## List of Figures 

1 Numbering scheme for aldopyranoses rings. . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 

2 Different ring shapes for stable ring conformers: chairs (left); boats (center); skews (right). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 

3 Puckering free energy landscape (already corrected with the results from the umbrella sampling phase) of β -d- Glc using the standard 45a4 parameter set. Upper panel: the ( θ, φ ) plane is shown, with isolines drawn every 10 kJ/mol starting from the absolute minimum. Lower panel: projection of the free en- ergy profile onto the φ = 0 plane. Darker colors correspond to lower energies. . 35 

4 Contribution to the total puckering free energy of β -d- Glc (45a4 parameters) from the equilibrium sampling, − k b T ln ρ$_{bias}$ ( θ, φ ). An immaterial constant has been added, so that the correction term is zero at the position of the free energy global minimum. Isolines are drawn every 2.5 kJ/mol (upper panel). The projection onto the φ = 0 plane of the correction term (lower panel). . . . . 36 

5 Inverted chair free energy difference for the β (upper panel) and α (lower panel) series of aldopyranoses. The three curves refer to the simulation results obtained using the 45a4 parameter set (squares) and the predictions of Ref. 62 (triangles) and Ref. 63 (circles). Lines are a guide to the eye, and error bars are always smaller than the symbols (0.5 kJ/mol). . . . . . . . . . . . . . . . . . . . . . . 37 

6 Results of the unbiased molecular dynamics simulation of β -d- Glc. Histogram of the population along the θ puckering coordinate (upper panel) and time evolution of the number of inverted chairs (lower panel). . . . . . . . . . . . . . . . . . 38 

7 Inverted chair free energy difference for the β (upper panel) and α (lower panel) series of aldopyranoses. The three curves refer to the simulation re- sults using the new parameter set (squares) and the predictions of Ref. 62 (triangles) and Ref. 63 (circles). Lines are a guide to the eye, and error bars are always smaller than the symbols (0.5 kJ/mol). . . . . . . . . . . . . . . . . . . . . . . 39 

8 Puckering free energy landscapes (in kJ/mol) obtained by the combined meta- dynamics – umbrella sampling, for the series of β -d- aldopyranoses simulated using the new force field parameters. Isolines are drawn every 10 kJ/mol, starting from the global minimum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 

