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Oligomerization Reaction (oligomerization + reaction)
Selected AbstractsEffect of Counter Ions on the Silica Oligomerization ReactionCHEMPHYSCHEM, Issue 11 2009Thuat T. Trinh Abstract The silicate oligomerization reaction is key to sol-gel chemistry and zeolite synthesis. Numerous experimental and theoretical studies have addressed the physical chemistry of silicate oligomers in the prenucleation stage of siliceous zeolite formation. Here we report a study of a silica condensation reaction in aqueous solution in the presence of counter ions (Li+ and NH4+). Ab-initio molecular dynamics simulations have been used to construct reaction energy diagrams including transition state free energies. Contact with Li+ as well as NH4+ increases the activation energies of the dimerization step compared to the situation in the absence of counterions. The presence of NH4+ has no effect on consecutive oligomerization steps. Hence NH4+ will increase the relative formation rate of larger oligomers. [source] Oligo(triacetylene) Derivatives with Pendant Long Alkyl ChainsHELVETICA CHIMICA ACTA, Issue 6 2004Jean-François Nierengarten Substituted (E)-2-(ethynyl)but-2-ene and (E)-hex-3-ene-1,5-diyne derivatives 6 and 10, respectively, were prepared by dicyclohexylcarbodiimide(DCC)-mediated esterification of tris(dodecyloxy)benzoic acid (4) with (E)-2-[(triisopropylsilyl)ethynyl]but-2-ene-1,4-diol (3) and (E)-2,3-bis[(trimethylsilyl)ethynyl]but-2-ene-1,4-diol (8), respectively, followed by deprotection with Bu4NF in wet THF (Schemes,1 and 2). Oligomerization reactions of diyne derivative 10 were attempted by treatment with the Hay catalyst in the presence of mono-alkyne 6 as an end-capping reagent. Under these conditions, only compound 7 resulting from the homocoupling of 6 (Scheme,1), and polymers of 10 were obtained due to the difference in reactivity of the alkyne groups in 6 and 10. In contrast, when phenylacetylene was used as the stopper, the oligomerization of 10 afforded a mixture of end-capped oligomers, from which 11,13 were isolated by column chromatography (Scheme,3). The poly(triacetylenes) (PTA) 16,18 were prepared in a similar manner starting from diol 8 and stearic acid (Schemes,4 and 5). Whereas the end-capped monomers and dimers 11, 12, 16, and 17 with pendant long alkyl chains do not exhibit any liquid-crystalline behavior, the trimeric derivatives 13 and 18 show mesomorphic properties, thus demonstrating that the poly(triacetylene) backbone can behave as a mesogenic unit. [source] An enigmatic peptide ligation reaction: Protease-catalyzed oligomerization of a native protein segment in neat aqueous solutionPROTEIN SCIENCE, Issue 4 2000Sangaralingam Kumaran Abstract We report an enigmatic peptide ligation reaction catalyzed by Glu-specific Staphylococcus aureus V8 protease that occurs in neat aqueous solution around neutral pH utilizing a totally unprotected peptide substrate containing free ,-carboxyl and ,-amino groups. V8 protease catalyzed a chain of ligation steps between pH 6 and 8 at 4 °C, producing a gamut of covalent oligomers (dimer through octamer or higher) of a native protein segment TAAAKFE (S39) derived from ribonuclease A (RNAse A). Size-exclusion chromatography suggested the absence of strong interaction between the reacting peptides. The circular dichroism spectra of monomer through pentamer showed length-dependent enhancement of secondary structure in the oligomers, suggesting that protease-catalyzed ligation of a monomer to an oligomer resulted in a product that was more structured than its precursor. The relative conformational stability of the oligomers was reflected in their ability to resist proteolysis, indicating that the oligomerization reaction was facilitated as a consequence of the "conformational trapping" of the product. The ligation reaction proceeded in two phases,slow formation and accumulation of the dimer followed by a fast phase of oligomerization, implying that the conformational trap encountered in the oligomerization reaction was a two-step process. The Gly substitution at any position of the TAAAKFE sequence was deleterious, suggesting that the first step of the conformational trap, namely the dimerization reaction, that proceeded very slowly even with the parent peptide, was quite sensitive to amino acid sequence. In contrast, the oligomerization reaction of an Ala analog, AAAAKFE, occurred in much the same way as S39, albeit with faster rate, suggesting that Ala substitution stabilized the overall conformational trapping process. The results suggest the viability of the product-directed "conformational trap" as a mechanism to achieve peptide ligation of totally unprotected peptide fragments in neat aqueous solution. Further, the study projects the presence of considerable innate synthetic potential in V8 protease, baring rich possibilities of protein engineering of this enzyme to generate a "V8 peptide ligase." [source] ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2009Andreas Vitalis Abstract A new implicit solvation model for use in Monte Carlo simulations of polypeptides is introduced. The model is termed ABSINTH for self- Assembly of Biomolecules Studied by an Implicit, Novel, and Tunable Hamiltonian. It is designed primarily for simulating conformational equilibria and oligomerization reactions of intrinsically disordered proteins in aqueous solutions. The paradigm for ABSINTH is conceptually similar to the EEF1 model of Lazaridis and Karplus (Proteins 1999, 35, 133). In ABSINTH, the transfer of a polypeptide solute from the gas phase into a continuum solvent is the sum of a direct mean field interaction (DMFI), and a term to model the screening of polar interactions. Polypeptide solutes are decomposed into a set of distinct solvation groups. The DMFI is a sum of contributions from each of the solvation groups, which are analogs of model compounds. Continuum-mediated screening of electrostatic interactions is achieved using a framework similar to the one used for the DMFI. Promising results are shown for a set of test cases. These include the calculation of NMR coupling constants for short peptides, the assessment of the thermal stability of two small proteins, reversible folding of both an ,-helix and a ,-hairpin forming peptide, and the polymeric properties of intrinsically disordered polyglutamine peptides of varying lengths. The tests reveal that the computational expense for simulations with the ABSINTH implicit solvation model increase by a factor that is in the range of 2.5,5.0 with respect to gas-phase calculations. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] | ||||||||||