In this thesis a series of experiments on collisions between atomic projectile ions at keV energies and target vapors of either isolated molecules or van der Waals clusters is presented and analyzed. The atomic ions are produced in an Electron Cyclotron Resonance (ECR) ion source, accelerated and guided into the target volume. The charged target collision products are mass-to-charge analyzed in a time-of-flight spectrometer. The Polycyclic Aromatic Hyrdrocarbons (PAHs) Anthracene (C₁₄H₁₀), Coronene (C₂₄H₁₂), two C₁₆H₁₀ isomers, Pyrene and Fluoranthene, and the fullerene C₆₀ are examined.

For projectile ions in low charge states, small impact parameter collisions dominate, which leads to internal heating of the target. With isolated molecules as targets, this typically results in ionization and often also in fragmentation. For cluster targets energy and charge are rapidly distributed among the cluster building blocks. This is followed by cluster evaporation and very limited fragmentation of the individual molecules. C₁₁₉⁺ and C₁₁₈⁺ are observed as products. These are due to the formation of the reactive C_58/59⁺ ions by direct knockout processes, which react with another C₆₀ of the cluster to form dumb-bell shaped molecules.

For projectile ions of high charge (Xe²⁰⁺) larger impact parameters dominate, leading to little internal heating. For isolated molecule targets, intact molecular ions are the main collision products. Charged fragments stem mostly from multifragmentation following ionization to high charge states. For cluster targets, the collision products consist mainly of singly charged monomers. Fragmentation of the individual molecules is comparatively strong. This suggests a quick distribution of charges followed by a Coulomb explosion, which leads to internal heating.

The results show that weakly bound clusters do not sustain the impact of keV-ions and that it is possible to form new molecular structures.