CHEMISTRY, BIOPHYSICS. For the article “Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms,” by Jason A. Wagoner and Nathan A. Baker, which appeared in issue 22, May 30, 2006, of Proc Natl Acad Sci USA (103:8331–8336; first published May 18, 2006; 10.1073/pnas.0600118103), the authors note that an error in the implementation of Eq. 10 in the original paper led to improper scaling of the solvent-accessible volume forces for highly exposed surface atoms. The error in the original implementation of Eq. 10 affects Tables 1 and 2 of the original manuscript as well as Tables 3 and 4 and Figs. 2 B and C and 3 in the original supporting information. Corrected versions of Tables 1 and 2 appear below. A correction to the supporting information has been published online. This error does not affect the conclusions of the article.
Table 1.
Optimized 6/12 and WCA implicit solvent nonpolar MF parameter values and goodness-of-fit metrics
| MF model 6/12 |
MF model WCA |
|||||
|---|---|---|---|---|---|---|
| Parameters | Attractive | Repulsive | Total | Attractive | Repulsive | Total |
| σs, Å | 0.89 [0.87–0.91] | 1.29 [1.16–1.44] | 1.68 [1.57–1.80] | 0.8 [0.73–0.86] | 1.29 [1.18–1.41] | 1.25 [1.16–1.39] |
| γ, cal·mol−1·Å−2 | — | 15(1) | 1(1) | — | 2(1) | 0(1) |
| p, cal·mol−1·Å−3 | — | 94(2) | 55(2) | — | 52(2) | 55(2) |
| r | 0.88 | 0.56 | 0.83 | 0.84 | 0.87 | 0.86 |
| R | 0.97 | 0.91 | 0.94 | 0.97 | 0.94 | 0.94 |
| χ2, 10−3 kcal2·mol−2·Å−2 | 6.99 | 3.35 | 6.47 | 0.56 | 4.87 | 4.63 |
Separate fits of nonpolar solvation MFs were performed as follows: Attractive, a comparison of attractive implicit (Eq. 15) and attractive explicit; Repulsive, a comparison of repulsive implicit (Eq. 10) and repulsive explicit; and Total, a comparison of the total implicit (Eq. 21) and total explicit (Eq. 8) nonpolar MFs. Where applicable, standard errors are presented in parentheses; 99% confidence intervals (see text) are presented in brackets.
Table 2.
Comparison of total solvation energies (kcal/mol) for small alkane solutes
| Compound | WCA 1.25 | WCA 0.65 | OPLS | AMBER | Exp. |
|---|---|---|---|---|---|
| Methane | 6.40 | 1.93 | 2.40 | 2.69 | 2.00 |
| Ethane | 8.41 | 2.25 | 2.63 | — | 1.83 |
| Propane | 10.5 | 2.84 | 2.89 | 3.02 | 1.96 |
| Butane | 11.8 | 2.93 | 3.21 | 3.19 | 2.08 |
| Pentane | 13.7 | 3.48 | 3.78 | — | 2.33 |
| Hexane | 15.6 | 3.90 | 3.78 | — | 2.49 |
| Isobutane | 12.0 | 3.16 | 3.03 | 3.27 | 2.52 |
| 2-Methylbutane | 13.4 | 3.45 | 3.51 | — | 2.38 |
| Neopentane | 13.2 | 3.46 | 3.23 | — | 2.50 |
| Cyclopentane | 11.3 | 2.25 | 2.80 | — | 1.20 |
| Cyclohexane | 13.7 | 3.18 | 2.34 | — | 1.23 |
WCA energy values were obtained by using the methods described in the text with σs = 1.25 and 0.65 Å. OPLS energies were taken from Gallicchio et al. (35) by using values in table 2 of their paper. AMBER energies are from Shirts et al. (64), ′van der Waals′ values in table II of their paper. Experimental (Exp.) values are from table VII of Cabini et al. (65).