Mode of action of antitumour antibiotics-III: Modulation of permeability of nuclear membrane in the presence of the antibiotics

The binding characteristics of the antibiotics to nuclei and their effect on the permeability of nuclear membrane with respect to histones and ribonucleic acids have been investigated. The binding constant for chromomycin A3 was found to be 1.4 × 104M?1 and number of binding sites was equal to 3.48 ± 1.08 × 1012 molecules/nuclei. The antibiotic chromomycin A3 enhanced the uptake of lysine-rich histone, actinomycin D decreased the uptake and ethidium bromide had no effect. Chromomycin A3 also enhanced the release of acid insoluble fraction containing RNA from the nuclei, actinomycin D and ethidium bromide inhibited the release of acid insoluble fraction containing RNA. The relevance of this finding to the role of nuclear envelope in understanding the mechanism of action of the antibiotic has been discussed.

Use of 2-pyrimidineamidoxime to generate polynuclear homo-/heterometallic assemblies: synthesis, crystal structures and magnetic study with theoretical investigations on the exchange mechanism

Three new transition metal complexes using 2-pyrimidineamidoxime (pmadH(2)) as multidentate chelating and/or bridging ligand have been synthesized and characterized. The ligand pmadH(2) has two potential bridging functional groups mu-O and mu-(N-O)] and consequently shows several coordination modes. While a polymeric 1D Cu-II complex Cu(pmadH(2))(2)(NO3)](NO3) (1) was obtained upon treatment of Cu(NO3)(2)center dot 3H(2)O with pmadH(2) at room temperature in the absence of base, a high temperature reaction in the presence of base yielded a tetranuclear Cu-II-complex Cu-4(pmad)(2)(pmadH)(2)(NO3)](NO3)(H2O) (2). One of the Cu-II centers is in a square pyramidal environment while the other three are in a square planar geometry. Reaction of the same ligand with an equimolar mixture of both Cu(NO3)(2)center dot 3H(2)O and NiCl2 center dot 6H(2)O yielded a tetranuclear heterometallic (Cu2Ni2II)-Ni-II complex Cu2Ni2(pmad)(2)(pmadH)(2)Cl-2]center dot H2O (3) containing both square planar (Ni-II) and square pyramidal (Cu-II) metal centers. Complexes 1-3 represent the first examples of polynuclear metal complexes of 2-pyrimidineamidoxime. The analysis of variable temperature magnetic susceptibility data of 2 reveals that both ferromagnetic and antiferromagnetic interactions exist in this complex (J(1) = +10.7 cm(-1) and J(2) = -2.7 cm(-1) with g = 2.1) leading to a resultant ferromagnetic behavior. Complex 3 shows expected antiferromagnetic interaction between two Cu-II centers through -N-O- bridging pathway with J(1) = -3.4 cm(-1) and g = 2.08. DFT calculations have been used to corroborate the magnetic results.

Computer modelling studies on the mechanism of action of ribonuclease T1

The mechanism of action of ribonuclease (RNase) T1 is still a matter of considerable debate as the results of x-ray, 2-D nmr and site-directed mutagenesis studies disagree regarding the role of the catalytically important residues. Hence computer modelling studies were carried out by energy minimisation of the complexes of RNase T1 and some of its mutants (His40Ala, His40Lys, and Glu58Ala) with the substrate guanyl cytosine (GpC), and of native RNase T1 with the reaction intermediate guanosine 2',3'-cyclic phosphate (G greater than p). The puckering of the guanosine ribose moiety in the minimum energy conformer of the RNase T1-GpC (substrate) complex was found to be O4'-endo and not C3'-endo as in the RNase T1-3'-guanylic acid (inhibitor/product) complex. A possible scheme for the mechanism of action of RNase T1 has been proposed on the basis of the arrangement of the catalytically important amino acid residues His40, Glu58, Arg77, and His92 around the guanosine ribose and the phosphate moiety in the RNase T1-GpC and RNase T1-G greater than p complexes. In this scheme, Glu58 serves as the general base group and His92 as the general acid group in the transphosphorylation step. His40 may be essential for stabilising the negatively charged phosphate moiety in the enzyme-transition state complex.

Unfolding of Plasmodium falciparum triosephosphate isomerase in urea and guanidinium chloride solutions. Evidence for a novel disulfide exchange reaction in a covalently crosslinked mutant

The conformational stability of Plasmodium falciparum triosephosphate isomerase (TIMWT) enzyme has been investigated in urea and guanidinium chloride (GdmCl) solutions using circular dichroism, fluorescence, and size-exclusion chromatography. The dimeric enzyme is remarkably stable in urea solutions. It retains considerable secondary, tertiary, and quaternary structure even in 8 M urea. In contrast, the unfolding transition is complete by 2.4 M GdmCl. Although the secondary as well as the tertiary interactions melt before the perturbation of the quaternary structure, these studies imply that the dissociation of the dimer into monomers ultimately leads to the collapse of the structure, suggesting that the interfacial interactions play a major role in determining multimeric protein stability. The Cm(urea)/Cm(GdmCl) ratio (where Cm is the concentration of the denaturant required at the transition midpoint) is unusually high for triosephosphate isomerase as compared to other monomeric and dimeric proteins. A disulfide cross-linked mutant protein (Y74C) engineered to form two disulfide cross-links across the interface (13-74‘) and (13‘-74) is dramatically destablized in urea. The unfolding transition is complete by 6 M urea and involves a novel mechanism of dimer dissociation through intramolecular thiol−disulfide exchange.

One pot synthesis of polycyclic oxygen aromatics. Part III mechanism of formation

Reaction of 6-Image -butyl-1-bromomethyl-2-(2-tetrahydropyranyloxy)-naphthalene2c with tetrachlorocatechol (TCC) in acetone in presence of K2CO3 gave diastereomers 6c and 7c. A mechanism (Scheme-1) invoking the base induced cleavage of the pyranyl ether 2 to 1,2-naphthoquinone-1-methide 8 as the first step has been postulated. The cleavage of the pyranyl ether linkage in 2 to give dimers 4 and 5 of 1,2-naphthoquinone-1-methide has been demonstrated with different bases. 1,2-Naphthoquinone-1-methide 8, thus generated, undergoes Michael addition with TCC followed by elimination of chloride ions to give a diketone, which further undergoes aldolisation with acetone to give diastereomers 6 and 7. Michael reaction of 8, generated Image from pyranyl ethers 2a-c, with tetrabromocatechol (TBC) under similar-reaction conditions gave the expected monobromo compounds 6h, 6i, 6k, 7n, 7n and 7q. The last step in the proposed mechanism, Image ., aldolisation has also been demonstrated using different ketonic solvents. Thus, reaction of 2a-c with TCC/TBC in diethyl ketone/methyl ethyl ketone under similar reaction conditions gave the expected compounds 6 and 7.

Rearrangements in the cerium(IV) and manganese(III) oxidations of substituted naphthalenes and the nih shift mechanism

Ceric ammonium sulphate oxidation of 1- and 1,4- disubstituted naphthalenes gives 2- and/or 2,3- disubstituted 1,4- naphthoquinones through migration of substituents (D, Br, Ph). Similar rearrangements are also observed in the manganese(III) oxidation and also in the anodic oxidation of these substrates. The results are consistent with the proposal that these oxidations go through the formation of radical cation followed by reaction with H2O and further oxidation of the radical to the carbocationic intermediate on the way to the corresponding 1,4-naphthoquinone. Oxidation of 1,4-diphenylnaphthalene gives 2,3-diphenyl-1,4-naphthoquinone or 4-hydroxy- 2,4- diphenyl - 1(4)R - naphthalenone. The results are in accordance with the conclusion that such rearrangements do not require prior formation of arene oxide intermediates, originally proposed for the NM shift mechanism.

Sonochemical reaction engineering

Ultrasound has been widely used by chemists to enhance yields as well as rates of homogeneous as well as heterogeneous chemical reactions. The effect of ultrasound on the course of chemical reactions is mediated through cavitation bubbles it generates. High temperatures and pressures are attained inside the cavitating bubbles when they collapse. The extreme conditions so generated lead to the formation of reactive intermediates, e.g., free radiacls, inside the bubbles, which cause chemical reactions to occur when they enter the surrounding liquid. This is the mechanism through which ultrasound influences the path of homogeneous reactions. The cavitation bubbles collapse asymmetrically in the vicinity of solids, e.g., catalyst particles. Asymmetric collapse lead to formation of high speed microjets. The microjets can enhance transport rates, the increase surface area through pitting as well as particle fragmentation through collisions. Both can alter the rates of heterogeneous reaction rates. It however appears that these effects do not exhaust the scope of the influence of ultrasound on heterogeneous reactions. Modelling and quantitative prediction of the effect of ultrasound on chemical reactions is however at a stage of infancy as the phenomena are complex. Only a few examples of modelling exist in literature. Apart from this, reactor design and scaleup pose significant problems. Thus sonochemical reaction engineering offers large scope for research and development efforts.

Kinetics and mechanism for dye degradation with ionic Pd-substituted ceria

The degradation of the dye, Orange G, was carried out in the presence of H2O2 and Pd-substituted/impregnated CeO2. The effects of pH, initial dye concentration, initial H2O2 concentration, temperature, catalyst loading, and Pd content in the catalyst on the degradation of the dye were investigated. Eight to twelve percent degradation of the dye was obtained in 1 h when the reaction was carried out in the presence of CeO2 or H2O2 or Pd-substituted/impregnated CeO2 while 17% and 97% degradation was obtained when H2O2 was used with Pd-impregnated CeO2 and Pd-substituted CeO2, respectively. This difference clearly indicated that the ionic substitution of Pd played a key role in the degradation of the dye. A mechanism for the reaction was proposed based upon the catalyst structure and the electron transfer processes that take place in the metal ion substituted system in a reducible oxide. The reaction was found to follow first order kinetics and the influence of all the parameters on the degradation kinetics was compared using the rate constants. (c) 2011 Elsevier B.V. All rights reserved.

The intercalation reaction of pyridine with manganese thiophosphate, MnPS3

The intercalation of pyridine in the layered manganese thiophosphate, MnPS3, has been examined in detail by a variety of techniques. The reaction is interesting since none of the anticipated changes in optical and electrical properties associated with intercalation of electron donating molecules is observed. The only notable change in the properties of the host lattice is in the nature of the low-temperature magnetic ordering; while MnPS3 orders antiferromagnetically below 78 K, the intercalated compound shows weak ferromagnetism probably due to a canted spin structure. Vibrational spectra clearly show that the intercalated species are pyridinium ions solvated by neutral pyridine molecules. The corresponding reduced sites of the host lattice, however, were never observed. The molecules in the solvation shell are exchangeable. Although the reaction appears to be topotactic and reversible, from XRD, a more detailed analysis of the products of deintercalation reveal that it is not so. The intercalation proceeds by an ion exchange/intercalation mechanism wherein the intercalated species are pyridinium ions solvated by neutral molecules with charge neutrality being preserved not by electron transfer but by a loss of Mn2+ ions from the lattice. The experimental evidence leading to this conclusion is discussed and it is shown that this model can account satisfactorily for the observed changes (or lack of it) in the optical, electrical, vibrational, and magnetic properties.

Isomerisation of 4-aryl-4-methylhex-5-en-2-ones to 5-aryl-4-methylhex-5-en-2-ones by an intramolecular ene-retro ene reaction sequence

Acid-catalysed thermal rearrangement of 4-aryl-4-methylhex-5-en-2-ones (products of the Claisen rearrangement of beta-methylcinnamyl alcohols and 2-methoxypropene) to isomeric 5-aryl-4-methylhex-5-en-2-ones via an intramolecular ene reaction of the enol tautomer followed by a retro ene reaction of the resultant acetylcyclopropane is described. Formation of the known diketone 13 via the ozonolysis of the rearrangement product 10, confirmed the structures of the rearranged enones, whereas formation of the enone 15 containing an extra methyl group on the styrene double bond confirmed the proposed mechanism. Finally, the rearrangement has been extended to the formal synthesis of beta-cuparenone 20 via the enones 22 and 23.

Structure, function, and mechanism of HhaI DNA methyltransferases

A vast amount of literature has accumulated on the characterization of DNA methyltransferases. The HhaI DNA methyltransferase, a C5-cytosine methyltransferase, has been the subject of investigation for the last 2 decades. Biochemical and kinetic characterization have led to an understanding of the catalytic and kinetic mechanism of the methyltransfer reaction. The HhaI methyltransferase has also been subjected to extensive structural analysis, with the availability of 12 structures with or without a cofactor and a variety of DNA substrates. The mechanism of base flipping, first described for the HhaI methyltransferase, is conserved among all DNA methyltransferases and is also found to occur in numerous DNA repair enzymes. Studies with other methyltransferase reveal a significant structural and functional similarity among different types of methyltransferases. This review aims to summarize the available information on the HhaI DNA methyltransferase.

Carbothermal reduction and nitridation reaction of SiOx and preoxidized SiOx: Formation of α-Si3N4 fibers

The chemical composition of amorphous SiOx has been analyzed by oxidation studies and is found to be SiO1.7. SiO1.7 appears to be a monophasic amorphous material on the basis of 29Si nuclear magnetic resonance, high resolution electron microscopy, and comparative behavior of a physical mixture of Si and SiO2. Carbothermal reduction and nitridation reactions have been carried out on amorphous SiO1.7 and on amorphous SiO2 obtained from oxidation of SiO1.7. At 1623 K reactions of SiO1.7 lead exclusively to the formation of Si2N2O, while those of SiO2 lead exclusively to the formation of Si3N4. Formation of copious fibers of α-Si3N4 was observed in the latter reaction. It is suggested that the partial pressure of SiO in equilibrium with reduced SiO1.7 and SiO2 during the reaction is the crucial factor that determines the chemistry of the products. The differences in the structures of SiO2 and SiO1.7 have been considered to be the origin of the differences in the SiO partial pressures of the reduction products formed prior to nitridation. The effect of the ratios, C:SiO1.7 and C:SiO2, in the reaction mixture as well as the effect of the temperature on the course of the reactions have also been investigated.

Production of niobium powder by electronically mediated reaction (EMR) using calcium as a reductant

Explored in this study is an electronically mediated reaction (EMR) route for the production of niobium powder using calcium as a reductant for niobium oxide (Nb2O5). Feed material, Nb2O5, and reductant calcium alloy containing aluminum and nickel were charged into electronically isolated locations in a molten salt (e.g. CaCl2) at 1173 K. The current flow through an external path between the feed and reductant locations was monitored. A current approximately 0.4 A was measured during the reaction in the external circuit connecting cathode and anode location. Niobium powder with low aluminum and nickel content was obtained although liquid Ca–Al–Ni alloy was used as the reductant. This clearly demonstrates that niobium metal powder can be produced by an electronically mediated reaction (EMR), without direct physical contact between feed (Nb2O5) and reductant (calcium). Mechanism of calciothermic reduction of Nb2O5 in the molten salt is discussed using an isothermal chemical potential diagram.

Differential Reaction Kinetics, Cleavage Complex Formation, and Nonamer Binding Domain Dependence Dictate the Structure-Specific and Sequence-Specific Nuclease Activity of RAGs

During V(D)J recombination, RAG (recombination-activating gene) complex cleaves DNA based on sequence specificity. Besides its physiological function, RAG has been shown to act as a structure-specific nuclease. Recently, we showed that the presence of cytosine within the single-stranded region of heteroduplex DNA is important when RAGs cleave on DNA structures. In the present study, we report that heteroduplex DNA containing a bubble region can be cleaved efficiently when present along with a recombination signal sequence (RSS) in cis or trans configuration. The sequence of the bubble region influences RAG cleavage at RSS when present in cis. We also find that the kinetics of RAG cleavage differs between RSS and bubble, wherein RSS cleavage reaches maximum efficiency faster than bubble cleavage. In addition, unlike RSS, RAG cleavage at bubbles does not lead to cleavage complex formation. Finally, we show that the ``nonamer binding region,'' which regulates RAG cleavage on RSS, is not important during RAG activity in non-B DNA structures. Therefore, in the current study, we identify the possible mechanism by which RAG cleavage is regulated when it acts as a structure-specific nuclease. (C) 2011 Elsevier Ltd. All rights reserved.

Structural characterisation of reaction zone for friction stir welded aluminium-stainless steel joint

In the present investigation, commercially pure Al has been joined with 304 stainless steel (SS) by friction stir welding. The assembly finds widespread application in the field of cryogenics, nuclear, structural industries and domestic appliances. Microstructural characterisation was carried out using scanning and transmission electron microscopes. It has been found that diffusion of Fe, Cr and Ni is substantial within Al; however, diffusion of Al within 304SS is limited. Owing to interdiffusion of chemical species across the bondline, discrete islands of Fe3Al intermetallic form within the reaction zone. The rubbing action of tool over the butting edge of 304SS removed fine particles from 304SS, which were embedded in the stirring zone of Al matrix. Subsequently, austenite underwent phase transformation to ferrite due to large strain within this grain. Fracture path mainly moves through stirring zone of Al alloy under tensile loading; however, in some places, presence of Fe3Al compound has been also found.