Ab Initio Structure Research Articles

Ab Initio Structure Determination of La34Mo8O75 Using Powder X-ray and Neutron Diffraction Data

We report the synthesis, the structure determination, and the structure analysis of La34Mo8O75, which comprises 68 mol % La2O3 in the binary system La2O3–MoO3, in place of the previously reported compound La4MoO9, 66.7 mol % La2O3. This latter compound, which was reported in the literature without any structural information, is presented in this Article as part of the exploration of the La2O3–Nb2O5–MoO3 ternary phase diagram. Several diffraction techniques were used for the structural resolution of this compound such as powder X-ray and neutron diffraction as well as transmission electron microscopy in diffraction mode. La34Mo8O75 crystallizes in the monoclinic space group C2/m with the cell parameters: a = 17.070 A, b = 12.204 A, c = 9.742 A, β = 109.58°. The structure, related to fluorite, can be described as an anion-deficient fluorite with the global formula La34Mo8O75□9. The oxygen conduction of the compound was also investigated by means of complex impedance spectroscopy.

Fermi surface complexity, effective mass, and conduction band alignment in n-type thermoelectric Mg3Sb2 – xBix from first principles calculations

Using first principles calculations, we study the conduction band alignment, effective mass, and Fermi surface complexity factor of n-type Mg3Sb2 – xBix (x = 0, 1, and 2) from the full ab initio band structure. We find that with an increase in the Bi content, the K and M band minima move away from the conduction band minimum CB1 while the singly-degenerate Г band minimum shifts rapidly downward and approaches the conduction band minimum. However, the favorable sixfold degenerate CB1 band minimum keeps dominating the conduction band minimum and there is no band crossing between the Г and CB1 band minima. In addition, we show that the connection of the CB1 carrier pockets with the energy level close to the band minimum M can strongly enhance the carrier pocket anisotropy and Fermi surface complexity factor, which is likely the electronic origin for the local maximum in the theoretical power factor. Our calculations also show that the density of states effective mass, Seebeck coefficient, and Fermi surface complexity factor decrease with an increase in the Bi content, which is unfavorable to the electrical transport. In contrast, reducing the conductivity effective mass with an increase in the Bi content is beneficial to the electrical transport by improving carrier mobility and weighted mobility as long as the detrimental bipolar effect is insignificant. As a result, in comparison with n-type Mg3Sb2, n-type Mg3SbBi shows higher power factors and a much lower optimal carrier concentration for the theoretical power factor at 300 K, which can be easily achieved by the experiment.

Improved fragment sampling for ab initio protein structure prediction using deep neural networks

A typical approach to predicting unknown native structures of proteins is to assemble the amino acid residues (fragments) extracted from known structures. The quality of these extracted fragments, which are used to build protein-specific fragment libraries, can determine the success or failure of sampling near-native conformations. Here we show how a high-quality fragment library can be built using deep contextual learning techniques. Our algorithm, called DeepFragLib, employs bidirectional long short-term-memory recurrent neural networks with knowledge distillation for initial fragment classification, followed by an aggregated residual transformation network with cyclically dilated convolution for detecting near-native fragments. DeepFragLib improves the position-averaged proportion of near-native fragments by 12.2% over existing methods and, consequently, produces better near-native structures for 72.0% of the free-modelling domain targets tested when integrated with Rosetta. DeepFragLib is fully parallelized and available for use in conjunction with structure prediction programs. An approach to protein structure prediction is to assemble candidate structures from template fragments, which are extracted from known protein structures. Wang et al. demonstrate that combining deep neural network architectures with a relatively small but high-resolution fragment dataset can improve the quality of the sample fragment libraries used for protein structure prediction.

Automated electron diffraction tomography - development and applications.

Electron diffraction tomography (EDT) has gained increasing interest, starting with the development of automated electron diffraction tomography (ADT) which enables the collection of three-dimensional electron diffraction data from nano-sized crystals suitable for ab initio structure analysis. A basic description of the ADT method, nowadays recognized as a reliable and established method, as well as its special features and general applicability to different transmission electron microscopes is provided. In addition, the usability of ADT for crystal structure analysis of single nano-sized crystals with and without special crystallographic features, such as twinning, modulations and disorder is demonstrated.

The equilibrium molecular structure of 2-cyanopyridine from combined analysis of gas-phase electron diffraction and microwave data and results of ab initio calculations

The gas-phase electron diffraction study of 2-cyanopyridine was carried out for the first time. Results of ab initio structure calculations performed at the CCSD(T) level of theory agree well with the equilibrium structure determined by the electron diffraction method in combination with vibrational spectroscopy data and microwave rotational constants. The deviations between them are only a few thousandths of A units and a few tenths of degree in the bond lengths and bond angles, respectively. The structure in the solid state is more different from that in the gas phase. The observed discrepancies between these structures are up to 0.02 A and 2° in the bond lengths and bond angles, respectively. The influence of the ortho-, meta-, and para-cyano substituents on the geometry of pyridine ring is discussed. The pyridine ring is noticeably distorted due to cyano substituents. The Cipso–N and/or Cipso–C bond lengths are elongated both in 2-CNP and 4-CNP by 0.004 A in comparison to those in pyridine, whereas the Cipso–C bond lengths are increased by 0.005 and 0.009 A in 3-CNP.

Complex interaction of hydrogen with the monolayer TiS2 decorated with Li and Li2O clusters: an ab initio random structure searching approach

We have applied ab initio random structure searching to study the structure, stability and hydrogen storage properties of monolayer TiS2 coated with Li and small Li2O clusters. For the low Li covered system we found a complex adsorption mechanism: some hydrogen molecules were adsorbed due to polarization with Li, others due to polarization with S near the surface of TiS2. The peculiarities of the interaction of the H2 molecules with each other and the preferred adsorption sites allowed us to formulate a series of recommendations that can be useful when selecting the material for the most effective support. Moreover, the findings also show that the storage capacity of this system can reach up to 9.63 wt%, presenting a good potential as hydrogen storage material. As for the Li2O clusters supported on TiS2, we found that the polarization of the Li–O bond increases upon the adsorption of the Li2O nanocluster. Moreover, the polarized Li–S bonds appear in addition to the already existing Li–O bonds. All this is possible due to the extraction of 1.46 electrons from the S atom of the substrate by O atom of the cluster, and should contribute to an increase in both the adsorption energy and the maximum capacity. The adsorption energies of H2 for the systems studied here are within 0.11–0.16 eV/H2 which is a recommended range for reversible hydrogen physisorption under standard test conditions. This study may stimulate experimental efforts to check the claims of high-capacity, stable and reversible hydrogen adsorption reported here.

The Crystal Structure of Orthocetamol Solved by 3D Electron Diffraction.

Orthocetamol is a regioisomer of the well-known pain medication paracetamol and a promising analgesic and an anti-arthritic medicament itself. However, orthocetamol cannot be grown as single crystals suitable for X-ray diffraction, so its crystal structure has remained a mystery for more than a century. Here, we report the ab-initio structure determination of orthocetamol obtained by 3D electron diffraction, combining a low-dose acquisition method and a dedicated single-electron detector for recording the diffracted intensities. The structure is monoclinic, with a pseudo-tetragonal cell that favors multiple twinning on a scale of a few tens of nanometers. The successful application of 3D electron diffraction to orthocetamol introduces a new gold standard of total structure solution in all cases where X-ray diffraction and electron-microscope imaging methods fail.

B-site disorder driven multiple-magnetic phases: Griffiths phase, re-entrant cluster glass, and exchange bias in Pr2CoFeO6

The magnetic spin ordering and the magnetization dynamics of a double perovskite Pr2CoFeO6 have been investigated by employing the (dc and ac) magnetization and neutron powder diffraction techniques. The study revealed that Pr2CoFeO6 adopted a B-site disordered orthorhombic structure (Pnma). Furthermore, ab initio band structure calculations suggested an insulating antiferromagnetic ground state. Magnetization measurements revealed that the system possesses a spectrum of competing magnetic phases, viz., long range canted antiferromagnetic (AFM) spin ordering (TN ∼ 269 K), Griffiths-like phase, re-entrant cluster glass (TG ∼ 34 K), and exchange bias effects. The neutron diffraction study divulged the exhibition of a long range G-type of canted AFM spin ordering. The random nonmagnetic dilution of magnetic Fe3+ (high spin) ions by Co3+ (low spin) ions due to B-site disorder essentially played a crucial role in manifesting such magnetic properties of the system.

Structural Model of the ETR1 Ethylene Receptor Transmembrane Sensor Domain

The structure, mechanism of action and copper stoichiometry of the transmembrane sensor domain of the plant ethylene receptor ETR1 and homologs have remained elusive, hampering the understanding on how the perception of the plant hormone ethylene is transformed into a downstream signal. We generated the first structural model of the transmembrane sensor domain of ETR1 by integrating ab initio structure prediction and coevolutionary information. To refine and independently validate the model, we determined protein-related copper stoichiometries on purified receptor preparations and explored the helix arrangement by tryptophan scanning mutagenesis. All-atom molecular dynamics simulations of the dimeric model reveal how ethylene can bind proximal to the copper ions in the receptor, illustrating the initial stages of the ethylene perception process.

Near-unity spin Hall ratio in Ni x Cu1-x alloys.

We report a large spin Hall effect in the 3d transition metal alloy Ni x Cu1-x for x ∈ {0.3, 0.75}, detected via the ferromagnetic resonance of a permalloy (Py = Ni80Fe20) film deposited in a bilayer with the alloy. A thickness series at x = 0.6, for which the alloy is paramagnetic at room temperature, allows us to determine the spin Hall ratio θ SH ≈ 1, spin diffusion length λs, spin mixing conductance G ⇅, and damping due to spin memory loss αSML. We compare our results with similar experiments on Py/Pt bilayers measured using the same method. Ab initio band structure calculations with disorder and spin-orbit coupling suggest an intrinsic spin Hall effect in Ni x Cu1-x alloys, although the experiments here cannot distinguish between extrinsic and intrinsic mechanisms.

Predicting three-dimensional icosahedron-based boron B60

The icosahedron-based bulk boron structures have extremely chemical and structural complexity, and are usually semiconductors at ambient conditions. Here we predict bulk boron phases with a 60-atom orthorhombic unit cell from an ab initio evolutionary structure search, termed as ${\mathrm{B}}_{60}$. The metastable structures can be either a conductor or a semimetal depending on their interstitial atomic positions. In particular, an orthorhombic structure with $Pnma$ symmetry ($Pnma\ensuremath{-}{\mathrm{B}}_{60}$), consisting of ${\mathrm{B}}_{12}$ icosahedra and twisted interstitial two-atom wide boron ribbons, is identified to be a topological node-line semimetal with potential superior electronic transport. The band structure and simulated electron-diffraction pattern of $Pnma\ensuremath{-}{\mathrm{B}}_{60}$ are in satisfactory agreement with the experimental data, suggesting that it may exist in the form of nanomaterials.

Three-body calculations for (p,pN) reactions: Kinematically inclusive, semi-inclusive, and fully exclusive cross sections

Background: Nucleon knockout reactions have been previously used to extract single particle information from nuclei. The analysis of nucleon knockout from a stable projectile in the collision with a proton target and the comparison with the experimental data is a key test for the reaction and structure models used to evaluate the reaction observables.Purpose: We analyze $p$ and $n$ knockout from $^{12}\mathrm{C}$, assuming that only the heavy fragment or core $C$ (taken as inert), the knockout particle $N$, and the proton target $p$ participate in the collision process with the aim of (i) getting insight to the dominant kinematic conditions of the emitted particles; (ii) clarifying the dynamics of the reaction; (iii) exploring the isospin dependence (here $p$ and $n$ knockout) of the calculated reaction cross sections.Method: We solve three-body Faddeev/Alt-Grassberger-Sandhas (Faddeev/AGS) equations for transition operators and calculate kinematically fully exclusive, semi-inclusive, and inclusive cross sections.Results: We show that (i) the dominant final-state kinematic conditions are consistent with the assumption of quasifree scattering reaction mechanism; (ii) the distortions due to higher order multiple scattering terms depend on the final-state kinematics, and the $N\ensuremath{-}C$ and $p\ensuremath{-}C$ final state interaction provide significant effects in the calculated observables; (iii) the twofold energy--polar angle and polar angle--polar angle cross sections exhibit distinct $p$- and $n$-knockout behaviors. Finally we also show that the Faddeev/AGS formalism is able to a certain extent to reproduce the available experimental data for the $p$ knockout.Conclusions: Kinematically fully exclusive measurements of $p$ and $n$ knockout are needed to rigorously assess the role of the distortion, as it cannot be taken into account as an overall reduction factor. This is a prerequisite for a reliable understanding of the structure of the projectile and the reaction mechanism. In addition, realistic interactions inferred from ab initio structure models are needed for analyzing experimental data.

Protein Structure Determination in Living Cells.

To date, in-cell NMR has elucidated various aspects of protein behaviour by associating structures in physiological conditions. Meanwhile, current studies of this method mostly have deduced protein states in cells exclusively based on ‘indirect’ structural information from peak patterns and chemical shift changes but not ‘direct’ data explicitly including interatomic distances and angles. To fully understand the functions and physical properties of proteins inside cells, it is indispensable to obtain explicit structural data or determine three-dimensional (3D) structures of proteins in cells. Whilst the short lifetime of cells in a sample tube, low sample concentrations, and massive background signals make it difficult to observe NMR signals from proteins inside cells, several methodological advances help to overcome the problems. Paramagnetic effects have an outstanding potential for in-cell structural analysis. The combination of a limited amount of experimental in-cell data with software for ab initio protein structure prediction opens an avenue to visualise 3D protein structures inside cells. Conventional nuclear Overhauser effect spectroscopy (NOESY)-based structure determination is advantageous to elucidate the conformations of side-chain atoms of proteins as well as global structures. In this article, we review current progress for the structure analysis of proteins in living systems and discuss the feasibility of its future works.

Electron diffraction determines molecular absolute configuration in a pharmaceutical nanocrystal.

Determination of the absolute configuration of organic molecules is essential in drug development and the subsequent approval process. We show that this determination is possible through electron diffraction using nanocrystalline material. Ab initio structure determination by electron diffraction has so far been limited to compounds that maintain their crystallinity after a dose of one electron per square angstrom or more. We present a complete structure analysis of a pharmaceutical cocrystal of sofosbuvir and l-proline, which is about one order of magnitude less stable. Data collection on multiple positions of a crystal and an advanced-intensity extraction procedure enabled us to solve the structure ab initio. We further show that dynamical diffraction effects are strong enough to permit unambiguous determination of the absolute structure of material composed of light scatterers.

Nuclear Charge Radii of ^{10,11}B.

The first laser spectroscopic determination of the change in the nuclear charge radius for a five-electron system is reported. This is achieved by combining high-accuracy abinitio mass-shift calculations and a high-accuracy measurement of the isotope shift in the 2s^{2}2p ^{2}P_{1/2}→2s^{2}3s ^{2}S_{1/2} ground state transition in boron atoms. Accuracy is increased by orders of magnitude for the stable isotopes ^{10,11}B and the results are used to extract their difference in the mean-square charge radius ⟨r_{c}^{2}⟩^{11}-⟨r_{c}^{2}⟩^{10}=-0.49(12) fm^{2}. The result is qualitatively explained by a possible cluster structure of the boron nuclei and quantitatively used to benchmark new abinitio nuclear structure calculations using the no-core shell model and Green's function MonteCarlo approaches. These results are the foundation for a laser spectroscopic determination of the charge radius of the proton-halo candidate ^{8}B.

Two-dimensional antiferromagnetic boron form first principles

A new two-dimensional (2D) antiferromagnetic semiconducting boron structure, named as M-B28, is predicted using ab initio evolutionary structure searching. First-principles calculations show that M-B28 has a lower energy than other 2D magnetic boron structures and is dynamically stable. The unpaired electrons from the caps of B26 clusters lead to magnetism in M-B28, while making its highest valence band flat and isolated. The Néel temperature and mechanical properties of M-B28 are evaluated with the Ising model and strain-stress method, respectively, revealing a transition temperature of 32 K and the ideal strengths of 43.7 N/m along x direction and 38.5 N/m along y direction.

Structural characterization and ab-initio resolution of natural occurring zaccariniite (RhNiAs) by means of Precession Electron Diffraction

The crystal structure of naturally occurring zaccariniite from Loma Peguera (Republica Dominicana) has been studied in Transmission Electron Microscopy (TEM) with variable angle Precession Electron Diffraction (PED) techniques: 0.7° Precession Electron Diffraction Tomography (Precession EDT) for unit cell and Laue class sorting, 0.5° Scanning Precession Diffraction (SPED) for crystal orientation mapping and grain alignment, and high symmetry zone axis 1.2° to 2.2° Zone Axis High Angle Precession Electron Diffraction (ZA high angle PED) for Space Group assessment and supercell information gathering. The natural sample has been prepared into an electron thin lamella by means of Focused Ion Beam (FIB). The analysis of the data has yielded tetragonal cell parameters of 3.86, 3.86, 6.77 Å and space group of P4/nmm for the basic structure, and its constituent atom positions for Ni, As and Rh were determined as well by ab-initio structure resolution method in accordance to the elemental composition of the natural zaccariniite obtained with Energy Dispersive X-ray (EDX) and High Magnification Electron Microscopy (HMEM) analysis. A modulation of the crystal basic structure of 3 by 1 in the basal plane has been reported for the first time on natural occurring zaccariniite.

X-ray study and computational model of the solid solvate of [1,2,5]oxadiazolo[3,4-е][1,2,3,4]tetrazine 4,6-dioxide (FTDO) with benzene and ab initio crystal structure prediction of pure FTDO

X-ray study and computational modeling of [1,2,5]oxadiazole [3,4-e][1,2,3,4]tetrazine 4,6-dioxide (FTDO)–benzene (1 : 1) solvate structure have been carried out. Using the Atom-Atom Potentials Method, the original methodology and elaborated program packings the crystal structure of pure FTDO was predicted.

Performance comparison of ab initio protein structure prediction methods

Abstract Wet Lab methods used to resolve the native structure of a given protein such as X-ray Diffraction and NMR spectroscopy are time-consuming, expensive, and could be done multiple times due to failure. Those pitfalls led to the development of computationally automated prediction methods. Predicting the structure of a protein using its peptide sequence only — also known as ab initio Protein Structure Prediction “PSP”— is computationally challenging because of the large conformational space to be searched and the complexity of energy functions. Some successful predictive methods have been developed to solve PSP problem. In this paper, by using a set of peptide sequences, we compare a collection of PSP ab initio-based methods. Experiments show that using a metaheuristic-based search method that utilizes genetic algorithm can achieve same or better results than time consuming methods.

Valence band hard x-ray photoelectron spectroscopy on 3d transition-metal oxides containing rare-earth elements

Here we report on our study to quantitatively describe the intensities of the valence band hard x-ray photoemission spectra (HAXPES) of a rare earth element containing 3d transition metal oxides. Using LaCoO3 as a representative model compound, we compared the experimental data to the results of ab initio one-step photoemission band structure calculations as well as to the sum of the partial density of states of the atomic constituents weighted by their tabulated photoionization cross sections. We discovered that the semicore La 5p density of states surprisingly contributes in a significant manner to the valence band spectrum: Although the La 5p partial density of states in the valence band region is negligible compared to that of the O 2p or the Co 3d, the La 5p cross section in the hard x-ray range is found to be orders of magnitude larger than that of the other subshells. This explains the long-standing issue of why the hard x-ray valence band spectra of a rare-earth element containing materials have line shapes that are very different from those taken at lower photon energies and why they cannot be described in terms of partial density of states of the subshells usually considered for the lower photon energy spectra. We infer that the contribution of the rare-earth 5p must be taken into account and cannot be ignored.