Lattice animals: Supplementation of perimeter polynomial data by graph-theoretic methods

Application of graph-theoretic methods to new perimeter polynomials for connected clusters on a lattice yields extra data on the total number of clusters and for the coefficients in the series expansion for the mean size of clusters at low densities. The lattices studied are the square, the square with next nearest neighbors, the triangular, and the simple cubic.     

Effect of pH on the self-exchange reactivity of the plant plastocyanin from parsley

The self-exchange rate constant (25 degrees C) for parsley plastocyanin is 5.0 x 10(4) M-1 s-1 at pH* 7.5 (I = 0.10 M). This value is quite large for a higher plant plastocyanin and can be attributed to a diminished upper acidic patch in this protein. The self-exchange rate constant is almost independent of pH* in the range 7.5-5.6, with a value (25 degrees C) of 5.6 x 10(4) M-1 s-1 at pH* 5.6 (I = 0.10 M). At this pH*, the ligand His87 is protonated in approximately 50% of the reduced protein molecules (pKa* 5.6), and this would be expected to hinder electron transfer between the two oxidation states. However, this effect is counterbalanced by the enhanced association of two parsley plastocyanins at lower pH* due to the partial protonation of the acidic patch.     

Shape-tunable polymer nodules grown from liposomes via ring-opening metathesis polymerization

A new inisurf (acting as surfactant and initiator) molecule for ring-opening metathesis polymerization (ROMP) was synthesized and used in aqueous solution in order to control the size and shape of polymer nodules grown from liposomes. Nodules were observed to grow in size with conversion of monomer, and depending on the monomer used, they adopted either a spherical or comet-like shape. Here, we investigate polymer production from a liposome surface. We use a hydrophobic derivative of the Grubbs catalyst positioned at the liposome surface to allow for ROMP of monomers dissolved in the aqueous outer phase. We obtain nodules of polymer that can grow up to tens of micrometers, unveiling new efficient possibilities of polymerization from a membrane in an aqueous solution.     

Calculations of hydrogen—fluorine and fluorine—fluorine nuclear magnetic spinspin coupling anisotropies for fluorinated ethenes and benzenes oriented in liqiud crystal solvents

Spinspin coupling tensors are calculated using self-consistent perturbation theory and INDO wavefunctions, in order to estimate whether neglect of their anisotropy influences molecular dimensions deduced from the NMR spectra of partially oriented solutes. It is found that anisotropy of cis and trans and many aromatic HF couplings can be neglected but that trans FF couplings are markedly anisotropic. Comparisons are made with the limited experimental results.     

Determination of residues of pirimicarb and its desmethyl and desmethylformamido metabolites in fruits and vegetables by liquid chromatography-electrospray/mass spectrometry

A method was developed for the simultaneous determination of residues of pirimicarb (I) and its desmethylformamido (II) and desmethyl (III) metabolites in plums, peas, green beans, broad beans, carrots, and swedes. The compounds were extracted with ethyl acetate and determined, without cleanup, by reversed-phase liquid chromatography and electrospray mass spectrometry (MS). MS and MS/MS were used concurrently to monitor the protonated molecules and their common collision-induced dissociation product. The limit of detection (signal-to-noise ratio of >3) was 1 ng/mL, corresponding to crop concentrations of <0.0015 mg/kg. All 3 compounds were determined in plums, broad beans, and green beans by MS without interference. Interferences which affected the determination of desmethylformamido-pirimicarb in peas, and to a lesser extent in carrots and swedes, were eliminated by MS/ MS. Recoveries for all 3 compounds, at 0.05 mg/kg for plums and 0.005 mg/kg for other commodities, were in the range 83-124%. No interconversion of I, II and III, occurred during extraction, and the compounds were stable in extracts for > or = 7 days under appropriate conditions.     

New approach to molecular docking and its application to virtual screening of chemical databases

This paper describes the validation of a molecular docking method and its application to virtual database screening. The code flexibly docks ligand molecules into rigid receptor structures using a tabu search methodology driven by an empirically derived function for estimating the binding affinity of a protein-ligand complex. The docking method has been tested on 70 ligand-receptor complexes for which the experimental binding affinity and binding geometry are known. The lowest energy geometry produced by the docking protocol is within 2.0 A root mean square of the experimental binding mode for 79% of the complexes. The method has been applied to the problem of virtual database screening to identify known ligands for thrombin, factor Xa, and the estrogen receptor. A database of 10,000 randomly chosen "druglike" molecules has been docked into the three receptor structures. In each case known receptor ligands were included in the study. The results showed good separation between the predicted binding affinities of the known ligand set and the database subset.     

Aqueous Solution Chemistry of the Mo(3)PdS(4) Cube: Substitution Reactions and the Double to Single Cube Interconversion Induced by CO, Two Phosphines, Cl(-), Br(-), and NCS(-)

The kinetics of conversion of an edge-linked double cube, in this case [{Mo(3)PdS(4)(H(2)O)(9)}(2)](8+), to the corresponding single cube [Mo(3)(PdX)S(4)(H(2)O)(9)](4+), has been studied for the first time. Reaction is induced by six reagents X = CO, two water-soluble phosphines, Cl(-), Br(-), and NCS(-), which complex at the tetrahedral Pd. The first stage of reaction is fast and is accompanied by color changes, e.g. purple to dark blue in the case of Cl(-), assigned as double to single cube conversion. With X = CO and the two phosphines, when absorbance changes are intense enough for stopped-flow monitoring with reactants at Pd-SCN. On removal of e.g. Cl(-) by chromatography or addition of Ag(+), the double cube re-forms.     

The chemistry of constrained crown ring systems and fluorescence sensor applications

Using anthraquinone as a useful synthetic scaffold and the ability of anthraquinone to form stable intermediate reduction products (i.e. anthrones and anthranols), we have synthesized a wide variety of constrained crown ring systems where the receptor includes several types and patterns of Lewis bases that can tune receptor selectivity for different metal cations. Constrained crown ring systems are defined as macrocycles that contain an intraannular heteroatom, in addition to the normal peripheral Lewis bases that compose the outer ring of the macrocycle. These fluorescence sensors predominantly utilizes the internal charge transfer mechanism to promote fluorescence, but has also led to the development of new photophysical mechanisms, i.e. metal-mediated tautomerization, to selectively detect Zn(II) ion in solution. We are currently pursuing a number of synthetic avenues to incorporate new functional groups and lumophores such that a myiad of different photophysical mechanisms under optimal conditions can be employed to improve solubility, sensitivity and take advantage of the cross pollination of electrochemistry and fluorescence spectroscopy with these sensors which incorporate closely integrated electrochemical, fluorescence and receptor subunits.     

On the spatial-temporal averaging method for modeling transport in porous media

The spatial-temporal averaging procedure is considered with a nonhomogeneous distribution of elementary domains in the spatial-temporal space and the probabilistic interpretation of the ST-averaging is also given. Several averaging theorems and corollaries about the averages of spatial and temporal derivatives are presented and rigorously proved which allow elementary domain to vary in space and time. The macroscopic transport equation in the most general condition and the simplified macroscopic equation under the special form of distributions are developed which may be reduced to the classical macroscopic transport equation as the spatial-temporal average degenerates into the volume average.