Evolutionary Structure Prediction Research Articles

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.

Ordered structures in III-Nitride ternary alloys

An efficient evolutionary structure prediction algorithm in combination with ab initio calculations is implemented in order to reveal energetically favorable superstructures of the III-Nitride ternary alloys. Several 2×2×2 32-atom supercells are used to explore the full range of concentrations, from x=0 to 1. The formation enthalpies, bandgaps, clustering and/or ordering of the atoms are investigated and the results are discussed.The formation enthalpy plots show local minima at specific concentrations, namely for x=0.25, 0.50 and 0.75, that correspond to ordered structures. The valance band maxima, conduction band minima, bandgaps and the composition-independent bowing parameters for 2nd order Vegard’s equation are calculated. The bandgap deviations from 1st order Vegard’s law show total maxima at specific concentrations. The formation enthalpies and the bandgaps cannot be accurately described by single composition-independent bowing parameters, but the bandgaps are sufficiently described by composition-dependent bowing parameters, that are established.In order to verify the rationality of the results against the size of the ab initio supercells, molecular dynamics calculations of 14×14×14 supercells of ∼104atoms using bond-order interatomic potentials are performed. The obtained local minima of the formation enthalpy for the specific alloy compositions concur with those predicted by ab initio calculations proving the results are not influenced by the supercell size.

Investigation of exotic stable calcium carbides using theory and experiment.

It is well known that pressure causes profound changes in the properties of atoms and chemical bonding, leading to the formation of many unusual materials. Here we systematically explore all stable calcium carbides at pressures from ambient to 100 GPa using variable-composition evolutionary structure predictions using the USPEX code. We find that Ca5C2, Ca2C, Ca3C2, CaC, Ca2C3 and CaC2 have stability fields on the phase diagram. Among these, Ca2C and Ca2C3 are successfully synthesized for the first time via high-pressure experiments with excellent structural correspondence to theoretical predictions. Of particular significance is the base-centred monoclinic phase (space group C2/m) of Ca2C, a quasi-two-dimensional metal with layers of negatively charged calcium atoms, and the primitive monoclinic phase (space group P21/c) of CaC with zigzag C4 groups. Interestingly, strong interstitial charge localization is found in the structure of R-3m-Ca5C2 with semi-metallic behaviour.

Computational Materials design by Evolutionary Structure Prediction

Crystal structure prediction (CSP) has been viewed as a major challenge in condensed matter science for a long time. Until recently, we developed a USPEX method based on evolutionary algorithms, and it proved to be a powerful tool enabling accurate and reliable prediction of structures from the beginning. How does it work - and why? In this lecture, I will summarize the principles, recent developments, and some applications of the USPEX code. 1) Optimizing chemical compositional space for compounds and co-crystals. A scheme is proposed to allow the automatic search for all the stable compounds with variation of chemical compositions. This function can be applied to study binary/ternary systems composed of both atomic/molecular blocks (Na-Cl, Mg-O, CaCl2-H2O, etc) [1]. 2) Predicting structures containing complex inorganic/organic molecular motifs. We designed a constrained evolutionary algorithm [2]. The key feature of this new approach is that each motif is treated as a building block which significantly reduces the search space. This method has been applied to a wide range of systems including inorganic complex, small molecular crystals, pharmaceuticals and even polymers crystals. 3) Predicting low dimensional system is different from predicting the bulk crystals. Surface brings another independent thermodynamic parameter, chemical potential. Since the stability of surface configuration depends on the chemical potential, the established phase diagram for multi-component system is quite different from that of bulk crystals [3].

Synthesis of β-Mg(2)C(3): a monoclinic high-pressure polymorph of magnesium sesquicarbide.

A new monoclinic variation of Mg2C3 was synthesized from the elements under high-pressure (HP), high-temperature (HT) conditions. Formation of the new compound, which can be recovered to ambient conditions, was observed in situ using X-ray diffraction with synchrotron radiation. The structural solution was achieved by utilizing accurate theoretical results obtained from ab initio evolutionary structure prediction algorithm USPEX. Like the previously known orthorhombic Pnnm structure (α-Mg2C3), the new monoclinic C2/m structure (β-Mg2C3) contains linear C3(4-) chains that are isoelectronic with CO2. Unlike α-Mg2C3, which contains alternating layers of C3(4-) chains oriented in opposite directions, all C3(4-) chains within β-Mg2C3 are nearly aligned along the crystallographic c-axis. Hydrolysis of β-Mg2C3 yields C3H4, as detected by mass spectrometry, while Raman and NMR measurements show clear C═C stretching near 1200 cm(-1) and (13)C resonances confirming the presence of the rare allylenide anion.

Tuning the crystal structure and electronic states ofAg2Se: Structural transitions and metallization under pressure

We performed synchrotron x-ray diffraction and infrared (IR) experiments combined with evolutionary structure predictions and band structure calculations on ${\text{Ag}}_{2}\text{Se}$ to \ensuremath{\sim}20 GPa. We present evidence for phase I (\ensuremath{\beta}-${\text{Ag}}_{2}\text{Se}$) as a potential three-dimensional topological insulator by its increase in optical band gap and the topologically nontrivial nature of its band structure. Higher pressures induce a triple-layer stacking pattern and significantly increase the crystallographic inequivalence of the two Ag sites, where $P$2${}_{1}$2${}_{1}$2${}_{1}$ phase I first reconstructs into a Pnma phase II, and then transforms into a topologically different Cmcm phase III. The radical changes in IR spectra and electronic band structures indicate the metallic nature of the high-pressure phases. Our results highlight the effects of pressure in tuning the crystal structure and electronic states of ${\text{Ag}}_{2}\text{Se}$.

A metallic carbon consisting of helical carbon triangle chains

Carbon is the basis of life on Earth and many technological applications. We computationally report an sp3-hybridization-assembled carbon allotrope constructed by helical triangle chains through the evolutionary structure prediction method. Different from the previous metallic carbon K4, this carbon, called Tri-carbon, is mechanically and dynamically stable at ambient pressure. High ring strain in the carbon triangle blocks forces the C–C bond in Tri-carbon to be a ‘bent bond’, rather than the common single bond in diamond or the π bond in graphite. Unlike the unstrained sp3-hybridization in semiconductive diamond, valence electrons in the ‘bent bond’ are recombined to form extremely anisotropic sp3-hybridized bonds, thus conferring metallicity to Tri-carbon. Under nonhydrostatic conditions, Tri-carbon shows significantly anisotropic ideal tensile and compressive strength. Tri-carbon is expected to be achieved through chemical methods, such as the synthesis of cyclopropane derivatives (e.g. triangulane and tetrahedrane). These methods eliminate the restriction of ultra-high pressure to obtain metallic carbons.

New developments in evolutionary structure prediction algorithm USPEX

We present new developments of the evolutionary algorithm USPEX for crystal structure prediction and its adaptation to cluster structure prediction. We show how to generate randomly symmetric structures, and how to introduce ‘smart’ variation operators, learning about preferable local environments. These and other developments substantially improve the efficiency of the algorithm and allow reliable prediction of structures with up to ∼200 atoms in the unit cell. We show that an advanced version of the Particle Swarm Optimization (PSO) can be created on the basis of our method, but PSO is strongly outperformed by USPEX. We also show how ideas from metadynamics can be used in the context of evolutionary structure prediction for escaping from local minima. Our cluster structure prediction algorithm, using the ideas initially developed for crystals, also shows excellent performance and outperforms other state-of-the-art algorithms.

Pressure-induced structural transitions of LiNH2: A first-principle study

The pressure-induced phase transformations in LiNH2 have been studied by using ab initio total-energy calculations and evolutionary structure prediction simulations. Two stable high-pressure polymorphs of LiNH2 are found: β-LiNH2 (orthorhombic, NaNH2-type, Fddd) and γ-LiNH2 (orthorhombic, P21212). The β→γ structural transition occurs at 10.7GPa, which is in good agreement with experimental observation. Further analysis of the structural properties, charge density distribution, and calculated phonon density of states indicates that the possibility of the N–H⋯N hydrogen bond occurring in the high-pressure γ-LiNH2 is extremely high. The existence of hydrogen bond weakens the N–H polar covalent bonds within NH2 groups, which can facilitate the hydrogen desorption.

Fe–C and Fe–H systems at pressures of the Earth's inner core

The solid inner core of Earth is predominantly composed of iron alloyed with several percent Ni and some lighter elements, Si, S, O, H, and C being the prime candidates. To establish the chemical composition of the inner core, it is necessary to find the range of compositions that can explain its observed characteristics. Recently, there have been a growing number of papers investigating C and H as possible light elements in the core, but the results were contradictory. Here, using ab initio simulations, we study the Fe–C and Fe–H systems at inner core pressures (330–364 GPa). Based on the evolutionary structure prediction algorithm USPEX, we have determined the lowest-enthalpy structures of all possible carbides (FeC, Fe2C, Fe3C, Fe4C, FeC2, FeC3, FeC4, Fe7C3) and hydrides (Fe4H, Fe3H, Fe2H, FeH, FeH2, FeH3, FeH4) and have found that Fe2C (space group Pnma) is the most stable iron carbide at pressures of the inner core, while FeH, FeH3, and FeH4 are the most stable iron hydrides at these conditions. For Fe3C, the cementite structure (space group Pnma) and the Cmcm structure recently found by random sampling are less stable than the I-4 and C2/m structures predicted here. We have found that FeH3 and FeH4 adopt chemically interesting thermodynamically stable crystal structures, containing trivalent iron in both compounds. We find that the density of the inner core can be matched with a reasonable concentration of carbon, 11–15 mol.% (2.6–3.7 wt.%) at relevant pressures and temperatures, yielding the upper bound to the C content in the inner core. This concentration matches that in CI carbonaceous chondrites and corresponds to the average atomic mass in the range 49.3–51.0, in close agreement with inferences from Birch's law for the inner core. Similarly made estimates for the maximum hydrogen content are unrealistically high: 17–22 mol.% (0.4–0.5 wt.%), which corresponds to the average atomic mass of the core in the range 43.8–46.5. We conclude that carbon is a better candidate light alloying element than hydrogen.

Mechanical properties and chemical bonding of the Os–B system: A first-principles study

The mechanical properties of Os–B compounds containing different boron contents have been investigated systemically by first-principles calculations. Two previously unreported crystal structures of Os2B5 and OsB3, crystallizing in space groups R3m and P-6m2 respectively, are determined using the ab initio evolutionary structure prediction. The calculated elastic constants, bulk modulus, shear modulus, Young’s modulus, Poisson’s ratio, and hardness for Os–B compounds are in good agreement with the available experimental values. Our results show that the hardness of osmium borides increases with increasing boron content. Os2B5 and OsB3, with hardnesses of 34.4 and 36.9GPa respectively, can almost be considered as potential superhard materials. Further analyses on density of states, crystal orbital Hamilton population, and electron localization function demonstrate that the electronic structure of Os–B compounds is directly responsible for their particular mechanical properties. High hardness in Os2B5 and OsB3 is mainly attributed to the occurrence of strong B–B covalent bonds and the disappearance of some ductile Os–Os metallic bonds.

Theoretical Studies of High-Pressure Phases, Electronic Structure, and Vibrational Properties of NaNH2

Thermodynamically stable phases of sodium amide (NaNH2) at pressures up to 20 GPa have been determined using the ab initio evolutionary structure prediction. We find that the ground-state phase α-NaNH2 (orthorhombic, Fddd) first transforms into β-NaNH2 (orthorhombic, P21212) at 2.2 GPa; then, γ-NaNH2 (monoclinic, C2/c) becomes stable at 9.4 GPa. In addition to strong ionic bonding between Na+ and [NH2]− ions and covalent bonding between H and N in NH2 groups, the N–H···N hydrogen bonding between neighboring NH2 groups could not be ignored anymore in the high-pressure β-NaNH2, as suggested by the analysis of charge density distribution and structural and vibrational properties. The covalent N–H bonds in the high-pressure phase of NaNH2 are weakened by additional hydrogen bonding, which could be favorable for the hydrogen desorption.

Evolutionary structure prediction and electronic properties of indium oxide nanoclusters

Indium sesquioxide is widely used as a transparent conducting oxide in modern optoelectronic devices; the rising cost of indium has generated interest in the nanoscale properties of In(2)O(3), and questions arise as to the nature of its physicochemical properties below the bulk regime. We report the stable and metastable stoichiometric clusters of (In(2)O(3))(n), where n = 1-10, as predicted from an evolutionary search within the classical interatomic potential and quantum density functional energy landscapes. In contrast to the paradigm set by ZnO, which favours high symmetry bubble-like structures, the In(2)O(3) nanoclusters are found to tend towards dense, low symmetry structures approaching the bulk system at remarkably small molecular masses. Electronic characterisation is performed at the hybrid density functional and many-body GW levels to obtain accurate predictions of the spectroscopic properties, with mean values of the ionisation potentials and electron affinities calculated as 7.7 and 1.7 eV, respectively.

Ionic high-pressure form of elemental boron

Boron is an element of fascinating chemical complexity. Controversies have shrouded this element since its discovery was announced in 1808: the new 'element' turned out to be a compound containing less than 60-70% of boron, and it was not until 1909 that 99% pure boron was obtained. And although we now know of at least 16 polymorphs, the stable phase of boron is not yet experimentally established even at ambient conditions. Boron's complexities arise from frustration: situated between metals and insulators in the periodic table, boron has only three valence electrons, which would favour metallicity, but they are sufficiently localized that insulating states emerge. However, this subtle balance between metallic and insulating states is easily shifted by pressure, temperature and impurities. Here we report the results of high-pressure experiments and ab initio evolutionary crystal structure predictions that explore the structural stability of boron under pressure and, strikingly, reveal a partially ionic high-pressure boron phase. This new phase is stable between 19 and 89 GPa, can be quenched to ambient conditions, and has a hitherto unknown structure (space group Pnnm, 28 atoms in the unit cell) consisting of icosahedral B(12) clusters and B(2) pairs in a NaCl-type arrangement. We find that the ionicity of the phase affects its electronic bandgap, infrared adsorption and dielectric constants, and that it arises from the different electronic properties of the B(2) pairs and B(12) clusters and the resultant charge transfer between them.

Evolutionary rate variation and RNA secondary structure prediction

Predicting RNA secondary structure using evolutionary history can be carried out by using an alignment of related RNA sequences with conserved structure. Accurately determining evolutionary substitution rates for base pairs and single stranded nucleotides is a concern for methods based on this type of approach. Determining these rates can be hard to do reliably without a large and accurate initial alignment, which ideally also has structural annotation. Hence, one must often apply rates extracted from other RNA families with trusted alignments and structures. Here, we investigate this problem by applying rates derived from tRNA and rRNA to the prediction of the much more rapidly evolving 5′-region of HIV-1. We find that the HIV-1 prediction is in agreement with experimental data, even though the relative evolutionary rate between A and G is significantly increased, both in stem and loop regions. In addition we obtained an alignment of the 5′ HIV-1 region that is more consistent with the structure than that currently in the database. We added randomized noise to the original values of the rates to investigate the stability of predictions to rate matrix deviations. We find that changes within a fairly large range still produce reliable predictions and conclude that using rates from a limited set of RNA sequences is valid over a broader range of sequences.