Structure, dynamics and reactivity of carbohydrates NMR spectroscopic studies Jerk Rönnols © Jerk Rönnols, Stockholm 2013 Cover picture: Man, machine and molecule by Sara Alfredsson ISBN 978-91-7447-730-6 Printed in Sweden by US-AB, Stockholm 2013 Distributor: Department of Organic Chemistry, Stockholm University ii Petrokemi Det kan man Inte bada i /Arbete & Fritid iii iv Abstract The main focus of this thesis is on the ring conformations of carbohydrate molecules; how the conformational equilibria and the rates of the associated interconversions are affected by the molecular constitution and their sur- roundings. The conformational equilibria of a group of amine linked pseudodisaccha- rides, designed as potential glycosidase inhibitors, comprising α-D-altrosides O are described in Chapter 3. The S2 conformation was largely populated, and the ring conformation was found to depend on the charge of the amine func- tionality. The conformations of β-D-xylopyranoside derivatives with naphthyl- based aglycones, which are potential anti-cancer agents, are described in chapter 4. Solvent dependent flexibility was observed. Intramolecular hy- 1 drogen bonds were concluded to be involved in the stabilization of C4 con- formers in non-hydrogen bonding solvents of low polarity. Chapter 5 describes the first measurements of the conformational ex- 4 1 change rates of mannuronic acid ester derivatives between the C1 and C4 conformations, through DNMR measurements. The relative reactivity of glycosyl triflates as electrophiles in glycosylation reactions were investigat- ed with NMR-based competition experiments. In Chapter 6, investigations of ruthenium-catalyzed epimerizations of the allylic alcohols of glycal derivatives, and stereoselective synthesis of esters through a DYKAT protocol, are described. The kinetics of the epimeriza- tions were elaborated through different NMR-spectroscopic methods. Chapter 7 describes additions of NMR chemical shift data of mono- and oligosaccharides to database of the computer program CASPER, and appli- cations thereof. v vi List of papers This thesis is based on the following papers, which are referred to in the text by their Roman numerals. Reprints were made with kind permission from the publishers. I. pKa-Determination and conformational studies by NMR spectroscopy of D-altrose-containing and other pseudodisaccharides as glycosidase inhibitor candidates Rönnols, J.; Burkhardt, A.; Cumpstey, I.; Widmalm, G. Eur. J. Org. Chem. 2012, 74–84. II. Synthesis, conformation and biology of naphthoxylosides Siegbahn, A.; Aili, U.; Ochocinska, A.; Olofsson, M.; Rönnols, J.; Mani, K.; Widmalm, G.; Ellervik, U. Bioorg. Med. Chem. 2011, 19, 4114–4126. III. Exploration of conformational flexibility and hydrogen bonding of xylosides in different solvents, as a model system for enzyme active site interactions Rönnols, J.; Manner, S.; Siegbahn, A.; Ellervik, U.; Widmalm, G. Org. Biomol. Chem. 2013, 11, 5465–5472. IV. Chair interconversion and reactivity of mannuronic acid esters Rönnols, J.; Walvoort, M. T. C.; van der Marel, G. A.; Codée, J. D. C.; Widmalm G. Submitted V. Rapid epimerization and DYKAT of glycal derivatives, with a cyclopentadienylruthenium catalyst Lihammar, R.; Rönnols, J.; Widmalm, G.; Bäckvall, J. -E. Manuscript vii VI. Complete 1H and 13C NMR chemical shift assignments of mono- to tetrasaccharides as basis for NMR chemical shift predictions of oligosaccharides using the computer program CASPER Rönnols, J.; Pendrill, R.; Fontana, C.; Hamark, C.; Angles D’Ortoli, T.; Engström, O.; Ståhle, J.; Zaccheus, M. V.; Säwén, E.; Hahn, L. E.; Iqbal, S.; Widmalm, G. Carbohydr. Res. 2013, In press. Papers not included in this thesis Synthesis and molecular dynamics simulations on a tetrasaccharide corresponding to the repeating unit of the capsular polysaccharide from Salmonella enteritidis Olsson, J. D. M.; Landström, J.; Rönnols, J.; Oscarson, S.; Widmalm, G. Org. Biomol. Chem. 2009, 7, 1612–1618. Complete 1H and 13C NMR chemical shift assignments of mono-, di-, and trisaccharides as basis for NMR chemical shift predictions of polysaccharides using the computer program CASPER Roslund, M. U.; Säwén, E.; Landström, J.; Rönnols, J.; Jonsson, K. H. M.; Lundborg, M.; Svensson, M. V.; Widmalm, G. Carbohydr. Res. 2011, 346, 1311–1319. viii Contents Abstract ......................................................................................................... v List of papers .............................................................................................. vii Papers not included in this thesis .......................................................................... viii 1 Introduction ......................................................................................... 1 1.1 Carbohydrates ................................................................................................... 1 1.2 Carbohydrate conformation ............................................................................ 3 1.2.1 Ring conformation .................................................................................. 3 1.2.2 Exocyclic torsions ................................................................................... 5 1.2.3 Hydrogen bonds ..................................................................................... 6 1.3 Reactions of the glycosidic bond ................................................................... 7 1.3.1 Enzymatic reactions .............................................................................. 7 1.3.2 Synthetic glycosylation ......................................................................... 7 2 NMR spectroscopy .............................................................................. 9 2.1 J-couplings and conformational analysis ..................................................... 9 2.2 Nuclear Overhauser effect ............................................................................ 11 2.3 Dynamic NMR .................................................................................................. 12 3 Conformational studies of pseudodisaccharides (Paper I) ...... 15 3.1 Results and discussion ................................................................................... 16 3.1.1 NMR assignments ................................................................................. 16 3.1.2 Conformational analysis ..................................................................... 16 3.2 Conclusions ...................................................................................................... 20 4 Conformational studies of xylose derivatives (Papers II and III) ............................................................................................................. 21 4.1 Results and discussion ................................................................................... 22 4.1.1 Initial measurements .......................................................................... 22 4.1.2 Dynamics of compound 16 ................................................................ 24 4.1.3 Solvent effects ...................................................................................... 26 4.1.4 Fluorinated compounds ...................................................................... 28 4.1.5 C-Methyl compounds ........................................................................... 30 4.1.6 3-substitution ........................................................................................ 32 4.2 Conclusions ...................................................................................................... 34 ix 5 Chair interconversions and reactivity of mannuronic acid esters (Paper IV) ....................................................................................... 36 5.1 Results ............................................................................................................... 37 5.1.1 NMR spectroscopy ................................................................................ 37 5.1.2 Conformational distribution ............................................................... 38 5.1.3 Dynamics ............................................................................................... 40 5.1.4 Competition experiments ................................................................... 42 5.2 Discussion ......................................................................................................... 43 5.2.1 Kinetics and conformational itinerary .............................................. 43 5.2.2 Conformational equilibria ................................................................... 45 5.3 Conclusions ...................................................................................................... 45 6 Epimerization and DYKAT of glycal derivatives (Paper V) ....... 46 6.1 Results and discussion ................................................................................... 47 6.1.1 Epimerization ........................................................................................ 47 6.1.2 Equilibrium populations and conformations ................................... 50 6.1.3 DYKAT ..................................................................................................... 52 6.2 Conclusions ...................................................................................................... 53 7 Development of the NMR-database for CASPER (Paper VI) ... 54 7.1 Results and discussion ..................................................................................