An approach to the application of free energy perturbation methods using molecular dynamics: applications to the transformations of methanol .fwdarw. ethane, oxonium .fwdarw. ammonium, glycine .fwdarw. alanine, and alanine .fwdarw. phenylalanine in aqueous solution and to H3O+(H2O)3 .fwdarw. NH4+(H2O)3 in the gas phase