Multiple single-photon ionization of a polyatomic system induced by an intense X-ray pulse triggers a complicated relaxation dynamics. Exceptional molecules, like fullerenes, allows to study this dynamics in a remarkably detailed way. General features derived here can serve as a paradigm for more complex systems like clusters consisting of small molecules.

We study systematically the electronic sequence of methane CH4, ammonia NH4, and water H2O clusters, augmented by the "atomic limit" of neon clusters.

Those containing hydrogen do eject fast protons when illuminated by short X-ray pulses. Surprisingly, a suitable overall charging of the cluster -- controlled by the X-ray intensity -- induces electron migration from the surface to the bulk leading to efficient segregation of the protons. This "dynamical segregation" hinders globally the explosion of the heavy atoms even outside the screened volume.

In contrast to core-shell systems where the outer shell is sacrificed to reduce radiation damage, the intricate proton dynamics of hydride clusters allows one to keep the entire backbone of heavy atoms intact. Further studies on large molecules -- being neither as homogeneous nor as spherical as the molecular cluster -- confirm this segregation effect.