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Glycosidic linkage conformation of methyl-alpha-mannopyranoside

J. Chem. Phys. 129, 045102 (2008); doi:10.1063/1.2958916

Published 31 July 2008

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Orkid Coskuner,1,2 Denis E. Bergeron,1 Luis Rincon,1,3 Jeffrey W. Hudgens,1 and Carlos A. Gonzalez1
1Physical and Chemical Properties Division, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 8380, Gaithersburg, Maryland 20899, USA
2Computational Materials Sciences Center, George Mason University, Research I, Fairfax, Virginia 22030, USA
3Departamento de Química, Universidad de los Andes, Mérida 5101, Venezuela
We study the preferred conformation of the glycosidic linkage of methyl-alpha-mannopyranoside in the gas phase and in aqueous solution. Results obtained utilizing Car–Parrinello molecular dynamics (CPMD) simulations are compared to those obtained from classical molecular dynamics (MD) simulations. We describe classical simulations performed with various water potential functions to study the impact of the chosen water potential on the predicted conformational preference of the glycosidic linkage of the carbohydrate in aqueous solution. In agreement with our recent studies, we find that results obtained with CPMD simulations differ from those obtained from classical simulations. In particular, this study shows that the trans (t) orientation of the glycosidic linkage of methyl-alpha-mannopyranoside is preferred over its gauche anticlockwise (g−) orientation in aqueous solution. CPMD simulations indicate that this preference is due to intermolecular hydrogen bonding with surrounding water molecules, whereas no such information could be demonstrated by classical MD simulations. This study emphasizes the importance of ab initio MD simulations for studying the structural properties of carbohydrates in aqueous solution. ©2008 American Institute of Physics
History: Received 10 March 2008; accepted 24 June 2008; published 31 July 2008
Permalink: http://link.aip.org/link/?JCPSA6/129/045102/1
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KEYWORDS and PACS

Keywords
PACS
  • 87.15.B-
    Structure of biomolecules
  • 87.15.hp
    Conformational changes of biomolecules
  • 87.15.Fh
    Bonding of biomolecules; mechanisms of bond breakage
  • 87.15.ap
    Molecular dynamics simulation in molecular biophysics
  • 87.14.Df
    Carbohydrates
  • YEAR: 2008

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ISSN:
0021-9606 (print)   1089-7690 (online)
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