The pypadf package: computing the pair angle distribution function from fluctuation scattering data.

The pair angle distribution function (PADF) is a three- and four-atom correlation function that characterizes the local angular structure of disordered materials, particles or nanocrystalline materials. The PADF can be measured using X-ray or electron fluctuation diffraction data, which can be collected by scanning or flowing a structurally disordered sample through a focused beam. It is a natural generalization of established pair distribution methods, which do not provide angular information. The software package pypadf provides tools to calculate the PADF from fluctuation diffraction data. The package includes tools for calculating the intensity correlation function, which is a necessary step in the PADF calculation and also the basis for other fluctuation scattering analysis techniques.

Pressure-Induced Metallization of BaH2 and the Effect of Hydrogenation.

Using optical spectroscopy, X-ray diffraction, and electrical transport measurements, we have studied the pressure-induced metallization in BaH2 and Ba8H46. Our combined measurements suggest a structural phase transition from BaH2-II to BaH2-III accompanied by band gap closure and transformation to a metallic state at 57 GPa. The metallization is confirmed by resistance measurements as a function of the pressure and temperature. We also confirm that, with further hydrogenation, BaH2 forms the previously observed Weaire-Phelan Ba8H46, synthesized at 45 GPa and 1200 K. In this compound, metallization pressure is shifted to 85 GPa. Through a comparison of the properties of these two compounds, a question is raised about the importance of the hydrogen content in the electronic properties of hydride systems.

Synthesis and characterization of XeAr2 under high pressure.

The binary Xe-Ar system has been studied in a series of high pressure diamond anvil cell experiments up to 60 GPa at 300 K. In-situ x-ray powder diffraction and Raman spectroscopy indicate the formation of a van der Waals compound, XeAr2, at above 3.5 GPa. Powder x-ray diffraction analysis demonstrates that XeAr2 adopts a Laves MgZn2-type structure with space group P63/mmc and cell parameters a = 6.595 Å and c = 10.716 Å at 4 GPa. Density functional theory calculations support the structure determination, with agreement between experimental and calculated Raman spectra. Our DFT calculations suggest that XeAr2 would remain stable without a structural transformation or decomposition into elemental Xe and Ar up to at least 80 GPa.

Probing ion-binding at a protein interface: Modulation of protein properties by ionic liquids.

Ions are important to modulate protein properties, including solubility and stability, through specific ion effects. Ionic liquids (ILs) are designer salts with versatile ion combinations with great potential to control protein properties. Although protein-ion binding of common metals is well-known, the IL effect on proteins is not well understood. Here, we employ the model protein lysozyme in dilute and concentrated IL solutions to determine the specific ion binding effect on protein phase behaviour, activity, size and conformational change, aggregation and intermolecular interactions. A combination of spectroscopic techniques, activity assays, small-angle X-ray scattering, and crystallography highlights that ILs, particularly their anions, bind to specific sites in the protein hydration layer via polar contacts on charged, polar and aromatic residues. The specific ion binding can induce more flexible loop regions in lysozyme, while the ion binding in the bulk phase can be more dynamic in solution. Overall, the protein behaviour in ILs depends on the net effect of nonspecific interactions and specific ion binding. Compared to formate, the nitrate anion induced high protein solubility, low activity, elongated shape and aggregation, which is largely owing to its higher propensity for ion binding. These findings provide new insights into protein-IL binding interactions and using ILs to modulate protein properties.

Automation of liquid crystal phase analysis for SAXS, including the rapid production of novel phase diagrams for SDS-water-PIL systems.

Lyotropic liquid crystal phases (LCPs) are widely studied for diverse applications, including protein crystallization and drug delivery. The structure and properties of LCPs vary widely depending on the composition, concentration, temperature, pH, and pressure. High-throughput structural characterization approaches, such as small-angle x-ray scattering (SAXS), are important to cover meaningfully large compositional spaces. However, high-throughput LCP phase analysis for SAXS data is currently lacking, particularly for patterns of multiphase mixtures. In this paper, we develop semi-automated software for high throughput LCP phase identification from SAXS data. We validate the accuracy and time-savings of this software on a total of 668 SAXS patterns for the LCPs of the amphiphile hexadecyltrimethylammonium bromide (CTAB) in 53 acidic or basic ionic liquid derived solvents, within a temperature range of 25-75 °C. The solvents were derived from stoichiometric ethylammonium nitrate (EAN) or ethanolammonium nitrate (EtAN) by adding water to vary the ionicity, and adding precursor ions of ethylamine, ethanolamine, and nitric acid to vary the pH. The thermal stability ranges and lattice parameters for CTAB-based LCPs obtained from the semi-automated analysis showed equivalent accuracy to manual analysis, the results of which were previously published. A time comparison of 40 CTAB systems demonstrated that the automated phase identification procedure was more than 20 times faster than manual analysis. Moreover, the high throughput identification procedure was also applied to 300 unpublished scattering patterns of sodium dodecyl-sulfate in the same EAN and EtAN based solvents in this study, to construct phase diagrams that exhibit phase transitions from micellar, to hexagonal, cubic, and lamellar LCPs. The accuracy and significantly low analysis time of the high throughput identification procedure validates a new, rapid, unrestricted analytical method for the determination of LCPs.

Chemically Assisted Precompression of Hydrogen Molecules in Alkaline-Earth Tetrahydrides.

Through a series of high pressure diamond anvil experiments, we report the synthesis of alkaline earth (Ca, Sr, Ba) tetrahydrides, and investigate their properties through Raman spectroscopy, X-ray diffraction, and density functional theory calculations. The tetrahydrides incorporate both atomic and quasi-molecular hydrogen, and we find that the frequency of the intramolecular stretching mode of the H2δ- units downshifts from Ca to Sr and to Ba upon compression. The experimental results indicate that the larger the host cation, the longer the H2δ- bond. Analysis of the electron localization function (ELF) demonstrates that the lengthening of the H-H bond is caused by the charge transfer from the metal to H2δ- and by the steric effect of the metal host on the H-H bond. This effect is most prominent for BaH4, where the precompression of H2δ- units at 50 GPa results in bond lengths comparable to that of pure H2 above 275 GPa.

Observations of phase changes in monoolein during high viscous injection.

Serial crystallography of membrane proteins often employs high-viscosity injectors (HVIs) to deliver micrometre-sized crystals to the X-ray beam. Typically, the carrier medium is a lipidic cubic phase (LCP) media, which can also be used to nucleate and grow the crystals. However, despite the fact that the LCP is widely used with HVIs, the potential impact of the injection process on the LCP structure has not been reported and hence is not yet well understood. The self-assembled structure of the LCP can be affected by pressure, dehydration and temperature changes, all of which occur during continuous flow injection. These changes to the LCP structure may in turn impact the results of X-ray diffraction measurements from membrane protein crystals. To investigate the influence of HVIs on the structure of the LCP we conducted a study of the phase changes in monoolein/water and monoolein/buffer mixtures during continuous flow injection, at both atmospheric pressure and under vacuum. The reservoir pressure in the HVI was tracked to determine if there is any correlation with the phase behaviour of the LCP. The results indicated that, even though the reservoir pressure underwent (at times) significant variation, this did not appear to correlate with observed phase changes in the sample stream or correspond to shifts in the LCP lattice parameter. During vacuum injection, there was a three-way coexistence of the gyroid cubic phase, diamond cubic phase and lamellar phase. During injection at atmospheric pressure, the coexistence of a cubic phase and lamellar phase in the monoolein/water mixtures was also observed. The degree to which the lamellar phase is formed was found to be strongly dependent on the co-flowing gas conditions used to stabilize the LCP stream. A combination of laboratory-based optical polarization microscopy and simulation studies was used to investigate these observations.

Preferred orientation and its effects on intensity-correlation measurements.

Intensity-correlation measurements allow access to nanostructural information on a range of ordered and disordered materials beyond traditional pair-correlation methods. In real space, this information can be expressed in terms of a pair-angle distribution function (PADF) which encodes three- and four-body distances and angles. To date, correlation-based techniques have not been applied to the analysis of microstructural effects, such as preferred orientation, which are typically investigated by texture analysis. Preferred orientation is regarded as a potential source of error in intensity-correlation experiments and complicates interpretation of the results. Here, the theory of preferred orientation in intensity-correlation techniques is developed, connecting it to the established theory of texture analysis. The preferred-orientation effect is found to scale with the number of crystalline domains in the beam, surpassing the nanostructural signal when the number of domains becomes large. Experimental demonstrations are presented of the orientation-dominant and nanostructure-dominant cases using PADF analysis. The results show that even minor deviations from uniform orientation produce the strongest angular correlation signals when the number of crystalline domains in the beam is large.

Stability, flow alignment and a phase transition of the lipidic cubic phase during continuous flow injection.

Continuous flow injection is a key technology for serial crystallography measurements of protein crystals suspended in the lipidic cubic phase (LCP). To date, there has been little discussion in the literature regarding the impact of the injection process itself on the structure of the lipidic phase. This is despite the fact that the phase of the injection matrix is critical for the flow properties of the stream and potentially for sample stability. Here we report small-angle X-ray scattering measurements of a monoolein:water mixture during continuous delivery using a high viscosity injector. We observe both an alignment and modification of the LCP as a direct result of the injection process. The orientation of the cubic lattice with respect to the beam was estimated based on the anisotropy of the diffraction pattern and does not correspond to a single low order zone axis. The solvent fraction was also observed to impact the stability of the cubic phase during injection. In addition, depending on the distance traveled by the lipid after exiting the needle, the phase is observed to transition from a pure diamond phase (Pn3m) to a mixture containing both gyriod (Ia3d) and lamellar (Lα) phases. Finite element modelling of the observed phase behaviour during injection indicates that the pressure exerted on the lipid stream during extrusion accounts for the variations in the phase composition of the monoolein:water mixture.

Superionicity, disorder, and bandgap closure in dense hydrogen chloride.

Hydrogen bond networks play a crucial role in biomolecules and molecular materials such as ices. How these networks react to pressure directs their properties at extreme conditions. We have studied one of the simplest hydrogen bond formers, hydrogen chloride, from crystallization to metallization, covering a pressure range of more than 2.5 million atmospheres. Following hydrogen bond symmetrization, we identify a previously unknown phase by the appearance of new Raman modes and changes to x-ray diffraction patterns that contradict previous predictions. On further compression, a broad Raman band supersedes the well-defined excitations of phase V, despite retaining a crystalline chlorine substructure. We propose that this mode has its origin in proton (H+) mobility and disorder. Above 100 GPa, the optical bandgap closes linearly with extrapolated metallization at 240(10) GPa. Our findings suggest that proton dynamics can drive changes in these networks even at very high densities.

High-temperature phase transitions in dense germanium.

Through a series of high-pressure x-ray diffraction experiments combined with in situ laser heating, we explore the pressure-temperature phase diagram of germanium (Ge) at pressures up to 110 GPa and temperatures exceeding 3000 K. In the pressure range of 64-90 GPa, we observe orthorhombic Ge-IV transforming above 1500 K to a previously unobserved high-temperature phase, which we denote as Ge-VIII. This high-temperature phase is characterized by a tetragonal crystal structure, space group I4/mmm. Density functional theory simulations confirm that Ge-IV becomes unstable at high temperatures and that Ge-VIII is highly competitive and dynamically stable at these conditions. The existence of Ge-VIII has profound implications for the pressure-temperature phase diagram, with melting conditions increasing to much higher temperatures than previous extrapolations would imply.

Pressure-Induced Synthesis and Properties of an H2S-H2Se-H2 Molecular Alloy.

The chalcogens are known to react with one another to form interchalcogens, which exhibit a diverse range of bonding and conductive behavior due to the difference in electronegativity between the group members. Through a series of high-pressure diamond anvil experiments combined with density functional theory calculations, we report the synthesis of an S-Se hydride. At pressures above 4 GPa we observe the formation of a single solid composed of both H2Se and H2S molecular units. Further compression in a hydrogen medium leads to the formation of an alloyed compound (H2SxSe1-x)2H2, after which there is a sequence of pressure-induced phase transitions associated with the arrested rotation of molecules. At pressures above 50 GPa, there is a symmetrization of hydrogen bonds concomitantly with a closing band gap and increased reflectivity of the compound, indicative of a transition to a metallic state.

Synthesis of Weaire-Phelan Barium Polyhydride.

By combining pressures up to 50 GPa and temperatures of 1200 K, we synthesize the novel barium hydride, Ba8H46, stable down to 27 GPa. We use Raman spectroscopy, X-ray diffraction, and first-principles calculations to determine that this compound adopts a highly symmetric Pm3¯n structure with an unusual 534:1 hydrogen-to-barium ratio. This singular stoichiometry corresponds to the well-defined type-I clathrate geometry. This clathrate consists of a Weaire-Phelan hydrogen structure with the barium atoms forming a topologically close-packed phase. In particular, the structure is formed by H20 and H24 clathrate cages showing substantially weakened H-H interactions. Density functional theory (DFT) demonstrates that cubic Pm3¯n Ba8H46 requires dynamical effects to stabilize the H20 and H24 clathrate cages.

Synthesis of Superconducting Cobalt Trihydride.

The Co-H system has been investigated through high-pressure, high-temperature X-ray diffraction experiments combined with first-principles calculations. On compression of elemental cobalt in a hydrogen medium, we observe face-centered cubic cobalt hydride (CoH) and cobalt dihydride (CoH2) above 33 GPa. Laser heating CoH2 in a hydrogen matrix at 75 GPa to temperatures in excess of ∼800 K produces cobalt trihydride (CoH3) which adopts a primitive structure. Density functional theory calculations support the stability of CoH3. This phase is predicted to be thermodynamically stable at pressures above 18 GPa and to be a superconductor below 23 K. Theory predicts that this phase remains dynamically stable upon decompression above 11 GPa where it has a maximum Tc of 30 K.

Counterintuitive effects of isotopic doping on the phase diagram of H2-HD-D2 molecular alloy.

Molecular hydrogen forms the archetypical quantum solid. Its quantum nature is revealed by behavior which is classically impossible and by very strong isotope effects. Isotope effects between [Formula: see text], [Formula: see text], and HD molecules come from mass difference and the different quantum exchange effects: fermionic [Formula: see text] molecules have antisymmetric wavefunctions, while bosonic [Formula: see text] molecules have symmetric wavefunctions, and HD molecules have no exchange symmetry. To investigate how the phase diagram depends on quantum-nuclear effects, we use high-pressure and low-temperature in situ Raman spectroscopy to map out the phase diagrams of [Formula: see text]-HD-[Formula: see text] with various isotope concentrations over a wide pressure-temperature (P-T) range. We find that mixtures of [Formula: see text], HD, and [Formula: see text] behave as an isotopic molecular alloy (ideal solution) and exhibit symmetry-breaking phase transitions between phases I and II and phase III. Surprisingly, all transitions occur at higher pressures for the alloys than either pure [Formula: see text] or [Formula: see text] This runs counter to any quantum effects based on isotope mass but can be explained by quantum trapping of high-kinetic energy states by the exchange interaction.

Complex Hydrogen Substructure in Semimetallic RuH4.

When compressed in a matrix of solid hydrogen, many metals form compounds with increasingly high hydrogen contents. At high density, hydrogenic sublattices can emerge, which may act as low-dimensional analogues of atomic hydrogen. We show that at high pressures and temperatures, ruthenium forms polyhydride species that exhibit intriguing hydrogen substructures with counterintuitive electronic properties. Ru3H8 is synthesized from RuH in H2 at 50 GPa and at temperatures in excess of 1000 K, adopting a cubic structure with short H-H distances. When synthesis pressures are increased above 85 GPa, we observe RuH4 which crystallizes in a remarkable structure containing corner-sharing H6 octahedra. Calculations indicate this phase is semimetallic at 100 GPa.

Author Correction: Band gap closure, incommensurability and molecular dissociation of dense chlorine.

The original version of this Article omitted references to previous experimental reports on solid hydrogen that are relevant for a full understanding of the context of the previous work. The added references are: 47. Akahama, Y. et al. Evidence from x-ray diffraction of orientational ordering in phase III of solid hydrogen at pressures up to 183 GPa. Phys. Rev. B 82, 060101 (2010). 48. Zha, C.-S., Liu, Z. & Hemley, R. J. Synchrotron infrared measurements of dense hydrogen to 360 GPa. Phys. Rev. Lett. 108, 146402 (2012). 49. Dias, R. & Silvera, I. Observation of the Wigner-Huntington transition to metallic hydrogen. Science 355, 715-718 (2017). 50. Eremets, M. I. & Drozdov, A. P. Comments on the claimed observation of the Wigner-Huntington transition to metallic hydrogen. Preprint at http://arxiv.org/abs/1702.05125 (2017). 51. Loubeyre, P., Occelli, F. & Dumas, P. Comment on: "Observation of the Wigner-Huntington transition to metallic hydrogen". Preprint at http://arxiv.org/abs/1702.07192 (2017). 52. Goncharov, A. F. & Struzhkin, V. V. Comment on "Observation of the Wigner-Huntington transition to metallic hydrogen". Science 357, eaam9736 (2017). 53. Liu, X.-D., Dalladay-Simpson, P., Howie, R. T., Li, B. & Gregoryanz, E. Comment on "Observation of the Wigner-Huntington transition to metallic hydrogen". Science 357, eaan2671 (2017). Citations to these reference, plus reference 21, have been added to the fourth sentence of the Introduction: 'The experimental realisation of atomic metallic hydrogen has remained elusive despite intense research efforts lasting over 30 years4-7,21,47-53.' This has been corrected in the PDF and HTML versions of the Article.

Band gap closure, incommensurability and molecular dissociation of dense chlorine.

Diatomic elemental solids are highly compressible due to the weak interactions between molecules. However, as the density increases the intra- and intermolecular distances become comparable, leading to a range of phenomena, such as structural transformation, molecular dissociation, amorphization, and metallisation. Here we report, following the crystallization of chlorine at 1.15(30) GPa into an ordered orthorhombic structure (oC8), the existence of a mixed-molecular structure (mC8, 130(10)-241(10) GPa) and the concomitant observation of a continuous band gap closure, indicative of a transformation into a metallic molecular form around 200(10) GPa. The onset of dissociation of chlorine is identified by the observation of the incommensurate structure (i-oF4) above 200(10) GPa, before finally adopting a monatomic form (oI2) above 256(10) GPa.

Direct Reaction between Copper and Nitrogen at High Pressures and Temperatures.

Transition-metal nitrides have applications in a range of technological fields. Recent experiments have shown that new nitrogen-bearing compounds can be accessed through a combination of high temperatures and pressures, revealing a richer chemistry than was previously assumed. Here, we show that at pressures above 50 GPa and temperatures greater than 1500 K  elemental copper reacts with nitrogen, forming copper diazenide (CuN2). Through a combination of synchrotron X-ray diffraction and first-principles calculations we have explored the stability and electronic structure of CuN2. We find that the novel compound remains stable down to 25 GPa before decomposing to its constituent elements. Electronic structure calculations show that CuN2 is metallic and exhibits partially filled N2 antibonding orbitals, leading to an ambiguous electronic structure between Cu+/Cu2+. This leads to weak Cu-N bonds and the lowest bulk modulus observed for any transition-metal nitride.

Unusually complex phase of dense nitrogen at extreme conditions.

Nitrogen exhibits an exceptional polymorphism under extreme conditions, making it unique amongst the elemental diatomics and a valuable testing system for experiment-theory comparison. Despite attracting considerable attention, the structures of many high-pressure nitrogen phases still require unambiguous determination. Here, we report the structure of the elusive high-pressure high-temperature polymorph ι-N2 at 56 GPa and ambient temperature, determined by single crystal X-ray diffraction, and investigate its properties using ab initio simulations. We find that ι-N2 is characterised by an extraordinarily large unit cell containing 48 N2 molecules. Geometry optimisation favours the experimentally determined structure and density functional theory calculations find ι-N2 to have the lowest enthalpy of the molecular nitrogen polymorphs that exist between 30 and 60 GPa. The results demonstrate that very complex structures, similar to those previously only observed in metallic elements, can become energetically favourable in molecular systems at extreme pressures and temperatures.