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Nogueira JJ, Plasser F, González L. Electronic delocalization, charge transfer and hypochromism in the UV absorption spectrum of polyadenine unravelled by multiscale computations and quantitative wavefunction analysis. Chem Sci 2017; 8:5682-5691. [PMID: 28989607 PMCID: PMC5621053 DOI: 10.1039/c7sc01600j] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/09/2017] [Indexed: 12/23/2022] Open
Abstract
The characterization of the electronically excited states of DNA strands populated upon solar UV light absorption is essential to unveil light-induced DNA damage and repair processes. We report a comprehensive analysis of the electronic properties of the UV spectrum of single-stranded polyadenine based on theoretical calculations that include excitations over eight nucleobases of the DNA strand and environmental effects by a multiscale quantum mechanics/molecular mechanics scheme, conformational sampling by molecular dynamics, and a meaningful interpretation of the electronic structure by quantitative wavefunction analysis. We show that electronic excitations are extended mainly over two nucleobases with additional important contributions of monomer-like excitations and excitons delocalized over three monomers. Half of the spectral intensity derives from locally excited and Frenkel exciton states, while states with partial charge-transfer character account for the other half and pure charge-transfer states represent only a minor contribution. The hypochromism observed when going from the isolated monomer to the strand occurs independently from delocalization and charge transfer and is instead explained by long-range environmental perturbations of the monomer states.
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Affiliation(s)
- Juan J Nogueira
- Institute of Theoretical Chemistry , Faculty of Chemistry , University of Vienna , Währinger Straße 17 , 1090 Vienna , Austria . ; ;
| | - Felix Plasser
- Institute of Theoretical Chemistry , Faculty of Chemistry , University of Vienna , Währinger Straße 17 , 1090 Vienna , Austria . ; ;
| | - Leticia González
- Institute of Theoretical Chemistry , Faculty of Chemistry , University of Vienna , Währinger Straße 17 , 1090 Vienna , Austria . ; ;
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Briggs JS, Eisfeld A. Equivalence of quantum and classical coherence in electronic energy transfer. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:051911. [PMID: 21728575 DOI: 10.1103/physreve.83.051911] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Indexed: 05/31/2023]
Abstract
To investigate the effect of quantum coherence on electronic energy transfer, which is the subject of current interest in photosynthesis, we solve the problem of transport for the simplest model of an aggregate of monomers interacting through dipole-dipole forces using both quantum and classical dynamics. We conclude that for realistic coupling strengths quantum and classical coherent transport are identical. This is demonstrated by numerical calculations for a linear chain and for the photosynthetic Fenna-Matthews-Olson complex.
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Affiliation(s)
- John S Briggs
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.
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Eisfeld A, Kniprath R, Briggs JS. Theory of the absorption and circular dichroism spectra of helical molecular aggregates. J Chem Phys 2007; 126:104904. [PMID: 17362084 DOI: 10.1063/1.2464097] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A theory of the electronic circular dichroism (CD) and optical rotatory dispersion (ORD) of infinite aggregates exhibiting cylindrical symmetry is presented in which, to the authors' knowledge, for the first time vibrational structure is included explicitly. It is shown that, with the coherent exciton scattering approximation in the Green function approach, the detailed vibrational structure of the aggregate absorption. CD and ORD bands can be calculated from a knowledge of the electronic coupling and the monomer absorption line shape alone. Detailed model calculations for a single helix are made and the results are used to expose the origin of different spectral features. A good reproduction of experimental J-aggregate spectra is obtained, using the same electronic interaction to fit both absorption and CD spectral line shapes. The theory allows some prediction of aggregate geometry to be made, but it is shown that an unambiguous geometrical assignment can only be made where experimental spectra for light of different propagation directions with respect to the cylinder axis are available.
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Affiliation(s)
- A Eisfeld
- Theoretical Quantum Dynamics, University of Freiburg, Hermann-Herder-Strasse 3, D-79104 Freiburg, Germany.
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Hansen AE, Bouman TD. Natural Chiroptical Spectroscopy: Theory and Computations. ADVANCES IN CHEMICAL PHYSICS 2007. [DOI: 10.1002/9780470142639.ch5] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Mikhonin AV, Asher SA, Bykov SV, Murza A. UV Raman spatially resolved melting dynamics of isotopically labeled polyalanyl peptide: slow alpha-helix melting follows 3(10)-helices and pi-bulges premelting. J Phys Chem B 2007; 111:3280-92. [PMID: 17388440 DOI: 10.1021/jp0654009] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We used UV resonance Raman (UVRR) to examine the spatial dependence of the T-jump secondary structure relaxation of an isotopically labeled 21-residue mainly Ala peptide, AdP. The AdP penultimate Ala residues were perdeuterated, leaving the central residues hydrogenated, to allow separate monitoring of melting of the middle versus the end peptide bonds. For 5 to 30 degrees C T-jumps, the central peptide bonds show a approximately 2-fold slower relaxation time (189 +/- 31 ns) than do the exterior peptide bonds (97 +/- 15 ns). In contrast, for a 20 to 40 degrees C T-jump, the central peptide bond relaxation appears to be faster (56 +/- 6 ns) than that of the penultimate peptide bonds (131 +/- 46 ns). We show that, if the data are modeled as a two-state transition, we find that only exterior peptide bonds show anti-Arrhenius folding behavior; the middle peptide bonds show both normal Arrhenius-like folding and unfolding. This anti-Arrhenius behavior results from the involvement of pi-bulges/helices and 3(10)-helix states in the melting. The unusual temperature dependence of the (un)folding rates of the interior and exterior peptide bonds is due to the different relative (un)folding rates of 3(10)-helices, alpha-helices, and pi-bulges/helices. Pure alpha-helix unfolding rates are approximately 12-fold slower (approximately 1 micros) than that of pi-bulges and 3(10)-helices. In addition, we also find that the alpha-helix is most stable at the AdP N-terminus where eight consecutive Ala occur, whereas the three hydrophilic Arg located in the middle and at the C-terminus destabilize the alpha-helix in these regions and induce defects such as pi-bulges and 3(10)-helices.
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Affiliation(s)
- Aleksandr V Mikhonin
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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MORI T, YAMAMURA T. Development of a Program to Estimate Dye-Configurations in Chirogenic Porphyrin Ensembles from UV-Vis. and CD Spectra. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2005. [DOI: 10.2477/jccj.4.107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Briggs JS, Herzenberg A. Vibrational effects in the absorption spectrum of polymer rods. ACTA ACUST UNITED AC 2002. [DOI: 10.1088/0370-1328/92/1/322] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Theoretical investigation on the optical bandshape properties of chromophore aggregates by use of the incoherent dynamic interaction model. Chem Phys 1989. [DOI: 10.1016/0301-0104(89)80252-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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The circular dichroism of helical chromophore aggregates as studied by a self-consistent non-linear response theory. Chem Phys 1986. [DOI: 10.1016/0301-0104(86)80011-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Rabenold DA, Rhodes W. Linear response theory of long‐range solvent effects on ππ* circular dichroism of helical polypeptides. J Chem Phys 1984. [DOI: 10.1063/1.447167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Rabenold DA, Rhodes W. Linear response theory of long range solvent effects on nπ* circular dichroism of helical polypeptides. J Chem Phys 1984. [DOI: 10.1063/1.447168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Rabenold DA. Linear response theory of dye–polymer complex circular dichroism. J Chem Phys 1984. [DOI: 10.1063/1.446813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Kamiya M. A theoretical study for the dynamic interchromophoric interaction effects upon the susceptibility and hypersusceptibility of chromophore aggregates. J Chem Phys 1983. [DOI: 10.1063/1.445862] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ito H, I’Haya YJ. UV absorption and circular dichroism calculations of three Drosophila virilis satellite DNA’s: Use of linear response polarizability theory. J Chem Phys 1982. [DOI: 10.1063/1.443831] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Rabenold DA. Linear response theory of polypeptide circular dichroism: Bogoliubov exciton theory. J Chem Phys 1982. [DOI: 10.1063/1.444427] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Kamiya M. Dynamic perturbation effects upon the circular dichroism intensity induced in an aggregate of dye chromophores bound to biopolymers. Chem Phys 1980. [DOI: 10.1016/0301-0104(80)85237-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Kamiya M. Remarks on the dynamic perturbation effects upon the circular dichroism intensity for chromophore aggregates in the Frenkel exciton model. J Chem Phys 1980. [DOI: 10.1063/1.439095] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Applequist J. A dipole interaction treatment of the polarizabilities and low energy π–π* transitions of amides of formic acid and acetic acid. J Chem Phys 1979. [DOI: 10.1063/1.438238] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Applequist J. A full polarizability treatment of the π–π* absorption and circular dichroic spectra of α‐helical polypeptides. J Chem Phys 1979. [DOI: 10.1063/1.438239] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Applequist J. Dipole coupling effects of nonchromophoric groups in molecules on frequencies, dipole strengths, and rotational strengths of chromophoric groups. J Chem Phys 1979. [DOI: 10.1063/1.438517] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Texter J, Stevens ES. Random‐phase circular dichroism calculations of the σ/3s←n transition in chiral alcohols. J Chem Phys 1979. [DOI: 10.1063/1.437582] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Texter J, Stevens ES. Random‐phase calculation of the circularly dichroic 3000 Å band of (+)−D‐camphor. J Chem Phys 1978. [DOI: 10.1063/1.436745] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Rabenold DA. Circular dichroism theory for unordered polypeptides: A Green operator technique. J Chem Phys 1976. [DOI: 10.1063/1.432956] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ito H, Eri T, I'haya Y. Linear response polarizability theory of the ORD and the CD spectra of helical biopolymers. Chem Phys Lett 1976. [DOI: 10.1016/0009-2614(76)85217-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Ivanov VT, Kogan GA, Meshcheryakova EA, Shilin VV, Ovchinnikov YA. A study of the conformational states of cyclopeptide systems III. Cyclohexapeptides as systems of interacting amide chromophores. Chem Nat Compd 1971. [DOI: 10.1007/bf00569004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Pullman B, Pullman A. Quantum-mechanical investigations of the electronic structure of nucleic acids and their constituents. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1969; 9:327-402. [PMID: 4305447 DOI: 10.1016/s0079-6603(08)60772-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Bullough RK. Complex Refractive Index and a Two‐Band Model in the Theory of Hypochromism. J Chem Phys 1968. [DOI: 10.1063/1.1669675] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Volkenstein MV, Zubkov VA. Rotatory dispersion of the beta-form of polypeptides. PEDIATRIA 1967; 16:465-72. [PMID: 6043413 DOI: 10.1002/bip.1967.360050507] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Vol'kenshtein MV, Zubkov VA. Dispersion of the optical activity of the ?-form of polypeptides. J STRUCT CHEM+ 1967. [DOI: 10.1007/bf00745641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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DeVoe H. Optical Properties of Molecular Aggregates. II. Classical Theory of the Refraction, Absorption, and Optical Activity of Solutions and Crystals. J Chem Phys 1965. [DOI: 10.1063/1.1697294] [Citation(s) in RCA: 235] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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