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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

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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.

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References

  1. Genicot-Joncour S, Poinas A, Richard O, Potin P, Rudolph B, Kloareg B, Helbert W (2009) Am Soc Plant Biol 151:1609–1616

    Google Scholar 

  2. Stortz CA (2006) Carbohydr Res 341:2531–2542

    Article  CAS  Google Scholar 

  3. Stortz CA (2005) In: Yarema KJ (ed) In: Handbook of carbohydrate engineering. Taylor and Francis, Boca Raton, pp 211–245

    Chapter  Google Scholar 

  4. Campo VL, Kawano DF, da Silva DB Jr, Carvalho I (2009) Carbohydr Polymers 77:167–180

    Article  CAS  Google Scholar 

  5. Strati GL, Willett JL, Momany FA (2002) Carbohydr Res 337:1851–1859

    Article  CAS  Google Scholar 

  6. Navarro DA, Stortz CA (2003) Carbohydr Res 338:2111–2118

    Article  CAS  Google Scholar 

  7. Le Questel JY, Cros S, Mackie W, Perez S (1995) Int J Biol Macromol 17:161–175

    Article  Google Scholar 

  8. Parra E, Caro HN, Jimènez-Barbero J, Martin-Lomas M, Bernabé M (1990) Carbohydr Res 208:83–92

    Article  CAS  Google Scholar 

  9. Urbani R, Di Blas A, Cesàro A (1993) Int J Biol Macromol 15:24–29

    Article  CAS  Google Scholar 

  10. Ueda K, Ochiai H, Imamura A, Nakagawa S (1995) Bull Chem Soc Jpn 68:95–106

    Article  CAS  Google Scholar 

  11. Ueda K, Brady JW (1996) Biopolymers 38:461–469

    Article  CAS  Google Scholar 

  12. Stortz CA, Cerezo AS (2000) J Carbohydr Chem 19:1115–1130

    Article  CAS  Google Scholar 

  13. Stortz CA, Cerezo AS (1994) J Carbohydr Chem 13:235

    Article  CAS  Google Scholar 

  14. Stortz CA, Cerezo AS (1995) An Asoc Quim Argent 83:171–181

    CAS  Google Scholar 

  15. Stortz CA, Cerezo AS (1998) J Carbohydr Chem 17:1405–1419

    Article  CAS  Google Scholar 

  16. Stortz CA (1999) Carbohydr Res 322:77–86

    Article  CAS  Google Scholar 

  17. Ragazzi M, Ferro D, Provasoli A (1986) J Comput Chem 7:105–112

    Article  CAS  Google Scholar 

  18. Ferro DR, Pumilia P, Cassinari A, Ragazzi M (1995) Int J Biol Macromol 17:131–136

    Article  CAS  Google Scholar 

  19. Huige CJM, Altona C (1995) J Comput Chem 16:56–79

    Article  CAS  Google Scholar 

  20. Ferro DR, Pumilia P, Ragazzi M (1997) J Comput Chem 18:351–367

    Article  CAS  Google Scholar 

  21. Lamba D, Glover S, Mackie W, Rashid A, Sheldrick B, Pérez S (1994) Glycobiology 4:151–163

    Article  CAS  Google Scholar 

  22. Ueda K, Saiki M, Brady JW (2001) J Phys Chem B 105:8629–8638

    Article  CAS  Google Scholar 

  23. Ueda K, Iwama K, Nakayama H (2001) Bull Chem Soc Jpn 74:2269–2277

    Article  CAS  Google Scholar 

  24. Schnupf U, Willett JL, Bosma WB, Momany FA (2007) Carbohydr Res 342:2270–2285

    Article  CAS  Google Scholar 

  25. Ha SN, Madson LJ, Brady JW (1988) Biopolymers 27:1927–1952

    Article  CAS  Google Scholar 

  26. Tran V, Buleon A, Imberty A, Pérez S (1989) Biopolymers 28:679–690

    Article  CAS  Google Scholar 

  27. Dowd MK, Zeng J, French AD, Reilly PJ (1992) Carbohydr Res 230:223–244

    Article  CAS  Google Scholar 

  28. Kouwijzer MLC, Grootenhuis PDJ (1995) J Phys Chem 99:13426–13436

    Article  Google Scholar 

  29. Kuttel MM, Naidoo K (2005) J Phys Chem B 109:7468–7474

    Article  CAS  Google Scholar 

  30. Gould IR, Bettley HA, Bryce RA (2007) J Comput Chem 28:1965–1973

    Article  CAS  Google Scholar 

  31. Landström J, Widmalm G (2010) Carbohydr Res 345:330–333

    Article  Google Scholar 

  32. Hatcher E, Säwén E, Widmalm G, MacKerell AD Jr (2011) J Phys Chem B 115:597–608

    Article  CAS  Google Scholar 

  33. Perič-Hassler L, Hansen HS, Baron R, Hünenberger PH (2010) Carbohydr Res 345:1781–1801

    Article  Google Scholar 

  34. Stortz CA, Johnson GP, French AD, Csonka GI (2009) Carbohydr Res 344:2217–2228

    Article  CAS  Google Scholar 

  35. Momany FA, Appell M, Willett JL, Schnupf U, Bosma WB (2006) Carbohydr Res 341:525–537

    Article  CAS  Google Scholar 

  36. Da Silva CO, Nascimento MAC (2004) Carbohydr Res 339:113–122

    Article  Google Scholar 

  37. French AD, Johnson GP, Kelterer AM, Csonka GI (2005) Tetrahedron-Asymmetry 16:577–586

    Article  CAS  Google Scholar 

  38. Momany FA, Willett JL (2000) J Comput Chem 21:1204–1219

    Article  CAS  Google Scholar 

  39. Strati GL, Willett JL, Momany FA (2002) Carbohydr Res 337:1833–1849

    Article  CAS  Google Scholar 

  40. Bosma WB, Appell M, Willett JL, Momany FA (2006) J Mol Struct (THEOCHEM) 776:1–19

    Article  CAS  Google Scholar 

  41. Bosma WB, Appell M, Willett JL, Momany FA (2006) J Mol Struct (THEOCHEM) 776:13–24

    Google Scholar 

  42. Appell M, Strati GL, Willett JL, Momany FA (2004) Carbohydr Res 339:537–551

    Article  CAS  Google Scholar 

  43. Appell M, Willett JL, Momany FA (2005) Carbohydr Res 340:459–468

    Article  CAS  Google Scholar 

  44. Schnupf U, Willett JL, Bosma WB, Momany FA (2007) Carbohydr Res 342:196–216

    Article  CAS  Google Scholar 

  45. Momany FA, Appell MA, Strati GL, Willett JL (2004) Carbohydr Res 339:553–567

    Article  CAS  Google Scholar 

  46. Hricovini M, Scholtzovà E, Bizik F (2007) Carbohydr Res 342:1350–1356

    Article  CAS  Google Scholar 

  47. Lii J-H, Ma B, Allinger NL (1999) J Comput Chem 20:1593–1603

    Article  CAS  Google Scholar 

  48. Tvaroska I, Taravel FR, Utille JP, Carver JP (2002) Carbohydr Res 337:353–367

    Article  CAS  Google Scholar 

  49. Tissot B, Salpin JY, Martinez M, Gaigeot MP, Daniel R (2006) Carbohydr Res 341:598–609

    Article  CAS  Google Scholar 

  50. Momany FA, Appell M, Willett JL, Bosma WB (2005) Carbohydr Res 340:1638–1655

    Article  CAS  Google Scholar 

  51. Pogány P, Kovács A (2009) Carbohydr Res 344:1745–1752

    Article  Google Scholar 

  52. Dauchez M, Lagant P, Derreumaux P, Vergoten G, Sekkal M (1994) Spectrochim Acta A Mol Spectrosc 50:105–118

    Article  Google Scholar 

  53. Dauchez M, Derreumaux P, Lagant P, Vergoten G, Sekkal M, Legrand P (1994) Spectrochim Acta A Mol Biomol Spectrosc 50:87–104

    Article  Google Scholar 

  54. Kuttel JM, Brady W, Naidoo K (2002) J Comput Chem 23:1236–1243

    Article  CAS  Google Scholar 

  55. Schnupf U, Willett JL, Momany FA (2010) J Comput Chem 31:2087–2097

    Article  CAS  Google Scholar 

  56. Yousfi N, Sekkal-Rahal M, Sayede A, Springborg M (2010) J Comput Chem 31:1312–1320

    CAS  Google Scholar 

  57. Gonçalves PFB, Stassen H (2002) J Comput Chem 23:706–714

    Article  Google Scholar 

  58. Langella E, Rega N, Improta R, Crescenzi O, Barone B (2002) J Comput Chem 23:650–661

    Article  CAS  Google Scholar 

  59. Curutchet C, Cramer CJ, Truhlar DG, Ruiz-Lopez MF, Rinaldi D, Orozco M, Luque FJ (2003) J Comput Chem 24:284–297

    Article  CAS  Google Scholar 

  60. Fattebert JL, Gygi F (2002) J Comput Chem 23:662–666

    Article  CAS  Google Scholar 

  61. Csonka GI, French AD, Johnson GP, Stortz CA (2009) J Chem Theor Comput 5:679–692

    Article  CAS  Google Scholar 

  62. Kristyan S, Pulay P (1994) Chem Phys Lett 229:175–180

    Article  CAS  Google Scholar 

  63. IUPAC-IUB Commission on Biochemical Nomenclature (1971) Arch Biochem Biophys 145:405

    Article  Google Scholar 

  64. Arnott S, Scott WE Rees DA, McNab CGA (1974) J Mol Biol 90:253–267

    Article  CAS  Google Scholar 

  65. Janaswamy S, Chandrasekaran R (2001) Carbohydr Res 335:181–194

    Article  CAS  Google Scholar 

  66. Janaswamy S, Chandrasekaran R (2002) Carbohydr Res 337:523–535

    Article  CAS  Google Scholar 

  67. French AD, Dowd MK (1993) J Mol Struct (THEOCHEM) 286:183–201

    Article  Google Scholar 

  68. Onsager L (1936) J Am Chem Soc 58:1486–1493

    Article  CAS  Google Scholar 

  69. Foresman JB, Frisch A (1996) Gaussian94 user’s guide. Exploring chemistry with electronic structure methods, 2nd edn. Gaussian, Inc, Pittsburgh

  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, PA

  71. Golden Software, Inc (2002) Surface mapping system. Golden Software, Inc. Golden, CO

  72. Marchessault RH, Pérez S (1979) Biopolymers 18:2369–2374

    Article  CAS  Google Scholar 

  73. Navarro DA, Stortz CA (2008) Carbohydr Res 343:2292–2298

    Article  CAS  Google Scholar 

  74. Engelsen SB, Kocà J, Braccini I, du Hervé PC, Pérez S (1995) Carbohydr Res 276:1–30

    Article  CAS  Google Scholar 

  75. Dowd MK, French AD, Reilly PJ (1994) Carbohydr Res 264:1–19

    Article  CAS  Google Scholar 

  76. Wong CHS, Siu FM, Ma NL, Tsang CW (2001) J Mol Struct (THEOCHEM) 536:227–234

    Article  CAS  Google Scholar 

  77. Lii J-H, Chen K-H, Durkin KA, Allinger NL (2003) J Comput Chem 24:1473–1489

    Article  CAS  Google Scholar 

  78. Lii J-H, Chen K-H, Allinger NL (2003) J Comput Chem 24:1504–1513

    Article  CAS  Google Scholar 

  79. Momany FA, Willett JL (2000) Carbohydr Res 326:194–209

    Article  CAS  Google Scholar 

  80. Momany FA, Willett JL (2000) Carbohydr Res 326:210–226

    Article  CAS  Google Scholar 

  81. Navarro DA, Stortz CA (2005) Carbohydr Res 340:2030–2038

    Article  CAS  Google Scholar 

  82. Jeffrey GA (1990) Acta Crystallogr B46:89–103

    CAS  Google Scholar 

  83. Longchambon F, Gillier-Pandraud H (1977) Acta Crystallogr B32:1822–1826

    Google Scholar 

  84. Van Eijck BP, Mooij WTM, Kroon J (2001) J Phys Chem B 105:10573–10578

    Article  Google Scholar 

  85. McDonnell C, López O, Murphy P, Fernández Bolanõs JG, Hazell R, Bols M (2004) J Am Chem Soc 126:12374–12385

    Article  CAS  Google Scholar 

  86. Barone V, Cossi M, Tomasi J (1998) J Comput Chem 19:404–417

    Article  CAS  Google Scholar 

  87. Rashid A, Mackie W (1992) Carbohydr Res 223:147–155

    Article  CAS  Google Scholar 

  88. Millane RP, Chandrasekaran R, Arnott S, Dea ICM (1988) Carbohydr Res 182:1–17

    Article  CAS  Google Scholar 

Download references

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

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Authors and Affiliations

  1. L2MSM, Faculté des Sciences, Université Djillali Liabes de Sidi Bel Abbes, B.P. 89, 22000, Sidi Bel Abbes, Algeria

    Noreya Bestaoui-Berrekhchi-Berrahma, Majda Sekkal-Rahal, Noureddine Yousfi & Abd-Ed-Daim Kadoun

  2. Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13, rue Pierre et Marie Curie, 75005, Paris, France

    Philippe Derreumaux

  3. Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005, Paris, France

    Philippe Derreumaux

  4. Physikalische und Theoretische Chemie, Universitaet des Saarlandes, Postfach 15 11 50, Saarbruecken, 66041, Germany

    Michael Springborg

  5. UCCS-CNRS UMR 8181, Faculté des Sciences de Lens, Université d’Artois, Rue, Jean-Souvraz SP-18, Lens, 62300, France

    Adlane Sayede

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  1. Noreya Bestaoui-Berrekhchi-Berrahma
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  2. Philippe Derreumaux
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Correspondence to Majda Sekkal-Rahal.

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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)

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)

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)

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)

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)

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)

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Bestaoui-Berrekhchi-Berrahma, N., Derreumaux, P., Sekkal-Rahal, M. et al. 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. J Mol Model 19, 893–904 (2013). https://doi.org/10.1007/s00894-012-1621-y

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