Computer Assisted Pathway Generation for Atrazine Degradation in Advanced Oxidation Processes
Affiliation(s)
Department of Computer Science, University of Georgia, Athens, GA 30605. Faculty of Engineering, University of Georgia, Athens, GA 30605.
Department of Computer Science, University of Georgia, Athens, GA 30605. Faculty of Engineering, University of Georgia, Athens, GA 30605.
ABSTRACT
A model was developed to generate the complex degradation pathway of contaminants initiated by hydroxyl radical in the advanced oxidation processes. The model abstracts chemical structures into mathematic graphs. The manipulation of the graphs enumerates the reactions among the large number of molecules, radicals, and other intermediates in the advanced oxidation processes. Using Canonical Simplified Molecular Input Line Entry Specification (Canonical SMILE) representation, the algorithm was able to simulate the reaction of contaminants containing both chain and ring structures. The input chemicals, reaction pattern, and the reaction rules could be specified by users through a graphical user interface. The degradation pathway of Atrazine was used as an example to demonstrate the capability of the algorithm. The generated reaction pathways were compared with those reported in literatures.
A model was developed to generate the complex degradation pathway of contaminants initiated by hydroxyl radical in the advanced oxidation processes. The model abstracts chemical structures into mathematic graphs. The manipulation of the graphs enumerates the reactions among the large number of molecules, radicals, and other intermediates in the advanced oxidation processes. Using Canonical Simplified Molecular Input Line Entry Specification (Canonical SMILE) representation, the algorithm was able to simulate the reaction of contaminants containing both chain and ring structures. The input chemicals, reaction pattern, and the reaction rules could be specified by users through a graphical user interface. The degradation pathway of Atrazine was used as an example to demonstrate the capability of the algorithm. The generated reaction pathways were compared with those reported in literatures.
Cite this paper
X. Li, F. Zeng and K. Li, "Computer Assisted Pathway Generation for Atrazine Degradation in Advanced Oxidation Processes," Journal of Environmental Protection, Vol. 4 No. 1, 2013, pp. 62-69. doi: 10.4236/jep.2013.41B012.
X. Li, F. Zeng and K. Li, "Computer Assisted Pathway Generation for Atrazine Degradation in Advanced Oxidation Processes," Journal of Environmental Protection, Vol. 4 No. 1, 2013, pp. 62-69. doi: 10.4236/jep.2013.41B012.
References
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[6] Hendrickson, J.B., Descriptions of reactions: Their logic and applications. Recueil des Travaux Chimiques des Pays-Bas, 1992. 111(6): p. 323-334. [7] Abe, H., et al., A convenient notation system for organic structure on the basis of connectivity stack. Journal of Chemical Information and Computer Sciences, 1984. 24(4): p. 212-216. [8] Weininger, D., SMILES, a chemical language and information system. 1. introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci., 1988. 28(1): p. 31-36. [9] Homer, R.W., et al., SYBYL Line Notation (SLN): A Single Notation To Represent Chemical Structures, Queries, Reactions, and Virtual Libraries. Journal of Chemical Information and Modeling, 2008. 48(12): p. 2294-2307. [10] Weininger, D., A. Weininger, and J.L. Weininger, SMILES. 2. Algorithm for generation of unique SMILES notation. Journal of Chemical Information and Computer Sciences, 1989. 29(2): p. 97-101. [11] LLC, G.S.S., Indigo. Web. [12] Asmus, K.D., H. Moeckel, and A. Henglein, Pulse radiolytic study of the site of hydroxyl radical attack on aliphatic alcohols in aqueous solution. The Journal of Physical Chemistry, 1973. 77(10): p. 1218-1221. [13] Schuchmann, M.N. and C. Von Sonntag, Hydroxyl radical-induced oxidation of diethyl ether in oxygenated aqueous solution. A product and pulse radiolysis study. The Journal of Physical Chemistry, 1982. 86(11): p. 1995-2000. [14] Ulanski, P., et al., Hydroxyl-radical-induced reactions of poly (acrylic acid); a pulse radiolysis, EPR and product study. Part II. Oxygenated aqueous solutions. Journal of the Chemical Society, Perkin Transactions 2, 1996(1): p. 23-28. [15] Pryor, W.A., Free Radicals1966, New York: McGraw-Hill Book Company. [16] Huyser, E.S., Free-Radical Chain Reactions1970, New York: Johns Wiley & Sons, Inc. [17] Alfassi, Z.B., ed. General Aspects of the Chemistry of Radicals. 1999, Wiley: Chichester, UK. [18] von Sonntag, C.a.H.-P.S., Peroxyl Radicals in Aqueous Solutions, in Peroxyl Radicals, Z.B. Alfassi, Editor 1997, John Wiley & Sons: New York. p. 172-234. [19] Ilan, Y., J. Rabani, and A. Henglein, Pulse radiolytic investigations of peroxy radicals produced from 2-propanol and methanol. The Journal of Physical Chemistry, 1976. 80(14): p. 1558-1562. [20] Gilbert, B.C., R. G. G. Holmes and R. O. C. Norman, Electron spin resonance studies. Part LII. Reactions of secondary alkoxyl radicals. J. Chem. Res., Synopses, 1977(1): p. 1. [21] Schuchmann, H.-P. and C. von Sonntag, Photolysis at 185 nm of dimethyl ether in aqueous solution: involvement of the hydroxymethyl radical. Journal of Photochemistry, 1981. 16(4): p. 289-295. [22] Stefan, M.I. and J.R. Bolton, Mechanism of the Degradation of 1,4-Dioxane in Dilute Aqueous Solution Using the UV/Hydrogen Peroxide Process. Environmental Science & Technology, 1998. 32(11): p. 1588-1595. [23] Vel Leitner, N.K., P. Berger, and B. Legube, Oxidation of Amino Groups by Hydroxyl Radicals in Relation to the Oxidation Degree of the α-Carbon. Environmental Science & Technology, 2002. 36(14): p. 3083-3089. [24] Stefan, M.I., A.R. Hoy, and J.R. Bolton, Kinetics and Mechanism of the Degradation and Mineralization of Acetone in Dilute Aqueous Solution Sensitized by the UV Photolysis of Hydrogen Peroxide. Environmental Science & Technology, 1996. 30(7): p. 2382-2390. [25] Koltzenburg, G., G. Behrens, and D. Schulte-Frohlinde, Fast hydrolysis of alkyl radicals with leaving groups in the β position. Journal of the American Chemical Society, 1982. 104(25): p. 7311-7312. [26] Richard A. Larson, E.J.W., Reaction Mechanisms in Environmental Organic Chemistry1994: CRC Press. [27] Getoff, N., Peroxyl radicals in the treatment of waste solutions, in Peroxyl Radical, Z.B. Alfassi, Editor 1997, John Wiley & Sons: New York. [28] Merenyi, G., J. Lind, and L. Engman, One- and two-electron reduction potentials of peroxyl radicals and related species. Journal of the Chemical Society, Perkin Transactions 2, 1994(12): p. 2551-2553. [29] Schuchmann, M.N. and C. von Sonntag, Hydroxyl radical induced oxidation of diethyl ether in oxygenated aqueous solution. A product and pulse radiolysis study. [Gamma radiation]. Journal Name: J. Phys. Chem.; (United States); Journal Volume: 86:11, 1982: p. Medium: X; Size: Pages: 1995-2000. [30] Schuchmann, M.N., H. Zegota and C. v. Sonntag, Acetate Peroxyl Radicals, *O2CHCO2-: A Study on the r-Radiolysis and Pulse Radiolysis of Acetate in Oxygenated Aqueous Solutions. Z. Naturforsch, 1985(40B): p. 215. [31] McMurray, T.A., P.S.M. Dunlop, and J.A. Byrne, The photocatalytic degradation of atrazine on nanoparticulate TiO2 films. Journal of Photochemistry and Photobiology A: Chemistry, 2006. 182(1): p. 43-51. [32] Ou, X., et al., Atrazine Photodegradation in Aqueous Solution Induced by Interaction of Humic Acids and Iron: Photoformation of Iron(II) and Hydrogen Peroxide. Journal of Agricultural and Food Chemistry, 2007. 55(21): p. 8650-8656. [33] Chan, K.H. and W. Chu, Model applications and mechanism study on the degradation of atrazine by Fenton's system. Journal of Hazardous Materials, 2005. 118(1-3): p. 227-237. [34] Chan, K.-H. and W. Chu, Model Applications and Intermediates Quantification of Atrazine Degradation by UV-Enhanced Fenton Process. Journal of Agricultural and Food Chemistry, 2006. 54(5): p. 1804-1813. [35] Arnold, S.M., W.J. Hickey, and R.F. Harris, Degradation of Atrazine by Fenton's Reagent: Condition Optimization and Product Quantification. Environmental Science & Technology, 1995. 29(8): p. 2083-2089. [36] Nélieu, S., L. Kerhoas, and J. Einhorn, Degradation of Atrazine into Ammeline by Combined Ozone/Hydrogen Peroxide Treatment in Water. Environmental Science & Technology, 1999. 34(3): p. 430-437. [37] Torrents, A., et al., Atrazine photolysis: Mechanistic investigations of direct and nitrate mediated hydroxy radical processes and the influence of dissolved organic carbon from the Chesapeake Bay. Environmental Science & Technology, 1997. 31(5): p. 1476-1482. [38] Balci, B., et al., Degradation of atrazine in aqueous medium by electrocatalytically generated hydroxyl radicals. A kinetic and mechanistic study. Water Research, 2009. 43(7): p. 1924-1934. [39] Acero, J.L., K. Stemmler, and U. von Gunten, Degradation Kinetics of Atrazine and Its Degradation Products with Ozone and OH Radicals:? A Predictive Tool for Drinking Water Treatment. Environmental Science & Technology, 2000. 34(4): p. 591-597. [40] Bianchi, C.L., et al., Mechanism and efficiency of atrazine degradation under combined oxidation processes. Applied Catalysis B: Environmental, 2006. 64(1–2): p. 131-138. [41] Granados-Oliveros, G., et al., Degradation of atrazine using metalloporphyrins supported on TiO2 under visible light irradiation. Applied Catalysis B: Environmental, 2009. 89(3-4): p. 448-454. [42] Mackul’ak, T., J. Prousek, and L.u. ?vorc, Degradation of atrazine by Fenton and modified Fenton reactions. Monatshefte für Chemie / Chemical Monthly, 2011. 142(6): p. 561-567. [43] Rebelo, S.L.H., et al., Catalytic oxidative degradation of s-triazine and phenoxyalkanoic acid based herbicides with metalloporphyrins and hydrogen peroxide: Identification of two distinct reaction schemes. Journal of Molecular Catalysis A: Chemical, 2009. 297(1): p. 35-43. [44] Hiskia, A., et al., Sonolytic, photolytic, and photocatalytic decomposition of atrazine in the presence of polyoxometalates. Environmental Science & Technology, 2001. 35(11): p. 2358-2364. [45] Pelizzetti, E., et al., Photocatalytic degradation of atrazine and other s-triazine herbicides. Environmental Science & Technology, 1990. 24(10): p. 1559-1565.
[1] Glaze, W.H., J.-W. Kang, and D.H. Chapin, The Chemistry of Water Treatment Processes Involving Ozone, Hydrogen Peroxide and Ultraviolet Radiation. Ozone: Science & Engineering, 1987. 9(4): p. 335-352. [2] Rosenfeldt, E.J. and K.G. Linden, Degradation of Endocrine Disrupting Chemicals Bisphenol A, Ethinyl Estradiol, and Estradiol during UV Photolysis and Advanced Oxidation Processes. Environmental Science & Technology, 2004. 38(20): p. 5476-5483. [3] Huber, M.M., et al., Oxidation of Pharmaceuticals during Ozonation and Advanced Oxidation Processes. Environmental Science & Technology, 2003. 37(5): p. 1016-1024. [4] Li, K. and J. Crittenden, Computerized Pathway Elucidation for Hydroxyl Radical-Induced Chain Reaction Mechanisms in Aqueous Phase Advanced Oxidation Processes. Environmental Science & Technology, 2009. 43(8): p. 2831-2837. [5] Temkin, O.N., A.V. Zeigarnik, and D.G. Bonchev, Chemical Reaction Networks: A Graph-Theoretical Approach. Book, 1996. [6] Hendrickson, J.B., Descriptions of reactions: Their logic and applications. Recueil des Travaux Chimiques des Pays-Bas, 1992. 111(6): p. 323-334. [7] Abe, H., et al., A convenient notation system for organic structure on the basis of connectivity stack. Journal of Chemical Information and Computer Sciences, 1984. 24(4): p. 212-216. [8] Weininger, D., SMILES, a chemical language and information system. 1. introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci., 1988. 28(1): p. 31-36. [9] Homer, R.W., et al., SYBYL Line Notation (SLN): A Single Notation To Represent Chemical Structures, Queries, Reactions, and Virtual Libraries. Journal of Chemical Information and Modeling, 2008. 48(12): p. 2294-2307. [10] Weininger, D., A. Weininger, and J.L. Weininger, SMILES. 2. Algorithm for generation of unique SMILES notation. Journal of Chemical Information and Computer Sciences, 1989. 29(2): p. 97-101. [11] LLC, G.S.S., Indigo. Web. [12] Asmus, K.D., H. Moeckel, and A. Henglein, Pulse radiolytic study of the site of hydroxyl radical attack on aliphatic alcohols in aqueous solution. The Journal of Physical Chemistry, 1973. 77(10): p. 1218-1221. [13] Schuchmann, M.N. and C. Von Sonntag, Hydroxyl radical-induced oxidation of diethyl ether in oxygenated aqueous solution. A product and pulse radiolysis study. The Journal of Physical Chemistry, 1982. 86(11): p. 1995-2000. [14] Ulanski, P., et al., Hydroxyl-radical-induced reactions of poly (acrylic acid); a pulse radiolysis, EPR and product study. Part II. Oxygenated aqueous solutions. Journal of the Chemical Society, Perkin Transactions 2, 1996(1): p. 23-28. [15] Pryor, W.A., Free Radicals1966, New York: McGraw-Hill Book Company. [16] Huyser, E.S., Free-Radical Chain Reactions1970, New York: Johns Wiley & Sons, Inc. [17] Alfassi, Z.B., ed. General Aspects of the Chemistry of Radicals. 1999, Wiley: Chichester, UK. [18] von Sonntag, C.a.H.-P.S., Peroxyl Radicals in Aqueous Solutions, in Peroxyl Radicals, Z.B. Alfassi, Editor 1997, John Wiley & Sons: New York. p. 172-234. [19] Ilan, Y., J. Rabani, and A. Henglein, Pulse radiolytic investigations of peroxy radicals produced from 2-propanol and methanol. The Journal of Physical Chemistry, 1976. 80(14): p. 1558-1562. [20] Gilbert, B.C., R. G. G. Holmes and R. O. C. Norman, Electron spin resonance studies. Part LII. Reactions of secondary alkoxyl radicals. J. Chem. Res., Synopses, 1977(1): p. 1. [21] Schuchmann, H.-P. and C. von Sonntag, Photolysis at 185 nm of dimethyl ether in aqueous solution: involvement of the hydroxymethyl radical. Journal of Photochemistry, 1981. 16(4): p. 289-295. [22] Stefan, M.I. and J.R. Bolton, Mechanism of the Degradation of 1,4-Dioxane in Dilute Aqueous Solution Using the UV/Hydrogen Peroxide Process. Environmental Science & Technology, 1998. 32(11): p. 1588-1595. [23] Vel Leitner, N.K., P. Berger, and B. Legube, Oxidation of Amino Groups by Hydroxyl Radicals in Relation to the Oxidation Degree of the α-Carbon. Environmental Science & Technology, 2002. 36(14): p. 3083-3089. [24] Stefan, M.I., A.R. Hoy, and J.R. Bolton, Kinetics and Mechanism of the Degradation and Mineralization of Acetone in Dilute Aqueous Solution Sensitized by the UV Photolysis of Hydrogen Peroxide. Environmental Science & Technology, 1996. 30(7): p. 2382-2390. [25] Koltzenburg, G., G. Behrens, and D. Schulte-Frohlinde, Fast hydrolysis of alkyl radicals with leaving groups in the β position. Journal of the American Chemical Society, 1982. 104(25): p. 7311-7312. [26] Richard A. Larson, E.J.W., Reaction Mechanisms in Environmental Organic Chemistry1994: CRC Press. [27] Getoff, N., Peroxyl radicals in the treatment of waste solutions, in Peroxyl Radical, Z.B. Alfassi, Editor 1997, John Wiley & Sons: New York. [28] Merenyi, G., J. Lind, and L. Engman, One- and two-electron reduction potentials of peroxyl radicals and related species. Journal of the Chemical Society, Perkin Transactions 2, 1994(12): p. 2551-2553. [29] Schuchmann, M.N. and C. von Sonntag, Hydroxyl radical induced oxidation of diethyl ether in oxygenated aqueous solution. A product and pulse radiolysis study. [Gamma radiation]. Journal Name: J. Phys. Chem.; (United States); Journal Volume: 86:11, 1982: p. Medium: X; Size: Pages: 1995-2000. [30] Schuchmann, M.N., H. Zegota and C. v. Sonntag, Acetate Peroxyl Radicals, *O2CHCO2-: A Study on the r-Radiolysis and Pulse Radiolysis of Acetate in Oxygenated Aqueous Solutions. Z. Naturforsch, 1985(40B): p. 215. [31] McMurray, T.A., P.S.M. Dunlop, and J.A. Byrne, The photocatalytic degradation of atrazine on nanoparticulate TiO2 films. Journal of Photochemistry and Photobiology A: Chemistry, 2006. 182(1): p. 43-51. [32] Ou, X., et al., Atrazine Photodegradation in Aqueous Solution Induced by Interaction of Humic Acids and Iron: Photoformation of Iron(II) and Hydrogen Peroxide. Journal of Agricultural and Food Chemistry, 2007. 55(21): p. 8650-8656. [33] Chan, K.H. and W. Chu, Model applications and mechanism study on the degradation of atrazine by Fenton's system. Journal of Hazardous Materials, 2005. 118(1-3): p. 227-237. [34] Chan, K.-H. and W. Chu, Model Applications and Intermediates Quantification of Atrazine Degradation by UV-Enhanced Fenton Process. Journal of Agricultural and Food Chemistry, 2006. 54(5): p. 1804-1813. [35] Arnold, S.M., W.J. Hickey, and R.F. Harris, Degradation of Atrazine by Fenton's Reagent: Condition Optimization and Product Quantification. Environmental Science & Technology, 1995. 29(8): p. 2083-2089. [36] Nélieu, S., L. Kerhoas, and J. Einhorn, Degradation of Atrazine into Ammeline by Combined Ozone/Hydrogen Peroxide Treatment in Water. Environmental Science & Technology, 1999. 34(3): p. 430-437. [37] Torrents, A., et al., Atrazine photolysis: Mechanistic investigations of direct and nitrate mediated hydroxy radical processes and the influence of dissolved organic carbon from the Chesapeake Bay. Environmental Science & Technology, 1997. 31(5): p. 1476-1482. [38] Balci, B., et al., Degradation of atrazine in aqueous medium by electrocatalytically generated hydroxyl radicals. A kinetic and mechanistic study. Water Research, 2009. 43(7): p. 1924-1934. [39] Acero, J.L., K. Stemmler, and U. von Gunten, Degradation Kinetics of Atrazine and Its Degradation Products with Ozone and OH Radicals:? A Predictive Tool for Drinking Water Treatment. Environmental Science & Technology, 2000. 34(4): p. 591-597. [40] Bianchi, C.L., et al., Mechanism and efficiency of atrazine degradation under combined oxidation processes. Applied Catalysis B: Environmental, 2006. 64(1–2): p. 131-138. [41] Granados-Oliveros, G., et al., Degradation of atrazine using metalloporphyrins supported on TiO2 under visible light irradiation. Applied Catalysis B: Environmental, 2009. 89(3-4): p. 448-454. [42] Mackul’ak, T., J. Prousek, and L.u. ?vorc, Degradation of atrazine by Fenton and modified Fenton reactions. Monatshefte für Chemie / Chemical Monthly, 2011. 142(6): p. 561-567. [43] Rebelo, S.L.H., et al., Catalytic oxidative degradation of s-triazine and phenoxyalkanoic acid based herbicides with metalloporphyrins and hydrogen peroxide: Identification of two distinct reaction schemes. Journal of Molecular Catalysis A: Chemical, 2009. 297(1): p. 35-43. [44] Hiskia, A., et al., Sonolytic, photolytic, and photocatalytic decomposition of atrazine in the presence of polyoxometalates. Environmental Science & Technology, 2001. 35(11): p. 2358-2364. [45] Pelizzetti, E., et al., Photocatalytic degradation of atrazine and other s-triazine herbicides. Environmental Science & Technology, 1990. 24(10): p. 1559-1565.