The Solution Structure of [Cu(aq)]2+ and Its Implications for Rack-Induced Bonding in Blue Copper Protein Active Sites

Structure and complexation mechanism of aqueous Zn(II)-acetate complex studied by XAFS and Raman spectroscopies

In this work, the structure of Zn acetate has been determined by a combination of X-ray absorption fine structure and Raman spectroscopy. We have analyzed the local atomic environment and the main vibrational bands of the acetate and Zn acetate at different pH. The results suggest that Zn acetate complex acquires a bidentate structure that modifies its first coordination shell. Meanwhile, the coordination shell of the hydrated Zn cation is formed by 6 hydroxides at a mean distance of 2.06 Å, the coordination shell of the Zn cation in the complex is formed by 2 hydroxides and 2 oxygens from the carboxyl group of the acetate, at a mean Zn-O distance of 1.96 Å. The structure of the Zn acetate complex is compared to those of Zn malonate and Zn citrate, none of which present a reduction in the coordination shell neither a shrinkage of the Zn-O shell distance.

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.

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.

A Tb3+ ion encapsulated anionic indium-organic framework as logical probe for distinguishing quenching Fe3+ and Cu2+ ions

We successfully synthesized a stable anionic microporous metal-organic framework (MOF) HDU-1 ([Me2NH2]2In2[(TATAB)4(DMF)4](DMF)4(H2O)4) and constructed a fluorescent probe Tb@HDU-1 by an exchange strategy. Because of its suspension distinct fluorescent response of Tb(III) characteristic transition and ligand emission, the Tb@HDU-1 can be used as fluorescent probe for sensing towards Fe3+ and Cu2+ ions. It is surprising that Tb@HDU-1 is used as a ratiometric fluorescent probe for Cu2+ ions while only single peak detection for Fe3+ ions, which describes a particular rare example of a sensor based on Ln-MOFs to distinguish quenching Fe3+ and Cu2+ ions. Hence we designed a molecular logic gate device for making the distinction of Fe3+ and Cu2+ ions more clearly and appropriately. In addition, the different quenching effect between Fe3+ and Cu2+ ions may be ascribed to the differences of competitive absorption and interaction between frameworks and metal ions.

The Role of the CuCl Active Complex in the Stereoselectivity of the Salt-Induced Peptide Formation Reaction: Insights from Density Functional Theory Calculations

The salt-induced peptide formation (SIPF) reaction is a prebiotically plausible mechanism for the spontaneous polymerization of amino acids into peptides on early Earth. Experimental investigations of the SIPF reaction have found that in certain conditions, the l enantiomer is more reactive than the d enantiomer, indicating its potential role in the rise of biohomochirality. Previous work hypothesized that the distortion of the CuCl active complex toward a tetrahedral-like structure increases the central chirality on the Cu ion, which amplifies the inherent parity-violating energy differences between l- and d-amino acid enantiomers, leading to stereoselectivity. Computational evaluations of this theory have been limited to the protonated-neutral l + l forms of the CuCl active complex. Here, density functional theory methods were used to compare the energies and geometries of the homochiral (l + l and d + d) and heterochiral (l + d) CuCl-amino acid complexes for both the positive-neutral and neutral-neutral forms for alanine, valine, and proline. Significant energy differences were not observed between different chiral active complexes (i.e., d + d, l + l vs. l + d), and the distortions of active complexes between stereoselective systems and non-selective systems were not consistent, indicating that the geometry of the active complex is not the primary driver of the observed stereoselectivity of the SIPF reaction.

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.

Persistence of a Delocalized Radical in Larger Clusters of Hydrated Copper(II) Hydroxide, CuOH+(H2O)3-7

The structures, vibrational spectra, and electronic properties of copper hydroxide hydrates CuOH+(H2O)3-7 were investigated with quantum chemistry computations. As a follow-up to a previous analysis of CuOH+(H2O)0-2, this investigation examined the progression as the square-planar metal coordination environment was filled and as solvation shells expanded. Four-, five-, and six-coordinate structures were found to be low-energy isomers. The delocalized radical character, which was discovered in the small clusters, was found to persist upon continued hydration, although the hydrogen-bonded water network in the larger clusters was found to play a more significant role in accommodating this spin. Partial charges indicated that the electronic structure includes more Cu2+···OH- character than was observed in smaller clusters, but this structure remains decidedly mixed with Cu+···OH· configurations and yields roughly half-oxidation of the water network in the absence of any electrochemical potential. Computed vibrational spectra for n = 3 showed congruence with spectra from recent predissociation spectroscopy experiments, provided that the role of the D2 tag was taken into account. Spectra for n = 4-7 were predicted to exhibit features that are reflective of both the mixed electronic character and proton-/hydrogen-shuttling motifs within the hydrogen-bonded water network.

A Combined Wave Function and Density Functional Approach for K-Edge X-ray Absorption Near-Edge Spectroscopy: A Case Study of Hydrated First-Row Transition Metal Ions

The prediction of X-ray absorption spectra (XAS) of transition metal complexes has important and broad application areas in chemistry and biology. In this letter, we have investigated the predictive ability of multiconfiguration pair-density functional theory (MC-PDFT) for X-ray absorption spectra by calculating the metal K pre-edge features of aquated 3d transition metal ions in common oxidation states. MC-PDFT results were compared with experimentally measured spectra as well as analyzed against results from restricted active-space second-order perturbation theory (RASPT2) and time-dependent density functional theory (TDDFT). As expected, TDDFT performs well for excited states that can be accurately represented by singly excited configurations but fails for excited states where higher order excitations become important. On the other hand, both RASPT2 and MC-PDFT provide quantitatively accurate results for all excited states irrespective of their character. While core-level spectroscopy with RASPT2 is accurate, it is computationally expensive. Our results show that MC-PDFT performs equally well with significantly lower computational cost and is an encouraging alternate approach for X-ray spectroscopies.

Near-Quantitative Predictions of the First-Shell Coordination Structure of Hydrated First-Row Transition Metal Ions Using K-Edge X-ray Absorption Near-Edge Spectroscopy

The solvation structure of transition metal ions is important for applications in geochemistry, biochemistry, energy storage, and environmental chemistry. We study the X-ray absorption pre-edge and near-edge spectra at the K-edge of a nearly complete series of hydrated first-row transition metal ions with d orbital occupancy from d² to d¹⁰. We optimize all of the structures at the density functional theory (DFT) level with explicit solvation and then compute the pre-edge X-ray absorption spectra with time-dependent DFT (TDDFT) and restricted active space second-order perturbation theory (RASPT2). TDDFT provides accurate results for spectra that are dominated by single excitations, while RASPT2 correctly distinguishes between singly and doubly excited states with quantitative accuracy compared with experiment. We analyze the pre-edge features for each metal ion to reveal the impact of the variations in d orbital occupancy on the first-shell coordination environment. We also report the lowest-energy ligand field d-d transitions using complete active space second-order perturbation theory.

Informing our Understanding of the Copper-Cuprizone Reaction with Computational Chemistry

The reaction of copper with bis(cyclohexanone)oxaldihydrazone (cuprizone) is a challenging coordination chemistry problem that has confounded attempts at elucidation for the past 70 years. The product of the reaction, a...

Symmetry Breaking in Solution-Phase [Cu(tsc)2(H2O)2]2+: Emergent Asymmetry in Cu-S Distances and in Covalence

The structure of aqueous Cu(II)-bis-thiosemicarbazide, [Cu(tsc)₂]²⁺, is reported following EXAFS and MXAN analyses of the copper K-edge X-ray absorption (XAS) spectrum. The rising K-edge feature at 8987.1 eV is higher energy than those of crystalline models, implying unique electronic and structural solution states. EXAFS analysis (k = 2-13 Å^-1; 2 × Cu-N = 2.02 ± 0.01 Å; 2 × Cu-S = 2.27 ± 0.01 Å; Cu-O_ax = 2.41 ± 0.04 Å) could not resolve 5- versus 6-coordinate models. However, MXAN fits converged to an asymmetric broken symmetry 6-coordinate model with cis-disposed TSC ligands (Cu-O_ax = 2.07 and 2.54 Å; Cu-N = 1.94 Å, 1.98 Å; Cu-S = 2.20 Å, 2.41 Å). Transition dipole integral evaluation of the sulfur K-edge XAS 1s → 3p valence transition feature at 2470.7 eV yielded a Cu-S covalence of 0.66 e^-, indicating Cu^1.34+. The high Cu-S covalence and short Cu-S bond in aqueous [Cu(tsc)₂(H₂O)₂]²⁺ again contradict the need for a protein rack to explain the unique structure of the blue copper active site. MXAN models of dissolved Cu(II) complex ions have invariably featured broken centrosymmetry. The potential energy ground state for dissolved Cu(II) evidently includes the extended solvation field, providing a target for improved physical theory. A revised solvation model for aqueous Cu(II), |[Cu(H₂O)₅]·14H₂O|²⁺, is presented.

Electronic Structure and Vibrational Signatures of the Delocalized Radical in Hydrated Clusters of Copper("II") Hydroxide CuOH+(H2O)0-2

The copper hydroxide ion, CuOH⁺, serves as the catalytic core in several recently developed water-splitting catalysts, and an understanding of its chemistry is critical to determining viable catalytic mechanisms. In spite of its importance, the electronic structure of this open-shell ion has remained ambiguous in the literature. In particular, computed values for both the thermodynamics of hydration and the vibrational signatures of the mono- and dihydrates have shown prohibitively large errors compared to values from recent experimental measurements. In this work, the source of this discrepancy is demonstrated to be the propensity of this ion to exist between traditional Cu(I) and Cu(II) oxidation-state limits. The spin density of the radical is accordingly shown to delocalize between the metal center and surrounding ligands, and increasing the hydration serves to exacerbate this behavior. Equation-of-motion coupled-cluster methods demonstrated the requisite accuracy to resolve the thermodynamic discrepancies. Such methods were also needed for spectral simulations, although the latter also required a direct simulation of the role of the deuterium "tag" molecules that are used in modern predissociation spectroscopy experiments. This nominally benign tag molecule underwent direct complexation with the open-valence metal ion, thereby forming a species akin to known metal-H₂ complexes and strongly impacting the resulting spectrum. Thermal populations of this configuration and other more traditional noncovalently bound isomers led to a considerable broadening of the spectral lineshapes. Therefore, at least for the CuOH⁺(H₂O)_0-2 hydrates, these benchmark ions should be considered to be delocalized radical systems with some degree of multireference character at equilibrium. They also serve as a cautionary tale for the spectroscopy community, wherein the role of the D₂ tag is far from benign.

A spectroscopic study of solvent effects on the formation of Cu(ii)-chloride complexes in aqueous solution

A combination of electronic (UV-vis) and X-ray absorption (EXAFS, XANES) spectroscopies has been used to investigate the formation of copper(ii)/chloride complexes in concentrated aqueous solutions. It is established that lowering the water activity by the addition of Mg(ClO₄)₂ at a constant Cl^-/Cu(ii) ratio results in the replacement of water molecules by Cl^- ions in the primary coordination shell of Cu(ii). This behavior closely parallels the effect of increasing the Cl^-/Cu(ii) ratio and demonstrates that full understanding of the stoichiometry and structures of the complexes formed in concentrated metal-ion chloride solutions requires explicit consideration of the role of the solvent.

Framework coordination of single-ion Cu2+ sites in hydrated 17O-ZSM-5 zeolite

The interfacial coordination chemistry of water solvated single Cu²⁺ sites in ZSM-5 is assessed through pulsed EPR spectroscopy and selective ¹⁷O isotopic labelling.

A coumarin derivative-Cu2+ complex-based fluorescent chemosensor for detection of biothiols

Herein, a novel fluorescent sensor has been developed for the detection of biothiols based on theoretical calculations of the stability constant of the complex between a Cu2+ ion and (E)-3-((2-(benzo[d]thiazol-2-yl)hydrazono)methyl)-7-(diethylamino) coumarin (BDC) as a fluorescent ligand. In this study, on the basis of density functional theory method, the Gibbs free energy of ligand-exchange reaction and the solvation model were carried out using thermodynamic cycles. The obtained results are in good agreement with the experimental data. The BDC-Cu2+ complex can be used as a fluorescent sensor for the detection of biothiols in the presence of non-thiol containing amino acids, with a detection limit for cysteine at 0.3 μM. Moreover, theoretical calculations of excited states were used to elucidate variations in the fluorescence properties. The computed results show that the excited doublet states D2 and D1 are dark doublet states, which quench the fluorescence of the complex.

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.

Evaluating Density Functionals by Examining Molecular Structures, Chemical Bonding, and Relative Energies of Mononuclear Ru-Cl-H-PR3 Isomers

In order to define a robust level of theory using density functionals for investigating the reactivity of ruthenium complexes, we used benchmark wave function theory, with saturated basis sets to validate generalized gradient approximation (GGA), meta-GGA, and hyper-GGA functionals in the presence and absence of empirical dispersion and range-separated corrections. We first selected potentially suitable functionals that gave accurate predictions of the relative energetics of coordination isomers. These functionals were further evaluated for the chemical accuracy of their predicted geometric and electronic structures. For the latter, both the ionic and covalent interactions were considered. The reference level of theory for comparison was coupled-cluster perturbation theory using full treatment of singles and doubles (CCSD) with a saturated triple-ζ quality basis set (TZVP) and corresponding small-core, effective core potentials for ruthenium. Several population analysis methods were evaluated to predict the ionic interactions. We found that the atomic charges obtained from fitting the electrostatic potential provided the most reasonable estimates for the ruthenium complexes. The covalent interactions were quantified by considering the atomic compositions of Ru 4d _{x²- y²}- and 4d _z²-based frontier unoccupied orbitals. Comparison of more than two dozen functionals with reference data from high-level wave function calculations revealed trends that allowed for the formulation of an optimal hybrid density functional: PBE exchange and correlation functionals with 50% HF exchange component. This level of theory was found to reproduce the experimental structure of Ru^(II) complexes. These complexes were used to investigate chemical speciation in a simplified model for an ionic liquid environment.

Can a temporary bond between dye and redox mediator increase the efficiency of p-type dye-sensitized solar cells?

Efficient n-type dye-sensitized solar cells are known since the seminal work of O'Reagan and Grätzel in 1991. However, highly efficient p-type dye-sensitized solar cells have not been developed so far. This hinders the construction of tandem dye-sensitized solar cells, which can surpass the performance of n-type devices. Within this work, we investigate if a temporary coordination of transition metal-based redox mediators at a sensitizer can increase the efficiency of p-type dye-sensitized solar cells. Based on a computational screening, diverse Cu, Ni, and Co redox mediators were selected to construct p-type dye-sensitized solar cells. Unfortunately, the efficiency of the investigated devices does not surpass analogous cells with iodide-triiodide as redox mediator. While Ni and Cu complexes might be reduced to Ni(0) and Cu(0), respectively, the investigated Co-complex quenches the excited state efficiently. As a result, the necessary electron injection from the semiconductor is too slow, which hinders the construction of a highly efficient p-type dye-sensitized solar cell. Graphical Abstract Comparison of the mode of action of p-type dye-sensitized solar cells. While top shows the traditional one, bottom shows the investigated devices where a temporary link between dye and redox mediator plays a crucial role.

[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.

Composition-driven Cu-speciation and reducibility in Cu-CHA zeolite catalysts: a multivariate XAS/FTIR approach to complexity

The small pore Cu-CHA zeolite is attracting increasing attention as a versatile platform to design novel single-site catalysts for deNO _x applications and for the direct conversion of methane to methanol. Understanding at the atomic scale how the catalyst composition influences the Cu-species formed during thermal activation is a key step to unveil the relevant composition-activity relationships. Herein, we explore by in situ XAS the impact of Cu-CHA catalyst composition on temperature-dependent Cu-speciation and reducibility. Advanced multivariate analysis of in situ XANES in combination with DFT-assisted simulation of XANES spectra and multi-component EXAFS fits as well as in situ FTIR spectroscopy of adsorbed N₂ allow us to obtain unprecedented quantitative structural information on the complex dynamics during the speciation of Cu-sites inside the framework of the CHA zeolite.

Identifying Coordination Geometries of Metal Aquaions in Water: Application to the Case of Lanthanoid and Actinoid Hydrates

The angular distribution function (ADF) associated with the oxygen-metal ion-oxygen angle (OMO) of several trivalent lanthanoid and actinoid aquaions has been used to identify the most probable coordination geometry of these aquaions in aqueous solutions. The ADFs extracted from the molecular dynamics trajectories have been compared with continuous distribution functions corresponding to the geometry of a reference polyhedron pattern. The procedure incorporates specific quantum-mechanical information on the aquaion under study. The new method is applied to the analysis of four M(H₂O)_n³⁺ aquaions in water, M = Lu and Cf for n = 8, and M = La and Ac for n = 9. For those that are 8-coordinated, the square antiprism (SA) coordination geometry is preferred. For the 9-fold coordination, the simulation ADFs are more similar to the continuous ADF derived from a Gyro-elongated-SA rather than to the usually proposed trigonal tricapped prism. Advantages of these continuous distributions with respect to the usually employed discrete distributions are emphasized as well as further applications are suggested.

Solvation structure of the halides from x-ray absorption spectroscopy

Three-dimensional models for the aqueous solvation structures of chloride, bromide, and iodide are reported. K-edge extended X-ray absorption fine structure (EXAFS) and Minuit X-ray absorption near edge (MXAN) analyses found well-defined single shell solvation spheres for bromide and iodide. However, dissolved chloride proved structurally distinct, with two solvation shells needed to explain its strikingly different X-ray absorption near edge structure (XANES) spectrum. Final solvation models were as follows: iodide, 8 water molecules at 3.60 ± 0.13 Å and bromide, 8 water molecules at 3.40 ± 0.14 Å, while chloride solvation included 7 water molecules at 3.15 ± 0.10 Å, and a second shell of 7 water molecules at 4.14 ± 0.30 Å. Each of the three derived solvation shells is approximately uniformly disposed about the halides, with no global asymmetry. Time-dependent density functional theory calculations simulating the chloride XANES spectra following from alternative solvation spheres revealed surprising sensitivity of the electronic state to 6-, 7-, or 8-coordination, implying a strongly bounded phase space for the correct structure during an MXAN fit. MXAN analysis further showed that the asymmetric solvation predicted from molecular dynamics simulations using halide polarization can play no significant part in bulk solvation. Classical molecular dynamics used to explore chloride solvation found a 7-water solvation shell at 3.12 (-0.04/+0.3) Å, supporting the experimental result. These experiments provide the first fully three-dimensional structures presenting to atomic resolution the aqueous solvation spheres of the larger halide ions.

Equilibrium between 5- and 6-Fold Coordination in the First Hydration Shell of Cu(II)

The hydration structure dynamics of Cu(II) ion is characterized by a combination of classical molecular dynamics simulation and X-ray absorption near-edge spectroscopy. Previous experimental data have been analyzed on the basis of 5- or 6-fold first hydration structure, with a quite well-established equatorial structure. This 4-fold equatorial geometry has been our starting point to develop a simple but effective in silico model, which provides ab initio theoretical X-ray absorption spectra in very good agreement with the experimental data. Our results point out two equally populated 6- and 5-fold hydration structures with remarkable different water residence times of 5 and 98 ps, respectively, and a low free energy barrier between first and second hydration shell.

Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations

We apply two recently developed computational methods, DFTB3 and VALBOND, to study copper oxidation/reduction processes in solution and protein. The properties of interest include the coordination structure of copper in different oxidation states in water or in a protein (plastocyanin) active site, the reduction potential of the copper ion in different environments, and the environmental response to copper oxidation. The DFTB3/MM and VALBOND simulation results are compared to DFT/MM simulations and experimental results whenever possible. For a copper ion in aqueous solution, DFTB3/MM results are generally close to B3LYP/MM with a medium basis, including both solvation structure and reduction potential for Cu(II); for Cu(I), however, DFTB3/MM finds a two-water coordination, similar to previous Born-Oppenheimer molecular dynamics simulations using BLYP and HSE, whereas B3LYP/MM leads to a tetrahedron coordination. For a tetraammonia copper complex in aqueous solution, VALBOND and DFTB3/MM are consistent in terms of both structural and dynamical properties of solvent near copper for both oxidation states. For copper reduction in plastocyanin, DFTB3/MM simulations capture the key properties of the active site, and the computed reduction potential and reorganization energy are in fair agreement with experiment, especially when the periodic boundary condition is used. Overall, the study supports the value of VALBOND and DFTB3(/MM) for the analysis of fundamental copper redox chemistry in water and protein, and the results also help highlight areas where further improvements in these methods are desirable.

A method to calculate redox potentials relative to the normal hydrogen electrode in nonaqueous solution by using density functional theory-based molecular dynamics

We demonstrate the redox potential calculation relative to the normal hydrogen electrode (NHE) in nonaqueous solution using a density functional theory-based molecular dynamics (DFT-MD) simulation. The calculation of the NHE in nonaqueous solution consists of two processes: the first step is the equilibrated simulation for a proton in nonaqueous solution to determine the space for inserting a proton in solution, and the second step is the thermodynamic integration method to calculate the solvation energy of the proton in the nonaqueous solution. In this work, we apply the method for a cation and an anion, i.e., copper(ii)/copper(i) and iodine/iodide in acetonitrile solution, and show that the errors in the calculated redox potential from experiments are within 0.21 V.

Absorption mechanisms of Cu(2+) on a biogenic bixbyite-like Mn2O3 produced by Bacillus CUA isolated from soil

BACKGROUND

Although most reported biogenic Mn oxides are hexagonal birnessites, other types of biogenic Mn oxides also commonly occur in the environment. However, sorption characteristics and underlying mechanisms of the adsorption of heavy-metal ions on these biogenic Mn oxides are still rarely addressed. In this study, the sorption mechanisms of Cu(II) on a low valence biogenic Mn oxide, poorly crystallized bixbyite-like Mn2O3 (α-Mn2O3), were investigated.

RESULTS

The maximum adsorption capacity of Cu(II) onto this biogenic Mn oxide at pH 6.00 was 796 mmol/kg (0.45 mol Cu mol(-1) Mn). The complex structure of adsorbed Cu(II) was constrained using Cu extended X-ray absorption fine structure (EXAFS) analysis, combined with structural parameters of the biogenic Mn oxide with alternately arranged regular and distorted MnO6 octahedra obtained through multiple-FEFF fitting of Mn EXAFS data. The sorbed Cu(II) was found to coordinate with the biogenic Mn oxide particle edges as inner-sphere complexes. At a relatively low Cu(2+) loading (233 mmol/kg, pH 6.00), Cu(II) adsorbed onto the biogenic Mn oxide with two types of coordinated complexes, i.e., (1) coordinated with one regular/distorted MnO6 octahedron as a monodentate-mononuclear complex and (2) with two adjacent MnO6 octahedra as a bidentate-binuclear complex. While, at a relatively high Cu(2+) loading (787 mmol/kg, pH 6.00), only one type of coordinated complex was constrained, the adsorbed Cu(II) coordinated with one regular/distorted MnO6 octahedron as a monodentate-mononuclear complex.

CONCLUSIONS

This research extends further insight into the bacterial Mn(II) oxidation in the environment and serves as a good reference for understanding the interactions between metal ions and biogenic low valence Mn oxides, which are still poorly explored either theoretically or practically.