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-RahalEmail author
  • Michael Springborg
  • Adlane Sayede
  • Noureddine Yousfi
  • Abd-Ed-Daim Kadoun
Original Paper


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.


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



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)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Noreya Bestaoui-Berrekhchi-Berrahma
    • 1
  • Philippe Derreumaux
    • 2
    • 3
  • Majda Sekkal-Rahal
    • 1
    Email author
  • 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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