A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part II: A ChemTraYzer Study of Chlorinated Dibenzofuran Formation and Decomposition Processes.
ChemTraYzer
Chlorinated organic compounds
Dibenzofurans
ParAMS
Reactive force fields
Self-learning transition-state search
Journal
Chemphyschem : a European journal of chemical physics and physical chemistry
ISSN: 1439-7641
Titre abrégé: Chemphyschem
Pays: Germany
ID NLM: 100954211
Informations de publication
Date de publication:
03 Apr 2023
03 Apr 2023
Historique:
revised:
09
12
2022
received:
18
10
2022
medline:
14
12
2022
pubmed:
14
12
2022
entrez:
13
12
2022
Statut:
ppublish
Résumé
In our two-paper series, we first present the development of ReaxFF CHOCl parameters using the recently published ParAMS parametrization tool. In this second part, we update the reactive Molecular Dynamics - Quantum Mechanics coupling scheme ChemTraYzer and combine it with our new ReaxFF parameters from Part I to study formation and decomposition processes of chlorinated dibenzofurans. We introduce a self-learning method for recovering failed transition-state searches that improves the overall ChemTraYzer transition-state search success rate by 10 percentage points to a total of 48 %. With ChemTraYzer, we automatically find and quantify more than 500 reactions using transition state theory and DFT. Among the discovered chlorinated dibenzofuran reactions are numerous reactions that are new to the literature. In three case studies, we discuss the set of reactions that are most relevant to the dibenzofuran literature: (i) bimolecular reactions of the chlorinated-dibenzofuran precursors phenoxy radical and 1,3,5-trichlorobenzene, (ii) dibenzofuran chlorination and pyrolysis, and (iii) oxidation of chlorinated dibenzofurans.
Identifiants
pubmed: 36511423
doi: 10.1002/cphc.202200783
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e202200783Subventions
Organisme : German Federal Ministry of Education and Research (BMBF)
ID : 03EW0009 C
Organisme : European Union's Horizon 2020
ID : 814143
Organisme : Research Board of Ghent University (BOF)
Organisme : RWTH Aachen University
ID : rwth0631
Informations de copyright
© 2022 The Authors. ChemPhysChem published by Wiley-VCH GmbH.
Références
J.-C. Lizardo-Huerta, B. Sirjean, L. Verdier, R. Fournet, P.-A. Glaude, J. Phys. Chem. A 2018, 122, 249.
H. Babad, A. G. Zeiler, Chem. Rev. 1973, 73, 75.
D. Noort, A. G. Hulst, A. Fidder, R. A. van Gurp, L. P. A. de Jong, H. P. Benschop, Chem. Res. Toxicol. 2000, 13, 719.
V. B. Arce, C. O. Della Védova, A. J. Downs, S. Parsons, R. M. Romano, J. Org. Chem. 2006, 71, 3423.
P. S. Kulkarni, J. G. Crespo, C. A. Afonso, Environ. Int. 2008, 34, 139.
D. Consonni, A. C. Pesatori, C. Zocchetti, R. Sindaco, L. C. D'Oro, M. Rubagotti, P. A. Bertazzi, Am. J. Epidemiol. 2008, 167, 847.
R. Madaj, E. Sobiecka, H. Kalinowska, Int. J. Sci. Environ. Technol. 2018, 15, 471.
I. Amato, Science 1993, 261, 152.
M. Altarawneh, B. Z. Dlugogorski, E. M. Kennedy, J. C. Mackie, Prog. Energy Combust. Sci. 2009, 35, 245.
M. Altarawneh, B. Z. Dlugogorski, E. M. Kennedy, J. C. Mackie, J. Phys. Chem. A 2006, 110, 13560.
M. Altarawneh, B. Z. Dlugogorski, E. M. Kennedy, J. C. Mackie, J. Phys. Chem. A 2007, 111, 7133.
M. Altarawneh, E. M. Kennedy, B. Z. Dlugogorski, J. C. Mackie, J. Phys. Chem. A 2008, 112, 6960.
M. Altarawneh, M. W. Radny, P. V. Smith, J. C. Mackie, E. M. Kennedy, B. Z. Dlugogorski, A. Soon, C. Stampfl, Appl. Surf. Sci. 2010, 256, 4764.
M. Altarawneh, B. Z. Dlugogorski, Phys. Chem. Chem. Phys. 2015, 17, 1822.
N. Bai, W. Wang, Y. Zhao, W. Feng, P. Li, ACS Omega 2019, 4, 358.
K. Zhang, S. Sun, H. Zhang, RSC Adv. 2015, 5, 81153.
W. Wang, Y. Wang, W. Feng, W. Wang, P. Li, Molecules 2018, 23.
Z. Wen, Z. Wang, J. Xu, Y. Liu, K. Cen, Chemosphere 5 2013, 92, 293.
Z. Wen, P. Kang, Z. Wang, J. Xu, K. Cen, Asian J. Chem. 2015, 27.
Z. Wen, S. Li, H. Li, Y. Li, Int. J. Environ. Pollut. 2019, 65, 337.
N. Zeinali, I. Oluwoye, M. Altarawneh, B. Z. Dlugogorski, Ecotoxicol. Environ. Saf. 2019, 184, 109605.
Y. Fernández Pulido, E. Suárez, R. López, M. I. Menéndez, Chemosphere 2016, 145, 77.
X. Sun, C. Zhang, Y. Zhao, J. Bai, Q. Zhang, W. Wang, Environ. Sci. Technol. 2012, 46, 8148.
C. J. E. Bajamundi, P. Vainikka, M. Hedman, J. Konttinen, Fuel 2014, 134, 688.
O. V. Dorofeeva, V. S. Iorish, N. F. Moiseeva, J. Chem. Eng. Data 1999, 44, 516.
D. Thompson, B. C. R. Ewan, J. Phys. Chem. A 2007, 111, 5043.
M. Takaoka, A. Shiono, K. Nishimura, T. Yamamoto, T. Uruga, N. Takeda, T. Tanaka, K. Oshita, T. Matsumoto, H. Harada, Environ. Sci. Technol. 2005, 39, 5878.
P.-M. Marquaire, R. Bounaceur, F. Baronnet, Organohalogen Compd. 2003, 63, 377.
M. Döntgen, M.-D. Przybylski-Freund, L. C. Kröger, W. A. Kopp, A. E. Ismail, K. Leonhard, J. Chem. Theory Comput. 2015, 11, 2517.
M. Döntgen, F. Schmalz, W. A. Kopp, L. C. Kröger, K. Leonhard, J. Chem. Inf. Model. 2018, 58, 1343.
L.-P. Wang, A. Titov, R. McGibbon, F. Liu, V. S. Pande, T. J. Martínez, Nat. Chem. 2014, 6, 1044.
J. Ford, S. Seritan, X. Zhu, M. N. Sakano, M. M. Islam, A. Strachan, T. J. Martínez, J. Phys. Chem. A 2021, 125, 1447.
L.-P. Wang, R. T. McGibbon, V. S. Pande, T. J. Martinez, J. Chem. Theory Comput. 2016, 12, 638.
E. Martìnez-Núñez, J. Comput. Chem. 2015, 36, 222.
E. Martìnez-Núñez, Phys. Chem. Chem. Phys. 2015, 17, 14912.
A. Rodrìguez, R. Rodrìguez-Fernàndez, S. A. Vázquez, G. L. Barnes, J. J. P. Stewart, E. Martínez-Núñez, J. Comput. Chem. 2018, 39, 1922.
S. Maeda, Y. Harabuchi, WIREs Comput. Mol. Sci. 2021, 11, e1538.
G. N. Simm, M. Reiher, J. Chem. Theory Comput. 2017, 13, 6108.
V. Warth, F. Battin-Leclerc, R. Fournet, P. Glaude, G. Côme, G. Scacchi, Comput. Chem. 2000, 24, 541.
S. Rangarajan, A. Bhan, P. Daoutidis, Ind. Eng. Chem. Res. 2010, 49, 10459.
D. Rappoport, C. J. Galvin, D. Y. Zubarev, A. Aspuru-Guzik, J. Chem. Theory Comput. 2014, 10, 897.
D. Rappoport, A. Aspuru-Guzik, J. Chem. Theory Comput. 2019, 15, 4099.
C. W. Gao, J. W. Allen, W. H. Green, R. H. West, Comput. Phys. Commun. 2016, 203, 212.
P. L. Bhoorasingh, B. L. Slakman, F. Seyedzadeh Khanshan, J. Y. Cain, R. H. West, J. Phys. Chem. A 2017, 121, 6896.
R. Van de Vijver, K. M. Van Geem, G. B. Marin, J. Zàdor, Combust. Flame 2018, 196, 500.
R. Van de Vijver, J. Zàdor, Comput. Phys. Commun. 2020, 248, 106947.
Y. Kim, J. W. Kim, Z. Kim, W. Y. Kim, Chem. Sci. 2018, 9, 825.
P. M. Zimmerman, J. Comput. Chem. 2013, 34, 1385.
A. L. Dewyer, P. M. Zimmerman, Org. Biomol. Chem. 2017, 15, 501.
Y. V. Suleimanov, W. H. Green, J. Chem. Theory Comput. 2015, 11, 4248.
S. Habershon, J. Chem. Phys. 2015, 143, 094106.
S. Habershon, J. Chem. Theory Comput. 2016, 12, 1786.
C. Robertson, S. Habershon, Catal. Sci. Technol. 2019, 9, 6357.
T. A. Young, J. J. Silcock, A. J. Sterling, F. Duarte, Angew. Chem. Int. Ed. 2021, 60, 4266.
C. A. Grambow, A. Jamal, Y.-P. Li, W. H. Green, J. Zàdor, Y. V. Suleimanov, J. Am. Chem. Soc. 2018, 140, 1035.
A. L. Dewyer, A. J. Argüelles, P. M. Zimmerman, WIREs Comput. Mol. Sci. 2018, 8, e1354.
A. L. Dewyer, A. J. Argüelles, P. M. Zimmerman, WIREs Comput. Mol. Sci. 2018, 8, e1354.
G. N. Simm, A. C. Vaucher, M. Reiher, J. Phys. Chem. A 2019, 123, 385.
J. P. Unsleber, M. Reiher, Annu. Rev. Phys. Chem. 2020, 71, 121.
J. A. Miller, R. Sivaramakrishnan, Y. Tao, C. F. Goldsmith, M. P. Burke, A. W. Jasper, N. Hansen, N. J. Labbe, P. Glarborg, J. Zádor, Prog. Energy Combust. Sci. 2021, 83, 100886.
L. Komissarov, L. Krep, F. Schmalz, W. Kopp, K. Leonhard, T. Verstraelen 2022, submitted.
M. Altarawneh, B. Dlugogorski, E. M. Kennedy, J. C. Mackie, Mechanisms for PCDF and PCB Formation from Fires: Pathways from Oxidation of Chlorobenzenes, in Seventh Asia-Oceania symposium on fire sci- ence and technology, Hong Kong 2007.
R. J. Kee, F. M. Rupley, J. A. Miller, Chemkin-II: A Fortran chemical kinetics package for the analysis of gas-phase chemical kinetics 1989.
A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard, J. Phys. Chem. A 2001, 105, 9396.
K. Chenoweth, A. C. T. van Duin, W. A. Goddard, J. Phys. Chem. A 2008, 112, 1040.
S. Plimpton, J. Comput. Phys. 1995, 117, 1.
H. Aktulga, J. Fogarty, S. Pandit, A. Grama, Parallel Comput. 2012, 38, 245.
F. Rüger, Y. Trnka, P. van Lenthe, van Vuren, B. Klumpers, T. Soini, Amsterdam Modeling Suite 2020.
L. C. Kröger, W. A. Kopp, M. Döntgen, K. Leonhard, J. Chem. Theory Comput. 2017, 13, 3955.
L. Krep, I. S. Roy, W. Kopp, F. Schmalz, C. Huang, K. Leonhard, J. Chem. Inf. Model. 2022, 62, 890.
M. R. Sørensen, A. F. Voter, J. Chem. Phys. 2000, 112, 9599.
S. Chekmarev, S. Krivov, Chem. Phys. Lett. 1998, 287, 719.
S. Chekmarev, S. Krivov, Eur. Phys. J. D 1999, 9, 201.
S. F. Chekmarev, Phys. Rev. E 2001, 64, 036703.
S. Krivov, S. Chekmarev, Eur. Phys. J. D 1999, 9, 205.
P. Pracht, S. Grimme, Chem. Sci. 2021, 12, 6551.
E. Martìnez-Núñez, D. V. Shalashilin, J. Chem. Theory Comput. 2006, 2, 912.
D. R. Glowacki, E. Paci, D. V. Shalashilin, J. Phys. Chem. B 2009, 113, 16603.
D. R. Glowacki, E. Paci, D. V. Shalashilin, J. Chem. Theory Comput. 2011, 7, 1244.
M. O'Connor, E. Paci, S. McIntosh-Smith, D. R. Glowacki, Faraday Discuss. 2016, 195, 395.
J. Booth, S. Vazquez, E. Martinez-Nunez, A. Marks, J. Rodgers, D. R. Glowacki, D. V. Shalashilin, Phil. Trans. R. Soc. A 2014, 372, 20130384.
R. J. Shannon, S. Amabilino, M. O'Connor, D. V. Shalishilin, D. R. Glowacki, J. Chem. Theory Comput. 2018, 14, 4541.
R. A. Jara-Toro, G. A. Pino, D. R. Glowacki, R. J. Shannon, E. Martínez-Núñez, ChemSystemsChem 2020, 2, e1900024.
M. Hutchings, J. Liu, Y. Qiu, C. Song, L.-P. Wang, J. Chem. Theory Comput. 2020, 16, 1606.
G. Schmitz, Ö. Yönder, B. Schnieder, R. Schmid, C. Hättig, J. Comput. Chem. 2021, 42, 2264.
T. R. Cundari, J. Organomet. Chem., CRC Press, Boca Raton, Fla 2001.
G. Henkelman, B. P. Uberuaga, H. Jónsson, J. Chem. Phys. 2000, 113, 9901.
P. M. Zimmerman, Mol. Simul. 2015, 41, 43.
L. Pattanaik, J. B. Ingraham, C. A. Grambow, W. H. Green, Phys. Chem. Chem. Phys. 2020, 22, 23618.
W. Kabsch, Acta Crystallogr. Sect. A 1976, 32, 922.
P. Virtanen, R. Gommers, T. E. Oliphant, M. Haberland, T. Reddy, D. Cournapeau, E. Burovski, P. Peterson, W. Weckesser, J. Bright, S. J. van der Walt, M. Brett, J. Wilson, K. J. Millman, N. Mayorov, A. R. J. Nelson, E. Jones, R. Kern, E. Larson, C. J. Carey, İ. Polat, Y. Feng, E. W. Moore, J. Vander-Plas, D. Laxalde, J. Perktold, R. Cimrman, I. Henriksen, E. A. Quintero, C. R. Harris, A. M. Archibald, A. H. Ribeiro, F. Pedregosa, P. van Mulbregt, SciPy 1.0 Contributors, Nat. Methods 2020, 17, 261.
N. M. O'Boyle, M. Banck, C. A. James, C. Morley, T. Vandermeersch, G. R. Hutchison, J. Cheminf. 2011, 3, 33.
L. Martínez, R. Andrade, E. G. Birgin, J. M. Martínez, J. Comput. Chem. 2009, 30, 2157.
L. Krep, W. A. Kopp, L. C. Kröger, M. Döntgen, K. Leonhard, ChemSystemsChem 2020, 2, e1900043.
M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. Marenich, J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young, F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, K. Throssell, J. A. M. Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi, J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, J. B. Foresman, D. J. Fox, Gaussian 09, Revision D.01 2013.
L. Goerigk, A. Hansen, C. Bauer, S. Ehrlich, A. Najibi, S. Grimme, Phys. Chem. Chem. Phys. 2017, 19, 32184.
Y. Zhang, X. Xu, W. A. Goddard, Proc. Natl. Acad. Sci. USA 2009, 106, 4963.
I. Y. Zhang, J. Wu, X. Xu, Chem. Commun. 2010, 46, 3057.
M. Saeys, M.-F. Reyniers, G. B. Marin, V. Van Speybroeck, M. Waroquier, J. Phys. Chem. A 2003, 107, 9147.
M. Cieplik, O. Epema, R. Louw, Eur. J. Org. Chem. 2002, 2002, 2792.
B. Yang, L. Gagliardi, D. G. Truhlar, Phys. Chem. Chem. Phys. 2018, 20, 4129.