2 Background, Tasks, Modeling Methods …
35
71. Hammett LP (1936) The effect of structure upon the reactions of organic compounds. Benzene
derivatives. J Am Chem Soc 59(1):96–103
72. Hansch C, Maloney PP, Fujita T (1962) Correlation of biological activity of phenoxyacetic
acids with Hammett substituent constants and partition coefficients. Nature 194(4824):178
73. Cronin MTD, Schultz TW (2003) Pitfalls in QSAR. J Mol Struct-Theochem 622(1–2):39–51
74. Ekins S (2014) Progress in computational toxicology. J Pharmacol Toxicol Methods
69(2):115–140
75. Todeschini R, Consonni V (2009) Molecular descriptors for chemoinformatics, vol I & II.
Wiley, Weinheim
76. Flach P (2012) Machine learning: the art and science of algorithms that make sense of data.
Cambridge University Press, Cambridge
77. Yang X, Xie H, Chen J, Li X (2013) Anionic phenolic compounds bind stronger with
transthyretin than their neutral forms: nonnegligible mechanisms in virtual screening of
endocrine disrupting chemicals. Chem Res Toxicol 26(9):1340–1347
78. Olsen L, Rydberg P, Rod TH, Ryde U (2006) Prediction of activation energies for hydrogen
abstraction by cytochrome P450. J Med Chem 49(22):6489–6499
79. Rydberg P, Ryde U, Olsen L (2008) Prediction of activation energies for aromatic oxidation
by cytochrome P450. J Phys Chem A 112(50):13058–13065
80. Rydberg P, Ryde U, Olsen L (2008) Sulfoxide, sulfur, and nitrogen oxidation and dealkylation
by cytochrome P450. J Chem Theory Comput 4(8):1369–1377
81. Rydberg P, Gloriam DE, Zaretzki J, Breneman C, Olsen L (2010) SMARTCyp: a 2D method for
prediction of cytochrome P450-mediated drug metabolism. ACS Med Chem Lett 1(3):96–100
82. Li C, Chen J, Xie H-B, Zhao Y, Xia D, Xu T, Li X, Qiao X (2017) Effects of atmospheric
water on •OH-initiated oxidation of organophosphate flame retardants: a DFT investigation on
TCPP. Environ Sci Technol 51(9):5043–5051
83. Li C, Xie HB, Chen JW, Yang XH, Zhang YF, Qiao XL (2014) Predicting gaseous reaction
rates of short chain chlorinated paraffins with •OH: overcoming the difficulty in experimental
determination. Environ Sci Technol 48(23):13808–13816
84. Fu Z, He N, Zhou P, Liu J, Xie H-B, Yu Q, Ma F, Fu Z, Wang Z, Chen J (2017) Adsorption
of nitrobenzene on the surface of ice: a grand canonical monte carlo simulation study. J Phys
Chem C 121(29):15746–15755
85. Van Straalen N (2003) Ecotoxicology becomes stress ecology. Environ Sci Technol
37(17):324A–330A
86. Celander MC, Goldstone JV, Denslow ND, Iguchi T, Kille P, Meyerhoff RD, Smith BA,
Hutchinson TH, Wheeler JR (2011) Species extrapolation for the 21st century. Environ Toxicol
Chem 30(1):52–63
87. Brinkmann M, Schlechtriem C, Reininghaus M, Eichbaum K, Buchinger S, Reifferscheid G,
Hollert H, Preuss TG (2016) Cross-species extrapolation of uptake and disposition of neutral organic chemicals in fish using a multispecies physiologically-based toxicokinetic model
framework. Environ Sci Technol 50(4):1914–1923
88. Bordoli L, Kiefer F, Arnold K, Benkert P, Battey J, Schwede T (2009) Protein structure homology modeling using SWISS-MODEL workspace. Nat Protoc 4(1):1–13
89. Doering JA, Wiseman S, Giesy JP, Hecker M (2018) A cross-species quantitative adverse
outcome pathway for activation of the aryl hydrocarbon receptor leading to early life stage
mortality in birds and fishes. Environ Sci Technol 52(13):7524–7533
90. Fu Z, Wang Y, Chen J, Wang Z, Wang X (2016) How PBDEs are transformed into dihydroxylated and dioxin metabolites catalyzed by the active center of cytochrome P450s: a DFT study.
Environ Sci Technol 50(15):8155–8163
91. Wang X, Wang Y, Chen J, Ma Y, Zhou J, Fu Z (2012) Computational toxicological investigation
on the mechanism and pathways of xenobiotics metabolized by cytochrome P450: a case of
BDE-47. Environ Sci Technol 46(9):5126–5133
92. Li F, Xie Q, Li X, Li N, Chi P, Chen J, Wang Z, Hao C (2010) Hormone activity of hydroxylated polybrominated diphenyl ethers on human thyroid receptor-β: in vitro and in silico
investigations. Environ Health Perspect 118(5):602–606
35
71. Hammett LP (1936) The effect of structure upon the reactions of organic compounds. Benzene
derivatives. J Am Chem Soc 59(1):96–103
72. Hansch C, Maloney PP, Fujita T (1962) Correlation of biological activity of phenoxyacetic
acids with Hammett substituent constants and partition coefficients. Nature 194(4824):178
73. Cronin MTD, Schultz TW (2003) Pitfalls in QSAR. J Mol Struct-Theochem 622(1–2):39–51
74. Ekins S (2014) Progress in computational toxicology. J Pharmacol Toxicol Methods
69(2):115–140
75. Todeschini R, Consonni V (2009) Molecular descriptors for chemoinformatics, vol I & II.
Wiley, Weinheim
76. Flach P (2012) Machine learning: the art and science of algorithms that make sense of data.
Cambridge University Press, Cambridge
77. Yang X, Xie H, Chen J, Li X (2013) Anionic phenolic compounds bind stronger with
transthyretin than their neutral forms: nonnegligible mechanisms in virtual screening of
endocrine disrupting chemicals. Chem Res Toxicol 26(9):1340–1347
78. Olsen L, Rydberg P, Rod TH, Ryde U (2006) Prediction of activation energies for hydrogen
abstraction by cytochrome P450. J Med Chem 49(22):6489–6499
79. Rydberg P, Ryde U, Olsen L (2008) Prediction of activation energies for aromatic oxidation
by cytochrome P450. J Phys Chem A 112(50):13058–13065
80. Rydberg P, Ryde U, Olsen L (2008) Sulfoxide, sulfur, and nitrogen oxidation and dealkylation
by cytochrome P450. J Chem Theory Comput 4(8):1369–1377
81. Rydberg P, Gloriam DE, Zaretzki J, Breneman C, Olsen L (2010) SMARTCyp: a 2D method for
prediction of cytochrome P450-mediated drug metabolism. ACS Med Chem Lett 1(3):96–100
82. Li C, Chen J, Xie H-B, Zhao Y, Xia D, Xu T, Li X, Qiao X (2017) Effects of atmospheric
water on •OH-initiated oxidation of organophosphate flame retardants: a DFT investigation on
TCPP. Environ Sci Technol 51(9):5043–5051
83. Li C, Xie HB, Chen JW, Yang XH, Zhang YF, Qiao XL (2014) Predicting gaseous reaction
rates of short chain chlorinated paraffins with •OH: overcoming the difficulty in experimental
determination. Environ Sci Technol 48(23):13808–13816
84. Fu Z, He N, Zhou P, Liu J, Xie H-B, Yu Q, Ma F, Fu Z, Wang Z, Chen J (2017) Adsorption
of nitrobenzene on the surface of ice: a grand canonical monte carlo simulation study. J Phys
Chem C 121(29):15746–15755
85. Van Straalen N (2003) Ecotoxicology becomes stress ecology. Environ Sci Technol
37(17):324A–330A
86. Celander MC, Goldstone JV, Denslow ND, Iguchi T, Kille P, Meyerhoff RD, Smith BA,
Hutchinson TH, Wheeler JR (2011) Species extrapolation for the 21st century. Environ Toxicol
Chem 30(1):52–63
87. Brinkmann M, Schlechtriem C, Reininghaus M, Eichbaum K, Buchinger S, Reifferscheid G,
Hollert H, Preuss TG (2016) Cross-species extrapolation of uptake and disposition of neutral organic chemicals in fish using a multispecies physiologically-based toxicokinetic model
framework. Environ Sci Technol 50(4):1914–1923
88. Bordoli L, Kiefer F, Arnold K, Benkert P, Battey J, Schwede T (2009) Protein structure homology modeling using SWISS-MODEL workspace. Nat Protoc 4(1):1–13
89. Doering JA, Wiseman S, Giesy JP, Hecker M (2018) A cross-species quantitative adverse
outcome pathway for activation of the aryl hydrocarbon receptor leading to early life stage
mortality in birds and fishes. Environ Sci Technol 52(13):7524–7533
90. Fu Z, Wang Y, Chen J, Wang Z, Wang X (2016) How PBDEs are transformed into dihydroxylated and dioxin metabolites catalyzed by the active center of cytochrome P450s: a DFT study.
Environ Sci Technol 50(15):8155–8163
91. Wang X, Wang Y, Chen J, Ma Y, Zhou J, Fu Z (2012) Computational toxicological investigation
on the mechanism and pathways of xenobiotics metabolized by cytochrome P450: a case of
BDE-47. Environ Sci Technol 46(9):5126–5133
92. Li F, Xie Q, Li X, Li N, Chi P, Chen J, Wang Z, Hao C (2010) Hormone activity of hydroxylated polybrominated diphenyl ethers on human thyroid receptor-β: in vitro and in silico
investigations. Environ Health Perspect 118(5):602–606