Structure and size of complete hydration shells of metal ions and inorganic anions in aqueous solution

The structures of nine hydrated metal ions in aqueous solution have been redetermined by large angle X-ray scattering to obtain experimental data of better quality than those reported 40-50 years ago. Accurate M-OI and M-(OI-H)⋯OII distances and M-OI(H)⋯OII bond angles are reported for the hydrated magnesium(II), aluminium(III), manganese(II), iron(II), iron(III), cobalt(II), nickel(II), copper(II) and zinc(II) ions; the subscripts I and II denote oxygen atoms in the first and second hydration sphere, respectively. Reported structures of hydrated metal ions in aqueous solution are summarized and evaluated with emphasis on a possible relationship between M-OI-OII bond angles and bonding character. Metal ions with high charge density have M-OI-OII bond angles close to 120°, indicative of a mainly electrostatic interaction with the oxygen atom in the water molecule in the first hydration shell. Metal ions forming bonds with a significant covalent contribution, as e.g. mercury(II) and tin(II), have M-OI-OII bond angles close to 109.5°. This implies that they bind to one of the free electron pairs in the water molecule. Comparison of M-O bond distances of hydrated metal ions in the solid state with one hydration shell, and in aqueous solution with in most cases at least two hydration shells, shows no significant differences. On the other hand, the X-O bond distance in hydrated oxoanions increases by ca. 0.02 Å in aqueous solution in comparison with the corresponding X-O distance in the solid state. A linear correlation is observed between volume, calculated from the van der Waals radius of the hydrated ion, and the ionic diffusion coefficient in aqueous solution. This correlation strongly indicates that monovalent metal ions, except lithium and silver(I), and singly-charged monovalent oxoanions have a single hydration shell. Divalent metal ions, bismuth(III) and the lanthanoid(III) and actinoid(III) ions have two hydration shells. Trivalent transition and tetravalent metal ions have two full hydration shells and portion of a third one. Doubly charged oxoanions have one well-defined hydration shell and an ill-defined second one.

Fingerprint of Dipole Moment Orientation of Water Molecules in Cu2+ Aqueous Solution Probed by X-ray Photoelectron Spectroscopy

The electronic structure and geometrical organization of aqueous Cu2+ have been investigated by using X-ray photoelectron spectroscopy (XPS) at the Cu L-edge combined with state-of-the-art ab initio molecular dynamics and a quantum molecular approach designed to simulate the Cu 2p X-ray photoelectron spectrum. The calculations offer a comprehensive insight into the origin of the main peak and satellite features. It is illustrated how the energy drop of the Cu 3d levels (≈7 eV) following the creation of the Cu 2p core hole switches the nature of the highest singly occupied molecular orbitals (MOs) from the dominant metal to the dominant MO nature of water. It is particularly revealed how the repositioning of the Cu 3d levels induces the formation of new bonding (B) and antibonding (AB) orbitals, from which shakeup mechanisms toward the relaxed H-SOMO operate. As highlighted in this study, the appearance of the shoulder near the main peak corresponds to the characteristic signature of shakeup intraligand (1a1 → H-SOMO(1b1)) excitations in water, providing insights into the average dipole moment distribution (≈36°) of the first-shell water molecules surrounding the metal ion and its direct impact on the broadening of the satellite. It is also revealed that the main satellite at 8 eV from the main peak corresponds to (metal/1b2 → H-SOMO(1b1) of water) excitations due to a bonding/antibonding (B/AB) interaction of Cu 3d levels with the deepest valence O2p/H1s 1b2 orbitals of water. This finding underscores the sensitivity of XPS to the electronic structure and orientation of the nearest water molecules around the central ion.

Structural, Thermodynamic, and Spectroscopic Evolution in the Hydration of Copper(II) Ions, Cu2+(H2O)2-8

Gas-phase clusters of the hydrated Cu(II) cation with 2-8 water molecules were investigated using ab initio quantum chemistry. Isomer structures, energies, and vibrational spectra were computed across this size range, yielding a qualitative picture of this ion as an intact Cu2+ hydrate that also partially oxidizes the surrounding water network at equilibrium. At sufficient cluster sizes, these ion hydrates also become thermodynamically preferred over competitive Cu(II) hydroxide hydrates. Competitive coordination environments were found to exist at some cluster sizes, due to both hydrogen-bonding and d-orbital chemical effects, and the dominant coordination number was found in some cases to be temperature-dependent. Clear spectral signatures of the ion's coordination environment were computed to exist at each cluster size, which should make experimental verification of these computational predictions straightforward. Through comparison to recent studies of hydrated CuOH+, the effective charge on the metal center was shown to converge to approximately +1.5 in both cases, despite qualitatively different behavior of their radical spin densities. Therefore, nominally Cu(II) ions exhibit considerable electronic, chemical, and structural flexibility. The electronic origins of this flexibility─including key roles played by the water network itself─are investigated in this work and should provide a conceptual foundation for future studies of copper-based, water-oxidation catalysts.

Cu(II) assisted peroxymonosulfate for antibiotic resistant bacteria inactivation: A potential disinfection technology in swimming pool

Alternative disinfection technology to chlorination is required to control the risk of antibiotic resistance in swimming pools. In this study, copper ions (Cu(II)), which often exist in swimming pools as algicides, were used to activate peroxymonosulfate (PMS) for the inactivation of ampicillin-resistant E. coli. Cu(II) and PMS showed synergistic effects on E. coli inactivation in weak alkaline conditions, obtaining 3.4 log inactivation in 20 min with 10 μM Cu(II) and 100 μM PMS at pH 8.0. Quenching experiments indicated that radicals (i.e., OH and SO₄^-) were not the main disinfectors for E. coli inactivation. Based on the structure of Cu(II) and density functional theory calculations, the Cu(II)-PMS complex (Cu(H₂O)₅SO₅) was recommended as the active species for E. coli inactivation. Under the experimental conditions, the PMS concentration had a greater influence on E. coli inactivation than the Cu(II) concentration, possibly because increasing PMS concentration accelerates ligand exchange reaction and facilitates active species generation. By forming hypohalous acids, halogen ions could improve the disinfection efficiency of Cu(II)/PMS. The addition of HCO₃^- concentration (from 0 to 1.0 mM) and humic acid (0.5 and 1.5 mg/l) did not significantly inhibit the E. coli inactivation. The feasibility of adding PMS to waters containing Cu(II) for the inactivation of antibiotic-resistant bacteria was validated in actual swimming pool waters, where 4.7 log inactivation of E. coli was achieved in 60 min.

Femtosecond symmetry breaking and coherent relaxation of methane cations via x-ray spectroscopy

Understanding the relaxation pathways of photoexcited molecules is essential to gain atomistic level insight into photochemistry. Herein, we performed a time-resolved study of ultrafast molecular symmetry breaking via geometric relaxation (Jahn-Teller distortion) on the methane cation. Attosecond transient absorption spectroscopy with soft X-rays at the carbon K-edge revealed that the distortion occurred within 10 ± 2 femtoseconds after few-femtosecond strong-field ionization of methane. The distortion activated coherent oscillations in the asymmetric scissoring vibrational mode of the symmetry broken cation, which were detected in the X-ray signal. These oscillations were damped within 58 ± 13 femtoseconds, as vibrational coherence was lost with the energy redistributing into lower-frequency vibrational modes. This study completely reconstructs the molecular relaxation dynamics of this prototypical example and opens new avenues for exploring complex systems.

Quantum-mechanical characteristics of apigenin: Antiradical, metal chelation and inhibitory properties in physiologically relevant media

Density functional theory was used to examine the antioxidant activity of apigenin. All protonated species that are present in a non-negligible population at physiological pH were considered in the study. The ability to scavenge the hydroperoxide radical was evaluated in lipid and aqueous environments. The capacity to halt the Fenton reaction by chelating Fe(III) and Cu(II) ions was also investigated, as was the ability to inhibit xanthine oxidase. The results indicate that these activities may be particularly important in describing the beneficial effects of apigenin, especially because of its lower anti-•OOH potential than Trolox or vitamin C. The findings underscore the significant role of dianion in the antiradical and chelating properties, despite its presence in much lower molar fractions than other ions.

An Atomistic Model Describing the Structure and Morphology of Cu-Doped C-S-H Hardening Accelerator Nanoparticles

Calcium silicate hydrate (C-S-H) is the main binding phase in Portland cement. The addition of C-S-H nanoparticles as nucleation seeds has successfully been used to accelerate the hydration process and the precipitation of binding phases either in conventional Portland cement or in alternative binders. Indeed, the modulation of the hydration kinetics during the early-stage dissolution-precipitation reactions, by acting on the nucleation and growth of binding phases, improves the early strength development. The fine-tuning of concrete properties in terms of compressive strength and durability by designed structural modifications can be achieved through the detailed description of the reaction products at the atomic scale. The nano-sized, chemically complex and structurally disordered nature of these phases hamper their thorough structural characterization. To this aim, we implement a novel multi-scale approach by combining forefront small-angle X-ray scattering (SAXS) and synchrotron wide-angle X-ray total scattering (WAXTS) analyses for the characterization of Cu-doped C-S-H nanoparticles dispersed in a colloidal suspension, used as hardening accelerator. SAXS and WAXTS data were analyzed under a unified modeling approach by developing suitable atomistic models for C-S-H nanoparticles to be used to simulate the experimental X-ray scattering pattern through the Debye scattering equation. The optimization of atomistic models against the experimental pattern, together with complementary information on the structural local order from ²⁹Si solid-state nuclear magnetic resonance and X-ray absorption spectroscopy, provided a comprehensive description of the structure, size and morphology of C-S-H nanoparticles from the atomic to the nanometer scale. C-S-H nanoparticles were modeled as an assembly of layers composed of 7-fold coordinated Ca atoms and decorated by silicate dimers and chains. The structural layers are a few tens of nanometers in length and width, with a crystal structure resembling that of a defective tobermorite, but lacking any ordering between stacking layers.

Effects of Cu(II) and Zn(II) on PbO2 Reductive Dissolution under Drinking Water Conditions: Short-term Inhibition and Long-term Enhancement

Lead oxide (PbO₂) has the lowest solubility with free chlorine among Pb corrosion products, but depletion of free chlorine or a switch from free chlorine to monochloramine can cause its reductive dissolution. We previously reported that Cu(II) and Zn(II) inhibited PbO₂ reductive dissolution within 12 h. Here, we expanded on this work by performing longer duration experiments and further exploring the underlying mechanisms. Between 12 and 48 h, Cu(II) and Zn(II) had no discernible effect on PbO₂ reductive dissolution. From 48 to 192 h, Cu(II) and Zn(II) enhanced PbO₂ reductive dissolution. Dissolved oxygen (DO) concentrations followed the same trends as PbO₂ reductive dissolution, indicating that the DO was produced by PbO₂ reductive dissolution. On the basis of extended X-ray absorption fine structure spectra, we hypothesize that the inhibitory effect of Cu(II) and Zn(II) on PbO₂ reductive dissolution (<12 h) is caused by decreasing abundance of protonated sites on the PbO₂ surface. The enhanced dissolution (>48 h) may be caused by competitive adsorption of Cu(II) and Zn(II) with Pb(II), which could limit the adsorption of Pb(II) onto PbO₂ that could otherwise inhibit reductive dissolution. This study indicates that stagnation time plays a vital role in determining cations' effects on the stability of Pb corrosion products.

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.

Study of interaction of metal ions with methylthymol blue by chemometrics and quantum chemical calculations

In this study, we determine the acidity constants of methylthymol blue (MTB) and association constants of its complexes with the ZnII, CuII, and FeII metal ions (MIs), through theoretical and experimental means. The complexes were characterized using UV-Visible absorption spectroscopy combined with soft/hard chemometrics methods and quantum chemical calculations. Quantum chemical calculations revealed that electronic transitions in the UV-Visible spectra of MTB have mixed n → π* and π → π* characters. The results of molar ratio and multivariate curve resolution alternating least squares (MCR-ALS) revealed the formation of successive 1:2 and 1:1 complexes (MI:MTB) for the ZnII and CuII systems. However, the formation of successive 1:1 and 2:1 complexes are suggested for FeII by the molar ratio and MCR-ALS. The majority of transitions observed in the UV-Visible spectra of the Zn(MTB) and Cu(MTB) complexes have ligand-to-ligand charge transfer (LLCT) characters. However, the transitions in the UV-Visible spectrum of the Fe(MTB) complex have LLCT and metal-to-ligand charge transfer (MLCT) characters. For the Fe2(MTB) complex, the lowest energy transition of has an LLCT character. However, its higher energy transitions are a mixture of LLCT, MLCT, and metal-to-metal charge transfer (MMCT) characters. The correlation between experimental and computed wavelengths revealed that the 1:1 complexes of ZnII and CuII prefer square pyramidal geometries. However, the FeII complexes always show octahedral geometry.

Theoretical investigation of tetrahedral distortion of four-coordinate iron(II) centres in FePd(CN)4

The tetrahedral distortion of iron(ii) centres in the cyanide-bridged framework FePd(CN)4 was recently demonstrated experimentally. Here, we theoretically confirmed the electronically driven tetrahedral distortion of iron(ii) by comparing the density of states and total energies of FePd(CN)4 (d6) and ZnPd(CN)4 (d10). The calculation results suggested that a Jahn-Teller-like effect is caused on the tetrahedral geometry by the electronic effect of unequally occupied non-bonding 3d orbitals in the corresponding structure.

Selective Recovery of Ammonia Nitrogen from Wastewaters with Transition Metal-Loaded Polymeric Cation Exchange Adsorbents

Extracting valuable products from wastewaters with nitrogen-selective adsorbents can offset energy-intensive ammonia production, rebalance the nitrogen cycle, and incentivize environmental remediation. Separating nitrogen (N) as ammonium from other wastewater cations (e.g., K⁺ , Ca²⁺ ) presents a major challenge to N removal from wastewater and N recovery as high-purity products. High selectivity and capacity were achieved through ligand exchange of ammonia with ammine-complexing transition metals loaded onto polymeric cation exchange resins. Compared to commercial resins, metal-ligand exchange adsorbents exhibited higher ammonia removal capacity (8 mequiv g^-1 ) and selectivity (N/K⁺ equilibrium selectivity of 10.1) in binary equimolar solutions. Considering optimal ammonia concentrations (200-300 mequiv L^-1 ) and pH (9-10) for metal-ligand exchange, hydrolyzed urine was identified as a promising candidate for selective TAN recovery. However, divalent cation exchange increased transition metal elution and reduced ammonia adsorption. Ultimately, metal-ligand exchange adsorbents can advance nitrogen-selective separations from wastewaters.

Evaluating the Performance of a Non-Bonded Cu2+ Model Including Jahn-Teller Effect into the Binding of Tyrosinase Inhibitors

Tyrosinase (TYR) is a metalloenzyme classified as a type-3 copper protein, which is involved in the synthesis of melanin through a catalytic process beginning with the conversion of the amino acid l-Tyrosine (l-Tyr) to l-3,4-dihydroxyphenylalanine (l-DOPA). It plays an important role in the mechanism of melanogenesis in various organisms including mammals, plants, and fungi. Herein, we used a combination of computational molecular modeling techniques including molecular dynamic (MD) simulations and the linear interaction energy (LIE) model to evaluate the binding free energy of a set of analogs of kojic acid (KA) in complex with TYR. For the MD simulations, we used a dummy model including the description of the Jahn–Teller effect for Cu²⁺ ions in the active site of this enzyme. Our results show that the LIE model predicts the TYR binding affinities of the inhibitor in close agreement to experimental results. Overall, we demonstrate that the classical model provides a suitable description of the main interactions between analogs of KA and Cu²⁺ ions in the active site of TYR.

EXAFS Study on the Coordination Chemistry of the Solvated Copper(II) Ion in a Series of Oxygen Donor Solvents

The structures of the solvated copper(II) ion in water and nine organic oxygen donor solvents with similar electron-pair donor ability, but with different space-demanding properties at coordination, have been studied by EXAFS. N,N′-Dimethylpropyleneurea and N,N,N′,N′-tetramethylurea are sufficiently space demanding at coordination to make the axial positions not accessible, resulting in square-planar copper(II) solvate complexes with an intense green color. The mean Cu–O bond distances in these two solvate complexes are 1.939(3) and 1.935(3) Å, respectively. The best fits of the remaining solvates, which are light blue in different hues, are obtained with a Jahn–Teller distorted-octahedral model consisting of four strongly bound solvent molecules in the equatorial positions at 1.96(2) Å and two in the axial positions but with different Cu–O_ax bond distances: ca. 2.15 and 2.32 Å. This is in agreement with observations in solid-state structures of compounds containing hexaaquacopper(II) complexes crystallizing in noncentrosymmetric space groups and all reported crystal structures containing a [Cu(H₂O)₅(O-ligand)] complex with Jahn–Teller distortion. Such a structure is in agreement with previous EPR and EXAFS studies proving the hydrated copper(II) ion to be a noncentrosymmetric complex in aqueous solution. The refinements of the EXAFS data of the solids [Cu(H₂O)₆](ClO₄)₂, [Cu(H₂O)₆](BrO₃)₂, [Cu(H₂O)₆]SiF₆, Cu(NO₃)₂·2.5H₂O, and CuSO₄·5H₂O gave Cu–O bond distances significantly different from those reported in the crystallographic studies but similar to the configuration and bond distances in the hydrated copper(II) ion in aqueous solution. This may depend on whether the orientation of the axial positions is random in one or three dimensions, giving a mean structure of the solid with symmetry higher than that of the individual complexes. This study presents the very first experimental data from the new X-ray absorption spectroscopy beamline Balder at the MAX IV synchrotron radiation facility in Lund, Sweden, as well as the utilized properties of the beamline.

The coordination chemistry of the solvated copper(II) ion has been studied in 10 solvents, including water. The copper(II) ion has a noncentrosymmetric Jahn−Teller distorted-octahedral geometry with the axial Cu−O bond distances differing by ca. 0.2 Å.

Electrochemical Deposition of Copper on Epitaxial Graphene

Understanding the mechanism of metal electrodeposition on graphene as the simplest building block of all graphitic materials is important for electrocatalysis and the creation of metal contacts in electronics. The present work investigates copper electrodeposition onto epitaxial graphene on 4H-SiC by experimental and computational techniques. The two subsequent single-electron transfer steps were coherently quantified by electrochemistry and density functional theory (DFT). The kinetic measurements revealed the instantaneous nucleation mechanism of copper (Cu) electrodeposition, controlled by the convergent diffusion of reactant to the limited number of nucleation sites. Cu can freely migrate across the electrode surface. These findings provide fundamental insights into the nature of copper reduction and nucleation mechanisms and can be used as a starting point for performing more sophisticated investigations and developing real applications.

Nanocellulose/graphene oxide layered membranes: elucidating their behaviour during filtration of water and metal ions in real time

The deposition of a thin layer of graphene oxide onto cellulose nanofibril membranes, to form CNF-GO layered-composite membranes, dramatically enhances their wet-mechanical stability, water flux and capacity to adsorb water pollutants (P. Liu, C. Zhu and A. P. Mathew, J. Hazard. Mater., 2019, 371, 484-493). In this work, we studied in real time the behavior of these layered membranes during filtration of water and metal ion solutions by means of in situ SAXS and reactive molecular dynamics (ReaxFF) computational simulations. SAXS confirms that the GO layers limit the swelling and structural deformations of CNFs during filtration of aqueous solutions. Moreover, during filtration of metal ion solutions, the connection of the CNF-GO network becomes highly complex mass-fractal like, with an increment in the correlation length. In addition, after ion adsorption, the SAXS data revealed apparent formation of nanoparticles during the drying stage and particle size increase as a function of time during drying. The molecular dynamics simulations, on the other hand, provide a deep insight into the assembly of both components, as well as elucidating the motion of the metal ions that potentially lead to the formation of metal clusters during adsorption, confirming the synergistic behavior of GO and CNFs for water purification applications.

Application of the 3D-RISM-KH molecular solvation theory for DMSO as solvent

The molecular solvation theory in the form of the Three-Dimensional Reference Interaction Site Model (3D-RISM) with Kovalenko-Hirata (KH) closure relation is benchmarked for use with dimethyl sulfoxide (DMSO) as solvent for (bio)-chemical simulation within the framework of integral equation formalism. Several force field parameters have been tested to correctly reproduce solvation free energy in DMSO, ion solvation in DMSO, and DMSO coordination prediction. Our findings establish a united atom (UA) type parameterization as the best model of DMSO for use in 3D-RISM-KH theory based calculations.

The Jahn-Teller effect in mixed aqueous solution: the solvation of Cu2+ in 18.6% aqueous ammonia obtained from ab initio quantum mechanical charge field molecular dynamics

The solvation structure and dynamics of Cu2+ in 18.6 % aqueous ammonia have been investigated using an ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation approach at the Hartree–Fock (HF) level of theory applying the LANL2DZ ECP and Dunning DZP basis sets for Cu2+, ammonia and water, respectively. During a simulation time of 20 ps, only NH3 molecules are observed within the first solvation shell of Cu2+, resulting in the formation of an octahedral [Cu(NH3)6]2+ complex. While no exchange of these ligands with the second solvation shell are observed along the simulation, the monitoring of the associated N-Ntrans distances highlight the dynamics of the associated Jahn-Teller distortions, showing on average 2 elongated axial (2.19 Å) and 4 equatorial Cu–N bonds (2.39 Å). The observed structural properties are found in excellent agreement with experimental studies. In addition, an NBO analysis was carried out, confirming the strong electrostatic character of the Cu2+–NH3 interaction.

Binding of Copper Ions with Octapeptide Region in Prion Protein: Simulations with Charge Transfer Model

Copper ions are important cofactors of many metalloproteins. The binding dynamics of proteins to the copper ion is important for biological functions but is less understood at the microscopic level. What are the key factors determining the recognition and the stabilization of the copper ion during the binding? Our work investigates the binding dynamics of the copper ion with a simple system (the N-terminus of PrP) using simulation methods. To precisely characterize the protein?ion interaction, we build up an effective copper?peptide force field based on quantum chemistry calculations. In our model, the effects of charge transfer, protonation/deprotonation, and induced polarization are considered. With this force field, we successfully characterize the local structures and the complex interactions of the octapeptide around the copper ion. Furthermore, using an enhanced sampling method, the binding/unbinding processes of the copper ion with the octapeptide are simulated. Free-energy landscapes are generated in consequence, and multiple binding pathways are characterized. It is observed that various native ligands contribute differently to the binding processes. Some residues are related to the capture of the ion (behaving like ?arm?s), and some others contribute to the stabilization of the coordination structure (acting like ?core?s). These different interactions induce various pathways. Besides, a nonnative binding ligand is determined, and it has essential contributions and modulations to the binding pathways. With all these results, the picture of copper?octapeptide binding is outlined. These features are believed to happen in many ion?peptide interactions, such as the cooperative stabilization between the coordinations with neighboring backbone nitrogens and an auxiliary intermediate coordination with the neighboring oxygen from the N-terminal direction. We believe that our studies are valuable to understand the complicated ion?peptide binding processes.

[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.

Molecular Facts on the Structure and Dynamics of Electrolyte Species in Cu-Cl Cycle for Hydrogen Generation: An Insight from Molecular Dynamic Simulations

The Cu complex, which is the key chemical species in well-known Cu-Cl hybrid thermochemical cycles and also in numerous metal hydrometallurgical and sedimentary deposit processes, displays a wide variety of structural and dynamical characteristics that are further complicated by the presence of multiple oxidation states of Cu ions with different coordination chemistries, therefore they are difficult to explore from experiments alone. In this article, an attempt has been made to understand the coordination behavior of the Cu complex using MD simulations. The study provides compelling evidence of the experimentally observed multiple stoichiometries of Cu ions, i.e., 1:6:0, 1:5:1, and 1:4:2 for Cu⁺:H₂O:Cl^- and 1:6:0 for Cu²⁺:H₂O:Cl^-. The presence of the anionic Cu complex, [Cu⁺Cl₂]^-·2H₂O, [Cu⁺Cl₂]^-·3H₂O, [Cu²⁺Cl₃]^-·H₂O, and [Cu²⁺Cl₃]^-·2H₂O, was captured in the presence of excess chloride ions. Furthermore, the probability distribution profiles have been estimated to determine the most possible complex in the considered systems. The results establish structural and dynamical reformation of the Cu complex with change in the salt concentration or variation in the solvent medium in which they are dissolved. Moreover, the structure and kinetics of the Cu ions in the Cu-Cl electrolyzer have been explored over a large range of the electric field by extending the simulated systems for varied strengths of the electric fields. It has been observed that with an increase in the strength of the electric field, the water molecules lose their coordination strength with central Cu ions, which, on the other hand, results in a significant change in the structure of the captured complex. The diffusion dynamics of the ions is altered while applying the electric field, which is furthermore modified while increasing the strength of electric field beyond a critical limit. In fact, the diffusion mechanism of the ions was seen to be transformed from Brownian-like to linear motion and then to hopping diffusion with the increasing strength of the electric field. To the best of our knowledge, this is the first time when the multiple oxidation states of the Cu ion are explored using MD simulations, and the coexisting pictures of the multiple coordinations and the solvent effects have been clearly revealed. Also to date, the present article is the first one to report the insights of the structure and the dynamics of the ions in the Cu-Cl electrolyzer over a wide range of the electric field. The present studies will be very helpful in understanding the mechanism involved in numerous metal hydrometallurgical and sedimentary deposit processes and to comprehend the analogies involved in the electrode reactions of the Cu-Cl cycle for hydrogen generation.

Genistein Binding to Copper(II)-Solvent Dependence and Effects on Radical Scavenging

Genistein, but not daidzein, binds to copper(II) with a 1:2 stoichiometry in ethanol and with a 1:1 stoichiometry in methanol, indicating chelation by the 5-phenol and the 4-keto group of the isoflavonoid as demonstrated by the Jobs method and UV-visible absorption spectroscopy. In ethanol, the stability constants had the value 1.12 × 10¹¹ L²∙mol^-2 for the 1:2 complex and in methanol 6.0 × 10⁵ L∙mol^-1 for the 1:1 complex at 25 °C. Binding was not detected in water, as confirmed by an upper limit for the 1:1 stability constant of K = 5 mol^-1 L as calculated from the difference in solvation free energy of copper(II) between methanol and the more polar water. Solvent molecules compete with genistein as demonstrated in methanol where binding stoichiometry changes from 1:2 to 1:1 compared to ethanol and methanol/chloroform (7/3, v/v). Genistein binding to copper(II) increases the scavenging rate of the stable, neutral 2,2-diphenyl-1-picrylhydrazyl radical by more than a factor of four, while only small effects were seen for the short-lived but more oxidizing β-carotene radical cation using laser flash photolysis. The increased efficiency of coordinated genistein is concluded to depend on kinetic rather than on thermodynamic factors, as confirmed by the small change in reduction potential of -0.016 V detected by cyclic voltammetry upon binding of genistein to copper(II) in methanol/chloroform solutions.

The Role of the Secondary Coordination Sphere in a Fungal Polysaccharide Monooxygenase

Polysaccharide monooxygenases (PMOs) are secreted metalloenzymes that catalyze the oxidative degradation of polysaccharides in a copper-, oxygen-, and reductant-dependent manner. Cellulose-active fungal PMOs degrade cellulosic substrates to be utilized as a carbon source for fungal growth. To gain insight into the PMO mechanism, the role of conserved residues in the copper coordination sphere was investigated. Here, we report active-site hydrogen-bonding motifs in the secondary copper coordination sphere of MtPMO3*, a C1-oxidizing PMO from the ascomycete fungus Myceliophthora thermophila. A series of point substitutions that disrupt this conserved network are used to interrogate its function. Activity assays, in conjunction with EPR spectroscopy, demonstrate that residues H161 and Q167 are involved in stabilizing bound oxygen, and H161 appears to play a role in proton transfer. Additionally, Q167 increases the ligand donor strength of Y169 to the copper via a hydrogen-bonding interaction. Altogether, H161 and Q167 are important for oxygen activation, and the results are suggestive of a copper-oxyl active intermediate.

Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase

Lytic polysaccharide monooxygenases have attracted vast attention owing to their abilities to disrupt glycosidic bonds via oxidation instead of hydrolysis and to enhance enzymatic digestion of recalcitrant substrates including chitin and cellulose. We have determined high-resolution X-ray crystal structures of an enzyme from Neurospora crassa in the resting state and of a copper(II) dioxo intermediate complex formed in the absence of substrate. X-ray crystal structures also revealed "pre-bound" molecular oxygen adjacent to the active site. An examination of protonation states enabled by neutron crystallography and density functional theory calculations identified a role for a conserved histidine in promoting oxygen activation. These results provide a new structural description of oxygen activation by substrate free lytic polysaccharide monooxygenases and provide insights that can be extended to reactivity in the enzyme-substrate complex.