Janitra Regaputra S, Destiarani Wanda, Hardianto Ari, Baroroh Umi, Rohmatulloh Fauzian G, Subroto Toto, Yusuf Muhammad
Biotechnology Master Program, Postgraduate School, Universitas Padjadjaran, Jl. Dipatiukur 35, Bandung 40132, West Java, Indonesia.
Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Jl. Singaperbangsa 2, Bandung 40132, West Java, Indonesia.
J Phys Chem B. 2023 Aug 17;127(32):7103-7110. doi: 10.1021/acs.jpcb.3c00771. Epub 2023 Aug 4.
Studies on the interaction between gold nanoparticles (AuNPs) and functional proteins have been useful in developing diagnostic and therapeutic agents. Such studies require a realistic computational model of AuNPs for successful molecular design works. This study offers a new multilayer model of AuNPs to address the inconsistency between its molecular mechanics' interpretation and AuNP's plasmonic nature. We performed partial charge quantum calculation of AuNPs using Au and Au models. The result showed that it has partial negative charges on the surface and partial positive charges on the inner part, indicating that the AuNP model should be composed of multiatom types. We tested the partial charge parameters of these gold (Au) atoms in classical molecular dynamics simulation (CMD) of AuNPs. The result showed that our parameters performed better in simulating the adsorption of Na and dicarboxy acetone in terms of consistency with surface charge density than the zero charges Au in the interface force field (IFF). We proposed that the multiple-charged AuNP model can be developed further into a simpler four-atom type of Au in a larger AuNP size.
