Comparison of the IR spectra of the Cu-phthalocyanine (CuPc) nanocrystals obtained using surface sensitive attenuated total reflectance (ATR) and bulk sensitive transmittance sample configurations revealed small but measurable changes of some vibrational frequencies of the molecules at the surface of nanocrystals with the outermost part of the surface CuPc molecules being the most affected. These changes are caused by electrostatic interactions between the polar components of the molecules on the surface of nanocrystals and external polar molecular species vicinal to the nanocrystals. The external polar species can be either chemically bonded to the CuPc nanocrystal's surface or they can reside in its vicinity without forming a chemical bond with the nanocrystal. Molecular modeling (DMOL3 - Materials Studio and Gaussian calculations) of the impact of selected external polar species vicinal to a CuPc molecule on the CuPc molecular vibrations confirmed experimentally observed changes in the vibrational frequencies of the selected CuPc molecular bonding configurations and provided detailed information on the forces involved in these interactions. The population of external polar species vicinal to the CuPc surface can be modified by washing the nanocrystals or by introducing polar molecular additives miscible with the CuPc nanocrystals. Reduction in the number of external polar additives was accomplished by either centrifuging the aqueous dispersion of the nanocrystals or by organic solvent-based Soxhlet extraction, while their number was increased by soaking (followed by drying) the nanocrystals in high and low pH aqueous solutions containing SO3- and OH- ions. These quantitative and qualitative modifications of the population of external polar species surrounding CuPc nanocrystals were reflected in the corresponding changes of the selected vibrational frequencies of the CuPc surface molecules providing an effective tool for not only recognizing the molecular species vicinal to a nanocrystal but also quantifying their concentration. Some of these modifications can also be observed with a naked eye in the form of noticeable color changes of the CuPc nancrystalline powder. This is due to the extremely high visible extinction coefficient of the CuPc nanocrystals causing that the impinging light is mostly absorbed/reflected within the surface region of the nanocrystals. Changes of the electronic structure within this region, caused by the interactions with the vicinal polar species, shift the vis absorption/reflection spectra changing the observed color of the nanocrystalline powder. Similar results were obtained for other molecular nanocrystals, including yellow chromophore molecules. Preliminary data indicate that the described analytical method of analyzing the molecular polar species vicinal to a molecular nanocrystal could find variety of applications ranging from molecular device fabrication to pharmaceutical materials.