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Original Articles

MM3 MODELING OF ALDOPENTOSE PYRANOSE RINGS

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Pages 11-25 | Received 10 May 2001, Accepted 10 Dec 2001, Published online: 28 Oct 2011

REFERENCES

  • Dowd , M. K. , French , A. D. and Reilly , P. J. 1994 . Modeling of aldopyranosyl ring puckering with MM3(92) . Carbohydr. Res. , 264 : 1 – 19 .
  • Bock , K. and Thøgersen , H. 1982 . Nuclear magnetic resonance spectroscopy in the study of mono- and oligosaccharides . Ann. Rep. NMR Spectrosc. , 13 : 1 – 57 .
  • Angyal , S. J. 1984 . The composition of reducing sugars in solution . Adv. Carbohydr. Chem. Biochem. , 42 : 15 – 68 .
  • Dowd , M. K. , French , A. D. and Reilly , P. J. 2000 . MM3 modeling of ribose and 2-deoxyribose ring puckering . J. Carbohydr. Chem. , 19 ( 9 ) : 1091 – 1114 .
  • Farrell , R. L. and Skerker , P. S. 1992 . “ Chlorine-Free Bleaching with Cartazyme™ HS Treatment ” . In Xylans and Xylanases Edited by: Visser , J. 315 – 324 . Amsterdam : Elsevier Science Publications .
  • Paice , M. G. , Gurnagul , N. , Page , D. H. and Jurasek , L. 1992 . Mechanism of hemicellulose-directed prebleaching of kraft pulps . Enzyme Microb. Technol. , 14 : 272 – 276 .
  • Wakarchuk , W. W. , Campbell , R. L. , Sung , W. L. , Davoodi , J. and Yaguchi , M. 1994 . Mutational and crystallographic analyses of the active site residues of the Bacillus circulans xylanase . Protein Sci. , 3 : 467 – 475 .
  • Sabini , E. , Sulzenbacher , G. , Dauter , M. , Dauter , Z. , Jørgensen , P. L. , Schülein , M. , Dupont , C. , Davies , G. J. and Wilson , K. S. 1999 . Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5 B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase . Chem. Biol. , 6 ( 7 ) : 483 – 492 .
  • Sidhu , G. , Withers , S. G. , Nguyen , N. T. , McIntosh , L. P. , Ziser , L. and Brayer , G. D. 1999 . Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase . Biochemistry , 38 ( 17 ) : 5346 – 5354 .
  • Allinger , N. L. , Yuh , Y. H. and Lii , J. H. 1989 . Molecular mechanics. The MM3 force field for hydrocarbons. 1 . J. Am. Chem. Soc. , 111 ( 23 ) : 8551 – 8566 .
  • Lii , J. H. and Allinger , N. L. 1989 . The MM3 force field for hydrocarbons. 2. Vibrational frequencies and thermodynamics . J. Am. Chem. Soc. , 111 ( 23 ) : 8566 – 8575 .
  • Allinger , N. L. , Rahman , M. and Lii , J. H. 1990 . A molecular mechanics force field (MM3) for alcohols and ethers . J. Am. Chem. Soc. , 112 ( 23 ) : 8293 – 8307 .
  • French , A. D. and Dowd , M. K. 1993 . Exploration of disaccharide conformations by molecular mechanics . J. Mol. Struct. (Theochem) , 286 : 183 – 201 .
  • Cremer , D. and Pople , J. A. 1975 . A general definition of ring puckering coordinates . J. Am. Chem. Soc. , 97 ( 6 ) : 1354 – 1358 .
  • Pickett , H. M. and Strauss , H. L. 1970 . Conformational structure, energy, and inversion rates of cyclohexane and some related oxanes . J. Am. Chem. Soc. , 92 : 7281 – 7290 .
  • Haasnoot , C.A. G. , de Leeuw , F.A.A. M. and Altona , C. 1980 . The relationship between proton–proton NMR coupling constants and substituent electronegativities-I . Tetrahedron , 36 ( 19H ) : 2783 – 2792 .
  • Allen , F. H. and Kennard , O. 1993 . 3D search and research using the Cambridge structural database . Chem. Des. Autom. News , 8 ( 1 ) : 31 – 37 .
  • Berman , H. M. , Westbrook , J. , Feng , Z. , Gilliland , G. , Bhat , T. N. , Wessig , H. , Shindyalov , I. N. and Bourne , P. E. 2000 . The protein data bank . Nucleic Acids Res. , 28 : 235 – 242 .
  • Richards , G. F. 1973 . An x-ray crystallographic study of a metal–carbohydrate complex: α-d-xylose·CaCl2·3H2O . Carbohydr. Res. , 26 : 448 – 449 .
  • Moran , R. A. and Richards , G. F. 1973 . The crystal and molecular structure of an aldotriourionic acid trihydrate: O-(4-O-Methyl-α-d-glucopyranosyluronic acid)-(1-2)-O-β-d-xylopyranosyl-(1-4)-d-xylopyranose trihydrate . Acta Crystallogr., Sect. B , 29 : 2770 – 2783 .
  • Leung , F. and Marchessault , R. H. 1973 . Crystal structure of β-d,1→4 xylobiose hexahydrate . Can. J. Chem. , 51 : 1215 – 1222 .
  • James , V. J. and Stevens , J. D. 1974 . Methyl 2,3,4-tri-O-acetyl-α-d-xylopyranose. C12H18O8 . Cryst. Struct. Commun. , 3 : 27 – 30 .
  • Delbaere , L.T. J. , Kamenar , B. and Prout , K. 1975 . The crystal and molecular structure of O-(β-d-xylopyranosyl)-l-serine and its copper(II) complex . Acta Crystallogr., Sect. B , 31 : 862 – 865 .
  • James , V. J. , Nimgirawath , K. and Stevens , J. D. 1976 . 1,2,3,4-Tetra-O-acetyl-β-d-xylopyranose. C13H18O9 . Cryst. Struct. Commun. , 5 : 851 – 856 .
  • Takagi , S. and Jeffrey , G. A. 1977 . A neutron diffraction refinement of the crystal structures of β-l-arabinose and methyl β-d-xylopyranoside . Acta Crystallogr., Sect. B , 33 : 3033 – 3040 .
  • Takagi , S. and Jeffrey , G. A. 1978 . Methyl β-d-xylopyranoside . Acta Crystallogr., Sect. B , 34 : 3104 – 3107 .
  • Takagi , S. and Jeffrey , G. A. 1979 . α-l-Xylopyranoside: a neutron diffraction refinement . Acta Crystallogr., Sect. B , 35 : 1482 – 1486 .
  • Luger , P. , Kothe , G. , Vangehr , K. , Paulsen , H. and Heiker , F. R. 1979 . Konformationen von 1,2,3,4-tetra-O-benzoyl-β-d-xylopyranose, 1,5-anhydro-2,3,4-tri-O-benzoylxylitol und 1,5-anhydro-2,3,4-tri-O-benzoylribitol . Carbohydr. Res. , 68 : 207 – 223 .
  • Vangehr , K. , Luger , P. and Paulsen , H. 1980 . Twist-boat-konformation von methyl-2,3,4-tri-O-benzoyl-β-d-xylopyranosid im kristall . Chem. Ber. , 113 : 2609 – 2615 .
  • Vorontsova , L. G. , Dekaprilevich , M. O. and Chizhov , O. S. 1985 . An x-ray diffraction structural study of 2,3,4-tri-O-acetyl-β-methyl-d-xylopyranoside . Izv. Akad. Nauk SRRC, Ser. Khim. , : 824 – 826 .
  • Vorontsova , L. G. , Dekaprilevich , M. O. and Chizhov , O. S. 1985 . Molecular and crystal structure of β-methyl-2,3-di-O-acetyl-4-O-trityl-d-xylopyranoside . Izv. Akad. Nauk SRRC, Ser. Khim. , : 1563 – 1567 .
  • Tavanaiepour , I. , Watson , W. H. , Gao , F. and Mabry , T. J. 1987 . Structure of a diterpene ent-Labdane xyloside . Acta Crystallogr., Sect. C: Cryst. Struct. Commun. , 43 : 754 – 756 .
  • Beagley , B. , Larson , D. S. , Pritchard , R. G. and Stoodley , R. J. 1990 . Asymmetric Diels–Alder reactions. Part 5. Influence of sugar substituents upon the diastereofacial reactivity of (E)-3-(t-butyldimethylsiloxy)-1-(d-glucopyranosyloxy)buta-1,3-dienes . J. Chem. Soc., Perkin Trans. 1 , : 3113 – 3127 .
  • Il'in , S. G. , Reshetnyak , M. V. , Shedrin , A. P. , Struchkov , Y. T. , Kapustina , I. I. , Stonik , V. A. and Elyakov , G. B. 1990 . The crystal and molecular structure of 6α,8β,15β-trihydroxy-3β-24R-di(O-β-d-xylopyranosyl)-5α-cholest-22(23)-ene trihydrate . Dokl. Akad. Nauk , 312 ( 3 ) : 637 – 639 .
  • van der Sluis , P. and Kroon , J. 1990 . Conformation of the xyl-β-(1→2)-man glycosidic linkage. Structure of 2,4,6-tri-O-acetyl-1-O-methyl-2-O-(2,3,4-tri-O-acetyl-β-d-xylopyranosyl)-β-d-mannopyranose . Acta Crystallogr., Sect. C: Cryst. Struct. Commun. , 46 : 2171 – 2174 .
  • Taga , T. , Inagaki , E. , Fujimori , Y. , Fujita , K. and Hana , K. 1992 . The crystal and molecular structure of α-d-fructofuranosyl α-d-xylopyranoside hemihydrate . Carbohydr. Res. , 241 : 63 – 69 .
  • Il'in , S. G. , Lindeman , S. V. , Struchkov , Y. T. , Levina , E. V. , Stonik , V. A. and Elyakov , G. B. 1992 . Crystalline and molecular structure of 24-O-(2,4-di-O-methyl-β-d-xylopyranosyl-(1-2)-α-l-arabinofuranosyl)-5α-cholestan-3β-4β-6α,8,15β,24S-hexaol hydrate . Dokl. Akad. Nauk , 323 ( 2 ) : 290 – 293 .
  • Le Questel , J. Y. , Mouhous-Riou , N. and Pérez , S. 1994 . The crystal and molecular structure of 4-cyanophenyl and 4-nitrophenyl β-d-xylopyranosides . Carbohydr. Res. , 265 : 291 – 298 .
  • Tomić , S. , van Eijck , B. P. , Kojić-Prodić , B. , Kroon , J. , Magnus , V. , Nigović , B. , Laćan , G. , Ilić , N. , Duddeck , H. and Hiegemann , M. 1995 . Synthesis and conformational analysis of the plant hormone (auxin) related 2-(indol-3-yl)ethyl and 2-phenylethyl β-d-xylopyranosides and their 2,3,4-tri-O-acetyl derivatives . Carbohydr. Res. , 270 : 11 – 32 .
  • Kanie , O. , Takeda , T. and Hatano , K. 1995 . Molecular and crystal structure of methyl 2,3,4-tri-O-acetyl-β-d-xylopyranosyl-(1→2)-3-O-benzyl-4,6-O-benzylidene-α-d-mannopyranoside . Carbohydr. Res. , 276 : 409 – 416 .
  • Takeda , T. , Gonda , R. and Hatano , K. 1997 . Constitution of lucumin and its related glycosides from Calocarpum sapota Merrill . Chem. Pharm. Bull. , 45 ( 4 ) : 697 – 699 .
  • Venugopalan , N. , Noguchi , K. , Okuyama , K. , Kitamura , S. and Takeo , K. 1998 . Molecular and crystal structure of ethyl 2,3,4-tri-O-acetyl-β-d-xylopyranosyl-(1→3)-2,4-di-O-acetyl-1-thio-β-d-xylopyranoside . Carbohydr. Res. , 306 : 563 – 565 .
  • James , V. J. and Stevens , J. D. 1974 . 1,2,3,4-tetra-O-acetyl-α-d-arabinopyranose. C13H18O9 . Cryst. Struct. Commun. , 3 : 19 – 22 .
  • James , V. J. and Stevens , J. D. 1974 . 1,2,3,4-Tetra-O-acetyl-α-d-arabinopyranose C13H18O9 . Cryst. Struct. Commun. , 3 : 187 – 190 .
  • McConnell , J. F. , Schwartz , A. and Stevens , J. D. 1979 . Methyl β-d-arabinopyranoside, C6H12O5 . Cryst. Struct. Commun. , 8 : 19 – 25 .
  • Terzis , A. 1978 . α-l-Arabinose-calcium chloride tetrahydrate, C5H10CaCl2O5·4H2O . Cryst. Struct. Commun. , 7 : 95 – 99 .
  • Takagi , S. and Jeffrey , G. A. 1978 . The crytal structures of methyl α-l-arabinopyranoside and methyl β-l-arabinopyranoside . Acta Crystallogr., Sect. B , 34 : 1591 – 1596 .
  • Longchambon , F. , Gillier-Pandraud , H. , Wiest , R. , Rees , B. , Mitschler , A. , Feld , R. , Lehmann , M. and Becker , P. 1985 . Etude structurale et densité de déformation electronique X-N à 75 K dans la région anomère du β-dl-arabinose . Acta Crystallogr., Sect. B , 41 : 47 – 56 .
  • Sakata , K. , Yamauchi , H. , Yagi , A. , Ina , K. , Párkányi , L. and Clardy , J. 1989 . 2-O-(β-l-Arabinopyranosyl)-myo-inositol as a main constituent of tea (Camellia sinensis) . Agric. Biol. Chem. , 53 : 2975 – 2979 .
  • Tomić , S. , van Eijck , B. P. , Kroon , J. , Kojić-Prodić , B. , Laćan , G. , Magnus , V. , Duddeck , H. and Hiegemann , M. 1994 . Synthesis and conformational analysis of 2-(indol-3-yl)ethyl α-l-arabinopyranoside and its 2,3,4-tri-O-acetyl derivative . Carbohydr. Res. , 259 : 175 – 190 .
  • Popek , T. , Mazurek , J. and Lis , T. 1996 . 1-O-Benzyl-β-l-arabinopyranose, 1-O-benzyl-3,4-O-isopropylidene-β-l-arabinopyranose and 1-O-benzyl-2-O-benzoyl-3,4-O-isopropylidene-β-l-arabinopyranose . Acta Crystallogr., Sect. C: Cryst. Struct. Commun. , 52 : 1558 – 1563 .
  • Martínez-Váquez , M. , García-Argáez , A. N. , Bueno , J. L. , Espinosa , G. and Calderon , J. S. 1998 . Two isomeric glycoside sesquiterpenes from Machaeranthera tanacetifolia . Phytochemistry , 48 ( 7 ) : 1221 – 1224 .
  • Herpin , P. , Famery , R. , Augé , J. and David , S. 1976 . Etude structurale du tétra-O-acetyl-α-d-lyxopyranose, C13O9H18 . Acta Crystallogr., Sect. B , 32 : 215 – 220 .
  • Evdokimov , A. G. and Frolow , F. 1996 . Methyl α-d-lyxopyranoside . Acta Crystallogr., Sect. C: Cryst. Struct. Commun. , 52 : 3218 – 3219 .
  • Nordensen , S. , Takagi , S. and Jeffrey , G. A. 1978 . β-l-Lyxopyranose: a neutron diffraction refinement . Acta Crystallogr., Sect. B , 34 : 3809 – 3811 .
  • James , V. J. and Stevens , J. D. 1981 . Methyl 2,3,4-tri-O-acetyl-β-d-lyxopyranoside C12H18O8 . Cryst. Struct. Commun. , 10 : 719 – 722 .
  • French , A. D. , Kelterer , A.-M. , Cramer , C. J. , Johnson , G. P. and Dowd , M. K. 2000 . A QM/MM analysis of the conformations of crystalline sucrose moieties . Carbohydr. Res. , 326 : 305 – 322 .

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