The conformational dynamics of humic polyanions in model organic and organo-mineral aggregates

Molecular mechanics calculations and simulated annealing were applied to model humic polyanions originating from lignin. The dynamic behavior of such oxidized lignins in model soil organic complexes, such as an oxidized lignin-carbohydrate complex (LCC) and humic (oxidized LCC)-clay aggregates, was analyzed. Neither ionization nor hydrogen bonding bring significant changes in the conformational properties of oxidized lignin and LCC. Oxidized lignin and LCC oligomers (humic substances in soil) bind to the mineral surfaces, a process that was exemplified in computational experiments on complexes with muscovite. Upon ionization, a lignin-derived oligomer develops strong attractive organo-mineral interactions through cation bridges. Without metal cations, electrostatic repulsion between negatively charged anions and the oxygen-mineral surface prevails, and the two parts of the organo-mineral complex drift apart. This tendency is typical of an oxidized lignin oligomer but not of a topological oxidized LCC.     

The formation of methyl cations from acetone and 1,2-epoxypropane molecular cations

The technique of photoelectron—photoion coincidence spectroscopy is used to determine the breakdown curves of CH⁺₃ from acetone and 1,2-epoxypropane. The experimental appearance energies of CH⁺₃ from both isomers are found to be identical with the calculated thresholds for the formation of CH⁺₃ + CH₃ + CO, i.e. the secondary fragmentation of C₃H₆O⁺.     

Fluorescence anisotropy and FRET studies of G-quadruplex formation in presence of different cations

Results of the steady-state fluorescence, anisotropy and FRET measurements of G-quadruplex formation in the presence of selected cations (Li(+), Na(+), K(+), NEt(4)(+) and Mg(2+)) are reported. Three different fluorescent oligonucleotides with human telomeric sequence labeled with fluorescein (FAM) and tetramethylrhodamine (TAMRA) were investigated: a dual-labeled 21-mer denoted as PSO (Potassium Sensing Oligonucleotide) and two 5'- and 3'- single-labeled probes, FAM-21 and 21-TAMRA, respectively. The fluorescence signal of FAM-21 increased significantly for all systems and the fluorescence enhancement was comparable in magnitude for monovalent cations but it was more pronounced for Mg(2+) cation. This phenomenon was attributed to the protolytic equilibria of FAM affected by the variation in ionic strength. On the other hand, fluorescence of TAMRA was enhanced selectively by Na(I) cation that was explained by the dequenching of TAMRA emission originated from the peculiarity of the basket-type structure of Na(I)-quadruplex. Anisotropy of FAM-21 (but not 21-TAMRA) appeared to be sensitive to the G-quadruplex formation, showing significant increase with an increase in cation concentration and indicating some restrictions in rotational depolarization of FAM. FRET experiments revealed that all tested cations caused quenching of FAM fluorescence in PSO, but only Na(+) and K(+) ions produced sensitized emission of TAMRA acceptor. Higher FRET efficiency observed in the presence of sodium ion was attributed to the specific spectral factor and steric interactions in the basket-type Na(I)-quadruplex.     

The formation and structure of radical cations

ions generated from a number of different presursors have been studied by high kinetie energy ion—molecule reations. It has been shown that at least four distinct stable species oeeur, of which acetonitrile and methyl isoeyanide retain their original structure. With imidazole or pyrazole as precursors, a mixture of open thain radical cations, not identical to the above species and probably interconvertible via the 1H-azirine radocal cation, is formed. From butrynitrile, pyrrole, crotonitrile, allyl interconvertible via the and cyanocyopropane a fourth species, probably the vinylidenimine ion, is formed.     

Reaction of triarylphosphine radical cations generated from photoinduced electron transfer in the presence of oxygen

[reaction: see text] The 9,10-dicyanoanthracene (DCA)-sensitized photoreaction of triarylphosphines (1) was carried out in acetonitrile under aerobic conditions. Phosphine 1 was oxidized to the corresponding phosphine oxide with no appreciable side reactions. Product analysis and laser flash photolysis experiments suggest that the radical cation of 1 formed by the electron transfer from 1 to DCA in the singlet excited state ((1)DCA) reacts with O(2) to eventually afford the phosphine oxide.     

ATP and AMP formation from ADP in the presence of cyclodextrin

A new nonenzymatic formation of ATP from ADP was observed in the presence of cyclodextrin in a phosphate buffer of pH 7.00 at 37.0°C under at mospheric conditions. Time conversion curves were obtained in the presence of -cyclodextrin and heptakis-(2,6-dimethyl)--cyclodextrin. The effect of adding -cyclodextrin, MgCl₂, phosphate buffer and creatine was examined kinetically as well as the effect of cyclohexanol as an inhibtor.     

Effect of hydrophilic walls on the hydration of sodium cations in planar nanopores

A computer simulation of the structure of Na⁺ ion hydration shells with sizes in the range of 1 to 100 molecules in a planar model nanopore 0.7 nm wide with structureless hydrophilic walls is performed using the Monte Carlo method at a temperature of 298 K. A detailed model of many-body intermolecular interactions, calibrated with reference to experimental data on the free energy and enthalpy of reactions after gaseous water molecules are added to a hydration shell, is used. It is found that perturbations produced by hydrophilic walls cause the hydration shell to decay into two components that differ in their spatial arrangement and molecular orientational order.     

Ion-chromatographic separation of metal cations in the presence of a-hydroxyisobutyric acid

Separations of metal cations on a column packed with the strongly acidic cation exchanger Separon SGX CX were investigated in the presence of -hydroxyisobutyric acid (HIBA) in the mobile phase. A retention model based on the general theory of side equilibria was elaborated and relations describing dependences of capacity factors of analytes on the compositon of the mobile phase were derived. Effects of HIBA concentration and pH of the mobile phase on the analyte retention were studied in detail. Stability constants of divalent metal cations (Cd²⁺, Co²⁺, Mn²⁺, Ni²⁺ and Zn²⁺) with HIBA were calculated from the experimental dependences of the reciprocal values of capacity factors on the ligand concentration.     

Electrochemical behaviour of graphite cathodes in the presence of tetraalkylammonium cations

A graphite cathode in N,N-dimethylformamide with tetraalkylammonium salts as supporting electrolyte was found to be able to accept reversibly a rather large charge in a way somewhat akin to the formation of anion radicals and ion pairs of polycondensed aromatic hydrocarbons. The charged graphite has certain similarities with an amalgam, it can thus be used as an insoluble chemical reducing agent. The charging of the graphite depends on the size of the cation, in the presence of very large cations the cathode disintegrates. The nature of the charge is discussed on the basis of i-E curves and coulometric results.     

Probing the mechanical stability of DNA in the presence of monovalent cations

We examine the interaction between monovalent cations and DNA using several different assays that measure the stability of double-stranded DNA (dsDNA). The thermal melting of dsDNA and the mechanical separation of dsDNA into two single strands both depend on the stability of dsDNA with respect to ssDNA and are sensitive to the interstrand phosphate repulsion. We find that the experimentally measured melting temperatures and unzipping forces are approximately the same for all of the ions considered in this study. Likewise, the force required to transform B-DNA into the overstretched form is also similar for all of the ions. In contrast, for a given ion concentration, the force at which the overstretched state fully relaxes back to the canonical B-DNA form depends on the cation; however, for all cations, the overstretching force decreases with decreasing ion concentration, suggesting that this force is sensitive to screening. We observe a general trend for smaller ions to produce more efficient relaxation. Finally, for a given cation, the relaxation can also depend on the anion.     

The role of selected cations in the formation of pseudomicelles in aqueous humic acid

The fluorescence intensity enhancement of a pyrene probe in aqueous humic acid solutions was assessed in terms of added lanthanide and thorium cations. Among the trivalent ions it was found that size played a role, with the small Lu(3+) ion producing the greatest increase in pyrene emission. This was attributed to its superior ability to cause pseudomicellization in the humic acid polymer. Slow kinetic effects were observed, leading to substantial fluorescence enhancement over a period of 7 h. This was ascribed to a continuous aggregation process in aqueous humic acid, leading to ever more viscous microenvironments for the probe molecule.     

Turing pattern formation in anisotropic medium

Diffusion of reacting species in chemical and biochemical systems in anisotropic medium is markedly different from those occurring in isotropic medium, therefore approximating diffusion coefficients as constants may not be desirable as this has dynamical consequences. This paper is devoted to the analytical and numerical investigation of the development of spatial patterns in such systems. To this end we consider a general reaction–diffusion system with concentration-dependent diffusion and formulate a scheme to derive the general form of envelope equation for such systems. The theory is applied to the chlorite–iodide–malonic acid system, a standard paradigm for activator–inhibitor mechanism, to derive the instability condition in terms of the anisotropy parameters (\(\kappa _{i}, i = u, v\) that impart concentration-dependence to the diffusion coefficients) and identify the supercritical and subcritical Turing regions in the bifurcation diagram. The theoretical predictions are in good agreement with the numerical simulations.     

Voltammetry of lead cations on a new type of silver composite electrode in the presence of other cations

A new type of silver composite electrode was examined, prepared from silver, graphite powder, and methacrylate resin. The effects of the presence of various cations (cadmium, copper, bismuth, thallium), anions (chlorides), surface-active substances (Triton X-100), and oxygen on the anodic-stripping voltammetric determination of lead were studied. It was found that the effect of underpotential deposition at the composite electrode differs from that produced at a metallic silver electrode, mainly at low concentrations of the deposited metal. The use of this type of silver composite electrode in differential pulse anodic-stripping voltammetry enables direct determination of lead in natural water samples without elimination of surface-active substances (LOD about 3 g L^–1).     

Micromechanics and contact forces of colloidal aggregates in the presence of surfactants

We report measurements of the bending mechanics of colloidal aggregates consisting of poly(methyl methacrylate) (PMMA) flocculated with 250 mM MgCl2 in the presence of either pentaethylene glycol monododecyl ether (C(12)E(5)), a nonionic surfactant, or sodium dodecyl sulfate (SDS), an anionic surfactant. In the absence of surfactant, singly bonded aggregates exhibit a substantial bond rigidity, kappa(0), in the linear bending regime. With the addition of surfactant, the tangential restoring force between particles becomes weaker; aggregates exhibit nonlinear mechanics at a lower critical bending moment, M(c), and the bond rigidity decreases. The decrease in kappa(0) is related to the reduction of the surface energy of adhesion between particles, W(SL). We find that W(SL) decreases with increasing surfactant concentration below the critical micelle concentration (cmc). However, above the cmc, W(SL) remains constant within experimental error. These results confirm the relation between the bond rigidity and the surface energy of adhesion and clearly demonstrate that, on the basis of this relationship, surface-active agents provide a means of tuning the macroscopic elasticity and yield stress of colloidal gels. Last, the mechanics of the critical moment is consistent with the surfactant lowering the stress at which the contact line between the particles de-pins.     

In search of fully uncomplexed cyclodextrin in the presence of micellar aggregates

The chemical behavior of beta-cyclodextrin/nonionic surfactant mixed systems has been investigated using the basic hydrolysis of N-methyl-N-nitroso-p-toluenesulfonamide as a chemical probe. The experimental results prove that at the cmc, there are significant quantities of uncomplexed beta-CD in equilibrium with the micellar aggregates. In contrast to the expected situation, the percentage of uncomplexed beta-CD in equilibrium with the micellar system increases on increasing the hydrophobicity of the surfactant molecule. This behavior is due to the existence of two simultaneous processes: complexation of surfactant monomers by cyclodextrin and the process of self-assembly to form micellar aggregates. The autoaggregation of surfactant monomers is expected to be more important than the complexation process in this mixed system. Varying the hydrophobicity of the surfactant monomer enabled us to determine that the percentages of uncomplexed cyclodextrin in equilibrium with the micellar system were in the range of 5-95%.     

Charge-induced facial-selectivity in the formation of new cationic planar chiral iridacycles derived from aniline

The reaction of chiral chlorido-iridacyclic 2-(4-N,N-dimethylaminophenyl)pyridines with solvato-type [Cp*M(S)(3)](q+) (M = Ru, S = MeCN, q = 1; M = Ir, S = MeC(O)Me, q = 2) complexes produces new cationic racemic planar chiral iridacycles in an efficient and diastereospecific way.     

Novel polysiloxane formation process from dimethyldiethoxysilane in the presence of oxalic acid

Polysiloxane formation in dimethyldiethoxysilane (DMDES)-ethyl alcohol (EtOH(D))-oxalic acid (OA) (DMDES:EtOH(D):OA=1:2:0.5) and DMDES-dimethylsulfoxide (DMSO)-OA (DMDES:DMSO:OA=1:2:0.5) systems was investigated by gas chromatography-mass spectrometry and ²⁹Si-nuclear magnetic resonance. While the DMDES-EtOH(D)-OA system was homogeneous, the DMDES-DMSO-OA system consisted of two immiscible phases. In both systems, ethoxy-terminated linear oligomers ((EtO)Me₂SiO(Me₂SiO)_nSiMe₂(OEt); n=0–4, Et = C₂H₅, Me = CH₃) and cyclic tetramer ((Me₂SiO)₄) were identified. The reaction mechanism for polysiloxane formation is discussed.     

The formation of polyethylene terephthalate in the presence of dicarboxylic acids

The process of polyethylene terephthalate (PET) formation in the presence of dicarboxylic acids has been studied. Certain amounts of terephthalic acid (TPA) have two- to threefold accelerating efficiency in the polycondensation process. To elucidate the causes of the acceleration the main reactions leading to PET formation in the presence of dicarboxylic acids have been investigated by the use of models. The evaluation of kinetic and equilibrium parameters obtained for model reactions made it possible to conclude that the influence of carboxyl-containing additives on the apparent rate of polycondensation manifests itself in accelerating direct reactions and facilitating the liberation of the eliminated by-product; that is, ethylene glycol (EG) from the polymer melt. Carboxylic acid acts as a catalyst on the ester interchange of 2-hydroxyethyl ester end groups and thus increases the rate of polymer formation in this reaction 10–40 times. The parallel interaction between the 2-hydroxyethyl ester end group and the carboxyl group of the added acid is also catalyzed by the acid and its rate constant is four times larger than that of the catalytic polycondensation of 2-hydroxyethyl ester end groups. Unlike EG, the reaction water formed in the process is more readily removed from the reaction system and thus promotes the intensification of the process. In addition, the carboxyl groups react with the eliminated EG to decrease its amount and shift the equilibrium toward polymer formation. The investigation of the consequent parallel reactions on models made it possible to draw a conclusion about the higher reactivity of 2-hydroxyethyl esters in the esterification processes. This fact has been explained by strengthening the nucleophilicity of the oxygen atom in the hydroxyl of a 2-hydroxyethyl ester group compared with that of EG; for example, by the formation of an intramolecular cycle involving a hydrogen bond. Simultaneously, it has been found that in the system simulating PET polycondensation in the presence of dicarboxylic acids the reaction mechanism involves the catalysis by a proton formed during the carboxyl group dissociation and accepted by the 2-hydroxyethyl ester group.