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Preferred conformation of the glycosidic linkage of methyl--mannose
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10.1063/1.2747238
/content/aip/journal/jcp/127/1/10.1063/1.2747238
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/1/10.1063/1.2747238
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Figures

Image of FIG. 1.
FIG. 1.

The methyl--mannose molecule with the conventional numbering of specific heavy atoms.

Image of FIG. 2.
FIG. 2.

Calculated torsional energy change of the glycosidic linkage of methyl--mannose in the gas phase: (—, 엯) , (---, ◻) CPMD simulations, and (⋯, ◇) classical MD simulations. Errors were calculated using the time dependent standard deviation method.

Image of FIG. 3.
FIG. 3.

Calculated torsional free energy change of the glycosidic linkage of methyl--mannose with the potential of mean force method in solution: (—, ◻) CPMD simulations, (---, 엯) classical MD simulations using TIP5P model for water, (⋯, ◇) classical MD simulations utilizing TIP4P model for water, and (— ∙ —, ▵) classical MD simulations using TIP3P model for water. The inset plot presents the calculated energy differences of the glycosidic linkage of methyl--mannose with the potential of mean force (---, 엯) and perturbation methods (—∙∙—, ) by classical MD simulations utilizing TIP5P model for water. Errors were calculated using the time dependent standard deviation method.

Image of FIG. 4.
FIG. 4.

Calculated proximal distribution functions for (a) , (b) , (c) , and (d) at room temperature using (a) TIP5P model for water via classical MD simulations and (b) CPMD simulations; (—) orientation, (⋯) orientation, and (— ∙ —) orientation of the glycosidic linkage of methyl--mannose.

Image of FIG. 5.
FIG. 5.

Average numbers of hydrogen bonds between specific methyl--mannose oxygens and water molecules; for the (—) , (---) , and (⋯) orientations of the glycosidic linkage of methyl--mannose via CPMD simulations at room temperature.

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/content/aip/journal/jcp/127/1/10.1063/1.2747238
2007-07-02
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Preferred conformation of the glycosidic linkage of methyl-β-mannose
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/1/10.1063/1.2747238
10.1063/1.2747238
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