KAJIAN STRUKTUR DAN DINAMIKA SOLVASI ION MANGAN(III) DALAM AIR MENGGUNAKAN SIMULASI DINAMIKA MOLEKULAR QM/MM (QUANTUM MECHANICS/MOLECULAR MECHANICS)

Ayyasy Mufid Habibullah, NIM.: 20106030022 (2024) KAJIAN STRUKTUR DAN DINAMIKA SOLVASI ION MANGAN(III) DALAM AIR MENGGUNAKAN SIMULASI DINAMIKA MOLEKULAR QM/MM (QUANTUM MECHANICS/MOLECULAR MECHANICS). Skripsi thesis, UIN SUNAN KALIJAGA YOGYAKARTA.

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Abstract

The reactivity of manganese metal ions in water can influence the properties and structure of the complexes formed. Experimental research has not been able to predict the static and dynamic properties directly derived from interactions at the atomic or molecular level. This study aims to investigate the structure and dynamics of Mn3+ ion solvation in water through QM/MM molecular dynamics simulations. The subject of the research is Mn3+ ions, while the object is the structure and dynamics of Mn3+ ions in water. The procedure involved determining and testing simulation parameters according to the Lennard-Jones potential graph. The next step was to develop and modify computational programs in LAMMPS and Gromacs to solve the 2-body and 3-body potential equations using QM/MM molecular dynamics simulations, which resulted in trajectory file data. The trajectory files were then processed to generate RDF and ADF graphs. The dynamics of ion and ligand movements were analyzed using YASARA software, which produced RMSF and RMSD data. The research results showed the regularity of Mn3+ ion structure in water. The angles formed, based on ADF analysis, were 89º and 176º, identifying an octahedral shape surrounded by six water ligands. The RMSD and RMSF analysis results indicated average values of ≤ 2.5Å from the simulation results over 500 picoseconds. This suggests that the ion and ligands do not exhibit high flexibility and can be considered to have stable interactions or bonds. The stable complexation of manganese(III) ions with water makes them more toxic in the body.

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