Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Borosilicide with Clathrate VIII Structure.

ABSTRACT: The high-pressure phase Na₈B_xSi_46-x (3 < x < 5) is the first representative of a borosilicide crystallizing in the rarely occurring clathrate VIII type structure. Crystals with composition Na₈B₄Si₄₂ (space group I43̅m; a = 9.7187(2) Å; Pearson symbol cI54) were obtained at 5-8 GPa and 1200 K. The clathrate I modification exists for the same composition at lower pressure with a larger cell volume (Pm3̅n; a = 9. 977(2) Å; cP54). Profound structural adaptions allow for a higher density of the clathrate VIII type than clathrate I, opening up the perspective of obtaining clathrate VIII type compounds as high-pressure forms of clathrate I.

SUBMITTER: Hubner JM

PROVIDER: S-EPMC9377393 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A Borosilicide with Clathrate VIII Structure.

Hübner Julia-Maria JM Carrillo-Cabrera Wilder W Kozelj Primoz P Prots Yurii Y Baitinger Michael M Schwarz Ulrich U Jung Walter W

Journal of the American Chemical Society 20220725 30

The high-pressure phase Na8BxSi46-x (3 < x < 5) is the first representative of a borosilicide crystallizing in the rarely occurring clathrate VIII type structure. Crystals with composition Na8B4Si42 (space group I43̅m; a = 9.7187(2) Å; Pearson symbol cI54) were obtained at 5-8 GPa and 1200 K. The clathrate I modification exists for the same composition at lower pressure with a large ...[more]

PMID: 35875975

Similar Datasets

Prediction of giant thermoelectric power factor in type-VIII clathrate Si46.

Project description:Clathrate materials have been the subject of intense interest and research for thermoelectric application. Nevertheless, from the very large number of conceivable clathrate structures, only a small fraction of them have been examined. Since the thermal conductivity of clathrates is inherently small due to their large unit cell size and open-framework structure, the current research on clathrates is focused on finding the ones with large thermoelectric power factor. Here we predict an extraordinarily large power factor for type-VIII clathrate Si(46). We show the existence of a large density of closely packed elongated ellipsoidal carrier pockets near the band edges of this so far hypothetical material structure, which is higher than that of the best thermoelectric materials known today. The high crystallographic symmetry near the energy band edges for Si(46)-VIII clathrates is responsible for the formation of such a large number of carrier pockets.

| S-EPMC5382702 | biostudies-literature

Factor VIII-antibody structure and membrane binding.

Project description: Not available

| S-EPMC8160506 | biostudies-literature

Polyhydride CeH9 with an atomic-like hydrogen clathrate structure.

Project description:Compression of hydrogen-rich hydrides has been proposed as an alternative way to attain the atomic metallic hydrogen state or high-temperature superconductors. However, it remains a challenge to get access to these states by synthesizing novel polyhydrides with unusually high hydrogen-to-metal ratios. Here we synthesize a series of cerium (Ce) polyhydrides by a direct reaction of Ce and H2 at high pressures. We discover that cerium polyhydride CeH9, formed above 100 GPa, presents a three-dimensional hydrogen network composed of clathrate H29 cages. The electron localization function together with band structure calculations elucidate the weak electron localization between H-H atoms and confirm its metallic character. By means of Ce atom doping, metallic hydrogen structure can be realized via the existence of CeH9. Particularly, Ce atoms play a positive role to stabilize the sublattice of hydrogen cages similar to the recently discovered near-room-temperature lanthanum hydride superconductors.

| S-EPMC6671988 | biostudies-literature

Effects of the CO₂ Guest Molecule on the sI Clathrate Hydrate Structure.

Project description:This paper analyzes the structural, energetic and mechanical properties of carbon dioxide hydrate clathrates calculated using finite cluster and periodic ab initio density-functional theory methodologies. Intermolecular interactions are described by the exchange-hole dipole moment method. The stability, gas saturation energetics, guest-host interactions, cage deformations, vibrational frequencies, and equation of state parameters for the low-pressure sI cubic phase of the CO₂@H₂O clathrate hydrate are presented. Our results reveal that: (i) the gas saturation process energetically favors complete filling; (ii) carbon dioxide molecules prefer to occupy the larger of the two cages in the sI structure; (iii) blue shifts occur in both the symmetric and antisymmetric stretching frequencies of CO₂ upon encapsulation; and (iv) free rotation of guest molecules is restricted to a plane parallel to the hexagonal faces of the large cages. In addition, we calculate the librational frequency of the hindered rotation of the guest molecule in the plane perpendicular to the hexagonal faces. Our calculated spectroscopic data can be used as signatures for the detection of clathrate hydrates in planetary environments.

| S-EPMC5457105 | biostudies-literature

Modeling of Structure H Carbon Dioxide Clathrate Hydrates: Guest-Lattice Energies, Crystal Structure, and Pressure Dependencies.

Project description:We performed first-principles computations to investigate the complex interplay of molecular interaction energies in determining the lattice structure and stability of CO2@sH clathrate hydrates. Density functional theory computations using periodic boundary conditions were employed to characterize energetics and the key structural properties of the sH clathrate crystal under pressure, such as equilibrium lattice volume and bulk modulus. The performance of exchange-correlation functionals together with recently developed dispersion-corrected schemes was evaluated in describing interactions in both short-range and long-range regions of the potential. Structural relaxations of the fully CO2-filled and empty sH unit cells yield crystal structure and lattice energies, while their compressibility parameters were derived by including the pressure dependencies. The present quantum chemistry computations suggest anisotropy in the compressibility of the sH clathrate hydrates, with the crystal being less compressible along the a-axis direction than along the c-axis one, in distinction from nearly isotropic sI and sII structures. The detailed results presented here give insight into the complex nature of the underlying guest-host interactions, checking earlier assumptions, providing critical tests, and improving estimates. Such entries may eventually lead to better predictions of thermodynamic properties and formation conditions, with a direct impact on emerging hydrate-based technologies.

| S-EPMC9465682 | biostudies-literature

Mainly on the Plane: Deep Subsurface Bacterial Proteins Bind and Alter Clathrate Structure.

Project description:Gas clathrates are both a resource and a hindrance. They store massive quantities of natural gas but also can clog natural gas pipelines, with disastrous consequences. Eco-friendly technologies for controlling and modulating gas clathrate growth are needed. Type I Antifreeze Proteins (AFPs) from cold-water fish have been shown to bind to gas clathrates via repeating motifs of threonine and alanine. We tested whether proteins encoded in the genomes of bacteria native to natural gas clathrates bind to and alter clathrate morphology. We identified putative clathrate-binding proteins (CBPs) with multiple threonine/alanine motifs in a putative operon (cbp) in metagenomes from natural clathrate deposits. We recombinantly expressed and purified five CbpA proteins, four of which were stable, and experimentally confirmed that CbpAs bound to tetrahydrofuran (THF) clathrate, a low-pressure analogue for structure II gas clathrate. When grown in the presence of CbpAs, the THF clathrate was polycrystalline and platelike instead of forming single, octahedral crystals. Two CbpAs yielded branching clathrate crystals, similar to the effect of Type I AFP, while the other two produced hexagonal crystals parallel to the [1 1 1] plane, suggesting two distinct binding modes. Bacterial CBPs may find future utility in industry, such as maintaining a platelike structure during gas clathrate transportation.

| S-EPMC7786625 | biostudies-literature

Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental 129 Xe NMR Spectroscopy.

Project description:An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o- and m-fluorophenol, whose previously unknown clathrate structures have been studied by 129 Xe NMR spectroscopy. The high sensitivity of the 129 Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures.

| S-EPMC5763392 | biostudies-literature

Structure-driven CO2 selectivity and gas capacity of ionic clathrate hydrates.

Project description:Ionic clathrate hydrates can selectively capture small gas molecules such as CO2, N2, CH4 and H2. We investigated CO2 + N2 mixed gas separation properties of ionic clathrate hydrates formed with tetra-n-butylammonium bromide (TBAB), tetra-n-butylammonium chloride (TBAC), tetra-n-butylphosphonium bromide (TBPB) and tetra-n-butylphosphonium chloride (TBPC). The results showed that CO2 selectivity of TBAC hydrates was remarkably higher than those of the other hydrates despite less gas capacity of TBAC hydrates. The TBAB hydrates also showed irregularly high CO2 selectivity at a low pressure. X-ray diffraction and Raman spectroscopic analyses clarified that TBAC stably formed the tetragonal hydrate structure, and TBPB and TBPC formed the orthorhombic hydrate structure. The TBAB hydrates showed polymorphic phases which may consist of the both orthorhombic and tetragonal hydrate structures. These results showed that the tetragonal hydrate captured CO2 more efficiently than the orthorhombic hydrate, while the orthorhombic hydrate has the largest gas capacity among the basic four structures of ionic clathrate hydrates. The present study suggests new potential for improving gas capacity and selectivity of ionic clathrate hydrates by choosing suitable ionic guest substances for guest gas components.

| S-EPMC5722917 | biostudies-literature

Structural and Electrochemical Properties of Type VIII Ba8Ga16-δSn30+δ Clathrate (δ ≈ 1) during Lithiation.

Project description:Clathrates of the tetrel (Tt = Si, Ge, Sn) elements are host-guest structures that can undergo Li alloying reactions with high capacities. However, little is known about how the cage structure affects the phase transformations that take place during lithiation. To further this understanding, the structural changes of the type VIII clathrate Ba8Ga16-δSn30+δ (δ ≈ 1) during lithiation are investigated and compared to those in β-Sn with ex situ X-ray total scattering measurements and pair distribution function (PDF) analysis. The results show that the type VIII clathrate undergoes an alloying reaction to form Li-rich amorphous phases (LixBa0.17Ga0.33Sn0.67, x = 2-3) with local structures similar to those in the crystalline binary Li-Sn phases that form during the lithiation of β-Sn. As a result of the amorphous phase transition, the type VIII clathrate reacts at a lower voltage (0.25 V vs Li/Li+) compared to β-Sn (0.45 V) and goes through a solid-solution reaction after the initial conversion of the crystalline clathrate phase. Cycling experiments suggest that the amorphous phase persists after the first lithiation and results in considerably better cycling than in β-Sn. Density functional theory (DFT) calculations suggest that topotactic Li insertion into the clathrate lattice is not favorable due to the high energy of the Li sites, which is consistent with the experimentally observed amorphous phase transformation. The local structure in the clathrate featuring Ba atoms surrounded by a cage of Ga and Sn atoms is hypothesized to kinetically circumvent the formation of Li-Sn or Li-Ga crystalline phases, which results in better cycling and a lower reaction voltage. Based on the improved electrochemical performance, clathrates could act as tunable precursors to form amorphous Li alloying phases with novel electrochemical properties.

| S-EPMC8447186 | biostudies-literature

The tertiary structure and domain organization of coagulation factor VIII.

Project description:Factor VIII (fVIII) is a serum protein in the coagulation cascade that nucleates the assembly of a membrane-bound protease complex on the surface of activated platelets at the site of a vascular injury. Hemophilia A is caused by a variety of mutations in the factor VIII gene and typically requires replacement therapy with purified protein. We have determined the structure of a fully active, recombinant form of factor VIII (r-fVIII), which consists of a heterodimer of peptides, respectively containing the A1-A2 and A3-C1-C2 domains. The structure permits unambiguous modeling of the relative orientations of the 5 domains of r-fVIII. Comparison of the structures of fVIII, fV, and ceruloplasmin indicates that the location of bound metal ions and of glycosylation, both of which are critical for domain stabilization and association, overlap at some positions but have diverged at others.

| S-EPMC2214755 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data