Structure determination of the 2:1 derivatives of copper(I) bromide and iodide with bis(diphenylphosphino)methane. A simple structural scheme for the formation of (CuX)nLm species

The structures of the complexes (CuX)₂DPM (X = Br, I; DMP = bis(diphenylphosphino)methane) were determined from three dimensional X-ray data collected by counter methods. The iodine derivative crystallizes in the space group Pbca with eight units in a cell defined by a = 17.128(9), b = 18.306(9) c, = 16.508 (8) Å. The structure was refined by the least-squares method to a final R factor of 0.054 for 1336 non-zero independent reflections. The bromine derivative crystallizes in the space group P2₁/c with eight units in a cell defined by a = 23.707(1), b = 17.805(9), c = 16.991(1) Å, β = 136.10(5)°. The final least-squares refinement, based on 2489 non-zero independent reflections, gave an R factor of 0.074.Both the compounds have similar structures with a centrosymmetric (CuX)₄ core, in which two copper atoms have a tetrahedral geometry, while the other two are trigonal.The above structures are compared with those already reported for other compounds (CuX)_nL_m and a single scheme is proposed to rationalize the different geometries of the (CuX)_n core on the basis of steric and electronic effects.     

Di-organocobalt complexes of macrocyclic ligands

Three new di-metallorganic cobalt complexes of the type trans-(Bz)₂Co(chel), where Bz is a benzyl group σ-bonded to cobalt atom and chel is an equatorial chelating system constituted by an amino-oximic ligand and its conjugated base, were synthesised. The protonated and the unprotonated ligands interact through an O-H ? O bridge stabilising the entire structure. The complexes differ in the equatorial moiety which is derived from the following ligands: HLN-py=3-[(2-pyridyl)ethylimino]-butan-2-one oxime), HLN-Ph=3-[(2-phenyl)ethylimino]-butan-2-one oxime and the analogous HLN-PhCl=3-[(2-chlorophenyl)ethylimino]-butan-2-one oxime. Two of these compounds, namely those derived from HLN-py and HLN-PhCl were structurally characterised by means X-ray diffractometry. Data reveal that each complex is characterised by the presence of two unusually long cobalt-carbon bonds which are 2.120(4) Å (mean value) in complex with HLN-py ligand and 2.119(4) Å (mean value) in complex with HLN-PhCl. These data are consistent with a strong mutual trans-influence exerted by one ligand on the other.     

Binding of nitrite and its reductive activation to nitric oxide at biomimetic copper centers

The reactivity of nitrite towards the copper(II) and copper(I) centers of a series of complexes with tridentate nitrogen donor ligands has been investigated. The ligands are bis[(1-methylbenzimidazol-2-yl)methyl]amine (1-bb), bis[2-(1-methylbenzimidazol-2-yl)ethyl]amine (2-bb), and bis[2-(3,5-dimethyl-1-pyrazolyl)ethyl]amine (ddah) and carry two terminal benzimidazole (1-bb, 2-bb) or pyrazole (ddah) rings and a central amine donor residue. While 2-bb and ddah form two adjacent six-membered chelate rings on metal coordination, 1-bb forms two smaller rings of five members. The binding affinity of nitrite and azide to the Cu(II) complexes (ClO₄ ⁻ as counterion) has been determined in solution. The association constants for the two ligands are similar, but nitrite is a slightly stronger ligand than azide when it binds as a bidentate donor. The X-ray crystal structure of the nitrite complex [Cu(ddah)(NO₂)]ClO₄ (final R=0.056) has been determined: triclinic P1ˉspace group, a=8.200(2) ?, b=9.582(3) ?, c=15.541(4) ?. It may be described as a perchlorate salt of a “supramolecular” species resulting from the assembly of two complex cations and one sodium perchlorate unit. The copper stereochemistry in the complex is intermediate between SPY and TBP, and nitrite binds to Cu(II) asymmetrically, with Cu-O distances of 2.037(2) and 2.390(3) ? and a nearly planar CuO₂N cycle. On standing, solutions of [Cu(ddah)(NO₂)]ClO₄ in methanol produce the dinuclear complex [Cu(ddah)(OMe)]₂(ClO₄)₂, containing dibridging methoxy groups. In fact the crystal structure analysis (final R=0.083) showed that the crystals are built up by dinuclear cations, arranged on a crystallographic symmetry center, and perchlorate anions. Electrochemical analysis shows that binding of nitrite to the Cu(II) complexes of 2-bb and ddah shifts the reduction potential of the Cu(II)/Cu(I) couple towards negative values by about 0.3 V. The thermodynamic parameters of the Cu(II)/Cu(I) electron transfer have also been analyzed. The mechanism of reductive activation of nitrite to nitric oxide by the Cu(I) complexes of 1-bb, 2-bb, and ddah has been studied. The reaction requires two protons per molecule of nitrite and Cu(I). Kinetic experiments show that the reaction is first order in [Cu(I)] and [H⁺] and exhibits saturation behavior with respect to nitrite concentration. The kinetic data show that [Cu(2-bb)]⁺ is more efficient than [Cu(1-bb)]⁺ and [Cu(ddah)]⁺ in reducing nitrite. Received: 19 November 1999 / Accepted: 20 January 2000     

Cleavage of the iron-methionine bond in c-type cytochromes: Crystal structure of oxidized and reduced cytochrome c2 from Rhodopseudomonas palustris and its ammonia complex

The three-dimensional structures of the native cytochrome c(2) from Rhodopseudomonas palustris and of its ammonia complex have been obtained at pH 4.4 and pH 8.5, respectively. The structure of the native form has been refined in the oxidized state at 1.70 A and in the reduced state at 1.95 A resolution. These are the first high-resolution crystal structures in both oxidation states of a cytochrome c(2) with relatively high redox potential (+350 mV). The differences between the two oxidation states of the native form, including the position of internal water molecules, are small. The unusual six-residue insertion Gly82-Ala87, which precedes the heme binding Met93, forms an isolated 3(10)-helix secondary structural element not previously observed in other c-type cytochromes. Furthermore, this cytochrome shows an external methionine residue involved in a strained folding near the exposed edge of the heme. The structural comparison of the present cytochrome c(2) with other c-type cytochromes has revealed that the presence of such a residue, with torsion angles phi and psi of approximately -140 and -130 degrees, respectively, is a typical feature of this family of proteins. The refined crystal structure of the ammonia complex, obtained at 1.15 A resolution, shows that the sulphur atom of the Met93 axial ligand does not coordinate the heme iron atom, but is replaced by an exogenous ammonia molecule. This is the only example so far reported of an X-ray structure with the heme iron coordinated by an ammonia molecule. The detachment of Met93 is accompanied by a very localized change in backbone conformation, involving mainly the residues Lys92, Met93, and Thr94. Previous studies under typical denaturing conditions, including high-pH values and the presence of exogenous ligands, have shown that the detachment of the Met axial ligand is a basic step in the folding/unfolding process of c-type cytochromes. The ammonia adduct represents a structural model for this important step of the unfolding pathway. Factors proposed to be important for the methionine dissociation are the strength of the H-bond between the Met93 and Tyr66 residues that stabilizes the native form, and the presence in this bacterial cytochrome c(2) of the rare six-residue insertion in the helix 3(10) conformation that increases Met loop flexibility.     

Miniaturized heme proteins: crystal structure of Co(III)-mimochrome IV

Protein design provides an attractive approach to test the essential features required for folding and function. Previously, we described the design and structural characterization in solution of mimochromes, a series of miniaturized metalloproteins, patterned after the F-helix of the hemoglobin beta-chain. Mimochromes consist of two medium-sized helical peptides, covalently linked to the deuteroporphyrin. CD and NMR characterization of the prototype, mimochrome I, revealed that the overall structure conforms well to the design. However, formation of Delta and Lambda diastereomers was observed. To overcome the problem of diastereomer formation, we re-designed mimochrome I, by engineering intramolecular, interchain interactions. The resulting model was mimochrome IV: the solution structural characterization showed the presence of the Lambda isomer as a unique form. To examine the extent to which the stereochemical stability and uniqueness of mimochrome IV was retained in the solid state, the crystal structure of Co(III)-mimochrome IV was solved by X-ray diffraction, and compared to the solution structure of the same derivative. Co(III)-mimochrome IV structures, both in solution and in the solid state, are characterized by the following common features: a bis-His axial coordination, a Lambda configuration around the metal ion, and a predominant helical conformation of the peptide chains. However, in the crystal structure, intrachain Glu1-Arg9 ion pairs are preferred over the designed, and experimentally found in solution, interchain interactions. This ion pairing switch may be related to strong packing interactions.     

Metal-stabilized rare tautomers of nucleobases

 A Pt^II complex containing N4 bound neutral 1-methylcytosine (1-MeC), trans–[Pt(NH₃)₂(1-MeC-N4)₂](ClO₄)₂ (5), has been prepared and characterized by X-ray analysis. The complex contains the rare iminooxo tautomer form of the cytosine nucleobase. Pt^II binding is through the exocyclic N4 position of the nucleobases, with Pt and the N3 positions in a syn orientation. As a consequence, the proton at N3 is pointing toward the heavy metal, thereby allowing an agostic Pt···HN interaction. Formation of 5 is achieved via oxidation of the linkage isomer trans–[Pt(NH₃)₂(1-MeC-N3)₂]²⁺ (1) to a Pt^IV species (2), followed by metal migration to N4, and subsequent reduction to Pt^II. This process is a text-book example for a redox-assisted metal migration at a heterocyclic ligand. The existence of various rotamers of 5 in aqueous solution is evident from ¹H NMR spectroscopy. The possible role of these rotamers of the metalated rare tautomer, and in particular of those having Pt and the N3 position in an anti arrangement, with regard to base mispairing is discussed. Received: 27 February 1996 / Accepted: 10 June 1996     

Reaction of PtOH complexes with CO2: synthesis and X-ray structure of (PBz3)4Pt2(Ph)2(η1,η1,μ-CO3)·(toluene)

The reaction of (diphoe)Pt(CH₂CN)(OH) and trans-(PBz₃)₂Pt(Ph)(OH) with CO₂ is reported as producing dimeric, bridged carbonato complexes of the type: P₄Pt₂(R)₂(CO₃). The crystal and molecular structure of (PBz₃)₄Pt₂(Ph)₂(μ-CO₃)·(toluene) is also reported, showing η¹, η¹ bonding. The reaction is recognized to proceed in a stepwise fashion through bicarbonato intermediates.     

Structural study on ligand specificity of human vitamin B12 transporters

Studies comparing the binding of genuine cobalamin (vitamin B12) to that of its natural or synthetic analogues have long established increasing ligand specificity in the order haptocorrin, transcobalamin and intrinsic factor, the high-affinity binding proteins involved in cobalamin transport in mammals. In the present study, ligand specificity was investigated from a structural point of view, for which comparative models of intrinsic factor and haptocorrin are produced based on the crystal structure of the homologous transcobalamin and validated by results of published binding assays. Many interactions between cobalamin and its binding site in the interface of the two domains are conserved among the transporters. A structural comparison suggests that the determinant of specificity regarding cobalamin ligands with modified nucleotide moiety resides in the beta-hairpin motif beta3-turn-beta4 of the smaller C-terminal domain. In haptocorrin, it provides hydrophobic contacts to the benzimidazole moiety through the apolar regions of Arg357, Trp359 and Tyr362. Together, these large side chains may compensate for the missing nucleotide upon cobinamide binding. Intrinsic factor possesses only the tryptophan residue and transcobalamin only the tyrosine residue, consistent with their low affinity for cobinamide. Relative affinity constants for other analogues are rationalized similarly by analysis of steric and electrostatic interactions with the three transporters. The structures also indicate that the C-terminal domain is the first site of cobalamin-binding since part of the beta-hairpin motif is trapped between the nucleotide moiety and the N-terminal domain in the final holo-proteins.