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

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.

Ionization Energies and Redox Potentials of Hydrated Transition Metal Ions: Evaluation of Domain-Based Local Pair Natural Orbital Coupled Cluster Approaches

Hydrated transition metal ions are prototypical systems that can be used to model properties of transition metals in complex chemical environments. These seemingly simple systems present challenges for computational chemistry and are thus crucial in evaluations of quantum chemical methods for spin-state and redox energetics. In this work, we explore the applicability of the domain-based pair natural orbital implementation of coupled cluster (DLPNO-CC) theory to the calculation of ionization energies and redox potentials for hydrated ions of all first transition row (3d) metals in the 2+/3+ oxidation states, in connection with various solvation approaches. In terms of model definition, we investigate the construction of a minimally explicitly hydrated quantum cluster with a first and second hydration layer. We report on the convergence with respect to the coupled cluster expansion and the PNO space, as well as on the role of perturbative triple excitations. A recent implementation of the conductor-like polarizable continuum model (CPCM) for the DLPNO-CC approach is employed to determine self-consistent redox potentials at the coupled cluster level. Our results establish conditions for the convergence of DLPNO-CCSD(T) energetics and stress the absolute necessity to explicitly consider the second solvation sphere even when CPCM is used. The achievable accuracy for redox potentials of a practical DLPNO-based approach is, on average, 0.13 V. Furthermore, multilayer approaches that combine a higher-level DLPNO-CCSD(T) description of the first solvation sphere with a lower-level description of the second solvation layer are investigated. The present work establishes optimal and transferable methodological choices for employing DLPNO-based coupled cluster theory, the associated CPCM implementation, and cost-efficient multilayer derivatives of the approach for open-shell transition metal systems in complex environments.

Benchmarking Plane Waves Quantum Mechanical Calculations of Iron(II) Tris(2,2′-bipyridine) Complex by X-ray Absorption Spectroscopy

In this work, we used, for the first time, a computational Self-Consistent Field procedure based on plane waves to describe the low and high spin conformational states of the complex [Fe(bpy)3]2+. The results obtained in the study of the minimum energy structures of this complex, a prototype of a wide class of compounds called Spin Cross Over, show how the plane wave calculations are in line with the most recent studies based on gaussian basis set functions and, above all, reproduce within acceptable errors the experimental spectra of X-ray absorption near-edge structure spectroscopy (XANES). This preliminary study shows the capabilities of plane wave methods to correctly describe the molecular structures of metal-organic complexes of this type and paves the way for future even complex computational simulations based on the energy gradient, such as Nudge Elastic Band or ab-initio Born-Oppenheimer molecular dynamics.

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.

Cu2+ in liquid ammonia-The impact of solvent flexibility and electron correlation in ab initio quantum mechanical charge field molecular dynamics

The impact of solvent flexibility and electron correlation on the simulation results of Cu²⁺ in liquid ammonia has been investigated via an ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation approach. To achieve this, three different simulation systems were considered in this study, namely Cu²⁺ in rigid and flexible ammonia at Hartree-Fock (HF) level of theory, as well as resolution of identity second order Møller-Plesset (MP2) perturbation theory in the rigid body case. In all cases, a stable octahedral [Cu(NH₃ )₆ ]²⁺ complex subject to dynamic Jahn-Teller distortions without the occurrence of ligand exchange was observed. The Cu²⁺  - NH₃ distance in the first shell agrees well with the experimental and other theoretical data. In all three cases, the structural data shows that the rigid-body ammonia model in conjunction with the HF level of theory provides accurate data for the first solvation shell, while at the same time, the computational demand and thus the achievable simulation time are much more beneficial. The vibrational analysis of the Cu²⁺  - NH₃ interaction yields similar force constants in the three investigated systems indicating that there is no distinct difference on the dynamical properties of the first solvation shell. In addition to the QMCF MD simulations, a number of natural bond orbital (NBO) analyses were carried out, confirming the strong electrostatic character of the Cu²⁺  - NH₃ interaction.

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.

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.

Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin

We present a detailed analysis of the X-ray absorption near-edge structure (XANES) data on the Fe K-edge of CO Myoglobin based on a combined procedure of Molecular Dynamics (MD) calculations and MXAN (Minuit XANes) data analysis that we call D-MXAN. The ability of performing quantitative XANES data analysis allows us to refine classical force field MD parameters, thus obtaining a reliable tool for the atomic investigation of this important model system for biological macromolecules. The iterative procedure here applied corrects the greatest part of the structural discrepancy between classical MD sampling and experimental determinations. Our procedure, moreover, is able to discriminate between different heme conformational basins visited during the MD simulation, thus demonstrating the necessity of a sampling on the order of tens of nanoseconds, even for an application such X-ray absorption spectroscopy data analysis.

[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.