Polymerised bicontinuous microemulsions as stationary phases for capillary electrochromatography

Summary Polymerisation of bicontinuous microemulsions yields porous monolithic structures with well defined pore sizes that are potentially suitable for use as stationary phases for capillary electrochromatography (CEC). A variety of pore sizes can be achieved by altering the composition of the microemulsion, which typically consists of butyl methacrylate (BMA) and ethylene glycol dimethacrylate (EGDMA) as the polymerisable oil phase. The aqueous phase consists of water, a surfactant (sodium dodecyl sulphate, SDS) and a co-surfactant (1-propanol). 2-acrylamido-2-methyl-1-propane sulfonic acid (AMPS) is also added to provide charges along the polymer backbone to allow electroosmotic flow (EOF) to occur. SEM analysis shows that in-situ polymerisation yields a monolithic structure with a porous topography. Investigations have shown that these monoliths are easy to prepare, robust and suitable for the separation of phthalates. They generate higher linear velocities than are achieved using the silica based HPLC packings normally used for CEC.     

Fully automated molecular mechanics based induced fit protein-ligand docking method

We describe a method for docking a ligand into a protein receptor while allowing flexibility of the protein binding site. The method employs a multistep procedure that begins with the generation of protein and ligand conformations. An initial placement of the ligand is then performed by computing binding site hotspots. This initial placement is followed by a protein side-chain refinement stage that models protein flexibility. The final step of the process is an energy minimization of the ligand pose in the presence of the rigid receptor. Thus the algorithm models flexibility of the protein at two stages, before and after ligand placement. We validated this method by performing docking and cross docking studies of eight protein systems for which crystal structures were available for at least two bound ligands. The resulting rmsd values of the 21 docked protein-ligand complexes showed values of 2 A or less for all but one of the systems examined. The method has two critical benefits for high throughput virtual screening studies. First, no user intervention is required in the docking once the initial binding site selection has been made in the protein. Second, the initial protein conformation generation needs to be performed only once for a given binding region. Also, the method may be customized in various ways depending on the particular scenario in which dockings are being performed. Each of the individual steps of the method is fully independent making it straightforward to explore different variants of the high level workflow to further improve accuracy and performance.     

Z-Selective and Syndioselective Ring-Opening Metathesis Polymerization (ROMP) Initiated by MonoAryloxidePyrrolide (MAP) Catalysts

We report the Z-selective and syndioselective polymerization of 2,3-bis(trifluoromethyl)bicyclo[2.2.1]hepta-2,5-diene (NBDF6) and 3-methyl-3-phenylcyclopropene (MPCP) by monoaryloxide monopyrrolide imido alkylidene (MAP) catalysts of Mo. The mechanism of polymerization with syn-Mo(NAd)(CHCMe(2)Ph)(Pyr)(OHIPT) (1; Ad = 1-adamantyl, OHIPT = O-2,6-(2,4,6-i-Pr(3)C(6)H(2))(2)C(6)H(3)) as the initiator is proposed to consist of addition of monomer to the syn initiator to yield a syn first insertion product and propagation via syn insertion products. In contrast, the mechanism of polymerization with syn-Mo(NAr)(CHCMe(2)Ph)(Pyr)(OTPP) (4; Ar = 2,6-i-Pr(2)C(6)H(3), OTPP = 2,3,5,6-Ph(4)C(6)H) as the initiator at -78 °C consists of addition of monomer to the syn initiator to yield an anti first insertion product and propagation via anti insertion products. Polymerizations of NBDF6 and MPCP at room temperature initiated by 4 led to polymers without a regular structure. We propose that the syndiotacticity of cis polymers is the consequence of the required inversion at the metal center with each insertion of monomer, i.e., stereogenic metal control of the polymer structure. We also propose that the two mechanisms for forming cis,syndiotactic polymers arise as a consequence of the relative steric bulk of the imido and phenoxide ligands.     

GESA--a two-dimensional processing system using knowledge base techniques

The successful analysis of two-dimensional (2-D) polyacrylamide electrophoresis gels demands considerable experience and understanding of the protein system under investigation as well as knowledge of the separation technique itself. The present work concerns the development of a computer system for analysing 2-D electrophoretic separations which incorporates concepts derived from artificial intelligence research such that non-experts can use the technique as a diagnostic or identification tool. Automatic analysis of 2-D gel separations has proved to be extremely difficult using statistical methods. Non-reproducibility of gel separations is also difficult to overcome using automatic systems. However, the human eye is extremely good at recognising patterns in images, and human intervention in semi-automatic computer systems can reduce the computational complexities of fully automatic systems. Moreover, the expertise and understanding of an "expert" is invaluable in reducing system complexity if it can be encapsulated satisfactorily in an expert system. The combination of user-intervention in the computer system together with the encapsulation of expert knowledge characterises the present system. The domain within which the system has been developed is that of wheat grain storage proteins (gliadins) which exhibit polymorphism to such an extent that cultivars can be uniquely identified by their gliadin patterns. The system can be adapted to other domains where a range of polymorpic protein sub-units exist. In its generalised form, the system can also be used for comparing more complex 2-D gel electrophoretic separations.     

A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction

A range of methods has been developed to predict transmembrane helices and their topologies. Although most of these algorithms give good predictions, no single method consistently outperforms the others. However, combining different algorithms is one approach that can potentially improve the accuracy of the prediction. We developed a new method that initially uses a hidden Markov model to predict alternative models for membrane spanning helices in proteins. The algorithm subsequently identifies the best among models by ranking them using a novel scoring function based on the folding energy of transmembrane helical fragments. This folding of helical fragments and the incorporation into membrane is modeled using CHARMm, extended with the Generalized Born surface area solvent model (GBSA/IM) with implicit membrane. The combined method reported here, TMHGB significantly increases the accuracy of the original hidden Markov model-based algorithm.     

Synthesis of cis,syndiotactic ROMP polymers containing alternating enantiomers

Ring-opening metathesis polymerization (ROMP) of rac-endo,exo-5,6-dicarbomethoxynorbornene (inter alia) yields a cis,syndio,alt-polymer, one in which the sequential units in the cis,syndiotactic polymer consist of alternating enantiomers. Cis selectivity arises through addition of the monomer to produce an all-cis-metallacyclobutane intermediate, while syndioselectivity and alternating enantiomer structures arise as a consequence of inversion of configuration at the metal center with each metathesis step.     

Polymerised bicontinuous microemulsions as stationary phases for capillary electrochromatography. Effect of pore size on chromatographic performance

Monolithic columns for capillary electrochromatography (CEC) were prepared by in situ polymerisation of bicontinuous microemulsions containing butyl methacrylate. The resulting monoliths were found to be permeable to mobile phase flow and their behaviour as CEC stationary phases was investigated. It was found that the monoliths were able to separate a simple test mixture of phthalates, but that efficiencies were low. However, several advantages of the monoliths compared to conventional ODS packed columns were found: preparation time is short, many columns can be prepared from the same batch of microemulsion and column conditioning is much faster. The columns show promise as stationary phases for CEC, but more development is required to improve efficiencies.     

Separation of inorganic anions on a high capacity porous polymeric monolithic column and application to direct determination of anions in seawater

A commercially available 4.6 mm id x 50 mm polymethacrylate-based monolithic strong anion exchange column (ProSwift SAX-1S) designed for the separation of proteins has been successfully used to separate small inorganic anions in the presence of a seawater sample matrix. Using a hydroxide eluent with suppressed conductivity detection the ion exchange capacity of this column declined over time; however, using KCl as the eluent, the column performance was stable with a capacity of 530 microequiv. for nitrate. The optimum conditions for the separation of iodate, bromate, nitrite, bromide and nitrate were assessed by constructing van Deemter plots using 1.00 and 0.100 M KCl. Efficiencies of up to 26 700 plates/m were recorded using 1.00 M KCl, at a flow rate of 0.20 mL/min but iodate was not baseline resolved from the void peak. By reducing the concentration of the eluent to 0.100 M, efficiencies of up to 39 900 plates/m could be obtained at 0.35 mL/min. By employing a linear gradient ranging from 0.05 to 1.00 M KCl the ions dissolved in distilled water or a salt water matrix could be baseline separated in less than 3 min at a flow rate of 2.50 mL/min.     

Ortho-hydroxylation of benzoic acids with hydrogen peroxide at a non-heme iron center

The iron-assisted hydroxylation of benzoic acid to salicylic acid by 1/H2O2 has been achieved in good yield under mild conditions (where is [Fe(II)(BPMEN)(CH3CN)2](ClO4)2 and BPMEN =N,N'-dimethyl-N,N'-bis(2-pyridylmethyl)ethane-1,2-diamine); the product of this reaction is a novel mononuclear iron(III) complex with a chelating salicylate.