Skip to main content
Log in

An ab initio study on tunability of σ-hole interactions in XHS:PH2Y and XH2P:SHY complexes (X = F, Cl, Br; Y = H, OH, OCH3, CH3, C2H5, and NH2)

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

Abstract

Quantum chemical calculations are performed to investigate the tunability of σ-hole interactions in chalcogen-bonded XHS:PH2Y and pnicogen-bonded XH2P:SHY complexes, where X = F, Cl, Br and Y = H, OH, OCH3, CH3, C2H5, NH2. The formation of these binary complexes can be understood in terms of molecular electrostatic potentials (MEPs), considering the P and S atoms as an electron acceptor or an electron donor in the chalcogen and pnicogen bonds. The strength of the XHS:PH2Y and XH2P:SHY complexes for a given Y increases as follows: X = Br < Cl < F. In addition, an acceptable linear relationship is found between the interaction energies and the magnitudes of the product of most positive and negative MEPs. This finding along with the electron density difference maps provides a clear picture of the electrostatic nature of the interactions in the XHS:PH2Y and XH2P:SHY complexes. The calculated spin–spin coupling constants across the chalcogen bond interactions in the XHS:PH2Y complexes display a quadratic dependence with the P···S binding distance.

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

Access this article

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

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. 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 

  3. Priimagi A, Cavallo G, Metrangolo P, Resnati G (2013) The halogen bond in the design of functional supramolecular materials: recent advances. Acc Chem Res 46:2686–2695

    Article  CAS  Google Scholar 

  4. Esrafili MD, Solimannejad M (2013) Revealing substitution effects on the strength and nature of halogen-hydride interactions: a theoretical study. J Mol Model 19:3767–3777

    Article  CAS  Google Scholar 

  5. Esrafili MD, Juyban P (2014) CNXeCl and CNXeBr species as halogen bond donors: a quantum chemical study on the structure, properties, and nature of halogen · · · nitrogen interactions. J Mol Model 20:2203

    Article  Google Scholar 

  6. Clark T, Hennemann M, Murray JS, Politzer P (2007) Halogen bonding: the σ-hole. J Mol Model 13:291–296

    Article  CAS  Google Scholar 

  7. 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 

  8. 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 

  9. 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 

  10. Riley KE, Murray JS, Fanfrlík J, Řezáč J, Solá RJ, Concha MC, Ramos FM, Politzer P (2011) Halogen bond tunability I: the effects of aromatic fluorine substitution on the strengths of halogen-bonding interactions involving chlorine, bromine, and iodine. J Mol Model 17:3309–3318

    Article  CAS  Google Scholar 

  11. 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

  12. 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 

  13. Politzer P, Murray JS (2012) Halogen bonding and beyond: factors influencing the nature of CN–R and SiN–R complexes with F–Cl and Cl2. Theor Chem Acc 131:1114

    Article  Google Scholar 

  14. Politzer P, Murray JS (2013) Halogen bonding: an interim discussion. ChemPhysChem 14:278–294

    Article  CAS  Google Scholar 

  15. Politzer P, Murray JS, Clark T (2015) σ-Hole bonding: a physical interpretation. Top Curr Chem 358:19–42

  16. Murray JS, Lane P, Clark T, Politzer P (2007) σ‐Hole bonding: molecules containing group VI atoms. J Mol Model 13:1033–1038

    Article  CAS  Google Scholar 

  17. Murray JS, Lane P, Politzer P (2008) Simultaneous σ-hole and hydrogen bonding by sulfur- and selenium-containing heterocycles. Int J Quantum Chem 108:2770–2781

    Article  CAS  Google Scholar 

  18. Murray JS, Lane P, Politzer P (2009) Expansion of the σ-hole concept. J Mol Model 15:723–729

    Article  CAS  Google Scholar 

  19. Politzer P, Murray JS, Clark T (2013) Halogen bonding and other σ-hole interactions: a perspective. Phys Chem Chem Phys 15:11178–11189

    Article  CAS  Google Scholar 

  20. Li QZ, Li R, Guo P, Li H, Li WZ, Cheng JB (2012) Competition of chalcogen bond, halogen bond, and hydrogen bond in SCS–HOX and SeCSe–HOX (X = Cl and Br) complexes. Comput Theor Chem 980:56–61

    Article  CAS  Google Scholar 

  21. Bauzá A, Quiñonero D, Deyà PM, Frontera A (2013) Halogen bonding versus chalcogen and pnicogen bonding: a combined Cambridge structural database and theoretical study. CrystEngComm 15:3137–31440

    Article  Google Scholar 

  22. Brezgunova ME, Lieffrig J, Aubert E, Dahaoui S, Fertey P, Lebègue S, Ángyán JG, Fourmigué M, Espinosa E (2013) Chalcogen bonding: experimental and theoretical determinations from electron density analysis. Geometrical preferences driven by electrophilic − nucleophilic interactions. Cryst Growth Des 13:3283–3289

    Article  CAS  Google Scholar 

  23. Scheiner S (2013) Detailed comparison of the pnicogen bond with chalcogen, halogen, and hydrogen bonds. Int J Quantum Chem 113:1609–1620

    Article  CAS  Google Scholar 

  24. Esrafili MD, Mohammadian-Sabet F, Solimannejad M (2014) A theoretical evidence for mutual influence between S · · · N(C) and hydrogen/lithium/halogen bonds: competition and interplay between π-hole and σ-hole interactions. Struct Chem 25:1197–1205

    Article  CAS  Google Scholar 

  25. Cozzolino AF, Vargas-Baca I, Mansour S, Mahmoudkhani AH (2005) The nature of the supramolecular association of 1,2,5-Chalcogenadiazoles. J Am Chem Soc 127:3184–3190

    Article  CAS  Google Scholar 

  26. Tauer TP, Derrick ME, Sherrill CD (2005) Estimates of the ab initio limit for sulfur-π interactions: the H2S-benzene dimer. J Phys Chem A 109:191–196

    Article  CAS  Google Scholar 

  27. Saczewski J, Frontera A, Gdaniec M, Brzozowski Z, Saczewski F, Tabin P, Quiñonero D, Deyà PM (2006) Synthesis, X-ray structure analysis and computational studies of novel bis(thiocarbamoyl) disulfides with non-covalent S⋯N and S⋯S interactions. Chem Phys Lett 422:234–239

    Article  CAS  Google Scholar 

  28. Esrafili MD, Vakili M (2014) Cooperativity effects between σ-hole interactions: a theoretical evidence for mutual influence between chalcogen bond and halogen bond interactions in F2S∙∙∙NCX∙∙∙NCY complexes (X = F, Cl, Br, I; Y = H, F, OH). Mol Phys 112:2746–2752

  29. Esrafili MD, Mohammadian-Sabet F (2015) Does single-electron chalcogen bond exist? Some theoretical insights. J Mol Model 21:65

    Article  Google Scholar 

  30. Iwaoka M, Takemoto S, Tomoda S (2002) Statistical and theoretical investigations on the directionality of nonbonded S · · · O interactions. Implications for molecular design and protein engineering. J Am Chem Soc 124:10613–10620

    Article  CAS  Google Scholar 

  31. Saparov B, He H, Zhang X, Greene R, Bobev S (2010) Synthesis, crystallographic and theoretical studies of the new Zintl phases Ba2Cd2Pn3 (Pn = As, Sb), and the solid solutions (Ba1–xSrx)2Cd2Sb3 and Ba2Cd2(Sb1–xAsx)3. Dalton Trans 39:1063–1070

    Article  CAS  Google Scholar 

  32. Riley KE, Murray JS, Fanfrlík J, Rezáč J, Solá RJ, Concha MC, Ramos FM, Politzer P (2013) Halogen bond tunability II: the varying roles of electrostatic and dispersion contributions to attraction in halogen bonds. J Mol Model 19:4651–4659

    Article  CAS  Google Scholar 

  33. Alkorta I, Elguero J, Del Bene JE (2013) Pnicogen-bonded cyclic trimers (PH2X)3 with X = F, Cl, OH, NC, CN, CH3, H, and BH2. J Phys Chem A 117:4981–4987

    Article  CAS  Google Scholar 

  34. Esrafili MD, Fatehi P, Solimannejad M (2014) Mutual interplay between pnicogen bond and dihydrogen bond in HMH · · · HCN · · · PH2X complexes (M = Be, Mg, Zn; X = H, F, Cl). Comput Theor Chem 1034:1–6

    Article  CAS  Google Scholar 

  35. 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 

  36. Guo X, Liu Y, Li Q, Li W, Cheng J (2015) Competition and cooperativity between tetrel bond and chalcogen bond in complexes involving F2CX(X = Se and Te). Chem Phys Chem 620:7–12

    CAS  Google Scholar 

  37. 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 

  38. Politzer P, Murray JS, Janjić GV, Zarić SD (2014) σ-Hole interactions of covalently-bonded nitrogen, phosphorus and arsenic: a survey of crystal structures. Crystals 4:12–31

    Article  Google Scholar 

  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. Kozuch S, Martin JML (2013) Halogen bonds: benchmarks and theoretical analysis. J Chem Theory Comput 9:1918–1931

    Article  CAS  Google Scholar 

  41. 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 

  42. Bader RFW (1990) Atoms in molecules-a quantum theory. Oxford University Press, New York

    Google Scholar 

  43. Biegler-Konig F, Schonbohm J, Bayles D (2001) AIM 2000. J Comput Chem 22:545–559

    Article  Google Scholar 

  44. 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 

  45. Wolinski K, Hilton JF, Pulay P (1990) Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations. J Am Chem Soc 112:8251–8260

    Article  CAS  Google Scholar 

  46. Politzer P, Lane P, Murray JS, Concha MC (2005) Comparative analysis of surface electrostatic potentials of carbon, boron/nitrogen and carbon/boron/nitrogen model nanotubes. J Mol Model 11:1–7

    Article  CAS  Google Scholar 

  47. Esrafili MD, Behzadi H (2013) A comparative study on carbon, boron-nitride, boron-phosphide and silicon-carbide nanotubes based on surface electrostatic potentials and average local ionization energies. J Mol Model 19:2375–2382

    Article  CAS  Google Scholar 

  48. Cozzolino AF, Vargas-Baca I, Mansour S, Mahmoudkhani AH (2005) The nature of the supramolecular association of 1,2,5-chalcogenadiazoles. J Am Chem Soc 127:3184–3190

  49. Bleiholder C, Werz DB, Köppel H, Gleiter R (2006) Theoretical investigations on chalcogen-chalcogen interactions: what makes these nonbonded interactions bonding? J Am Chem Soc 128:2666–2674

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

    Article  CAS  Google Scholar 

  51. Blake AJ, Davis MJ, Rankin DWH (1990) Instant ligands: Part 5. The molecular structures of (PF2)OCH2CCCH2O(PF2) in the gas phase and PF2OCH2CH2CN in gaseous and crystalline phases. J Mol Struct 221:25–44

    Article  CAS  Google Scholar 

  52. Hennemann M, Murray JS, Politzer P, Riley KE, Clark T (2012) Polarization-induced σ-holes and hydrogen bonding. J Mol Model 18:2461–2469

    Article  CAS  Google Scholar 

  53. Clark T, Murray JS, Politzer P (2013) Role of polarization in halogen bonds. Aust J Chem 67:451–456

    Article  Google Scholar 

  54. Koch U, Popelier PLA (1995) Characterization of C-H · · · O hydrogen bonds on the basis of the charge density. J Phys Chem 99:9747–9754

    Article  CAS  Google Scholar 

  55. Del Bene JE, Alkorta I, Sanchez-Sanz G, Elguero J (2011) 31P–31P spin–spin coupling constants for pnicogen homodimers. Chem Phys Lett 512:184–187

    Article  Google Scholar 

  56. Esrafili MD, Mahdavinia G, Javaheri M, Sobhi HR (2014) A theoretical study of substitution effects on halogen–π interactions. Mol Phys 112:1160–1166

    Article  CAS  Google Scholar 

  57. Del Bene JE, Alkorta I, Elguero J (2013) Properties of complexes H2C = (X)P:PXH2, for X = F, Cl, OH, CN, NC, CCH, H, CH3, and BH2:P · · · P pnicogen bonding at σ–holes and π–holes. J Phys Chem A 117:11592–11604

    Article  Google Scholar 

  58. Alkorta I, Sánchez-Sanz G, Elguero J, Del Bene JE (2014) Pnicogen bonds between X = PH3 (X = O, S, NH, CH2) and phosphorus and nitrogen bases. J Phys Chem A 118:1527–1537

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Mehdi D. Esrafili.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(DOC 2541 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Esrafili, M.D., Mohammadirad, N. An ab initio study on tunability of σ-hole interactions in XHS:PH2Y and XH2P:SHY complexes (X = F, Cl, Br; Y = H, OH, OCH3, CH3, C2H5, and NH2). J Mol Model 21, 176 (2015). https://doi.org/10.1007/s00894-015-2727-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-015-2727-9

Keywords

Navigation