Skip to main content
SpringerLink
Log in

Structural and electronic properties of adsorbed nucleobases on pristine and Al-doped coronene in absence and presence of external electric fields: a computational study

  • Original Research
  • Published:
Structural Chemistry Aims and scope Submit manuscript

Abstract

The adsorption of nucleobases (NBs) on pristine and aluminum-doped coronene (Al-coronene) has been studied theoretically using density functional theory (DFT) method in the presence/absence of external electric fields (EFs) having different strengths. The changes in geometric and electronic structures upon the adsorption were analyzed in order to reveal the sensitivity of pristine coronene and Al-coronene toward NBs. The results of theoretical calculations at wB97XD/6–31G(d,p) level of theory showed that the molecular adsorption of NBs on Al-coronene under the external EFs can induce significant change in Al-coronene conductivity. On the basis of calculated changes in band gap energy (ΔEg) and adsorption energy (Eads), it was found that electronic properties of Al-coronene, especially in presence of the applied EFs, are very sensitive to the adsorption of NBs. Finally, electronic structures analysis and full characterization of the surface interactions were performed using the quantum theory of atoms in molecules (QTAIM) to elucidate the nature of NB adsorption interaction. As a result, the enhanced electrical properties of NBs/Al-coronene-adsorbed complexes in the presence of the applied external EFs indicated promising perspectives for fabrication of new NBs-sensing devices.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

References

  1. Hanawalt PC, Spivak G (2008) Transcription–coupled DNA repair: two decades of progress and surprises. Nat Rev Mol Cell Biol 9(12):958–970

    CAS  PubMed  Google Scholar 

  2. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136(2):215–233

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Lister JH (2009) The chemistry of heterocyclic compounds, fused pyrimidines: the purines. Wiley

  4. Horton HR, Moran LA, Ochs RS, Rawn JD, Scrimgeour KG (1996) Principles of biochemistry. Prentice Hall Upper Saddle River, NY

    Google Scholar 

  5. Baei MT, Taghartapeh MR, Lemeski ET, Soltani A (2014) A computational study of adenine, uracil, and cytosine adsorption upon AlN and BN nano–cages. Phys B Condens Matter 444:6–13

    CAS  Google Scholar 

  6. Borhani B, Mohsennia M, Shakourian-Fard M (2019) Structural and electronic properties of adsorbed nucleobases on Si–doped hexagonal boron nitride nanoflake: a computational study. Struct Chem:1–11

  7. Mirzaei M, Yousefi M (2012) Computational studies of the purine–functionalized graphene sheets. Superlattice Microst 52(4):612–617

    CAS  Google Scholar 

  8. Cazorla C (2010) Ab initio study of the binding of collagen amino acids to graphene and A–doped (A= H, Ca) graphene. Thin Solid Films 518(23):6951–6961

    CAS  Google Scholar 

  9. Shtogun YV, Woods LM, Dovbeshko GI (2007) Adsorption of adenine and thymine and their radicals on single–wall carbon nanotubes. J Phys Chem C 111(49):18174–18181

    CAS  Google Scholar 

  10. Meyer M, Steinke T, Brandl M, Sühnel J (2001) Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes. J Comput Chem 22(1):109–124

    CAS  Google Scholar 

  11. Rauls E, Blankenburg S, Schmidt WG (2008) DFT calculations of adenine adsorption on coin metal (1 1 0) surfaces. Surf Sci 602(13):2170–2174

    CAS  Google Scholar 

  12. Artiles MS, Rout CS, Fisher TS (2011) Graphene–based hybrid materials and devices for biosensing. Adv Drug Deliv Rev 63:1352–1360

    CAS  PubMed  Google Scholar 

  13. Furukawa M, Yamada T, Katano S, Kawai M, Ogasawara H, Nilsson A (2007) Geometrical characterization of adenine and guanine on Cu (1 1 0) by NEXAFS, XPS, and DFT calculation. Surf Sci 601(23):5433–5440

    CAS  Google Scholar 

  14. Pagliai M, Caporali S, Muniz-Miranda M, Pratesi G, Schettino V (2012) SERS, XPS, and DFT study of adenine adsorption on silver and gold surfaces. J Phys Chem Lett 3(2):242–245

    CAS  PubMed  Google Scholar 

  15. Arsawang U, Saengsawang O, Rungrotmongkol T, Sornmee P, Wittayanarakul K, Remsungnen T, Hannongbua S (2011) How do carbon nanotubes serve as carriers for gemcitabine transport in a drug delivery system? J Mol Graph Model 29(5):591–596

    CAS  PubMed  Google Scholar 

  16. Saikia N, Deka RC (2011) Density functional calculations on adsorption of 2–methylheptylisonicotinate antitubercular drug onto functionalized carbon nanotube. Comput Theor Chem 964(1–3):257–261

    CAS  Google Scholar 

  17. Rosa M, Corni S, Di Felice R (2012) A density functional theory study of cytosine on Au (111). J Phys Chem C 116(40):21366–21373

    CAS  Google Scholar 

  18. Novoselov KS, Geim AK, Morozov SV, Jiang D, Zhang Y, Dubonos SV, Grigorieva IV, Firsov AA (2004) Electric field effect in atomically thin carbon films. Science 306(5696):666–669

    CAS  PubMed  Google Scholar 

  19. Ramraj A, Hillier IH, Vincent MA, Burton NA (2010) Assessment of approximate quantum chemical methods for calculating the interaction energy of nucleic acid bases with graphene and carbon nanotubes. Chem Phys Lett 484(4–6):295–298

    CAS  Google Scholar 

  20. Stepanian SG, Karachevtsev MV, Glamazda AY, Karachevtsev VA, Adamowicz L (2008) Stacking interaction of cytosine with carbon nanotubes: MP2, DFT and Raman spectroscopy study. Chem Phys Lett 459(1–6):153–158

    CAS  Google Scholar 

  21. Panigrahi S, Bhattacharya A, Banerjee S, Bhattacharyya D (2012) Interaction of nucleobases with wrinkled graphene surface: dispersion corrected DFT and AFM studies. J Phys Chem C 116(7):4374–4379

    CAS  Google Scholar 

  22. Umadevi D, Sastry GN (2011) Quantum mechanical study of physisorption of nucleobases on carbon materials: graphene versus carbon nanotubes. J Phys Chem Lett 2(13):1572–1576

    CAS  Google Scholar 

  23. Ataka K, Osawa M (1999) In situ infrared study of cytosine adsorption on gold electrodes. J Electroanal Chem 460(1–2):188–196

    CAS  Google Scholar 

  24. Otero R, Lukas M, Kelly RE, Xu W, Lægsgaard E, Stensgaard I, Kantorovich LN, Besenbacher F (2008) Elementary structural motifs in a random network of cytosine adsorbed on a gold (111) surface. Science 319(5861):312–315

    CAS  PubMed  Google Scholar 

  25. Vetterl V (1976) Electric field effect in the adsorption of adenosine and cytosine. Bioeletrochem Bioenerg 3(2):338–345

    CAS  Google Scholar 

  26. Yamada T, Shirasaka K, Takano A, Kawai M (2004) Adsorption of cytosine, thymine, guanine and adenine on Cu (1 1 0) studied by infrared reflection absorption spectroscopy. Surf Sci 561(2–3):233–247

    CAS  Google Scholar 

  27. Cristine E, Carneiro A, Berndt G, de Souza Junior IG, Cláudio M, de Souza D, Paesano A, Antonio C, Da Costa S, Di Mauro E, de Santana H (2011) Adsorption of adenine, cytosine, thymine, and uracil on sulfide–modified montmorillonite: FT–IR, Mossbauer and EPR spectroscopy and X–ray diffractometry studies. Orig Life Evol Biosph 41(5):453–468

    Google Scholar 

  28. Lone B (2016) Adsorption of cytosineon single–walled carbon nanotubes. J Nanomed Nanotechnol 7:354–357

    Google Scholar 

  29. Ricca A, Bauschlicher Jr CW, Boersma C, Tielens AG, Allamandola LJ (2012) The infrared spectroscopy of compact polycyclic aromatic hydrocarbons containing up to 384 carbons. J Astrophys J 754(1):75–96

    Google Scholar 

  30. Goumans TP, Uppal MA, Brown WA (2008) Formation of CO2 on a carbonaceous surface: a quantum chemical study. Mon Not R Astron Soc 384(3):1158–1164

    CAS  Google Scholar 

  31. Mahns B, Roth F, Knupfer M (2012) Absence of photoemission from the Fermi level in potassium intercalated picene and coronene films: Structure, polaron, or correlation physics? J Chem Phys 136(13):134503–134517

    PubMed  Google Scholar 

  32. Xu C, Que Y, Zhuang Y, Lin Z, Wu X, Wang K, Xiao X (2017) Growth behavior of pristine and potassium doped coronene thin films on substrates with tuned coupling strength. J Phys Chem B 122(2):601–611

    PubMed  Google Scholar 

  33. Zhang YH, Chen YB, Zhou KG, Liu CH, Zeng J, Zhang HL, Peng Y (2009) Improving gas sensing properties of graphene by introducing dopants and defects: a first–principles study. Nanotechnology 20(18):185504–185511

    PubMed  Google Scholar 

  34. Niu F, Tao LM, Deng YC, Wang QH, Song WG (2014) Phosphorus doped graphene nanosheets for room temperature NH3 sensing. New J Chem 38(6):2269–2272

    CAS  Google Scholar 

  35. Shokuhi Rad A, Zareyee D (2016) Adsorption properties of SO2 and O3 molecules on Pt–decorated graphene: a theoretical study. Vacuum 130:113–118

    CAS  Google Scholar 

  36. Anota EC, Soto AT, Cocoletzi GH (2014) Studies of graphene–chitosan interactions and analysis of the bioadsorption of glucose and cholesterol. Appl Nanosci 4(8):911–918

    Google Scholar 

  37. Shokuhi Rad A, Esfahanian M, Maleki S, Gharati G (2016) Application of carbon nanostructures toward SO2 and SO3 adsorption: a comparison between pristine graphene and N–doped graphene by DFT calculations. J Sulfur Chem 37(2):176–188

    CAS  Google Scholar 

  38. Rad AS, Abedini E (2016) Chemisorption of NO on Pt–decorated graphene as modified nanostructure media: a first principles study. Appl Surf Sci 360:1041–1046

    CAS  Google Scholar 

  39. Rad AS (2016) Adsorption of C2H2 and C2H4 on Pt–decorated graphene nanostructure: ab–initio study. Synth Met 211:115–120

    CAS  Google Scholar 

  40. Shokuhi Rad A (2016) Density functional theory study of the adsorption of MeOH and EtOH on the surface of Pt–decorated graphene. Phys E 83:135–140

    Google Scholar 

  41. Cortés-Arriagada D, Toro-Labbé A (2015) Improving As (iii) adsorption on graphene based surfaces: impact of chemical doping. Phys Chem Chem Phys 17:12056–12064

    PubMed  Google Scholar 

  42. Cortés-Arriagada D (2016) Expanding the environmental applications of metal (Al, Ti, Mn, Fe) doped graphene: adsorption and removal of 1, 4–dioxane. Phys Chem Chem Phys 18:32281–32292

    PubMed  Google Scholar 

  43. Cortés-Arriagada D, Toro-Labbé A (2016) Aluminum and iron doped graphene for adsorption of methylated arsenic pollutants. Appl Surf Sci 386:84–95

    Google Scholar 

  44. Rad AS, Zareyee D, Peyravi M, Jahanshahi M (2016) Surface study of gallium–and aluminum–doped graphenes upon adsorption of cytosine: DFT calculations. Appl Surf Sci 390:444–451

    Google Scholar 

  45. Rad AS, Jouibary YM, Foukolaei VP, Binaeian E (2016) Study on the structure and electronic property of adsorbed guanine on aluminum doped graphene: first principles calculations. Appl Phys 16(5):527–533

    Google Scholar 

  46. Hussain E, Cheng C, Li Y, Niu N, Zhou H, Jin X, Kong J, Yu C (2019) Benzo [ghi] perylene & coronene as ratiometric reversible optical oxygen nano-sensors. Sensors Actuators B Chem 287:27–34

    CAS  Google Scholar 

  47. Ganji MD, Hosseini-Khah SM, Amini-Tabar Z (2015) Theoretical insight into hydrogen adsorption onto graphene: a first–principles B3LYP–D3 study. Phys Chem Chem Phys 17(4):2504–2511

    Google Scholar 

  48. Velázquez-López LF, Pacheco-Ortin SM, Mejía-Olvera R, Agacino-Valdés E (2019) DFT study of CO adsorption on nitrogen/boron doped-graphene for sensor applications. J Mol Model 25(4):91–101

    PubMed  Google Scholar 

  49. Acharya CK, Turner CH (2007) Effect of an electric field on the adsorption of metal clusters on boron–doped carbon surfaces. J Phys Chem C 111(40):14804–14812

    CAS  Google Scholar 

  50. Tomanek D, Kreuzer HJ, Block JH (1985) Tight–binding approach to field desorption: N2 ON Fe (111). Surf Sci 157(1):315–322

    Google Scholar 

  51. Freitas A, Azevedo S, Kaschny JR (2013) Effects of a transverse electric field on the electronic properties of single–and multi–wall BN nanotubes. Solid State Commun 153(1):40–45

    CAS  Google Scholar 

  52. Chen CW, Lee MH, Clark CJ (2004) Band gap modification of single–walled carbon nanotube and boron nitride nanotube under a transverse electric field. Nanotechnology 15(12):1837–1843

    CAS  Google Scholar 

  53. Mohsennia M, Rakhshi M, Rasa H. (2018) A computational study on interactions of Ni– and Pt–doped boron nitride nano tubes with NH3 in presence and absence of electric fields Comput Theor Chem 1136:1–9

    CAS  Google Scholar 

  54. Rakhshi M, Mohsennia M, Rasa H, Sameti MR (2018) First–principle study of ammonia molecules adsorption on boron nitride nanotubes in presence and absence of static electric field and ion field. Vacuum 155:456–464

    CAS  Google Scholar 

  55. Afshari T, Mohsennia M (2018) Effect of external electric field on the adsorption of ethylene oxide on pristine and Al–doped coronenes: a DFT study. J Theor Comput Chem 17:1850032–1850043

    CAS  Google Scholar 

  56. Farmanzadeh D, Ghazanfary S (2009) First principle electric field response of single–walled boron nitride nanotube: a case study of zigzag (4, 0) model. Struct Chem 20(4):709–717

    CAS  Google Scholar 

  57. Chai JD, Head-Gordon M (2008) Long–range corrected hybrid density functionals with damped atom–atom dispersion corrections. Phys Chem Chem Phys 10(44):6615–6620

    CAS  PubMed  Google Scholar 

  58. Frisch M, Trucks G, Schlegel H, Scuseria G, Robb M, Cheeseman J, Scalmani G, Barone V, Mennucci B, Petersson G (2010) GAUSSIAN 09, Rev. C. 01, D. 01. Gaussian. Inc, Wallingford CT

  59. Grimme S (2006) Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J Comput Chem 27(15):1787–1799

    CAS  PubMed  Google Scholar 

  60. Liao MS, Huang MJ, Watts JD (2013) Binding of O2 and NO to heme in heme–nitric oxide/oxygen–binding (H–NOX) proteins. A Theoretical Study. J Phys Chem B 117(35):10103–10114

    CAS  PubMed  Google Scholar 

  61. Davidson ER, Feller D (1986) Basis set selection for molecular calculations. Chem Rev 86(4):681–696

    CAS  Google Scholar 

  62. Cortés-Arriagada D, Villegas-Escobar N, Miranda-Rojas S, Toro-Labbé A (2017) Adsorption/desorption process of formaldehyde onto iron doped graphene: a theoretical exploration from density functional theory calculations. Phys Chem Chem Phys 19(6):4179–4189

    PubMed  Google Scholar 

  63. Xu G, Lv W, Liu Y (2009) Effect of external electric field on the optical excitation of silicon dioxide. Acta Phys Sin 58(5):3058–3063

    CAS  Google Scholar 

  64. Bader R, Biegler-König F, Schönbohm J (2002) AIM2000—aprogram to analyze and visualize atoms in molecules, version. University of Applied Sciences, Bielefield, p 2

    Google Scholar 

  65. Bader RF (1990) Atoms in molecules: a quantum theory, vol 22, international series of monographs on chemistry. Oxford University Press, Oxford

    Google Scholar 

  66. Boys SF, Bernardi FJMP (1970) The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol Phys 19(4):553–566

    CAS  Google Scholar 

  67. Chattaraj PK, Sarkar U, Roy DR (2007) Update 1 of: electrophilicity index. Chem Rev 107(9):46–74

    Google Scholar 

  68. Koopmans TJP (1934) Über die Zuordnung von Wellenfunktionen und Eigenwerten zu den einzelnen Elektronen eines Atoms. Physica 1(1–6):104–113

    Google Scholar 

  69. Phillips J (1961) Generalized Koopmans’ Theorem. Phys Rev 123:420–424

    CAS  Google Scholar 

  70. Roohi H, Jahantab MJPCR (2017) Sensitivity of perfect and stoneWales defective BNNTs toward NO molecule: a DFT/M06–2X approach. Phys Chem Res 5(1):167–183

    CAS  Google Scholar 

  71. Cukrowski I, de Lange JH, Mitoraj M (2014) Physical nature of interactions in ZnII complexes with 2, 2′–bipyridyl: quantum theory of atoms in molecules (QTAIM), interacting quantum atoms (IQA), noncovalent interactions (NCI), and extended transition state coupled with natural orbitals for chemical valence (ETS–NOCV) comparative studies. J Phys Chem A 118(3):623–637

    CAS  PubMed  Google Scholar 

  72. Espinosa E, Alkorta I, Elguero J, Molins E (2002) From weak to strong interactions: a comprehensive analysis of the topological and energetic properties of the electron density distribution involving X–H⋯ F–Y systems. J Chem Phys 117(12):5529–5542

    CAS  Google Scholar 

  73. Grabowski SJ (2011) What is the covalency of hydrogen bonding? Chem Rev 111(4):2597–2625

    CAS  PubMed  Google Scholar 

Download references

Funding

This study received partial financial support from the University of Kashan, Iran.

Author information

Authors and Affiliations

  1. Department of Chemistry, University of Kashan, Kashan, Iran

    Tooba Afshari & Mohsen Mohsennia

  2. Institute of Nanoscience and Nanotechnology, University of Kashan, Kashan, Iran

    Mohsen Mohsennia

Authors
  1. Tooba Afshari
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mohsen Mohsennia
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mohsen Mohsennia.

Ethics declarations

Conflict of interest

The authors declare that they have no any conflict of interest.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Afshari, T., Mohsennia, M. Structural and electronic properties of adsorbed nucleobases on pristine and Al-doped coronene in absence and presence of external electric fields: a computational study. Struct Chem 31, 795–807 (2020). https://doi.org/10.1007/s11224-019-01455-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11224-019-01455-1

Keywords

Search

Navigation