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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.
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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
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2
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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.
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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.
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Caricato M. A Perspective on the Simulation of Electronic Circular Dichroism and Circularly Polarized Luminescence Spectra in Chiral Solid Materials. J Phys Chem A 2024; 128:1197-1206. [PMID: 38295762 DOI: 10.1021/acs.jpca.3c08095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Chiral materials have shown tremendous potential for many technological applications, such as optoelectronics, sensing, magnetism, information technology, and imaging. Characterization of these materials is mostly based on chiroptical spectroscopies, such as electronic circular dichroism (ECD) and circularly polarized luminescence (CPL). These experimental measurements would greatly benefit from theoretical simulations for interpretation of the spectra as well as predictions on new materials. While ECD and CPL simulations are well established for molecular systems, they are not for materials. In this Perspective, we describe the theoretical quantities necessary to simulate ECD and CPL spectra in oriented systems. Then, we discuss the approximate strategies currently used to perform these calculations, what computational machinery is already available to develop more general approaches, and some of the open challenges for the simulation of ECD and CPL spectra in solid materials. When methods that are as reliable and computationally efficient as those for molecules are developed, these simulations will provide invaluable insight and guidance for the rational design of optically active materials.
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Affiliation(s)
- Marco Caricato
- Department of Chemistry, University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
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4
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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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5
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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.
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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
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6
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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.
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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.
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7
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8
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Chakravarty C, Aksu H, Martinez B JA, Ramos P, Pavanello M, Dunietz BD. Role of Dielectric Screening in Calculating Excited States of Solvated Azobenzene: A Benchmark Study Comparing Quantum Embedding and Polarizable Continuum Model for Representing the Solvent. J Phys Chem Lett 2022; 13:4849-4855. [PMID: 35617015 DOI: 10.1021/acs.jpclett.2c00982] [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: 06/15/2023]
Abstract
The low energy excited states of the conformational isomers of solvated azobenzene are calculated with several DFT methods accounting for the solute-solvent interaction implicitly with the polarizable continuum model or explicitly with subsystem DFT. For the latter, embedding potentials are calculated for 21 sampled snapshots of the solvent molecules. First, we find that accounting for the solvent implicitly or explicitly has little effect on the predicted cis-trans S1 excitation energy gap. Second, we find that azobenzene's S1 cis and trans energies are accurate as long as a screened range-separated hybrid exchange-correlation functional is employed. Finally, we also tested a simplified workflow whereby a single, averaged, embedding potential is used. Unfortunately, we find larger deviations against the experiment for the simplified workflow. This highlights a basic flaw in the approach, where the time scale of solvent averaging is much longer than that of the solute's electronic polarization.
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Affiliation(s)
- Chandrima Chakravarty
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Huseyin Aksu
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
- Computational Physics Laboratory, Department of Physics, Pamukkale University, 20010 Denizli, Turkey
| | - Jessica A Martinez B
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Pablo Ramos
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Michele Pavanello
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Barry D Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
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9
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Gendron F, Grasser M, Le Guennic B. Near-infrared circular dichroism of the ytterbium DOTMA complex: an ab initio investigation. Phys Chem Chem Phys 2022; 24:5404-5410. [PMID: 35170600 DOI: 10.1039/d1cp01675j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electronic structure and circular dichroism spectra of the ytterbium(III) complex [Yb(DOTMA)]- are calculated using complete and restricted active space self-consistent field wavefunction methods with the spin-orbit coupling treated by the state interaction approach. The influence of the dynamical correlation effect is then included via the 2nd order perturbation method. The experimental circular dichroism spectrum is well reproduced by calculations, both in terms of relative energy excitations and in terms of rotatory strength intensities. The results allow highlighting the mechanism that drives the chiroptical properties in Yb(III) complexes and reveal the importance of taking into account the 4f125d1 electronic configurations in the calculated wavefunctions to properly describe the chiroptical properties of the 4f-4f transitions.
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Affiliation(s)
- Frédéric Gendron
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) UMR 6226, F-35000 Rennes, France.
| | - Maxime Grasser
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) UMR 6226, F-35000 Rennes, France.
| | - Boris Le Guennic
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes) UMR 6226, F-35000 Rennes, France.
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10
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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.
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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:
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11
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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.
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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
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12
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Ozcelik A, Pereira-Cameselle R, Alonso-Gómez JL. From Allenes to Spirobifluorenes: On the Way to Device-compatible Chiroptical Systems. CURR ORG CHEM 2020. [DOI: 10.2174/1385272824999201013164534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The last decade has seen a huge growth in the construction of chiral systems to
expand the scope of chiroptical applications. Dependence of chiroptical response on molecular
conformation typically leads to low chiroptical intensities of chiral systems that feature
several conformations in solution. In this respect, allenes were employed for the preparation
of open and cyclic oligomers as well as molecular cages, presenting remarkable chiroptical
responses in solution. Their molecular chirality was also transferred to metal surfaces, yet
photoisomerization of allenes limited their further exploration. In search of a more robust
chiral axis, theoretical and experimental studies confirmed that spirobifluorenes could give
rise to stable systems with tailored optical and chiroptical properties. Additionally, incorporating
a conformational lock into spirobifluorene cyclic architectures served as an efficient
strategy towards the generation of distinct helical molecular orbitals. This review article outlines our results on developing
device-compatible chiroptical systems through axially chiral allenes and spirobifluorenes. The contribution
from other research groups is presented briefly.
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Affiliation(s)
- Ani Ozcelik
- Department of Organic Chemistry, Faculty of Chemistry, University of Vigo, Vigo, Spain
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13
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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
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14
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Abstract
It is well established that chiroptical responses, based on the unique reaction to circularly polarized light by chiral non-racemic systems, are sensitive to the stereochemistry of the featuring systems. This behavior has promoted the use of chiroptical spectroscopies as a mandatory tool in the structure determination of molecules for decades. Recently, the higher sensitivity of chiroptical techniques compared to the conventional UV/Vis absorption and fluorescence spectroscopies or electrochemistry has awakened much interest in the development of chiroptical everyday applications. While chiroptical responses could be predicted by ab initio calculations, large systems calculated at a high level of theory may have an important computational cost; therefore, more intuitive methods are desired to design systems with tailored chiroptical responses. In this regard, the exciton chirality method has been often used in conformationally stable systems incorporating at least two independent chromophores. Taking this method into consideration, in our previous work, we described the chiroptical symmetry analysis (CSA) based on symmetry selection rules. To explore the scope of the CSA, herein we perform the chiroptical symmetry analysis of diverse trianglimines and draw general conclusions to assist on the design of chiroptical systems with high symmetry.
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15
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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
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16
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Gendron F, Moore Ii B, Cador O, Pointillart F, Autschbach J, Le Guennic B. Ab Initio Study of Circular Dichroism and Circularly Polarized Luminescence of Spin-Allowed and Spin-Forbidden Transitions: From Organic Ketones to Lanthanide Complexes. J Chem Theory Comput 2019; 15:4140-4155. [PMID: 31125219 DOI: 10.1021/acs.jctc.9b00286] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Complete and restricted active space self-consistent field (CAS-/RAS-SCF) wave function methods are applied for the calculation of circular dichroism (CD) and circularly polarized luminescence (CPL) of a series of molecules comprising four organic ketones, the chiral cobalt(III) complex [Co(en)3]3+, and the europium(III) complex [Eu(DPA)3]3-. The ab initio results are in good agreement with the experimental data and previous results obtained with Kohn-Sham density functional theory in the case of the spin-allowed transitions. CD and CPL properties are calculated ab initio for the spin-forbidden transitions of both a transition metal and a lanthanide complex.
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Affiliation(s)
- Frédéric Gendron
- Univ Rennes, CNRS , ISCR (Institut des Sciences Chimiques de Rennes) , UMR 6226, F-35000 Rennes , France
| | - Barry Moore Ii
- Department of Chemistry , University at Buffalo, State University of New York , Buffalo , New York 14260-3000 , United States
| | - Olivier Cador
- Univ Rennes, CNRS , ISCR (Institut des Sciences Chimiques de Rennes) , UMR 6226, F-35000 Rennes , France
| | - Fabrice Pointillart
- Univ Rennes, CNRS , ISCR (Institut des Sciences Chimiques de Rennes) , UMR 6226, F-35000 Rennes , France
| | - Jochen Autschbach
- Department of Chemistry , University at Buffalo, State University of New York , Buffalo , New York 14260-3000 , United States
| | - Boris Le Guennic
- Univ Rennes, CNRS , ISCR (Institut des Sciences Chimiques de Rennes) , UMR 6226, F-35000 Rennes , France
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17
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Marazzi M, Gattuso H, Monari A, Assfeld X. Steady-State Linear and Non-linear Optical Spectroscopy of Organic Chromophores and Bio-macromolecules. Front Chem 2018; 6:86. [PMID: 29666792 PMCID: PMC5891624 DOI: 10.3389/fchem.2018.00086] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/12/2018] [Indexed: 01/05/2023] Open
Abstract
Bio-macromolecules as DNA, lipid membranes and (poly)peptides are essential compounds at the core of biological systems. The development of techniques and methodologies for their characterization is therefore necessary and of utmost interest, even though difficulties can be experienced due to their intrinsic complex nature. Among these methods, spectroscopies, relying on optical properties are especially important to determine their macromolecular structures and behaviors, as well as the possible interactions and reactivity with external dyes—often drugs or pollutants—that can (photo)sensitize the bio-macromolecule leading to eventual chemical modifications, thus damages. In this review, we will focus on the theoretical simulation of electronic spectroscopies of bio-macromolecules, considering their secondary structure and including their interaction with different kind of (photo)sensitizers. Namely, absorption, emission and electronic circular dichroism (CD) spectra are calculated and compared with the available experimental data. Non-linear properties will be also taken into account by two-photon absorption, a highly promising technique (i) to enhance absorption in the red and infra-red windows and (ii) to enhance spatial resolution. Methodologically, the implications of using implicit and explicit solvent, coupled to quantum and thermal samplings of the phase space, will be addressed. Especially, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are explored for a comparison with solely QM methods, in order to address the necessity to consider an accurate description of environmental effects on spectroscopic properties of biological systems.
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Affiliation(s)
- Marco Marazzi
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France.,Departamento de Química, Centro de Investigacíon en Síntesis Química (CISQ), Universidad de La Rioja, Logroño, Spain
| | - Hugo Gattuso
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
| | - Antonio Monari
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
| | - Xavier Assfeld
- Laboratoire de Physique et Chimie Théoriques, Université de Lorraine-Nancy, UMR 7019, Vandoeuvre-lés-Nancy, France.,Laboratoire de Physique et Chimie Théoriques, Centre National de la Recherche Scientifique, UMR 7019, Vandoeuvre-lès-Nancy, France
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18
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Fujita T, Mochizuki Y. Development of the Fragment Molecular Orbital Method for Calculating Nonlocal Excitations in Large Molecular Systems. J Phys Chem A 2018; 122:3886-3898. [DOI: 10.1021/acs.jpca.8b00446] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
- Institute for Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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19
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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
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20
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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
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21
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Giovannini T, Del Frate G, Lafiosca P, Cappelli C. Effective computational route towards vibrational optical activity spectra of chiral molecules in aqueous solution. Phys Chem Chem Phys 2018; 20:9181-9197. [DOI: 10.1039/c8cp00487k] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A polarizable QM/MM approach to accurately compute the Vibrational Optical Activity (VOA) spectra of chiral systems is proposed and applied to aqueous solutions of (l)-methyl lactate and (S)-glycidol.
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22
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Jurinovich S, Cupellini L, Guido CA, Mennucci B. EXAT: EXcitonic analysis tool. J Comput Chem 2017; 39:279-286. [PMID: 29151259 DOI: 10.1002/jcc.25118] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 01/09/2023]
Abstract
We introduce EXcitonic Analysis Tool (EXAT), a program able to compute optical spectra of large excitonic systems directly from the output of quantum mechanical calculations performed with the popular Gaussian 16 package. The software is able to combine in an excitonic scheme the single-chromophore properties and exciton couplings to simulate energies, coefficients, and excitonic spectra (UV-vis, CD, and LD). The effect of the environment can also be included using a Polarizable Continuum Model. EXAT also presents a simple graphical user interface, which shows on-screen both site and exciton properties. To show the potential of the method, we report two applications on a a chiral perturbed BODIPY system and DNA G-quadruplexes, respectively. The program is available online at http://molecolab.dcci.unipi.it/tools/. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Sandro Jurinovich
- Dipartimento di Chimica, Università di Pisa, Via G. Moruzzi 13, Pisa, 56124, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica, Università di Pisa, Via G. Moruzzi 13, Pisa, 56124, Italy
| | - Ciro A Guido
- Laboratoire CEISAM - UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Benedetta Mennucci
- Dipartimento di Chimica, Università di Pisa, Via G. Moruzzi 13, Pisa, 56124, Italy
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23
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Wu X, Teuler JM, Cailliez F, Clavaguéra C, Salahub DR, de la Lande A. Simulating Electron Dynamics in Polarizable Environments. J Chem Theory Comput 2017; 13:3985-4002. [DOI: 10.1021/acs.jctc.7b00251] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaojing Wu
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Jean-Marie Teuler
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Fabien Cailliez
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Carine Clavaguéra
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Dennis R. Salahub
- Department
of Chemistry, Centre for Molecular Simulation, Institute for Quantum
Science and Technology and Quantum Alberta, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
- College
of Chemistry and Chemical Engineering, Henan University of Technology, No. 100, Lian Hua Street, High-Tech Development Zone, Zhengzhou 450001, P. R. China
| | - Aurélien de la Lande
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
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24
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Gattuso H, García-Iriepa C, Sampedro D, Monari A, Marazzi M. Simulating the Electronic Circular Dichroism Spectra of Photoreversible Peptide Conformations. J Chem Theory Comput 2017; 13:3290-3296. [DOI: 10.1021/acs.jctc.7b00163] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Hugo Gattuso
- Théorie-Modélisation-Simulation, Université de Lorraine − Nancy, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
- Théorie-Modélisation-Simulation,
CNRS, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
| | - Cristina García-Iriepa
- Departamento
de Química, Centro de Investigación en Síntesis
Química (CISQ), Universidad de La Rioja, Madre de Dios
53, E-26006 Logroño, Spain
- Unidad
Docente de Química Física, Universidad de Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Diego Sampedro
- Departamento
de Química, Centro de Investigación en Síntesis
Química (CISQ), Universidad de La Rioja, Madre de Dios
53, E-26006 Logroño, Spain
| | - Antonio Monari
- Théorie-Modélisation-Simulation, Université de Lorraine − Nancy, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
- Théorie-Modélisation-Simulation,
CNRS, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
| | - Marco Marazzi
- Théorie-Modélisation-Simulation, Université de Lorraine − Nancy, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
- Théorie-Modélisation-Simulation,
CNRS, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, Nancy, France
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25
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Padula D, Jurinovich S, Di Bari L, Mennucci B. Simulation of Electronic Circular Dichroism of Nucleic Acids: From the Structure to the Spectrum. Chemistry 2016; 22:17011-17019. [PMID: 27699878 DOI: 10.1002/chem.201602777] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Indexed: 12/18/2022]
Abstract
We present a quantum mechanical (QM) simulation of the electronic circular dichroism (ECD) of nucleic acids (NAs). The simulation combines classical molecular dynamics, to obtain the structure and its temperature-dependent fluctuations, with a QM excitonic model to determine the ECD. The excitonic model takes into account environmental effects through a polarizable embedding and uses a refined approach to calculate the electronic couplings in terms of full transition densities. Three NAs with either similar conformations but different base sequences or similar base sequences but different conformations have been investigated and the results were compared with experimental observations; a good agreement was seen in all cases. A detailed analysis of the nature of the ECD bands in terms of their excitonic composition was also carried out. Finally, a comparison between the QM and the DeVoe models clearly revealed the importance of including fluctuations of the excitonic parameters and of accurately determining the electronic couplings. This study demonstrates the feasibility of the ab initio simulation of the ECD spectra of NAs, that is, without the need of experimental structural or electronic data.
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Affiliation(s)
- Daniele Padula
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| | - Lorenzo Di Bari
- 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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26
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Loco D, Jurinovich S, Di Bari L, Mennucci B. A fast but accurate excitonic simulation of the electronic circular dichroism of nucleic acids: how can it be achieved? Phys Chem Chem Phys 2016; 18:866-77. [PMID: 26646952 DOI: 10.1039/c5cp06341h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present and discuss a simple and fast computational approach to the calculation of electronic circular dichroism spectra of nucleic acids. It is based on a exciton model in which the couplings are obtained in terms of the full transition-charge distributions, as resulting from TDDFT methods applied on the individual nucleobases. We validated the method on two systems, a DNA G-quadruplex and a RNA β-hairpin whose solution structures have been accurately determined by means of NMR. We have shown that the different characteristics of composition and structure of the two systems can lead to quite important differences in the dependence of the accuracy of the simulation on the excitonic parameters. The accurate reproduction of the CD spectra together with their interpretation in terms of the excitonic composition suggest that this method may lend itself as a general computational tool to both predict the spectra of hypothetic structures and define clear relationships between structural and ECD properties.
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Affiliation(s)
- Daniele Loco
- 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.
| | - Lorenzo Di Bari
- 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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27
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Pratumyot Y, Chen S, Hu L, Polen SM, Hadad CM, Badjić JD. Assembly and Folding of Twisted Baskets in Organic Solvents. Org Lett 2016; 18:4238-41. [PMID: 27513214 DOI: 10.1021/acs.orglett.6b01976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A synthetic method for obtaining enantiopure and twisted baskets of type (P)-3 is described. These chiral cavitands were found to fold quinoline gates, at the rim of their twisted platform, in acetonitrile and give molecular capsules that assemble into large unilamellar vesicles. In a less polar dichloromethane, however, cup-shaped (P)-3 packed into vesicles but with the quinoline gates in an unfolded orientation. The ability of twisted baskets to form functional nanostructured materials could be of interest for building stereoselective sensors and catalysts.
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Affiliation(s)
- Yaowalak Pratumyot
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shigui Chen
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Lei Hu
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shane M Polen
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Christopher M Hadad
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jovica D Badjić
- Department of Chemistry and Biochemistry, The Ohio State University , 100 West 18th Avenue, Columbus, Ohio 43210, United States
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28
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Padula D, Di Bari L, Pescitelli G. The “Case of Two Compounds with Similar Configuration but Nearly Mirror Image CD Spectra” Refuted. Reassignment of the Absolute Configuration of N-Formyl-3′,4′-dihydrospiro[indan-1,2′(1′H)-pyridine]. J Org Chem 2016; 81:7725-32. [DOI: 10.1021/acs.joc.6b01416] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniele Padula
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi
13, 56124 Pisa, Italy
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, U.K
| | - Lorenzo Di Bari
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi
13, 56124 Pisa, Italy
| | - Gennaro Pescitelli
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi
13, 56124 Pisa, Italy
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29
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Enamullah M, Makhloufi G, Ahmed R, Joy BA, Islam MA, Padula D, Hunter H, Pescitelli G, Janiak C. Synthesis, X-ray, and Spectroscopic Study of Dissymmetric Tetrahedral Zinc(II) Complexes from Chiral Schiff Base Naphthaldiminate Ligands with Apparent Exception to the ECD Exciton Chirality. Inorg Chem 2016; 55:6449-64. [DOI: 10.1021/acs.inorgchem.6b00403] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mohammed Enamullah
- Department of Chemistry, Jahangirnagar University, Dhaka-1342, Bangladesh
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Canada
| | - Gamall Makhloufi
- Institut
für Anorganische Chemie und Strukturchemie, Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Rifat Ahmed
- Department of Chemistry, Jahangirnagar University, Dhaka-1342, Bangladesh
| | - Baitul Alif Joy
- Department of Chemistry, Jahangirnagar University, Dhaka-1342, Bangladesh
| | | | - Daniele Padula
- Department of Chemistry, University of Pisa, via Moruzzi 13, 56124 Pisa, Italy
| | - Howard Hunter
- Department of Chemistry, York University, 4700 Keele Street, Toronto, Canada
| | - Gennaro Pescitelli
- Department of Chemistry, University of Pisa, via Moruzzi 13, 56124 Pisa, Italy
| | - Christoph Janiak
- Institut
für Anorganische Chemie und Strukturchemie, Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
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30
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Gattuso H, Spinello A, Terenzi A, Assfeld X, Barone G, Monari A. Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy To Unravel Complex Structures. J Phys Chem B 2016; 120:3113-21. [DOI: 10.1021/acs.jpcb.6b00634] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hugo Gattuso
- Theory-Modeling-Simulation,
SRSMC, Université de Lorraine Nancy, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
| | - Angelo Spinello
- Dipartimento
di Scienze Biologiche, Chimiche e Farmaceutiche, Universitá di Palermo, Viale delle Scienze, Palermo, Italy
| | - Alessio Terenzi
- Dipartimento
di Scienze Biologiche, Chimiche e Farmaceutiche, Universitá di Palermo, Viale delle Scienze, Palermo, Italy
- Institute
of Inorganic Chemistry, University of Vienna, Währingerstrasse 42, Vienna, Austria
| | - Xavier Assfeld
- Theory-Modeling-Simulation,
SRSMC, Université de Lorraine Nancy, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
| | - Giampaolo Barone
- Dipartimento
di Scienze Biologiche, Chimiche e Farmaceutiche, Universitá di Palermo, Viale delle Scienze, Palermo, Italy
| | - Antonio Monari
- Theory-Modeling-Simulation,
SRSMC, Université de Lorraine Nancy, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
- CNRS, Theory-Modeling-Simulation, SRSMC, Boulevard des Aiguillettes, 54506 Vandoeuvre-lès-Nancy, France
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31
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Sundar MS, Bedekar AV. Synthesis of enantiomerically pure helicene-like mono 1,3-oxazines from 1,1′-binaphthyl-2,2′,7-triol and study of their chiroptical properties. RSC Adv 2016. [DOI: 10.1039/c6ra10496g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Several helicene-like molecules have been synthesized and characterized. The effect of helicene-like structural arrangement was more prominent in the chiroptical properties as compared to the stereogenic center of the diastereomeric compounds.
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Affiliation(s)
- M. Shyam Sundar
- Department of Chemistry
- Faculty of Science
- M. S. University of Baroda
- Vadodara 390 002
- India
| | - Ashutosh V. Bedekar
- Department of Chemistry
- Faculty of Science
- M. S. University of Baroda
- Vadodara 390 002
- India
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32
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Berardozzi R, Di Bari L. Optical Activity in the Near-IR Region: Theλ=980 nm Multiplet of Chiral Yb3+Complexes. Chemphyschem 2015. [DOI: 10.1002/cphc.201500355] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Abbate S, Mazzeo G, Meneghini S, Longhi G, Boiadjiev SE, Lightner DA. Bicamphor: a prototypic molecular system to investigate vibrational excitons. J Phys Chem A 2015; 119:4261-7. [PMID: 25871493 DOI: 10.1021/acs.jpca.5b02332] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vibrational circular dichroism (VCD) and IR spectra have been recorded in the fingerprint and carbonyl stretching regions for endo,endo-bicamphor (1), exo,exo-bicamphor (2), endo,exo-bicamphor (3), 3,3'-bicamphorylidene (4), and exo,exo-bis-thiocamphor (5). The C2 symmetry possessed by these molecular systems (except in one case), as well as their limited conformational mobility associated with well-defined degrees of freedom, allow for optimal test of the vibrational circular dichroism exciton chirality (VCDEC) rule introduced by Taniguchi and Monde. Density functional theory calculations are employed not only to predict the entire aspect of the VCD and IR spectra but also to study how the VCDEC rule may be impacted by the coupling between C═O stretchings and from C═O stretchings with other vibrational modes and by the rotation about the C-C bond connecting the two camphors. Comments are provided about the limitations and potentialities of the VCDEC method and about the manifestation of different vibrational excitons in other regions of the VCD spectra, either in the mid-IR or in the CH-stretching regions.
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Affiliation(s)
- Sergio Abbate
- †Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy.,‡CNISM Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia,Via della Vasca Navale, 84, 00146 Roma, Italy
| | - Giuseppe Mazzeo
- †Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Silvia Meneghini
- †Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy.,§Dipartimento di Scienze del Farmaco, viale Taramelli 12, Università di Pavia, 27100 Pavia, Italy
| | - Giovanna Longhi
- †Dipartimento di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy.,‡CNISM Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia,Via della Vasca Navale, 84, 00146 Roma, Italy
| | - Stefan E Boiadjiev
- ∥Department of Chemistry and Biochemistry, Medical University-Pleven, 1 St. Kl. Ohridski Str., 5800 Pleven, Bulgaria
| | - David A Lightner
- ⊥Department of Chemistry, University of Nevada, 1664 North Virginia Street, Reno, Nevada 89557-0020, United States
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34
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Gattuso H, Assfeld X, Monari A. Modeling DNA electronic circular dichroism by QM/MM methods and Frenkel Hamiltonian. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1640-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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35
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Di Meo F, Pedersen MN, Rubio-Magnieto J, Surin M, Linares M, Norman P. DNA Electronic Circular Dichroism on the Inter-Base Pair Scale: An Experimental-Theoretical Case Study of the AT Homo-Oligonucleotide. J Phys Chem Lett 2015; 6:355-359. [PMID: 26261947 DOI: 10.1021/jz502696t] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens the field for using circular dichroism spectroscopy as a sensitive nanoscale probe of DNA to reveal its complex interactions with the environment.
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Affiliation(s)
- Florent Di Meo
- †Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-58183 Linköping, Sweden
| | - Morten N Pedersen
- †Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-58183 Linköping, Sweden
- ‡Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Jenifer Rubio-Magnieto
- ||Laboratory for Chemistry of Novel Materials, Center for Innovation and Research in Materials and Polymers, University of Mons - UMONS, 20 Place du Parc, B-7000 Mons, Belgium
| | - Mathieu Surin
- ||Laboratory for Chemistry of Novel Materials, Center for Innovation and Research in Materials and Polymers, University of Mons - UMONS, 20 Place du Parc, B-7000 Mons, Belgium
| | - Mathieu Linares
- †Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-58183 Linköping, Sweden
- ||Laboratory for Chemistry of Novel Materials, Center for Innovation and Research in Materials and Polymers, University of Mons - UMONS, 20 Place du Parc, B-7000 Mons, Belgium
| | - Patrick Norman
- †Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-58183 Linköping, Sweden
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36
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Olsen JMH, Steinmann C, Ruud K, Kongsted J. Polarizable Density Embedding: A New QM/QM/MM-Based Computational Strategy. J Phys Chem A 2015; 119:5344-55. [DOI: 10.1021/jp510138k] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jógvan Magnus Haugaard Olsen
- Laboratory of
Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense
M, Denmark
| | - Casper Steinmann
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense
M, Denmark
| | - Kenneth Ruud
- Centre for Theoretical
and Computational Chemistry, Department of Chemistry, University of Tromsø—The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense
M, Denmark
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37
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Egidi F, Russo R, Carnimeo I, D'Urso A, Mancini G, Cappelli C. The electronic circular dichroism of nicotine in aqueous solution: a test case for continuum and mixed explicit-continuum solvation approaches. J Phys Chem A 2015; 119:5396-404. [PMID: 25568940 DOI: 10.1021/jp510542x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In this paper, we extend an integrated QM/MM/polarizable continuum model (PCM) method, which combines a fluctuating charge (FQ) approach to the MM polarization with the PCM, to describe electronic circular dichroism (ECD) spectra of systems in aqueous solution. The main features of the approach are presented, and then applications to the UV and ECD spectra of neutral (S)-nicotine in aqueous solution are reported. The performance of the QM/FQ/PCM is compared with that of the PCM against newly measured UV ECD spectra, which are in agreement with previous findings. The inclusion of specific solvation effects via the QM/FQ/PCM method leads to an improvement in the calculated spectra compared to the experimental findings, though the pure PCM results are still qualitatively correct and are a useful tool for the characterization of the states.
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Affiliation(s)
- Franco Egidi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| | - Rosario Russo
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| | - Ivan Carnimeo
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| | - Alessandro D'Urso
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| | - Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), via Morego 30, I-16163 Genova, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Department of Chemical Sciences, University of Catania, Viale A. Doria 6, I-95125 Catania, Italy.,Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Giuseppe Moruzzi 3, I-56124 Pisa, Italy
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38
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Hermann K, Pratumyot Y, Polen S, Hardin AM, Dalkilic E, Dastan A, Badjić JD. Twisted baskets. Chemistry 2015; 21:3550-5. [PMID: 25604262 DOI: 10.1002/chem.201406492] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Indexed: 11/09/2022]
Abstract
A preparative procedure for obtaining a pair of twisted molecular baskets, each comprising a chiral framework with either right ((P)-1syn) or left ((M)-1syn) sense of twist and six ester groups at the rim has been developed and optimized. The racemic (P/M)-1syn can be obtained in three synthetic steps from accessible starting materials. The resolution of (P/M)-1syn is accomplished by its transesterification with (1R,2S,5R)-(-)-menthol in the presence of a Ti(IV) catalyst to give diastereomeric 8(P) and 8(M). It was found that dendritic-like cavitands 8(P) and 8(M), in CD2Cl2, undergo self-inclusion ((1)H NMR spectroscopy) with a menthol moiety occupying the cavity of each host. Importantly, the degree of inclusion of the menthol group was ((1)H NMR spectroscopy) found to be greater in the case of 8(P) than 8(M). Accordingly, it is suggested that different folding characteristic of 8(P) and 8(M) ought to affect the physicochemical characteristics of the hosts to permit their effective separation by column chromatography. The absolute configuration of 8(P)/8(M), encompassing right- and left-handed "cups", was determined with the exciton chirality method and also verified in silico (DFT: B3LYP/TZVP). Finally, the twisted baskets are strongly fluorescent due to three naphthalene chromophores, having a high fluorescence quantum yield within the rigid framework of 8(P)/8(M).
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Affiliation(s)
- Keith Hermann
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue (USA)
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39
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Jurinovich S, Guido CA, Bruhn T, Pescitelli G, Mennucci B. The role of magnetic–electric coupling in exciton-coupled ECD spectra: the case of bis-phenanthrenes. Chem Commun (Camb) 2015; 51:10498-501. [DOI: 10.1039/c5cc03167b] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The intrinsic magnetic moment of phenanthrene1Bbtransition has a strong impact on exciton-coupled CD spectra of some bis(phenanthrenes).
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Affiliation(s)
- Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Ciro A. Guido
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Torsten Bruhn
- Institut für Organische Chemie
- Universität Würzburg Am Hubland
- 97074 Würzburg
- Germany
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale
- Università di Pisa
- I-56124 Pisa
- Italy
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40
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Bruhn T, Pescitelli G, Jurinovich S, Schaumlöffel A, Witterauf F, Ahrens J, Bröring M, Bringmann G. Axial-chirale BODIPY-DYEmers: eine offensichtliche Ausnahme für die Exciton-Chiralitäts-Methode. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408398] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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41
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Bruhn T, Pescitelli G, Jurinovich S, Schaumlöffel A, Witterauf F, Ahrens J, Bröring M, Bringmann G. Axially Chiral BODIPY DYEmers: An Apparent Exception to the Exciton Chirality Rule. Angew Chem Int Ed Engl 2014; 53:14592-5. [DOI: 10.1002/anie.201408398] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Indexed: 01/16/2023]
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42
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Jurinovich S, Curutchet C, Mennucci B. The Fenna-Matthews-Olson protein revisited: a fully polarizable (TD)DFT/MM description. Chemphyschem 2014; 15:3194-204. [PMID: 25080315 DOI: 10.1002/cphc.201402244] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Indexed: 01/21/2023]
Abstract
We report a combined molecular dynamics and quantum mechanics (QM)/molecular mechanics (MM) analysis of the excitonic properties of the Fenna-Matthews-Olson (FMO) protein by using a polarizable MM model combined with a time-dependent density functional theory description. Overall, our results indicate that structural fluctuations, electrostatic interactions, and short-range quantum effects can significantly modulate the model Hamiltonian parameters (site energies and couplings). We find that the specific interactions with the axial ligand and the hydrogen-bonded residues are responsible for the energy ladder, with their effects being mainly due to electrostatic interactions, but with short-range quantum contributions that are not negligible. In addition, a striking modulation of the screening effects experienced by the BChl pairs, due to the heterogeneous polarizability of the FMO and solvent environment, is observed. Finally, we find that the exciton model gives a reliable description of the delocalized excited states in the complex.
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Affiliation(s)
- Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via Risorgimento 35, I-56126 Pisa (Italy)
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