Multiple binding modes of the camptothecin family to DNA oligomers

The binding constants of camptothecin, topotecan and its lactone ring-opened carboxylate derivative to DNA octamers were measured by UV and NMR spectroscopy. The self-association of topotecan (TPT) was also measured. The carboxylate form of TPT binds in the same way as the lactone, but more weakly. Titration of TPT into d(GCGATCGC)2 shows a preferred location stacked onto the terminal G1 base. However, the intermolecular NOEs cannot be reconciled with a single conformation of the complex, and suggest a model of a limited number of conformations in fast exchange. MD calculations on four pairs of starting structures with TPT stacked onto the G1-C8 base pair in different orientations were therefore performed. The use of selected experimental "docking" restraints yielded ten MD trajectories covering a wide conformational space. From a combination of calculated free energies, NOEs and chemical shifts, some of the structures produced could be eliminated, and it is concluded that the data are consistent with two major families of conformations in fast exchange. One of these is the conformation found in a crystal of a TPT/DNA/topoisomerase I ternary complex [Proc. Natl. Acad. Sci. USA 2002, 99, 15 387-15 392].     

Investigation of the electrokinetic properties of paraffin suspension. 2. In cationic and anionic surfactant solutions

Electrical phenomena at nonionogenic hydrophobic surfaces (solid or liquid) in water, electrolyte, and/or surfactant solutions still attract research. In part 1 of this paper we described the electrokinetic behavior of paraffin wax suspension in water and electrolyte solutions (NaCl or LaCl3). On the basis of the latest data of water structure near hydrophobic surfaces it was concluded that immobilized water dipoles at the interface can play an essential role in the zeta potential formation. In this paper were investigated the zeta potentials of paraffin wax in cationic surfactants cetyltrimethylammonium bromide, C16H33(CH3)3NBr, and octadecyltrimethylammonium chloride, C18H37(CH3)3NCl, and anionic surfactant sodium dodecyl sulfate, C12H25SO4Na. Also changes in wettability of the paraffin surface due to the surfactant's adsorption were studied via wetting contact angle measurements and calculation of the surface free energy. It was concluded that at a low surfactant concentration (10(-6) M) the water dipole structure still contributes to the zeta potential, but at a higher one the zeta potential is determined by the surfactant molecules' adsorption. A special role of OH- ions is also clearly seen. Moreover, a functional relationship was found between the surface free energy of the surfactant-covered paraffin surface and the zeta potential.     

Electron localization function and electron localizability indicator applied to study the bonding in the peroxynitrous acid HOONO

The ground‐state electronic structure of peroxynitrous acid (HOONO) and its singlet biradicaloid form (HO ··· ONO) have been studied using topological analysis of the electron localization function (ELF), together with the electron localizability indicator (ELI‐D), at the DFT (B3LYP, M05, M052X, and M06), CCSD, and CASSCF levels. Three isomers of HOONO (cis‐cis, cis‐perp, and trans‐perp) have been considered. The results show that from all functionals applied, only B3LYP yields the correct geometrical structure. The ELF and ELI‐D‐topology of the O? O and central N? O bonds strongly depends on the wave function used for analysis. Calculations carried out at CAS (14,12)/aug‐cc‐pVTZ//CCSD(T)/aug‐cc‐pVTZ level reveal two bonds of the charge‐shift type: a protocovalent N? O bond with a basin population of 0.82–1.08e, and a more electron depleted O? O bond with a population of 0.66–0.71e. The most favorable dissociation channel (HOONO → HO + ONO) corresponds to breaking of the most electron‐deficient bond (O? O). In the case of cis‐ and trans‐HO ··· ONO, the ELF, ELI‐D, and electron density fields results demonstrate a closed‐shell O ··· O interaction. The α‐spin electrons are found mainly (0.64e) in the lone pairs of oxygen V_{i = 1,2} (O) from the OH group. The β‐spin electrons are delocalized over the ONO group, with the largest concentration (0.34e) on the lone pair of nitrogen V(N). © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Immobilization and electrochemical redox behavior of cytochrome c on fullerene film-modified electrodes

Two different fullerene film-modified electrodes were prepared and used for surface immobilization and electrochemical property investigation of horse heart cytochrome c (cyt c). Both a pristine fullerene film and fullerene-palladium (C(60)-Pd) polymer film-modified platinum, glassy carbon and indium-tin-oxide (ITO) electrodes were used. The immobilized cyt c was characterized by piezoelectric microgravimetry at a quartz crystal microbalance (QCM), UV-visible absorption, and X-ray photoelectron spectroscopy (XPS), as well as cyclic voltammetry (CV) techniques. The UV-visible spectral studies revealed a small blue shift of both the Soret and Q band of the heme moiety of cyt c, immobilized on the C(60)-Pd polymer film-modified ITO electrode, as compared to the bands of cyt c in solution suggesting that molecules of cyt c are densely packed onto the surface of the modified electrode. The CV studies revealed a quasi-reversible electrode behavior of the heme moiety indicating the occurrence of kinetically hindered electron transfer. A good agreement was found between the values of cyt c electrode surface coverage determined by piezoelectric microgravimetry and cyclic voltammetry. For piezoelectric microgravimetry, these values ranged from 0.5 x 10(-10) to 2.5 x 10(-10) mol cm(-2), depending upon the amount of cyt c present in solution and the time allowed for immobilization, which compared with a value of 3.6+/-0.4 x 10(-10) mol cm(-2) determined by CV. The possible mechanisms of cyt c immobilization on the C(60) film and C(60)-Pd film-modified electrodes are also discussed.     

meso-Alkylidene (m-benzi)pentaphyrin: a modified pentaphyrin bearing exocyclic double bonds at meso-positions

meso-Alkylidene (m-benzi)pentaphyrin containing exocyclic C=C double bonds at two meso-positions is synthesized and fully characterized for the first time. The single crystal X-ray crystallographic analysis shows a concave conformation with two pyrrole rings inverted. The first protonation occurs exclusively at core nitrogen. The synthesized compound displays concentration dependent chromogenic responses for fluoride anion in organic solvent.     

Cocrystals of 2,3,5,6‐tetrafluorobenzene‐1,4‐diol with diaza aromatic compounds

2,3,5,6‐Tetrafluorobenzene‐1,4‐diol easily forms cocrystals with heteroaromatic bases containing the pyrazine unit. In the 1:1 complexes with pyrazine, C₆H₂F₄O₂·C₄H₄N₂, (I), and quinoxaline, C₆H₂F₄O₂·C₈H₆N₂, (II), the crystal components are linked via O—H...N hydrogen bonds into one‐dimensional chains. With the largest base, phenazine, the 1:2 benzenediol–phenazine complex, C₆H₂F₄O₂·2C₁₂H₈N₂, (III), was obtained, with the molecules linked via O—H...N interactions into a discrete heterotrimer. In all three cocrystals, the two types of molecules are organized into layers via softer C—H...O and C—H...F interactions and π–π stacking interactions, with stronger hydrogen bonds linking molecules of adjacent layers. In (II) and (III), molecules are arranged into heterostacks, whereas in (I) separate stacks are formed by the heterocyclic base and the benzenediol molecule.     

Pyrolytic and catalytic conversion of rape oil into aromatic and aliphatic fractions in a fixed bed reactor on Al2O3 and Al2O3/B2O3 catalysts

In the, at present, unstable fuel market, much attention is devoted to alternative technologies for fuel production and development of alternative products of the petrochemical industry. One of the prospective sources of fuel and alternative petrochemical products is biomass, and the use of oil plants is one of the possibilities. This paper reports on a possible conversion of rapeseed oil produced in Poland into intermediate hydrocarbon fractions by pyrolysis combined with parallel catalytic conversion. The products were analysed by gas chromatography coupled with a mass detector. The process was performed in a fixed-bed reactor and was monitored by FTIR and ¹H NMR. Depending on the catalysts applied, the products contained: water, carbon oxides, hydrogen, aliphatic or aromatic hydrocarbons accompanied by some amount of C2-C5 hydrocarbons formed during the cracking process. Presented at the 35th International Conference of the Slovak Society of Chemical Engineering, Tatranské Matliare, 26–30 May 2008.     

Heterologous Production of Fungal Maleidrides Reveals the Cryptic Cyclization Involved in their Biosynthesis

Fungal maleidrides are an important family of bioactive secondary metabolites that consist of 7, 8, or 9‐membered carbocycles with one or two fused maleic anhydride moieties. The biosynthesis of byssochlamic acid (a nonadride) and agnestadride A (a heptadride) was investigated through gene disruption and heterologous expression experiments. The results reveal that the precursors for cyclization are formed by an iterative highly reducing fungal polyketide synthase supported by a hydrolase, together with two citrate‐processing enzymes. The enigmatic ring formation is catalyzed by two proteins with homology to ketosteroid isomerases, and assisted by two proteins with homology to phosphatidylethanolamine‐binding proteins.