Table 2.

Examples of two proteins and two small molecules for which optimal vdW and MS based dielectric boundary definitions yield equally accurate PB estimates of ΔG_el, kcal/mol. The vdW DB calculations are based on BONDI + 0.2 Å atomic radii. For the proteins the standard value of ρ_w = 1.4 Å was used to compute the MS. Since, in the case of the small molecules and MS DB, the 3 common radii sets did no yield an optimal agreement with the explicit solvent for any solvent probe radius ρ_w < 7 Å, fig. 6, we increased all the atomic radii slightly to reach the optimum at a reasonable ρ_w. Specifically, a uniform scaling (multiplication) of all the radii in the BONDI set by 1.096 gave a clear minimum at ρ_w = 3 Å in the PB vs. explicit solvent ΔG_el average error curve (graph not shown); here we used this value of ρ_w to define MS for the PB calculations on small molecules.

Structure class	small protein	small protein	small molecule	small molecule
Name	1BH4	1BRV	3-methyl-1h-indole	1-naphthol
Number of atoms	427	265	19	19
ΔGel, PB vdW	−237.9	−210.0	−7.5	−8.0
ΔGel, PB MS	−240.9	−213.4	−7.4	−8.1
ΔGel, TIP3P	−239.7	−206.7	−7.5	−8.3