How did the carrier shell Xenophora crispa (König, 1825) build its shell? Evidence from the Recent and fossil record

The genus Xenophora comprises species of marine gastropods (Cretaceous-Recent) able to add fragments of various origins to their shell surface. Agglutination potentials vary, from species lacking attachments to species completely covered by agglutinated materials, as in the Mediterranean species Xenophora crispa. Here, we analyse Recent and fossil specimens of Xenophora crispa from the Mediterranean area using SEM and XRD, to better understand their biomineralization patterns and the mechanisms leading to the agglutination of shells, bioclasts and lithoclasts, and their evolution in time. We also provide new data on poorly studied gastropod shell microstructures. We conclude that: (1) most of the Xenophora crispa shell consists of an aragonitic crossed lamellar fabric, but fibrous to spherulitic prismatic fabrics, seemingly of calcite, have been found in the columella and peripheral edge (the thickest parts of the shell); (2) attachment of objects is mediated by a prismatic microstructure, indicating that this may be the most functional fabric in attachment areas in molluscs; and (3) the functional purpose of the agglutination in Xenophora crispa may be related to a snowshoe strategy to successfully colonize muddy substrates, coupled with tactile and olfactory camouflage. Indeed, this species secretes in the columella and peripheral edge a less dense and a more organic rich calcitic fabric, possibly to lighten the shell thickest parts in order not to sink in soft sediments and to facilitate the shell raising from the substrate to create a protected feeding area. This behaviour seems to have been maintained by X. crispa over 2 My time span

MOLECULAR MODELING OF EBOLA VIRUS INHIBITORS

In this PhD thesis computational methods have been employed in order to study different biologically relevant systems. In the first part of the thesis two Ebola virus proteins were studied, namely Viral Protein 24 (VP24) and Viral Protein 35 (VP35), responsible for the inhibition of the immune response . After a brief theoretical introduction to the main computational methods employed in the thesis, a study of VP35 in complex with small organic molecules is presented. These compounds are able to inhibit the interaction between VP35 and viral nucleoprotein. This study confirms the experimental findings highlighting new important key interactions between the protein the inhibitors. Moreover, an Essential Dynamics analysis points out an interesting collective motion of the apo-form that is hindered by the presence of the ligands. Afterwards, the protein-protein interaction VP24-Karyopherin (KPNA) is studied. An atomistic analysis of the interactions at the interface leads to the design of a nonapeptide with VP24 binding capability. The peptide is derived from a KPNA subsequence and could potentially inhibit the VP24-KPNA interaction. Subsequently an analysis on the pockets present on VP24 surface in different solvents is performed. Once the most promising pocket has been located, a virtual screening on a subset of ZINC database is carried out, leading to the identification of few classes of molecules potentially able to bind VP24. Finally the effect of the osmolytes on VP24 protein structure is studied, pointing out how osmoprotectants and urea have opposite effects on the protein, the former stabilizing the folded state and the latter shifting the equilibrium to the denatured state. In the second part of the manuscript the study of the interaction of an antimicrobial peptide with a lipid membrane is presented. This work was carried out in the University of Groningen under the supervision of Prof. Siewert Jan Marrink in order to deepen the Coarse Grain method

Structural Study of Nano-Sized Gahnite (ZnAl2O4): From the Average to the Local Scale

Spinel gahnite (ZnAl2O4) has been obtained through a hydrothermal synthesis method with a grain size of about 2 nm. The sample was calcined for a few hours at two different temperatures (800 and 900 °C) in order to obtain larger grain sizes to be analyzed by means of powder diffraction with the Rietveld method, and by means of total scattering with the Pair Distribution Function (PDF) method. The idea is to compare the average to the local structure, as a function of increasing grain size. The total scattering data were collected at the European Synchrotron Radiation Facility (ESRF), Grenoble. The samples have been also characterised by means of high resolution Transmission Electron Microscopy (TEM), showing an increasing grain size up to about 9 nm. The average structure presented variations in the inversion degree and an increase in grain size. TEM observations demonstrated that the small crystals are well crystallised: the high resolution images neatly showed the atomic planes, even in the smallest particles. However, the average structure did not properly fit the PDF data in the local region, owing to a slightly different coordination among the octahedra. A new structural model is proposed for the local region of the PDF, that helped our understanding of the differences between a real nanostructured sample and that of a microcrystalline one. The oxygen disorder, due to the inversion grade of the spinel, is demonstrates to be at the basis of the local deviation. No signals of interstitial Zn atoms were detected

Synthesis and biological evaluation of new 3-amino-2-azetidinone derivatives as anticolorectal cancer agents

Several synthetic combretastatin A4 (CA-4) derivatives were recently prepared to increase the drug efficacy and stability of the natural product isolated from the South African tree Combretum caffrum. A group of ten 3-amino-2-azetidinone derivatives, as combretastatin A4 analogues, was selected through docking experiments, synthesized and tested for their anti-proliferative activity against the colon cancer SW48 cell line. These molecules, through the formation of amide bonds in position 3, allow the synthesis of various derivatives that can modulate the activity with great resistance to hydrolytic conditions. The cyclization to obtain the 3-aminoazetidinone ring is highly diastereoselective and provides a trans biologically active isomer under mild reaction conditions with better yields than the 3-hydroxy-2-azetidinone synthesis. All compounds showed IC50 values ranging between 14.0 and 564.2 nM, and the most active compound showed inhibitory activity against tubulin polymerization in vitro, being a potential therapeutic agent against colon cancer

Halogen bonding in the framework of classical force fields: The case of chlorine

Halogen bonding is nowadays a consolidated tool in chemistry. Only recently, the importance of halogen bonding has been demonstrated also in biological systems, owing to the presence of halogens in drugs. This interaction is due to the anisotropy of the electron density around the halogen that leads to the formation of the \u2018\u3c3-hole\u2019, which is responsible for the interaction with a nucleophile site. Unfortunately, classical force fields used in the study of ligand-receptor systems are not able to describe the \u2018\u3c3-hole\u2019. Here, we propose a pseudo-atom based methodology able to correctly describe halogen bonding involving chlorine using classical force field

A valence bond description of the bromine halogen bond

A theoretical investigation on the nature of the halogen bond through a valence-bond approach has been carried out with two main goals: (a) finding further confirmations of already existing explanations on the physical origins of the halogen bond and (b) possibly enriching the current models with new details. To achieve these goals we have exploited the spin-coupled method and we have performed computations on RBr efNH3 dimers characterized by a different electron withdrawing power of substituent \uf8ffR to the bromine atom. The analysis of typical spin-coupled descriptors (eg, shapes and overlaps of the spin-coupled orbitals, weights of the spin-coupled structures) in the different cases and in function of the distance between the monomers allowed us to draw qualitative conclusions about the formation and the strength of the halogen bonds. In particular, the investigation not only confirmed the validity of already existing models (ie, \u3c3-hole and lump-hole models) but also highlighted interesting new features, such as the fact that the depletion of electron density around the bromine atom does not extend only toward the acceptor of the halogen bond, but also in the opposite direction (toward the substituent of the halogen), thus forming a sort of \u3c3-tunnel, rather than a simple \u3c3-hole

Multiscale understanding of tricalcium silicate hydration reactions

Tricalcium silicate, the main constituent of Portland cement, hydrates to produce crystalline calcium hydroxide and calcium-silicate-hydrates (C-S-H) nanocrystalline gel. This hydration reaction is poorly understood at the nanoscale. The understanding of atomic arrangement in nanocrystalline phases is intrinsically complicated and this challenge is exacerbated by the presence of additional crystalline phase(s). Here, we use calorimetry and synchrotron X-ray powder diffraction to quantitatively follow tricalcium silicate hydration process: i) its dissolution, ii) portlandite crystallization and iii) C-S-H gel precipitation. Chiefly, synchrotron pair distribution function (PDF) allows to identify a defective clinotobermorite, Ca11Si9O28(OH)2.8.5H2O, as the nanocrystalline component of C-S-H. Furthermore, PDF analysis also indicates that C-S-H gel contains monolayer calcium hydroxide which is stretched as recently predicted by first principles calculations. These outcomes, plus additional laboratory characterization, yielded a multiscale picture for C-S-H nanocomposite gel which explains the observed densities and Ca/Si atomic ratios at the nano- and meso- scales.This work has been supported by Spanish MINECO through BIA2014-57658-C2-2-R, which is co-funded by FEDER, BIA2014-57658-C2-1-R and I3 (IEDI-2016-0079) grants. We also thank CELLS-ALBA (Barcelona, Spain) for providing synchrotron beam time at BL04-MSPD beamline

Nearest-neighbour distribution of distances in crystals from extended X-ray absorption fine structure

Extended X-ray absorption fine structure (EXAFS) is a powerful probe of the distribution of nearest-neighbour distances around selected atomic species. We consider here the effect of vibrational disorder in crystals. The potential of EXAFS for the accurate evaluation of the coefficient of bond thermal expansion and its temperature dependence is discussed, with the aim of stimulating and facilitating the comparison with the results from total scattering experiments. The meaning of the distribution asymmetry in crystals and its connection with the effective potential anharmonicity and the bond expansion is quantitatively explored by comparing the results for a number of different systems. The extent of the relative atomic vibrations perpendicular to the bond direction and the perpendicular to parallel anisotropy are correlated with the extent of lattice negative thermal expansion as well as with the ionic mobility in superionic crystals

The local and average structure of Ba(Ti, Ce)O3 perovskite solid solution: effect of cerium concentration and particle size

The amazing properties of ferroelectric perovskite BaTiO3 (BT) and its solid solutions make them indispensable for many technological applications (e.g. multilayer capacitors). Unfortunately, the so-called `size effect' limits their use. Indeed, under a certain critical particle size, these materials show a suppression of the spontaneous polarization and thus of the ferroelectric properties. In pure nanometric BaTiO3, this is related to a certain local structural disorder. However, only a few studies have explored BT solid solutions, where the doping effect, coupled to the reduced particle size, can play an important role. Therefore, in this work, the structure of BaCexTi1\u2013xO3 (x = 0.02\u20130.20) was explored by traditional Rietveld method and Pair Distribution Function. Samples present a particle size from 80\u2013160 nm to 400\u20131000 nm depending on increasing x. The carbox approach was applied, investigating the evolution of the local structure, its modifications and the structural coherent correlation length, as a function of cerium amount. Results demonstrate a cooperative effect of composition and reduced size in the ferroelectricity loss. The two, in fact, contribute to intensify the local structural disorder, decreasing the structural coherent correlation length. The local structural disorder is thus confirmed to be a relevant factor in the ferroelectric properties degradation