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Time-Dependent and Time-Independent Approaches for the Computation of Absorption Spectra of Uracil Derivatives in Solution (62 visite)

Improta R, Lami A, Barone V SF

International Journal Of Quantum Chemistry (ISSN: 0020-7608), 2010 Mar 5; 110(3): 624-636.

Tipo di articolo: Journal Article,

Impact factor: 1.302

Impact factor a 5 anni: 1.305


Parole chiave: Non disponibili.

Url: Non disponibile.

In this contribution we discuss the most significant benefits and drawbacks of the alternative time-independent (TI) and time-dependent (TD) approaches to the Calculation of absorption spectra of molecules in solutions. Eigenstate-free TD methods are in principle the most suitable route to face with the calculation of optical spectra in nonadiabatic systems, most of all in presence of conical intersections easily accessible from the Franck-Condon region. However, here we show that, in selected cases, a combined strategy that adopts TD methods to assess the impact of nonadiabatic Couplings on the spectrum and subsequently applies TI methods to include all the degrees of freedom can reveal very convenient. Such a combined TD/TI strategy has been applied to the calculation of the spectrum of Uracil and 5Fluoro-Uracil in acetonitrile. TD studies on reduced dimensionality diabatic models indicate that nonadiabatic effects are moderate and are not the main origin of the diffuse spectral shapes observed in experiments. Subsequent full-coordinate TI calculations allow assigning this feature to intrinsic characteristics of a pi pi* excitation of a small molecular ring structure. This latter introduces remarkable deformation in all the ring structure thus inducing a FC activity in many molecular normal modes both due to displacements of the equilibrium structures and to Duschinsky mixings of the normal coordinates. (C) 2009 Wiley Periodicals, Inc. Int J Quantum Chem 110: 624-636, 20 10
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Avila Ferrer FJ, Cerezo J, Stendardo E, Improta R, Santoro F
J Chem Theory Comput (ISSN: 1549-9618, 1549-9626electronic), 2013 Apr; 9(4): 2072-2082.
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Banyasz A, Douki T, Improta R, Gustavsson T, Onidas D, Vaya I, Perron M, Markovitsi D
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Ruggiero A, Smaldone G, Squeglia F, Berisio R
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Weigel A, Pfaffe M, Sajadi M, Mahrwald R, Improta R, Barone V, Polli D, Cerullo G, Ernsting NP, Santoro F
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Stendardo E, Avila FJA, Santoro F, Improta R
J Chem Theory Comput (ISSN: 1549-9618, 1549-9626electronic, 1549-9618linking), 2012; 8(11): 4483-4493.
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Improta R
Comput Strateg For Spectrosc (ISSN: 9780-4704), 2011; N/D: 37-75.
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Palma G, Comerci M, Prinster A, Quarantelli M, Alfano B
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Langella E, Pierre S, Ghattas W, Giorgi M, Rglier M, Saviano M,  Esposito L, Hardr R
Chemmedchem, 2010; 5: 1568-1576.
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Palma G, Comerci M, Prinster A, Quarantelli M, Alfano B
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Illario M, Monaco S, Cavallo AL, Esposito I, Formisano P, D'Andrea LD, Cipolletta E, Trimarco B, Fenzi G, Rossi G, Vitale M
Cell Signal Cellular Signalling (ISSN: 0898-6568), 2009 May; 21(5): 786-792.
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* Photoinduced dynamics of guanosine monophosphate in water from broad-band transient absorption spectroscopy and quantum-chemical calculations (67 visite)
Karunakaran V, Kleinermanns K, Improta R, Kovalenko SA
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2009; 131(16): 5839-5850.
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Dudar GK, D'Andrea LD, Di Stasi R, Pedone C, Wallace JL
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Improta R, Barone V
Theor Chem Acc (ISSN: 1432-881x), 2008 Jul; 120(4-6): 491-497.
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Santoro F, Lami A, Improta R, Bloino J, Barone V
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Barone V, Improta R, Rega N
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Gallotta G, Palmieri V, Piedimonte V, Rendina D, De Bonis S, Russo V, Celentano A, Di Minno M, Postiglione A, Di Minno G
Int J Cardiol (ISSN: 0167-5273, 1874-1754electronic, 0167-5273linking), 2008 Mar 14; 124(3): 351-357.
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* Liver Fat Is Increased In Type 2 Diabetes Independently Of Visceral Fat And Insulin-Sensitivity (65 visite)
Bozzetto L, Annuzzi G, Prinster A, Mancini M, Giacco R, De Natale C, Salvatore M, Riccardi G, Rivellese AA
Nutr Metab Cardiovasc Dis, 2008; N/D: N/D-N/D.
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J Neurol Sci (ISSN: 0022-510x), 2007 Dec 15; 263(1-2): 15-19.
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* Toward effective and reliable fluorescence energies in solution by a new state specific polarizable continuum model time dependent density functional theory approach (60 visite)
Improta R, Scalmani G, Frisch MJ, Barone V
J Chem Physj Chem Phys (ISSN: 0021-9606), 2007 Sep 21; 127(7): N/D-N/D.
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* Involvement of H4(D10S170) protein in ATM-dependent response to DNA damage (69 visite)
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Oncogene (ISSN: 0950-9232, 1476-5594), 2007 Sep 13; 26(42): 6167-6175.
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* Absorption flattening as one cause of distortion of circular dichroism spectra of Δ-RuPhen3·H2TPPS complex (94 visite)
Castiglioni E, Abbate S, Longhi G, Gangemi R, Lauceri R, Purrello R
Chirality (ISSN: 0899-0042), 2007 Sep; 19(8): 642-646.
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* Solvent effects on the steady-state absorption and fluorescence spectra of uracil, thymine and 5-fluorouracil (68 visite)
Gustavsson T, Sarkar N, Banyasz A, Markovitsi D, Improta R
Photochem Photobiol (ISSN: 0031-8655), 2007 May; 83(3): 595-599.
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* Does Tetracycline Bind Helix 2 Of Prion? An Integrated Spectroscopical And Computational Study Of The Interaction Between The Antibiotic And Alpha Helix 2 Human Prion Protein Fragments (119 visite)
Ronga L, Langella E, Palladino P, Marasco D, Tizzano B, Saviano M, Pedone C, Improta R, Ruvo M
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2007 Feb 15; 66(3): 707-715.
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* Ab initio calculations of absorption spectra of large molecules in solution: Coumarin C153 (72 visite)
Improta R, Barone V, Santoro F
Angew Chem Int Ed (ISSN: 1433-7851, 1521-3773electronic), 2007; 46(3): 405-408.
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* Influence of base stacking on excited-state behavior of polyadenine in water, based on time-dependent density functional calculations (50 visite)
Santoro F, Barone V, Improta R
Proc Natl Acad Sci U S A (ISSN: 0027-8424, 1091-6490, 0027-8424print), 2007; 104(24): 9931-9936.
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* Solvent effect on the singlet excited-state lifetimes of nucleic acid bases: A computational study of 5-fluorouracil and uracil in acetonitrile and water (57 visite)
Santoro F, Barone V, Gustavsson T, Improta R
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2006 Dec 20; 128(50): 16312-16322.
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* A state-specific polarizable continuum model time dependent density functional theory method for excited state calculations in solution (69 visite)
Improta R, Barone V, Scalmani G, Frisch MJ
J Chem Physj Chem Phys (ISSN: 0021-9606), 2006 Sep 7; 125(5): N/D-N/D.
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* Atomoxetine occupies the norepinephrine transporter in a dose-dependent fashion: A PET study in nonhuman primate brain using (S, S)-[18F] FMeNER-D2 (83 visite)
Seneca N, Gulyas B, Varrone A, Schou M, Airaksinen A, Tauscher J, Vandenhende F, Kielbasa W, Farde L, Innis R, Halldin C
Psychopharmacology (ISSN: 0033-3158), 2006 Sep; 188(1): 119-127.
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* Singlet excited-state behavior of uracil and thymine in aqueous solution: A combined experimental and computational study of 11 uracil derivatives (113 visite)
Gustavsson T, Banyasz A, Lazzarotto E, Markovitsi D, Scalmani G, Frisch MJ, Barone V, Improta R
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2006 Jan 18; 128(2): 607-619.
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* A computational protocol to probe the role of solvation effects on the reduction potential of azurin mutants (55 visite)
Barone V, De Rienzo F, Langella E, Menziani MC, Rega N, Sola M
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2006 Jan 1; 62(1): 262-269.
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* Tyrosine phosphorylation of phosphoinositide-dependent kinase 1 by the insulin receptor is necessary for insulin metabolic signaling (81 visite)
Fiory F, Alberobello AT, Miele C, Oriente F, Esposito I, Corbo V, Ruvo M, Tizzano B, Rasmussen TE, Gammeltoft S, Formisano P, Beguinot F
Mol Cell Biol (ISSN: 0270-7306, 1098-5549), 2005 Dec; 25(24): 10803-10814.
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* Survival benefit after revascularization is independent of left ventricular ejection fraction improvement in patients with previous myocardial infarction and viable myocardium (62 visite)
Acampa W, Petretta M, Spinelli L, Ibello F, De Lauro F, Sansone V, Salvatore M, Cuocolo A
Eur J Nucl Med Mol Imaging (ISSN: 1619-7070, 1619-7089, 0340-6997), 2005 Apr; 32(4): 430-437.
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* Nicergoline, a drug used for age-dependent cognitive impairment, protects cultured neurons against β-amyloid toxicity (213 visite)
Filippo C, Mariangela C, Giuseppina F, Pier Luigi C, Angelo B, Marco C, Giuseppe B, Paolo B, Ferdinando N, Agata C, Maria Angela S
Brain Res (ISSN: 0006-8993), 2005; 1047(1): 30-37.
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* Absorption and fluorescence spectra of uracil in the gas phase and in aqueous solution: A TD-DFT quantum mechanical study (140 visite)
Improta R, Barone V
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2004 Nov 10; 126(44): 14320-14321.
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* Computation of protein pK's values by an integrated density functional theory/Polarizable Continuum Model approach (76 visite)
Barone V, Improta R, Rega N
Theor Chem Acc (ISSN: 1432-881x), 2004; 111(2-6): 237-245.
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* Time dependent DFT investigation on the two lowest 1B u states of the trans isomer of stilbene and stiff-stilbenes (73 visite)
Improta R, Santoro F, Dietl C, Papastathopoulos E, Gerber G
Chemical Physics Letters (ISSN: 0009-2614), 2004; 387(4-6): 509-516.
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* An integrated structural and computational study of the thermostability of two thioredoxin mutants from Alicyclobacillus acidocaldarius (80 visite)
Bartolucci S, De Simone G, Galdiero S, Improta R, Menchise V, Pedone C, Pedone E, Saviano M
J Bacteriol Journal Of Bacteriology (ISSN: 0021-9193, 1098-5530), 2003 Jul; 185(14): 4285-4289.
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* Relationship between contractile reserve, TI-201 uptake, and collateral angiographic circulation in collateral-dependent myocardium: Implications regarding the evaluation of myocardial viability (75 visite)
Piscione F, De Luca G, Perrone-filardi P, Prastaro M, Pace L, Galasso G, Marrazzo G, Salvatore M, Chiariello M
J Nucl Cardiol (ISSN: 1071-3581, 1532-6551, 1532-6551electronic), 2003 Jan; 10(1): 17-27.
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* Increased carotid artery intima-media thickness is associated with a novel mutation of low-density lipoprotein receptor independently of major cardiovascular risk factors (76 visite)
Pauciullo P, Giannino A, De Michele M, Gentile M, Liguori R, Argiriou A, Carlotto A, Faccenda F, Mancini M, Bond MG, De Simone V, Rubba P
Metab Clin Exp (ISSN: 0026-0495, 1532-8600), 2003; 52(11): 1433-1438.
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* Radiolabeling approaches for cholecystokinin B receptor imaging (113 visite)
Aloj L, Panico M, Caracó C, Zannetti A, Del Vecchio S, Di Nuzzo C, Arra C, Morelli G, Tesauro D, De Luca S, Pedone C, Salvatore M
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2002; 66(6): 370-380.
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* Solvent polarity and pH effects on the magnetic properties of ionizable nitroxide radicals: A combined computational and experimental study of 2, 2, 5, 5-tetramethyl-3-carboxypyrrolidine and 2, 2, 6, 6-tetramethyl-4-carboxypiperidine nitroxides (65 visite)
Saracino GAA, Tedeschi A, D'Errico G, Improta R, Franco L, Ruzzi M, Corvaia C, Barone V
J Phys Chem A (ISSN: 1089-5639, 1520-5215electronic), 2002; 106(44): 10700-10706.
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Computational procedures to explain the different biological activity of DNA/DNA, DNA/PNA and PNA/PNA hybrid molecules mimicking NF-κB binding sites (76 visite)
Saviano M, Romanelli A, Bucci E, Pedone C, Mischiati C, Bianchi N, Feriotto G, Borgatti M, Gambari R
J Biomol Struct Dyn (ISSN: 0739-1102, 1538-0254electronic), 2000 Dec; 18(3): 353-362.
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Urokinase receptor interacts with alpha(v)beta(5) vitronectin receptor, promoting urokinase-dependent cell migration in breast cancer (94 visite)
Carriero M, Del Vecchio S, Capozzoli M, Franco P, Fontana L, Zannetti A, Botti G, D'Aiuto G, Salvatore M, Stoppelli M
Cancer Res (ISSN: 0008-5472, 1538-7445, 1538-7445electronic), 1999 Oct 15; 59(20): N/D-N/D.
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Mechanisms Of The Hypoglycemic Effect Of Water Solubile Fiber In Non Insulin Dependent Diabetic Patients (45 visite)
Giacco R, Clemente G, Mancini M, D'Avanzo A, Mansueto G, Brighenti F, Lasorella G, Rivieccio AM, Rivellese AA, Riccardi G
Amyloid, 1998 Dec; N/D: 1025-1025.
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Effects of superoxide on nitric oxide-dependent n-nitrosation reactions (52 visite)
Miles AM, Gibson MF, Kirshina M, Cook JC, Pacelli R, Wink D, Grisham MB
Free Radic Res Free Radical Research (ISSN: 1071-5762), 1995 Oct; 23(4): 379-390.
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CRYSTALLIZATION AND PRELIMINARY-X-RAY ANALYSIS OF AN NAD+-DEPENDENT ALCOHOL-DEHYDROGENASE FROM THE EXTREME THERMOPHILIC ARCHAEBACTERIUM SULFOLOBUS-SOLFATARICUS (66 visite)
PEARL L, DEMASI D, HEMMINGS A, SICA F, MAZZARELLA L, RAIA C, DAURIA S, ROSSI M
J Mol Biol Journal Of Molecular Biology (ISSN: 0022-2836, 1089-8638, 1089-8638electronic), 1993 Feb 5; 229(3): 782-784.
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Cerebrovascular Reactivity By Transcranial Doppler Ultrasonography In Insulin-Dependent Diabetic Patients (52 visite)
De Simone C, Mancini M, Vaccaro O, Riccardi G, Gallotta LA, Ferrara G, Cicerano U, Postiglione A
Cerebrovasc Dis, 1993; 3(2): 111-115.
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Relationship between urinary neopterin excretion and islet cell antibodies in type 1 (insulin-dependent) diabetes (61 visite)
Manna R, Salvatore M, Di Leo MA, Scuderi F, Greco AV, Ghirlanda G, Gambassi G
Diabetes Res (ISSN: 0265-5985), 1991 May; 17(1): 33-36.
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86 Records (73 escludendo Abstract e Conferenze).
Impact factor totale: 353.558 (305.927 escludendo Abstract e Conferenze).
Impact factor a 5 anni totale: 363.317 (316.027 escludendo Abstract e Conferenze).

Interrogazione bibliografica effettuata: (([btitle] "Dependent" OR [btitle] "Independent" OR [btitle] "Approaches" OR [btitle] "Computation" OR [btitle] "Absorption") AND NOT [id] = 8967)







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