Characterization and three-dimensional structural modeling of humic acid via molecular mechanics and molecular dynamic simulation

The humic acid(HA) sample obtained from the alluvial soil was characterized by elemental composition, pyrolysis gas chromatography-mass spectrometry(Py-GC-MS) and solid-state C-13 nuclear magnetic resonance (C-13 NMR) spectroscopy. There is high fat content and a few nitrogen-containing functional groups in HA. Py-GC-MS demonstrates the characterization and structural identification of HA. One long list of identified pyrolysis products was proposed for the construction of conceptual model of HA. Solid-state 13C NMR data indicate there are higher values of alkyl-C, O-alkyl-C and aryl-C in HA. The elemental composition, structural carbon distribution and C-13 NMR spectroscopy of simulated HA are consistent with those of experimental HA. HyperChemA (R) was used to simulate the three-dimensional molecular structure of the monomer, which was optimized by the molecular mechanics of the optimized potential for liquid simulations(OPLS) force field and molecular dynamics simulation to get the stable and balanced conformation. The deprotonation process study depicts that the degree of ionization of HA gets deeper, while the electronegativity of HA and the energy of van der Waals(vdW) increase. Moreover, the 3D structure of humic acid with -4 charges is the most stable. The deprotonation process is an endothermic process.