Probing organic layers on the TiO2(110) surface

In this work, we use first principles simulations to provide features of the dynamic scanning force microscopy imaging of adsorbed organic layers on insulating surfaces. We consider monolayers of formic (HCOOH) and acetic (CH(3)COOH) acid and a mixed layer of acetic and trifluoroacetic acids (CF(3)COOH) on the TiO(2)(110) surface and study their interaction with a silicon dangling bond tip. The results demonstrate that the silicon tip interacts more strongly with the substrate and the COO(-) group than the adsorbed acid headgroups, and, therefore, molecules would appear dark in images. The pattern of contrast and apparent height of molecules is determined by the repulsion between the tip and the molecular headgroups and by significant deformation of the monolayer and individual molecules. The height of the molecule on the surface and the size of the headgroup play a large role in determining access of the tip to the substrate and, hence, the contrast in images. Direct imaging of the molecules themselves could be obtained by providing a functionalized tip with attraction to the molecular headgroups, for example, a positive potential tip.     

A simple and general chiral silicon Lewis acid for asymmetric synthesis: highly enantioselective [3+2] acylhydrazone-enol ether cycloadditions

A highly diastereo- and enantioselective [3 + 2] acylhydrazone-enol ether cycloaddition mediated by a simple chiral silane Lewis acid is described. The reactions are highly practical, as demonstrated by a larger scale (5 g of the hydrazone) reaction in which the product was obtained after recrystallization in 93% yield and 99% ee. Evidence for a stepwise mechanism and a model for the asymmetric induction are presented, as well.     

Trypsin activity assay in substrate-specific one- and two-dimensional gels: a powerful method to separate and characterize novel proteases in active form in biological samples

To separate and identify the proteases, a substrate-specific, sensitive assay in sodium dodecyl sulfate (SDS)-polyacrylamide gels after two-dimensional (2-D) electrophoresis has been developed. This method allows simultaneous determination of protease cleavage specificity, molecular weight, isoelectric point, and if necessary, amino acid sequencing. After isoelectric focusing in immobilized pH gradient (IPG) strips (pH 6-11) (first dimension), trypsin was electrophoresed in 12% SDS polyacrylamide gels (second dimension) copolymerized with Boc-Gln-Ala-Arg-MCA (4-methyl-coumaryl-7-amide). The gels were washed in cold 2.5% Triton X-100 and water, and incubated in assay buffer (6.3 mM Bicine, 100 mM NaCl). Trypsin cleavage of the peptide-MCA generated fluorescent 7-amino-4-methyl-coumarin. In 1-D gels, as low as 500 pg trypsin could be detected and trypsin band volumes correlated linearly with the amounts of trypsin (R(2) = 0.999). In 2-D gels, the lowest amount of trypsin detected was 1 ng. The linear regression of spot volume and loading amount was still good (R(2) = 0.974). To optimize renaturation conditions, 5x5 min washes with 2.5% Triton X-100 and water, respectively, gave the strongest band volume. For fluorescence development, an assay buffer at pH 9 was the best; incubation at 37 degrees C for 30 min was sufficient. The method has application for identifying novel proteases as it does not rely on antibodies.     

A microwave-assisted sequential extraction of water and dilute acid soluble arsenic species from marine plant and animal tissues

This paper describes the use of dilute nitric acid for the extraction and quantification of arsenic species. A number of extractants (e.g. water, 1.5 M orthophosphoric acid, methanol-water and dilute nitric acid) were tested for the extraction of arsenic from marine biological samples, such as plants that have proved difficult to quantitatively extract. Dilute 2% (v/v) nitric acid was found to give the highest recoveries of arsenic overall and was chosen for further optimisation. The optimal extraction conditions for arsenic were 2% (v/v) HNO₃, 6 min⁻¹, 90 °C. Arsenic species were found to be stable under the optimised conditions with the exception of the arsenoriboses which degraded to a product eluting at the same retention time as glycerol arsenoribose. Good agreement was found between the 2% (v/v) HNO₃ extraction and the methanol-water extraction for the certified reference material DORM-2 (AB 17.1 and 16.2 μg g⁻¹, respectively, and TETRA 0.27 and 0.25 μg g⁻¹, respectively), which were in close agreement with the certified concentrations of AB 16.4 ± 1.1 μg g⁻¹ and TETRA 0.248 ± 0.054 μg g⁻¹.To preserve the integrity of arsenic species, a sequential extraction technique was developed where the previously methanol-water extracted pellet was further extracted with 2% (v/v) HNO₃ under the optimised conditions. Increases in arsenic recoveries between 13% and 36% were found and speciation of this faction revealed that only inorganic and simple methylated species were extracted.     

Complete ozonolysis of alkyl substituted ethenes at -60 degrees C: distributions of ozonide and oligomeric products

The distribution of ozonide and oligomeric structures formed on complete ozonolysis of alkenes in a non-participating solvent at -60 degrees C is governed by the alkyl substitution around the carbon-carbon double bond. The ozonolysis of a 1,1-alkyl substituted ethene generally favours the formation of an ozonide (a 1,2,4-trioxolane). Whereas the ozonolysis of a 1,1,2-alkyl substituted ethene also produces ozonide, a considerable amount of the ozonised products are oligomeric in nature. For example, the ozonolysis of 3-methylpent-2-ene in solution to high conversion in pentane yields oligomers with structural units derived from the fragmentation products of the primary ozonide (a 1,2,3-trioxolane) which are namely butanone carbonyl oxide and acetaldehyde; these can be characterised by electrospray ionisation mass spectroscopy (ESI-MS) under soft ionisation conditions. The predominant oligomers formed are rich in carbonyl oxide units (80 + mol%) and are cyclic in nature. A small proportion of the oligomers formed are open chain compounds with end groups that suggest that chain termination is brought about either by water or by hydrogen peroxide. Residual water in the solvent will react with the carbonyl oxides to produce 2-methoxybut-2-yl hydroperoxide, which we propose readily decomposes generating hydrogen peroxide. A significant yield of oligomers also is obtained from the ozonolysis of a 1,2-alkyl substituted ethene. The ozonolysis of trans-hex-2-ene in pentane yields oligomers containing up to four structural units and are predicted to be mainly cyclic.     

Synthesis, structure, and complexation of a large 28-mer macrocycle containing two binding sites for either anions or metal ions

The "one-pot" synthesis and characterization of a large 28-mer macrocycle (H(4)L(2)) with oxamido units capable of complexing guest ions through oxygen or nitrogen donor atoms is reported. Single-crystal structure determination of H(8)L(2)(NO(3))(4) and (Cu(2)[H(2)L(2)](H(2)O)(2))(NO(3))(2) demonstrated that the macrocycle contains two sites capable of complexing two nitrate anions or two copper(II) ions, involving a large structural reorganization in the conformation of the macrocyclic framework on coordination of the copper(II) ions when compared to the nitrate. Electrochemical and magnetic susceptibility measurements on the dinuclear Cu(II) complex and the related mononuclear and trinuclear Cu(II) complexes derived from the related 14-mer macrocycle were carried out and illustrate the role of the oxamido groups in mediating metal-metal interaction and delocalization.     

Isotope effects in electron-donor-acceptor complexes involving aromatic hydrocarbons and fluoranil from NMR shift measurements

Equilibrium constants and NMR shift parameters have been determined for complexes of benzene, toluene and p-xylene and their perdeutero-analogues with fluoranil in cyclohexane solution from NMR shift measurements. Isotope effects are observed in the 1:1 equilibrium constants for the complexes of p-xylene $\text{(}\text{K}{}_1\text{(D)}\text{K}{}_1\text{(H)}$= 1.1₀) and toluene $\text{(}\text{K}{}_1\text{(D)}\text{K}{}_1\text{(H)}$ = 1.0₉). A much smaller effect was observed for the benzene complex which could not be quantified. These results may be interpreted through either the larger electronegativity of H over D, or the greater steric requirements of H over D.     

Discovery of a small molecule that inhibits the interaction of anthrax edema factor with its cellular activator, calmodulin

The catalytic efficiency of adenylyl cyclase activity of edema factor (EF) from Bacillus anthracis is enhanced by approximately 1000-fold upon its binding to mammalian protein calmodulin (CaM). A tandem cell-based and protein binding-based screen of a 10,000 member library identified a molecule that inhibits the EF-CaM interaction and therefore the adenylyl cyclase activity. A combination of fluorescence spectroscopy and photolabeling studies showed that the molecule targets the CaM binding region of EF. A series of related compounds were synthesized and evaluated to identify one compound, 4-[4-(4-nitrophenyl)-thiazolylamino]-benzenesulfonamide, that maintained activity against EF but showed minimal toxicity to two cultured cell lines. This compound represents an important reagent to study the role of EF in anthrax pathology and may represent a drug lead against anthrax infection.     

Fragmentation and reaction processes in cluster-surface collisions

We review the processes which have been observed from collisions between alkali-halide clusters and solid surfaces. Soft impact of nanocrystalline Na_nF _n?1 ⁺ clusters against solid surfaces causes them to cleave along the lowest energy (100) plane. At higher collision energies (E_i>1 eV/atom), an evaporative cascade occurs which is characteristic of a transformation of the nanocrystal to a molten state. Efficient F^? transfer from the cluster to the surface can occur for the larger clusters (>60 atoms) scattering from Si(111), in direct competition with the cleaving channel at low energies. In this regime, strong bonds can form between the F^? and silicon surface. The reaction probability increases with cluster size indicating that an impact-initiated shock wave is needed to enhance the reactive process.     

Solution-phase parallel synthesis of a pharmacophore library of HUN-7293 analogues: a general chemical mutagenesis approach to defining structure-function properties of naturally occurring cyclic (depsi)peptides

HUN-7293 (1), a naturally occurring cyclic heptadepsipeptide, is a potent inhibitor of cell adhesion molecule expression (VCAM-1, ICAM-1, E-selectin), the overexpression of which is characteristic of chronic inflammatory diseases. Representative of a general approach to defining structure-function relationships of such cyclic (depsi)peptides, the parallel synthesis and evaluation of a complete library of key HUN-7293 analogues are detailed enlisting solution-phase techniques and simple acid-base liquid-liquid extractions for isolation and purification of intermediates and final products. Significant to the design of the studies and unique to solution-phase techniques, the library was assembled superimposing a divergent synthetic strategy onto a convergent total synthesis. An alanine scan and N-methyl deletion of each residue of the cyclic heptadepsipeptide identified key sites responsible for or contributing to the biological properties. The simultaneous preparation of a complete set of individual residue analogues further simplifying the structure allowed an assessment of each structural feature of 1, providing a detailed account of the structure-function relationships in a single study. Within this pharmacophore library prepared by systematic chemical mutagenesis of the natural product structure, simplified analogues possessing comparable potency and, in some instances, improved selectivity were identified. One potent member of this library proved to be an additional natural product in its own right, which we have come to refer to as HUN-7293B (8), being isolated from the microbial strain F/94-499709.