Characterizing the complex structure of such molecules with highly resolving, vacuum-based methods like scanning probe microscopy requires their transfer into the gas phase and further onto an atomically clean surface in ultrahigh vacuum without causing additional contamination. Conventionally this is done via sublimation in vacuum. However, similar to biological molecules, large synthetic compounds can be non-volatile and decompose upon heating. Soft-landing ion beam deposition using soft ionization methods represents an alternative approach to vacuum deposition. Using different oligoyne derivatives of the form of R-1-(C equivalent to C)(n)-R-2, here we demonstrate that even sensitive molecules can be handled by soft-landing electrospray ion beam deposition. We generate intact molecular ions as well as fragment ions with intact hexayne parts and deposit them on clean metal surfaces. Scanning tunneling microscopy shows that the reactive hexayne segments of the molecules of six conjugated triple bonds are intact. The molecules agglomerate into ribbon-like islands, whose internal structure can be steered by the choice of the substituents. Our results suggest the use of ion beam deposition to arrange reactive precursors for subsequent polymerization reactions. (C) 2014 The Authors. Published by Elsevier B.V.