Biomedical subjects

Giampaolo Barone

Publications and source records attributed to Giampaolo Barone.

7 recordsLinked to original sources

PubMed2006

The prediction of the nuclear quadrupole splitting of 119Sn Mössbauer spectroscopy data by scalar relativistic DFT calculations.

The electric field gradient components for the tin nucleus of 34 tin compounds of experimentally known structures and (119)Sn Mössbauer spectroscopy parameters were computed at the scalar relativistic density functional theory level of approximation. The theoretical values of the electric field gradient components were used to determine a quantity, V, which is proportional to the nuclear quadrupole splitting parameter (DeltaE). In a subsequent linear regression analysis the effective nuclear quadrupole moment, Q, was evaluated. The value of (11.9+/-0.1) fm(2) is a significant improvement over the non-relativistic result of (15.2+/-4.4) fm(2) and is in agreement with the experimental value of (10.9+/-0.8) fm(2). The average mean square error DeltaE(calcd)-DeltaE(exptl)=+/-0.3 mm s(-1) is a factor of two smaller than in the non-relativistic case. Thus, the approach has a quality which provides accurate support for the structure interpretation by (119)Sn spectroscopy. It was noted that geometry optimization at the relativistic level does not significantly increase the quality of the results compared with non-relativistic optimized structures. The accuracy in the approach called on us to consider the singlet-triplet state nature of the electronic structure of one of the investigated compounds.

Journal Article↗

PubMed2006

Photochemistry of 1,2,4-oxadiazoles. A DFT study on photoinduced competitive rearrangements of 3-amino- and 3-n-methylamino-5-perfluoroalkyl-1,2,4-oxadiazoles.

The photoinduced competitive rearrangements of 5-perfluoroalkyl-3-amino(N-alkylamino)-1,2,4-oxadiazoles have been investigated by DFT calculations and UV-vis spectroscopy. The observed product selectivity depends on the number of hydrogen atoms present in the amino moiety and involves two or three possible routes: (i) ring contraction-ring expansion (RCRE), (ii) internal-cyclization isomerization (ICI), or (iii) C3-N2 migration-nucleophilic attack-cyclization (MNAC). UV absorption and fluorescence spectra of the reactants, and vertical excitation energy values, calculated by time dependent DFT, support the involvement of a neutral singlet excited state in the photoexcitation process. The values of the standard free energy of the most stable prototropic tautomers of reactant, products, proposed reaction intermediates, and deprotonated anionic transition states allowed us to rationalize the competition among the three rearrangements, in agreement with chemical trapping experiments, in terms of: (i) the evolution of the excited state toward three stable ground-state intermediates, (ii) tautomeric and deprotonation equilibria occurring in methanol solution for each intermediate, and (iii) relative stabilization of intermediates and transition states in the thermally driven section of the reaction.

Models, Chemical↗

PubMed2005

DFT calculations of the electric field gradient at the tin nucleus as a support of structural interpretation by 119Sn Mössbauer spectroscopy.

DFT calculations, using an all-electron basis set and with full geometry optimization, were performed on 34 Sn(II) and Sn(IV) compounds of known structure and (119)Sn Mössbauer parameters, to obtain the theoretical values of the electric field gradient components, V(xx), V(yy), and V(zz), at the tin nucleus. These were used to determine the quantity V = V(zz)[1+ 1/3((V(xx) - V(yy))/((V(zz))(2)](1/2), for each investigated compound, which is related to the quadrupole splitting (DeltaE) parameter according to DeltaE = 1/2eQV, where e is the electronic charge and Q is the quadrupole moment of the tin nucleus. The linear fitting of the correlation plot of the experimental DeltaE, versus the corresponding calculated V values, produced a slope that is equal to 0.93 +/- 0.03 and a correlation coefficient R = 0.982. The value of Q obtained, 15.2 +/- 4.4 fm(2), is in agreement with that previously experimentally determined or calculated by analogous procedures. The calculation method is able to establish the sign of the electric field gradient component V(zz), in agreement with the sign of DeltaE determined experimentally by Mössbauer-Zeeman spectroscopy. The calculated structural parameters are in good agreement with the corresponding experimental data, determined by X-ray crystallography in the solid state, with average structural deviations of about 3 % for bond lengths and angles in the tin environment. Calculated values of DeltaE were obtained from the calibration fitting constant and from the values of V. By comparing experimental and calculated DeltaE parameters, the structure assignment of configurational isomers was successful in two test cases, in agreement with the experimental X-ray crystallographic structures. These results indicate that the method can be used as a tool to support the routine structure interpretation of tin compounds by (119)Sn Mössbauer spectroscopy.

Journal Article↗

PubMed2004

The interaction of native DNA with iron(III)- N ,N'-ethylene-bis(salicylideneiminato)-chloride.

The interaction between native calf thymus deoxyribonucleic acid (DNA) and Fe(III)- N ,N'-ethylene-bis (salicylideneiminato)-chloride, Fe(Salen)Cl, was investigated in aqueous solutions by UV-visible (UV-vis) absorption, circular dichroism (CD), thermal denaturation and viscosity measurements. The results obtained from CD, UV-vis and viscosity measurements exclude DNA intercalation and can be interpreted in terms of an electrostatic binding between the Fe(Salen)(+) cation and the phosphate groups of DNA. The trend of the UV-vis absorption band of the Fe(Salen)Cl complex at different ratios [DNA(phosphate)]/[Fe(Salen)Cl] and the large increase of the melting temperature of DNA in the presence of Fe(Salen)Cl, support the hypothesis of an external electrostatic interaction between the negatively charged DNA double helix and the axially stacked positively charged Fe(Salen)(+) moieties, analogously to what reported for a number of porphyrazines and metal-porphyrazine complexes interacting with DNA.

Animals↗

PubMed2002

Structure validation of natural products by quantum-mechanical GIAO calculations of 13C NMR chemical shifts.

Geometry optimization and GIAO (gauge including atomic orbitals) (13)C NMR chemical shift calculations at Hartree-Fock level, using the 6-31G(d) basis set, are proposed as a tool to be applied in the structural characterization of new organic compounds, thus providing useful support in the interpretation of experimental NMR data. Parameters related to linear correlation plots of computed versus experimental (13)C NMR chemical shifts for fourteen low-polar natural products, containing 10-20 carbon atoms, were employed to assess the reliability of the proposed structures. A comparison with the hybrid B3LYP method was carried out to evaluate electron correlation contributions to the calculation of (13)C NMR chemical shifts and, eventually, to extend the applicability of such computational methods to the interpretation of NMR spectra in apolar solutions. The method was tested by studying three examples of revised structure assignments, analyzing how the theoretical (13)C chemical shifts of both correct and incorrect structures matched the experimental data.

Biological Products↗

PubMed2002

Determination of the relative stereochemistry of flexible organic compounds by Ab initio methods: conformational analysis and Boltzmann-averaged GIAO 13C NMR chemical shifts.

Ab initio calculations at the Hartree-Fock level with full-geometry optimization using the 6-31G(d) basis set, and GIAO (gauge including atomic orbitals) (13)C NMR chemical shifts, are presented here as a support in the study of the stereochemistry of low-polar organic compounds having an open-chain structure. Four linear stereoisomers, fragments of a natural product previously characterized by experimental (13)C NMR spectra, which possesses three stereogenic centers, 11 carbon atoms, and 38 atoms in total, were considered. Conformational searches, by empirical force-field molecular dynamics, pointed out the existence of 8-13 relevant conformers per stereoisomer. Thermochemical calculations at the ab initio level in the harmonic approximation of the vibrational modes, allowed the evaluation, at 298.15 K, of the standard Gibbs free energy of the conformers. The (13)C NMR chemical shift of a given carbon atom in each stereoisomer was considered as the average chemical shift value of the same atom in the different conformers. The averages were obtained by the Boltzmann distribution, using the relative standard free energies as weighting factors. Computed parameters related to linear correlation plots of experimental (13)C chemical shifts versus the corresponding computed average data allowed us to distinguish among the four stereoisomers.

Journal Article↗

PubMedDate not supplied

SCSA code: applications on the cyclopeptide renieramide.

SCSA is an algorithm designed to get information on molecular conformational properties. The most stable conformers are determined by the homemade SCSA code, performing a multistep systematic conformational search, which involves energy and structure quantum chemical optimizations at low-level and high-level. The SCSA method was employed to analyze the conformational space of the in vacuo cyclopeptide renieramide at AM1 and B3LYP/6-31G(d) levels. Calculations at B3LYP level of the GIAO (13)C NMR chemical shifts were also performed on the final conformers. In fact, to validate the conformational search results experimental and calculated (13)C NMR spectra of renieramide were compared. Slight disagreements observed between experimental and calculated spectra could be attributed to solute-solvent interactions, which were not taken into account in the algorithm proposed here.

Models, Molecular↗