Skip to main content
SpringerLink
Log in

Competition between chalcogen bond and halogen bond interactions in YOX4:NH3 (Y = S, Se; X = F, Cl, Br) complexes: An ab initio investigation

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

Abstract

Using ab initio calculations, the geometries, interaction energies and bonding properties of chalcogen bond and halogen bond interactions between YOX4 (Y = S, Se; X = F, Cl, Br) and NH3 molecules are studied. These binary complexes are formed through the interaction of a positive electrostatic potential region (σ-hole) on the YOX4 with the negative region in the NH3. The ab initio calculations are carried out at the MP2/aug-cc-pVTZ level, through analysis of molecular electrostatic potentials, quantum theory of atoms in molecules and natural bond orbital methods. Our results indicate that even though the chalcogen and halogen bonds are mainly dominated by electrostatic effects, but the polarization and dispersion effects also make important contributions to the total interaction energy of these complexes. The examination of interaction energies suggests that the chalcogen bond is always favored over the halogen bond for all of the binary YOX4:NH3 complexes.

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

Similar content being viewed by others

References

  1. Scheiner S (1997) Hydrogen bonding. A theoretical perspective. Oxford University Press, New York

    Google Scholar 

  2. Pochorovski I, Milić J, Kolarski D, Gropp C, Schweizer WB, Diederich F (2014) Evaluation of hydrogen-bond acceptors for redox-switchable resorc in [4] arene cavitands. J Am Chem Soc 136:3852–3858

    Article  CAS  Google Scholar 

  3. Nichols DA, Hargis JC, Sanishvili R, Jaishankar P, Defrees K, Smith EW, Wang KK, Prati F, Renslo AR, Woodcock HL, Chen Y (2015) Ligand-induced proton transfer and low-barrier hydrogen bond revealed by X-ray crystallography. J Am Chem Soc 137:8086–8095

    Article  CAS  Google Scholar 

  4. Nick TU, Lee W, Koßmann S, Neese F, Stubbe J, Bennati M (2015) Hydrogen bond network between amino acid radical intermediates on the proton-coupled electron transfer pathway of E. coli α2 ribonucleotide reductase. J Am Chem Soc 137:289–298

    Article  CAS  Google Scholar 

  5. Metrangolo P, Carcenac Y, Lahtinen M, Pilati T, Rissanen K, Vij A, Resnati G (2009) Nonporous organic solids capable of dynamically resolving mixtures of diiodoperfluoroalkanes. Science 323:1461–1464

    Article  CAS  Google Scholar 

  6. Voth AR, Khuu P, Oishi K, Ho PS (2009) Halogen bonds as orthogonal molecular interactions to hydrogen bonds. Nat Chem 1:74–79

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  8. Esrafili MD, Ahmadi B (2012) A theoretical investigation on the nature of Cl···N and Br···N halogen bonds in FArX···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 

  9. 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 

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

    Article  CAS  Google Scholar 

  11. 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 

  12. 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 

  13. 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 

  14. 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 

  15. Shields ZP, Murray JS, Politzer P (2010) Directional tendencies of halogen and hydrogen bonds. Int J Quantum Chem 110:2823–2832

    Article  CAS  Google Scholar 

  16. 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 

  17. 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 

  18. 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 

  19. Murray JS, Macaveiu L, Politzer P (2014) Factors affecting the strengths of σ-hole electrostatic potentials. J Comput Sci 5:590–596

    Article  Google Scholar 

  20. 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 

  21. Wang Y-H, Zou J-W, Lu Y-X, Yu Q-S, Xu H-Y (2007) Single-electron halogen bond: Ab initio study. Int J Quantum Chem 107:501–506

    Article  CAS  Google Scholar 

  22. Li Q, Li R, Yi S, Li W, Cheng J (2012) The single-electron hydrogen, lithium, and halogen bonds with HBe, H2B, and H3C radicals as the electron donor: an ab initio study. Struct Chem 23:411–416

    Article  CAS  Google Scholar 

  23. Li QZ, Li R, Liu XF, Li WZ, Cheng JB (2012) Concerted interaction between pnicogen and halogen bonds in XCl-FH2P-NH3 (X = F, OH, CN, NC, and FCC). ChemPhysChem 13:1205–1212

    Article  CAS  Google Scholar 

  24. Zhang Y, Ma N, Wang W (2012) A new class of halogen bonds that avoids the σ-hole. Chem Phys Lett 532:27–30

    Article  CAS  Google Scholar 

  25. Esrafili MD, Vakili M (2014) Halogen bonds enhanced by σ-hole and π-hole interactions: a comparative study on cooperativity and competition effects between X···N and S···N interactions in H3N···XCN···SF2 and H3N···XCN···SO2 complexes (X = F, Cl, Br and I). J Mol Model 20:2291

    Article  Google Scholar 

  26. Metrangolo P, Resnati G, Pilati T, Biella S (2008) Halogen bonding in crystal engineering. Springer, Berlin

    Book  Google Scholar 

  27. Cinčić D, Friščić T, Jones W (2011) Experimental and database studies of three-centered halogen bonds with bifurcated acceptors present in molecular crystals, cocrystals and salts. CrystEngComm 13:3224–3231

    Article  Google Scholar 

  28. Ji B, Wang W, Deng D, Zhang Y (2011) Symmetrical bifurcated halogen bond: design and synthesis. Crys Growth Des 11:3622–3628

    Article  CAS  Google Scholar 

  29. Troff RW, Mäkelä T, Topić F, Valkonen A, Raatikainen K, Rissanen K (2013) Alternative motifs for halogen bonding. Eur J Org Chem 2013:1617–1637

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  31. Bundhun A, Ramasami P, Murray J, Politzer P (2013) Trends in σ-hole strengths and interactions of F3MX molecules (M = C, Si, Ge and X = F, Cl, Br, I). J Mol Model 19:2739–2746

    Article  CAS  Google Scholar 

  32. Wang W, Ji B, Zhang Y (2009) Chalcogen bond: a sister noncovalent bond to halogen bond. J Phys Chem A 113:8132–8135

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  34. Adhikari U, Scheiner S (2014) Effects of charge and substituent on the S···N chalcogen bond. J Phys Chem A 118:3183–3192

    Article  CAS  Google Scholar 

  35. Nziko VdPN, Scheiner S (2014) Chalcogen bonding between tetravalent SF4 and amines. J Phys Chem A 118:10849–10856

    Article  CAS  Google Scholar 

  36. Azofra LM, Alkorta I, Scheiner S (2015) Chalcogen bonds in complexes of SOXY (X, Y = F, Cl) with nitrogen bases. J Phys Chem A 119:535–541

    Article  CAS  Google Scholar 

  37. Esrafili MD, Mohammadian-Sabet F (2015) Bifurcated chalcogen bonds: a theoretical study on the structure, strength and bonding properties. Chem Phys Lett 634:210–215

    Article  CAS  Google Scholar 

  38. Esrafili MD, Mohammadian-Sabet F (2015) An ab initio study on chalcogen–chalcogen bond interactions in cyclic (SHX)3 complexes (X = F, Cl, CN, NC, CCH, OH, OCH3, NH2). Chem Phys Lett 628:71–75

    Article  CAS  Google Scholar 

  39. Li Q-Z, Li R, Guo P, Li H, Li W-Z, Cheng J-B (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 

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

    Article  Google Scholar 

  41. 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 

  42. Esrafili MD, Mohammadian-Sabet F (2014) Halogen-bond interactions enhanced by charge-assisted hydrogen bonds: an ab Initio study. Bull Chem Soc Jpn 87:882–889

    Article  CAS  Google Scholar 

  43. 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 

  44. 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

    Article  CAS  Google Scholar 

  45. Adhikari U, Scheiner S (2012) Substituent effects on Cl···N, S···N, and P···N noncovalent bonds. J Phys Chem A 116:3487–3497

    Article  CAS  Google Scholar 

  46. Esrafili MD, Mohammadian-Sabet F (2014) Ab initio calculations of cooperativity effects on chalcogen bonding: linear clusters of (OCS)2–8 and (OCSe)2–8. Struct Chem 26:199–206

    Article  Google Scholar 

  47. 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

    Article  CAS  Google Scholar 

  48. Esrafili MD, Mohammadirad N (2015) Substituent effects in cooperativity of chalcogen bonds. Mol Phys 113:3282–3290

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  50. Alkorta I, Blanco F, Solimannejad M, Elguero J (2008) Competition of hydrogen bonds and halogen bonds in complexes of hypohalous acids with nitrogenated bases. J Phys Chem A 112:10856–10863

    Article  CAS  Google Scholar 

  51. Esrafili MD, Mohammadirad N (2016) Characterization of σ-hole interactions in 1:1 and 1:2 complexes of YOF2X (X = F, Cl, Br, I; Y = P, As) with ammonia: competition between halogen and pnicogen bonds. Struct Chem 27:617–625

    Article  CAS  Google Scholar 

  52. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark MJ, Heyd J, Brothers EN, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell AP, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam NJ, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09, in. Gaussian Inc, Wallingford

    Google Scholar 

  53. 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 

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

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  56. Bulat F, Toro-Labbé A, Brinck T, Murray J, 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 

  57. Biegler-Konig F, Schonbohm J, Bayles D (2001) AIM2000. J Comput Chem 22:545–559

    Article  Google Scholar 

  58. Reed AE, Curtiss LA, Weinhold F (1988) Intermolecular interactions from a natural bond orbital, donor–acceptor viewpoint. Chem Rev 88:899–926

    Article  CAS  Google Scholar 

  59. Lu T, Chen F (2012) Multiwfn: a multifunctional wavefunction analyzer. J Comput Chem 33:580–592

    Article  Google Scholar 

  60. Hedberg L, Hedberg K (1982) Thionyl tetrafluoride. Reanalysis of the molecular structure and resolution of the multiple model problem. J Phys Chem 86:598–602

    Article  CAS  Google Scholar 

  61. Esrafili MD, Mohammadian-Sabet F (2016) σ-Hole bond tunability in YO2X2:NH3 and YO2X2: H2O complexes (X = F, Cl, Br; Y = S, Se): trends and theoretical aspects. Struct Chem 27:617–625

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  63. Alkorta I, Sánchez-Sanz G, Elguero J, Del Bene JE (2012) Exploring (NH2F)2, H2FP: NFH2, and (PH2F)2 potential surfaces: hydrogen bonds or pnicogen bonds? J Phys Chem A 117:183–191

    Article  Google Scholar 

  64. Alkorta I, Elguero J, Del Bene JE (2013) Pnicogen bonded complexes of PO2X (X = F, Cl) with nitrogen bases. J Phys Chem A 117:10497–10503

    Article  CAS  Google Scholar 

  65. Alkorta I, Elguero J, Grabowski SJ (2015) Pnicogen and hydrogen bonds: complexes between PH3X(+) and PH2X systems. Phys Chem Chem Phys 17:3261–3272

    Article  CAS  Google Scholar 

  66. Cremer D, Kraka E (1984) A description of the chemical bond in terms of local properties of electron density and energy. Croat Chem Acta 57:1259–1281

    Google Scholar 

  67. Rozas I, Alkorta I, Elguero J (2000) Behavior of ylides containing N, O, and C atoms as hydrogen bond acceptors. J Am Chem Soc 122:11154–11161

    Article  CAS  Google Scholar 

  68. Grabowski SJ (2009) Covalent character of hydrogen bonds enhanced by π-electron delocalization. Croat Chem Acta 82:185–192

    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 & Soheila Asadollahi

  2. Environmental Heath Research Center, Golestan University of Medical Sciences, Gorgan, Iran

    Yousef Dadban Shahamat

Authors
  1. Mehdi D. Esrafili
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Soheila Asadollahi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yousef Dadban Shahamat
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mehdi D. Esrafili.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 306 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., Asadollahi, S. & Dadban Shahamat, Y. Competition between chalcogen bond and halogen bond interactions in YOX4:NH3 (Y = S, Se; X = F, Cl, Br) complexes: An ab initio investigation. Struct Chem 27, 1439–1447 (2016). https://doi.org/10.1007/s11224-016-0763-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11224-016-0763-4

Keywords

Search

Navigation