Skip to main content
Log in

Intermolecular interactions between the heavy-atom analogues of acetylene T2H2 (T = Si, Ge, Sn, Pb) and HCN

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

Abstract

Methods

The intermolecular interactions between the heavy-atom analogues of acetylene T2H2 (T = Si, Ge, Sn, Pb) and HCN have been investigated by theoretical calculations at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVDZ level.

Results

The global energy minimum of T2H2 is the butterfly structure A, and another energy minimum is the planar structure B. Both structures A and B exhibit the dual behavior when binding with HCN. The various hydrogen bond (HB), dihydrogen bond (DB) and tetrel bond (TB) complexes can be found according to the MEP maps of T2H2. One TB and three HB complexes formed between structure A and HCN can be located for Si2H2 and Ge2H2. One TB, two HB and one DB complexes formed between structure A and HCN can be located for Sn2H2 and Pb2H2. Four TB and one HB complexes formed between structure B and HCN can be located for all the T2H2. The geometries and binding strengths of the complexes are compared and analyzed.

Conclusions

The interactions in these complexes are generally weak, and the interaction energies of these complexes range from −0.53 to −8.23 kcal/mol. The interaction energies of the TB complexes are larger than those of the corresponding HB and DB complexes for structure A···HCN systems. The relative binding strength of the four TB complexes exhibits different order for different structure B···HCN systems, which is consistent with the MEP maps of the isolated monomers.

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
Fig. 6

Similar content being viewed by others

Data availability

All data generated or analysed during this study are included in this published article.

Code availability

N/A.

References

  1. Wheeler SE, Seguin TJ, Guan Y, Doney AC (2016) Noncovalent interactions in organocatalysis and the prospect of computational catalyst design. Acc Chem Res 49:1061–1069

    Article  CAS  Google Scholar 

  2. Vallavoju N, Sivaguru J (2014) Supramolecular photocatalysis: combining confinement and non-covalent interactions to control light initiated reactions. Chem Soc Rev 43:4084–4101

    Article  CAS  Google Scholar 

  3. Georgakilas V, Tiwari JN, Kemp KC, Perman JA, Bourlinos AB, Kim KS, Zboril R (2016) Noncovalent functionalization of graphene and graphene oxide for energy materials, Biosensing, Catalytic, and Biomedical Applications. Chem Rev 116:5464–5519

    Article  CAS  Google Scholar 

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

    Google Scholar 

  5. Bauzá A, Mooibroek TJ, Frontera A (2013) Tetrel-bonding interaction: rediscovered supramolecular force? Angew Chem Int Ed 52:12317–12321

    Article  Google Scholar 

  6. Chehayber JM, Nagy ST, Lin CS (1984) Ab initio studies of complexes between SiF4 and ammonia. Can J Chem 62:27–31

    Article  CAS  Google Scholar 

  7. Clark T, Hennemann M, Murray JS, Politzer P (2007) Halogen bonding: the sigma-hole. Proceedings of “Modeling interactions in biomolecules II”, Prague, September 5th-9th, 2005. J Mol Model 13:291–296

    Article  CAS  Google Scholar 

  8. 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 

  9. Bundhun A, Ramasami P, Murray JS, 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 

  10. Grabowski SJ (2014) Tetrel bond-σ-hole bond as a preliminary stage of the SN2 reaction. Phys Chem Chem Phys 16:1824–1834

    Article  CAS  Google Scholar 

  11. Grabowski SJ (2018) Tetrel bonds with π-electrons acting as Lewis bases—theoretical results and experimental evidences. Molecules 23:1183

    Article  Google Scholar 

  12. Thomas SP, Pavan MS, Row TNG (2014) Experimental evidence for ‘carbon bonding’ in the solid state from charge density analysis. Chem Commun 50:49–51

    Article  CAS  Google Scholar 

  13. McDowell SAC, Joseph JA (2014) The effect of atomic ions on model σ-hole bonded complexes of AH3Y (A = C, Si, Ge; Y = F, Cl, Br). Phys Chem Chem Phys 16:10854–10860

    Article  CAS  Google Scholar 

  14. Mani D, Arunan E (2014) The X-C···π (X = F, Cl, Br, CN) carbon bond. J Phys Chem A 118:10081–10089

    Article  CAS  Google Scholar 

  15. Southern SA, Bryce DL (2015) NMR investigations of noncovalent carbon tetrel bonds. Computational assessment and initial experimental observation. J Phys Chem A 119:11891–11899

    Article  CAS  Google Scholar 

  16. Scheiner S (2015) Comparison of CH···O, SH···O, Chalcogen, and Tetrel bonds formed by neutral and cationic sulfur-containing compounds. J Phys Chem A 119:9189–9199

    Article  CAS  Google Scholar 

  17. Azofra LM, Scheiner S (2015) Tetrel, chalcogen, and CH···O hydrogen bonds in complexes pairing carbonyl-containing molecules with 1, 2, and 3 molecules of CO2. J Chem Phys 142:034307

    Article  Google Scholar 

  18. Bauzá A, Mooibroek TJ, Frontera A (2016) Tetrel bonding interactions. Chem Rec 16:473–487

    Article  Google Scholar 

  19. Bauzá A, Frontera A, Mooibroek TJ (2016) 1,1,2,2-Tetracyanocyclopropane (TCCP) as supramolecular synthon. Phys Chem Chem Phys 18:1693–1698

    Article  Google Scholar 

  20. Liu MX, Li QZ, Li WZ, Cheng JB (2017) Carbene tetrel-bonded complexes. Struct Chem 28:823–831

    Article  CAS  Google Scholar 

  21. Liu MX, Li QZ, Cheng JB, Li WZ, Li HB (2016) Tetrel bond of pseudohalide anions with XH3F (X = C, Si, Ge, and Sn) and its role in SN2 reaction. J Chem Phys 145:224310

    Article  Google Scholar 

  22. Bene JED, Alkorta I, Elguero J (2017) Carbon-carbon bonding between nitrogen heterocyclic carbenes and CO2. J Phys Chem A 121:8136–8146

    Article  Google Scholar 

  23. Liu MX, Li QZ, Scheiner S (2017) Comparison of tetrel bonds in neutral and protonated complexes of pyridineTF3 and furanTF3 (T = C, Si, and Ge) with NH3. Phys Chem Chem Phys 19:5550–5559

    Article  CAS  Google Scholar 

  24. Legon AC (2017) Tetrel, pnictogen and chalcogen bonds identified in the gas phase before they had names: a systematic look at non-covalent interactions. Phys Chem Chem Phys 19:14884–14896

    Article  CAS  Google Scholar 

  25. Scheiner S (2018) Comparison of various means of evaluating molecular electrostatic potentials for noncovalent interactions. J Comput Chem 39:500–510

    Article  CAS  Google Scholar 

  26. Chen Y, Wang F (2020) Intermolecular interactions involving heavy alkenes H2Si=TH2 (T = C, Si, Ge, Sn, Pb) with H2O and HCl: tetrel bond and hydrogen bond. ACS Omega 5:30210–30225

    Article  CAS  Google Scholar 

  27. Zierkiewicz W, Michalczyk M, Scheiner S (2018) Implications of monomer deformation for tetrel and pnicogen bonds. Phys Chem Chem Phys 20:8832–8841

    Article  CAS  Google Scholar 

  28. Liu MX, Yang L, Li QZ, Li WZ, Cheng JB, Xiao B, Yu XF (2016) Modulating the strength of tetrel bonding through beryllium bonding. J Mol Model 22:192

    Article  CAS  Google Scholar 

  29. McDowell SAC (2014) Sigma-hole cooperativity in anionic [FX···CH3···YF] (X, Y = Cl, Br) complexes. Chem Phys Lett 598:1–4

    Article  CAS  Google Scholar 

  30. Esrafili MD, Mohammadirad N, Solimannejad M (2015) Tetrel bond cooperativity in open-chain (CH3CN)n and (CH3NC)n clusters (n = 2–7): an ab initio study. Chem Phys Lett 628:16–20

    Article  CAS  Google Scholar 

  31. Solimannejad M, Orojloo M, Amani S (2015) Effect of cooperativity in lithium bonding on the strength of halogen bonding and tetrel bonding: (LiCN)n···ClYF3 and (LiCN)n···YF3Cl (Y = C, Si and n = 1-5) complexes as a working model. J Mol Model 21:183

    Article  Google Scholar 

  32. Yourdkhani S, Korona T, Hadipour NL (2015) Interplay between tetrel and triel bonds in RC6H4CN···MF3CN···BX3 complexes: a combined symmetry-adapted perturbation theory, Møller-Plesset, and quantum theory of atoms-in-molecules study. J Comput Chem 36:2412–2428

    Article  CAS  Google Scholar 

  33. Marín-Luna M, Alkorta I, Elguero J (2016) Cooperativity in tetrel bonds. J Phys Chem A 120:648–656

    Article  Google Scholar 

  34. Esrafili MD, Mohammadian-Sabet F (2016) Cooperativity of tetrel bonds tuned by substituent effects. Mol Phys 114:1528–1538

    Article  CAS  Google Scholar 

  35. Rezaei Z, Solimannejad M, Esrafili MD (2015) Interplay between hydrogen bond and single-electron tetrel bond: H3C···COX2···HY and H3C···CSX2···HY (X = F, Cl; Y = CN, NC) complexes as a working model. Comput Theor Chem 1074:101–106

    Article  CAS  Google Scholar 

  36. Chen YS, Yao LF, Wang F (2021) Intermolecular interactions between the heavy alkenes H2Si = TH2 (T = C, Si, Ge, Sn, Pb) and acetylene. J Mol Model 27:110

    Article  CAS  Google Scholar 

  37. Chen YS, Yao LF, Wang F (2019) Synergistic and antagonistic interplay between tetrel bond and pnicogen bond in complexes involving ring compounds. J Mol Model 25:351

    Article  Google Scholar 

  38. Xu HL, Cheng JB, Yang X, Liu ZB, Xiao B, Li QZ (2017) Interplay between the σ-tetrel bond and σ-halogen bond in PhSiF3···4-iodopyridine···N-base. RSC Adv 7:21713–21720

    Article  CAS  Google Scholar 

  39. Li W, Zeng Y, Li X, Sun Z, Meng L (2016) Insight into the pseudo π-hole interactions in the M3H6(NCF)n (M = C, Si, Ge, Sn, Pb; n = 1, 2, 3) complexes. Phys Chem Chem Phys 18:24672–24680

    Article  CAS  Google Scholar 

  40. Quiñonero D (2017) Sigma-hole carbon-bonding interactions in carbon–carbon double bonds: an unnoticed contact. Phys Chem Chem Phys 19:15530–15540

    Article  Google Scholar 

  41. Remyaa K, Suresh CH (2015) Intermolecular carbon–carbon, nitrogen–nitrogen and oxygen–oxygen non-covalent bonding in dipolar molecules. Phys Chem Chem Phys 17:18380–18392

    Article  Google Scholar 

  42. Varadwaj PR, Varadwaja A, Jin BY (2014) Significant evidence of C···O and C···C long-range contacts in several heterodimeric complexes of CO with CH3–X, should one refer to them as carbon and dicarbon bonds! Phys Chem Chem Phys 16:17238–17252

    Article  CAS  Google Scholar 

  43. Alkorta I, Rozas I, Elguero J (2001) Molecular complexes between silicon derivatives and electron-rich groups. J Phys Chem A 105:743–749

    Article  CAS  Google Scholar 

  44. Scheiner S (2020) The ditetrel bond noncovalent bond between neutral tetrel atoms. Phys Chem Chem Phys 22:16606–16614

    Article  CAS  Google Scholar 

  45. Sethio D, Oliveira V, Kraka E (2018) Quantitative assessment of tetrel bonding utilizing vibrational spectroscopy. Molecules 23:2763

    Article  Google Scholar 

  46. Wei YX, Li QZ, Scheiner S (2018) The π-tetrel bond and its influence on hydrogen bonding and proton transfer. ChemPhysChem 19:736–743

    Article  CAS  Google Scholar 

  47. Li QZ, Guo X, Yang X, Li WZ, Cheng JB, Li HB (2014) A σ-hole interaction with radical species as electron donors: does single-electron tetrel bonding exist? Phys Chem Chem Phys 16:11617–11625

    Article  CAS  Google Scholar 

  48. Zierkiewicz W, Michalczyk M, Scheiner S (2018) Comparison between tetrel bonded complexes stabilized by σ and π hole interactions. Molecules 23:1416

    Article  Google Scholar 

  49. Scheiner S (2021) Origins and properties of the tetrel bond. Phys Chem Chem Phys 23:5702–5717

    Article  CAS  Google Scholar 

  50. Scheiner S (2021) Relative strengths of a pnicogen and a tetrel bond and their mutual effects upon one another. J Phys Chem A 125:2631–2641

    Article  CAS  Google Scholar 

  51. Lischka H, Köhler H (1983) Ab initio investigation on the lowest singlet and triplet state of disilyne (Si2H2). J Am Chem Soc. 105:6646–6649

    Article  CAS  Google Scholar 

  52. Binkley JS (1984) Theoretical study of the relative stabilities of C2H2 and Si2H2 conformers. J Am Chem Soc 106:3603–3609

    Article  Google Scholar 

  53. Grev RS, Deleeuw BJ, Schaefer HF (1990) Germanium-germanium multiple bonds: the singlet electronic ground state of Ge2H2. Chem Phys Lett 165:257–264

    Article  CAS  Google Scholar 

  54. Nagase S, Kobayashi K, Takagi N (2000) Triple bonds between heavier Group 14 elements. A theoretical approach. J. Organomet. Chem. 611:264–271

    Article  CAS  Google Scholar 

  55. Bogey M, Bolvin H, Demuynck C, Destombes JL (1991) Nonclassical double-bridged structure in silicon-containing molecules: experimental evidence in Si2H2 from its submillimeter-wave spectrum. Phys Rev Lett 66:413–416

    Article  CAS  Google Scholar 

  56. Wang X, Andrews L, Kushto G (2002) Infrared spectra of the novel Ge2H2 and Ge2H4 species and the reactive GeH1,2,3 intermediates in solid neon, deuterium and argon. J Phys Chem A 106:5809–5816

    Article  CAS  Google Scholar 

  57. Power PP (1999) π-bonding and the lone pair effect in multiple bonds between heavier main group elements. Chem Rev 99:3463–3504

    Article  CAS  Google Scholar 

  58. Lein M, Krapp A, Frenking G (2005) Why do the heavy-atom analogues of acetylene E2H2 (E = Si−Pb) exhibit unusual structures? J Am Chem Soc 127:6290–6299

    Article  CAS  Google Scholar 

  59. Hermann M, Jones C, Frenking G (2014) Reaction mechanisms of small-molecule activation by amidoditetrylynes R2N–EE–NR2 (E = Si, Ge, Sn). Inorg Chem 53:6482–6490

    Article  CAS  Google Scholar 

  60. Emilie B, Guidez MS, Gordon KR (2020) Why is Si2H2 not linear? An intrinsic quasi-atomic bonding analysis. J Am Chem Soc 142:13729–13742

    Article  Google Scholar 

  61. Y. Sert,M. Gümü, H. Gkce,I. Kani,I. Koca, Molecular docking, Hirshfeld surface, structural, spectroscopic, electronic, NLO and thermodynamic analyses on novel hybrid compounds containing pyrazole and coumarin cores. J Mol Struct 2018, 1171, 850-866.

    Article  CAS  Google Scholar 

  62. Abdulridha AA, Allah MAAH, Makki SQ, Sert Y, Salman HE, Balakit AA (2020) Corrosion inhibition of carbon steel in 1 M H2SO4 using new azo Schiff compound: electrochemical, gravimetric, adsorption, surface and DFT studies. J Mol Liq 315:113690

    Article  CAS  Google Scholar 

  63. Hay Allah MAA, Balakit AA, Salman HI, Abdulridha AA, Sert Y (2022) New heterocyclic compound as carbon steel corrosion inhibitor in 1 M H2SO4, high efficiency at low concentration: experimental and theoretical studies. J Adh Sci Technol https://doi.org/10.1080/01694243.2022.2034588

  64. Dege N, Gökce H, Doğan OE, Alpaslan G, Ağar T, Muthu S, Sert Y (2022) Quantum computational, spectroscopic investigations on N-(2-((2-chloro-4,5-dicyanophenyl)amino)ethyl)-4-methylbenzenesulfonamide by DFT/TD-DFT with different solvents, molecular docking and drug-likeness researches. Colloid Surface A 638:128311

    Article  CAS  Google Scholar 

  65. 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 AV, Bloino J, Janesko BG, Gomperts R, Mennucci B, Hratchian HP, Ortiz JV et al (2013) Gaussian 09, Revision D.01. Gaussian, Inc., Wallingford CT

    Google Scholar 

  66. Feller D (1996) The role of databases in support of computational chemistry calculations. J Comput Chem 17:1571–1586

    Article  CAS  Google Scholar 

  67. 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 

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

    Article  Google Scholar 

  69. 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 

Download references

Funding

This work was supported by the Scientific Research Funds from the Educational Department of Yunnan Province, China, grant no. 2020J0634.

Author information

Authors and Affiliations

Authors

Contributions

Yishan Chen: investigation, conceptualization, writing—original draft. Lifeng Yao: writing—review and editing. Fan Wang: resources, supervision.

Corresponding author

Correspondence to Yishan Chen.

Ethics declarations

Conflict of interest

The authors declare no competing interests.

Additional information

Publisher’s note

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

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chen, Y., Yao, L. & Wang, F. Intermolecular interactions between the heavy-atom analogues of acetylene T2H2 (T = Si, Ge, Sn, Pb) and HCN. J Mol Model 29, 52 (2023). https://doi.org/10.1007/s00894-023-05459-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-023-05459-x

Keywords

Navigation