Unwinding dynamics of double-stranded polymers

We consider the unwinding of two lattice polymer strands of length N that are initially wound around each other in a double-helical conformation and evolve through Rouse dynamics. The problem relates to quickly bringing a double-stranded polymer well above its melting temperature, i.e., the binding interactions between the strands are neglected, and the strands separate from each other as it is entropically favorable for them to do so. The strands unwind by rotating around each other until they separate. We find that the process proceeds from the ends inward; intermediate conformations can be characterized by a tightly wound inner part, from which loose strands are sticking out, with length l～t(0.39). The total time needed for the two strands to unwind scales as a power of N as τ(u)～N(2.57±0.03). We present a theoretical argument, which suggests that during this unwinding process, these loose strands are far out of equilibrium.     

Facile synthesis of TMS-protected trifluoromethylated alcohols using trifluoromethyltrimethylsilane (TMSCF3) and various nucleophilic catalysts in DMF

Organofluorine compounds are becoming increasingly important in different fields, such as material science, agro chemistry, and the pharmaceutical industry. Nucleophilic trifluoromethylation is one of the widely used methods to incorporate a trifluoromethyl moiety into organic molecules. We have carried out extensive studies to develop varieties of easily accessible nucleophilic catalysts to promote such reactions. TMS-protected trifluoromethylated alcohols were prepared from both aldehydes and ketones in excellent yields using catalytic amount of amine N-oxide. Carbonate and phosphate salts also showed efficient catalytic activity toward this reaction. These reactions were highly solvent dependent, and DMF was found to be the most suitable one among the various solvents studied. All these reactions proceeded under very mild conditions, giving clean products and avoiding the use of any fluoride initiators or expensive catalysts, and extremely water-free conditions. The mechanism for the reaction is discussed in detail. DFT calculations were performed on the possible reaction intermediates using the Gaussian 03 program at B3LYP/6-311+G* level to support the proposed mechanism.     

A Rhodamine-Based Dual Chemosensor for Cu(II) and Fe(III)

An “off-on” rhodamine-based fluorescence probe for the selective signaling of Cu(II) and Fe(III) has been designed and synthesized. The optical properties of this compound have been investigated in acetonitrile-water (1:1) binary solution. Very interestingly, this compound showed sensitivity and selectivity towards Cu(II) during absorption process and towards Fe(III) during emission process. So this is a nice example of an excellent dual chemosensor for two biologically/physiologically very important transition metal ions using only the two very different techniques (absorption and emission); both cases displayed only intensity enhancement.     

A Spray Reagent for Identification of Amino Acids on Thin-Layer Chromatography Plates

JPC – Journal of Planar Chromatography – Modern TLC -     

Cluster Formation through Hydrogen Bond Bridges across Chloride Anions in a Hydroxyl-Functionalized Ionic Liquid

Several recent studies of hydroxyl-functionalized ionic liquids (ILs) have shown that cation-cation interactions can be dominating these materials at the molecular level when the anion involved is weakly interacting. The hydrogen bonds between the like ions led to the formation of interesting chain-like, ring-like, or distinct dimeric (i. e. two ion pairs) supermolecular clusters. In the present work, vibrational spectroscopy (ATR-IR and Raman) and density functional theory (DFT) calculations of the hydroxyl-functionalized imidazolium ionic liquid C₂OHmimCl indicate that anion-cation hydrogen bonding interactions are dominating, leading to the formation of distinct dimeric ion pair clusters. In this arrangement, the Cl⁻ anions function as a bridge between the cations by establishing bifurcated hydrogen bonds with the OH group of one cation and the C(2)-H of another cation. Cation–cation interactions, on the other hand, do not play a significant role in the observed clusters.     

A comparative kinetic study for the oxidation of 2‐mercaptoethanol by di‐μ‐oxo‐bis(1,4,7,10‐tetraazacyclododecane)‐dimanganese(III,IV) and di‐μ‐oxo‐bis(1,4,8,11‐tetraazacyclotetradecane)‐dimanganese(III,IV) complexes: Influence of copper(II)

A comparative kinetic study of the reactions of two mixed valence manganese(III,IV) complexes with macrocyclic ligands, [L¹Mn^IV(O)₂Mn^IIIL¹], 1 (L¹ = 1,4,7,10‐tetraazacyclododecane) and [L²Mn^IV(O)₂Mn^IIIL²], 2 (L² = 1,4,8,11‐tetraazacyclotetradecane) with 2‐mercaptoethanol (RSH) has been carried out by spectrophotometry in aqueous buffer at (30 ± 0.1)°C. Rate of the reactions between the oxidants and the reductant was found to be negligibly slow with no systematic dependence on either redox partners. Externally added copper(II) (usually 5 × 10^?7 mol dm^?3), however, increases the rate of the reduction of 1 and 2 significantly. In the presence of catalytic amount of copper(II), the rate of the reaction is nearly proportional to [RSH] at lower concentration of the reductant but follows a saturation kinetics at higher concentration of the latter for the reaction between 1 and the thiol. Reaction rate was found to be strongly influenced by the variation of acidity of the medium and the observed kinetics suggests that the two reductant species ([Cu(RSH)]²⁺ and [Cu(RS)]⁺) are significant for the reaction between 1 and the thiol. The dependence of the rate on [RSH] for the reduction of 2 by the thiol was complex and rationalized considering two equilibria involving the catalyst (Cu²⁺) and the reductant. The pH rate profile suggests that both the μ‐O protonated [Mn^III(O)(OH)Mn^IV] and the deprotonated [Mn^III(O)₂Mn^IV] forms of the oxidant 2 become important. The kinetic results presented in this study indicate the domination of outer‐sphere path. © 2003 Wiley Periodicals, Inc. Int J Chem Kinet 36: 129–137, 2004     

Long-Time-Tail Effects on Lyapunov Exponents of a Random, Two-Dimensional Field-Driven Lorentz Gas

We study the Lyapunov exponents for a moving, charged particle in a two-dimensional Lorentz gas with randomly placed, nonoverlapping hard-disk scatterers in a thermostatted electric field, . The low-density values of the Lyapunov exponents have been calculated with the use of an extended Lorentz–Boltzmann equation. In this paper we develop a method to extend theses results to higher density, using the BBGKY hierarchy equations and extending them to include the additional variables needed for calculation of the Lyapunov exponents. We then consider the effects of correlated collision sequences, due to the so-called ring events, on the Lyapunov exponents. For small values of the applied electric field, the ring terms lead to nonanalytic, field-dependent contributions to both the positive and negative Lyapunov exponents which are of the form ~ ²ln~, where ~ is a dimensionless parameter proportional to the strength of the applied field. We show that these nonanalytic terms can be understood as resulting from the change in the collision frequency from its equilibrium value due to the presence of the thermostatted field, and that the collision frequency also contains such nonanalytic terms.     

Translocation of DNA molecules through nanopores with salt gradients: the role of osmotic flow

Recent experiments of translocation of double-stranded DNA through nanopores [M. Wanunu et al., Nature Nanotech. 5, 160 (2009)] reveal that the DNA capture rate can be significantly influenced by a salt gradient across the pore. We show that osmotic flow combined with electrophoretic effects can quantitatively explain the experimental data on the salt-gradient dependence of the capture rate.     

Rhodamine-linked pyridyl thiourea as a receptor for selective recognition of F–, Al3+ and Ag+ under different conditions

A new rhodamine-labelled pyridyl thiourea-based compound 1 has been designed and synthesised. While the receptor selectively recognises F^– and Al³⁺ ions in CH₃CN, Al³⁺ and Ag⁺ ions are selectively screened from other cations in CH₃CN/water (4/1, v/v; 10 μM Tris–HCl buffer, pH 6.8) by observing different emission characteristics and colour changes. While Ag⁺ is sensed through an increase in emission at 416 nm, Al³⁺ is detected by a ratiometric change in emission of 1 with a band at 585 nm. The receptor shows in vitro detection of both the ions in human cervical cancer (HeLa) cells.