For large molecules, electronically excited stales are denser than can be simply judged from the gap between the ground state and excited states. This is particularly true for large open shell systems, such as peptide cations. In such systems, short laser pulses can be used to prepare initial electronic states that are not stationary. These are non Born-Oppenheimer states, and therefore, the motion of the nuclei is not determined by a single potential. It is argued that such states could offer the possibility of control of reactivity. They can impede the usually facile vibrational energy redistribution, which is characteristic for a motion on a potential surface with a well. After a localized ionization, the dependence of site-selective fragmentation of small peptide ions on time is discussed with computational results based on a Pariser-Parr-Pople Like electronic Hamiltonian. We predict a strong nonstatistical and site selective reactivity on a short time scale and also a dependence on the nature of the initial excitation. Results are presented for the fragmentation of Leu-Leu-Leu-Trp(+) and Ala-Ala-Ala-Tyr(+) ions and are compared with nanosecond laser pulse experiments.