1
|
Della Sala P, Calice U, Iuliano V, Geremia S, Hickey N, Belviso S, Summa FF, Monaco G, Gaeta C, Superchi S. Chirality Sensing of Cryptochiral Guests with Prism[n]arenes. Chemistry 2024; 30:e202401625. [PMID: 38717117 DOI: 10.1002/chem.202401625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Indexed: 06/11/2024]
Abstract
Optical chirality sensing has gained significant attention in recent years. Within this field, the quest for stereodynamic chiroptical probes capable of detecting cryptochiral guests presents a formidable challenge. Macrocycles exhibiting planar chirality have emerged as promising candidates for amplifying the chirality of cryptochiral guests. In this study, we demonstrate that the formation of host-guest complexes between cryptochiral molecules and planar chiral prismarenes triggers electronic circular dichroism (ECD) signals via host-guest complexation-induced chirality amplification. The absolute configuration of the most stable chiral macrocyclic host-guest complex has been established by resorting to both exciton model and DFT computations. Furthermore, we demonstrated that this supramolecular chirality sensing system can be employed to determine the enantiomeric composition of scalemic mixtures by measuring the ECD bands intensity. The information described here opens the way for the use of prismarenes as stereodynamic probes for sensing of cryptochiral guests.
Collapse
Affiliation(s)
- Paolo Della Sala
- Laboratory of Supramolecular Chemistry, Dipartimento di Chimica e Biologia "A. Zambelli", Università degli Studi di Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, Salerno, Italy
| | - Umberto Calice
- Dipartimento di Scienze, Università della Basilicata, Via dell'Ateneo Lucano, 10, 85100, Potenza, Italy
| | - Veronica Iuliano
- Laboratory of Supramolecular Chemistry, Dipartimento di Chimica e Biologia "A. Zambelli", Università degli Studi di Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, Salerno, Italy
| | - Silvano Geremia
- Centro di Eccellenza in Biocristallografia, Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Neal Hickey
- Centro di Eccellenza in Biocristallografia, Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Sandra Belviso
- Dipartimento di Scienze, Università della Basilicata, Via dell'Ateneo Lucano, 10, 85100, Potenza, Italy
| | - Francesco F Summa
- Laboratory of Supramolecular Chemistry, Dipartimento di Chimica e Biologia "A. Zambelli", Università degli Studi di Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, Salerno, Italy
| | - Guglielmo Monaco
- Laboratory of Supramolecular Chemistry, Dipartimento di Chimica e Biologia "A. Zambelli", Università degli Studi di Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, Salerno, Italy
| | - Carmine Gaeta
- Laboratory of Supramolecular Chemistry, Dipartimento di Chimica e Biologia "A. Zambelli", Università degli Studi di Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, Salerno, Italy
| | - Stefano Superchi
- Dipartimento di Scienze, Università della Basilicata, Via dell'Ateneo Lucano, 10, 85100, Potenza, Italy
| |
Collapse
|
2
|
Ennist NM, Wang S, Kennedy MA, Curti M, Sutherland GA, Vasilev C, Redler RL, Maffeis V, Shareef S, Sica AV, Hua AS, Deshmukh AP, Moyer AP, Hicks DR, Swartz AZ, Cacho RA, Novy N, Bera AK, Kang A, Sankaran B, Johnson MP, Phadkule A, Reppert M, Ekiert D, Bhabha G, Stewart L, Caram JR, Stoddard BL, Romero E, Hunter CN, Baker D. De novo design of proteins housing excitonically coupled chlorophyll special pairs. Nat Chem Biol 2024; 20:906-915. [PMID: 38831036 PMCID: PMC11213709 DOI: 10.1038/s41589-024-01626-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
Natural photosystems couple light harvesting to charge separation using a 'special pair' of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C2-symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.
Collapse
Affiliation(s)
- Nathan M Ennist
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - Shunzhi Wang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Madison A Kennedy
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Mariano Curti
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | | | | | - Rachel L Redler
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Valentin Maffeis
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | - Saeed Shareef
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain
| | - Anthony V Sica
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ash Sueh Hua
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Arundhati P Deshmukh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Adam P Moyer
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Derrick R Hicks
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Avi Z Swartz
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ralph A Cacho
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nathan Novy
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Amala Phadkule
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Damian Ekiert
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Gira Bhabha
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Justin R Caram
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Elisabet Romero
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | - C Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| |
Collapse
|
3
|
Dai Y, Rambaldi F, Negri F. Eclipsed and Twisted Excimers of Pyrene and 2-Azapyrene: How Nitrogen Substitution Impacts Excimer Emission. Molecules 2024; 29:507. [PMID: 38276585 PMCID: PMC11154402 DOI: 10.3390/molecules29020507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Due to their unique photophysical and electronic properties, pyrene and its analogues have been the subject of extensive research in recent decades. The propensity of pyrene and its derivatives to form excimers has found wide application in various fields. Nitrogen-substituted pyrene derivatives display similar photophysical properties, but for them, excimer emission has not been reported to date. Here, we use time-dependent density functional theory (TD-DFT) calculations to investigate the low-lying exciton states of dimers of pyrene and 2-azapyrene. The excimer equilibrium structures are determined and the contribution of charge transfer (CT) excitations and intermolecular interactions to the exciton states is disclosed using a diabatization procedure. The study reveals that the dimers formed by the two molecules have quite similar exciton-state patterns, in which the relevant CT contributions govern the formation of excimer states, along with the La/Lb state inversion. In contrast with pyrene, the dipole-dipole interactions in 2-azapyrene stabilize the dark eclipsed excimer structure and increase the barrier for conversion into a bright twisted excimer. It is suggested that these differences in the nitrogen-substituted derivative might influence the excimer emission properties.
Collapse
Affiliation(s)
- Yasi Dai
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, 40126 Bologna, Italy; (Y.D.); (F.R.)
- Center for Chemical Catalysis—C3, Alma Mater Studiorum—Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Filippo Rambaldi
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, 40126 Bologna, Italy; (Y.D.); (F.R.)
| | - Fabrizia Negri
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, 40126 Bologna, Italy; (Y.D.); (F.R.)
- Center for Chemical Catalysis—C3, Alma Mater Studiorum—Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
- Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Research Unit of Bologna, 40126 Bologna, Italy
| |
Collapse
|
4
|
Ozaydin B, Curutchet C. Unraveling the role of thermal fluctuations on the exciton structure of the cryptophyte PC612 and PC645 photosynthetic antenna complexes. Front Mol Biosci 2023; 10:1268278. [PMID: 37790875 PMCID: PMC10544999 DOI: 10.3389/fmolb.2023.1268278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/30/2023] [Indexed: 10/05/2023] Open
Abstract
Protein scaffolds play a crucial role in tuning the light harvesting properties of photosynthetic pigment-protein complexes, influencing pigment-protein and pigment-pigment excitonic interactions. Here, we investigate the influence of thermal dynamic effects on the protein tuning mechanisms of phycocyanin PC645 and PC612 antenna complexes of cryptophyte algae, featuring closed or open quaternary structures. We employ a dual molecular dynamics (MD) strategy that combines extensive classical MD simulations with multiple short Born-Oppenheimer quantum/molecular mechanical (QM/MM) simulations to accurately account for both static and dynamic disorder effects. Additionally, we compare the results with an alternative protocol based on multiple QM/MM geometry optimizations of the pigments. Subsequently, we employ polarizable QM/MM calculations using time-dependent density functional theory (TD-DFT) to compute the excited states, and we adopt the full cumulant expansion (FCE) formalism to describe the absorption and circular dichroism spectra. Our findings indicate that thermal effects have only minor impacts on the energy ladder in PC612, despite its remarkable flexibility owing to an open quaternary structure. In striking contrast, thermal effects significantly influence the properties of PC645 due to the absence of a hydrogen bond controlling the twist of ring D in PCB β82 bilins, as well as the larger impact of fluctuations on the excited states of MBV pigments, which possess a higher conjugation length compared to other bilin types. Overall, the dual MD protocol combined with the FCE formalism yields excellent spectral properties for PC612 and PC645, and the resultant excitonic Hamiltonians pave the way for future investigations concerning the implications of open and closed quaternary structures on phycocyanin light harvesting properties.
Collapse
Affiliation(s)
- Beste Ozaydin
- Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona (UB), Barcelona, Spain
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona (UB), Barcelona, Spain
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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.
Collapse
Affiliation(s)
- Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy
| |
Collapse
|
7
|
Cupellini L, Qian P, Nguyen-Phan TC, Gardiner AT, Cogdell RJ. Quantum chemical elucidation of a sevenfold symmetric bacterial antenna complex. PHOTOSYNTHESIS RESEARCH 2023; 156:75-87. [PMID: 35672557 PMCID: PMC10070313 DOI: 10.1007/s11120-022-00925-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The light-harvesting complex 2 (LH2) of purple bacteria is one of the most studied photosynthetic antenna complexes. Its symmetric structure and ring-like bacteriochlorophyll arrangement make it an ideal system for theoreticians and spectroscopists. LH2 complexes from most bacterial species are thought to have eightfold or ninefold symmetry, but recently a sevenfold symmetric LH2 structure from the bacterium Mch. purpuratum was solved by Cryo-Electron microscopy. This LH2 also possesses unique near-infrared absorption and circular dichroism (CD) spectral properties. Here we use an atomistic strategy to elucidate the spectral properties of Mch. purpuratum LH2 and understand the differences with the most commonly studied LH2 from Rbl. acidophilus. Our strategy exploits a combination of molecular dynamics simulations, multiscale polarizable quantum mechanics/molecular mechanics calculations, and lineshape simulations. Our calculations reveal that the spectral properties of LH2 complexes are tuned by site energies and exciton couplings, which in turn depend on the structural fluctuations of the bacteriochlorophylls. Our strategy proves effective in reproducing the absorption and CD spectra of the two LH2 complexes, and in uncovering the origin of their differences. This work proves that it is possible to obtain insight into the spectral tuning strategies of purple bacteria by quantitatively simulating the spectral properties of their antenna complexes.
Collapse
Affiliation(s)
- Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124, Pisa, Italy.
| | - Pu Qian
- Materials and Structure Analysis, Thermofisher Scientific, Achtseweg Nordic 5, 5651 GTC, Eindhoven, The Netherlands
| | - Tu C Nguyen-Phan
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Alastair T Gardiner
- Laboratory of Anoxygenic Phototrophs, Centre Algatech, Novohradská 237 - Opatovický mlýn, 379 01, Třeboň, Czech Republic
| | - Richard J Cogdell
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, G12 8QQ, UK
| |
Collapse
|
8
|
Asha H, Green JA, Esposito L, Santoro F, Improta R. Computing the electronic circular dichroism spectrum of DNA quadruple helices of different topology: A critical test for a generalized excitonic model based on a fragment diabatization. Chirality 2023; 35:298-310. [PMID: 36775278 DOI: 10.1002/chir.23540] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 02/14/2023]
Abstract
In this study, we exploit a recently developed fragment diabatization-based excitonic model, FrDEx, to simulate the electronic circular dichroism (ECD) spectra of three guanine-rich DNA sequences arranged in guanine quadruple helices with different topologies: thrombin binding aptamer (antiparallel), c-Myc promoter (parallel), and human telomeric sequence (3+1 hybrid). Starting from time-dependent density functional theory (TD-DFT) calculations with the M052X functional, we apply our protocol to parameterize the FrDEX Hamiltonian, which accounts for electron density overlap and includes both the coupling with charge transfer transitions and the effect of the surrounding bases on the local excitation of each chromophore. The TD-DFT/M052X spectral shapes are in good agreement with the experimental ones, the main source of discrepancy being related to the intrinsic error on the computed transition energies of guanine monomer. FrDEx spectra are fairly close to the reference TD-DFT ones, allowing a significant advance with respect to a more standard excitonic Hamiltonian. We also show that the ECD spectra are sensitive to the inclusion of the inner K + $$ {}^{+} $$ cation in the calculation.
Collapse
Affiliation(s)
- Haritha Asha
- Istituto di Biostrutture e Bioimmagini, CNR, Napoli, Italy
| | - James A Green
- Institut für Physikalische Theoretische Chemie, Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | | | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Pisa, Italy
| | | |
Collapse
|
9
|
Gu Y, Guberman-Pfeffer MJ, Srikanth V, Shen C, Giska F, Gupta K, Londer Y, Samatey FA, Batista VS, Malvankar NS. Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity. Nat Microbiol 2023; 8:284-298. [PMID: 36732469 PMCID: PMC9999484 DOI: 10.1038/s41564-022-01315-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 12/20/2022] [Indexed: 02/04/2023]
Abstract
OmcZ nanowires produced by Geobacter species have high electron conductivity (>30 S cm-1). Of 111 cytochromes present in G. sulfurreducens, OmcZ is the only known nanowire-forming cytochrome essential for the formation of high-current-density biofilms that require long-distance (>10 µm) extracellular electron transport. However, the mechanisms underlying OmcZ nanowire assembly and high conductivity are unknown. Here we report a 3.5-Å-resolution cryogenic electron microscopy structure for OmcZ nanowires. Our structure reveals linear and closely stacked haems that may account for conductivity. Surface-exposed haems and charge interactions explain how OmcZ nanowires bind to diverse extracellular electron acceptors and how organization of nanowire network re-arranges in different biochemical environments. In vitro studies explain how G. sulfurreducens employ a serine protease to control the assembly of OmcZ monomers into nanowires. We find that both OmcZ and serine protease are widespread in environmentally important bacteria and archaea, thus establishing a prevalence of nanowire biogenesis across diverse species and environments.
Collapse
Affiliation(s)
- Yangqi Gu
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
- PNAC division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Matthew J Guberman-Pfeffer
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vishok Srikanth
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Cong Shen
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Microbiology, Yale University, New Haven, CT, USA
| | - Fabian Giska
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Kallol Gupta
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Yuri Londer
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Fadel A Samatey
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Nikhil S Malvankar
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
| |
Collapse
|
10
|
Dai Y, Calzolari A, Zubiria-Ulacia M, Casanova D, Negri F. Intermolecular Interactions and Charge Resonance Contributions to Triplet and Singlet Exciton States of Oligoacene Aggregates. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010119. [PMID: 36615311 PMCID: PMC9822017 DOI: 10.3390/molecules28010119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022]
Abstract
Intermolecular interactions modulate the electro-optical properties of molecular materials and the nature of low-lying exciton states. Molecular materials composed by oligoacenes are extensively investigated for their semiconducting and optoelectronic properties. Here, we analyze the exciton states derived from time-dependent density functional theory (TDDFT) calculations for two oligoacene model aggregates: naphthalene and anthracene dimers. To unravel the role of inter-molecular interactions, a set of diabatic states is selected, chosen to coincide with local (LE) and charge-transfer (CT) excitations within a restricted orbital space including two occupied and two unoccupied orbitals for each molecular monomer. We study energy profiles and disentangle inter-state couplings to disclose the (CT) character of singlet and triplet exciton states and assess the influence of inter-molecular orientation by displacing one molecule with respect to the other along the longitudinal translation coordinate. The analysis shows that (CT) contributions are relevant, although comparably less effective for triplet excitons, and induce a non-negligible mixed character to the low-lying exciton states for eclipsed monomers and for small translational displacements. Such (CT) contributions govern the La/Lb state inversion occurring for the low-lying singlet exciton states of naphthalene dimer and contribute to the switch from H- to J-aggregate type of the strongly allowed Bb transition of both oligoacene aggregates.
Collapse
Affiliation(s)
- Yasi Dai
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, 40126 Bologna, Italy
| | - Alessandro Calzolari
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, 40126 Bologna, Italy
| | - Maria Zubiria-Ulacia
- Donostia International Physics Center (DIPC), 20018 Donostia-San Sebastian, Euskadi, Spain
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Manuel Lardizabal 3, 20018 Donostia-San Sebastian, Euskadi, Spain
| | - David Casanova
- Donostia International Physics Center (DIPC), 20018 Donostia-San Sebastian, Euskadi, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Euskadi, Spain
| | - Fabrizia Negri
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, 40126 Bologna, Italy
- INSTM UdR Bologna, 40126 Bologna, Italy
- Correspondence:
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Rogers DM, Do H, Hirst JD. Electronic circular dichroism of proteins computed using a diabatisation scheme. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2133748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Affiliation(s)
- David M. Rogers
- School of Chemistry, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Hainam Do
- Department of Chemical and Environmental Engineering and Key Laboratory of Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, Ningbo, People’s Republic of China
- New Materials Institute, University of Nottingham Ningbo China, Ningbo, People’s Republic of China
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham, United Kingdom
| |
Collapse
|
13
|
Segalina A, Aranda D, Green JA, Cristino V, Caramori S, Prampolini G, Pastore M, Santoro F. How the Interplay among Conformational Disorder, Solvation, Local, and Charge-Transfer Excitations Affects the Absorption Spectrum and Photoinduced Dynamics of Perylene Diimide Dimers: A Molecular Dynamics/Quantum Vibronic Approach. J Chem Theory Comput 2022; 18:3718-3736. [PMID: 35377648 PMCID: PMC9202308 DOI: 10.1021/acs.jctc.2c00063] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Indexed: 12/12/2022]
Abstract
In this contribution we present a mixed quantum-classical dynamical approach for the computation of vibronic absorption spectra of molecular aggregates and their nonadiabatic dynamics, taking into account the coupling between local excitations (LE) and charge-transfer (CT) states. The approach is based on an adiabatic (Ad) separation between the soft degrees of freedom (DoFs) of the system and the stiff vibrations, which are described by the quantum dynamics (QD) of wave packets (WPs) moving on the coupled potential energy surfaces (PESs) of the LE and CT states. These PESs are described with a linear vibronic coupling (LVC) Hamiltonian, parameterized by an overlap-based diabatization on the grounds of time-dependent density functional theory computations. The WPs time evolution is computed with the multiconfiguration time-dependent Hartree method, using effective modes defined through a hierarchical representation of the LVC Hamiltonian. The soft DoFs are sampled with classical molecular dynamics (MD), and the coupling between the slow and fast DoFs is included by recomputing the key parameters of the LVC Hamiltonians, specifically for each MD configuration. This method, named Ad-MD|gLVC, is applied to a perylene diimide (PDI) dimer in acetonitrile and water solutions, and it is shown to accurately reproduce the change in the vibronic features of the absorption spectrum upon aggregation. Moreover, the microscopic insight offered by the MD trajectories allows for a detailed understanding of the role played by the fluctuation of the aggregate structure on the shape of the vibronic spectrum and on the population of LE and CT states. The nonadiabatic QD predicts an extremely fast (∼50 fs) energy transfer between the two LEs. CT states have only a moderate effect on the absorption spectrum, despite the fact that after photoexcitation they are shown to acquire a fast and non-negligible population, highlighting their relevance in dictating the charge separation and transport in PDI-based optical devices.
Collapse
Affiliation(s)
- Alekos Segalina
- Université
de Lorraine and CNRS, LPCT, UMR 7019, F-54000 Nancy, France
| | - Daniel Aranda
- Instituto
de Ciencia Molecular (ICMol), Universidad
de Valencia, Catedrático J. Beltrán 2, 46980 Paterna, Valencia, Spain
| | - James A. Green
- Consiglio
Nazionale delle Ricerche, Istituto di Biostrutture
e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| | - Vito Cristino
- Dipartimento
di Scienze Chimiche, Farmaceutiche ed Agrarie, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Stefano Caramori
- Dipartimento
di Scienze Chimiche, Farmaceutiche ed Agrarie, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Giacomo Prampolini
- Istituto
di Chimica dei Composti Organo Metallici, Consiglio Nazionale delle Ricerche, (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi
1, I-56124 Pisa, Italy
| | | | - Fabrizio Santoro
- Istituto
di Chimica dei Composti Organo Metallici, Consiglio Nazionale delle Ricerche, (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi
1, I-56124 Pisa, Italy
| |
Collapse
|
14
|
Structure of the stress-related LHCSR1 complex determined by an integrated computational strategy. Commun Biol 2022; 5:145. [PMID: 35177775 PMCID: PMC8854571 DOI: 10.1038/s42003-022-03083-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/25/2022] [Indexed: 11/08/2022] Open
Abstract
Light-harvesting complexes (LHCs) are pigment-protein complexes whose main function is to capture sunlight and transfer the energy to reaction centers of photosystems. In response to varying light conditions, LH complexes also play photoregulation and photoprotection roles. In algae and mosses, a sub-family of LHCs, light-harvesting complex stress-related (LHCSR), is responsible for photoprotective quenching. Despite their functional and evolutionary importance, no direct structural information on LHCSRs is available that can explain their unique properties. In this work, we propose a structural model of LHCSR1 from the moss P. patens, obtained through an integrated computational strategy that combines homology modeling, molecular dynamics, and multiscale quantum chemical calculations. The model is validated by reproducing the spectral properties of LHCSR1. Our model reveals the structural specificity of LHCSR1, as compared with the CP29 LH complex, and poses the basis for understanding photoprotective quenching in mosses. The structure of the moss P. patens light-harvesting complex stress-related 1 (LHCSR1) is determined using a multi-scale computational approach for investigations of its photoprotective function.
Collapse
|
15
|
Impact of Charge-Resonance Excitations on CT-Mediated J-Type Aggregation in Singlet and Triplet Exciton States of Perylene Di-Imide Aggregates: A TDDFT Investigation. COMPUTATION 2022. [DOI: 10.3390/computation10020018] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The modulation of intermolecular interactions upon aggregation induces changes in excited state properties of organic molecules that can be detrimental for some optoelectronic applications but can be exploited for others. The time-dependent density functional theory (TDDFT) is a cost-effective approach to determining the exciton states of molecular aggregates, and it has been shown to provide reliable results when coupled with the appropriate choice of the functional. Here we apply a general procedure to analyze the aggregates’ exciton states derived from TDDFT calculations in terms of diabatic states chosen to coincide with local (LE) and charge-transfer (CT) excitations within a restricted orbital space. We apply the approach to study energy profiles, interstate couplings, and the charge-transfer character of singlet and triplet exciton states of perylene di-imide aggregates (PDI). We focus on the intermolecular displacement along the longitudinal translation coordinate, which mimics different amounts of slip-stacking observed in PDI crystals. The analysis, in terms of symmetry-adapted Frenkel excitations (FE) and charge-resonance (CR) states and their interactions, discloses how the interchange of the H/J character for small longitudinal shifts, previously reported for singlet exciton states, also occurs for triplet excitons.
Collapse
|
16
|
Fujita T, Noguchi Y. Fragment-Based Excited-State Calculations Using the GW Approximation and the Bethe-Salpeter Equation. J Phys Chem A 2021; 125:10580-10592. [PMID: 34871000 DOI: 10.1021/acs.jpca.1c07337] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein, we present a fragment-based approach for calculating the charged and neutral excited states in molecular systems, based on the many-body Green's function method within the GW approximation and the Bethe-Salpeter equation (BSE). The implementation relies on the many-body expansion of the total irreducible polarizability on the basis of fragment molecular orbitals. The GW quasi-particle energies in complex molecular environments are obtained by the GW calculation for the target fragment plus induced polarization contributions of the surrounding fragments at the static Coulomb-hole plus screened exchange level. In addition, we develop a large-scale GW/BSE method for calculating the delocalized excited states of molecular aggregates, based on the fragment molecular orbital method and the exciton model. The accuracy of fragment-based GW and GW/BSE methods was evaluated on molecular clusters and molecular crystals. We found that the accuracy of the total irreducible polarizability can be improved systematically by including two-body correction terms, and the fragment-based calculations can reasonably reproduce the results of the corresponding unfragmented calculations with a relative error of less than 100 meV. The proposed approach enables efficient excited-state calculations for large molecular systems with reasonable accuracy.
Collapse
Affiliation(s)
- Takatoshi Fujita
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai, Ibaraki 319-1106, Japan
| | - Yoshifumi Noguchi
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu, Shizuoka 432-8561, Japan
| |
Collapse
|
17
|
Pescitelli G. ECD exciton chirality method today: a modern tool for determining absolute configurations. Chirality 2021; 34:333-363. [PMID: 34791704 PMCID: PMC9299504 DOI: 10.1002/chir.23393] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 02/02/2023]
Abstract
The application of the exciton chirality method (ECM) to interpret electronic circular dichroism (ECD) spectra is a well‐established and still popular approach to assign the absolute configuration (AC) of natural products, chiral organic compounds, and organometallic species. The method applies to compounds containing at least two chromophores with electric dipole allowed transitions (e.g., π–π* transitions). The exciton chirality rule correlates the sign of an exciton couplet (two ECD bands with opposite sign and similar intensity) with the overall molecular stereochemistry, including the AC. A correct application of the ECM requires three main prerequisites: (a) the knowledge of the molecular conformation, (b) the knowledge of the directions of the electric transition moments (TDMs), and (c) the assumption that the exciton coupling mechanism must be the major source of the observed ECD signals. All these prerequisites can be easily verified by means of quantum‐mechanical (QM) calculations. In the present review, we shortly introduce the general principles that underpin the use of the ECM for configurational assignments and survey its applications, both classic ones and some reported in the recent literature. Based on these examples, we will stress the advantages of the ECM but also the key requisites for its correct application. Additionally, we will discuss the dependence of the couplet sign on geometrical parameters (angles α,β,γ between TDMs), which can be helpful for discerning the sign of exciton chirality in ambiguous situations. Finally, we will present a molecular orbital (MO) description of the exciton coupling phenomenon.
Collapse
Affiliation(s)
- Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Pisa, Italy
| |
Collapse
|
18
|
Asha H, Green JA, Martinez-Fernandez L, Esposito L, Improta R. Electronic Circular Dichroism Spectra of DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations including Charge Transfer States. Molecules 2021; 26:molecules26164789. [PMID: 34443377 PMCID: PMC8398971 DOI: 10.3390/molecules26164789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/18/2022] Open
Abstract
We here investigate the Electronic Circular Dichroism (ECD) Spectra of two representative Guanine-rich sequences folded in a Quadruple helix (GQ), by using a recently developed fragment diabatisation based excitonic model (FrDEx). FrDEx can include charge transfer (CT) excited states and consider the effect of the surrounding monomers on the local excitations (LEs). When applied to different structures generated by molecular dynamics simulations on a fragment of the human telomeric sequence (Tel21/22), FrDEx provides spectra fully consistent with the experimental one and in good agreement with that provided by quantum mechanical (QM) method used for its parametrization, i.e., TD-M05-2X. We show that the ECD spectrum is moderately sensitive to the conformation adopted by the bases of the loops and more significantly to the thermal fluctuations of the Guanine tetrads. In particular, we show how changes in the overlap of the tetrads modulate the intensity of the ECD signal. We illustrate how this correlates with changes in the character of the excitonic states at the bottom of the La and Lb bands, with larger LE and CT involvement of bases that are more closely stacked. As an additional test, we utilised FrDEx to compute the ECD spectrum of the monomeric and dimeric forms of a GQ forming sequence T30695 (5′TGGGTGGGTGGGTGGG3′), i.e., a system containing up to 24 Guanine bases, and demonstrated the satisfactory reproduction of the experimental and QM reference results. This study provides new insights on the effects modulating the ECD spectra of GQs and, more generally, further validates FrDEx as an effective tool to predict and assign the spectra of closely stacked multichromophore systems.
Collapse
Affiliation(s)
- Haritha Asha
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy; (H.A.); (J.A.G.); (L.E.)
| | - James A. Green
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy; (H.A.); (J.A.G.); (L.E.)
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and IADCHEM (Institute for Advanced Research in Chemistry), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain;
| | - Luciana Esposito
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy; (H.A.); (J.A.G.); (L.E.)
| | - Roberto Improta
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via Mezzocannone 16, I-80136 Napoli, Italy; (H.A.); (J.A.G.); (L.E.)
- Correspondence:
| |
Collapse
|
19
|
Segatta F, Nenov A, Nascimento DR, Govind N, Mukamel S, Garavelli M. iSPECTRON: A simulation interface for linear and nonlinear spectra with ab-initio quantum chemistry software. J Comput Chem 2021; 42:644-659. [PMID: 33556195 DOI: 10.1002/jcc.26485] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 12/18/2022]
Abstract
We introduce iSPECTRON, a program that parses data from common quantum chemistry software (NWChem, OpenMolcas, Gaussian, Cobramm, etc.), produces the input files for the simulation of linear and nonlinear spectroscopy of molecules with the Spectron code, and analyzes the spectra with a broad range of tools. Vibronic spectra are expressed in term of the electronic eigenstates, obtained from quantum chemistry computations, and vibrational/bath effects are incorporated in the framework of the displaced harmonic oscillator model, where all required quantities are computed at the Franck-Condon point. The program capabilities are illustrated by simulating linear absorption, transient absorption and two dimensional electronic spectra of the pyrene molecule. Calculations at two levels of electronic structure theory, time-dependent density functional theory (with NWChem) and RASSCF/RASPT2 (with OpenMolcas) are presented and compared where possible. The iSPECTRON program is available online at https://github.com/ispectrongit/iSPECTRON/ and distributed open source under the terms of the Educational Community License version 2.0 (ECL 2.0).
Collapse
Affiliation(s)
- Francesco Segatta
- Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Bologna, Italy
| | - Daniel R Nascimento
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Niranjan Govind
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Shaul Mukamel
- Department of Chemistry and Department of Physics and Astronomy, University of California, Irvine, California, USA
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Bologna, Italy
| |
Collapse
|
20
|
Canola S, Bagnara G, Dai Y, Ricci G, Calzolari A, Negri F. Addressing the Frenkel and charge transfer character of exciton states with a model Hamiltonian based on dimer calculations: Application to large aggregates of perylene bisimide. J Chem Phys 2021; 154:124101. [PMID: 33810656 DOI: 10.1063/5.0045913] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
To understand the influence of interchromophoric arrangements on photo-induced processes and optical properties of aggregates, it is fundamental to assess the contribution of local excitations [charge transfer (CT) and Frenkel (FE)] to exciton states. Here, we apply a general procedure to analyze the adiabatic exciton states derived from time-dependent density functional theory calculations, in terms of diabatic states chosen to coincide with local excitations within a restricted orbital space. In parallel, motivated by the need of cost-effective approaches to afford the study of larger aggregates, we propose to build a model Hamiltonian based on calculations carried out on dimers composing the aggregate. Both approaches are applied to study excitation energy profiles and CT character modulation induced by interchromophore rearrangements in perylene bisimide aggregates up to a tetramer. The dimer-based approach closely reproduces the results of full-aggregate calculations, and an analysis in terms of symmetry-adapted diabatic states discloses the effects of CT/FE interactions on the interchange of the H-/J-character for small longitudinal shifts of the chromophores.
Collapse
Affiliation(s)
- Sofia Canola
- Università di Bologna, Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi, 2, 40126 Bologna, Italy
| | - Giuseppe Bagnara
- Università di Bologna, Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi, 2, 40126 Bologna, Italy
| | - Yasi Dai
- Università di Bologna, Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi, 2, 40126 Bologna, Italy
| | - Gaetano Ricci
- Università di Bologna, Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi, 2, 40126 Bologna, Italy
| | - Alessandro Calzolari
- Università di Bologna, Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi, 2, 40126 Bologna, Italy
| | - Fabrizia Negri
- Università di Bologna, Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi, 2, 40126 Bologna, Italy
| |
Collapse
|
21
|
Guido CA, Rotunno E, Zanfrognini M, Corni S, Grillo V. Exploring the Spatial Features of Electronic Transitions in Molecular and Biomolecular Systems by Swift Electrons. J Chem Theory Comput 2021; 17:2364-2373. [PMID: 33646769 PMCID: PMC8047794 DOI: 10.1021/acs.jctc.1c00045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
We
devise a new kind of experiment that extends the technology
of electron energy loss spectroscopy to probe (supra-)molecular systems: by using
an electron beam in a configuration that avoids
molecular damage and a very recently introduced electron optics setup
for the analysis of the outcoming electrons, one can obtain information
on the spatial features of the investigated excitations. Physical
insight into the proposed experiment is provided by means of a simple
but rigorous model to obtain the transition rate and selection rule.
Numerical simulations of DNA G-quadruplexes and other biomolecular
systems, based on time dependent density functional theory calculations,
point out that the conceived new technique can probe the multipolar
components and even the chirality of molecular transitions, superseding
the usual optical spectroscopies for those cases that are problematic,
such as dipole-forbidden transitions, at a very high spatial resolution.
Collapse
Affiliation(s)
- Ciro A Guido
- Dipartimento di Scienze Chimiche, Università di Padova, via F. Marzolo 1, 35131 Padova, Italy
| | - Enzo Rotunno
- CNR-NANO, Institute of Nanoscience, via Campi 213/A, Modena, Italy
| | | | - Stefano Corni
- Dipartimento di Scienze Chimiche, Università di Padova, via F. Marzolo 1, 35131 Padova, Italy.,CNR-NANO, Institute of Nanoscience, via Campi 213/A, Modena, Italy
| | - Vincenzo Grillo
- CNR-NANO, Institute of Nanoscience, via Campi 213/A, Modena, Italy
| |
Collapse
|
22
|
Green JA, Asha H, Santoro F, Improta R. Excitonic Model for Strongly Coupled Multichromophoric Systems: The Electronic Circular Dichroism Spectra of Guanine Quadruplexes as Test Cases. J Chem Theory Comput 2021; 17:405-415. [PMID: 33378185 DOI: 10.1021/acs.jctc.0c01100] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We here propose a general and flexible approach, based on fragment diabatization, which incorporates charge transfer states and significantly increases the reliability of excitonic Hamiltonians for systems where the chromophores are very close. This model (FrDEx) is used to compute the electronic circular dichroism and absorption spectra of two prototype guanine-rich DNA sequences folded in quadruple helices (GQs), i.e., a fragment of the human telomeric sequence (Tel21, antiparallel), and (TGGGGT)4 (TG4T, parallel). Calculations on different subsets of Tel21 and TG4T, from dimers to tetramers, show that FrDEx provides spectra close to the reference full quantum mechanical (QM) ones (obtained with time-dependent density functional theory), with significant improvements with respect to "standard" excitonic Hamiltonians. Furthermore, these tests enable the most cost-effective procedure for the whole GQ to be determined. FrDEx spectra of Tel21 and TG4T are also in good agreement with the QM and experimental ones and give access to interesting insights into the chemical-physical effects modulating the spectral signals. FrDEx could be profitably used to investigate many other biological and nanotechnological materials, from DNA to (opto)electronic polymers.
Collapse
Affiliation(s)
- James A Green
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| | - Haritha Asha
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| | - 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-56124 Pisa, Italy
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy
| |
Collapse
|
23
|
Coccia E, Fregoni J, Guido CA, Marsili M, Pipolo S, Corni S. Hybrid theoretical models for molecular nanoplasmonics. J Chem Phys 2020; 153:200901. [PMID: 33261492 DOI: 10.1063/5.0027935] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The multidisciplinary nature of the research in molecular nanoplasmonics, i.e., the use of plasmonic nanostructures to enhance, control, or suppress properties of molecules interacting with light, led to contributions from different theory communities over the years, with the aim of understanding, interpreting, and predicting the physical and chemical phenomena occurring at molecular- and nano-scale in the presence of light. Multiscale hybrid techniques, using a different level of description for the molecule and the plasmonic nanosystems, permit a reliable representation of the atomistic details and of collective features, such as plasmons, in such complex systems. Here, we focus on a selected set of topics of current interest in molecular plasmonics (control of electronic excitations in light-harvesting systems, polaritonic chemistry, hot-carrier generation, and plasmon-enhanced catalysis). We discuss how their description may benefit from a hybrid modeling approach and what are the main challenges for the application of such models. In doing so, we also provide an introduction to such models and to the selected topics, as well as general discussions on their theoretical descriptions.
Collapse
Affiliation(s)
- E Coccia
- Dipartimento di Scienze Chimiche e Farmaceutiche, Universit di Trieste, via L. Giorgieri 1, 34127 Trieste, Italy
| | - J Fregoni
- Dipartimento di Scienze Fisiche, Informatiche e Matematiche, Universit di Modena e Reggio Emilia, via Campi 213/A, 41125 Modena, Italy
| | - C A Guido
- Dipartimento di Scienze Chimiche, Universit di Padova, via F. Marzolo 1, 35131 Padova, Italy
| | - M Marsili
- Dipartimento di Scienze Chimiche, Universit di Padova, via F. Marzolo 1, 35131 Padova, Italy
| | - S Pipolo
- Université de Lille, CNRS, Centrale Lille, ENSCL, Université d'Artois UMR 8181-UCCS Unité de Catalyse et Chimie du Solide, F-59000 Lille, France
| | - S Corni
- Istituto Nanoscienze-CNR, via Campi 213/A, 41125 Modena, Italy
| |
Collapse
|
24
|
Ozcelik A, Aranda D, Gil‐Guerrero S, Pola‐Otero XA, Talavera M, Wang L, Behera SK, Gierschner J, Peña‐Gallego Á, Santoro F, Pereira‐Cameselle R, Alonso‐Gómez JL. Distinct Helical Molecular Orbitals through Conformational Lock**. Chemistry 2020; 26:17342-17349. [DOI: 10.1002/chem.202002561] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Ani Ozcelik
- Departamento de Química Orgánica Universidad de Vigo Campus Universitario 36310 Vigo Spain
| | - Daniel Aranda
- Istituto di Chimica dei Composti Organometallici Consiglio Nazionale delle Ricerche Pisa Italy
- Departamento de Química Física Universidad de Málaga Bulevar Louis Pasteur 31 Málaga 29010 Spain
| | - Sara Gil‐Guerrero
- Departamento de Química Física Universidad de Vigo Campus Universitario 36310 Vigo Spain
| | - Xaquín A. Pola‐Otero
- Departamento de Química Orgánica Universidad de Vigo Campus Universitario 36310 Vigo Spain
| | - Maria Talavera
- Department of Chemistry Humboldt Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Liangxuan Wang
- Madrid Institute for Advanced Studies IMDEA Nanoscience C/ Faraday 9, Ciudad Universitaria de Cantoblanco 28049 Madrid Spain
| | - Santosh Kumar Behera
- Madrid Institute for Advanced Studies IMDEA Nanoscience C/ Faraday 9, Ciudad Universitaria de Cantoblanco 28049 Madrid Spain
| | - Johannes Gierschner
- Madrid Institute for Advanced Studies IMDEA Nanoscience C/ Faraday 9, Ciudad Universitaria de Cantoblanco 28049 Madrid Spain
| | - Ángeles Peña‐Gallego
- Departamento de Química Física Universidad de Vigo Campus Universitario 36310 Vigo Spain
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici Consiglio Nazionale delle Ricerche Pisa Italy
| | | | | |
Collapse
|
25
|
Rivera M, Dommett M, Sidat A, Rahim W, Crespo-Otero R. fromage: A library for the study of molecular crystal excited states at the aggregate scale. J Comput Chem 2020; 41:1045-1058. [PMID: 31909830 PMCID: PMC7079081 DOI: 10.1002/jcc.26144] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/27/2019] [Accepted: 12/03/2019] [Indexed: 12/31/2022]
Abstract
The study of photoexcitations in molecular aggregates faces the twofold problem of the increased computational cost associated with excited states and the complexity of the interactions among the constituent monomers. A mechanistic investigation of these processes requires the analysis of the intermolecular interactions, the effect of the environment, and 3D arrangements or crystal packing on the excited states. A considerable number of techniques have been tailored to navigate these obstacles; however, they are usually restricted to in‐house codes and thus require a disproportionate effort to adopt by researchers approaching the field. Herein, we present the FRamewOrk for Molecular AGgregate Excitations (fromage), which implements a collection of such techniques in a Python library complemented with ready‐to‐use scripts. The program structure is presented and the principal features available to the user are described: geometrical analysis, exciton characterization, and a variety of ONIOM schemes. Each is illustrated by examples of diverse organic molecules in condensed phase settings. The program is available at https://github.com/Crespo-Otero-group/fromage.
Collapse
Affiliation(s)
- Miguel Rivera
- Department of Chemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Michael Dommett
- Department of Chemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Amir Sidat
- Department of Chemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Warda Rahim
- Department of Chemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Rachel Crespo-Otero
- Department of Chemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| |
Collapse
|
26
|
Martínez-Fernández L, Esposito L, Improta R. Studying the excited electronic states of guanine rich DNA quadruplexes by quantum mechanical methods: main achievements and perspectives. Photochem Photobiol Sci 2020; 19:436-444. [DOI: 10.1039/d0pp00065e] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calculations are providing more and more useful insights into the interaction between light and DNA quadruplexes.
Collapse
Affiliation(s)
- Lara Martínez-Fernández
- Departamento de Química
- Facultad de Ciencias
- Modulo 13 Universidad Autónoma de Madrid
- Campus de Excelencia UAM-CSIC Cantoblanco
- 28049 Madrid
| | | | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini
- CNR
- I-80134 Napoli
- Italy
| |
Collapse
|
27
|
Cardoso Ramos F, Nottoli M, Cupellini L, Mennucci B. The molecular mechanisms of light adaption in light-harvesting complexes of purple bacteria revealed by a multiscale modeling. Chem Sci 2019; 10:9650-9662. [PMID: 32055335 PMCID: PMC6988754 DOI: 10.1039/c9sc02886b] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/23/2019] [Indexed: 12/27/2022] Open
Abstract
The light-harvesting in photosynthetic purple bacteria can be tuned in response to the light conditions during cell growth. One of the used strategies is to change the energy of the excitons in the major fight-harvesting complex, commonly known as LH2. In the present study we report the first systematic investigation of the microscopic origin of the exciton tuning using three complexes, namely the common (high-light) and the low-light forms of LH2 from Rps. acidophila plus a third complex analogous to the PucD complex from Rps. palustris. The study is based on the combination of classical molecular dynamics of each complex in a lipid membrane and excitonic calculations based on a multiscale quantum mechanics/molecular mechanics approach including a polarizable embedding. From the comparative analysis, it comes out that the mechanisms that govern the adaptation of the complex to different light conditions use the different H-bonding environment around the bacteriochlorophyll pigments to dynamically control both internal and inter-pigment degrees of freedom. While the former have a large effect on the site energies, the latter significantly change the electronic couplings, but only the combination of the two effects can fully reproduce the tuning of the final excitons and explain the observed spectroscopic differences.
Collapse
Affiliation(s)
- Felipe Cardoso Ramos
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , Via G. Moruzzi 13 , 56124 Pisa , Italy .
| | - Michele Nottoli
- 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 .
| |
Collapse
|
28
|
Shiraogawa T, Ehara M. Theoretical Study on the Optical Properties of Multichromophoric Systems Based on an Exciton Approach: Modification Guidelines. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Takafumi Shiraogawa
- SOKENDAIThe Graduate University for Advanced Studies Nishigonaka 38, Myodaiji Okazaki 444-8585 Japan
| | - Masahiro Ehara
- SOKENDAIThe Graduate University for Advanced Studies Nishigonaka 38, Myodaiji Okazaki 444-8585 Japan
- Institute for Molecular Science and Research Center for Computational Science Nishigonaka 38, Myodaiji Okazaki 444-8585 Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB)Kyoto University Kyoto 615-8245 Japan
| |
Collapse
|
29
|
Plasser F, Gómez S, Menger MFSJ, Mai S, González L. Highly efficient surface hopping dynamics using a linear vibronic coupling model. Phys Chem Chem Phys 2018; 21:57-69. [PMID: 30306987 DOI: 10.1039/c8cp05662e] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We report an implementation of the linear vibronic coupling (LVC) model within the surface hopping dynamics approach and present utilities for parameterizing this model in a blackbox fashion. This results in an extremely efficient method to obtain qualitative and even semi-quantitative information about the photodynamical behavior of a molecule, and provides a new route toward benchmarking the results of surface hopping computations. The merits and applicability of the method are demonstrated in a number of applications. First, the method is applied to the SO2 molecule showing that it is possible to compute its absorption spectrum beyond the Condon approximation, and that all the main features and timescales of previous on-the-fly dynamics simulations of intersystem crossing are reproduced while reducing the computational effort by three orders of magnitude. The dynamics results are benchmarked against exact wavepacket propagations on the same LVC potentials and against a variation of the electronic structure level. Four additional test cases are presented to exemplify the broader applicability of the model. The photodynamics of the isomeric adenine and 2-aminopurine molecules are studied and it is shown that the LVC model correctly predicts ultrafast decay in the former and an extended excited-state lifetime in the latter. Futhermore, the method correctly predicts ultrafast intersystem crossing in the modified nucleobase 2-thiocytosine and its absence in 5-azacytosine while it fails to describe the ultrafast internal conversion to the ground state in the latter.
Collapse
Affiliation(s)
- Felix Plasser
- Department of Chemistry, Loughborough University, Loughborough, LE11 3TU, UK.
| | | | | | | | | |
Collapse
|
30
|
Abstract
The subtle details of the mechanism of energy flow from carotenoids to chlorophylls in biological light-harvesting complexes are still not fully understood, especially in the ultrafast regime. Here we focus on the antenna complex peridinin–chlorophyll a–protein (PCP), known for its remarkable efficiency of excitation energy transfer from carotenoids—peridinins—to chlorophylls. PCP solutions are studied by means of 2D electronic spectroscopy in different experimental conditions. Together with a global kinetic analysis and multiscale quantum chemical calculations, these data allow us to comprehensively address the contribution of the potential pathways of energy flow in PCP. These data support dominant energy transfer from peridinin S2 to chlorophyll Qy state via an ultrafast coherent mechanism. The coherent superposition of the two states is functional to drive population to the final acceptor state, adding an important piece of information in the quest for connections between coherent phenomena and biological functions. Energy transfer from carotenoids to chlorophylls in light-harvesting is still not fully understood, especially in the ultrafast regime. Here, the authors investigate the coherent dynamics of this process in peridinin-chlorophyll a-protein complex via 2D electronic spectroscopy and quantum chemical calculations.
Collapse
|
31
|
Nottoli M, Jurinovich S, Cupellini L, Gardiner AT, Cogdell R, Mennucci B. The role of charge-transfer states in the spectral tuning of antenna complexes of purple bacteria. PHOTOSYNTHESIS RESEARCH 2018; 137:215-226. [PMID: 29502240 DOI: 10.1007/s11120-018-0492-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 02/23/2018] [Indexed: 05/21/2023]
Abstract
The LH2 antenna complexes of purple bacteria occur, depending on light conditions, in various different spectroscopic forms, with a similar structure but different absorption spectra. The differences are related to point changes in the primary amino acid sequence, but the molecular-level relationship between these changes and the resulting spectrum is still not well understood. We undertook a systematic quantum chemical analysis of all the main factors that contribute to the exciton structure, looking at how the environment modulates site energies and couplings in the B800-850 and B800-820 spectroscopic forms of LH2. A multiscale approach combining quantum chemistry and an atomistic classical embedding has been used where mutual polarization effects between the two parts are taken into account. We find that the loss of hydrogen bonds following amino acid changes can only explain a part of the observed blue-shift in the B850 band. The coupling of excitonic states to charge-transfer states, which is different in the two forms, contributes with a similar amount to the overall blue-shift.
Collapse
Affiliation(s)
- Michele Nottoli
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124, Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124, Pisa, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124, Pisa, Italy
| | - Alastair T Gardiner
- Glasgow Biomedical Research Centre, Institute of Molecular Cell and Systems Biology, University of Glasgow, 126 University Place, Glasgow, G12 8TA, Scotland, UK
| | - Richard Cogdell
- Glasgow Biomedical Research Centre, Institute of Molecular Cell and Systems Biology, University of Glasgow, 126 University Place, Glasgow, G12 8TA, Scotland, UK
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124, Pisa, Italy.
| |
Collapse
|
32
|
Ianeselli A, Orioli S, Spagnolli G, Faccioli P, Cupellini L, Jurinovich S, Mennucci B. Atomic Detail of Protein Folding Revealed by an Ab Initio Reappraisal of Circular Dichroism. J Am Chem Soc 2018; 140:3674-3682. [DOI: 10.1021/jacs.7b12399] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alan Ianeselli
- Centre for Integrative Biology, Trento University, Via Sommarive 9, 38128 Povo, Trento, Italy
| | - Simone Orioli
- Physics Department, Trento University, Via Sommarive 14, 38128 Povo, Trento, Italy
- INFN-TIFPA, Via Sommarive 14, 38128 Povo, Trento, Italy
| | - Giovanni Spagnolli
- Centre for Integrative Biology, Trento University, Via Sommarive 9, 38128 Povo, Trento, Italy
| | - Pietro Faccioli
- Physics Department, Trento University, Via Sommarive 14, 38128 Povo, Trento, Italy
- INFN-TIFPA, Via Sommarive 14, 38128 Povo, Trento, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, via G. Moruzzi 13, 56124, Pisa, Italy
| | - Sandro Jurinovich
- 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
| |
Collapse
|
33
|
Shiraogawa T, Ehara M, Jurinovich S, Cupellini L, Mennucci B. Frenkel-exciton decomposition analysis of circular dichroism and circularly polarized luminescence for multichromophoric systems. J Comput Chem 2018; 39:931-935. [DOI: 10.1002/jcc.25169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 01/03/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Takafumi Shiraogawa
- SOKENDAI, The Graduate University for Advanced Studies, Nishigonaka; Myodaiji Okazaki 444-8585 Japan
| | - Masahiro Ehara
- SOKENDAI, The Graduate University for Advanced Studies, Nishigonaka; Myodaiji Okazaki 444-8585 Japan
- Institute for Molecular Science and Research Center for Computational Science, Nishigonaka; Myodaiji Okazaki 444-8585 Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB); Kyoto University; Kyoto 615-8520 Japan
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale; University of Pisa, Via G. Moruzzi 13; Pisa 56124 Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale; University of Pisa, Via G. Moruzzi 13; Pisa 56124 Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale; University of Pisa, Via G. Moruzzi 13; Pisa 56124 Italy
| |
Collapse
|
34
|
Cupellini L, Jurinovich S, Campetella M, Caprasecca S, Guido CA, Kelly SM, Gardiner AT, Cogdell R, Mennucci B. An Ab Initio Description of the Excitonic Properties of LH2 and Their Temperature Dependence. J Phys Chem B 2016; 120:11348-11359. [PMID: 27791372 DOI: 10.1021/acs.jpcb.6b06585] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The spectroscopic properties of light-harvesting (LH) antennae in photosyntehtic organisms represent a fingerprint that is unique for each specific pigment-protein complex. Because of that, spectroscopic observations are generally combined with structural data from X-ray crystallography to obtain an indirect representation of the excitonic properties of the system. Here, an alternative strategy is presented which goes beyond this empirical approach and introduces an ab initio computational description of both structural and electronic properties and their dependence on the temperature. The strategy is applied to the peripheral light-harvesting antenna complex (LH2) present in purple bacteria. By comparing this model with the one based on the crystal structure, a detailed, molecular level explanation of the absorption and circular dichroism (CD) spectra and their temperature dependence is achieved. The agreement obtained with the experiments at both low and room temperature lays the groundwork for an atomistic understanding of the excitation dynamics in the LH2 system.
Collapse
Affiliation(s)
- Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Marco Campetella
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Stefano Caprasecca
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Ciro A Guido
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Sharon M Kelly
- Life Sciences Biomolecular Sci, Joseph Black Building, University of Glasgow , Glasgow G12 8QQ, Scotland
| | - Alastair T Gardiner
- Glasgow Biomedical Research Centre, Institute of Molecular Cell and Systems Biology, University of Glasgow , 126 University Place, Glasgow G12 8TA, Scotland
| | - Richard Cogdell
- Glasgow Biomedical Research Centre, Institute of Molecular Cell and Systems Biology, University of Glasgow , 126 University Place, Glasgow G12 8TA, Scotland
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa , Via G. Moruzzi 13, I-56124 Pisa, Italy
| |
Collapse
|