Davide Viterbo

Structural Characterization of Siliceous Spicules from Marine Sponges

Siliceous sponges, one of the few animal groups involved in a biosilicification process, deposit hydrated silica in discrete skeletal elements called spicules. A multidisciplinary analysis of the structural features of the protein axial filaments inside the spicules of a number of marine sponges, belonging to two different classes (Demospongiae and Hexactinellida), is presented, together with a preliminary analysis of the biosilicification process. The study was carried out by a unique combination of techniques: fiber diffraction using synchrotron radiation, scanning electron microscopy (SEM), thermogravimetric analysis (TGA), differential scanning calorimetric (DSC), Fourier transform infrared spectroscopy (FTIR), and molecular modeling. From a phylogenetic point of view, the main result is the structural difference between the dimension and packing of the protein units in the spicule filaments of the Demospongiae and the Hexactinellida species. Models of the protein organization in the spicule axial filaments, consistent with the various experimental evidences, are given. The three different species of demosponges analyzed have similar general structural features, but they differ in the degree of order. The structural information on the spicule axial filaments can help shed some light on the still unknown molecular mechanisms controlling biosilicification.

Kinematic diffraction on a structure with periodically varying scattering function.

A theory is developed to describe the kinematic diffraction response of a crystal when it is subjected to a periodically varying external perturbation. It is shown that if a part of the local electron density varies linearly with an external stimulus, the diffracted signal is not only a function of the stimulation frequency Ω, but also of its double 2Ω. These frequency components can provide, under certain conditions, selective access to partial diffraction contributions that are normally summed up in the interference pattern. A phasing process applied to partial diffraction terms would allow recovery of the substructure actively responding to the stimulus. Two ways of frequency filtering are discussed (demodulation and correlation) with respect to extracting information from such an experiment. Also considered is the effect of the variation of different structural parameters on the diffraction intensity that have to be accounted for while planning modulation-enhanced experiments. Finally, the advantages and limitations of the proposed concept are discussed, together with possible experiments.

14β-Hydroxy-10-deacetylbaccatin III, a new taxane from Himalayan yew (Taxus wallichiana Zucc.)

The needles of T. wallichiana Zucc. gave a new taxane, whose structure was established as 14β-hydroxy-10-deacetylbaccatin III on the basis of chemical reactions, spectroscopic data and X-ray analysis.

An NMR and molecular mechanics study of squalene and squalene derivatives

Various squalene derivatives, including squalene, squalene 2,3-epoxide (monoepoxide, SQME), squalene 2,3;22,23-diepoxide (SQDE), 2-aza-2,3-dihydrosqualene (SQN) and 2-aza-2,3-dihydrosqualene N-oxide (SQNO), were studied in chloroform solutions using ID high-resolution 1H spectra and 13C longitudinal relaxation studies, 2D proton NOESY and COSY and 2D proton-carbon HETCOR spectroscopy. A full interpretation of the 1H and 13C-NMR spectra is presented. Staggered conformations along the C11-C12 bond are favoured and a relatively rigid structure of the central part of the chain is indicated in relaxation and coupling data, while further away from the central part the molecular mobility grows. A detected NOE dipolar interaction between terminal and central parts of the molecule indicates the presence of dynamically folded structures in solution. The proposed model also explains the selective reactivity of the mobile chain endings with respect to the central part which is protected by these moving ends. Different solvents at different concentrations induce some variations in this molecular model with a shortening or a lengthening of the mean path covered by the tail endings. Molecular mechanics and molecular dynamics calculations on the free squalene molecule indicate that the mobility of the chain is almost equivalent in all its isoprenic moieties, and the greater mobility of the chain ends may be ascribed to co-operative movements from the center to the tails. The solvent probably plays an important role in hindering the motion of the central part of the molecule.

Synthesis, biological activity, and conformational analysis of CD-ring modified trans-decalin 1 alpha,25-dihydroxyvitamin D analogs

A novel series of analogs of 1,25-dihydroxyvitamin D3, the hormonally active metabolite of vitamin D3, characterised by the presence of a trans-fused decalin CD-ring system, possesses surprising biological activities in combination with specific structural modifications in the flexible parts of the molecule, when compared with the natural hydrindane derivatives. (1) A large difference in biological activity is observed between the 20-epimeric trans-decalin analogs that follows a pattern opposite to what is usually observed for the natural ring size. (2) Several trans-decalin analogs that are modified in the seco-B-ring region, including previtamin derivatives, possess a pronounced vitamin D-like activity, whereas the corresponding hydrindane derivatives are inactive. The molecular origin of this behavior is still under study.

Isolation and characterization of the acyl complexestrans-[Pt(PPh3)2(COR)Cl] (R =nBu orsBu) and their relevance to the hydroformylation of linear butenes catalyzed by platinum/tin/triphenylphosphine catalytic systems. Molecular structure ofcis- [Pt(PPh3)2Cl(SnCl3)]

Abstract The acyl complex trans -[Pt(PPh 3 ) 2 (CO n Bu)Cl] ( A ) has been synthesized by reaction of [Pt(PPh 3 ) 2 Cl 2 ] with 1-butene under 100 atm of CO at 80–100°C, in ethanol. With 2-butene rather than 1-butene under the same conditions, a mixture of the above acyl complex and of trans - [Pt(PPh 3 ) 2 (CO s Bu)Cl] ( B ) was formed. Complexes A and B do not interconvert. The new acyl complexes A and B have been characterized by IR and 1 H NMR and 13 C NMR spectroscopy. The ratio A / B increases with PPh 3 /Pt ratio and with temperature. The formation of two isomers when 2-butene is used involves an isomerization process which is likely to be limited to the alkyl precursor complexes. The reactivity of complexes A and B has been tested in reactions with SnCl 2 , H 2 , HCl and trans -[Pt(PPh 3 ) 2 HCl]. From the reaction solutions crystals of cis -[Pt(PPh 3 ) 2 Cl(SnCl 3 )] have been obtained. Its molecular structure has been determined by X-ray diffraction. The Pt atom has cis square planar coordination, with angular distortions due to steric factors. The strong trans influence of the SnCl 3 group is confirmed by the lengthening of the trans Pt-P distance. The SnCl 3 group has the pyramidal geometry found in all related compounds.

Structural characterization and thermal and chemical stability of bioactive molecule–hydrotalcite (LDH) nanocomposites

Layered double hydroxides (LDH) are versatile materials used for intercalating bioactive molecules, both in pharmaceutical and cosmetic fields, with the purpose of protecting them from degradation, enhancing their water solubility to increase bioavailability, and/or obtaining modified release properties. The properties of the intercalation compounds of Mg/Al_LDH and Zn/Al_LDH with different drugs and sunscreens, namely diclofenac, ketoprofen, gliclazide, retinoic acid, furosemide, para-aminobenzoic acid and 2-phenylbenzimidazolsulfonic (Eusolex) acid, have been studied by crystallographic, spectroscopic and thermogravimetric techniques and by solid state NMR, to shed light on their structure, their molecular interactions and their stability from the thermal and chemical viewpoint. The structural features were described with particular attention to the interaction between the organic and inorganic components and to the stability of the intercalation products. For the first time two synchrotron radiation powder diffraction patterns of organic-containing LDH were solved and refined by Rietveld methods to obtain an experimental crystal structure.

Sonochemical Synthesis and Structural Characterization and DFT Calculations of a Novel Nano Flower Pb(II) Coordination Compound [Pb(phen)2(4-abs)2]n

Nano-structures of a new coordination polymer of divalent Pb with the ligands 1,10-phenanthroline (phen) and 4-aminobenzene sulfonic acid (4-abs), [Pb(phen)2(4-abs)2]n (1), were synthesized by a sonochemical method that produced a coordination polymer of nanometer size. The new nano-structure was characterized by scanning electron microscopy, X-ray powder diffraction and IR spectroscopy and elemental analysis. Compound 1 was structurally characterized by single crystal X-ray diffraction and showed that the coordination number of the Pb(II) ions is six; i.e. (PbN4O2). Compound 1 also has a stereochemically active lone pair of electrons and a hemi-directed coordination sphere. The chains interact with each other through π–π stacking to create a 3D framework. The structure of 1 was optimized by density functional theory calculations. The calculated structural parameters and IR spectra of 1 are consistent with the crystal structure.

Patterson selectivity by modulation-enhanced diffraction

Modulation excitation spectroscopy is a powerful and well established technique for investigating the dynamic behaviour of chemical and physical systems. Recently, an expansion of this technique for diffraction was proposed and the theory deriving the diffraction response of a crystal subjected to a periodically varying external perturbation was developed [Chernyshov, van Beek, Emerich, Milanesio, Urakawa, Viterbo, Palin & Caliandro (2011). Acta Cryst. A67, 327–335]. The result of this is that a substructure composed of atoms actively responding to the stimulus may be separated out by analysing the diffraction signal at a frequency twice that of the stimulus. This technique is called modulation-enhanced diffraction. Here, a version of the theory dealing with the modulation of the site occupancies of a selected subset of atoms is formulated, and this is supported by experiments carried out at the Swiss–Norwegian Beam Lines at the ESRF, involving periodic variation of the xenon content of a polycrystalline zeolite as a function of temperature. The data analysis involves three steps: (i) data selection is carried out to mimic a linear response; (ii) phase-sensitive detection is applied to obtain contributions both from the responding part of the electron density associated with the Xe atoms and from the interference term; (iii) a phasing procedure is applied to both. A Patterson deconvolution technique has been successfully used to phase the demodulated diffraction patterns and obtain the active substructure.

A Short Intramolecular Diels−Alder Route to Himbacine Derivatives

The intramolecular cycloaddition of 5 yields the unsaturated lactones 17a, 17b, and 17c as three major isomeric adducts. These were further reduced to the corresponding derivatives 21a, 21b, and 21c, which are intermediates for the synthesis of (+)-himbacine and stereoisomers thereof. Precursor 5 was obtained in a short convergent way using Sonogashira and Stille coupling reactions as the main C−C bond construction reactions.