A theoretical study on the chirality detection of serine amino acid based on carbon nanotubes with and without Stone-Wales defects

  • Zeynab Mohammad Hosseini Naveh
  • Mohaddeseh Mehmandoust KhajehdadEmail author
  • Masoud Majidiyan Sarmazdeh
Original Research


In the present study, the interaction of serine (SER) amino acid (AA) with the pristine and defected carbon nanotubes (CNTs) has been investigated by employing the molecular dynamics (MD) and the density functional theory (DFT) approaches. Furthermore, the potential application of CNTs with and without the Stone-Wales (SW) defects in sensing of SER chirality has been studied. Our results confirm that introducing the chiral l and d SERs (LSER and DSER) exerts a significant effect on the electronic and optical properties of the CNTs with and without the SW defect. According to the MD results, it is observed that for all the structures, the obtained minimum distance is among the SER aliphatic segments and the tube atoms. The calculated structural and electronic properties of pristine and defected CNT are in good agreement with the reported research studies. The results indicate that pyramidalization angles (θp) at C atoms are altered in the presence of the SW defects. The overall increment of θp suggests that the reactivity has increased at the defective regions. In the case of CNT with one SW defect (CNTSW1), the central C–C bond of the SW defect is the most chemically reactive site. Our results establish that pristine CNT is a semiconductor when the LSER and DSER are adsorbed (with the band gap of 0.30 eV and 0.32 eV, respectively). The LSER-adsorbing CNT with two SW defects (CNTSW2) is a semiconductor with a reduced band gap (0.41 eV), while the DSER-adsorbing CNTSW2 is an n-type semiconductor (with a band gap of 0.70 eV). The optical properties are inferred from the dielectric functions of the CNTs. The most remarkable result belongs to the CNTSW2; the imaginary part of the CNTSW2 dielectric function can sensitively distinguish the chirality of the SER amino acid.


Density functional theory Molecular dynamics simulation Carbon nanotube SER amino acid Chirality Stone-Wales defect Biosensor 


Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


  1. 1.
    Iijima S (1991) Helical microtubules of graphitic carbon. Nature 354:56–58CrossRefGoogle Scholar
  2. 2.
    Kong J, Franklin NR, Zhou C, Chapline MG, Peng S, Cho K, Dai H (2000) Nanotube molecular wires as chemical sensors. Science 287:622–625CrossRefGoogle Scholar
  3. 3.
    Collins PG, Bradley K, Ishigami M, Zettl A (2000) Extreme oxygen sensitivity of electronic properties of carbon nanotubes. Science 287:1801–1804CrossRefGoogle Scholar
  4. 4.
    Besteman K, Lee JO, Wiertz FGM, Heering HA, Dekker C (2003) Enzyme-coated carbon nanotubes as single-molecule biosensors. Nano Lett 3:727–730CrossRefGoogle Scholar
  5. 5.
    Chen RJ, Bangsaruntip S, Drouvalakis KA, Wong Shi Kam N, Shim M, Li Y, Kim W, Utz PJ, Dai H (2003) Non-covalent sidewall functionalization of carbon nanotubes for highly specific biosensors. PNAS 100:4984–4989CrossRefGoogle Scholar
  6. 6.
    Bradley K, Grner G, Star A, Gabriel JCP (2003) Electronic detection of specific protein binding using nanotube FET devices. Nano Lett 3:459–463CrossRefGoogle Scholar
  7. 7.
    Roman T, Dino WA, Nakanishi H, Kasai H (2006) Amino acid adsorption on single-walled carbon nanotubes. Eur Phys J D 38:117CrossRefGoogle Scholar
  8. 8.
    Su Z, Mui K, Daub E, Leung T, Honek J (2007) Single-walled carbon nanotube binding peptides: probing tryptophans importance by unnatural amino acid substitution. J Phys Chem B 111:14411–14417CrossRefGoogle Scholar
  9. 9.
    Leon D, Jalbout AF, Basiuk VA (2008) SWNT-amino acid interactions: a theoretical study. Chem Phys Lett 457:185–190CrossRefGoogle Scholar
  10. 10.
    Ganji MD (2009) Density functional theory based treatment of amino acids adsorption, on single-walled carbon nanotubes. Diamond and Relat Mater 18:662–668CrossRefGoogle Scholar
  11. 11.
    Monajjemi M, Kharghanian L, Khaleghian M, Chegini H (2014) Quantum study of amino acid bind to carbon nanotube in view of magnetic properties. Fullerenes Nanotubes Carbon Nanostruc 22:709–725CrossRefGoogle Scholar
  12. 12.
    Cuihong W, Yue J, Guangwu Y (2015) Comprehensive study of threonine adsorption on carbon nanotube: a dispersion complemented density functional theory-based treatment. Int J Quantum Chem 115:1606–1612CrossRefGoogle Scholar
  13. 13.
    Jiang L, Zhu C, Fu Y, Yang G (2017) Amino acid functionalization of doped single-walled carbon nanotubes: effects of dopants and side chains as well as zwitterionic stabilizations. J Phys Chem B 121:2721–2730CrossRefGoogle Scholar
  14. 14.
    He Z, Zhou J (2014) Probing carbon nanotube-amino acid interactions in aqueous solution with molecular dynamics simulations. Carbon 78:500–509CrossRefGoogle Scholar
  15. 15.
    Az’hari S, Ghayeb Y (2014) Effect of chirality, length and diameter of carbon nanotubes on the adsorption of 20 amino acids: a molecular dynamics simulation study. Mol Simul 40:392–398CrossRefGoogle Scholar
  16. 16.
    Wu E, Coppens MO, Garde S (2015) Role of arginine in mediating protein-carbon nanotube interactions. Langmuir 31:1683–1692CrossRefGoogle Scholar
  17. 17.
    Barzegar A, Mansouri A, Azamat J (2016) Molecular dynamics simulation of non-covalent single-walled carbon nanotube functionalization with surfactant peptides. J Mol Graph Model 64:75–84CrossRefGoogle Scholar
  18. 18.
    Al-Qattan MN, Deb PK, Rakesh K (2018) Molecular dynamics simulation strategies for designing carbon-nanotube-based targeted drug delivery. Drug Discov Today 23:235–250CrossRefGoogle Scholar
  19. 19.
    Grabill L, Riemann A (2018) Conformational impact on amino acid-surface π-π interactions on a (7,7) single-walled carbon nanotube: a molecular mechanics approach. J Phys Chem A 122:1713–1726CrossRefGoogle Scholar
  20. 20.
    Walus K, Abadir GB, Pulfrey DL (2010) Bias-dependent amino-acid-induced conductance changes in short semi-metallic carbon nanotubes. Nanotechnology 21:015202CrossRefGoogle Scholar
  21. 21.
    Wang J (2018) Near infrared optical biosensor based on peptide functionalized single-walled carbon nanotubes hybrids for 2,4,6-trinitrotoluene (TNT) explosive detection. Anal Biochem 550:49–53CrossRefGoogle Scholar
  22. 22.
    Cai Y, Wei Z, Song C, Tang C, Han W, Dong X (2019) Optical nano-agents in the second near-infrared window for biomedical applications. Chem Soc Rev 48:22–37CrossRefGoogle Scholar
  23. 23.
    Hong G, Antaris AL, Dai H (2017) Near-infrared fluorophores for biomedical imaging, nature biomedical engineering. Nat Biomed Eng 1:0010CrossRefGoogle Scholar
  24. 24.
    Antonucci A, Kupis-Rozmysowicz J, Boghossian AA (2017) Noncovalent protein and peptide functionalization of single-walled carbon nanotubes for biodelivery and optical sensing applications. ACS Appl Mater Interfaces 9:11321–11331CrossRefGoogle Scholar
  25. 25.
    O’Connell MJ, Bachilo SM, Huffman CB, Moore VC, Strano MS, Haroz EH, Rialon KL, Boul PJ, Noon WH, Kittrell C, Ma J, Hauge RH, Weisman RB, Smalley RE (2002) Band gap fluorescence from individual single-walled carbon nanotubes. Science 297:593CrossRefGoogle Scholar
  26. 26.
    Lee K, Nojoomi A, Jeon J, Lee CY, Yum K (2018) Near-infrared fluorescence modulation of refolded DNA aptamer-functionalized single-walled carbon nanotubes for optical sensing. ACS Appl Nano Mater 1:5327–5336CrossRefGoogle Scholar
  27. 27.
    Yoon H, Ahn JH, Barone PW, Yum K, Sharma R, Boghossian A, Han JH, Strano MS (2011) Periplasmic binding proteins as optical modulators of single-walled carbon nanotube fluorescence: amplifying a nanoscale actuator. Angewandte Chemie-Int Ed 50:1828–1831CrossRefGoogle Scholar
  28. 28.
    Tsai TW, Heckert G, Neves LF, Tan Y, Kao DY, Harrison RG, Resasco DE, Schmidtke DW (2009) Adsorption of glucose oxidase onto single-walled carbon nanotubes and its application in layer-by-layer biosensors. Anal Chem 81:7917–7925CrossRefGoogle Scholar
  29. 29.
    Heller DA, Baik S, Eurell TE, Strano MS (2005) Single-walled carbon nanotube spectroscopy in live cells: towards long-term labels and optical sensors. Adv Mater 17:2793–2799CrossRefGoogle Scholar
  30. 30.
    Liu Z, Davis C, Cai W, He L, Chen X, Dai H (2008) Circulation and long-term fate of functionalized, biocompatible single-walled carbon nanotubes in mice probed by Raman spectroscopy. Proc Natl Acad Sci U S A 105:1410–1415CrossRefGoogle Scholar
  31. 31.
    Zavaleta C, de la Zerda A, Liu Z, Keren S, Cheng Z, Schipper M, Chen X, Dai H, Gambhir SS (2008) Noninvasive Raman spectroscopy in living mice for evaluation of tumor targeting with carbon nanotubes. Nano Lett 8:2800–2805CrossRefGoogle Scholar
  32. 32.
    Liu Z, Tabakman S, Sherlock S, Li X, Chen Z, Jiang K, Fan S, Dai H (2010) Multiplexed five-color molecular imaging of cancer cells and tumor tissues with carbon nanotube Raman tags in the near-infrared. Nano Res 3:222–233CrossRefGoogle Scholar
  33. 33.
    Gong H, Peng R, Liu Z (2013) Carbon nanotubes for biomedical imaging: the recent advances. Adv Drug Deliv Rev 65:1951–1963CrossRefGoogle Scholar
  34. 34.
    Stone AJ, Wales DJ (1986) Theoretical studies of icosahedral C60 and some related species. Chem Phys Lett 128:501CrossRefGoogle Scholar
  35. 35.
    Prachamon W, Limpijumnong S, Komin S (2018) Optical transitions of native defects in single-walled carbon nanotubes: time-dependent density functional theory study. Integr Ferroelectr 187:1–13CrossRefGoogle Scholar
  36. 36.
    Badehian HA, Gharbavi K, Ghazi SM (2019) First-principle investigation of the mechanical and transport properties of the zigzag carbon nanotubes (n, 0) (n=4, 5) with Stone-Wales defects. Iran J Sci Technol Trans A Sci 43:1303–1309CrossRefGoogle Scholar
  37. 37.
    Dinadayalane TC, Leszczynski J (2016) Fundamental structural, electronic, and chemical properties of carbon nanostructures: graphene, fullerenes, carbon nanotubes, and their derivatives. In: Leszczynski J (ed) Handbook of computational chemistry. Springer, Dordrecht, pp 793–867Google Scholar
  38. 38.
    Zanolli Z, Charlier JC (2009) Defective carbon nanotubes for single-molecule sensing. Phys Rev B 80:155447CrossRefGoogle Scholar
  39. 39.
    Roh S, Lee J, Jang M, Shin M, Ahn J, Park T, Yi W (2010) Characteristic features of Stone-Wales defects in single-walled carbon nanotube; adsorption, dispersion, and field emission. J Nanomater 2010:398621CrossRefGoogle Scholar
  40. 40.
    Arasteh J, Naseh M (2018) DFT study of arsine (AsH3) gas adsorption on pristine, Stone-Wales defected, and Fe-doped single-walled carbon nanotubes. Struct Chem 30:97–105CrossRefGoogle Scholar
  41. 41.
    McConathy J, Owens MJ (2003) Stereochemistry in drug action. Prim Care Companion J Clin Psychiatry 5:70–73CrossRefGoogle Scholar
  42. 42.
    Grant SL, Shulman Y, Tibbo P, Hampson DR, Baker GB (2006) Determination of D-serine and related neuroactive amino acids in human plasma by high-performance liquid chromatography with uorimetric detection. J Chromatogr B 844:278–282CrossRefGoogle Scholar
  43. 43.
    Panizzutti R, Fisher M, Garrett C, Man WH, Sena W, Madeira C, Vinogradov S (2018) Association between increased serum D-serine and cognitive gains induced by intensive cognitive training in schizophrenia. Schizophr Res 207:63–69CrossRefGoogle Scholar
  44. 44.
    Butyrskaya E, Zapryagaev S, Izmailova E, Nechaeva L (2017) Sorption interactions between l/d-alanine and carbon nanotubes in aqueous solutions. J Phys Chem C 121:20524–20531CrossRefGoogle Scholar
  45. 45.
    Hohenberg P, Kohn W (1964) Inhomogeneous electron gas. Phys Rev 136:B864CrossRefGoogle Scholar
  46. 46.
    Sanchez-Portal D, Artacho E, Ordejon P, Soler JM (1997) Density-functional method for very large systems with LCAO basis sets. Int J Quantum Chem 65:453–461CrossRefGoogle Scholar
  47. 47.
    Ordejon P, Artacho E, Soler JM (1996) Self-consistent order-N density-functional calculations for very large systems. Phys Rev B 53:R10441CrossRefGoogle Scholar
  48. 48.
    Perdew JP, Burke K, Ernzerhof M (1996) Generalized gradient approximation made simple. Phys Rev Lett 77:3865–3868CrossRefGoogle Scholar
  49. 49.
    Troullier N, Martins JL (1990) A straightforward method for generating soft transferable pseudopotentials. Solid State Comm 74:613–616CrossRefGoogle Scholar
  50. 50.
    Troullier N, Martins JL (1991) Efficient pseudopotentials for plane-wave calculations. II. Operators for fast iterative diagonalization. Phys Rev B 43:8861–8869CrossRefGoogle Scholar
  51. 51.
    Monkhorst HJ, Pack JD (1976) Special points for brillouin-zone integrations. Phys Rev B 13:5188–5192CrossRefGoogle Scholar
  52. 52.
    Wooten F (1972) Optical properties of solids. Academic Press, New YorkGoogle Scholar
  53. 53.
    Bachilo SM, Strano MS, Kittrell C, Hauge RH, Smalley RE, Weisman RB (2002) Structure-assigned optical spectra of single-walled carbon nanotubes. Science 298:2361–2366CrossRefGoogle Scholar
  54. 54.
    Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781–1802CrossRefGoogle Scholar
  55. 55.
    Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) Charmm: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187–217CrossRefGoogle Scholar
  56. 56.
    Jorgensen W, Chandrasekhar J, Madura J, Impey R, Klein M (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935CrossRefGoogle Scholar
  57. 57.
    Lasdon LS, Mitter SK, Waren AD (1967) The conjugate gradient method for optimal control problems. IEEE Trans Autom Control 12:132–138CrossRefGoogle Scholar
  58. 58.
    Quigley D, Probert MIJ (2004) Langevin dynamics in constant pressure extended systems. J Chem Phys 120:11432–11441CrossRefGoogle Scholar
  59. 59.
    Allen MP, Tildesley DJ (1989) Computer simulation of liquids. Oxford Science publications, Oxford University Press, USAGoogle Scholar
  60. 60.
    Darden T, York D, Pedersen L (1993) Particle mesh ewald: an n log(n) method for ewald sums in large systems. J Chem Phys 98:10089–10093CrossRefGoogle Scholar
  61. 61.
    Lefebvre J, Ding J, Li Z, Finnie P, Lopinski G, Malenfant PRL (2017) High-purity semiconducting single-walled carbon nanotubes: a key enabling material in emerging electronics. Acc Chem Res 50:2479–2486CrossRefGoogle Scholar
  62. 62.
    Cao Q, Tersoff J, Farmer DB, Zhu Y, Han S (2017) Carbon nanotube transistors scaled to a 40-nanometer footprint. Science 356:1369–1372CrossRefGoogle Scholar
  63. 63.
    Otsuka K, Inoue T, Maeda E, Kometani R, Chiashi S, Maruyama S (2017) On-chip sorting of long semiconducting carbon nanotubes for multiple transistors along an identical array. ACS Nano 11:11497–11504CrossRefGoogle Scholar
  64. 64.
    Jain A, Homayoun A, Bannister CW, Yum K (2015) Single-walled carbon nanotubes as near-infrared optical biosensors for life sciences and biomedicine. Biotechnol J 10:447–459CrossRefGoogle Scholar
  65. 65.
    Liu Z, Tabakman S, Welsher K, Dai H (2009) Carbon nanotubes in biology and medicine: in vitro and in vivo detection, imaging and drug delivery. Nano Res 2:85–120CrossRefGoogle Scholar
  66. 66.
    Dai M, Zhao L, Gao H, Sun P, Liu F, Zhang S, Shimanoe K, Yamazoe N, Lu G Hierarchical assembly of α-Fe2O3 nanorods on multiwall carbon nanotubes as a high-performance sensing material for gas sensors. ACS Appl Mater Interfaces 9:8919–8928Google Scholar
  67. 67.
    Haddon RC (1993) Chemistry of the fullerenes: the manifestation of strain in a class of continuous aromatic molecules. Science 261:1545–1550CrossRefGoogle Scholar
  68. 68.
    Gulseren O, Yildirim T, Ciraci S (2001) Tunable adsorption on carbon nanotubes. Phys Rev Lett 87:116802CrossRefGoogle Scholar
  69. 69.
    Dinadayalane TC, Leszczynski J (2007) Stone-Wales defects with two different orientations in (5, 5) single-walled carbon nanotubes: a theoretical study. Chem Phys Lett 434:86–91CrossRefGoogle Scholar
  70. 70.
    Pan L, Shenaand Z, Jia Y, Dai X (2012) First-principle s study of electronic and elastic properties of Stone-Wales defective zigzag car bon nanotubes. Physica B 407:2763–2767CrossRefGoogle Scholar
  71. 71.
    Wong H, Akinwande D (2010) Carbon nanotube equilibrium properties. Carbon nanotube and graphene device physics. Cambridge University Press, Cambridge, pp 102–127CrossRefGoogle Scholar
  72. 72.
    Rao AM, Richter E, Bandow S, Chase B, Eklund PC, Williams KA, Fang S, Subbaswamy KR, Menon M, Thess A, Smalley RE, Dresselhaus G, Dresselhaus MS (1997) Diameter-selective Raman scattering from vibrational modes in carbon nanotubes. Science 275:187–191CrossRefGoogle Scholar
  73. 73.
    Hoddon RC (2001) Comment on the relationship of the pyramidalization angle at a conjugated carbon atom to the bond angles. J Phys Chem A 105:4164–4165CrossRefGoogle Scholar
  74. 74.
    Doudou BB, Chen J, Vivet A, Poîlane C, Ayachi M (2011) Role of Stone–Wales defects on the functionalization of (8, 0) single wall carbon nanotubes by the amine group: ab initio study. Physica E 44:120–123CrossRefGoogle Scholar
  75. 75.
    Zhou QX, Wang CY, Fu ZB, Tang YJ, Zhang H (2014) Effects of various defects on the electronic properties of single-walled carbon nanotubes : a first principle study. Front Phys 9:200–209CrossRefGoogle Scholar
  76. 76.
    Molarooy T, Hosseini SM, Kompany A, Shahtahmasebi N (2011) Ab initio calculations of electronic structure and optical spectra of (13,0) carbon nanotube. Int J Nanosci 10:587–590CrossRefGoogle Scholar
  77. 77.
    Molarooy T, Kompany A, Hosseini SM, Shahtahmasebi N (2010) Optical absorption and electron energy loss spectra of single-walled carbon nanotubes. Comput Mater Sci 49:450–456CrossRefGoogle Scholar
  78. 78.
    Fa W, Yang X, Chen J, Dong J (2004) Optical properties of the semiconductor carbon nanotube intra-molecular junctions. Phys Lett A 323:122–131CrossRefGoogle Scholar

Copyright information

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Authors and Affiliations

  • Zeynab Mohammad Hosseini Naveh
    • 1
  • Mohaddeseh Mehmandoust Khajehdad
    • 2
    Email author
  • Masoud Majidiyan Sarmazdeh
    • 3
  1. 1.Kashmar Higher Education InstituteKashmarIran
  2. 2.Department of PhysicsPayame Noor University (PNU)TehranIran
  3. 3.School of PhysicsDamghan UniversityDamghanIran

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