  Self-assembled molecular structures have been intensively used in molecular
electronics and spintronics. However, detailed nature of the interfaces between
molecular layers and extended metallic contacts used to bias the real devices
remains unclear. Buried interfaces greatly restrict application of standard
techniques such as Raman or scanning electron microscopies. Here we introduce
low frequency noise spectroscopy as a tool to characterize buried
molecular-metal interfaces. We take advantage of vibrational heating of the
molecules with incomplete contacts to the interface. Electrons, being the main
spin and charge carriers propagating through the interfaces involving
self-assembled molecules, interact inelastically with charged atomic ions. Such
interactions produce quantum molecular vibrations (phonons). Detailed
investigation of both conductance and conductance fluctuations in magnetic
tunnel junctions with few nm Perylenetetracarboxylic dianhydride (PTCDA) allows
to map vibrational heating at specific biases taking place in 'hot spots' where
self-assembled layers weaker contact the metallic electrodes. We follow this
effect as a function of PTCDA thickness and find the best molecular-metal order
for the lowest (3-5 monolayers) barriers. Moreover, we unveil interplay between
spin and phonons at interface showing experimentally and by modelling
spin-control over molecular vibrational heating. We find that vibrational
heating related low frequency noise essentially depends on the relative
alignment of the electrodes with noise changes well beyond expectations from
fluctuation-dissipation theorem.
