Application of computational models to the study of molecular sensors

Festa, Gaetano (2006) Application of computational models to the study of molecular sensors. [Tesi di dottorato] (Inedito)

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Abstract

In the present work we have considered various topics concerning spectroscopic properties simulation (Part I) and basic aspects involved in nanoscience (Part II). In the first part the IR spectra of uracil in vacuo was simulated by the Fourier Transform of the dipole autocorrelation function. This function has been generated by the sampling of the 10 ps ADMP (ab initio Density Matrix Propagation) trajectory. The results were compared with the experimental spectra of uracil in argon matrix so as to reproduce as much as possible the neglect of intermolecular interaction characteristic of the current simulation conditions. Moreover, the results were also compared with frequencies calculations within harmonic and anharmonic approximations. In the second part we studied basic aspects related to the synthesis of DNA/RNA biosensors. Full characterization of 1-amino-3cyclopentene (ACP) reaction path along both chemical functionalities was reported outlying the effective competitiveness of both reactions on silicon surface reaction sites. Differently from others works mainly focused on a radicalic mechanism, here we found another mechanism of reaction based on the separation of charges in silicon surface dimer with no radicals formation. The reaction path through ACP double bond has been studied in collaboration with the Departement of Physics of the University of Naples "Federico II" in order to compare computational results obtained within density functional theory (DFT) with both Gaussian Type Orbitals and Plane Waves basis set functions. To simulate the Si(100)-2x1 surface we used both cluster and slab models. Furthermore, it has been considered a further step in the surface functionalization considering the product of reactions of sulfo-succinimidyl-4-(N-maleimidomethyl)-cyclohexane-1-carboxilate (SSMCC) and thio-oligonucleotide on the ACP hybrid surface.

Tipologia di documento:Tesi di dottorato
Parole chiave:ADMP IR spectra simulation, silicon surface (100)-2x1, biosensing
Settori scientifico-disciplinari MIUR:Area 03 Scienze chimiche > CHIM/02 CHIMICA FISICA
Coordinatori della Scuola di dottorato:
Coordinatore del Corso di dottoratoe-mail (se nota)
Lanzetta, Rosa
Tutor della Scuola di dottorato:
Tutor del Corso di dottoratoe-mail (se nota)
Cossi, Maurizio
Stato del full text:Accessibile
Data:2006
Numero di pagine:103
Istituzione:Università degli Studi di Napoli Federico II
Dipartimento o Struttura:Chimica
Tipo di tesi:Dottorato
Stato dell'Eprint:Inedito
Denominazione del dottorato:Scienze Chimiche
Ciclo di dottorato:XVIII
Numero di sistema:729
Depositato il:31 Luglio 2008
Ultima modifica:04 Febbraio 2009 09:39

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