有机化学 ›› 2021, Vol. 41 ›› Issue (10): 3995-4006.DOI: 10.6023/cjoc202102036 上一篇 下一篇
所属专题: 南开大学化学学科创立100周年
综述与进展
收稿日期:
2021-02-20
修回日期:
2021-03-18
发布日期:
2021-03-25
通讯作者:
彭谦
基金资助:
Kairui Zhang, Yaya Wang, Hongdan Zhu, Qian Peng()
Received:
2021-02-20
Revised:
2021-03-18
Published:
2021-03-25
Contact:
Qian Peng
Supported by:
文章分享
准经典分子动态学模拟方法结合了经典分子动力学和电子结构理论, 从原子/分子层面研究化学反应的动态机制, 不但能模拟反应体系中相应产物或中间体的统计学分布, 还可提供时间尺度下化学键生成/断裂的信息. 密度泛函理论(DFT)计算在反应机制研究中已被广泛应用, 但从准经典分子动态学角度的研究还相对较少, 比如分叉过渡态的现象及其选择性、环加成协同机制中出现的分步过程以及绕过常见的中间体而直接生成产物等. 这些新颖机制的研究通常需要分子动态学, 有些甚至打破了传统过渡态理论的认知. 综述了近年来有机化学反应机制的准经典分子动态学研究进展, 强调机制中的动态学效应, 旨在加深人们对有机反应机制的理解并拓宽有机化学理论.
张凯瑞, 王亚亚, 朱宏丹, 彭谦. 有机反应机制的准经典分子动态学研究进展[J]. 有机化学, 2021, 41(10): 3995-4006.
Kairui Zhang, Yaya Wang, Hongdan Zhu, Qian Peng. Advances on Quasi-classical Molecular Dynamics of Organic Reaction Mechanisms[J]. Chinese Journal of Organic Chemistry, 2021, 41(10): 3995-4006.
Structure | ΔG | Structure | ΔG | Structure | ΔG |
---|---|---|---|---|---|
50 | 0.0 | 50F | 0.0 | 50Cl | 0.0 |
TS-51 | 41.0 | TSF-51 | 45.8 | TSCl-51 | 44.8 |
TS-52 | 36.9 | TSF-52 | 43.6 | TSCl-52 | 35.8 |
53 | –11.5 | 53F | –6.9 | 53Cl | –18.9 |
54 | –11.5 | 54F | –10.9 | 54Cl | –10.7 |
Structure | ΔG | Structure | ΔG | Structure | ΔG |
---|---|---|---|---|---|
50 | 0.0 | 50F | 0.0 | 50Cl | 0.0 |
TS-51 | 41.0 | TSF-51 | 45.8 | TSCl-51 | 44.8 |
TS-52 | 36.9 | TSF-52 | 43.6 | TSCl-52 | 35.8 |
53 | –11.5 | 53F | –6.9 | 53Cl | –18.9 |
54 | –11.5 | 54F | –10.9 | 54Cl | –10.7 |
Gas | Solution | Solution+OEEF | |
---|---|---|---|
Uncatalyzed | 100 (0c) [5d] | 100 (0c) [6d] | — |
6-c 4Fea | 100 (21c) [40d] | 130 (26c) [50d] | 130 (86c) [174d] |
5-c 4Feb | 130 (39c) [59d] | 130 (54c) [98d] | 130 (88c) [235d] |
5-c 6Feb | 100 (74c) [103d] | 130 (87c) [199d] | 130 (96c) [414d] |
Gas | Solution | Solution+OEEF | |
---|---|---|---|
Uncatalyzed | 100 (0c) [5d] | 100 (0c) [6d] | — |
6-c 4Fea | 100 (21c) [40d] | 130 (26c) [50d] | 130 (86c) [174d] |
5-c 4Feb | 130 (39c) [59d] | 130 (54c) [98d] | 130 (88c) [235d] |
5-c 6Feb | 100 (74c) [103d] | 130 (87c) [199d] | 130 (96c) [414d] |
[1] |
Blais, N. C.; Bunker, D. L. J. Chem. Phys. 1962, 37, 2713.
doi: 10.1063/1.1733079 |
[2] |
Bunker, D. L. J. Chem. Phys. 1964, 40, 1946.
doi: 10.1063/1.1725427 |
[3] |
Bunker, D. L. J. Chem. Phys. 1962, 37, 393.
doi: 10.1063/1.1701333 |
[4] |
Hohenberg, P.; Kohn, W. Phys. Rev. 1964, 136, 864.
|
[5] |
Kohn, W.; Sham, L. J. Phys. Rev. 1965, 140, 1133.
|
[6] |
Zhang, D. H.; Collins, M. A.; Lee, S.-Y. Science 2000, 290, 961.
pmid: 11062123 |
[7] |
Xie, Y.; Zhao, H.; Wang, Y.; Huang, Y.; Wang, T.; Xu, X.; Xiao, C.; Sun, Z.; Zhang, D. H.; Yang, X. Science 2020, 368, 767.
doi: 10.1126/science.abb1564 |
[8] |
Paranjothy, M.; Sun, R.; Zhuang, Y.; Hase, W. L. Comput. Mol. Sci. 2013, 3, 296.
doi: 10.1002/wcms.1132 |
[9] |
Pratihar, S.; Ma, X.; Homayoon, Z.; Barnes, G. L.; Hase, W. L. J. Am. Chem. Soc. 2017, 139, 3570.
doi: 10.1021/jacs.6b12017 pmid: 28118543 |
[10] |
Verlet, L. Phys. Rev. 1967, 159, 98.
doi: 10.1103/PhysRev.159.98 |
[11] |
Hollingsworth, S. A.; Dror, R. O. Neurone 2018, 99, 1129.
doi: 10.1016/j.neuron.2018.08.011 |
[12] |
Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471.
pmid: 10032153 |
[13] |
Helgaker, T.; Uggerud, E.; Jensen, H. J. A. Chem. Phys. Lett. 1990, 173, 145.
doi: 10.1016/0009-2614(90)80068-O |
[14] |
Uggerud, E.; Helgaker, T. J. Am. Chem. Soc. 1992, 114, 4265.
doi: 10.1021/ja00037a033 |
[15] |
Barnett, R. N.; Landman, U. Phys. Rev. B 1993, 48, 2081.
pmid: 10008598 |
[16] |
Hase, W. L.; Duchovic, R. J.; Hu, X.; Komornicki, A.; Lim, K.; Lu, D.-H.; Peslherbe, G. H.; Swamy, K. N.; Vande Linde, S. R.; Wang, H.; Wolfe, R. J. Quant. Chem. Prog. Ex. 1996, 16, 671.
|
[17] |
Li, G.; Hase, W. L. J. Am. Chem. Soc. 1999, 121, 7124.
doi: 10.1021/ja990607j |
[18] |
Xie, J.; Sun, R.; Siebert, M. R.; Otto, R.; Wester, R.; Hase, W. L. J. Phys. Chem. A 2013, 117, 7162.
doi: 10.1021/jp4008027 |
[19] |
Peslherbe, G. H.; Hase, W. L. J. Chem. Phys. 1996, 104, 7882.
doi: 10.1063/1.471504 |
[20] |
Singleton, D. A.; Hang, C.; Szymanski, M. J.; Greenwald, E. E. J. Am. Chem. Soc. 2003, 125, 1176.
pmid: 12553813 |
[21] |
Carlsen, R.; Wohlgemuth, N.; Carlson, L.; Ess, D. H. J. Am. Chem. Soc. 2018, 140, 11039.
doi: 10.1021/jacs.8b05238 pmid: 30066561 |
[22] |
Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery Jr, J. A. J. Comput. Chem. 1993, 14, 1347.
doi: 10.1002/(ISSN)1096-987X |
[23] |
Ess, D. H.; Wheeler, S. E.; Iafe, R. G.; Xu, L.; Çelebi-Ölçüm, N.; Houk, K. N. Angew. Chem., Int. Ed. 2008, 47, 7592.
doi: 10.1002/anie.v47:40 |
[24] |
Hare, S. R.; Tantillo, D. J. Pure Appl. Chem. 2017, 89, 679.
doi: 10.1515/pac-2017-0104 |
[25] |
Caramella, P.; Quadrelli, P.; Toma, L. J. Am. Chem. Soc. 2002, 124, 1130.
doi: 10.1021/ja016622h |
[26] |
Zhang, L.; Wang, Y.; Yao, Z.-J.; Wang, S.-Z.; Yu, Z.-X. J. Am. Chem. Soc. 2015, 137, 13290.
doi: 10.1021/jacs.5b05971 pmid: 26407120 |
[27] |
Burns, J. M.; Boittier, E. D. J. Org. Chem. 2019, 84, 5997.
doi: 10.1021/acs.joc.8b03236 pmid: 30700089 |
[28] |
Fu, C.; Lora, N.; Kirchhoefer, P. L.; Lee, D. R.; Altenhofer, E.; Barnes, C. L.; Hungerford, N. L.; Krenske, E. H.; Harmata, M. Angew. Chem., Int. Ed. 2017, 56, 14682.
doi: 10.1002/anie.v56.46 |
[29] |
Yu, P.; Chen, T. Q.; Yang, Z.; He, C. Q.; Patel, A.; Lam, Y.-H.; Liu, C.-Y.; Houk, K. N. J. Am. Chem. Soc. 2017, 139, 8251.
doi: 10.1021/jacs.7b02966 |
[30] |
Patel, A.; Chen, Z.; Yang, Z.; Gutiérrez, O.; Liu, H.-W.; Houk, K. N.; Singleton, D. A. J. Am. Chem. Soc. 2016, 138, 3631.
doi: 10.1021/jacs.6b00017 |
[31] |
Black, K.; Liu, P.; Xu, L.; Doubleday, C.; Houk, K. N. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 12860.
doi: 10.1073/pnas.1209316109 |
[32] |
Yu, P.; Patel, A.; Houk, K. N. J. Am. Chem. Soc. 2015, 137, 13518.
doi: 10.1021/jacs.5b06656 |
[33] |
Zhang, C.; Wang, X.; Chen, Y.; He, Z.; Yu, P.; Liang, Y. J. Org. Chem. 2020, 85, 9440.
doi: 10.1021/acs.joc.0c01187 pmid: 32567858 |
[34] |
Salomon-Ferrer, R.; Case, D. A.; Walker, R. C. Comput. Mol. Sci. 2013, 3, 198.
doi: 10.1002/wcms.1121 |
[35] |
Xue, X.-S.; Jamieson, C. S.; Garcia-Borràs, M.; Dong, X.; Yang, Z.; Houk, K. N. J. Am. Chem. Soc. 2019, 141, 1217.
doi: 10.1021/jacs.8b12674 |
[36] |
Roth, W. R.; Wollweber, D.; Offerhaus, R.; Rekowski, V.; Lennartz, H.-W.; Sustmann, R.; Müller, W. Chem. Ber. 1993, 126, 2701.
doi: 10.1002/(ISSN)1099-0682 |
[37] |
Hrovat, D. A.; Duncan, J. A.; Borden, W. T. J. Am. Chem. Soc. 1999, 121, 169.
doi: 10.1021/ja983032j |
[38] |
Debbert, S. L.; Carpenter, B. K.; Hrovat, D. A.; Borden, W. T. J. Am. Chem. Soc. 2002, 124, 7896.
pmid: 12095322 |
[39] |
Villar López, R.; Faza, O. N.; Silva López, C. J. Org. Chem. 2017, 82, 4758.
doi: 10.1021/acs.joc.7b00425 |
[40] |
Hare, S. R.; Tantillo, D. J. Beilstein J. Org. Chem. 2016, 12, 377.
doi: 10.3762/bjoc.12.41 |
[41] |
Siebert, M. R.; Zhang, J.; Addepalli, S. V.; Tantillo, D. J.; Hase, W. L. J. Am. Chem. Soc. 2011, 133, 8335.
doi: 10.1021/ja201730y |
[42] |
Blümel, M.; Nagasawa, S.; Blackford, K.; Hare, S. R.; Tantillo, D. J.; Sarpong, R. J. Am. Chem. Soc. 2018, 140, 9291.
doi: 10.1021/jacs.8b05804 |
[43] |
Xu, L.; Doubleday, C. E.; Houk, K. N. J. Am. Chem. Soc. 2011, 133, 17848.
doi: 10.1021/ja207051b |
[44] |
Yu, P.; Yang, Z.; Liang, Y.; Hong, X.; Li, Y.; Houk, K. N. J. Am. Chem. Soc. 2016, 138, 8247.
doi: 10.1021/jacs.6b04113 |
[45] |
Yang, Y.; Zhang, X.; Zhong, L.-P.; Lan, J.; Li, X.; Li, C.-C.; Chung, L. W. Nat. Commun. 2020, 11, 1850.
doi: 10.1038/s41467-020-15599-w |
[46] |
Zheng, C. Chin. J. Chem. 2020, 38, 1579.
doi: 10.1002/cjoc.v38.12 |
[47] |
Zheng, C.; Xia, Z.-L.; You, S.-L. Chem 2018, 4, 1952.
doi: 10.1016/j.chempr.2018.06.006 |
[48] |
Xie, J.; Otto, R.; Mikosch, J.; Zhang, J.; Wester, R.; Hase, W. L. Acc. Chem. Res. 2014, 47, 2960
doi: 10.1021/ar5001764 |
[49] |
Xie, J.; Hase, W. L. Science 2016, 352, 32.
doi: 10.1126/science.aaf5172 |
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