#06. 2012-01-20 Quiz 1: Thursday 26 Jan 2012 from 11 AM to 12 noon GG Building Ground Floor #06. 2012-01-20 Last class... Clarification on torsion potential: periodicity 2 and 3 Conformer selection, active/inactive conformations, activation by ligands, etc. - alternative models Inter- and intra-molecular interactions Non-covalent / non-bonded interactions Bonded and non-bonded atoms Hard-sphere approximation Steric effect Preference of trans over gauche conformation for bulky groups #06. 2012-01-20 Monosubstituted cyclohexanes Me Me Bulky group is axially Bulky group is equatorially oriented: gauche to both oriented: trans to both vicinal carbon atoms vicinal carbon atoms #06. 2012-01-20 Monosubstituted cyclohexanes Me Me Bulky group is axially Bulky group is equatorially oriented: gauche to both oriented: trans to both vicinal carbon atoms vicinal carbon atoms #06. 2012-01-20 Cis 1,2-disubstituted cyclohexane Me 4 5 6 Me 3 2 1 #06. 2012-01-20 Trans 1,4-disubstituted cyclohexane 4 5 6 Me Me 3 2 1 #06. 2012-01-20 What governs the conformational preferences? Conformation “a” Conformation “b” Unfolded Folded (protein, DNA, RNA) Monomers (homo/hetero) Oligomer(s) (protein, lipid) A + B A·B (binding) ∆∆∆G = ∆∆∆H – T ∆∆∆S Steric criterion – (approximation of) van der Waals interactions Often, van der Waals contribution is not predominant #06. 2012-01-20 Conformation of 1,3,5-trineopentylbenzene CH 2-tBu tBu-H2C CH 2-tBu Two neopentyl groups are on one side, All the three neopentyl groups are on third on the other side of the ring the same side of the ring view along the plane of the ring Nishio & Hirota (1989) Tetrahedron 45:7201 #06. 2012-01-20 Conformation of Ph-CH(Me)-CH 2-tBu Ph-CH(Me)-X-tBu gauche X= CH 2, CHOH, S, SO, SO 2 Preferred: Tertiary butyl (tBu) group is trans to the methyl group, trans gauche to the phenyl group Expected solely based on steric criterion: Tertiary butyl (tBu) group is gauche to the methyl group, trans to the phenyl group Nishio & Hirota (1989) Tetrahedron 45:7201 #06. 2012-01-20 Gauche preference n-pentane CH 3-CH 2-CH 2-CH 2-CH 3 CH 3-CH 2-CH 2-CH 2-CH 3 trans to each other trans to each other Dimethoxymethane CH 3-O-CH 2-O-CH 3 gauche preferred over trans #06. 2012-01-20 Conformation of n-alkanes: chain length & solvent effect C6D6 1-Chloronaphthalene n-Hexane Extended Extended n-Dodecane Open “U” shaped J Chem Soc Perkin Trans. 2, (2001) 2370-3 (no volume #) Summary #06. 2012-01-20 Steric criterion helps us to rationalize preferred conformations only when van der Waals contribution is predominant Exceptions discussed: 1,3,5-trineopentylbenzene Ph-CHMe-CH2-tBu Dimethoxymethane – anomeric effect n-Decane in different solvents Relationship among monosaccharides – chemists’#06. view 2012-01-20 Notation HCO H OH = HOCH 2 Glyceraldehyde HCO HCO D-series HOCH HOCH 2 2 ET Erythrose Threose HCO HCO HCO HCO HOCH 2 HOCH 2 HOCH 2 HOCH 2 Right AXLe Ribose Arabinose Xylose Lyxose HCO HCO HCO HCO HCO HCO HCO HCO ALL ALTRuists GLadly MAke GUm In GALlon HOCH 2 HOCH 2 HOCH 2 HOCH 2 HOCH 2 HOCH 2 HOCH 2 HOCH 2 TAnks Allose Altrose Glucose Mannose Gulose Idose Galactose Talose #06. 2012-01-20 Different ring forms of glucose 4C 3 ααα-D-Glucopyranose ( 1) ααα-D-Glucofuranose ( E) D-Glucose 4C 3 βββ-D-Glucopyranose ( 1) βββ-D-Glucofuranose ( E) #06. 2012-01-20 Monosaccharides: glucose, prototypical example 6 6 1 5 5 4 1 3 2 4 3 2 4C 1C Pyranose ring conformation: 1 Pyranose ring conformation: 4 #06. 2012-01-20 1C Pyranose ring in 4 conformation (cyclodextrin) C6 C1 C5 C4 C3 C2 Cambridge structural database code: HEZWAK01 Rendered using RasMol 2.7.2 Caira et al., (1994) J Chem Soc Perkin Trans 2:2071 #06. 2012-01-20 Effect of substituents on ring conformation Xylopyranose derivatives CSD refcode OACXPF C4 C5 CSD refcode C3 OBZXYP10 C1 C2 Luger et al., (1979) Carbohydr. Res. 68, 207 Kothe et al., (1979) C5 Acta Cryst. B30, 365 C1 C4 C3 C2 O-acetyl derivative O-benzoyl derivative #06. 2012-01-20 Idose, an “unusual” monosaccharides CHO CHO H OH HO H HO H H OH H OH HO H H OH H OH CH 2OH CH 2OH D-Glucose D-Idose (stereoisomer) βββ-D-Glucose #06. 2012-01-20 Biological systems: L-enantiomer / uronic acid CHO CHO CHO HO H H OH H OH H OH HO H HO H HO H H OH H OH H OH HO H HO H CH 2OH CH 2OH COOH D-Idose L-Idose L-Iduronic acid Constituent of glycosaminoglycans (e.g., heparin, heparan sulphate) #06. 2012-01-20 Conformational preferences of idose 4C 1C 2S 1-ααα-L-idopyranose 4-ααα-L-idopyranose O-ααα-L-iduronopyranose -CH 2OH - axial All 4 –OH - axial Staggered, but not maximally Considerable fraction of monosaccharide exists in furanose form Biochemistry by Stryer, L., p257 (2nd ed.) – heparin as anticoagulant #06. 2012-01-20 Skew-boat conformation skew-boat conformation: atoms i and i+2 out of plane ααα-L-Iduronic acid (monosaccharide; aldohexose derivative) Skew-boat conformation 2S ( O) Chair / boat conformations: atoms i and i+3 out of plane #06. 2012-01-20 Pyranose ring in skew-boat conformation C3 C1 C4 C6 Heparin heptasaccharide C5 C2 Protein database id: 1SR5:NT1 Rendered using RasMol 2.7.2 In complex with antithrombin Nat Struct Mol Biol 2004 11:863 #06. 2012-01-20 Conformation of heparin heptasaccharide Protein database id: 1SR5:NT1 Rendered using RasMol 2.7.2 In complex with antithrombin Nat Struct Mol Biol 2004 11:863 1. Changes in the conformation of the pyranose rings 2. Rotations around the single bonds, especially those that link the pyranose rings These will alter the spatial positions of the sulfate groups with respect to each other #06. 2012-01-20 Chair-boat transitions in polysaccharides Polysaccharide elasticity is governed by chair-boat transitions of the glucopyranose ring Comparison of ααα- and βββ-linked polysaccharides 4C 4C ααα-D-Glucopyranose ( 1) βββ-D-Glucopyranose ( 1) Nature (1998) 396:661 #06. 2012-01-20 Half-chair conformation atoms i and i+1 out of plane ααα-D-Glucose (Glc694) part of a nonasaccharide in complex with D229N-E257Q-cyclodextringlycosyltransferase (CGTase) from Bacillus circulans strain 251 (PDB id 1CXK) 2H Distorted towards a 3-half chair conformation Uitdehaag et al., (1999) Nat Struct Biol 6:432-6 #06. 2012-01-20 Ribose: in solution and in nucleic acids CHO H OH βββ-D-Ribofuranose (3E) H OH H OH CH 2-OH D-Ribose 4C βββ-D-Ribopyranose ( 1) #06. 2012-01-20 Distorted conformations of pyranose rings Nature (2001) 412:835-838 Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate D J Vocadlo, G J Davies, R Laine, S G Withers Carbohydrate Research (2001) 331:461-467 Boat conformations: synthesis, NMR spectroscopy and molecular dynamics of methyl 4,6-O-benzylidene-3- deoxy-3-phthalimido-ααα-D-altropyranoside derivatives B Coxon, R C Reynolds Examples chosen arbitrarily.