Synergy of machine learning and density functional theory calculations for predicting experimental Lewis base affinity and Lewis polybase binding atoms.
Lewis acid-base adducts
Lewis base affinity
density functional theory
graph neural network
machine learning
Journal
Journal of computational chemistry
ISSN: 1096-987X
Titre abrégé: J Comput Chem
Pays: United States
ID NLM: 9878362
Informations de publication
Date de publication:
18 Mar 2024
18 Mar 2024
Historique:
revised:
26
01
2024
received:
31
10
2023
accepted:
31
01
2024
medline:
19
3
2024
pubmed:
19
3
2024
entrez:
19
3
2024
Statut:
aheadofprint
Résumé
Investigation of Lewis acid-base interactions has been conducted by ab initio calculations and machine learning (ML) models. This study aims to resolve two critical tasks that have not been quantitatively investigated. First, ML models developed from density functional theory (DFT) calculations predict experimental BF
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2024 Wiley Periodicals LLC.
Références
M. Zhu, C. Li, B. Li, J. Zhang, Y. Sun, W. Guo, Z. Zhou, S. Pang, Y. Yan, Mater. Horiz. 2020, 7, 2208.
C. Li, X. Wang, E. Bi, F. Jiang, S. M. Park, Y. Li, L. Chen, Z. Wang, L. Zeng, H. Chen, Y. Liu, C. R. Grice, A. Abudulimu, J. Chung, Y. Xian, T. Zhu, H. Lai, B. Chen, R. J. Ellingson, F. Fu, D. S. Ginger, Z. Song, E. H. Sargent, Y. Yan, Science 2023, 379, 690.
D. W. Stephan, J. Am. Chem. Soc. 2015, 137, 10018.
G. C. Welch, R. Coffin, J. Peet, G. C. Bazan, J. Am. Chem. Soc. 2009, 131, 10802.
G. C. Welch, G. C. Bazan, J. Am. Chem. Soc. 2011, 133, 4632.
P. Zalar, Z. B. Henson, G. C. Welch, G. C. Bazan, T.-Q. Nguyen, Angew. Chem. 2012, 124, 7613.
H. Phan, T. J. Kelly, A. Zhugayevych, G. C. Bazan, T.-Q. Nguyen, E. A. Jarvis, S. Tretiak, J. Phys. Chem. Lett. 2019, 10, 4632.
F. Bessac, G. Frenking, Inorg. Chem. 2003, 42, 7990.
A. Khorief Nacereddine, L. Merzoud, C. Morell, H. Chermette, J. Comput. Chem. 2021, 42, 1296.
Z.-F. Zhang, M.-D. Su, J. Comput. Chem. 2022, 43, 1783.
S. Mebs, S. Grabowsky, D. Förster, R. Kickbusch, M. Hartl, L. L. Daemen, W. Morgenroth, P. Luger, B. Paulus, D. Lentz, J. Phys. Chem. A 2010, 114, 10185.
T. Baruah, M. R. Pederson, J. Chem. Theory Comput. 2009, 5, 834.
A. Vlček, S. Záliš, Coord. Chem. Rev. 2007, 251, 258.
C. Laurence, J.-F. Gal, Lewis Basicity and Affinity Scales: Data and Measurement, John Wiley & Sons, Hoboken 2009.
I. Kang, H.-J. Yun, D. S. Chung, S.-K. Kwon, Y.-H. Kim, J. Am. Chem. Soc. 2013, 135, 14896.
J.-R. Pouliot, B. Sun, M. Leduc, A. Najari, Y. Li, M. Leclerc, Polym. Chem. 2014, 6, 278.
M. M. Wienk, M. Turbiez, J. Gilot, R. A. J. Janssen, Adv. Mater. 2008, 20, 2556.
X. Zhang, L. J. Richter, D. M. DeLongchamp, R. J. Kline, M. R. Hammond, I. McCulloch, M. Heeney, R. S. Ashraf, J. N. Smith, T. D. Anthopoulos, B. Schroeder, Y. H. Geerts, D. A. Fischer, M. F. Toney, J. Am. Chem. Soc. 2011, 133, 15073.
V. Jonas, G. Frenking, M. T. Reetz, J. Am. Chem. Soc. 1994, 116, 8741.
J.-F. Gal, P.-C. Maria, M. Yáñez, O. Mó, Molecules 2021, 26, 6659.
X. Qu, D. A. Latino, J. Aires-de-Sousa, J. Cheminformatics 2013, 5, 34.
H. Huynh, T. J. Kelly, L. Vu, T. Hoang, P. A. Nguyen, T. C. Le, E. A. Jarvis, H. Phan, ACS Omega 2023, 8, 19119.
D. M. Wilkins, A. Grisafi, Y. Yang, K. U. Lao, R. A. DiStasio, M. Ceriotti, Proc. Natl. Acad. Sci. USA 2019, 116, 3401.
N. Lubbers, J. S. Smith, K. Barros, J. Chem. Phys. 2018, 148, 241715.
O. T. Unke, M. Meuwly, J. Chem. Theory Comput. 2019, 15, 3678.
P. B. Jørgensen, K. W. Jacobsen, M. N. Schmidt, Neural Message Passing with Edge Updates for Predicting Properties of Molecules and Materials. arXiv June 8. 2018 https://doi.org/10.48550/arXiv.1806.03146
H. Sahu, W. Rao, A. Troisi, H. Ma, Adv. Energy Mater. 2018, 8, 1801032.
C. A. Bauer, G. Schneider, A. H. Göller, J. Cheminformatics 2019, 11, 59.
A. Zhavoronkov, Y. A. Ivanenkov, A. Aliper, M. S. Veselov, V. A. Aladinskiy, A. V. Aladinskaya, V. A. Terentiev, D. A. Polykovskiy, M. D. Kuznetsov, A. Asadulaev, Y. Volkov, A. Zholus, R. R. Shayakhmetov, A. Zhebrak, L. I. Minaeva, B. A. Zagribelnyy, L. H. Lee, R. Soll, D. Madge, L. Xing, T. Guo, A. Aspuru-Guzik, Nat. Biotechnol. 2019, 37, 1038.
G. Schneider, U. Fechner, Nat. Rev. Drug Discov. 2005, 4, 649.
R. Batra, H. Chan, G. Kamath, R. Ramprasad, M. J. Cherukara, S. K. R. S. Sankaranarayanan, J. Phys. Chem. Lett. 2020, 11, 7058.
T. Le, V. C. Epa, F. R. Burden, D. A. Winkler, Chem. Rev. 2012, 112, 2889.
T. C. Le, M. Ballard, P. Casey, M. S. Liu, D. A. Winkler, Mol. Inf. 2015, 34, 18.
R. Todeschini, V. Consonni, Molecular Descriptors for Chemoinformatics. Weinheim 2009. https://doi.org/10.1002/9783527628766.fmatter
G. Pilania, A. Mannodi-Kanakkithodi, B. P. Uberuaga, R. Ramprasad, J. E. Gubernatis, T. Lookman, Sci. Rep. 2016, 6, 19375.
V. Botu, R. Batra, J. Chapman, R. Ramprasad, J. Phys. Chem. C 2017, 121, 511.
C. Xu, Y. Wang, A. Barati Farimani, Npj Comput. Mater. 2023, 9, 1.
J. Schmidt, L. Pettersson, C. Verdozzi, S. Botti, M. A. L. Marques, Sci. Adv. 2021, 7, eabi7948.
K. T. Schütt, H. E. Sauceda, P.-J. Kindermans, A. Tkatchenko, K.-R. Müller, J. Chem. Phys. 2018, 148, 241722.
P. C. St. John, C. Phillips, T. W. Kemper, A. N. Wilson, Y. Guan, M. F. Crowley, M. R. Nimlos, R. E. Larsen, J. Chem. Phys. 2019, 150, 234111.
V. Fung, J. Zhang, E. Juarez, B. G. Sumpter, Npj Comput. Mater. 2021, 7, 1.
RDKit. https://www.rdkit.org/ (accessed: 29 September 2023)
S. Kim, J. Chen, T. Cheng, A. Gindulyte, J. He, S. He, Q. Li, B. A. Shoemaker, P. A. Thiessen, B. Yu, L. Zaslavsky, J. Zhang, E. E. Bolton, Nucleic Acids Res. 2023, 51, D1373.
L. A. Curtiss, P. C. Redfern, K. Raghavachari, J. Chem. Phys. 2007, 126, 084108.
J. Foresman, A. Frisch, Exploring Chemistry With Electronic Structure Methods, 3rd ed., Gaussian, Inc. Wallingford 2015.
A. Austin, G. A. Petersson, M. J. Frisch, F. J. Dobek, G. Scalmani, K. Throssell, J. Chem. Theory Comput. 2012, 8, 4989.
C. A. Bauer, G. Schneider, A. H. Göller, Mol. Inf. 2019, 38, 1800115.
H. Moriwaki, Y.-S. Tian, N. Kawashita, T. Takagi, J. Cheminformatics 2018, 10, 4.
F. Pedregosa, G. Varoquaux, A. Gramfort, V. Michel, B. Thirion, O. Grisel, M. Blondel, P. Prettenhofer, R. Weiss, V. Dubourg, J. Mach. Learn. Res. 2011, 12, 2825.
A. Géron, Hands-On Machine Learning with Scikit-Learn, Keras, and TensorFlow, 2nd ed., O'Reilly Media, Inc., Sebastopol 2019.
B. Ramsundar, P. Eastman, P. Walters, V. Pande, K. Leswing, Z. Wu, Deep Learning for the Life Sciences,O'Reilly Media, Sebastopol 2019.
P. W. Ayers, Faraday Discuss. 2006, 135, 161.
P. W. Ayers, J. Chem. Phys. 2005, 122, 141102.
C. Cárdenas, P. W. Ayers, Phys. Chem. Chem. Phys. 2013, 15, 13959.
M.-H. Lee, Org. Electron. 2020, 76, 105465.
E. Scornet, Ann. inst. Henri Poincare Probab. Stat. 2023, 59, 21.
M. Sandri, P. Zuccolotto, Stat. Comput. 2010, 20, 393.
A. P. Cassidy, F. A. Deviney, 2014 IEEE Int. Conf. Big Data (Big Data); 2014; pp 23-28. https://doi.org/10.1109/BigData.2014.7004352
J. D. Hunter, Computing in Science & Engineering 2007, 9, 90.