Electronic and solvent effects on monosaccharide conformations

 

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dc.contributor.advisor Naidoo, Kevin J en_ZA
dc.contributor.author Barnett, Christopher Bevan en_ZA
dc.date.accessioned 2014-09-15T07:34:24Z
dc.date.available 2014-09-15T07:34:24Z
dc.date.issued 2007 en_ZA
dc.identifier.citation Barnett, C. 2007. Electronic and solvent effects on monosaccharide conformations. University of Cape Town. en_ZA
dc.identifier.uri http://hdl.handle.net/11427/7487
dc.description.abstract The hydroxymethyl group rotational preferences of the monosaccharides glucose and galactose are different from each other and non-intuitive (from a steric point of view) in their preferences for gauche conformers. These molecules exhibit very different biological and thermodynamic properties in, for example their binding to glycosides or their liquid crystalline phases in glycolipids. The preference for gauche conformations has been attributed to solvent effects, stereo-electronic effects and hydrogen bonding; yet the experimentally obtained hydroxymethyl rotational populations have not yet been fully rationalised. In this dissertation, I have used a range of ab initio, Molecular Dynamics (MD), Quantum Mechanics/Molecular Mechanics (QM/MM) and free energy computational methods to resolve and explain this observation. The hydroxymethyl free energy surface was calculated using the Potential of Mean Force (PMF), umbrella sampling and Weighted Histogram Analysis Methods (WHAM). The PMF calculations were performed in the canonical (NVT) ensemble in the gaseous and aqueous phase where each monosaccharide was modelled with Parameter Model 3 for Carbohydrates (PM3CARB-I). Density Functional Theory (OFT) calculations were also carried out and Atoms in Molecules (AIM) and Natural Bond Orbital (NBO) analyses were applied. Gaseous phase simulation results for both glucose and galactose gave hydroxymethyl rotational preferences of gg>tg>gt and gt>gg>tg respectively. These conformational preferences can be rationalised in terms of an intrinsic stereo-electronic effect (found from NBO calculations) and strong intramolecular hydrogen bonding (found in the tg conformer of glucose and the gg conformer of galactose using AIM) in the gaseous phase. The addition of solvent (water) was found to disrupt the intramolecular hydrogen bonding present in the gaseous phase. Hydroxymethyl rotational preferences in the solution phase were gg>gt>tg for glucose and gt>tg>gg for galactose. The population distributions in solution were also calculated for glucose as gg:gt:tg = 59.21 :34.88:0.83 and for galactose as gg:gt:tg = 3.32:79.60: 1 0.15. These populations agree favourably with experimental NMR populations. The solvent conformational preference is dominated by the intrinsic stereoeIectronic effect and steric interactions. The gauche effect in monosaccharides has been successfully rationalised. en_ZA
dc.language.iso eng en_ZA
dc.subject.other Chemistry en_ZA
dc.title Electronic and solvent effects on monosaccharide conformations en_ZA
dc.type Master Thesis
uct.type.publication Research en_ZA
uct.type.resource Thesis en_ZA
dc.publisher.institution University of Cape Town
dc.publisher.faculty Faculty of Science en_ZA
dc.publisher.department Department of Chemistry en_ZA
dc.type.qualificationlevel Masters
dc.type.qualificationname MSc en_ZA
uct.type.filetype Text
uct.type.filetype Image
dc.identifier.apacitation Barnett, C. B. (2007). <i>Electronic and solvent effects on monosaccharide conformations</i>. (Thesis). University of Cape Town ,Faculty of Science ,Department of Chemistry. Retrieved from http://hdl.handle.net/11427/7487 en_ZA
dc.identifier.chicagocitation Barnett, Christopher Bevan. <i>"Electronic and solvent effects on monosaccharide conformations."</i> Thesis., University of Cape Town ,Faculty of Science ,Department of Chemistry, 2007. http://hdl.handle.net/11427/7487 en_ZA
dc.identifier.vancouvercitation Barnett CB. Electronic and solvent effects on monosaccharide conformations. [Thesis]. University of Cape Town ,Faculty of Science ,Department of Chemistry, 2007 [cited yyyy month dd]. Available from: http://hdl.handle.net/11427/7487 en_ZA
dc.identifier.ris TY - Thesis / Dissertation AU - Barnett, Christopher Bevan AB - The hydroxymethyl group rotational preferences of the monosaccharides glucose and galactose are different from each other and non-intuitive (from a steric point of view) in their preferences for gauche conformers. These molecules exhibit very different biological and thermodynamic properties in, for example their binding to glycosides or their liquid crystalline phases in glycolipids. The preference for gauche conformations has been attributed to solvent effects, stereo-electronic effects and hydrogen bonding; yet the experimentally obtained hydroxymethyl rotational populations have not yet been fully rationalised. In this dissertation, I have used a range of ab initio, Molecular Dynamics (MD), Quantum Mechanics/Molecular Mechanics (QM/MM) and free energy computational methods to resolve and explain this observation. The hydroxymethyl free energy surface was calculated using the Potential of Mean Force (PMF), umbrella sampling and Weighted Histogram Analysis Methods (WHAM). The PMF calculations were performed in the canonical (NVT) ensemble in the gaseous and aqueous phase where each monosaccharide was modelled with Parameter Model 3 for Carbohydrates (PM3CARB-I). Density Functional Theory (OFT) calculations were also carried out and Atoms in Molecules (AIM) and Natural Bond Orbital (NBO) analyses were applied. Gaseous phase simulation results for both glucose and galactose gave hydroxymethyl rotational preferences of gg>tg>gt and gt>gg>tg respectively. These conformational preferences can be rationalised in terms of an intrinsic stereo-electronic effect (found from NBO calculations) and strong intramolecular hydrogen bonding (found in the tg conformer of glucose and the gg conformer of galactose using AIM) in the gaseous phase. The addition of solvent (water) was found to disrupt the intramolecular hydrogen bonding present in the gaseous phase. Hydroxymethyl rotational preferences in the solution phase were gg>gt>tg for glucose and gt>tg>gg for galactose. The population distributions in solution were also calculated for glucose as gg:gt:tg = 59.21 :34.88:0.83 and for galactose as gg:gt:tg = 3.32:79.60: 1 0.15. These populations agree favourably with experimental NMR populations. The solvent conformational preference is dominated by the intrinsic stereoeIectronic effect and steric interactions. The gauche effect in monosaccharides has been successfully rationalised. DA - 2007 DB - OpenUCT DP - University of Cape Town LK - https://open.uct.ac.za PB - University of Cape Town PY - 2007 T1 - Electronic and solvent effects on monosaccharide conformations TI - Electronic and solvent effects on monosaccharide conformations UR - http://hdl.handle.net/11427/7487 ER - en_ZA


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