The electrons transfer (ET) from an atom or a molecule, donor (D), to another, acceptor (A) is the basis of many fundamental chemical and physical processes. The ET mechanism is controlled by spatial arrangements of donor and acceptors: it’s the particular spatial arrangement and thus the particular distance and the orientation between the electron donors and acceptors that controls the efficiency in charge separation processes in nature. Here, we stress the importance of this concept reviewing how spatial distribution of atomic and molecular self-assembly can determine the quality and physical features of ET process from biology to material science. In this context, we propose novel lab-on-chip techniques to be used to control spatial distribution of molecules at nanoscale. Synchrotron source brightness jointly to focusing optics fabrication allows one nowadays to monitor and visualize structures with sub-micrometric spatial resolution. This can give us a new powerful tool to set up sophisticated X-ray imaging techniques as well as spectroscopic elemental and chemical mapping to investigate the structure-function relationship controlling the spatial arrangement of the molecules at nanoscale. Finally, we report intriguing recent case studies on the possibility to manipulate and control this spatial distribution and material functionality at nanoscale by using X ray illumination.