Supporting Information. S1: NMR Spectroscopy and resonance assignments ( 1 H, 13 C)
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1 Supporting Information S1: NMR Spectroscopy and resonance assignments ( 1 H, 13 C) All NMR spectra were recorded at 25 C. Heteronuclear [ 1 H, 13 C] HSQC spectra were standard experiments in D 2 O (99.990%) recorded at natural abundance and conducted with a 1 H frequency of 600 MHz on a Bruker spectrometer equipped with a z gradient TXI cryoprobe. Vicinal couplings reported in in Figure 2 were measured from [ 1 H] 1D spectra recorded with 32,768 complex points at 900 MHz. The Varian INOVA 900 MHz NMR Spectrometer was from the Henry Wellcome Building for Biomolecular Spectroscopy, University of Birmingham, UK. [ 1 H ] and [ 13 C ]chemical shift assignments (ppm, relative to DSS) for the three monosaccharides: 600 MHz [ 1 H, 13 C] HSQC spectra of IdoA (red) and IdoA2S (blue) are overlayed in the figure below
2 S2: Annotated 900 MHz [ 1 H] 1D NMR spectrum of 1 O Me α L iduronic acid (full spectrum in S19)
3 S3: Annotated 900 MHz [ 1 H] 1D NMR spectrum of 1 O Me α L iduronic acid 2 sulfate (full spectrum in S20)
4 S4: Annotated 900 MHz [ 1 H] 1D NMR spectrum of 1 O Me β D glucuronic acid (full spectrum in S21)
5 S5: Cremer Pople analysis for 1 O Me α L iduronic acid
6 S6: Cremer Pople analysis for 1 O Me α L iduronic acid 2 sulfate
7 S7: Cremer Pople analysis for 1 O Me β D glucuronic acid
8 S8: Equilibration of monosaccharide conformation (convergence of the Cremer Pople polar angle θ) IdoA (black), IdoA2S (red) and GlcA (green) simulations (initialized as 1 C 4 and 4 C 1 ) are illustrated dynamic average of the cos(θ); the mean value of cos(θ) over the entire trajectory
9 S9: Population analysis (normalized occupancy of 1 C 4, 2 S 0 and 4 C 1 conformations in each simulation) IdoA: 1 C 4 IdoA: 4 C 1 IdoA2S: 1 C 4 IdoA2S: 4 C 1 GlcA: 1 C 4 GlcA: 4 C 1 1 C S C S10: Free energy, conformational exchange rate and vicinal coupling calculations Free energies were derived from ΔG = RTln(p 1 /p 2 ); where p 1 and p 2 are the equilibrium populations. Conformational exchange rates for IdoA were derived by (a) counting transitions ( 1 C 4 > 4 C 1 and 4 C 1 > 1 C 4 ), (b) determining the lifetimes and (c) the rates (μs 1 ). The reported equilibrium constants are the ratio of the rates. Errors in the vicinal coupling calculations reported on Figure 2 were calculated as standard deviations. Each 10 μs trajectory was split into ten 1 μs sub trajectories. Vicinal couplings were calculated for each 1 μs sub trajectory and the standard deviations of the 10 values are reported to 1 decimal place in Figure 2 (i.e. standard deviation of < 0.05 Hz is reported as 0.0). S11: Molecular dynamics: Sulfate parameterization and simulation initiation The sulfate topology for use in the model IdoA2S was appended manually. Sulfate parameters not present in the GLYCAM06 parameter set (the angle O S O and the torsion C2 O2 S O) were appended using values from the General Amber Forcefield. 1 Merz Singh Kollman 2 electrostatic potential derived partial charges for this modified residue were computed using Gaussian 03 3 following gas phase geometry optimization at the HF/6 31G(d)//HF/6 31G(d) level of theory (see below). This approach and level of theory is consistent with GLYCAM06. Each system was energy minimized prior to molecular dynamics simulation. The systems were then heated from 0K to 298K over 1 ns. Bonds to hydrogen atoms were constrained using the M SHAKE algorithm (Krutler, V.; van Gunsteren, W. F.; Hnenberger, P. H. J. Comput. Chem. 2001, 22, )
10 AMBER PREP file for IdoA2S 1 DUMM DU M DUMM DU M DUMM DU M C1 CG M H1 H2 E C5 CG M H5 H1 E C6 C B O6A O2 E O6B O2 E C4 CG M H4 H1 E O4 OH S H4O HO E C3 CG M H3 H1 E O3 OH S H3O HO E C2 CG M H2 H1 E O2 OS S SO2 S OS1 O2 E OS2 O2 E OS3 O2 E
11 S12: Conformational free energies (ΔG, kcal mol 1 ) derived from equilibrium populations, Figure 1 data CP θ ΔG IdoA ΔG IdoA2S ΔG GlcA n/s n/s n/s n/s n/s n/s n/s n/s n/s n/s CP θ: Cremer Pople polar angle θ (reaction coordinate). Value represents half way point in each bin (i.e. 2.5 represents a bin of θ values in the range 1 5). Data were normalized. n/s: not sampled at 298K
12 S13: Experimental and calculated pyranose ring 1 H 1 H vicinal couplings ( 3 J H,H, Hz), Figure 2 data Expt. HB AH Expt. Error HB Error AH Error IdoA_J 1, IdoA _J 2, IdoA _J 3, IdoA _J 4, IdoA2S_J 1, IdoA2S _J 2, IdoA2S _J 3, IdoA2S _J 4, GlcA_J 1, GlcA_J 2, GlcA_J 3, GlcA_J 4, Expt.: Measured or modeled (line fit) from 900 MHz 1H 1D NMR spectra (see S2 4 and S19 S21) HB: Calculated (Hricovini and Bizik) 4 AH: Calculated (Altona and Haasnoot) 5
13 S14: Synthesis of L iduronic acid and 2 O sulfated L iduronic acid methyl glycosides. The compounds used for NMR studies were synthesized according to the following scheme: Methyl 3 O benzyl α L iduronic acid pyranoside (4). To cyanohydrin 3 6 (4.1 g, 13.4 mmol) was added MeOH (25 ml) and then slowly AcCl (4 ml). The mixture was stirred 16 hours and the solvents evaporated. The residue was redissolved in EtOAc (200 ml) and extracted with water (200 ml). The organic phase was dried with MgSO 4 and evaporated to give 4.08 g of a crude mixture of furanoside and pyranoside forms of the L iduronic acid methyl ester methyl glycosides that could not be separated by column chromatography. This crude was dissolved in a mixture of THF/MeOH (30 ml/ 15 ml) and KOH (807 mg, 14.4 mmol) dissolved in water (15 ml) was added with stirring. After 2 hours the mixture was extracted with EtOAc (200 ml) and aqueous HCl (100 ml, 0.3M). The organic phase was dried with MgSO 4 and evaporated. Column chromatography using EtOAc/Hexane 1:1 with 1% HCOOH as the eluent yielded 2.05 g of a
14 mixture of Methyl L iduronic acid pyranosides (51%). From this crude 310 mg of 4 crystallized out as white needles from a mixture of EtOAc/Hexane (dissolved in EtOAc (50 ml) and hexane (50mL) added). Mp C. 1 H NMR (400 MHz, CD 3 OD) δ (m, 5H, Ph), (broad s, 1H, COOH), (m, 1H, H 1), 4.71 (d, J = 12.0 Hz, 1H, CH a Ph), 4.64 (d, J = 11.2 Hz, 1H, CH b Ph), (m, 1H, H 5), (m, 1H, H 4), (m, 1H, H 2), (m, 1H, H 3), 3.42 (s, 3H, OCH 3 ). 13 C NMR (100 MHz, CD 3 OD) δ 173.4, 139.5, 129.4, 128.9, 128.8, 103.8, 77.9, 73.0, 69.9, 69.5, 68.4, ESI HRMS: m/z: calcd for C 14 H 18 O 7 Na [M+Na] + : ; found: Methyl L iduronic acid pyranoside sodium salt (1). To 4 (35 mg, mmol) was added MeOH/H 2 O (1mL/1mL), NaOH (4.7 mg, mmol), 10% Pd(OH) 2 /C (47 mg) and the flask was fitted with a balloon containing hydrogen. The mixture was stirred vigorously over night, then filtered over celite and evaporated to give 27 mg of 1 (100%). ESI HRMS: m/z: calcd for C 7 H 11 O 7 [M Na] : ; found: Methyl 3 O benzyl 2 O sulfonato α L iduronic acid pyranoside disodium salt (5). To 4 (112 mg, 0.37 mmol) was added dry pyridine (3 ml) and pyridine sulfurtrioxide complex (111 mg, 0.74 mmol) and the mixture stirred under a nitrogen atmosphere for 2 hours. The reaction was then quenched with aqueous NaHCO 3 and evaporated. Column chromatography using CHCl 3 /MeOH 5:1 with 1% HCOOH as eluent, followed by conversion to the disodium salt by titration with NaOH (aq), yielded 72 mg of 5 (45%). 1 H NMR (400 MHz, CD 3 OD) δ (m, 5H, Ph), (m, 1H, H 1), 4.74 (d, J = 12.0 Hz, 1H, CH a Ph), 4.60 (d, J = 12.0 Hz, 1H, CH b Ph), (m, 1H, H 5), (m, 1H, H 2), (m, 1H, H 4), (m, 1H, H 3), 3.42 (s, 3H, OCH 3 ). 13 C NMR (100 MHz, CD 3 OD) δ 177.0, 139.4, 129.3, 129.0, 128.7, 101.9, 76.7, 72.6, 71.6, 69.6, 68.7, 56.2, ESI HRMS: m/z: calcd for C 14 H 17 O 10 S [M 2Na+H] : ; found: Methyl 2 O sulfonato L iduronic acid pyranoside disodium salt (2). To 5 (21 mg, mmol) was added MeOH/H 2 O (1mL/1mL), 10% Pd(OH) 2 /C (36 mg) and the flask was fitted with a balloon containing hydrogen. The mixture was stirred vigorously over night, then filtered over celite and evaporated to give 16 mg of 2 (100%). ESI HRMS: m/z: calcd for C 7 H 11 O 10 S [M 2Na+H] : ; found:
15 S15: 1 H NMR (400 MHz, CD 3 OD) 4:
16 S16: 13 C NMR (100 MHz, CD 3 OD) 4:
17 S17: 1 H NMR (400 MHz, CD 3 OD) 5:
18 S18: 13 C NMR (100 MHz, CD 3 OD) 5:
19 S19: 900 MHz [ 1 H] 1D NMR spectrum of 1 O Me α L iduronic acid
20 S20: 900 MHz [ 1 H] 1D NMR spectrum of 1 O Me α L iduronic acid 2 sulfate
21 S21: 900 MHz [ 1 H] 1D NMR spectrum of 1 O Me β D glucuronic acid
22 References (1) Wang, J. M.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Journal of Computational Chemistry 2004, 25, (2) Singh, U. C.; Kollman, P. A. Journal of Computational Chemistry 1984, 5, (3) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A.; Gaussian, Inc.,: Wallingford CT, (4) Hricovini, M.; Bizik, F. Carbohydr Res 2007, 342, (5) Altona, C.; Haasnoot, C. A. G. Org Magn Reson 1980, 13, (6) Hansen, S. U.; Barath, M.; Salameh, B. A.; Pritchard, R. G.; Stimpson, W. T.; Gardiner, J. M.; Jayson, G. C. Org Lett 2009, 11,
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