Higher Coordination Number Research Articles

Coordination and binding properties of zwitterionic glutathione with transition metal cations

The interaction of metal cations at different nucleophilic sites of zwitterionic forms of glutathione complexes (Glu-A, Glu-B)-M2+ were studied using the hybrid density functional theory (DFT-B3LYP) and second order Moller-plesset perturbation theory (MP2) methods. The metal ions coordinate with glutathione complexes in tri and tetra dentate manner. The zwitterionic forms of glutathione (Glu-A) and (Glu-B) are found to be neutralized during interaction with transition metal cations in the gas phase. The tetrahedral or square pyramidal with multi membered chelating ring complexes and higher coordination numbers quite favors for stabilizing the Cd2+, Hg2+ and Zn2+ metal cations in Glu-A-M2+ and Glu-B-M2+ complexes to form the most stable complexes. The overall structural parameters of zwitterionic forms of glutathione (GSH) complexes are not altered by metal ion substitution; however the metal ion binding site has undergone a noticeable change. The metal ion affinity and basis set superposition error (BSSE) corrected interaction energy was computed for all the complexes. The stability orders of the zwitterionic form of glutathione complexes remain the same in relative energy, interaction energy and metal ion affinity (MIA) values. Solvent effects, with explicit water molecules and polarizable continuum model (PCM), were considered to study the most stable Cd2+, Hg2+ and Zn2+ complexes.

Effect of ionic radius on the assemblies of first row transition metal–5-tert-butylisophthalates–(2,2′-bipyridine or phenanthroline) coordination compounds

18 coordination compounds of Mn2+, Fe2+, Co2+, Ni2+, Cu2+ and Zn2+, with mixed organic ligands 5-tert-butylisophthalic acid, 2,2′-bipyridine or phenanthroline, have been hydrothermally synthesized and characterized. Structure analysis shows that the ionic radius of a metal ion determines the form of the metal centre and the structure of the product. Large metal ions tend to have higher coordination numbers, connect to more bridging ligands and form multinuclear metal centres. On the contrary, small metal ions tend to connect to fewer bridging ligands, and act as mononuclear metal centres for discrete coordination compounds or low dimensional coordination polymers. The influences of other factors such as molar ratio of reactants, pH and temperature, have also been discussed. The magnetic properties of the temperature dependent cobalt compounds have been investigated.

Molecular Dynamics Study of the Structural Properties of Calcium Aluminosilicate Slags with Varying Al2O3/SiO2 Ratios

Molecular dynamics simulation was explored to investigate the change of structure of calcium aluminosilicate slags with varying Al2O3/SiO2 ratios at a fixed CaO content. In practice the results of the study are relevant to the significant changes in slag structure caused by the changes in chemical composition during continuous casting of steels containing high amounts of dissolved aluminum. It was found that Q4 tetrahedral species (tetrahedron with four bridging oxygens) increase while NBOs (non-bridging oxygen) decreases with increasing Al2O3/SiO2 mole ratio, suggesting that a more polymerized network was formed. The concentration of oxygen tricluster increased dramatically up to 24% with increasing Al2O3/SiO2 mole ratio, and the coordination number for Al (CNAl–O) was also observed to increase from 4.02 for sample CAS1 to 4.11 for sample CAS11, suggesting that high coordination number of Al presents in the slag melt with the substitution of [AlO4] for [SiO4]. NBOs prefer to be coordinated with Si and Al tends to be localized in more polymerized environment as network intermediate phases. The degree of Al avoidance was calculated and the Al avoidance principle is applicable in the SiO2 rich regions.

A Cyano‐Bridged Vanadium–Niobium Bimetal Assembly Exhibiting a High Curie Temperature of 210 K

AbstractWe report a cyano‐bridged V–Nb bimetal assembly, K0.59VII1.59VIII0.41[NbIV(CN)8]·(SO4)0.50·6.9H2O, exhibiting ferrimagnetism with a high Curie temperature (TC) of 210 K, which is the highest TC value among those of octacyano‐bridged bimetal assemblies. Such a high TC value originates from the high coordination number of octacyanoniobate and the strong superexchange interaction between VII (S = 3/2) and NbIV (S = 1/2) through the CN groups.

Coordination chemistry of copper proteins: How nature handles a toxic cargo for essential function

Biological copper is coordinated predominantly by just three ligand types: the side chains of histidine, cysteine, and methionine, with of course some exceptions. The arrangement of these components, however, is fascinating. The diversity provided by just these three ligands provides choices of nitrogen vs. sulfur, neutral vs. charged, hydrophilic vs. hydrophobic, susceptibility to oxidation, and degree of pH-sensitivity. In this review we examine how the total number of ligands, their spatial arrangement and solvent accessibility, the various combinations of imidazole, thiolate, and thioether donors, all work together to provide binding sites that either enable copper to carry out a function, or safely transport it in a way that prevents toxic reactivity. We separate copper proteins into two broad classes, those that utilize the metal as a cofactor, or those that traffic the metal. Enzymes and proteins that utilize copper as a cofactor use high affinity sites of high coordination numbers of 4–5 that prevent loss of the metal during redox cycling. Copper trafficking proteins, on the other hand, promote metal transfer either by having low affinity binding sites with moderate coordination number ~ 4, or by having lower coordinate binding sites of 2–3 ligands that bind with high affinity. Both strategies retain the metal but allow transfer under appropriate conditions. Analysis of studies from our own lab on model peptides, combined with those from other labs, raises an interesting hypothesis that various methionine/histidine/cysteine combinations provide organisms with dynamic, multifunctional domains on copper trafficking proteins that facilitate copper transfer under different extracellular, subcellular, and tissue-specific scenarios of pH, redox environment, and presence of other copper carriers or target proteins.

Coordination Numbers of Hydrated Divalent Transition Metal Ions Investigated with IRPD Spectroscopy

Hydration of the divalent transition metal ions, Mn, Fe, Co, Ni, Cu, and Zn, with 5-8 water molecules attached was investigated using infrared photodissociation spectroscopy and photodissociation kinetics. At 215 K, spectral intensities in both the bonded-OH and free-OH stretch regions indicate that the average coordination number (CN) of Mn(2+), Fe(2+), Co(2+), and Ni(2+) is ~6, and these CN values are greater than those of Cu(2+) and Zn(2+). Ni has the highest CN, with no evidence for any population of structures with a water molecule in a second solvation shell for the hexa-hydrate at temperatures up to 331 K. Mn(2+), Fe(2+), and Co(2+) have similar CN at low temperature, but spectra of Mn(2+)(H(2)O)(6) indicate a second population of structures with a water molecule in a second solvent shell, i.e., a CN < 6, that increases in abundance at higher temperature (305 K). The propensity for these ions to undergo charge separation reactions at small cluster size roughly correlates with the ordering of the hydrolysis constants of these ions in aqueous solution and is consistent with the ordering of average CN values established from the infrared spectra of these ions.

Analysis of crystallographic and structural data of polymeric iron-alkaline metal complexes

Abstract The present review covers almost 100 polymeric MFe (M=Li, Na, K, Rb, and Cs) compounds. The metal atoms of group 1 as partners with iron atom build up complex polymeric chains. The iron atoms are found in the oxidation states 0, +2, and +3, of which the oxidation state +3 prevails. The coordination number of the iron atom ranges from 2 to 10 (sandwiched). The coordination sphere about the main group 1 metals varies, ranging from tetrahedral to mostly trigonal bipyramid. There are also higher coordination numbers involved, namely, from 6 to 10. The most common ligand atoms are oxygen and nitrogen. There are three compounds displaying distortion isomerism. Several relationships between structural parameters are found and discussed.

Electronic stress tensor analysis of hydrogenated palladium clusters

We study the chemical bonds of small palladium clusters Pd_n (n=2-9) saturated by hydrogen atoms using electronic stress tensor. Our calculation includes bond orders which are recently proposed based on the stress tensor. It is shown that our bond orders can classify the different types of chemical bonds in those clusters. In particular, we discuss Pd-H bonds associated with the H atoms with high coordination numbers and the difference of H-H bonds in the different Pd clusters from viewpoint of the electronic stress tensor. The notion of "pseudo-spindle structure" is proposed as the region between two atoms where the largest eigenvalue of the electronic stress tensor is negative and corresponding eigenvectors forming a pattern which connects them.

Building a Bridge between Coordination Compounds and Clusters: Bonding Analysis of the Icosahedral Molecules [M(ER)12] (M = Cr, Mo, W; E = Zn, Cd, Hg)

The bonding situation of the icosahedral compounds [M(EH)(12)] (M = Cr, Mo, W; E = Zn, Cd, Hg), which are model systems for the isolated species [Mo(ZnCp*)(3)(ZnMe)(9)] possessing the coordination number 12 at the central atom M, have been analyzed with a variety of charge and energy decomposition methods (AIM, EDA-NOCV, WBI, MO). The results give a coherent picture of the electronic structure and the nature of the interatomic interactions. The compounds [M(EH)(12)] are transition metal complexes that possess 12 M-EH radial bond paths (AIM) that can be described as 6 three-center two-electron bonds (MO). The radial M-EH bonds come from the electron sharing interactions mainly between the singly occupied valence s and d AOs of the central atom M and the singly occupied EH valence orbitals (MO, EDA-NOCV). The orbital interactions provide ~42% of the total attraction, while the electrostatic attraction contributes ~58% to the metal-ligand bonding (EDA-NOCV). There is a weak peripheral E-E bonding in [M(EH)(12)] that explains the unusually high coordination number (MO). The peripheral bonding leads for some compounds [M(EH)(12)] to the emergence of E-E bond paths, while in others it does not (AIM). The relative strength of the radial and peripheral bonding in [Al(13)](-) and [Pt@Pb(12)](2-) is clearly different from the situation in [M(EH)(12)], which supports the assignments of the former species as cluster compounds or inclusion compounds (MO, WBI). The bonding situation in [WAu(12)] is similar to that in [M(EH)(12)].

A new rhombohedral modification of EuNi5In

A rhombohedral modification of europium pentanickel indide, r-EuNi(5)In, crystallizes in the R ̅3m space group and adopts the UCu(5)In structure type. The structure is closely related to the hexagonal, h-EuNi(5)In, form (CeNi(5)Sn type). Both EuNi(5)In modifications are composed of CaCu(5) (EuNi(5))-, MgCu(2) (InNi(2))- and NiAs (EuNi)-type slabs in a 1:2:1 ratio. The atoms in the structure have high coordination numbers, viz. 20 and 18 for europium, 14 for indium, and 12 and 10 for nickel. The structure features a two-dimensional network of (2)(∞)[Ni(8)] tetrahedral clusters arranged in the ab plane.

Enhancing performance of FSP SnO 2-based gas sensors through Sb-doping and Pd-functionalization

Via flame spray pyrolysis (FSP), SnO 2 gas sensing layers have been doped with 0.01–4 wt% Sb as well as 0.01 wt% Pd in combination with 1 wt% Sb. Characterization of these materials through X-ray diffraction (XRD), Brunauer–Emmett–Teller (BET) surface analysis, and transmission electron microscopy (TEM) revealed particle grain sizes and crystallinity unchanged by the presence of Sb and/or Pd. The addition of Sb to SnO 2 resulted in the significant decrease in baseline resistance; up to two orders of magnitude in dry air at 300 °C and three orders of magnitude in humid air at 300 °C, which is significant for FSP-prepared gas sensors with high porosity and low particle coordination number since they typically suffer from high baseline resistance. While the baseline resistance was improved with Sb-doping, the sensor signal ( R 0/ R gas) remained constant over all concentrations explored. Moreover, regarding the surface functionalization of SnO 2 with Pd in combination with Sb-doping, the reduction of baseline resistance was preserved without influencing sensor signal.

Chemical bonding in complexes with high coordination numbers: a charge density study

The topological analysis of an experimental charge-density distribution in crystalline tris(pyridine)bis(o-hydroxybenzoato)cadmium(ii) revealed that the metal–ligand bonds occupy nearly the same place in the energetic scale as the hydrogen bonds do, thus being extremely sensitive to steric and crystal-packing effects.

Neodymium triflate modified nafion composite membrane for reduced alcohol permeability in direct alcohol fuel cell

This paper reports an experimental study on the modification of nafion membrane with neodymium triflate, Nd(SO3CF3)3, a rare earth triflate. The triflate ion resembles nafion in structure and has high lewis acidity, high coordination number, hygroscopic nature and thermal stability. These properties make the neodymium triflate (NdTfO) suitable to improve the performance of NdTfO/nafion membranes in direct alcohol fuel cell by reducing fuel permeability without compromising other properties. The NdTfO/nafion membranes reduced alcohol permeability by nearly 48%. The proton conductivity of 1% NdTfO/nafion was increased by at least 24% as compared to pure cast nafion membrane. The mechanical strength of 1% NdTfO/nafion was higher than that of pure cast nafion. The composite membrane was thermally and chemically stable and has potential for use in direct alcohol fuel cells. A DMFC was developed and its performance was evaluated using the composite membrane, which showed encouraging results.

Pore networks in continental and marine mudstones: Characteristics and controls on sealing behavior

Mudstone pore networks are strong modifiers of sedimentary basin fluid dynamics and have a critical role in the distribution of hydrocarbons and containment of injected fluids. Using core samples from continental and marine mudstones, we investigate properties of pore types and networks from a variety of geologic environments, together with estimates of capillary breakthrough pressures by mercury intrusion porosimetry. Analysis and interpretation of quantitative and qualitative three-dimensional (3D) observations, obtained by dual focused ion beam–scanning electron microscopy, suggest seven dominant mudstone pore types distinguished by geometry and connectivity. A dominant planar pore type occurs in all investigated mudstones and generally has high coordination numbers (i.e., number of neighboring connected pores). Connected networks of pores of this type contribute to high mercury capillary pressures due to small pore throats at the junctions of connected pores and likely control most matrix transport in these mudstones. Other pore types are related to authigenic (e.g., replacement or pore-lining precipitation) clay minerals and pyrite nodules; pores in clay packets adjacent to larger, more competent clastic grains; pores in organic phases; and stylolitic and microfracture-related pores. Pores within regions of authigenic clay minerals often form small isolated networks (<3 μm). Pores in stringers of organic phases occur as tubular pores or slit- and/or sheet-like pores. These form short, connected lengths in 3D reconstructions, but appear to form networks no larger than a few microns in size. Sealing efficiency of the studied mudstones increases with greater distal depositional environments and greater maximum depth of burial.

The Atomic Site Occupancies in the Fe-Cr σ-Phase

The atomic site distribution of the complex σ-phase structure (P42/mnm) has been studied using density functional theory (within the EMTO and WIEN2k codes) applying the cluster expansion method in a mean field approximation at finite temperatures. We found that at low temperatures Fe atoms predominantly occupy the icosahedrally coordinated (A,D) sites, Cr atoms prefer the (B,E) sites with the high coordination numbers, while the C site remains mixed. However, at higher temperature close to 1000 K all occupations become more and more mixed and reproduce well the available experimental data.

Lanthanide-centered organic–inorganic hybrids through a functionalized aza-crown ether bridge: coordination bonding assembly, microstructure and multicolor luminescence

This work focuses on the synthesis of a series of chemically bonded lanthanide/inorganic/organic hybrid materials (CE-15-Si-Ln, CE-16-Si-Ln, CE-18-Si-Ln) containing a novel aza-crown ether organic component. The materials show red emission (Ln = Eu), green emission (Ln = Tb) and near-infrared (NIR) luminescence (Ln = Nd). Three functional molecular precursors (denoted as CE-15-Si, CE-16-Si, CE-18-Si) have been synthesized with two or three N-substituted pendant arms containing chelating groups which can not only fulfill the high coordination numbers of Ln(3+) ions but also form an inorganic Si-O-Si network with tetraethoxysilane (TEOS). The resulting amorphous materials exhibit regular uniform microstructures for the organic and the inorganic components which are covalently linked through Si-O bonds via a self-assembly process. These hybrids present strong luminescent intensities in red, green and NIR ranges by embedding selected Ln(3+) ions into the hybrid system, which may lead to potential applications in organic electroluminescence displays, light emitting devices, functional membranes or chemical/biomedical sensors.

Europium environment and clustering in europium doped silica and sodium silicate glasses

The local environment and distribution of rare earth ions are important to the optical properties of rare earth doped oxide glasses. In this paper, we report studies of the structures of europium doped (around 1 mol% Eu 2O 3) silica and sodium silicate glasses using molecular dynamics simulations. By using effective partial charge potentials, systems with over 24,000 atoms were modeled in order to obtain better statistics of rare earth ion distribution. The simulated glass structures were validated by comparing the calculated neutron and X-ray structure factors with experimental data. It was found that europium ions have higher coordination number (5.9 versus 4.8) and more symmetric environments in sodium silicate glasses than in the silica glass. Rare earth ion clustering has been characterized in detail and it was found that the clustering probability of europium ions in sodium silicate glass is consistently less than that predicted from a random distribution, while the probability of clustering in pure silica glass is higher than that of random distribution at the 1 mol% doping level.

Chemistry of Group IV Metal Ion‐Containing Polyoxometalates

AbstractThe chemistry of Group IV metal ion (TiIV, ZrIV and HfIV)‐containing polyoxometalates (POMs) is presented as a sharply focused microreview, introducing an aspect of our own research. The synthesis, structure, and solid/solution state behavior of the POMs, which are prepared by the reactions of various lacunary species of POMs with TiIV, ZrIV and HfIV atoms, are described in several sections, classified with Keggin and Dawson POM families. Because of the ionic radius of TiIV (0.75 Å), close to that of WVI (0.74 Å), the TiIV atom can fit nicely into the mono‐lacunary site of the POM, but ZrIV and HfIV atoms (0.85–0.86 Å), larger than TiIV atom, do not fit into the mono‐lacunary site of the POM. Thus, the mono‐lacunary site of the POM acts as the oxygen‐donor pentadentate ligand to the TiIV atom, whereas it acts as the tetradentate ligand to ZrIV and HfIV atoms. The TiIV atom in the POM takes on six‐coordinate geometry, whereas the ZrIV and HfIV atoms have higher coordination numbers (6, 7 and 8) due to their larger ionic radii. Consequently, most Ti‐substituted Keggin POMs are isolated as oligomers formed by corner‐sharing Ti–O–Ti bonds, whereas Zr/Hf‐containing Keggin/Dawson POMs are usually isolated as di‐, tri‐, tetra‐Zr/Hf cluster cations sandwiched between two lacunary POMs, the cluster cations of which are formed by edge‐sharing M(OH)2M (M = Zr, Hf) bonds. These compounds show quite different behavior under pH‐dependent conditions. The pH‐dependent interconversion between the dimeric and monomeric species of Ti‐substituted Dawson POMs is quite an opposite tendency from those of Zr/Hf‐containing Dawson POMs. The Ti‐substituted Dawson POM oligomers have a tendency to undergo base hydrolysis to give monomers, whereas the Zr/Hf‐containing Dawson POM oligomers have a tendency to undergo acid hydrolysis to provide monomers. In the Group IV metal ion‐containing POMs, the Zr/Hf atoms function very similarly to each other, but show quite different behavior from the Ti atom.

Ab initio ternary [formula omitted]-phase diagram: The Cr–Mo–Re system

For the first time, the formation enthalpies at 0 K of every ordered configuration of a ternary σ -phase, i.e. 5 3=243 configurations, have been calculated using the electronic density functional theory. The Cr–Mo–Re system has been chosen for the present investigation since the two binary Cr–Re and Mo–Re σ -phase are known to show opposite Re site preference: high coordination number sites in Cr–Re and low coordination number sites in Mo–Re. The ternary Cr–Mo–Re σ -phase diagram has been computed at 0 K. It presents at this temperature several distinct single-phase regions separated by a large number of miscibility gaps. Finite temperature properties have been calculated using only the configurational entropy, in the Bragg–Williams approximation. Only above 800 K, the Gibbs energy surface becomes convex. The occupancies of the inequivalent sites have been computed as a function of composition at several temperatures. Re site preference is shown to change progressively in the ternary field when passing from Cr–Re to Mo–Re binary borders.

Phase diagrams of the mixed spin-1 and spin-1/2 Ising–Heisenberg model on the diamond-like decorated Bethe lattice

The ground-state and finite-temperature behavior of the mixed spin-1 and spin-1/2 Ising–Heisenberg model on the diamond-like decorated Bethe lattice is investigated within the framework of two rigorous methods: the decoration-iteration transformation and exact recursion relations. The model under consideration describes a hybrid classical-quantum system consisting of the Ising and Heisenberg spins, which interact among themselves either through the Ising or XXZ Heisenberg nearest-neighbor interaction. Both sublattice magnetizations of the Ising and Heisenberg spins are exactly calculated with the aim to examine phase diagrams, thermal variations of the total and sublattice magnetizations. The finite-temperature phase diagrams form continuous (second-order) phase transition lines only, which exhibit a small reentrant region if the diamond-like decorated Bethe lattice with a sufficiently high coordination number is considered.