RuC nanosheet as a promising biosensing material for detecting the aromatic amino acids: a DFT study

Mahmoud A A Ibrahim; Nada K M Ahmed; Amna H M Mahmoud; Mohamed A El-Tayeb; Ashraf M M Abdelbacki; Shahzeb Khan; Mahmoud E S Soliman; Tamer Shoeib

doi:10.1039/d4na00670d

RuC nanosheet as a promising biosensing material for detecting the aromatic amino acids: a DFT study

Nanoscale Adv. 2024 Oct 25;6(24):6398-6407. doi: 10.1039/d4na00670d. Online ahead of print.

Authors

Mahmoud A A Ibrahim^{1

2}, Nada K M Ahmed¹, Amna H M Mahmoud¹, Mohamed A El-Tayeb³, Ashraf M M Abdelbacki⁴, Shahzeb Khan⁵, Mahmoud E S Soliman⁶, Tamer Shoeib⁷

Affiliations

¹ Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt [email protected].
² School of Health Sciences, University of KwaZulu-Natal Westville Campus Durban 4000 South Africa.
³ Department of Botany and Microbiology, College of Science, King Saud University P.O. Box 2455 Riyadh 11451 Saudi Arabia.
⁴ Deanship of Skills Development, King Saud University P.O. Box 2455 Riyadh 11451 Saudi Arabia.
⁵ Centre for Pharmaceutical Engineering Science, Faculty of Life Science, School of Pharmacy and Medical Sciences, University of Bradford BD7 1DP UK.
⁶ Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal Westville Campus Durban 4000 South Africa.
⁷ Department of Chemistry, The American University in Cairo New Cairo 11835 Egypt [email protected].

Abstract

Density functional theory (DFT) calculations were performed to examine the potential of the RuC nanosheet as a biosensor towards the aromatic amino acids (AAA; tryptophan (TRP), histidine (HIS), tyrosine (TYR), and phenylalanine (PHE)). The AAA molecules were placed vertically and horizontally with respect to the RuC surface and then subjected to geometrical relaxation. According to the geometry relaxation results, it was found that all AAA molecules preferred to be adsorbed on the RuC surface in a horizontal configuration rather than a vertical one, except the HIS molecule, which desired to be vertically adsorbed on the RuC nanosheet. From the energy manifestations, the adsorption process within the TRP⋯RuC complexes had the greatest desired negative adsorption energy (E _ads), followed by HIS⋯, TYR⋯, and then PHE⋯RuC complexes (E _ads = -40.22, -36.54, -23.95, and -16.62 kcal mol^-1, respectively). As indicated by the FMO data, changes in the E _HOMO, E _LUMO, and E _gap values of the RuC nanosheet following the adsorption process demonstrated the capacity of the RuC nanosheet to adsorb the AAA molecules. The outcomes of Bader charge transfer revealed that the RuC nanosheet had the ability to donate electrons to the AAA molecules during the adsorption process, supported by the positive Q _t values. Consistent with the E _ads conclusions, the TRP⋯RuC complexes had the largest Q _t values, indicating the potential affinity of the RuC nanosheet to adsorb the TRP molecule. Following the adsorption of AAA molecules on the RuC nanosheet, new peaks and bands were discovered based on the DOS and the band structure plots, respectively, revealing the validity of the adsorption process. Additionally, the current adsorption findings on the RuC nanosheet were compared to those on the graphene (GN) nanosheet. The outcomes of the comparison demonstrated the outperformance of the RuC nanosheet over the GN nanosheet in adsorbing the AAA molecules. These outcomes provide a solid foundation for further research on the RuC nanosheets to detect small biomolecules.