The Exchange Processes in Zinc-Complexes of o-Vanillin Salicyloylhydrazone as studied by 2-Dimensional NMR

Zinc forms two types of complexes with o-vanillin salicyloylhydrazone. The H-1 and C-13 nmr studies suggest that it coordinates with azomethine nitrogen, the carbonyl oxygen and with one or both of the phenolic oxygens. The H-1-H-1 and H-1 decoupled C-13-C-13 two-dimensional nuclear Overhauser and exchange spectra show that there is an exchange between the two types of complexes.

DockYard-a repository to assist modeling of protein-protein docking

In the absence of interlogs, building docking models is a time intensive task, involving generation of a large pool of docking decoys followed by refinement and screening to identify near native docking solutions. This limits the researcher interested in building docking methods with the choice of benchmarking only a limited number of protein complexes. We have created a repository called dockYard (http://pallab.serc.iisc.ernet.in/dockYard), that allows modelers interested in protein-protein interaction to access large volume of information on protein dimers and their interlogs, and also download decoys for their work if they are interested in building modeling methods. dockYard currently offers four categories of docking decoys derived from: Bound (native dimer co-crystallized), Unbound (individual subunits are crystallized, as well as the target dimer), Variants (match the previous two categories in at least one subunit with 100% sequence identity), and Interlogs (match the previous categories in at least one subunit with >= 90% or >= 50% sequence identity). The web service offers options for full or selective download based on search parameters. Our portal also serves as a repository to modelers who may want to share their decoy sets with the community.

Photolysis of arene chromium tricarbonyl complexes in presence of amine-boranes: Observation of sigma-borane complexes in solution

Activation of the B-H sigma-bond of amine-boranes on the chromium(0) center of arene chromium tricarbonyl complexes (eta(6)-arene) Cr(CO)(3) (arene = fluorobenzene, 1a; benzene, 1b and mesitylene, 1c) has been studied. Photolysis of 1b in presence of ammonia-borane (H3N center dot BH3, AB) and tert-butylamine-borane ((BuH2N)-Bu-t center dot BH3, TBAB) resulted in H-2 evolution and precipitation of a BNHx polymer. On the other hand, photolysis in the presence of trimethylamine-borane (Me3N center dot BH3, TMAB) resulted in the formation of a sigma-borane complex (2) along with Cr(CO)(5)(eta(1)-HBH2 center dot NMe3) (3). The sigma-borane complexes (eta(6)-arene) Cr-( CO)(2)(eta(1)-HBH2 center dot NMe3) (arene = fluorobenzene, 2a; benzene, 2b and mesitylene, 2c) were characterized in solution by H-1, B-11, and C-13 NMR spectroscopy. Electron withdrawing substituents on the arene ring provide the more stable sigma-borane moiety in this series of complexes. (C) 2011 Elsevier B.V. All rights reserved.

Chelating and bridging bis(diphenylphosphino)aniline complexes of copper(I)

The ligand bis(diphenylphosphino)aniline (dppan) has been shown to be a versatile ligand sporting different coordination modes and geometries as dictated by copper(I) and the counter ion. The molecular structures of its Cu(I) complexes were characterized by X-ray crystallography. The ligand was found in a chelating mode and monomeric complexes were formed when the ligand to copper ratio was 2: 1 and the anion was non-coordinating. However, with thiocyanate as the counter anion, the ligand was found to adopt two different modes, with one ligand chelating and the other acting as a monodentate ligand. With CuX (X = Cl, Br), dppan formed a tetrameric complex when the ligand and metal were reacted in the ratio of 1:1. But reactions containing ligand and metal in the ratios of 1: 2 or 2: 1, resulted in the formation of a mixture of species in solution. Crystallization however, led to the isolation of the tetrameric complex. Variable temperature P-31{H-1} NMR spectra of the isolated tetramers did not show the presence of chelated structures in solution. Tetra-alkylammonium salts were added to solutions of various complexes of dppan and studied by P-31{H-1} NMR to probe the effect of anions on the stability of complexes in solution. The Cu-dppan complexes were robust and did not interconvert with other structures in solution unlike the bis(diphenylphosphino) isopropylamine complexes. (C) 2011 Elsevier B.V. All rights reserved.

Synthesis and structures of oxyanion encapsulated copper(I)-dppm complexes (dppm = bis(diphenylphosphino) methane)

Copper(I)-dppm complexes encapsulating the oxyanions ClO4-, NO3-, CH3C6H4CO2-, SO42-, and WO42- have been synthesized either by reduction of the corresponding Cu(II) salts and treatment with dppm, or by treating the complex [Cu-2(dppm)(2)(dmcn)(3)](BF4)(2) (1) (dmcn = dimethyl cyanamide) with the respective anion. The isolated complexes [Cu-2(dppm)(2)(dmcn)(2)(ClO4)] (ClO4) (2), [Cu-2(dppm)(2)(dmcn)(2)(NO3)] (NO3) (3), Cu-2(dppm)(2)(NO3)(2) (4), [Cu-2(dppm)(2)(CH3C6H4CO2)(2)]dmcn.2THF (5), Cu-2(dppm)(2)(SO4) (6), and [Cu-3(dppm)(3)(Cl)(WO4)] 0.5H(2)O (7) have been characterized by IR, H-1 and P-31{H-1} NMR, UV-vis, and emission spectroscopy. The solid-state molecular structure of complexes 1, 2, 4, and 7 were determined by single-crystal X-ray diffraction. Pertinent crystal data are as follows: for 1, monoclinic P2(1)/c, a = 11.376(10) Angstrom, b = 42.503(7) Angstrom, c = 13.530(6) Angstrom, beta = 108.08(2)degrees, V = 6219(3) Angstrom(3), Z = 4; for 2, monoclinic P2(1)/c, a = 21.600(3) Angstrom, b = 12.968(3) Angstrom, c = 23.050(3) Angstrom, beta = 115.97(2)degrees, V = 5804(17) Angstrom(3), Z = 4; for 4, triclinic , a = 10.560(4) Angstrom, b = 10.553(3) Angstrom, c = 22.698(3) Angstrom, alpha = 96.08(2)degrees, beta = 96.03(2)degrees, gamma = 108.31(2)degrees, V = 2362(12) Angstrom(3), Z = 2; and for 7, orthorhombic P2(1)2(1)2(1), a = 14.407(4) Angstrom, b = 20.573(7) Angstrom, c = 24.176(6) Angstrom, V = 7166(4) Angstrom(3), Z = 4. Analyses of the crystallographic and spectroscopic data of these complexes reveal the nature of interactions between the Cu-I-dppm core and oxyanion. The anchoring of the oxyanion to the Cu-n(dppm)(n) unit is primarily through coordination to the metal, but the noncovalent C-H ... O interactions between the methylene and phenyl protons of the dppm and oxygen atoms of the oxyanion play a significant role. The solid-state emission spectra for complexes 1-6 are very similar but different from 7. In CDCl3 solution, addition of ClO4- or NO3- (as their tetrabutylammonium salts) to 1 establishes a rapid equilibrium between the anion-complexed and uncomplexed forms. The association constant values for ClO4- and NO3- have been estimated from the P-31{H-1} NMR spectra.

Chemistry of dihydrogen complexes containing only phosphorus co-ligands

A series of new dicationic dihydrogen complexes of ruthenium of the type cis-[(dppm)(2)Ru(eta(2)-H-2)(L)][BF4](2) (dppm = Ph2PCH2PPh2; L = phosphite) have been prepared by protonating the precursor hydride complexes cis-[(dPPM)(2)Ru(H)(L)][BF4] using HBF4.Et2O. The precursor hydride complexes have been obtained from trans-[(dppm)(2)Ru(H)(L)][BF4][(L = phospfiite) via a rare acid-catalysed isomerization reaction in six coordinate species. The trans-[(dppm)(2)Ru(H)(L)][BF4] complexes (L = phosphine) upon protonation gave the isomerized derivatives, however, further addition of acid resulted in a five-coordinate species, [(dppm)(2)RuCl](+) presumably via an intermediate phosphine dihydrogen complex. The electronic as well as the steric properties of the co-ligands seem to strongly influence the structure-reactivity behaviour of this series of complexes.

Organometallic chemistry of diphosphazanes. Part 15. Half-sandwich cyclopentadienyl ruthenium complexes of achiral and chiral diphosphazanes

Reaction of [CpRu(PPh3)(2)Cl] (1) {Cp = eta(5)-(C5H5)} with X2PN(CHMe2) PYY' {X = Y = Y' = Ph (L-1); X = Y = Ph, Y' = OC6H4Me-4 (L-4); X = Y = Ph, Y' = OC6H3Me2- 3,5 (L-5); X = Y = Ph, Y' = N2C3HMe2 (L-6)} yields the cationic chelate complexes, [CpRu(eta(2)-(X2PN(CHMe2) PYY')) PPh3] Cl. On the other hand, the reaction of 1 with X2PN(CHMe2)PYY' {X = Ph, YY' = O2C6H4(L-3)} gives the complex, [CpRu(eta(1)-L-2)(2)PPh3] Cl. Both types of complexes are formed with X2PN(CHMe2) PYY' {X = Ph, YY' = O2C6H4 (L-3)}. The reaction of 1 with (R),(S)-(H12C20O2) PN(CHMe2) PPh2 (L-7) yields both cationic and neutral complexes, [CpRu{eta(2)-(L-7)} PPh3] Cl and [CpRu{eta(1)-(L-7)}(2)PPh3] Cl and [CpRu{eta(2)-(L-7)}Cl]. The reactions of optically pure diphosphazane, Ph2PN(*CHMePh) PPhY (Y = Ph (L-8); Y = N2C3HMe2-3,5 (L-9)) with 1 give the neutral and cationic ruthenium complexes, [CpRu{eta(2)-(Ph2PN(R) PPhY)} Cl] and [CpRu{eta(2)-(Ph2PN(R)PPhY)} PPh3] Cl. "Chiral-at-metal" ruthenium complexes of diphosphazanes have been synthesized with high diastereoselectivity. The absolute configuration of a novel ruthenium complex, (SCSPRRu)-[(eta(5)-C5H5) Ru*{eta(2)-(Ph2PN(*CHMePh)P*Ph( N2C3HMe2-3,5))} Cl] possessing three chiral centers, is established by X-ray crystallography. The reactions of [CpRu{eta(2)-(L-8)} Cl] with mono or diphosphanes in the presence of NH4PF6 yield the cationic complexes, [CpRu{eta(2)-(L-8)}{eta(1)-(P)}] PF6 {P = P(OMe)(3), PPh3, Ph2P(CH2)(n)PPh2 (n = 1 or 2)}.

Trans -> Cis isomerization of trans-[(dPPM)(2)Ru(H)(L)][BF4] (L = P(OR)(3)) Complexes: Preparation of cis-[(dppm)(2)Ru(eta(2)-H-2)(L)][BF4](2)

A series of new dicationic dihydrogen complexes of ruthenium of the type cis-[(dppm)(2)Ru(eta(2)-H-2)(L)][BF4](2) (dppm = Ph2PCH2PPh2; L = P(OMe)(3), P(OEt)(3), PF((OPr)-Pr-i)(2)) have been prepared by protonating the precursor hydride complexes cis-[(dppm)(2)Ru(H)(L)][BF4] (L = P(OMe)(3), P(OEt)(3), P((OPr)-Pr-i)(3)) using HBF4.Et2O. The cis-[(dppm)(2)Ru(H)(L)][BF4] complexes were obtained from the trans hydrides via an isomerization reaction that is acid-accelerated. This isomerization reaction gives mixtures of cis and trans hydride complexes, the ratios of which depend on the cone angles of the phosphite ligands: the greater the cone angle, the greater is the amount of the cis isomer. The eta(2)-H-2 ligand in the dihydrogen complexes is labile, and the loss of H-2 was found to be reversible. The protonation reactions of the starting hydrides with trans PMe3 or PMe2Ph yield mixtures of the cis and the trans hydride complexes; further addition of the acid, however, give trans-[(dPPM)(2)Ru(BF4)Cl]. The roles of the bite angles of the dppm ligand as well as the steric and the electronic properties of the monodentate phosphorus ligands in this series of complexes are discussed. X-ray crystal structures of trans-[(dppm)(2)Ru(H)(P(OMe)(3))][BF4], cis-[(dppm)(2)Ru-(H)(P(OMe)(3))][BF4], and cis-[(dppm)(2)Ru(H)(P((OPr)-Pr-i)(3))][BF4] complexes have been determined.

Synthesis, X-ray crystal structure, DNA binding, antioxidant and cytotoxicity studies of Ni(II) and Pd(II) thiosemicarbazone complexes

New complexes, [Ni(HL)(PPh3)]Cl (1), [Pd(L)(PPh3)](2), and [Pd(L)(AsPh3)](3), were synthesized from the reactions of 4-chloro-5-methyl-salicylaldehyde thiosemicarbazone [H2L] with [NiCl2(PPh3)(2)], [PdCl2(PPh3)(2)] and [PdCl2(AsPh3)(2)]. They were characterized by IR, electronic, H-1-NMR spectral data. Further, the structures of the complexes have been determined by single crystal X-ray diffraction. While the thiosemicarbazone coordinated as binegative tridentate (ONS) in complexes 2 and 3, it is coordinated as mono negative tridentate (ONS) in 1. The interactions of the new complexes with calf thymus DNA was examined by absorption and emission spectra, and viscosity measurements. Moreover, the antioxidant properties of the new complexes have also been tested against DPPH radical in which complex 1 exhibited better activity than that of the other two complexes 2 and 3. The in vitro cytotoxicity of complexes 1-3 against A549 and HepG2 cell lines was assayed, and the new complexes exhibited higher cytotoxic activity with lower IC50 values indicating their efficiency in killing the cancer cells even at very low concentrations.

The Nature of Bond Critical Points in Dinuclear Copper(I) Complexes

Closed-shell contacts between two copper(I) ions are expected to be repulsive. However, such contacts are quite frequent and are well documented. Crystallographic characterization of such contacts in unsupported and bridged multinuclear copper(I) complexes has repeatedly invited debates on the existence of cuprophilicity. Recent developments in the application of Baders theory of atoms-in-molecules (AIM) to systems in which weak hydrogen bonds are involved suggests that the copper(I)copper(I) contacts would benefit from a similar analysis. Thus the nature of electron-density distributions in copper(I) dimers that are unsupported, and those that are bridged, have been examined. A comparison of complexes that are dimers of symmetrical monomers and those that are dimers of two copper(I) monomers with different coordination spheres has also been made. AIM analysis shows that a bond critical point (BCP) between two Cu atoms is present in most cases. The nature of the BCP in terms of the electron density, ?, and its Laplacian is quite similar to the nature of critical points observed in hydrogen bonds in the same systems. The ? is inversely correlated to Cu?Cu distance. It is higher in asymmetrical systems than what is observed in corresponding symmetrical systems. By examining the ratio of the local electron potential-energy density (Vc) to the kinetic energy density (Gc), |Vc|/Gc at the critical point suggests that these interactions are not perfectly ionic but have some shared nature. Thus an analysis of critical points by using AIM theory points to the presence of an attractive metallophilic interaction similar to other well-documented weak interactions like hydrogen bonding.

Evaluation of DNA binding, antioxidant and cytotoxic activity of mononuclear Co(III) complexes of 2-oxo-1,2-dihydrobenzoh]quinoline-3-carbaldehyde thiosemicarbazones

Four new 2-oxo-1,2-dihydrobenzoh]quinoline-3-carbaldehyde N-substituted thiosemicarbazone ligands (H-2-LR, where R = H, Me, Et or Ph) and their corresponding new cobalt(III) complexes have been synthesized and characterized. The structures of the complexes 2 and 3 were determined by single crystal X-ray diffraction analysis. The interactions of the new complexes with DNA were investigated by absorption, emission and viscosity studies which indicated that the complexes bind to DNA via intercalation. Antioxidant studies of the new complexes showed that the significant antioxidant activity against DPPH radical. In addition, the in vitro cytotoxicity of complexes 1-4 against A549 cell line was assayed which showed higher cytotoxic activity with lower IC50 values indicating their efficiency in killing the cancer cells even at very low concentrations. (C) 2012 Elsevier Masson SAS. All rights reserved.

Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins

Abstract: Background: Most signalling and regulatory proteins participate in transient protein-protein interactions during biological processes. They usually serve as key regulators of various cellular processes and are often stable in both protein-bound and unbound forms. Availability of high-resolution structures of their unbound and bound forms provides an opportunity to understand the molecular mechanisms involved. In this work, we have addressed the question "What is the nature, extent, location and functional significance of structural changes which are associated with formation of protein-protein complexes?" Results: A database of 76 non-redundant sets of high resolution 3-D structures of protein-protein complexes, representing diverse functions, and corresponding unbound forms, has been used in this analysis. Structural changes associated with protein-protein complexation have been investigated using structural measures and Protein Blocks description. Our study highlights that significant structural rearrangement occurs on binding at the interface as well as at regions away from the interface to form a highly specific, stable and functional complex. Notably, predominantly unaltered interfaces interact mainly with interfaces undergoing substantial structural alterations, revealing the presence of at least one structural regulatory component in every complex. Interestingly, about one-half of the number of complexes, comprising largely of signalling proteins, show substantial localized structural change at surfaces away from the interface. Normal mode analysis and available information on functions on some of these complexes suggests that many of these changes are allosteric. This change is largely manifest in the proteins whose interfaces are altered upon binding, implicating structural change as the possible trigger of allosteric effect. Although large-scale studies of allostery induced by small-molecule effectors are available in literature, this is, to our knowledge, the first study indicating the prevalence of allostery induced by protein effectors. Conclusions: The enrichment of allosteric sites in signalling proteins, whose mutations commonly lead to diseases such as cancer, provides support for the usage of allosteric modulators in combating these diseases.

Highly Stable Hexacoordinated Nonoxidovanadium(IV) Complexes of Sterically Constrained Ligands: Syntheses, Structure, and Study of Antiproliferative and Insulin Mimetic Activity

Three highly stable, hexacoordinated nonoxidovanadium(IV), V-IV(L)(2), complexes (1-3) have been isolated and structurally characterized with tridentate aroylhydrazonates containing ONO donor atoms. All the complexes are stable in the open air in the solid state as well as in solution, a phenomenon rarely observed in nonoxidovanadium(IV) complexes. The complexes have good solubility in organic solvents, permitting electrochemical and various spectroscopic investigations. The existence of nonoxidovanadium(IV) complexes was confirmed by elemental analysis, ESI mass spectroscopy, cyclic voltammetry, EPR, and magnetic susceptibility measurements. X-ray crystallography showed the N3O3 donor set to define a trigonal prismatic geometry in each case. All the complexes show in vitro insulin mimetic activity against insulin responsive L6 myoblast cells, with complex 3 being the most potent, which is comparable to insulin at the complex concentration of 4 mu M, while the others have moderate insulin mimetic activity. In addition, the in vitro antiproliferative activity of complexes 1-3 against the He La cell line was assayed. The cytotoxicity of the complexes is affected by the various functional groups attached to the bezoylhydrazone derivative and 2 showed considerable antiproliferative activity compared to the most commonly used chemotherapeutic drugs.

Photocytotoxic luminescent lanthanide complexes of DTPA-bisamide using quinoline as photosensitizer

Lanthanide complexes Ln(DTPAAQ)(DMF)] (1-3) (Ln - Pr (1), Eu (2), Tb (3), H(3)DTPAAQ - N, N `'-bis(3-amidoquinolyl) diethylenetriamine-N, N', N `'-triacetic acid, DMF - N, N-dimethylformamide) were studied for their structures, photophysical properties, DNA and protein binding, DNA photocleavage, photocytotoxicity and cellular internalization. The crystal structures of complexes Ln(DTPAAQ)(DMF)] (1-3) display a discrete mononuclear nine-coordinate {LnN(3)O(6)} tricapped-trigonal prism (TTP) coordination geometry. The europium and terbium complexes show strong luminescence properties in the visible region having a long luminescence lifetime (tau = 0.51-0.64 ms). The conjugated 3-aminoquinoline moieties act as efficient light harvesting antennae, which upon photoexcitation transfer their energy to Eu(III) or Tb(III) for their characteristic D-5(0) -> F-7(J) or D-5(4) -> F-7(J) f-f transitions respectively. The complexes display efficient binding affinity to DNA (K-b = 3.4 x 10(4) - 9.8 x 10(4) M-1) and BSA (KBSA = 3.03 x 10(4) - 6.57 x 10(4) M-1). Europium and terbium complexes give enhanced luminescence upon interacting with CT-DNA suggesting possible luminescence-based sensing applications for these complexes. Complexes 1-3 show moderate cleavage of supercoiled (SC) DNA to its nicked circular (NC) form on exposure to UV-A light of 312 nm involving formation of singlet oxygen (O-1(2)) and hydroxyl radicals (cOH) in type-II and photoredox pathways. Eu(III) and Tb(III) complexes exhibit remarkable photocytotoxicity with human cervical cancer cell line (HeLa) (IC50 = 20.7-28.5 mM) while remaining essentially noncytotoxic up to 150 mM in the dark. Complexes are nontoxic in nature thus suitable for designing cellular imaging agents. Fluorescence microscopy data reveal primarily cytosolic localization of the Eu(III) and Tb(III) complexes in HeLa cells.

Proton magnetic resonance studies of ribonucleic acid complexes. I. Complexes of biological bases and oligonucleotides with RNA. II. Template recognition and the degeneracy of the genetic code

Part I. Complexes of Biological Bases and Oligonucleotides with RNA

The physical nature of complexes of several biological bases and oligonucleotides with single-stranded ribonucleic acids have been studied by high resolution proton magnetic resonance spectroscopy. The importance of various forces in the stabilization of these complexes is also discussed.

Previous work has shown that purine forms an intercalated complex with single-stranded nucleic acids. This complex formation led to severe and stereospecific broadening of the purine resonances. From the field dependence of the linewidths, T₁ measurements of the purine protons and nuclear Overhauser enhancement experiments, the mechanism for the line broadening was ascertained to be dipole-dipole interactions between the purine protons and the ribose protons of the nucleic acid.

The interactions of ethidium bromide (EB) with several RNA residues have been studied. EB forms vertically stacked aggregates with itself as well as with uridine, 3'-uridine monophosphate and 5'-uridine monophosphate and forms an intercalated complex with uridylyl (3' → 5') uridine and polyuridylic acid (poly U). The geometry of EB in the intercalated complex has also been determined.

The effect of chain length of oligo-A-nucleotides on their mode of interaction with poly U in D₂0 at neutral pD have also been studied. Below room temperatures, ApA and ApApA form a rigid triple-stranded complex involving a stoichiometry of one adenine to two uracil bases, presumably via specific adenine-uracil base pairing and cooperative base stacking of the adenine bases. While no evidence was obtained for the interaction of ApA with poly U above room temperature, ApApA exhibited complex formation of a 1:1 nature with poly U by forming Watson-Crick base pairs. The thermodynamics of these systems are discussed.

Part II. Template Recognition and the Degeneracy of the Genetic Code

The interaction of ApApG and poly U was studied as a model system for the codon-anticodon interaction of tRNA and mRNA in vivo. ApApG was shown to interact with poly U below ~20°C. The interaction was of a 1:1 nature which exhibited the Hoogsteen bonding scheme. The three bases of ApApG are in an anti conformation and the guanosine base appears to be in the lactim tautomeric form in the complex.

Due to the inadequacies of previous models for the degeneracy of the genetic code in explaining the observed interactions of ApApG with poly U, the "tautomeric doublet" model is proposed as a possible explanation of the degenerate interactions of tRNA with mRNA during protein synthesis in vivo.