mol Sci 2023; 24:12614. [PMID: 37628797 PMCID: PMC10454157 DOI: 10.3390/ijms241612614] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
I-motifs are non-canonical DNA structures formed by intercalated hemiprotonated (CH·C)+ pairs, i.e., formed by a cytosine (C) and a protonated cytosine (CH+), which are currently drawing great attention due to their biological relevance and promising nanotechnological properties. It is important to characterize the processes occurring in I-motifs following irradiation by UV light because they can lead to harmful consequences for genetic code and because optical spectroscopies are the most-used tools to characterize I-motifs. By using time-dependent DFT calculations, we here provide the first comprehensive picture of the photoactivated behavior of the (CH·C)+ core of I-motifs, from absorption to emission, while also considering the possible photochemical reactions. We reproduce and assign their spectral signatures, i.e., infrared, absorption, fluorescence and circular dichroism spectra, disentangling the underlying chemical-physical effects. We show that the main photophysical paths involve C and CH+ bases on adjacent steps and, using this basis, interpret the available time-resolved spectra. We propose that a photodimerization reaction can occur on an excited state with strong C→CH+ charge transfer character and examine some of the possible photoproducts. Based on the results reported, some future perspectives for the study of I-motifs are discussed.
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Affiliation(s)
- Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy
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12
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Boichenko AN, Bochenkova AV. Accurate Vertical Electron Detachment Energies and Multiphoton Resonant Photoelectron Spectra of Biochromophore Anions in Aqueous Solution. J Chem Theory Comput 2023. [PMID: 37146177 DOI: 10.1021/acs.jctc.2c01082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We introduce a new methodology for calculating vertical electron detachment energies (VDEs) of biologically relevant chromophores in their deprotonated anionic forms in aqueous solution. It combines a large-scale mixed DFT/EFP/MD approach with the high-level multireference perturbation theory XMCQDPT2 and the Effective Fragment Potential (EFP) method. The methodology includes a multiscale flexible treatment of inner (∼1000 water molecules) and outer (∼18000 water molecules) water shells around a charged solute, capturing both the effects of specific solvation and the properties of bulk water. VDEs are calculated as a function of system size for getting a converged value at the DFT/EFP level of theory. The XMCQDPT2/EFP approach, adapted for calculating VDEs, supports the DFT/EFP results. When corrected for a solvent polarization contribution, the XMCQDPT2/EFP method yields the most accurate estimate to date of the first VDE for aqueous phenolate (7.3 ± 0.1 eV), which agrees well with liquid-jet X-ray photoelectron spectroscopy data (7.1 ± 0.1 eV). We show that the geometry of the water shell and its size are essential for accurate VDE calculations of aqueous phenolate and its biologically relevant derivatives. By simulating photoelectron spectra of aqueous phenolate upon two-photon excitation at wavelengths resonant with the S0 → S1 transition, we also provide interpretation of recent multiphoton UV liquid-microjet photoelectron spectroscopy experiments. We show that its first VDE is consistent with our estimate of 7.3 eV, when experimental two-photon binding energies are corrected for the resonant contribution.
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Affiliation(s)
- Anton N Boichenko
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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13
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Sen S, Visscher L. Towards the description of charge transfer states in solubilised LHCII using subsystem DFT. PHOTOSYNTHESIS RESEARCH 2023; 156:39-57. [PMID: 35988131 PMCID: PMC10070235 DOI: 10.1007/s11120-022-00950-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/04/2022] [Indexed: 05/05/2023]
Abstract
Light harvesting complex II (LHCII) in plants and green algae have been shown to adapt their absorption properties, depending on the concentration of sunlight, switching between a light harvesting and a non-harvesting or quenched state. In a recent work, combining classical molecular dynamics (MD) simulations with quantum chemical calculations (Liguori et al. in Sci Rep 5:15661, 2015) on LHCII, it was shown that the Chl611-Chl612 cluster of the terminal emitter domain can play an important role in modifying the spectral properties of the complex. In that work the importance of charge transfer (CT) effects was highlighted, in re-shaping the absorption intensity of the chlorophyll dimer. Here in this work, we investigate the combined effect of the local excited (LE) and CT states in shaping the energy landscape of the chlorophyll dimer. Using subsystem Density Functional Theory over the classical [Formula: see text]s MD trajectory we look explicitly into the excitation energies of the LE and the CT states of the dimer and their corresponding couplings. Upon doing so, we observe a drop in the excitation energies of the CT states, accompanied by an increase in the couplings between the LE/LE and the LE/CT states facilitated by a shorter interchromophoric distance upon equilibration. Both these changes in conjunction, effectively produces a red-shift of the low-lying mixed exciton/CT states of the supramolecular chromophore pair.
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Affiliation(s)
- Souloke Sen
- Division of Theoretical Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Lucas Visscher
- Division of Theoretical Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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14
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Maity S, Kleinekathöfer U. Recent progress in atomistic modeling of light-harvesting complexes: a mini review. PHOTOSYNTHESIS RESEARCH 2023; 156:147-162. [PMID: 36207489 PMCID: PMC10070314 DOI: 10.1007/s11120-022-00969-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
In this mini review, we focus on recent advances in the atomistic modeling of biological light-harvesting (LH) complexes. Because of their size and sophisticated electronic structures, multiscale methods are required to investigate the dynamical and spectroscopic properties of such complexes. The excitation energies, in this context also known as site energies, excitonic couplings, and spectral densities are key quantities which usually need to be extracted to be able to determine the exciton dynamics and spectroscopic properties. The recently developed multiscale approach based on the numerically efficient density functional tight-binding framework followed by excited state calculations has been shown to be superior to the scheme based on pure classical molecular dynamics simulations. The enhanced approach, which improves the description of the internal vibrational dynamics of the pigment molecules, yields spectral densities in good agreement with the experimental counterparts for various bacterial and plant LH systems. Here, we provide a brief overview of those results and described the theoretical foundation of the multiscale protocol.
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Affiliation(s)
- Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany.
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15
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Segatta F, Ruiz DA, Aleotti F, Yaghoubi M, Mukamel S, Garavelli M, Santoro F, Nenov A. Nonlinear Molecular Electronic Spectroscopy via MCTDH Quantum Dynamics: From Exact to Approximate Expressions. J Chem Theory Comput 2023; 19:2075-2091. [PMID: 36961952 PMCID: PMC10100531 DOI: 10.1021/acs.jctc.2c01059] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
We present an accurate and efficient approach to computing the linear and nonlinear optical spectroscopy of a closed quantum system subject to impulsive interactions with an incident electromagnetic field. It incorporates the effect of ultrafast nonadiabatic dynamics by means of explicit numerical propagation of the nuclear wave packet. The fundamental expressions for the evaluation of first- and higher-order response functions are recast in a general form that can be used with any quantum dynamics code capable of computing the overlap of nuclear wave packets evolving in different states. Here we present the evaluation of these expressions with the multiconfiguration time-dependent Hartree (MCTDH) method. Application is made to pyrene, excited to its lowest bright excited state S2 which exhibits a sub-100-fs nonadiabatic decay to a dark state S1. The system is described by a linear vibronic coupling Hamiltonian, parametrized with multiconfiguration electronic structure methods. We show that the ultrafast nonadiabatic dynamics can have a remarkable effect on the spectral line shapes that goes beyond simple lifetime broadening. Furthermore, a widely employed approximate expression based on the time scale separation of dephasing and population relaxation is recast in the same theoretical framework. Application to pyrene shows the range of validity of such approximations.
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Affiliation(s)
- Francesco Segatta
- Dipartimento di Chimica Industriale "Toso Montanari", University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Daniel Aranda Ruiz
- ICMol, Universidad de Valencia, Catedrático José Beltrán Martínez, 2, 46980 Paterna, Spain
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Flavia Aleotti
- Dipartimento di Chimica Industriale "Toso Montanari", University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Martha Yaghoubi
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Shaul Mukamel
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California 92697, United States
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari", University of Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
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16
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Toldo JM, do Casal MT, Ventura E, do Monte SA, Barbatti M. Surface hopping modeling of charge and energy transfer in active environments. Phys Chem Chem Phys 2023; 25:8293-8316. [PMID: 36916738 PMCID: PMC10034598 DOI: 10.1039/d3cp00247k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
An active environment is any atomic or molecular system changing a chromophore's nonadiabatic dynamics compared to the isolated molecule. The action of the environment on the chromophore occurs by changing the potential energy landscape and triggering new energy and charge flows unavailable in the vacuum. Surface hopping is a mixed quantum-classical approach whose extreme flexibility has made it the primary platform for implementing novel methodologies to investigate the nonadiabatic dynamics of a chromophore in active environments. This Perspective paper surveys the latest developments in the field, focusing on charge and energy transfer processes.
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Affiliation(s)
| | | | - Elizete Ventura
- Departamento de Química, CCEN, Universidade Federal da Paraíba, 58059-900, João Pessoa, Brazil.
| | - Silmar A do Monte
- Departamento de Química, CCEN, Universidade Federal da Paraíba, 58059-900, João Pessoa, Brazil.
| | - Mario Barbatti
- Aix-Marseille University, CNRS, ICR, Marseille, France.
- Institut Universitaire de France, 75231, Paris, France
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17
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Sen S, Senjean B, Visscher L. Characterization of excited states in time-dependent density functional theory using localized molecular orbitals. J Chem Phys 2023; 158:054115. [PMID: 36754801 DOI: 10.1063/5.0137729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Localized molecular orbitals are often used for the analysis of chemical bonds, but they can also serve to efficiently and comprehensibly compute linear response properties. While conventional canonical molecular orbitals provide an adequate basis for the treatment of excited states, a chemically meaningful identification of the different excited-state processes is difficult within such a delocalized orbital basis. In this work, starting from an initial set of supermolecular canonical molecular orbitals, we provide a simple one-step top-down embedding procedure for generating a set of orbitals, which are localized in terms of the supermolecule but delocalized over each subsystem composing the supermolecule. Using an orbital partitioning scheme based on such sets of localized orbitals, we further present a procedure for the construction of local excitations and charge-transfer states within the linear response framework of time-dependent density functional theory (TDDFT). This procedure provides direct access to approximate diabatic excitation energies and, under the Tamm-Dancoff approximation, also their corresponding electronic couplings-quantities that are of primary importance in modeling energy transfer processes in complex biological systems. Our approach is compared with a recently developed diabatization procedure based on subsystem TDDFT using projection operators, which leads to a similar set of working equations. Although both of these methods differ in the general localization strategies adopted and the type of basis functions (Slaters vs Gaussians) employed, an overall decent agreement is obtained.
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Affiliation(s)
- Souloke Sen
- Division of Theoretical Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Bruno Senjean
- ICGM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
| | - Lucas Visscher
- Division of Theoretical Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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18
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Cignoni E, Cupellini L, Mennucci B. Machine Learning Exciton Hamiltonians in Light-Harvesting Complexes. J Chem Theory Comput 2023; 19:965-977. [PMID: 36701385 PMCID: PMC9933434 DOI: 10.1021/acs.jctc.2c01044] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We propose a machine learning (ML)-based strategy for an inexpensive calculation of excitonic properties of light-harvesting complexes (LHCs). The strategy uses classical molecular dynamics simulations of LHCs in their natural environment in combination with ML prediction of the excitonic Hamiltonian of the embedded aggregate of pigments. The proposed ML model can reproduce the effects of geometrical fluctuations together with those due to electrostatic and polarization interactions between the pigments and the protein. The training is performed on the chlorophylls of the major LHC of plants, but we demonstrate that the model is able to extrapolate well beyond the initial training set. Moreover, the accuracy in predicting the effects of the environment is tested on the simulation of the small changes observed in the absorption spectra of the wild-type and a mutant of a minor LHC.
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19
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Feighan O, Manby FR, Bourne-Worster S. An efficient protocol for excited states of large biochromophores. J Chem Phys 2023; 158:024107. [PMID: 36641400 DOI: 10.1063/5.0132417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Efficient energy transport in photosynthetic antenna is a long-standing source of inspiration for artificial light harvesting materials. However, characterizing the excited states of the constituent chromophores poses a considerable challenge to mainstream quantum chemical and semiempirical excited state methods due to their size and complexity and the accuracy required to describe small but functionally important changes in their properties. In this paper, we explore an alternative approach to calculating the excited states of large biochromophores, exemplified by a specific method for calculating the Qy transition of bacteriochlorophyll a, which we name Chl-xTB. Using a diagonally dominant approximation to the Casida equation and a bespoke parameterization scheme, Chl-xTB can match time-dependent density functional theory's accuracy and semiempirical speed for calculating the potential energy surfaces and absorption spectra of chlorophylls. We demonstrate that Chl-xTB (and other prospective realizations of our protocol) can be integrated into multiscale models, including concurrent excitonic and point-charge embedding frameworks, enabling the analysis of biochromophore networks in a native environment. We exploit this capability to probe the low-frequency spectral densities of excitonic energies and interchromophore interactions in the light harvesting antenna protein LH2 (light harvesting complex 2). The impact of low-frequency protein motion on interchromophore coupling and exciton transport has routinely been ignored due to the prohibitive costs of including it in simulations. Our results provide a more rigorous basis for continued use of this approximation by demonstrating that exciton transition energies are unaffected by low-frequency vibrational coupling to exciton interaction energies.
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Affiliation(s)
- Oliver Feighan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Susannah Bourne-Worster
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
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20
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Asha H, Green JA, Esposito L, Martinez-Fernandez L, Santoro F, Improta R. Effect of the Thermal Fluctuations of the Photophysics of GC and CG DNA Steps: A Computational Dynamical Study. J Phys Chem B 2022; 126:10608-10621. [PMID: 36508709 DOI: 10.1021/acs.jpcb.2c05688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Here we refine and assess two computational procedures aimed to include the effect of thermal fluctuations on the electronic spectra and the ultrafast excited state dynamics of multichromophore systems, focusing on DNA duplexes. Our approach is based on a fragment diabatization procedure that, from a given Quantum Mechanical (QM) reference method, can provide the parameters (energy and coupling) of the reference diabatic states on the basis of the isolated fragments, either for a purely electronic excitonic Hamiltonian (FrDEx) or a linear vibronic coupling Hamiltonian (FrD-LVC). After having defined the most cost-effective procedure for DNA duplexes on two smaller fragments, FrDEx is used to simulate the absorption and Electronic Circular Dichroism (ECD) spectra of (GC)5 sequences, including the coupling with the Charge Transfer (CT) states, on a number of structures extracted from classical Molecular Dynamics (MD) simulations. The computed spectra are close to the reference TD-DFT calculations and fully consistent with the experimental ones. We then couple MD simulations and FrD-LVC to simulate the interplay between local excitations and CT transitions, both intrastrand and interstrand, in GC and CG steps when included in a oligoGC or in oligoAT DNA sequence. We predict that for both sequences a substantial part of the photoexcited population on G and C decays, within 50-100 fs, to the corresponding intrastrand CT states. This transfer is more effective for GC steps that, on average, are more closely stacked than CG ones.
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Affiliation(s)
- Haritha Asha
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy
| | - James A Green
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy.,Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438Frankfurt am Main, Germany
| | - Luciana Esposito
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autònoma de Madrid, Campus de Excelencia UAM-CSIC, 28049Madrid, Spain
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124Pisa, Italy
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy.,DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800Kongens Lyngby, Denmark
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21
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Castaldo D, Jahangiri S, Delgado A, Corni S. Quantum Simulation of Molecules in Solution. J Chem Theory Comput 2022; 18:7457-7469. [PMID: 36351289 DOI: 10.1021/acs.jctc.2c00974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Quantum chemical calculations on quantum computers have been focused mostly on simulating molecules in the gas phase. Molecules in liquid solution are, however, most relevant for chemistry. Continuum solvation models represent a good compromise between computational affordability and accuracy in describing solvation effects within a quantum chemical description of solute molecules. In this work, we extend the variational quantum eigensolver to simulate solvated systems using the polarizable continuum model. To account for the state dependent solute-solvent interaction we generalize the variational quantum eigensolver algorithm to treat non-linear molecular Hamiltonians. We show that including solvation effects does not impact the algorithmic efficiency. Numerical results of noiseless simulations for molecular systems with up to 12 spin-orbitals (qubits) are presented. Furthermore, calculations performed on a simulated noisy quantum hardware (IBM Q, Mumbai) yield computed solvation free energies in fair agreement with the classical calculations.
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Affiliation(s)
- Davide Castaldo
- Dipartimento di Scienze Chimiche, Università degli studi di Padova, Via Marzolo 1, Padova35131, Italy
| | | | | | - Stefano Corni
- Dipartimento di Scienze Chimiche, Università degli studi di Padova, Via Marzolo 1, Padova35131, Italy.,Istituto Nanoscienze─CNR, via Campi 213/A, Modena41125, Italy.,Padua Quantum Technologies Research Center, Università di Padova, Padova35131, Italy
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22
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Nicoli L, Giovannini T, Cappelli C. Assessing the quality of QM/MM approaches to describe vacuo-to-water solvatochromic shifts. J Chem Phys 2022; 157:214101. [PMID: 36511555 DOI: 10.1063/5.0118664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The performance of different quantum mechanics/molecular mechanics embedding models to compute vacuo-to-water solvatochromic shifts is investigated. In particular, both nonpolarizable and polarizable approaches are analyzed and computed results are compared to reference experimental data. We show that none of the approaches outperform the others and that errors strongly depend on the nature of the molecular transition to be described. Thus, we prove that the best choice of embedding model highly depends on the molecular system and that the use of a specific approach as a black box can lead to significant errors and, sometimes, totally wrong predictions.
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Affiliation(s)
- Luca Nicoli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | | | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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23
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Marchetti L, Nifosì R, Martelli PL, Da Pozzo E, Cappello V, Banterle F, Trincavelli ML, Martini C, D’Elia M. Quantum computing algorithms: getting closer to critical problems in computational biology. Brief Bioinform 2022; 23:6758194. [PMID: 36220772 PMCID: PMC9677474 DOI: 10.1093/bib/bbac437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/15/2022] [Accepted: 09/08/2022] [Indexed: 12/14/2022] Open
Abstract
The recent biotechnological progress has allowed life scientists and physicians to access an unprecedented, massive amount of data at all levels (molecular, supramolecular, cellular and so on) of biological complexity. So far, mostly classical computational efforts have been dedicated to the simulation, prediction or de novo design of biomolecules, in order to improve the understanding of their function or to develop novel therapeutics. At a higher level of complexity, the progress of omics disciplines (genomics, transcriptomics, proteomics and metabolomics) has prompted researchers to develop informatics means to describe and annotate new biomolecules identified with a resolution down to the single cell, but also with a high-throughput speed. Machine learning approaches have been implemented to both the modelling studies and the handling of biomedical data. Quantum computing (QC) approaches hold the promise to resolve, speed up or refine the analysis of a wide range of these computational problems. Here, we review and comment on recently developed QC algorithms for biocomputing, with a particular focus on multi-scale modelling and genomic analyses. Indeed, differently from other computational approaches such as protein structure prediction, these problems have been shown to be adequately mapped onto quantum architectures, the main limit for their immediate use being the number of qubits and decoherence effects in the available quantum machines. Possible advantages over the classical counterparts are highlighted, along with a description of some hybrid classical/quantum approaches, which could be the closest to be realistically applied in biocomputation.
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Affiliation(s)
| | | | - Pier Luigi Martelli
- Corresponding authors: Pier Luigi Martelli. Tel.: +39 0512094005; Fax: +39 0512094005; E-mail: ; Claudia Martini. Tel.: +39 0502219522; Fax: +39 050 2210680; E-mail:
| | - Eleonora Da Pozzo
- University of Pisa, Department of Pharmacy, via Bonanno 6, 56126 Pisa Italy
| | - Valentina Cappello
- Italian Institute of Technology, Center for Materials Interfaces, Viale Rinaldo Piaggio 34, 56025 Pontedera (PI), Italy
| | | | | | - Claudia Martini
- Corresponding authors: Pier Luigi Martelli. Tel.: +39 0512094005; Fax: +39 0512094005; E-mail: ; Claudia Martini. Tel.: +39 0502219522; Fax: +39 050 2210680; E-mail:
| | - Massimo D’Elia
- University of Pisa, Department of Physics, Largo Bruno Pontecorvo 3, 56127, Pisa Italy
- INFN, Sezione di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
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24
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Cordier BA, Sawaya NPD, Guerreschi GG, McWeeney SK. Biology and medicine in the landscape of quantum advantages. J R Soc Interface 2022; 19:20220541. [PMID: 36448288 PMCID: PMC9709576 DOI: 10.1098/rsif.2022.0541] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Quantum computing holds substantial potential for applications in biology and medicine, spanning from the simulation of biomolecules to machine learning methods for subtyping cancers on the basis of clinical features. This potential is encapsulated by the concept of a quantum advantage, which is contingent on a reduction in the consumption of a computational resource, such as time, space or data. Here, we distill the concept of a quantum advantage into a simple framework to aid researchers in biology and medicine pursuing the development of quantum applications. We then apply this framework to a wide variety of computational problems relevant to these domains in an effort to (i) assess the potential of practical advantages in specific application areas and (ii) identify gaps that may be addressed with novel quantum approaches. In doing so, we provide an extensive survey of the intersection of biology and medicine with the current landscape of quantum algorithms and their potential advantages. While we endeavour to identify specific computational problems that may admit practical advantages throughout this work, the rapid pace of change in the fields of quantum computing, classical algorithms and biological research implies that this intersection will remain highly dynamic for the foreseeable future.
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Affiliation(s)
- Benjamin A. Cordier
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97202, USA
| | | | | | - Shannon K. McWeeney
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97202, USA,Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97202, USA,Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR 97202, USA
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25
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King DS, Hermes MR, Truhlar DG, Gagliardi L. Large-Scale Benchmarking of Multireference Vertical-Excitation Calculations via Automated Active-Space Selection. J Chem Theory Comput 2022; 18:6065-6076. [PMID: 36112354 PMCID: PMC9558375 DOI: 10.1021/acs.jctc.2c00630] [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: 11/29/2022]
Abstract
![]()
We have calculated state-averaged complete-active-space
self-consistent-field
(SA-CASSCF), multiconfiguration pair-density functional theory (MC-PDFT),
hybrid MC-PDFT (HMC-PDFT), and n-electron valence
state second-order perturbation theory (NEVPT2) excitation energies
with the approximate pair coefficient (APC) automated active-space
selection scheme for the QUESTDB benchmark database of 542 vertical
excitation energies. We eliminated poor active spaces (20–40%
of calculations) by applying a threshold to the SA-CASSCF absolute
error. With the remaining calculations, we find that NEVPT2 performance
is significantly impacted by the size of the basis set the wave functions
are converged in, regardless of the quality of their description,
which is a problem absent in MC-PDFT. Additionally, we find that HMC-PDFT
is a significant improvement over MC-PDFT with the translated PBE
(tPBE) density functional and that it performs about as well as NEVPT2
and second-order coupled cluster on a set of 373 excitations in the
QUESTDB database. We optimized the percentage of SA-CASSCF energy
to include in HMC-PDFT when using the tPBE on-top functional, and
we find the 25% value used in tPBE0 to be optimal. This work is by
far the largest benchmarking of MC-PDFT and HMC-PDFT to date, and
the data produced in this work are useful as a validation of HMC-PDFT
and of the APC active-space selection scheme. We have made all the
wave functions produced in this work (orbitals and CI vectors) available
to the public and encourage the community to utilize this data as
a tool in the development of further multireference model chemistries.
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Affiliation(s)
- Daniel S. King
- Department of Chemistry, University of Chicago, Chicago Illinois 60637, United States
| | - Matthew R. Hermes
- Department of Chemistry, University of Chicago, Chicago Illinois 60637, United States
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputng Institute, University of Minnesota, Minneapolis Minnesota 55455-0431, United States
| | - Laura Gagliardi
- Department of Chemistry, Pritzker School of Molecular Engineering, James Franck Institute, Chicago Center for Theoretical Chemistry, University of Chicago, Chicago Illinois 60637, United States
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26
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Martínez Fernández L, Santoro F, Improta R. Nucleic Acids as a Playground for the Computational Study of the Photophysics and Photochemistry of Multichromophore Assemblies. Acc Chem Res 2022; 55:2077-2087. [PMID: 35833758 DOI: 10.1021/acs.accounts.2c00256] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
ConspectusThe interaction between light and multichromophoric assemblies (MCAs) is the primary event of many fundamental processes, from photosynthesis to organic photovoltaics, and it triggers dynamical processes that share remarkable similarities at the molecular scale: light absorption, energy and charge transfer, internal conversions, emission, and so on. Those events often involve many chromophores and different excited electronic states that are coupled on an ultrafast time scale. This Account aims to discuss some of the chemical physical effects ruling these processes, a fundamental step toward their control, based on our experience on nucleic acids.In the last 15 years, we have, indeed, studied the photophysics and photochemistry of DNA and its components. By combining different quantum mechanical methods, we investigated the molecular processes responsible for the damage of the genetic code or, on the contrary, those preventing it by dissipating the excess energy deposited in the system by UV absorption. Independently of its fundamental biological role, DNA, with its fluctuating closely stacked bases stabilized by weak nonbonding interactions, can be considered a prototypical MCA. Therefore, it allows one to tackle within a single system many of the conceptual and methodological challenges involved in the study of photoinduced processes in MCA.In this Account, by using the outcome of our studies on oligonucleotides as a guideline, we thus highlight the most critical modellistic issues to be faced when studying, either experimentally or computationally, the interaction between UV light and DNA and, at the same time, bring out their general relevance for the study of MCAs.We first discuss the rich photoactivated dynamics of nucleobases (the chromophores), highlighting the main effects modulating the interplay between their excited states and how the latter can affect the photoactivated dynamics of the polynucleotides, either providing effective monomer-like nonradiative decay routes or triggering reactive processes (e.g., triplet generation).We then tackle the reaction paths involving multiple bases, showing that in the DNA duplex the most important ones involve two stacked bases, forming a neutral excimer or a charge transfer (CT) state, which exhibit different spectral signatures and photochemical reactivity. In particular, we analyze the factors affecting the dynamic equilibrium between the excimer and CT, such as the fluctuations of the backbone or the rearrangement of the solvent.Next, we highlight the importance of the effects not directly connected to the chromophores, such as the flexibility of the backbone or the solvent effect. The former, affecting the stacking geometry of the bases, can determine the preference between different deactivation paths. The latter is particularly influential for CT states, making very important an accurate treatment of dynamical solvation effects, involving both the solvent bulk and specific solute-solvent interactions.In the last section, we describe the main methodological challenges related to the study of polynucleotide excited states and stress the benefits derived by the integration of complementary approaches, both computational and experimental. Only exploiting different point of views, in our opinion, it is possible to shed light on the complex phenomena triggered by light absorption in DNA, as in every MCA.
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Affiliation(s)
- Lara Martínez Fernández
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy
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27
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Sarngadharan P, Maity S, Kleinekathöfer U. Spectral densities and absorption spectra of the core antenna complex CP43 from photosystem II. J Chem Phys 2022; 156:215101. [DOI: 10.1063/5.0091005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Besides absorbing light, the core antenna complex CP43 of photosystem II is of great importance in transferring excitation energy from the antenna complexes to the reaction center. Excitation energies, spectral densities, and linear absorption spectra of the complex have been evaluated by a multiscale approach. In this scheme, quantum mechanics/molecular mechanics molecular dynamics simulations are performed employing the parameterized density functional tight binding (DFTB) while the time-dependent long-range-corrected DFTB scheme is applied for the excited state calculations. The obtained average spectral density of the CP43 complex shows a very good agreement with experimental results. Moreover, the excitonic Hamiltonian of the system along with the computed site-dependent spectral densities was used to determine the linear absorption. While a Redfield-like approximation has severe shortcomings in dealing with the CP43 complex due to quasi-degenerate states, the non-Markovian full second-order cumulant expansion formalism is able to overcome the drawbacks. Linear absorption spectra were obtained, which show a good agreement with the experimental counterparts at different temperatures. This study once more emphasizes that by combining diverse techniques from the areas of molecular dynamics simulations, quantum chemistry, and open quantum systems, it is possible to obtain first-principle results for photosynthetic complexes, which are in accord with experimental findings.
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Affiliation(s)
- Pooja Sarngadharan
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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28
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Liang W, Pei Z, Mao Y, Shao Y. Evaluation of molecular photophysical and photochemical properties using linear response time-dependent density functional theory with classical embedding: Successes and challenges. J Chem Phys 2022; 156:210901. [DOI: 10.1063/5.0088271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Time-dependent density functional theory (TDDFT) based approaches have been developed in recent years to model the excited-state properties and transition processes of the molecules in the gas-phase and in a condensed medium, such as in a solution and protein microenvironment or near semiconductor and metal surfaces. In the latter case, usually, classical embedding models have been adopted to account for the molecular environmental effects, leading to the multi-scale approaches of TDDFT/polarizable continuum model (PCM) and TDDFT/molecular mechanics (MM), where a molecular system of interest is designated as the quantum mechanical region and treated with TDDFT, while the environment is usually described using either a PCM or (non-polarizable or polarizable) MM force fields. In this Perspective, we briefly review these TDDFT-related multi-scale models with a specific emphasis on the implementation of analytical energy derivatives, such as the energy gradient and Hessian, the nonadiabatic coupling, the spin–orbit coupling, and the transition dipole moment as well as their nuclear derivatives for various radiative and radiativeless transition processes among electronic states. Three variations of the TDDFT method, the Tamm–Dancoff approximation to TDDFT, spin–flip DFT, and spin-adiabatic TDDFT, are discussed. Moreover, using a model system (pyridine–Ag20 complex), we emphasize that caution is needed to properly account for system–environment interactions within the TDDFT/MM models. Specifically, one should appropriately damp the electrostatic embedding potential from MM atoms and carefully tune the van der Waals interaction potential between the system and the environment. We also highlight the lack of proper treatment of charge transfer between the quantum mechanics and MM regions as well as the need for accelerated TDDFT modelings and interpretability, which calls for new method developments.
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Affiliation(s)
- WanZhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Zheng Pei
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
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29
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Cignoni E, Cupellini L, Mennucci B. A fast method for electronic couplings in embedded multichromophoric systems. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:304004. [PMID: 35552268 DOI: 10.1088/1361-648x/ac6f3c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Electronic couplings are key to understanding exciton delocalization and transport in natural and artificial light harvesting processes. We develop a method to compute couplings in multichromophoric aggregates embedded in complex environments without running expensive quantum chemical calculations. We use a transition charge approximation to represent the quantum mechanical transition densities of the chromophores and an atomistic and polarizable classical model to describe the environment atoms. We extend our framework to estimate transition charges directly from the chromophore geometry, i.e., bypassing completely the quantum mechanical calculations using a regression approach. The method allows to rapidly compute accurate couplings for a large number of geometries along molecular dynamics trajectories.
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Affiliation(s)
- Edoardo Cignoni
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124, Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124, Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124, Pisa, Italy
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30
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Cignoni E, Slama V, Cupellini L, Mennucci B. The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol. J Chem Phys 2022; 156:120901. [DOI: 10.1063/5.0086275] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The function of light-harvesting complexes is determined by a complex network of dynamic interactions among all the different components: the aggregate of pigments, the protein, and the surrounding environment. Complete and reliable predictions on these types of composite systems can be only achieved with an atomistic description. In the last few decades, there have been important advances in the atomistic modeling of light-harvesting complexes. These advances have involved both the completeness of the physical models and the accuracy and effectiveness of the computational protocols. In this Perspective, we present an overview of the main theoretical and computational breakthroughs attained so far in the field, with particular focus on the important role played by the protein and its dynamics. We then discuss the open problems in their accurate modeling that still need to be addressed. To illustrate an effective computational workflow for the modeling of light harvesting complexes, we take as an example the plant antenna complex CP29 and its H111N mutant.
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Affiliation(s)
- Edoardo Cignoni
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Vladislav Slama
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124 Pisa, Italy
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31
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Tölle J, Neugebauer J. The Seamless Connection of Local and Collective Excited States in Subsystem Time-Dependent Density Functional Theory. J Phys Chem Lett 2022; 13:1003-1018. [PMID: 35061387 DOI: 10.1021/acs.jpclett.1c04023] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The theoretical understanding of photoinduced processes in multichromophoric systems requires, as an essential ingredient, the possibility of accurately describing their electronically excited states. However, the size of these systems often prohibits the usage of conventional electronic-structure methods, so that often multiscale approaches based on phenomenologically motivated models are employed. In contrast, subsystem time-dependent density functional theory (sTDDFT) allows for a subsystem-based ab initio description of multichromophoric systems and therefore allows for, in principle, an exact description of photoinduced processes. This Perspective aims to outline the theoretical foundations and commonly used practical realizations as well as to illustrate benefits of recent developments and open issues in the field of sTDDFT. Prospective, potential future applications and possible methodological developments are discussed.
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Affiliation(s)
- Johannes Tölle
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
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32
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Villa M, Ceroni P, Fermi A. Tetrachromophoric Systems Based on Rigid Tetraphenylmethane (TPM) and Tetraphenylethylene (TPE) Scaffolds. Chempluschem 2022; 87:e202100558. [DOI: 10.1002/cplu.202100558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/01/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Marco Villa
- Universita di Bologna Department of Chemistry "Giacomo Ciamician" ITALY
| | - Paola Ceroni
- Universita di Bologna Depatment of Chemistry "G. Ciamician" ITALY
| | - Andrea Fermi
- Universita degli Studi di Bologna Dipartimento di Chimica Giacomo Ciamician Dipartimento di Chimica "Giacomo Ciamician" via Selmi 2 40126 Bologna ITALY
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33
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Bertoni AI, Fogarty RM, Sánchez CG, Horsfield AP. QM/MM optimization with quantum coupling: Host–guest interactions in a pentacene-doped p-terphenyl crystal. J Chem Phys 2022; 156:044110. [DOI: 10.1063/5.0079788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Andrés I. Bertoni
- Instituto Interdisciplinario de Ciencias Básicas (ICB-CONICET), Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, Mendoza 5502, Argentina
| | - Richard M. Fogarty
- Department of Materials and Thomas Young Centre, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Cristián G. Sánchez
- Instituto Interdisciplinario de Ciencias Básicas (ICB-CONICET), Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, Mendoza 5502, Argentina
| | - Andrew P. Horsfield
- Department of Materials and Thomas Young Centre, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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34
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Carreras A, Casanova D. Simple evaluation of dynamic disorder effects on exciton transport. J Chem Phys 2022; 156:044112. [DOI: 10.1063/5.0078406] [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] Open
Affiliation(s)
- Abel Carreras
- Donostia International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain
| | - David Casanova
- Donostia International Physics Center (DIPC), 20018 Donostia, Euskadi, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Euskadi, Spain
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35
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Wang K, Xie Z, Luo Z, Ma H. Low-Scaling Excited State Calculation Using the Block Interaction Product State. J Phys Chem Lett 2022; 13:462-470. [PMID: 35015548 DOI: 10.1021/acs.jpclett.1c03445] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We develop an automatic and efficient scheme for the accurate construction of the bases for excitonic models, which can enable "black-box" excited state structure calculations for large molecular systems. These new and optimized bases, which are named the block interaction product state (BIPS), can be expressed as the direct products of the local states for each chromophore. Each chromophore's local states are selected by diagonalization of its reduced density matrix, which is obtained by quantum chemical calculation of the small subsystem composed of the chromophore and its nearest neighbors. We implemented the BIPS framework with fragment-based calculations considering two- and three-body interactions. Test calculations for eight different molecular aggregates demonstrate that this framework provides an accurate description of not only the excitation energies but also the first-order wave function properties (dipole moment and transition dipole moment) of the low-lying excited states at a low-scaling computational cost.
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Affiliation(s)
- Ke Wang
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
| | - Zhaoxuan Xie
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
| | - Zhen Luo
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
| | - Haibo Ma
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
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36
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Xu C, Lin K, Hu D, Gu FL, Gelin MF, Lan Z. Ultrafast Internal Conversion Dynamics through the on-the-Fly Simulation of Transient Absorption Pump-Probe Spectra with Different Electronic Structure Methods. J Phys Chem Lett 2022; 13:661-668. [PMID: 35023755 DOI: 10.1021/acs.jpclett.1c03373] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
An on-the-fly surface-hopping simulation protocol is developed for the evaluation of transient absorption (TA) pump-probe (PP) signals of molecular systems exhibiting internal conversion to the electronic ground state. We study the nonadiabatic dynamics of azomethane and the associating TA PP spectra at three levels of the electronic-structure theory, OM2/MRCI, SA-CASSCF, and XMS-CASPT2. The impact of these methods on the population dynamics and time-resolved TA PP signals is substantially different. This difference is attributed to the strong non-Condon effects that must be taken into account for the proper understanding and interpretation of time-resolved TA PP signals of nonadiabatic polyatomic systems. This shows that the combination of the dynamical and spectral simulations definitely provides more accurate and detailed information on the microscopic mechanisms of photophysical and photochemical processes. Hence the simulation of time-resolved spectroscopic signals provides another important dimension to examine the accuracy of quantum chemistry methods.
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Affiliation(s)
- Chao Xu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education; School of Chemistry, South China Normal University, Guangzhou, 510006, P. R. China
| | - Kunni Lin
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education; School of Chemistry, South China Normal University, Guangzhou, 510006, P. R. China
| | - Deping Hu
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou, 510006, P. R. China
| | - Feng Long Gu
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education; School of Chemistry, South China Normal University, Guangzhou, 510006, P. R. China
| | - Maxim F Gelin
- School of Sciences, Hangzhou Dianzi University, Hangzhou, 310018, P. R. China
| | - Zhenggang Lan
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou, 510006, P. R. China
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37
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Gil ES, Granucci G, Persico M. Surface Hopping Dynamics with the Frenkel Exciton Model in a Semiempirical Framework. J Chem Theory Comput 2021; 17:7373-7383. [PMID: 34843643 PMCID: PMC8675141 DOI: 10.1021/acs.jctc.1c00942] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
We present an implementation
of the Frenkel exciton model in the
framework of the semiempirical floating occupation molecular orbitals-configuration
interaction (FOMO-CI) electronic structure method, aimed at simulating
the dynamics of multichromophoric systems, in which excitation energy
transfer can occur, by a very efficient approach. The nonadiabatic
molecular dynamics is here dealt with by the surface hopping method,
but the implementation we proposed is compatible with other dynamical
approaches. The exciton coupling is computed either exactly, within
the semiempirical approximation considered, or by resorting to transition
atomic charges. The validation of our implementation is carried out
on the trans-azobenzeno-2S-phane (2S-TTABP), formed
by two azobenzene units held together by sulfur bridges, taken as
a minimal model of multichromophoric systems, in which both strong
and weak exciton couplings are present.
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Affiliation(s)
- Eduarda Sangiogo Gil
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via Moruzzi 13, 56124 Pisa, Italy
| | - Giovanni Granucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via Moruzzi 13, 56124 Pisa, Italy
| | - Maurizio Persico
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via Moruzzi 13, 56124 Pisa, Italy
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38
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Liu YH, Wang K, Ma HB. Evaluating first-order molecular properties of delocalized ionic or excited states in molecular aggregates by renormalized excitonic method. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2108133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Yun-hao Liu
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
| | - Ke Wang
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
| | - Hai-bo Ma
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
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39
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Sirohiwal A, Pantazis DA. Electrostatic profiling of photosynthetic pigments: implications for directed spectral tuning. Phys Chem Chem Phys 2021; 23:24677-24684. [PMID: 34708851 DOI: 10.1039/d1cp02580e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photosynthetic pigment-protein complexes harvest solar energy with a high quantum efficiency. Protein scaffolds are known to tune the spectral properties of embedded pigments principally through structured electrostatic environments. Although the physical nature of electrostatic tuning is straightforward, the precise spatial principles of electrostatic preorganization remain poorly explored for different protein matrices and incompletely characterized with respect to the intrinsic properties of different photosynthetic pigments. In this work, we study the electronic structure features associated with the lowest excited state of a series of eight naturally occurring (bacterio)chlorophylls and pheophytins to describe the precise topological differences in electrostatic potentials and hence determine intrinsic differences in the expected mode and impact of electrostatic tuning. The difference electrostatic potentials between the ground and first excited states are used as fingerprints. Both the spatial profile and the propensity for spectral tuning are found to be unique for each pigment, indicating spatially and directionally distinct modes of electrostatic tuning. The results define a specific partitioning of the protein matrix around each pigment as an aid to identify regions with a maximal impact on spectral tuning and have direct implications for dimensionality reduction in protein design and engineering. Thus, a quantum mechanical basis is provided for understanding, predicting, and ultimately designing sequence-modified or pigment-exchanged biological systems, as suggested for selected examples of pigment-reconstituted proteins.
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Affiliation(s)
- Abhishek Sirohiwal
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
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40
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Liu J, Lan Z, Yang J. An efficient implementation of spin-orbit coupling within the framework of semiempirical orthogonalization-corrected methods for ultrafast intersystem crossing dynamics. Phys Chem Chem Phys 2021; 23:22313-22323. [PMID: 34591049 DOI: 10.1039/d1cp03477d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We implement spin-orbit coupling (SOC) within the framework of semiempirical orthogonalization-corrected methods (OMx). The excited-state wavefunction is generated from configuration interaction with single excitations (CIS). The SOC Hamiltonian in terms of the one-electron Breit-Pauli operator with effective nuclear charges is adopted in this work. Benchmark calculations show that SOCs evaluated using the OMx/CIS method agree very well with those obtained from time-dependent density functional theory. As a particularly attractive application, we incorporate SOCs between singlet and triplet states into Tully's fewest switches surface hopping algorithm to enable excited-state nonadiabatic dynamics simulations, treating internal conversion and intersystem crossing on an equal footing. This semiempirical dynamics simulation approach is applied to investigate ultrafast intersystem crossing processes in core-substituted naphthalenediimides.
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Affiliation(s)
- Jie Liu
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Zhenggang Lan
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Jinlong Yang
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China.
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41
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Ordóñez-Hernández J, Arcos-Ramos R, Alvarez-Venicio V, Basiuk VA, González-Antonio O, Flores-Álamo M, García-Ortega H, Farfán N, Carreón-Castro MDP. Engineering coumarin-BODIPY thin-films and molecular crystals: Tailoring supramolecular self-assembly for organic electronic applications. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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42
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Westermayr J, Marquetand P. Machine Learning for Electronically Excited States of Molecules. Chem Rev 2021; 121:9873-9926. [PMID: 33211478 PMCID: PMC8391943 DOI: 10.1021/acs.chemrev.0c00749] [Citation(s) in RCA: 162] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Indexed: 12/11/2022]
Abstract
Electronically excited states of molecules are at the heart of photochemistry, photophysics, as well as photobiology and also play a role in material science. Their theoretical description requires highly accurate quantum chemical calculations, which are computationally expensive. In this review, we focus on not only how machine learning is employed to speed up such excited-state simulations but also how this branch of artificial intelligence can be used to advance this exciting research field in all its aspects. Discussed applications of machine learning for excited states include excited-state dynamics simulations, static calculations of absorption spectra, as well as many others. In order to put these studies into context, we discuss the promises and pitfalls of the involved machine learning techniques. Since the latter are mostly based on quantum chemistry calculations, we also provide a short introduction into excited-state electronic structure methods and approaches for nonadiabatic dynamics simulations and describe tricks and problems when using them in machine learning for excited states of molecules.
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Affiliation(s)
- Julia Westermayr
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
| | - Philipp Marquetand
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Vienna
Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Data
Science @ Uni Vienna, University of Vienna, Währinger Strasse 29, 1090 Vienna, Austria
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43
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Abstract
Electronically excited states of molecules are at the heart of photochemistry, photophysics, as well as photobiology and also play a role in material science. Their theoretical description requires highly accurate quantum chemical calculations, which are computationally expensive. In this review, we focus on not only how machine learning is employed to speed up such excited-state simulations but also how this branch of artificial intelligence can be used to advance this exciting research field in all its aspects. Discussed applications of machine learning for excited states include excited-state dynamics simulations, static calculations of absorption spectra, as well as many others. In order to put these studies into context, we discuss the promises and pitfalls of the involved machine learning techniques. Since the latter are mostly based on quantum chemistry calculations, we also provide a short introduction into excited-state electronic structure methods and approaches for nonadiabatic dynamics simulations and describe tricks and problems when using them in machine learning for excited states of molecules.
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Affiliation(s)
- Julia Westermayr
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
| | - Philipp Marquetand
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Vienna Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
- Data Science @ Uni Vienna, University of Vienna, Währinger Strasse 29, 1090 Vienna, Austria
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44
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Avagliano D, Bonfanti M, Garavelli M, González L. QM/MM Nonadiabatic Dynamics: the SHARC/COBRAMM Approach. J Chem Theory Comput 2021; 17:4639-4647. [PMID: 34114454 DOI: 10.1021/acs.jctc.1c00318] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the SHARC/COBRAMM approach to enable easy and efficient excited-state dynamics simulations at different levels of electronic structure theory in the presence of complex environments using a quantum mechanics/molecular mechanics (QM/MM) setup. SHARC is a trajectory surface-hoping method that can incorporate the simultaneous effects of nonadiabatic and spin-orbit couplings in the excited-state dynamics of molecular systems. COBRAMM allows ground- and excited-state QM/MM calculations using a subtractive scheme, with electrostatic embedding and a hydrogen link-atom approach. The combination of both free and open-source program packages provides a modular and extensive framework to model nonadiabatic processes after light irradiation from the atomistic scale to the nano-scale. As an example, the relaxation of acrolein from S1 to T1 in solution is provided.
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Affiliation(s)
- Davide Avagliano
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1180 Vienna, Austria
| | - Matteo Bonfanti
- Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Viale Del Risorgimento, 4, I-40136 Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Viale Del Risorgimento, 4, I-40136 Bologna, Italy
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, A-1180 Vienna, Austria.,Vienna Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währinger Straße 17, A-1180 Vienna, Austria
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45
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Green JA, Yaghoubi Jouybari M, Asha H, Santoro F, Improta R. Fragment Diabatization Linear Vibronic Coupling Model for Quantum Dynamics of Multichromophoric Systems: Population of the Charge-Transfer State in the Photoexcited Guanine-Cytosine Pair. J Chem Theory Comput 2021; 17:4660-4674. [PMID: 34270258 DOI: 10.1021/acs.jctc.1c00416] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We introduce a method (FrD-LVC) based on a fragment diabatization (FrD) for the parametrization of a linear vibronic coupling (LVC) model suitable for studying the photophysics of multichromophore systems. In combination with effective quantum dynamics (QD) propagations with multilayer multiconfigurational time-dependent Hartree (ML-MCTDH), the FrD-LVC approach gives access to the study of the competition between intrachromophore decays, like those at conical intersections, and interchromophore processes, like exciton localization/delocalization and the involvement of charge-transfer (CT) states. We used FrD-LVC parametrized with time-dependent density functional theory (TD-DFT) calculations, adopting either CAM-B3LYP or ωB97X-D functionals, to study the ultrafast photoexcited QD of a guanine-cytosine (GC) hydrogen-bonded pair, within a Watson-Crick arrangement, considering up to 12 coupled diabatic electronic states and the effect of all of the 99 vibrational coordinates. The bright excited states localized on C and, especially, on G are predicted to be strongly coupled to the G → C CT state, which is efficiently and quickly populated after an excitation to any of the four lowest energy bright local excited states. Our QD simulations show that more than 80% of the excited population on G and ∼50% of that on C decay to this CT state in less than 50 fs. We investigate the role of vibronic effects in the population of the CT state and show that it depends mainly on its large reorganization energy so that it can occur even when it is significantly less stable than the bright states in the Franck-Condon region. At the same time, we document that the formation of the GC pair almost suppresses the involvement of dark nπ* excited states in the photoactivated dynamics.
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Affiliation(s)
- James A Green
- Istituto di Biostrutture e Bioimmagini (IBB-CNR), Consiglio Nazionale delle Ricerche, via Mezzocannone 16, I-80136 Napoli, Italy
| | - Martha Yaghoubi Jouybari
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), Consiglio Nazionale delle Ricerche, SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Haritha Asha
- Istituto di Biostrutture e Bioimmagini (IBB-CNR), Consiglio Nazionale delle Ricerche, via Mezzocannone 16, I-80136 Napoli, Italy
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), Consiglio Nazionale delle Ricerche, SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini (IBB-CNR), Consiglio Nazionale delle Ricerche, via Mezzocannone 16, I-80136 Napoli, Italy
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46
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Nottoli M, Cupellini L, Lipparini F, Granucci G, Mennucci B. Multiscale Models for Light-Driven Processes. Annu Rev Phys Chem 2021; 72:489-513. [PMID: 33561359 DOI: 10.1146/annurev-physchem-090419-104031] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Multiscale models combining quantum mechanical and classical descriptions are a very popular strategy to simulate properties and processes of complex systems. Many alternative formulations have been developed, and they are now available in all of the most widely used quantum chemistry packages. Their application to the study of light-driven processes, however, is more recent, and some methodological and numerical problems have yet to be solved. This is especially the case for the polarizable formulation of these models, the recent advances in which we review here. Specifically, we identify and describe the most important specificities that the polarizable formulation introduces into both the simulation of excited-state dynamics and the modeling of excitation energy and electron transfer processes.
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Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy;
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy;
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy;
| | - Giovanni Granucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy;
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy;
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47
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Santoro F, Green JA, Martinez-Fernandez L, Cerezo J, Improta R. Quantum and semiclassical dynamical studies of nonadiabatic processes in solution: achievements and perspectives. Phys Chem Chem Phys 2021; 23:8181-8199. [PMID: 33875988 DOI: 10.1039/d0cp05907b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We concisely review the main methodological approaches to model nonadiabatic dynamics in isotropic solutions and their applications. Three general classes of models are identified as the most used to include solvent effects in the simulations. The first model describes the solvent as a set of harmonic collective modes coupled to the solute degrees of freedom, and the second as a continuum, while the third explicitly includes solvent molecules in the calculations. The issues related to the use of these models in semiclassical and quantum dynamical simulations are discussed, as well as the main limitations and perspectives of each approach.
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Affiliation(s)
- Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - James A Green
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
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48
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Maity S, Daskalakis V, Elstner M, Kleinekathöfer U. Multiscale QM/MM molecular dynamics simulations of the trimeric major light-harvesting complex II. Phys Chem Chem Phys 2021; 23:7407-7417. [PMID: 33876100 DOI: 10.1039/d1cp01011e] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photosynthetic processes are driven by sunlight. Too little of it and the photosynthetic machinery cannot produce the reductive power to drive the anabolic pathways. Too much sunlight and the machinery can get damaged. In higher plants, the major Light-Harvesting Complex (LHCII) efficiently absorbs the light energy, but can also dissipate it when in excess (quenching). In order to study the dynamics related to the quenching process but also the exciton dynamics in general, one needs to accurately determine the so-called spectral density which describes the coupling between the relevant pigment modes and the environmental degrees of freedom. To this end, Born-Oppenheimer molecular dynamics simulations in a quantum mechanics/molecular mechanics (QM/MM) fashion utilizing the density functional based tight binding (DFTB) method have been performed for the ground state dynamics. Subsequently, the time-dependent extension of the long-range-corrected DFTB scheme has been employed for the excited state calculations of the individual chlorophyll-a molecules in the LHCII complex. The analysis of this data resulted in spectral densities showing an astonishing agreement with the experimental counterpart in this rather large system. This consistency with an experimental observable also supports the accuracy, robustness, and reliability of the present multi-scale scheme. To the best of our knowledge, this is the first theoretical attempt on this large complex system is ever made to accurately simulate the spectral density. In addition, the resulting spectral densities and site energies were used to determine the exciton transfer rate within a special pigment pair consisting of a chlorophyll-a and a carotenoid molecule which is assumed to play a role in the balance between the light harvesting and quenching modes.
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Affiliation(s)
- Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.
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49
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Freixas VM, White AJ, Nelson T, Song H, Makhov DV, Shalashilin D, Fernandez-Alberti S, Tretiak S. Nonadiabatic Excited-State Molecular Dynamics Methodologies: Comparison and Convergence. J Phys Chem Lett 2021; 12:2970-2982. [PMID: 33730495 DOI: 10.1021/acs.jpclett.1c00266] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Direct atomistic simulation of nonadiabatic molecular dynamics is a challenging goal that allows important insights into fundamental physical phenomena. A variety of frameworks, ranging from fully quantum treatment of nuclei to semiclassical and mixed quantum-classical approaches, were developed. These algorithms are then coupled to specific electronic structure techniques. Such diversity and lack of standardized implementation make it difficult to compare the performance of different methodologies when treating realistic systems. Here, we compare three popular methods for large chromophores: Ehrenfest, surface hopping, and multiconfigurational Ehrenfest with ab initio multiple cloning (MCE-AIMC). These approaches are implemented in the NEXMD software, which features a common computational chemistry model. The resulting comparisons reveal the method performance for population relaxation and coherent vibronic dynamics. Finally, we study the numerical convergence of MCE-AIMC algorithms by considering the number of trajectories, cloning thresholds, and Gaussian wavepacket width. Our results provide helpful reference data for selecting an optimal methodology for simulating excited-state molecular dynamics.
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Affiliation(s)
- Victor M Freixas
- Universidad Nacional de Quilmes, Roque Saénz Peña 352, B1876BXD Bernal, Argentina
| | - Alexander J White
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Tammie Nelson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Huajing Song
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Dmitry V Makhov
- School of Chemistry, University of Leeds, Leeds LS2 9JT, U.K
- School of Mathematics, University of Bristol, Bristol BS8 1TW, U.K
| | | | | | - Sergei Tretiak
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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50
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Aleotti F, Aranda D, Yaghoubi Jouybari M, Garavelli M, Nenov A, Santoro F. Parameterization of a linear vibronic coupling model with multiconfigurational electronic structure methods to study the quantum dynamics of photoexcited pyrene. J Chem Phys 2021; 154:104106. [PMID: 33722019 DOI: 10.1063/5.0044693] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
With this work, we present a protocol for the parameterization of a Linear Vibronic Coupling (LVC) Hamiltonian for quantum dynamics using highly accurate multiconfigurational electronic structure methods such as RASPT2/RASSCF, combined with a maximum-overlap diabatization technique. Our approach is fully portable and can be applied to many medium-size rigid molecules whose excited state dynamics requires a quantum description. We present our model and discuss the details of the electronic structure calculations needed for the parameterization, analyzing critical situations that could arise in the case of strongly interacting excited states. The protocol was applied to the simulation of the excited state dynamics of the pyrene molecule, starting from either the first or the second bright state (S2 or S5). The LVC model was benchmarked against state-of-the-art quantum mechanical calculations with optimizations and energy scans and turned out to be very accurate. The dynamics simulations, performed including all active normal coordinates with the multilayer multiconfigurational time-dependent Hartree method, show good agreement with the available experimental data, endorsing prediction of the excited state mechanism, especially for S5, whose ultrafast deactivation mechanism was not yet clearly understood.
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Affiliation(s)
- Flavia Aleotti
- Dipartimento di Chimica Industriale "Toso Montanari," Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Daniel Aranda
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Martha Yaghoubi Jouybari
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari," Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari," Università di Bologna, Viale del Risorgimento 4, 40136 Bologna, Italy
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
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