Potential energy surfaces of α-(1→3)-linked disaccharides calculated with the MM3 force-field

Journal of Carbohydrate Chemistry

Volumn 21, Issue 5, 2002, Pages 355-371

  Stortz, Carlos A ^a   Cerezo, Alberto S ^a  

^a UNIVERSIDAD DE BUENOS AIRES   (Argentina)

Author keywords

Axial; Conformational analysis; Disaccharide maps; Equatorial; MM3

Indexed keywords

DISACCHARIDE; HYDROXYL GROUP;

ARTICLE; CONFORMATION; DIELECTRIC CONSTANT; MATHEMATICAL COMPUTING; SYNTHESIS;

EID: 0036412624     PISSN: 07328303     EISSN: None     Source Type: Journal    
DOI: 10.1081/CAR-120014900     Document Type: Article

References (38)

1. a) French, A.D.; Brady, J.W. Computer modeling of carbohydrates. ACS Symp. Ser. 1990, 430, 1-19;
2. b) Engelsen, S.B.; Rasmussen, K. Conformations of disaccharides by empirical force field calculations. Part V: Conformational maps of β-gentiobiose in an optimized consistent force field. Int. J. Biol. Macromol. 1993, 15 (1), 56-62.
3. French, A.D.; Dowd, M.K. Exploration of disaccharide conformations by molecular mechanics. J. Mol. Struct., Theochem. 1993, 286, 183-201.
4. a) Lemieux, R.U.; Koto, S. The conformational properties of glycosidic linkages. Tetrahedron 1974, 30, 1933-1944;
5. b) Thøgersen, H.; Lemieux, R.U.; Bock, K.; Meyer, B. Further justification for the exo-anomeric effect. Conformational analysis based on nuclear magnetic resonance spectroscopy of oligosaccharides. Can. J. Chem. 1982, 60, 44-57.
6. a) Melberg, S.; Rasmussen, K. Conformations of disaccharides by empirical force-field calculations. Part I, β-maltose. Carbohydr. Res. 1979, 69, 27-38;
7. b) Melberg, S.; Rasmussen, K. Conformations of disaccharides by empirical force-field calculations. Part II, β-cellobiose. Carbohydr. Res. 1979, 71, 25-34.
8. c) Melberg, S.; Rasmussen, K. Conformations of disaccharides by empirical. Force-field calculations. Part III, β-gentiobiose. Carbohydr. Res. 1980, 78, 215-224.
9. a) Tvaroška, I.; Pérez, S. Conformational energy calculations for oligosaccharides: A comparison of methods and a strategy of calculation. Carbohydr. Res. 1986, 149 (2), 389-410;
10. b) French, A.D. Rigid- and relaxed-residue conformational analyses of cellobiose using the computer program MM2. Biopolymers 1988, 27 (9), 1519-1525;
11. c) Ha, S.N.; Madsen, L.J.; Brady, J.W. Conformational analysis and molecular dynamics simulations of maltose. Biopolymers 1988, 27 (12), 1927-1952;
12. d) French, A.D. Comparison of rigid and relaxed conformational maps for cellobiose and maltose. Carbohydr. Res. 1989, 188, 206-211;
13. e) Tran, V.; Buléon, A.; Imberty, A.; Pérez, S. Relaxed potential energy surfaces of maltose. Biopolymers 1989, 28, 679-690;
14. f) Imberty, A.; Tran, V.; Pérez, S. Relaxed potential energy surfaces of N-linked oligosaccharides: The mannose-α-(1→3)-mannose case. J. Comput. Chem. 1989, 11 (2), 205-216.
15. a) Allinger, N.L.; Yuh, Y.H.; Lii, J.-H. Molecular mechanics. The MM3 force field for hydrocarbons. J. Am. Chem. Soc. 1989, 111 (23), 8551-8566;
16. b) Allinger, N.L.; Rahman, M.; Lii, J.-H. A molecular mechanics force field (MM3) for alcohols and ethers. J. Am. Chem. Soc. 1990, 112 (23), 8293-8307.
17. a) Koca, J.; Pérez, S.; Imberty, A. Conformational analysis and flexibility of carbohydrates using the CICADA approach with MM3. J. Comput. Chem. 1995, 16 (3), 296-310;
18. b) Koca, J. Potential energy hypersurface and molecular flexibility. J. Mol. Struct. 1993, 291, 255-269.
19. a) Dowd, M.K.; Reilly, P.J.; French, A.D. Conformational analysis of trehalose disaccharides and analogues using MM3. J. Comput. Chem. 1992, 13 (1), 102-114;
20. b) Dowd, M.K.; French, A.D.; Reilly, P.J. Conformational analysis of the anomeric forms of sophorose, laminaribiose, and cellobiose using MM3. Carbohydr. Res. 1992, 233, 15-34;
21. c) Dowd, M.K.; French, A.D.; Reilly, P.J. Molecular mechanics modeling of α-(1→2), α-(1→3), and α-(1→6)-linked mannosyl disaccharides with MM3(92). J. Carbohydr. Chem. 1995, 14 (4&5), 589-600.
22. Dowd, M.K.; Zeng, J.; French, A.D.; Reilly, P.J. Conformational analysis of the anomeric forms of kojibiose, nigerose, and maltose using MM3. Carbohydr. Res. 1992, 230, 223-244.
23. Stortz, C.A. Disaccharide conformational maps: How adiabatic is an adiabatic map? Carbohydr. Res. 1999, 322, 77-86.
24. French, A.D.; Kelterer, A.-M.; Johnson, G.P.; Dowd, M.K.; Cramer, C.J. HF/6-31G* energy surfaces for disaccharide analogs. J. Comput. Chem. 2001, 22 (1), 65-78.
25. a) French, A.D.; Kelterer, A.-M.; Cramer, C.J.; Johnson, G.P.; Dowd, M.K. A QM/MM analysis of the conformations of crystalline sucrose moieties. Carbohydr. Res. 2000, 326, 305-322;
26. b) French, A.D.; Kelterer, A.-M.; Johnson, G.P.; Dowd, M.K.; Cramer, C.J. Constructing and evaluating energy surfaces of crystalline disaccharides. J. Mol. Graph. Model. 2000, 18 (2), 95-107.
27. Rees, D.A. Polysaccharide Shapes; Chapman & Hall: London, 1977; 51.
28. Stortz, C.A.; Cerezo, A.S. Conformational analysis of neocarrabiose and its sulfated and/or pyruvylated derivatives using the MM3 force-field. J. Carbohydr. Chem. 2000, 19 (9), 1115-1130.
29. Stortz, C.A.; Cerezo, A.S. Conformational analysis of sulfated α-(1→3)-linked D-galactobioses using the MM3 force-field. J. Carbohydr. Chem. 1998, 17 (9), 1405-1419.
30. MM3 (96). Bull. QCPE 1997, 17 (1), 3.
31. Engelsen, S.B.; Rasmussen, K. β-lactose in the view of a CFF-optimized force field. J. Carbohydr. Chem. 1997, 16 (6), 773-788.
32. a) Neuman, A.; Avenel, D.; Arène, F.; Gillier-Pandraud, H.; Pougny, J.-R.; Sinaÿ, P. Structure cristalline du méthyl-3-O-α-D-glucopyranosyl-α-D-glucopyranoside (méthyl-α-nigéroside). Carbohydr. Res. 1980, 80 (1), 15-24;
33. b) Luger, P.; Vangehr, K.; Bock, K.; Paulsen, H. Bestimmung der konformation der 2-acetamido-3-O-(2-acetamido-3,4,6-tri-O-acetyl-2-desoxy-α-D- galactopyranosyl)-1,4,6-tri-O-acetyl-2-desoxy-α-D-galactopyranose durch röntgenstrukturanalyse, NOE-messungen und HSEA-berechnungen. Carbohydr. Res. 1983, 117, 23-38;
34. c) Warin, V.; Baert, F.; Fouret, R.; Strecker, G.; Spik, G.; Fournet, B.; Montreuil, J. The crystal and molecular structure of O-α-D-mannopyranosyl-(1→3)-O-β-D-mannopyranosyl-(1→4)- 2-acetamido-2-deoxy-α-D-glucopyranose. Carbohydr. Res. 1979, 76, 11-22.
35. Rees, D.A.; Scott, W.E. Polysaccharide conformation. Part VI. Computer model-building for linear and branched pyranoglycans. Correlations with biological function. Preliminary assessment of inter-residue forces in aqueous solution. Further interpretation of optical rotation in terms of chain conformation. J. Chem. Soc., B 1971, 469-479.
36. 13C chemical shifts on the spatial interaction of protons, and its application in structural and conformational studies of oligo- and polysaccharides. Carbohydr. Res. 1984, 133, 173-185;
37. 13C chemical shifts in carbohydrates. Magn. Reson. Chem. 1988, 26, 735-747.
38. 13C nuclear magnetic resonance chemical shifts in oligosaccharides. J. Chem. Soc., Perkin Trans. 2 1986, 1711-1713.