Metal Coordination Polyhedron Research Articles

Structural influence of hydrophobic core residues on metal binding and specificity in carbonic anhydrase II.

Aromatic residues in the hydrophobic core of human carbonic anhydrase II (CAII) influence metal ion binding in the active site. Residues F93, F95, and W97 are contained in a beta-strand that also contains two zinc ligands, H94 and H96. The aromatic amino acids contribute to the high zinc affinity and slow zinc dissociation rate constant of CAII [Hunt, J. A., and Fierke, C. A. (1997) J. Biol. Chem. 272, 20364-20372]. Substitution of these aromatic amino acids with smaller side chains enhances Cu(2+) affinity while decreasing Co(2+) and Zn(2+) affinity [Hunt, J. A., Mahiuddin, A., & Fierke, C. A. (1999) Biochemistry 38, 9054-9062]. Here, X-ray crystal structures of zinc-bound F93I/F95M/W97V and F93S/F95L/W97M CAIIs reveal the introduction of new cavities in the hydrophobic core, compensatory movements of surrounding side chains, and the incorporation of buried water molecules; nevertheless, the enzyme maintains tetrahedral zinc coordination geometry. However, a conformational change of direct metal ligand H94 as well as indirect (i.e., "second-shell") ligand Q92 accompanies metal release in both F93I/F95M/W97V and F93S/F95L/W97M CAIIs, thereby eliminating preorientation of the histidine ligands with tetrahedral geometry in the apoenzyme. Only one cobalt-bound variant, F93I/F95M/W97V CAII, maintains tetrahedral metal coordination geometry; F93S/F95L/W97M CAII binds Co(2+) with trigonal bipyramidal coordination geometry due to the addition of azide anion to the metal coordination polyhedron. The copper-bound variants exhibit either square pyramidal or trigonal bipyramidal metal coordination geometry due to the addition of a second solvent molecule to the metal coordination polyhedron. The key finding of this work is that aromatic core residues serve as anchors that help to preorient direct and second-shell ligands to optimize zinc binding geometry and destabilize alternative geometries. These geometrical constraints are likely a main determinant of the enhanced zinc/copper specificity of CAII as compared to small molecule chelators.

Ligand field spectroscopy and chemical bonding in Cr 3+-, Fe 3+-, Co 2+- and Ni 2+-containing oxidic solids : Influence of the inductive effect of the competing bonds and magnetic interactions on the degree of covalency of the 3d M–O bonds

The correlations between B 35 and the ionic-covalent parameter ICP nn for various 3d n electronic configurations (3d 3, 3d 5, 3d 7, 3d 8) in mixed oxides reveal the effect of the nearest cationic shell on bonding in the transition metal coordination polyhedron. The variations of B 35 with the optical basicity calculated from the valence and coordination numbers of the component cations show that the physical interpretation of the Racah parameter in terms of so-called covalency effects should be viewed with some caution. A much closer correlation between the Racah parameters and the degree of covalency of M–O bonds is achieved when the inductive effect and the influence of magnetic interactions are taken into account.

Crystal structures of isomorphous triaquatris(3-aminobenzoato-O, O)yttrium(III) trihydrate and triaquatris(3-aminobenzoato-0,0)lanthanide(III) trihydrate

The space group and unit cell parameters of yttrium(III) and lanthanide(III) 3-aminobenzoate hexahydrate crystals have been determined. All compounds have the formula [M(C 7 H 6 NO 2 ) 3 · 3H 2 O] · 3H 2 0 and their crystals are isomorphous in the non-centrosymmetric trigonal space group R 3 c . Crystal structures of three of these salts have been determined: Y(III), Er(III) and Lu(III). The structures consist of the metal cation coordinated by water molecules, bidentate chelating 3-aminobenzoate anions, and crystallization water. The metal coordination polyhedron, with crystallographically imposed threefold symmetry axis, is formed by nine oxygen atoms: six of carboxylate groups and three of water molecules. The crystal structure is stabilized by interligand hydrogen bonding between water molecules and either carboxylate or amino groups.

Carboxylate-histidine-zinc interactions in protein structure and function

The three-dimensional structures of proteins contained in the Brookhaven Protein Data Bank were analyzed for bound metal ions. Well over 150 unique protein structures are available which contain seven different types of bound metal ions. Iron, calcium, and zinc are most commonly observed, and the extended coordination polyhedra of biological zinc are the subject of this study. In particular, histidine residues ligating zinc ions are often found to bridge both the zinc ion and the carboxylate side chain of a nearby aspartate (sometimes glutamate) residue. We refer to the carboxylate-histidine-zinc interaction as indirect carboxylate-metal coordination, and we observe this feature in all zinc enzymes of reported three-dimensional structure. Additionally, we also observe a related carbonyl-histidine-zinc interaction in some metalloproteins. We observe some direct carboxylate-zinc interactions, and their coordination stereochemistry is exclusively syn with respect to the carboxylate. On the basis of available protein structures and known homologues thereof, more than 30 examples of indirect carboxylate-zinc coordination across bridging histidine can be identified. The carboxylate-histidine-zinc triad may be important in the function of many zinc-containing proteins and enzymes, e.g., by strengthening metal complexation or modulating the nucleophilicity of zinc-bound water. The presence of an uncomplexed carboxylate-histidine couple (a grouping more basic than histidine alone) in a native protein can also signal a regulatory metal binding site. Indeed, the Asp—His couple of the serine protease active site may comprise a structural, evolutionary link to the Asp—His of the zinc protease metal coordination polyhedron.

Neopentyl and trimethylsilylmethyl compounds of rhodium(III) and iridium (III) with ortho-metallated triphenylphosphine. X-Ray crystal structure of [Ir(C6H4PPh2)(CH2SiMe3)(η5-C5Me5)

The compound [RhCl2(η5-C5Me5)(PPh3)] reacts with Li(CH2SiMe3) to give the ortho-metallated complex [R[graphic omitted]Ph2)(CH2SiMe3)(η5-C5Me5)](2), and with Mg(CH2SiMe3)Cl in CH2Cl2(molar ratio 1:1) to yield [RhCl(CH2SiMe3)(η5-C5Me5)(PPh3)], (3). Complex (3) is converted by the action of Li(CH2SiMe3) into the ortho-metallated compound (2). The reaction of [IrCl2(η5-C5Me5)-(PPh3)] with Mg(CH2SiMe3)Cl in CH2Cl2 gives [I[graphic omitted]Ph2)(CH2SiMe3)(η5-C5Me5)], (6), and [lrCl(Me)(η5-C5Me5)(PPh3)]. Reaction of [RhCl2(η5-C5Me5)(PPh3)] with Mg(CH2CMe3)Cl or Li(CH2CMe3) in diethyl ether affords a mixture of [R[graphic omitted]H2)(η5-C5Me5)(PPh3)], [R[graphic omitted]Ph2)(CH2CMe3)(η5-C5Me5)], and [Rh(η5-C5Me5)(C2H4)(PPh3)], while reaction in CH2Cl2 in equimolar amounts gives [RhCl(CH2CMe3)(η5-C5Me5)(PPh3)]. Reaction of [lrCl2(η5-C5Me5)(PPh3)] with Mg(CH2CMe3)Cl gives [I[graphic omitted]Ph2)(CH2CMe3)(η5-C5Me5)]. The X-ray crystal structure analysis of compound (6) has been carried out: a= 17.537(7), b= 11.304(4), c= 15.410(7)A, β= 94.49(1)°, space group P21/n, Z= 4, R= 0.0361 for 4114 observed reflections. The ‘piano-stool’ metal co-ordination polyhedron is deformed by ortho-metallation which imposes a 67.0(2)° angle at iridium in the metallacycle, while the other angles, P-Ir-C(17) 89.0(2) and C(17)-Ir-C(36) 89.2(2)°, between the ‘legs’ of the ‘stool’ are near to 90°. The bulky C5Me5 ligand (effective cone angle 146°), in approaching the metal, produces large widenings of the other co-ordination polyhedron angles: Cp–Ir–P 137.0(3), Cp–Ir–C(36)(benzene)133.4(3)°, and Cp–Ir–C(17)(silyl)122.6(3)°(Cp = centroid of C5Me5). The ortho-metallated ring is nearly planar, (P–Ir–C)⁁(P–C–C) 5.3(3)°, and bent by only 6.6(2)° with respect to the metal-bound benzene ring which maintains its planarity; the only deformation this ring suffers involves the endocyclic angles at the carbon bound to phosphorus which widen to 124.5(5)° and at the ortho carbons which narrow to 115.9(6) and 116.7(5)°.

Reaction of NO2 with palladium(II) and platinum(II) aryl complexes; the crystal structure of tans-[Pd(ONO2)2(OPPh3)(PPh3)

[Pd(C6H4NO2-p)I(PPh3)2] and [Pd(Ph)Cl(Ph2PCH2PPh2)] do not react with NO but react with NO2 to give [Pd(NO3)2(OPPh3)(PPh3)] and [PdCl(NO3)(Ph2PCH2CH2PPh2)] respectively. The structure of [Pd(NO3)2(OPPh3)(PPh3)] has been confirmed by X-ray crystallography, the metal co-ordination polyhedron being planar with trans monodentate nitrato groups. Reaction of [Pt(R)I(PPh3)2](R = C6H4NO2-p or Ph) with NO2 gave [Pt(R)(NO3)(PPh3)2], species shown spectroscopically to contain monodentate nitrate. Treatment of [Pd(NO2)2(PPh3)2] with NO2 gave [Pd(NO3)2(PPh3)2], while NO or CO caused deoxygenation of [Pd(NO3)2L2](L = PPh3 or PEt3) and [Pt(Ph)(NO3)(PPh3)2] to the nitro species [Pd(NO2)2L2] and [Pt(Ph)(NO2)(PPh3)2]. Reaction of [Ni(NO3)2(PEt3)2] with NO or NO2 afforded [Ni(NO3)2(OPEt3)2]. The possible mechanisms of these oxygen-transfer reactions are briefly discussed.

Application of Ligand Field Spectroscopy to Problems of Chemical Bonding in Solids

Selected examples (dn systems) are presented to illustrate the interpretation of ligand field spectra (remission spectra) of solid inorganic compounds. In particular, this article demonstrates possible means for the investigation of weak cooperative interactions between transition metal coordination polyhedra and for the determination of the cation distribution in crystal lattices. The information value of the spectroscopic method to the chemist is critically discussed.