A Benchmark Study of Density Functional Theory (DFT) Methods for Mo-Catalyzed Carbonyl Oxidative Addition

doi:10.6023/cjoc202507040

Abstract

In molybdenum chemistry, the oxidative addition of o-quinone or 1,2-dicarbonyl compounds to molybdenum has been widely used in Mo-catalyzed C—C bond construction. The carbonyl oxidative addition to Mo(0) or Mo(II) is the critical elementary reaction of molybdenum catalysis. However, the relevant density functional theory (DFT) studies are relatively scarce, especially regarding the rational selection of functionals. In this work, 14 functionals were employed to investigate the Mo-catalyzed carbonyl oxidative addition step. A benchmark study was carried out to evaluate their performance in structure optimization and energy calculation. Analyses of mean absolute error (MAE) and mean squared error (MSE) indicated that the B3LYP-D3(BJ), TPSSh, and ωB97X-D functionals exhibited superior performance in structure optimization. Using the DLPNO-CCSD(T) functional as the reference, the M06, M06-L, and MN15-L functionals exhibited good performance for energy calculation based on the structures optimized using the B3LYP-D3(BJ) functional. In particular, MN15-L provided the best performance with the smallest MAE and MSE.

Key words: molybdenum catalysis, carbonyl oxidation addition, density functional theory (DFT) calculation, DFT benchmark study

Cite this article

Zitong Chen, Liwei Wang, Xiao Shen, Xiaotian Qi. A Benchmark Study of Density Functional Theory (DFT) Methods for Mo-Catalyzed Carbonyl Oxidative Addition[J]. Chinese Journal of Organic Chemistry, 2026, 46(2): 507-514.

Export EndNote|Reference Manager|ProCite|BibTeX|RefWorks

share this article

Fig. & Tab. 6

Scheme 1. Mo-catalyzed carbonyl oxidative addition reactions

Figure 1. (a) X-ray crystal structure of Mo(0) catalysts 1 and 2; (b) MAE and MSE values of the benchmark results compared to the X-ray crystal structures

Figure 2. DFT study of three representative carbonyl oxidative addition steps in Mo catalysis The activation free energies were calculated using DLPNO-CCSD(T) based on the structures optimized by B3LYP-D3, ωB97X-D, and TPSSh, respectively. The 3D structures were optimized using B3LYP-D3(BJ).

Figure 3. Benchmark results of DFT functionals for energy calculation of TPSSh optimized carbonyl oxidative addition transition states The activation free energy calculated by DLPNO-CCSD(T) is used as the standard of energy.

Figure 4. Benchmark results of DFT functionals for energy calculation of ωB97X-D optimized carbonyl oxidative addition transition states The activation free energy calculated by DLPNO-CCSD(T) is used as the standard of energy.

Figure 5. Benchmark results of DFT functionals for energy calculation of B3LYP-D3(BJ) optimized carbonyl oxidative addition transition states The activation free energy calculated by DLPNO-CCSD(T) is used as the standard of energy.

References 42

[1]	(a) Novotny J. A.; Peterson C. A. Adv. Nutr. 2018, 9, 272. doi: 10.1093/advances/nmx001 pmid: 29767695
	(b) Hu C.-Z. J.;Huang Z. D.; Fu H. H.; Peng X. H. Chin. J. Org. Chem. 2018, 38, 486 (in Chinese). doi: 10.6023/cjoc201707017 pmid: 29767695
	(胡传峰, 周建豪, 黄志达, 傅惠惠, 彭新华, 有机化学, 2018, 38, 486.) doi: 10.6023/cjoc201707017 pmid: 29767695
	(c) Li C.-S.; Chun C. L. Chin. J. Org. Chem. 2001, 21, 1009 (in Chinese). pmid: 29767695
	(宋礼成, 罗春成, 有机化学, 2001, 21, 1009.) pmid: 29767695
[2]	Metz S.; Thiel W. Coord. Chem. Rev. 2011, 255, 1085. doi: 10.1016/j.ccr.2011.01.027
[3]	(a) Hille R. Chem. Rev. 1996, 96, 2757. pmid: 12114025
	(b) Hille R. Trends Biochem. Sci 2002, 27, 360. doi: 10.1016/s0968-0004(02)02107-2 pmid: 12114025
	(c) Mendel R. R. Dalton Trans. 2005, 3404. pmid: 12114025
[4]	(a) Lennartson A. Nat. Chem. 2014, 6, 746. doi: 10.1038/nchem.2011 pmid: 25054948
	(b) Carmona E. Chem. Eur. J. 2019, 25, 11. doi: 10.1002/chem.v25.1 pmid: 25054948
[5]	(a) Schrock R. R. Angew. Chem. Int. Ed. 2006, 45, 3748. doi: 10.1002/anie.v45:23 pmid: 27126041
	(b) Nguyen T. T.; Koh M. J.; Shen X.; Romiti F.; Schrock R. R.; Hoveyda A. H. Science 2016, 352, 569. doi: 10.1126/science.aaf4622 pmid: 27126041
	(c) Korber J. N.; Wille C.; Leutzsch M.; Fürstner A. J. Am. Chem. Soc. 2023, 145, 26993. doi: 10.1021/jacs.3c10430 pmid: 27126041
[6]	Margulieux G. W.; Bezdek M. J.; Turner Z. R.; Chirik P. J. J. Am. Chem. Soc. 2017, 139, 6110. doi: 10.1021/jacs.7b03070 pmid: 28414434
[7]	Poli R. Chem. Eur. J. 2004, 10, 332. doi: 10.1002/chem.v10:2
[8]	(a) Hille R.; Hall J.; Basu P. Chem. Rev. 2014, 114, 3963. doi: 10.1021/cr400443z pmid: 34045715
	(b) McSkimming A.; Suess D. L. M. Nat. Chem. 2021, 13, 666. doi: 10.1038/s41557-021-00701-6 pmid: 34045715
	(c) Miyazaki T.; Tanaka H.; Tanabe Y.; Yuki M.; Nakajima K.; Yoshizawa K.; Nishibayashi Y. Angew. Chem. Int. Ed. 2014, 53, 11488. doi: 10.1002/anie.v53.43 pmid: 34045715
	(d) Lehnert N.; Musselman B. W.; Seefeldt L. C. Chem. Soc. Rev. 2021, 50, 3640. doi: 10.1039/D0CS00923G pmid: 34045715
[9]	(a) Hu Z.-N.; Ai Y.; Zhao Y.; Wang Y.; Ding K.; Zhang W.; Guo R.; Zhang X.; Cai X.; Wang N.; Hu J.; Liang Q.; Liu H.; Huang F.; Wu L.; Zhang J.; Sun H.-B. Nano Res. 2023, 16, 2302. doi: 10.1007/s12274-022-5277-3
	(b) Wang L.; Liu X.; Zhang Q.; Zhou G.; Pei Y.; Chen S.; Wang J.; Rao A. M.; Yang H.; Lu B. Nano Energy 2019, 61, 194. doi: 10.1016/j.nanoen.2019.04.060
[10]	Cao L.-Y.; Luo J.-N.; Yao J.-S.; Wang D.-K.; Dong Y.-Q.; Zheng C.; Zhuo C.-X. Angew. Chem. Int. Ed. 2021, 60, 15254. doi: 10.1002/anie.v60.28
[11]	Dong Y.-Q.; Shi X.-N.; Cao L.-Y.; Bai J.; Zhuo C.-X. Org. Chem. Front. 2023, 10, 3544. doi: 10.1039/D3QO00567D
[12]	Qing H.-S, Bao X. G. Chin. J. Org. Chem. 2024, 44, 3518 (in Chinese). doi: 10.6023/cjoc202405018
	(孙庆浩, 鲍晓光, 有机化学, 2024, 44, 3518.) doi: 10.6023/cjoc202405018
[13]	(a) Rui Y.; Chen Y.; Ivanova E.; Kumar V. B.; Śmiga S.; Grabowski I.; Dral P. O. Adv. Sci. 2024, 11, 2408239. doi: 10.1002/advs.v11.47
	(b) Licht R. B.; Bell A. T. ACS Catal. 2017, 7, 161. doi: 10.1021/acscatal.6b02523
[14]	(a) Ziane M.; Amitouche F.; Bouarab S.; Vega A. J. Nanopart. Res. 2017, 19, 380. doi: 10.1007/s11051-017-4072-7 pmid: 29206033
	(b) Mallick S.; Lu Y.; Luo M. H.; Meng M.; Tan Y. N.; Liu C. Y.; Zuo J.-L. Inorg. Chem. 2017, 56, 14888. doi: 10.1021/acs.inorgchem.7b02133 pmid: 29206033
[15]	(a) Kanungo B.; Zimmerman P. M.; Gavini V. Nat. Commun. 2019, 10, 4497. doi: 10.1038/s41467-019-12467-0 pmid: 31582755
	(b) Su N. Q.; Xu X. Annu. Rev. Phys. Chem. 2017, 68, 155. doi: 10.1146/physchem.2017.68.issue-1 pmid: 31582755
[16]	Oueis Y.; Staroverov V. N. J. Chem. Phys 2022, 157, 204107. doi: 10.1063/5.0128508
[17]	Albavera-Mata A.; Botello-Mancilla K.; Trickey S. B.; Gázquez J. L.; Vela A. Phys. Rev. B 2020, 102, 035129. doi: 10.1103/PhysRevB.102.035129
[18]	Gould T.; Pittalis S. Phys. Rev. X 2024, 14, 041045.
[19]	Garza A. J.; Bell A. T.; Head-Gordon M. J. Chem. Theory Comput. 2018, 14, 3083. doi: 10.1021/acs.jctc.8b00288
[20]	Frisch, M. J. T. G. W.; Schlegel H. B.; Scuseria G. E.; Robb M. A.; Cheeseman J. R.; Scalmani G.; Barone V.; Mennucci B.; Petersson G. A.; Nakatsuji H.; Caricato M.; Li X.; Hratchian H. P.; Izmaylov A. F.; Bloino J.; Zheng G.; Sonnenberg J. L.; Hada M.; Ehara M.; Toyota K.; Fukuda R.; Hasegawa J.; Ishida M.; Nakajima T.; Honda Y.; Kitao O.; Nakai H.; Vreven T.; Montgomery J. A., Jr.; ; Peralta J. E.; Ogliaro F.; Bearpark M.; Heyd J. J.; Brothers E.; Kudin K. N.; Staroverov V. N.; Kobayashi R.; Normand J.; Raghavachari K.; Rendell A.; Burant J. C.; Iyengar S. S.; Tomasi J.; Cossi M.; Rega N.; Millam N. J.; Klene M.; Knox J. E.; Cross J. B.; Bakken V.; Adamo C.; Jaramillo J.; Gomperts R.; Stratmann R. E.; Yazyev O.; Austin A. J.; Cammi R.; Pomelli C.; Ochterski J. W.; Martin R. L.; Morokuma K.; Zakrzewski V. G.; Voth G. A.; Salvador P.; Dannenberg J. J.; Dapprich S.; Daniels A. D.; Farkas O.; Foresman J. B.; Ortiz J. V.; Cioslowski J.; Fox D. J. Gaussian 16, Revision C.01; Gaussian, Inc.: Wallingford, CT, 2019.
[21]	(a) Neese F. WIREs Comput. Mol. Sci. 2012, 2, 73. doi: 10.1002/wcms.v2.1
	(b) Neese F. WIREs Comput. Mol. Sci. 2018, 8, e1327.
	(c) Neese F.; Wennmohs F.; Becker U.; Riplinger C. J. Chem. Phys. 2020, 152, 224108. doi: 10.1063/5.0004608
[22]	Verma P.; Truhlar D. G. Trends Chem. 2020, 2, 302. doi: 10.1016/j.trechm.2020.02.005
[23]	Perdew J. P. Phys. Rev. B 1986, 33, 8822. doi: 10.1103/PhysRevB.33.8822
[24]	(a) Stephens P. J.; Devlin F. J.; Chabalowski C. F.; Frisch M. J. J. Phys. Chem. 1994, 98, 11623. doi: 10.1021/j100096a001
	(b) Becke A. D. J. Chem. Phys 1993, 98, 5648. doi: 10.1063/1.464913
[25]	Adamo C.; Barone V. J. Chem. Phys. 1999, 110, 6158. doi: 10.1063/1.478522
[26]	Shimazaki T.; Nakajima T. Chem. Phys. Lett. 2016, 647, 132. doi: 10.1016/j.cplett.2015.12.069
[27]	Grimme S.; Antony J.; Ehrlich S.; Krieg H. J. Chem. Phys. 2010, 132, 154104. doi: 10.1063/1.3382344
[28]	Chai J.-D.; Head-Gordon M. Phys. Chem. Chem. Phys. 2008, 10, 6615. doi: 10.1039/b810189b
[29]	Zhao Y.; Truhlar D. G. J. Chem. Phys. 2006, 125, 194101. doi: 10.1063/1.2370993
[30]	Peverati R.; Truhlar D. G. J. Phys. Chem. Lett. 2012, 3, 117. doi: 10.1021/jz201525m
[31]	Yu H. S.; He X.; Truhlar D. G. J. Chem. Theory Comput. 2016, 12, 1280. doi: 10.1021/acs.jctc.5b01082
[32]	Zhao Y.; Truhlar D. G. Theor. Chem. Acc. 2008, 120, 215. doi: 10.1007/s00214-007-0310-x
[33]	Peverati R.; Truhlar D. G. J. Phys. Chem. Lett. 2011, 2, 2810. doi: 10.1021/jz201170d
[34]	Yu H. S.; He X.; Li S. L.; Truhlar D. G. Chem. Sci. 2016, 7, 5032. doi: 10.1039/C6SC00705H
[35]	(a) Tao J.; Perdew J. P.; Staroverov V. N.; Scuseria G. E. Phys. Rev. Lett. 2003, 91, 146401. doi: 10.1103/PhysRevLett.91.146401
	(b) Staroverov V. N.; Scuseria G. E.; Tao J.; Perdew J. P. J. Chem. Phys. 2004, 121, 11507. doi: 10.1063/1.1795692
[36]	Xu X.; Goddard W. A. Proc. Natl. Acad. Sci. 2004, 101, 2673. doi: 10.1073/pnas.0308730100
[37]	Gray M.; Herbert J. M. J. Chem. Phys 2024, 161, 054114. doi: 10.1063/5.0206533
[38]	(a) Weigend F.; Ahlrichs R. Phys. Chem. Chem. Phys. 2005, 7, 3297. doi: 10.1039/b508541a
	(b) Weigend F. Phys. Chem. Chem. Phys. 2006, 8, 1057. doi: 10.1039/b515623h
[39]	Marenich A. V.; Cramer C. J.; Truhlar D. G. J. Phys. Chem. B. 2009, 113, 6378. doi: 10.1021/jp810292n
[40]	(a) Weigend F. J. Comput. Chem. 2008, 29, 167. doi: 10.1002/jcc.v29:2
	(b) Hellweg A.; Hättig C.; Höfener S.; Klopper W. Theor. Chem. Acc. 2007, 117, 587. doi: 10.1007/s00214-007-0250-5
[41]	Legault C. Y. C. 1.0b, Université de Sherbrooke, Sher-brooke, Quebec, Canada, 2009, http://www Cylview.org.
[42]	Li W.; Huang M.; Liu J.; Huang Y.-L.; Lan X.-B.; Ye Z.; Zhao C.; Liu Y.; Ke Z. ACS Catal. 2021, 11, 10377. doi: 10.1021/acscatal.1c02956

钼催化羰基氧化加成步骤的密度泛函理论(DFT)方法评估研究