Skip to main content
SpringerLink
Log in

Insights into the strength and nature of carbene···halogen bond interactions: a theoretical perspective

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

Abstract

Halogen-bonding, a noncovalent interaction between a halogen atom X in one molecule and a negative site in another, plays critical roles in fields as diverse as molecular biology, drug design and material engineering. In this work, we have examined the strength and origin of halogen bonds between carbene CH2 and XCCY molecules, where X = Cl, Br, I, and Y = H, F, COF, COOH, CF3, NO2, CN, NH2, CH3, OH. These calculations have been carried out using M06-2X, MP2 and CCSD(T) methods, through analyses of surface electrostatic potentials V S(r) and intermolecular interaction energies. Not surprisingly, the strength of the halogen bonds in the CH2···XCCY complexes depend on the polarizability of the halogen X and the electron-withdrawing power of the Y group. It is revealed that for a given carbene···X interaction, the electrostatic term is slightly larger (i.e., more negative) than the dispersion term. Comparing the data for the chlorine, bromine and iodine substituted CH2···XCCY systems, it can be seen that both the polarization and dispersion components of the interaction energy increase with increasing halogen size. One can see that increasing the size and positive nature of a halogen’s σ-hole markedly enhances the electrostatic contribution of the halogen-bonding interaction.

Halogen bonding interactions between carbene and X-CC-Y molecules (X = Cl, Br, and I; Y = H, F, COF, COOH, CF3, NO2, CN, OH, NH2, CH3)

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

Similar content being viewed by others

References

  1. Auffinger P, Hays FA, Westhof E, Ho PS (2004) Halogen bonds in biological molecules. Proc Natl Acad Sci U S A 101:16789–16794

    Article  CAS  Google Scholar 

  2. Riley KE, Hobza P (2008) Investigations into the nature of halogen bonding including symmetry adapted perturbation theory analyses. J Chem Theory Comput 4:232–242

    Article  CAS  Google Scholar 

  3. Jabłoński M, Palusiak M (2012) Nature of a hydride − halogen bond. A SAPT-, QTAIM-, and NBO-based study. J Phys Chem A 116:2322–2332

    Article  Google Scholar 

  4. Jabłoński M (2012) Energetic and geometrical evidence of nonbonding character of some intramolecular halogen···oxygen and other Y···Y interactions. J Phys Chem A 116:3753–3764

    Article  Google Scholar 

  5. Riley KE, Merz KM Jr (2007) Insights into the strength and origin of halogen bonding: the halobenzene-formaldehyde dimer. J Phys Chem A 111:1688–1694

    Article  CAS  Google Scholar 

  6. Beweries T, Brammer L, Jasim NA, McGrady JE, Perutz RN, Whitwood AC (2011) Energetics of halogen bonding of group 10 metal fluoride complexes. J Am Chem Soc 133:14338–14348

    Article  CAS  Google Scholar 

  7. Parker AJ, Stewart J, Donald KJ, Parish CA (2012) Halogen bonding in DNA base pairs. J Am Chem Soc 134:5165–5172

    Article  CAS  Google Scholar 

  8. El-Sheshtawy HS, Bassil BS, Assaf KI, Kortz U, Nau WM (2012) Halogen bonding inside a molecular container. J Am Chem Soc 134:19935–19941

    Article  CAS  Google Scholar 

  9. Politzer P, Murray JS, Concha MC (2007) Halogen bonding and the design of new materials: organic bromides, chlorides and perhaps even fluorides as donors. J Mol Model 13:643–650

    Article  CAS  Google Scholar 

  10. McAllister LJ, Bruce DW, Karadakov PB (2011) Halogen bonding interaction between fluorohalides and isocyanides. J Phys Chem A 115:11079–11086

    Article  CAS  Google Scholar 

  11. Duarte DJR, de las Vallejos MM, Peruchena NM (2010) Topological analysis of aromatic halogen/hydrogen bonds by electron charge density and electrostatic potentials. J Mol Model 16:737–748

    Article  CAS  Google Scholar 

  12. Lu Y, Zou J, Wang Y, Jiang Y, Yu Q (2007) Ab Initio investigation of the complexes between bromobenzene and several electron donors: some insights into the magnitude and nature of halogen bonding interactions. J Phys Chem A 111:10781–10788

    Article  CAS  Google Scholar 

  13. Zhu S, Xing C, Xu W, Jin G, Li Z (2004) Halogen bonding and hydrogen bonding coexist in driving self-assembly. Cryst Growth Des 4:53–56

    Article  CAS  Google Scholar 

  14. Mukherjee A, Desiraju GR (2011) Halogen bonding and structural modularity in 2,3,4- and 3,4,5-trichlorophenol. Cryst Growth Des 11:3735–3739

    Article  CAS  Google Scholar 

  15. Hardegger LA, Kuhn B, Spinnler B, Anselm L, Ecabert R, Stihle M, Gsell B, Thoma R, Diez J, Benz J, Plancher JM, Hartmann G, Banner DW, Haap W, Diederich F (2011) Systematic investigation of halogen bonding in protein-ligand interactions. Angew Chem Int Ed 50:314–318

    Article  CAS  Google Scholar 

  16. Riley KE, Murray JS, Politzer P, Concha MC, Hobza P (2009) Br···O complexes as probes of factors affecting halogen bonding: interactions of bromobenzenes and bromopyrimidines with acetone. J Chem Theory Comput 5:155–163

    Article  CAS  Google Scholar 

  17. Bertani R, Chaux F, Gleria M, Metrangolo P, Milani R, Pilati T, Resnati G, Sansotera M, Venzo A (2007) Supramolecular rods via halogen bonding-based self-assembly of fluorinated phosphazene nanopillars. Inorg Chim Acta 360:1191–1199

    Article  CAS  Google Scholar 

  18. Cariati E, Forni A, Biella S, Metrangolo P, Meyer F, Resnati G, Righetto S, Tordin E, Ugo R (2007) Tuning second-order NLO responses through halogen bonding. Chem Commun 2590–2592

  19. Wang F, Ma N, Chen Q, Wang W, Wang L (2007) Halogen bonding as a new driving force for layer-by-layer assembly. Langmuir 23:9540–9542

    Article  CAS  Google Scholar 

  20. Metrangolo P, Neukirch H, Pilati T, Resnati G (2005) Halogen bonding based recognition processes: a world parallel to hydrogen bonding. Acc Chem Res 38:386–395

    Article  CAS  Google Scholar 

  21. Politzer P, Lane P, Concha MC, Ma YG, Murray JS (2007) An overview of halogen bonding. J Mol Model 13:305–311

    Article  CAS  Google Scholar 

  22. Grabowski SJ (2012) QTAIM characteristics of halogen bond and related interactions. J Phys Chem A 116:1838–1845

    Article  CAS  Google Scholar 

  23. Esrafili MD, Hadipour NL (2011) Characteristics and nature of halogen bonds in linear clusters of NCX (X = Cl, and Br): an ab initio, NBO and QTAIM study. Mol Phys 109:2451–2460

    Article  CAS  Google Scholar 

  24. Awwadi FF, Willett RD, Peterson KA, Twamley B (2006) The nature of halogen···halogen synthons: crystallographic and theoretical studies. Chem Eur J 12:8952–8960

    Article  CAS  Google Scholar 

  25. Politzer P, Murray JS, Concha MC (2008) σ-hole bonding between like atoms; a fallacy of atomic charges. J Mol Model 14:659–665

    Article  CAS  Google Scholar 

  26. Murray JS, Lane P, Clark T, Riley KE, Politzer P (2012) σ-Holes, π-holes and electrostatically-driven interactions. J Mol Model 18:541–548

    Article  CAS  Google Scholar 

  27. Murray JS, Concha MC, Lane P, Hobza P, Politzer P (2008) Blue shifts vs red shifts in σ-hole bonding. J Mol Model 14:699–704

    Article  CAS  Google Scholar 

  28. Li Q, Yuan H, Jing B, Liu Z, Li W, Cheng J, Gong B, Sun J (2010) Theoretical study of halogen bonding between FnH3-nCBr(n = 0,1, 2, 3) and HMgH. J Mol Struct (THEOCHEM) 942:145–148

    Article  CAS  Google Scholar 

  29. Esrafili MD, Ahmadi B (2012) A theoretical investigation on the nature of Cl···N and Br···N halogen bonds in F-Ar-X···NCY complexes (X = Cl, Br and Y = H, F, Cl, Br, OH, NH2, CH3 and CN). Comput Theor Chem 997:77–82

    Article  CAS  Google Scholar 

  30. Bundhun A, Ramasami P, Murray JS, Politzer P (2013) Trends in σ-hole strengths and interactions of F3MX molecules (M 0 C, Si, Ge and X 0 F, Cl, Br, I). J Mol Model doi: 10.1007/s00894-012-1571-4

  31. Metrangolo P, Murray JS, Pilati T, Politzer P, Resnati G, Terraneo G (2011) Fluorine-centered halogen bonding: a factor in recognition phenomena and reactivity. Cryst Growth Des 11:4238–4246

    Article  CAS  Google Scholar 

  32. Valerio G, Raos G, Meille SV, Metrangolo P, Resnati G (2000) Halogen bonding in fluoroalkylhalides: a quantum chemical study of increasing fluorine substitution. J Phys Chem A 104:1617–1620

    Article  CAS  Google Scholar 

  33. Metrangolo P, Murray JS, Pilati T, Politzer P, Resnati G (2011) The fluorine atom as a halogen bond donor, viz. a positive site. Cryst Eng Comm 13:6593–6596

    Article  CAS  Google Scholar 

  34. Palusiak M (2010) On the nature of halogen bond – The Kohn–Sham molecular orbital approach. J Mol Struct (THEOCHEM) 945:89–92

    Article  CAS  Google Scholar 

  35. Politzer P, Riley KE, Bulat FA, Murray JS (2012) Perspectives on halogen bonding and other σ-hole interactions: Lex parsimoniae (Occam’s Razor). Comput Theor Chem 998:2–8

    Article  CAS  Google Scholar 

  36. Riley KE, Murray JS, Fanfrlík J, Řezáč J, Solá RJ, Concha MC, Ramos FM, Politzer P (2012) Halogen bond tunability II: the varying roles of electrostatic and dispersion contributions to attraction in halogen bonds. J Mol Model doi: 10.1007/s00894-012-1428-x

  37. Esrafili MD (2012) Investigation of H-bonding and halogen-bonding effects in dichloroacetic acid: DFT calculations of NQR parameters and QTAIM analysis. J Mol Model 18:5005–5016

    Article  CAS  Google Scholar 

  38. Esrafili MD (2012) A theoretical investigation of the characteristics of hydrogen/halogen bonding interactions in dibromo-nitroaniline. J Mol Mod doi: 10.1007/s00894-012-1691-x

  39. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su SJ, Windus TL, Dupuis M, Montgomery JA (1993) General atomic and molecular electronic structure system. J Comput Chem 14:1347–1363

    Article  CAS  Google Scholar 

  40. Zhao Y, Schultz NE, Truhlar DG (2005) Exchange-correlation functional with broad accuracy for metallic and nonmetallic compounds, kinetics, and noncovalent interactions. J Chem Phys 123:161103

    Article  Google Scholar 

  41. Zhao Y, Schultz NE, Truhlar DG (2006) Design of density functionals by combining the method of constraint satisfaction with parametrization for thermochemistry, thermochemical kinetics, and noncovalent interactions. J Chem Theory Comput 2:364–382

    Article  Google Scholar 

  42. Zhao Y, Truhlar DG (2006) A new local density functional for main-group thermochemistry, transition metal bonding, thermochemical kinetics, and noncovalent interactions. J Chem Phys 125:194101

    Article  Google Scholar 

  43. Zhao Y, Truhlar DG (2008) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functional. Theor Chem Accounts 120:215–241

    Article  CAS  Google Scholar 

  44. Zhao Y, Truhlar DG (2007) Density functionals for noncovalent interaction energies of biological importance. J Chem Theory Comput 3:289–300

    Article  CAS  Google Scholar 

  45. Gu JD, Wang J, Leszczynski J, Xie YM, Schaefer HF (2008) To stack or not to stack: performance of a new density functional for the uracil and thymine dimers. Chem Phys Lett 459:164–166

    Article  CAS  Google Scholar 

  46. Dunning TH (1989) Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J Chem Phys 90:1007–1023

    Article  CAS  Google Scholar 

  47. Peterson KA, Figgen D, Goll E, Stoll H, Dolg M (2003) Systematically convergent basis sets with relativistic pseudopotentials. II. Small-core pseudopotentials and correlation consistent basis sets for the post-d group 16–18 elements. J Chem Phys 119:11113–11123

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  49. Bulat FA, Toro-Labbe A, Brinck T, Murray JS, Politzer P (2010) Quantitative analysis of molecular surfaces: areas, volumes, electrostatic potentials and average local ionization energies. J Mol Model 16:1679–1691

    Article  CAS  Google Scholar 

  50. Su P, Li H (2009) Energy decomposition analysis of covalent bonds and intermolecular interactions. J Chem Phys 131:014102

    Article  Google Scholar 

  51. Bader RFW, Carroll MT, Cheeseman JR, Chang C (1987) Properties of atoms in molecules: atomic volumes. J Am Chem Soc 109:7968–7979

    Article  CAS  Google Scholar 

  52. Bondi A (1964) van der Waals volumes and radii. J Phys Chem 68:441–451

    Article  CAS  Google Scholar 

  53. Torii H, Yoshida M (2010) Properties of halogen atoms for representing intermolecular electrostatic interactions related to halogen bonding and their substituent effects. J Comput Chem 31:107–116

    Article  CAS  Google Scholar 

  54. Hobza P, Zahradnik R, Muller-Dethlefs K (2006) The world of non-covalent interactions. Coll Czech Chem Commun 71:443–531

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Laboratory of Theoretical Chemistry, Department of Chemistry, University of Maragheh, P.O. Box: 5513864596, Maragheh, Iran

    Mehdi D. Esrafili & Nafiseh Mohammadirad

Authors
  1. Mehdi D. Esrafili
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nafiseh Mohammadirad
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mehdi D. Esrafili.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Esrafili, M.D., Mohammadirad, N. Insights into the strength and nature of carbene···halogen bond interactions: a theoretical perspective. J Mol Model 19, 2559–2566 (2013). https://doi.org/10.1007/s00894-013-1804-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00894-013-1804-1

Keywords

Search

Navigation