Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
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A Minimalist Model of Single Molecule Spectroscopy in a Dynamic Environment Studied by Metadynamics

  • Oh, In-Rok (Department of Chemistry, Seoul National University) ;
  • Lee, Eun-Sang (Department of Chemistry, Seoul National University) ;
  • Jung, Youn-Joon (Department of Chemistry, Seoul National University)
  • Received : 2011.12.10
  • Accepted : 2012.01.11
  • Published : 2012.03.20
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Abstract

In this paper we develop a minimalist model of single molecule spectroscopy in a dynamic environment. Our model is based upon a lattice system consisting of a probe molecule embedded in an Ising-model like environment. We assume that the probe molecule interacts with the Ising spins via a dipole-dipole potential, and calculate free energy curves and lineshapes of the system. To investigate fluctuation behavior of the system we exploit the metadynamics sampling method. In particular, using the method, we calculate the free energy curve of magnetization of the lattice and that of the transition energy of the probe molecule. Furthermore, we compare efficiencies of three different sampling methods used; unbiased, umbrella, and metadynamics sampling methods. Finally, we explore the lineshape behavior of the probe molecule as the system undergoes a phase transition from a sub-critical and to a super-critical temperature. We show that the transition energy of a probe molecule is broadly distributed due to the heterogeneous, local environments.

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References

  1. Basche, T.; Moerner, W. E.; Orrit, M.; Wild, U. P. Single-Molecule Detection, Imaging, and Spectroscopy; VCH: New York, 1996.
  2. Barkai, E.; Brown, F. L. H.; Orrit, M.; Yang, H. Theory and Evaluation of Single-Molecule Signals; World Scientific Press: Singapore, 2008.
  3. Moerner, W. E.; Kador, L. Phys. Rev. Lett. 1989, 62, 2535-2538 https://doi.org/10.1103/PhysRevLett.62.2535
  4. Orrit, M.; Bernard, J. Phys. Rev. Lett. 1990, 65, 2716-2719. https://doi.org/10.1103/PhysRevLett.65.2716
  5. Empedocles, S.; Norris, D.; Bawendi, M. Phys. Rev. Lett. 1996, 77, 3873-3876 https://doi.org/10.1103/PhysRevLett.77.3873
  6. Xie, X. S.; Trautman, J. K. Annu. Rev. Phys. Chem. 1998, 49, 441- 480. https://doi.org/10.1146/annurev.physchem.49.1.441
  7. Weiss, S. Science 1999, 283, 1676-1683. https://doi.org/10.1126/science.283.5408.1676
  8. Moerner, W. E.; Orrit, M. Science 1999, 283, 1670-1676. https://doi.org/10.1126/science.283.5408.1670
  9. Zumbusch, A.; Fleury, L.; Brown, R.; Bernard, J.; Orrit, M. Phys. Rev. Lett. 1993, 70, 3584-3587. https://doi.org/10.1103/PhysRevLett.70.3584
  10. Kuno, M.; Fromm, D. P.; Hamann, H. F.; Gallagher, A.; Nesbitt, D. J. J. Chem. Phys. 2000, 112, 3117. https://doi.org/10.1063/1.480896
  11. Jung, Y.; Barkai, E.; Silbey, R. J. Chem. Phys. 2002, 284, 181-194. https://doi.org/10.1016/S0301-0104(02)00547-5
  12. Cao, J.; Silbey, R. J. J. Phys. Chem. B, 2008, 112, 12867-12880. https://doi.org/10.1021/jp803347m
  13. Fleury, L.; Segura, J.; Zumofen, G.; Hecht, B.; Wild, U. P. J. Luminescence 2001, 94, 805-809. https://doi.org/10.1016/S0022-2313(01)00367-2
  14. Lounis, B.; Moerner, W. E. Nature 2000, 407, 491-493. https://doi.org/10.1038/35035032
  15. Jung, Y.; Barkai, E.; Silbey, R. J. Adv. Chem. Phys. 2002, 199-266
  16. Barkai, E.; Jung, Y.; Silbey, R. Annu. Rev. Phys. Chem. 2004, 55, 457-507. https://doi.org/10.1146/annurev.physchem.55.111803.143246
  17. Zheng, Y.; Brown, F. L. H. Phys. Rev. Lett. 2003, 90, 238305. https://doi.org/10.1103/PhysRevLett.90.238305
  18. Mukamel, S. Phys. Rev. A 2003, 68, 063821. https://doi.org/10.1103/PhysRevA.68.063821
  19. He, Y.; Barkai, E. Phys. Rev. Lett. 2004, 93, 068302. https://doi.org/10.1103/PhysRevLett.93.068302
  20. Sung, J.; Silbey, R. J. Chem. Phys. Lett. 2005, 415, 10-14. https://doi.org/10.1016/j.cplett.2005.08.057
  21. Deschenes, L.; Vanden Bout, D. J. Phys. Chem. B 2002, 106, 11438-11445. https://doi.org/10.1021/jp025843m
  22. Vallee, R.; Cotlet, M.; Hofkens, J.; De Schryver, F. Macromolecules 2003, 36, 7752-7758. https://doi.org/10.1021/ma034710b
  23. Jung, Y.; Garrahan, J. P.; Chandler, D. J. Chem. Phys. 2005, 123, 084509. https://doi.org/10.1063/1.2001629
  24. Jung, Y.; Garrahan, J. P.; Chandler, D. Phys. Rev. E 2004, 69, 061205. https://doi.org/10.1103/PhysRevE.69.061205
  25. Jeong, D.; Choi, M. Y.; Kim, H. J.; Jung, Y. Phys. Chem. Chem. Phys. 2010, 12, 2001-2010. https://doi.org/10.1039/b921725h
  26. Schuler, B.; Eaton, W. A. Curr. Opin. Struct. Biol. 2008, 18, 16- 26. https://doi.org/10.1016/j.sbi.2007.12.003
  27. Lee, E.; Jung, Y. Bull. Kor. Chem. Soc. 2011, 32, 3051-3056. https://doi.org/10.5012/bkcs.2011.32.8.3051
  28. Kollman, P. Chem. Rev. 1993, 93, 2395-2417. https://doi.org/10.1021/cr00023a004
  29. Beveridge, D. L.; DiCapua, F. M. Annu. Rev. Biophys. Biophys. Chem. 1989, 18, 431-492. https://doi.org/10.1146/annurev.bb.18.060189.002243
  30. Chandler, D. Introduction to Modern Statistical Mechanics; Oxford University Press: New York, USA, 1987.
  31. Sugita, Y.; Okamoto, Y. Chem. Phys. Lett. 1999, 314, 141-151. https://doi.org/10.1016/S0009-2614(99)01123-9
  32. Jarzynski, C. Phys. Rev. Lett. 1997, 78, 2690-2693. https://doi.org/10.1103/PhysRevLett.78.2690
  33. Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. USA 2002, 99, 12562. https://doi.org/10.1073/pnas.202427399
  34. Michel, C.; Laio, A.; Mohamed, F.; Krack, M.; Parrinello, M.; Milet, A. Organometallics 2007, 26, 1241-1249. https://doi.org/10.1021/om060980h
  35. Spiwok, V.; Lipovova, P.; Kralova, B. J. Phys. Chem. B 2007, 111, 3073-3076. https://doi.org/10.1021/jp068587c
  36. Ambrose, W. P.; Moerner, W. E. Nature 1991, 349, 225-227. https://doi.org/10.1038/349225a0
  37. Tanimura, Y.; Takano, H.; Klafter, J. J. Chem. Phys. 1998, 108, 1851-1858. https://doi.org/10.1063/1.475563
  38. Laio, A.; Rodriguez-Fortea, A.; Gervasio, F. L.; Ceccarelli, M.; Parrinello, M. J. Phys. Chem. B 2005, 109, 6714-6721. https://doi.org/10.1021/jp045424k
  39. Torrie, G.; Valleau, J. J. Comput. Phys. 1977, 23, 187-199. https://doi.org/10.1016/0021-9991(77)90121-8