Molecular dynamics and FEP Monte Carlo studies of calix[4]arene-derived complexes of Eu3+: The role of the counterions investigated

Journal of Physical Chemistry A

Volumn 101, Issue 15, 1997, Pages 2755-2765

  Van Veggel, Frank C J M ^a  

^a UNIVERSITY OF TWENTE   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0041774309     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp962160w     Document Type: Article

References (83)

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22. 3+ is relatively far away.
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36. See for instance: Shirts, R. B.; Stolworthy, L. D. J. Inclusion Phenom. Mol. Recognit. 1995, 20, 297. Perera, L.; Essmann, U.; Berkowitz, M. L. J. Chem. Phys. 1995, 102, 450. Lau, K. F.; Alper, H. E.; Thacher, T. S.; Stouch, T. R. J. Phys. Chem. 1994, 98, 8785. Saito, M. J. Chem. Phys. 1994, 101, 4055. Roberts, J. E.; Schnitker, J. J. Phys. Chem. 1995, 99, 1322. Brooks, C. L., III; Pettitt, B. M.; Karplus, M. J. Chem. Phys. 1985, 83, 5897. Tasaki, K.; McDonald, S.; Brady, J. W. J. Comput. Chem. 1993, 14, 278. Brooks, C. L., III. J. Chem. Phys. 1987, 86, 5156. Loncharich, R. J.; Brooks, B. R. Proteins: Struct., Funct., Genet. 1989, 6, 32. York, D. M.; Darden, T. A.; Pedersen, L. G. J. Chem. Phys. 1993, 99, 8345. Steinbach, P. J.; Brooks, B. R. J. Comput. Chem. 1994, 15, 667.
37. See for instance: Shirts, R. B.; Stolworthy, L. D. J. Inclusion Phenom. Mol. Recognit. 1995, 20, 297. Perera, L.; Essmann, U.; Berkowitz, M. L. J. Chem. Phys. 1995, 102, 450. Lau, K. F.; Alper, H. E.; Thacher, T. S.; Stouch, T. R. J. Phys. Chem. 1994, 98, 8785. Saito, M. J. Chem. Phys. 1994, 101, 4055. Roberts, J. E.; Schnitker, J. J. Phys. Chem. 1995, 99, 1322. Brooks, C. L., III; Pettitt, B. M.; Karplus, M. J. Chem. Phys. 1985, 83, 5897. Tasaki, K.; McDonald, S.; Brady, J. W. J. Comput. Chem. 1993, 14, 278. Brooks, C. L., III. J. Chem. Phys. 1987, 86, 5156. Loncharich, R. J.; Brooks, B. R. Proteins: Struct., Funct., Genet. 1989, 6, 32. York, D. M.; Darden, T. A.; Pedersen, L. G. J. Chem. Phys. 1993, 99, 8345. Steinbach, P. J.; Brooks, B. R. J. Comput. Chem. 1994, 15, 667.
38. See for instance: Shirts, R. B.; Stolworthy, L. D. J. Inclusion Phenom. Mol. Recognit. 1995, 20, 297. Perera, L.; Essmann, U.; Berkowitz, M. L. J. Chem. Phys. 1995, 102, 450. Lau, K. F.; Alper, H. E.; Thacher, T. S.; Stouch, T. R. J. Phys. Chem. 1994, 98, 8785. Saito, M. J. Chem. Phys. 1994, 101, 4055. Roberts, J. E.; Schnitker, J. J. Phys. Chem. 1995, 99, 1322. Brooks, C. L., III; Pettitt, B. M.; Karplus, M. J. Chem. Phys. 1985, 83, 5897. Tasaki, K.; McDonald, S.; Brady, J. W. J. Comput. Chem. 1993, 14, 278. Brooks, C. L., III. J. Chem. Phys. 1987, 86, 5156. Loncharich, R. J.; Brooks, B. R. Proteins: Struct., Funct., Genet. 1989, 6, 32. York, D. M.; Darden, T. A.; Pedersen, L. G. J. Chem. Phys. 1993, 99, 8345. Steinbach, P. J.; Brooks, B. R. J. Comput. Chem. 1994, 15, 667.
39. See for instance: Shirts, R. B.; Stolworthy, L. D. J. Inclusion Phenom. Mol. Recognit. 1995, 20, 297. Perera, L.; Essmann, U.; Berkowitz, M. L. J. Chem. Phys. 1995, 102, 450. Lau, K. F.; Alper, H. E.; Thacher, T. S.; Stouch, T. R. J. Phys. Chem. 1994, 98, 8785. Saito, M. J. Chem. Phys. 1994, 101, 4055. Roberts, J. E.; Schnitker, J. J. Phys. Chem. 1995, 99, 1322. Brooks, C. L., III; Pettitt, B. M.; Karplus, M. J. Chem. Phys. 1985, 83, 5897. Tasaki, K.; McDonald, S.; Brady, J. W. J. Comput. Chem. 1993, 14, 278. Brooks, C. L., III. J. Chem. Phys. 1987, 86, 5156. Loncharich, R. J.; Brooks, B. R. Proteins: Struct., Funct., Genet. 1989, 6, 32. York, D. M.; Darden, T. A.; Pedersen, L. G. J. Chem. Phys. 1993, 99, 8345. Steinbach, P. J.; Brooks, B. R. J. Comput. Chem. 1994, 15, 667.
40. See for instance: Shirts, R. B.; Stolworthy, L. D. J. Inclusion Phenom. Mol. Recognit. 1995, 20, 297. Perera, L.; Essmann, U.; Berkowitz, M. L. J. Chem. Phys. 1995, 102, 450. Lau, K. F.; Alper, H. E.; Thacher, T. S.; Stouch, T. R. J. Phys. Chem. 1994, 98, 8785. Saito, M. J. Chem. Phys. 1994, 101, 4055. Roberts, J. E.; Schnitker, J. J. Phys. Chem. 1995, 99, 1322. Brooks, C. L., III; Pettitt, B. M.; Karplus, M. J. Chem. Phys. 1985, 83, 5897. Tasaki, K.; McDonald, S.; Brady, J. W. J. Comput. Chem. 1993, 14, 278. Brooks, C. L., III. J. Chem. Phys. 1987, 86, 5156. Loncharich, R. J.; Brooks, B. R. Proteins: Struct., Funct., Genet. 1989, 6, 32. York, D. M.; Darden, T. A.; Pedersen, L. G. J. Chem. Phys. 1993, 99, 8345. Steinbach, P. J.; Brooks, B. R. J. Comput. Chem. 1994, 15, 667.
41. See for instance: Shirts, R. B.; Stolworthy, L. D. J. Inclusion Phenom. Mol. Recognit. 1995, 20, 297. Perera, L.; Essmann, U.; Berkowitz, M. L. J. Chem. Phys. 1995, 102, 450. Lau, K. F.; Alper, H. E.; Thacher, T. S.; Stouch, T. R. J. Phys. Chem. 1994, 98, 8785. Saito, M. J. Chem. Phys. 1994, 101, 4055. Roberts, J. E.; Schnitker, J. J. Phys. Chem. 1995, 99, 1322. Brooks, C. L., III; Pettitt, B. M.; Karplus, M. J. Chem. Phys. 1985, 83, 5897. Tasaki, K.; McDonald, S.; Brady, J. W. J. Comput. Chem. 1993, 14, 278. Brooks, C. L., III. J. Chem. Phys. 1987, 86, 5156. Loncharich, R. J.; Brooks, B. R. Proteins: Struct., Funct., Genet. 1989, 6, 32. York, D. M.; Darden, T. A.; Pedersen, L. G. J. Chem. Phys. 1993, 99, 8345. Steinbach, P. J.; Brooks, B. R. J. Comput. Chem. 1994, 15, 667.
42. See for instance: Shirts, R. B.; Stolworthy, L. D. J. Inclusion Phenom. Mol. Recognit. 1995, 20, 297. Perera, L.; Essmann, U.; Berkowitz, M. L. J. Chem. Phys. 1995, 102, 450. Lau, K. F.; Alper, H. E.; Thacher, T. S.; Stouch, T. R. J. Phys. Chem. 1994, 98, 8785. Saito, M. J. Chem. Phys. 1994, 101, 4055. Roberts, J. E.; Schnitker, J. J. Phys. Chem. 1995, 99, 1322. Brooks, C. L., III; Pettitt, B. M.; Karplus, M. J. Chem. Phys. 1985, 83, 5897. Tasaki, K.; McDonald, S.; Brady, J. W. J. Comput. Chem. 1993, 14, 278. Brooks, C. L., III. J. Chem. Phys. 1987, 86, 5156. Loncharich, R. J.; Brooks, B. R. Proteins: Struct., Funct., Genet. 1989, 6, 32. York, D. M.; Darden, T. A.; Pedersen, L. G. J. Chem. Phys. 1993, 99, 8345. Steinbach, P. J.; Brooks, B. R. J. Comput. Chem. 1994, 15, 667.
43. See for instance: Shirts, R. B.; Stolworthy, L. D. J. Inclusion Phenom. Mol. Recognit. 1995, 20, 297. Perera, L.; Essmann, U.; Berkowitz, M. L. J. Chem. Phys. 1995, 102, 450. Lau, K. F.; Alper, H. E.; Thacher, T. S.; Stouch, T. R. J. Phys. Chem. 1994, 98, 8785. Saito, M. J. Chem. Phys. 1994, 101, 4055. Roberts, J. E.; Schnitker, J. J. Phys. Chem. 1995, 99, 1322. Brooks, C. L., III; Pettitt, B. M.; Karplus, M. J. Chem. Phys. 1985, 83, 5897. Tasaki, K.; McDonald, S.; Brady, J. W. J. Comput. Chem. 1993, 14, 278. Brooks, C. L., III. J. Chem. Phys. 1987, 86, 5156. Loncharich, R. J.; Brooks, B. R. Proteins: Struct., Funct., Genet. 1989, 6, 32. York, D. M.; Darden, T. A.; Pedersen, L. G. J. Chem. Phys. 1993, 99, 8345. Steinbach, P. J.; Brooks, B. R. J. Comput. Chem. 1994, 15, 667.
44. See for instance: Shirts, R. B.; Stolworthy, L. D. J. Inclusion Phenom. Mol. Recognit. 1995, 20, 297. Perera, L.; Essmann, U.; Berkowitz, M. L. J. Chem. Phys. 1995, 102, 450. Lau, K. F.; Alper, H. E.; Thacher, T. S.; Stouch, T. R. J. Phys. Chem. 1994, 98, 8785. Saito, M. J. Chem. Phys. 1994, 101, 4055. Roberts, J. E.; Schnitker, J. J. Phys. Chem. 1995, 99, 1322. Brooks, C. L., III; Pettitt, B. M.; Karplus, M. J. Chem. Phys. 1985, 83, 5897. Tasaki, K.; McDonald, S.; Brady, J. W. J. Comput. Chem. 1993, 14, 278. Brooks, C. L., III. J. Chem. Phys. 1987, 86, 5156. Loncharich, R. J.; Brooks, B. R. Proteins: Struct., Funct., Genet. 1989, 6, 32. York, D. M.; Darden, T. A.; Pedersen, L. G. J. Chem. Phys. 1993, 99, 8345. Steinbach, P. J.; Brooks, B. R. J. Comput. Chem. 1994, 15, 667.
45. See for instance: Shirts, R. B.; Stolworthy, L. D. J. Inclusion Phenom. Mol. Recognit. 1995, 20, 297. Perera, L.; Essmann, U.; Berkowitz, M. L. J. Chem. Phys. 1995, 102, 450. Lau, K. F.; Alper, H. E.; Thacher, T. S.; Stouch, T. R. J. Phys. Chem. 1994, 98, 8785. Saito, M. J. Chem. Phys. 1994, 101, 4055. Roberts, J. E.; Schnitker, J. J. Phys. Chem. 1995, 99, 1322. Brooks, C. L., III; Pettitt, B. M.; Karplus, M. J. Chem. Phys. 1985, 83, 5897. Tasaki, K.; McDonald, S.; Brady, J. W. J. Comput. Chem. 1993, 14, 278. Brooks, C. L., III. J. Chem. Phys. 1987, 86, 5156. Loncharich, R. J.; Brooks, B. R. Proteins: Struct., Funct., Genet. 1989, 6, 32. York, D. M.; Darden, T. A.; Pedersen, L. G. J. Chem. Phys. 1993, 99, 8345. Steinbach, P. J.; Brooks, B. R. J. Comput. Chem. 1994, 15, 667.
46. Quanta was bought from Molecular Simulations Inc., Burlington, MA.
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48. Brooks, B. R.; Bruccoleri, R. E.; Olafsen, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187. Momany, F. A.; Klimkowski, V. J.; Schäfer, L. J. Comput. Chem. 1990, 11, 654. Momany, F. A.; Rone, R.; Kunz, H.; Frey, R. F.; Newton, S. Q.; Schäfer, L. J. Mol. Struct. 1993, 286, 1.
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50. n clusters; see: Howell, J. M.; Sapse, A. M.; Singma, E.; Snijder, G. J. Phys. Chem. 1982, 86, 2345.
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53. Jorgensen, W. L. BOSS version 3.5; Yale University: New Haven, CT, 1994. Jorgensen, W. L. J. Phys. Chem. 1983, 87, 5304. Jorgensen, W. L. Acc. Chem. Res. 1989, 22, 184. Duffy, E. M.; Jorgensen, W. L. J. Am. Chem. Soc. 1994, 116, 6337, Kaminski, G.; Duffy, E. M.; Matsui, T.; Jorgensen, W. L. J. Phys. Chem. 1994, 98, 13077.
54. Jorgensen, W. L. BOSS version 3.5; Yale University: New Haven, CT, 1994. Jorgensen, W. L. J. Phys. Chem. 1983, 87, 5304. Jorgensen, W. L. Acc. Chem. Res. 1989, 22, 184. Duffy, E. M.; Jorgensen, W. L. J. Am. Chem. Soc. 1994, 116, 6337, Kaminski, G.; Duffy, E. M.; Matsui, T.; Jorgensen, W. L. J. Phys. Chem. 1994, 98, 13077.
55. Jorgensen, W. L. BOSS version 3.5; Yale University: New Haven, CT, 1994. Jorgensen, W. L. J. Phys. Chem. 1983, 87, 5304. Jorgensen, W. L. Acc. Chem. Res. 1989, 22, 184. Duffy, E. M.; Jorgensen, W. L. J. Am. Chem. Soc. 1994, 116, 6337, Kaminski, G.; Duffy, E. M.; Matsui, T.; Jorgensen, W. L. J. Phys. Chem. 1994, 98, 13077.
56. Jorgensen, W. L. BOSS version 3.5; Yale University: New Haven, CT, 1994. Jorgensen, W. L. J. Phys. Chem. 1983, 87, 5304. Jorgensen, W. L. Acc. Chem. Res. 1989, 22, 184. Duffy, E. M.; Jorgensen, W. L. J. Am. Chem. Soc. 1994, 116, 6337, Kaminski, G.; Duffy, E. M.; Matsui, T.; Jorgensen, W. L. J. Phys. Chem. 1994, 98, 13077.
57. Jorgensen, W. L. BOSS version 3.5; Yale University: New Haven, CT, 1994. Jorgensen, W. L. J. Phys. Chem. 1983, 87, 5304. Jorgensen, W. L. Acc. Chem. Res. 1989, 22, 184. Duffy, E. M.; Jorgensen, W. L. J. Am. Chem. Soc. 1994, 116, 6337, Kaminski, G.; Duffy, E. M.; Matsui, T.; Jorgensen, W. L. J. Phys. Chem. 1994, 98, 13077.
58. Methods to avoid singularities have been discussed. See for instance: Beutler, T. C.; Mark, A. E.; van Schaik, R. C.; Gerber, P. R.; van Gunsteren, W. F. Chem. Phys. Lett. 1994, 222, 529. Carlson, H. A.; Jorgensen, W. L. Tetrahedron 1995, 51, 449. Sun, Y.; Spellmeyer, D.; Pearlman, D. A.; Kollman, P. J. Am. Chem. Soc. 1992, 114, 6798.
59. Methods to avoid singularities have been discussed. See for instance: Beutler, T. C.; Mark, A. E.; van Schaik, R. C.; Gerber, P. R.; van Gunsteren, W. F. Chem. Phys. Lett. 1994, 222, 529. Carlson, H. A.; Jorgensen, W. L. Tetrahedron 1995, 51, 449. Sun, Y.; Spellmeyer, D.; Pearlman, D. A.; Kollman, P. J. Am. Chem. Soc. 1992, 114, 6798.
60. Methods to avoid singularities have been discussed. See for instance: Beutler, T. C.; Mark, A. E.; van Schaik, R. C.; Gerber, P. R.; van Gunsteren, W. F. Chem. Phys. Lett. 1994, 222, 529. Carlson, H. A.; Jorgensen, W. L. Tetrahedron 1995, 51, 449. Sun, Y.; Spellmeyer, D.; Pearlman, D. A.; Kollman, P. J. Am. Chem. Soc. 1992, 114, 6798.
61. A study on the difference between linear and nonlinear coupling parameters has been published: Cross, A. J. Chem. Phys. Lett. 1986, 128, 198.
62. Arnaud-Neu, F. Chem. Soc. Rev. 1994, 23, 235.
63. Holz, R. C.; Chang, C. A.; Horrocks, W. DeW., Jr. Inorg. Chem. 1991, 30, 3270.
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65. Kowell, Th.; Foglia, F.; Helm, L.; Merbach, A. E.; J. Am. Chem. Soc. 1995, 117, 3790. Kowell, Th.; Foglia, F.; Helm, L.; Merbach, A. E. Chem. Eur. J. 1996, 2, 285.
66. Switch truncations of 10-11 and 12-16 Å both resulted in constantly increasing temperatures. Truncation of 10-11 Å showed only species vibrating around an averaged position; that is, no diffusion of particles was observed.
67. Kirby, A. F.; Foster, D.; Richardson, F. S. Chem. Phys. Lett. 1983, 95, 507.
68. Li, M.; Selvin, P. R. J. Am. Chem. Soc. 1995, 117, 8132. Selvin, P. R.; Jancarik, J.; Li, M.; Hung, L.-W. Inorg. Chem. 1996, 35, 700.
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70. This procedure is similar to that used by among others Miyamoto and Kollman, Åqvist, and Blake and Jorgensen. Miyamoto and P. A. Kollman (J. Am. Chem. Soc. 1992, 114, 3668) have determined the absolute binding free energy of calixspherands by perturbing an alkali metal ion into a dummy atom with no interaction with its surrounding. Similarly, J. Åqvist (J. Phys. Chem. 1990, 94, 8021) has determined, widely used, parameters for the alkali and alkaline earth metal ions by the creation of the charge in a discrete number of steps. J. F. Blake and W. L. Jorgensen (J. Am. Chem. Soc. 1990, 112, 7269) calculated the absolute binding free energy between adenine and a "molecular tweezer".
71. This procedure is similar to that used by among others Miyamoto and Kollman, Åqvist, and Blake and Jorgensen. Miyamoto and P. A. Kollman (J. Am. Chem. Soc. 1992, 114, 3668) have determined the absolute binding free energy of calixspherands by perturbing an alkali metal ion into a dummy atom with no interaction with its surrounding. Similarly, J. Åqvist (J. Phys. Chem. 1990, 94, 8021) has determined, widely used, parameters for the alkali and alkaline earth metal ions by the creation of the charge in a discrete number of steps. J. F. Blake and W. L. Jorgensen (J. Am. Chem. Soc. 1990, 112, 7269) calculated the absolute binding free energy between adenine and a "molecular tweezer".
72. This procedure is similar to that used by among others Miyamoto and Kollman, Åqvist, and Blake and Jorgensen. Miyamoto and P. A. Kollman (J. Am. Chem. Soc. 1992, 114, 3668) have determined the absolute binding free energy of calixspherands by perturbing an alkali metal ion into a dummy atom with no interaction with its surrounding. Similarly, J. Åqvist (J. Phys. Chem. 1990, 94, 8021) has determined, widely used, parameters for the alkali and alkaline earth metal ions by the creation of the charge in a discrete number of steps. J. F. Blake and W. L. Jorgensen (J. Am. Chem. Soc. 1990, 112, 7269) calculated the absolute binding free energy between adenine and a "molecular tweezer".
73. 3+. The fact that occasionally one acetonitrile is bound at a longer distance than the other eight donors is consistent with observations from the MD calculations (see Table 3, entries 10-13). The MC sampling efficiency seems, therefore, adequate. For a comparison between MD and MC see: Mordasini Denti, T. Z.; Beutler, T. C.; van Gunsteren, W. F.; Diederich, F. J. Phys. Chem. 1996, 100, 4256. Jorgensen, W. L.; Tirado-Rives, J. J. Phys. Chem. 1996, 100, 14508.
74. 3+. The fact that occasionally one acetonitrile is bound at a longer distance than the other eight donors is consistent with observations from the MD calculations (see Table 3, entries 10-13). The MC sampling efficiency seems, therefore, adequate. For a comparison between MD and MC see: Mordasini Denti, T. Z.; Beutler, T. C.; van Gunsteren, W. F.; Diederich, F. J. Phys. Chem. 1996, 100, 4256. Jorgensen, W. L.; Tirado-Rives, J. J. Phys. Chem. 1996, 100, 14508.
75. The referee correctly pointed out that the torsions between the two pyridine rings have not been sampled and that they will certainly affect the calculations. They have not been sampled to decrease the already heavy CPU demands. I do not think that including them will change the order of magnitude, and therefore the conclusion that the equilibrium in eq 1 is to the right remains valid.
76. Straatsma, T. P.; Berendsen, H. J. C. J. Chem. Phys. 1988, 89, 5876.
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79. Fréchette, M.; Butler, I. A.; Hynes, R.; Detellier, C. Inorg. Chem. 1992, 31, 1650. Fréchette, M. Can. J. Chem. 1993, 71, 377. Fréchette, M.; Bensimon, C. Inorg. Chem. 1995, 34, 3520.
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82. 3+ and the nitrates of 7.5 and 10 Å, respectively, should give the same equilibrium structure. This should be a matter of time.
83. 3+ are probably the most approximate. Currently, I am deriving parameters for the trivalent lanthanide ions that reproduce accurately the hydration free energy, i.e. within a standard deviation of 1%.