This invention refers to a method of changing a molecular structure of a hydrocarbon-containing material, the method comprising producing an ion beam comprising a first distribution of ion energies having a full width at half maximum of W; adjusting the energies of at least some of the ions to produce a second distribution of ion energies in the ion beam having a full width at half maximum of more than W; and exposing the hydrocarbon-containing material to the adjusted ion beam; wherein adjusting is based on a thickness of the hydrocarbon-containing material; and wherein adjusting the energies of at least some of the ions comprises increasing the full width at half maximum of a Bragg peak of the expected ion dose profile in the material enough to reduce a difference between the thickness of the hydrocarbon-containing material and the full width at half maximum of the Bragg peak, wherein the hydrocarbon-containing material is selected from the group consisting of oil sands, oil shale, tar sands, bitumen, and coal.