Influence of Anions on Electrochemical Properties of Polypyrrole-Modified Electrodes

The influence of anions ClO₄ ^–, NO₃ ^–, Cl^–, SO₄ ^2–, and DDS^– (dodecyl sulfate) on the cyclic voltammetric response of polypyrrole-modified electrodes is studied. The change in the film composition is examined by electron probe microanalysis. It is established that essential changes in the shape of voltammograms take place during cycling if the anions are not sufficiently freely mobile in the polymer film and insertion of cations from the solution is necessary to guarantee electroneutrality of the system. Some differences between the mobility of Cl^– ions and ClO₄ ^– or NO₃ ^– ions are in good agreement with the results of semi-empirical quantum chemical calculations showing that the interaction of Cl^– and Br^– ions with pyrrole oligomers is stronger than that of NO₃ ^– or ClO₄ ^– ions. Nevertheless, it is established that the peak current determined from voltammograms increases linearly with the increase of the scan rate with very high correlation coefficient. It means that it is possible to describe the behavior of ClO₄ ^–, NO₃ ^– and Cl^– ions in the framework of the model of free ions. The redox behavior of the PPy films doped with anions of low mobility such as SO₄ ^2– and DDS^– depends essentially on the nature of cations in the test solution. It is found that the mobility of cations increases in the row Li⁺ < Na⁺ < K⁺ < Cs⁺. The mobility of DDS^– ions in the PPy in ethanolic solution is significantly higher and their electrochemical properties are quite similar to PPy|Cl or NO₃ ^– film in aqueous solution.     

Carbocyclic analogues of nucleosides from bis-(Hydroxymethyl)-cyclopentane: synthesis,antiviral and cytostatic activities of adenosine,inosine and uridine analogues

Six new carbocyclic nucleosides were prepared by constructing a purine base (in compounds 9-11) or pyrimidine base (in 6-8) on the amino groups of (+/-)-(1 beta,2 alpha,4 beta)-4-amino-1,2-cyclopentanedimethanol (4) and (+/-)-(1 beta,3 alpha,4 beta)-4-amino-1,3-cyclopentanedimethanol (5), and their activities against a variety of viruses and tumour cell lines were determined.     

Synthesis of 2′-Deoxy-5-(isothiazol-5-yl)uridine and Its Interaction with the HSV-1 Thymidine Kinase

2′-Deoxy-5-(isothiazol-5-yl)uridine ( 12 ) was synthesized starting from 2′-deoxy-5-iodouridine using a Pd-catalysed cross-coupling reaction with propiolaldehyde diethyl acetal followed by deprotection and ring closure using thiosulfate. 2′-Deoxyuridine 12 has a particular place among the 5-heteroaryl-substituted 2′-deoxyuridines in that it has a high affinity for herpes simplex virus type 1 (HSV-1)-encoded thymidine kinase (TK) without antiviral activity. Biochemical studies revealed that 12 is a substrate for viral TK. We further investigated the interaction of 12 with the HSV-1 thymidine kinase. The conformation of 12 in solution was established by NMR spectroscopy. The most stable conformer 12A has the S-atom of the isothiazole ring placed in the neighbourhood of the C(4)?O group of the pyrimidine moiety. The compound was docked in its most stable conformation in the active site of HSV-1 TK and subjected to energy minimization. This demonstrated that the isothiazole moiety binds in a cavity lined by the side chains of Tyr-132, Arg-163, Ala-167, and Ala-168 and that the C(3) atom of the isothiazole moiety is located in close proximity of the phenolic O-atom of Tyr-132 and the aliphatic part of the Arg-163 side chain.     

GROMACS: fast, flexible, and free

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.     

Self-consistent solution of the Dyson equation for atoms and molecules within a conserving approximation

We have calculated the self-consistent Green's function for a number of atoms and diatomic molecules. This Green's function is obtained from a conserving self-energy approximation, which implies that the observables calculated from the Green's functions agree with the macroscopic conservation laws for particle number, momentum, and energy. As a further consequence, the kinetic and potential energies agree with the virial theorem, and the many possible methods for calculating the total energy all give the same result. In these calculations we use the finite temperature formalism and calculate the Green's function on the imaginary time axis. This allows for a simple extension to nonequilibrium systems. We have compared the energies from self-consistent Green's functions to those of nonselfconsistent schemes and also calculated ionization potentials from the Green's functions by using the extended Koopmans' theorem.     

Intercalating nucleic acids (INAs) with insertion of N-(pyren-1-ylmethyl)-(3R,4R)-4-(hydroxymethyl)pyrrolidin-3-ol. DNA (RNA) duplex and DNA three-way junction stabilities

N-(Pyren-1-ylmethyl)-(3R,4R)-4-(hydroxymethyl)pyrrolidin-3-ol was synthesised from (3R,4R)-4-(hydroxymethyl)pyrrolidin-3-ol and (3R,4S)-4-[(1S)-1,2-dihydroxyethyl] pyrrolidin-3-ol using alkylation with 1-(chloromethyl)pyrene or reductive amination with pyrene-1-carbaldehyde and NaCNBH3. The incorporation of N-(pyren-1-ylmethyl)azasugar moiety into oligodeoxynucleotides (ODN) as a bulge to form an intercalating nucleic acid (INA) induced a slight destabilization of INA-DNA duplex, whereas the INA-RNA duplex was strongly destabilized and 9 degrees C difference per modification in thermal stability between INA-DNA over INA-RNA duplexes was observed. The stabilization of a DNA three way junction (TWJ) was improved when the intercalator moiety was inserted into the junction region as a bulge.     

Beitrag zur Frage der qualitativen und quantitativen Bestimmung einiger Pyridinderivate mit Hilfe der IR-Absorptionsspektroskopie

Zusammenfassung Es wird die Möglichkeit einer qualitativen und quantitativen Reinheitsprüfung mit Mitteln der IR-Absorptionsspektroskopie an einer Anzahl von Pyridinderivaten untersucht. Zu diesem Zweck werden die IR-Absorptionsspektren der reinen Substanzen, sowie von binären und ternären Gemischen aufgenommen. Die Spektren werden aus-gewertet und die Nachweisgrenzen angegeben.Dem Verband der Chemischen Industrie und der Deutschen Forschungsgemeinschaft danken wir für die Unterstützung dieser Arbeit.     

Effect of concentrate solution pH and mineral composition of a whey protein diluate solution on membrane fouling formation during conventional electrodialysis

The aim of this work was to study the effect of the concentrate solution pH and the composition in calcium, carbonate and protein of the diluate solution to be treated by conventional electrodialysis on the fouling of ion-exchange membranes. Conductivity, system resistance, pH of the diluate and cation migration were monitored to follow the evolution of the demineralization. Total cation migration was similar for all conditions although different forms of fouling were identified after three consecutive 100 min electrodialysis treatments. The nature of fouling and the membrane surface fouled depended on the concentrate pH value, the diluate mineral composition and the intrinsic composition of the whey isolate. Once conditions leading to membrane fouling were identified, an alternative configuration for our electrodialysis stack is proposed to prevent fouling onset.     

Electron-rich radicals by neutralizationreionization mass spectrometry. Generation, dissociations and energetics of the hydrogen atom adduct to acetamide

Protonated acetamide exists as two planar conformers, the more stable anti-form (anti-1(+)) and the syn-form (syn-1(+)), DeltaG(degree) (298) (anti-->syn) = 10.8 kJ mol(-1). Collisional neutralization of 1(+) produces 1-hydroxy-1-amino-1-ethyl radicals (anti-1 and syn-1) which in part survive for 3.7 micros. The major dissociation of 1 is loss of the hydroxyl hydrogen atom (approximately 95%) which is accompanied by loss of one of the methyl hydrogen atoms (approximately 3%) and loss of the methyl group (approximately 2%). The most favorable dissociation of the OH bond is calculated to be only 34 kJ mol(1) endothermic but requires 88 kJ mol(-1) in the transition state. Other dissociations of 1, e.g., loss of one of the amide hydrogens, methyl hydrogens, and loss of ammonia are calculated to proceed through higher- energy transition states and are not kinetically competitive if proceeding from the ground doublet electronic state of 1. The unimolecular dissociation of 1 following collisional electron transfer is promoted by large Franck-Condon effects that result in 8090 kJ mol(-1) vibrational excitation in the radicals. Radicals 1 are calculated to exoergically abstract hydrogen atoms from acetamide in water, but not in the gas phase. The different reactivity is due to solvent effects that favor the products, (.)CH(2)CONH(2) and CH(3)CH(OH)NH(2), over the reactants.