Coordination Bond Distances Research Articles

Structural and elastic properties of zirconium silicate glasses: Insight from molecular dynamic simulation

Using Morse potentials, we performed molecular dynamics simulations to study the effect of ZrO2/SiO2 substitution on the structure and mechanical properties of SiO2-ZrO2 glasses with various ZrO2 concentrations (5, 10, 20, 30, 40, and 50 mol%). We computed the pair distribution function (PDF) for all atomic pairs and extracted the cation-oxygen coordination number and bond distance as a function of composition for Zr4+ and other cations. We found that Zr entered the glass network as distorted [ZrO6] octahedra. Our results showed that the ZrO2 content was positively associated with the number of non-bridging oxygens and the emergence of tricluster oxygens, which consequently reduced the glass transition temperature. The elastic constants such as Young’s, bulk and shear modulus, increase with rising zirconium content.

Mapping the structural trends in zinc aluminosilicate glasses.

The structure of zinc aluminosilicate glasses with the composition (ZnO)x(Al2O3)y(SiO2)1-x-y, where 0 ≤ x < 1, 0 ≤ y < 1, and x + y < 1, was investigated over a wide composition range by combining neutron and high-energy x-ray diffraction with 27Al magic angle spinning nuclear magnetic resonance spectroscopy. The results were interpreted using an analytical model for the composition-dependent structure in which the zinc ions do not act as network formers. Four-coordinated aluminum atoms were found to be in the majority for all the investigated glasses, with five-coordinated aluminum atoms as the main minority species. Mean Al-O bond distances of 1.764(5) and 1.855(5) Å were obtained for the four- and five-coordinated aluminum atoms, respectively. The coordination environment of zinc was not observed to be invariant. Instead, it is dependent on whether zinc plays a predominantly network-modifying or charge-compensating role and, therefore, varies systematically with the glass composition. The Zn-O coordination number and bond distance were found to be 4.36(9) and 2.00(1) Å, respectively, for the network-modifying role vs 5.96(10) and 2.08(1) Å, respectively, for the charge-compensating role. The more open coordination environment of the charge-compensator is related to an enhanced probability of zinc finding bridging oxygen atoms as nearest-neighbors, reflecting a change in the connectivity of the glass network comprising four-coordinated silicon and aluminum atoms as the alumina content is increased.

X-ray Absorption Spectroscopy for Estimation of Oxidation State, Chemical Fraction and Local Atomic Structure of Materials

This work discussed the role of X-ray absorption spectroscopy (XAS) in determining the oxidation state, chemical fraction, and local atomic structure of the materials. These aspects of XAS were discussed by taking LiNiO2 and Mn3O4 as prototype materials. The oxidation state of metal ions in these oxides was estimated with the help of XAS spectra of the reference oxides such as NiO (in the case of LiNiO2), MnO, Mn2O3, and MnO2 (in the case of Mn3O4). Analysis of the oxidation state was performed from the main absorption edge which was estimated from half of the step height. This showed that the Ni K-edge absorption edge of LiNiO2 is slightly above that of NiO. In the case of Mn ions, the main absorption edges show a linear variation with the oxidation states. This estimates the presence of a mixed oxidation state (2.6+) of Mn ions in Mn3O4. Linear combination fitting results exhibit that almost 35% of ions are in a 2+ oxidation state. The remaining ions are in a 3+ oxidation state. Thus, XAS can determine the fractions of each oxidation state of a particular ion in a given material. Quantitative information on coordination number and bond distance of nearest neighbor for a given element of a material is another important use of this technique.

Understanding X-ray absorption spectra by means of descriptors and machine learning algorithms

X-ray absorption near-edge structure (XANES) spectra are the fingerprint of the local atomic and electronic structures around the absorbing atom. However, the quantitative analysis of these spectra is not straightforward. Even with the most recent advances in this area, for a given spectrum, it is not clear a priori which structural parameters can be refined and how uncertainties should be estimated. Here, we present an alternative concept for the analysis of XANES spectra, which is based on machine learning algorithms and establishes the relationship between intuitive descriptors of spectra, such as edge position, intensities, positions, and curvatures of minima and maxima on the one hand, and those related to the local atomic and electronic structure which are the coordination numbers, bond distances and angles and oxidation state on the other hand. This approach overcoms the problem of the systematic difference between theoretical and experimental spectra. Furthermore, the numerical relations can be expressed in analytical formulas providing a simple and fast tool to extract structural parameters based on the spectral shape. The methodology was successfully applied to experimental data for the multicomponent Fe:SiO2 system and reference iron compounds, demonstrating the high prediction quality for both the theoretical validation sets and experimental data.

Efficient Electronic Modulation of g-C 3 N 4 Photocatalyst by Implanting Atomically Dispersed Ag 1 -N 3 for Extremely High Hydrogen Evolution Rates

Efficient Electronic Modulation of g-C ₃ N ₄ Photocatalyst by Implanting Atomically Dispersed Ag ₁ -N ₃ for Extremely High Hydrogen Evolution Rates

Defect Induced Charge Redistribution and Enhanced Adsorption of Lysozyme on Hydroxyapatite for Efficient Antibacterial Activity.

Defects in hydroxyapatite (HA) have attracted increasing research interest due to their significant functions to increase the bioactivity and antibacterial ability of hard-tissue implants. However, little is known about the natural property and functional mechanism of the defects in HA. Herein, we reported on the defect property concerned with the coordination state and charge distribution in Al doped HA, as well as the consequent interface and protein capture ability for improved antibacterial activity. Systemic investigations suggested that Al replacing Ca in HA induced coordination defect with decreased coordination number and bond distance, caused charge transfer and redistribution of surrounding O atom and resulted in an increase in negative charge of coordinated O atoms. These O atoms coordinated with Al further served as docking sites for lysozyme molecules via electrostatic and H-bonding interaction. The capacity of lysozyme adsorption for Al-HA increased approximately 10-fold more than that of HA, which significantly increased the antibacterial activity through lysozyme-catalyzed splitting of cell wall of bacteria. Moreover, in vitro studies indicated that Al-HA materials showed good cytocompatibility. These findings not only provided new insights into the important effect of defects on the performances of HA biomaterials by modulation of the coordination state, charge distribution, and chemical activity, but also proposed a promising method for efficient antibacterial activity of HA biomaterials.

Thermodynamics Perspective on the Stepwise Conversion of Methane to Methanol over Cu-Exchanged SSZ-13

Transition-metal exchanged zeolites are known to convert methane to methanol with high selectivity, in a stepwise process, involving exposure to oxidants, followed by exposure to methane, and finally by exposure to water vapor. However, a comprehensive theoretical study on the nature of the possible active sites and their respective changes during this stepwise process is still lacking. Here, we use a combination of density functional theory calculations in its generalized-gradient approximation (DFT-GGA) and post-DFT methods to identify the thermodynamically preferred sites in Cu-exchanged zeolite SSZ-13 during the stepwise conversion of methane to methanol. We develop a thermodynamic model for an extensive set of possible active sites, that is, Cu monomers, dimers, and trimers, which are anchored in different ring structures and supported by a series of different local Al distributions. Subsequently, phase diagrams are constructed and used to identify thermodynamically favored sites at each step during the stepwise conversion of methane to methanol. We find that during exposure to O2, hydroxylated dimers—Cu2O2H2 and, depending on the local Al configuration, Cu2OH—are preferred. Upon exposure to methane, site-bound methanol molecules are formed. With the subsequent increase in water vapor pressure, a thermodynamic preference for monoatomic Cu and the release of methanol are observed. Furthermore, we compare our predicted results to experimental measurements published in the literature and find close agreement in terms of Cu coordination number and bond distances for some of the sites considered. We expect that the insights obtained here can be used to improve our understanding of the reaction mechanism and to optimize the stepwise conversion of methane to methanol.

Local Electronic Structure of Calcite Investigated Using X-ray Absorption Spectroscopy at Different Span of Time.

For the present work, calcite nanoparticles was synthesized from calcium nitrate by annealing precursor at 300, 400, 500 and 600°C. Ca K-edge near edge X-ray absorption fine structure measurements revealed spectral features characteristics to the amorphous phase of calcium carbonate at 300 and 400°C. At 500 and 600°C, the spectra were analogues to the calcite phase of calcium carbonate. Simulation of extended X-ray absorption fine structure spectra envisaged that both coordination number and bond distance for Ca-O bonds decreased with annealing temperature. Both parameters attained values close to standard calcite when annealed at 600°C. The spectral features at Ca L-, O K- and C K-edge near edge X-ray absorption fine structure appeared at same positions for different ages, which envisaged the occurrence of almost same local electronic structure for different span of times.

Derivation of Relation between a parameter of Inverse correlation and effective Charge of X-ray absorbing K-Edge of Copper atom in it’s different Compounds

The article gives an overview of the XANES technique contribution to the analysis of multi-component catalysts. The theoretical basis of the technique, the interpretation of the energy position and intensity of XANES features, and the numerical methods developed to interpret XANES data on catalytic systems are described and discussed. XANES in the K-edge of copper in the systems. CuO, Cu(NO3)2, La2CuO4, CuCl2, and CuBr have been investigated and transitions have been assigned to the observed structures. The measurements have been used for calculating the first coordination bond distance in the above systems. It is observed that the values so determined agree fairly well with crystallographic values

Synchrotron X-Ray Absorption Spectroscopy (XAS) Studies on Structural and Magnetic Properties of T’-Pr&lt;sub&gt;2-x&lt;/sub&gt;Ce&lt;sub&gt;x&lt;/sub&gt;CuO&lt;sub&gt;4&lt;/sub&gt; Nanocrystals

We have succeeded in synthesizing electron-doped cuprates T’-Pr2-xCexCuO4 (PCCO) with x = 0 and 0.10 nanocrystals prepared by the chemically dissolved method. Reduction annealing of the PCCO samples at 700°C under a flowing argon gas atmosphere has been performed for the removal of excess oxygen in the apical sites. The XRD data showed that the reduction annealing process decreases c-axis length indicating successful removal of the excess oxygen. The bond distortion of PCCO including coordination number and bond distance between the absorber atoms with the nearest neighboring atoms (Cu-O) was investigated by extended x-ray absorption fine structure (EXAFS) using Cu K-edge. The implication of our results is discussed on the basis of tremendous influence of oxygen vacancies on the magnetism of the nanosized T’-cuprates at the normal state.

Understanding metal-ligand interactions in coordination polymers using Hirshfeld surface analysis.

Properties related to the size and shape of Hirshfeld surfaces provide insight into the nature and strength of interactions among the building blocks of molecular crystals. In this work, we demonstrate that functions derived from the curvatures of the surface at a point, namely, shape index (S) and curvedness (C), as well as the distances from the surface to the nearest external (de) and internal (di) nuclei, can be used to help understand metal-ligand interactions in coordination polymers. The crystal structure of catena-poly[[[(1,10-phenanthroline-κ2N,N')copper(II)]-μ-4-nitrophthalato-κ2O1:O2] trihydrate], {[Cu(C8H3NO6)(C12H8N2)]·3H2O}n, described here for the first time, was used as a prototypical system for our analysis. Decomposition of the coordination polymer into its metal centre and ligand molecules followed by joint analysis of the Hirshfeld surfaces generated for each part unveil qualitative and semi-quantitative information that cannot be easily obtained either from conventional crystal packing analysis or from Hirshfeld surface analysis of the entire polymeric units. The shape index function S is particularly sensitive to the coordination details and its mapping on the surface of the metallic centre is highly dependent on the nature of the ligand and the coordination bond distance. Correlations are established between the shape of the Hirshfeld surface of the metal and the geometry of the metal-ligand contacts in the crystals. This could be applied not only to estimate limiting coordination distances in metal-organic compounds, but also to help establish structure-property relationships potentially useful for the crystal engineering of such materials.

Structural and spectroscopic investigations of redox active seven coordinate luminescent lanthanide complexes

The ligand H3L and its corresponding tris(phenolato) lanthanide complexes L-Tb, L-Gd, L-Yb and L-Lu were synthesized. The X-Ray crystal structures demonstrated a monocapped octahedron environment of the lanthanide ion, with exclusion of all solvent molecules from the coordination sphere due to the protection by the tert-butyl groups. The coordination bond distances followed the lanthanide contraction, with Ln-O bond lengths in the range 2.148–2.217 Å and Ln-Nimine bond lengths in the range 2.405–2.535 Å. Each of the complexes showed three one-electron oxidation processes. These potentials changed as a function of the lanthanide due to the difference in size of the metal ions. Both chemical and electrochemical oxidations of these complexes permitted the one-electron oxidised species to be generated. They all show a sharp absorption band at around 420 nm in their UV-Vis spectra, which demonstrated phenoxyl radical formation. Consistently, the radical species L-Lu+ displays a resonance at g = 2.001 in its EPR spectrum. The other cations are EPR-silent or difficult to detect due to magnetic interactions, confirming the proximity of the phenoxyl radical to the metal centre. For both L-Lu+ and L-Yb+ DFT calculations predict the radical to be delocalized over the three arms. The L-Tb and L-Yb complexes experienced a quenching of the luminescence upon oxidation to the radical species whereby the quenching of up to 83% in the visible region and 93% in the NIR was observed.

Examination of lutetium(III)-DOTA and copper(II)-NOTA solution structures using EXAFS

Targeted radionuclide therapy generally relies on the chelation of select short-lived isotopes such as 177Lu and 67Cu. The majority of Lu(III) and Cu(II) chelate structural information is derived from solid state diffraction data. Herein, the complexes Lu(DOTA)−, Cu(NOTA)− were examined in solution using EXAFS for the first time. Both ligands were fully deprotonated and coordinated to the metal with four and three carboxylic sites for Lu(DOTA)− and Cu(NOTA)−, respectively. Near-neighbor correlations from nitrogen atoms on the macrocyclic cages were also visible in the spectra in addition to the adjacent carbon backbones. Coordination numbers, bond distances, and Debye-Waller factors are reported and discussed alongside differences with known crystal structures.

Monte Carlo simulations of bulk and nano amorphous silica (a-SiO2) melts

Monte Carlo simulations were carried on bulk and nano amorphous silica (SiO2) melts under different thermodynamic conditions and nano-sizes. The potential developed by Ersan, Tahir, Norman and William (ETNW) was used to model the interatomic interactions of SiO2 melts in both cases (bulk and nano systems). The bulk system was developed using periodic boundary conditions. The nano SiO2 melts were prepared by cutting out a sphere from the bulk amorphous SiO2 melt structure to the required size, and then simulated under free boundary conditions. The high-pressure, high-temperature and nano-size effects on the structure and properties of the melts were investigated and studied via radial distribution functions, radial density profiles, potential energy, density, ring size analysis, coordination number distributions, bond distances and angles. In addition, to understand the difference in properties of bulk and nano silica melts, a comparative study was done at the same thermodynamic conditions. Details of the modelling, simulation results and the study are presented in this paper.

Seven-coordinate lanthanide complexes with a tripodal redox active ligand: structural, electrochemical and spectroscopic investigations.

The tripodal ligand TREN-(3,5-di-tert-butylsalicylidene)3 (H3L) was synthesized and its tris(phenolato) lanthanide complexes L-Ln (Ln = NdIII, EuIII, TbIII, GdIII, ErIII, YbIII and LuIII) were prepared. The X-Ray crystal structures confirm that each metal ion resides in a similar monocapped octahedral geometry, excluding water molecules from the coordination sphere. The coordination bond distances are in agreement with the lanthanide contraction, with Ln-O bond lengths in the range 2.139-2.216 Å. The complexes show three reversible monoelectronic oxidation waves, which are assigned to the successive oxidation of the phenolate moieties to phenoxyl radicals. The L-Nd complex is the easiest to oxidize, with E = 0.11, E = 0.21 and E = 0.34 V vs. Fc+/Fc, due to the larger size of the lanthanide ion. The ΔE1/2 value (ΔE1/2 = E-E) is correlated to the lanthanide radius, with values of 0.10 V for L-Nd and 0.22 V for L-Lu. The monoradical species were persistent in solution, allowing for their characterisation. All exhibit a distinct absorption band at around 445 nm due to the phenoxyl π-π* transitions. The EPR spectrum of L-Lu+ consists of a single resonance at giso = 1.999, confirming the radical nature of the oxidized product. Most of the other complexes (L-Gd, L-Er, L-Yb) show a quenching of the LnIII-based resonances upon oxidation, indicative of magnetic interactions between the metal and the radical spins. The L-Ln (L = Nd, Er, Yb) complexes exhibit a metal-based luminescence upon excitation of the ligand. A significant quenching of the luminescence was observed upon radical formation: 92%, 83% and 79% respectively for L-Nd+, L-Er+ and L-Yb+.

Photoluminescent properties of three lanthanide compounds of formulae LnCl3(diphenyl((5-phenyl-1H-pyrazol-3-yl)methyl)phosphine oxide)2, Ln = Sm, Eu and Tb: X-ray structural, emission and vibrational spectroscopies, DFT and thermogravimetric studies

Abstract The synthesis and properties of a new sensitizing bidentate ligand, diphenyl((5-phenyl-1H-pyrazol-3-yl)methyl)phosphine oxide, 2, capable of demonstrating the emissive properties of lanthanide elements, is described. Two ligands are attached to LnCl3 moieties, Ln = Sm, Eu and Tb, resulting in complexes of formulae LnCl3(2)2. These complexes were structurally characterized by single-crystal X-ray crystallography and have geometries that are pentagonal bipyramidal with the two bidentate ligands in a cisoid conformation on the equatorial plane and the three chloride ligands in a mer-configuration. The coordination bond distances decrease from Sm to Tb paralleling the decrease in lanthanide ionic radii. The photoluminescent properties of these complexes were examined and, one of them, TbCl3(2)2, was assessed a ΦF of ca. 1.00. DFT calculations were conducted to understand the mechanism of proton transfer in ligand 2 for a hydrogen atom hopping between nitrogen atoms on the pyrazolyl moiety and, to assess aspects of the coordination sphere of the lanthanide complexes.

A review of the structural architecture of tellurium oxycompounds

AbstractRelative to its extremely low abundance in the Earth's crust, tellurium is the most mineralogically diverse chemical element, with over 160 mineral species known that contain essential Te, many of them with unique crystal structures. We review the crystal structures of 703 tellurium oxysalts for which good refinements exist, including 55 that are known to occur as minerals. The dataset is restricted to compounds where oxygen is the only ligand that is strongly bound to Te, but most of the Periodic Table is represented in the compounds that are reviewed. The dataset contains 375 structures that contain only Te4+cations and 302 with only Te6+, with 26 of the compounds containing Te in both valence states. Te6+was almost exclusively in rather regular octahedral coordination by oxygen ligands, with only two instances each of 4- and 5-coordination. Conversely, the lone-pair cation Te4+displayed irregular coordination, with a broad range of coordination numbers and bond distances. A threshold was applied for Te4+–O links of ∼2.45 Å or 0.3 valence units with some flexibility, as a criterion to define strongly bound Te–O polymers and larger structural units. Using this criterion, Te4+cations display one-sided 3-, 4- or 5-coordination by oxygen (with rare examples of coordination numbers 2 and 6). For both valence states of Te, examples are known of TemOncomplexes which are monomeric (m= 1; neso), noncyclic finite oligomers (soro), rings (cyclo), infinite chains (ino), layers (phyllo) and frameworks (tecto tellurates). There is a clear analogy to the polymerization classes that are known for silicate anions, but the behaviour of Te is much richer than that of Si for several reasons: (1) the existence of two cationic valence states for Te; (2) the occurrence of multiple coordination numbers; (3) the possibility of edge-sharing by TeOnpolyhedra; (4) the possibility for oxygen ligands to be 3-coordinated by Te; and (5) the occurrence of TemOnpolymers that are cationic, as well as neutral or anionic. While most compounds contain only one or two symmetrically distinct types of Te atom, Pauling's Fifth Rule is frequently violated, and stoichiometrically simple compounds such as CaTeO3can have polymorphs with up to 18 distinct Te sites. There is a tendency for local symmetry features such as the threefold axis of a TeO6octahedron or the acentric symmetry of a Te4+Onpolyhedron to be inherited by the host structure; the latter in particular can lead to useful physical properties such as nonlinear optical behaviour. We develop for the first time a hierarchical taxonomy of Te-oxysalt structures, based upon (1) valence state of Te; (2) polymerization state of TemOncomplexes; (3) polymerization state of larger strongly-bound structural units that include non-Te cations. Structures are readily located and compared within this classification.

Syntheses of a pyrene-based π-expanded ligand and the corresponding platinum(II) complex, bis[2-[(octylimino)methyl]-1-pyrenolato-N,O] platinum(II)

A pyrene-based new ligand (1) attaching hydroxyl and imine group, i.e., a salicylaldimine-style ligand based on pyrene, was designed and synthesized. The ligand was prepared from the commercially available pyrene in five steps. A treatment of this ligand 1 (L) with Pt(II)Cl2(PhCN)2 in the presence of AcONa in PhCl afforded the corresponding metal complex, Pt(II)L2 (2) (80%). Single crystal diffraction study revealed that the complex is a square planar four-coordinated platinum(II) complex. The ligands bind to the metal in trans-manner. The coordination geometry, i.e., bond distances and angles for the coordination site, is the typical of the reported platinum(II) salicylaldiminatos, e.g., the mean Pt–N distance (d(Pt–N)): 2.011 and d(Pt–O): 1.994Å, respectively. The expansion of the π-system of the ligand induces the bathochromic shift in absorption spectra. The lowest excitation energy of 2 was found at 520nm. Theoretical studies suggest that this phenomenon is attributable to the narrowing intramolecular HOMO–LUMO gap of 2.

Heterometallic coordination framework by sodium carboxylate subunits and cobalt (III) centers obtained from a highly hydrogen bonding stabilized cobalt (II) monomeric complex

Coordination cobalt and nickel complexes (1) and (2) were obtained serendipitously by the reaction of M(NO3)2·6H2O (M=Co and Ni) and methyliminodiacetic acid (H2L) in a mixture of solvents. The X-ray diffraction showed the unusual structures with Z′=4 of (1) and (2), showing the four monomers highly stabilized by hydrogen bonding interactions which corresponds to the tris-(aqua)-(N-methyliminodiacetato)-cobalt (II) and nickel (II) respectively. The Wiberg Bond Indices (WBIs) were computed on (1) and (2) to evaluate the stability of the hydrogen bonding interactions and showed a good correlation with the experimental X-ray diffraction data. Finally, the complex [Co (L)2 Na]n (3) corresponds to the heterometallic coordination framework which was obtained by addition of a second equiv. of methyliminodiacetic acid (H2L) in basic sodium hydroxide media. The oxidation of the cobalt atom in (3) was confirmed by the experimental coordination bond distances observed by XRD, which are in the range from 1.882 to 1.957Å.

Amorphous W–S–N thin films: The atomic structure behind ultra-low friction

Amorphous W–S–N in the form of thin films has been identified experimentally as an ultra-low friction material, enabling easy sliding by the formation of a WS2 tribofilm. However, the atomic-level structure and bonding arrangements in amorphous W–S–N, which give such optimum conditions for WS2 formation and ultra-low friction, are not known. In this study, amorphous thin films with up to 37at.% N are deposited, and experimental as well as state-of-the-art ab initio techniques are employed to reveal the complex structure of W–S–N at the atomic level. Excellent agreement between experimental and calculated coordination numbers and bond distances is demonstrated. Furthermore, the simulated structures are found to contain N bonded in molecular form, i.e. N2, which is experimentally confirmed by near edge X-ray absorption fine structure and X-ray photoelectron spectroscopy analysis. Such N2 units are located in cages in the material, where they are coordinated mainly by S atoms. Thus this ultra-low friction material is shown to be a complex amorphous network of W, S and N atoms, with easy access to W and S for continuous formation of WS2 in the contact region, and with the possibility of swift removal of excess nitrogen present as N2 molecules.