A gradient descent algorithm for minimizing amino acid coupling reactions when synthesizing cyclic-peptide libraries

Combinatorial chemistry has become an invaluable tool in medicinal chemistry for the identification of new drug leads. For example, libraries of predetermined sequences and head-to-tail cyclized peptides are routinely synthesized in our laboratory using the IRORI approach. Such libraries are used as molecular toolkits that enable the development of pharmacophores that define activity and specificity at receptor targets. These libraries can be quite large and difficult to handle, due to physical and chemical constraints imposed by their size. Therefore, smaller sub-libraries are often targeted for synthesis. The number of coupling reactions required can be greatly reduced if the peptides having common amino acids are grouped into the same sub-library (batching). This paper describes a schedule optimizer to minimize the number of coupling reactions by rotating and aligning sequences while simultaneously batching. The gradient descent method thereby reduces the number of coupling reactions required for synthesizing cyclic peptide libraries. We show that the algorithm results in a 75% reduction in the number of coupling reactions for a typical cyclic peptide library.

Mammalian L-to-D-amino-acid-residue isomerase from platypus venom

The presence Of D-amino-acid-containing polypeptides, defensin-like peptide (DLP)-2 and Ornithorhyncus venom C-type natriuretic peptide (OvCNP)b, in platypus venom suggested the existence of a mammalian D-amino-acid-residue isomerase(s) responsible for the modification of the all-L-amino acid precursors. We show here that this enzyme(s) is present in the venom gland extract and is responsible for the creation of DLP-2 from DLP-4 and OvCNPb from OvCNPa. The isomerisation reaction is freely reversible and under well defined laboratory conditions catalyses the interconversion of the DLPs to full equilibration. The isomerase is similar to 50-60 kDa and is inhibited by methanol and the peptidase inhibitor amastatin. This is the first known L-to-D-amino-acid-residue isomerase in a mammal. (c) 2006 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Nucleic acid amplification testing for Neisseria gonorrhoeae: An ongoing challenge

Nucleic acid amplification tests (NAATs) for the detection of Neisseria gonorrhoeae became available in the early 1990s. Although offering several advantages over traditional detection methods, N. gonorrhoeae NAATs do have some limitations. These include cost, risk of carryover contamination, inhibition, and inability to provide antibiotic resistance data. In addition, there are sequence-related limitations that are unique to N. gonorrhoeae NAATs. In particular, false-positive results are a major consideration. These primarily stem from the frequent horizontal genetic exchange occurring within the Neisseria genus, leading to commensal Neisseria species acquiring N. gonorrhoeae genes. Furthermore, some N. gonorrhoeae subtypes may lack specific sequences targeted by a particular NAAT. Therefore, NAAT false-negative results because of sequence variation may occur in some gonococcal populations. Overall, the N. gonorrhoeae species continues to present a considerable challenge for molecular diagnostics. The need to evaluate N. gonorrhoeae NAATs before their use in any new patient population and to educate physicians on the limitations of these tests is emphasized in this review.

Inhibition studies of purple acid phosphatases: Implications for the catalytic mechanism

Purple acid phosphatases (PAPs) belong to the family of binuclear metallohydrolases and catalyse the hydrolysis of a large group of phosphoester substrates at acidic pH. Despite structural conservation in their active sites PAPs appear to display mechanistic versatility. Here, aspects of the catalytic mechanism of two PAPs are investigated using the inhibitors vanadate and fluoride as probes. While the magnitude of their vanadate inhibition constants are similar the two enzymes differ with respect to the mode of inhibition; vanadate interacts in a non-competitive fashion with pig PAP (K-i = 40 mu mol L-1) while it inhibits red kidney bean PAP competitively (K-i = 30 mu mol L-1). Similarly, fluoride also acts as a competitive inhibitor for red kidney bean PAP, independent of pH, while the inhibition of pig PAP by fluoride is uncompetitive at low pH and non-competitive at higher pH, independent of metal ion composition. Furthermore, while fluoride acts as a slow-binding inhibitor in pig PAP it binds rapidly to the catalytic site of the red kidney bean enzyme. Since vanadate and fluoride are proposed to act as transition state and nucleophile mimics, respectively, the observed differences in inhibition kinetics indicate subtle but distinct variations in the reaction mechanism of these enzymes.

Synthesis and structure characterization of chromium oxide prepared by solid thermal decomposition reaction

Mesoporous chromium oxide (Cr2O3) nanocrystals were first synthesized by the thermal decomposition reaction of Cr(NO3)(3)(circle)9H(2)O using citric acid monohydrate (CA) as the mesoporous template agent. The texture and chemistry of chromium oxide nanocrystals were characterized by N-2 adsorption-desorption isotherms, FTIR, X-ray diffraction (XRD), UV-vis, and thermoanalytical methods. It was shown that the hydrate water and CA are the crucial factors in influencing the formation of mesoporous Cr2O3 nanocrystals in the mixture system. The decomposition of CA results in the formation of a mesoporous structure with wormlike pores. The hydrate water of the mixture provides surface hydroxyls that act as binders, making the nanocrystals aggregate. The pore structures and phases of chromium oxide are affected by the ratio of precursor-to-CA, thermal temperature, and time.

Aryliminopropadienone-C-amidoketenimine-amidinoketene-2-aminoquinolone cascades and the ynamine-isocyanate reaction

Imidoylketenes 11 and oxoketenimines 12 are generated by flash vacuum thermolysis of Meldrum's acid derivatives 9, pyrrolediones 17 and 18, and triazole 19 and are observed by IR spectroscopy. Ketenimine-3-carboxylic acid esters 12a are isolable at room temperature. Ketenes 11 and ketenimines 12 undergo rapid interconversion in the gas phase, and the ketenes cyclize to 4-quinolones 13. When using an amine leaving group in Meldrum's acid derivatives 9c, the major reaction products are aryliminopropadienones, ArN=C=C=C=O (15). The latter react with 1 equiv of nucleophile to produce ketenimines 12 and with 2 equiv to afford maIonic acid imide derivatives 16. N-Arylketenimine-C-carboxamides 12c cyclize to quinolones 13c via the transient amidinoketenes 11c at temperatures of 25-40 degrees C. This implies rapid interconversion of ketenes and ketenimines by a 1,3-shift of the dimethylamino group, even at room temperature. This interconversion explains previously poorly understood outcomes of the ynamine-isocyanate reaction. The solvent dependence of the tautomerism of 4-quinolones/4-quinolinols is discussed. Rotational barriers of NMe2 groups in amidoketenimines 12c and malonioc amides and amidines 16 (24) are reported.

Bio-inspired carbon electro-catalysis for the oxygen reduction reaction

We report the synthesis, characterisation and catalytic performance of two nature-inspired biomass-derived electro-catalysts for the oxygen reduction reaction in fuel cells. The catalysts were prepared via pyrolysis of a real food waste (lobster shells) or by mimicking the composition of lobster shells using chitin and CaCO3 particles followed by acid washing. The simplified model of artificial lobster was prepared for better reproducibility. The calcium carbonate in both samples acts as a pore agent, creating increased surface area and pore volume, though considerably higher in artificial lobster samples due to the better homogeneity of the components. Various characterisation techniques revealed the presence of a considerable amount of hydroxyapatite left in the real lobster samples after acid washing and a low content of carbon (23%), nitrogen and sulphur (<1%), limiting the surface area to 23 m2/g, and consequently resulting in rather poor catalytic activity. However, artificial lobster samples, with a surface area of ≈200 m2/g and a nitrogen doping of 2%, showed a promising onset potential, very similar to a commercially available platinum catalyst, with better methanol tolerance, though with lower stability in long time testing over 10,000 s.

The polymerization of lactic acid anhydrosulphite by anionic initiators

This thesis is primarily concerned with the synthesis and polymerization of 5-methyl-1;3, 2-dioxathiolan-4-one-2-oxide (lactic acid anhydrosulphite (LAAS)) using anionic initiators under various conditions. Poly(lactic acid) is a biodegradable polymer which finds many uses in biomedical applications such as drug-delivery and wound-support systems. For such applications it is desirable to produce polymers having predictable molecular weight distributions and crystallinity, The use of anionic initiators offers a potential route to the creation of living polymers. The synthesis of LAAS was achieved by means of an established route though the procedure was modified to some extent and a new method of purification of the monomer using copper oxides was introduced, Chromatographic purification methods were also examined but found to be ineffective. An unusual impurity was discovered in some syntheses and this was identified by means of 1H and 13C NMR, elemental analysis and GC-MS. Since poly-α-esters having hydroxyl-bearing substituents might be expected to have high equilibrium water contents and hence low surface tension characteristics which might aid bio-compatibility, synthesis of gluconic acid anhydrosulphite was also attempted and the product characterised by 1H and 13C NMR. The kinetics of the decomposition of lactic acid anhydrosulphite by lithium tert-butoxide in nitrobenzene has been examined by means of gas evolution measurements. The kinetics of the reaction with potassium tert-butoxide (and also sec-butyl lithium) in tetrahydrofuran has been studied using calorimetric techniques. LAAS was block co-polymerized with styrene and also with 1,3-butadiene in tetrahydrofuran (in the latter case a statistical co-polymer was also produced).

Mass transfer and chemical reaction on a distillation plate

A multistage distillation column in which mass transfer and a reversible chemical reaction occurred simultaneously, has been investigated to formulate a technique by which this process can be analysed or predicted. A transesterification reaction between ethyl alcohol and butyl acetate, catalysed by concentrated sulphuric acid, was selected for the investigation and all the components were analysed on a gas liquid chromatograph. The transesterification reaction kinetics have been studied in a batch reactor for catalyst concentrations of 0.1 - 1.0 weight percent and temperatures between 21.4 and 85.0 °C. The reaction was found to be second order and dependent on the catalyst concentration at a given temperature. The vapour liquid equilibrium data for six binary, four ternary and one quaternary systems are measured at atmospheric pressure using a modified Cathala dynamic equilibrium still. The systems with the exception of ethyl alcohol - butyl alcohol mixtures, were found to be non-ideal. Multicomponent vapour liquid equilibrium compositions were predicted by a computer programme which utilised the Van Laar constants obtained from the binary data sets. Good agreement was obtained between the predicted and experimental quaternary equilibrium vapour compositions. Continuous transesterification experiments were carried out in a six stage sieve plate distillation column. The column was 3" in internal diameter and of unit construction in glass. The plates were 8" apart and had a free area of 7.7%. Both the liquid and vapour streams were analysed. The component conversion was dependent on the boilup rate and the reflux ratio. Because of the presence of the reaction, the concentration of one of the lighter components increased below the feed plate. In the same region a highly developed foam was formed due to the presence of the catalyst. The experimental results were analysed by the solution of a series of simultaneous enthalpy and mass equations. Good agreement was obtained between the experimental and calculated results.

Modelling a biochemical reaction with computational fluid dynamics

Earlier investigations (Cartland Glover et al., 2004) into the use of computational fluid dynamics (CFD) for the modelling of gas-liquid and gas-liquid-solid flow allowed a simple biochemical reaction model to be implemented. A single plane mesh was used to represent the transport and reaction of molasses, the mould Aspergillus niger and citric acid in a bubble column with a height to diameter aspect ratio of 20:1. Two specific growth rates were used to examine the impact that biomass growth had on the local solids concentration and the effect this had on the local hydrodynamics of the bubble column.

Multiscale modelling of heterogeneously catalysed transesterification reaction process:an overview

Biodiesel is fast becoming one of the key transport fuels as the world endeavours to reduce its carbon footprint and find viable alternatives to oil derived fuels. Research in the field is currently focusing on more efficient ways to produce biodiesel, with the most promising avenue of research looking into the use of heterogeneous catalysis. This article presents a framework for kinetic reaction and diffusive transport modelling of the heterogeneously catalysed transesterification of triglycerides into fatty acid methyl esters (FAMEs), unveiled by a model system of tributyrin transesterification in the presence of MgO catalysts. In particular, the paper makes recommendations on multicomponent diffusion calculations such as the diffusion coefficients and molar fluxes from infinite dilution diffusion coefficients using the Wilke and Chang correlation, intrinsic reaction kinetic studies using the Eley-Rideal kinetic mechanism with methanol adsorption as the rate determining steps and multiscale reaction-diffusion process simulation between catalytic porous and bulk reactor scales. © 2013 The Royal Society of Chemistry.

Zr-containing hybrid organic-inorganic mesoporous materials:hydrophobic acid catalysts for biodiesel production

Zirconium-containing periodic mesoporous organosilicas (Zr-PMOs) with varying framework organic content have been synthesized through a direct synthesis method. These materials display the excellent textural properties of the analogous inorganic solid acid Zr-SBA-15 material. However, the substitution of silica by organosilicon species provides a strong hydrophobic character. This substitution leads to meaningful differences in the environment surrounding the zirconium metal sites, leading the modification of the catalytic properties of these materials. Although lower metal incorporation is accomplished in the final materials, leading to a lower population of metal sites, hydrophobisation leads to an impressive beneficial effect on the intrinsic catalytic activity of the zirconium sites in biodiesel production by esterification/transesterification of free fatty acid -containing feedstock. Moreover, the catalytic activity of the highly hybridised materials is hardly affected in presence of large amounts of water, confirming their very good water-tolerance. This makes Zr-PMO materials interesting catalysts for biodiesel production from highly acidic water-containing feedstock. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optimising catalytic properties of supported sulfonic acid catalysts

Siliceous mesoporous molecular sieves (SBA-15) have been functionalised with propylsulfonic acid groups by both co-condensing 3-mercaptopropyltrimethoxysilane with the solid at the synthesis (sol-gel) stage and by grafting the same compound to pre-prepared SBA-15, followed, in both cases, by oxidation to sulfonic acid. The acidic and catalytic properties of the supported sulfonic acids prepared in the two ways have been compared, using ammonia adsorption calorimetry and the benzylation reaction between benzyl alcohol and toluene. Using a combination of X-ray photoelectron spectroscopy and other analytical techniques, the level of functionalisation and the extent of subsequent oxidation of tethered thiol to sulfonic acid, both in the bulk and close to the surface of SBA-15 particles, have been assessed. The research shows that the co-condensing route leads to higher levels of functionalisation than the grafting route. The extent of oxidation of added thiol to acid groups is similar using the two routes, about 70% near the surface and only 50% in the bulk. Comparison is made with polymer supported sulfonic acid catalysts, Amberlysts 15 and 35, and Nafion. Nafion shows the highest acid strength and the highest specific catalytic activity of all materials studied. Amongst the other materials, average acid strengths are broadly similar but there appears to be a relationship between the concentration of acid sites on the catalysts and their specific activity in the benzylation reaction. A model is proposed to explain this, in which clustering of sulfonic acid groups, even to a small extent, leads to disproportionately enhanced catalytic activity. © 2009 Elsevier B.V. All rights reserved.

Zirconium phosphate supported tungsten oxide solid acid catalysts for the esterification of palmitic acid

A series of zirconium phosphate supported WOx solid acid catalysts with W loadings from 1–25 wt% have been prepared on high surface area zirconium phosphate by a surface grafting method. Catalysts were characterized by N2 adsorption, FTIR, Raman, UV-Vis, 31P MAS NMR, pyridine TPD and X-ray methods. Spectroscopic measurements suggest a Keggin-type structure forms on the surface of zirconium phosphate as a ([triple bond, length as m-dash]ZrOH2+)(ZrPW11O405−) species. All catalysts show high activity in palmitic acid esterification with methanol. These materials can be readily separated from the reaction system for re-use, and are resistant to leaching of the active heteropolyacid, suggesting potential industrial applications in biodiesel synthesis. © The Royal Society of Chemistry 2006.

Kinetic study of the pyrolysis of miscanthus and its acid hydrolysis residue by thermogravimetric analysis

The kinetic parameters of the pyrolysis of miscanthus and its acid hydrolysis residue (AHR) were determined using thermogravimetric analysis (TGA). The AHR was produced at the University of Limerick by treating miscanthus with 5 wt.% sulphuric acid at 175 °C as representative of a lignocellulosic acid hydrolysis product. For the TGA experiments, 3 to 6 g of sample, milled and sieved to a particle size below 250 μm, were placed in the TGA ceramic crucible. The experiments were carried out under non-isothermal conditions heating the samples from 50 to 900 °C at heating rates of 2.5, 5, 10, 17 and 25 °C/min. The activation energy (EA) of the decomposition process was determined from the TGA data by differential analysis (Friedman) and three isoconversional methods of integral analysis (Kissinger–Akahira–Sunose, Ozawa–Flynn–Wall, Vyazovkin). The activation energy ranged from 129 to 156 kJ/mol for miscanthus and from 200 to 376 kJ/mol for AHR increasing with increasing conversion. The reaction model was selected using the non-linear least squares method and the pre-exponential factor was calculated from the Arrhenius approximation. The results showed that the best fitting reaction model was the third order reaction for both feedstocks. The pre-exponential factor was in the range of 5.6 × 1010 to 3.9 × 10+ 13 min− 1 for miscanthus and 2.1 × 1016 to 7.7 × 1025 min− 1 for AHR.