Efficient Combination of Environment Change and Alchemical
Perturbation within the Enveloping Distribution Sampling (EDS) Scheme:
Twin-System EDS and Application to the Determination of Octanol–Water
Partition Coefficients
posted on 2016-02-19, 18:50authored byNiels Hansen, Philippe H. Hünenberger, Wilfred F. van Gunsteren
The
methodology of Enveloping Distribution Sampling (EDS) is extended
to probe a single-simulation alternative to the thermodynamic cycle
that is standardly used for measuring the effect of a modification
of a chemical compound, e.g. from a given species to a chemical derivative
for a ligand or solute molecule, on the free-enthalpy change associated
with a change in environment, e.g. from the unbound state to the bound
state for a protein–ligand system or from one solvent to another
one for a solute molecule. This alternative approach relies on the
coupled simulation of two systems (computational boxes) 1 and 2, and
the method is therefore referred to as twin-system EDS. Systems 1
and 2 account for the two choices of environment. The end states of
the alchemical perturbation for the twin-system associate the two
alternative forms X and Y of the molecule to systems 1 and 2 or 2
and 1, respectively. In this way, the processes of transforming one
molecule into the other are carried out simultaneously in opposite
directions in the two environments, leading to a change in free enthalpy
that is smaller than for the two individual processes and to an energy-difference
distribution that is more symmetric. As an illustration, the method
is applied to the calculation of octanol–water partition coefficients
for C4 to C8 alkanes, 1-hexanol and 1,2-dimethoxyethane.
It is shown in particular that the consideration of the residual hydration
of octanol leads to calculated partition coefficients that are in
better agreement with reported experimental numbers.