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

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

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

Computer aided design and NMR characterization of an oligopeptide targeting the Ebola virus VP24 protein

The Ebola viral Protein 24 (VP24) inhibits interferon signaling through its interaction with the human protein Karyopherin, thus impairing the immune response of the host against the infection and increasing its rate of diffusion into the organism and its lethality. This makes VP24 a potential pharmacological target, as the inhibition of its interaction with Karyopherin could reduce Ebola virulence. In this work, we carried out an atomic level study of the network of interactions between VP24 and Karyopherin using molecular dynamics and computational alanine scanning. Modeling the VP24-Karyopherin complex allowed us to identify the amino acid residues responsible for protein-protein binding and led to the identification of a nonapeptide with VP24 binding potential. Subsequently, the ability of this peptide to actually bind VP24 in solution has been assayed using Saturation Transfer Difference NMR and Circular Dichroism. Experimental and molecular modeling data concerning the VP24-peptide complex have been compared and putative peptide binding sites and modes are discussed

Local distortion and octahedral tilting in BaCexTi1−xO3perovskite

Ceramics with perovskite structure and composition BaCexTi1 12xO3(x = 0.02\u20130.30) show a progressive evolution with increasing x, from the long-range polar order of ferroelectric BaTiO3to the short-range polar order typical of relaxors. The ionic size mismatch between Ti4+and Ce4+determines strong local strains which have a significant impact on dielectric properties and phase transitions. The pair distribution function, coupled with transmission electron microscopy analysis, was applied to study the local structure. Because of the inner B-cation sizes, the superposition of rigid B\u2014O octahedra with different volumes is not compatible with the construction of an ideal perovskite structure. In this light, local structure can be described by an original model which allows (i) different Ti\u2014O and Ce\u2014O distances and (ii) the typical distortions of the two end members: off-center displacement of Ti occurring in BaTiO3and octahedral tilt in BaCeO3. The results show a clear difference, in terms of volumes, between oxygen octahedra with titanium and those related to cerium. In addition, the inclusion of cerium causes a tilt of its oxygen cage, as occurs in pure BaCeO3, creating contra-rotations and distortions of the octahedra containing titanium. This complex arrangement entails a substantial distortion, increasing as a function of cerium amount, which strongly influences the directions of titanium displacements, their local correlation and consequently their long-range cooperative effects

Molecular dynamics simulations of p97 including covalent, allosteric and ATP-competitive inhibitors

Binary (nucleotide-protein dimer and hexamer complexes) and ternary (nucleotide-protein-inhibitor complexes) p97 complexes were subjected to molecular dynamics simulations in an attempt to further our understanding of the p97 protein oligomer domain stability and, more importantly, of the recently reported diverse molecular mechanisms of inhibition including allosteric, ATP-competitive and covalent inhibitors. Analysis of stable states following equilibration phases indicated a higher intrinsic stability of the homohexamer as opposed to the dimer, and of N-D1 domains as opposed to the D2 domain. The molecular dynamics of the proposed allosteric binding model reproduced important molecular interactions identified experimentally with high frequency throughout the trajectory. Observed conformational changes occurring in the D2 nucleotide binding site provided a novel bind-rearrange-react hypothesis of stepwise molecular events involved in the specific covalent inhibitor mode of actio

Investigation on viscosity and non-isothermal crystallization behavior of P-bearing steelmaking slags with varying TiO2 content

The viscous flow and crystallization behavior of CaO-SiO2-MgO-Al2O3-FetO-P2O5-TiO2 steelmaking slags have been investigated over a wide range of temperatures under Ar (High purity, >99.999 pct) atmosphere, and the relationship between viscosity and structure was determined. The results indicated that the viscosity of the slags slightly decreased with increasing TiO2 content. The constructed nonisothermal continuous cooling transformation (CCT) diagrams revealed that the addition of TiO2 lowered the crystallization temperature. This can mainly be ascribed to that addition of TiO2 promotes the formation of [TiO6]-octahedra units and, consequently, the formation of MgFe2O4-Mg2TiO4 solid solution. Moreover, the decreasing viscosity has a significant effect on enhancing the diffusion of ion units, such as Ca2+ and [TiO4]-tetrahedra, from bulk melts to the crystal–melt interface. The crystallization of CaTiO3 and CaSiTiO5 was consequently accelerated, which can improve the phosphorus content in P-enriched phase (n2CaO·SiO2-3CaO·P2O5). Finally, the nonisothermal crystallization kinetics was characterized and the activation energy for the primary crystal growth was derived such that the activation energy increases from −265.93 to −185.41 KJ·mol−1 with the addition of TiO2 content, suggesting that TiO2 lowered the tendency for the slags to crystallize