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. 2015 Jan 22;119(3):637-52.
doi: 10.1021/jp412696m. Epub 2014 Feb 24.

Polarizable empirical force field for hexopyranose monosaccharides based on the classical Drude oscillator

Dhilon S Patel  1 , Xibing He, Alexander D MacKerell Jr
Affiliations

Polarizable empirical force field for hexopyranose monosaccharides based on the classical Drude oscillator

Dhilon S Patel et al. J Phys Chem B. .

Abstract

A polarizable empirical force field based on the classical Drude oscillator is presented for the hexopyranose form of selected monosaccharides. Parameter optimization targeted quantum mechanical (QM) dipole moments, solute-water interaction energies, vibrational frequencies, and conformational energies. Validation of the model was based on experimental data on crystals, densities of aqueous-sugar solutions, diffusion constants of glucose, and rotational preferences of the exocylic hydroxymethyl of d-glucose and d-galactose in aqueous solution as well as additional QM data. Notably, the final model involves a single electrostatic model for all sixteen diastereomers of the monosaccharides, indicating the transferability of the polarizable model. The presented parameters are anticipated to lay the foundation for a comprehensive polarizable force field for saccharides that will be compatible with the polarizable Drude parameters for lipids and proteins, allowing for simulations of glycolipids and glycoproteins.

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Figures

Figure 1
Figure 1
Chemical structures of the α anomer of each of the eight hexapyranose diasteromers is shown with the numbering of the carbons shown on α-d-allose. Shown in parentheses are the configuration (eq – equatorial; ax – axial) of the hydroxyls of each diastereomer at the C2, C3 and C4 positions.
Figure 2
Figure 2
α- and β-d-glucose–water interaction geometries. (a) Acceptor type interactions from α-d-glucose with water hydrogen, where LP represents lone pair direction and BIS represents bisector angle based interactions. (b) Donor type interactions (PR) from α-d-glucose with water oxygen. (c) Acceptor type interactions from β-d-glucose with water hydrogen, where LP represents lone pair direction and BIS represents bisector angle based interactions. (d) Donor type interactions (PR) from β-d-glucose with water oxygen.
Figure 3
Figure 3
Hexopyranose monosaccharide relative energies from the MP2/cc-pVTZ//MP2/6-31G(d) model chemistry (black), from the Drude force field before torsion fitting (green), and from the Drude force field after torsion fitting (red). Both sets of MM data have been RMS aligned to the QM data.
Figure 4
Figure 4
Conformational energies of β-allose (a), β-gulose (b) and α-mannose (c) at the MP2/cc-pVTZ//MP2/6-31G(d) model chemistry (black), from the Drude force field (red) and from the additive C36 force field (blue). Dipole moment comparisons are given for β-allose (d), β-gulose (e), and α-mannose (f).
Figure 5
Figure 5
Probability distribution of α1 (a), α2 (b) and α3 (c). All figures also include average values from experimental structures, from average structures of the simulations and from ensemble averages of the simulation. Note that the ensemble average dotted lines cannot be seen as they coincide with the average structure dashed lines in all cases.
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