The Orbital Interaction Component of Conformational Effects
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University of Cape Town
CHEMICAL AND CONFORMATIONAL STUDIES OF BACTERIAL CELL SURFACE POLYSACCHARIDE REPEATING UNITS Zaheer Timol University of Cape Town Supervisors: Neil Ravenscroft, Michelle Kuttel and David Gammon A thesis presented for the degree of Master in Science University of Cape Town March 2017 The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town Abstract Bacterial cell surface polysaccharides are primarily present as lipopolysaccharides or capsular polysac- charides. They are used by cells for both structure and function and have been shown to be a virulence factor of bacterial pathogens. Cell surface polysaccharides are widely utilised as antigenic components in vaccines and play an important role in the protection against numerous diseases including meningo- coccal disease and shigellosis. This study is composed of two parts: a computational section, which investigates the capsular polysaccharide (CPS) repeating unit (RU) conformations of meningococcal Y and W CPS vaccines and a second experimental component that involves synthetic studies toward the O-specific polysaccharide (O-SP) RU of Shigella sonnei. The CPS RU of MenY [!6)-a-D-Glc(1!4)-a-D-NeuNAc-(2!] and MenW [!6)-a-D-Gal(1!4)-a- D-NeuNAc-(2!] differ only in the orientation of the C-4 hydroxyl: equatorial in MenY and axial in MenW. -
Stereoelectronic Effects in Nucleosides and Nucleotides and Their Structural Implications
Stereoelectronic Effects in Nucleosides and Nucleotides and their Structural Implications (including Appendix on literature up to 2005) Christophe Thibaudeau, Parag Acharya and Jyoti Chattopadhyaya* *To whom correspondence should be addressed. E-mail: [email protected] F +4618554495 T +46184714577 www.boc.uu.se Department of Bioorganic Chemistry Biomedical Center, Uppsala University, Sweden 2 Christophe Thibaudeau, Parag Acharya and Jyoti Chattopadhyaya* Dept of Bioorganic Chemistry Uppsala University Biomedical Center, Box 581 S-751 23 Uppsala Dr C. Thibaudeau has completed his Ph.D in Feb, 1999 at the Dept of Bioorganic Chemistry under the supervision of Prof J. Chattopadhyaya Dr P. Acharya has completed his Ph.D in Dec, 2003 at the Dept of Bioorganic Chemistry under the supervision of Prof J. Chattopadhyaya Dr J. Chattopadhyaya is professor of Bioorganic Chemistry at the Uppsala University Use the following for citation in your reference: Uppsala University Press First Edition: 1999; Second Edition, 2005 Copyright © May, 1999 by J. Chattopadhyaya, C. Thibaudeau and P. Acharaya ISBN 91-506-1351-0 pp 166 Chattopadhyaya et al, "Stereoelectronic Effects in Nucleosides & Nucleotides and their Structural Implications", Dept of Bioorganic Chemistry, Box 581, Uppsala University, S-75123 Uppsala, Sweden, Ver 160205 [email protected] 3 The intrinsic flexibility of pentoses in natural PREFACE nucleosides and nucleotides, owing to their lower energy barrier for interconversions compared to the The three essential components of DNA and RNA are hexopyranoses, is dictated by the energetics of the aglycone, the pentofuranose sugar in β-D stereochemistry stereoelectronic effects, which simply can be tuned and the phosphodiester. The phosphates at the backbone and modulated by choice of substituents and their makes DNA/RNA to behave as polyelectrolyte, the pentose ionization state as well as by their complexation with sugar gives the intrinsic flexibility with relatively low energy potential ligands present in the medium. -
Determination of Carbohydrates in Honey Manali Aggrawal, Jingli Hu and Jeff Rohrer, Thermo Fisher Scientific, Sunnyvale, CA
Determination of carbohydrates in honey Manali Aggrawal, Jingli Hu and Jeff Rohrer, Thermo Fisher Scientific, Sunnyvale, CA ABSTRACT RESULTS SAMPLE ANALYSIS METHOD ACCURACY Table 7. Adulteration parameters for HS6 adulterated with 10% SS1 through SS5. Purpose: To develop an HPAE-PAD method for the determination of carbohydrates in honey Honey sugar analysis Sample Recovery HS6 (Wild Mountain Honey) samples to evaluate their quality and to assess the possibility of adulteration. Separation Adulteration Honey sugars were separated using a Dionex CarboPac PA210-Fast-4μm column (150 × 4 mm) in Method accuracy was evaluated by measuring recoveries of 10 sugar standards spiked into honey Parameters 100% + 10% + 10% + 10% + 10% + 10% For this study, we purchased 12 commercial honey samples (Table 1) and analyzed them using Honey SS1 SS2 SS3 SS4 SS5 Methods: Separation of individual honey sugars was achieved on the recently introduced Thermo series with a Dionex CarboPac PA210 guard column (50 × 4 mm). The column selectivity allow samples. For spiking experiments, four honey samples were used (HS7–HS10) and spiked with a 10- HPAE-PAD. Figure 3 shows the representative chromatograms of 3 honey samples. For all 12 Glucose(G), mg/L 121 115 116 117 119 107 Scientific™ Dionex™ CarboPac™ PA210-Fast-4μm column. Carbohydrate detection was by pulsed carbohydrates to be separated with only a hydroxide eluent generated using an eluent generator. A sugar standard mix at two concentration levels. Figure 4 shows the representative chromatograms investigated honey samples, fructose and glucose (Peak 2 and Peak 3), were found to be the major Fructose(F), mg/L 127 115 115 116 126 116 amperometric detection (PAD) with a gold working electrode and, therefore, no sample derivatization solution of honey sugar standards was prepared and an aliquot (10 μL) of the solution was injected of unspiked and spiked honey sample HS7. -
Carbohydrates: Occurrence, Structures and Chemistry
Carbohydrates: Occurrence, Structures and Chemistry FRIEDER W. LICHTENTHALER, Clemens-Schopf-Institut€ fur€ Organische Chemie und Biochemie, Technische Universit€at Darmstadt, Darmstadt, Germany 1. Introduction..................... 1 6.3. Isomerization .................. 17 2. Monosaccharides ................. 2 6.4. Decomposition ................. 18 2.1. Structure and Configuration ...... 2 7. Reactions at the Carbonyl Group . 18 2.2. Ring Forms of Sugars: Cyclic 7.1. Glycosides .................... 18 Hemiacetals ................... 3 7.2. Thioacetals and Thioglycosides .... 19 2.3. Conformation of Pyranoses and 7.3. Glycosylamines, Hydrazones, and Furanoses..................... 4 Osazones ..................... 19 2.4. Structural Variations of 7.4. Chain Extension................ 20 Monosaccharides ............... 6 7.5. Chain Degradation. ........... 21 3. Oligosaccharides ................. 7 7.6. Reductions to Alditols ........... 21 3.1. Common Disaccharides .......... 7 7.7. Oxidation .................... 23 3.2. Cyclodextrins .................. 10 8. Reactions at the Hydroxyl Groups. 23 4. Polysaccharides ................. 11 8.1. Ethers ....................... 23 5. Nomenclature .................. 15 8.2. Esters of Inorganic Acids......... 24 6. General Reactions . ............ 16 8.3. Esters of Organic Acids .......... 25 6.1. Hydrolysis .................... 16 8.4. Acylated Glycosyl Halides ........ 25 6.2. Dehydration ................... 16 8.5. Acetals ....................... 26 1. Introduction replacement of one or more hydroxyl group (s) by a hydrogen atom, an amino group, a thiol Terrestrial biomass constitutes a multifaceted group, or similar heteroatomic groups. A simi- conglomeration of low and high molecular mass larly broad meaning applies to the word ‘sugar’, products, exemplified by sugars, hydroxy and which is often used as a synonym for amino acids, lipids, and biopolymers such as ‘monosaccharide’, but may also be applied to cellulose, hemicelluloses, chitin, starch, lignin simple compounds containing more than one and proteins. -