Mechanistic Insights into Bioengineered Antibiofilm Enamel Pellicles.

Dental caries remains the most widespread chronic disease worldwide. Basically, caries originates within biofilms accumulated on dental enamel. Despite the nonrenewable nature of the enamel tissue, targeted preventive strategies are still very limited. We previously introduced customized multifunctional proteinaceous pellicles (coatings) for controlling bacterial attachment and subsequent biofilm succession. Stemmed from our whole proteome/peptidome analysis of the in vivo acquired enamel pellicle, we designed these pellicles using hybrid mixtures of the most abundant and complementary-acting antimicrobial and antifouling proteins/peptides for synergetic suppression of early biofilms. In conjugating these domains synthetically, their bioinhibitory efficacy was remarkably boosted. Herein, we sought to explore the key structure-function relationship of these potent de novo hybridized conjugates in comparison with their individual domains, solely or in physical mixtures. Specifically, we interrelated the following facets: physicochemical and 3-dimensional folding characteristics via molecular dynamics simulations, adopted secondary structure by circular dichroism, immobilization capacity on enamel through high-spatial resolution multiphoton microscopy, and biofilm suppression potency. Our data showed consistent associations among the increased preference for protein folding structures, α-helix content, and enamel-immobilization capacity; all were inversely correlated with the attached bioburden. The expressed phenotypes could be explained by the adopted strongly amphipathic helical conformation upon conjugation, mediated by the highly anionic and acidic N-terminal pentapeptide shared region/motif for enhanced immobilization on enamel. In conclusion, conjugating bioactive proteins/peptides is a novel translational approach to engineer robust antibiofilm pellicles for caries prevention. The adopted α-helical conformation is key to enhance the antibiofilm efficacy and immobilization capacity on enamel that are promoted by certain physicochemical properties of the constituent domains. These data are valuable for bioengineering versatile therapeutics to prevent/arrest dental caries, a condition that otherwise requires invasive treatments with substantial health care expenditures.

Sensitivity of the Kß″ X-ray Emission Line to Coordination Changes in GeO2 and TiO2.

The hard X-ray Kß″ emission line shows sensitivity with respect to a wide range of cation-ligand coordination, which we investigate in the cases of GeO2 and TiO2 on the basis of ab initio spectral calculations on amorphous and crystalline structures. In compressed amorphous GeO2, the sampling of a large number of instantaneous coordination polyhedra from an ab initio molecular dynamics trajectory reveals that the functional relation between the Kß″ shift and coordination is close to linear between 4-fold and 7-fold coordination. A similar sensitivity of the Kß″ emission line exists in the coordination range between six and nine of crystalline high-pressure TiO2 polymorphs. Our results demonstrate the potential of the Kß″ emission line in research on the structure of amorphous oxide material.

Mechanisms for pressure-induced crystal-crystal transition, amorphization, and devitrification of SnI4.

The pressure-induced amorphization and subsequent recrystallization of SnI4 have been investigated using first principles molecular dynamics calculations together with high-pressure (119)Sn nuclear resonant inelastic x-ray scattering measurements. Above ∼8 GPa, we observe a transformation from an ambient crystalline phase to an intermediate crystal structure and a subsequent recrystallization into a cubic phase at ∼64 GPa. The crystalline-to-amorphous transition was identified on the basis of elastic compatibility criteria. The measured tin vibrational density of states shows large amplitude librations of SnI4 under ambient conditions. Although high pressure structures of SnI4 were thought to be determined by random packing of equal-sized spheres, we detected electron charge transfer in each phase. This charge transfer results in a crystal structure packing determined by larger than expected iodine atoms.

Using ecological niche modelling to predict spatial and temporal distribution patterns in Chinese gibbons: lessons from the present and the past.

Ecological niche modelling (ENM) is used to predict species' tolerance to changing environmental conditions. Understanding changes in the spatial distribution of species across time is essential in order to develop effective conservation strategies. Here we map the past and present distribution of gibbons across China, a country experiencing extensive anthropogenic habitat destruction and ongoing biodiversity loss. The distribution of gibbons across three time intervals is described based on fossil, historical and modern-day data, and ENM, implemented using DIVA-GIS, is used to predict how modern-day gibbon distributions might respond to future climate change. Predictions based on modern-day data alone fail to reveal patterns of environmental tolerance and geographical distribution shown by gibbons in the relatively recent historical period, emphasizing the need to incorporate past as well as present data in conservation analyses.

Large amplitude fluxional behaviour of elemental calcium under high pressure.

Experimental evidences are presented showing unusually large and highly anisotropic vibrations in the "simple cubic" (SC) unit cell adopted by calcium over a broad pressure ranging from 30-90 GPa and at temperature as low as 40 K. X-ray diffraction patterns show a preferential broadening of the (110) Bragg reflection indicating that the atomic displacements are not isotropic but restricted to the [110] plane. The unusual observation can be rationalized invoking a simple chemical perspective. As the result of pressure-induced s → d transition, Ca atoms situated in the octahedral environment of the simple cubic structure are subjected to Jahn-Teller distortions. First-principles molecular dynamics calculations confirm this suggestion and show that the distortion is of dynamical nature as the cubic unit cell undergoes large amplitude tetragonal fluctuations. The present results show that, even under extreme compression, the atomic configuration is highly fluxional as it constantly changes.

Stability, elastic and electronic properties of palladium nitride.

The crystal structure, stability, elastic constants and electronic properties of PdN(2) for four polymorph structures: pyrite, marcasite, CoSb(2) and ST(AA), have been investigated using first-principles calculations. At zero pressure all four polymorphs are metallic and thermodynamically unstable but mechanically stable. Pyrite PdN(2) is found to be the lowest energy phase. It is metallic at ambient pressure but becomes a semiconductor at pressures higher than 18 GPa. The calculated phonon band structures of pyrite PdN(2) show the structure is dynamically stable up to 60 GPa. Good agreement between calculated and observed Raman frequencies was found, indicating that the recently synthesized palladium nitride at high pressure is likely to have a pyrite structure.

Pressure-induced hydrogen-dominant metallic state in aluminum hydride.

Two structural transitions in covalent aluminum hydride AlH3 were characterized at high pressure. A metallic phase stable above 100 GPa is found to have a remarkably simple cubic structure with shortest first-neighbor H-H distances ever measured except in H2 molecule. Although the high-pressure phase is predicted to be superconductive, this was not observed experimentally down to 4 K over the pressure range 120-164 GPa. The results indicate that the superconducting behavior may be more complex than anticipated.

Superconductivity in hydrogen dominant materials: silane.

The metallization of hydrogen directly would require pressure in excess of 400 gigapascals (GPa), out of the reach of present experimental techniques. The dense group IVa hydrides attract considerable attention because hydrogen in these compounds is chemically precompressed and a metallic state is expected to be achievable at experimentally accessible pressures. We report the transformation of insulating molecular silane to a metal at 50 GPa, becoming superconducting at a transition temperature of Tc = 17 kelvin at 96 and 120 GPa. The metallic phase has a hexagonal close-packed structure with a high density of atomic hydrogen, creating a three-dimensional conducting network. These experimental findings support the idea of modeling metallic hydrogen with hydrogen-rich alloy.

Novel superconductivity in metallic SnH(4) under high pressure.

From first-principles calculations, a high-pressure metallic phase of SnH(4) with a novel layered structure intercalated by "H(2)" units is revealed. This structure is stable at pressure between 70 and 160 GPa. A remarkable feature of this structure is the presence of soft modes in the phonon band structure induced by Fermi surface nesting and Kohn anomalies that lead to very strong electron-phonon coupling. The application of the Allen-Dynes modified McMillan equation with the calculated electron-phonon coupling parameter lambda shows that a superconducting critical temperature close to 80 K can be achieved at 120 GPa.

Hydrogen-bond dynamics and Fermi resonance in high-pressure methane filled ice.

High-pressure, variable temperature infrared spectroscopy and first-principles calculations on the methane filled ice structure (MH-III) at high pressures are used to investigate the vibrational dynamics related to pressure induced modifications in hydrogen bonding. Infrared spectroscopy of isotopically dilute solutions of H(2)O in D(2)O is employed together with first-principles calculations to characterize proton dynamics with the pressure induced shortening of hydrogen bonds. A Fermi resonance is identified and shown to dominate the infrared spectrum in the pressure region between 10 and 30 GPa. Significant differences in the effects of the Fermi resonance observed between 10 and 300 K arise from the double-well potential energy surface of the hydrogen bond and quantum effects associated with the proton dynamics.

Anharmonic motions of Kr in the clathrate hydrate.

The anomalous glass-like thermal conductivity of crystalline clathrates has been suggested to be the result of the scattering of thermal phonons of the framework by 'rattling' motions of the guests in the clathrate cages. Using the site-specific (83)Kr nuclear resonant inelastic scattering spectroscopy in combination with conventional incoherent inelastic neutron scattering and molecular-dynamics simulations, we provide unambiguous evidence and characterization of the effects on these guest-host interactions in a structure-II Kr clathrate hydrate. The resonant scattering of phonons led to unprecedented large anharmonic motions of the guest atoms. The anharmonic interaction underlies the anomalous thermal transport in this system. Clathrates are prototypical models for a class of crystalline framework materials with glass-like thermal conductivity. The explanation of the unusual molecular dynamics has a wide implication for the understanding of the thermal properties of disordered solids and structural glasses.

Ordering of hydrogen bonds in high-pressure low-temperature H2O.

The near K-edge structure of oxygen in liquid water and ices III, II, and IX at 0.25 GPa and several low temperatures down to 4 K has been studied using inelastic x-ray scattering at 9884.7 eV with a total energy resolution of 305 and 175 meV. A marked decrease of the preedge intensity from the liquid phase and ice III to ices II and IX is attributed to ordering of the hydrogen bonds in the proton-ordered lattice of the latter phases. Density functional theory calculations including the influence of the Madelung potential of the ice IX crystal correctly account for the remaining preedge feature. Furthermore, we obtain spectroscopic evidence suggesting a possible new phase of ice at temperatures between 4 and 50 K.

Adsorption sites and rotational tunneling of methyl groups in cubic I methyl fluoride water clathrate.

Neutron spectroscopy in the microeV and meV regime and quasielastic scattering is applied to characterize the dynamics of methyl groups of methyl fluoride guest molecules in cubic I CH3F-water clathrate. Only above T approximately 60 K quasielastic spectra are unaffected by quantum effects. They are well described by two Lorentzians representing the CH3F species in the small and large cages of the structure. The intensities show that both cages are completely filled. The linear broadenings with temperature follow the model of rotational diffusion. Two clearly separated tunneling bands were observed at T = 4.2 K and are also assigned to the two types of water cages. Disorder of the environment (H-bonds) is reflected in the shape of the bands. For the less hindered species housing the large cages the tunneling band can be quantitatively converted into a potential distribution function within the model of single particle rotation. Transitions to excited rotational states show the dominance of a sixfold potential term V6 = 13 meV modified by a weak threefold term distributed around a characteristic value V3 = 0.9 meV. The potential distribution of V3 influences the barrier for classical reorientation only weakly in agreement with the results from quasielastic data. Adsorption sites with the guest molecules oriented towards a hydrogen bond along one of twelve local twofold axes of the cage are proposed. Such sites are consistent with the sixfold rotational potential and earlier results from methyl iodide clathrate. Rotation-translation coupling as an alternative dynamical process is excluded.

Formation and structure of a dense octahedral glass.

We have performed in situ x-ray and neutron-diffraction measurements, and molecular dynamics simulations, of GeO2, an archetypal network-forming glass under pressure. Below 5 GPa, additional atoms encroaching on the first tetrahedral shell are seen to be a precursor of local coordination change. Between 6 and 10 GPa, we observe structures with a constant average coordination of approximately 5, indicating a new metastable, intermediate form of the glass. At 15 GPa, the structure of a fully octahedral glass has been measured. This structure is not retained upon decompression and, therefore, must be studied in situ.

The structure of methane hydrate under geological conditions a combined Rietveld and maximum entropy analysis.

We present a study of the structure of a fully deuterated methane hydrate under the geological conditions found in the world's oceans. In situ high-resolution neutron diffraction experiments have been performed at temperatures of 220, 275, and 280 K and a pressure of 100 bar, corresponding to the conditions at 1000 m water depth. The data were analyzed with a combination of Rietveld refinement and maximum entropy methods. From the Rietveld refinement, precise atomic parameters of the host lattice could be determined, indicating increasing distortions of the structure of the cages at elevated temperatures and pressures. Debye-Waller factors of the encaged CD(4) molecules have been found to exceed the values of the Debye-Waller factors of the D(2)O molecules considerably. In the large cage of structure type I the thermal center-of-mass displacements of the guests are 5-10 times larger than those of the water molecules. From the maximum entropy analysis maps of the scattering length density have been obtained, showing details of the vibrational amplitudes of the atoms in methane hydrate. The Debye-Waller factors of all molecules have been found to deviate considerably from a simple spherical geometry.