Conductance through glycine in a graphene nanogap

  • Puspitapallab ChaudhuriEmail author
  • H. O. Frota
  • Cicero Mota
  • Angsula Ghosh
Research Paper


We report theoretical analysis of charge transport process through a single glycine molecule utilizing graphene nanogaps. Density functional theory and non-equilibrium Green’s function method are employed to investigate the transport properties of glycine inside the gap. The projected density of states, transmittance, and the current–voltage characteristics are determined with changes in the molecular orientation inside the nanogap of c.a 0.8 nm. The current values demonstrate a high sensitivity on the orientation of the molecule. The conductance of the molecule is also dependent on the voltage.


Glycine Graphene nanogap DFT Molecular electronics Nanoelectronics Modeling and simulation 


Funding information

This study received financial support from the Brazilian funding agency CNPq.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


  1. Acik M, Chabal YJ (2011) Nature of graphene edges. Jpn J Appl Phys 50:070101CrossRefGoogle Scholar
  2. Albrecht T, Guckian A, Kuznetsov AM, Vos JG, Ulstrup JJ (2006) Mechanism of electrochemical charge transport in individual transition metal complexes. J Am Chem Soc 128:17132–17138CrossRefGoogle Scholar
  3. Albrecht T, Guckian A, Ulstrup J, Vos JG (2005) Transistor-like behavior of transition metal complexes. Nano Lett 5:1451–1455CrossRefGoogle Scholar
  4. Arjmandi-Tash H, Belyaeva LA, Schneider GF (2016) Single molecule detection with graphene and other two-dimensional materials: nanopores and beyond. Chem Soc Rev 45:476–493CrossRefGoogle Scholar
  5. Avdoshenko SM, Nozaki D, da Rocha CG, González JW, Lee MH, Gutierrez R, Cuniberti G (2013) Dynamic and electronic transport properties of DNA translocation through graphene. Nanopores Nano Lett 13:1969–1976CrossRefGoogle Scholar
  6. Aviram A, Ratner MA (1974) Molecular rectifiers. Chem Phys Lett 29:277–283CrossRefGoogle Scholar
  7. Burg TP, Godin M, Knudsen SM, Shen W, Carlson G, Foster JS, Babcock K, Manalis SR (2007) Weighing of biomolecules, single cells and single nanoparticles in fluid. Nature 446:1066–1069CrossRefGoogle Scholar
  8. Calzolari A, Marzari N Souza I, Nardelli MB (2004) Ab initio transport properties of nanostructures from maximally localized Wannier functions. Phys. Rev B 69:035108CrossRefGoogle Scholar
  9. Cao W, Kang J, Liu W, Khatami Y, Sarkar D, Banerjee K (2013) 2D electronics: graphene and beyond. In: Proc Eur Solid-State Device Res Conf, pp 37–44Google Scholar
  10. Chang S, Huang S, He J, Liang F, Zhang P, Li S, Chen X, Sankey O, Lindsay S (2010) Electronic signatures of all four DNA nucleosides in a tunneling gap. Nano Lett 10:1070–1075CrossRefGoogle Scholar
  11. Cobden DH (2001) Molecular electronics: nanowires begin to shine. Nature 409:32–33CrossRefGoogle Scholar
  12. Cui A, Dong H, Hu W (2015) Nanogap electrodes towards solid state single-molecule transistors. Small 11:6115–6141CrossRefGoogle Scholar
  13. Dadosh T, Gordin Y, Krahne R, Khivrich I, Mahalu D, Frydman V, Sperling J, Yacoby A, Bar-Joseph I (2005) Measurement of the conductance of single conjugated molecules. Nature 436:677–680CrossRefGoogle Scholar
  14. Dasgupta NP, Sun J, Liu C, Brittman S, Andrews SC, Lim J, Gao H, Yan R, Yang P (2014) 25th anniversary article: semiconductor nanowires–synthesis, characterization, and applications. Adv Mater 26:2137–2184CrossRefGoogle Scholar
  15. Deen MJ, Shinwari MW, Ranuárez JC, Landheer D (2006) Noise considerations in field-effect biosensors. J Appl Phys 100:074703–074703-8CrossRefGoogle Scholar
  16. Dekker C (2007) Solid-state nanopores. Nat Nanotechnol 2:209–215CrossRefGoogle Scholar
  17. Dennington R, Keith T, Millam J (2006) GaussView, Version 4.1.2. Semichem Inc., Shawnee MissionGoogle Scholar
  18. Du K, Knutson CR, Glogowski E, McCarthy KD, Shenhar R, Rotello VM, Tuominen MT, Emrick T, Russell TP, Dinsmore AD (2009) Self-assembled electrical contact to nanoparticles using metallic droplets. Small 5:1974– 1977CrossRefGoogle Scholar
  19. Facchetti A (2011) π-conjugated polymers for organic electronics and photovoltaic cell applications. Chem Mater 223:733–758CrossRefGoogle Scholar
  20. Fanget A, Traversi F, Khlybov S, Granjon P, Magrez A, Forro L, Radenovic A (2014) Nanopore integrated nanogaps for DNA detection. Nano Lett 14:244–249CrossRefGoogle Scholar
  21. Ferretti F, Bonferroni B, Calzolari A, Buongiorno MN (2010) WanT Code,
  22. Fiori G, Bonaccorso F, Lannaccone G, Palacios T, Neumaier D, Seabaugh A, Banerjee SK, Colombo L (2014) Electronics based on two-dimensional materials. Nat Nanotech 9:768–779CrossRefGoogle Scholar
  23. Gaudioso J, Lauhon LJ, Ho W (2000) Vibrationally mediated negative differential resistance in a single molecule. Phys Rev Lett 85:1918–1921CrossRefGoogle Scholar
  24. Galperin M, Ratner MA, Nitzan A (2007) Molecular transport junctions: vibrational effects. J Phys: Condens Matter 103201:19Google Scholar
  25. Giannozzi P et al. (2009) QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials. J Phys Condens Matter 21:1–19CrossRefGoogle Scholar
  26. Girit CO, Meyer JC, Emi R, Rossell MD, Kisielowski C, Yang L, Park C-H, Crommie MF, Cohen ML, Louie SG, Zettl A (2009) Controlled formation of sharp zigzag and armchair edges in graphitic nanoribbons. Science 323:1705–1708CrossRefGoogle Scholar
  27. Goto H, Uesugi E, Eguchi R, Fujiwara A, Kubozono Y (2013) Edge-dependent transport properties in graphene. Nano Lett 13:1126–1130CrossRefGoogle Scholar
  28. Haiss W, Albrecht T, van Zalinge H, Higgins SL, Bethell D, Höbenreich H, Schiffrin DJ, Nichols RJ, Kuznetsov AM, Zhang J, Chi Q, Ulstrup J (2007) Single molecule condutance of redox molecules in electrochemical scanning tunneling microscopy. J Phys Chem B 111:6703–6712CrossRefGoogle Scholar
  29. Hatzor A, Weiss PS (2001) Molecular rulers for scaling down nanostructures. Science 291:1019–1020Google Scholar
  30. He J, Lin L, Zhang P, Lindsay S (2007) Identification of DNA basepairing via tunnel-current decay. Nano Lett 7:3854–3858CrossRefGoogle Scholar
  31. He YH, Scheicher RH, Grigoriev A, Ahuja R, Long SB, Huo ZL, Liu M (2001) Enhanced DNA sequencing performance through edge-hydrogenation of graphene electrodes. Adv Funct Mater 21:2674–2679CrossRefGoogle Scholar
  32. Heerema SJ, Dekker C (2016) Graphene nanodevices for DNA sequencing. Nat Nanotechnol 11:127–134CrossRefGoogle Scholar
  33. Hong G, Wu Q-H, Ren J, Wang C, Zhang W, Lee S-T (2013) Recent progress in organic molecule/graphene interfaces. Nano Today 8:388–402CrossRefGoogle Scholar
  34. Horri A, Faez R, Pourfath M, Darvish G (2017a) A computational study of vertical tunneling transistors based on graphene-WS2 heterostructure. J Appl Phys 121:214503CrossRefGoogle Scholar
  35. Horri A, Faez R, Pourfath M, Darvish G (2017b) Modelling of a vertical tunneling transistors based on graphene-WS2 heterostructure. IEEE Trans Elect Dev 99:1–7Google Scholar
  36. Horri A, Faez R, Darvish G (2017c) Numerical simulation of vertical tunneling transistor with bilayer graphene as source and drain regions. Phys Sta Solidi A 214:1700155CrossRefGoogle Scholar
  37. Howorka S, Siwy Z (2009) Nanopore analytics: sensing of single molecules. Chem Soc Rev 38:2360–2384CrossRefGoogle Scholar
  38. Iqbal SM, Akin D, Bashir R (2007) Solid-state nanopore channels with DNA selectivity. Nat Nanotechnol 2:243–248CrossRefGoogle Scholar
  39. Ivanov AP, Instuli E, McGilvery CM, Baldwin G, McComb DW, Albrecht T, Ede JB (2011) DNA tunneling detector embedded in a nanopore. Nano Lett 11:279–285CrossRefGoogle Scholar
  40. Jo G, Choe M, Cho CY, Kim JH, Park W, Lee S, Hong WK, Kim TW, Park SJ, Hong BH, Kahng YH, Lee T (2010) Large-scale patterned multi-layer graphene films as transparent conducting electrodes for GaN light-emitting diodes. Nanotechnology 21:175201–175206CrossRefGoogle Scholar
  41. Jo G, Choe M, Lee S, Park W, Kahng YH, Lee T (2012) The application of graphene as electrodes in electrical and optical devices. Nanotechnology 23:112001CrossRefGoogle Scholar
  42. Kima T, Liu Z-F, Lee C, Neaton JB, Venkataramana L (2014) Charge transport and rectification in molecular junctions formed with carbon-based electrodes. PNAS 111:10928–10932CrossRefGoogle Scholar
  43. Kokalj A (2003) Computer graphics and graphical user interfaces as tools in simulations of matter at the atomic scale. Compl Mat Sci 28:155–168CrossRefGoogle Scholar
  44. Krems M, Zwolak M, Pershin YV, Di Ventra M (2009) Effect of noise on DNA sequencing via transverse electronic transport. Biophys J 97:1990–1996CrossRefGoogle Scholar
  45. Lagerqvist J, Zwolak M, Ventra M (2006) Fast DNA sequencing via transverse electronic transport. Nano Lett 6:779–782CrossRefGoogle Scholar
  46. Lagerqvist J, Zwolak M, Di Ventra M (2007a) Comment on characterization of the tunneling conductance across DNA bases. Phys Rev E 76:013901/1–3CrossRefGoogle Scholar
  47. Lagerqvist J, Zwolak M, Ventra M (2007b) Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport. Biophys J 93:2384–2390CrossRefGoogle Scholar
  48. Landheer D, Aers G, McKinnon WR, Deen MJ, Ranuarez JC (2005) Model for the field effect from layers of biological macromolecules on the gates of metal-oxide-semiconductor transistors. J Appl Phys 98:044701/1–15CrossRefGoogle Scholar
  49. Landheer D, McKinnon WR, Aers G, Jiang W, Deen MJ, Shinwari MW (2007) Calculation of the response of field-effect transistors to charged biological molecules. IEEE Sens J 7:1233–1242CrossRefGoogle Scholar
  50. Liu H, He J, Tang J, Liu H, Pang P, Cao D, Krstic P, Joseph S, Lindsay S, Nuckolls C (2010) Translocation of single-stranded DNA through single-walled carbon nanotubes. Science 327:64–67CrossRefGoogle Scholar
  51. Mol JA, Lau CS, Lewis WJM, Sadeghi H, Roche C, Cnossen A, Warner JH, Lambert CJ, Anderson HL, Briggs GAD (2015) Graphene-porphyrin single-molecule transistors. Nanoscale 7:13181–13185CrossRefGoogle Scholar
  52. Nakada K, Fujita M, Dresselhaus MS, Dresselhaus MM (1996) Edge state in graphene ribbons: nanometer size effect and edge shape dependence. Phys Rev B 54:17954–17961CrossRefGoogle Scholar
  53. Nelson T, Zhang B, Prezhdo OV (2010) Detection of nucleic acids with graphene nanopores: ab initio characterization of a novel sequencing device. Nano Lett 10:3237–3242CrossRefGoogle Scholar
  54. Nicewarner-Pena SR, Freeman RG, Reiss BD, He L, Pena DJ, Walton ID, Cromer R, Keating CD, Natan MJ (2001) Submicrometer metallic barcodes. Science 294:137–141CrossRefGoogle Scholar
  55. Park H, Lim AKL, Alivisatos AP, Park J, McEuen PL (1999) Fabrication of metallic electrodes with nanometer separation by electromigration. Appl Phys Lett 75:301–303CrossRefGoogle Scholar
  56. Postma HWCh (2010) Rapid sequencing of individual DNA molecules in graphene nanogaps. Nano Lett 10:420–425CrossRefGoogle Scholar
  57. Prasongkit J, Grigoriev A, Pathak B, Ahuja R, Scheicher RH (2011) Transverse conductance of dna nucleotides in a graphene nanogap from first principles. Nano Lett 11:1941–1945CrossRefGoogle Scholar
  58. Prasongkit J, Grigoriev A, Pathak B, Ahuja R, Scheicher RH (2013) Theoretical study of electronic transport through DNA nucleotides in a double-functionalized graphene nanogap. J Phys Chem C 117:15421–15428CrossRefGoogle Scholar
  59. Qin L, Park S, Huang L, Mirkin CA (2005) On-wire lithography. Science 309:113–115CrossRefGoogle Scholar
  60. Reed MA, Zhou C, Muller CJ, Burgin TP, Tour JM (1997) Conductance of a molecular junction. Science 278:252–254CrossRefGoogle Scholar
  61. Ritter KA, Lyding JW (2009) The influence of edge structure on the electronic properties of graphene quantum dots and nanoribbons. Nat Mater 8:235–242CrossRefGoogle Scholar
  62. Rogers JA, Somya T, Huang Y (2010) Materials and mechanics for stretchable electronics. Science 327:1603–1607CrossRefGoogle Scholar
  63. Sader JE, Uchihashi T, Higgins MJ, Farrell A, Nakayama Y, Jarvis SP (2005) Quantitative force measurements using frequency modulation atomic force microscopy—theoretical foundations. Nanotechnology 16:S94–S101CrossRefGoogle Scholar
  64. Saha KK, Drndić M, Nikolić BK (2012) DNA base-specific modulation of a transverse edge currents through a metallic graphene nanoribbon with a nanopore. Nano Lett 12:50–55CrossRefGoogle Scholar
  65. Sathe C, Zou X, Leburton J-P, Schulten K (2011) Computational investigation of DNA detection using graphene nanopores. ACS Nano 5:8842–8851CrossRefGoogle Scholar
  66. Schneider GF, Kowalczyk SW, Calado VE, Pandraud G, Zandbergen H, Vandersypen LMK, Dekker C (2010) DNA translocation through graphene nanopores. Nano Lett 630 10:3163–3167CrossRefGoogle Scholar
  67. Shinwari MW, Deen MJ, Landheer D (2007) Study of the electrolyte-insulator-semiconductor field-effect transistor (EISFET) with applications in biosensor design. Microelectron Reliab 47:2025–2057CrossRefGoogle Scholar
  68. Shinwari MW, Deen MJ, Starikov EB, Cuniberti G (2010) Electrical conductance in biological molecules. Adv Func Mater 20:1865–1883CrossRefGoogle Scholar
  69. Son Y-W, Cohen ML, Louie SG (2006) Energy gaps in graphene nanoribbons. Phys Rev Lett 97:216803CrossRefGoogle Scholar
  70. Sorgenfrei S, Chiu C-y, Gonzalez Jr RL, Yu Y-J, Kim P, Nuckolls C, Shepard KL (2011) Label-free single-molecule detection of DNA-hybridization kinetics with a carbon nanotube field-effect transistor. Nat Nanotechnol 6:126– 132CrossRefGoogle Scholar
  71. Storm AJ, Storm C, Chen JH, Zanderbergen H, Joanny JF, Dekker C (2005) Fast DNA translocation through a solid-state nanopore. Nano Lett 5:1193–1197CrossRefGoogle Scholar
  72. Sun L, Diaz-Fernandez YA, Gschneidtner TA, Westerlund F, Lara-Avilab S, Moth-Poulsen K (2014) Single-molecule electronics: from chemical design to functional devices. Chem Soc Rev 43:7378–7411CrossRefGoogle Scholar
  73. Taniguchi M, Tsutsui M, Yokota K, Kawai T (2009) Fabrication of the gating nanopore device. Appl Phys Lett 95:123701–123703CrossRefGoogle Scholar
  74. Tetienne JP, THingant T, Kim JV, Diez LH, Adam JP, Garcia K, Roch JF, Rohart S, Thiaville A, Ravelosona D, Jacques V (2014) Nanoscale imaging and control of domain-wall hopping with a nitrogen-vacancy center microscope. Science 344:1366–1369CrossRefGoogle Scholar
  75. Tour JM (2000) Molecular electronics. Synthesis and testing of components. Acc Chem Res 33:791–804CrossRefGoogle Scholar
  76. Troisi A, Ratner MA (2006) Molecular signatures in the transport properties of molecular wire junctions: what makes a junction molecular Small 2:172–181CrossRefGoogle Scholar
  77. Ventra MD, Pantelides ST, Lang ND (2000) First-principles calculation of transport properties of a molecular device. Phys Rev Lett 84:979–982CrossRefGoogle Scholar
  78. Wang J, Shen F, Wang Z, He G, Qin J, Cheng N, Yao M, Li L, Guo X (2014) Point decoration of silicon nanowires: an approach toward single-molecule electrical detection. Angew Chem 53:5038–5043Google Scholar
  79. Wang W, Lee T, Reed MA (2007) Electrical characterization of self-assembled monolayers. In: Lyshevski SE (ed) Nano and molecular electronics handbook. Chapter 1, pp 3. CRC Press, Boca RatonGoogle Scholar
  80. Wolf SA, Awschalom DD, Buhrman RA, Daughton JM, Molnar von S, Roukes ML, Chtchelkanova AY, Treger DM (2001) Spintronics: a spin-based electronics vision for the future. Science 294:1488–1495CrossRefGoogle Scholar
  81. Wu M-Y, Smeets RMM, Zandbergen M, Ziese U, Krapf D, Batson PE, Dekker NH, Dekker C, Zandbergen HW (2009) Control of shape and material composition of solid-state nanopores. Nano Lett 9:479–484CrossRefGoogle Scholar
  82. Wu Y, Farmer DB, Xia F, Avouris P (2013) Graphene electronics, materials, devices, and circuits. Proc IEEE 101:1620–1637CrossRefGoogle Scholar
  83. Xu BQ, Xiao XY, Tao NJ (2003) Measurements of single-molecule electromechanical properties. J Am Chem Soc 125:16164–16165CrossRefGoogle Scholar
  84. Yaghmaie F, Fleck J, Gusman A, Prohaska R (2010) Improvement of PMMA electron-beam lithography performance in metal liftoff through a poly-imide bi-layer system. Microelectron Eng 87:2629–2632CrossRefGoogle Scholar
  85. Yan Y, Erickson BW, Tropsha A (1995) Free energies for folding and refolding of four types of .beta. Turns: simulation of the role of D/L chirality. J Amer Chem Soc 117:7592–7593CrossRefGoogle Scholar
  86. Zhao Y, Ashcroft B, Zhang P, Liu H, Sen S, Song W, Im J, Gyarfas B, Manna S, Biswas S, Borges C, Lindsay S (2014) Single molecule spectroscopy of amino acids and peptides by recognition tunneling. Nat Nanotechnol 9:466–473CrossRefGoogle Scholar
  87. Zhang J, Kuznetsov AM, Medvedev IG, Chi Q, Albrecht T, Jensen PS, Mertens SFL, Ulstrup J (2007) Intrinsic multistate switching of gold clusters through electrochemical gating. J Am Chem Soc 129:9162–9167CrossRefGoogle Scholar
  88. Zhou Y-h, Y-l Peng, Yuan L-z (2013) World congress on medical physics and biomedical engineering. IFMBE Proc 39:317CrossRefGoogle Scholar
  89. Zikic R, Krstic PS, Zhang X-G, Fuentes-Cabrera M, Wells J, Zhao X (2006) Characterization of the tunneling conductance across DNA bases. Phys Rev E 74:011919/1–9CrossRefGoogle Scholar
  90. Zwolak M, Di Ventra M (2005) Electronic signature of DNA nucleotides via transverse transport. Nano Lett 5:421–424CrossRefGoogle Scholar
  91. Zwolak M, Di Ventra M (2008) Colloquium: physical approaches to DNA sequencing and detection. Rev Mod Phys 80:141–165CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  • Puspitapallab Chaudhuri
    • 1
    • 4
    Email author
  • H. O. Frota
    • 1
  • Cicero Mota
    • 2
  • Angsula Ghosh
    • 1
    • 3
  1. 1.Department of PhysicsFederal University of AmazonasManausBrazil
  2. 2.Department of MathematicsFederal University of AmazonasManausBrazil
  3. 3.Institute of PhysicsUniversity of São PauloSão PauloBrazil
  4. 4.Institute for Theoretical PhysicsSão Paulo State UniversitySão PauloBrazil

Personalised recommendations