We present a study of first principles computational techniques for the description of chemical systems in the nanometer scale: clusters, nanostructures and biomolecules. The scope of our methodology comprises linear and non-linear interactions of electromagnetic fields with nanostructures, the latter being described through the point-nuclei approximation, whereas the electromagnetic fields are described classically. We have focused on both small to medium sized inorganic clusters and on small organic and biological systems. We have considered both their linear photoresponse (e.g. optical absorption) and their non-linear interaction with intense femtosecond lasers. Also, the underlying nuclear structure is not inert: the coupling of the excited electronic states with the vibronic degrees of freedom is also studied -- which may lead to processes such as photodissociation, photoisomerization, etc. In these latter cases, we have investigated non-adiabatic molecular dynamics simulations within our formalism.