STRUKTUR DAN DINAMIKA SOLVASI KROMIUM(III) DALAM AMONIA: STUDI SIMULASI DINAMIKA MOLEKULAR QUANTUM MECHANICS/ MOLECULAR MECHANICS (QM/MM)

Muhammad Rafiq Al Mahdi, NIM.: 20106030050 (2024) STRUKTUR DAN DINAMIKA SOLVASI KROMIUM(III) DALAM AMONIA: STUDI SIMULASI DINAMIKA MOLEKULAR QUANTUM MECHANICS/ MOLECULAR MECHANICS (QM/MM). Skripsi thesis, UIN SUNAN KALIJAGA YOGYAKARTA.

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Abstract

Molecular dynamics simulation studies using the QM/MM (Quantum Mechanics/Molecular Mechanics) method have been carried out. These metal ions have the potential to cause toxicity if they enter the body. This research aims to study the structure and dynamics of chromium solvation in ammonia through QM/MM molecular dynamics simulation studies. In the research, the subject used was Cr3+ with the research object being the structure and dynamics of Cr ions in ammonia. The research begins by determining the simulation parameters with the Lennard-Jones potential. The simulation is arranged in a simulation box with a length of 40x40x40 with picosecond (ps) time units. Next, QM/MM molecular structure and dynamics simulations were carried out on 2-body and 3-body potential analysis using LAMMPS with modifications in solving equations whose results were in the form of trajectory data. The data obtained will later be presented in the form of RDF and ADF graphs. RMSD and RMSF analyzes were obtained from the solvation dynamics of ion-ligand interactions processed in GROMACS software. The angle distribution analysis carried out obtained results of 91° and 178°, which indicates that the geometry formed is octahedral surrounded by six ammonia ligands in Cr. Then, the dynamic properties of solvation resulting from RMSD and RMSF data show that it is stable with simulation results of RMSD values ≤ 2Å and RMSF values ≤ 2.5 Å. The results obtained from research on Cr3+ ions in ammonia show agreement.

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