Abstract

COMPUTATIONAL INSIGHTS INTO THE THERMODYNAMIC STABILITY AND QUANTUM-CHEMICAL REACTIVITY OF CYTOSINE-INITIATED DNA TRINUCLEOTIDES: AN AM1 SEMI-EMPIRICAL STUDY

*Dr. Bojja Rajeshwar Rao

ABSTRACT

The physicochemical and electronic behaviour of short DNA sequences underlies fundamental processes such as base-pair recognition, strand stability, and susceptibility to oxidative or electrophilic damage. In this work, all sixteen cytosine-initiated DNA trinucleotides (5′-C–N–N-3′; N = A, C, G, T) were investigated using the Austin Model 1 (AM1) semi-empirical Hamiltonian implemented in MOPAC2016. Fully optimised geometries were used to extract the heat of formation (ΔHf), dipole moment, frontier molecular orbital (FMO) energies (EHOMO, ELUMO), conductor-like screening model (COSMO) surface area and volume, and molecular weight for each trinucleotide. These primary outputs were further used, within Koopmans’ theorem and conceptual density functional theory (DFT), to derive a complete set of global reactivity descriptors: the HOMO–LUMO gap (ΔE), ionisation potential (IP), electron affinity (EA), electronegativity (χ), chemical hardness (η), softness (S), chemical potential (μ), and electrophilicity index (ω). The pyrimidine-terminated sequence CTT was found to be the most thermodynamically stable trinucleotide (ΔHf = −1025.78 kcal mol⁻¹) and, together with CTC and CCT, possessed the widest HOMO–LUMO gaps, indicating high kinetic (chemical) stability. In contrast, CGC and CAT exhibited the narrowest gaps and were identified as the most chemically reactive species, while CCA and CAC showed the highest electrophilicity indices. A strong linear relationship (r > 0.99) was found between ΔE and  chemical hardness, consistent with the theoretical definition η ≈ ΔE/2, while molecular weight correlated positively with COSMO volume (r = 0.84). Sequence-averaged analysis further revealed that thymine occupying the second or third position of the triplet systematically stabilises the trinucleotide relative to adenine-containing analogues. These results provide a quantitative, sequence-resolved reactivity map of cytosine-initiated trinucleotides and establish a computational benchmark for future studies on point mutations, oxidative lesions, and ligand/drug interactions at the trinucleotide level.

Keywords: DNA trinucleotides, AM1 semi-empirical method, MOPAC2016, frontier molecular orbitals, conceptual density functional theory, chemical reactivity descriptors, electrophilicity index, COSMO.