Molecular Mechanics (MM4) study of fluorinated hydrocarbons

Journal of Physical Chemistry A

Volumn 110, Issue 22, 2006, Pages 7202-7227

  Chen, Kuo Hsiang ^a   Lii, Jenn Huei ^a   Walker, Gerald A ^a   Xie, Yaoming ^a   Schaefer III, Henry F ^a   Allinger, Norman L ^a  

^a UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; FLUORINE; MOLECULAR DYNAMICS; PARAFFINS; POLYTETRAFLUOROETHYLENES; STRETCHING; VIBRATION CONTROL;

ELECTRONEGATIVITY; MOLECULAR MECHANICS; POLYFLUORINATED ALKANES; POLYFLUORINATED COMPOUNDS;

HYDROCARBONS;

EID: 33745445674     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp060430x     Document Type: Article

References (118)

1. Allinger, N. L.; Yuh, Y. H.; Lii, J.-H. J. Am. Chem. Soc. 1989, 111, 8551, 8566, 8576.
2. The MM3 program is available to all users from Tripos Associates, 1699 South Hanley Road, St. Louis, MO 63144, and to nonprofit organizations only from Norman L. Allinger, Center for Computational Chemistry, Chemistry Annex, University of Georgia, Athens, GA 30602-2526. The MM4 program is also available (UNIX version) from Tripos Incorporated. It is also available from N.L.A. to nonprofit organizations only. A Windows version will be available shortly from Wavefunction, 18401 Von Karman Avenue, Suite 370, Irvine, CA 92612. Those interested should contact the appropriate distributor.
3. Allinger, N. L.; Chen, K.; Lii, J.-H. J. Comput. Chem. 1996, 17, 642.
4. Nevins, N.; Chen, K.; Allinger, N. L. J. Comput. Chem. 1996, 17, 669.
5. Nevins, N.; Allinger, N. L. J. Comput. Chem. 1996, 17, 730.
6. Allinger, N. L.; Chen, K.; Katzenellenbogen, J. A.; Wilson, S. R.; Anstead, G. M. J. Comput. Chem. 1996, 17, 747.
7. Allinger, N. L.; Fan, Y. J. Comput. Chem. 1997, 18, 1827.
8. Allinger, N. L.; Durkin, K. A. J. Comput. Chem. 2000, 21, 1229.
9. Langley, C. H.; Lii, J.-H.; Allinger, N. L. J. Comput. Chem. 2001, 22, 1396.
10. Mastryukov, V. S.; Chen, K.-H.; Allinger, N. L. J. Phys. Chem. A 2001, 105, 8562.
11. Chen, K.-H.; Allinger, N. L. THEOCHEM 2002, 581, 215.
12. Langley, C. H.; Allinger, N. L. J. Phys. Chem. A 2002, 106, 5638.
13. Lii, J.-H. J. Phys. Chem. A 2002, 106, 8667.
14. Langley, C. H.; Allinger, N. L. J. Phys. Chem. A 2003, 107, 5208.
15. Allinger, N. L.; Chen, K.-H.; Lii, J.-H.; Durkin, K. J. Comput. Chem. 2003, 24, 1447.
16. Sakakibara, K.; Naka, K.; Yamaguchi, Y.; Asami, M.; Chen, K.-H.; Lii, J.-H.; Allinger, N. L. J. Phys. Chem. A 2004, 108, 3048.
17. Langley, C. H.; Lii, J.-H.; Allinger, N. L. J. Comput. Chem. 2001, 22, 1426.
18. Langley, C. H.; Lii, J.-H.; Allinger, N. L. J. Comput. Chem. 2001, 22, 1451.
19. Langley, C. H.; Lii, J.-H.; Allinger, N. L. J. Comput. Chem. 2001, 22, 1476.
20. Allinger, N. L.; Chen, K.-H.; Lii, J.-H.; Durkin, K. J. Comput. Chem. 2003, 24, 1447.
21. Lii, J.-H.; Chen, K.-H.; Durkin, K.; Allinger, N. L. J. Comput. Chem. 2003, 24, 1473.
22. Lii, J.-H.; Chen, K.-H.; Grindley, T. B.; Allinger, N. L. J. Comput. Chem. 2003, 24, 1490.
23. Lii, J.-H.; Chen, K.-H.; Allinger, N. L. J. Comput. Chem. 2003, 24, 1504.
24. Lii, J.-H.; Chen, K.-H.; Allinger, N. L. J. Phys. Chem. A 2004, 108, 3006.
25. Lu, J.-H.; Chen, K.-H.; Johnson, G. P.; French, A.; Allinger, N. L. Carbohydr. Res. 2006, 340, 853.
26. The MM4 program is available to all users from Tripos Associates, 1699 South Hanley Road, St. Louis, MO 63144, and to nonprofit organizations only from Norman L. Allinger, Center for Computational Chemistry, Chemistry Annex, University of Georgia, Athens, GA 30602-2526.
27. Ma, B.; Lii, J.-H.; Schaefer, H. F.; Allinger, N. L. J. Phys. Chem. 1996, 100, 8763.
28. Ma, B.; Lii, J.-H.; Chen, K.-H.; Allinger, N. L. J. Am. Chem. Soc. 1997, 119, 2570.
29. Meyer, A. Y.; Allinger, N. L. Tetrahedron 1975, 31, 1971.
30. Chen, K.-H.; Walker, G. A.; Allinger, N. L. THEOCHEM 1999, 490, 87.
31. (a) Bohlmann, F. Angew Chem. 1957, 69, 641.
32. (b) Bohlmann F. Chem. Ber. 1958, 91, 2157.
33. (c) Thomas, H.; Chen, K.; Allinger, N. L. J. Am. Chem. Soc. 1994, 116, 5887.
34. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Gill, P. M. W.; Johnson, B. G.; Wong, M. W.; Foresman, J. B.; Robb, M. A.; Head-Gordon, M.; Replogle, E. S.; Gomperts, R.; Andres, J. L.; Raghavachari, K.; Binkley, J. S.; Stewart, J. J. P.; Pople, J. A. Gaussian 94/DFT, revision E.2; Gaussian, Inc.: Pittsburgh, PA, 1993.
35. Pulay's method: Baker, J.; Pulay, P. J. Comput. Chem. 1998, 19, 1187.
36. Allinger, N. L. J. Am. Chem. Soc. 1977, 99, 8127.
37. Allinger, N. L.; Imam, M. R.; Frierson, M. R.; Yuh, Y.; Schafer, L. In Mathematics and Computational Concepts in Chemistry; Trinajstic, N., Ed.; E. Horwood, Ltd.: London, 1986; p 8.
38. Crowder, G. A.; Jackson, D. Spectrochim. Acta 1971, 27A, 2505.
39. Crowder, G. A. J. Fluorine Chem. 1973, 3, 125.
40. Branch, G. E. K.; Calvin, M. The Theory of Organic Chemistry; Prentice-Hall: New York, 1941; p 217.
41. Egawa, T.; Yamamoto, S.; Nakata, M.; Kuchitsu, K. J. Mol. Struct. 1987, 156, 213.
42. Beagley, B.; Jones, M. O.; Yavari, P. J. Mol. Struct. 1981, 71, 203.
43. Kakubari, H.; Iijima, T.; Kimura, M. Bull. Chem. Soc. Jpn. 1975, 48, 1984.
44. Haas, B.; Haas, J.; Zeil, W. Z. Naturforschg. 1967, 22a, 1646.
45. Bent, H. Chem. Rev. 1961, 61, 275.
46. (a) King, W. C.; Gordy, W. Phys. Rev. 1954, 93, 407.
47. (b) Lide, D. R., Jr. J. Am. Chem. Soc. 1952, 74, 3548.
48. (c) Kawashima, Y.; Cox, A. P. J. Mol. Struct. 1978, 72, 423.
49. (d) Takami, M. J. Chem. Phys. 1981, 74, 4276.
50. (e) Zeil, W.; Christen, D. J. Phys. Chem. 1980, 84, 1790.
51. (f) Solimene, N.; Dailey, B. P. J. Chem. Phys. 1954, 22, 2042.
52. (g) Butcher, S. S. Cohen, R. A.; Rounds, T. C. J. Chem. Phys. 1971, 54, 4123.
53. (h) Edgell, W. F.; Miller, G. B.; Amy, J. W. J. Am. Chem. Soc. 1957, 79, 2391.
54. (i) Tipton, A. B.; Britt, C. O.; Boggs, J. E. J. Chem. Phys. 1967, 46, 1606.
55. (j) Hayashi, M.; Fujitake, M. J. Mol. Struct. 1986, 146, 9.
56. (k) Griffiths, J. H.; Owen, N. L.; Sheridan, J. J. Chem. Soc., Faraday Trans. 2 1973, 69, 1359.
57. (l) Durig, J. R.; Guirgis, G. A.; Li, Y. S. J. Chem. Phys. 1981, 74, 5946.
58. (m) Andersen, F. A.; Bak, B.; Rastrup-Andersen, J. Acta Chem. Scand. 1953, 7, 643.
59. (n) Pierce, L.; Nelson, R. J. Am. Chem. Soc. 1966, 88, 216.
60. (o) Pierce, L.; Beecher, J. F. J. Am. Chem. Soc. 1966, 88, 5406.
61. (p) Damiani, D.; Ferretti, L. Chem. Phys. Lett. 1974, 24, 357.
62. (a) Pawlowski, F.; Jorgensen, P.; Olsen, J.; Hegelund, F.; Helgaker, T.; Gauss, J.; Bak, K. L.; Stanton, J. F. J. Chem. Phys. 2002, 116, 6482.
63. (b) Allen, W. D.; East, A. L. L.; Csaszar, A. G. In Structures and Conformations of Non-Rigid Molecules; Laane, J., Kakkouri, M., Van der Veken, B., Oberhammer H., Eds.; Kluwer: Dordrecht, The Netherlands, 1993;p 343.
64. Kuchitsu, K. In Molecular Structures and Vibrations; Cyvin, S. J., Ed.; Elsevier: New York, 1972.
65. Hedberg, L.; Mills, I. M. J. Mol. Spectrosc. 1993, 160, 117.
66. Hayashi, M.; Fujtake, M. J. Mol. Struct. 1986, 146, 9.
67. Chu, P.-S.; True, N. S. J. Phys. Chem. 1985, 89, 5613.
68. Pierce, L.; Nelson, R. J. Am. Chem. Soc. 1966, 88, 5406.
69. Wiberg, K. J. Org. Chem. 1999, 64, 6387.
70. Houk, K. N.; Eksterowicz, J. E.; Wu, Y.-D.; Fuglesang, C. D.; Mitchell, D. B. J. Am. Chem. Soc. 1993, 115, 4170.
71. Nygaard, L. Spectrochim. Acta 1966, 22, 1261.
72. Bak, B.; Detoni, S.; Hansen-Nygaard, L.; Nielson, J.; Rastrup-Andersen, J. Spectrochim. Acta 1960, 16, 376.
73. Schwendeman, R. H.; Jacobs, G. D. J. Chem. Phys. 1962, 36, 1245.
74. Kraitchman, J.; Dailey, B. P. J. Chem. Phys. 1955, 23, 184.
75. Herschbach, D. R. J. Chem. Phys. 1956, 25, 358.
76. Lide, D. R., Jr. J. Chem. Phys. 1959, 30, 37.
77. Durig, J. R.; Bucy, W. E.; Carreira, L. A.; Wurrey, C. J. J. Chem. Phys. 1974, 60, 1754.
78. Sage, G.; Klemperer, W. J. Chem. Phys. 1963, 39, 371.
79. Brier, P. N. J. Mol. Struct. 1970, 6, 23.
80. Pace, E. L.; Aston, J. G. J. Am. Chem. Soc. 1948, 70, 566.
81. Mann, D. E.; Plyler, E. K. J. Chem. Phys. 1953, 21, 1116.
82. Eggers, D. F., Jr.; Lord, R. C.; Wickstrom, C. W. J. Mol. Spectrosc. 1976, 59, 63.
83. Wolfe, S. Acc. Chem. Res. 1972, 5, 102.
84. Radom, L.; Lathan, W. A.; Hehre, W. J.; Pople, J. A. J. Am. Chem. Soc. 1973, 95, 693.
85. Durig, J. R.; Liu, J.; Little, T. S.; Kalasinsky, V. F. J. Phys. Chem. 1992, 96, 8224.
86. Wiberg, K. B.; Murcko, M. A.; Laidig, K. E.; MacDougall, P. J. J. Phys. Chem. 1990, 94, 6956.
87. Butcher, S. S.; Cohen, R. A.; Rounds, T. C. J. Chem. Phys. 1971, 54, 4123.
88. Friesen, D.; Hedberg, K. J. Am. Chem. Soc. 1980, 102, 3987.
89. Beagley, B.; Brown, D. E. J. Mol. Struct. 1979, 54, 175.
90. Klaboe, P.; Nielsen, J. R. J. Chem. Phys. 1960, 32, 899.
91. Brown, D. E.; Beagley, B. J. Mol. Struct. 1977, 38, 167.
92. Reeves, R. E. J. Am. Chem. Soc. 1950, 72, 1499.
93. Stoddart, J. F. Stereochemistry of Carbohydrates; Wiley-Interscience: New York, 1971; p 71.
94. McClellan, A. L. Tables of Experimental Dipole Moments; Rahara Enterprise: E. Cerrito, CA, 1989.
95. Fateley, W. G.; Miller, F. A. Spectrochim. Acta 1961, 17, 857.
96. Brown, F.; Clague, A.; Heitkamp, N.; Koster, D.; Danti, A. J. Mol. Spectrosc. 1967, 24, 163.
97. Abraham, R. J.; Kemp, R. H. J. Chem. Soc. B 1971, 1240.
98. Verdlov, L. M. S., Kovner, M. A., Krainov, E. P., Eds. Vibrational Spectra of Polyatomic Molecules; John Wiley and Sons: New York, Toronto, 1974; Moscow, 1970.
99. Smith, D. C.; Saunders, R. A.; Nielsen, J. R.; Ferguson, E. E. J. Chem. Phys. 1952, 20, 847.
100. Durig, J. R.; Craven, S. M.; Hawley, C. W.; Bragin, J. J. Chem. Phys. 1972, 57, 131.
101. Durig, J. R.; Liu, J.; Little, T. S.; Kalasinsky, V. F. J. Phys. Chem. 1992, 96, 8224.
102. Harris, W. C.; Holtzclaw, J. R.; Kalasinsky, V. F. J. Chem. Phys. 1977, 67, 3330.
103. Edgell, W. F.; Riethof, T. R.; Ward, C. J. Mol. Spectrosc. 1963, 11, 92.
104. Danti, A.; Wood, J. L. J. Chem. Phys. 1959, 30, 582.
105. Kalasinsky, V. F.; Anjaria, H. V.; Little, T. S. J. Phys. Chem. 1982, 86, 1351.
106. Klaboe, P.; Nielsen, J. R. J. Chem. Phys. 1960, 32, 899.
107. Nielsen, J. R.; Claassen, H. H.; Moran, N. B. J. Chem. Phys. 1955, 23, 329.
108. Nielsen, J. R.; Liang, C. Y.; Smith, R. M.; Smith, D. C. J. Chem. Phys. 1953, 21, 383.
109. Schachtschneider, J. H.; Snyder, R. G. Spectrochim. Acta 1963, 19, 117.
110. -1 with MM4, and thus, errors of this order are acceptable. Attaching up to two fluorines to a C-C bond generally leads to errors that are smaller than this, and therefore is not of any present concern. The effect becomes important only when three or more fluorines are attached to the same bond, although it is included for all numbers of fluorines with the equation given. In principle, this effect should also apply for any other electronegative or electropositive substituents added to the hydrocarbon framework. However, since fluorine is the most electronegative atom, presumably adding less than three of some other atom would have a smaller effect than in the case of fluorines, and thus can be ignored at the present level of approximation. In particular, the MM4 force field has already been decided upon for carbohydrates-and related compounds, containing C-O bonds. This effect was not included in those structures, but since there are very few carbohydrates that have more than three oxygens attached to the same C-C bond, we do not believe that this constitutes a problem. The program automatically applies this kind of correction to any compound that contains fluorine, and hence, it will apply to compounds that contain both fluorine and oxygen attached to the same bond. This may introduce some inconsistency into the calculations, but we believe that these inconsistencies are negligible for pfactical purposes.
111. Schachtschneider, J. H.; Shell Development Co. Technol. Repts., Nos. 231-264 and 57-65, 1965.
112. Mack, H.-G.; Dakkouri, M.; Oberhammer, H. J. Phys. Chem. 1991, 95, 3136.
113. Albinsson, B.; Michl, J. J. Am. Chem. Soc. 1995, 117, 6378.
114. Smith, G. D.; Jaffe, R. L.; Yoon, D. Y. Macromolecules 1994, 27, 3166.
115. Albinsson, B.; Michl, J. J. Phys. Chem. 1996, 100, 3418.
116. Antic, D.; Michl, J. Personal communications to NLA.
117. Sperati, C. A.; Starkweather, H. W., Jr. Fortschr. Hochpolym.-Forsch. Bd. S 1961, 2, 465.
118. 6, term improves the shape of the actual torsion curve as determined experimentally, for example. In the general case, all of these can be used, according to the general equation above.