Atoms In Crystal Structures Research Articles

First-principles calculation of chalcogen-doped Sr2M2O7 (M=Nb and Ta) for visible light photocatalysis

Doped Sr2M2O7 (M ​= ​Nb and Ta) crystals with various chalcogen X (X ​= ​S, Se, and Te) concentrations have been studied by using first-principles calculations combined with hybrid functional (HSE06). Our results indicate that the more stable doping site of X generally induces the less distortion of the lattice. The calculated formation energies reveal that the doping becomes more difficult in the order S ​< ​Se ​< ​Te. Some localized X np states are located above the VBM of pure semiconductors, which results in the narrowing of band gaps. For Sr2Nb2O7, an increase of the X concentration has negative effect on the narrowing of band gap since the X np states moves towards the VBM of pristine semiconductor. As to Sr2Ta2O7, the higher doping level of X elements leads to the further narrowing of energy gap compared with the lower doping level. The formation of Sr2M2X7 (X ​= ​S and Se) by replacing all the O atoms in crystal structures by chalcogens extends the absorption edges to near-infrared region and loses the abilities to oxidize water. Our findings demonstrate that S-doped Sr2Nb2O7, Se-doped Sr2Nb2O7 and Se-doped Sr2Ta2O7 at a higher doping level, and Te-doped Sr2Ta2O7 at a lower doping level can catalyze overall splitting water reaction under visible light irradiation. Furthermore, they possess stronger capabilities of photo-oxidation and photo-reduction than pristine semiconductors. Therefore, these systems mentioned above are potential visible-light-driven photocatalytic materials, which are worthy of further experimental investigations.

Effect of atomic tessellations on structural and functional properties of additive manufactured lattice structures

The properties of lattice structure are influenced by cell morphology, cell size, relative density and tessellations. In this study, the concept of tessellation has been evaluated for structural and functional properties of additively manufactured lattice structures using PA-12 material. The tessellation design of unit lattice cell is inspired by arrangement of atoms in crystal structures. The strategy of mimicking these different arrangements at atomic level to generate mesoscale cellular structures is termed as ‘Atomic Tessellation’. In the current study, arrangement of metallic crystal structures: BCC, FCC and HCP were compared with conventional periodically tessellated SC structure using sea-urchin unit cell for mechanical, energy absorption and structural behaviour properties. The tessellated lattice structures were printed with hybrid AM technology using HP-MJF 4200. The significant effect of tessellations was observed during compression testing of printed samples in terms of their stress-strain behaviour. Lattice structures such as SC, BCC, FCC and HCP_90 shows ‘degradation-prone deformation behaviour’ which is similar to stretch dominated behaviour in structural elements (thin struts and thin walls). On the other hand, HCP tessellation (HCP_0) converts ‘degradation-prone deformation behaviour’ into ‘progressive deformation behaviour’ that is similar to bending dominated behaviour in structural elements. Moreover, significant effects of tessellations were also observed in load bearing and energy absorption properties. Although the study has attempted to introduce the design concept of atomic tessellations from structural point of view, further studies are required to strengthen tessellation based design principles for obtaining different structural and functional properties. • The novel concept of ‘Atomic Tessellation’ have been introduced in design of cellular lattice structures. • Metallic crystal structures: SC, BCC, FCC and HCP were designed in mesoscale using Sea Urchin (SU) inspired unit cell. • Mechanical properties and energy absorption capacity was affected by tessellation strategy. • Tessellation strategy converts stretch-dominated behavior of lattice structure to bending dominated behavior and vice versa. • HCP tessellated structure behaves as bending dominated in 0˚orientation whereas as stretch dominated behavior was observed in 90˚orientation.

Augmenting Structure-Based Design with Experimental Protein-Ligand Interaction Data: Molecular Recognition, Interactive Visualization, and Rescoring.

The previously introduced ratio of frequencies (RF ) framework provides statistically sound information on the relative interaction preferences of atoms in crystal structures. By applying the methodology to protein-ligand complexes, we can investigate the significance of interactions that are employed in structure-based drug design. Here, we revisit three aspects of molecular recognition in the light of the RF framework, namely stacking interactions of heteroaromatic rings with protein amide groups, interactions of acidified C-H groups, and interaction differences between syn and anti lone pairs of carboxylate groups. In addition, we introduce a highly interactive visualization tool that facilitates design idea generation in structure-enabled drug discovery projects. Finally, we show that applying the RF analysis as a simple rescoring tool after docking improves enrichment factors for the DUD-E diverse targets subset supporting the relevance of our approach.

Crystal and electronic structure of poly-halogenated lanthanide Schiff base complex: Insights into halogen bond from structural and theoretical analysis

With the aim to explore the electronic structure and the influence of halogen bonds to the supramolecular networks of lanthanide Schiff base complexes, halogenated salen-type Schiff-base and cerium nitrate were chosen as starting materials and isolated a new salen-type cerium(IV) complex [CeIV(3,5Br-salpn)2] (1) where 3,5Br-salpn = N,N’-bis(3,5‑bromo salicylidene)-1,3-diaminopropane. The complex was investigated in the solid state by single-crystal X-ray diffraction. Structural analysis reveal the substitutional halogen atoms play an important role in tuning the molecule structure and supramolecular networks. The electronic structure of halogen bonds was confirmed by theoretical calculation, which uncovered an interesting phenomenon that the σ-hole of bromine atoms of different substituents present quite different molecular electrostatic surface potential (5-Br: Vmax = 6.8 kcal/mol and 3-Br: Vmax = 13.2 kcal/mol). Hirshfeld surface analysis showed that bromine atoms involved intermolecular contacts donate 56.6% contribution of all the interactions, indicating the significant role of bromine atoms in crystal structures. Additionally, fluorescence experiments proved that the halogenated ligand has an important influence on the fluorescence behavior of the complex.

A computational approach to study the optoelectronic properties of F-BODIPY derivatives at the bulk level for photovoltaic applications

The Dipyrrin compounds are recognized as imminent and hi-tech organic semiconductor materials (OSMs) designed for photovoltaic applications owing to low-cost, flexible, and eco-friendly nature. In a latest study, several optoelectronic properties of conjugated F-BODIPY derivatives were studied by using the density functional theory (DFT) at (GGA/PBE) level. This analysis classifies Comp_1 (5,5-difluoro-1,37,9-tetramethyloctahydro-1H,5H-5l4-dipyrrolo[1,2-c:2′,1′-f][1,3,2] diazaborinine) as a direct band-gap semiconductor with a band-gap of 2.81 eV. The band-gap of Comp_2 (2-ethyl-5,5-difluoro-1,3,7,9-tetramethyloctahydro-1H,5H-5l4-dipyrrolo[1,2-c:2′,1′-f][1,3,2]diazaborinine) and Comp_3 (2,8-diethyl-5,5-difluoro-1,3,7,9-tetramethyloctahydro-1H,5H-5l4-dipyrrolo[1,2-c:2′,1′-f] [1,3,2] diazaborinine) are reduced by 1.25 and 1.09 eV, respectively in comparison with parent molecule Comp_1 owing to the influence of p- orbitals of all atoms in crystal structures. The reduction in energy and density of states (DOS) for these compounds in this study validated that band-gap could be improved to a required value for optoelectronic applications by derivatives modeling. Additionally, optoelectronic properties at the solid-state bulk level were also computed. Several features of interest at solid-state bulk level exposed the F-BODIPY derivatives as competent compounds for organic semiconductor devices applications.

Supramolecular synthons involving fluorine atoms in crystal structures of fluorobenzamides

Supramolecular synthons involving fluorine atoms in crystal structures of fluorobenzamides

Erratum to: Tautomerism in acyl-pyrazolones and in a novel photolysis product—importance and impact of the accurate localization of hydrogen atoms in crystal structures

Erratum to: Tautomerism in acyl-pyrazolones and in a novel photolysis product—importance and impact of the accurate localization of hydrogen atoms in crystal structures

Tautomerism in acyl-pyrazolones and in a novel photolysis product—importance and impact of the accurate localization of hydrogen atoms in crystal structures

Acyl-pyrazolones exist in four different tautomeric forms (two keto and two enol) in crystal structures. Routine crystal structure refinements using an independent atom model and routine isolated-molecule calculations fail in locating the mobile hydrogen atoms accurately in 22 investigated acyl-pyrazolone examples. However, a combination of both within the framework of quantum crystallography represented by the method of Hirshfeld atom refinement accurately locates the mobile hydrogen atom in a resonance-assisted hydrogen bond of title compound 3, a novel photolysis product. The impact of the hydrogen atom position on the resonance system of the non-hydrogen framework of the various tautomers is discussed, and the importance of intermolecular interactions for the positioning of the hydrogen atom is highlighted.

Using the Plan View To Teach Basic Crystallography in General Chemistry

The plan view is used in crystallography and materials science to show the positions of atoms in crystal structures. However, it is not widely used in teaching general chemistry. In this contribution, we introduce the plan view, and show these views for the simple cubic, body-centered cubic, face-centered cubic, hexagonal close packed, CsCl, NaCl, diamond cubic, ZnS, and CaF2 unit cells. A survey administered to college-level general chemistry students indicates that the plan view helps them to better understand crystal structures.

Likelihood of atom-atom contacts in crystal structures of halogenated organic compounds.

The likelihood of occurrence of intermolecular contacts in crystals of halogenated organic compounds has been analysed statistically using tools based on the Hirshfeld surface. Several families of small halogenated molecules (containing organic F, Cl, Br or I atoms) were analysed, based on chemical composition and aromatic or aliphatic character. The behaviour of crystal contacts was also probed for molecules containing O or N. So-called halogen bonding (a halogen making short interactions with O or N, or a π interaction with C) is generally disfavoured, except when H is scarce on the molecular surface. Similarly, halogen⋯halogen contacts are more rare than expected, except for molecules that are poor in H. In general, the H atom is found to be the preferred partner of organic halogen atoms in crystal structures. On the other hand, C⋯C interactions in parallel π-stacking have a high propensity to occur in halogenated aromatic molecules. The behaviour of the four different halogen species (F, Cl, Br, I) is compared in several chemical composition contexts. The analysis tool can be refined by distinguishing several types for a given chemical species, such as H atoms bound to O or C. Such distinction shows, for instance, that C-H⋯Cl and O-H⋯O are the preferred interactions in compounds containing both O and Cl.

Packing schemes of cavities in selected clathrasils and zeolites and the analogous packings of atoms in crystal structures

Sizes of cavities and their packing schemes in selected zeolites and clathrasils were studied by means of least squares fitting of circumscribed spheres to them. Resulting packing of spheres of different diameters was analyzed by the coordinates of their centers, their volumes and sphericity, and interpreted by comparison with analogous packings of atoms in inorganic compounds and alloys. The topology is described qualitatively as “negative” structures formed by the cavities. Melanophlogite and dodecasils 3C and 1H are all clathrasils with isolated cavities. They all have pentagonal dodecahedral [5 12 ] cages, associated with other cavity types. The packing of cavities in melanophlogite is analogous to the packing of atoms in the structure of Cr 3 Si, where the Cr atoms form icosahedra around the Si sites. Dodecasil 3C has a cubic arrangement of [5 12 ] cavities, which is described as ABC stacking of kagome nets and its cavity packing is an analog to the packing scheme of atoms in the cubic Laves phase MgCu 2 . Dodecasil 1H has an arrangement of [5 12 ] cavities in an AA stacking of kagome nets and is analogous to the alloy structure type CaZn 5 . Edingtonite and natrolite are built from two types of cavities, tetragonal scalenohedra and [8 6 ] cavities. The [8 6 ] cavities have different shape and packing in the two structures. In paulingite, the largest cavity, a large rhombicuboctahedron [4 12 6 8 8 6 ] with a diameter of 11.02 A is in a body centered configuration. It is interspaced by six other types of cavities with diameters from 5.10 to 8.20 A, arranged in a complex pattern. In this structure, there are three non-intersecting channel systems. Their cavity arrangements mimic sodalite and a modified ReO 3 structure. The cubic structure of sodalite has only one type of cavity, a truncated octahedron [4 6 6 8 ] with a diameter of 6.41 A, arranged in a body-centered packing analogous to α-Fe. Chabasite has a rhombohedral packing of elongate cavities [4 12 6 2 8 6 ], whereas Linde Type A has [4 6 6 8 ] and [4 12 6 8 8 6 ] cavities in a CsCl-type arrangement. The cavity representation used here gives a clear picture of cavities and interconnections even for complicated cases.

The coordination polyhedra GaS n in crystal structures

Voronoi-Dirichlet polyhedra (VDP) and the intersecting sphere method were used to perform coordination analysis of 204 crystallographically different gallium atoms in the structures of all known compounds containing GaS n polyhedra. The Ga(III) atoms in crystal structures were found to be linked to 6, 4, or three sulfur atoms to form coordination octahedra, tetrahedra, and triangles, respectively, whereas Ga(II) atoms are bound only to three sulfur atoms and a gallium atom. The effect of the valence state and the coordination number of gallium atoms on the key parameters of the VDP is considered. A common linear dependence of the solid angles of the VDP faces corresponding to the Ga-S bonds on the corresponding interatomic distances, which vary from 2.09 to 2.53 A, was established to exist.

Maximum filling principle and sublattices of actinide atoms in crystal structures

The most important characteristics of the Voronoi-Dirichlet polyhedra (VDP) of A atoms (A is actinide) in chemically homogeneous sublattices in the crystal structures of 3479 inorganic, coordination, and organometallic compounds are determined. The effect of the actinide nature on the A-A interatomic distances in the crystal structures is considered. In the Th, U, Np, or Pu sublattices, VDP have most often 14 faces and the Fedorov cuboctahedron is the most abundant type of VDP, whereas in Ac, Pa, Am, Cm, Bk, or Cf sublattices, the VDP have mainly 12 faces and are shaped like rhomobododecahedra. In A sublattices that typically form VDP with 14 faces, the actinide atoms occupy, most often, sites with C 1 symmetry (47 to 59% of the sample size). In the case of actinides whose A sublattices tend to form VDP with 12 faces, the C 1 site symmetry is found either very rarely (Pa, Am, Cf) or not at all (Ac, Cm, Bk).

Maximum filling principle and sublattices of lanthanide atoms in crystal structures

Maximum filling principle and sublattices of lanthanide atoms in crystal structures

Predictability of ion transport properties from the structure of solid electrolytes

The concept of bond valence (BV) is widely used in crystal chemical considerations, e.g. to assess equilibrium positions of atoms in crystal structures from an empirical relationship between bond lengthR M−X and bond valenceS A−X =exp [(R 0 −R M−X ) /b] as sites where the BV sumV(A)=∑ s M−X equals the formal valenceV id of the cationM + . Our modified BV approach that systematically accounts for the softness of the bond may then be effectively used to study the interplay between structure and properties of solid electrolytes. This is exemplified for correlations to experimental data from IR, NMR, and impedance spectroscopy. Combining the bond valence approach with reverse Monte Carlo (RMC) modeling or molecular dynamics (MD) simulations provides a deeper understanding of ion transport mechanisms, especially in highly disordered or amorphous solids. Local structure models for crystalline electrolytes are derived by combining crystallographic structure information with simulations. A method for the prediction of the activation energy of the ionic conductivity from the bond valence analysis of the crystal structure is proposed. Taking into account the mass dependence of the conversion factor from bond valence mismatch into an activation energy scale, we could establish a correlation that holds for different types of mobile ions. The strong coupling of the H+ transfer to the anion motion in proton conductors requires a special treatment. For glassy solid electrolytes RMC structure models are BV-analyzed to assess the total number of equilibrium sites and to identify transport pathways for the mobile ions. Recently, we have reported a correlation between the pathway volume fraction and the transport properties that permits to predict both absolute value and activation energy of the dc ionic conductivities of disordered solids (including mixed alkali glasses) directly from their structural models. Here we discuss a corresponding BV analysis of molecular dynamics simulation trajectories that allows quantifying the evolution of pathways in time and the influence of temperature on the transport pathways.

Reliable computation of the points of intersection of $n$ spheres in $R^n$

The problem of determining the points of intersection of n spheres in R n has many applications. Examples in 3-D include problems in navigation, in positioning of specific atoms in crystal structures, in reconstructing torso geometries in experimental cardiology, in the `Pentacle Problem,' and in many other problems of distance geometry. The problem is easily formulated as a system of n nonlinear equations in the coordinates of the unknown point(s) of intersection and it is of interest to determine an efficient and reliable method of solution. It is shown that apart from a few square roots the problem is usually easily and robustly solved without iteration by employing standard techniques from linear algebra. In some applications, however, the radii of the spheres may not be known accurately and this can lead to difficulties, particularly when the required point is close to lying in the affine subspace defined by the n centres of the spheres. In such cases it is more appropriate to formulate a nonlinear least squares problem in order to identify a `best approximate solution.' The special structure of this nonlinear least squares problem allows a solution to be calculated through an efficient safeguarded Newton iteration.

Workshop focuses on protein crystallography with neutrons

The challenge in protein structure research is to visualize hydrogen positions at 8, resolution in biological structures. Neutrons are the ideal probe to detect hydrogen atoms in crystal structures, but in practice only a very limited number of protein structure papers using neutrons are published. The main drawbacks come from the large sample size required and the long data acquisition times in com- parison with X-ray measurements. Improvement in instrument performance and availability of more powerful neutron sources by next generation spallation-based facilities could solve these problems and, in complementarity to X-rays, open up the fieId of protein crystallography with neutrons.

The Form of the Carbon Atom in Crystal Structure

A. GERSTACKER, H. Moller, and A. Reis have published an account of the crystal structure of pentaerythritol tetra-acetate (Zeitsch. f. Kryst., 66, 355; Jan. 1928), in which they assign the crystals to the space-group C34h with a simple tetragonal lattice (Γt). There are two molecules of pentaerythritol tetraacetate to the unit cell and the space-group C34h with a Γt lattice requires eight asymmetric molecules per unit cell. Therefore the molecules of pentaerythritol tetra-acetate must have some kind of fourfold symmetry. There are two types of fourfold symmetry possible in this space-group—either a simple fourfold rotation axis or a fourfold alternating axis. Messrs. Gerstacker, Moller, and Reis have chosen the former, since it leads to a molecule which can be built into a chain-like structure, and the latter does not.