In this research, through the use of molecular dynamics (MD) simulations, the ability of gold nanoparticles (AuNPs) functionalized by different groups, such as 3-mercaptoethylsulfonate (Mes), undecanesulfonic acid (Mus), octanethiol (Ot), and a new peptide, to inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was investigated. According to the crystal structure of angiotensin-converting enzyme 2 (ACE2), which binds to the SARS-CoV-2 receptor binding domain (RBD), 15 amino acids of ACE2 have considerable interaction with RBD. Therefore, a new peptide based on these amino acids was designed as the functional group for AuNP. On the basis of the obtained results, functionalized AuNPs have remarkable effects on the RBD and strongly interact with this protein of SARS-CoV-2. Among the studied nanoparticles, the AuNP functionalized by new peptide forms a more stable complex with RBD in comparison with ACE2, which is the human receptor for SARS-CoV-2. Different analyses confirm that the designed AuNPs can be good candidates for antiviral agents against COVID-19 disease.

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Graphical abstract Theoretical simulations reveal that phosphorene nanosheet has a considerable ability as a sensor for SARS-CoV-2 detection.

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Improving the stability of the gold nanoparticles (AuNPs) is an important challenge in nanoscience, given that the activity and ubiquitous application of the AuNPs in different fields depend largely on their stability in the solution phase. Ionic liquids (ILs) can be used as new alternatives in comparison to water and organic solvents due to their considerable properties to elevate the stability and resistance of the AuNPs against aggregation for a long period of storage. In this study, we employ molecular dynamics simulation and quantum chemistry calculations to investigate the effects of amino acid ILs ( and [BMIM][Ala]) on the stability and aggregation process of the AuNPs from the molecular viewpoint. Our results suggest that ILs can prevent AuNP aggregation. These ILs penetrate the solvation shell of the nanoparticles and by increasing the electrostatic repulsions on the surface of the AuNPs improve their stability against aggregation. Moreover, the [BMIM] + cation is more effective on the stability of the AuNPs in comparison with the corresponding anions. The ring of the cation, due to the stronger interaction with the AuNPs compared to the side chain, contributes predominantly to the stability of the nanostructures. Our quantum chemistry calculations confirm that dispersion interactions between the cation and anions of the ILs and the surface of gold play a key role in the stability of the IL−AuNP complexes. [Leu] − anion has the strongest dispersion interactions with the metal surface and forms the most stable complex with the AuNPs. Overall, the results of this study offer new insights into the properties of amino acid ILs as effective agents to improve the stability of AuNPs for long-term storage.