The atomic level understanding and control of the electron transport has important advantages for many applications, such as molecular electronics, solar cells and sensors. The target of my Ph.D. work is to investigate electronic and chemical properties of molecular nanosystems using scanning tunneling microscopy (STM) and spectroscopy (STS), which can be subdivided into two key objects. The first target is to control the electron transport of the Phthalocyanine (H2Pc) molecule deposited on the gate-tunable graphene device by applying electric filed. It is known that the electron transport properties can be controlled by the intramolecular reaction which reshapes the electronic configuration without any significant change in the conformation. The STM-induced tautomerization, i.e the interconversion between two isomers due to the migration of Hydrogen, can be observed in the form of telegraphic noise. Several methods to control the intramolecular Hydrogen-transfer by changing the chemical environment of the molecule have been developed, such as locating adatoms or introducing defects. However, these affect the molecules only in the nm range. In this work, using the gate-tunable STM, I want to demonstrate a global control of the chemical environment of the device which results in the changing of the switching rate of the Hydrogen-transfer. The second target of my Ph.D. work is to provide the atomic structure and its electronic properties of various charge traps in organic-inorganic perovskite surfaces and interfaces, particularly the surface of the CH3NH3MX3 crystal and its interface structure with TiO2, which will enable to provide new insight to design improved solar cells with better efficiency.