Computational prediction of new magnetic materials.

The discovery of new magnetic materials is a big challenge in the field of modern materials science. We report the development of a new extension of the evolutionary algorithm USPEX, enabling the search for half-metals (materials that are metallic only in one spin channel) and hard magnetic materials. First, we enabled the simultaneous optimization of stoichiometries, crystal structures, and magnetic structures of stable phases. Second, we developed a new fitness function for half-metallic materials that can be used for predicting half-metals through an evolutionary algorithm. We used this extended technique to predict new, potentially hard magnets and rediscover known half-metals. In total, we report five promising hard magnets with high energy product (|BH|MAX), anisotropy field (Ha), and magnetic hardness (κ) and a few half-metal phases in the Cr-O system. A comparison of our predictions with experimental results, including the synthesis of a newly predicted antiferromagnetic material (WMnB2), shows the robustness of our technique.

Programmable nano-reactors for stochastic sensing.

Chemical reactions of single molecules, caused by rapid formation or breaking of chemical bonds, are difficult to observe even with state-of-the-art instruments. A biological nanopore can be engineered into a single molecule reactor, capable of detecting the binding of a monatomic ion or the transient appearance of chemical intermediates. Pore engineering of this type is however technically challenging, which has significantly restricted further development of this technique. We propose a versatile strategy, "programmable nano-reactors for stochastic sensing" (PNRSS), by which a variety of single molecule reactions of hydrogen peroxide, metal ions, ethylene glycol, glycerol, lactic acid, vitamins, catecholamines or nucleoside analogues can be observed directly. PNRSS presents a refined sensing resolution which can be further enhanced by an artificial intelligence algorithm. Remdesivir, a nucleoside analogue and an investigational anti-viral drug used to treat COVID-19, can be distinguished from its active triphosphate form by PNRSS, suggesting applications in pharmacokinetics or drug screening.

Correction: The stability and unexpected chemistry of oxide clusters.

Correction for 'The stability and unexpected chemistry of oxide clusters' by Xiaohu Yu et al., Phys. Chem. Chem. Phys., 2018, 20, 30437-30444.

The stability and unexpected chemistry of oxide clusters.

Using evolutionary structure prediction and ab initio thermodynamics, we determine stable compositions and structures of small CemOn and FemOn clusters at realistic temperatures and oxygen pressures. We use second energy differences as the criterion determining clusters of particular stability ("magic" clusters), whereas HOMO-LUMO gaps are used to gauge chemical inertness - i.e. the ability of a cluster to survive in a complex chemical environment. We find that, similar to atomic nuclei (which are clusters made of neutrons and protons), compositional space of two-component clusters also has ridges and islands of stability, surrounded by sea of instability. Long ridges of stability correspond to stoichiometric compositions - e.g., (CeO2)k, (Ce2O3)k, (FeO)k, (Fe2O3)k and (Fe3O4)k series of clusters, while "islands of stability" can have very unexpected compositions. For example, at room temperature and ambient atmosphere, superoxidized Fe4O8 clusters will be dominant among the Fe4On clusters. We emphasize that stability is dictated not only by closed geometric and electronic shells, but also by magnetism.

Mechanism of the fcc-to-hcp phase transformation in solid Ar.

We present an atomistic description of the fcc-to-hcp transformation mechanism in solid argon (Ar) obtained from transition path sampling molecular dynamics simulation. The phase transition pathways collected during the sampling for an 8000-particle system reveal three transition types according to the lattice deformation and relaxation details. In all three transition types, we see a critical accumulation of defects and uniform growth of a less ordered transition state, followed by a homogeneous growth of an ordered phase. Stacking disorder is discussed to describe the transition process and the cooperative motions of atoms in {111} planes. We investigate nucleation with a larger system: in a system of 18 000 particles, the collective movements of atoms required for this transition are facilitated by the formation and growth of stacking faults. However, the enthalpy barrier is still far beyond the thermal fluctuation. The high barrier explains previous experimental observations of the inaccessibility of the bulk transition at low pressure and its sluggishness even at extremely high pressure. The transition mechanism in bulk Ar is different from Ar nanoclusters as the orthorhombic intermediate structure proposed for the latter is not observed in any of our simulations.

A stable compound of helium and sodium at high pressure.

Helium is generally understood to be chemically inert and this is due to its extremely stable closed-shell electronic configuration, zero electron affinity and an unsurpassed ionization potential. It is not known to form thermodynamically stable compounds, except a few inclusion compounds. Here, using the ab initio evolutionary algorithm USPEX and subsequent high-pressure synthesis in a diamond anvil cell, we report the discovery of a thermodynamically stable compound of helium and sodium, Na2He, which has a fluorite-type structure and is stable at pressures >113 GPa. We show that the presence of He atoms causes strong electron localization and makes this material insulating. This phase is an electride, with electron pairs localized in interstices, forming eight-centre two-electron bonds within empty Na8 cubes. We also predict the existence of Na2HeO with a similar structure at pressures above 15 GPa.

Diverse Chemistry of Stable Hydronitrogens, and Implications for Planetary and Materials Sciences.

Nitrogen hydrides, e.g., ammonia (NH3), hydrazine (N2H4) and hydrazoic acid (HN3), are compounds of great fundamental and applied importance. Their high-pressure behavior is important because of their abundance in giant planets and because of the hopes of discovering high-energy-density materials. Here, we have performed a systematic investigation on the structural stability of N-H system in a pressure range up to 800 GPa through evolutionary structure prediction. Surprisingly, we found that high pressure stabilizes a series of previously unreported compounds with peculiar structural and electronic properties, such as the N4H, N3H, N2H and NH phases composed of nitrogen backbones, the N9H4 phase containing two-dimensional metallic nitrogen planes and novel N8H, NH2, N3H7, NH4 and NH5 molecular phases. Another surprise is that NH3 becomes thermodynamically unstable above ~460 GPa. We found that high-pressure chemistry of hydronitrogens is much more diverse than hydrocarbon chemistry at normal conditions, leading to expectations that N-H-O and N-H-O-S systems under pressure are likely to possess richer chemistry than the known organic chemistry. This, in turn, opens a possibility of nitrogen-based life at high pressure. The predicted phase diagram of the N-H system also provides a reference for synthesis of high-energy-density materials.

Combined Theoretical and in Situ Scattering Strategies for Optimized Discovery and Recovery of High-Pressure Phases: A Case Study of the GaN-Nb2O5 System.

The application of pressure in solid-state synthesis provides a route for the creation of new and exciting materials. However, the onerous nature of high-pressure techniques limits their utility in materials discovery. The systematic search for novel oxynitrides-semiconductors for photocatalytic overall water splitting-is a representative case where quench high-pressure synthesis is useful and necessary in order to obtain target compounds. We utilize state of the art crystal structure prediction theory (USPEX) and in situ synchrotron-based X-ray scattering to speed up the discovery and optimization of novel compounds using high-pressure synthesis. Using this approach, two novel oxynitride phases were discovered in the GaN-Nb2O5 system. The (Nb2O5)0.84:(NbO2)0.32:(GaN)0.82 rutile structured phase was formed at 1 GPa and 900 °C and gradually transformed to a α-PbO2-related structure above 2.8 GPa and 1000 °C. The low-pressure rutile type phase was found to have a direct optical band gap of 0.84 eV and an indirect gap of 0.51 eV.

Antiferromagnetic Stabilization in the Ti8O12 Cluster.

Using the evolutionary algorithm USPEX and DFT+U calculations, we predicted a high-symmetry geometric structure of the bare Ti8 O12 cluster composed of 8 Ti atoms forming a cube, in which O atoms are at midpoints of all of its edges, in excellent agreement with experimental results. Using natural bond orbital analysis, adaptive natural density partitioning algorithm, electron localization function, and partial charge plots, we find the origin of the particular stability of bare Ti8 O12 cluster: unique chemical bonding where eight electrons of Ti atoms interacting with each other in antiferromagnetic fashion to lower the total energy of the system. The bare Ti8 O12 is thus an unusual molecule stabilized by d-orbital antiferromagnetic coupling.

Novel superhard B-C-O phases predicted from first principles.

We explored the B-C-O system at pressures in the range 0-50 GPa by ab initio variable-composition evolutionary simulations in the hope of discovering new stable superhard materials. A new tetragonal thermodynamically stable phase B4CO4, space group I4[combining macron], and two low-enthalpy metastable compounds (B6C2O5, B2CO2) have been discovered. Computed phonons and elastic constants show that these structures are dynamically and mechanically stable both at high pressure and zero pressure. B4CO4 is thermodynamically stable at pressures above 23 GPa, but should remain metastable under ambient conditions. Its computed hardness is about 38-41 GPa, which suggests that B4CO4 is potentially superhard.

Nitrogen oxides under pressure: stability, ionization, polymerization, and superconductivity.

Nitrogen oxides are textbook class of molecular compounds, with extensive industrial applications. Nitrogen and oxygen are also among the most abundant elements in the universe. We explore the N-O system at 0 K and up to 500 GPa though ab initio evolutionary simulations. Results show that two phase transformations of stable molecular NO2 occur at 7 and 64 GPa, and followed by decomposition of NO2 at 91 GPa. All of the NO(+)NO3(-) structures are found to be metastable at T = 0 K, so experimentally reported ionic NO(+)NO3(-) is either metastable or stabilized by temperature. N2O5 becomes stable at 9 GPa, and transforms from P-1 to C2/c structure at 51 GPa. NO becomes thermodynamically stable at 198 GPa. This polymeric phase is superconducting (Tc = 2.0 K) and contains a -N-N- backbone.

A novel phase of beryllium fluoride at high pressure.

A previously unknown thermodynamically stable high-pressure phase of BeF2 has been predicted using the evolutionary algorithm USPEX. This phase occurs in the pressure range 18-27 GPa. Its structure has C2/c space group symmetry and contains 18 atoms in the primitive unit cell. Given the analogy between BeF2 and SiO2, silica phases have been investigated as well, but the new phase has not been observed to be thermodynamically stable for this system. However, it is found to be metastable and to have comparable energy to the known metastable phases of SiO2, suggesting a possibility of its synthesis.

Backbone NxH compounds at high pressures.

Optical and synchrotron x-ray diffraction diamond anvil cell experiments have been combined with first-principles theoretical structure predictions to investigate mixtures of N2 and H2 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 N2, H2, 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.

The phase diagram and hardness of carbon nitrides.

Novel superhard materials, especially those with superior thermal and chemical stability, are needed to replace diamond. Carbon nitrides (C-N), which are likely to possess these characteristics and have even been expected to be harder than diamond, are excellent candidates. Here we report three new superhard and thermodynamically stable carbon nitride phases. Based on a systematic evolutionary structure searches, we report a complete phase diagram of the C-N system at 0-300 GPa and analyze the hardest metastable structures. Surprisingly, we find that at zero pressure, the earlier proposed graphitic-C3N4 structure () is dynamically unstable, and we find the lowest-energy structure based on s-triazine unit and s-heptazine unit.

Novel hydrogen hydrate structures under pressure.

Gas hydrates are systems of prime importance. In particular, hydrogen hydrates are potential materials of icy satellites and comets, and may be used for hydrogen storage. We explore the H2O-H2 system at pressures in the range 0-100 GPa with ab initio variable-composition evolutionary simulations. According to our calculation and previous experiments, the H2O-H2 system undergoes a series of transformations with pressure, and adopts the known open-network clathrate structures (sII, C0), dense "filled ice" structures (C1, C2) and two novel hydrate phases. One of these is based on the hexagonal ice framework and has the same H2O:H2 ratio (2:1) as the C0 phase at low pressures and similar enthalpy (we name this phase Ih-C0). The other newly predicted hydrate phase has a 1:2 H2O:H2 ratio and structure based on cubic ice. This phase (which we name C3) is predicted to be thermodynamically stable above 38 GPa when including van der Waals interactions and zero-point vibrational energy, and explains previously mysterious experimental X-ray diffraction and Raman measurements. This is the hydrogen-richest hydrate and this phase has a remarkable gravimetric density (18 wt.%) of easily extractable hydrogen.

Pressure-induced stabilization and insulator-superconductor transition of BH.

Diborane (B(2)H(6)), a high energy density material, was believed to be stable in a wide P, T interval. A systematic investigation of the B-H system using the ab initio variable-composition evolutionary simulations shows that boron monohydride (BH) is thermodynamically stable and can coexist with solid B, H(2), and B(2)H(6) in a wide pressure range above 50 GPa. B(2)H(6) becomes unstable and decomposes into the Ibam phase of BH and H(2) (C2/c) at 153 GPa. The semiconducting layered Ibam structure of BH at 168 GPa transforms into a metallic phase with space group P6/mmm and a 3D topology with strong B-B and B-H covalent bonds. The Ibam-P6/mmm transformation pathway suggests the possibility of obtaining the metastable Pbcm phase on cold decompression of the P6/mmm phase. The electron-phonon coupling calculations indicate that P6/mmm-BH is a phonon-mediated superconductor with a critical temperature of superconductivity (T(c)) of 14.1-21.4 K at 175 GPa.

An ab initio study on the transition paths from graphite to diamond under pressure.

We calculate and compare the transition paths from graphite to two types of diamond using the variable cell nudged elastic band method. For the phase transition from graphite to cubic diamond, we analyze in detail how the π bonds transit to the σ bonds in an electronic structure. Meanwhile, a new transition path with a lower energy barrier for the transformation from graphite to hexagonal diamond is discovered. The path has its own peculiar sp(2)-sp(3) bonding configurations, serving as a transition state. Further calculation suggests that the sp(2)-sp(3) transition state represents an expected general phenomenon for cold-compressed graphite.

FastUniq: a fast de novo duplicates removal tool for paired short reads.

The presence of duplicates introduced by PCR amplification is a major issue in paired short reads from next-generation sequencing platforms. These duplicates might have a serious impact on research applications, such as scaffolding in whole-genome sequencing and discovering large-scale genome variations, and are usually removed. We present FastUniq as a fast de novo tool for removal of duplicates in paired short reads. FastUniq identifies duplicates by comparing sequences between read pairs and does not require complete genome sequences as prerequisites. FastUniq is capable of simultaneously handling reads with different lengths and results in highly efficient running time, which increases linearly at an average speed of 87 million reads per 10 minutes. FastUniq is freely available at http://sourceforge.net/projects/fastuniq/.

First-principles determination of the structure of magnesium borohydride.

The energy landscape of Mg(BH(4))(2) under pressure is explored by ab initio evolutionary calculations. Two new tetragonal structures, with space groups P4 and I4(1)/acd, are predicted to be lower in enthalpy by 15.4 and 21.2 kJ/mol, respectively, than the earlier proposed P4(2)nm phase. We have simulated x-ray diffraction spectra, lattice dynamics, and equations of state of these phases. The density, volume contraction, bulk modulus, and simulated x-ray diffraction patterns of I4(1)/acd and P4 structures are in excellent agreement with the experimental results.