Self-assembling a molecular pegboard

This paper describes the design, construction, and application of a self-assembled, chemically addressable DNA nanogrid composed of DNA tiles of nanometer dimensions. This self-assembled structure permits precise placement of molecules at predetermined locations on a "molecular pegboard". We used the indexed DNA nanogrids to identify single molecules of DNA that hybridize at particular locations.     

Preferred orientation in filtercakes of kaolinite

The orientational order parameter of dense colloidal dispersions of plate-like particles as a function of volume fraction is measured using neutron diffraction. This non-invasive experimental approach directly provides the full particle orientation distribution from which the order parameters can be calculated. The orientation parameters are shown to be linked to the solids fractions of the cakes and the macroscopic permeability of the samples. However, this study suggests that, although orientation can be relevant for a given system, other factors can have a stronger influence, for example, the degree of dispersion or colloidal stability of the clay and may be the principle factor that controls permeability. In addition, we report enhanced ordering of these materials under the influence of an external cross-flow field.     

Development of the continuously variable volume reactor for flow injection analysis: Part 1. Design, capabilities and testing

A new apparatus for mixing sample and reagent in flow injection analysis (FIA) is described. The continuously variable volume reactor (CVVR) replaces the conventional mixing coil in a flow injection (FI) manifold to provide mixing and dilution. A linear actuator motor allows control of the chamber volume via LabVIEW software. The chamber volume can be incremented in steps of 1 μl over the range 68-1704 μl. In addition, the chamber has an integral variable-speed stirring unit that is also under computer control. Experiments were performed to evaluate the dispersion characteristics of this new device, evaluate the volume reproducibility, and understand the mixing characteristics. Use of the chamber is shown in the determination of iron(II) in pond water, and in NIST SRM 1643d with excellent results and a detection limit of 3.7 μg/l iron(II). Advantages of the CVVR and future research activities using the device are discussed.     

Identification of diastereomeric chlorophyll allomers by atmospheric pressure chemical ionisation liquid chromatography/tandem mass spectrometry

Atmospheric pressure chemical ionisation liquid chromatography/mass spectrometry (APCI-LC/MS) has been used for identification of the epimers of hydroxy, methoxy and methoxylactone allomers of chlorophyll a (13(2)-HO-chl a, 13(2)-MeO-chl a and 15(1)-MeO-lact-chl a), the hydroxy allomer of bacteriochlorophyll a (13(2)-HO-bchl a) and the hydroxy and methoxylactone allomers of bacterioviridin a (13(2)-HO-bvir a and 15(1)-MeO-lact-bvir a). The APCI mass spectra show that facile fragmentations involve the methoxyl or hydroxyl groups at the C-13(2) or C-15(1) chiral centres. Losses involving the C-13(2) or C-15(1) hydroxyl or methoxyl groups occur more easily from the S-epimer than from the R-epimer due to the greater relief of the steric strain associated with interaction with the bulky C-17 substituent. The differences in mass spectrometric fragmentation can be used as a diagnostic tool for the assignment of the stereochemical configuration at the C-13(2) or C-15(1) chiral centres.     

Stereocontrol in Organic Synthesis Using the Diphenylphosphoryl Group

In 1959, Horner showed that metalated alkyldiphenylphosphane oxides react with aldehydes or ketones to give alkenes. With this reaction, the diphenylphosphoryl (Ph₂PO) group made its entrance into synthetic organic chemistry. In the thirty-six years since that date, extensive research has shown that this olefination, the Horner–Wittig reaction, has unique properties that make it much more than simply the phosphane oxide cousin of the more famous phosphorus-based olefinations—the Wittig reaction (based on phosphonium salts) and the Wadsworth–Emmons reaction (based on phosphonate esters). Early work on the Horner–Wittig reaction concentrated on the reactivity of phosphane oxides and the regioselectivity of their reactions, but more recently the power of the Ph₂PO group to control the stereochemistry of alkenes, and to produce “on demand” either stereoisomer in high stereochemical purity, has emerged. From the study of these stereocontrolled Horner–Wittig reactions arose the realization that the Ph₂PO group is useful not only for the control of the two-dimensional stereochemistry of alkenes, but also of three-dimensional stereochemistry in general. After a brief introduction to phosphane oxide chemistry, this review will examine the Horner–Wittig reaction, in both its original and “stereocontrolled” varieties. From there, we will move on to an account of the stereoselective construction of molecules containing the Ph₂PO group, concentrating on the stereochemical directing effects of the Ph₂PO group and on the role of its unique combination of attributes—steric bulk, electronegativity, and Lewis basicity—in controlling these reactions. Finally, we will present what is intended as a practical guide to this chemistry, covering the type of functionalized alkenes that have been made with the help of the Ph₂PO group and giving guidelines that we hope will help the organic chemist to make the most of the chemistry the Ph₂PO group has to offer.     

Synthesis with migrating phenylthio groups: connective routes to 2-phenylthioallyl alcohols and 2-phenylthio enones

The title compounds may be made from bis(phenylthio) acetals and aldehydes by routes involving PhS migration.     

The Bohlmann-Rahtz route to functionalised pyridine scaffolds and their use in library synthesis

The Bohlmann-Rahtz reaction has been used to prepare 2,3,6-trisubstituted pyridines suitable for use in library synthesis. The synthesis of piperidine substituted nicotinic acid derivative 9 has been optimised and carried out on a large scale to give ca. 500 g of scaffold which was used in the generation of the pyridine library 11.     

Influence of NaCl on the behavior of PEO-PPO-PEO triblock copolymers in solution, at interfaces, and in asymmetric liquid films

The solution behavior of the polymeric surfactant Pluronic F127 (PEO(99)PPO(65)PEO(99)) and its adsorption behavior on aqueous-silica and aqueous-air interfaces, as well as the disjoining pressure isotherms of asymmetric films (silica/aqueous film/air) containing F127, are studied. The interfacial properties of adsorbed F127 layers (the adsorbed amount Gamma and the thickness h) as well as the aqueous wetting film properties [film thickness (h) and refractive indexes] were studied via ellipsometry. The solution properties of F127 were investigated using surface tensiometry and light scattering. The interactions between the air-water and silica-water interfaces were measured with a thin film pressure balance technique (TFB) and interpreted in terms of disjoining pressure as a function of the film thickness. The relations between the behaviors of the asymmetric films, adsorption at aqueous air, and aqueous silica interfaces and the solution behavior of the polymeric surfactant are discussed. Special attention is paid to the influence of the concentrations of F127 and NaCl. Addition of electrolyte lowers the critical micelle concentration, diminishes adsorption on silica, and increases the thickness of the asymmetric film.     

Functionally relevant protein motions: extracting basin-specific collective coordinates from molecular dynamics trajectories

Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion along so-called "collective coordinates." We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fluctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation. Conformational clustering is performed using automated histogram filtering of the inter-C(alpha) distances. Orthogonal (varimax) rotation of the vectors obtained by principal component analysis of these interresidue distances for the members of individual clusters is key to the interpretation of collective coordinates dominating each conformational class. The rotated loadings plots isolate significant variation in interresidue distances, and these are associated with entire mobile secondary structure elements. From this we infer concerted motions of these structural elements. For the Spo0F simulations employing an implicit-solvent representation, collective coordinates obtained in this fashion are consistent with the location of the protein's known active sites and experimentally determined mobile regions.     

Synthesis of cationic dialkylgold(III) complexes: nature of the facile reductive elimination of alkane

A series of gold(III) cations of the type cis-[CH₃)₂AuL₂]⁺ X^? where L  Ph₃, PMePh₂, PMe₂Ph, PMe₃, AsPh₃, AsPh₃, SbPh₃, $\text{1}\text{2}$H₂NCH₂CH₂NH₂, $\text{1}\text{2}$ Ph₂PCH₂CH₂-PPh₂, $\text{1}\text{2}$ Ph₂AsCH₂CH₂AsPh₂, and $\text{1}\text{2}$o-C₆H₄(AsMe₂)₂ and X  BF₄^?, PF₆^?, ClO₄^?, and F₃CSO₃^? has been prepared. In addition, the cis complexes [(CH₃)(CD₃)-Au(PPh₃)₂]F₃CSO₃, [(C₂H₅)₂Au(PPh₃)₂]F₃CSO and [(n-C₄H₉)₂Au(PPh₃)₂]F₃-CSO₃ have been synthesized. All have been characterized by PMR, Raman and infrared spectroscopy. These [R₂AuL₂]X compounds yield only ethane, butane, or octane via reductive elimination, and no disproportionation is observed. The alkane eliminations have been studied in CHCl₃, CH₃Cl₂, and CH₃COCH₃ solution as a function of temperature, concentration of the complex, and concentration of added ligand L. Elimination is fastest when L is bulky (PPh₃ > PMePh₂ > PMe₂Ph > PMe₃), decreases in the sequence SbPh₃ > AsPh₃ > PPh₃, is slow with chelating ligands, is inhibited by excess ligand, and there is small anion effect as X is varied. As R is varied, the rate of elimination decreases Bu ? Et > Me. An intramolecular dissociative mechanism is proposed which involves rapid elimination of alkane from an electron deficient dialkylgold(III) complex with nonequivalent gold—carbon bonds and produces the corresponding [AuL₂]X complex.