Characterization and Three-Dimensional Structural Modeling of Humic Acid Using Molecular Dynamics

Abstract

The humic acid (HA) that was obtained from an alluvial soil from the experimental station under conservation tillage in Luancheng County, Hebei Province, China, is the object of this study. HA was characterized by elemental composition and infrared and 13C-nuclear magnetic resonance (NMR) spectroscopy. ChemBioOffice was used to construct the two-dimensional molecular structure of the HA monomers. By comparing the actual and simulated spectra, we determined that the two-dimensional structure of the HA molecular model had better suitability. This study also used HyperChem to simulate the three-dimensional molecular structure of the monomers, which was optimized by the molecular mechanics of the MM+, AMBER, and OPLS force fields. After optimization, the bond energy, bond-angle energy, dihedral-angle energy, van der Waals energy, electrostatic energy, and total potential energy were all found to have changed, which show no rules during the variation. At the same time, a molecular dynamics simulation was also used. Under the OPLS force field, the three-dimensional structure of the HA monomers had the smallest heat of formation (−1,485.99 kJ mol−1), which indicates that it is the most stable of the three force fields. The molecular structure and total potential energy in the simulated environment changed after optimization, but all of the various energy states were generally stable.