A Molecular Dynamics Study of the Thermodynamic Properties of Calcium Apatites. 1. Hexagonal Phases

Porous isoreticular non-metal organic frameworks

Metal-organic frameworks (MOFs) are useful synthetic materials that are built by the programmed assembly of metal nodes and organic linkers1. The success of MOFs results from the isoreticular principle2, which allows families of structurally analogous frameworks to be built in a predictable way. This relies on directional coordinate covalent bonding to define the framework geometry. However, isoreticular strategies do not translate to other common crystalline solids, such as organic salts3-5, in which the intermolecular ionic bonding is less directional. Here we show that chemical knowledge can be combined with computational crystal-structure prediction6 (CSP) to design porous organic ammonium halide salts that contain no metals. The nodes in these salt frameworks are tightly packed ionic clusters that direct the materials to crystallize in specific ways, as demonstrated by the presence of well-defined spikes of low-energy, low-density isoreticular structures on the predicted lattice energy landscapes7,8. These energy landscapes allow us to select combinations of cations and anions that will form thermodynamically stable, porous salt frameworks with channel sizes, functionalities and geometries that can be predicted a priori. Some of these porous salts adsorb molecular guests such as iodine in quantities that exceed those of most MOFs, and this could be useful for applications such as radio-iodine capture9-12. More generally, the synthesis of these salts is scalable, involving simple acid-base neutralization, and the strategy makes it possible to create a family of non-metal organic frameworks that combine high ionic charge density with permanent porosity.

Structure and thermodynamics of empty clathrate hydrates below the freezing point of water

Recently prepared as a new H2O phase, ice XVI was obtained by degassing a Ne-sII clathrate hydrate under vacuum, however very little is known of that crystalline solid under temperatures (T ≤ 220 K) and pressures (p ≤ 5000 bar) relevant for the Earth's environment and geochemistry. In this work, atomically detailed calculations using long time-scale molecular simulations, seldom paralelled before, are employed to probe empty sII clathrate hydrates. It is found that the volumetric response to an applied pressure-temperature gradient is accurately described by the Parsafar and Mason equation of state with an accuracy of at least 99.7%. Structural deformation induced upon the crystals is interpreted by monitoring the unit cell length and isobaric thermal expansivity, whilst benchmarked against previous neutron diffraction measurements of ice XVI and hexagonal ice under room pressure conditions; a critical comparison is established with other sII guest occupied lattices (CH4, CO2 and CnH2n+2 with n = 2, 3, 4), often found in permafrost regions and in the margins of continental shelves. Such an analysis reveals that empty sII frameworks are slightly more stable to thermal deformation than their sI analogues and that hexagonal ice is the structurally most stable of the condensed H2O phases addressed here. Of paramount importance for the oil and natural gas industries, heat capacities obtained from enthalpy profiles are identical for the sI and sII empty clathrates up to 2000 bar and diverge by only ∼7.3% at 5000 bar. The canonical tetrahedral symmetry of water-bonded networks is analysed in terms of an angular and a distance order parameters, which are observed to decrease (increase) as pressure (temperature) increases (decreases). The results now being reported constitute a landmark for future studies dealing with high-pressure and very low-temperature conditions, characteristic of the Earth's permafrost environment and other planetary interiors, whilst contributing to expand our knowledge regarding the recently discovered ice XVI phase.

A review on hydroxyapatite coatings for the biomedical applications: experimental and theoretical perspectives

The production of hydroxyapatite (HAP) composite coatings has continuously been investigated for bone tissue applications during the last few decades due to their significant bioactivity and osteoconductivity.

Specific ion effects control the thermoelastic behavior of nanolayered materials: the case of crystalline alkali-silica reaction products

We perform molecular simulations to characterize the structure and the thermo-mechanical behavior of crystalline alkali-silica reaction (ASR) products, which are layered silicate analogous to shlykovite.

Computational insights of K1444N substitution in GAP-related domain of NF1 gene associated with neurofibromatosis type 1 disease: a molecular modeling and dynamics approach

The NF1 gene encodes for neurofibromin protein, which is ubiquitously expressed, but most highly in the central nervous system. Non-synonymous SNPs (nsSNPs) in the NF1 gene were found to be associated with Neurofibromatosis Type 1 disease, which is characterized by the growth of tumors along nerves in the skin, brain, and other parts of the body. In this study, we used several in silico predictions tools to analyze 16 nsSNPs in the RAS-GAP domain of neurofibromin, the K1444N (K1423N) mutation was predicted as the most pathogenic. The comparative molecular dynamic simulation (MDS; 50 ns) between the wild type and the K1444N (K1423N) mutant suggested a significant change in the electrostatic potential. In addition, the RMSD, RMSF, Rg, hydrogen bonds, and PCA analysis confirmed the loss of flexibility and increase in compactness of the mutant protein. Further, SASA analysis revealed exchange between hydrophobic and hydrophilic residues from the core of the RAS-GAP domain to the surface of the mutant domain, consistent with the secondary structure analysis that showed significant alteration in the mutant protein conformation. Our data concludes that the K1444N (K1423N) mutant lead to increasing the rigidity and compactness of the protein. This study provides evidence of the benefits of the computational tools in predicting the pathogenicity of genetic mutations and suggests the application of MDS and different in silico prediction tools for variant assessment and classification in genetic clinics.

New Insight into Mixing Fluoride and Chloride in Bioactive Silicate Glasses

Adding fluoride into bioactive glasses leads to fluorapatite formation and a decrease in glass transition temperature. Recently, chloride has been introduced into glasses as an alternative to fluoride. The presence of the large chloride ion lowers glass crystallisation tendency and increases glass molar volume, which effectively facilitates glass degradation and bone-bonding apatite-like layer formation. However, there is no information regarding the effect of mixing fluoride and chloride on the glass structure and properties. This study aims to synthesize mixed fluoride and chloride containing bioactive glasses; investigate the structural role of fluoride and chloride and their effects on glass properties. The chloride content measurements reveal that 77–90% of chloride was retained in these Q² type glasses. Glass transition temperature reduced markedly with an increase in CaX₂ (X = F + Cl) content, while the glass molar volume increased. ²⁹Si MAS-NMR results show that the incorporation of mixed fluoride and chloride did not cause significant change in the polymerization of the silicate network and no detectable concentration of Si-F/Cl bands were present. This agrees with ¹⁹F NMR spectra showing that F existed as F-Ca(n) species.

Thickness of hydroxyapatite nanocrystal controls mechanical properties of the collagen-hydroxyapatite interface

Collagen-hydroxyapatite interfaces compose an important building block of bone structures. While it is known that the nanoscale structure of this elementary building block can affect the mechanical properties of bone, a systematic understanding of the effect of the geometry on the mechanical properties of this interface between protein and mineral is lacking. Here we study the effect of geometry, different crystal surfaces, and hydration on the mechanical properties of collagen-hydroxyapatite interfaces from an atomistic perspective, and discuss underlying deformation mechanisms. We find that the presence of hydroxyapatite significantly enhances the tensile modulus and strength compared with a tropocollagen molecule alone. The stiffening effect is strongly dependent on the thickness of the mineral crystal until a plateau is reached at 2 nm crystal thickness. We observe no significant differences due to the mineral surface (Ca surface vs OH surface) or due to the presence of water. Our result shows that the hydroxyapatite crystal with its thickness confined to the nanometer size efficiently increases the tensile modulus and strength of the collagen-hydroxyapatite composite, agreeing well with experimental observations that consistently show the existence of extremely thin mineral flakes in various types of bones. We also show that the collagen-hydroxyapatite interface can be modeled with an elastic network model which, based on the results of atomistic simulations, provides a good estimate of the surface energy and other mechanical features.

Adsorption processes of Gly and Glu amino acids on hydroxyapatite surfaces at the atomic level

The regulation mechanism of organic additives on the crystallization of inorganic crystal is fundamentally important in biomineralization. Experimentally, it was found that the amino acids glycine (Gly) and glutamic acid (Glu) could lead to the formation of rod- and plate-like hydroxyapatite (HAP) crystallites, respectively. The detailed adsorption behavior of Gly and Glu on HAP crystal faces was studied by molecular dynamics (MD) simulation. The specific adsorption sites and patterns of Gly and Glu on the (100) and (001) faces of HAP crystals were revealed at the atomic level. The amino acids adsorbed on the HAP (001) and (100) faces with their positive amino groups occupied vacant calcium sites, and their negative carboxylate groups occupied vacant P or OH sites precisely and formed an ordered adsorption layer. The atomic force microscopy pulling simulation and free energy calculation showed that Glu was much more difficult to depart from the HAP (001) face than that from the (100) face. This result indicated that Glu preferred to adsorb strongly onto the HAP (001) face, which resulted in the formation of plate-like HAP. However, Gly did not show any significantly preferential adsorption between these two HAP faces. Thus, the habits of HAP, rod-like crystallites, were not altered during the HAP crystallization in the presence of Gly. Combined with experimental results, our study demonstrated that the MD simulation of interfacial structures could improve our understanding of biological regulation in mineralization processes at the atomic level.

Molecular Force Field for Ionic Liquids III: Imidazolium, Pyridinium, and Phosphonium Cations; Chloride, Bromide, and Dicyanamide Anions

This is the third set of parameters of a force field for the molecular simulation of ionic liquids, developed within the spirit of the OPLS-AA model and thus oriented toward the calculation of equilibrium thermodynamic and structural properties. The parameter sets reported here concern the cations alkylimidazolium, tetra-alkylphosphonium, and N-alkylpyridinium, and the anions chloride, bromide, and dicyanamide. The force field is built in a stepwise manner that allows the construction of models for an entire family of cations, with alkyl side chains of different length, for example. Due to the transferability of the present force field, the ions studied here can be combined with those reported in our two previous publications to create a large variety of ionic liquids that can be studied by molecular simulation. The parameters reported were obtained through different series of ab initio calculations concerning the geometry, force constants, torsion energy profiles, and electrostatic charge distributions of the ions under study. Validation of the force field consisted of comparison with experimental crystal structure and liquid density data.