Biomedical subjects

Dario Duca

Publications and source records attributed to Dario Duca.

4 recordsLinked to original sources

PubMed2004

Comparison of different theory models and basis sets in the calculation of 13C NMR chemical shifts of natural products.

The influence of the calculation method in mimicking experimental (13)C NMR chemical shifts of 15 low-polarity natural products singularly containing 10-20 carbon atoms was investigated by employing different quantum chemistry approaches and basis sets, both in the preliminary geometry optimizations and in the following single-point (13)C GIAO calculations of the NMR chemical shifts. The geometries of the involved species were optimized at the PM3, HF, B3LYP and mPW1PW91 levels whereas the (13)C NMR parameters were determined at the HF, B3LYP and mPW1PW91 levels. Different combinations of basis sets were also tested. The consistency and efficiency of the considered combinations of geometry optimizations and GIAO (13)C NMR calculations were thoroughly checked by the analysis of statistical parameters concerning computed and experimental (13)C NMR chemical shift values.

Biological Products↗

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↗