Free energy perturbation calculations were used to determine how the size of an internally bound monovalent cation affects the stability of an antiparallel G-DNA quadruplex in water. A free energy cost was incurred as the cation size was increased in both water and within the DNA ’host’ complex. In water the free energy tends to level off as the ionic radius increases and charge density correspondingly decreases. In contrast, in the DNA complex the free energy change became progressively steeper as the growing ion began to induce conformational deformations in the relatively constrained binding site. The minimum point in the energy curve obtained by subtracting the free energy curves for water and DNA indicates the favored cation for binding within the complex. Two sets of ionic Lennard-Jones ’6-12’ van der Waals parameters were tested and gave similar results. In both cases the minimum free energy is in the middle of the size range of the monovalent monoatomic cations, in qualitative agreement with experimental results. However, K+ is apparently tao big for the DNA cavity, leading to weakening of the solvent-exposed, outer hydrogen bonds, so that Na+ is wrongly preferred. Thus, in contrast to expectation, the steric fit of group IA cations may not be the sole determinant of ion selectivity; e.g., K+-specific electronic effects may be involved. An antiparallel closed-loop model for the DNA sequence d(T(2)G(4))(4) was also constructed by adding two covalently-connected thymidine residues to close each major groove at one end of the quadruplex stem and each minor groove at the other end. Interloop thymidine-thymidine base pairing interactions formed at each end during molecular dynamics trajectories that were started from several different initial loop configurations.