Citation: ZHAO Dong-Bo, RONG Chun-Ying, JENKINS Samantha, KIRK Steven R., YIN Du-Lin, LIU Shu-Bin. Origin of the cis-Effect: a Density Functional Theory Study of Doubly Substituted Ethylenes[J]. Acta Physico-Chimica Sinica, ;2013, 29(01): 43-54. doi: 10.3866/PKU.WHXB201211121 shu

Origin of the cis-Effect: a Density Functional Theory Study of Doubly Substituted Ethylenes

1.
1 Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China) and Key Laboratory of Resource Fine-Processing and Advanced Materials of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, P. R. China;
2 Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, U. S. A.

Received Date: 21 August 2012
Available Online: 12 November 2012
Fund Project: 杰出人才项目(23040609)资助 (23040609) 赵东波受湖南省研究生创新项目(CX2012B223)资助 (CX2012B223)

It is well known that the trans isomer of a doubly substituted ethylene is more stable than its cis counterpart because of the more favorable electrostatic and steric interactions in the trans conformer. Exceptions do exist nevertheless. 1,2-Difluoroethylene is such an example, so is 1,2-dichloroethylene. The unusual stability of the cis isomer of these doubly substituted ethylene compounds is referred to as the cis-effect, whose nature and origin are still not well understood. In this work, using 12 simple molecules, XHC=CHY (X, Y=F, Cl, Br, CN, CH₃, OCH₃, C₂H₆), as examples, we perform systematic studies to investigate the validity, nature, and origin of this effect. Among the systems studied, 9 of them exhibit the existence of the cis-effect and the remaining 3 systems are conventional systems used for the comparison purpose. We employ a large number of density functionals and basis sets to confirm its validity. We also use a few well-established analysis tools, such as natural bond orbital (NBO), energy decomposition analysis (EDA), density functional reactivity theory (DFRT), and non-covalent interaction (NCI) analysis, to pinpoint its nature and origin. We found that there exists a weak but attractive non-covalent interaction between the two substituting groups in the cis conformer. We also found that electrostatic, steric, and kinetic energies all play important roles for the validity of the cis-effect. Nevertheless, none of these quantities can be solely used as the single reason verning the general validity of the cis-effect, suggesting that the origin of the effect is complicated and its validity results from compound interactions from a number of interactions. In this work, we employ two-variable explanations to justify its validity through the electrostatic interaction plus steric effect or kinetic energy, with which reasonable fits with R²=0.86-0.87 were obtained.
- Density functional theory,
- cis-Effect,
- Natural bond orbital analysis,
- Steric effect,
- Non-covalent interaction
1. [1]
  
  (1) (a) Craig, N. C.; Entemann, E. A. J. Am. Chem. Soc. 1961, 83,3047. doi: 10.1021/ja01475a019
2. [2]
  (b) Craig, N. C.; Overend, J. J. Chem. Phys. 1969, 51, 1127.
3. [3]
  (c) Craig, N. C.; Piper, L. G.; Wheeler, V. L. J. Phys. Chem.1971, 76, 1453.
4. [4]
  (d) Craig, N. C.; Chen, A.; Suh, K. H.; Klee, S.; Mellau, G.;Winnewiser, B. P.;Winnewisser, M. J. Phys. Chem. A 1997,101, 9302.
5. [5]
  (e) Craig, N. C.; Brandon, D.W.; Stone, S. C.; Lafferty,W. J.J. Phys. Chem. 1992, 96, 1598.
6. [6]
  (2) Craig, N. C.; Lo, Y. S.; Piper, L. G.; Wheeler, J. C. J. Phys. Chem. 1970, 74, 1712. doi: 10.1021/j100703a011
7. [7]
  (3) (a)Wood, R. E.; Stevenson, D. P. J. Am. Chem. Soc. 1941, 63,1650. doi: 10.1021/ja01851a042
8. [8]
  (b) Gardner, D. V.; McGreer, D. E. Can. J. Chem. 1970, 48,2104.
9. [9]
  (4) (a) Salomma, P.; Nissi, P. Acta Chim. Scand. 1967, 21, 1386.doi: 10.3891/acta.chem.scand.21-1386
10. [10]
  (b) Crump, J.W. J. Org. Chem. 1963, 28, 953.
11. [11]
  (c) Harwell, K. E.; Hatch, L. F. J. Am. Chem. Soc. 1955, 77,1682.
12. [12]
  (5) Waldron, J. T.; Snyder,W. H. J. Am. Chem. Soc. 1973, 95, 5491.doi: 10.1021/ja00798a010
13. [13]
  (6) Huber-Wälchli, P.; Günthard, H. H. Spectrochim. Acta 1981,37, 285. doi: 10.1016/0584-8539(81)80159-6
14. [14]
  (7) Durig, J. R.; Liu, J.; Little, T. S.; Kalasinsky, V. F. J. Phys. Chem. 1992, 96, 8224. doi: 10.1021/j100200a006
15. [15]
  (8) Connor, T. M.; McLauchlan, K. A. J. Phys. Chem. 1965, 69,1888. doi: 10.1021/j100890a018
16. [16]
  (9) Epiotis, N. D. J. Am. Chem. Soc. 1973, 95, 3087. doi: 10.1021/ja00791a001
17. [17]
  (10) Kollman, P. A. J. Am. Chem. Soc. 1974, 96, 4363. doi: 10.1021/ja00821a003
18. [18]
  (11) Bemardi, F.; Bottoni, A.; Epiotis, N. D.; Guena, M. J. Am. Chem. Soc. 1978, 100, 6018. doi: 10.1021/ja00487a007
19. [19]
  (12) (a) Cremer, D. J. Am. Chem. Soc. 1981, 103, 3633. doi: 10.1021/ja00403a003
20. [20]
  (b) Cremer, D. Chem. Phys. Lett. 1981, 81, 481.
21. [21]
  (13) Carlos, J. L.; Karl, R. R.; Bauer, S. H. J. Chem. Soc. Faraday Trans. 2 1974, 2, 177.
22. [22]
  (14) Gandhi, S. R.; Benzel, M. A.; Dykstra, C. E.; Fukunaga, T.J. Phys. Chem. 1982, 86, 3121. doi: 10.1021/j100213a013
23. [23]
  (15) Saebø, S.; Sellers, H. J. Phys. Chem. 1988, 92, 4269. doi: 10.1021/j100326a006
24. [24]
  (16) Dixon, D. A.; Smart, B. E.; Fukunaga, T. Chem. Phys. Lett.1986, 125, 447. doi: 10.1016/0009-2614(86)87076-2
25. [25]
  (17) Yamamoto, T.; Kaneno, D.; Tomoda, S. Chem. Lett. 2005, 34,1190. doi: 10.1246/cl.2005.1190
26. [26]
  (18) Parr, R. G.; Yang,W. Density-Functional Theory of Atoms andMolecules. In International Series of Monographs on Chemistry;Clarendon Press: Oxford, England, 1989; Vol.16, p 333.
27. [27]
  (19) Liu, S. B. J. Chem. Phys. 2007, 126, 244103. doi: 10.1063/1.2747247
28. [28]
  (20) Liu, S. B.; vind, N.; Pedersen, L. G. J. Chem. Phys. 2008,129, 094104. doi: 10.1063/1.2976767
29. [29]
  (21) Liu, S. B.; Hu, H.; Pedersen, L. G. J. Phys. Chem. A 2010, 114,5913. doi: 10.1021/jp101329f
30. [30]
  (22) Ess, D. H.; Liu, S. B.; DeProft, F. J. Phys. Chem. A 2010, 114,12952. doi: 10.1021/jp108577g
31. [31]
  (23) Tsirelson,V. G.; Stash, A. I.; Liu, S. B. J. Chem. Phys. 2010,133, 114110. doi: 10.1063/1.3492377
32. [32]
  (24) Huang, Y.; Zhong, A. G.; Yang, Q. S.; Liu, S. B. J. Chem. Phys.2011, 134, 084103. doi: 10.1063/1.3555760
33. [33]
  (25) Torrent-Sucarrat, M.; Liu, S. B.; DeProft, F. J. Phys. Chem. A2009, 113, 3698. doi: 10.1021/jp8096583
34. [34]
  (26) Hohenberg, P.; Kohn,W. Phys. Rev. B 1964, 136, 864.doi: 10.1103/PhysRev.136.B864
35. [35]
  (27) Becke, A. D. Modern Electronic Structure Theory; Yarkony, D.R. Ed.;World Scientific: River Edge, N. J., 1995; pp 1022-1046.
36. [36]
  (28) Cohen, A. J.; Mori-Sánchez, P.; Yang,W. Science 2008, 321,792. doi: 10.1126/science.1158722
37. [37]
  (29) Xu, H. Y.;Wang,W. Acta Phys. -Chim. Sin. 2011, 27, 2565.[许惠英, 王维. 物理化学学报, 2011, 27, 2565.] doi: 10.3866/PKU.WHXB20111127
38. [38]
  (30) Bader, R. F.W.; Essén, H. J. Chem. Phys. 1984, 80, 1943. doi: 10.1063/1.446956
39. [39]
  (31) Johnson, E. R.; Keinan, S.; Mori-Sánchez, P.; Contreras-García,J.; Cohen, A. J.; Yang,W. J. Am. Chem. Soc. 2010, 132, 6498.doi: 10.1021/ja100936w
40. [40]
  (32) Geerlings, P.; DeProft, F.; Langenaeker,W. Chem. Rev. 2003,103, 1793. doi: 10.1021/cr990029p
41. [41]
  (33) Liu, S. B. Acta Phys. -Chim. Sin. 2009, 25, 590. [刘述斌. 物理化学学报, 2009, 25, 590.] doi: 10.3866/PKU.WHXB20090332
42. [42]
  (34) Woon, D. E.; Dunning, T. H., Jr. J. Chem. Phys. 1993, 98, 1358.doi: 10.1063/1.464303
43. [43]
  (35) Dunning, T. H., Jr.; Hay, P. J. Modern Theoretical Chemistry;Schaefer, H. F., III. Ed.; Plenum: New York, 1976; Vol. 3, pp1-28.
44. [44]
  (36) Frisch, M. J.; Trucks, G.W.; Schlegel, H. B.; et al. Gaussian-09,Revision B.01; Gaussian Inc.:Wallingford, CT, 2009.
45. [45]
  (37) NBO Version 3.1, Glendening, E. D.; Reed, A. E.; Carpenter, J.E.;Weinhold, F. doi: 10.3878/j.issn.1006-9585.2012.11212
46. [46]
  (38) Valiev, M.; Bylaska, E. J.; vind, N.; Kowalski, K.; Straatsma,T. P.; van Dam, H. J. J.;Wang, D.; Nieplocha, J.; Apra, E.;Windus, T. L.; De Jong,W. A. Comput. Phys. Commun. 2010,181, 1477. doi: 10.1016/j.cpc.2010.04.018
47. [47]
  (39) Dunning, T. H., Jr. J. Chem. Phys. 1989, 90, 1007. doi: 10.1063/1.456153
48. [48]
  (40) NBO Version 5.0, Glendening, E. D.; Badenhoop, J. K.; Reed,A. E.; Carpenter, J. E.; Bohmann, J. A.; Morales, C. M.;Weinhold, F. (Theoretical Chemistry Institute, University ofWisconsin, Madison, WI, 2001). http://www.chem.wisc.edu/-nbo5.
49. [49]
  (41) Weinhold, F.; Landis, C. Valency and Bonding: A Natural Bond Orbital Donor-Acceptor Perspective; Cambridge UniversityPress: UK, 2005.
50. [50]
  (42) Contreras-García, J.; Johnson, E. R.; Keinan, S.; Chaudret, R.;Piquemal, J. P.; Beratan, D. N.; Yang,W. J. Chem. Theory Comput. 2011, 7, 625. doi: 10.1021/ct100641a
51. [51]
  (43) Humphrey,W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996,14, 133.
52. [52]
  (44) AIMAll (Version 11.08.23), Keith, T. A. TK Gristmill Software,Overland Park KS, USA, 2012 (aim.tkgristmill.com); Bader, R.F.W. Atoms inMolecules: AQuantum Theory; Oxford UniversityPress: Oxford, 1990; Popeplier, P. L.; Hall, P. Atoms in Molecules: An Introduction; London, 2000; Matta, C. F., Boyd, R. J. Eds.;The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design;Wiley:Weinham, 2007.
53. [53]
  (45) Feller, D.; Peterson, K. A.; Dixon, D. A. J. Phys. Chem. A 2011,115, 1440.
54. [54]
  (46) (a) Liu, S. B. Phys. Rev. A 1996, 54, 1328. doi: 10.1103/PhysRevA.54.1328
55. [55]
  (b) Liu, S. B.; Parr, R. G. Phys. Rev. A 1996, 53, 2211.
56. [56]
  (c) Nagy, A.; Liu, S. B.; Parr, R. G. Phys. Rev. A 1999, 59, 3349.
57. [57]
  (d) Liu, S. B.; Morrison, R. C.; Parr, R. G. J. Chem. Phys. 2006,125, 174109.
58. [58]
  (47) (a) Liu, S. B.; Pedersen, L. G. J. Phys. Chem. A 2009, 113,3648. doi: 10.1021/jp811250r
59. [59]
  (b) Liu, S. B.; Schauer, C. K.; Pedersen, L. G. J. Chem. Phys.2009, 131, 164107.
60. [60]
  (c) Burger, S. K.; Liu, S. B.; Ayers, P.W. J. Phys. Chem. A 2011,115, 1293.
61. [61]
  (d) Huang, Y.; Liu, L.; Liu,W.; Liu, S. G.; Liu, S. B. J. Phys. Chem. A 2011, 115, 14697.
62. [62]
  (e) Huang, Y.; Liu, L.; Liu, S. B. Chem. Phys. Lett. 2012, 527,73.
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