The molecules modeled in the present study: (a) indole, (c) para-methyl-phenol, (b) -glucopyranose, and (d) -glucopyranose. Both glucose molecules are shown with their primary alcohol groups in the gt conformation (Ref. 16).
Definition of the reaction coordinates.
Potentials of mean force as function of center-of-mass separation for -glucopyranose-indole (solid black), -glucopyranose-indole (dashed black), -glucopyranose-para-methyl-phenol (solid gray), and -glucopyranose-para-methyl-phenol (dashed gray).
Free energy surfaces for glucose-aromatic systems: -glucopyranose-indole (a), -glucopyranose-indole (b), -glucopyranose-para-methyl-phenol (c), and -glucopyranose-para-methyl-phenol (d). Energies are given as a function of separation and , for two values of ; (left) for which the glucose is tilted with respect to the aromatic molecule, and (right) which corresponds to a planar arrangement (see Fig. 2 and text).
Free energy surfaces for glucose-aromatic systems: -glucopyranose-indole (a), -glucopyranose-indole (b), -glucopyranose-para-methyl-phenol (c), and -glucopyranose-para-methyl-phenol (d). Energy contours are in kJ/mol.
Contour plots of the free energy landscape for -glucopyranose interacting with indole, for two different values of , 0.42 and 0.62 nm, along with illustrations of the relative orientations represented by three specific points, indicated on the plots by the corresponding letters. All energy contours are in kJ/mol.
Standard free energies of binding, calculated using different values for the cutoff for the bound region, . The first value is calculated using Eq. (4) and the approximation described in the previous section. The second value is calculated using Eq. (3) assuming spherical symmetry. are the well depths of the one dimensional pmfs in Fig. 3. All values are given in kJ/mol.
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