Giampaolo Barone

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.

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.

Spectroscopic study of the interaction of NiII-5-triethyl ammonium methyl salicylidene ortho-phenylendiiminate with native DNA

The interaction of native calf thymus DNA with the cationic Ni(II) complex of 5-triethyl ammonium methyl salicylidene ortho-phenylendiimine (NiL(2+)), in 1mM Tris-HCl aqueous solutions at neutral pH, has been monitored as a function of the metal complex-DNA molar ratio by UV absorption spectrophotometry, circular dichroism (CD) and fluorescence spectroscopy. The dramatic modification of the DNA CD spectrum, the appearance of a broad induced CD band in the range 350-400nm, the strong increase of the DNA melting temperature (T(m)) and the fluorescence quenching of ethidium bromide-DNA solutions, in the presence of increasing amounts of the NiL(2+) metal complex, support the existence of a tight intercalative interaction of NiL(2+) with DNA, analogous to that recently reported for both ZnL(2+) and CuL(2+). The intrinsic binding constant (K(b)) and the interaction stoichiometry (s), determined by UV spectrophotometric titration, are equal to 4.3x10(6)M(-1) and 1.0 base pair per metal complex, respectively. Interestingly, the value of K(b) is slightly higher and 10 times higher than that relative to the CuL(2+)-DNA and the ZnL(2+)-DNA systems, respectively. Speculations can be performed to rationalize the observed trend, on the basis of the electronic and geometrical structures of the three complexes of the same ligand. Analogously to what previously observed for CuL(2+), the shape of the CD of the NiL(2+)-DNA system at NiL(2+)-DNA molar ratios higher than 0.5 is indicative of the formation of supramolecular aggregates in solutions, as a possible consequence of the electrostatic interaction between the cationic complex and the negatively charged phosphate groups of DNA.

Deposition of tin sulfide thin films from tin(IV) thiolate precursors

AACVD (aerosol-assisted chemical vapour deposition) using (PhS)(4)Sn as precursor leads to the deposition of Sn3O4 in the absence of H2S and tin sulfides when H2S is used as co-reactant. At 450 degreesC the film deposited consists of mainly SnS2 while at 500 degreesC SnS is the dominant component. The mechanism of decomposition of (PhS)(4)Sn is discussed and the structure of the precursor presented.

Analytic high-order Douglas-Kroll-Hess electric field gradients

In this work we present a comprehensive study of analytical electric field gradients in hydrogen halides calculated within the high-order Douglas-Kroll-Hess (DKH) scalar-relativistic approach taking picture-change effects analytically into account. We demonstrate the technical feasibility and reliability of a high-order DKH unitary transformation for the property integrals. The convergence behavior of the DKH property expansion is discussed close to the basis set limit and conditions ensuring picture-change-corrected results are determined. Numerical results are presented, which show that the DKH property expansion converges rapidly toward the reference values provided by four-component methods. This shows that in closed-shell cases, the scalar-relativistic DKH(2,2) approach which is of second order in the external potential for both orbitals and property operator yields a remarkable accuracy. As a parameter-dependence-free high-order DKH model, we recommend DKH(4,3). Moreover, the effect of a finite-nucleus model, different parametrization schemes for the unitary matrices, and the reliability of standard basis sets are investigated.

Toward a rationale for the PTC124 (Ataluren) promoted readthrough of premature stop codons: a computational approach and GFP-reporter cell-based assay.

The presence in the mRNA of premature stop codons (PTCs) results in protein truncation responsible for several inherited (genetic) diseases. A well-known example of these diseases is cystic fibrosis (CF), where approximately 10% (worldwide) of patients have nonsense mutations in the CF transmembrane regulator (CFTR) gene. PTC124 (3-(5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl)-benzoic acid), also known as Ataluren, is a small molecule that has been suggested to allow PTC readthrough even though its target has yet to be identified. In the lack of a general consensus about its mechanism of action, we experimentally tested the ability of PTC124 to promote the readthrough of premature termination codons by using a new reporter. The reporter vector was based on a plasmid harboring the H2B histone coding sequence fused in frame with the green fluorescent protein (GFP) cDNA, and a TGA stop codon was introduced in the H2B-GFP gene by site-directed mutagenesis. Additionally, an unprecedented computational study on the putative supramolecular interaction between PTC124 and an 11-codon (33-nucleotides) sequence corresponding to a CFTR mRNA fragment containing a central UGA nonsense mutation showed a specific interaction between PTC124 and the UGA codon. Altogether, the H2B-GFP-opal based assay and the molecular dynamics (MD) simulation support the hypothesis that PTC124 is able to promote the specific readthrough of internal TGA premature stop codons.

Structure-Directing and High-Efficiency Photocatalytic Hydrogen Production by Ag Clusters

H2 production by water splitting is hindered mainly by the lack of low-cost and efficient photocatalysts. Here we show that sub-nanometric silver clusters can catalyze the anisotropic growth of gold nanostructures by preferential adsorption at certain crystal planes of Au seeds, with the result that the final nanostructure can be tuned via the cluster/seed ratio. Such semiconducting Ag clusters are extremely stable and retain their electronic structure even after adsorption at the tips of Au nanorods, enabling various photocatalytic experiments, such as oxygen evolution from basic solutions. In the absence of electron scavengers, UV irradiation generates photoelectrons, which are stored within the nanorods, increasing their Au Fermi level up to the redox pinning limit at 0 V (RHE), where hydrogen evolution occurs with an estimated high efficiency of 10%. This illustrates the considerable potential of very small zerovalent, nonmetallic clusters as novel atomic-level photocatalysts.

Selective G-quadruplex stabilizers: Schiff-base metal complexes with anticancer activity

The affinity of three square-planar nickel(II) (1), copper(II) (2) and zinc(II) (3) Schiff-base complexes for wild-type human telomeric (h-Telo) and protooncogene c-myc G-quadruplex (G4) DNA was investigated by UV-visible absorption spectroscopy and circular dichroism. DNA-binding constants (Kb) were determined by spectrophotometric titrations for both G4-DNA and B-DNA. The results obtained point out that the three metal complexes selectively bind G4-DNA with higher affinity, up to two orders of magnitude, with respect to B-DNA. The nickel(II) complex 1 was found to be the most effective G4-DNA stabilizer and the Kb values decrease in the order 1 > 2 ≈ 3. Innovative computational investigations, consisting of molecular dynamics (MD) simulations followed by density functional theory/molecular mechanics (DFT/MM) calculations, provide atomistic support for the interpretation of the binding mechanism to G4-DNA by end stacking and also of the experimental affinity order. Interestingly, 1 is able to induce G4-DNA formation of h-Telo sequences, also in the absence of K+ cations. This last result is nicely confirmed and highlighted by polymerase chain reaction (PCR) stop assays, which show the ability of the title compounds to induce and stabilize G4 structures inhibiting the amplification of PCR products. Finally, compounds 1–3 showed concentration and time-dependent cytotoxicity towards HeLa and MCF-7 human cancer cell lines, inducing significant effects on cell cycle distribution with G2/M arrest in HeLa cells and G0/G1 arrest in MCF-7 cells. Overall, the PCR inhibition and anticancer activity of the three compounds decreases in the same order 1 > 2 ≈ 3, in excellent correlation with the G4-DNA-binding affinity, implying that G4-DNA is the biotarget for their biological activity.

Hydrogenation of acetylene–ethylene mixtures on Pd catalysts: computational study on the surface mechanism and on the influence of the carbonaceous deposits

A time-dependent Monte Carlo algorithm was employed to study the effects of carbonaceous surface species on the hydrogenation mechanism of acetylene–ethylene mixtures on a Pd catalyst. Simulations of tail-end and front-end mixture hydrogenation were performed employing the same set of predetermined event probabilities. The involvement of the steric hindrance of the surface species was essential to simulate the experimental data. The catalyst activity and selectivity were promoted or inhibited by different concentrations of surface polymeric species formed along with the hydrocarbon hydrogenation. Tools to get a new interpretation of the catalytic reaction mechanism and an innovative basis to perform catalyst design were suggested by the approach illustrated.

Hsp60, a novel target for antitumor therapy: Structure-function features and prospective drugs design

Heat shock protein 60 kDa (Hsp60) is a chaperone classically believed to be involved in assisting the correct folding of other mitochondrial proteins. Hsp60 also plays a role in cytoprotection against cell stressors, displaying for example, antiapoptotic potential. Despite the plethora of studies devoted to the mechanism of Hsp60s function, especially in prokaryotes, fundamental issues still remain unexplored, including the definition of its role in cancer. Key questions still unanswered pertain to the differences in structure-function features that might exist between the well-studied prokaryotic GroEL and the largely unexplored eukaryotic Hsp60 proteins. In this article we discuss these differences in sequence, structure, and roles of Hsp60, focusing on the human ortholog with the view of devising compounds to block its ability to favour tumor-cell growth and survival. Compounds currently known to directly or indirectly affect Hsp60 functions, such as protein folding, HIF-1α accumulation, or Hsp60-induced cell proliferation, are discussed along with strategies that might prove effective for developing Hsp60-targeting drugs for anticancer therapy.