Conformational Analysis of Gentiobiose Using Genetic Algorithm Search and GIAO DFT Calculations with ¹³C CPMAS NMR as a Verification Method

REFERENCES

• Webster, A.; Osifo P.O.; Neomagus, H.W.J.P.; Grant, D.M. A comparison of glycans and polyglycans using solid-state NMR and X-ray powder diffraction. Solid STATE NMR. 2006, 30, 150–161.
   PubMed Web of Science ®Google Scholar
• Jeffrey, G.A.; Saenger, W. Hydrogen Bonding in Biological Structures. Springer-Verlag: Berlin 1991.
   Google Scholar
• Earl, W.L.; Parish, A.F.W. A cross-polarisation-magic-angle sample spinning N.M.R. study of several crystal forms of lactose. Carbohydr. Res. 1983, 115, 23–32.
   Web of Science ®Google Scholar
• Jeffrey, G.A.; Wood, R.A; Pfefel, P.E.; Hicks, K.B. Crystal structure and solid-state NMR analysis of lactulose. J. Am. Chem. Soc. 1983, 105, 21–26.
   Web of Science ®Google Scholar
• Gray, G.A, Hill, H.D.W. Solid-state NMR spectroscopy. Distinction of diastereomers and determination of optical purity. Ind. Res. And Dev. 1980, 22, 131–136.
   Google Scholar
• Zang, P.; Klymachyov, W.N.; Brown, S.; Ellington J.G.; Grandinetti P.J. Solid-state 13C NMR investigations of the glycosidic linkage in α-α′ trehalose. Solid State NMR 1998, 12, 221–225.
   PubMed Web of Science ®Google Scholar
• Yates, J.R.; Titman, J.J. Carbon-13 chemical shift tensors of disaccharides: Measurement. J. Phys. Chem. A 2007, 111, 13126.
   PubMed Web of Science ®Google Scholar
• Swalina, C.W.; Zauhar, R.J.; DeGrazia, M.J.; Moyna, G.J. Derivation of 13C chemical shift surfaces for the anomeric carbons of oligosaccharides and glycopeptides using ab initio methodology. Biomol. NMR 2001, 21, 49–61.
   PubMed Web of Science ®Google Scholar
• Sayers, E.W.; Prestegard, J.H. Solution conformations of a trimannoside from nuclear magnetic resonance and molecular dynamics simulations. Biophys. J. 2000, 79, 3313–3329.
   PubMed Web of Science ®Google Scholar
• Pereira, C.S.; Kony, D.; Baron, R.; Müller, M.; Van Gunsterenand, W.F.; Hünenberger, P.H. Conformational and dynamical properties of disaccharides in water: A molecular dynamics study. Biophys. J. 2006, 90, 4337–4344.
   PubMed Web of Science ®Google Scholar
• Ramakrishna, C. Ramachandran and his map. Resonance 2001, 6, 48–56.
   Google Scholar
• Perez, S.; Kouwijzer, M.; Mazeru, K.; Engelsen, S.B. Modeling polysaccharides: Present status and challenges. J. Mol.Graph. 1998, 14, 307–321.
   Google Scholar
• Stortz, C.A. Disaccharide conformational maps: how adiabatic is an adiabatic map? Carbohydr. Res. 1999, 322, 77–86.
   PubMed Web of Science ®Google Scholar
• Frank, M.; Lutteke, T.; Von der Lieth, C.W. GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages. Nuclei Acids Res. 2007, 35, 287–290.
   PubMed Web of Science ®Google Scholar
• Nahmany, A.; Strino, F.; Rosen J.; Kemp, G.J.; Nyholm, P.G. The use of a genetic algorithm search for molecular mechanics (MM3) based conformational analysis of oligosaccharides. Carbohydr Res. 2005, 340, 1059–1064.
   PubMed Web of Science ®Google Scholar
• Strino, F.; Nahmany, A.; Rosen, J.; Kemp, G.J.L; Sa-Correia, I.; Nyholm, P.G. Conformation of the exopolysaccharide of Burkholderia cepacia predicted with Molecular Mechanics (MM3) using genetic algorithm search. Carbohydr. Res. 2005, 340, 1019–1024.
   PubMed Web of Science ®Google Scholar
• Goldberg, D.E. Genetic Algorithms in Search, Optimization and Machine Learning, Addison Wesley: New York, 1989.
   Google Scholar
• Rohrer, D.C.; Sarko, A.; Bluh, T.L., Lee, Y.N. The structure of gentiobiose. Acta Crystallogr. B 1980, 36, 650–654.
   Web of Science ®Google Scholar
• Arene, F.; Neuman, A.; Longchambon, F. Solid-state and solution conformation of scleroglucan. C.R. Acad. Sci., Ser C 1979, 288, 331–334.
   Google Scholar
• Yui, T.; Goto, K.; Kawano, Y.; Ogawa, K. Molecular modeling study of highly branching (1–>3)-alpha-D-glucan, a model polysaccharide for cariogenic glucan, using the N-H mapping method. Biosci. Biotechnol. Biochem. 2000, 64, 52–60.
   PubMed Web of Science ®Google Scholar
• Wawer, A. Evolutionary algorithm in conformational analysis. Polish-Japanese Institute Information Technology2003.
   Google Scholar
• HyperChem ™ Professional 8.0, Hypercube, Inc. 1115 NW 4th Street, Gainesville, Florida 32601, USA.
   Google Scholar
• Hocquet, A.; Laggard, M. An evaluation of the MM+ force field. J. Mol. Model. 1998, 4, 94–112.
   Web of Science ®Google Scholar
• Stortz, C.A.; Johnson, G.P.; French, A.D.; Csonka, G.I. Comparison of different force fields for the study of disaccharides. Carbohydr. Res. 2009, 344, 2217–2228.
   PubMed Web of Science ®Google Scholar
• Gaussian 09, Revision, Frisch, M.J.; Trucks, G.W.; Schlegel, H.B.; Scuseria, G.E.; Robb, M.A.; Cheeseman, J.R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G.A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H.P.; Izmaylov, A.F.; Bloino, J.; Zheng, G.; Sonnenberg, J.L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, J.A.; Peralta, Jr., J.E.; Ogliaro, F.; Bearpark, M.; Heyd, J.J.; Brothers, E.; Kudin, K.N.; Staroverov, V.N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J.C.; Iyengar, S.S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, J.M.; Klene, M.; Knox, J.E.; 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.; Martin, R.L.; Morokuma, K.; Zakrzewski, V.G.; Voth, G.A.; Salvador, P.; Dannenberg, J.J.; Dapprich, S.; Daniels, A.D.; Farkas, Ö.; Foresman, J.B.; Ortiz, J.V.; Cioslowski, J.; Fox, D.J. Gaussian, Inc., Wallingford CT, 2009.
   Google Scholar
• Klein, R.A. Hydrogen bonding in diols and binary diol-water systems investigated using DFT methods. II. Calculated infrared OH-stretch frequencies, force constants, and NMR chemical shifts correlate with hydrogen bond geometry and electron density topology. A reevaluation of geometrical criteria for hydrogen bonding. J. Am. Chem. Soc. 2002, 124, 13931–13937.
   PubMed Web of Science ®Google Scholar
• Roslund, M.U.; Tähtinen, P.; Niemitz, M.; Sjöholm, R. Complete assignments of the (1)H and (13)C chemical shifts and J(H,H) coupling constants in NMR spectra of D-glucopyranose and all D-glucopyranosyl-D-glucopyranosides. Carbohydr. Res. 2008, 343, 101–112.
   PubMed Web of Science ®Google Scholar
• Temeriusz, A.; Gubica, T.; Rogowska, P.; Paradowska, K.; Cyrański, M.K. Crystal structure and solid state 13C NMR analysis of nitrophenyl 2,3,4,6-tetra-O-acetyl-β-D-gluco and D-galactopyranosides. Carbohydr. Res. 2005, 340, 1175–1184.
   PubMed Web of Science ®Google Scholar
• Paradowska, K.; Gubica, T.; Temeriusz, A.; Cyrański, M.K.; Wawer, I. 13C CPMAS NMR and crystal structure of methyl glycopyranosides. Carbohydr. Res. 2008, 343, 2299–2307.
   PubMed Web of Science ®Google Scholar
• Horii, F.; Hirai, A.; Kitamaru, R. Solid-state 13C-NMR study of conformations of oligosaccharides and cellulose. Conformation of CH2OH group about the exo-cyclic C-C bond. Polym. Bull. 1983, 10, 357–361.
   Web of Science ®Google Scholar
• Kupka, T.; Pasterna, G.; Lodowski, P.; Szeja, W. GIAO -DFT prediction of accurate NMR parameters in selected glucose derivatives. Magn. Reson. Chem. 1999, 37, 421–426.
   Web of Science ®Google Scholar
• Forsyth, D.A.; Sebag, A.B. Computed 13C NMR chemical shifts via empirically scaled GIAO shieldings and molecular mechanics geometries. Conformation and configuration from 13C shifts. J. Am. Chem. Soc. 1997, 119, 9483–9494.
   Web of Science ®Google Scholar
• Lefort, R.; Bordat, P.; Cesaro, A.; Descamps, M. Exploring the conformational energy landscape of glassy disaccharides by cross polarization magic angle spinning 13C nuclear magnetic resonance and numerical simulations. II. Enhanced molecular flexibility in amorphous trehalose. J. Chem. Phys. 2007, 126, 014510–9.
   Web of Science ®Google Scholar
• Javaroni, F.; Ferreira, A.B.B.; da Silva, C.O. The (alpha-1,6) glycosidic bond of isomaltose: A tricky system for theoretical conformational studies. Carbohydr. Res. 2009, 344, 1235–1247.
   PubMed Web of Science ®Google Scholar
• Olsson, U.; Säwén, E.; Stenutz, R.; Widmalm, G. Conformational flexibility and dynamics of two (1–>6)-linked disaccharides related to an oligosaccharide epitope expressed on malignant tumour cells. Chem.-Eur. J. 2009, 15, 8886–8894.
   PubMed Web of Science ®Google Scholar
• Sergeyev, I.; Moyna, G. Determination of the three-dimensional structure of oligosaccharides in the solid state from experimental 13C NMR data and ab initio chemical shift surfaces. Carbohydr. Res. 2005, 340, 1165–1174.
   PubMed Web of Science ®Google Scholar