Side-chain polarity. The most interesting contributions arise from the polarity of the fluorinated side chain. The large, positive electrostatic potential affecting hydration waters adds an average +0.4 kcal mol 1 to the DDG Hyd of all partially fluorinated amino acids, and a near-zero, positive, contribution to the trifluorinated amino acids; the largest deviations come from I1G and I3D, for which this contribution is +0.8 kcal mol 1 . As indicated above, this contribution stems from the partial shielding of the positively charged carbons occurring in partially fluorinated groups. Regarding the water-fluorine hydrogen bonds, they are much weaker than those with the carbonyl or amine groups, and decrease in stability in the order -CH 2 F > -CHF 2 /-CF 2 -> -CF 3 , as indicated by the relative magnitudes of the relevant parameters in Table . These trends are expected: our simulations show that the distance between the water oxygen and the fluorine is smaller in groups with fewer fluorines (SI Table ) indicating an increase in hydrogen bond strength, and other experiments and ab initio calculations have shown the same trends . Despite the weakness of the hydrogen bonds between water and the diand tri-fluorinated groups, they nevertheless play an important role: e.g., they are present ⇡15% of the time per fluorine in CF 3 groups (SI Table ); for comparison, the number of water-methyl configurations per side chain CH group meeting the hydrogen bond criteria in the non-fluorinated amino acids is almost negligible (⇡3%). The magnitude of the hydrogen bond contributions to DDG Hyd per fluorine atom also follows the order -CH 2 F > -CHF 2 /-CF 2 -> -CF 3 , with the average values being 1.79, 0.60 and 0.13 kcal mol 1 per fluorine, respectively † ; the weak water-fluorine hydrogen bonds to -CF 3 contribute on average a non-negligible -0.39 kcal mol 1 -CF 1 3 . Contributions of the side chain to DDG Hyd are largely constant per CF x substituent. The values of the free energy contribution per water-fluorine hydrogen bond yielded by the multivariate model anticorrelate surprisingly well with the LJ contribution of the area per fluorine atom (SI Figure ), suggesting that the energy cost associated with (overall repulsive) waterfluoromethyl LJ interactions is partially offset by the energy gain from the formation of water-fluorine hydrogen bonds. This point is illustrated in Figure , where the ratio of the area and waterfluorine hydrogen bond contributions is plotted against the number of fluorine atoms. It is clear that the contribution of each For one hydrogen ! fluorine substitution, the hydrogen bonding over-compensates the cavity-formation cost. As the number of substitutions increases, the penalty for cavity formation per fluorine is reduced, showing that the perturbation due to the insertion of the first fluorine atom is large but further insertions perturb the water network to a smaller extent. Simultaneously, the energy gain per fluorine from water-fluorine hydrogen bonds is decreased for multiple fluorine insertions, likely due to the less negative partial charges on fluorine and the fewer H F atoms, which interact favorably with water (see SI section 2.3). Interestingly, there is a crossover point, associated with the number of fluorine substitutions, after which the energy cost surpasses the energy gain; in other words, there is a transition between a locally hydrophilic moiety to a locally hydrophobic moiety. Inspecting Figure we find that the number of fluorine atoms required to perform the transition is 2.8. This crossover point has associated uncertainty arising from the systematic deviations in the hydration free energies observed for small alkanes with the GAFF/Amber force field (see Figure and discussion above). Even considering this uncertainty, it appears that trifluoromethyl groups, by themselves, impart only a small increase in amino acid hydrophobicity, because the positive Lennard-Jones component of the hydration free energy is partially offset by the weak but still favorable waterfluorine hydrogen bonds.