Molecular model for hydrated biological tissues

A density-functional microscopic model for soft tissues (STmod) is presented. The model was based on a prototype molecular structure from experimentally resolved type I collagen peptide residues and water clusters treated in periodic boundary conditions. We obtained the optimized geometry, binding and coupling energies, dipole moments, and vibrational frequencies. The results concerning the stability of the confined water clusters, the water-water, and water-collagen interactions were successfully correlated to some important experimental trends of normal and inflammatory tissues.

Figure 1

(a) Structural scheme of a connective tissue showing the collagen fibers and the fibrils. These are constituted by water and collagen molecules. (b) The construction of the STmod unit cell compared the original collagen fibers structure. (c) STmod unit cell example ($C_4$ structure) chosen from a experimentally resolved hydrated peptide structure. (d) $C_4$ structure enclosing four water molecules clusters. In (c) and (d) hydrogen bond inside water clusters were indicated by yellow. Hydrogen, carbon, nitrogen, and oxygen atoms were in white, green, blue, and red, respectively.

Figure 2

$C_0,C_{1s}$, and $D_0$ structures.

Figure 3

(a) Normalized total energy per atom for optimized and non-optimized $C$ structures. (b) Histogram for atomic coordinates of $C_0$ showing the effect of geometry optimization. (c) Binding $E_B$ (open circle) and coupling $E_C$ (closed square) energies as defined in Eqs. (2) and (3), respectively, for the various structures.

Figure 4

Total dipole moment $\left(\mu \right)$ for each structure.

Figure 5

Raman spectra obtained for each confinement and the experimental curves of normal (NM) (a) and inflammatory fibrous hyperplasia (IFH) (b) tissues. Numbers (1) to (10) indicate the vibrational bands discussed in the text.