A first-principle calculation of the XANES spectrum of Cu2+ in water

Probing the Dynamic Landscape: From Static to Time-Resolved X-Ray Absorption Spectroscopy to Investigate Copper Redox Chemistry in Neurodegenerative Disorders

Copper (Cu), with its ability to exist in various oxidation states, notably Cu(I) and Cu(II), plays a crucial role in diverse biological redox reactions. This includes its involvement in pathways associated with oxidative stress in neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and Transmissible Spongiform Encephalopathies. This paper offers an overview of X-ray Absorption Spectroscopy (XAS) studies designed to elucidate the interactions between Cu ions and proteins or peptides associated with these neurodegenerative diseases. The emphasis lies on XAS specificity, revealing the local coordination environment, and on its sensitivity to Cu oxidation states. Furthermore, the paper focuses on XAS applications targeting the characterization of intermediate reaction states and explores the opportunities arising from recent advancements in time-resolved XAS at ultrabright synchrotron and Free Electron Laser radiation sources.

New Hybrid Compounds Incorporating Natural Products as Multifunctional Agents against Alzheimer's Disease

A series of new hybrid derivatives 1a-c, 2a-c, 3a-c, 4a-c, 5a-c, inspired by nature, were synthesized and studied as multifunctional agents for the treatment of Alzheimer's disease (AD). These compounds were designed to merge together the trifluoromethyl benzyloxyaminic bioactive moiety, previously identified, with different acids available in nature. The ability of the synthesized compounds to chelate biometals, such as Cu2+, Zn2+ and Fe2+, was studied by UV-Vis spectrometer, and through a preliminary screening their antioxidant activity was evaluated by DPPH. Then, selected compounds were tested by in vitro ABTS free radical method and ex vivo rat brain TBARS assay. Compounds 2a-c, combining the strongest antioxidant and biometal chelators activities, were studied for their ability to contrast Aβ1-40 fibrillization process. Finally, starting from the promising profile obtained for compound 2a, we evaluated if it could be able to induce a positive cross-interaction between transthyretin (TTR) and Aβ in presence and in absence of Cu2+.

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.

Analysis of the First Ion Coordination Sphere: A Toolkit to Analyze the Coordination Sphere of Ions

Rapid and accurate approaches to characterizing the coordination structure of an ion are important for designing ligands and quantifying structure-property trends. Here, we introduce AFICS (Analysis of the First Ion Coordination Sphere), a tool written in Python 3 for analyzing the structural and geometric features of the first coordination sphere of an ion over the course of molecular dynamics simulations. The principal feature of AFICS is its ability to quantify the distortion a coordination geometry undergoes compared to uniform polyhedra. This work applies the toolkit to analyze molecular dynamics simulations of the well-defined coordination structure of aqueous Cr³⁺ along with the more ambiguous structure of aqueous Eu³⁺ chelated to ethylenediaminetetraacetic acid. The tool is targeted for analyzing ions with fluxional or irregular coordination structures (e.g., solution structures of f-block elements) but is generalized such that it may be applied to other systems.

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.

Ab initio molecular dynamics free energy study of enhanced copper (II) dimerization on mineral surfaces

Understanding the adsorption of isolated metal cations from water on to mineral surfaces is critical for toxic waste retention and cleanup in the environment. Heterogeneous nucleation of metal oxyhydroxides and other minerals on material surfaces is key to crystal growth and dissolution. The link connecting these two areas, namely cation dimerization and polymerization, is far less understood. In this work we apply ab initio molecular dynamics calculations to examine the coordination structure of hydroxide-bridged Cu(II) dimers, and the free energy changes associated with Cu(II) dimerization on silica surfaces. The dimer dissociation pathway involves sequential breaking of two Cu²⁺-OH^- bonds, yielding three local minima in the free energy profiles associated with 0-2 OH^- bridges between the metal cations, and requires the design of a (to our knowledge) novel reaction coordinate for the simulations. Cu(II) adsorbed on silica surfaces are found to exhibit stronger tendency towards dimerization than when residing in water. Cluster-plus-implicit-solvent methods yield incorrect trends if OH^- hydration is not correctly depicted. The predicted free energy landscapes are consistent with fast equilibrium times (seconds) among adsorbed structures, and favor Cu²⁺ dimer formation on silica surfaces over monomer adsorption.

Metal Ion Binding in Wild-Type and Mutated Frataxin: A Stability Study

This work studies the stability of wild-type frataxin and some of its variants found in cancer tissues upon Co2+ binding. Although the physiologically involved metal ion in the frataxin enzymatic activity is Fe2+, as it is customarily done, Co2+ is most often used in experiments because Fe2+ is extremely unstable owing to the fast oxidation reaction Fe2+ → Fe3+. Protein stability is monitored following the conformational changes induced by Co2+ binding as measured by circular dichroism, fluorescence spectroscopy, and melting temperature measurements. The stability ranking among the wild-type frataxin and its variants obtained in this way is confirmed by a detailed comparative analysis of the XAS spectra of the metal-protein complex at the Co K-edge. In particular, a fit to the EXAFS region of the spectrum allows positively identifying the frataxin acidic ridge as the most likely location of the metal-binding sites. Furthermore, we can explain the surprising feature emerging from a detailed analysis of the XANES region of the spectrum, showing that the longer 81-210 frataxin fragment has a smaller propensity for Co2+ binding than the shorter 90-210 one. This fact is explained by the peculiar role of the N-terminal disordered tail in modulating the protein ability to interact with the metal.

Polyphenols as Potential Metal Chelation Compounds Against Alzheimer's Disease

Alzheimer's disease (AD) is the most common neurodegenerative disease affecting more than 50 million people worldwide. The pathology of this multifactorial disease is primarily characterized by the formation of amyloid-β (Aβ) aggregates; however, other etiological factors including metal dyshomeostasis, specifically copper (Cu), zinc (Zn), and iron (Fe), play critical role in disease progression. Because these transition metal ions are important for cellular function, their imbalance can cause oxidative stress that leads to cellular death and eventual cognitive decay. Importantly, these transition metal ions can interact with the amyloid-β protein precursor (AβPP) and Aβ42 peptide, affecting Aβ aggregation and increasing its neurotoxicity. Considering how metal dyshomeostasis may substantially contribute to AD, this review discusses polyphenols and the underlying chemical principles that may enable them to act as natural chelators. Furthermore, polyphenols have various therapeutic effects, including antioxidant activity, metal chelation, mitochondrial function, and anti-amyloidogenic activity. These combined therapeutic effects of polyphenols make them strong candidates for a moderate chelation-based therapy for AD.

An Atomic-Scale Understanding of the Solution Chemistry of Antimony(V): Insights from First-Principles Molecular Dynamics Simulation

In this study, the structure, hydrolysis, and complexation of Sb(V) in aqueous solution has been elucidated by using first-principles molecular dynamics (FPMD) simulations. The results show that both antimonic acid and its deprotonated form have an octahedral configuration, with average Sb-OH₂ and Sb-OH distances of 2.25 and 2.05 Å, respectively. The computed pK_a of [Sb(OH)₅(OH₂)] is 1.8, while [Sb(OH)₆]^- has an extremely high pK_a. Consequently, [Sb(OH)₆]^- is the most dominant species of Sb(V) under common environmental conditions. A stable aqueous complex can form between [Sb(OH)₆]^- and common cations, and an Sb-Al bidentate complex has the largest dissociation free energy, followed by a Sb-Mg bidentate complex, indicating that they have significantly higher stabilities. For Na⁺ and Ca²⁺, their respective monodentate and bidentate complexes have similar dissociation free energies, indicating very close possibilities. These findings provide a comprehensive understanding of the solution chemistry of Sb(V) from a quantitative and microscopic perspective.

A model for the effect of ion pairing on an outer sphere electron transfer

Ion pairing can strongly affect the rates of electron transfer reactions. To explain this effect, we propose a model Hamiltonian that describes the interactions between the pairing ion and the reactant, solvent and inner sphere reorganization, and bond breaking. Explicit expressions for the energies of the initial and final states, and for the energy of activation are derived in the weak adiabatic limit. The model is applied to the reduction of Cu(ii) in the presence of chloride ions. For this purpose, the pertinent system parameters are obtained from density functional theory. Our model explains why the chloride ion enhances the rate of the first electron transfer in copper deposition.

The Potential of EuPRAXIA@SPARC_LAB for Radiation Based Techniques

A proposal for building a Free Electron Laser, EuPRAXIA@SPARC_LAB, at the Laboratori Nazionali di Frascati, is at present under consideration. This FEL facility will provide a unique combination of a high brightness GeV-range electron beam generated in a X-band RF linac, a 0.5 PW-class laser system and the first FEL source driven by a plasma accelerator. The FEL will produce ultra-bright pulses, with up to 10 12 photons/pulse, femtosecond timescale and wavelength down to 3 nm, which lies in the so called “water window”. The experimental activity will be focused on the realization of a plasma driven short wavelength FEL able to provide high-quality photons for a user beamline. In this paper, we describe the main classes of experiments that will be performed at the facility, including coherent diffraction imaging, soft X-ray absorption spectroscopy, Raman spectroscopy, Resonant Inelastic X-ray Scattering and photofragmentation measurements. These techniques will allow studying a variety of samples, both biological and inorganic, providing information about their structure and dynamical behavior. In this context, the possibility of inducing changes in samples via pump pulses leading to the stimulation of chemical reactions or the generation of coherent excitations would tremendously benefit from pulses in the soft X-ray region. High power synchronized optical lasers and a TeraHertz radiation source will indeed be made available for THz and pump–probe experiments and a split-and-delay station will allow performing XUV-XUV pump–probe experiments.

X-Ray Absorption Spectroscopy Measurements of Cu-ProIAPP Complexes at Physiological Concentrations

The amyloidogenic islet amyloid polypeptide (IAPP) and the associated pro-peptide ProIAPP1–48 are involved in cell death in type 2 diabetes mellitus. It has been observed that interactions of this peptide with metal ions have an impact on the cytotoxicity of the peptides as well as on their deposition in the form of amyloid fibrils. In particular, Cu(II) seems to inhibit amyloid fibril formation, thus suggesting that Cu homeostasis imbalance may be involved in the pathogenesis of type 2 diabetes mellitus. We performed X-ray Absorption Spectroscopy (XAS) measurements of Cu(II)-ProIAPP complexes under near-physiological (10 μM), equimolar concentrations of Cu(II) and peptide. Such low concentrations were made accessible to XAS measurements owing to the use of the High Energy Resolved Fluorescence Detection XAS facility recently installed at the ESRF beamline BM16 (FAME-UHD). Our preliminary data show that XAS measurements at micromolar concentrations are feasible and confirm that ProIAPP1–48-Cu(II) binding at near-physiological conditions can be detected.

[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.

Multi-scale theoretical approach to X-ray absorption spectra in disordered systems: an application to the study of Zn(ii) in water

We develop a multi-scale theoretical approach aimed at calculating from first principles X-ray absorption spectra of liquid solutions and disordered systems.

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.

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.

Local environment of metal ions in phthalocyanines: K-edge X-ray absorption spectra

We describe a model for interpreting XAFS spectra of metal phthalocyanines. The near edge spectra are reproduced in a full potential approach.