Structural features of the adenosine conjugate in means of vibrational spectroscopy and DFT

Vibrational spectra of adenosine bearing benzo-15-crown ether moiety [N6-4′-(benzo-15-crown-5)-adenosine, AC] have been recorded in solid phase (FT-IR, FT-Raman) and in aqueous solution on the silver colloid surface (SERS). To interpret a very complex vibrational pattern of experimental data, geometrical parameters (molecular structure) as well as harmonic frequencies of the isolated molecule were calculated at the density functional theory level [B3LYP/6-31G(d)]. Assignment of the observed vibrational modes is discussed on the basis of the theoretical results obtained for N6-4′-(benzo-15-crown-5)-adenosine as well as its molecular isolated fragments, i.e. adenosine and benzo-15-crown ether. Our analysis of SERS spectrum indicates that adenine and benzo-15-crown ether take tilted orientation while the imino group and ribose adopt almost vertical position in respect to the metal surface. Moreover, calculated atomic charge distribution gives interesting insights into changes of electron density allocation in investigated fragments.