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

The Solvation of Cu2+ with Gas-Phase Clusters of Water and Ammonia

A detailed study has been undertaken of the gas-phase chemistry of [Cu(H2O)N]2+ and [Cu(NH3)N]2+ complexes. Ion intensity distributions and fragmentation pathways (unimolecular and collision-induced) have been recorded for both complexes out as far as N=20. Unimolecular fragmentation is dominated by Coulomb explosion (separation into two single charged units) on the part of the smaller ions, but switches to neutral molecule loss for N>7. In contrast, collisional activation promotes extensive electron capture from the collision gas, with the appearance of particular singly charged fragment ions being sensitive to the size and composition of the precursor. The results show clear evidence of the unit [Cu(X)8]2+ being of special significance, and it is proposed that the hydrogen-bonded structure associated with this ion is responsible for stabilizing the dipositive charge on Cu2+ in aqueous solution.

Comprehensive Molecular Mechanics Model for Oxidized Type I Copper Proteins: Active Site Structures, Strain Energies, and Entatic Bulging

The ligand field molecular mechanics (LFMM) model has been applied to the oxidized Type 1 copper center. In conjunction with the AMBER94 force field implemented in DommiMOE, the ligand field extension of the molecular operating environment (MOE), LFMM parameters for Cu-N(imidazole), Cu-S(thiolate), Cu-S(thioether), and Cu-O(carbonyl) interactions were developed on the basis of experimental and theoretical data for homoleptic model systems. Subsequent LFMM optimizations of the active site model complex [Cu(imidazole)2(SMe)(SMe2]+ agree with high level quantum results both structurally and energetically. Stable trigonal and tetragonal structures are located with the latter about 1.5 kcal mol-1 lower in energy. Fully optimized unconstrained structures were computed for 24 complete proteins containing T1 centers spanning four-coordinate, plastocyanin-like CuN2SS' and stellacyanin-like CuN2SO sites, plus the five-coordinate CuN2SS'O sites of the azurins. The initial structures were based on PDB coordinates augmented by a 10 A layer of water molecules. Agreement between theory and experiment is well within the experimental uncertainties. Moreover, the LFMM results for plastocyanin (Pc), cucumber basic protein (CBP) and azurin (Az) are at least as good as previously reported QM/MM structures and are achieved several orders of magnitude faster. The LFMM calculations suggest the protein provides an entatic strain of about 10 kcal mol-1. However, when combined with the intrinsic 'plasticity' of d9 Cu(II), different starting protein/solvent configurations can have a significant effect on the final optimized structure. This 'entatic bulging' results in relatively large fluctuations in the calculated metal-ligand bond lengths. For example, simply on the basis of 25 different starting configurations of the solvent molecules, the optimized Cu-S(thiolate) bond lengths in Pc vary by 0.04 A while the Cu-S(thioether) distance spans over 0.3 A. These variations are the same order of magnitude as the differences often quoted to correlate the spectroscopic properties from a set of proteins. Isolated optimizations starting from PDB coordinates (or indeed, the PDB structures themselves) may only accidentally correlate with spectroscopic measurements. The present calculations support the work of Warshel who contends that adequate configurational averaging is necessary to make proper contact with experimental properties measured in solution. The LFMM is both sufficiently accurate and fast to make this practical.

X-ray structure analysis of a metalloprotein with enhanced active-site resolution using in situ x-ray absorption near edge structure spectroscopy

X-ray absorption spectroscopy is exquisitely sensitive to the coordination geometry of an absorbing atom and therefore allows bond distances and angles of the surrounding atomic cluster to be measured with atomic resolution. By contrast, the accuracy and resolution of metalloprotein active sites obtainable from x-ray crystallography are often insufficient to analyze the electronic properties of the metals that are essential for their biological functions. Here, we demonstrate that the combination of both methods on the same metalloprotein single crystal yields a structural model of the protein with exceptional active-site resolution. To this end, we have collected an x-ray diffraction data set to 1.4-A resolution and Fe K-edge polarized x-ray absorption near edge structure (XANES) spectra on the same cyanomet sperm whale myoglobin crystal. The XANES spectra were quantitatively analyzed by using a method based on the multiple scattering approach, which yielded Fe-heme structural parameters with +/-(0.02-0.07)-A accuracy on the atomic distances and +/-7 degrees on the Fe-CN angle. These XANES-derived parameters were subsequently used as restraints in the crystal structure refinement. By combining XANES and x-ray diffraction, we have obtained an cyanomet sperm whale myoglobin structural model with a higher precision of the bond lengths and angles at the active site than would have been possible with crystallographic analysis alone.

Factors governing the metal coordination number in metal complexes from Cambridge Structural Database analyses

The metal coordination number (CN) is a key determinant of the structure and properties of metal complexes. It also plays an important role in metal selectivity in certain metalloproteins. Despite its central role, the preferred CN for several metal cations remains ambiguous, and the factors determining the metal CN are not fully understood. Here, we evaluate how the CN depends on (1) the metal's size, charge, and charge-accepting ability for a given set of ligands, and (2) the ligand's size, charge, charge-donating ability, and denticity for a given metal by analyzing the Cambridge Structural Database (CSD) structures of metal ions in the periodic table. The results show that for a given ligand type, the metal's size seems to affect its CN more than its charge, especially if the ligand is neutral, whereas, for a given metal type, the ligand's charge and charge-donating ability appear to affect the metal CN more than the ligand's size. Interestingly, all 98 metal cations surveyed could adopt more than than one CN, and most of them show an apparent preference toward even rather than odd CNs. Furthermore, as compared to the preferred metal CNs observed in the CSD, those in protein binding sites generally remain the same. This implies that the protein matrix (excluding amino acid residues in the metal's first and second coordination shell) does not impose severe geometrical restrictions on the bound metal cation.

Electron spin relaxation of copper(II) complexes in glassy solution between 10 and 120 K

The temperature dependence, between 10 and 120 K, of electron spin-lattice relaxation at X-band was analyzed for a series of eight pyrrolate-imine complexes and for ten other copper(II) complexes with varying ligands and geometry including copper-containing prion octarepeat domain and S100 type proteins. The geometry of the CuN4 coordination sphere for pyrrolate-imine complexes with R=H, methyl, n-butyl, diphenylmethyl, benzyl, 2-adamantyl, 1-adamantyl, and tert-butyl has been shown to range from planar to pseudo-tetrahedral. The fit to the recovery curves was better for a distribution of values of T1 than for a single time constant. Distributions of relaxation times may be characteristic of Cu(II) in glassy solution. Long-pulse saturation recovery and inversion recovery measurements were performed. The temperature dependence of spin-lattice relaxation rates was analyzed in terms of contributions from the direct process, the Raman process, and local modes. It was necessary to include more than one process to fit the experimental data. There was a small contribution from the direct process at low temperature. The Raman process was the dominant contribution to relaxation between about 20 and 60 K. Debye temperatures were between 80 and 120 K. For samples with similar Debye temperatures the coefficient of the Raman process tended to increase as gz increased, as expected if modulation of spin-orbit coupling is a major factor in relaxation rates. Above about 60 K local modes with energies in the range of 260-360 K (180-250 cm-1) dominated the relaxation. For molecules with similar geometry, relaxation rates were faster for more flexible molecules than for more rigid ones. Relaxation rates for the copper protein samples were similar to rates for small molecules with comparable coordination spheres. At each temperature studied the range of relaxation rates was less than an order of magnitude. The spread was smaller between 20 and 60 K where the Raman process dominates, than at higher temperatures where local modes dominate the relaxation. Spin echo dephasing time constants, Tm, were calculated from two-pulse spin echo decays. Near 10 K Tm was dominated by proton spins in the surroundings. As temperature was increased motion and spin-lattice relaxation made increasing contributions to Tm. Near 100 K spin-lattice relaxation dominated Tm.

The hydration of Cu2+: Can the Jahn-Teller effect be detected in liquid solution?

The long elusive structure of Cu(II) hydrate in aqueous solutions, classically described as a Jahn-Teller distorted octahedron and recently proposed to be a fivefold coordination structure [Pasquarello et al., Science 291, 856 (2001)], has been probed with x-ray-absorption spectroscopy by performing a combined theoretical and experimental analysis. Two absorption channels were needed to obtain a proper reproduction of the x-ray-absorption near-edge structure (XANES) region spectrum, as already observed in other Cu(II) complexes [Chaboy et al., Phys. Rev. B 71, 134208 (2005)]. The extended x-ray-absorption fine-structure (EXAFS) spectrum was analyzed as well within this approach. Quite good reproductions of both XANES and EXAFS spectra were attained for several distorted and undistorted structures previously proposed. Nevertheless, there is not a clearly preferred structure among those including four-, five-, and sixfold coordinated Cu(II) ions. Taking into account our results, as well as many more from several other authors using different techniques, the picture of a distorted octahedron for the Cu(II) hexahydrate in aqueous solution, paradigm of the Jahn-Teller effect, is no longer supported. In solution a dynamical view where the different structures exchange among themselves is the picture that better suits the results presented here.

MXAN Analysis of the XANES Energy Region of a Mononuclear Copper Complex: Applications to Bioinorganic Systems

The near edge XAS spectra of the mononuclear copper complex [Cu(TMPA)(OH(2))](ClO(4))(2) (1) have been simulated using the multiple scattering edge simulation package MXAN (or Minuit XANes). These simulations, which employ the muffin-tin (MT) approximation, have been compared to simulations generated using the finite-difference method (FDM) to evaluate the effect of MT corrections. The sensitivity of the MXAN method was tested using structural models that included several different variations on the bond angles and bond distances for the first-shell atoms of 1. The sensitivity to small structural changes was also evaluated by comparing MXAN simulations of 1 and of structurally modified [Cu(TMPA)(L)](n)(+) complexes [where L = -O-(F(8)TPP)Fe(III), -F, -OPO(2)(O-p-nitrophenyl)Zn(II)(TMPA), and -NCMe] to the experimental data. The accuracy of the bond distances obtained from the MXAN simulations was then examined by comparison to the metrics of the crystal structures. The results show that MXAN can successfully extract geometric information from the edge structure of an XAS spectrum. The systematic application of MXAN to 1 indicates that this approach is sensitive to small structural changes in the molecule that are manifested in the XAS edge spectrum. These results represent the first step toward the application of this methodology to bioinorganic and biological systems.