Ab Initio Structure Research Articles

Ab Initio Structure and Dynamics of Beryllium Monofluoride and Its Anion.

The accurate potential energy functions of beryllium monofluoride, BeF, and its anion, BeF-, have been determined from ab initio calculations using the coupled-cluster approach, up to the CCSDTQP level of approximation, in conjunction with the augmented correlation-consistent core-valence basis sets, aug-cc-pCVnZ, up to septuple-zeta quality. The vibration-rotation energy levels of the two species were predicted to near the "spectroscopic" accuracy. Changes in the electron density distribution upon formation of the Be-F chemical bond are discussed.

Equilibrium Structures of Propane and 2,2-Difluoropropane and Comparison with Other Two-Top Molecules

The Born–Oppenheimer ab initio equilibrium structures of propane (CH3)2CH2 and 2,2-difluoropropane (CH3)2CF2 were computed at the CCSD(T) level of theory using a basis set of quadruple zeta quality. The semiexperimental structure of propane was also determined from the ground state rotational constants corrected for rovibrational corrections calculated at the MP2 level of theory. Structural comparisons are made with other molecules and are discussed in terms of the quantum theory of atoms in molecules.

Signature of pressure-induced topological phase transition in ZrTe5

The layered van der Waals material ZrTe5 is known as a candidate topological insulator (TI), however its topological phase and the relation with other properties such as an apparent Dirac semimetallic state is still a subject of debate. We employ a semiclassical multicarrier transport (MCT) model to analyze the magnetotransport of ZrTe5 nanodevices at hydrostatic pressures up to 2 GPa. The temperature dependence of the MCT results between 10 and 300 K is assessed in the context of thermal activation, and we obtain the positions of conduction and valence band edges in the vicinity of the chemical potential. We find evidence of the closing and re-opening of the band gap with increasing pressure, which is consistent with a phase transition from weak to strong TI. This matches expectations from ab initio band structure calculations, as well as previous observations that CVT-grown ZrTe5 is a weak TI in ambient conditions.

The crystal structure of olanzapine form III.

The antipsychotic drug olanzapine is well known for its complex polymorphism. Although widely investigated, the crystal structure of one of its anhydrous polymorphs, form III, is still unknown. Its appearance, always in concomitance with forms II and I, and the impossibility of isolating it from that mixture, have prevented its structure determination so far. The scenario has changed with the emerging field of 3D electron diffraction (3D ED) and its great advantages in the characterization of polyphasic mixtures of nanosized crystals. In this study, we show how the application of 3D ED allows the ab initio structure determination and dynamical refinement of this elusive crystal structure that remained unknown for more than 20 years. Olanzapine form III is monoclinic and shows a similar but shifted packing with respect to form II. It is remarkably different from the lowest-energy structures predicted by the energy-minimization algorithms of crystal structure prediction.

Even-integer quantum Hall effect in an oxide caused by a hidden Rashba effect.

In the presence of a high magnetic field, quantum Hall systems usually host both even- and odd-integer quantized states because of lifted band degeneracies. Selective control of these quantized states is challenging but essential to understand the exotic ground states and manipulate the spin textures. Here we demonstrate the quantum Hall effect in Bi2O2Se thin films. In magnetic fields as high as 50 T, we observe only even-integer quantum Hall states, but there is no sign of odd-integer states. However, when reducing the thickness of the epitaxial Bi2O2Se film to one unit cell, we observe both odd- and even-integer states in this Janus (asymmetric) film grown on SrTiO3. By means of a Rashba bilayer model based on the ab initio band structures of Bi2O2Se thin films, we can ascribe the only even-integer states in thicker films to the hidden Rasbha effect, where the local inversion-symmetry breaking in two sectors of the [Bi2O2]2+ layer yields opposite Rashba spin polarizations, which compensate with each other. In the one-unit-cell Bi2O2Se film grown on SrTiO3, the asymmetry introduced by the top surface and bottom interface induces a net polar field. The resulting global Rashba effect lifts the band degeneracies present in the symmetric case of thicker films.

First-principle study of two-photon absorption in Fe3O4.

Utilizing the length gauge and the electron density operator, we calculate the two-photon absorption (2PA) coefficient of Fe3O4 based on a full ab initio band structure. The pure two-photon interband transitions and those modulated by intraband transitions have been separated explicitly to determine their impact on the 2PA spectrum. A single main absorption peak instead of two will present in the spectrum by including the hybridization of inter- and intra-band transitions, which can be identified easily in future experimental studies. In addition, we find that in almost the whole 2PA-active spectral range, circularly polarized light can be absorbed with a much lower threshold power than the linearly polarized one. But the linearly polarized light is more easily to be manipulated. One can control the magnitude and resonance frequency of the 2PA coefficient by simply adjusting the polarization angle of the incident light. Our findings will deepen the understanding of the 2PA phenomenon in Fe3O4 nanoparticles.

Clogauite, PbBi4Te4S3, a new member of the aleksite series

AbstractClogauite, ideally PbBi4Te4S3 is the new n = 1 member of the aleksite series, PbnBi4Te4Sn+2, where n is the homologue number. Clogauite is named from the type locality, the Clogau gold mine, Dolgellau Gold belt, Gwynedd, North Wales, United Kingdom. The mineral and name have been approved by the Commission on New Minerals, Nomenclature and Classification of the International Mineralogical Association (IMA2023–062). The aleksite series is an accretional homologous series in which each member is derived from the same 5-atom tetradymite archetype. Clogauite crystallises in the trigonal crystal system (space group: P$\bar{3}$m1, #164). Three distinct polytypes of clogauite are recognised, corresponding to identical chemistry but different layer sequences, expressed as (57), (5559) and (557.559), respectively, in reference to the number of atoms in individual layer sequences. These are clogauite-12H, a = 4.277(4) Å, c = 23.46(14) Å, V = 371.598 Å3 and Z = 1; clogauite-24H, a = 4.278(4) Å, c = 46.88(31) Å, V = 743.053 Å3 and Z = 2; and clogauite-36H, a = 4.278(4) Å, c = 70.36(32) Å, V = 1115.283 Å3 and Z = 3. Clogauite is opaque, with a pale grey colour in reflected light. Reflectance is higher than tetradymite or galena. Bireflectance and anisotropy are strong. Structural data were determined from measurement of atomic-scale HAADF STEM imaging showing the internal arrangement of component atoms and characteristic selected area electron diffraction patterns for each polytype. The structures were then further constrained from ab initio total energy calculations and structure relaxation using density functional theory (DFT) using the measured parameters as input data. The relaxed crystal structure for each polytype was modelled to generate crystallographic information files (cif). STEM and electron diffraction simulations based on the crystallographic information data obtained from the DFT calculations show an excellent match to the empirical measurements.

New Findings on the Crystal Polymorphism of Imepitoin.

Scientific and industrial reasons dictate the study of the solid state of imepitoin, a highly safe and tolerable anticonvulsant drug used in the therapy of epileptic dogs that was approved in the Europe Union in 2013. Our investigations allowed us to discover the existence of a new polymorph of imepitoin, which finds itself in a monotropic relationship with the crystalline form (polymorph I) already known and present on the market. This form (polymorph II), obtained by crystallization from xylene, remains metastable under ambient conditions for at least 1 year. Both solid forms were characterized by thermal (DSC and TGA), spectroscopic (FT-IR and Raman), microscopic (SEM and HSM), and diffractometric techniques. The thermodynamic relationship between the two polymorphs (monotropic) is such that it is not possible to study the melting of polymorph II, not even by adopting appropriate experimental strategies. Our measurements highlighted that the melting peak of imepitoin actually also includes an onset of melt decomposition. The ab initio structure solution, obtained from synchrotron X-ray powder diffraction data collected at room temperature, allowed us to determine the crystal structure of the new polymorph (II). It crystallizes in the monoclinic crystal structure, P21/c space group (#14), with a = 14.8687(6) Å, b = 7.2434(2) Å, c = 12.5592(4) Å, β = 107.5586(8)°, V = 1289.61(8) Å3, and Z = 4.

Towards heavy-mass ab initio nuclear structure: Open-shell Ca, Ni and Sn isotopes from Bogoliubov coupled-cluster theory

Recent developments in nuclear many-body theory enabled the description of open-shell medium-mass nuclei from first principles by exploiting the spontaneous breaking of symmetries within correlation expansion methods. Once combined with systematically improvable inter-nucleon interactions consistently derived from chiral effective field theory, modern ab initio nuclear structure calculations provide a powerful framework to deliver first-principle predictions accompanied with theoretical uncertainties. In this Letter, controlled ab initio Bogoliubov coupled cluster (BCC) calculations are performed for the first time, targeting the ground-state of all calcium, nickel and tin isotopes up to mass A≈180. While showing good agreement with available experimental data, the shell structure evolution in neutron-rich isotopes and the location of the neutron drip-lines are predicted. The BCC approach constitutes a key development towards reliable first-principles simulations of heavy-mass open-shell nuclei.

On the performance of composite schemes in determining equilibrium molecular structures.

Determination of equilibrium molecular structures is an essential ingredient in predicting spectroscopic parameters that help in identifying molecular carriers of microwave transitions. Here, the performance of two different ab initio composite approaches for obtaining equilibrium structures, "energy scheme" and "geometry scheme," is explored and compared to semi-experimental equilibrium structures. This study is performed for a set of 11 molecules which includes diatomics, linear triatomics, and a few non-linear molecules. The ab initio calculations were performed using three tiers of composite chemical recipes. The current results show that as the overall rigor of calculation is increased, the semi-experimental and the ab initio numbers agree to within 0.0003 Å for all molecules in the test set. The composite approach based on correcting the potential energy surface (energy scheme) and the one based on correcting the geometry directly (geometry scheme) show excellent agreement with each other. This work represents a step toward development of efficient and highly accurate procedures for computing ab initio equilibrium structures.

A comprehensive exploration of structural and electronic properties of molybdenum clusters

Molybdenum clusters, characterized by their unique structure and intriguing catalytic properties, have gained significant attention in recent years. In several existing studies, density functional theory (DFT) methods have been used to find the lowest energy Mo clusters and explore their electronic and magnetic structure. In all cases, with the exception of a single recent study, where a genetic algorithm was employed, initial geometries of the clusters, prior to geometry optimization, were chosen using heuristic approaches based on symmetry considerations and known structures. DFT calculations were performed using different types of pseudopotentials, from soft to hard, and different types of basis sets. However, no comprehensive study has yet been carried out in which a DFT method with the best control on its precision would be complemented by a reliable global minimum search method to find the lowest energy Mo clusters. In this work, we employ a combination of a plane wave-based DFT method and ab initio random structure searching technique to find the lowest energy clusters of up to 10 Mo atoms. In each case, the search has been performed for clusters with different spin multiplicities, which enabled us to explore their magnetic structure. The results are compared for both hard and soft pseudopotentials stressing the importance of treating more electrons explicitly, in agreement with some of the previous studies. For most of the low-energy magnetic structures found, we investigate the distribution of their spin densities, and for all low energy clusters, we confirm their stability by calculating their vibrational structure. For a few smallest clusters, the results of multiconfigurational quantum chemistry calculations are also discussed. Finally, free energies of the Mo clusters, within the quasi-harmonic approximation, are also calculated and discussed.

3D atomic structure from a single X-ray free electron laser pulse

X-ray Free Electron Lasers (XFEL) are cutting-edge pulsed x-ray sources, whose extraordinary pulse parameters promise to unlock unique applications. Several new methods have been developed at XFELs; however, no methods are known, which allow ab initio atomic level structure determination using only a single XFEL pulse. Here, we present experimental results, demonstrating the determination of the 3D atomic structure from data obtained during a single 25 fs XFEL pulse. Parallel measurement of hundreds of Bragg reflections was done by collecting Kossel line patterns of GaAs and GaP. To the best of our knowledge with these measurements, we reached the ultimate temporal limit of the x-ray structure solution possible today. These measurements open the way for obtaining crystalline structures during non-repeatable fast processes, such as structural transformations. For example, the atomic structure of matter at extremely non-ambient conditions or transient structures formed in irreversible physical, chemical, or biological processes may be captured in a single shot measurement during the transformation. It would also facilitate time resolved pump-probe structural studies making them significantly shorter than traditional serial crystallography.

TiO2 II: The high‐pressure Zr‐free srilankite endmember in impact rocks

AbstractTiO2II, a high‐pressure polymorph of titanium dioxide, is a diagnostic indicator of shock metamorphism in impact rocks. Due to its typical micro‐to‐nanometer scale, there are no ab initio structure solutions of natural TiO2II, thereby generating uncertainty about its crystal structure and its known similarity with srilankite (Ti0.67,Zr0.33)O2. Nanoscale electron diffraction investigation of TiO2II from the Australasian tektite strewn field provides the first ab initio structure solution revealing a primitive orthorhombic lattice with cell parameters a = 4.547 Å, b = 5.481 Å, c = 4.891 Å, and space group Pbcn, that is, the same as srilankite and scrutinyite α‐PbO2. The linear a and c decrease, and b increase with Ti content indicate TiO2II as Zr‐free srilankite endmember in the binary system ZrO2‐TiO2. Thereby the name srilankite should be used referring to TiO2II, according to the International Mineralogical Association recommendations. We provide the first evidence for a topotactic subsolidus rutile‐to‐TiO2II transition, founding their finely intermixing nanocrystals in the same TiO2 crystal, where TiO2II is within the crystal and surrounded by rutile in direct contact. They also show recurrent iso‐orientation, with TiO2II [100] parallel to rutile [100], TiO2II [010] parallel to rutile [011], and TiO2II [001] parallel to rutile (0–11). The rutile‐TiO2II iso‐orientation suggests the compression of rutile (0–11) planes as a possible transition mechanism from rutile to TiO2II, with a consequent shortening of ~0.5 Å per cell. The presence of TiO2II in the distal (~1200 km) impact ejecta from the Australasian tektite strewn field indicates shock pressures of ~12–15 GPa and post‐shock temperatures below 500°C followed by rapid quenching.

Candidate ferroelectrics via ab initio high-throughput screening of polar materials

Ferroelectrics are a class of polar and switchable functional materials with diverse applications, from microelectronics to energy conversion. Computational searches for new ferroelectric materials have been constrained by accurate prediction of the polarization and switchability with electric field, properties that, in principle, require a comparison with a nonpolar phase whose atomic-scale unit cell is continuously deformable from the polar ground state. For most polar materials, such a higher-symmetry nonpolar phase does not exist or is unknown. Here, we introduce a general high-throughput workflow that screens polar materials as potential ferroelectrics. We demonstrate our workflow on 1978 polar structures in the Materials Project database, for which we automatically generate a nonpolar reference structure using pseudosymmetries, and then compute the polarization difference and energy barrier between polar and nonpolar phases, comparing the predicted values to known ferroelectrics. Focusing on a subset of 182 potential ferroelectrics, we implement a systematic ranking strategy that prioritizes candidates with large polarization and small polar-nonpolar energy differences. To assess stability and synthesizability, we combine information including the computed formation energy above the convex hull, the Inorganic Crystal Structure Database id number, a previously reported machine learning-based synthesizability score, and ab initio phonon band structures. To distinguish between previously reported ferroelectrics, materials known for alternative applications, and lesser-known materials, we combine this ranking with a survey of the existing literature on these candidates through Google Scholar and Scopus databases, revealing ~130 promising materials uninvestigated as ferroelectric. Our workflow and large-scale high-throughput screening lays the groundwork for the discovery of novel ferroelectrics, revealing numerous candidates materials for future experimental and theoretical endeavors.

Prediction of BiS2-type pnictogen dichalcogenide monolayers for optoelectronics

In this work, we introduce a 2D materials family with chemical formula MX2 (M={As, Sb, Bi} and X={S, Se, Te}) having a rectangular 2D lattice. This materials family has been predicted by systematic ab-initio structure search calculations in two dimensions. Using density-functional theory and many-body perturbation theory, we study the structural, vibrational, electronic, optical, and excitonic properties of the predicted MX2 family. Our calculations reveal that the predicted SbX2 and BiX2 monolayers are stable while the AsX2 layers exhibit an in-plane ferroelectric instability. All materials display strong excitonic effects and good optical absorption within the infrared-to-visible range. Hence, these monolayers can harvest solar energy and serve in optoelectronics applications. Furthermore, our results indicate that exfoliation of the predicted MX2 monolayers from their bulk counterparts is experimentally viable.

Water-carbon disulfide dimers: observation of a new isomer and ab initio structure theory.

The weakly bound dimer water-carbon disulfide is studied by ab initio structure theory and high-resolution infrared spectroscopy. The calculations yield three stable minima in the potential energy surface, all planar. The most stable, isomer 1, was observed previously by microwave spectroscopy. It has C2v symmetry, an S-O bond, and a linear O-S-C-S backbone. Isomer 2, the next most stable, has not been considered previously by theory or experiment. It also has C2v symmetry, but with a side-by-side structure. Isomer 3, which is slightly less stable, is side-by-side with one O-H bond pointing toward an S atom. The first gas phase water-CS2 infrared spectra are reported. For isomer 1, H2O-, HDO-, and D2O-CS2 are observed in the CS2ν1 + ν3 region, H2O-CS2 in the H2O ν2 bend region, and D2O-CS2 in the D2O ν1 and ν3 stretch regions. The latter ν3 spectrum enables an experimental determination of the A rotational parameter, which turns out to be larger than expected. The new isomer 2 is observed by means of a band in the H2O ν2 region, confirming its C2v symmetry and calculated structure.

STEM SerialED: achieving high-resolution data for ab initio structure determination of beam-sensitive nanocrystalline materials.

Serial electron diffraction (SerialED), which applies a snapshot data acquisition strategy for each crystal, was introduced to tackle the problem of radiation damage in the structure determination of beam-sensitive materials by three-dimensional electron diffraction (3DED). The snapshot data acquisition in SerialED can be realized using both transmission and scanning transmission electron microscopes (TEM/STEM). However, the current SerialED workflow based on STEM setups requires special external devices and software, which limits broader adoption. Here, we present a simplified experimental implementation of STEM-based SerialED on Thermo Fisher Scientific STEMs using common proprietary software interfaced through Python scripts to automate data collection. Specifically, we utilize TEM Imaging and Analysis (TIA) scripting and TEM scripting to access the STEM functionalities of the microscope, and DigitalMicrograph scripting to control the camera for snapshot data acquisition. Data analysis adapts the existing workflow using the software CrystFEL, which was developed for serial X-ray crystallography. Our workflow for STEM SerialED can be used on any Gatan or Thermo Fisher Scientific camera. We apply this workflow to collect high-resolution STEM SerialED data from two aluminosilicate zeolites, zeolite Y and ZSM-25. We demonstrate, for the first time, ab initio structure determination through direct methods using STEM SerialED data. Zeolite Y is relatively stable under the electron beam, and STEM SerialED data extend to 0.60 Å. We show that the structural model obtained using STEM SerialED data merged from 358 crystals is nearly identical to that using continuous rotation electron diffraction data from one crystal. This demonstrates that accurate structures can be obtained from STEM SerialED. Zeolite ZSM-25 is very beam-sensitive and has a complex structure. We show that STEM SerialED greatly improves the data resolution of ZSM-25, compared with serial rotation electron diffraction (SerialRED), from 1.50 to 0.90 Å. This allows, for the first time, the use of standard phasing methods, such as direct methods, for the ab initio structure determination of ZSM-25.

Li2GeS3: New Structural Type of Lithium Solid Electrolyte for All-Solid-State Batteries

Sulfide inorganic materials exhibit favorable qualities such as high ionic conductivity and mechanical softness, making them promising candidates for solid electrolytes in Li-ion all-solid-state batteries. Sulfide solid electrolytes exist in various structural types, including β-Li3PS4, Li10GeP2S12, argyrodite, Li4PS4I, Li7P3S11, and Li1.82SiP0.036S3. While these materials exhibit high ionic conductivities of up to ~10− 2 S cm− 1 at room temperature and possess mechanical softness, they also have limitations, such as a narrow electrochemical stability window and air instability, which can hinder their scalability. The electrochemical and air stabilities of a solid electrolyte (Li–M–S, where M = non-Li metal ions) are largely governed by its stability of crystal structure consisting of MSn polyhedra and Li ions. A material with a different crystal structure would show its distinct properties. However, despite extensive research, no single structure known to date has proven superior in all aspects of performance. Given the importance of crystal structure in developing high-performance solid electrolytes, exploring and identifying novel ion-conducting materials with unique crystal structures is imperative. Additionally, once a new structural type of material is discovered, its performance can be adjusted, enhanced, or optimized through various techniques, such as chemical substitution, morphology and particle size control, and surface coating. In this work, we discovered a new crystal structural type of Li-ion conductor Li2GeS3. It was first known in 2000 by Kanno et al., with only orthorhombic unit cell dimension reported. However, our study using ab initio structure determination techniques from powder X-ray diffraction data, similar to our previous works, unveiled its structure possessing a hexagonal P61 symmetry with lattice parameters of a = 6.80098(4) Å and c = 17.92827(11) Å, revealing a new type of crystal structure. Its structure is comprised of a distorted hexagonal close-packed arrangement of sulfur anions with three asymmetric metal atoms: Ge and Li2 are in tetrahedral cavities surrounded by sulfur atoms; Li1 is in the trigonal bipyramidal cavity. The material displayed an ionic conductivity of 1.63 × 10− 8 S cm− 1 at 303 K and 2.45 × 10− 7 S cm− 1 at 383 K. Bond valence energy landscape calculations revealed three-dimensional lithium diffusion pathways within the structure. These results suggest that Li2GeS3 is expected to be a host structure from which improved ionic conductors can be derived through appropriate chemical substitution.

Ab initio protein structure prediction: the necessary presence of external force field as it is delivered by Hsp40 chaperone

BackgroundThe aqueous environment directs the protein folding process towards the generation of micelle-type structures, which results in the exposure of hydrophilic residues on the surface (polarity) and the concentration of hydrophobic residues in the center (hydrophobic core). Obtaining a structure without a hydrophobic core requires a different type of external force field than those generated by a water. The examples are membrane proteins, where the distribution of hydrophobicity is opposite to that of water-soluble proteins. Apart from these two extreme examples, the process of protein folding can be directed by chaperones, resulting in a structure devoid of a hydrophobic core.ResultsThe current work presents such example: DnaJ Hsp40 in complex with alkaline phosphatase PhoA-U (PDB ID—6PSI)—the client molecule. The availability of WT form of the folding protein—alkaline phosphatase (PDB ID—1EW8) enables a comparative analysis of the structures: at the stage of interaction with the chaperone and the final, folded structure of this biologically active protein. The fuzzy oil drop model in its modified FOD-M version was used in this analysis, taking into account the influence of an external force field, in this case coming from a chaperone.ConclusionsThe FOD-M model identifies the external force field introduced by chaperon influencing the folding proces. The identified specific external force field can be applied in Ab Initio protein structure prediction as the environmental conditioning the folding proces.

Ab initio based study of the diamagnetism of diamond, silicon and germanium

Diamond, silicon and germanium are widely used technological materials, whose electron structures are tabulated and understood very well. Yet the detailed picture of various diamagnetic contributions and their interplay with the paramagnetic effect, especially at the ab initio level, due to the complexity of this problem remains largely unknown. In our study, based on the ab initio electron band structure approach, all possible magnetic contributions, including the Langevin (Larmor) diamagnetism and the Van Vleck paramagnetism accounted in the second order of the perturbation treatment, are analyzed quantitatively. The Van Vleck contribution has been adapted to the band structure calculations by performing integration over k-points. Also, the partial diamagnetic contributions of core and valence electrons are obtained and discussed in detail. Of all terms there is only one — the Langevin diamagnetism of the valence electrons, which is not well defined quantitatively due to the contribution from the interstitial region. We discuss possible approaches to partitioning this contribution among neighboring crystal sites, based on the Bader charge separation and introducing the area of depleted electron density, excluded from the integration. Under various assumptions for the interstitial region, we have found that the magnetic susceptibilities for diamond, silicon and germanium lie in the range -13.4/-9.3, -4.7/-4.0 and -8.4/-8.8 (volume values, in units of 10−7), correspondingly. In general, this is consistent with the available experimental values, albeit the numerical uncertainty typically reaches tens of percent.