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

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Multiscale and Multiphysics Computational Frameworks for Nano- and Bio-Systems

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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.

Reprinted with permission from Kim, H; Goddard, W. A.; Jang S. S.; Dichtel, W. R.; Heath, J. R.; Stoddart J. F. J. Phys. Chem. A 2009, 113 (10), 2136-2143. Copyright 2009 American Chemical Society.

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Bibliography

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  3. Anelli, P. L.; Spencer, N.; Stoddart, J. F. J. Am. Chem. Soc. 1991, 113, 5131–5133.

    Article  CAS  Google Scholar 

  4. Bissell, R. A.; Cordova, E.; Kaifer, A. E.; Stoddart, J. F. Nature 1994, 369, 133–137.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  8. Barboiu, M.; Lehn, J.-M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 5201–5206.

    Article  CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  10. Zheng, X.; Mulcahy, M. E.; Horinek, D.; Galeotti, F.; Magnera, T. F.; Michl, J. J. Am. Chem. Soc. 2004, 126, 4540–4542.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  12. de Jong, J. J. D.; Lucas, L. N.; Kellogg, R. M.; van Esch, J. H.; Reringa, B. L. Science 2004, 304, 278–281.

    Article  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  18. Credi, A.; Balzani, V.; Langford, S. J.; Stoddart, J. F. J. Am. Chem. Soc. 1997, 119, 2679–2681.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  20. Elizarov, A. M.; Chiu, S. H.; Stoddart, J. F. J. Org. Chem. 2002, 67, 9175–9181.

    Article  CAS  Google Scholar 

  21. Carroll, R. L.; Gorman, C. B. Angew. Chem. Int. Ed. 2002, 41, 4379–4400.

    Article  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  23. Heath, J. R.; Ratner, M. A. Phys. Today 2003, 56, 43–49.

    Article  CAS  Google Scholar 

  24. Balzani, V.; Gomez-Lopez, M.; Stoddart, J. F. Acc. Chem. Res. 1998, 31, 405–414.

    Article  CAS  Google Scholar 

  25. Balzani, V.; Credi, A.; Raymo, F. M.; Stoddart, J. F. Angew. Chem. Int. Ed. 2000, 39, 3349–3391.

    Google Scholar 

  26. Chia, S. Y.; Cao, J. G.; Stoddart, J. F.; Zink, J. I. Angew. Chem. Int. Ed. 2001, 40, 2447–2451.

    Article  CAS  Google Scholar 

  27. Belohradsky, M.; Elizarov, A. M.; Stoddart, J. F. Collect. Czech. Chem. Commun. 2002, 67, 1719–1728.

    Article  CAS  Google Scholar 

  28. Hernandez, R.; Tseng, H. R.; Wong, J. W.; Stoddart, J. F.; Zink, J. I. J. Am. Chem. Soc. 2004, 126, 3370–3371.

    Article  CAS  Google Scholar 

  29. Badjic, J. D.; Balzani, V.; Credi, A.; Silvi, S.; Stoddart, J. F. Science 2004, 303, 1845–1849.

    Article  CAS  Google Scholar 

  30. Tseng, H. R.; Vignon, S. A.; Stoddart, J. F. Angew. Chem., Int. Ed. 2003, 42, 1491–1495.

    Article  CAS  Google Scholar 

  31. Jeppesen, J. O.; Perkins, J.; Becher, J.; Stoddart, J. F. Angew. Chem. Int. Ed. 2001, 40, 1216–1221.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  35. Kang, S. S.; Vignon, S. A.; Tseng, H. R.; Stoddart, J. F. Chem. Eur. J. 2004, 10, 2555–2564.

    Article  CAS  Google Scholar 

  36. Livoreil, A.; Dietrichbuchecker, C. O.; Sauvage, J. P. J. Am. Chem. Soc. 1994, 116, 9399–9400.

    Article  CAS  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  40. Tseng, H. R.; Wu, D. M.; Fang, N. X. L.; Zhang, X.; Stoddart, J. F. ChemPhysChem 2004, 5, 111–116.

    Article  CAS  Google Scholar 

  41. Raehm, L.; Kern, J. M.; Sauvage, J. P.; Hamann, C.; Palacin, S.; Bourgoin, J. P. Chem. Eur. J. 2002, 8, 2153–2162.

    Article  CAS  Google Scholar 

  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. 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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  45. Jang, Y. H.; Jang, S. S.; Goddard, W. A., III J. Am. Chem. Soc. 2005, 127, 4959–4964.

    Article  CAS  Google Scholar 

  46. Jang, Y. H.; Goddard, W. A., III J. Phys. Chem. B 2006, 110, 7660–7665.

    Article  CAS  Google Scholar 

  47. Kim, Y.-H.; Goddard, W. A., III J. Phys. Chem. C 2007, 111, 4831–4837.

    Article  CAS  Google Scholar 

  48. Jeppesen, J. O.; Nygaard, S.; Vignon, S. A.; Stoddart, J. F. Eur. J. Org. Chem. 2004, 196, 220.

    Google Scholar 

  49. Dichtel, W. R.; Heath, J. R.; Stoddart, J. F. Philos. Trans. R. Soc. A, Math. Phys. Eng. Sci. 2007, 365, 1607–1625.

    Article  CAS  Google Scholar 

  50. Carter, E. A.; Ciccotti, G.; Hynes, J. T.; Kapral, R. Chem. Phys. Lett. 1989, 156, 472–477.

    Article  CAS  Google Scholar 

  51. Sprik, M.; Ciccotti, G. J. Chem. Phys. 1998, 109, 7737–7744.

    Article  CAS  Google Scholar 

  52. Trzesniak, D.; Kunz, A. P. E.; van Gunsteren, W. F. ChemPhysChem 2007, 8, 162–169.

    Article  CAS  Google Scholar 

  53. Jaguar, V. 5.0 ed.; Schrödinger Inc.: Portland, 2003.

    Google Scholar 

  54. Evans, D. J.; Morriss, G. P. Statistical Mechanics of Nonequilibrium Liquids; Academic Press: London, 1990.

    Google Scholar 

  55. Fixman, M. Proc. Natl. Acad. Sci. U.S.A. 1974, 71, 3050–3053.

    Article  CAS  Google Scholar 

  56. Mayo, S. L.; Olafson, B. D.; Goddard, W. A., III J. Phys. Chem. 1990, 94, 8897–8909.

    Article  CAS  Google Scholar 

  57. Jang, S. S.; Molinero, V.; Cagin, T.; Goddard, W. A., III J. Phys. Chem. B 2004, 108, 3149–3157.

    Article  CAS  Google Scholar 

  58. Jang, S. S.; Lin, S.-T.; Cagin, T.; Molinero, V.; Goddard, W. A., III J. Phys. Chem. B 2005, 109, 10154–10167.

    Article  CAS  Google Scholar 

  59. Jang, S. S.; Goddard, W. A. J. Phys. Chem. C 2007, 111, 2759–2769.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  61. Jang, S. S.; Goddard, W. A. J. Phys. Chem. B 2006, 110, 7992–8001.

    Article  CAS  Google Scholar 

  62. Plimpton, S. J. J. Comput. Phys. 1995, 117, 1–19.

    Article  CAS  Google Scholar 

  63. Plimpton, S. J.; Pollock, R.; Stevens, M. The Eighth SIAM Conference on Parallel Processing for Scientific Computing Minneapolis; 1997.

    Google Scholar 

  64. Swope, W. C.; Andersen, H. C.; Berens, P. H.; Wilson, K. R. J. Chem. Phys. 1982, 76, 637–649.

    Article  CAS  Google Scholar 

  65. Castro, R.; Nixon, K. R.; Evanseck, J. D.; Kaifer, A. E. J. Org. Chem. 1996, 61, 7298–7303.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  67. Bryce, M. R.; Cooke, G.; Duclairoir, F. M. A.; Rotello, V. M. Tetrahedron Lett. 2001, 42, 1143–1145.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  69. Leigh, D. A.; Murphy, A.; Smart, J. P.; Deleuze, M. S.; Zerbetto, F. J. Am. Chem. Soc. 1998, 120, 6458–6467.

    Article  CAS  Google Scholar 

  70. Leigh, D. A.; Troisi, A.; Zerbetto, F. Chem. Eur. J. 2001, 7, 1450–1454.

    Article  CAS  Google Scholar 

  71. Deleuze, M. S.; Leigh, D. A.; Zerbetto, F. J. Am. Chem. Soc. 1999, 121, 2364–2379.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  73. Lin, S. T.; Blanco, M.; Goddard, W. A. J. Chem. Phys. 2003, 119, 11792–11805.

    Article  CAS  Google Scholar 

  74. Lin, S. T.; Jang, S. S.; Cagin, T.; Goddard, W. A. J. Phys. Chem. B 2004, 108, 10041–10052.

    Article  CAS  Google Scholar 

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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.

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  1. Center for Materials Simulations & Design, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea

    Hyungjun Kim

  2. Materials and Process Simulation Center, California Institute of Technology, Pasadena, USA

    Hyungjun Kim

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Kim, H. (2011). Free Energy Barrier for Molecular Motions in Bistable [2]Rotaxane Molecular Electronic Devices. In: Multiscale and Multiphysics Computational Frameworks for Nano- and Bio-Systems. Springer Theses. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-7601-7_3

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