Perfluoroalkanes in AMBER-ii Force Field

Perfluoroalkanes are famous for their properties similar to normal alkanes, but with interesting differences that determine their practical application. One of the practically useful but difficult to model properties is the mutual insolubility of higher liquid alkanes and perfluoroalkanes. Because of assigning a relatively high partial charge of −0.37e to fluorine atoms, the AMBER-ii reproduces the mutual insolubility¹.

Simulation of phase separation in a mixture of C₁₂H₂₆ and C₉F₂₀

start	1 ns	2 ns	4 ns	8 ns	16 ns

It is interesting to note that the obtained parameters provide the conformational properties of linear perfluoroalkanes without the introduction of torsion potentials¹.

¹ Alexei M. Nikitin, Yury V. Milchevskiy and Alexander P. Lyubartsev AMBER-ii: New Combining Rules and Force Field for Perfluoroalkanes. J. Phys. Chem. B, 2015, 119 (46), pp 14563–14573 DOI 10.1021/acs.jpcb.5b07233