Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
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Calculation of the Solvation Free Energy of the Proton in Methanol

  • Hwang, Sun-Gu (School of Free Major, Miryang National University) ;
  • Chung, Doo-Soo (School of Chemistry, NS 60, Seoul National University)
  • Published : 2005.04.20
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Abstract

The solvation free energy of proton in methanol was calculated by B3LYP flavor of density functional calculations in combination with the Poisson-Boltzmann continuum solvation model. In order to check the adequacy of the computation level, the free energies of clustering in the gas phase were compared with the experimental data. The solvents were taken into account in a hybrid manner, i.e. one to five molecules of methanol were explicitly considered while other solvent molecules were represented with an implicit solvation model.

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References

  1. Chen, J. L.; Noodleman, L.; Case, D. A.; Bashford, D. J. Phys. Chem. 1994, 98, 11059 https://doi.org/10.1021/j100094a013
  2. Li, J.; Fisher, C. L.; Chen, J. L.; Bashford, D.; Noodleman, L. Inorg. Chem. 1996, 35, 4694 https://doi.org/10.1021/ic951428f
  3. Kallies, B.; Mitzner, R. J. Phys. Chem. B 1997, 101, 2959 https://doi.org/10.1021/jp962708z
  4. Richardson, W. H.; Peng, C.; Bashford, D.; Noodleman, L.; Case, D. A. Int. J. Quantum Chem. 1997, 61, 207 https://doi.org/10.1002/(SICI)1097-461X(1997)61:2<207::AID-QUA3>3.0.CO;2-#
  5. Topol, I. A.; Tawa, G. J.; Burt, S. K.; Rashin, A. A. J. Phys. Chem. A 1997, 101, 10075 https://doi.org/10.1021/jp9723168
  6. Perakyla, M. J. Am. Chem. Soc. 1998, 120, 12895 https://doi.org/10.1021/ja981405a
  7. Schuurmann, G.; Cossi, M.; Barone, V.; Tomasi, J. J. Phys. Chem. A 1998, 102, 6706 https://doi.org/10.1021/jp981922f
  8. Shapley, W. A.; Bacskay, G. B.; Warr, G. G. J. Phys. Chem. B 1998, 102, 1938 https://doi.org/10.1021/jp9734179
  9. da Silva, C. O.; da Silva, E. C.; Nascimento, M. A. C. J. Phys. Chem. A 1999, 103, 11194 https://doi.org/10.1021/jp9836473
  10. Lyne, P. D.; Karplus, M. J. Am. Chem. Soc. 2000, 122, 166 https://doi.org/10.1021/ja991820i
  11. Silva, C. O.; da Silva, E. C.; Nascimento, M. A. C. J. Phys. Chem. A 2000, 104, 2402 https://doi.org/10.1021/jp992103d
  12. Topol, I. A.; Burt, S. K.; Rashin, A. A.; Erickson, J. W. J. Phys. Chem. A 2000, 104, 866 https://doi.org/10.1021/jp992691v
  13. Topol, I. A.; Tawa, G. J.; Caldwell, R. A.; Eissenstat, M. A.; Burt, S. K. J. Phys. Chem. A 2000, 104, 9619 https://doi.org/10.1021/jp001938h
  14. Wiberg, K. B.; Clifford, S.; Jorgensen, W. L.; Frisch, M. J. J. Phys. Chem. A 2000, 104, 7625 https://doi.org/10.1021/jp000944a
  15. Jang, Y. H.; Sowers, L. C.; Cagin, T.; Goddard III, W. A. J. Phys. Chem. A 2001, 105, 274 https://doi.org/10.1021/jp994432b
  16. Kubicki, J. D. J. Phys. Chem. A 2001, 105, 8756 https://doi.org/10.1021/jp011793u
  17. Liptak, M. D.; Shields, G. C. J. Am. Chem. Soc. 2001, 123, 7314 https://doi.org/10.1021/ja010534f
  18. Liptak, M. D.; Shields, G. C. Int. J. Quantum Chem. 2001, 85, 727 https://doi.org/10.1002/qua.1703
  19. Toth, A. M.; Liptak, M. D.; Phillips, D. L.; Shields, G. C. J. Chem. Phys. 2001, 114, 4595 https://doi.org/10.1063/1.1337862
  20. Klicic, J. J.; Friesner, R. A.; Liu, S.-Y.; Guida, W. C. J. Phys. Chem. A 2002, 106, 1327 https://doi.org/10.1021/jp012533f
  21. Liptak, M. D.; Gross, K. C.; Seybold, P. G.; Feldgus, S.; Shields, G. C. J. Am. Chem. Soc. 2002, 124, 6421 https://doi.org/10.1021/ja012474j
  22. Lopez, X.; Schaefer, M.; Dejaegere, A.; Karplus, M. J. Am. Chem. Soc. 2002, 124, 5010 https://doi.org/10.1021/ja011373i
  23. Jang, Y. H.; Goddard III, W. A.; Noyes, K. T.; Sowers, L. C.; Hwang, S.; Chung, D. S. Chem. Res. Toxicol. 2002, 15, 1023 https://doi.org/10.1021/tx010146r
  24. Hwang, S.; Jang, Y. H.; Chung, D. S. Bull. Korean Chem. Soc. 2005, 26, 585 https://doi.org/10.5012/bkcs.2005.26.4.585
  25. Lim, C.; Bashford, D.; Karplus, M. J. Phys. Chem. 1991, 95, 5610 https://doi.org/10.1021/j100167a045
  26. Tissandier, M. D.; Cowen, K. A.; Feng, W. Y.; Gundlach, E.; Cohen, M. H.; Earhart, A. D.; Coe, J. V.; Tuttle, T. R. Jr. J. Phys. Chem. A 1998, 102, 7787 https://doi.org/10.1021/jp982638r
  27. Tawa, G. J.; Topol, I. A.; Burt, S. K.; Caldwell, R. A.; Rashin, A. A. J. Chem. Phys. 1998, 109, 4852 https://doi.org/10.1063/1.477096
  28. Mejias, J. A.; Lago, S. J. Chem. Phys. 2000, 113, 7306 https://doi.org/10.1063/1.1313793
  29. Zhan, C.-G.; Dixon, D. A. J. Phys. Chem. A 2001, 105, 11534 https://doi.org/10.1021/jp012536s
  30. Chang, H.-C.; Jiang, J.-C.; Lin, S. H.; Lee, Y. T.; Chang, H.-C. J. Phys. Chem. A 1999, 103, 2941
  31. Chang, H. C.; Jiang, J. C.; Chang, H. C.; Wang, L. R.; Lee, Y. T. Isr. J. Chem. 1999, 39, 231 https://doi.org/10.1002/ijch.199900030
  32. Hwang, S.; Chung, D. S. Chem. Lett. 2002, 1220
  33. Hagemeister, F. C.; Gruenloh, C. J.; Zwier, T. S. J. Phys. Chem. A 1998, 102, 82 https://doi.org/10.1021/jp963763a
  34. Mo, O.; Yanez, M.; Elguero, J. J. Chem. Phys. 1997, 107, 3592 https://doi.org/10.1063/1.474486
  35. Provencal, R. A.; Paul, J. B.; Roth, K.; Chapo, C.; Casaes, R. N.; Saykally, R. J.; Tschumper, G. S.; Schaefer III, H. F. J. Chem. Phys. 1999, 110, 4258 https://doi.org/10.1063/1.478309
  36. Yamaguchi, Y.; Yasutake, N.; Nagaoka, M. J. Phys. Chem. A 2002, 106, 404 https://doi.org/10.1021/jp012831c
  37. Jaguar v4.1; Schrodinger Inc.: Portland, Oregon, 2000
  38. Slater, J. C. Self-Consistent Field for Molecules and Solids; McGraw-Hill: New York, 1974
  39. Vosko, S. H.; Wilk, L.; Nusair, M. Can. J. Phys. 1980, 58, 1200 https://doi.org/10.1139/p80-159
  40. Becke, A. D. Phys. Rev. A 1988, 38, 3098 https://doi.org/10.1103/PhysRevA.38.3098
  41. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785 https://doi.org/10.1103/PhysRevB.37.785
  42. Marten, B.; Kim, K.; Cortis, C.; Friesner, R. A.; Murphy, R. B.; Ringnalda, M. N.; Sitkoff, D.; Honig, B. J. Phys. Chem. 1996, 100, 11775 https://doi.org/10.1021/jp953087x
  43. Morrone, J. A.; Tuckerman, M. E. J. Chem. Phys. 2002, 117, 4403 https://doi.org/10.1063/1.1496457
  44. Grimsrud, E. P.; Kebarle, P. J. Am. Chem. Soc. 1973, 95, 7939 https://doi.org/10.1021/ja00805a002
  45. Scott, A. P.; Radom, L. J. Phys. Chem. 1996, 100, 16502 https://doi.org/10.1021/jp960976r

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