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Effects of molecular dynamics and solvation on the electronic structure of molecular probes (97 visite)

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.

Tipo di articolo: Journal Article,

Impact factor: 2.233

Impact factor a 5 anni: 3.151


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

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

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.
*** 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
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Contiene: [X]      Estesa  

Autori: [X]   E Tipo di lavoro: [X]

E Data iniziale: Data finale: [X]   E Sede:  E    Affiliazione IBB   [Pulisci modulo]

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* Insights into structure, stability, and toxicity of monomeric and aggregated polyglutamine models from molecular dynamics simulations (91 visite)
Esposito L, Paladino A, Pedone C, Vitagliano L
Biophysical Journal (ISSN: 1542-0086, 0006-3495), 2008 May 15; 94(10): 4031-4040.
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* Structure, dynamics, and stability of assemblies of the human prion fragment SNQNNF (112 visite)
De Simone A, Pedone C, Vitagliano L
Biochem Biophys Res Commun (ISSN: 1090-2104, 0006-291x, 1090-2104electronic), 2008 Feb 15; 366(3): 800-806.
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* 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 (104 visite)
Staiano M, Saviano M, Herman P, Grycznyski Z, Fini C, Varriale A, Parracino A, Kold AB, Rossi M, D'Auria S
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2008; 89(4): 284-291.
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* An NMR and molecular dynamics investigation of the avian prion hexarepeat conformational features in solution (88 visite)
Pietropaolo A, Raiola L, Muccioli L, Tiberio G, Zannoni C, Fattorusso R, Isernia C, La Mendola D, Pappalardo G, Rizzarelli E
Chemical Physics Letters (ISSN: 0009-2614), 2007 Jul 6; 442(1-3): 110-118.
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* Tracking the dynamics of secondary degeneration after stroke (62 visite)
Pappata S
J Neurol Neurosurg Psychiatry (ISSN: 0022-3050), 2007 Jun; 78(6): 554-554.
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* A Molecular Dynamics Study of Pilus Subunits: Insights into Pilus Biogenesis (108 visite)
Vitagliano L, Ruggiero A, Pedone C, Berisio R
J Mol Biol Journal Of Molecular Biology (ISSN: 0022-2836, 1089-8638, 1089-8638electronic), 2007 Apr 6; 367(4): 935-941.
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* Dynamics of prefrontal and cingulate activity during a reward-based logical deduction task (97 visite)
Landmann C, Dehaene S, Pappata S, Jobert A, Bottlaender M, Roumenov D, Le Bihan D
Cereb Cortex (ISSN: 1047-3211), 2007 Apr; 17(4): 749-759.
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* Ab initio calculations of absorption spectra of large molecules in solution: Coumarin C153 (83 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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* Quantum dynamics of ultrafast photoinduced processes in biological molecules (79 visite)
Santoro F, Barone V, Improta R, Lami A, Olivucci M
Aip Conf Proc (ISSN: 0094-243x), 2007; 963(2): 667-670.
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* Steered molecular dynamics studies reveal different unfolding pathways of prions from mammalian and non-mammalian species (90 visite)
Pappalardo M, Milardi D, Grasso D, La Rosa C
New Journal Of Chemistry (ISSN: 1144-0546), 2007; 31(6): 901-905.
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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 (79 visite)
Santoro F, Gustavsson T, Lami S, Barone V, Improta R
Aip Conf Proc (ISSN: 0094-243x), 2007; 963(2): 631-634.
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* Tryptophan phosphorescence studies of the D-galactose/ D-glucose-binding protein from Escherichia coli provide a molecular portrait with structural and dynamics features of the protein (349 visite)
D'Auria S, Varriale A, Gonnelli M, Saviano M, Staiano M, Rossi M, Strambini GB
J Proteome Res Journal Of Proteome Research (ISSN: 1535-3893), 2007; 6(4): 1306-1312.
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* Singlet excited state dynamics of uracil and thymine derivatives: A femtosecond fluorescence upconversion study in acetonitrile (70 visite)
Gustavsson T, Sarkar N, Lazzarotto E, Markovitsi D, Improta R
Chemical Physics Letters (ISSN: 0009-2614), 2006 Oct 5; 429(4-6): 551-557.
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* Molecular dynamics analyses of cross-beta-spine steric zipper models: beta-sheet twisting and aggregation (126 visite)
Esposito L, Pedone C, Vitagliano L
Proc Natl Acad Sci U S A (ISSN: 0027-8424, 1091-6490, 0027-8424print), 2006 Sep 1; 103(31): 11533-11538.
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* Femtosecond study on the isomerization dynamics of NK88. I. Ground-state dynamics after photoexcitation (77 visite)
Nuernberger P, Vogt G, Gerber G, Improta R, Santoro F
J Chem Phys (ISSN: 0021-9606, 0021-9606print), 2006 Jul 28; 125(4): 44512-44544.
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* Femtosecond study on the isomerization dynamics of NK88. II. Excited-state dynamics (98 visite)
Vogt G, Nuernberger P, Gerber G, Improta R, Santoro F, Nuernberger P, Vogt G, Gerber G, Improta R, Santoro F
J Chem Physj Chem Phys (ISSN: 0021-9606), 2006 Jul 28; 125(4): 44512-44512.
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* Solvent effect on the singlet excited-state dynamics of 5-fluorouracil in acetonitrile as compared with water (81 visite)
Gustavsson T, Sarkar N, Lazzarotto E, Markovitsi D, Barone V, Improta R
J Phys Chem B (ISSN: 1520-6106, 1520-5207, 1520-5207electronic), 2006 Jul 6; 110(26): 12843-12847.
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* Assessing the acid-base and conformational properties of histidine residues in human prion protein (125-228) by means of pKα calculations and molecular dynamics simulations (137 visite)
Langella E, Improta R, Crescenzi O, Barone V
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2006 Jul 1; 64(1): 167-177.
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* Polyglutamine Repeats And Beta-Helix Structure: Molecular Dynamics Study (109 visite)
Merlino A, Esposito L, Vitagliano L
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2006 Jun 1; 63(4): 918-927.
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* Conformation analysis of aspartame-based sweeteners by NMR spectroscopy, molecular dynamics simulations, and X-ray diffraction studies (159 visite)
De Capua A, Goodman M, Amino Y, Saviano M, Benedetti E
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-7633electronic), 2006 Feb; 7(2): 377-387.
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* The importance of dynamic effects on the enzyme activity: X-ray structure and molecular dynamics of onconase mutants (97 visite)
Merlino A, Mazzarella L, Carannante A, Di Fiore A, Di Donato A, Notomista E, Sica F
J Biol Chem Journal Of Biological Chemistry (ISSN: 0021-9258, 1083-351x), 2005 May 6; 280(18): 17953-17960.
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* Insight into ribonuclease A domain swapping by molecular dynamics unfolding simulations (82 visite)
Esposito L, Daggett V
Biochemistry (ISSN: 0006-2960, 1520-4995, 1520-4995electronic), 2005 Mar 8; 44(9): 3358-3368.
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* Open interface and large quaternary structure movements in 3D domain swapped proteins: Insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease (114 visite)
Merlino A, Ceruso MA, Vitagliano L, Mazzarella L
Biophysical Journal (ISSN: 0006-3495, 1542-0086), 2005 Mar; 88(3): 2003-2012.
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* Checking the pH-induced conformational transition of prion protein by molecular dynamics simulations: Effect of protonation of histidine residues (102 visite)
Langella E, Improta R, Barone V
Biophysical Journal (ISSN: 0006-3495, 1542-0086), 2004 Dec; 87(6): 3623-3632.
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* A molecular dynamics study on the conformational stability of PrP 180-193 helix II prion fragment (87 visite)
Pappalardo M, Milardi D, La Rosa C, Zannoni C, Rizzarelli E, Grasso D
Chemical Physics Letters (ISSN: 0009-2614), 2004 Jun 1; 390(4-6): 511-516.
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* Early and late effects of coronary artery bypass grafting on cardiac haemodynamics during daily physical activities in patients with coronary artery disease (83 visite)
Imbriaco M, Ferro A, Storto G, Pellegrino T, Sica G, Cuocolo A
Eur J Nucl Med Mol Imaging (ISSN: 1619-7070, 1619-7089, 0340-6997), 2004 Jun; 31(6): 852-856.
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* Solution structure and backbone dynamics of the K18G/R82E Alicyclobacillus acidocaldarius thioredoxin mutant: A molecular analysis of its reduced thermal stability (80 visite)
Leone M, Di Lello P, Ohlenschläger O, Pedone E, Bartolucci S, Rossi M, Di Blasio B, Pedone C, Saviano M, Isernia C, Fattorusso R
Biochemistry (ISSN: 0006-2960, 1520-4995, 1520-4995electronic), 2004 May 25; 43(20): 6043-6058.
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* 3-Amino Derivative Of Beta-Cyclodextrin: Thermodynamics Of Copper (ii) Complexes And Exploitation Of Its Enantioselectivity In The Separation Of Amino Acid Racemates By Ligand Exchange Capillary Electrophoresis (98 visite)
Cucinotta V, Giuffrida A, La Mendola D, Maccarrone G, Puglisi A, Rizzarelli E, Vecchio G
And Life Sciencesjournal Of Chromatography B Analytical Technologies In The Biomedical, 2004 Feb 5; 800(1-2): 127-133.
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* Free energy perturbation and molecular dynamics calculations of copper binding to azurin (93 visite)
Pappalardo M, Milardi D, Grasso DM, La Rosa C
J Comput Chem (ISSN: 0192-8651, 1096-987xelectronic), 2003 Apr 30; 24(6): 779-785.
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* Global and local motions in ribonuclease A: A molecular dynamics study (87 visite)
Merlino A, Vitagliano L, Ceruso M, Di Nola A, Mazzarella L
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2002 Nov 15; 65(4): 274-283.
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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 (86 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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OPTIMAL DETERMINATION OF RIGHT-VENTRICULAR FILLING DYNAMICS IN SYSTEMIC HYPERTENSION (68 visite)
Cittadini A, Fazio S, Strömer H, Cuocolo A, Sabatini D, Imbriaco M, Saccá L, Douglas PS
American Heart Journal (ISSN: 0002-8703), 1995 Nov; 130(5): 1074-1082.
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BIOACTIVE PEPTIDES - SOLID-STATE, SOLUTION AND MOLECULAR-DYNAMICS STUDIES OF A CYCLOLINOPEPTIDE-A RELATED CYSTINYL CYCLOPENTAPEPTIDE (91 visite)
Rossi F, Saviano M, Di Blasio B, Zanotti G, Maione AM, Tancredi T, Pedone C
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 1994 Feb; 34(2): 273-284.
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Noninvasive evaluation of cardiac hemodynamics during exercise in patients with chronic heart failure: Effects of short-term Coenzyme Q10 treatment (78 visite)
Morisco C, Nappi A, Argenziano L, Sarno D, Fonatana D, Imbriaco M, Nicolai E,  Romano M, Rosiello G, Cuocolo A
Molecular Aspects Of Medicine (ISSN: 0098-2997, 1872-9452), 1994; 15(SUPPL.1): s155-s155.
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Molecular dynamics simulation in vacuo and in solution of [Aib5, 6-D- Ala8] Cyclolinopeptide A: A conformational and comparative study (79 visite)
Saviano M, Rossi F, Pavone V, Di Blasio B, Pedone C
J Biomol Struct Dyn (ISSN: 0739-1102, 1538-0254electronic, 0739-1102linking), 1992 Jun; 9(6): 1045-1060.
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Peripheral Haemodynamics In Hypertensive Patients (60 visite)
Mancini M, Iannuzzi R, Marotta T, Ferrara LA
J Hum Hypertens, 1992 May; N/D: 39A-39A.
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Regional Hemodynamics During Ketanserin Treatment In Hypertensive Patients (64 visite)
Ferrara LA, Mancini M, Soricelli A, Postiglione A, Iannuzzi A, Iannuzzi R
Fifth European Meeting On Hypertension European Society Of Hypertension Milan, 1991 Oct; N/D: 209-209.
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Regional Haemodynamics During Ketanserin In Hypertensive Patients (64 visite)
Ferrara LA, Mancini Marcello, Soro S, Soricelli A, Postiglione A, Iannuzzi A, Iannuzzi R
Acta Therapeuthica, 1991; N/D: 229-238.
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77 Records (68 escludendo Abstract e Conferenze).
Impact factor totale: 262.217 (246.788 escludendo Abstract e Conferenze).
Impact factor a 5 anni totale: 265.966 (242.497 escludendo Abstract e Conferenze).

Interrogazione bibliografica effettuata: (([btitle] "Absorption Spectra" OR [btitle] "Dynamics" OR [btitle] "Electron Density Analysis" OR [btitle] "Epr Spectra" OR [btitle] "Nitroxides") AND NOT [id] = 10620)







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