Coordination Bond Lengths Research Articles

Crystal and Molecular Structure of Bis(O,O"-diisopropyldithiophosphato-S,S")(dimethylglyoximato-N,N")rhodium(III)

The crystal and molecular structure of bis(O,O"-diisopropyldithiophosphato-S,S")(dimethylglyoximato-N,N")rhodium(III) (I) was studied using X-ray diffraction analysis: space group P21/c, a = 13.644 A, b = 10.350 A, c = 20.906 A, β = 109.02°, Z = 4. The structure was solved by the direct method and anisotropically refined by the full-matrix least-squares method to R = 0.029 using 5447 independent reflections (CAD-4 autodiffractometer, λMoKα). Compound I is a mononuclear tris-chelate complex whose three ligands are singly charge anions. The individual molecule of the complex has a noncrystallographic two-fold axis; its Rh atom is coordinated by four S atoms and two N atoms, forming a distorted octahedron. The average coordination bond lengths are Rh–S 2.402 and Rh–N 2.023 A. The molecules in structureI are joined into infinite chains via weak intramolecular C–H···S hydrogen bonds and intermolecular N–O–H···O–N hydrogen bonds.

Studies on electronic structures and related properties of complexes M(tap)32+ (M = Fe, Ru, Os) by the DFT method

Studies on a series of complexes M(tap)32+ (M = Fe, Ru, Os; tap = 1,4,5,8-tetraazaphenanthrene) are carried out using the DFT method at the B3LYP/LanL2DZ level. The electronic structures and related chemical properties of complexes M(tap)32+, e.g. the energies and components of some frontier molecular orbitals, the spectral properties, and the net charge populations of some main atoms of the complexes, etc. have been investigated. In addition, computations on the complex Ru(phen)32+(phen = 1,10-phenanthroline) are also performed for comparison. The computational results show some very interesting trends in electronic structures and related properties of complexes M(tap)32+. First, the computational energies of some frontier molecular orbitals of Ru(tap)32+ are all lower than those of Ru(phen)32+. In particular, the energies of LUMOs of the complexes Os(tap)32+ and Ru(tap)32+ are all rather low and their electron affinities are rather high, leading to the prediction that an electron is very easily transferred from DNA guanine base to the LUMO of the complexes. This may be a major reason why these cations are excellent photoreagents for DNA. Second, the components of the HOMO of the four complexes all arise mainly from d orbitals of the central metal ions, and the components of the LUMO arise mainly from p orbitals of C and N atoms in the ligands, so their electronic ground state bands are theoretically all assigned to singlet metal-to-ligand charge-transfer (1MLCT) transitions in absorption spectra, similar to those of Ru(bpy)32+. Third, for M(tap)32+, the most negative charges are populated on N1, with the next populated on N4. Fourth, the chemical stabilities (S) of the complexes are in order SIII > SII > SI, according to coordination energy computations. In addition, the central atom M has little effect on the coordination bond lengths and bond angles of the complexes. The obtained results should be important references for the synthesis of the complexes, mechanistic analysis of their photochemistry, electrochemistry and catalysis chemistry.

Theoretical studies on the electronic structures and related properties of [Ru(L)3]2+ (L=bpy, bpm, bpz) with DFT method

Theoretical studies on the complexes [Ru(L)3]2+ (L=bpy, bpm, bpz) are carried out using the density functional theory (DFT) method and the B3LYP/LanL2DZ level of theory. The effects of the ligands on the electronic structures and related properties, e.g. the components and the energies of some frontier molecular orbitals, the spectral characteristics, and the net charge populations of some main atoms of the complexes, and the effect of N atom position on total energy of different isomer, etc. have been investigated. The results show that the different ligands (bpy, bpm, bpz) have some interesting effects on the electronic structures and related properties of complexes [Ru(L)3]2+. First, the energies of corresponding frontier molecular orbitals of the three complexes all greatly reduce in the order of εi(I)>εi(II)>εi(III). The energy intervals (ΔεL–H) between LUMO and HOMO for the three complexes are in the order of ΔεL–H(I)<ΔεL–H(II)<ΔεL–H(III). Second, the HOMOS of Ru(L)32+ can be characterized by d orbitals of Ru2+, whereas for the LUMOS, although their components may be characterized by p orbitals of the ligands, the contributions of N atomic orbitals in different complexes are greatly different. Third, the most negative charges are all populated on N1 for each of the three complexes, and among them that on N1 (−0.5015) of II is the most. On the other hand, as for C atoms of the main ligand, the most negative charges are populated on C5 of complex II. Fourth, the iso-complexes II and III with identical types of bonds have different total energies. The characteristics of atomic charge populations in the poly-heteroatomic systems as well as the effects of N atom positions on total energies of different isomers can be simply and satisfactorily interpreted applying the schematic map based on the law of polarity alternation and the idea of polarity interference. Final, the different ligand has a little effect on the coordination bond length, and the trend agrees with references. The above theoretical results should be very useful in the analysis of DNA-binding mechanism of complexes and the designs of binding agents to DNA, etc.

AMORPHOUS AND NANOCRYSTALLINE ZrO2·Y2O3(15%) STUDIED BY EXTENDED X-RAY ABSORPTION FINE STRUCTURE

Chemical coprecipitated amorphous and nanocrystalline ZrO2·Y2O3(15%) was studied by Powder X-ray diffraction(XRD) and extended X-ray absorption fine structure(EXAFS). XRD result shows that the sample is an amorphous phase annealed below 300℃; and it crystallizes into cubic nanocrystalline zirconia at 500℃. EXAFS analysis indicates that the coordination number and bond length of Zr-O shell has not changed when transforming from amorphous into nanocrystalline. This suggests that at 300℃,it has formed the same nearest-neighbor local structure as at 900℃. For Zr-Zr(Y) shell, with the reducing of grain size, the coordination number decreases obviously: the bond length is shorter and the disorder becomes larger. This result suggests that the grain size effect is much stronger for more distant coordination shell (Zr-Zr ) than for the first nearest-neighbor shell(Zr-O).

Metal chelates of N-carbamoylmethyl-iminodiacetate(2−) ion : Part IV. Isostructural ternary mixed-ligand cobalt(II) and nickel(II) chelates with N-carbamoylmethyl-iminodiacetate(2−) ion, imidazole and aqua ligands. Synthesis, molecular and crystal structures and properties of [M(ADA)(Him)(H 2O)]·1.5H 2O (M=Co, Ni)

Stoichiometric reaction of CoCO 3·Co(OH) 2·2H 2O, or NiCO 3·2Ni(OH) 2·4H 2O with H 2ADA and imidazole (Him) in water yields crystalline samples of compounds aqua(imidazole)( N-carbamoylmethyl-iminodiacetato)metal(II), [M(ADA)(Him)(H 2O)]·1.5H 2O (M=Co, compound I, dark pink; M=Ni, compound II, bluish). Single-crystal X-ray diffraction studies were carried out. Both complexes are isostructural (orthorhombic system, space group Pna2(1), Z=8). These crystals consist of slightly asymmetrical octahedral coordination units linked in a tridimensional network stabilised by hydrogen bonds where all N–H bonds of ADA and Him and probably O–H bonds of water molecules are involved. The asymmetric unit has two independent but very similar complex molecules and three water ones. Coordination bond distances for I (average in Å): Co–N(amino)=2.14(1), Co–O(carboxyl)=2.06(1), Co–O(carboxyl)=2.08(1) and Co–O( amide)=2.15(1) with ADA, Co–N(Him)=2.04(1), and Co–O(aqua)=2.13(1). Coordination bond lengths for II (average in Å): Ni–N(amino)=2.08(1), Ni–O(carboxyl)=2.04(1), Ni–O(carboxyl)=2.06(1) and Ni–O(amide)=2.012(1) with ADA, Ni–N(Him)=2.01(1), and Ni–O(aqua)=2.12(1). The ADA ligand acts as a tripodal tetradentate chelating one. On the basis of the octahedral structures of [Ni(ADA)(H 2O) 2], reported in the literature, and of the new compounds, it is concluded that there is a preference for the N(Him)donor atom to occupy the trans-position to the M–N(ADA) bond.

In Situ X‐Ray Absorption Spectroscopy Study of Li ( 1 − z ) Ni ( 1 + z ) O 2 ( z ≤ 0.02 ) Cathode Material

In situ X‐ray absorption spectroscopy study of phases shows that the Ni K edge continuously shifts to higher energies with a decrease in Li content in a manner consistent with oxidation of Ni(III) to Ni(IV) The Ni K‐edge energy for is consistent with that observed for chemically prepared quadrivalent Ni in . Variations in the coordination numbers, bond lengths, and disorders as a function of state of charge (i.e., the value of x) are consistent with the following facts: (i) a Jahn‐Teller distortion for Ni(III), (ii) an undistorted environment for Ni(IV), and (iii) an electrochemical oxidation of Ni(III) to Ni(IV). © 2000 The Electrochemical Society. All rights reserved.

Mononuclear Fe(II) and Fe(III) complexes with the tetradentate ligand N, N′-bisbenzyl- N, N′-bis(2-pyridylmethyl)-ethane-1,2-diamine. Synthesis and characterisation

Two new mononuclear iron complexes, [(LBzl 2)Fe(II)Cl 2]·H 2O and [(LBzl 2) Fe(III)Cl 2]·PF 6, (LBzl 2= N, N′-bisbenzyl- N, N′-bis(2-pyridylmethyl)-ethane-1,2-diamine) have been synthesised in view of generating complexes to mimic the active site of methane monooxygenase. Their structures have been determined by X-ray analysis. In both species, the iron atom shows a pseudo-octahedral coordination with two pyridine nitrogen atoms in axial positions and two amine nitrogen atoms in the equatorial plane. Two other equatorial positions are occupied by chloride ions. The coordination bond lengths clearly indicate the sensitivity of the ligand to the oxidation state of the iron. Thus, the FeN and FeCl bond distances in Fe(II) complex are more elongated than corresponding distances in Fe(III). A statistical examination of the bond distances of hexacoordinated Fe(II) and Fe(III) complexes using the Cambridge Structural Database provides evidence to relate both complexes to their spin state. The redox potential of the Fe(III)/Fe(II) couple was determined by cyclic voltammetry. The UV–Vis spectra are dominated by charge transfer transitions. The X-band EPR spectrum of [(LBzl 2) FeCl 2]·PF 6 is characteristic of an S=5/2 species with an unusual zero-field splitting.

Complexation of ω-thiocaprolactam with heavy metals: terminal and bridging coordination modes in cadmium and silver compounds

The soft base w-thiocaprolactam (1-azacycloheptane-2-thione, Hthcl) reacts with Cd II and Ag I nitrate salts, giving two new coordination complexes, [Cd(NO 3 ) 2 (C 6 H 11 NS) 4 ] and [Ag 4 (C 6 H 11 NS) 8 ](NO 3 ) 4 . The first compound, tetrakis(1-azacycloheptane-2-thione-S)bis(nitrate-O)cadmium(II), presents a slightly distorted octahedral coordination geometry, with two η 1 -NO 3 fragments in a cis arrangement and four Hthcl molecules bonded via the S atom of the thiocarbonyl group; coordination bond lengths involving S atoms range from 2.5768 (19) to 2.6828 (18) A. The cationic moiety of the silver compound, tetrakis[μ-(1-azacycloheptane-2-thione-S)]tetrakis[(1-azacycloheptane-2-thione-S)silver(I)] tetranitrate, is a centrosymmetric tetranuclear cluster containing eight Hthcl molecules, four of which are in terminal positions [coordination distances 2.4850(19) and 2.478 (2) A], as in the Cd complex, while the other four bridge two metallic ions each, with coordination distances in the range 2.4608 (17)-2.6976(18) A.

An In Situ X‐Ray Absorption Spectroscopic Study of Charged Li ( 1 − z ) Ni ( 1 + z ) O 2 Cathode Material

We have measured in situ the Ni K‐edge X‐ray absorption spectra of cathode material charged in a nonaqueous cell. The material was charged to various states of charge (i.e., Li content) which corresponded to x = 0.0, 0.12, 0.24, 0.37, 0.49, and 0.86 in . We have determined variations in the Ni‒O and Ni‒Ni coordination numbers, bond lengths, and local disorders as well as the Ni K‐edge energies as a function of Li content. We show that in the pristine state, the composition of the material can be described by the formula (i.e., x = 0 and = 0.14). That is, the material consists of (25%) and (75%) with half the atoms residing in Li sites and the other half in the slabs. Upon charging, initially is oxidized to up to a state of charge which corresponds to x = 2. Upon further charging to states corresponding to 2z <x≤1 − z, is oxidized to with fractions being dependent on the values of x and z. Analysis of the edge energies for NiO, stoichiometric , and as reference compounds for , , and , respectively, shows a quadratic dependence for edge energy vs. oxidation state. This type of correlation is consistent with variations observed in earlier studies for some Mn reference compounds in the same range of oxidation states. Oxidation‐state determination of Ni in as a function of state of charge (i.e., Li content or x) on the basis of edge energies yielded results which are in excellent agreement with oxidation state determinations made on the basis of the mole fractions for , , and extracted from extended X‐ray absorption fine structure spectra. © 1999 The Electrochemical Society. All rights reserved.

Study on the local atomic structure of germanium in organic germanium compounds by EXAFS

Organic germanium compounds have been extensively applied in medicine as tonics. In this paper, the local structures of two organic germanium compounds, carboxyethylgermanium sesquioxide and polymeric germanium glutamate, were determined by EXAFS. The structure parameters including coordination numbers and bond lengths were reported, and possible structure patterns were discussed.

Structure and dynamics of magnesium in silicate melts; a high-temperature25Mg NMR study

25 Mg NMR spectra for several silicate and aluminosilicate melts were obtained from 1000-1470 °C. The peaks are initially very broad, but narrow with increasing temperature to near 500 Hz at the highest temperatures. The peak positions for most of the melts do not shift noticeably with temperature in the range studied, except for a sodium magnesium silicate composition that was previously studied by Fiske and Stebbins (1994). This material showed a decrease in frequency of the peak position by about 4 ppm between 1150-1360 °C in both this and the previous study, consistent with an increase in the average size of the site. The chemical shifts vary with composition as well, ranging from 31 ppm for a potassium sodium magnesium silicate melt to 22 ppm for diopside melt (CaMgSi 2 O 6 ) at 1400 °C. Compositions with higher field strength cations have lower frequency chemical shifts, which correspond to larger coordination numbers and bond lengths for Mg 2+ . All of the peak positions obtained fall to slightly higher frequency than the range for sixfoldcoordinated Mg in crystals and well below the fourfold-coordinated range, indicating that the Mg is in fivefold to sixfold coordination in the melts. Spin-lattice relaxation times show that measurements are on the high-temperature side of the T 1 minima, and a simple expression for quadrupolar relaxation can be used to obtain correlation times for the motion responsible for the relaxation. The correlation times obtained in this manner are very similar to the correlation time τ shear obtained from viscosity measurements, implying that the Mg motion is strongly coupled to the network motion at these temperatures. Line widths also scale with T 1 in this temperature range, leading to the conclusion that the viscosity is the fundamental limit to observing the 25 Mg signal in the melt.

On the Coordination and Oxidation States of the Active-Site Copper Ion in Prokaryotic Cu,Zn Superoxide Dismutases

The active-site copper ion of the prokaryotic Cu,Zn superoxide dismutase fromP. leiognathiis found to undergo reversible reduction upon irradiation of the protein solution with a high-intensity X-ray beam from a third-generation synchrotron source. The same phenomenon is observed for the enzyme crystals, whose diffraction pattern has been obtained from synchrotron sources. In this case the active-site copper–ligand coordination bond lengths and in particular the Cu–NE2(His61) distance are consistent with a copper ion in the reduced state. These results are in line with previous studies on the eukaryotic Cu,Zn superoxide dismutases and suggest the conservation of an identical catalytic mechanism in both the prokaryotic and eukaryotic enzymes.

Steric Hindrance in a Mixed Solvated Nickel(II) Complex: Bis(acetonitrile-N)tetrakis(N,N-dimethylacetamide-O)nickel(II) Bis(tetrafluoroborate)

The title compound, [Ni(CH3CN)2{(CH3)2NCOCH3}4](BF4)2, has an octahedral coordination structure with the centre of symmetry at the Ni atom. Both of the two crystallographically inequivalent N,N-dimethylacetamide (DMA) molecules have normal coordination bond lengths Ni—O and angles Ni—O-C, but one of the Ni—O-C-N torsion angles deviates from 180°, indicating that the Ni—O bond is displaced from the direction of the lone pair of the sp2 O atom. It is ascribed to the steric hindrance of DMA coordination in an octahedral environment, which is imposed by the non-bonding contact of the acetyl methyl group with the ligating oxygen atom of the adjacent DMA molecule.

Investigation of Aquo and Chloro Complexes of UO(2)(2+), NpO(2)(+), Np(4+), and Pu(3+) by X-ray Absorption Fine Structure Spectroscopy.

U, Np, and Pu L(II,III)-edge X-ray absorption fine structure (XAFS) spectra were collected for the UO(2)(2+), NpO(2)(+), Np(4+), and Pu(3+) ions as a function of chloride concentration in aqueous solution. At low chloride concentration, the hydration numbers and corresponding bond lengths for the different ions are as follows: UO(2)(2+), N= 5.3, R = 2.41 Å; NpO(2)(+), N = 5.0, R = 2.50 Å; Np(4+), N = 11.2, R = 2.40 Å; Pu(3+), N = 10.2, R = 2.51 Å. As the Cl(-) concentration increases, inner-sphere Cl(-) complexation occurs, resulting in a decrease in the hydration numbers and an expansion of the actinide-oxygen (water) bond lengths. The Pu(3+) ion shows only a decrease in hydration number (40%) and no inner-sphere Cl(-) complexation for [Cl(-)] < 14 M. For concentrations up to 10-14 M Cl(-), the average Cl(-) coordination numbers and bond lengths are as follows: UO(2)(2+), N = 2.6, R = 2.73 Å; NpO(2)(+), N = 1.0, R = 2.84 Å; Np(4+), N = 2.0, R = 2.61 Å. Structural changes are observed in the near-edge spectral region as shown by significant changes in the white line intensities upon Cl(-) complexation. For ions with similar structures, i.e. Pu(3+) and Np(4+) or the actinyl ions NpO(2)(+) and UO(2)(2+), positive energy shifts are observed with increasing oxidation state. The ability to use XAFS speciation results to calculate equilibrium constants and the relationship of these results to previous studies are discussed.

XAFS Study on the Local Atomic Structures of Germanium in Organic Germanium Compounds

Organic germanium compounds have been extensively applied in medicine as tonics. In this paper, the local atomic structures in two organic germanium compounds, carboxyethylgermanium sesquioxide and polymeric germanium glutamate, are determined by using XAFS technique. The structural parameters including coordination number and bond lengths are reported, and possible structural patterns are discussed.

Single Crystal X-Ray Analyses of a Series of Hexamethylphosphoramide-Coordinated Complexes of Rare Earth Triflates: Existence of Tetrad Effects in the Coordinate Bonds

Abstract The molecular structures of [M(OTf)2(hmpa)4]OTf·CHCl3(OTf = OSO2CF3; M = Y, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu), [Sc(OTf)2(hmpa)4]OTf, and [La(η2-OTf)(OTf)(hmpa)4]OTf·CHCl3 were accurately determined by single crystal X-ray analyses. Tetrad effects are manifested in the series of the coordinate bond lengths.

Molecular Adducts of Inorganic Salts. VI. The Dimorphism of Cd(ReO4)2.2tu (tu = Thiourea)

The title compound, cadmium tetraoxorhenium bis(thiourea), Cd(ReO4)2.2CH4N2S, forms two polymorphs: monoclinic, (I), and triclinic, (II). Both are built up of infinite chains in which the Cd atoms are hexacoordinate. In (I), the centrosymmetric CdO4S2 octahedra are interlinked by double ReO4 bridges, while in (II), CdO3S3 octahedra are connected by alternating double ReO4 and S bridges. The Cd—S coordination bond length is 2.495 (2) Å in (I) and ranges from 2.576 (2) to 2.719 (2) Å in (II). The hydrogen bonding between chains is more developed in compound (II).

Structure determination of AgGeS glasses by isotopic substitution neutron diffraction

Structural studies of superionic glasses in the AgGeS system were performed using neutron diffraction with isotopic substitution of silver (107Ag, 109Ag and natAg) to understand the local environment of Ag+ ions. Real-space correlations, with and without Ag contributions, have been obtained from the first differences of the differential functions, D(r). The second differences of the D(r) functions yielded the AgAg correlation function. GeS and AgS correlations were also identified and their coordination numbers and bond lengths estimated.

EXAFS of bromide ion in solvents and at air/solution interface

Solvation structures of Br − ion dissolved in 23 solvents have been studied at the Br K-edge using extended X-ray absorption fine structure (EXAFS). The results are summarized as follows. 1) Coordination bond lengths r are 0.31–0.32 nm for BrO in protic solvents and 0.35–0.36 nm for BrC in aprotic solvents. 2) The r values for water and formamide are larger than those for other protic solvents, possibly due to the strong solvent-solvent interactions of these two solvents. 3) Coordination numbers N widely differ, ranging between 3–6, from solvent to solvent. The value of N for alcohol linearly correlates with the Mayer-Gutmann's acceptor number A N. 4) In aprotic solvents containing two methyl groups per molecule, Br − is found to contact with the two methyl groups, thus the number of primary solvent molecules must be equal to half the N value. 5) EXAFS amplitude is found to correlate with A N of the solvent. To study the surface structure, a new EXAFS technique, tocal-reflection total-conversion-electron-yield EXAFS, has been developed and applied. The new technique utilizes polarized X-rays from synchrotron radiation, providing not only information on the solvation structures of ions at the aqueous solution surface but also on the preferential orientation of coordination bond at the solution surface.

Extended x-ray-absorption fine-structure investigation of short-range order in a-Ge1-xSnx alloys.

The local environments of germanium and tin atoms in a-Ge 1-x Sn x alloys (0.0≤x≤0.2) have been investigated by measuring the extended x-ray-absorption fine structure (EXAFS) at the Ge K edge and at the Sn L III edge. The measured EXAFS at both edges could be described only by assuming the presence of a mixed first coordination shell composed of both Ge and Sn atoms. Coordination numbers, bond lengths, and relative mean-square displacement values characterizing the first coordination shell around Ge and Sn atoms were obtained