Skip to main content
SpringerLink
Log in

A post-HF study on the interaction of iodine with small polyaromatic hydrocarbons

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

In this work, we present a theoretical study of the interaction between a diatomic iodine molecule with planar naphthalene and several other small polyaromatic hydrocarbons (PAHs). Our aim was to understand the general characteristics of the potential energy surface (PES) of this system; that is locating various local minima, finding the variation of PES around these optimum points by means of first principle calculations at MP2, SCS-MP2 and CCSD(T) levels of theory. Two basic orientations of the iodine molecule, i.e., parallel or perpendicular with respect to the naphthalene plane, are discussed. The PES of the former was investigated in detail, including the translation and rotation of I2 (as a rigid rotor) along the naphtalene surface. It was concluded that, although the perpendicular conformations are usually 1 kcal mol−1 more stable than the parallel conformation, this small difference does not exclude the presence of both conformations in the gas phase. Both structures were stable enough to hold more than 20 vibrational states. NBO analysis showed that the mutual polarization effects were greater for the perpendicular conformation. It was also observed that the I2 + naphtalene dimer interaction is almost twice of that of I2 + naphtalene, showing the long range character of the interaction.

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.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6a,b
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11

Similar content being viewed by others

Abbreviations

PES:

Potential energy surface

COM:

Center of mass

MP2:

Second order Møller-Plesset perturbation theory

SCS-MP2:

Spin component-scaled second order Møller-Plesset perturbation theory

CCSD(T):

Coupled cluster theory including single double and perturbative triple excitations

CP:

Counterpoise

DFT:

Density functional theory

BSSE:

Basis set superposition error

References

  1. Geim AK, Novoselov KS (2007) The rise of graphene. Nat Mater 6:183

    Article  CAS  Google Scholar 

  2. Lee C, Wei XD, Kysar JW, Hone J (2008) Measurement of the elastic properties and intrinsic strength of monolayer graphene. Science 321:385

    Article  CAS  Google Scholar 

  3. Fowler JD, Allen MJ, Tung VC, Yang Y, Kaner RB, Weiller BH (2009) Practical chemical sensors from chemically derived graphene. ACS Nano 3:2:01:306

  4. Kong J, Franklin NR, Zhou C, Chapline MG, Peng S, Cho K, Dai H (2000) Nanotube molecular wires as chemical sensors. Science 287:622

    Article  CAS  Google Scholar 

  5. Lee SM, Lee YH (2000) Hydrogen storage in single-walled carbon nanotubes. Appl Phys Lett 76:2877

    Article  CAS  Google Scholar 

  6. Zhu XY, Lee SM, Lee YH, Frauenheim T (2000) Adsorption and desorption of an O2 molecule on carbon nanotubes. Phys Rev Lett 85:2757

    Article  CAS  Google Scholar 

  7. Jhi SH, Louie SG, Cohen ML (2000) Electronic properties of oxidized carbon nanotubes. Phys Rev Lett 85:1710

    Article  CAS  Google Scholar 

  8. Chang H, Do JL, Mi S, L, Hee Y (2001) Adsorption of NH3 and NO2 molecules on carbon nanotubes. Appl Phys Lett 79:3863

  9. Zhao J, Buldum A, Han J, Lu JP (2002) Gas molecule adsorption in carbon nanotubes and nanotube bundles. Nanotechnology 13:195

    Article  CAS  Google Scholar 

  10. Leenaerts O, Partoens B, Peeters FM (2008) Adsorption of H2O, NH3, CO, NO2, and NO on graphene: a first-principles study. Phys Rev B 77:125416

    Article  Google Scholar 

  11. Chen S, Cai W, Chen D, Ren Y, Li X, Zhu Y, Kang J, Ruoff RS (2010) Adsorption/desorption and electrically controlled flipping of ammonia molecules on graphene. New J Phys 12:125011

    Article  Google Scholar 

  12. Schedin F, Geim AK, Morozov SV, Hill EW, Blake P, Katsnelson MI, Novoselov KS (2007) Detection of individual gas molecules adsorbed on graphene. Nat Mater 6:652

    Article  CAS  Google Scholar 

  13. Robinson JA, Snow ES, Badescu SC, Reinecke TL, Perkins FK (2006) Role of defects in single-walled carbon nanotube chemical sensors. Nano Lett 6 :8:1747

  14. Donchev AG (2007) Ab initio study of the effects of orientation and corrugation for H2 adsorbed on polycyclic aromatic haydocarbons. J Chem Phys 126:124706

    Article  CAS  Google Scholar 

  15. Medeiros PVC, Mascarenhas AJS, de Brito MF, de Castilho CMC (2010) A DFT study of halogen atoms adsorbed on graphene layers. Nanotechnology 21:485701

    Article  Google Scholar 

  16. Ghosh S, Yamijala SRKCS, Pati SK, Rao CNR (2012) The interaction of halogen molecules with SWNTs and graphene. RSC Advances 2:1181

    Article  CAS  Google Scholar 

  17. Werner HJ, Knowles PJ, Lindh R, Manby FR, Schu¨tz M, Celani P, Korona T, Rauhut G, Amos RD, Bernhardsson A, Berning A, Cooper DL, Deegan MJO, Dobbyn AJ, Eckert F, Hampel C, Hetzer G, Lloyd AW, McNicholas SJ, Meyer W, Mura ME, Nicklass A, Palmieri P, Pitzer R, Schumann U, Stoll H, Stone AJ, Tarroni R, Thorsteinsson T MOLPRO, version 2009.1, a package of ab initio programs, see http://www.molpro.net

  18. Bond length of I2 molecule, in NIST chemistry web book. In: Howard WF, Andrews L (eds) NIST standard reference database number 69. National Institute of Standards and Technology, Gaithersburg, MD, 20899, (http://webbook.nist.gov)

  19. Yurtsever E (2009) π-stack dimers of small polyaromatic hydrocarbons: a path to the packing of graphenes. J Phys Chem A 113:924

  20. Yurtsever E (2010) Stacking of triphenylene: characterization of the potential energy surface. Theo Chem Acc 127:133

    Article  CAS  Google Scholar 

  21. Hobza P (ed) (2008) Non-standard base pairing and stacked structures in methyl xanthine clusters. Phys Chem Chem Phys 10:19:2561:2868

  22. Grimme S (2003) Improved second-order Møller–Plesset perturbation theory by separate scaling of parallel- and antiparallel-spin pair correlation energies. J Chem Phys 118:9095

    Article  CAS  Google Scholar 

  23. Grimme S (2004) Accurate description of van der Waals complexes by density functional theory including empirical corrections. J Comput Chem 25:1463

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  25. Jansen G, Haßelmann A (2001) Comment on: using Kohn-Sham orbitals in symmetry-adapted perturbation theory to investigate intermolecular interactions. J Phys Chem A 105:11156

    Article  CAS  Google Scholar 

  26. Haßelmann A, Jansen G (2002) First-order intermolecular interaction energies from Kohn-Sham orbitals. Chem Phys Lett 357:464

    Article  Google Scholar 

  27. Haßelmann A, Jansen G (2002) Intermolecular induction and exchange-induction energies from coupled-perturbed Kohn-Sham density functional theory. Chem Phys Lett 362:319

    Article  Google Scholar 

  28. Haßelmann A, Jansen G (2003) Intermolecular dispersion energies from time-dependent density functional theory. Chem Phys Lett 367:778

    Article  Google Scholar 

  29. Bergner A, Dolg M, Kuechle W, Stoll H, Preuss H (1993) Ab initio energy-adjusted pseudopotentials for elements of groups 13–17. Mol Phys 80:1431

    Article  CAS  Google Scholar 

  30. LEVEL program, version 8.0, RJ Le Roy 519: 888:4051. http://leroy.uwaterloo.ca/programs/

  31. Rudenko AN, Keil FJ, Katsnelson MI, Lichtenstein AI (2010) Adsorption of diatomic halogen molecules on graphene: a van der Waals density functional study. Phys Rev B 82:035427

    Article  Google Scholar 

  32. Politzer P, Riley KE, Bulat FA, Murray JS (2012) Perspectives on halogen bonding and other σ-hole interactions. Comp Theo Chem 998:2

    Article  CAS  Google Scholar 

  33. Politzer P, Murray JS (2013) Halogen bonding: an interim discussion. ChemPhysChem 14:278

    Article  CAS  Google Scholar 

  34. Politzer P, Murray JS, Clark T (2013) Halogen bonding and other σ-hole interactions: a perspective. Phys Chem Chem Phys 15:11178

    Article  CAS  Google Scholar 

Download references

Acknowledgments

We acknowledge the computational resources provided by the National Center for High Performance Computing of Turkey (UHEM), Informatics Institute of Istanbul Technical University and the High Performance Computer Laboratory of Koç University.

Author information

Authors and Affiliations

  1. Department of Chemistry, Koç University, 34450, Istanbul, Turkey

    Ersin Yurtsever

  2. Department of Chemistry, Istanbul Technical University, 34469, Istanbul, Turkey

    Berkay Sütay & Mine Yurtsever

Authors
  1. Berkay Sütay
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mine Yurtsever
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ersin Yurtsever
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Mine Yurtsever or Ersin Yurtsever.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sütay, B., Yurtsever, M. & Yurtsever, E. A post-HF study on the interaction of iodine with small polyaromatic hydrocarbons. J Mol Model 20, 2445 (2014). https://doi.org/10.1007/s00894-014-2445-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-014-2445-8

Keywords

Search

Navigation