Theoretical investigation on the effect of cluster size and level of density funcitonals in bonding case study on glycine and cytidine

This research investigated the theoretical calculation of the electron density for glycine and cytidine system using Density Functional Theory (DFT). This is because DFT offers a good balance between computational cost and accuracy for studying electron density distribution. The structure of glycine and cytidine was constructed using GaussView from a CIF file obtained from Hara et al. (2024). Topological analyses were performed using the Multiwfn program to identify bond critical points (BCPs) and compute |VBCP|/GBCP, and Vesta was used to visualise the electron density distribution. The result showed that the C-N, C-C and C-H bonds were covalent with high |VBCP|/GBCP ratios (>2). The Valence Electron Density (VED) plots resembled the experimental curves more closely. The findings showed that the cluster size of neighbouring molecules have an impact on electron distributions, thus fulfilling the first objective. Although the two functionals used, APFD/def2tzvp and LC-BLYP/cc-pVTZ displayed similar bonding trends, LC-BLYP/cc-pVTZ results was slightly better in terms of long-range interactions, achieving the second objective. In conclusion, it has been shown in paper that cluster size does indeed influence the bonding interactions and electron density.