New dimension indices for the characterization of the solvent-accessible surface

A method for the computation of a dimension index D is implemented in progr am TOPO and applied to calculate the solvent-accessible surfaces of molecul es. Our algorithm distinguishes external from internal atoms, and uses such a feature to give two fractal-like dimension indices, D and D'. The D' - D difference is a sensitive method to elucidate the occurrence of atoms that are hidden to solvents. For molecules with buried atoms this difference is great (e.g., faujasite). The procedure is compared with the GEPOL code, wh ich provides high-quality results. TOPO systematic error can be easily corr ected by simple addition of a small constant value (0.011). Correlation mod els between indices D and D', globularity, rugosity, dipole moment and othe r properties make clear the existence of a homogeneous molecular structure in each series. Additional applications are the extrapolation of D to infin ite polymers, the variation of the D with generations of dendrimers and a r evision of D for lysozyme. (C) 2001 John Wiley & Sons, Inc.