Recognition of G-1:C73 atomic groups by Escherichia coli histidyl-tRNA synthetase

This work focuses on the RNA-protein interactions necessary for efficient aminoacylation of tRNAHis by Escherichia coli histidyl-tRNA synthetase (HisRS). The E. coli tRNAHis acceptor stem is characterized by a unique "extra" G-1:C73 base pair. Previous in vivo and in vitro studies showed that G-1:C73 is a major recognition element for E. coli HisRS. To further probe the role of the G-1:C73 base pair in specific aminoacylation, we carried out atomic group "mutagenesis" studies. Systematic base analogue substitutions at the -1:73 position of chemically synthesized microhelixHis substrates suggest that the G-1 base serves to position the 5'-monophosphate, which is critical for aminoacylation. Additionally, the C73 and G-1 bases contain major groove exocyclic atomic groups that contribute to HisRS recognition.     

Unusual solid-state behavior in a neutral [2]catenane bearing a hydrolyzable component

A template-directed strategy to forming a bis(diimide) macrocycle through an intermediate asymmetric [2]catenane is reported. Saponification of the ester linkages within the crown ether component is much slower in the mechanically interlocked structure when compared to the free crown. The predominance of a single translational isomer leads to a dimeric structure, resulting in the generation of infinite channels within the crystal lattice. [structure: see text]     

Electrokinetic molecular separation in nanoscale fluidic channels

This report presents a study of electrokinetic transport in a series of integrated macro- to nano-fluidic chips that allow for controlled injection of molecular mixtures into high-density arrays of nanochannels. The high-aspect-ratio nanochannels were fabricated on a Si wafer using interferometric lithography and standard semiconductor industry processes, and are capped with a transparent Pyrex cover slip to allow for experimental observations. Confocal laser scanning microscopy was used to examine the electrokinetic transport of a negatively charged dye (Alexa 488) and a neutral dye (rhodamine B) within nanochannels that varied in width from 35 to 200 nm with electric field strengths equal to or below 2000 V m-1. In the negatively charged channels, nanoconfinement and interactions between the respective solutes and channel walls give rise to higher electroosmotic velocities for the negatively charged dye than for the neutral dye, towards the negative electrode, resulting in an anomalous separation that occurs over a relatively short distance (<1 mm). Increasing the channel widths leads to a switch in the electroosmotic transport behavior observed in microscale channels, where neutral molecules move faster because the negatively charged molecules are slowed by the electrophoretic drag. Thus a clear distinction between "nano-" and "microfluidic" regimes is established. We present an analytical model that accounts for the electrokinetic transport and adsorption (of the neutral dye) at the channel walls, and is in good agreement with the experimental data. The observed effects have potential for use in new nano-separation technologies.     

On the nature of the Møller-Plesset critical point

It has been suggested [F. H. Stillinger, J. Chem. Phys. 112, 9711 (2000)] that the convergence or divergence of M?ller-Plesset perturbation theory is determined by a critical point at a negative value of the perturbation parameter z at which an electron cluster dissociates from the nuclei. This conjecture is examined using configuration-interaction computations as a function of z and using a quadratic approximant analysis of the high-order perturbation series. Results are presented for the He, Ne, and Ar atoms and the hydrogen fluoride molecule. The original theoretical analysis used the true Hamiltonian without the approximation of a finite basis set. In practice, the singularity structure depends strongly on the choice of basis set. Standard basis sets cannot model dissociation to an electron cluster, but if the basis includes diffuse functions then it can model another critical point corresponding to complete dissociation of all the valence electrons. This point is farther from the origin of the z plane than is the critical point for the electron cluster, but it is still close enough to cause divergence of the perturbation series. For the hydrogen fluoride molecule a critical point is present even without diffuse functions. The basis functions centered on the H atom are far enough from the F atom to model the escape of electrons away from the fluorine end of the molecule. For the Ar atom a critical point for a one-electron ionization, which was not previously predicted, seems to be present at a positive value of the perturbation parameter. Implications of the existence of critical points for quantum-chemical applications are discussed.     

Fluorescence study of an immobilized ligand—metal ion complex

A ligand known to form a fluorescent complex with aluminum ion was immobilized on silica gel. The immobilization sequence was verified by cross-polarization magicangle spinning n.m.r. spectroscopy and diffuse reflectance u.v. spectroscopy. The solid-state fluorescence of the immobilized ligand complexed with aluminum ion was similar to the fluorescence of a solvated complex of a model ligand. The potential to eliminate possible interfering species by isolating the complex from solution was demonstrated.     

Esters of 5-carboxyl-5-methyl-1-pyrroline N-oxide: a family of spin traps for superoxide

Apparent rate constants, at acidic pH and neutral pH for the reaction of a family of ester-containing 5-carboxyl-5-methyl-1-pyrroline N-oxides with superoxide (O2*-) were estimated, using ferricytochrome c as a competitive inhibitor. It was of interest to note that the rate constants were similar among the different nitrones and not that significantly different from that found for 5-(diethoxyphosphoryl)-5-dimethyl-1-pyrroline N-oxide. At acidic pH, the rate constant for spin trapping O2*- was 3-fold greater than that at physiological pH. Subsequent experiments determined the half-life of aminoxyls, derived from the reaction of these nitrones with O2*-. The EPR spectra were modeled by using a global analysis method. The results clearly demonstrated that EPR spectra of all the aminoxyls were inconsistent with a model that included a single gamma-hydrogen splitting. A better interpretation modeled them as two diastereomers with identical nitrogen splittings and slightly different beta-hydrogen splittings. Detailed line width analyses slightly favored an equal line width-unequal population ratio for the two diastereomers.     

In situ observations of water production and distribution in an operating H2/O2 PEM fuel cell assembly using 1H NMR microscopy

Proton NMR imaging was used to investigate in situ the distribution of water in a polymer electrolyte membrane fuel cell operating on H2 and O2. In a single experiment, water was monitored in the gas flow channels, the membrane electrode assembly, and in the membrane surrounding the catalysts. Radial gradient diffusion removes water from the catalysts into the surrounding membrane. This research demonstrates the strength of 1H NMR microscopy as an aid for designing fuel cells to optimize water management.     

Studies of photoinitiation and phototermination of free radical polymerization using dual pulsed laser techniques

Studies of free radical polymerization are described in which the initiation and termination events are independently controlled using two laser pulses of different wavelength. Flash photolysis of azobisisobutyronitrile (AIBN) was used to initiate the polymerization of styrene. After a predefined period the polymerization was terminated by laser photolysis of 2-naphthylmethyl 1-naphthylacetate (NMNA). The molecular weights of the polymer were controlled by the time interval between laser pulses. Irradiation with high intensity laser pulses in the presence of preformed polystyrene yields a fluorescent-labelled polymer. A two-photon process is proposed to explain the mechanism of photoaddition of naphthylmethyl groups to the polymer chain.     

A graph-theoretic approach to quantitative structure—activity/reactivity studies

Characterization of molecular species based on the use of suitable graph invariants (graph paths, in particular) can provide a quantitative means of encoding structure; the technique is complementary to commoner approaches to studies of quantitative structure— activity relationships. Graph path encoding is here applied to quantitative studies of relationships between molecular structures and biological activity; the examples are the rates of various substrate reactions with hexoldnase, and the potential opiate-like activity of enkephalin analogs.     

Kinetics of two-phase bulk polymerization. II. The influence of dissolved polymer

The effect of dissolved polybutadiene on the initial rate of polymerization of styrene was investigated by using high-precision dilatometric techniques. The dissolved polymer reduced the rate of polymerization by amounts greater than can be accounted for by a reduction in monomer concentration. Rate reductions increased with the amount of dissolved polybutadiene and with its molecular weight and were greater for benzoyl peroxide initiator than for equal concentrations of azobisisobutyronitrile. Surprisingly, analogous rate reductions were observed when polystyrene were substituted for the polybutadienes, except that at high polystyrene concentrations, the expected autoacceleration was observed. These rate reductions showed no correlation with the viscosity of the reaction mass, nor did the dissolved polymer affect initiator efficiency. At a given level of a particular dissolved polybutadiene, rate reductions were diminished by increasing levels of each initiator, and by adding a chain-transfer agent. Good quantitative agreement was obtained with the number-average length of the growing polymer chains, whether varied by using different initiators, changing initiator level, or adding chain-transfer agent. These results are inconsistent with a chemical mechanism, but they are explained by a proposal originated by North and Reed whereby the dissolved polymer makes the reaction mass a “poorer” solvent for the growing polymer chains, reducing their overall coil dimensions and enhancing their rate of diffusion together for termination.