To understand and engineer plant metabolism, we need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we generated genome-scale metabolic pathway databases of 126 algal and plant genomes, ranging from model organisms to crops to medicinal plants (). Of these, 104 have not been reported before. We systematically evaluated the quality of the databases, which revealed that our semi-automated validation pipeline dramatically improves the quality. We then compared the metabolic content across the 126 organisms using multiple correspondence analysis and found that Brassicaceae, Poaceae, and Chlorophyta appeared as metabolically distinct groups. To demonstrate the utility of this resource, we used recently published sorghum transcriptomics data to discover previously unreported trends of metabolism underlying drought tolerance. We also used single-cell transcriptomics data from the Arabidopsis root to infer cell type-specific metabolic pathways. This work shows the quality and quantity of our resource and demonstrates its wide-ranging utility in integrating metabolism with other areas of plant biology.

Optical and synchrotron x-ray diffraction diamond anvil cell experiments have been combined with first-principles theoretical structure predictions to investigate mixtures of N-2 and H-2 up to 55 GPa. Our experiments show the formation of structurally complex van der Waals compounds [see also D. K. Spaulding et al., Nat. Commun. 5, 5739 (2014)] above 10 GPa. However, we found that these NxH (0.5 < x < 1.5) compounds transform abruptly to new oligomeric materials through barochemistry above 47 GPa and photochemistry at pressures as low as 10 GPa. These oligomeric compounds can be recovered to ambient pressure at T < 130 K, whereas at room temperature, they can be metastable on pressure release down to 3.5 GPa. Extensive theoretical calculations show that such oligomeric materials become thermodynamically more stable in comparison to mixtures of N-2, H-2, and NH3 above approximately 40 GPa. Our results suggest new pathways for synthesis of environmentally benign high energy-density materials. These materials could also exist as alternative planetary ices. (C) 2015 AIP Publishing LLC.

Pressure dependent angle-dispersive x-ray powder diffraction measurements of alpha-phase aluminum trifluoride (alpha-AlF3) and separately, aluminum triiodide (AlI3) were conducted using a diamond-anvil cell. Results at 295 K extend to 50 GPa. The equations of state of AlF3 and AlI3 were determined through refinements of collected x-ray diffraction patterns. The respective bulk moduli and corresponding pressure derivatives are reported for multiple orders of the Birch-Murnaghan (B-M), finite-strain (F-f), and higher pressure finite-strain (G-g) EOS analysis models. Aluminum trifluoride exhibits an apparent isostructural phase transition at approximately 12 GPa. Aluminum triiodide also undergoes a second-order atomic rearrangement: applied stress transformed a monoclinically distorted face centered cubic (fcc) structure into a standard fcc structural arrangement of iodine atoms. Results from semi-empirical thermochemical computations of energetic materials formulated with fluorine containing reactants were obtained with the aim of predicting the yield of halogenated products. (C) 2015 AIP Publishing LLC.

The elastic moduli, elastic anisotropy coefficients, sound velocities and Poisson's ratio of hcp solid helium have been calculated using density functional theory in generalized gradient approximation (up to 30 TPa), and pair + triple semiempirical potentials (up to 100 GPa). Zero-point vibrations have been treated in the Debye approximation assuming He-4 isotope (we exclude the quantum- crystal region at very low pressures from consideration). Both methods give a reasonable agreement with the available experimental data. Our calculations predict significant elastic anisotropy of helium (Delta P approximate to 1.14, Delta S-1 approximate to 1.7, Delta S-2 approximate to 0.93 at low pressures). Under terapascal (TPa) pressures helium becomes more elastically isotropic. At the metallization point, there is a sharp feature in the elastic modulus C-S, which is the stiffness with respect to the isochoric change of the c/a ratio. This is connected with the previously obtained sharp minimum of the c/a ratio at the metallization point. Our calculations confirm the previously measured decrease of the Poisson's ratio with increasing pressure. This is not a quantum effect, as the same sign of the pressure effect was obtained when we disregarded zero-point vibrations. At TPa pressures, Poisson's ratio reaches the value of 0.31 at the theoretical metallization point (V-mol = 0.228 cm(3)/mol, p = 17.48 TPa) and 0.29 at 30 TPa. For p = 0, we predict a Poisson's ratio of 0.38, which is in excellent agreement with the low-p-low-T experimental data.

We present results of lattice dynamics calculations of Poisson's ratio (PR) for solid hydrogen and rare gas solids (He, Ne, Ar, Kr and Xe) under pressure. Using two complementary approaches-the semi-empirical many-body calculations and the first-principle density-functional theory calculations we found three different types of pressure dependencies of PR. While for solid helium PR monotonically decreases with rising pressure, for Ar, Kr, and Xe it monotonically increases with pressure. For solid hydrogen and Ne the pressure dependencies of PR are nonmonotonic displaying rather deep minimums. The role of the intermolecular potentials in this diversity of patterns is discussed. (C) 2015 AIP Publishing LLC.

The noble gases are elements of broad importance across science and technology and are primary constituents of planetary and stellar atmospheres, where they segregate into droplets or layers that affect the thermal, chemical, and structural evolution of their host body. We have measured the optical properties of noble gases at relevant high pressures and temperatures in the laser-heated diamond anvil cell, observing insulator-to-conductor transformations in dense helium, neon, argon, and xenon at 4,000-15,000 K and pressures of 15-52 GPa. The thermal activation and frequency dependence of conduction reveal an optical character dominated by electrons of low mobility, as in an amorphous semiconductor or poor metal, rather than free electrons as is often assumed for such wide band gap insulators at high temperatures. White dwarf stars having helium outer atmospheres cool slower and may have different color than if atmospheric opacity were controlled by free electrons. Helium rain in Jupiter and Saturn becomes conducting at conditions well correlated with its increased solubility in metallic hydrogen, whereas a deep layer of insulating neon may inhibit core erosion in Saturn.

The richness of the phase diagram of water reduces drastically at very high pressures where only two molecular phases, proton-disordered ice VII and proton-ordered ice VIII, are known. Both phases transform to the centered hydrogen bond atomic phase ice X above about 60 GPa, i.e., at pressures experienced in the interior of large ice bodies in the universe, such as Saturn and Neptune, where nonmolecular ice is thought to be the most abundant phase of water. In this work, we investigate, by Raman spectroscopy up to megabar pressures and ab initio simulations, how the transformation of ice VII in ice X is affected by the presence of salt inclusions in the ice lattice. Considerable amounts of salt can be included in ice VII structure under pressure via rock-ice interaction at depth and processes occurring during planetary accretion. Our study reveals that the presence of salt hinders proton order and hydrogen bond symmetrization, and pushes ice VII to ice X transformation to higher and higher pressures as the concentration of salt is increased.

Double stage diamond anvil cells (DACs) of two designs have been assembled and tested. We used a standard symmetric DAC with flat or beveled culets as a primary stage and CVD microanvils machined by a focused ion beam as a second. We evaluated pressure, stress, and strain distributions in gold and a mixture of gold and iron as well as in secondary anvils using synchrotron x-ray diffraction with a micro-focused beam. A maximum pressure of 240 GPa was reached independent of the first stage anvil culet size. We found that the stress field generated by the second stage anvils is typical of conventional DAC experiments. The maximum pressures reached are limited by strains developing in the secondary anvil and by cupping of the first stage diamond anvil in the presented experimental designs. Also, our experiments show that pressures of several megabars may be reached without sacrificing the first stage diamond anvils. (C) 2015 AIP Publishing LLC.

The high-pressure behavior of manganese-rich carbonate, rhodochrosite, has been characterized up to 62GPa by synchrotron-based midinfrared spectroscopy and X-ray diffraction. Modifications in both the infrared spectra and the X-ray diffraction patterns were observed above similar to 35GPa, indicating the presence of a high-pressure phase transition at these pressures. We found that rhodochrosite adopts a structure close to CaCO3-VI with a triclinic unit cell (a=2.87 angstrom, b=4.83 angstrom, c=5.49 angstrom, =99.86 degrees, =94.95 degrees, and =90.95 degrees at 62GPa). Using first-principles calculations based on density functional theory, we confirmed these observations and assigned modes in the new infrared signature of the high-pressure phase. These results suggest that high-pressure metastable phase of calcite may play an important role in carbon storage and transport in the deep Earth.

The phase diagram of H2O is extremely complex; in particular, it is believed that a second critical point exists deep below the supercooled water (SCW) region where two liquids of different densities coexist. The problem, however, is that SCW freezes at temperatures just above this hypothesized liquid liquid critical point (LLCP), so direct experimental verification of its existence has yet to be realized. Here, we report two anomalies in the complex dielectric constant during warming in the form of a peak anomaly near T-p = 203 K and a sharp minimum near T-m = 210 K from ice samples prepared from SCW under hydrostatic pressures of up to 760 MPa. The same features were observed about 4 K higher in heavy ice. T-p is believed to be associated with the nucleation process of metastable cubic ice Ic, and T-m, is the transitioning of ice Ic to either ice Ih or II depending on the pressure. Given that T-p and T-m, are nearly isothermal, present up to at least 620 MPa, and end as a critical point near 33-50 MPa, it is deduced that two types of SCWs with different density concentrations exist, which affects the surface energy of ice Ic nuclei in the "no man's land" region of the phase diagram. Our results are consistent with the LLCP theory and suggest that a metastable critical point exists in the region of 33-50 MPa and T-c >= 210 K.