Advertisement

Free Energy Barrier for Molecular Motions in Bistable [2]Rotaxane Molecular Electronic Devices

  • Hyungjun Kim
Chapter
Part of the Springer Theses book series (Springer Theses)

Abstract

Donor-acceptor binding of the π-electron-poor cyclophane cyclobis (paraquat-p-phenylene) (CBPQT4+) with the π-electron-rich tetrathiafulvalene (TTF) and 1,5-dioxynaphthalene (DNP) stations provides the basis for electrochemically switchable, bistable [2]rotaxanes, which have been incorporated and operated within solid state devices to form ultradense memory circuits [1, 2] and nanoelectromechanical systems. The rate of CBPQT4+ shuttling at each oxidation state of the [2]rotaxane dictates critical write-and-retention time parameters within the devices, which can be tuned through chemical synthesis. To validate how well computational chemistry methods can estimate these rates for use in designing new devices, we used molecular dynamics simulations to calculate the free energy barrier for the shuttling of the CBPQT4+ ring between the TTF and the DNP. The approach used here was to calculate the potential of mean force along the switching pathway, from which we calculated free energy barriers. These calculations find a turn-on time after the rotaxane is doubly oxidized of \(\sim\!\!10^{-7}\) s (suggesting that the much longer experimental turn-on time is determined by the time scale of oxidization). The return barrier from the DNP to the TTF leads to a predicted lifetime of 2.1 s, which is compatible with experiments.

Keywords

Neutral State Coulombic Energy Free Energy Barrier Free Energy Profile Charge Scheme 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgments

The computational work was initiated with support by the National Science Foundation (NIRT, W.A.G.). The collaboration was supported by the Microelectronics Advanced Research Corporation (MARCO; W.A.G. and J.F.S.) and its Focus Centers on Functional Engineered NanoArchitectonics (FENA) and Materials Structures and Devices, the Molectronics Program of the Defense Advanced Research Projects Agency (DARPA; J.F.S. and J.R.H.), the Center for Nanoscale Innovation for Defense (CNID; J.F.S.), and the MARCO Materials Structures and Devices Focus Center (J.R.H.). In addition, the facilities of the MSC (W.A.G.) were supported by ONR-DURIP and ARO-DURIP.

Bibliography

  1. 1.
    Luo, Y.; Collier, C. P.; Jeppesen, J. O.; Nielsen, K. A.; Delonno, E.; Ho, G.; Perkins, J.; Tseng, H. R.; Yamamoto, T.; Stoddart, J. F.; Heath, J. R. ChemPhysChem 2002, 3, 519–525.CrossRefGoogle Scholar
  2. 2.
    Green, J. E.; Choi, J. W.; Boukai, A.; Bunimovich, Y.; Johnston-Halperin, E.; DeIonno, E.; Luo, Y.; Sheriff, B. A.; Xu, K.; Shin, Y. S.; Tseng, H.-R.; Stoddart, J. F.; Heath, J. R. Nature 2007, 445, 414–417.CrossRefGoogle Scholar
  3. 3.
    Anelli, P. L.; Spencer, N.; Stoddart, J. F. J. Am. Chem. Soc. 1991, 113, 5131–5133.CrossRefGoogle Scholar
  4. 4.
    Bissell, R. A.; Cordova, E.; Kaifer, A. E.; Stoddart, J. F. Nature 1994, 369, 133–137.CrossRefGoogle Scholar
  5. 5.
    Asakawa, M.; Ashton, P. R.; Balzani, V.; Credi, A.; Hamers, C.; Mattersteig, G.; Montalti, M.; Shipway, A. N.; Spencer, N.; Stoddart, J. F.; Tolley, M. S.; Venturi, M.; White, A. J. P.; Williams, D. J. Angew. Chem. Int. Ed. 1998, 37, 333–337.CrossRefGoogle Scholar
  6. 6.
    Balzani, V.; Credi, A.; Mattersteig, G.; Matthews, O. A.; Raymo, F. M.; Stoddart, J. F.; Venturi, M.; White, A. J. P.; Williams, D. J. J. Org. Chem. 2000, 65, 1924–1936.CrossRefGoogle Scholar
  7. 7.
    Collier, C. P.; Mattersteig, G.; Wong, E. W.; Luo, Y.; Beverly, K.; Sampaio, J.; Raymo, F. M.; Stoddart, J. F.; Heath, J. R. Science 2000, 289, 1172–1175.CrossRefGoogle Scholar
  8. 8.
    Barboiu, M.; Lehn, J.-M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5201–5206.CrossRefGoogle Scholar
  9. 9.
    Hogg, L.; Leigh, D. A.; Lusby, P. J.; Morelli, A.; Parsons, S.; Wong, J. K. Y. Angew. Chem., Int. Ed. 2004, 43, 1218–1221.Google Scholar
  10. 10.
    Zheng, X.; Mulcahy, M. E.; Horinek, D.; Galeotti, F.; Magnera, T. F.; Michl, J. J. Am. Chem. Soc. 2004, 126, 4540–4542.CrossRefGoogle Scholar
  11. 11.
    Hawthorne, M. F.; Zink, J. I.; Skelton, J. M.; Bayer, M. J.; Liu, C.; Livshits, E.; Baer, R.; Neuhauser, D. Science 2004, 303, 1849–1851.CrossRefGoogle Scholar
  12. 12.
    de Jong, J. J. D.; Lucas, L. N.; Kellogg, R. M.; van Esch, J. H.; Reringa, B. L. Science 2004, 304, 278–281.CrossRefGoogle Scholar
  13. 13.
    Turberfield, A. J.; Mitchell, J. C.; Yurke, B.; Mills, A. P.; Blakey, M. I.; Simmel, F. C. Phys. Rev. Lett. 2003, 90, art. no.118102.CrossRefGoogle Scholar
  14. 14.
    Liu, H. Q.; Schmidt, J. J.; Bachand, G. D.; Rizk, S. S.; Looger, L. L.; Hellinga, H. W.; Montemagno, C. D. Nat. Mater. 2002, 1, 173–177.CrossRefGoogle Scholar
  15. 15.
    Choi, J. W.; Flood, A.; Steuerman, D. W.; Nygaard, S.; Braunschweig, A.; Moonen, N.; Laursen, B.; Luo, Y.; DeIonno, E.; Peters, A. J.; Jeppesen, J. O.; Stoddart, J. F.; Heath, J. R. Chem. Eur. J. 2006, 12, 261–279.CrossRefGoogle Scholar
  16. 16.
    Collier, C. P.; Jeppesen, J. O.; Luo, Y.; Perkins, J.; Wong, E. W.; Heath, J. R.; Stoddart, J. F. J. Am. Chem. Soc. 2001, 123, 12632–12641.CrossRefGoogle Scholar
  17. 17.
    Diehl, M. R.; Steuerman, D. W.; Tseng, H. R.; Vignon, S. A.; Star, A.; Celestre, P. C.; Stoddart, J. F.; Heath, J. R. ChemPhysChem 2003, 4, 1335–1339.CrossRefGoogle Scholar
  18. 18.
    Credi, A.; Balzani, V.; Langford, S. J.; Stoddart, J. F. J. Am. Chem. Soc. 1997, 119, 2679–2681.CrossRefGoogle Scholar
  19. 19.
    Collier, C. P.; Wong, E. W.; Belohradsky, M.; Raymo, F. M.; Stoddart, J. F.; Kuekes, P. J.; Williams, R. S.; Heath, J. R. Science 1999, 285, 391–394.CrossRefGoogle Scholar
  20. 20.
    Elizarov, A. M.; Chiu, S. H.; Stoddart, J. F. J. Org. Chem. 2002, 67, 9175–9181.CrossRefGoogle Scholar
  21. 21.
    Carroll, R. L.; Gorman, C. B. Angew. Chem. Int. Ed. 2002, 41, 4379–4400.CrossRefGoogle Scholar
  22. 22.
    Yu, H. B.; Luo, Y.; Beverly, K.; Stoddart, J. F.; Tseng, H. R.; Heath, J. R. Angew. Chem. Int. Ed. 2003, 42, 5706–5711.CrossRefGoogle Scholar
  23. 23.
    Heath, J. R.; Ratner, M. A. Phys. Today 2003, 56, 43–49.CrossRefGoogle Scholar
  24. 24.
    Balzani, V.; Gomez-Lopez, M.; Stoddart, J. F. Acc. Chem. Res. 1998, 31, 405–414.CrossRefGoogle Scholar
  25. 25.
    Balzani, V.; Credi, A.; Raymo, F. M.; Stoddart, J. F. Angew. Chem. Int. Ed. 2000, 39, 3349–3391.Google Scholar
  26. 26.
    Chia, S. Y.; Cao, J. G.; Stoddart, J. F.; Zink, J. I. Angew. Chem. Int. Ed. 2001, 40, 2447–2451.CrossRefGoogle Scholar
  27. 27.
    Belohradsky, M.; Elizarov, A. M.; Stoddart, J. F. Collect. Czech. Chem. Commun. 2002, 67, 1719–1728.CrossRefGoogle Scholar
  28. 28.
    Hernandez, R.; Tseng, H. R.; Wong, J. W.; Stoddart, J. F.; Zink, J. I. J. Am. Chem. Soc. 2004, 126, 3370–3371.CrossRefGoogle Scholar
  29. 29.
    Badjic, J. D.; Balzani, V.; Credi, A.; Silvi, S.; Stoddart, J. F. Science 2004, 303, 1845–1849.CrossRefGoogle Scholar
  30. 30.
    Tseng, H. R.; Vignon, S. A.; Stoddart, J. F. Angew. Chem., Int. Ed. 2003, 42, 1491–1495.CrossRefGoogle Scholar
  31. 31.
    Jeppesen, J. O.; Perkins, J.; Becher, J.; Stoddart, J. F. Angew. Chem. Int. Ed. 2001, 40, 1216–1221.CrossRefGoogle Scholar
  32. 32.
    Jeppesen, J. O.; Nielsen, K. A.; Perkins, J.; Vignon, S. A.; Di Fabio, A.; Ballardini, R.; Gandolfi, M. T.; Venturi, M.; Balzani, V.; Becher, J.; Stoddart, J. F. Chem. Eur. J. 2003, 9, 2982–3007.CrossRefGoogle Scholar
  33. 33.
    Yamamoto, T.; Tseng, H. R.; Stoddart, J. F.; Balzani, V.; Credi, A.; Marchioni, F.; Venturi, M. Collect. Czech. Chem. Commun. 2003, 68, 1488–1514.CrossRefGoogle Scholar
  34. 34.
    Tseng, H. R.; Vignon, S. A.; Celestre, P. C.; Perkins, J.; Jeppesen, J. O.; Di Fabio, A.; Ballardini, R.; Gandolfi, M. T.; Venturi, M.; Balzani, V.; Stoddart, J. F. Chem. Eur. J. 2004, 10, 155–172.CrossRefGoogle Scholar
  35. 35.
    Kang, S. S.; Vignon, S. A.; Tseng, H. R.; Stoddart, J. F. Chem. Eur. J. 2004, 10, 2555–2564.CrossRefGoogle Scholar
  36. 36.
    Livoreil, A.; Dietrichbuchecker, C. O.; Sauvage, J. P. J. Am. Chem. Soc. 1994, 116, 9399–9400.CrossRefGoogle Scholar
  37. 37.
    Flood, A. H.; Peters, A. J.; Vignon, S. A.; Steuerman, D. W.; Tseng, H.-R.; Kang, S.; Heath, J. R.; Stoddart, J. F. Chem. Eur. J. 2004, 24, 6558–6561.CrossRefGoogle Scholar
  38. 38.
    Steuerman, D. W.; Tseng, H.-R.; Peters, A. J.; Flood, A. H.; Jeppesen, J. O.; Nielsen, K. A.; Stoddart, J. F.; Heath, J. R. Angew. Chem. Int. Ed. 2004, 43, 6486–6491.CrossRefGoogle Scholar
  39. 39.
    Lee, I. C.; Frank, C. W.; Yamamoto, T.; Tseng, H.-R.; Flood, A. H.; Stoddart, J. F.; Jeppesen, J. O. Langmuir 2004, 20, 5809–5828.CrossRefGoogle Scholar
  40. 40.
    Tseng, H. R.; Wu, D. M.; Fang, N. X. L.; Zhang, X.; Stoddart, J. F. ChemPhysChem 2004, 5, 111–116.CrossRefGoogle Scholar
  41. 41.
    Raehm, L.; Kern, J. M.; Sauvage, J. P.; Hamann, C.; Palacin, S.; Bourgoin, J. P. Chem. Eur. J. 2002, 8, 2153–2162.CrossRefGoogle Scholar
  42. 42.
    Jang, Y. H.; Kim, Y. H.; Jang, S. S.; Hwang, S. G.; Goddard, W. A., III Abstr. Pap., Am. Chem. Soc. 2004, 227, U850–U850.Google Scholar
  43. 43.
    Jang, S. S.; Jang, Y. H.; Kim, Y.-H.; Goddard, W. A., III; Flood, A. H.; Laursen, B. W.; Tseng, H.-R.; Stoddart, J. F.; Jeppesen, J. O.; Choi, J. W.; Steuerman, D. W.; DeIonno, E.; Heath, J. R. J. Am. Chem. Soc. 2005, 127, 1563–1575.CrossRefGoogle Scholar
  44. 44.
    Jang, S. S.; Jang, Y. H.; Kim, Y. H.; Goddard, W. A., III; Choi, J. W.; Heath, J. R.; Laursen, B. W.; Flood, A. H.; Stoddart, J. F.; Norgaard, K.; Bjornholm, T. J. Am. Chem. Soc. 2005, 127, 14804–14816.CrossRefGoogle Scholar
  45. 45.
    Jang, Y. H.; Jang, S. S.; Goddard, W. A., III J. Am. Chem. Soc. 2005, 127, 4959–4964.CrossRefGoogle Scholar
  46. 46.
    Jang, Y. H.; Goddard, W. A., III J. Phys. Chem. B 2006, 110, 7660–7665.CrossRefGoogle Scholar
  47. 47.
    Kim, Y.-H.; Goddard, W. A., III J. Phys. Chem. C 2007, 111, 4831–4837.CrossRefGoogle Scholar
  48. 48.
    Jeppesen, J. O.; Nygaard, S.; Vignon, S. A.; Stoddart, J. F. Eur. J. Org. Chem. 2004, 196, 220.Google Scholar
  49. 49.
    Dichtel, W. R.; Heath, J. R.; Stoddart, J. F. Philos. Trans. R. Soc. A, Math. Phys. Eng. Sci. 2007, 365, 1607–1625.CrossRefGoogle Scholar
  50. 50.
    Carter, E. A.; Ciccotti, G.; Hynes, J. T.; Kapral, R. Chem. Phys. Lett. 1989, 156, 472–477.CrossRefGoogle Scholar
  51. 51.
    Sprik, M.; Ciccotti, G. J. Chem. Phys. 1998, 109, 7737–7744.CrossRefGoogle Scholar
  52. 52.
    Trzesniak, D.; Kunz, A. P. E.; van Gunsteren, W. F. ChemPhysChem 2007, 8, 162–169.CrossRefGoogle Scholar
  53. 53.
    Jaguar, V. 5.0 ed.; Schrödinger Inc.: Portland, 2003.Google Scholar
  54. 54.
    Evans, D. J.; Morriss, G. P. Statistical Mechanics of Nonequilibrium Liquids; Academic Press: London, 1990.Google Scholar
  55. 55.
    Fixman, M. Proc. Natl. Acad. Sci. U.S.A. 1974, 71, 3050–3053.CrossRefGoogle Scholar
  56. 56.
    Mayo, S. L.; Olafson, B. D.; Goddard, W. A., III J. Phys. Chem. 1990, 94, 8897–8909.CrossRefGoogle Scholar
  57. 57.
    Jang, S. S.; Molinero, V.; Cagin, T.; Goddard, W. A., III J. Phys. Chem. B 2004, 108, 3149–3157.CrossRefGoogle Scholar
  58. 58.
    Jang, S. S.; Lin, S.-T.; Cagin, T.; Molinero, V.; Goddard, W. A., III J. Phys. Chem. B 2005, 109, 10154–10167.CrossRefGoogle Scholar
  59. 59.
    Jang, S. S.; Goddard, W. A. J. Phys. Chem. C 2007, 111, 2759–2769.CrossRefGoogle Scholar
  60. 60.
    Jang, S. S.; Lin, S.-T.; Maiti, P. K.; Blanco, M.; Goddard, W. A., III; Shuler, P.; Tang, Y. J. Phys. Chem. B 2004, 108, 12130–12140.CrossRefGoogle Scholar
  61. 61.
    Jang, S. S.; Goddard, W. A. J. Phys. Chem. B 2006, 110, 7992–8001.CrossRefGoogle Scholar
  62. 62.
    Plimpton, S. J. J. Comput. Phys. 1995, 117, 1–19.CrossRefGoogle Scholar
  63. 63.
    Plimpton, S. J.; Pollock, R.; Stevens, M. The Eighth SIAM Conference on Parallel Processing for Scientific Computing Minneapolis; 1997.Google Scholar
  64. 64.
    Swope, W. C.; Andersen, H. C.; Berens, P. H.; Wilson, K. R. J. Chem. Phys. 1982, 76, 637–649.CrossRefGoogle Scholar
  65. 65.
    Castro, R.; Nixon, K. R.; Evanseck, J. D.; Kaifer, A. E. J. Org. Chem. 1996, 61, 7298–7303.CrossRefGoogle Scholar
  66. 66.
    Ashton, P. R.; Balzani, V.; Becher, J.; Credi, A.; Fyfe, M. C. T.; Mattersteig, G.; Menzer, S.; Nielsen, M. B.; Raymo, F. M.; Stoddart, J. F.; Venturi, M.; Williams, D. J. J. Am. Chem. Soc. 1999, 121, 3951–3957.CrossRefGoogle Scholar
  67. 67.
    Bryce, M. R.; Cooke, G.; Duclairoir, F. M. A.; Rotello, V. M. Tetrahedron Lett. 2001, 42, 1143–1145.CrossRefGoogle Scholar
  68. 68.
    Nielsen, M. B.; Jeppesen, J. O.; Lau, J.; Lomholt, C.; Damgaard, D.; Jacobsen, J. P.; Becher, J.; Stoddart, J. F. J. Org. Chem. 2001, 66, 3559–3563.CrossRefGoogle Scholar
  69. 69.
    Leigh, D. A.; Murphy, A.; Smart, J. P.; Deleuze, M. S.; Zerbetto, F. J. Am. Chem. Soc. 1998, 120, 6458–6467.CrossRefGoogle Scholar
  70. 70.
    Leigh, D. A.; Troisi, A.; Zerbetto, F. Chem. Eur. J. 2001, 7, 1450–1454.CrossRefGoogle Scholar
  71. 71.
    Deleuze, M. S.; Leigh, D. A.; Zerbetto, F. J. Am. Chem. Soc. 1999, 121, 2364–2379.CrossRefGoogle Scholar
  72. 72.
    Brough, B.; Northrop, B. H.; Schmidt, J. J.; Tseng, H. R.; Houk, K. N.; Stoddart, J. F.; Ho, C. M. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 8583–8588.CrossRefGoogle Scholar
  73. 73.
    Lin, S. T.; Blanco, M.; Goddard, W. A. J. Chem. Phys. 2003, 119, 11792–11805.CrossRefGoogle Scholar
  74. 74.
    Lin, S. T.; Jang, S. S.; Cagin, T.; Goddard, W. A. J. Phys. Chem. B 2004, 108, 10041–10052.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Hyungjun Kim
    • 1
    • 2
  1. 1.Center for Materials Simulations & DesignKorea Advanced Institute of Science and TechnologyDaejeonRepublic of Korea
  2. 2.Materials and Process Simulation CenterCalifornia Institute of TechnologyPasadenaUSA

Personalised recommendations