Ab initio study of the phase separation of argon in molten iron at high pressures

Using first-principles molecular dynamics (MD) simulations, we study the solubility of argon in molten iron at high pressures and temperatures. In particular we explore whether the low pressure immiscibility of liquid Fe and Ar persists to high pressure (130 GPa) and temperature (4500K), or whether they mix. Starting from a variety of Fe/Ar mixtures we find that they always separate rapidly into two liquids. We conclude that there is no evidence for a significant increase in the solubility of Ar in Fe at these conditions. We cannot, therefore, attribute the lower melting temperatures of Fe obtained from DAC experiments compared to those obtained from ab initio calculations and shock experiments, to eutectic melting between Fe and the Ar pressure medium

A round up on some of the latest in the chemistry and biology of carbohydrates and carbohydrate-processing enzymes

Bio-organic Synthesi

Mg partitioning between solid and liquid iron under extreme conditions

Recent studies show the Earth’s core may contain more magnesium (Mg) than previously thought, with perhaps up to 6 wt.% in the early core and ∼1 wt.% still existing now. The Mg partitioning between the liquid and solid iron (Fe) under the relevant conditions is needed, therefore, in order to establish whether the presence of magnesium will have an effect on core properties, particularly those of the inner core. Using the techniques of ab initio molecular dynamics (AIMD) and thermodynamic integration, we have calculated the chemical potential and partition coefficient of Mg between solid and liquid Fe at 360 GPa and 6500 K. We find Mg partitioning slightly favours liquid Fe but still allows a significant amount of Mg into the solid, which will likely make a small but important contribution to the light-element effects on core properties

The melting curve of iron at extreme pressures: implications for planetary cores

Exoplanets with masses similar to that of Earth have recently been discovered in extrasolar systems. A first order question for understanding their dynamics is to know whether they possess Earth like liquid metallic cores. However, the iron melting curve is unknown at conditions corresponding to planets of several times the Earth's mass (over 1500 GPa for planets with 10 times the Earth's mass (ME)). In the density-temperature region of the cores of those super-Earths, we calculate the iron melting curve using first principle molecular dynamics simulations based on density functional theory. By comparing this melting curve with the calculated thermal structure of Super Earths, we show that planets heavier than 2ME, have solid cores, thus precluding the existence of an internal metallic-core driven magnetic field. The iron melting curve obtained in this study exhibits a steeper slope than any calculated planetary adiabatic temperature profile rendering the presence of molten metallic cores less likely as sizes of terrestrial planets increase

The axial ratio of hcp iron at the conditions of the Earth's inner core

We present ab initio calculations of the high-temperature axial c/a ratio of hexagonal-close-packed (hcp) iron at Earth's core pressures, in order to help interpret the observed seismic anisotropy of the inner core. The calculations are based on density functional theory, which is known to predict the properties of high-pressure iron with good accuracy. The temperature dependence of c/a is determined by minimising the Helmholtz free energy at fixed volume and temperature, with thermal contributions due to lattice vibrations calculated using harmonic theory. Anharmonic corrections to the harmonic predictions are estimated from calculations of the thermal average stress obtained from ab initio molecular dynamics simulations of hcp iron at the conditions of the inner core. We find a very gradual increase of axial ratio with temperature. This increase is much smaller than found in earlier calculations, but is in reasonable agreement with recent high-pressure, high-temperature diffraction measurements. This result casts doubt on an earlier interpretation of the seismic anisotropy of the inner core

Ab initio study of the modification of elastic properties of alpha-iron by hydrostatic strain and by hydrogen interstitials

The effect of hydrostatic strain and of interstitial hydrogen on the elastic properties of $\alpha$-iron is investigated using \textit{ab initio} density-functional theory calculations. We find that the cubic elastic constants and the polycrystalline elastic moduli to a good approximation decrease linearly with increasing hydrogen concentration. This net strength reduction can be partitioned into a strengthening electronic effect which is overcome by a softening volumetric effect. The calculated hydrogen-dependent elastic constants are used to determine the polycrystalline elastic moduli and anisotropic elastic shear moduli. For the key slip planes in $\alpha$-iron, $[1\bar{1}0]$ and $[11\bar{2}]$, we find a shear modulus reduction of approximately 1.6% per at.% H.Comment: Updated first part of 1009.378

Molecular Basis for Inhibition of GH84 Glycoside Hydrolases by Substituted Azepanes: Conformational Flexibility Enables Probing of Substrate Distortion

Here we report the synthesis of a series of polyhydroxylated 3- and 5-acetamido azepanes and detail the molecular basis of their inhibition of family 84 glycoside hydrolases. These family 84 enzymes include human O-GlcNAcase, an enzyme involved in post-translational processing of intracellular proteins modified by O-linked β-N-acetylglucosamine residues. Detailed structural analysis of the binding of these azepanes to BtGH84, a bacterial homologue of O-GlcNAcase, highlights their conformational flexibility. Molecular mechanics and molecular dynamics calculations reveal that binding to the enzyme involves significant conformational distortion of these inhibitors from their preferred solution conformations. The binding of these azepanes provides structural insight into substrate distortion that likely occurs along the reaction coordinate followed by O-GlcNAcase during glycoside hydrolysis. This class of inhibitors may prove to be useful probes for evaluating the conformational itineraries of glycosidases and aid the development of more potent and specific glycosidase inhibitors

Structural and mechanistic insights into a Bacteroides vulgatus retaining N-acetyl-β-galactosaminidase that uses neighbouring group participation

Bacteroides vulgatus is a member of the human microbiota whose abundance is increased in patients with Crohn's disease. We show that a B. vulgatus glycoside hydrolase from the carbohydrate active enzyme family GH123, BvGH123, is an N-acetyl-β-galactosaminidase that acts with retention of stereochemistry, and, through a 3-D structure in complex with Gal-thiazoline, provide evidence in support of a neighbouring group participation mechanism

Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics

An extension of the constant pH method originally implemented by Mongan et al. (J. Comput. Chem.2004, 25, 2038−2048) is proposed in this study. This adapted version of the method couples the constant pH methodology with the enhanced sampling technique of accelerated molecular dynamics, in an attempt to overcome the sampling issues encountered with current standard constant pH molecular dynamics methods. Although good results were reported by Mongan et al. on application of the standard method to the hen egg-white lysozyme (HEWL) system, residues which possess strong interactions with neighboring groups tend to converge slowly, resulting in the reported inconsistencies for predicted pKa values, as highlighted by the authors. The application of the coupled method described in this study to the HEWL system displays improvements over the standard version of the method, with the improved sampling leading to faster convergence and producing pKa values in closer agreement to those obtained experimentally for the more slowly converging residues