The quantitative Jahn-teller distortion of the Cu2+ site in aqueous solution by xanes spectroscopy

Hydration numbers of biologically relevant divalent metal cations from ab initio molecular dynamics and continuum solvation methods

Hydration and, in particular, the coordination number of a metal ion is of paramount importance as it defines many of its (bio)physicochemical properties. It is not only essential for understanding its behavior in aqueous solutions but also determines the metal ion reference state and its binding energy to (bio)molecules. In this paper, for divalent metal cations Ca2+, Cd2+, Cu2+, Fe2+, Hg2+, Mg2+, Ni2+, Pb2+, and Zn2+, we compare two approaches for predicting hydration numbers: (1) a mixed explicit/continuum DFT-D3//COSMO-RS solvation model and (2) density functional theory based ab initio molecular dynamics. The former approach is employed to calculate the Gibbs free energy change for the sequential hydration reactions, starting from [M(H2O)2]2+ aqua complexes to [M(H2O)9]2+, allowing explicit water molecules to bind in the first or second coordination sphere and determining the most stable [M(H2O)n]2+ structure. In the latter approach, the hydration number is obtained by integrating the ion-water radial distribution function. With a couple of exceptions, the metal ion hydration numbers predicted by the two approaches are in mutual agreement, as well as in agreement with the experimental data.

Designing Reactive Bridging O2- at the Atomic Cu-O-Fe Site for Selective NH3 Oxidation

Surface oxidation chemistry involves the formation and breaking of metal-oxygen (M-O) bonds. Ideally, the M-O bonding strength determines the rate of oxygen absorption and dissociation. Here, we design reactive bridging O^2- species within the atomic Cu-O-Fe site to accelerate such oxidation chemistry. Using in situ X-ray absorption spectroscopy at the O K-edge and density functional theory calculations, it is found that such bridging O^2- has a lower antibonding orbital energy and thus weaker Cu-O/Fe-O strength. In selective NH₃ oxidation, the weak Cu-O/Fe-O bond enables fast Cu redox for NH₃ conversion and direct NO adsorption via Cu-O-NO to promote N-N coupling toward N₂. As a result, 99% N₂ selectivity at 100% conversion is achieved at 573 K, exceeding most of the reported results. This result suggests the importance to design, determine, and utilize the unique features of bridging O^2- in catalysis.

Resolving Configurational Disorder for Impurities in a Low-Entropy Phase

Hematite (α-Fe₂O₃) exerts a strong control over the transport of minor but critical metals in the environment and is used in multiple industrial applications; the photocatalysis community has explored the properties of hematite nanoparticles over a wide range of transition metal dopants. Nonetheless, simplistic assumptions are used to rationalize the local coordination environment of impurities in hematite. Here, we use ab initio molecular dynamics (AIMD)-guided structural analysis to model the extended X-ray absorption fine structure (EXAFS) of Cu²⁺- and Zn²⁺-doped hematite nanoparticles. Specific defect-impurity associations were identified, and the local coordination environments of Cu and Zn both displayed considerable configurational disorder that, in aggregate, approached Jahn-Teller-like distortion for Cu but, in contrast, maintained hematite-like symmetry for Zn. This study highlights the role of defects in accommodating impurities in a nominally low-entropy phase and the limits to traditional shell-by-shell fitting of EXAFS for dopants/impurities in unprecedented bonding environments.

Solvation structure of lanthanide(iii) bistriflimide salts in acetonitrile solution: a molecular dynamics simulation and EXAFS investigation

Lanthanide³⁺ ions in acetonitrile solutions of bistriflimide salts form 10-fold coordination complexes composed of both solvent molecules and counterions

[Cu(aq)]2+ is structurally plastic and the axially elongated octahedron goes missing

High resolution (k = 18 Å^-1 or k = 17 Å^-1) copper K-edge EXAFS and MXAN (Minuit X-ray Absorption Near Edge) analyses have been used to investigate the structure of dissolved [Cu(aq)]²⁺ in 1,3-propanediol (1,3-P) or 1,5-pentanediol (1,5-P) aqueous frozen glasses. EXAFS analysis invariably found a single axially asymmetric 6-coordinate (CN6) site, with 4×O_eq = 1.97 Å, O_ax1 = 2.22 Å, and O_ax2 = 2.34 Å, plus a second-shell of 4×O_water = 3.6 Å. However, MXAN analysis revealed that [Cu(aq)]²⁺ occupies both square pyramidal (CN5) and axially asymmetric CN6 structures. The square pyramid included 4×H₂O = 1.95 Å and 1×H₂O = 2.23 Å. The CN6 sites included either a capped, near perfect, square pyramid with 5×H₂O = 1.94 ± 0.04 Å and H₂O_ax = 2.22 Å (in 1,3-P) or a split axial configuration with 4×H₂O = 1.94, H₂O_ax1 = 2.14 Å, and H₂O_ax2 = 2.28 Å (in 1,5-P). The CN6 sites also included an 8-H₂O second-shell near 3.7 Å, which was undetectable about the strictly pyramidal sites. Equatorial angles averaging 94° ± 5° indicated significant departures from tetragonal planarity. MXAN assessment of the solution structure of [Cu(aq)]²⁺ in 1,5-P prior to freezing revealed the same structures as previously found in aqueous 1M HClO₄, which have become axially compressed in the frozen glasses. [Cu(aq)]²⁺ in liquid and frozen solutions is dominated by a 5-coordinate square pyramid, but with split axial CN6 appearing in the frozen glasses. Among these phases, the Cu-O axial distances vary across 1 Å, and the equatorial angles depart significantly from the square plane. Although all these structures remove the d_x²-y² , d_z² degeneracy, no structure can be described as a Jahn-Teller (JT) axially elongated octahedron. The JT-octahedral description for dissolved [Cu(aq)]²⁺ should thus be abandoned in favor of square pyramidal [Cu(H₂O)₅]²⁺. The revised ligand environments have bearing on questions of the Cu(i)/Cu(ii) self-exchange rate and on the mechanism for ligand exchange with bulk water. The plasticity of dissolved Cu(ii) complex ions falsifies the foundational assumption of the rack-induced bonding theory of blue copper proteins and obviates any need for a thermodynamically implausible protein constraint.

Cu(ii) sorption by biogenic birnessite produced by Pseudomonas putida strain MnB1: structural differences from abiotic birnessite and its environmental implications

Cu(ii) adsorbs predominantly at the layer edges of abiobirnessite, but at vacancies in bio-birnessite with larger interlayer space.

Structure and Stability of a Copper(II) Lactate Complex in Alkaline Solution: a Case Study by Energy-Dispersive X-ray Absorption Spectroscopy

Energy-dispersive X-ray absorption spectroscopy was applied, aimed at solving the problem of the structure and stability of a copper(II) lactate complex in alkaline solution, used as a precursor for the electrodeposition of Cu₂O. The application of multiple scattering calculations to the simulation of the X-ray absorption near-edge structure part of the spectra allowed an accurate resolution of the structure: the copper(II) cation is surrounded by four lactate ions in a distorted tetrahedral environment, with the lactate anions acting as monodentate ligands. This results in an atomic arrangement where copper is surrounded by four oxygen atoms located at quite a short distance (ca. 1.87 Å) and four oxygen atoms located quite far apart (ca. 3.1-3.2 Å). The complex was finally found to be stable in a wide range of applied potentials.

A high-resolution XAS study of aqueous Cu(II) in liquid and frozen solutions: pyramidal, polymorphic, and non-centrosymmetric

High-resolution EXAFS (k = 18 Å(-1)) and MXAN XAS analyses show that axially elongated square pyramidal [Cu(H2O)5](2+) dominates the structure of Cu(II) in aqueous solution, rather than 6-coordinate JT-octahedral [Cu(H2O)6](2+). Freezing produced a shoulder at 8989.6 eV on the rising XAS edge and an altered EXAFS spectrum, while 1s → 3d transitions remained invariant in energy position and intensity. Core square pyramidal [Cu(H2O)5](2+) also dominates frozen solution. Solvation shells were found at ∼3.6 Å (EXAFS) or ∼3.8 Å (MXAN) in both liquid and frozen phases. However, MXAN analysis revealed that about half the time in liquid solution, [Cu(H2O)5](2+) associates with an axially non-bonding 2.9 Å water molecule. This distant water apparently organizes the solvation shell. When the 2.9 Å water molecule is absent, the second shell is undetectable to MXAN. The two structural arrangements may represent energetic minima of fluxional dissolved aqueous [Cu(H2O)5](2+). The 2.9 Å trans-axial water resolves an apparent conflict of the [Cu(H2O)5](2+) core model with a dissociational exchange mechanism. In frozen solution, [Cu(H2O)5](2+) is associated with either a 3.0 Å axial non-bonded water molecule or an axial ClO4(-) at 3.2 Å. Both structures are again of approximately equal presence. When the axial ClO4(-) is present, Cu(II) is ∼0.5 Å above the mean O4 plane. This study establishes [Cu(H2O)5](2+) as the dominant core structure for Cu(II) in water solution, and is the first to both empirically resolve multiple extended solution structures for fluxional [Cu(H2O)5](2+) and to provide direct evidence for second shell dynamics.

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.

Development and validation of a ReaxFF reactive force field for Cu cation/water interactions and copper metal/metal oxide/metal hydroxide condensed phases

To enable large-scale reactive dynamic simulations of copper oxide/water and copper ion/water interactions we have extended the ReaxFF reactive force field framework to Cu/O/H interactions. To this end, we employed a multistage force field development strategy, where the initial training set (containing metal/metal oxide/metal hydroxide condensed phase data and [Cu(H(2)O)(n)](2+) cluster structures and energies) is augmented by single-point quantum mechanices (QM) energies from [Cu(H(2)O)(n)](2+) clusters abstracted from a ReaxFF molecular dynamics simulation. This provides a convenient strategy to both enrich the training set and to validate the final force field. To further validate the force field description we performed molecular dynamics simulations on Cu(2+)/water systems. We found good agreement between our results and earlier experimental and QM-based molecular dynamics work for the average Cu/water coordination, Jahn-Teller distortion, and inversion in [Cu(H(2)O)(6)](2+) clusters and first- and second-shell O-Cu-O angular distributions, indicating that this force field gives a satisfactory description of the Cu-cation/water interactions. We believe that this force field provides a computationally convenient method for studying the solution and surface chemistry of metal cations and metal oxides and, as such, has applications for studying protein/metal cation complexes, pH-dependent crystal growth/dissolution, and surface catalysis.

Host–Guest Chemistry of Copper(II)–Histidine Complexes Encaged in Zeolite Y

Structural analysis has been carried out on copper(II)-histidine (Cu(2+)/His) complexes after immobilization in the pore system of the zeolites NaY and de-aluminated NaY (DAY). The aim of this study was to determine the geometrical structure of Cu(2+)/His complexes after encaging, to obtain insight into both the effect of the zeolite matrix on the molecular structure and redox properties of the immobilized complexes. In addition to N(2) physisorption and X-ray fluorescence (XRF) analyses, a combination of UV/Vis/NIR, ESR, X-ray absorption (EXAFS and XANES), IR, and Raman spectroscopy was used to obtain complementary information on both the first coordination shell of the copper ion and the orientation of the coordinating His ligands. It was demonstrated that two complexes (A and B) are formed, of which the absolute and relative abundance depends on the Cu(2+)/His concentration in the ion-exchange solution and on the Si/Al ratio of the zeolite material. In complex A, one His ligand coordinates in a tridentate facial-like manner through N(am), N(im), and O(c), a fourth position being occupied by an oxygen atom from a zeolite Brønsted site. In complex B, two His ligands coordinate as bidentate ligands; one histamine-like (N(am), N(im)) and the other one glycine-like (N(am), O(c)). In particular the geometrical structure of complex A differs from the preferred structure of Cu(2+)/His complexes in aqueous solutions; this fact implies that the zeolite host material actively participates in the coordination and orientation of the guest molecules. The tendency for complex A to undergo reduction in inert atmosphere to Cu(1+) (as revealed by dynamic XANES studies) suggests activation of complex A by the interaction with the zeolite material. EXAFS analysis confirms the formation of a distorted four coordinate geometry of complex A, suggesting that the combination of zeolite and one His ligand force the Cu(2+) complex into an activated, entactic state.

The hydration of Cu2+: Can the Jahn-Teller effect be detected in liquid solution?

The long elusive structure of Cu(II) hydrate in aqueous solutions, classically described as a Jahn-Teller distorted octahedron and recently proposed to be a fivefold coordination structure [Pasquarello et al., Science 291, 856 (2001)], has been probed with x-ray-absorption spectroscopy by performing a combined theoretical and experimental analysis. Two absorption channels were needed to obtain a proper reproduction of the x-ray-absorption near-edge structure (XANES) region spectrum, as already observed in other Cu(II) complexes [Chaboy et al., Phys. Rev. B 71, 134208 (2005)]. The extended x-ray-absorption fine-structure (EXAFS) spectrum was analyzed as well within this approach. Quite good reproductions of both XANES and EXAFS spectra were attained for several distorted and undistorted structures previously proposed. Nevertheless, there is not a clearly preferred structure among those including four-, five-, and sixfold coordinated Cu(II) ions. Taking into account our results, as well as many more from several other authors using different techniques, the picture of a distorted octahedron for the Cu(II) hexahydrate in aqueous solution, paradigm of the Jahn-Teller effect, is no longer supported. In solution a dynamical view where the different structures exchange among themselves is the picture that better suits the results presented here.

Surface complexation of copper(II) on soil particles: EPR and XAFS studies

The interactions of transition metals with natural systems play an important role in the mobility and the bioavailability of these metals in soils. In this study, the adsorption of copper(II) onto natural soil particles was studied as a function of pH and metal concentration. The retention capacity of soil particles was determined at pH 6.2 to be equal to 6.7 mg of copper/g of solid. The Langmuir and Freundlich isotherm equations were then used to describe the partitioning behavior of the system at different pH values. A combination of EPR, extended X-ray absorption fine structure (EXAFS), and X-ray absorption near-edge structure (XANES) spectroscopies was used to probe the Cu atomic environment at the soil particles/aqueous interface. The spectroscopic study revealed that copper(II) ions are held in inner-sphere surface complexes. It also revealed that Cu was in an octahedral coordination with first-shell oxygen atoms. A weak tetragonal distortion was pointed out due to the Jahn-Teller effect, with a mean Cu-Oequatorial bond distance of 1.96 A and a Cu-Oaxial bond distance of 2.06 A. A detailed analysis of the spectroscopic data suggested that Cu(II) was bonded to organic matter coated onto the mineral fraction of soil particles.

EXAFS and XANES studies of retention of copper and lead by a lignocellulosic biomaterial

Lignocellulosic substrate (LS), which is a low cost biomaterial, has a strong complexing ability and can be used in the treatment of wastewaters as biosorbentto remove heavy metals. The speciation of copper and lead to this biomaterial has been studied by X-ray absorption spectroscopy. The copper(II) has a 6-coordinate structure with four oxygen atoms in the equatorial plane at 1.95 A and two in axial position at 2.35 A. In the case of lead a particularly low coordination number of about 3 has been obtained. The combination of extended X-ray absorption fine structure (EXAFS) and X-ray absorption near edge structure (XANES) suggested that Cu and Pb are bound to the surface of LS through carboxylic moieties.

First solvation shell of the Cu(II) aqua ion: evidence for fivefold coordination

We determined the structure of the hydrated Cu(II) complex by both neutron diffraction and first-principles molecular dynamics. In contrast with the generally accepted picture, which assumes an octahedrally solvated Cu(II) ion, our experimental and theoretical results favor fivefold coordination. The simulation reveals that the solvated complex undergoes frequent transformations between square pyramidal and trigonal bipyramidal configurations. We argue that this picture is also consistent with experimental data obtained previously by visible near-infrared absorption, x-ray absorption near-edge structure, and nuclear magnetic resonance methods. The preference of the Cu(II) ion for fivefold instead of sixfold coordination, which occurs for other cations of comparable charge and size, results from a Jahn-Teller destabilization of the octahedral complex.

X-Ray Absorption and EPR Spectroscopic Characterization of Adsorbed Copper(II) Complexes at the Boehmite (AlOOH) Surface

The chemical environment of Cu(II) adsorbed to the boehmite (AlOOH) surface at pH 6.5 is examined by electron paramagnetic resonance and X-ray absorption spectroscopy. Adsorbed Cu(II) is always coordinated by four oxygens in an axially symmetric ligand field when adsorbed under our experimental conditions. The Cu-O bond distance is approximately 1.94 A. An oriented, inner-sphere Cu(II) surface complex is observed at low surface loading (<0.2 μmol/M2). A second population of Cu(OH)N (H2O)X(2-N)+ outer-sphere complexes is proposed at higher surface loadings to explain X-ray absorption fine structure results. Cu(II) strongly resists any tendency to form a surface precipitate on boehmite at pH 6.5. The presence of specifically adsorbing anions had little effect on the local chemical environment of adsorbed Cu(II). Copyright 1997 Academic Press. Copyright 1997Academic Press

Theoretical study of oxyhemocyanin active site: a possible insight on the first step of phenol oxidation by tyrosinase

Extended Huckel theory calculations have been carried out on a model of the oxyhemocyanin active site that includes six imidazoles, the two copper cations, and a dioxygen molecule. The results obtained for the very likely mu-eta 2:eta 2 arrangement of the dioxygen molecule show that the most favorable orientation of O2 is such that the two long Cu-N coordination bonds are perpendicular to the plane formed by the two metal atoms and O2. This arrangement leads to pentacoordinated coppers with a distorted square pyramidal geometry. The molecular electrostatic potential maps of the complexes exhibit a potential well located close to the peroxo anion midbond. The dependence of the energy and of the molecular electrostatic maps on the precise orientation and location of the imidazole rings has been investigated. These results, which show the important role played by the third remote imidazole ligand, are discussed in relation with the first step of tyrosinase-mediated phenol oxidation.