Ab Initio Structure Research Articles

Computationally Directed Discovery of MoBi2.

Incorporating bismuth, the heaviest element stable to radioactive decay, into new materials enables the creation of emergent properties such as permanent magnetism, superconductivity, and nontrivial topology. Understanding the factors that drive Bi reactivity is critical for the realization of these properties. Using pressure as a tunable synthetic vector, we can access unexplored regions of phase space to foster reactivity between elements that do not react under ambient conditions. Furthermore, combining computational and experimental methods for materials discovery at high-pressures provides broader insight into the thermodynamic landscape than can be achieved through experiment alone, informing our understanding of the dominant chemical factors governing structure formation. Herein, we report our combined computational and experimental exploration of the Mo-Bi system, for which no binary intermetallic structures were previously known. Using the ab initio random structure searching (AIRSS) approach, we identified multiple synthetic targets between 0-50 GPa. High-pressure in situ powder X-ray diffraction experiments performed in diamond anvil cells confirmed that Mo-Bi mixtures exhibit rich chemistry upon the application of pressure, including experimental realization of the computationally predicted CuAl2-type MoBi2 structure at 35.8(5) GPa. Electronic structure and phonon dispersion calculations on MoBi2 revealed a correlation between valence electron count and bonding in high-pressure transition metal-Bi structures as well as identified two dynamically stable ambient pressure polymorphs. Our study demonstrates the power of the combined computational-experimental approach in capturing high-pressure reactivity for efficient materials discovery.

A putative origin of the insect chemosensory receptor superfamily in the last common eukaryotic ancestor.

The insect chemosensory repertoires of Odorant Receptors (ORs) and Gustatory Receptors (GRs) together represent one of the largest families of ligand-gated ion channels. Previous analyses have identified homologous 'Gustatory Receptor-Like' (GRL) proteins across Animalia, but the evolutionary origin of this novel class of ion channels is unknown. We describe a survey of unicellular eukaryotic genomes for GRLs, identifying several candidates in fungi, protists and algae that contain many structural features characteristic of animal GRLs. The existence of these proteins in unicellular eukaryotes, together with ab initio protein structure predictions, provide evidence for homology between GRLs and a family of uncharacterized plant proteins containing the DUF3537 domain. Together, our analyses suggest an origin of this protein superfamily in the last common eukaryotic ancestor.

Ab initio structure determination and morphology study of La1.26 Zr0.25 Na2.5 N0.24 O2.54 triclinic structure from powder x-ray diffraction data.

Ab initio structure determination and morphology study of La1.26 Zr0.25 Na2.5 N0.24 O2.54 triclinic structure from powder x-ray diffraction data.

Ab initio structure determination and morphology study of La1.26 Zr0.25 Na2.5 N0.24 O2.54 triclinic structure from powder x-ray diffraction data.

This paper deals with the ab initio structure determination of La1.26 N0.24 Na2.5 O2.54 Zr0.25 triclinic structure having triclinic crystal system via powder X-ray data using the Rietveld refinement method, and with physical properties characterization of a related solid solution at the room temperature structure of three compounds belonging to the Aurivillius family La1.26 N0.24 Na2.5 O2.54 Zr0.25 has been analyzed. La1.26 N0.24 Na2.5 O2.54 Zr0.25 crystallizes in a triclinic crystal system with P-1 space group. The starting material was Na2CO3,Zr(NO3)4 La2O3 for the Zr,La and Na analogues was derived from ab initio methods and refined using the Rietveld refinement method using JANA software package and visualization by Diamond computer program. The cations Na and La are disordered over the Zr sites while the La cation is found exclusively in the layers. The cell parameters are a=4.1040 Å b=9.9102 Å c=17.6117 Å α=98.4299° β=93.4378° γ=92.2041°.The morphology and electrical properties are carried out of cited oxide.

Nuclear spin-dependent parity-violating effects in light polyatomic molecules

Measurements of nuclear spin-dependent parity-violating (NSD-PV) effects provide an excellent opportunity to test nuclear models and to search for physics beyond the Standard Model. Molecules possess closely-spaced states with opposite parity which may be easily tuned to degeneracy to greatly enhance the observed parity-violating effects. A high-sensitivity measurement of NSD-PV effects using light triatomic molecules is in preparation [E. B. Norrgard, et al., Commun. Phys. 2, 77 (2019)]. Importantly, by comparing these measurements in light nuclei with prior and ongoing measurements in heavier systems, the contribution to NSD-PV from $Z^0$-boson exchange between the electrons and the nuclei may be separated from the contribution of the nuclear anapole moment. Furthermore, light triatomic molecules offer the possibility to search for new particles, such as the postulated $Z^{\prime}$ boson. In this work, we detail a sensitive measurement scheme and present high-accuracy molecular and nuclear calculations needed for interpretation of NSD-PV experiments on triatomic molecules composed of light elements Be, Mg, N, and C. The ab initio nuclear structure calculations, performed within the No-Core Shell Model (NCSM) provide a reliable prediction of the magnitude of different contributions to the NSD-PV effects in the four nuclei. These results differ significantly from the predictions of the standard single-particle model and highlight the importance of including many-body effects in such calculations. In order to extract the NSD-PV contributions from measurements, a parity-violating interaction parameter $W_{\text{PV}}$, which depends on molecular structure, needs to be known with high accuracy. We have calculated these parameters for the triatomic molecules of interest using the relativistic coupled-cluster approach.

Electronic band structure of semiconductor alloys: From ab initio to k[formula omitted]p via computational alchemy, on example of [formula omitted] alloy

First principles calculations are increasingly often used in device modelling. However, due to their complexity and high computational costs, simplified but reliable models are of great value. In this work, we present an original method of finding the 30-band k·p parameters on an example of Ge1-xSnx alloy. It allows to reproduce the electronic band structure in the full BZ and in the full composition range. The method uses the state-of-the-art supercell based ab initio calculations as the reference. A direct fitting of the k·p parameters from ab initio supercell band structures is difficult since the assignment of the k·p bands to correct eigenvalues of the reference band structures may be ambiguous. For this reason, the ab initio computational alchemy is used as an intermediate step. Owing to its properties, the supercell unfolded eigenvalues are approximated with continuous curves, which enables a straigthforward way to fit the 30-band k·p parameters. As an example of application, the optical gain in bulk Ge0.91Sn0.09 has been calculated. The advantage of using the 30-band over the often used 8-band k·p approach is clearly seen. The presented method can be applied to any mixed, isovalent and isostructural system, eg. III-V, or II-VI alloys.

Ab initio based description of the unusual increase of the electric field gradient with temperature at Ti sites in rutile TiO2

Combining a precise ab initio electron band structure calculation of the TiO2 rutile structure with the temperature evolution of the Ti mean-square displacements, we reproduce a puzzling temperature increase of the electric field gradient at Ti sites in TiO2, observed experimentally. Our method employs a procedure of averaging two quadrupole electron density components (L = 2) inside a sphere vibrating with the Ti nucleus at its center, where the key factor introducing the temperature dependence is the square root of the Debye-Waller factor. Although the Debye-Waller factor always reduces the corresponding Fourier component, in TiO2 due to the interplay between terms of opposite signs, it results in a net increase of the whole sum with temperature, leading to the growth of the electric field gradient. Quantitatively, we find that the increase of electric field gradient is only half of the experimental value, which we ascribe to anharmonic effects or a strong oxygen position influence. In addition, our method reproduces the unusual temperature dependence of the asymmetry parameter eta, which first decreases with temperature, goes to zero and then increases.

Magnetic Interactions in ZnMnO3: Active Role of Zn 3d10 Orbitals, in Comparison with MgMnO3.

The ilmenite-type MgMnO3 and ZnMnO3 with honeycomb Mn layers exhibit distinctive magnetic ground states. In experiments, MgMnO3 exhibits a Néel antiferromagnetic alignment, in which both nearest-neighbor (NN) J1 and next-nearest-neighbor (NNN) J2 exchange interactions are antiferromagnetic, while ZnMnO3 has zigzag antiferromagnetic ordering with NN ferromagnetic and NNN antiferromagnetic coupling. On the basis of ab initio band structure calculations, we explain the deviation of NN J1 exchange coupling from antiferromagnetic (MgMnO3) to ferromagnetic (ZnMnO3) as originating from the intensive hybridization between the occupied Zn 3d10 orbitals with those of the bridging O 2p states, strongly depending on the position of the orbitals. In addition, our results indicate that, in combination with the NN J1 coupling, the considerably large third-nearest-neighbor (TNN) J3 exchange interaction plays an important role in erecting the magnetic ground states, rather than the experimentally proposed NNN J2. Furthermore, our findings highlight the important role of not only the electronic configurations but also the positions of the nonmagnetic cations in determining the essence of the magnetic exchange interactions. Therefore, the hybridization effect of nonmagnetic cations should not be dismissed in an analysis of the magnetic properties of transition-metal oxides.

MAISE: Construction of neural network interatomic models and evolutionary structure optimization

Module for ab initio structure evolution (MAISE) is an open-source package for materials modeling and prediction. The code’s main feature is an automated generation of neural network (NN) interatomic potentials for use in global structure searches. The systematic construction of Behler–Parrinello-type NN models approximating ab initio energy and forces relies on two approaches introduced in our recent studies. An evolutionary sampling scheme for generating reference structures improves the NNs’ mapping of regions visited in unconstrained searches, while a stratified training approach enables the creation of standardized NN models for multiple elements. A more flexible NN architecture proposed here expands the applicability of the stratified scheme for an arbitrary number of elements. The full workflow in the NN development is managed with a customizable ‘MAISE-NET’ wrapper written in Python. The global structure optimization capability in MAISE is based on an evolutionary algorithm applicable for nanoparticles, films, and bulk crystals. A multitribe extension of the algorithm allows for an efficient simultaneous optimization of nanoparticles in a given size range. Implemented structure analysis functions include fingerprinting with radial distribution functions and finding space groups with the SPGLIB tool. This work overviews MAISE’s available features, constructed models, and confirmed predictions. Program summaryProgram Title: MAISECPC Library link to program files:https://doi.org/10.17632/vfzgt2gnsh.1Licensing provisions: GNU General Public License v3.0Programming language: CNature of problem: Construction of NN interatomic potentials suitable for evolutionary structure searches, molecular dynamics, phonon calculations, and other applications presents a host of challenges ranging from sampling relevant parts of vast configuration spaces to tuning multitudes of NN parameters.Solution method: Evolutionary data generation and modular NN training algorithms featured in the open-source parallelized MAISE package enable automated development of NN models for multiple chemical species. Customizable MAISE-NET wrapper streamlines all stages of the iterative process.Unusual features: NN training stratification allows one to build libraries of reusable models from the bottom up, starting from elements and proceeding to multielement chemical systems. A multitribe evolutionary algorithm improves the efficiency of ground state structure searches by simultaneously optimizing nanoparticles of different sizes and periodically exchanging best motifs between the tribes.

Properties of Alkaline-Earth-Metal Polynitrogen Ternary Materials at High Pressure.

We report the formation of cubic and tetragonal BaSrN3 at 100 GPa using an ab initio structure search method. Pressure ramping to 0 GPa reveals a reaction pressure threshold of 4.92 and 7.23 GPa for the cubic and tetragonal BaSrN3, respectively. The cubic phase is stabilized by coulombic interaction between the ions. Meanwhile, tetragonal BaSrN3 is stabilized through an expansion of the d-orbital in Ba and Sr atoms that is compensated by delocalization of π-electrons in N through reduction of π overlap. Elastic properties analysis suggests that both phases are mechanically stable. The structures also have high melting points as predicted using an empirical model, and all imaginary modes vanishes at about 2000 K. These results have significant implication for the design of cleaner and environmentally friendly high energy density materials.

A Guided Tour of ab initio Nuclear Many-Body Theory

Over the last decade, new developments in Similarity Renormalization Group techniques and nuclear many-body methods have dramatically increased the capabilities of ab initio nuclear structure and reaction theory. Ground and excited-state properties can be computed up to the tin region, and from the proton to the presumptive neutron drip lines, providing unprecedented opportunities to confront two- plus three-nucleon interactions from chiral Effective Field Theory with experimental data. In this contribution, I will give a broad survey of the current status of nuclear many-body approaches, and I will use selected results to discuss both achievements and open issues that need to be addressed in the coming decade.

Exotic silicon phases synthesized through ultrashort laser-induced microexplosion: Characterization with Raman microspectroscopy

Confined microexplosions induced in silicon by powerful ultrashort laser pulses can lead to new Si phases. Some of these have not previously been observed via near-equilibrium compression of silicon. In this study, confocal Raman micro-spectroscopy and Raman imaging of arrays of microexplosions have been conducted to search for Raman signatures of these novel allotropes of silicon. A microexplosion is generated at the interface between a thick silicon dioxide confinement layer and underlying silicon. It is characterised by a void at the interface above a region of compressed silicon. Raman data show a rich assembly of silicon phases within the modified silicon. Residual stresses up to 4.5 GPa in the modifications have been determined from the shift in the main diamond-cubic Si Raman peak. The computed Raman spectra for a number of Si allotropes show reasonable agreement with the experimental spectra. Two structurally similar tetragonal phases of silicon (the rhombohedral r8 and the body-centred bc8) phases as well as recently identified bt8-Si are all highly likely to be contained in Raman spectra from many laser-modified sites. Although the st12-Si phase, previously observed in our electron diffraction studies of the highly compressively stressed laser-modified regions, was not reliably identified from Raman data, we suggest this could be due to the possible difference in residual stress level in the sites analysed by the electron diffraction and Raman spectra. Several other unidentified Raman peaks were observed, suggesting the presence of other unknown silicon phases. All of these silicon phases are expected to have attractive semiconducting properties including narrow band gap that open up novel applications.

Synthesis and ab initio Determination of Bi1.25 V0.123 Ca 0.245 N1.24 O8 cubic structure via powder X-ray diffraction data

This paper deals with the ab initio structure determination of Bi1.25 V0.123 Ca 0.245 N1.24 O8 cubic structure from powder X-ray data using the Rietveld method, and with physical properties characterization of a related solid solution. Bi1.25 V0.123 Ca 0.245 N 1.24 O 8 obtained from the annealing of a quenched cubic high temperature of sample, is cubic crystal system and lattice a=14.1243 Å; Z =4. The structure refinement converged to Rp=0.018, R wp=0.0212 GOF=0.0102. The structure is built from cationic slabs parallel to (100) faces of the cubic cell. Each cell corresponds to one slab containing a mixed Bi1.25 V0.123 Ca 0.245 cationic layer (Bi(1)) sandwiched between two equivalent bismuth layers (Bi(2)). The cohesion of the cations in the slabs results from the presence of the oxygen atoms and nitrogen atoms distributed over three sites. Six O(1) and two O(2) atoms form a slightly distorted cubical polyhedron around the mixed cationic site (Bi(1)). (Bi(2)) atoms are surrounded by seven oxygen nitrogen atoms in a very distorted polyhedron. The important delocalization of (Bi(2)) lone pairs toward the integers spaces leads to significant bonds with the adjacent slabs and to the cohesion of the structure. Bi1.25 V0.123 Ca 0.245 O8 is the low symmetry variety of a particular sample of a wide solid solution domain that, formulated Bi1.25 V0.123 Ca0.245 O8, has been investigated. The formation of this phase from the irreversible transformation of quenched on heating and the subsequent transitions and non-transition metal oxides mixed valence have been evidenced by thermo diffractometry, conductivity measurements versus temperature, dilatometer, and thermal analyses. The morphological study was carried out by SEM.

DNSS2: Improved ab initio protein secondary structure prediction using advanced deep learning architectures

Accurate prediction of protein secondary structure (alpha-helix, beta-strand and coil) is a crucial step for protein inter-residue contact prediction and ab initio tertiary structure prediction. In a previous study, we developed a deep belief network-based protein secondary structure method (DNSS1) and successfully advanced the prediction accuracy beyond 80%. In this work, we developed multiple advanced deep learning architectures (DNSS2) to further improve secondary structure prediction. The major improvements over the DNSS1 method include (a) designing and integrating six advanced one-dimensional deep convolutional/recurrent/residual/memory/fractal/inception networks to predict 3-state and 8-state secondary structure, and (b) using more sensitive profile features inferred from Hidden Markov model (HMM) and multiple sequence alignment (MSA). Most of the deep learning architectures are novel for protein secondary structure prediction. DNSS2 was systematically benchmarked on independent test data sets with eight state-of-art tools and consistently ranked as one of the best methods. Particularly, DNSS2 was tested on the protein targets of 2018 CASP13 experiment and achieved the Q3 score of 81.62%, SOV score of 72.19%, and Q8 score of 73.28%. DNSS2 is freely available at: https://github.com/multicom-toolbox/DNSS2.

Twinning in Zr-Based Metal-Organic Framework Crystals

Ab initio structure determination of new metal-organic framework (MOF) compounds is generally done by single crystal X-ray diffraction, but this technique can yield incorrect crystal structures if crystal twinning is overlooked. Herein, the crystal structures of three Zirconium-based MOFs, that are especially prone to twinning, have been determined from twinned crystals. These twin laws (and others) could potentially occur in many MOFs or related network structures, and the methods and tools described herein to detect and treat twinning could be useful to resolve the structures of affected crystals. Our results highlight the prevalence (and sometimes inevitability) of twinning in certain Zr-MOFs. Of special importance are the works of Howard Flack which, in addition to fundamental advances in crystallography, provide accessible tools for inexperienced crystallographers to take twinning into account in structure elucidation.

Half-metallicity in [formula omitted] and V doped tin-carbide SnC

Electronic and magnetic properties of V and Mn doping SnC are investigated in this work. The ab-initio structure calculation based on the Korring-Kohn-Rostoker (KKR) method combined with the coherent potential approximation (CPA) have been used. We have found that the substitution of Sn atoms in Tin-Carbide by Mn and V Transition Metals brings a half-metallic ferromagnetic character with a double exchange mechanism. The partial moments of impurities in the compound varies slightly from 1.11 to 1.09 μB in V case and 3.56 to 3.5 μB for Mn case. While the polarization is found to be equal 100%, in both cases where the up-spins channel is conductive, while the down channel is insulating. Using the Vegard's law, we have determined the laticce parameter of the doping compounds as function of the impurities concentrations. Such features has a significant implications for the performance of spintronic instruments and boosts their magnetoresistance ability at an enormous rate. Hence, the critical temperature can be controlled by varying the concentration of impurities.

Electronic structure studies on single crystalline Nd2PdSi3, an exotic Nd-based intermetallic: evidence for Nd 4f hybridization

In the series R2PdSi3, Nd2PdSi3 is an anomalous compound in the sense that it exhibits ferromagnetic order unlike other members in this family. The magnetic ordering temperature is also unusually high compared to the expected value for a Nd-based system, assuming 4f localization. Here, we have studied the electronic structure of single crystalline Nd2PdSi3 employing high resolution photoemission spectroscopy and ab initio band structure calculations. Theoretical results obtained for the effective on-site Coulomb energy of 6 eV corroborate well with the experimental valence band spectra. While there is significant Pd 4d–Nd 4f hybridization, the states near the Fermi level are found to be dominated by hybridized Nd 4f–Si 3p states, which is possibly responsible for the ferromagnetism in Nd compound. Nd 3d core level spectrum exhibits multiple features manifesting strong final state effects due to electron correlation, charge transfer and collective excitations. These results serve as one of the rare demonstrations of hybridization of Nd 4f states with the conduction electrons possibly responsible for the exoticity of this compound.

Electron Diffraction on Flash-Frozen Cowlesite Reveals the Structure of the First Two-Dimensional Natural Zeolite.

Cowlesite, ideally Ca6Al12Si18O60·36H2O, is to date the only natural zeolite whose structure could not be determined by X-ray methods. In this paper, we present the ab initio structure determination of this mineral obtained by three-dimensional (3D) electron diffraction data collected from single-crystal domains of a few hundreds of nanometers. The structure of cowlesite consists of an alternation of rigid zeolitic layers and low-density interlayers supported by water and cations. This makes cowlesite the only two-dimensional (2D) zeolite known in nature. When cowlesite gets in contact with a transmission electron microscope vacuum, a phase transition to a conventional 3D zeolite framework occurs in few seconds. The original cowlesite structure could be preserved only by adopting a cryo-plunging sample preparation protocol usually employed for macromolecular samples. Such a protocol allows the investigation by 3D electron diffraction of very hydrated and very beam-sensitive inorganic materials, which were previously considered intractable by transmission electron microscopy crystallographic methods.

Ab initio construction of symmetry-adapted k·p Hamiltonians for the electronic structure of semiconductors

While $\mathbf{k}\ifmmode\cdot\else\textperiodcentered\fi{}\mathbf{p}$ Hamiltonians are frequently used for the description of electronic states in quantum nanostructures, a method is lacking to obtain them in their symmetrized form directly from ab initio band structure calculations of bulk material. We developed a method for obtaining the parameters and the symmetry-adapted form of the $\mathbf{k}\ifmmode\cdot\else\textperiodcentered\fi{}\mathbf{p}$ Hamiltonian from the output of an ab initio band structure calculation. The method consists of (i) evaluation of momentum matrix elements between the wave functions obtained from band structure calculation; (ii) identification of the unitary transformation that transforms these wave functions to the symmetry-adapted basis; (iii) transformation of the $\mathbf{k}\ifmmode\cdot\else\textperiodcentered\fi{}\mathbf{p}$ Hamiltonian to the symmetry-adapted basis. We illustrate the methodology by obtaining $\mathbf{k}\ifmmode\cdot\else\textperiodcentered\fi{}\mathbf{p}$ Hamiltonians that describe the band structure of zinc-blende CdSe and then we use the Hamiltonians obtained to calculate the electronic states in CdSe quantum wells. Excellent agreement between density functional theory and $\mathbf{k}\ifmmode\cdot\else\textperiodcentered\fi{}\mathbf{p}$ is obtained for the electronic structure, even for quite thin wells.

Influence of anisotropy, tilt and pairing of Weyl nodes: the Weyl semimetals TaAs, TaP, NbAs and NbP

By means of ab initio band structure methods and model Hamiltonians we investigate the electronic, spin and topological properties of four monopnictides crystallizing in bct structure. We show that the Weyl bands around a WP W1 or W2 possess a strong anisotropy and tilt of the accompanying Dirac cones. These effects are larger for W2 nodes than for W1 ones. The node tilts and positions in energy space significantly influence the DOS of single-particle Weyl excitations. The node anisotropies destroy the conventional picture of (anti)parallel spin and wave vector of a Weyl fermion. This also holds for the Berry curvature around a node, while the monopole charges are independent as integrated quantities. The pairing of the nodes strongly modifies the spin texture and the Berry curvature for wave vectors in between the two nodes. Spin components may change their orientation. Integrals over planes perpendicular to the connection line yield finite Zak phases and winding numbers for planes between the two nodes, thereby indicating the topological character.Graphical abstract