Skip to main content
SpringerLink
Log in

The chalcogen bond in F2P(S)N⋅⋅⋅SX2, F2PNS⋅⋅⋅SX2, F2PSN⋅⋅⋅SX2 (X = F, Cl, Br, OH, CH3, NH2) complexes

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

Abstract

As a kind of intermolecular noncovalent interaction, chalcogen bonding plays a critical role in the fields of chemistry and biology. In this paper, S⋅⋅⋅S chalcogen bonds in three groups of complexes, F2P(S)N⋅⋅⋅SX2, F2PNS⋅⋅⋅SX2, and F2PSN⋅⋅⋅SX2 (X = F, Cl, Br, OH, CH3, NH2), were investigated at the MP2/aug-cc-pVTZ level of theory. The calculated results show that the formation of S⋅⋅⋅S chalcogen bond is in the manner of attraction between the positive molecular electrostatic potential (VS,max) of chalcogen bond donator and the negative VS,min of chalcogen bond acceptor. It is found that a good correlation exists between the S⋅⋅⋅S bond length and the interaction energy. The energy decomposition indicates the electrostatic energy and polarization energy are closely correlated with the total interaction energy. NBO analysis reveals that the charge transfer is rather closely correlated with the polarization, and the charge transfer has a similar behavior as the polarization in the formation of complex. Our results provide a new example for interpreting the noncovalent interaction based on the σ-hole concept.

The chalcogen bonds in the studied binary complexes are Coulombic in nature, and the charge transfer has a similar behavior as the polarization in the formation of the complex.

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

Scheme 1
Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Kabelac M, Hobza PH (2007) Stability of nucleic acid bases and base pairs. Phys Chem Chem Phys 9:903–917

    Article  CAS  Google Scholar 

  2. Buckingham AD, Ben JE, Mcdowell SAC (2008) The hydrogen bond. Chem Phys Lett 463:1–10

    Article  CAS  Google Scholar 

  3. Wendler K, Thar J, Zahn S, Kirchner BE (2010) The hydrogen bond energy. J Phys Chem A 114:9529

    Article  CAS  Google Scholar 

  4. Chudzinski MG, Mcclary CA, Taylor MS (2011) Anion receptors composed of hydrogen- and halogen-bond donor groups: modulating selectivity with combinations of distinct noncovalent interactions. J Am Chem Soc 133:10559–10567

    Article  CAS  Google Scholar 

  5. Shokri A, Wang Y, O’doherty GA (2013) Hydrogen-bond networks: strengths of different types of hydrogen bonds and an alternative to the low barrier hydrogen-bond proposal. J Am Chem Soc 135:17919–17924

    Article  CAS  Google Scholar 

  6. Elstner M, Hobza P, Frauenheim T (2001) Hydrogen bonding andstacking interactions of nucleic acid base pairs: a density-functional-theory based treatment. J Chem Phys 114:5149–5155

    Article  CAS  Google Scholar 

  7. ToriiH YM (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  Google Scholar 

  8. Xu Z, Liu Z, Chen T (2011) Utilization of halogen bond in lead optimization: a case study of rational design of potent phosphodiesterase type 5 (PDE5) inhibitors. J Med Chem 54:5607–5611

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  10. Wilcken R, Zimmermann MO, Lange A (2013) Principles and applications of halogen bonding in medicinal chemistry and chemical biology. J Med Chem 56:1363–1388

    Article  CAS  Google Scholar 

  11. Murray JS, Lane P, Clark T (2007) Sigma-hole bonding: molecules containing group VI atoms. J Mol Model 13:1033–1038

    Article  CAS  Google Scholar 

  12. Scheiner S (2012) Sensitivity of noncovalent bonds to intermolecular separation: hydrogen, halogen, chalcogen, and pnicogen bonds. CrystEngComm 15:3119–3124

    Article  Google Scholar 

  13. Politzer P, Murray JS, Clark T (2010) Halogen bonding: an electrostatically-driven highly directional noncovalent interaction. Phys Chem Chem Phys 12:7748–7757

    Article  CAS  Google Scholar 

  14. 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 

  15. Esrafili MD, Mohammadian-Sabet F (2015) Pnicogen–pnicogen interactions in O2XP:PH2Y complexes (X=H, F, CN; Y=H, OH, OCH3, CH3, NH2). Chem Phys Lett 638:122–127

    Article  CAS  Google Scholar 

  16. Shishkin OV, Omelchenko IV, Kalyuzhny AL (2010) Intramolecular S…O chalcogen bond in thioindirubin. Struct Chem 21:1005–1011

    Article  CAS  Google Scholar 

  17. Azofra LM, Alkorta I, Scheiner S (2015) Chalcogen bonds in complexes of SOXY (X, Y = F, Cl) with nitrogen bases. J Phys Chem A119:535–541

    Article  Google Scholar 

  18. Nziko VP, Scheiner S (2014) Chalcogen bonding between tetravalent SF4 and amines. J Phys Chem A 11:10849–10856

    Article  Google Scholar 

  19. Li H, Wu Z, Li D (2015) A singlet thiophosphoryl nitrene and its interconversion with thiazyl and thionitroso isomers. J Am Chem Soc 137:10942–10945

    Article  CAS  Google Scholar 

  20. 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 

  21. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Petersson GA, Nakatsuji H, Li X, Caricato M, Marenich A, Bloino J, Janesko BG, Gomperts R, Mennucci B, Hratchian HP, Ortiz JV, Izmaylov AF, Sonnenberg JL, Williams-Young D, Ding F, Lipparini F, Egidi F, Goings J, Peng B, Petrone A, Henderson T, Ranasinghe D, Zakrzewski VG, Gao J, Rega N, Zheng G, Liang W, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Throssell K, Montgomery Jr JA, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Keith T, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Millam JM, Klene M, Adamo C, Cammi R, Ochterski JW, Martin RL, Morokuma K, Farkas O, Foresman JB, Fox DJ (2013) Gaussian 09, revision A.02. Gaussian, Inc., Wallingford

    Google Scholar 

  22. Bulat FA, Toro-Labbe A, Brinck T (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 

  23. Schmidt MW, Baldridge KK, Boatz JA (1993) General atomic and molecular electronic structure system. J Comput Chem 14:1347–1363

    Article  CAS  Google Scholar 

  24. Weinhold F, Landis CR (2005) Valency and bonding: a natural bond orbital donor-acceptor perspective. Cambridge University Press, Cambridge

    Book  Google Scholar 

  25. Moon J, Baek H, Kim J (2016) Ab initio investigation of the ground states of F2P(S)N, F2PNS, and F2PSN. J Phys Chem A 120:9198–9202

    Article  CAS  Google Scholar 

  26. Solimannejad M, Gharabaghi M, Scheiner S (2011) SH…N and SH…P blue-shifting H-bonds and N…P interactions in complexes pairing HSN with amines and phosphines. J Chem Phys 134:024312

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  28. 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 

  29. Bondi (1964) A van der Waals Volumes and Radii. J Phys Chem 68:441–451

    Article  CAS  Google Scholar 

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

    Google Scholar 

  31. Scheiner S (2011) Effects of substituents upon the P…N noncovalent interaction: the limits of its strength. J Phys Chem A 115:11202–11209

    Article  CAS  Google Scholar 

  32. Scheiner S (2011) On the properties of X…N noncovalent interactions for first-, second-, and third-row X atoms. J Chem Phys 134:164313

    Article  Google Scholar 

  33. Scheiner S, Adhikari U (2011) Abilities of different electron donors (D) to engage in a P…D noncovalent interaction. J Phys Chem A 115:11101–11110

    Article  CAS  Google Scholar 

  34. Kuhne TD, Khaliullin RZ (2014) Nature of the asymmetry in the hydrogen-bond networks of hexagonal ice and liquid water. J Am Chem Soc 136:3395–3399

    Article  Google Scholar 

  35. Politzer P, Murray JS (2017) σ-Hole interactions: perspectives and misconceptions. Crystals 7:212

    Article  Google Scholar 

  36. Politzer P, Murray JS, Clark T (2017) Mathematical modeling and physical reality in noncovalent interactions. J Mol Model 21:52

    Article  Google Scholar 

  37. Clark T, Heßelmann A (2018) The coulombic σ-hole model describes bonding in CX3I⋯Y− complexes completely. Phys Chem Chem Phys 20:22849–22855 and the references cited therein

    Article  CAS  Google Scholar 

  38. Clark T, Murray JS, Politzer P (2018) The σ-Hole coulombic interpretation of trihalide anion formation. ChemPhysChem. https://doi.org/10.1002/cphc.201800750

  39. Guo X, An X, Li Q (2015) Se…N chalcogen bond and Se…X halogen bond involving F2C horizontal line Se: influence of hybridization, substitution, and cooperativity. J Phys Chem A 119:3518–3527

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by the National Natural Science Foundation of China (Contract Nos. 21373075, 21371045, 21372062), the Natural Science Foundation of Hebei Province (Contract No. B2016205042).

Author information

Authors and Affiliations

  1. College of Chemistry and Material Science, Hebei Normal University, Road East of 2nd Ring South, Shijiazhuang, 050024, China

    Nan Yan, Suhong Huo, Xiaoyan Li, Yanli Zeng & Lingpeng Meng

  2. Key Laboratory of Inorganic Nano-materials of Hebei Province, Shijiazhuang, 050024, China

    Xiaoyan Li, Yanli Zeng & Lingpeng Meng

Authors
  1. Nan Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Suhong Huo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xiaoyan Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yanli Zeng
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Lingpeng Meng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Lingpeng Meng.

Additional information

Publisher’s Note

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

Electronic supplementary material

ESM 1

(DOCX 767 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yan, N., Huo, S., Li, X. et al. The chalcogen bond in F2P(S)N⋅⋅⋅SX2, F2PNS⋅⋅⋅SX2, F2PSN⋅⋅⋅SX2 (X = F, Cl, Br, OH, CH3, NH2) complexes. J Mol Model 25, 19 (2019). https://doi.org/10.1007/s00894-018-3895-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-018-3895-1

Keywords

Search

Navigation