Handbook of Solvents - George Wypych - ChemTech - Ventech!

12.2 Chain conformations of polysaccharides 721
creasing number of MD simulations on sugars has been carried out. 11,13,56,57 The explicit representation
of solvent molecules is required especially in biological systems, where solvent
structuring plays an important role. Starting with an appropriate potential energy function
for sugar-water interactions, 13,58 the common solution simulations are carried out by placing
the solute molecule in the center of a cubic box of finite dimensions containing a given number
of solute molecules which usually corresponds to at least three solvation shells. 11 The
macroscopic system is then simulated by using the approximation known as “periodic
boundary conditions”, 59 in which the entire box is replicated in every direction, leaving solute
and solvent molecules to interact with each other both in central and in replica boxes and
setting the long-range interactions to smoothly decrease to zero by using the appropriate
switching functions. A pair distribution function, g(r), defined as:
()
gr
1
=
4πρr
2
()
dN r
dr
where:
r interatomic distance
ρ the bulk number density
N(r) number of atoms of given type at distance r
has been used to evaluate the normalized probability of finding a water oxygen atom at a
distance r from a given atom on the carbohydrate molecule. 11 In this way the anisotropic distribution
of solvent molecules around carbohydrate solutes was reported 11,60,61 showing an
exceptional structuring of water molecules which extends to greater distances around the
solute as compared to the pure solvent. One of the most interesting results of these simulations
is the identification of the spatial distribution of water molecules on the van der Waals’
surface of the carbohydrate molecules. Figure 12.2.10 shows a probability density excess of
the water molecules in a channel, which is effectively a bisector of the two closest sites for
hydrogen bonding.
When the energy maps have been obtained by molecular mechanics calculations, dynamics
simulations of disaccharides in various conformations are carried out to analyze the
Figure 12.2.10. Contours of solvent anisotropic density around the αα
, -trehalose disaccharide obtained from MD
simulation [unpublished figure kindly provided by J.W. Brady and Q. Liu].