The European Physical Journal Special Topics

, Volume 227, Issue 14, pp 1681–1692 | Cite as

Diamondoid-functionalized nanogaps: from small molecules to electronic biosensing

  • Frank C. Maier
  • Chandra S. Sarap
  • Maofeng Dou
  • Ganesh Sivaraman
  • Maria FytaEmail author
Regular Article
Part of the following topical collections:
  1. Particle Methods in Natural Science and Engineering


The potential of reading-out DNA molecules using functionalized electrodes embedded in nanopores is discussed here. Focus is given on functionalization using tiny diamond-like hydrogenated cages, the diamondoids. A derivative known as memantine of the smallest diamondoid is taken. This offers hydrogen bonding possibilities. Based on quantum-mechanical calculations, we first assess the interaction details of memantine with DNA units, the nucleotides. At a next step, nucleotides are placed within the nanogap formed by the diamondoid-functionalized electrodes. Quantum transport calculations are performed and show the high sensitivity of the electrodes in distinguishing among the different nucleotide types. We proceed by qualitatively revealing the influence of the DNA molecules by simply rotating the nucleotide within the nanogap. The effect of an aqueous environment is also included and the dynamic behavior of the conductance across the functionalized electrodes is addressed. In the end, we discuss the relevance of our results in detecting DNA sequences.


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  1. 1.
    D. Branton, D.W. Deamer, A. Marziali, H. Bayley, S.A. Benner, T. Butler, M. Di Ventra, S. Garaj, A. Hibbs, X. Huang, et al., Nat. Biotechnol. 26, 1146 (2008)Google Scholar
  2. 2.
    B.M. Venkatesan, R. Bashir, Nat. Nanotechnol. 6, 615 (2011)ADSGoogle Scholar
  3. 3.
    R.H. Scheicher, A. Grigoriev, R. Ahuja, J. Mater. Sci. 47, 7439 (2012)ADSGoogle Scholar
  4. 4.
    M. Fyta, J. Phys.: Condens. Matter 27, 273101 (2015)ADSGoogle Scholar
  5. 5.
    S. Agah, M. Zheng, M. Pasquali, A.B. Kolomeisky, J. Phys. D: Appl. Phys. 49, 413001 (2016)Google Scholar
  6. 6.
    C. Dekker, Nat. Nanotechnol. 2, 209 (2007)ADSGoogle Scholar
  7. 7.
    M. Zwolak, M. Di Ventra, Rev. Mod. Phys. 80, 141 (2008)ADSGoogle Scholar
  8. 8.
    M. Di Ventra, M. Taniguchi, Nat. Nano. 11, 117 (2016)Google Scholar
  9. 9.
    M. Zwolak, M. Di Ventra, Nano. Lett. 5, 421 (2005)ADSGoogle Scholar
  10. 10.
    J. Lagerqvist, M. Zwolak, M. Di Ventra, Nano. Lett. 6, 779 (2006)ADSGoogle Scholar
  11. 11.
    H. He, R.H. Scheicher, R. Pandey, A. Reily Rocha, S. Sanvito, A. Grigoriev, R. Ahuja, S. Karna, J. Phys. Chem. C 112, 3456 (2008)Google Scholar
  12. 12.
    F. Patolsky, A. Lichtenstein, I. Willner, Nat. Biotechnol. 19, 253 (2001)Google Scholar
  13. 13.
    E.M. Boon, D.M. Ceres, T.G. Drummond, M.G. Hill, J.K. Barton, Nat. Biotechnol. 18, 1096 (2000)Google Scholar
  14. 14.
    C. Merstorf, B. Cressiot, M. Pastoriza-Gallego, A. Oukhaled, J.M. Betton, L. Auvray, J. Pelta, ACS Chem. Biol. 7, 652 (2012)Google Scholar
  15. 15.
    A.C. Rajan, M.R. Rezapour, J. Yun, Y. Cho, W.J. Cho, S.K. Min, G. Lee, K.S. Kim, ACS Nano. 8, 1827 (2014)Google Scholar
  16. 16.
    M. Murtaza, S.J. Dawson, D.W. Tsui, D. Gale, T. Forshew, A.M. Piskorz, C. Parkinson, S.F. Chin, Z. Kingsbury, A.S. Wong, et al., Nature 497, 108 (2013)ADSGoogle Scholar
  17. 17.
    S. Huang, J. He, S. Chang, P. Zhang, F. Liang, S. Li, M. Tuchband, A. Fuhrmann, R. Ros, S. Lindsay, Nat. Nanotechnol. 5, 868 (2010)ADSGoogle Scholar
  18. 18.
    G. Sivaraman, R.G. Amorim, R.H. Scheicher, M. Fyta, Nanoscale 8, 10105 (2016)ADSGoogle Scholar
  19. 19.
    W.A. Clay, J.E.P. Dahl, R.M.K. Carlson, N.A. Melosh, Z.X. Shen, Rep. Prog. Phys. 78, 016501 (2015)ADSGoogle Scholar
  20. 20.
    J. Dahl, S. Liu, R. Carlson, Science 299, 96 (2003)ADSGoogle Scholar
  21. 21.
    W.L. Yang, J.D. Fabbri, T.M. Willey, J.R.I. Lee, J.E. Dahl, R.M.K. Carlson, P.R. Schreiner, A.A. Fokin, B.A. Tkachenko, N.A. Fokina, et al., Science 316, 1460 (2007)ADSGoogle Scholar
  22. 22.
    M. Vörös, T. Demjén, T. Szilvási, A. Gali, Phys. Rev. Lett. 108, 267401 (2012)ADSGoogle Scholar
  23. 23.
    A.A. Fokin, B.A. Tkachenko, P.A. Gunchenko, D.V. Gusev, P.R. Schreiner, Chem. Eur. J. 11, 7091 (2005)Google Scholar
  24. 24.
    M.A. Gunawan, J.C. Hierso, D. Poinsot, A.A. Fokin, N.A. Fokina, B.A. Tkachenko, P.R. Schreiner, New J. Chem. 38, 28 (2014)Google Scholar
  25. 25.
    Y. Zhou, A.D. Brittain, D. Kong, M. Xiao, Y. Meng, L. Sun, J. Mater. Chem. C 3, 6947 (2015)Google Scholar
  26. 26.
    A. Spasov, T. Khamidova, L. Bugaeva, I. Morozov, Pharm. Chem. J. 34, 1 (2000)Google Scholar
  27. 27.
    F.C. Maier, G. Sivaraman, M. Fyta, Eur. Phys. J. E 37, 95 (2014)Google Scholar
  28. 28.
    A. Nazem, G. Mansoori, J. Bioanal. Biomed. 6, 9 (2014)Google Scholar
  29. 29.
    B. Reisberg, R. Doody, A. Stöffler, F. Schmitt, S. Ferris, H.J. Möbius, New England J. Med. 348, 1333 (2003)Google Scholar
  30. 30.
    D.M. Robinson, G.M. Keating, Drugs 66, 1515 (2006)Google Scholar
  31. 31.
    M.W. Schmidt, K.K. Baldridge, J.A. Boatz, S.T. Elbert, M.S. Gordon, J.H. Jensen, S. Koseki, N. Matsunaga, K.A. Nguyen, S. Su, et al., J. Comput. Chem. 14, 1347 (1993)Google Scholar
  32. 32.
    M.S. Gordon, M.W. Schmidt, in Theory and applications of computational chemistry, edited by C.E. Dykstra, K.S. Kim, G.E. Scuseria (Elsevier, Amsterdam, 2005), pp. 1167–1189Google Scholar
  33. 33.
    J.M. Soler, E. Artacho, J.D. Gale, A. Garcia, J. Junquera, P. Ordejon, D. Sánchez-Portal, J. Phys.: Condens. Matter 14, 2745 (2002)ADSGoogle Scholar
  34. 34.
    Y. Zhao, D.G. Truhlar, Acc. Chem. Res. 41, 157 (2008)Google Scholar
  35. 35.
    H. Vovusha, S. Sanyal, B. Sanyal, J. Phys. Chem. Lett. 4, 3710 (2013)Google Scholar
  36. 36.
    D. Umadevi, G.N. Sastry, J. Phys. Chem. Lett. 2, 1572 (2011)Google Scholar
  37. 37.
    D. Branton, D.W. Deamer, A. Marziali, H. Bayley, S.A. Benner, T. Butler, M. Di Ventra, S. Garaj, A. Hibbs, X. Huang, et al., Nat. Biotechnol. 26, 1146 (2008)Google Scholar
  38. 38.
    V.R. Cooper, T. Thonhauser, D.C. Langreth, J. Chem. Phys. 128, 204102 (2008)ADSGoogle Scholar
  39. 39.
    S.F. Boys, F.d. Bernardi, Mol. Phys. 19, 553 (1970)ADSGoogle Scholar
  40. 40.
    J.P. Perdew, K. Burke, M. Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996)ADSGoogle Scholar
  41. 41.
    K. Stokbro, J. Taylor, M. Brandbyge, O. Pablo, Ann. N.Y. Acad. Sci. 1006, 212 (2003)ADSGoogle Scholar
  42. 42.
    J. Hutter, M. Iannuzzi, F. Schiffmann, J. VandeVondele, Wiley Interdiscip. Rev.: Comput. Mol. Sci. 4, 15 (2014)Google Scholar
  43. 43.
    S. Goedecker, M. Teter, J. Hutter, Phys. Rev. B 54, 1703 (1996)ADSGoogle Scholar
  44. 44.
    C. Hartwigsen, S. Goedecker, J. Hutter, Phys. Rev. B 58, 3641 (1998)ADSGoogle Scholar
  45. 45.
    J. VandeVondele, J. Hutter, J. Chem. Phys. 127, 114105 (2007)ADSGoogle Scholar
  46. 46.
    S. Grimme, J. Antony, S. Ehrlich, H. Krieg, J. Chem. Phys. 132, 154104 (2010)ADSGoogle Scholar
  47. 47.
    S.M. Foiles, M.I. Baskes, M.S. Daw, Phys. Rev. B 33, 7983 (1986)ADSGoogle Scholar
  48. 48.
    S. Plimpton, J. Comput. Phys. 117, 1 (1995)ADSGoogle Scholar
  49. 49.
    N. Sändig, F. Zerbetto, Chem. Commun. 46, 667 (2010)Google Scholar
  50. 50.
    F. Maseras, K. Morokuma, J. Comput. Chem. 16, 1170 (1995)Google Scholar
  51. 51.
    J. Pu, J. Gao, D.G. Truhlar, ChemPhysChem 6, 1853 (2005)Google Scholar
  52. 52.
    D. Golze, M. Iannuzzi, M.T. Nguyen, D. Passerone, J. Hutter, J. Chem. Theory Comput. 9, 5086 (2013)Google Scholar
  53. 53.
    C.S. Sarap, P. Partovi-Azar, M. Fyta, ACS Appl. Bio Mater. 1, 59 (2018)Google Scholar
  54. 54.
    M. Barbatti, A.J.A. Aquino, H. Lischka, Phys. Chem. Chem. Phys. 12, 4959 (2010)Google Scholar
  55. 55.
    D. Varsano, R. Di Felice, M.A.L. Marques, A. Rubio, J. Phys. Chem. B 110, 7129 (2006)Google Scholar
  56. 56.
    S.K. Min, W.Y. Kim, Y. Cho, K.S. Kim, Nat. Nanotechnol. 6, 162 (2011)ADSGoogle Scholar
  57. 57.
    P. Krstić, B. Ashcroft, S. Lindsay, Nanotechnology 26, 084001 (2015)ADSGoogle Scholar

Copyright information

© EDP Sciences, Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Frank C. Maier
    • 1
  • Chandra S. Sarap
    • 1
  • Maofeng Dou
    • 1
  • Ganesh Sivaraman
    • 1
    • 2
  • Maria Fyta
    • 1
    Email author
  1. 1.Institute for Computational Physics, University of StuttgartStuttgartGermany
  2. 2.Argonne Leadership Computing Facility, Argonne National LaboratoryArgonneUSA

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