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Journal of Molecular Modeling

, Volume 19, Issue 2, pp 893–904 | Cite as

Density functional conformational study of 2-O-sulfated 3,6 anhydro-α-D-galactose and of neo-κ- and ι-carrabiose molecules in gas phase and water

  • Noreya Bestaoui-Berrekhchi-Berrahma
  • Philippe Derreumaux
  • Majda Sekkal-Rahal
  • Michael Springborg
  • Adlane Sayede
  • Noureddine Yousfi
  • Abd-Ed-Daim Kadoun
Original Paper

Abstract

We examined the conformational preferences of the 2-O-sulfated-3,6-α-D-anhydrogalactose (compound I) and two 1,3 linked disaccharides constituting-κ or ι-carrageenans using density functional and ab initio methods in gas phase and aqueous solution. Systematic modifications of two torsion angles leading to 324 and 144 starting geometries for the compound I and each disaccharide were used to generate adiabatic maps using B3LYP/6-31G(d). The lower energy conformers were then fully optimized using B3LYP, B3PW91 and MP2 with several basis sets. Overall, we discuss the impact of full relaxation on the energy and structure of the dominant conformations, present the performance comparison with previous molecular mechanics calculations if available, and determine whether our results are impacted, when polarization and diffuse functions are added to the 6-31G(d) basis set, or when the MP2 level of theory is used.

Keywords

Adiabatic maps Conformers DFT methods Full optimization Gas and solvent 2-O-sulfated-3,6-α-D-anhydrogalactose Neo-κ-carrabiose Neo-ι-carrabiose 

Notes

Acknowledgments

N. B-B. B thanks D. J. Fox from his helpful suggestions to perform calculations and M. S-R thanks the Alexander von Humboldt foundation (Bonn) for grants

Supplementary material

894_2012_1621_MOESM1_ESM.doc (152 kb)
Figure SI.1 Structures including hydrogen bonds distances (in Å) of the four conformers of compound I in the gas phase, (a) obtained from the map 2a, and (b) after full optimization (DOC 151 kb)
894_2012_1621_MOESM2_ESM.doc (154 kb)
Figure SI.2 Structures including hydrogen bonds distances (in Å) of the four conformers of compound I in water, (a) obtained from the map 2b, and (b) after full optimization (DOC 153 kb)
894_2012_1621_MOESM3_ESM.doc (126 kb)
Figure SII.1 Structures including hydrogen bonds distances (in Å) of the two conformers of compound II in the gas phase, (a) obtained from the map 3a, and (b) after full optimization (DOC 126 kb)
894_2012_1621_MOESM4_ESM.doc (132 kb)
Figure SII.2 Structures including hydrogen bonds distances (in Å) of the two conformers of compound II in water, (a) obtained from the map 3b, and (b) after full optimization (DOC 132 kb)
894_2012_1621_MOESM5_ESM.doc (135 kb)
Figure SIII.1 Structures including hydrogen bonds distances (in Å) of the two conformers of compound III in the gas phase, (a) obtained from the map 4a, and (b) after full optimization (DOC 135 kb)
894_2012_1621_MOESM6_ESM.doc (172 kb)
Figure SIII.2 Structures including hydrogen bonds distances (in Å) of the three conformers of compound III in water, (a) obtained from the map 4b, and (b) after full optimization (DOC 172 kb)

References

  1. 1.
    Genicot-Joncour S, Poinas A, Richard O, Potin P, Rudolph B, Kloareg B, Helbert W (2009) Am Soc Plant Biol 151:1609–1616Google Scholar
  2. 2.
    Stortz CA (2006) Carbohydr Res 341:2531–2542CrossRefGoogle Scholar
  3. 3.
    Stortz CA (2005) In: Yarema KJ (ed) In: Handbook of carbohydrate engineering. Taylor and Francis, Boca Raton, pp 211–245CrossRefGoogle Scholar
  4. 4.
    Campo VL, Kawano DF, da Silva DB Jr, Carvalho I (2009) Carbohydr Polymers 77:167–180CrossRefGoogle Scholar
  5. 5.
    Strati GL, Willett JL, Momany FA (2002) Carbohydr Res 337:1851–1859CrossRefGoogle Scholar
  6. 6.
    Navarro DA, Stortz CA (2003) Carbohydr Res 338:2111–2118CrossRefGoogle Scholar
  7. 7.
    Le Questel JY, Cros S, Mackie W, Perez S (1995) Int J Biol Macromol 17:161–175CrossRefGoogle Scholar
  8. 8.
    Parra E, Caro HN, Jimènez-Barbero J, Martin-Lomas M, Bernabé M (1990) Carbohydr Res 208:83–92CrossRefGoogle Scholar
  9. 9.
    Urbani R, Di Blas A, Cesàro A (1993) Int J Biol Macromol 15:24–29CrossRefGoogle Scholar
  10. 10.
    Ueda K, Ochiai H, Imamura A, Nakagawa S (1995) Bull Chem Soc Jpn 68:95–106CrossRefGoogle Scholar
  11. 11.
    Ueda K, Brady JW (1996) Biopolymers 38:461–469CrossRefGoogle Scholar
  12. 12.
    Stortz CA, Cerezo AS (2000) J Carbohydr Chem 19:1115–1130CrossRefGoogle Scholar
  13. 13.
    Stortz CA, Cerezo AS (1994) J Carbohydr Chem 13:235CrossRefGoogle Scholar
  14. 14.
    Stortz CA, Cerezo AS (1995) An Asoc Quim Argent 83:171–181Google Scholar
  15. 15.
    Stortz CA, Cerezo AS (1998) J Carbohydr Chem 17:1405–1419CrossRefGoogle Scholar
  16. 16.
    Stortz CA (1999) Carbohydr Res 322:77–86CrossRefGoogle Scholar
  17. 17.
    Ragazzi M, Ferro D, Provasoli A (1986) J Comput Chem 7:105–112CrossRefGoogle Scholar
  18. 18.
    Ferro DR, Pumilia P, Cassinari A, Ragazzi M (1995) Int J Biol Macromol 17:131–136CrossRefGoogle Scholar
  19. 19.
    Huige CJM, Altona C (1995) J Comput Chem 16:56–79CrossRefGoogle Scholar
  20. 20.
    Ferro DR, Pumilia P, Ragazzi M (1997) J Comput Chem 18:351–367CrossRefGoogle Scholar
  21. 21.
    Lamba D, Glover S, Mackie W, Rashid A, Sheldrick B, Pérez S (1994) Glycobiology 4:151–163CrossRefGoogle Scholar
  22. 22.
    Ueda K, Saiki M, Brady JW (2001) J Phys Chem B 105:8629–8638CrossRefGoogle Scholar
  23. 23.
    Ueda K, Iwama K, Nakayama H (2001) Bull Chem Soc Jpn 74:2269–2277CrossRefGoogle Scholar
  24. 24.
    Schnupf U, Willett JL, Bosma WB, Momany FA (2007) Carbohydr Res 342:2270–2285CrossRefGoogle Scholar
  25. 25.
    Ha SN, Madson LJ, Brady JW (1988) Biopolymers 27:1927–1952CrossRefGoogle Scholar
  26. 26.
    Tran V, Buleon A, Imberty A, Pérez S (1989) Biopolymers 28:679–690CrossRefGoogle Scholar
  27. 27.
    Dowd MK, Zeng J, French AD, Reilly PJ (1992) Carbohydr Res 230:223–244CrossRefGoogle Scholar
  28. 28.
    Kouwijzer MLC, Grootenhuis PDJ (1995) J Phys Chem 99:13426–13436CrossRefGoogle Scholar
  29. 29.
    Kuttel MM, Naidoo K (2005) J Phys Chem B 109:7468–7474CrossRefGoogle Scholar
  30. 30.
    Gould IR, Bettley HA, Bryce RA (2007) J Comput Chem 28:1965–1973CrossRefGoogle Scholar
  31. 31.
    Landström J, Widmalm G (2010) Carbohydr Res 345:330–333CrossRefGoogle Scholar
  32. 32.
    Hatcher E, Säwén E, Widmalm G, MacKerell AD Jr (2011) J Phys Chem B 115:597–608CrossRefGoogle Scholar
  33. 33.
    Perič-Hassler L, Hansen HS, Baron R, Hünenberger PH (2010) Carbohydr Res 345:1781–1801CrossRefGoogle Scholar
  34. 34.
    Stortz CA, Johnson GP, French AD, Csonka GI (2009) Carbohydr Res 344:2217–2228CrossRefGoogle Scholar
  35. 35.
    Momany FA, Appell M, Willett JL, Schnupf U, Bosma WB (2006) Carbohydr Res 341:525–537CrossRefGoogle Scholar
  36. 36.
    Da Silva CO, Nascimento MAC (2004) Carbohydr Res 339:113–122CrossRefGoogle Scholar
  37. 37.
    French AD, Johnson GP, Kelterer AM, Csonka GI (2005) Tetrahedron-Asymmetry 16:577–586CrossRefGoogle Scholar
  38. 38.
    Momany FA, Willett JL (2000) J Comput Chem 21:1204–1219CrossRefGoogle Scholar
  39. 39.
    Strati GL, Willett JL, Momany FA (2002) Carbohydr Res 337:1833–1849CrossRefGoogle Scholar
  40. 40.
    Bosma WB, Appell M, Willett JL, Momany FA (2006) J Mol Struct (THEOCHEM) 776:1–19CrossRefGoogle Scholar
  41. 41.
    Bosma WB, Appell M, Willett JL, Momany FA (2006) J Mol Struct (THEOCHEM) 776:13–24Google Scholar
  42. 42.
    Appell M, Strati GL, Willett JL, Momany FA (2004) Carbohydr Res 339:537–551CrossRefGoogle Scholar
  43. 43.
    Appell M, Willett JL, Momany FA (2005) Carbohydr Res 340:459–468CrossRefGoogle Scholar
  44. 44.
    Schnupf U, Willett JL, Bosma WB, Momany FA (2007) Carbohydr Res 342:196–216CrossRefGoogle Scholar
  45. 45.
    Momany FA, Appell MA, Strati GL, Willett JL (2004) Carbohydr Res 339:553–567CrossRefGoogle Scholar
  46. 46.
    Hricovini M, Scholtzovà E, Bizik F (2007) Carbohydr Res 342:1350–1356CrossRefGoogle Scholar
  47. 47.
    Lii J-H, Ma B, Allinger NL (1999) J Comput Chem 20:1593–1603CrossRefGoogle Scholar
  48. 48.
    Tvaroska I, Taravel FR, Utille JP, Carver JP (2002) Carbohydr Res 337:353–367CrossRefGoogle Scholar
  49. 49.
    Tissot B, Salpin JY, Martinez M, Gaigeot MP, Daniel R (2006) Carbohydr Res 341:598–609CrossRefGoogle Scholar
  50. 50.
    Momany FA, Appell M, Willett JL, Bosma WB (2005) Carbohydr Res 340:1638–1655CrossRefGoogle Scholar
  51. 51.
    Pogány P, Kovács A (2009) Carbohydr Res 344:1745–1752CrossRefGoogle Scholar
  52. 52.
    Dauchez M, Lagant P, Derreumaux P, Vergoten G, Sekkal M (1994) Spectrochim Acta A Mol Spectrosc 50:105–118CrossRefGoogle Scholar
  53. 53.
    Dauchez M, Derreumaux P, Lagant P, Vergoten G, Sekkal M, Legrand P (1994) Spectrochim Acta A Mol Biomol Spectrosc 50:87–104CrossRefGoogle Scholar
  54. 54.
    Kuttel JM, Brady W, Naidoo K (2002) J Comput Chem 23:1236–1243CrossRefGoogle Scholar
  55. 55.
    Schnupf U, Willett JL, Momany FA (2010) J Comput Chem 31:2087–2097CrossRefGoogle Scholar
  56. 56.
    Yousfi N, Sekkal-Rahal M, Sayede A, Springborg M (2010) J Comput Chem 31:1312–1320Google Scholar
  57. 57.
    Gonçalves PFB, Stassen H (2002) J Comput Chem 23:706–714CrossRefGoogle Scholar
  58. 58.
    Langella E, Rega N, Improta R, Crescenzi O, Barone B (2002) J Comput Chem 23:650–661CrossRefGoogle Scholar
  59. 59.
    Curutchet C, Cramer CJ, Truhlar DG, Ruiz-Lopez MF, Rinaldi D, Orozco M, Luque FJ (2003) J Comput Chem 24:284–297CrossRefGoogle Scholar
  60. 60.
    Fattebert JL, Gygi F (2002) J Comput Chem 23:662–666CrossRefGoogle Scholar
  61. 61.
    Csonka GI, French AD, Johnson GP, Stortz CA (2009) J Chem Theor Comput 5:679–692CrossRefGoogle Scholar
  62. 62.
    Kristyan S, Pulay P (1994) Chem Phys Lett 229:175–180CrossRefGoogle Scholar
  63. 63.
    IUPAC-IUB Commission on Biochemical Nomenclature (1971) Arch Biochem Biophys 145:405CrossRefGoogle Scholar
  64. 64.
    Arnott S, Scott WE Rees DA, McNab CGA (1974) J Mol Biol 90:253–267CrossRefGoogle Scholar
  65. 65.
    Janaswamy S, Chandrasekaran R (2001) Carbohydr Res 335:181–194CrossRefGoogle Scholar
  66. 66.
    Janaswamy S, Chandrasekaran R (2002) Carbohydr Res 337:523–535CrossRefGoogle Scholar
  67. 67.
    French AD, Dowd MK (1993) J Mol Struct (THEOCHEM) 286:183–201CrossRefGoogle Scholar
  68. 68.
    Onsager L (1936) J Am Chem Soc 58:1486–1493CrossRefGoogle Scholar
  69. 69.
    Foresman JB, Frisch A (1996) Gaussian94 user’s guide. Exploring chemistry with electronic structure methods, 2nd edn. Gaussian, Inc, PittsburghGoogle Scholar
  70. 70.
    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, 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 JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2003) Gaussian 03, Revision D.02. Gaussian, Inc, Pittsburgh, PAGoogle Scholar
  71. 71.
    Golden Software, Inc (2002) Surface mapping system. Golden Software, Inc. Golden, COGoogle Scholar
  72. 72.
    Marchessault RH, Pérez S (1979) Biopolymers 18:2369–2374CrossRefGoogle Scholar
  73. 73.
    Navarro DA, Stortz CA (2008) Carbohydr Res 343:2292–2298CrossRefGoogle Scholar
  74. 74.
    Engelsen SB, Kocà J, Braccini I, du Hervé PC, Pérez S (1995) Carbohydr Res 276:1–30CrossRefGoogle Scholar
  75. 75.
    Dowd MK, French AD, Reilly PJ (1994) Carbohydr Res 264:1–19CrossRefGoogle Scholar
  76. 76.
    Wong CHS, Siu FM, Ma NL, Tsang CW (2001) J Mol Struct (THEOCHEM) 536:227–234CrossRefGoogle Scholar
  77. 77.
    Lii J-H, Chen K-H, Durkin KA, Allinger NL (2003) J Comput Chem 24:1473–1489CrossRefGoogle Scholar
  78. 78.
    Lii J-H, Chen K-H, Allinger NL (2003) J Comput Chem 24:1504–1513CrossRefGoogle Scholar
  79. 79.
    Momany FA, Willett JL (2000) Carbohydr Res 326:194–209CrossRefGoogle Scholar
  80. 80.
    Momany FA, Willett JL (2000) Carbohydr Res 326:210–226CrossRefGoogle Scholar
  81. 81.
    Navarro DA, Stortz CA (2005) Carbohydr Res 340:2030–2038CrossRefGoogle Scholar
  82. 82.
    Jeffrey GA (1990) Acta Crystallogr B46:89–103Google Scholar
  83. 83.
    Longchambon F, Gillier-Pandraud H (1977) Acta Crystallogr B32:1822–1826Google Scholar
  84. 84.
    Van Eijck BP, Mooij WTM, Kroon J (2001) J Phys Chem B 105:10573–10578CrossRefGoogle Scholar
  85. 85.
    McDonnell C, López O, Murphy P, Fernández Bolanõs JG, Hazell R, Bols M (2004) J Am Chem Soc 126:12374–12385CrossRefGoogle Scholar
  86. 86.
    Barone V, Cossi M, Tomasi J (1998) J Comput Chem 19:404–417CrossRefGoogle Scholar
  87. 87.
    Rashid A, Mackie W (1992) Carbohydr Res 223:147–155CrossRefGoogle Scholar
  88. 88.
    Millane RP, Chandrasekaran R, Arnott S, Dea ICM (1988) Carbohydr Res 182:1–17CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Noreya Bestaoui-Berrekhchi-Berrahma
    • 1
  • Philippe Derreumaux
    • 2
    • 3
  • Majda Sekkal-Rahal
    • 1
  • Michael Springborg
    • 4
  • Adlane Sayede
    • 5
  • Noureddine Yousfi
    • 1
  • Abd-Ed-Daim Kadoun
    • 1
  1. 1.L2MSM, Faculté des SciencesUniversité Djillali Liabes de Sidi Bel AbbesSidi Bel AbbesAlgeria
  2. 2.Laboratoire de Biochimie Théorique, CNRS, UPR 9080Université Paris Diderot, Sorbonne Paris CitéParisFrance
  3. 3.Institut Universitaire de FranceParisFrance
  4. 4.Physikalische und Theoretische ChemieUniversitaet des SaarlandesSaarbrueckenGermany
  5. 5.UCCS-CNRS UMR 8181, Faculté des Sciences de LensUniversité d’ArtoisLensFrance

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