Analysis Of Interatomic Distances Research Articles

Adhesion properties of the B- and N-doped graphene/Fe(110) interface

Influence of B and N substitutional impurities on the adhesion properties, electronic and magnetic characteristics of the external and internal graphene/Fe(110) semi-coherent interface was investigated by the projector augmented-wave method within the density functional theory. The analysis of interatomic distances, charge densities, charge transfer and magnetic states of atoms was performed. It was shown that B-doped graphene has a higher adhesion energy on the Fe(110) surface and in the iron bulk in comparison with the undoped systems; whereas, N-doped graphene in the Fe bulk demonstrates the opposite trend and on the surface it has no effect. Boron acts as electron donor that increases charges of the nearest C atoms by 0.5–0.6e. Nitrogen due to its high electronegativity is an acceptor and as a result the nearest C atoms lose 0.2–0.3e. Both impurities, depending on the position, influence differently on the magnetic moment of the nearest iron atoms.

Electronic phase transition in the Re3Ge7 endohedral cluster compound

${\mathrm{Re}}_{3}{\mathrm{Ge}}_{7}$ is a unique electronic material showing low-temperature metal--insulator-like phase transition. Furthermore, bulk superconductivity can be induced in ${\mathrm{Re}}_{3}{\mathrm{Ge}}_{7}$ by hole doping. Here, we present transport properties, temperature-dependent high-resolution powder x-ray diffraction study, and electronic structure of ${\mathrm{Re}}_{3}{\mathrm{Ge}}_{7}$ in the vicinity of the electronic phase transition. Electrical resistivity and heat capacity measurements confirm the anomaly at 58.5 K in zero magnetic field. The Seebeck coefficient changes its sign and exhibits a maximum below the transition temperature indicating substantial changes in the electronic structure. Temperature-dependent structural studies confirm the second-order nature of phase transition, where unit cell parameters show abrupt change at the transition temperature. An analysis of interatomic distances indicates that the shrinkage of the unit cell volume is due to the interatomic changes taking place in the second coordination sphere of Re atoms. Electronic structure calculations reveal strong $5d\ensuremath{-}4p$ hybridization of valence orbitals near the Fermi level, which is situated between two deep pseudogaps of the density of states. The transition to the semiconducting state is accompanied by the opening of a band gap at the Fermi level right above the narrow pocket of hybridized states.

«Ellestadite»-type anionic [PO4]3– → [SO4]2– substitutions in β-Ca3(PO4)2 type compounds: A new route to design the inorganic phosphors

Sulfate anion plays an important role in the development of inorganic phosphors and is considered as the path for for the enhancement of the luminescent properties. The heterovalent [PO4]3– → [SO4]2– anion substitution in the β-Ca3(PO4)2-type compounds was realized using the “ellestadite”-type strategy called by the analogy with the apatite-type structures. The novel compounds belonging to the Ca10.5–0.5x–yMy(PO4)7–x(SO4)x, M = Ca2+, Mg2+ and Zn2+ series have been synthesized using high-temperature solid state reaction. The used isomorphous scheme was [PO4]3– + ½ Ca2+ = [SO4]2– + ½ □ with the formation of the vacancy for the charge compensation. The successful incorporation of [SO4]2– groups was approved by Fourier-transform infrared spectroscopy, EDX method, and powder X-ray diffraction analysis. It was found that the sulfur atoms predominantly occupied T2 sites in the anionic sublattice according to crystal structure refinement based on the analysis of interatomic distances. The photoluminescent properties were studied for the Eu3+-doped samples and it was shown that Zn2+-containing samples exhibit a 1.5 times higher intensity in comparison with Mg2+-containing substituted phosphates. Thus, a new “ellestadite”-type substitution in β-Ca3(PO4)2-type structure significantly expands the crystal chemistry and give more insights into the deeper understanding of the dependence of luminescent properties on the cation distribution. The pathways of the [SO4]2– incorporation into the crystal structures are discussed in details.

Pattern of covalent and non‐covalent interactions within the pentaiodide anion in the structure of (3‐HOC5H9NH2)I5

Abstract3‐Hydroxypiperidinium pentaiodide was synthesized by a facile reaction in concentrated aqueous HI. Its crystal structure comprises 3‐hydroxypiperidinium cations and pentaiodide anions, the latter having geometry of cis‐shaped chains composed of I2 and I3− building units. The analysis of interatomic distances, Raman spectroscopy data, and results of DFT calculations, including non‐covalent interaction analysis, showed that the title compound exhibits a complex pattern of covalent and non‐covalent interactions. Those include I−I covalent bonds and I⋅⋅⋅I halogen bonds within the I5− anion as well as (N)H⋅⋅⋅I and (O)H⋅⋅⋅I hydrogen bonds and even weaker (C)H⋅⋅⋅I van‐der‐Waals interactions between the cations and anions.

The crystal structure and thermal expansion of novel substitutionally disordered Ca10TM0.5(VO4)7 (TM = Co, Cu) orthovanadates.

The whitlockite-related materials have attracted researchers' attention because of their potential application in various fields, especially in optoelectronics. In the present work, the structure of novel whitlockite-related oxides Ca10TM0.5(VO4)7 (TM = Co, Cu) is studied at room and high temperatures, using X-ray powder diffraction. These compounds form by fractional substitution of divalent transition metal atoms into the Ca3(VO4)2 lattice. Rietveld refinements provided the structural details. The lattice parameters are a = 10.78074(6) Å, c = 37.8196(2) Å, and V = 3806.67(4) Å3 for Ca10Co0.5(VO4)7 and a = 10.78710(7) Å, c = 37.8997(3) Å, and V = 3819.23(4) Å3 for Ca10Cu0.5(VO4)7. Structure refinement results show that among the five available sites (M1-M5), the M2+ ions select the M5 site. This finding is confirmed by analysis of interatomic distances: due to the difference in size between TM and Ca ions sharing the M5 site, the M5-O distance shortens by about 5.0% for Ca10Co0.5(VO4)7 and 2.7% for Ca10Cu0.5(VO4)7 with respect to the unsubstituted parent compound, Ca3(VO4)2. The observed trends in the crystallographic properties of the studied crystals are in line with those of previously reported structurally related phosphates, Ca10.5-xMx(PO4)7 (M = Mg or divalent transition metal). Moreover, the observed tendency for occupation of M5 by small divalent ions follows the earlier theoretical results. For cobalt and copper substituted orthovanadate and orthophosphate whitlockite related materials, a linear variation in the unit cell size is demonstrated. The common equation for evaluation of volume is applicable to the substitution of the two transition metals in orthovanadate and orthophosphate whitlockite related materials. Thermal expansion is investigated for both compounds. The variations of the lattice parameters and the thermal expansion coefficient with temperature are determined in the 300-810 K range. The lattice parameter, a, expands by 0.80% for Ca10Co0.5(VO4)7 and 0.74% for Ca10Cu0.5(VO4)7 in this range. The lattice parameter, c, enlarges by about 0.70% for both samples. In the studied temperature range, the volume thermal expansion coefficient of Ca10Co0.5(VO4)7 increases from 37.2 to 44.8 MK-1 and for Ca10Cu0.5(VO4)7, it increases from 35.1 to 45.2 MK-1; the observed expansion anisotropy is smaller than those of other related compounds.

Theoretical study of high-pressure phase stability of NaZr2(PO4)3 via elastic constants and equation of state

Phase stability of \(\mathrm {NaZr_2(PO_4)_3}\) has been studied through density functional theory calculations of elastic constants, equation of state and enthalpies. The changes in elastic constants as a function of pressure show that the ambient rhombohedral (R\(\bar{3}c\)) \(\mathrm {NaZr_2(PO_4)_3}\) becomes unstable above 8 GPa and this instability is driven by a softening of C\(_{44}\) elastic constant through one of the Born stability criteria. High-pressure equation-of-state and enthalpy calculations further show that the ambient rhombohedral (\(R\bar{3}c\)) structure transforms first into another rhombohedral (R3) phase and subsequently to LiZr\(_2\)(PO\(_4\))\(_3\)-type orthorhombic phase at pressures above 6 and 8 GPa respectively which are in agreement with a recent x-ray diffraction study. Analysis of interatomic distances show that LiZr\(_2\)(PO\(_4\))\(_3\)-type orthorhombic structure allows for shorter Na–O and Zr–P bonds at high pressures which appears to enable strong bonding and stability. Calculated formation enthalpy and bulk modulus of the ambient phase of \(\mathrm {NaZr_2(PO_4)_3}\) are found to be in reasonable agreement with the respective experimental values.

Structure determination of KLaS2, KPrS2, KEuS2, KGdS2, KLuS2, KYS2, RbYS2, NaLaS2and crystal-chemical analysis of the group 1 and thallium(I) rare-earth sulfide series

One of the purposes of this work is to provide a crystallographic review of group 1 and thallium rare-earth ternary sulfides M(+)Ln(3+)S2. We have therefore determined crystal structures of KLaS2, KPrS2, KEuS2, KGdS2, KLuS2, KYS2, RbYS2, which belong to the α-NaFeO2 structural family (R3m), as well as NaLaS2, which is derived from the disordered NaCl structural type (Fm3m). The determined structures were compared with known members of the group 1 as well as thallium(I) rare-earth sulfides by the standard tools of crystal-chemical analysis such as comparison of bond-valences, analysis of interatomic distances and comparison of the unit-cell parameters. The results indicate why the cubic structural type is limited to Li(+) and Na(+) members of the series only. The analysis has also revealed frequent problems in the reported crystal structures, especially in the determination of the K(+) compounds, probably due to severe absorption and different accuracy and sensitivity of various instruments. Intense diffuse scattering has been discovered in NaLaS2, which will be the subject of further investigation. The newly determined as well as already known structures are summarized, together with critical comments about possible errors in the previous structure determinations.

Identification of molecules in inorganic compounds from X-ray or neutron diffraction data and correction of their structures on the basis of vibrational spectroscopy data

A method of identification of molecules in inorganic crystals with asymmetric M-X...M bridges has been suggested on the basis of analysis of interatomic distances in the structure unit M (−X...M)n, which includes the atoms of the first and second coordination spheres. This analysis makes it possible to discern molecules (complex anions or cations) as a groups of atoms linked with each other by short M-X bonds, whereas the atoms of neighboring groups are linked by long M...X bonds. The symmetry of such a group is often lower than it follows from X-ray or neutron diffraction data. Studying vibrational spectra affords information on the true symmetry of a molecule. The use of the method is exemplified by the rhombohedral BaTiO3 phase.

Electronic Structure, Chemical Bonding, and Solid‐State NMR Spectroscopy of the Digallides of Ca, Sr, and Ba

Combined application of (69,71)Ga NMR spectroscopy and quantum mechanical calculations reveals the chemical bonding in the digallides of Ca, Sr, and Ba. An analysis of the electron localization function (ELF) shows honeycomb-like 6(3) nets of the Ga atoms as the most prominent structural features in SrGa(2) and BaGa(2). For CaGa(2) a description of a 3+1-coordinated Ga atom is revealed by the ELF and by an analysis of interatomic distances. The NMR spectroscopic signal shift is mainly due to the Knight shift and is almost equal for the investigated digallides, whereas the anisotropy of the signal shift decreases with the radius of the alkaline-earth metals. Calculated and observed values of the electric field gradient (EFG) are in good agreement for CaGa(2) and BaGa(2) but differ by about 21 % for SrGa(2) indicating structural instability. Better agreement is achieved by considering a puckering of the Ga layers. For BaGa(2) an instability of the structure is indicated by a peak in the density of states at the Fermi level, which is shifted to lower energies when taking puckering of the Ga layers into account. Both structural modifications are confirmed by crystallographic information. The Fermi velocity of the electrons is strongly anisotropic and is largest in the (001) plane of the crystal structure. This results in an alignment of the crystallites with the [001] axis perpendicular to the magnetic field as observed in (69,71)Ga NMR spectroscopy and magnetic susceptibility experiments. The electron transport is predominantly mediated by the Ga-Ga p(x)- and p(y)-like electrons in the (001) plane. The specific heat capacity of BaGa(2) was determined and indicated the absence of phase transitions between 1.8 and 320 K.

Some applications of the bond valence model to transition metal chalcogenides

The analysis of interatomic distances in complex transition metal chalcogenides of type A m [T n S p ] (A, alkali or alkaline earth metal; T, mainly Fe, Cu) can furnish interesting information on the oxidation state of the metal and also of sulfur. The charge distribution in complex anions can be estimated. Structural problems of the accommodation of the cations in framework structures leading to disorder can be detected.

An analysis of ATP binding with kinase catalytic subunit by molecular dynamics simulation of the CDK2 active kinase crystal lattice

Molecular dynamics simulation was used to analyze changes in the functionally significant structural elements of the crystal lattices of pT160-CDK2/cyclin and A/ATP-Mg2+/substrate complexes of the native (CDK2-G16) and mutant (CDK2-S16) active kinases at physiological temperatures (300 K). The structural rearrangement of ATP caused by changes in the kinase catalytic domain was studied. ATP was fixed by the ionic and H-bond interactions of several residues, including Lys33, Asp145, and side-chain amides of the G loop between β1 and β2. The binding of the kinases to complexes with cyclin and the phosphorylation of T160 in the active complex of the CDK2 kinase result in the ATP orientation more convenient for the transfer of the phosphate group to the substrate. An analysis of interatomic distances in the ATP active site region and Asp145, Asn132, Lys33 catalytic sites participating in the orientation of ATP phosphates revealed that the Asp 145 amino acid residue was situated noticeably closer to the ATP molecule in the native complex than in its mutant counterpart. The same is true of the arrangement of the Lys33 residue with respect to ATP.

Kaolinite:Dimethylsulfoxide IntercalateA Theoretical Study

Three models of the kaolinite:dimethylsulfoxide intercalate with 25, 50, and 100% saturation of dimethylsulfoxide (DMSO) have been investigated by means of density functional theory (DFT, fully periodic approach). The analysis of interatomic distances was used to characterize interactions between DMSO molecules and kaolinite layers. It was found that the most dominant forces in the formation of stable intercalates are the hydrogen bonds formed between the sulfonyl oxygen atom and surface hydroxyl groups. Weak hydrogen bonds, formed between the methyl groups and oxygen atoms of both adjacent layers, play an important role in the final localization and stabilization of the DMSO molecule in the interlayer space. Very good agreement was obtained between calculated (13.0 and 15.2 kJ mol-1) and experimental (13.0 and 16.5 kJ mol-1) energetic barriers for the free rotations of both methyl groups of the intercalated DMSO molecule. The calculation of the reaction energy of the intercalation process has shown a rel...

Magnetic properties and crystal structure of β-Ta

Polycrystalline samples of β-Ta with Frank-Kasper σ-phase structure prepared by electrolysis are studied. The atomic parameters are determined by the Rietveld method. The magnetic susceptibility is measured in the temperature range 4.2 < T < 273 K and the dependence of the magnetization on the magnetic field strength is measured at 4.2 and 77 K. The analysis of interatomic distances and the results of magnetic measurements indicate that clusters with a localized excess charge exist in β-Ta. The data obtained in this study suggest structural changes in β-Ta at T < 77 K.

Structural Properties and Stability of the becc and Omega Phases in the Zr-Nb System: Part Ill. Analysis of Interatomic Distances and Chemical Bonding Effects

This work is part of a systematic investigation of the composition dependence of the structural properties and relative stability of the bcc and omega phases in the Zr-Nb system. On the basis of our previous results on the lattice parameters of Zr-Nb alloys a detailed analysis is performed of the bonding distances in the quenched and aged omega phase. The analysis reveals striking regularities which are discussed in the light of recent first-principles calculations of the electronic structure of the omega phase in Zr. A picture of the structure bonding relations in the omega phase is proposed which accounts for the theoretical results as well as experimental data on lattice parameters, interatomic distances, and the composition dependence of the hexagonal/trigonal symmetry change in this phase. The present model is also used in discussing the possibility of atomic ordering in the Zr-Nb omega phase, and the Zr-Zr bonding distances in some AlB 2 -type structure compounds of Zr.

The crystal structure of CuVO 3(I), a distorted ilmenite-type derivative

The crystal structure of a high-pressure phase, CuVO 3(I), has been determined and refined by full-matrix least-squares procedures using automatic diffractometer data to a residual R = 0.055 ( R w = 0.070). The space group is triclinic, P1, with a = 4.9646(10), b = 5.4023(7), c = 4.9154(7)Å, α = 90.32(1), β = 119.13(1), and γ = 63.93(1)°; Z = 2. This structure is the first example of a triclinic distortion of the ilmenite structure-type and is discussed in terms of its crystal chemistry. Analysis of interatomic distances indicates the valence distribution to be Cu 2+V 4+O 3. The anomalous paramagnetic moment is discussed in terms of V 4+V 4+ interactions.