1
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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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3
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Xu Y, Huang X, Wang YC, Zhao Y, Liang W. Identification of the interchromophore interaction in the electronic absorption and circular dichroism spectra of bis-phenanthrenes. Phys Chem Chem Phys 2024; 26:6155-6163. [PMID: 38299862 DOI: 10.1039/d3cp05684h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
We characterize the low-lying excited electronic states of a series of bis-phenanthrenes using our newly developed diabatic scheme called the fragment particle-hole density (FPHD) method and calculate both the electronic absorption and circular dichroism (ECD) spectra using the time-dependent density functional theory (TDDFT) and the FPHD-based exciton model which couples intrachromophore local excitations (LEs) and the interchromophore charge-transfer excitations (CTEs). TDDFT treats each bis-phenanthrene as a single molecule while the mixed LE-CTE exciton model partitions the molecule into two phenanthrene-based aromatic moieties, and then applies the electronic coupling between the various quasi-diabatic states to cover the interactions. It is found that TDDFT and the mixed LE-CTE model reproduce all experimentally observed trends in the spectral profiles, and the hybridization between LE and CTE states is displayed differently in absorption and ECD spectral intensities, as it usually decreases the absorption maxima and affects the positive/negative extrema of the ECD irregularly. By comparing the results yielded by the LE-CTE model with and without the LE-CTE coupling, we identify the contribution of CTE on the main dipole-allowed transitions.
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Affiliation(s)
- Yuchuan Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Xunkun Huang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Yu-Chen Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - Yi Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
| | - WanZhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China.
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4
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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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5
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Sharma A, Athanasopoulos S, Kumarasamy E, Phansa C, Asadpoordarvish A, Sabatini RP, Pandya R, Parenti KR, Sanders SN, McCamey DR, Campos LM, Rao A, Tayebjee MJY, Lakhwani G. Pentacene-Bridge Interactions in an Axially Chiral Binaphthyl Pentacene Dimer. J Phys Chem A 2021; 125:7226-7234. [PMID: 34433272 DOI: 10.1021/acs.jpca.1c05254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular chirality can be exploited as a sensitive reporter of the nature of intra- and interchromophore interactions in π-conjugated systems. In this report, we designed an intramolecular singlet fission (iSF)-based pentacene dimer with an axially chiral binaphthyl bridge (2,2'-(2,2'-dimethoxy-[1,1'-binaphthalene]-3,3'-diyl) n-octyl-di-isopropyl silylethynyl dipentacene, BNBP) to utilize its chiroptical response as a marker of iSF chromophore-bridge-chromophore (SFC-β-SFC) interactions. The axial chirality of the bridge enforces significant one-handed excitonic coupling of the pentacene monomer units; as such, BNBP exhibits significant chiroptical response in the ground and excited states. We analyzed the chiroptical response of BNBP using the exciton coupling method and quadratic response density functional theory calculations to reveal that higher energy singlet transitions in BNBP involve significant delocalization of the electronic density on the bridging binaphthyl group. Our results highlight the promising application of chiroptical techniques to investigate the nature of SFC-β-SFC interactions that impact singlet fission dynamics.
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Affiliation(s)
- Ashish Sharma
- ARC Centre of Excellence in Exciton Science, School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Stavros Athanasopoulos
- Departamento de Física, Universidad Carlos III de Madrid, Avenida Universidad 30, Leganés 28911, Madrid, Spain
| | - Elango Kumarasamy
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Chanakarn Phansa
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Amir Asadpoordarvish
- ARC Centre of Excellence in Exciton Science, School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia.,ARC Centre of Excellence in Exciton Science, School of Physics, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Randy P Sabatini
- ARC Centre of Excellence in Exciton Science, School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Raj Pandya
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Kaia R Parenti
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Samuel N Sanders
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Dane R McCamey
- ARC Centre of Excellence in Exciton Science, School of Physics, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Luis M Campos
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Akshay Rao
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Murad J Y Tayebjee
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom.,School of Photovoltaic and Renewable Energy Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Girish Lakhwani
- ARC Centre of Excellence in Exciton Science, School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia
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6
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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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7
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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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8
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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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9
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Mądry T, Czapik A, Kwit M. Point-to-Axial Chirality Transmission: A Highly Sensitive Triaryl Chirality Probe for Stereochemical Assignments of Amines. J Org Chem 2020; 85:10413-10431. [PMID: 32806087 PMCID: PMC7458434 DOI: 10.1021/acs.joc.0c00734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Indexed: 01/17/2023]
Abstract
A readily available stereodynamic and the electronic circular dichroism (ECD)-silent 2,5-di(1-naphthyl)-terephthalaldehyde-based probe has been applied for chirality sensing of primary amines. The chiral amine (the inductor) forces a change in the structure of the chromophore system through the point-to-axial chirality transmission mechanism. As a result, efficient induction of optical activity in the chromophoric system is observed. The butterflylike structure of the probe, with the terminal aryl groups acting as changeable "wings", allowed for the generation of exciton Cotton effects in the region of 1Bb electronic transition in the naphthalene chromophores. The sign of the exciton couplets observed for inductor-reporter systems might be correlated with an absolute configuration of the inductor, whereas the linear relationship between amplitudes of the specific Cotton effect and enantiomeric excess of the parent amine gives potentiality for quantitative chirality sensing. Despite the structural simplicity, the probe turned out to be unprecedentedly highly sensitive to even subtle differences in the inductor structure (i.e., O vs CH2).
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Affiliation(s)
- Tomasz Mądry
- Department
of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61 614 Poznan, Poland
| | - Agnieszka Czapik
- Department
of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61 614 Poznan, Poland
| | - Marcin Kwit
- Department
of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61 614 Poznan, Poland
- Center
for Advanced Technologies, Adam Mickiewicz
University, Uniwersytetu
Poznanskiego 10, 61 614 Poznan, Poland
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10
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Swathi K, Sissa C, Painelli A, George Thomas K. Supramolecular chirality: a caveat in assigning the handedness of chiral aggregates. Chem Commun (Camb) 2020; 56:8281-8284. [PMID: 32572405 DOI: 10.1039/d0cc01922d] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The handedness of a supramolecular chiral aggregate is often assigned based on the sign of circular dichroism spectra, adopting the exciton chirality method. However, the method does not properly account for the nature of intermolecular interactions. We introduce a generalized picture on the use of the sign of chiral signals in determining the helicity of chiral aggregates, rooted in the exciton model, supported by TD-DFT results.
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Affiliation(s)
- K Swathi
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy.
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11
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Gao W, Chen Z, Yang Y, Jiang J, Feng Z, Zhang X, Yuan X, Zhang P. Base-catalyzed oxidative dearomatization of multisubstituted phloroglucinols: An easy access to C-glucosyl 3,5,6-trihydroxycyclohexa-2,4-dienone derivatives. Carbohydr Res 2019; 484:107756. [DOI: 10.1016/j.carres.2019.107756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 07/21/2019] [Accepted: 07/26/2019] [Indexed: 10/26/2022]
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12
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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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13
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Talele HR, Koval D, Severa L, Reyes-Gutiérrez PE, Císařová I, Sázelová P, Šaman D, Bednárová L, Kašička V, Teplý F. Diquats with Robust Chirality: Facile Resolution, Synthesis of Chiral Dyes, and Application as Selectors in Chiral Analysis. Chemistry 2018; 24:7601-7604. [PMID: 29575285 DOI: 10.1002/chem.201800369] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Indexed: 12/25/2022]
Abstract
Diquats with extremely high racemization barriers with ΔG≠theor of 233 kJ mol-1 at 180 °C are described. Reported configurational robustness is due to a combination of two structural features: the rigid o-xylylene tether connecting the nitrogen atoms and the presence of two substituents in the bay region of the bipyridinium scaffold. The straightforward synthesis of diquats, plus facile resolution and derivatization make them attractive for chiral application studies. This is demonstrated by: 1) synthesis of the first non-racemic diquat dyes with pronounced chiroptical properties, and 2) capability of diquats to interact stereospecifically with chiral molecules. This suggests potential for diquat derivatives to be used as chiral selectors in separation methods.
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Affiliation(s)
- Harish R Talele
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
| | - Dušan Koval
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
| | - Lukáš Severa
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
| | - Paul E Reyes-Gutiérrez
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry, Charles University, Hlavova 2030/8, 128 43, Prague 2, Czech Republic
| | - Petra Sázelová
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
| | - David Šaman
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
| | - Filip Teplý
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
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14
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Schies C, Alemayehu AB, Vazquez-Lima H, Thomas KE, Bruhn T, Bringmann G, Ghosh A. Metallocorroles as inherently chiral chromophores: resolution and electronic circular dichroism spectroscopy of a tungsten biscorrole. Chem Commun (Camb) 2018; 53:6121-6124. [PMID: 28530281 DOI: 10.1039/c7cc02027a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An inherently chiral metallocorrole has been resolved for the first time by means of HPLC on a chiral stationary phase. For the compound in question, a homoleptic tungsten biscorrole, the absolute configurations of the enantiomers were assigned using online HPLC-ECD measurements in conjunction with time-dependent CAM-B3LYP calculations, which provided accurate simulations of the ECD spectra.
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Affiliation(s)
- Christine Schies
- Institute of Organic Chemistry, University of Würzburg, 97074 Würzburg, Germany.
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15
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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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16
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M. dos Santos Jr. F, Bicalho KU, Calisto ÍH, S. Scatena G, Fernandes JB, Cass QB, Batista Jr. JM. Scope of the 2(5H)-furanone helicity rule: a combined ECD, VCD, and DFT investigation. Org Biomol Chem 2018; 16:4509-4516. [DOI: 10.1039/c8ob01085d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Combination of ECD, VCD and DFT calculations revealed a possible exception to the widely used helicity rule of the 2(5H)-furanone chromophore.
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Affiliation(s)
| | - Keylla U. Bicalho
- Institute of Chemistry
- São Paulo State University – UNESP
- Araraquara
- Brazil
| | - Ítalo H. Calisto
- Department of Chemistry
- Federal University of São Carlos – UFSCar
- São Carlos
- Brazil
| | - Gabriel S. Scatena
- Department of Chemistry
- Federal University of São Carlos – UFSCar
- São Carlos
- Brazil
| | - João B. Fernandes
- Department of Chemistry
- Federal University of São Carlos – UFSCar
- São Carlos
- Brazil
| | - Quezia B. Cass
- Department of Chemistry
- Federal University of São Carlos – UFSCar
- São Carlos
- Brazil
| | - João M. Batista Jr.
- Department of Chemistry
- Federal University of São Carlos – UFSCar
- São Carlos
- Brazil
- Institute of Science and Technology
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17
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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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18
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Covington CL, Raghavan V, Smuts JP, Armstrong DW, Polavarapu PL. Absolute configuration of an axially chiral sulfonate determined from its optical rotatory dispersion, electronic circular dichroism, and vibrational circular dichroism spectra. Chirality 2017; 29:670-676. [DOI: 10.1002/chir.22739] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/06/2017] [Accepted: 07/09/2017] [Indexed: 01/18/2023]
Affiliation(s)
- Cody L. Covington
- Department of Chemistry; Vanderbilt University; Nashville Tennessee USA
| | - Vijay Raghavan
- Department of Chemistry; Vanderbilt University; Nashville Tennessee USA
| | - Jonathan P. Smuts
- Department of Chemistry; University of Texas at Arlington; Arlington Texas USA
| | - Daniel W. Armstrong
- Department of Chemistry; University of Texas at Arlington; Arlington Texas USA
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19
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Affiliation(s)
- Gennaro Pescitelli
- Dipartimento Di Chimica E Chimica Industriale; Università Di Pisa; Pisa Italy
| | - Lorenzo Di Bari
- Dipartimento Di Chimica E Chimica Industriale; Università Di Pisa; Pisa Italy
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20
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Buffeteau T, Pitrat D, Daugey N, Calin N, Jean M, Vanthuyne N, Ducasse L, Wien F, Brotin T. Chiroptical properties of cryptophane-111. Phys Chem Chem Phys 2017; 19:18303-18310. [DOI: 10.1039/c7cp02045g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
How the presence or not of solvent molecules inside the cavity of enantiopure cryptophanes affects their chiroptical properties.
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Affiliation(s)
- Thierry Buffeteau
- Bordeaux University
- Institut des Sciences Moléculaires
- CNRS UMR 5255
- 33405 Talence
- France
| | - Delphine Pitrat
- Lyon 1 University
- Ecole Normale Supérieure de Lyon
- CNRS UMR 5182
- Laboratoire de Chimie
- 69364 Lyon
| | - Nicolas Daugey
- Bordeaux University
- Institut des Sciences Moléculaires
- CNRS UMR 5255
- 33405 Talence
- France
| | - Nathalie Calin
- Lyon 1 University
- Ecole Normale Supérieure de Lyon
- CNRS UMR 5182
- Laboratoire de Chimie
- 69364 Lyon
| | - Marion Jean
- Aix-Marseille University
- CNRS
- Centrale Marseille
- iSm2
- Marseille
| | | | - Laurent Ducasse
- Bordeaux University
- Institut des Sciences Moléculaires
- CNRS UMR 5255
- 33405 Talence
- France
| | - Frank Wien
- Synchrotron SOLEIL
- L'Orme des Merisiers
- 91192 Gif sur Yvette
- France
| | - Thierry Brotin
- Lyon 1 University
- Ecole Normale Supérieure de Lyon
- CNRS UMR 5182
- Laboratoire de Chimie
- 69364 Lyon
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21
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Abbate S, Bruhn T, Pescitelli G, Longhi G. Vibrational Optical Activity of BODIPY Dimers: The Role of Magnetic–Electric Coupling in Vibrational Excitons. J Phys Chem A 2016; 121:394-400. [DOI: 10.1021/acs.jpca.6b11327] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Sergio Abbate
- Dipartimento
di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Torsten Bruhn
- Institut
für Organische Chemie, Universität Würzburg Am Hubland, 97074 Würzburg, Germany
| | - Gennaro Pescitelli
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via Moruzzi
13, 56124 Pisa, Italy
| | - Giovanna Longhi
- Dipartimento
di Medicina Molecolare e Traslazionale, Università di Brescia, Viale Europa 11, 25123 Brescia, Italy
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22
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Li TX, Yang MH, Wang Y, Wang XB, Luo J, Luo JG, Kong LY. Unusual dimeric tetrahydroxanthone derivatives from Aspergillus lentulus and the determination of their axial chiralities. Sci Rep 2016; 6:38958. [PMID: 27941865 PMCID: PMC5150534 DOI: 10.1038/srep38958] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/31/2016] [Indexed: 12/25/2022] Open
Abstract
The research on secondary metabolites of Aspergillus lentulus afforded eight unusual heterodimeric tetrahydroxanthone derivatives, lentulins A-H (2-9), along with the known compound neosartorin (1). Compounds 1-6 exhibited potent antimicrobial activities especially against methicillin-resistant Staphylococci. Their absolute configurations, particularly the axial chiralities, were unambiguously demonstrated by a combination of electronic circular dichroism (ECD), Rh2(OCOCF3)4-induced ECD experiments, modified Mosher methods, and chemical conversions. Interestingly, compounds 1-4 were the first samples of atropisomers within the dimeric tetrahydroxanthone class. Further investigation of the relationships between their axial chiralities and ECD Cotton effects led to the proposal of a specific CD Exciton Chirality rule to determine the axial chiralities in dimeric tetrahydroxanthones and their derivatives.
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Affiliation(s)
- Tian-Xiao Li
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People’s Republic of China
| | - Ming-Hua Yang
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People’s Republic of China
| | - Ying Wang
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People’s Republic of China
| | - Xiao-Bing Wang
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People’s Republic of China
| | - Jun Luo
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People’s Republic of China
| | - Jian-Guang Luo
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People’s Republic of China
| | - Ling-Yi Kong
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, People’s Republic of China
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23
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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.
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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
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24
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Covington CL, Junior FMS, Silva JHS, Kuster RM, de Amorim MB, Polavarapu PL. Atropoisomerism in Biflavones: The Absolute Configuration of (-)-Agathisflavone via Chiroptical Spectroscopy. JOURNAL OF NATURAL PRODUCTS 2016; 79:2530-2537. [PMID: 27723329 DOI: 10.1021/acs.jnatprod.6b00395] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The first natural occurrence in optically active form of the dimeric flavonoid agathisflavone and definition of its axial chirality using chiroptical spectroscopic methods are described. The experimental electronic circular dichroism, electronic dissymmetry factor, optical rotatory dispersion, vibrational circular dichroism (VCD), and vibrational dissymmetry factor spectra of agathisflavone are presented and analyzed with their corresponding quantum chemical predictions to definitively assign the axial chirality of (-)-agathisflavone as (aS).
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Affiliation(s)
- Cody L Covington
- Department of Chemistry, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - Fernando M S Junior
- Department of Chemistry, Vanderbilt University , Nashville, Tennessee 37235, United States
- Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro , 21941-902, Rio de Janeiro, RJ, Brazil
| | - Jessica H S Silva
- Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro , 21941-902, Rio de Janeiro, RJ, Brazil
| | - Ricardo M Kuster
- Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro , 21941-902, Rio de Janeiro, RJ, Brazil
| | - Mauro B de Amorim
- Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro , 21941-902, Rio de Janeiro, RJ, Brazil
| | - Prasad L Polavarapu
- Department of Chemistry, Vanderbilt University , Nashville, Tennessee 37235, United States
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25
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Zinna F, Bruhn T, Guido CA, Ahrens J, Bröring M, Di Bari L, Pescitelli G. Circularly Polarized Luminescence from Axially Chiral BODIPY DYEmers: An Experimental and Computational Study. Chemistry 2016; 22:16089-16098. [PMID: 27658919 DOI: 10.1002/chem.201602684] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Indexed: 11/10/2022]
Abstract
With our new home-built circularly polarized luminescence (CPL) instrument, we measured fluorescence and CPL spectra of the enantiomeric pairs of two quasi-isomeric BODIPY DYEmers 1 and 2, endowed with axial chirality. The electronic circular dichroism (ECD) and CPL spectra of these atropisomeric dimers are dominated by the exciton coupling between the main π-π* transitions (550-560 nm) of the two BODIPY rings. Compound 1 has strong ECD and CPL spectra (glum =4×10-3 ) well reproduced by TD-DFT and SCS-CC2 (spin-component scaled second-order approximate coupled-cluster) calculations using DFT-optimized ground- and excited-state structures. Compound 2 has weaker ECD and CPL spectra (glum =4×10-4 ), partly due to the mutual cancellation of electric-electric and electric-magnetic exciton couplings, and partly to its conformational freedom. This compound is computationally very challenging. Starting from the optimized excited-state geometries, we predicted the wrong sign for the CPL band of 2 using TD-DFT with the most recommended hybrid and range-separated functionals, whereas SCS-CC2 or a DFT functional with full exact exchange provided the correct sign.
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Affiliation(s)
- Francesco Zinna
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi 13, 56124, Pisa, Italy
| | - Torsten Bruhn
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Ciro A Guido
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Moruzzi 13, 56124, Pisa, Italy
| | - Johannes Ahrens
- Institut für Anorganische und Analytische Chemie, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany.,Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Martin Bröring
- Institut für Anorganische und Analytische Chemie, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
| | - 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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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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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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28
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Bruhn T, Pescitelli G, Witterauf F, Ahrens J, Funk M, Wolfram B, Schneider H, Radius U, Bröring M. Cryptochirality in 2,2′-Coupled BODIPY DYEmers. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600585] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Torsten Bruhn
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale; Università di Pisa; Via Moruzzi 13 56124 Pisa Italy
| | - Franziska Witterauf
- Institut für Organische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Johannes Ahrens
- Institut für Anorganische und Analytische Chemie (IAAC); Technische Universität Braunschweig; Hagenring 30 38106 Braunschweig Germany
| | - Markus Funk
- Institut für Anorganische und Analytische Chemie (IAAC); Technische Universität Braunschweig; Hagenring 30 38106 Braunschweig Germany
| | - Benedikt Wolfram
- Institut für Anorganische und Analytische Chemie (IAAC); Technische Universität Braunschweig; Hagenring 30 38106 Braunschweig Germany
| | - Heidi Schneider
- Institut für Anorganische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Udo Radius
- Institut für Anorganische Chemie; Universität Würzburg; Am Hubland 97074 Würzburg Germany
| | - Martin Bröring
- Institut für Anorganische und Analytische Chemie (IAAC); Technische Universität Braunschweig; Hagenring 30 38106 Braunschweig Germany
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29
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Zhao L, Qi D, Wang K, Wang T, Han B, Tang Z, Jiang J. Integration of inherent and induced chirality into subphthalocyanine analogue. Sci Rep 2016; 6:28026. [PMID: 27294871 PMCID: PMC4904797 DOI: 10.1038/srep28026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/26/2016] [Indexed: 01/10/2023] Open
Abstract
Conventional conjugated systems are characteristic of only either inherent or induced chirality because of synthetic challenge in combination of chiral segment into the main chromophore. In this work, chiral binaphthyl segment is directly fused into the central chromophore of a subphthalocyanine skeleton, resulting in a novel type of chiral subphthalocyanine analogue (R/S)-1 of integrated inherent and induced chirality. Impressively, an obviously enhanced optical activity is discerned for (R/S)-1 molecules, and corresponding enhancement mechanism is elucidated in detail. The synthesis strategy based on rational molecular design will open the door towards fabrication of chiral materials with giant optical activity, which will have great potential in chiroptical devices.
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Affiliation(s)
- Luyang Zhao
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry, University of Science and Technology Beijing, Beijing 100083, China
| | - Dongdong Qi
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry, University of Science and Technology Beijing, Beijing 100083, China
| | - Kang Wang
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry, University of Science and Technology Beijing, Beijing 100083, China
| | - Tianyu Wang
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry, University of Science and Technology Beijing, Beijing 100083, China
| | - Bing Han
- Laboratory of Nanomaterials, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Zhiyong Tang
- Laboratory of Nanomaterials, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Jianzhuang Jiang
- Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry, University of Science and Technology Beijing, Beijing 100083, China
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30
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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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31
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Uchida Y, Hirose T, Nakashima T, Kawai T, Matsuda K. Synthesis and Photophysical Properties of a 13,13′-Bibenzo[b]perylenyl Derivative as a π-Extended 1,1′-Binaphthyl Analog. Org Lett 2016; 18:2118-21. [DOI: 10.1021/acs.orglett.6b00747] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yosuke Uchida
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takashi Hirose
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takuya Nakashima
- Graduate
School of Materials Science, Nara Institute of Science and Technology, NAIST, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Tsuyoshi Kawai
- Graduate
School of Materials Science, Nara Institute of Science and Technology, NAIST, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Kenji Matsuda
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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32
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Polavarapu PL. Structural Analysis Using Chiroptical Spectroscopy: Insights and Cautions. Chirality 2016; 28:445-52. [DOI: 10.1002/chir.22601] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/14/2016] [Accepted: 03/17/2016] [Indexed: 11/09/2022]
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33
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Nicu VP. Revisiting an old concept: the coupled oscillator model for VCD. Part 1: the generalised coupled oscillator mechanism and its intrinsic connection to the strength of VCD signals. Phys Chem Chem Phys 2016; 18:21202-12. [DOI: 10.1039/c6cp01282e] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
This work reports the development of a generalised coupled oscillator expression for VCD that is exact within the harmonic approximation and is applicable to all types of normal modes, regardless whether the considered molecule is symmetric or asymmetric.
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Affiliation(s)
- Valentin Paul Nicu
- Van't Hoff Institute for Molecular Sciences
- University of Amsterdam
- 1098 XH Amsterdam
- The Netherlands
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