Porphyrin films as discrete elements for nucleoside identification: Experimental and DFT study

Abstract

In this work, the interaction of metal-free octaethylporphyrin (P) and a Mn(III) octaethylporphyrin chloride (MnP) films with various RNA nucleoside molecules (adenosine [A], cytidine [C], guanosine [G] and uridine [U]) was investigated to elucidate a possible molecular recognition. The porphyrin film-nucleoside interaction took place in solution, which was analyzed to quantify the nucleoside adsorption. The films were investigated by using microscopy and spectroscopic techniques (SEM, AFM, UV-Vis and IR), in addition to the in-plane film conductivity. Experimental results were correlated with DFT calculations to investigate binding energies, separation distances, and adsorption sites, among others. From these results, it was observed that purine bases were preferably adsorbed by the metal-free porphyrin film, while pyrimidine bases were adsorbed on the manganese porphyrin surface. Conductivity results exhibited the highest resistance for the bare metal-free film, but its conductivity increases after nucleoside adsorption, being the purine molecules the most resistive and the pyrimidine molecules the most conductive. In contrast, the Mn porphyrin film showed the highest conductivity, but after nucleoside adsorption, the resistivity increased for purine and pyrimidine bases, being pyrimidines the less conductive. DFT calculations showed binding energies PG>PA>PC>PU and MnPC>MnPG>MnPA>MnPU, which were consistent with experimental findings. In general, the main interactions took place between the porphyrin core and the pentose of the nucleoside, while MnP formed Mn porphyrin-nucleoside arrangements with octahedral geometry. The calculated UV-Vis spectra were in agreement with the experimental plots. From these results, changes in nucleoside adsorption can lead to a selective recognition of nucleoside molecules.