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Towards the understanding of the excited state dynamics of nucleic acids: Solvent and stacking effect on the photophysical behavior of nucleobases (85 visite)

Santoro F, Gustavsson T, Lami S, Barone V, Improta R

Aip Conf Proc (ISSN: 0094-243x), 2007; 963(2): 631-634.

Tipo di articolo: Journal Article,

Impact factor: 0

Impact factor a 5 anni: 0


Parole chiave: Excited State, Nucleic Acids, Solvation, Spectroscopy, Time-Dependent Density Functional Theory,

Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-71449125084&partnerID=40&md5=47b843602cb7e97312a0b8b39ea8d2ba

This contribution describes the results of some recent studies concerning the excited state behavior of nucleic acid bases, where solvent and stacking effect are included. Our computational approach is based on PBE0 and TD-PBE0 geometry optimizations, while bulk solvent effects are taken into account by the Polarizable Continuum Model, with the possible inclusion of the solvent molecules of the first solvation shell. This approach provides accurate absorption and emission spectra both for pyrimidine and purine bases and is able to explain solvent effect on the excited state lifetimes of uracil-like molecules. Solvent indeed modulates the accessibility of an extra decay channel for the bright excited state, involving an underlying dark state. The effect of base stacking, investigated on 9-methyl-adenine stacked dimers and trimers, on the absorption and emission spectra is also fully reproduced by our calculations. Although light absorption leads to a state (SB) delocalized over different adenine molecules, excited state geometry optimization indicates that afterward it evolves into a state where the excitation is localized on a single base. Analysis of the excited state potential energy surfaces shows that SB can easily decay into the lowest energy excited state (SCT). SCT is a dark excimer produced by inter-monomer charge transfer between two stacked bases. © 2007 American Institute of Physics.
*** IBB - CNR ***

Istituto per i Processi Chimico-Fisici, CNR, Area della Ricerca del CNR Via Moruzzi, 1 I-56124 Pisa, Italy

Laboratoire Francis Perrin, CNRS URA 2453, CEA Saclay, F-91191 Gif-sur, Yvette, France

Dipartimento di Chimica, INSTM, Universita Federico II, Complesso Monte S. Angelo, via Cintia, I-80126 Napoli, Italy

Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, I-80134 Napoli, Italy
Crespo-Hernandez, C.E., Cohen, B., Hare, P.M., Kohler, B., (2004) Chem. Rev, 104, pp. 1977-201

Gustavsson, T., Sarkar, N., Lazzarotto, E., Markovitsi, D., Barone, V., Improta, R., (2006) J. Phys. Chem. B, 110, pp. 12843-12847

Markovitsi, D., Talbot, F., Gustavsson, T., Onidas, D., Lazzarotto, E., Marguet, S., (2006) Nature, 441, pp. E7

Kwok, W.-M., Ma, C., Phillips, D.L., (2006) J. Am. Chem. Soc, 128, pp. 11894-11905

Santoro, F., Barone, V., Gustavsson, T., Improta, R., (2006) J. Am. Chem. Soc, 128, pp. 16312-16322

Gustavsson, T., Banyasz, A., Lazzarotto, E., Markovitsi, D., Scalmani, G., Frisch, M.J., Barone, V., Improta, R., (2006) J. Am. Chem. Soc, 128, pp. 607-619

Improta, R., Barone, V., (2004) J. Am. Chem. Soc, 126, pp. 14320-14321

Hare, P.M., Crespo-Hernandez, C.E., Kohler, B., (2007) Proc. Nat. Acad. Sci, 104, p. 435

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Improta R
The Excited States Of Pi-Stacked 9-Methyl Adenine Oligomers: A Td-Dft Study In Aqueous Solution (79 visite)
Physical Chemistry Chemical Physics, 2008; 10: 2656-2664.
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Staiano M, Saviano M, Herman P, Grycznyski Z, Fini C, Varriale A, Parracino A, Kold AB, Rossi M, D'Auria S
* Time-resolved fluorescence spectroscopy and molecular dynamics simulations point out the effects of pressure on the stability and dynamics of the porcine odorant-binding protein (127 visite)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2008; 89(4): 284-291.
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Santoro F, Barone V, Benzi C, Improta R
* Excited state properties of sizable molecules in solution: From structure to reactivity (90 visite)
Theor Chem Acc (ISSN: 1432-881x), 2007 May; 117(5-6): 1073-1084.
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Roviello GN, Musumeci D, Moccia M, Castiglione M, Sapio R, Valente M, Bucci EM, Perretta G, Pedone C
* Dabpna: Design, Synthesis And Nucleic Acids Binding Studies (101 visite)
Nucleosides Nucleotides Nucleic Acids (ISSN: 1525-7770), 2007; 26(10-12): 1307-1310.
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Gustavsson T, Sarkar N, Lazzarotto E, Markovitsi D, Improta R
* Singlet excited state dynamics of uracil and thymine derivatives: A femtosecond fluorescence upconversion study in acetonitrile (78 visite)
Chemical Physics Letters (ISSN: 0009-2614), 2006 Oct 5; 429(4-6): 551-557.
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Improta R, Barone V, Scalmani G, Frisch MJ
* A state-specific polarizable continuum model time dependent density functional theory method for excited state calculations in solution (90 visite)
J Chem Phys (ISSN: 0021-9606, 0897-690online), 2006 Sep 7; 125(5): N/D-N/D.
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De Capua A, Goodman M, Amino Y, Saviano M, Benedetti E
* Conformation analysis of aspartame-based sweeteners by NMR spectroscopy, molecular dynamics simulations, and X-ray diffraction studies (171 visite)
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-7633electronic), 2006 Feb; 7(2): 377-387.
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Barone V, De Rienzo F, Langella E, Menziani MC, Rega N, Sola M
* A computational protocol to probe the role of solvation effects on the reduction potential of azurin mutants (73 visite)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2006 Jan 1; 62(1): 262-269.
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Improta R, Barone V, Scalmani G, Frisch MJ
* A State-Specific Pcm Td-Dft Method For Equilibrium And Non-Equilibrium Excited State Calculations In Solution (116 visite)
J Chem Phys (ISSN: 0897-690online, 0021-9606printed), 2006; 125(5): 54103-54103.
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Benzi C, Cossi M, Improta R, Barone V
* A Contribution To The Solvation Free Energy In Isotropic And Anisotropic Polarizable Continuum Model (102 visite)
Journal Of Computational Chemistry, 2005; 26: 1096-1105.
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Gulino A, Tabbì G
* CdO thin films: A study of their electronic structure by electron spin resonance spectroscopy (81 visite)
Appl Surf Sci (ISSN: 0169-4332), 2005; 245(1-4): 322-327.
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Borgatti M, Finotti A, Romanelli A, Saviano M, Bianchi N, Lampronti I, Lambertini E, Penolazzi L, Nastruzzi C, Mischiati C, Piva R, Pedone C, Gambari R
* Peptide nucleic acids (PNA)-DNA chimeras targeting transcription factors as a tool to modify gene expression (123 visite)
Curr Drug Targets (ISSN: 1389-4501), 2004 Nov; 5(8): 735-744.
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Cortesi R, Mischiati C, Borgatti M, Breda L, Romanelli A, Saviano M, Pedone C, Gambari R, Nastruzzi C
* Formulations for natural and peptide nucleic acids based on cationic polymeric submicron particles (92 visite)
The Aaps Journal (ISSN: 1522-1059, 1550-7416), 2004 Jan 20; 6(1): N/D-N/D.
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Gambari R, Borgatti M, Romanelli A, Capasso D, Saviano M, Bianchi N, Lampronti I, Mischiati C, Pedone C
* Transcription factor decoy (TFD) activity of peptide nucleic acids (PNA)-DNA chimeras (85 visite)
International Journal Of Molecular Medicine (ISSN: 1107-3756), 2003; 12(Supplement1): N/D-N/D.
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Sijens PE, Knopp MV, Brunetti A, Wicklow K, Alfano B, Bachert P, Sanders JA, Stillman AE, Kett H, Sauter R
1H MR spectroscopy in patients with metastatic brain tumors: A multicenter study (96 visite)
Magn Reson Med (ISSN: 0740-3194, 1522-2594electronic), 1995 Jun; 33(6): 818-826.
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BRUNETTI A, ALFANO B, STEFANO M, CARACO C, ARPAIA M, BRUNI G, ELMO M, COVELLI E, FREZZA P, SALVATORE M
METABOLIC CHARACTERIZATION OF CEREBRAL METASTASIS USING MR PROTON SPECTROSCOPY (92 visite)
Neuroradiology 1993, 1993; N/D: N/D-N/D.
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72 Records (64 escludendo Abstract e Conferenze).
Impact factor totale: 316.948 (303.259 escludendo Abstract e Conferenze).
Impact factor a 5 anni totale: 330.553 (310.747 escludendo Abstract e Conferenze).







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