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

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Abstract

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 13C nuclear magnetic resonance (13C 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 13C NMR spectroscopy of simulated HA are consistent with those of experimental HA. HyperChem® 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.

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Authors and Affiliations

  1. College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, P. R. China

    Nan Zhao & Yi-zhong Lü

  2. School of Chemistry and Environment, Beijing University of Aeronautics and Astronautics, Beijing, 100191, P. R. China

    Guang-jun Li

Authors
  1. Nan Zhao
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  2. Yi-zhong Lü
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  3. Guang-jun Li
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Corresponding author

Correspondence to Yi-zhong Lü.

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Supported by the National Natural Science Foundation of China(Nos.40771099, 41271331).

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Zhao, N., Lü, Yz. & Li, Gj. Characterization and three-dimensional structural modeling of humic acid via molecular mechanics and molecular dynamic simulation. Chem. Res. Chin. Univ. 29, 1180–1184 (2013). https://doi.org/10.1007/s40242-013-3156-x

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  • DOI: https://doi.org/10.1007/s40242-013-3156-x

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