Fig 1.
The glycosidic link in a GlcNH2 -GlcNH2 dimer.
a) The dihedral angles ϕ and ψ. Atoms defining ϕ and ψ are lablled. b) CG Topology. Atoms and bonds in the CG Model are drawn thick and in color. The all atom structure of the monomers is shown in gray for orientation. The centers of the CG interaction sites are shown in black, while the transparent gray spheres illustrate the range of steric interactions. c) A free energy map for ϕ and ψ.
Fig 2.
Components of the persistence length.
Decay of the bond vector correlation for simulations with and without electrostatic contributions.
Table 1.
Radius of gyration from different water models.
Fig 3.
Complete set of nine PMF maps for the nine possible combinations of monomers in a chitosan polymer.
Arrows indicate links that can change when the charge on monomer changes in a titration move.
Table 2.
Features of the PMF maps for all possible links.
Fig 4.
PMF specific persistence length.
a) Decay of the bond vector correlation for the nine different link types, and b) the correlation between the polymer stiffness (LP,0) and the energy of the second minimum (ΔG2).
Table 3.
Effects of map swapping.
Table 4.
Radius of gyration from simulation and experiment.
Fig 5.
MC acceptance rates as a function of DD and pH.
Fig 6.
Fitting pKi to titration data.
Comparison of simulated and experimental titration data for a) DD = 80% and pKi from 6.1 to 7.0; b) DD = 80% and pKi 6.5-6.7; c) DD = 76% and pKi 6.5-6.7.
Fig 7.
a) degree of dissociation vs pH. b) pKapp and c) n parameter as a function of cs for a polymer with DP = 1000 and DD = 89.4%.
Fig 8.
Equilibrium conformations at different pH and cs for chitosan with DD 89.4% and DP 1000.
Red numbers above each structure gives the root mean square RG (nm). Orange regions indicate regions where the conditions for model validity are no longer fulfilled.
Fig 9.
Contributions to the persistence length.
a)comparison of LP and LP,0 for cs = 0.1 and DD 59%, DP = 500; b) and c) effect of cs on LP,0 (b) and LP (c) for 89.4% DD for DP = 1000.
Fig 10.
pKapp versus degree of dissociation for different DD of (a) 95%, (b) 68% (c) 50% and (d) 30% for three different values of cs.
Fig 11.
Titration parameters as a function of DD.
(a)pKapp and (b) n parameter from a linear fit of pH vs in the range
0.5.
Fig 12.
The effect of DD on a) RG and (b and c) the contributions to LP at pH 4.5 (b) and pH 6.5 (c) for Chitosan with DP = 500.
Fig 13.
Effect of the pattern of acetylation RG of chitosan with 50% DD and DP = 500 for acetylation patterns with different blocksize and a random distribution.
Fig 14.
Characteristic ratio vs DP for different force field contributions at pH 4.5 and cs = 0.1.