Solution [Cu(amm)]²⁺ is a Strongly Solvated Square Pyramid: A Full Account of the Copper K-edge XAS Spectrum Within Single-Electron Theory

Abstract

The solution structure of Cu(II) in 4 M aqueous ammonia, [Cu(amm)]2+, was assessed using copper K-edge extended X-ray absorption fine structure (EXAFS) and Minuit XANes (MXAN) analyses. Tested structures included trigonal planar, planar and D 2 d -tetragonal, regular and distorted square pyramids, trigonal bipyramids, and Jahn−Teller distorted octahedra. Each approach converged to the same axially elongated square pyramid, 4 × Cu−Neq = 2.00 ± 0.02 Å and 1 × Cu−Nax=2.16 ± 0.02 Å (EXAFS) or 2.20 ± 0.07 Å (MXAN), with strongly localized solvation shells. In the MXAN model, four equatorial ammonias averaged 13° below the Cu(II) xy-plane, which was 0.45 ± 0.1 Å above the mean N4 plane. When the axial ligand equilibrium partial occupancies of about 0.65 ammonia and 0.35 water were included, EXAFS modeling found Cu−Lax distances of 2.16 and 2.31 Å, respectively, reproducing the distances found in the crystal structures of [Cu(NH3)5]2+ and [Cu(NH3)4(H2O)]2+. A transverse axially localized solvent molecule was found at 2.8 Å (EXAFS) or 3.1 Å (MXAN). Six second-shell solvent molecules were also found at about 3.4 ± 0.01 (EXAFS) or 3.8 ± 0.2 Å (MXAN). The structure of Cu(II) in 4 M pH 10 aqueous NH3 may be notationally described as {[Cu(NH3)4.62(H2O)0.38](solv)}2+·6solv, solv = H2O, NH3. The prominent shoulder and duplexed maximum of the rising K-edge XAS of [Cu(amm)]2+ primarily reflect the durable and well-organized solvation shells, not found around [Cu(H2O)5]2+, rather than two-electron shakedown transitions. Not accounting for solvent scattering thus may confound XAS-based estimates of metal−ligand covalency. [Cu(amm)]2+ continues the dissymmetry previously found for the solution structure of [Cu(H2O)5]2+, again contradicting the rack-bonding theory of blue copper proteins.

The x-ray absorption spectroscopy model of solvation about sulfur in aqueous L-cysteine

“…This fit is poor compared to the quality typically obtained using MXAN. 32,36,37 The poor quality of the fit is restricted to the rising Kedge energy region, and is primarily due to the constant normalization approximation used within extended continuum multiple scattering theory. This method treats XAS bound state transitions as very sharp scattering features, 69 in which the wave functions of bound and continuum states are normalized identically.…”

“…Therefore, the transitions cannot be solely assigned to S-C σ * or S-H σ * orbitals, as has been done in the past, 26, 85 but should be described as excitations into extremely delocalized orbitals with significant S-C and/or S-H σ * character. (33), LUMO+1 (34), LUMO+2 (35), and LUMO+3 (36). These orbitals have significant sulfur character and are expected to contribute to the sulfur K-edge XAS spectrum.…”

“…The first and second peaks are due to a combination of the sulfur 1s core-to-valence transitions (S1s → 33 plus S1s → 34), and (S1s → 35 plus S1s → 36), respectively (see Figure 9 for the contour plots of MO 33,34,35,and 36). As can be seen from Figure 10, DFT fails to address spectral features above ∼2475 eV, especially the broad peak at ∼2480 eV.…”

“…28,29 The improved application of extended continuum theory to x-ray absorption spectroscopy through Minuit XANES (MXAN) analysis, [30][31][32] now permits exploration of the threedimensional structures of dissolved small molecules. [33][34][35][36] The solution structural study reported here began when it was found that MXAN calculation of the sulfur K-edge XAS spectrum of aqueous cysteine required inclusion of at least one water molecule proximate to sulfur.…”

Metals in Alzheimer’s Disease: A Combined Experimental and Numerical Approach

“…-imidazole complex in water was studied by a combined theoretical analysis of EXAFS and XANES data, coming to the conclusion that a square-pyramidal geometry around Cu is preferred (over the planar or octahedral one) and persists through other Cu complexes like [Cu [87] and [88]). Remarkably, the ab initio simulations of the S 2 -Cu model system, besides confirming this conclusion, are able to give us the extra information that the Cu ligands in the Cu-A 1-14 complex are the His 6 , His 13 , His 14 and Tyr 10 residues, through the N , N , N and O atoms, respectively.…”