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Turn-on fluorescent sensor for the detection of lipopolysaccharides based on a novel bispyrenyl terephtalaldehyde-bis-guanylhydrazone
(2019-01-01)
Khownium, Kriangsak
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Romsaiyud, Jariya
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Borwornpinyo, Suparerk
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Wongkrasant, Preedajit
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Pongkorpsakol, Pawin
A novel bispyrene compound (BPTG) was developed as a selective lipopolysaccharide (LPS) sensor. The BPTG probe exhibited high selectivity and sensitivity toward LPS with a fluorescence 'off-on' behavior in HEPES-buffered DMSO-H<inf>2</inf>O (1:6 (v/v), HEPES = 10 mM, pH = 7.4) with a low detection limit of 5 nM. The turn-on flurescence sensing of the LPS occurred through monomer and excimer emissions. The mechanism of the probe was supported by computational experiments and was found to be unique for its sandwich conformation and self-quenching ability at ground state prior to the binding to the LPS with a butterfly-like skeleton. Upon binding with LPS in an aqueous medium, the probe showed a dose-dependent increase in fluorescent emissions and exhibited a typical excimer emission peak at 485 nm along with a monomer emission peak at 375 nm. BPTG is highly selective for LPS over heparin and other anionic biological species. Due to the expression of LPS on the cell surface of Gram negative bacteria, BPTG was successfully applied as a fluorescent dye to visualize live Vibrio cholerae, which are life-threatening bacteria causing diarrhoeal disease.
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Evaluating the enthalpic contribution to ligand binding using QM calculations: Effect of methodology on geometries and interaction energies
(2012-09-21)
Gleeson, Duangkamol
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Tehan, Ben
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Gleeson, M. Paul
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Limtrakul, Jumras
As a result of research on ligand efficiency in the pharmaceutical industry, there is greater focus on optimizing the strength of polar interactions within receptors, so that the contribution of overall size and lipophilicity to binding can be decreased. A number of quantum mechanical (QM) methods involving simple probes are available to assess the H-bonding potential of different heterocycles or functional groups. However, in most receptors, multiple features are present, and these have distinct directionality, meaning very minimalist models may not be so ideal to describe the interactions. We describe how the use of gas phase QM models of kinase protein-ligand complex, which can more closely mimic the polar features of the active site region, can prove useful in assessing alterations to a core template, or different substituents. We investigate some practical issues surrounding the use of QM cluster models in structure based design (SBD). These include the choice of the method; semi-empirical, density functional theory or ab-initio, the choice of the basis set, whether to include implicit or explicit solvation, whether BSSE should be included, etc. We find a combination of the M06-2X method and the 6-31G* basis set is sufficiently rapid, and accurate, for the computation of structural and energetic parameters for this system. © 2012 The Royal Society of Chemistry.
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The catalytic conversion of acetonitrile to acrylonitrile in zeolitic systems: Rationalization of experimental observations using theoretical simulations
(2007-12-15)
Gleeson, Duangkamol
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Limtrakul, Jumras
Quantum mechanical calculations have been performed on faujasite and silicalite models to investigate reported experimental differences in yields of two key catalytic products (propionitrile and acrylonitrile) formed from the reaction of acetonitrile with either methanol or formaldehyde, respectively. The calculations were performed using 12T and 10T cluster representations of faujasite and silicalite, respectively, and the results are in good overall agreement with experimental observations. Both reactions are predicted to proceed in a concerted manner, with the transfer of a proton to the basic zeolite oxygen atom in conjunction with the methyl group migration to form a reaction intermediate. The stationary points found on the reaction surface in both zeolites have been systematically assessed using principal components analysis to give us an insight into the correlated nature of the structural/electronic changes that occur on the reaction surfaces. © 2007 Elsevier B.V. All rights reserved.
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Application of ONIOM calculations in the study of the effect of the zeolite framework on the adsorption of alkenes to ZSM-5
(2006-08-18)
Namuangruk, Supawadee
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Tantanak, Duangkamol
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Limtrakul, Jumras
The structures and energetics associated with the adsorption of ethene and four butene isomers on H-ZSM-5 zeolite have been studied using a 46T cluster and calculated at the ONIOM2(B3LYP/6-311++G(d,p):UFF) level. The adsorption energy for ethene-zeolite complex is predicted to be -8.17 kcal/mol, which is in good agreement with the experimental data of -9.0 kcal/mol. The trend of the calculated adsorption energies (kcal/mol) for the butene isomers is as follows: 1-butene (-16.06) > cis-2-butene (-13.62) ≅ trans-2-butene (-13.25) > isobutene (-6.96). The isobutene-zeolite complex is the least stable due to the greatest steric repulsion between the methyl substituents around the C{double bond, long}C bond and zeolite framework; the more substituted the lower the adsorption energy. Although our own N-layered integrated molecular orbital and molecular mechanics (ONIOM) calculation results indicate that isobutene hardly approaches the acid site and has a weak interaction with the zeolite framework, NBO analysis shows that it has the maximum charge transfer from the active site and the largest stabilization energy. These findings explain the reason why ZSM-5 is selective towards isobutene produced from n-butene and indicate that the acidic proton from the zeolite is easy to transfer to isobutene. Thus, further catalytic conversion of isobutene would be facile. © 2006 Elsevier B.V. All rights reserved.
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Probing the structural and electronic factors affecting the adsorption and reactivity of alkenes in acidic zeolites using DFT calculations and multivariate statistical methods
(2005-01-01)
Tantanak, Duangkamol
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Limtrakul, Jumras
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Gleeson, Matthew Paul
Quantum mechanical (QM) cluster calculations have been performed on a model of ZSM-5 at DFT and MP2 levels. We investigated how the adsorption energies and the energetics of alkoxide intermediate formation of six different alkene substrates, ethene, propene, 1-butene, cis/trans butene, and isobutene, vary in this zeolite model. An analysis of the DFT geometric, electronic, and energetic parameters of the zeolite-substrate complexes, transition states, and alkoxide intermediates is performed using principal components analysis (PCA) and partial least squares (PLS). These deliver an insight into the correlated changes that occur between molecular structure and energy along the reaction coordinate between the physisorbed and chemisorbed species within the zeolite. To the best of our knowledge, this is the first occasion multivariate techniques such as PCA or PLS have been employed to profile the changes in electronics, distances, and angles in QM calculations of catalytic systems such as zeolites. We find the calculated adsorption and the alkoxide intermediate energies correlate strongly with the absolute charge on the substrate and the length of the substrate double bond. The transition states' energies are not affected by the zeolite framework as modeled, which explains why they correlate strongly with the gas-phase substrate protonation energy. Our cluster results show that for ethene, propene, 1-butene, and isobutene, the relative energetics associated with the formation of the alkoxide intermediate in ZSM-5 follow the same trends as calculations where the effects of the framework are included. © 2005 American Chemical Society.
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Activity enhancement by acetic acid in cyclohexane oxidation using Ti-containing zeolite catalyst
(2002-07-10)
Sooknoi, Tawan
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Limtrakul, Jumras
Titanium silicalite (TS-1) was hydrothermally crystallised from a titanosilicate gel. The solid material was characterised by XRD, IR, and SEM, and then used as a catalyst in the liquid phase oxidation of cyclohexane with hydrogen peroxide. The reaction was carried out for 6 h, at the temperature between 40 and 80 °C. It was found that a marked increase in the catalytic activity was observed in the reaction using acetic acid as the solvent, as compared to those using no solvent and methyl ethyl ketone. Further investigation was made on the cause of activity enhancement, and it was shown that acetic acid was readily oxidised to peracetic acid. This compound was believed to facilitate the complexation of the framework titanium active sites, and subsequently serve as a better oxidising agent, as compared to the original hydrogen peroxide. However, leaching of the titanium species was also observed in small amounts, from the reaction using acetic acid as the solvent. In the mechanistic point of view, there was an evidence suggesting that cyclohexanol might be a primary product from the cyclohexane oxidation, and can be consecutively re-oxidised to form cyclohexanone. It is noted that the direct oxidation from cyclohexane to cyclohexanone cannot be excluded. © 2002 Elsevier Science B.V. All rights reserved.
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