Description Of Crystal Structure Research Articles

Graphical Description and Classification of Crystal Structure of Borate Minerals

Graphical Description and Classification of Crystal Structure of Borate Minerals

Modeling of Crystal Structure in Li-Rich Layered Oxides for Rechargeable Lithium Cells

Lithium-Ion Batteries (LIBs) require further development in terms of safety and performance to establish also in the automotive market and new materials at both electrode sides as well as at the electrolyte side are necessary to overcome the state of-the-art and the commercial benchmarks. [1] The positive electrode materials constitute the bottleneck for present LIBs. They are based on layered structures (LiCoO2, NMC, NMA), spinel (LiMn2O4) and olivine LiFePO4, with rather moderate specific capacities (120–180 mAhg−1). [2] Therefore, the resulting specific energies are insufficient to meet market demand. Over-stoichiometric Li-rich layered oxides (LRLOs) are a family of positive electrode materials with promising theoretical electrochemical performance. [3] Indeed, they have received widespread attention due to their extremely high specific capacity (>250 mAhg−1) and low cost. Their extraordinary capacity has been confirmed to originate not only from the redox activities of transition metals, but also from the redox activities of oxygen anions. The crystal structure of LRLOs is an open playground of debate. There are two main hypotheses: a) a two phase nano-domain and b) a single phase solid solution. In this framework, the modeling of the crystal structure is quite challenging. Usually, the description of the structure of LRLOs can be done with rhombohedral or monoclinic unit cell. Nevertheless, the use of convention unit cells leads to a bad representation of the crystal structure because of the missing of structure features in the superstructure region (20<θ<30 in typical diffraction pattern with Cu Kα). In this communication, we demonstrate that extensive defectivities play a key role in the shape and intensity of diffractograms of LRLOs. In particular, we show how the use of supercells or defects (antisite defects and stacking faults) can help in the description of crystal structure of this class of materials.[1] Zubi, G.; Dufo-López, R.; Carvalho, M.; Pasaoglu, G. The Lithium-Ion Battery: State of the Art and Future Perspectives. Renewable and Sustainable Energy Reviews 2018, 89, 292–308.[2] Casas-Cabanas, M.; Ponrouch, A.; Palacín, M.R. Blended Positive Electrodes for Li-Ion Batteries: From Empiricism to Rational Design. Isr J Chem 2021, 61, 26–37.[3] Nie, L.; Chen, S.; Liu, W. Challenges and Strategies of Lithium-Rich Layered Oxides for Li-Ion Batteries. Nano Res 2022.

Atomic-scale imaging of polyvinyl alcohol crystallinity using electron ptychography

Polyvinyl alcohol (PVA) is considered to have great potential in medical, pharmaceutical, and packaging applications because of its outstanding biocompatibility, water solubility, low density and relatively low cost. PVA crystallinity, central to the materials properties, has been studied by X-ray diffraction, but two possible crystal structures are mooted. Electron microscopic techniques can potentially image PVA at high resolution. Still, it is challenging for conventional electron microscopies because of the relatively low crystallinity of PVA, its severe beam sensitivity, and the poor contrast of light elements. Electron ptychography makes use of a 4D STEM dataset comprising the intensity in the STEM detector plane recorded as a function of each probe position and has lower sample damage and better phase-contrast compared to traditional techniques. Here, we use electron ptychography to image PVA crystallinity. The reconstructed images, which show good agreement in the unit cell dimension with X-ray diffraction data, can show how the atoms order in the materials, however, deviations from previous models derived from X-ray diffraction are observed. To interpret the data, we propose a series of changes based on previous models to formulate a description of PVA crystal structure. Simulated results from this new model accord well with the experimental images. This study manages to image both carbon and oxygen atoms in PVA, which has not previously been achieved by any conventional method. The results are expected to bring a new and deeper understanding of PVA crystal structure, and illustrate the opportunity presented by this approach for directly imaging molecular order in polymer crystals.

Crystal Structure of Scapolite from Urdini Lakes, Northwestern Rila, Bulgaria

The paper provides new insight on the choice of correct space group for description of scapolite crystal structures, with a view of the preferred positions by Si and Al ions and their framework ordering. Samples of scapolite from a skarn zone around Urdini lakes, Northwestern Rila have been analysed with SEM-EDS and single crystal X-ray diffraction. The obtained value for the meionite component Me) is around 70. The crystal structure of the studied sample has been refined in the tetragonal I4/m and P42/n space groups, traditionally assigned to scapolite members. In addition, structural determination has been conducted in C2/m.

The flexibility of the T–X–T hinges between the coordination tetrahedra in various zeolitic frameworks: an empirical structural study

In recent years, a large number of precisely determined crystal structure determinations of zeolites, that is compounds based on open frameworks of coordination tetrahedra, has accumulated. This gives us the opportunity to evaluate them in terms of the flexibility of their bond angles T–X–T which serve as hinges between the coordination tetrahedra in zeolites containing various SiO4, AlO4, PO4 and similarly sized ions. Out of about 7,000 known crystal structure descriptions of zeolites we have selected 1187 which are based on single crystal diffraction studies and have estimated standard deviations of their T–O bond length of 0.01 Å or less. The mean Si–O–Si angle in zeolitic frameworks with T-sites fully occupied by one type of T atoms is 152.9° and these angles range from 127.0° to 180°, the mean for Al–O–Si is 141.9°, ranging from 124.8° to 179.3°. Straight angles Si–O–Si do occur in some zeolites.

Crystal structure of scapolite from Samurski Dol, Chepelare region, Central Rhodopes, Bulgaria

Samples of scapolite from the marble quarry from the Samurski Dol locality, situated nearby Chepelare, Central Rhodopes, Bulgaria have been subjected to chemical analyses and single crystal X-ray diffraction studies. The obtained values for the meionite component (Me) range between 70 and 75. The crystal structure of the studied sample has been solved in both I4/m and P42/n space groups, traditionally assigned to scapolite members. The paper provides new insight on the choice of correct space group for description of scapolites crystal structures, with a view of the preferred positions by silicon and aluminum ions and their framework ordering.

Centrosymmetric paddlewheel copper(II) complexes as potent intercalators: synthesis, crystal structure description and DNA-binding studies

ABSTRACT Two copper(II) paddlewheel carboxylate complexes 1 and 2 of the general formula ACuL4CuA, where A is DMSO (1) and meta-bromopyridine (2) and L is meta-chlorophenyl acetate, have been synthesised, isolated quantitatively, crystallised and characterised using FTIR, UV-Visible spectroscopy, electrochemistry and XRD. FTIR spectra contained all the required peaks with the most prominent peaks those of carboxylate moiety indicating the bridging bidentate carboxylate binding mode. Electrochemistry yielded results typical of complexes containing Cu2+ centres. The structures were completely solved by XRD technique assigning square pyramidal geometry to each copper ion of the dinuclear complexes. The square base is formed by four oxygen atoms of the carboxylate moiety while the apical position is occupied by the fifth oxygen (of the DMSO molecule in 1) or nitrogen of the meta-bromopyridine in complex 2. The DNA-binding potency of the complexes was explored by viscometry, cyclic voltammetry, UV-Visible spectrophotometry and spectrofluorimetry. All these techniques provided coincident results and showed that the complexes bonded with DNA via an intercalative-binding mode. Additionally, these complexes were found to scavenge the free radical DPPH effectively. The complexes add interesting and valuable addition to the existing treasury on the copper paddlewheel complexes and their biological relevance.

A New Thermophilic Ene-Reductase from the Filamentous Anoxygenic Phototrophic Bacterium Chloroflexus aggregans.

Aiming at expanding the biocatalytic toolbox of ene-reductase enzymes, we decided to explore photosynthetic extremophile microorganisms as unique reservoir of (new) biocatalytic activities. We selected a new thermophilic ene-reductase homologue in Chloroflexus aggregans, a peculiar filamentous bacterium. We report here on the functional and structural characterization of this new enzyme, which we called CaOYE. Produced in high yields in recombinant form, it proved to be a robust biocatalyst showing high thermostability, good solvent tolerance and a wide range of pH optimum. In a preliminary screening, CaOYE displayed a restricted substrate spectrum (with generally lower activities compared to other ene-reductases); however, given the amazing metabolic ductility and versatility of Chloroflexus aggregans, further investigations could pinpoint peculiar chemical activities. X-ray crystal structure has been determined, revealing conserved features of Class III (or thermophilic-like group) of the family of Old Yellow Enzymes: in the crystal packing, the enzyme was found to assemble as dimer even if it behaves as a monomer in solution. The description of CaOYE catalytic properties and crystal structure provides new details useful for enlarging knowledge, development and application of this class of enzymes.

Review on soft magnetic metal and inorganic oxide nanocomposites for power applications

• Summary of the state-of-the-art soft magnetic materials and applications in power electronics. • Characteristics of oxide-based, metal-insulator, and insulator-insulator type composites. • Overview on thermodynamics and kinetics of self-assembled nanocomposites. • Microstructure engineering of soft magnetic composites based on traditional and advanced powder processing techniques. Oxide-based nanocomposites have potential to offer much higher switching frequencies compared with state-of-the-art soft magnetic materials for applications in power electronics. However, scalable techniques for synthesizing high performance bulk oxide-based nanostructured and nanocomposite systems with superior performance compared to traditional materials are limited. This review aims at identifying existing and potential opportunities for the development of high performance nanocomposite systems through microstructure engineering specific to soft magnetic property optimization by traditional processing routes. The review begins with general introduction about soft magnetic properties of different classes of materials, followed by a detailed description of crystal structures and the underlying physics responsible for their magnetic performance. These include; soft ferrites, bulk crystalline alloys, metal-amorphous nanocomposites, and metal-oxide nanocomposites of various nature such as metal-insulator and insulator-insulator type composites. An overview on powder metallurgy techniques is provided and aspects relevant to optimizing the balance between competing requirements of high effective electrical resistivity to mitigate eddy current losses and high saturation magnetization are highlighted.

Unusual intra- and intermolecular Ni···H-C anagostic interactions in (N-(pyrrol-2-ylmethyl)-N-(2-phenylethyl)dithiocarbamato-S,S’)- (thiocyanato-κN)(triphenylphosphine)nickel(II): synthesis, spectral properties, crystal structure, Hirshfeld surface analysis and DFT studies

Two new Ni(II) complexes, bis(N-(pyrrol-2-ylmethyl)-N-(2-phenylethyl)dithiocarbamato-S,S′)nickel(II) (1) and ( N-(pyrrol-2-ylmethyl)-N-(2-phenylethyl)dithiocarbamato-S,S′)(thiocyanato-κN)(triphenylphosphine)nickel(II) (2) were synthesized and characterized by elemental analysis, IR, UV-vis and NMR spectroscopy. IR and 13C{1H} NMR spectra of both complexes suggest that the dithiocarbamate ligands interact with metal ion as bidentate ligands. Electron spectra reveal square planar geometry for both complexes. A detailed description of crystal structure, DFT calculations and Hirshfeld surface analysis of 2 is also reported. The structure determination of 2 by X-ray crystallography confirmed the presence of four coordinated Ni(II) with distorted square planar geometry. The optimized geometry, HOMO – LUMO energy gap, molecular electrostatic potential (MEP) map and global reactivity descriptors were obtained using DFT calculations. The geometric parameters calculated for 2 using the DFT method are in good agreement with those obtained from single crystal X-ray structure determination. One of the interesting structural features of 2 are the obvious intramolecular and intermolecular C-H···Ni anagostic interactions. Hirshfeld surface analysis showed the nature of intermolecular contacts. The largest contribution to the crystal packing is from H···H interactions.

From Simple to Complex: Design of Inorganic Crystal Structures with a Topologically Extended Zintl–Klemm Concept

We present a novel approach to the generation of new crystalline phases, which is based on a combination of the topological description of crystal structures as a periodic net and the extended Zintl-Klemm concept, which establishes the structural relations between chemically and structurally simpler and more complex inorganic compounds. With this approach, we have explored the structural similarities between all known binary sulfides, selenides, and the corresponding simple sulfates and selenates and have theoretically revealed seven new high-pressure phases in the last two groups of compounds. Using density functional theory methods, we have studied the thermodynamic and mechanical stability of the new phases, have adjusted the transition pathways in the sulfate and selenate systems, and have revealed new structural correlations of the baric polymorphism in these systems. The advantages of the topological approach compared to conventional methods of modeling crystal structures are discussed and illustrated.

On an extension of Krivovichev's complexity measures.

An extension is proposed of the Shannon entropy-based structural complexity measure introduced by Krivovichev, taking into account the geometric coordinational degrees of freedom a crystal structure has. This allows a discrimination to be made between crystal structures which share the same number of atoms in their reduced cells, yet differ in the number of their free parameters with respect to their fractional atomic coordinates. The strong additivity property of the Shannon entropy is used to shed light on the complexity measure of Krivovichev and how it gains complexity contributions due to single Wyckoff positions. Using the same property allows for combining the proposed coordinational complexity measure with Krivovichev's combinatorial one to give a unique quantitative descriptor of a crystal structure's configurational complexity. An additional contribution of chemical degrees of freedom is discussed, yielding an even more refined scheme of complexity measures which can be obtained from a crystal structure's description: the six C's of complexity.

Derived crystal structure of martensitic materials by solid-solid phase transformation.

A mathematical description of crystal structure is proposed consisting of two parts: the underlying translational periodicity and the distinct atomic positions up to the symmetry operations in the unit cell, consistent with the International Tables for Crystallography. By the Cauchy-Born hypothesis, such a description can be integrated with the theory of continuum mechanics to calculate a derived crystal structure produced by solid-solid phase transformation. In addition, the expressions for the orientation relationship between the parent lattice and the derived lattice are generalized. The derived structure rationalizes the lattice parameters and the general equivalent atomic positions that assist the indexing process of X-ray diffraction analysis for low-symmetry martensitic materials undergoing phase transformation. The analysis is demonstrated in a CuAlMn shape memory alloy. From its austenite phase (L21 face-centered cubic structure), it is identified that the derived martensitic structure has orthorhombic symmetry Pmmn with the derived lattice parameters ad = 4.36491, bd = 5.40865 and cd = 4.2402 Å, by which the complicated X-ray Laue diffraction pattern can be well indexed, and the orientation relationship can be verified.

Nuclear Egress Complexes of HCMV and Other Herpesviruses: Solving the Puzzle of Sequence Coevolution, Conserved Structures and Subfamily-Spanning Binding Properties.

Herpesviruses uniquely express two essential nuclear egress-regulating proteins forming a heterodimeric nuclear egress complex (core NEC). These core NECs serve as hexameric lattice-structured platforms for capsid docking and recruit viral and cellular NEC-associated factors that jointly exert nuclear lamina as well as membrane-rearranging functions (multicomponent NEC). The regulation of nuclear egress has been profoundly analyzed for murine and human cytomegaloviruses (CMVs) on a mechanistic basis, followed by the description of core NEC crystal structures, first for HCMV, then HSV-1, PRV and EBV. Interestingly, the highly conserved structural domains of these proteins stand in contrast to a very limited sequence conservation of the key amino acids within core NEC-binding interfaces. Even more surprising, although a high functional consistency was found when regarding the basic role of NECs in nuclear egress, a clear specification was identified regarding the limited, subfamily-spanning binding properties of core NEC pairs and NEC multicomponent proteins. This review summarizes the evolving picture of the relationship between sequence coevolution, structural conservation and properties of NEC interaction, comparing HCMV to α-, β- and γ-herpesviruses. Since NECs represent substantially important elements of herpesviral replication that are considered as drug-accessible targets, their putative translational use for antiviral strategies is discussed.

First Example of Antiparasitic Activity Influenced by Thermochromism: Leishmanicidal Evaluation of 5,7-dimethyl-1,2,4-triazolo[1,5-a]pyrimidine Metal Complexes.

The World Health Organization catalogues illnesses such as Leishmaniasis as neglected diseases, due to low investment in new drugs to fight them. The search of novel and non-side effects anti-parasitic compounds is one of the urgent needs for the Third World. The use of triazolopyrimidines and their metallic complexes has demonstrated hopeful results in this field. This work studies the antiparasitic efficacy of a series of 5,7-dimethyl-1,2,4- triazolo[1,5-a]pyrimidine first row transition metal complexes against three leishmania spp. strains. The in vitro antiproliferation of promastigote forms of different strains of leishmania spp. (L. infantum, L. braziliensis and L donovani) and the cytotoxicity in macrophage host cells are reported here. The antiparasitic assays have been complemented with enzymatic tests to elucidate the mechanisms of action. New crystal structure description, thermal analysis, magnetic susceptibility and magnetization experiments have also been carried out in order to present a whole characterization of the studied compounds and interesting physical properties besides the biological tests. The results of antiproliferation screening and cytotoxicity show great antiparasitic efficacy in the studied complexes. The superoxide dismutase enzymatic assays exhibit a different behaviour according to the thermochromic triazolopyrimidine form tested. Antiproliferative assays and enzymatic tests corroborate the synergetic leishmanicidal effect present in coordination triazolopyrimidine complexes. The changes in coordination sphere derived from thermochromism affect the physical properties as well as the biological efficacy.

High pressure exploration in the Li-Ln-V-O system.

Using in situ high pressure Raman spectroscopy, two structural changes were observed in a sample of the composition LiLa5O5(VO4)2. Taking this into account and by combining different conditions, three new compounds were further obtained from high pressure-high temperature synthesis. Their crystal structure description was done using the antiphase approach, which implies the presence of oxygen-centered [OLn4] building units, where Ln is La for (1) β-LiLa5O5(VO4)2 and (2) β-LiLa2O2(VO4) or Nd for (3) LiNd5O5(VO4)2 compounds. (1) crystallizes in the triclinic space group P1[combining macron] with unit cell parameters of a = 5.8167(15) Å, b = 12.2954(28) Å, c = 18.7221(69) Å, α = 102.03(2)°, β = 98.76(2)°, and γ = 103.54(2)°; a 3D structure was deduced from the ambient pressure polymorph. (2) also crystallizes in P1[combining macron] with a = 5.8144(7) Å, b = 5.8167(7) Å, c = 8.5272(1) Å, α = 98.184(7)°, β = 100.662(7)° and γ = 92.579(7)°. It shows a 2D structure with [La2O2]2+ layers surrounded by [LiO4] and [VO4] tetrahedra sharing corners and edges. (3) exhibits a 3D architecture isotypic with AP-LiLa5O5(VO4)2. The crucial role of high pressure in such types of synthesis and materials is also discussed.

Robocrystallographer: automated crystal structure text descriptions and analysis

Abstract

Mechanism for the Structural Transformation to the Modulated Superconducting Phase of Compressed Hydrogen Sulfide

A comprehensive description of crystal and electronic structures, structural transformations, and pressure-dependent superconducting temperature (Tc) of hydrogen sulfide (H2S) compressed from low pressure is presented through the analysis of the results from metadynamics simulations. It is shown that local minimum metastable crystal structures obtained are dependent on the choice of pressure-temperature thermodynamic paths. The origin of the recently proposed ‘high-Tc’ superconducting phase with a modulated structure and a diffraction pattern reproducing two independent experiments was the low pressure Pmc21 structure. This Pmc21 structure is found to transform to a Pc structure at 80 K and 80 GPa which becomes metallic and superconductive above 100 GPa. This structure becomes dynamically unstable above 140 GPa beyond which phonon instability sets in at about a quarter in the Γ to Y segment. This explains the transformation to a 1:3 modulation structure at high pressures proposed previously. The pressure trend of the calculated Tc for the Pc structure is consistent with the experimentally measured ‘low-Tc phase’. Fermi surface analysis hints that pressurized hydrogen sulfide may be a multi-band superconductor. The theoretical results reproduced many experimental characteristics, suggesting that the dissociation of H2S is unrequired to explain the superconductivity of compressed H2S at any pressure.

The Floppiness of It All: Bond Lengths Change with Atomic Displacement Parameters and the Flexibility of Various Coordination Tetrahedra in Zeolitic Frameworks. An Empirical Structural Study of Bond Lengths and Angles

We have evaluated more than 7000 crystal structures of zeolites in terms of the values of their bond-lengths T–O (T = Si, Al, P, Zn, Be, Ge, B, As, Ga, Co) and their variability as well as the flexibility of their bond angles O–T–O. Out of these known crystal structure descriptions of zeolites, we have selected 1179 which have estimated standard deviations of their T–O bond lengths of 0.01 A or less. For the most common bond lengths, we obtain 1.603(11) A for 1323 mean tetrahedral Si–O, 1.736(8) A for 416 Al–O, and 1.522(9) A for 228 P–O. It is unsettling that the spread of each of these values is large: about 0.07 A within the population studied by us. Furthermore, these values disagree by several hundredths of an Angstrom from some of the mean values of Si–O, Al–O, and P–O compiled from nonzeolitic types of compounds. This is at variance with the widespread conviction that such T–O distance values should be relatively constant across different types of inorganic compounds. Ever since Cruickshank (Acta C...

Lattice versus structure, dimensionality versus periodicity: a crystallographic Babel?

In this article, several mistakes occurring in the description of crystal structures are pointed out. (1) The term `lattice' is often used instead of `structure'. (2) The two terms `superlattice' and `sublattice' are incorrectly interchanged. (3) Substructures composed of a subset of the crystallographic orbits composing the structure are incorrectly called `sublattices'. (4) Subperiodic structures are incorrectly referred to as `low-dimensional' structures.