Simulation of 2D NMR Spectra of Carbohydrates Using GODESS Software
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1 Supporting Information Simulation of 2D NMR Spectra of Carbohydrates Using GODESS Software Roman R. Kapaev*, and Philip V. Toukach*, Higher Chemical College of the Russian Academy of Sciences, Miusskaya sq. 9, Moscow , Russia N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prosp. 47, Moscow , Russia * Corresponding authors: Roman R. Kapaev <kapaev_roman@mail.ru>, Philip V. Toukach <netbox@toukach.ru> ABSTRACT: Glycan Optimized Dual Empirical Spectrum Simulation (GODESS) is a web service, which has been recently shown to be one of the most accurate tools for simulation of 1 H and 13 C 1D NMR spectra of natural carbohydrates and their derivatives. The new version of GODESS supports visualization of the simulated 1 H and 13 C chemical shifts in the form of most 2D spin correlation spectra commonly used in carbohydrate research, such as 1 H- 1 H TOCSY, COSY/COSY-DQF/COSY-RCT and 1 H- 13 C edhsqc, HSQC-COSY, HSQC-TOCSY, and HMBC. Peaks in the simulated 2D spectra are color-coded and labeled according to the signal assignment, and can be exported in JCAMP-DX format. Peak widths are estimated empirically from the structural features. GODESS is available free of charge via the Internet at the platform of the Carbohydrate Structure Database (CSDB) project ( Page S-1
2 Section 1. Peak width estimation algorithm. Each 1 H chemical shift is given a width index I w. The peak width (PW, in Hz), is roughly estimated basing on typical values of spin coupling constants in carbohydrates and derivatives. 1-5 PW values are calculated according to the formula: = 3 The numerical term (3 Hz) is a step of coupling constant estimation, which was chosen to obtain 3-4 grades of spin-spin coupling range within 2-15 Hz. The I w is calculated as a sum of the following terms: 1. Geminal spin-spin coupling term a. is equal to 1 for geminal protons attached to sp 2 -carbons b. is equal to 3 for geminal protons attached to sp 3 -carbons c. is equal to 0 for non-geminal protons 2. Spin-spin couplings with vicinal protons (all vicinal protons are divided into groups, each group includes all atoms linked to the same carbon and is considered independently): a. in case the interacting protons are exocyclic I. is equal to 3 if both the current (simulated proton) and its vicinal protons are attached to sp 2 -carbons (e.g., H9-H10 of oleic acid) II. is equal to 2 if the current and/or its vicinal proton are attached to sp 3 -carbons (e.g., protons of stearic acid, ribitol, H6-H7 of ᴅ-glycero-ʟ-manno-heptose) b. in case the interacting protons are endocyclic I. if there is only one vicinal proton in a group, for furanose residues i. is equal to 2 if the current and the vicinal protons are in cis-configuration (e.g., tagatofuranose H3-H4) ii. is equal to 3 if the current and the vicinal protons are in transconfiguration (e.g., fructofuranose H3-H4) iii. is equal to 2.5 if the current proton has a geminal neighbor (e.g., tyvelose H3/H3 with H2 vicinal). In this case, I w = 2 for the one (cis) and I w = 3 for the other (trans) methylene proton. Mapping between these two crosspeaks and these two protons is impossible, so the values are averaged. iv. is equal to 1 in any other case (e.g., double bond) II. if there is only one vicinal proton in a group, for pyranose residues i. is equal to 3 if both protons are axial (e.g., Glcp H2-H3) ii. is equal to 1 if at least one of the protons is equatorial (e.g., α-glcp H1- H2, Manp H2-H3, Arap H5-H6/H6 with H5 vicinal) iii. is equal to 2 if the current proton has a geminal neighbor and the vicinal proton is axial (e.g., tyvelose H3/H3 with H2 vicinal). In this case, I w = 1 for the one (ax-eq) and I w = 3 for the other (ax-ax) methylene proton. Mapping between these two cross-peaks and these two protons is impossible, so the values are averaged. iv. is equal to 1 in any other case (e.g., double bond) III. is equal to 4 for pyranose and to 5 for furanose residues if there are two vicinal protons in a group (e.g., tyvelose H2 with deoxy H3/H3 vicinal) c. in case the interacting protons are both endo- and exocyclic I. is equal to 1 if there is only one vicinal proton in a group (e.g., Glc H6 with H5 vicinal, pseudaminic acid H6 with H7 vicinal) II. is equal to 2 if there are three vicinal protons in a group, implying a methyl group (e.g., rhamnopyranose H5 with H6 vicinal) III. is equal to 3 if there are two vicinal protons in a group (e.g., Glc H5 with H6 vicinal) d. is equal to 0 if there are no vicinal protons (e.g., fructofuranose H1) Along the 13 C axis, every cross-peak is considered 125 Hz wide, which is a typical value in heteronuclear 2D NMR spectra. Page S-2
3 Figure S1. GODESS structure input interface: (1) structure input options, (2) CSDB linear code input field, (3) simulation settings (clicking More parameters checkbox shows/hides the additional parameters). Figure S2. Residue assignment (a) and trustworthiness (b) visualization modes for the COSY spectrum of sucrose. In the assignment mode, glucose residue peaks are plotted in red and fructose peaks are plotted in green; the labels represent the signal assignment to atoms. In the trustworthiness mode, the greener peak stands for the more accurate simulation; the labels are a numeric metric of trustworthiness. Page S-3
4 Figure S3. edhsqc spectrum of sucrose (residue assignment visualization mode). Negative peaks are shown as rectangles and positive ones are shown as ellipses. Glucose residue peaks are plotted in red and fructose peaks are plotted in green. Figure S4. HMBC spectrum of sucrose (residue assignment visualization mode). Glucose residue peaks are plotted in red and fructose peaks are plotted in green. The inter-residue peak between glucose H1 and fructose C2 is plotted using both colors. Page S-4
5 Figure S5. Options available by mouse hovering over JDX. Clicking Live view NMR opens the cheminfo.org online 2D NMR viewer (see Figure S6). Figure S6. Simulated HSQC spectrum of α-lactose opened in the cheminfo.org online 2D NMR viewer. Page S-5
6 Figure S7. Simulated HSQC spectra of lactose (α-lactose, red; β-lactose, blue) exported to JCAMP-DX file and viewed in MestreNova in superposition with experimental HSQC spectrum of lactose. The experimental spectrum with slightly different recording options was adapted with DSS/TMS correction from record ID bmse in Biological Magnetic Resonance Data Bank 6. Page S-6
7 Figure S8. Experimental (black) and simulated (red) COSY spectra of the O-polysaccharide from Citrobacter freundii O22 strain PCM Figure S9. Experimental (black) and simulated (red) HSQC spectra of the O-polysaccharide from Proteus mirabilis G1. Page S-7
8 Figure S10. Experimental (black) and simulated (red) TOCSY spectra portions of Streptococcus suis serotype 2 capsular polysaccharide. Page S-8
9 References 1. Pretsch, E.; Bühlmann, P.; Affolter, C. In Structure determination of organic compounds; Pretsch, E.; Bhuhlmann, P.; Affolter, C., Ed.; Springer-Verlag Berlin Heidelberg: 2009; Vol. 13., Chapter 5, pp Altona, C.; Haasnoot, C. A., Prediction of Anti and Gauche Vicinal Proton Proton Coupling Constants in Carbohydrates: a Simple Additivity Rule for Pyranose Rings. Org. Magn. Resonance 1980, 13, De Leeuw, F. A.; Altona, C., Computer Assisted Pseudorotation Analysis of Five Membered Rings by Means of Proton Spin Spin Coupling Constants: Program PSEUROT. J. Comput. Chem. 1983, 4, Olson, W. K.; Sussman, J. L., How Flexible is the Furanose Ring? 1. A Comparison of Experimental and Theoretical Studies. J. Am. Chem. Soc. 1982, 104, Stenutz, R.; Carmichael, I.; Widmalm, G.; Serianni, A. S., Hydroxymethyl Group Conformation in Saccharides: Structural Dependencies of 2 J HH, 3 J HH, and 1 J CH Spin-Spin Coupling Constants. J. Org. Chem. 2002, 67, Ulrich, E. L.; Akutsu, H.; Doreleijers, J. F.; Harano, Y.; Ioannidis, Y. E.; Lin, J.; Livny, M.; Mading, S.; Maziuk, D.; Miller, Z., BioMagResBank. Nucl. Acids Res. 2008, 36, D402-D408. Page S-9
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