An apparatus that generates molecular ions and methods to generate molecular ions are disclosed. At least a first species is ionized in an ion source. The first species ions and/or first species combine to form molecular ions. These molecular ions may be transported to a second chamber, which may be an arc chamber or diffusion chamber, and are extracted. The molecular ions may have a larger atomic mass than the first species or first species ions. A second species also may be ionized with the first species to form molecular ions. In one instance, the first and second species are both molecules.