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Quantum mechanical computations and spectroscopy: From small rigid molecules in the gas phase to large flexible molecules in solution (83 visite)

Barone V, Improta R, Rega N

Acc Chem Res (ISSN: 0001-4842), 2008 May; 41(5): 605-616.

Tipo di articolo: Journal Article,

Impact factor: 12.176

Impact factor a 5 anni: 15.403


Parole chiave: Non disponibili.

Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-45749092976&partnerID=40&md5=fb9a10f9abaed7011ae30addc479a6eb

(Figure Presented) Interpretation of structural properties and dynamic behavior of molecules in solution is of fundamental importance to understand their stability, chemical reactivity, and catalytic action. While information can be gained, in principle, by a variety of spectroscopic techniques, the interpretation of the rich indirect information that can be inferred from the analysis of experimental spectra is seldom straightforward because of the subtle interplay of several different effects, whose spedfic role is not easy to separate and evaluate. In such a complex scenario, theoretical studies can be very helpful at two different levels: (i) supporting and complementing experimental results to determine the structure of the target molecule starting from its spectral properties; (ii) dissecting and evaluating the role of different effects in determining the observed spedroscopic properties. This is the reason why computational spectroscopy is rapidly evolving from a highly spedalized research field into a versatile and widespread tool for the assignment of experimental spectra and their interpretation in terms of chemical physical effects. In such a situation, it becomes important that both computationally and experimentally oriented chemists are aware that new methodological advances and integrated computational strategies are available, providing reliable estimates of fundamental spectral parameters not only for relatively small molecules in the gas phase but also for large and flexible molecules in condensed phases. In this Account, we review the most significant methodological contributions from our research group in this field, and by exploiting some recent results of their application to the computation of IR, UV-vis, NMR, and EPR spectral parameters, we discuss the microscopic mechanisms underlying solvent and vibrational effects on the spectral parameters. After reporting some recent achievements for the study of excited states by first prindple quantum mechanical approaches, we focus on the treatment of environmental effects by means of mixed discrete-continuum solvent models and on effective methods for computing vibronic contributions to the spectra. We then discuss some new developments, mainly based on time-dependent approaches, allowing us to go beyond the determination of spectroscopic parameters toward the simulation of line widths and shapes. Although further developments are surely needed to improve the accuracy and effectiveness of several items in the proposed approach, we try to show that the first important steps toward a direct comparison between the results obtained in vitro and those obtained in silico have been made, making easier fruitful crossovers among experiments, computations and theoretical models, which would be dedsive for a deeper understanding of the spectral behavior assodated with complex systems and processes. © 2008 American Chemical Society.
*** IBB - CNR ***

Chemistry Department Paolo Corradini, University Federico II, Complesso Universitario Monte S. Angelo, via Cintia, I-80126 Napoli, Italy
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* Vibrationally resolved absorption and emission spectra of dithiophene in the gas phase and in solution by first-principle quantum mechanical calculations (80 visite)
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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* Peptide bond distortions from planarity: New insights from quantum mechanical calculations and peptide/protein crystal structures (114 visite)
Improta R, Vitagliano L, Esposito L
Plos One (ISSN: 1932-6203, 1932-6203electronic), 2011 Sep 16; 6(9): e24533-e24533.
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* Probing membrane topology of the antimicrobial peptide distinctin by solid-state NMR spectroscopy in zwitterionic and charged lipid bilayers (99 visite)
Verardi R, Traaseth NJ, Shi L, Porcelli F, Monfregola L, De Luca S, Amodeo P, Veglia G, Scaloni A
Biochim Biophys Acta (ISSN: 0005-2736, 0006-3002, 0925-4439), 2011 Jan; 1808(1): 34-40.
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* Computing the inhomogeneous broadening of electronic transitions in solution: A first-principle quantum mechanical approach (80 visite)
Avila FF, Improta R, Santoro F, Barone V
Phys Chem Chem Phys (ISSN: 1463-9076, 1463-3907, 1463-9084electronic), 2011; 13(38): 17007-17012.
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* Sonographic hepatic-renal ratio as indicator of hepatic steatosis: comparison with (1)H magnetic resonance spectroscopy (100 visite)
Mancini M, Prinster A, Annuzzi G, Liuzzi R, Giacco R, Medagli C, Cremone M, Clemente G, Maurea S, Riccardi G, Rivellese AA, Salvatore M
Metab Clin Exp (ISSN: 1532-8600, 0026-0495), 2009 Dec; 58(12): 1724-1730.
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* A mass spectrometry and surface enhanced Raman spectroscopy study of the interaction between linear carbon chains and noble metals (113 visite)
Grasso G, D'Urso L, Messina E, Cataldo F, Puglisi O, Spoto G, Compagnini G
Carbon (ISSN: 0008-6223), 2009; 47(11): 2611-2619.
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* Colloidal particles composed of amphiphilic molecules binding gadolinium complexes and peptides as tumor-specific contrast agents in MRI: physico-chemical characterization (163 visite)
Vaccaro M, Mangiapia G, Radulescu A, Schillen K, D'Errico G, Morelli G, Paduano L
Soft Matter (ISSN: 1744-683x), 2009; 5(13): 2504-2512.
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* Photoinduced dynamics of guanosine monophosphate in water from broad-band transient absorption spectroscopy and quantum-chemical calculations (81 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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* Development of new molecules that compete with p53 for Binding to TFIIH (87 visite)
Zaccaro L, Del Gatto A, Saviano M, Langella E, Langlois C, Di Lello P, Baffreau J, Mas C, Legault P, Omichinski JG, Pedone C
J Pept Sci (ISSN: 1075-2617, 1099-1387, 1075-2617print), 2008 Sep; 14(8): N/D-N/D.
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* Effective method for the computation of optical spectra of large molecules at finite temperature including the Duschinsky and Herzberg-Teller effect: The Qx band of porphyrin as a case study (76 visite)
Santoro F, Lami A, Improta R, Bloino J, Barone V
J Chem Physj Chem Phys (ISSN: 0021-9606), 2008 Jun 14; 128(22): 17-17.
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* The identification and characterization of fusogenic domains in herpes virus glycoprotein B molecules (78 visite)
Galdiero S, Vitiello M, D'Isanto M, Falanga A, Cantisani M, Browne H, Pedone C, Galdiero M
Chembiochem (ISSN: 1439-7633, 1439-4227, 1439-7633electronic), 2008 Mar 25; 9(5): 758-767.
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* The cell cycle molecules behind neurodegeneration in Alzheimer's disease: Perspectives for drug development (99 visite)
Copani A, Guccione S, Giurato L, Caraci F, Calafiore M, Sortino MA
Curr Med Chem (ISSN: 0929-8673, 1875-533x, 1875-533xelectronic), 2008; 15(24): 2420-2432.
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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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* Effective method to compute vibrationally resolved optical spectra of large molecules at finite temperature in the gas phase and in solution (71 visite)
Santoro F, Lami A, Improta R, Barone V
J Chem Physj Chem Phys (ISSN: 0021-9606), 2007 May 14; 126(18): 184102-184102.
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* Excited state properties of sizable molecules in solution: From structure to reactivity (82 visite)
Santoro F, Barone V, Benzi C, Improta R
Theor Chem Acc (ISSN: 1432-881x), 2007 May; 117(5-6): 1073-1084.
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* Effective method to compute Franck-Condon integrals for optical spectra of large molecules in solution (77 visite)
Santoro F, Improta R, Lami A, Bloino J, Barone V
J Chem Physj Chem Phys (ISSN: 0021-9606), 2007 Feb 28; 126(8): 084509-084509.
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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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* Erratum: Effective Method To Compute Franck-Condon Integrals For Optical Spectra Of Large Molecules In Solution (55 visite)
Santoro F, Improta R, Lami A, Bloino J, Barone V
J Chem Physj Chem Phys (ISSN: 0021-9606), 2007; 126(16): N/D-N/D.
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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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* A Parameter Free Quantum Mechanical Approach To The Calculation Of Electron Transfer Rates For Large Systems In Solution (68 visite)
Improta R, Barone V, Newton MD
Chemphyschem (ISSN: 1439-4235, 1439-7641, 1439-7641electronic), 2006 Jun 12; 7(6): 1211-1215.
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* Water molecules as structural determinants among prions of low sequence identity (96 visite)
De Simone A, Dodson GG, Fraternali F, Zagari A
Febs Lett (ISSN: 0014-5793print, 0014-5793linking, 1873-3468electronic), 2006 May 1; 580(10): 2488-2494.
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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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* Peptide-based molecules in angiogenesis (126 visite)
D'Andrea LD, Del Gatto A, Pedone C, Benedetti E
Chem Biol Drug Des Chemical Biology And Drug Design (ISSN: 1747-0277, 1747-0285), 2006 Feb; 67(2): 115-126.
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* Identification of small molecules inhibitors of GCN5 histone acetyltransferase activity (86 visite)
Mai A, Rotili D, Ornaghi P, Tosi F, Vicidomini C, Sardella G, Nebbioso A, Altucci L, Filatici P
Arkivoc (ISSN: 1424-6376), 2006; 6(VIII): 24-37.
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* CdO thin films: A study of their electronic structure by electron spin resonance spectroscopy (72 visite)
Gulino A, Tabbì G
Appl Surf Sci (ISSN: 0169-4332), 2005; 245(1-4): 322-327.
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* Decoy molecules based on PNA-DNA chimeras and targeting Sp1 transcription factors inhibit the activity of urokinase-type plasminogen activator receptor (uPAR) promoter (93 visite)
Borgatti M, Boyd DD, Lampronti I, Bianchi N, Fabbri E, Saviano M, Romanelli A, Pedone C, Gambari R
Oncology Research (ISSN: 0965-0407), 2005; 15(7-8): 373-383.
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* Absorption and fluorescence spectra of uracil in the gas phase and in aqueous solution: A TD-DFT quantum mechanical study (155 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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* Nucleophilic Cyclopropane Ring Opening in Duocarmycin SA Derivatives by Methanol under Acid Conditions: A Quantum Mechanical Study in the Gas-Phase and in Solution (91 visite)
Cimino P, Improta R, Bifulco G, Riccio R, Gomez-paloma L, Barone V
J Org Chem (ISSN: 0022-3263), 2004; 69(8): 2816-2824.
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* Transcription factor decoy molecules based on a peptide nucleic acid (PNA)-DNA chimera mimicking Sp1 binding sites (90 visite)
Borgatti M, Lampronti I, Romanelli A, Pedone C, Saviano M, Bianchi N, Mischiati C, Gambari R
J Biol Chem Journal Of Biological Chemistry (ISSN: 0021-9258, 1083-351x), 2003 Feb 28; 278(9): 7500-7509.
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* Understanding the role of stereoelectronic effects in determining collagen stability. 2. A quantum mechanical/molecular mechanical study of (Proline-Proline-Glycine)n polypeptides (85 visite)
Improta R, Mele F, Crescenzi O, Benzi C, Barone V
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2002 Jul 3; 124(26): 7857-7865.
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* Study of systolic pressure variation (SPV) in presence of mechanical ventilation (59 visite)
Clemente F, De Lazzari C, Darowski M, Ferrari G, Mimmo R, Guaragno M, Tosti G
Int J Artif Organs (ISSN: 0391-3988, 0391-3988print), 2002 Apr; 25(4): 313-320.
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* Energetic parameter changes with mechanical ventilation in conjunction with BVAD assistance (57 visite)
De Lazzari C, Darowski M, Ferrari G, Clemente F, Guaragno M
J Med Eng Technol (ISSN: 0309-1902), 2002 Mar; 26(2): 63-70.
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* Quantum mechanical study of the conformational behavior of proline and 4R-hydroxyproline dipeptide analogues in vacuum and in aqueous solution (75 visite)
Benzi C, Improta R, Scalmani G, Barone V
J Comput Chem (ISSN: 0192-8651, 1096-987xelectronic), 2002 Feb; 23(3): 341-350.
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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 (87 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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1H MR spectroscopy in patients with metastatic brain tumors: A multicenter study (87 visite)
Sijens PE, Knopp MV, Brunetti A, Wicklow K, Alfano B, Bachert P, Sanders JA, Stillman AE, Kett H, Sauter R
Magn Reson Med (ISSN: 0740-3194, 1522-2594electronic), 1995 Jun; 33(6): 818-826.
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METABOLIC CHARACTERIZATION OF CEREBRAL METASTASIS USING MR PROTON SPECTROSCOPY (79 visite)
BRUNETTI A, ALFANO B, STEFANO M, CARACO C, ARPAIA M, BRUNI G, ELMO M, COVELLI E, FREZZA P, SALVATORE M
Neuroradiology 1993, 1993; N/D: N/D-N/D.
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Imaging of kinked configurations of DNA molecules undergoing orthogonal field alternating gel electrophoresis by fluorescence microscopy (63 visite)
Gurrieri S, Rizzarelli E, Beach D, Bustamante C
Biochemistry (ISSN: 0006-2960, 1520-4995, 1520-4995electronic), 1990 Apr 3; 29(13): 3396-3401.
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73 Records (63 escludendo Abstract e Conferenze).
Impact factor totale: 291.823 (269.087 escludendo Abstract e Conferenze).
Impact factor a 5 anni totale: 309.004 (282.956 escludendo Abstract e Conferenze).

Interrogazione bibliografica effettuata: (([btitle] "mechanical" OR [btitle] "computations" OR [btitle] "spectroscopy" OR [btitle] "molecules") AND NOT [id] = 9209)







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