Home | About Journal | Web Links | E-mail Alerts | RSS RSS Icon | Browse
Previous Article Next Article

Amino acid analogues bind to carbon nanotube via pi-pi interactions: Comparison of molecular mechanical and quantum mechanical calculations

Source: J. Chem. Phys. 136, 025103 (2012); http://dx.doi.org/10.1063/1.3675486

Published 10 January 2012

EPAPS
KEYWORDS and PACS
Keywords
PACS
  • 87.15.B-
    Structure of biomolecules
  • 87.15.R-
    Biochemical reactions and kinetics
  • 87.15.La
    Mechanical properties of biomolecules
  • YEAR: 2011
RELATED DATABASES
Web of Science

View this record in Web of Science

View Web of Science related articles

PUBLICATION DATA
ISSN:
1553-9628 (online)
Publisher:
AIP is a member of CrossRef AIP
Zaixing Yang,1,2 Zhigang Wang,3 Xingling Tian,1 Peng Xiu,1,2 and Ruhong Zhou4
1Bio-X Lab, Department of Physics, and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, China
2Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, China
3Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, China
4Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, USA
Understanding the interaction between carbon nanotubes (CNTs) and biomolecules is essential to the CNT-based nanotechnology and biotechnology. Some recent experiments have suggested that the pi-pi stacking interactions between protein's aromatic residues and CNTs might play a key role in their binding, which raises interest in large scale modeling of protein-CNT complexes and associated pi-pi interactions at atomic detail. However, there is concern on the accuracy of classical fixed-charge molecular force fields due to their classical treatments and lack of polarizability. Here, we study the binding of three aromatic residue analogues (mimicking phenylalanine, tyrosine, and tryptophan) and benzene to a single-walled CNT, and compare the molecular mechanical (MM) calculations using three popular fixed-charge force fields (OPLSAA, AMBER, and CHARMM), with quantum mechanical (QM) calculations using the density-functional tight-binding method with the inclusion of dispersion correction (DFTB-D). Two typical configurations commonly found in pi-pi interactions are used, one with the aromatic rings parallel to the CNT surface (flat), and the other perpendicular (edge). Our calculations reveal that compared to the QM results the MM approaches can appropriately reproduce the strength of pi-pi interactions for both configurations, and more importantly, the energy difference between them, indicating that the various contributions to pi-pi interactions have been implicitly included in the van der Waals parameters of the standard MM force fields. Meanwhile, these MM models are less accurate in predicting the exact structural binding patterns (matching surface), meaning there are still rooms to be improved. In addition, we have provided a comprehensive and reliable QM picture for the pi-pi interactions of aromatic molecules with CNTs in gas phase, which might be used as a benchmark for future force field developments. ©2012 American Institute of Physics
History: Received 12 September 2011; accepted 15 December 2011; published 10 January 2012
Digital Object Identifier: http://dx.doi.org/10.1063/1.3675486

REFERENCES (82)

  1. A. A. Bhirde, V. Patel, J. Gavard, G. Zhang, A. A. Sousa, A. Masedunskas, R. D. Leapman, R. Weigert, J. S. Gutkind, and J. F. Rusling, ACS Nano 3, 307 (2009).
  2. S. Jain, V. S. Thakare, M. Das, A. K. Jain, and S. Patil, Nanomedicine 5, 1277 (2010).
  3. R. J. Chen, S. Bangsaruntip, K. A. Drouvalakis, N. W. S. Kam, M. Shim, Y. M. Li, W. Kim, P. J. Utz, and H. J. Dai, Proc. Natl. Acad. Sci. U.S.A. 100, 4984 (2003).
  4. W. F. DeGrado, G. Grigoryan, Y. H. Kim, R. Acharya, K. Axelrod, R. M. Jain, L. Willis, M. Drndic, and J. M. Kikkawa, Science 332, 1071 (2011).
  5. D. Nepal and K. E. Geckeler, Small 2, 406 (2006).
  6. D. Nepal and K. E. Geckeler, Small 3, 1259 (2007).
  7. S. Q. Wang, E. S. Humphreys, S. Y. Chung, D. F. Delduco, S. R. Lustig, H. Wang, K. N. Parker, N. W. Rizzo, S. Subramoney, Y. M. Chiang, and A. Jagota, Nat. Mater. 2, 196 (2003). [MEDLINE]
  8. G. R. Dieckmann, A. B. Dalton, P. A. Johnson, J. Razal, J. Chen, G. M. Giordano, E. Munoz, I. H. Musselman, R. H. Baughman, and R. K. Draper, J. Am. Chem. Soc. 125, 1770 (2003). [MEDLINE]
  9. V. E. Kagan, N. V. Konduru, W. H. Feng, B. L. Allen, J. Conroy, Y. Volkov, I. I. Vlasova, N. A. Belikova, N. Yanamala, A. Kapralov, Y. Y. Tyurina, J. W. Shi, E. R. Kisin, A. R. Murray, J. Franks, D. Stolz, P. P. Gou, J. Klein-Seetharaman, B. Fadeel, A. Star, and A. A. Shvedova, Nat. Nanotechnol. 5, 354 (2010).
  10. Y. L. Zhao, G. M. Xing, and Z. F. Chai, Nat. Nanotechnol. 3, 191 (2008).
  11. G. Zuo, W. Gu, H. Fang, and R. Zhou, J. Phys. Chem. C 115, 12322 (2011).
  12. G. Zuo, Q. Huang, G. Wei, R. Zhou, and H. Fang, ACS Nano 4, 7508 (2010).
  13. C. C. Ge, J. F. Du, L. N. Zhao, L. M. Wang, Y. Liu, D. H. Li, Y. L. Yang, R. H. Zhou, Y. L. Zhao, Z. F. Chai, and C. Y. Chen, Proc. Natl. Acad. Sci. U.S.A. 108, 16968 (2011).
  14. S. S. Karajanagi, A. A. Vertegel, R. S. Kane, and J. S. Dordick, Langmuir 20, 11594 (2004). [ISI] [MEDLINE]
  15. P. Goldberg-Oppenheimer, and O. Regev, Small 3, 1894 (2007).
  16. J. Zhong, L. Song, J. Meng, B. Gao, W. Chu, H. Xu, Y. Luo, J. Guo, A. Marcelli, S. Xie, and Z. Wu, Carbon 47, 967 (2009).
  17. V. Zorbas, A. L. Smith, H. Xie, A. Ortiz-Acevedo, A. B. Dalton, G. R. Dieckmann, R. K. Draper, R. H. Baughman, and I. H. Musselman, J. Am. Chem. Soc. 127, 12323 (2005). [MEDLINE] [CAS]
  18. X. J. Li, W. Chen, Q. W. Zhan, L. M. Dai, L. Sowards, M. Pender, and R. R. Naik, J. Phys. Chem. B 110, 12621 (2006). [MEDLINE] [CAS]
  19. H. Xie, E. J. Becraft, R. H. Baughman, A. B. Dalton, and G. R. Dieckmann, J. Pept. Sci. 14, 139 (2008).
  20. Z. Su, K. Mui, E. Daub, T. Leung, and J. Honek, J. Phys. Chem. B 111, 14411 (2007).
  21. C. G. Salzmann, M. A. H. Ward, R. M. J. Jacobs, G. Tobias, and M. L. H. Green, J. Phys. Chem. C 111, 18520 (2007).
  22. T. Serizawa, Z. H. Gao, C. Y. Zhi, Y. Bando, and D. Golberg, J. Am. Chem. Soc. 132, 4976 (2010).
  23. J.-W. Shen, T. Wu, Q. Wang, and Y. Kang, Biomaterials 29, 3847 (2008).
  24. G. Gianese, V. Rosato, F. Cleri, M. Celino, and P. Morales, J. Phys. Chem. B 113, 12105 (2009).
  25. S. O. Nielsen, C. C. Chiu, and G. R. Dieckmann, J. Phys. Chem. B 112, 16326 (2008). [Inspec]
  26. M. S. P. Sansom, E. J. Wallace, R. S. G. D'Rozario, and B. M. Sanchez, Nanoscale 2, 967 (2010).
  27. C.-c. Chiu, M. C. Maher, G. R. Dieckmann, and S. O. Nielsen, ACS Nano 4, 2539 (2010).
  28. K. Balamurugan, R. Gopalakrishnan, S. S. Raman, and V. Subramanian, J. Phys. Chem. B 114, 14048 (2010).
  29. R. R. Johnson, B. J. Rego, A. T. C. Johnson, and M. L. Klein, J. Phys. Chem. B 113, 11589 (2009).
  30. Y. A. Cheng, D. C. Li, B. H. Ji, X. H. Shi, and H. J. Gao, J. Mol. Graphics Modell. 29, 171 (2010).
  31. Q. Wang, Y. Kang, Y. C. Liu, J. W. Shen, and T. Wu, J. Phys. Chem. B 114, 2869 (2010).
  32. T. R. Walsh, and S. D. Tomasio, Mol. Phys. 105, 221 (2007). [Inspec]
  33. T. R. Walsh, and S. M. Tomasio, J. Phys. Chem. C 113, 8778 (2009).
  34. S. Vaitheeswaran, and A. E. Garcia, J. Chem. Phys. 134, 125101 (2011). [MEDLINE]
  35. R. H. Zhou, X. H. Huang, C. J. Margulis, and B. J. Berne, Science 305, 1605 (2004).
  36. P. Liu, X. H. Huang, R. H. Zhou, and B. J. Berne, Nature (London) 437, 159 (2005). [MEDLINE]
  37. J. A. King, P. Das, and R. H. Zhou, Proc. Natl. Acad. Sci. U.S.A. 108, 10514 (2011).
  38. L. Zheng, M. Chen, and W. Yang, Proc. Natl. Acad. Sci. U.S.A. 105, 20227 (2008). [MEDLINE]
  39. H. Kamberaj and A. van der Vaart, J. Chem. Phys. 130, 074906 (2009).
  40. R. R. Johnson, A. Kohlmeyer, A. T. C. Johnson, and M. L. Klein, Nano Lett. 9, 537 (2009). [MEDLINE]
  41. S. Tsuzuki, K. Honda, T. Uchimaru, M. Mikami, and K. Tanabe, J. Am. Chem. Soc. 124, 104 (2002). [MEDLINE]
  42. E. C. Lee, D. Kim, P. Jurecka, P. Tarakeshwar, P. Hobza, and K. S. Kim, J. Phys. Chem. A 111, 3446 (2007). [MEDLINE]
  43. M. Pitonak, P. Neogrady, J. Rezac, P. Jurecka, M. Urban, and P. Hobza, J. Chem. Theory Comput. 4, 1829 (2008). [CAS]
  44. M. Lewis, M. W. Watt, M. L. K. E. Hardebeck, and C. C. Kirkpatrick, J. Am. Chem. Soc. 133, 3854 (2011).
  45. C. D. Sherrill and M. O. Sinnokrot, J. Phys. Chem. A 110, 10656 (2006). [MEDLINE]
  46. C. D. Sherrill, B. G. Sumpter, M. O. Sinnokrot, M. S. Marshall, E. G. Hohenstein, R. C. Walker, and I. R. Gould, J. Comput. Chem. 30, 2187 (2009).
  47. S. Grimme, J. Comput. Chem. 25, 1463 (2004). [MEDLINE]
  48. P. Jurecka, J. Sponer, J. Cerny, and P. Hobza, Phys. Chem. Chem. Phys. 8, 1985 (2006). [MEDLINE]
  49. M. O. Sinnokrot and C. D. Sherrill, J. Phys. Chem. A 108, 10200 (2004).
  50. T. Janowski and P. Pulay, Chem. Phys. Lett. 447, 27 (2007). [Inspec] [CAS]
  51. Y. Zhao and D. G. Truhlar, J. Phys. Chem. C 112, 4061 (2008). [CAS]
  52. W. L. Jorgensen and D. L. Severance, J. Am. Chem. Soc. 112, 4768 (1990).
  53. C. Chipot, R. Jaffe, B. Maigret, D. A. Pearlman, and P. A. Kollman, J. Am. Chem. Soc. 118, 11217 (1996). [ISI]
  54. A. T. Macias and A. D. MacKerell, J. Comput. Chem. 26, 1452 (2005). [ISI]
  55. Y. P. Pang, J. L. Miller, and P. A. Kollman, J. Am. Chem. Soc. 121, 1717 (1999).
  56. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. 117, 5179 (1996).
  57. A. de Leon, A. F. Jalbout, and V. A. Basiuk, Chem. Phys. Lett. 457, 185 (2008). [Inspec] [CAS]
  58. A. F. Jalbout, A. De Leon, and V. A. Basiuk, Comp Mater Sci 44, 310 (2008).
  59. R. Sharma, J. P. McNamara, R. K. Raju, M. A. Vincent, I. H. Hillier, and C. A. Morgado, Phys. Chem. Chem. Phys. 10, 2767 (2008).
  60. W. Fan, J. Zeng, and R. Zhang, J. Chem. Theory Comput. 5, 2879 (2009).
  61. M. Elstner, D. Porezag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B 58, 7260 (1998).
  62. B. Aradi, B. Hourahine, and T. Frauenheim, J. Phys. Chem. A 111, 5678 (2007). [MEDLINE]
  63. M. Elstner, P. Hobza, T. Frauenheim, S. Suhai, and E. Kaxiras, J. Chem. Phys. 114, 5149 (2001).
  64. W. L. Jorgensen, D. S. Maxwell, and J. TiradoRives, J. Am. Chem. Soc. 118, 11225 (1996).
  65. J. M. Wang, P. Cieplak, and P. A. Kollman, J. Comput. Chem. 21, 1049 (2000).
  66. A. D. Mackerell, M. Feig, and C. L. Brooks, J. Comput. Chem. 25, 1400 (2004). [MEDLINE]
  67. P. Hobza, J. Sponer, and T. Reschel, J. Comput. Chem. 16, 1315 (1995).
  68. Y. Zhao, X. Wu, J. Yang, and X. C. Zeng, Phys. Chem. Chem. Phys. 13, 11766 (2011).
  69. L. Zhechkov, T. Heine, S. Patchkovskii, G. Seifert, and H. A. Duarte, J. Chem. Theory Comput. 1, 841 (2005).
  70. J. R. Grover, E. A. Walters, and E. T. Hui, J. Phys. Chem. 91, 3233 (1987).
  71. Elkingto. Pa and G. Curthoys, J. Phys. Chem. 73, 2321 (1969). [ISI]
  72. E. Arunan and H. S. Gutowsky, J. Chem. Phys. 98, 4294 (1993).
  73. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, J. Chem. Theory Comput. 4, 435 (2008).
  74. W. Humphrey, A. Dalke, and K. Schulten, J. Mol. Graphics 14, 33 (1996). [MEDLINE]
  75. G. Hummer, J. C. Rasaiah, and J. P. Noworyta, Nature (London) 414, 188 (2001). [MEDLINE]
  76. P. Xiu, B. Zhou, W. P. Qi, H. J. Lu, Y. S. Tu, and H. P. Fang, J. Am. Chem. Soc. 131, 2840 (2009). [MEDLINE]
  77. P. Xiu, Z. X. Yang, B. Zhou, P. Das, H. P. Fang, and R. H. Zhou, J. Phys. Chem. B 115, 2988 (2011).
  78. F. Tournus, and J. C. Charlier, Phys. Rev. B 71, 165421 (2005).
  79. L. M. Woods, S. C. Badescu, and T. L. Reinecke, Phys. Rev. B 75, 155415 (2007).
  80. J. P. Lu, J. J. Zhao, J. Han, and C. K. Yang, Appl. Phys. Lett. 82, 3746 (2003).
  81. J. Lu, S. Nagase, X. W. Zhang, D. Wang, M. Ni, Y. Maeda, T. Wakahara, T. Nakahodo, T. Tsuchiya, T. Akasaka, Z. X. Gao, D. P. Yu, H. Q. Ye, W. N. Mei, and Y. S. Zhou, J. Am. Chem. Soc. 128, 5114 (2006). [MEDLINE] [CAS]
  82. See supplementary material at http://dx.doi.org/10.1063/1.3675486 for analysis of interaction energies of benzene dimer with different configurations for OPLSAA and CHARMM force fields, complete lists of interaction energies and equilibrium distances of benzene dimer obtained by different methods, nonbonded parameters for aromatic amino acid analogues in MM calculations, snapshots of equilibrium binding structures predicted by QM calculations, and comparison of equilibrium binding structures predicted by QM and MM calculations for the “edge” configuration. [EPAPS]
ADVERTISEMENT