Abstract: The covalent and noncovalent backbone binding interactions in RNA-peptide complexes were studied by DFT methods. RNA1 (GGCUAGCC) structure has been selected for eight protonated peptides (GR, VR, DR, ER, KR, RR, NGR, tmeGnd) interactions based on an experimental study (Anal. Chem. 2019, 91, 1659−1664). Several DFT-based global reactivity descriptors are used to study the reactivity of eight peptides by chemical reactivity method. High hardness reflects high stability and low reactivity for the protonated peptides. DR, ER, GR, KR, RR, VR, NGR show lower value of ω, µ while tmegnd has high value of ω, µ. Larger HOMO-LUMO gap (7.29 eV) show greater structural stability for peptides. Autodock results indicated that RNA1 form hairpin structure while interacting with peptide complexes. (RNA1-RR) has higher binding energies and RNA1-ER complexes have lower binding energies. Autodock results showed strong noncovalent interaction as compared to the covalent RNA backbone bonds interactions, which is also seen by NCIPLOT and IGMPLOT plots. The reason for it might be due to the proton transfer from protonated ligand to deprotonated RNA which initiated loss of the ligand and proton transfer becomes energetically unfavourable in presence of additional hydrogen bonds as verified by the experimental results.