Development of the 1D and 2D IR spectroscopy of small organic molecules and clusters opens yet another way of possible identification of small organic molecules in the state of motion in the graphene nanopore scanning device. With the advantage of obtaining qualitative and at least semi-quantitative information of specimens real-time and non-invasively, vibrational spectroscopy techniques, infrared (IR) and Raman have become more and more important in the analysis of biomolecular samples. At present, the sensitivity and spatial resolution of these techniques stands at the challenge of the detection and analysis of biosamples at very low concentration (single molecule) and high spatial resolution (nanometer/sub-nanometer scale). Spectral analysis requires theoretical assignment of vibrational modes to each biomolecule.
We considered vibrational spectra of DNA nucleobase at the time when they are translocated through the graphene nanopore. The Fourier transform of the density of states (DOS) of each base was calculated and the spectra of the base molecules and C atoms of graphene pore edge were obtained. Translocation rate was fixed to have maximum interaction of the base with 1.5 nm pore and single orientation of nucleobases was evaluated relative to molecular plane. Whether interaction of nucleobase and nanopore is able to enhance the signal is still remains unanswered. But we have shown that the spectra of each nucleobase are different and can be considered the fingerprint of the particular molecule.
The interaction forces between pore and base are structure dependent and time-limited by translocation time. In such case, transient correlation functions were utilized for the DOSes of the individual bases and forces on each atom of the particular base were sorted by intensity. The spectra of individual atoms in the bases as well as of whole molecule were compared and frequencies of most intense peaks were related to particular atoms. Molecular dynamics method is used for the DNA base and graphene nanopore calculations with the MM2/MM3 potentials for the base and REBO graphene potential. Interaction potential between the bases can simultaneously give additional information for the electronic transport calculations with possible tra and graphene are of the MM2/MM3 part of the Van der Waals interaction only has been considered. Possibility of base identification by spectral signature is confirmed. Calculated spectra are compared with results of the existing IR measurements for nucleobases.