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PubMed2002

Reactivity of [Re[kappa(3)-H(mu-H)B(tim(Me))(2)](CO)(3)] (tim(Me) = 2-mercapto-1-methylimidazolyl) toward neutral substrates.

The complex [Re[kappa(3)-H(mu-H)B(tim(Me))(2)](CO)(3)] (2a) (tim(Me) = 2-mercapto-1-methylimidazolyl) reacts with a variety of neutral substrates to afford new complexes featuring the dihydrobis(2-mercapto-1-methylimidazolyl)borate coordinated in a bidentate or unidentate fashion. By treating 2a with unidentate ligands, the mononuclear complexes [Re[kappa(2)-H(2)B(tim(Me))(2)](CO)(3)(L)] (L = imidazole (5), 4-(dimethylamino)pyridine (6), tert-butylisonitrile (7), triphenylphosphine (8)) were formed, upon replacement of the agostic B-H...Re bond by the correspondent unidentate ligand. With potentially bidentate substrates, 2a is transformed into mononuclear or dinuclear complexes, depending on the atom donor set of the reacting substrates. Reaction of compound 2a with ethylenediamine (en) gave the complex [Re[kappa(1)-H(2)B(tim(Me))(2)](CO)(3)(en)] (9), because of cleavage of the agostic interaction, dechelation of one mercaptoimidazolyl ring, and bidentate coordination of the amine. By contrast, 1,2-bis(diphenyl)phosphinoethane (dppe) is not able to replace the mercaptoimidazolyl ring, and the dimer [Re[kappa(2)-H(2)B(tim(Me))(2)](CO)(3)](2)(mu-dppe) (10) was formed. The novel Re(I) tricarbonyl complexes (5-10) have been fully characterized, including by X-ray diffraction analysis in the case of 6, 8, 9, and 10. The X-ray diffraction study confirmed the unprecedented unidentate coordination mode of the dihydrobis(2-mercapto-1-methylimidazolyl)borate in complex 9.

Journal Article↗
PubMed2002

Structural systematics for o-C(6)H(4)XY ligands with X,Y= O, NH, and S donor atoms. o-iminoquinone and o-iminothioquinone complexes of ruthenium and osmium.

The structural features of quinone ligands are diagnostic of charge. The o-benzoquinone, radical semiquinonate, and catecholate electronic forms have C-O bond lengths and a pattern of ring C-C bond lengths that point to a specific mode of coordination. This correlation between ligand charge and structure has been extended to iminoquinone and iminothioquinone ligands, giving a charge-localized view of electronic structure for complexes of redox-active metal ions. The radical semiquinonate form of these ligands has been found to be a surprisingly common mode of coordination; however, the paramagnetic character of the radical ligand is often obscured in complexes containing paramagnetic metal ions. In this report, diamagnetic iminosemiquinonate (isq) and iminothiosemiquinonate (itsq) complexes of ls-d(5) Ru(III) with related complexes of osmium are reported. With osmium, the Os(IV)-amidophenolate (ap) redox isomer is formed. Electrochemical and spectral properties are described for Ru(PPh(3))(2)(isq)Cl(2), Ru(PPh(3))(2)(itsq)Cl(2), Os(PPh(3))(2)(ap)Br(2), Os(PPh(3))(2)(atp)Br(2), and Os(PPh(3))(2)(ap)H(2). Crystallographic characterization of Ru(PPh(3))(2)(isq)Cl(2), Ru(PPh(3))(2)(itsq)Cl(2), and Os(PPh(3))(2)(ap)H(2) was used to assign charge distributions.

Journal Article↗
PubMed2005

An atomic resolution view of ICAM recognition in a complex between the binding domains of ICAM-3 and integrin alphaLbeta2.

Within the Ig superfamily (IgSF), intercellular adhesion molecules (ICAMs) form a subfamily that binds the leukocyte integrin alphaLbeta2. We report a 1.65-A-resolution crystal structure of the ICAM-3 N-terminal domain (D1) in complex with the inserted domain, the ligand-binding domain of alphaLbeta2. This high-resolution structure and comparisons among ICAM subfamily members establish that the binding of ICAM-3 D1 onto the inserted domain represents a common docking mode for ICAM subfamily members. The markedly different off-rates of ICAM-1, -2, and -3 appear to be determined by the hydrophobicity of residues that surround a metal coordination bond in the alphaLbeta2-binding interfaces. Variation in composition of glycans on the periphery of the interfaces influences on-rate.

Amino Acid Sequence↗
PubMed1984

Chromoxane cyanine R. II. Staining of animal tissues by the dye and its iron complexes.

The staining properties of chromoxane cyanine R (Colour Index No. 43820, Mordant blue 3; also known as eriochrome cyanine R and solochrome cyanine R) have been studied. Used alone, the dye imparted its red colour to nuclei, cytoplasm and collagen. The dye was extracted by mild alkali but not by acids. Stainability required ionized amino groups in the tissue, and there was also evidence for non-ionic binding of the dye. The colours obtained by staining with mixtures of chromoxane cyanine R and ferric chloride varied with the molar iron:dye ratio and with the pH. Useful staining was seen only between pH 1 and 2. The tissues were coloured either all blue (when Fe:dye was high), or both red and blue (when Fe:dye was low). Lower pH favoured the deposition of red, higher pH the deposition of blue colour. The red was mainly in cytoplasm, blue in nuclei and myelin. Collagen fibres were red or purple, depending on pH and iron:dye ratio. Red colours were differentiated by acid and changed to blue, but not extracted, by mild alkali. The red substance in the stained sections was clearly not the free dye, so it was probably an iron-dye complex. From the effects of various differentiating agents, it was deduced that the red and blue dye-metal complex molecules were bound to the tissue by the dye moiety, not by interposition of iron atoms. Staining by the complexes of iron(III) with chromoxane cyanine R did not involve nucleic acids or other polyanions or the amino groups of proteins. There was evidence for only non-ionic binding of both red and blue complexes. It is suggested that the red colour in sections stained by solutions with low iron:dye ratio is due to a simple carboxylate complex, [ Fe2H (dye)]-. The blue colour would then result from withdrawal of a proton from the red complex to give [Fe2(dye)]2-. The bases that remove the protons may be arginine-rich nucleoproteins of nuclei and phospholipid bases of myelin. Techniques are described for informative simultaneous staining in two colours, and for the selective staining of either nuclei or myelin.

Animals↗
PubMed2005

Sequential protonation and methylation of a hydride-osmium complex containing a cyclopentadienyl ligand with a pendant amine group.

Complex OsH{eta5-C5H4(CH2)2NMe2}(P(i)Pr3)2 (1) reacts with 1 equiv of trifluoromethanesulfonic acid (HOTf) and trifluoromethanesulfonic acid-d1 (DOTf) to produce the dihydride and hydride-deuteride complexes, [OsHE{eta5-C5H4(CH2)2NMe2}(P(i)Pr3)2]OTf (E = H (2), D (2-d1), respectively. Treatment of 2 and 2-d1 with a second equivalent of HOTf gives [OsHE{eta5-C5H4(CH2)2NHMe2}(P(i)Pr3)2][OTf]2 (E = H (3), D (3-d1) as a result of the protonation of the nitrogen atom. While the hydride and deuteride ligands of 2, 2-d1, 3, and 3-d1 do not undergo any H/D exchange process with the solvent, in acetone-d6, the NH proton of 3 and 3-d1 changes places with a deuterium atom of the solvent to yield [OsHE{eta5-C5H4(CH2)2NDMe2}(P(i)Pr3)2][OTf]2 (E = H (3-Nd1), D (3-d2)). Complex 3-Nd1 can also be obtained from the treatment of complex 2 with DOTf in dichloromethane. No exchange process between the hydride and the ND positions in 3-Nd1 or between the deuteride and NH positions in 3-d1 has been observed. Treatment of 3-Nd1 and 3-d1 with sodium methoxide results in a selective reaction of the base with the ammonium group to regenerate 2 and 2-d1, respectively. Complex 1 also reacts with methyl and methyl-d3 trifluoromethanesulfonate (CH3OTf and CD3OTf, respectively) to give [OsH{eta5-C5H4(CH2)2NMe2CE3}(P(i)Pr3)2]OTf (E = H (4), D (4-d3)) as a result of the addition of the CE3 (E = H, D) group to the nitrogen atom. Complex 4 has been characterized by an X-ray diffraction analysis. It reacts with a second molecule of CH3OTf or CD3OTf to produce [OsH{eta5-C5H4(CH2)2NMe3}{CH2CH(CH3)P(i)P2}(P(i)Pr3)[OTf]2 (5). Similarly, complex 4-d3 reacts with a second molecule of CH3OTf or CD3OTf to yield [OsH{eta5-C5H4(CH2)2NMe2CD3}{CH2CH(CH3)P(i)P2}(P(i)Pr3)[OTf]2 (5-d3). In acetonitrile, complex 5 evolves to an equilibrium mixture of the acetonitrile adducts [Os{eta5-C5H4(CH2)2NMe3}(NCCH3)(P(i)Pr3)2][OTf]2 (7) and [Os{eta5-C5H4(CH2)2NMe3}(NCCH3)2(P(i)Pr3)][OTf]2 (8). In methanol or methanol-d4, complex 4 is not stable and loses trimethylamine to give the vinylcyclopentadienyl derivatives [OsHE(eta5-C5H4CH=CH2)(P(i)Pr3)2]OTf (E = H (9), D (9-d1)) as a result of the protonation or deuteration of the metallic center and a subsequent Hofmann elimination. Protonation of 4 with HOTf gives the dihydride-trimethylammonium derivative [OsH2{eta5-C5H4(CH2)2NMe3}(P(i)Pr3)2][OTf]2 (10). Treatment of 9 with sodium methoxide produces OsH(eta5-C5H4CH=CH2)(P(i)Pr3)2 (11).

Journal Article↗
PubMed2001

The phosphoryl-transfer mechanism of Escherichia coli phosphoenolpyruvate carboxykinase from the use of AlF(3).

The mechanism of reversible transfer of the gamma-phosphate group of ATP by Escherichia coli phosphoenolpyruvate carboxykinase (PCK) on to its substrate is of great interest. It is known that metallofluorides are accurate analogs of the transition state in the context of kinase mechanisms. Therefore, two complexes of PCK, one with AlF(3), Mg(2+) and ADP (complex I), the other with AlF(3), Mg(2+), ADP and pyruvate (complex II) were crystallized. The X-ray crystal structures of these two complexes were determined at 2.0 A resolution. The Al atom has trigonal bipyramidal geometry that mimics the transition state of phosphoryl transfer. The Al atom is at a distance of 2.8 A and 2.9 A from an oxygen atom of the beta-phosphoryl group of ADP in complex I and II, respectively. A water molecule in complex I and an oxygen atom of the pyruvate in complex II are located along the axis of the trigonal bipyramid on the side opposite to the beta-phosphoryl oxygen with respect to the equatorial plane, suggesting that the complexes are close mimics of the transition state. Along with the presence of positively charged species around the AlF(3) moiety, these results indicate that phosphoryl transfer occurs via a direct displacement mechanism with associative qualities.

Adenosine Diphosphate↗
PubMed2005

Crystal structures and spectroscopic properties of zinc(II) ternary complexes of vitamin L, H' and their isomer m-aminobenzoic acid with bipyridine.

The crystal structures of the three Zn(II) complexes, [Zn(bpy)(o-AB)2] (1) (bpy=2,2'-bipyridine, o-AB=o-aminobenzoic acid=Vitamin L), [Zn(bpy)(m-AB)Cl]2 (2) (m-AB=m-aminobenzoic acid), [Zn(bpy)(p-AB)Cl]*p-AB*H2O (3) (p-AB=p-aminobenzoic acid=Vitamin H'), have been determined and the basic coordination geometries and architectures organized by hydrogen-bonds and pi-pi interactions also characterized. The substitute amine group at ortho-, meta-, and para-position of AB plays an important role to produce completely different coordination motif of these complexes, further, in all complexes, aromatic amines are not coordinated to Zn(II) atom. While two different types of coordination modes of the carboxylate O atoms are present in these complexes: one mode consists of the usual Zn-O bond lengths (2.009(2)-2.251(2) A) in complex 1, 2 and 3; another consists of a very long Zn-O bond lengths (2.422(2) A) in complex 1. Each of the complexes has the characteristic UV absorption bands around 250-310 nm region, and the intense fluorescence band at near 325 nm.

4-Aminobenzoic Acid↗
PubMed2005

Computational studies of the cationic aluminium(chloro) hydroxides by quantum chemical ab initio methods.

Cationic aluminium(chloro) hydroxide complexes with two to four aluminium atoms were studied using quantum chemical methods. Complexes were studied in both gas and liquid phase. The liquid environment was modeled by using a conductor-like screening model (COSMO). COSMO calculations were carried out as a single point calculation at the optimized gas phase structures. Water (epsilon = 78.54) was used as the solvent. The minimum energy structures obtained from the gas phase studies were mostly compact cyclic structures. Aluminium preferred to be five-coordinated in oxygen rich clusters. Core oxygen preferred three-fold coordination but in the largest clusters the four-coordinated oxygen was observed. Water reacted dissociatively with hydrogen poor clusters. The COSMO calculations showed that the optimal structures of cationic aluminium(chloro) hydroxides tend to be more open in the liquid than in the gas phase.

Aluminum↗
PubMed2006

The DNA binding preference of RAD52 and RAD59 proteins: implications for RAD52 and RAD59 protein function in homologous recombination.

We examined the double-stranded DNA (dsDNA) binding preference of the Saccharomyces cerevisiae Rad52 protein and its homologue, the Rad59 protein. In nuclease protection assays both proteins protected an internal sequence and the dsDNA ends equally well. Similarly, using electrophoretic mobility shift assays, we found the affinity of both Rad52 and Rad59 proteins for DNA ends to be comparable with their affinity for internal sequences. The protein-DNA complexes were also directly visualized using atomic force microscopy. Both proteins formed discrete complexes, which were primarily found (90-94%) at internal dsDNA sites. We also measured the DNA end binding behavior of human Rad52 protein and found a slight preference for dsDNA ends. Thus, these proteins have no strong preference for dsDNA ends over internal sites, which is inconsistent with their function at a step of dsDNA break repair that precedes DNA processing. Therefore, we conclude that S. cerevisiae Rad52 and Rad59 proteins and their eukaryotic counterparts function by binding to single-stranded DNA formed as intermediates of recombination rather than by binding to the unprocessed DNA double-strand break.

DNA Breaks, Double-Stranded↗
PubMed1999

Dichlorobis(1-methyl-1H-benzimidazole-N3)-cobalt(II).

The metal atom in the title complex, [CoCl2(C8H8N2)2], has a slightly distorted tetrahedral coordination involving two Cl- ions and two N atoms from the aromatic groups. The dihedral angle between the planes of the two 1-methylbenzimidazole ligands is 117.7 (7) degrees.

Cobalt↗
PubMed1987

Mitochondrial ATP synthase complex: interaction of its F1 adenosinetriphosphatase moiety with the heavy atom iodine.

Studies were carried out to determine whether a simple electron-dense "heavy atom" like iodine could be introduced selectively into one or more of the subunits of the mitochondrial ATP synthase complex of rat liver. Surprisingly, very low amounts of iodine are incorporated into the isolated F1 moiety of this complex under conditions which result in a marked loss of catalytic activity. ATPase activity is inactivated in a concentration-dependent manner at pH 7.5 with half-maximal inactivation occurring at about 40 microM iodine. A maximum of only 10 atoms of iodine are incorporated per F1 molecule under conditions where inhibition of ATPase activity is linearly related to iodine incorporation. The molecular size of F1 after iodination is unchanged, indicating that inactivation is due to modification of essential amino acid residues rather than subunit dissociation. Treatment of F1, with 20-50 microM [125I]iodine followed sequentially by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography showed that the beta subunit is preferentially labeled. Significantly, about two atoms of iodine per beta subunit are incorporated. Some iodine amounting to less than 23% of the total radioactivity placed on the gels is recovered in the alpha and gamma subunits whereas no radioactivity is detected in the delta and epsilon subunits. Iodination of F1 appears to modify essential residues other than those involved in substrate or product binding per se. Thus, nucleotide binding to F1 is unaltered by iodine, and neither phosphate, MgADP, nor MgATP protects F1 against inhibition by this agent.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1997

Chromatographic method involving inductively coupled plasma atomic emission spectrometric detection for the study of metal-protein complexes.

A chromatographic method has been used to study metal ion-protein complexes. It involves successively a gel filtration technique to separate and distinguish the complexed from the free metallic ions, and a spectrometric technique, inductively coupled plasma atomic emission spectrometry (ICP-AES), which allows us to calculate accurately the concentration of ionic metallic species in solution. In the chromatographic step, we applied a large-zone Hummel and Dreyer method. Thus, fractions can be collected throughout the chromatographic experiment and their metal concentration measured by ICP-AES, at constant and known protein concentration. This method has been tested on the copper complex of bovine serum albumin. Results of our study are in good agreement with previous studies on this complex.

Chromatography, Gel↗
PubMed2005

Atomic scale modelling of the cores of dislocations in complex materials part 1: methodology.

Dislocations influence many properties of crystalline solids, including plastic deformation, growth and dissolution, diffusion and the formation of polytypes. Some of these processes can be described using continuum methods but this approach fails when a description of the structure of the core is required. To progress in these types of problems, an atomic scale model is essential. So far, atomic scale modelling of the cores of dislocations has been limited to systems with rather simple crystal structures. In this article, we describe modifications to current methodology, which have been used for strongly ionic materials with simple structures. These modifications permit the study of dislocation cores in more structurally complex materials.

Biomedical Engineering↗
PubMed2002

Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution.

In enzyme catalysis, where exquisitely positioned functionality is the sine qua non, atomic coordinates for a Michaelis complex can provide powerful insights into activation of the substrate. We focus here on the initial proton transfer of the isomerization reaction catalyzed by triosephosphate isomerase and present the crystal structure of its Michaelis complex with the substrate dihydroxyacetone phosphate at near-atomic resolution. The active site is highly compact, with unusually short and bifurcated hydrogen bonds for both catalytic Glu-165 and His-95 residues. The carboxylate oxygen of the catalytic base Glu-165 is positioned in an unprecedented close interaction with the ketone and the alpha-hydroxy carbons of the substrate (C em leader O approximately 3.0 A), which is optimal for the proton transfer involving these centers. The electrophile that polarizes the substrate, His-95, has close contacts to the substrate's O1 and O2 (N em leader O < or = 3.0 and 2.6 A, respectively). The substrate is conformationally relaxed in the Michaelis complex: the phosphate group is out of the plane of the ketone group, and the hydroxy and ketone oxygen atoms are not in the cisoid configuration. The epsilon ammonium group of the electrophilic Lys-12 is within hydrogen-bonding distance of the substrate's ketone oxygen, the bridging oxygen, and a terminal phosphate's oxygen, suggesting a role for this residue in both catalysis and in controlling the flexibility of active-site loop.

Amino Acid Sequence↗
PubMed1997

Preparation, characterization, DNA binding, and in vitro cytotoxicity of the enantiomers of the platinum(II) complexes N-methyl-, N-ethyl- and N,N-dimethyl-(R)- and -(S)-3-aminohexahydroazepinedichloroplatinum(II).

A series of chiral diaminedichloroplatinum(II) complexes derived from [Pt(ahaz)Cl2] (ahaz = 3-aminohexahydroazepine) have been synthesized and tested for cytotoxic activity. Novel synthetic pathways were developed to produce the structural derivatives of the ahaz ligand, with alkyl substituents on the exocyclic nitrogen atom. The platinum(II) complexes of these ligands were synthesized and characterized by NMR and CD spectroscopy, confirming isomeric and enantiomeric purity. The crystal structures of three of these complexes, [Pt(S-meahaz)-Cl2], [Pt(R-etahaz)Cl2], and [Pt(S-dimeahaz)Cl2] (meahaz = N-methylahaz, etahaz = N-ethylahaz, dimeahaz = N,N-dimethylahaz), have been determined to establish the orientation of the protons and alkyl substituents on the nitrogen donor atoms. In vitro assays of the cytotoxic activity of the complexes have revealed a significant and reproducible enantioselective trend with the R-enantiomers more active than the S-enantiomers in all cell lines. Increasing the steric bulk on the amine groups was found to have only a modest effect on activity. No enantioselectivity was observed in the binding of R- and S-[Pt(etahaz)Cl2] to calf-thymus DNA.

Animals↗
PubMed2006

Thermodynamic, kinetic and solid-state study of divalent metal complexes of 1,4,8,11-tetraazacyclotetradecane (cyclam) bearing two trans (1,8-)methylphosphonic acid pendant arms.

Divalent metal complexes of macrocyclic ligand 1,4,8,11-tetraazacyclotetradecane-1,8-bis(methylphosphonic acid)) (1,8-H4te2p, H4L) were investigated in solution and in the solid state. The majority of transition-metal ions form thermodynamically very stable complexes as a consequence of high affinity for the nitrogen atoms of the ring. On the other hand, complexes with Mn2+, Pb2+ and alkaline earth ions interacting mainly with phosphonate oxygen atoms are much weaker than those of transition-metal ions and are formed only at higher pH. The same tendency is seen in the solid state. Zinc(II) ion in the octahedral trans-O,O-[Zn(H2L)] complex is fully encapsulated within the macrocycle (N4O2 coordination mode with protonated phosphonate oxygen atoms). The polymeric {[Pb(H2L)(H2O)2].6H2O}n complex has double-protonated secondary amino groups and the central atom is bound only to the phosphonate oxygen atoms. The phosphonate moieties bridge lead atoms creating a 3D-polymeric network. The [{(H2O)5Mn}2(micro-H2L)](H2L).21H2O complex contains two pentaaquamanganese(II) moieties bridged by a ligand molecule protonated on two nitrogen atoms. In the complex cation, oxygen atoms of the phosphonate groups on the opposite sites of the ring occupy one coordination site of each metal ion. The second ligand molecule is diprotonated and balances the positive charge of the complex cation. Complexation of zinc(II) and cadmium(II) by the ligand shows large differences in reactivity of differently protonated ligand species similarly to other cyclam-like complexes. Acid-assisted dissociations of metal(II) complexes occur predominantly through triprotonated species [M(H3L)]+ and take place at pH < 5 (Zn2+) and pH < 6 (Cd2+).

Combinatorial Chemistry Techniques↗