Polymer translocation through a nanopore induced by adsorption: Monte Carlo simulation of a coarse-grained model

Dynamic Monte Carlo simulation of a bead-spring model of flexible macromolecules threading through a very narrow pore in a very thin rigid membrane are presented, assuming at the cis side of the membrane a purely repulsive monomer-wall interaction, while the trans side is attractive. Two choices of monomer-wall attraction epsilon are considered, one choice is slightly below and the other slightly above the "mushroom to pancake" adsorption threshold epsilon(c) for an infinitely long chain. Studying chain lengths N=32, 64, 128, and 256 and varying the number of monomers N(trans) (time t=0) that have already passed the pore when the simulation started, over a wide range, we find for epsilonepsilon(c) a finite number N(trans)(t=0) suffices that the translocation probability is close to unity. In the case epsilonepsilon(c), we find that the translocation time scales as tau proportional, variant N(1.65+/-0.08). We suggest a tentative scaling explanation for this result. Also the distribution of translocation times is obtained and discussed.     

Thermodynamic properties of the silver ion in alcohol + water solvent mixtures from electromotive force measurements and thermodynamic solubility product constants of AgX (X = Cl,Br, I or CNS) at different temperatures

The standard potentials of the silver-silver ion electrode in alcohol+water solvent mixtures containing 10 and 20 wt% methanol, ethanol, 1-propanol and 2-propanol have been determined from the electromotive force measurements of the cell Ag(s), AgCl(s), NaCl(c), NaNO₃(c)// NaNO₃(c), AgNO₃(c), Ag(s) at seven different temperatures in the range 5–35°C. The standard potentials in each solvent have been represented as a function of temperature. The standard thermodynamic functions for the electrode reaction, the primary medium effects of various solvents upon Ag⁺, and the standard thermodynamic quantities for the transfer of 1 g-ion of Ag⁺ from water to the respective alcohol + water media have been evaluated and discussed in the light of ion-solvent interactions as well as the structural changes of the solvents. From the values of the standard potentials of the Ag/Ag⁺ and Ag/AgX, X^? electrodes, the thermodynamic solubility product constants of silver chloride, silver bromide, silver iodide and silver thiocyanate have been determined in alcohol + water solvent mixtures at different temperatures.     

Supramolecular interactions of [60]- and [70]fullerenes with calix[n]arenes

[60]- and [70]fullerenes have been shown to form 1:1 supramolecular complexes with (i) 24,26-dimethoxy-25,27-dihydroxy-5,11,17,23-tetra(4-tert-butyl)calix[4]arene (1) and (ii) 37,39,41-trimethoxy-38,40,42-trihydroxy-5,11,17,23,29,35-hexa(4-tert-butyl)calix[6]arene (2) in CCl(4) medium by absorption spectroscopy. Charge transfer absorption bands of the complexes have been located in each of the cases (except [70]fullerene-2 complex) studied from which the vertical ionisation potential of 1 has been obtained. Formation constants of the complexes have been determined at four different temperatures from which the enthalpies and entropies of formation of the complexes have been obtained. Moreover, the formation constant of [70]fullerene-2 complex is higher than that of the [60]fullerene-1 and [60]fullerene-2 complexes at all the four temperatures studied. This has been accounted in terms of greater cavity size of 2 which is a calix[6]arene compared to 1 which is a calix[4]arene and also by the fact that a high degree of preorganisation takes place in case of 2 through intramolecular H-bonding at its lower rim.     

Energies of charge transfer and supramolecular interactions of some mono O-substituted calix[6]arenes with [60]fullerene by absorption spectrometric method

Equilibria for the formation of supramolecular complexes of [60]fullerene with a series of mono O-substituted calix[6]arenes, namely: (i) 37-methoxy-38,39,40,41,42-pentahydroxy-5,11,17,23,29,35-hexa(4-tert-butyl)calix[6]arene (1), (ii) 37-allyl-38,39,40,41,42-pentahydroxy-5,11,17,23,29,35-hexa(4-tert-butyl)calix[6]arene (2), (iii) 37-phenacyl-38,39,40,41,42-pentahydroxy-5,11,17,23,29,35-hexa(4-tert-butyl)calix[6]arene (3), (iv) 37-ethylester-38,39,40,41,42-pentahydroxy-5,11,17,23,29,35-hexa(4-tert-butyl)calix[6]arene (4) and (v) 37-benzyl-38,39,40,41,42-pentahydroxy-5,11,17,23,29,35-hexa(4-tert-butyl)calix[6]arene (5) have been studied in CCl4 medium by absorption spectroscopic technique. The stoichiometry has been found to be 1:1 ([60]fullerene:calix[6]arene) in each case. An absorption band due to charge transfer (CT) transition is observed in each case in the visible region. The vertical ionisation potentials (I(D)(v)) of all the calix[6]arenes under study have been estimated utilising CT transition energy. The experimental I(D)(v) values also yield a good estimate of the electron affinity of [60]fullerene. The degrees of CT in the ground state of the complexes have been found to be very low (about 0.15%). Resonance energy of the complexes have been estimated. Thermodynamic parameters for the supramolecular complex formation of [60]fullerene with mono O-substituted calix[6]arene receptors are reported. It is observed that among the calix[6]arenes under the present study, only 1 and 4 form inclusion complexes with [60]fullerene. This has also been substantiated by theoretical calculation using PM3 method. Thus presence of one substituent group (of different types) on the lower rim of the calix[6]arene molecule has been shown to govern the host-guest complexation process.     

Oxidative damage by ruthenium complexes containing the dipyridophenazine ligand or its derivatives: a focus on intercalation

Interactions with DNA by a family of ruthenium(II) complexes bearing the dppz (dppz = dipyridophenazine) ligand or its derivatives have been examined. The complexes include Ru(bpy)(2)(dppx)(2+) (dppx = 7,8-dimethyldipyridophenazine), Ru(bpy)(2)(dpq)(2+) (dpq = dipyridoquinoxaline), and Ru(bpy)(2)(dpqC)(2+) (dpqC = dipyrido-6,7,8,9-tetrahydrophenazine). Their ground and excited state oxidation/reduction potentials have been determined using cyclic voltammetry and fluorescence spectroscopy. An intercalative binding mode has been established on the basis of luminescence enhancements in the presence of DNA, excited state quenching, fluorescence polarization values, and enantioselectivity. Oxidative damage to DNA by these complexes using the flash/quench method has been examined. A direct correlation between the amount of guanine oxidation obtained via DNA charge transport and the strength of intercalative binding was observed. Oxidative damage to DNA through DNA-mediated charge transport was also compared directly for two DNA-tethered ruthenium complexes. One contains the dppz ligand that binds avidly by intercalation, and the other contains only bpy ligands, that, while bound covalently, can only associate with the base pairs through groove binding. Long range oxidative damage was observed only with the tethered, intercalating complex. These results, taken together, all support the importance of close association and intercalation for DNA-mediated charge transport. Electronic access to the DNA base pairs, provided by intercalation of the oxidant, is a prerequisite for efficient charge transport through the DNA pi-stack.     

Quenching of fluorescence of 1-hydroxypyrene-3,6,8-trisulfonate (HPTS) by Cu2+, Co2+, Ni2+, I-, and cetylpyridinium (CP+) ions in water/AOT/heptane microemulsion

The quenching of the fluorescence of HPTS (1-hydroxypyrene-3,6,8-trisulfonate) by Cu(2+), Ni(2+), Co(2+), I(-), and CP(+) (cetylpyridinium cation) has been studied in the w/o microemulsion medium formed with water, AOT [sodium salt of bis (2-ethylhexyl) sulfosuccinic acid], and heptane as components at two [H(2)O]/[AOT] ratios (omega), 6 and 20. The quenching process has been found to be dynamic in nature. The lifetimes of HPTS in the microemulsion medium in the absence and in the presence of quencher have been determined. The analysis of the results has been performed in terms of the Stern-Volmer equation and the quenching sphere of action model. The Poisson distribution equation has been also used in the analysis of the probability of quencher distribution in the microemulsion compartment. The quenching of HPTS has been found to be much lower in microemulsion than in bulk water.     

Highly efficient and selective biocatalytic acylation studies on triazolylsugars

Different acid anhydrides (of C₂ to C₇ aliphatic fatty acids and benzoic acid) have been used to study the selective acylation of primary/secondary hydroxyl groups in 2-phenyl-4-(d-threo-1′,2′,3′-trihydroxypropyl)-2H-1,2,3-triazole, 2-phenyl-4-(d-erythro-1′,2′,3′-trihydroxypropyl)-2H-1,2,3-triazole, 2-phenyl-4-(d-arabino-1′,2′,3′,4′-tetrahydroxybutyl)-2H-1,2,3-triazole and 2-phenyl-4-(d-lyxo-1′,2′,3′,4′-tetrahydroxybutyl)-2H-1,2,3-triazole in the presence of Candida antarctica lipase B in diisopropyl ether. Among the different acid anhydrides, butanoic anhydride was found to be the most efficient acylating agent (for butanoylation); for acetylation, vinyl acetate gave the best results. The reactions with both these acylating agents were highly selective and efficient yielding exclusively the monoacylated products in 95-99% yields in 1-5 h.     

Preparation of57Fe enriched K4[Fe(CN)6] and K3[Fe(CN)6]

A simple method to prepare⁵⁷Fe enriched K₄[Fe(CN)₆] and K₃[Fe(CN)₆] is described. The yields of the products are much better than those reported in the literature so far. The enrichment is essential for⁵⁷Fe Mössbauer investigation in a variety of Prussiate type complexes and other inorganic compounds which are conveniently prepared from K₄[Fe(CN)₆] and K₃[Fe(CN)₆]. K₄[Fe(CN)₆] was obtained by reacting freshly prepared Fe(OH)₃ with glacial acetic acid and treating with iron acetate in boiling aqueous solution of KCN. The novel feature of the procedure to obtain K₃[Fe(CN)₆] is that the oxidation of K₄[Fe(CN)₆] has been carried out in the solid state by passing chlorine gas over the powdered specimen. K₃[Fe(CN)₆] was crystallised from alkaline solution of this oxidised powder. The compounds were characterised by Mössbauer spectroscopy.     

(S)‐3‐(Ammoniomethyl)‐5‐methylhexanoate (pregabalin)

The title compound, C₈H₁₇NO₂, exists as a zwitterion, adopting a propeller conformation. Molecules self‐assemble to form a hydrogen‐bonded layer parallel to the ab crystallographic plane connected by N⁺—H...O⁻ and C—H...O⁻ hydrogen bonds. These layers are stacked along the c axis and are stabilized by van der Waals interactions.