Reilly, Peter

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Conformational analysis of gossypol and its derivatives by molecular mechanics

2005-10-07 , Beisel, Chase , Dowd, Michael , Reilly, Peter , Reilly, Peter , Chemical and Biological Engineering

Conformations and inversion pathways leading to racemization of all the tautomers of gossypol, gossypolone, anhydrogossypol, and a diethylamine Schiff's base of gossypol were investigated with MM3(2000). All forms have hindered rotation because of clashes between the methyl carbon atom and oxygen-containing moieties ortho to the bond linking the two naphthalene rings. Inversion energies generally agree with available experimental data. Gossypol preferentially inverts in its dihemiacetal tautomeric form through the cis pathway (where similar groups clash). Gossypolone inverts more easily than gossypol, and preferentially through the trans pathway (where dissimilar groups clash) when one of its outer rings has an enol-keto group and the other has an aldehyde group. Anhydrogossypol racemizes through the cis pathway. The bridge bond and the ortho exo-cyclic bonds in all the structures bend from planarity, and the inner naphthalene rings pucker to accommodate the inversion. For gossypol, the transition is achieved through greater bending of the exo-cyclic bonds (up to 12°) and less distortion of the inner benzyl rings (q≤0.34 Å), (up to 12.7°) . For gossypolone the transition occurs with greater distortion of the inner benzyl rings (q≤0.63 Å) and less out-of-plane bending (up to 8.4°). By isolating individual clashes, their contribution to the overall barrier can be analyzed, as shown for the dialdehyde tautomer of gossypol.

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Automated Docking of α-(1,4)- and α-(1,6)-Linked Glucosyl Trisaccharides in the Glucoamylase Active Site

1998-03-18 , Coutinho, Pedro , Dowd, Michael , Reilly, Peter , Reilly, Peter , Chemical and Biological Engineering

Low-energy conformers of five α-(1,4)- and α-(1,6)-linked glucosyl trisaccharides were flexibly docked into the glucoamylase active site using AutoDock 2.2. To ensure that all significant conformational space was searched, the starting trisaccharide conformers for docking were all possible combinations of the corresponding disaccharide low-energy conformers. All docked trisaccharides occupied subsites −1 and +1 in very similar modes to those of corresponding nonreducing-end disaccharides. For linear substrates, full binding at subsite +2 occurred only when the substrate reducing end was α-(1,4)-linked, with hydrogen-bonding with the hydroxymethyl group being the only polar interaction there. Given the absence of other important interactions at this subsite, multiple substrate conformations are allowed. For the one docked branched substrate, steric hindrance in the α-(1,6)-glycosidic oxygen suggests that the active-site residues have to change position for hydrolysis to occur. Subsite +1 of the glucoamylase active site allows flexibility in binding but, at least inAspergillus glucoamylases, subsite +2 selectively binds substrates α-(1,4)-linked between subsites +1 and +2. Enzyme engineering to limit substrate flexibility at subsite +2 could improve glucoamylase industrial properties.

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MM# Modeling of Aldopentose Pyranose Rings

2002-01-01 , Dowd, Michael , Rockey, William , Reilly, Peter , French, Alfred , Reilly, Peter , Chemical and Biological Engineering

MM3 (version 1992, ϵ=3.0) was used to study the ring conformations of d-xylopyranose, d-lyxopyranose and d-arabinopyranose. The energy surfaces exhibit low-energy regions corresponding to chair and skew forms with high-energy barriers between these regions corresponding to envelope and half-chair forms. The lowest energy conformer is 4 C 1 for α- and β-xylopyranose and α- and β-lyxopyranose, and the lowest energy conformer is 1 C 4 for α- and β-arabinopyranose. Only α-lyxopyranose exhibits a secondary low-energy region (1 C 4) within 1 kcal/mol of its global minimum. Overall, the results are in good agreement with NMR and crystallographic results. For many of these molecules, skew conformations are found with relatively low energies (2.5 to 4 kcal/mol above lowest energy chair form). The 2 S O and 1 C 4conformers of crystalline benzoyl derivatives of xylopyranose are in secondary low-energy regions on the β-xylopyranose surface, within 3.8 kcal/mol of the global 4 C 1 minimum.

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Low Molecular Weight Organic Composition of Ethanol Stillage from Sugarcane Molasses, Citrus Waste, and Sweet Whey

1994-02-01 , Dowd, Michael , Johansen, Steven , Reilly, Peter , Cantarella, Laura , Reilly, Peter , Chemical and Biological Engineering

Filtered stillage from the distillation of ethanol made by yeast fermentation of sugarcane molasses, citrus waste, and sweet whey was analyzed by gas chromatography/mass spectroscopy and by high-performance liquid chromatography. Nearly all of the major peaks representing low molecular weight organic components were identified. The major components in cane stillage were, in decreasing order of concentration, lactic acid, glycerol, ethanol, and acetic acid. In citrus stillage they were lactic acid, glycerol, myo-inositol, acetic acid, chiro-inositol, and proline. Finally, in whey stillage the major components were lactose, lactic acid, glycerol, acetic acid, glucose, arabinitol, and ribitol.

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Modeling of deoxy- and dideoxyaldohexopyranosyl ring puckering with MM3(92)

2001-10-01 , Rockey, William , Dowd, Michael , Reilly, Peter , Reilly, Peter , French, Alfred , Chemical and Biological Engineering

Extensive variations of the ring structures of three deoxyaldohexopyranoses, l-fucose, d-quinovose, and l-rhamnose, and four dideoxyaldohexopyranoses, d-digitoxose, abequose, paratose, and tyvelose, were studied by energy minimization with the molecular mechanics algorithm MM3(92). Chair conformers, 4C1 ind-quinovose and the equivalent 1C4 in l-fucose and l-rhamnose, overwhelmingly dominate in the three deoxyhexoses; in the d-dideoxyhexoses, 4C1 is again dominant, but with increased amounts of 1C4 forms in the α anomers of the three 3,6-dideoxyhexoses, abequose, paratose, and tyvelose and in both α and β anomers of the 2,6-dideoxyhexose d-digitoxose. In general, modeled proton–proton coupling constants agreed well with experimental values. Computed anomeric ratios strongly favor the β configuration except ford-digitoxose, which is almost equally divided between α and β configurations, and l-rhamnose, where the β configuration is somewhat favored. MM3(92) appears to overstate the prevalence of the equatorial β anomer in all three deoxyhexoses, as earlier found with fully oxygenated aldohexopyranoses.

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Low Molecular Weight Organic Composition of Ethanol Stillage from Corn

1993-03-01 , Dowd, Michael , Reilly, Peter , Reilly, Peter , Trahanovsky, Walter , Chemical and Biological Engineering

Filtered stillage from the distillation of ethanol made by yeast fermentation of hydrolyzed corn starch was subjected to gas chromatography-mass spectroscopy and to high-performance liquid chromatography. Nearly all the major chromatographic peaks were identified and quantified. Low molecular weight organics in the soluble part of corn stillage were lactic acid, glycerol, and alanine, as well as smaller amounts of ethanol, and various nonnitrogenous and nitrogenous acids, polyhydroxy alcohols, sugars, and glucosides.