title: Molecular docking and molecular dynamics simulation analyses of urea with ammoniated and ammoxidized lignin.
abstract: Ammoniated lignin, prepared through the Mannich reaction of lignin, has more advantages as a slow-release carrier of urea molecules than ammoxidized lignin and lignin. The advantages of the ammoniated lignin include its amine groups added and its high molecular mass kept as similar as that of lignin. Three organic molecules including guaiacyl, 2-hydroxybenzylamine and 5-carbamoylpentanoic acid are monomers respectively in lignin, ammoniated lignin and ammoxidized lignin. We studied the difference between the interactions of lignin, ammoniated lignin and ammoxidized lignin with respect to urea, based on radial distribution functions (RDFs) results from molecular dynamics (MD) simulations. Glass transition temperature (Tg) and solubility parameter (δ) of ammoniated and ammoxidized lignin have been calculated by MD simulations in the constant-temperature and constant-pressure ensemble (NPT). Molecular docking results showed the interaction sites of the urea onto the ammoniated and ammoxidized lignin and three different interaction modes were identified. Root mean square deviation (RMSD) values could indicate the mobilities of the urea molecule affected by the three different interaction modes. A series of MD simulations in the constant-temperature and constant-volume ensemble (NVT) helped us to calculate the diffusivity of urea which was affected by the content of urea in ammoniated and ammoxidized lignin.
authors.affiliation: Department of Chemistry and Material Science, Nanjing Forestry University, Nanjing 210037, People's Republic of China. Electronic address: wzli@njfu.com.cn.
authors.forename: Wenzhuo
authors.initials: W
authors.lastname: Li
authors.affiliation: Department of Chemistry and Material Science, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
authors.forename: Song
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Department of Chemistry and Material Science, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
authors.forename: Yingying
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Department of Chemistry and Material Science, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
authors.forename: Shuaiyu
authors.initials: S
authors.lastname: Huang
authors.affiliation: Department of Chemistry and Material Science, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
authors.forename: Jiangshan
authors.initials: J
authors.lastname: Zhao
mesh_terms: D064751:Ammonium Compounds / Q000737:chemistry*; D008031:Lignin / Q000737:chemistry*; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011312:Pressure; D012995:Solubility; D013696:Temperature; D014508:Urea / Q000737:chemistry*
chemical_list: D064751:Ammonium Compounds; D014508:Urea; D008031:Lignin
keywords: Ammoniated lignin; Ammoxidized lignin; Molecular docking; Molecular dynamics simulations; Urea