Structure and lowest excitation properties of the backbone-modified GC PNA dimers

Abstract

The proposed research aims to investigate the structure and lowest excitation properties of GG-CC and GC-CG (G, guanine; C, cytosine) peptide nucleic acid (PNA) dimers, incorporating different amino acids such as serine, aspartic acid, and histidine using the density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods. The structures under consideration have been optimized at the Becke’s three-parameter hybrid density functional (B3) with correlation function of Lee, Yang and Parr (LYP)/6-31G* level of theory. The study involves calculating the backbone torsions and backbone-base linker torsions, correlating them with experimental data. The computed excitation energy for the GG-CC PNA system is compared with the natural GG-CC DNA system. The lowest excitation properties, such as excitation energy, wavelength, and oscillator strength, reveal their dependency on both the stacking arrangement and the molecular environment, irrespective of whether the PNA is modified or unmodified. Additionally, a highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) analyses were conducted. This study is intended to serve as a foundational tool for understanding the molecular behaviour of PNAs under light absorption, potentially leading to further exploitation in photo-related applications.

Graphical abstract