Accurate predictions of retention times, retention indices, and partition c
onstants are a long sought-after goal for theoretical studies in chromatogr
aphy. Configurational-bias Monte Carlo (CBMC) simulations in the Gibbs ense
mble using the transferable potentials for phase equilibria-united atom (Tr
aPPE-UA) force field have been carried out to obtain a microscopic picture
of the partitioning of 10 alkane isomers between a helium vapor phase and a
squalane Liquid phase, a prototypical gas-liquid chromatography system. Th
e alkane solutes include some topological isomers that differ only in the a
rrangement of their building blocks (e.g., 2,5-dimethylhexane and 3,4-dimet
hylhexane), for which the prediction of the retention order is particularly
difficult. The Kovats retention indices, a measure of the relative retenti
on times, are calculated directly from the partition constants and are in g
ood agreement with experimental values. The calculated Gibbs free energies
of transfer for the normal alkanes conform to Martin's equation which is th
e basis of linear free energy relationships used in many process modeling p
ackages. Analysis of radial distribution functions and the corresponding en
ergy integrals does not yield evidence for specific retention structures an
d shows that the internal energy of solvation is not the main driving force
for the separation of topological isomers in this system.