Effects of molecular dynamics and solvation on the electronic structure of molecular probes
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Effects of molecular dynamics and solvation on the electronic structure of molecular probes (526 views)

Caruso P, Causà M, Cimino P, Crescenzi O, D'Amore M, Improta R, Pavone M, Rega N

Theor Chem Acc (ISSN: 1432-881x), 2012 Apr; 131(4): 1211-1212.

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Paper type: Journal Article,

Impact factor: 2.233, 5-year impact factor: 3.151

Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-84860332862&partnerID=40&md5=48f2fee8b288c61c9a8ba76e7323e8d5

Keywords: Absorption Spectra, Adenine, Dynamics, Electron Density Analysis, Epr Spectra, Nitroxides, Quantum Mechanical Calculations, Solution,

Affiliations:
*** IBB - CNR ***

IIT, CRIB Center for Advanced Biomaterials for Healthcare, Italian Institute of Technology, p.le Tecchio 80, 80125 Napoli, Italy
Dipartimento di Chimica Paolo Corradini, Università Federico II di Napoli, Complesso Monte S. Angelo, via Cintia, 80126 Napoli, Italy
Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte don Melillo, 84084 Fisciano, SA, Italy
Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, 80134 Napoli, Italy


References:
Not available.
Effects of molecular dynamics and solvation on the electronic structure of molecular probes

Most spectroscopic parameters are influenced by nuclear dynamics and by the chemical environment. However, proper inclusion of these effects still represents a challenge in computational spectroscopy studies. In many cases, a route coupling satisfactory accuracy with reasonable computational costs consists in the integration of DFT-based methods to compute spectroscopic parameters, with ab initio molecular dynamics simulations to sample from the classical phase space of the system. Here, we discuss the application of this approach in two case studies of remarkable practical interest, namely the simulation of the absorption spectrum of 9-methyladenine, an adenine nucleoside model; and the prediction of electron spin resonance parameters for nitroxyl radicals, the prototypical spin probes. In both cases, the accuracy of the results increases significantly when the subtle interplay of intra-molecular dynamics and solvent effects is introduced. © 2012 Springer-Verlag.
Effects of molecular dynamics and solvation on the electronic structure of molecular probes

▼    Study of the interaction between UV light and nucleic acids: elucidating the molecular mechanisms responsible of the genetic stability and of the oxidative damaging processes by using computational methods
Effects of molecular dynamics and solvation on the electronic structure of molecular probes

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Ciaco S, Gavvala K, Greiner V, Mazzoleni V, Didier P, Ruff M, Martinez-fernandez L, Improta R, Mély Y
* Thienoguanosine brightness in DNA duplexes is governed by the localization of itsππ* excitation in the lowest energy absorption band (144 views)
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Impact Factor: 2.79
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Lizondo-aranda P, Martínez-fernández L, Miranda MA, Improta R, Gustavsson T, Lhiaubet-vallet V
* The Excited State Dynamics of a Mutagenic Cytidine Etheno Adduct Investigated by Combining Time-Resolved Spectroscopy and Quantum Mechanical Calculations (98 views)
J Phys Chem Lett (ISSN: 1948-7185linking, 1948-7185electronic), 2022 Jan 13; 13(1): 251-257.
Impact Factor: 6.475
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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 (173 views)
Molecules (ISSN: 1420-3049linking, 1420-3049electronic), 2021 Aug 7; 26(16): N/D-N/D.
Impact Factor: 4.411
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Green JA, Jouybari MY, Aranda D, Improta R, Santoro F
* Nonadiabatic Absorption Spectra and Ultrafast Dynamics of DNA and RNA Photoexcited Nucleobases (88 views)
Molecules (ISSN: 1420-3049linking, 1420-3049electronic), 2021 Mar 20; 26(6): N/D-N/D.
Impact Factor: 4.411
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Martinez-fernandez L, Gustavsson T, Diederichsen U, Improta R
* Excited State Dynamics of 8-Vinyldeoxyguanosine In Aqueous Solution Studied by Time-Resolved Fluorescence Spectroscopy and Quantum Mechanical Calculations (107 views)
Molecules (ISSN: 1420-3049linking, 1420-3049electronic), 2020 Feb 13; 25(4): N/D-N/D.
Impact Factor: 3.267
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Martinez-fernandez L, Banyasz A, Markovitsi D, Improta R
* Topology Controls the Electronic Absorption and Delocalization of Electron Holes in Guanine Quadruplexes (537 views)
Chemistry (ISSN: 1521-3765electronic, 0947-6539linking), 2018 Oct 12; 24(57): 15185-15189.
Impact Factor: 5.476
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Martinez-fernandez L, Improta R
* Photoactivated proton coupled electron transfer in DNA: Insights from quantum mechanical calculations (324 views)
Faraday Discuss (ISSN: 1359-6640, 1359-6640print), 2018; 207: 199-216.
Impact Factor: 3.427
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Martinez-fernandez L, Pepino AJ, Segarra-marti J, Jovaisaite J, Vaya I, Nenov A, Markovitsi D, Gustavsson T, Banyasz A, Garavelli M, Improta R
* Photophysics of Deoxycytidine and 5-Methyldeoxycytidine in Solution: A Comprehensive Picture by Quantum Mechanical Calculations and Femtosecond Fluorescence Spectroscopy (326 views)
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 0002-7863print), 2017 Jun 14; 139(23): 7780-7791.
Impact Factor: 14.357
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Musumeci D, Rozza L, Merlino A, Paduano L, Marzo T, Massai L, Messori L, Montesarchio D
* Interaction of anticancer Ru(III) complexes with single stranded and duplex DNA model systems (879 views)
Dalton T (ISSN: 1477-9226, 1477-9234, 1477-9226linking), 2015; 44(31): 13914-13925.
Impact Factor: 4.177
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Improta R
* Quantum mechanical calculations unveil the structure and properties of the absorbing and emitting excited electronic states of guanine quadruplex (763 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2014 Jun 23; 20(26): 8106-8115.
Impact Factor: 5.731
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Improta R, Vitagliano L,  Esposito L
* Correction: Peptide bond distortions from planarity: New insights from quantum mechanical calculations and peptide/protein crystal structures (PLoS ONE) (309 views)
Plosone (ISSN: 1932-6203, 1932-6203electronic, 1932-6203linking), 2014; 9(1): N/D-N/D.
Impact Factor: 3.234
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Banyasz A, Gustavsson T, Onidas D, Changenet-Barret P, Markovitsi D, Improta R
* Multi-pathway excited state relaxation of adenine oligomers in aqueous solution: A joint theoretical and experimental study (542 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2013 Mar; 19(11): 3762-3774.
Impact Factor: 5.696
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Stendardo E, Avila FJA, Santoro F, Improta R
* Vibrationally resolved absorption and emission spectra of dithiophene in the gas phase and in solution by first-principle quantum mechanical calculations (810 views)
J Chem Theory Comput (ISSN: 1549-9618, 1549-9626electronic, 1549-9618linking), 2012; 8(11): 4483-4493.
Impact Factor: 5.389
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Improta R, Vitagliano L, Esposito L
* Peptide bond distortions from planarity: New insights from quantum mechanical calculations and peptide/protein crystal structures (1225 views)
Plosone (ISSN: 1932-6203, 1932-6203electronic, 1932-6203linking), 2011 Sep 16; 6(9): e24533-e24533.
Impact Factor: 4.092
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Vagliasindi LI, Arena G, Bonomo RP, Pappalardo G, Tabbì G
* Copper complex species within a fragment of the N-terminal repeat region in opossum PrP protein (512 views)
Dalton T (ISSN: 1477-9226, 1477-9234, 1477-9234electronic), 2011 Mar 21; 40(11): 2441-2450.
Impact Factor: 3.838
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Improta R, Lami A, Barone V SF
* Time-Dependent and Time-Independent Approaches for the Computation of Absorption Spectra of Uracil Derivatives in Solution (403 views)
International Journal Of Quantum Chemistry (ISSN: 0020-7608), 2010 Mar 5; 110(3): 624-636.
Impact Factor: 1.302
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Improta R, Barone V
The excited states of adenine and thymine nucleoside and nucleotide in aqueous solution: A comparative study by time-dependent DFT calculations (336 views)
Theor Chem Acc (ISSN: 1432-881x), 2008 Jul; 120(4-6): 491-497.
Impact Factor: 2.37
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Santoro F, Lami A, Improta R, Barone V
* Effective method to compute vibrationally resolved optical spectra of large molecules at finite temperature in the gas phase and in solution (653 views)
J Chem Phys (ISSN: 0021-9606, 0897-690online), 2007 May 14; 126(18): 184102-184102.
Impact Factor: 3.044
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Santoro F, Barone V, Benzi C, Improta R
* Excited state properties of sizable molecules in solution: From structure to reactivity (344 views)
Theor Chem Acc (ISSN: 1432-881x), 2007 May; 117(5-6): 1073-1084.
Impact Factor: 2.537
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Santoro F, Improta R, Lami A, Bloino J, Barone V
* Effective method to compute Franck-Condon integrals for optical spectra of large molecules in solution (413 views)
J Chem Phys (ISSN: 0021-9606, 0897-690online), 2007 Feb 28; 126(8): 084509-084509.
Impact Factor: 3.044
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Improta R, Barone V, Santoro F
* Ab initio calculations of absorption spectra of large molecules in solution: Coumarin C153 (632 views)
Angew Chem Int Ed (ISSN: 1433-7851, 1521-3773electronic, 1433-7851linking), 2007; 46(3): 405-408.
Impact Factor: 10.031
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Saracino GAA, Tedeschi A, D'Errico G, Improta R, Franco L, Ruzzi M, Corvaia C, Barone V
* 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 (357 views)
J Phys Chem A (ISSN: 1089-5639, 1520-5215electronic, 1089-5639linking), 2002; 106(44): 10700-10706.
Impact Factor: 2.765
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22 Records (19 excluding Abstracts).
Total impact factor: 101.864 (91.684 excluding Abstracts).
Total 5 year impact factor: 96.158 (85.535 excluding Abstracts).

Last modified by Marco Comerci on Sunday 12 July 2020, 13:14:56
526 views. Last view on Sunday 13 October 2024, 1:51:35