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The association of π–π stacking and hydrogen bonding interactions in substituted Rebek imide with 2,6-di(isobutyramido)pyridine rings: theoretical insight into X-Rebek imide||pyr complexes

  • Sabereh Parvizi Moghadam
  • Marziyeh MohammadiEmail author
  • Reza Behjatmanesh-Ardakani
Original Research
  • 4 Downloads

Abstract

A host–guest model designed between two hemispheres as Rebek imide receptor and different ligands via triple hydrogen bonding and π−π stacking interactions was surveyed to investigate the substituent effects. The association of Rebek imide with 2,6-di(isobutyramido)pyridine (X-Rebek imide||pyr) in the presence of electron donating/withdrawing substituents was studied (X = (NCH3)2, OCH3, CH3, OH, H, F, Cl, Br and CN, CF3 and NO2, where || and ∙∙∙ denote π–π stacking and hydrogen bonding). It was explained the variation in binding energies, energy decomposition, geometries, NMR properties, and electron density of mentioned complexes and effect of different types of the substituents in studied complexes was identified via computational chemistry at M05-2X/6-311++G** level of theory on π–π stacking and hydrogen bonding interactions.

Keywords

π−π stacking Rebek imide Atoms in molecules SAPT 

Notes

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

References

  1. 1.
    Wheeler SE (2011) Local nature of substituent effects in stacking interactions. J Am Chem Soc 133:10262–10274PubMedCrossRefPubMedCentralGoogle Scholar
  2. 2.
    Hwang J, Li P, Smith MD, Shimizu KD (2016) Distance-dependent attractive and repulsive interactions of bulky alkyl groups. Angew Chem Int Ed 55:8086–8089CrossRefGoogle Scholar
  3. 3.
    Sinnokrot MO, Sherrill CD (2004) Substituent effects in π−π interactions: sandwich and T-shaped configurations. J Am Chem Soc 126:7690–7697PubMedCrossRefPubMedCentralGoogle Scholar
  4. 4.
    Parrish RM, Sherrill CD (2014) Quantum-mechanical evaluation of π–π versus substituent−π interactions in π stacking: direct evidence for the Wheeler–Houk picture. J Am Chem Soc 136:17386–17389PubMedCrossRefPubMedCentralGoogle Scholar
  5. 5.
    Seo J-I, Kim I, Lee YS (2009) π–π Interaction energies in monosubstituted-benzene dimers in parallel- and antiparallel-displaced conformations. Chem Phys Lett 474:101–106CrossRefGoogle Scholar
  6. 6.
    Rozas I, Alkorta I, Elguero J (2004) Modeling Protein−RNA Interactions: an electron-density study of the formamide and formic acid complexes with RNA bases. J Phys Chem B 108:3335–3341CrossRefGoogle Scholar
  7. 7.
    Meyer EA, Castellano RK, Diederich F (2003) Interactions with aromatic rings in chemical and biological recognition. Angew Chem Int Ed Eng 42:1210–1250CrossRefGoogle Scholar
  8. 8.
    Marsili S, Chelli R, Schettino V, Procacci P (2008) Thermodynamics of stacking interactions in proteins. Phys Chem Chem Phys 10:2673–2685PubMedCrossRefPubMedCentralGoogle Scholar
  9. 9.
    Olsen J, Seiler P, Wagner B, Fischer H, Tschopp T, Obst-Sander U, Banner DW, Kansy M, Meller K, Diederich F (2004) A fluorine scan of the phenylamidinium needle of tricyclic thrombin inhibitors: effects of fluorine substitution on pKa and binding affinity and evidence for intermolecular C–F⋯CN interactions. Org Biomol Chem 2:1339–1352PubMedCrossRefPubMedCentralGoogle Scholar
  10. 10.
    Morgenthaler M, Aebi JD, Groninger F, Mona D, Wagner B, Kansy M, Diederich F (2008) A fluorine scan of non-peptidic inhibitors of neprilysin: fluorophobic and fluorophilic regions in an enzyme active site. J Fluor Chem 129:852–865CrossRefGoogle Scholar
  11. 11.
    Gung BW, Emenike BU, Alverez CN, Rakovan J, Kirschbaum K, Jain N (2010) Relative substituent position on the strength of π–π stacking interactions. Tetrahedron Lett 51:1648–1650PubMedCentralCrossRefGoogle Scholar
  12. 12.
    Cozzi F, Siegel JS (1995) Interaction between stacked aryl groups in 1,8-diarylnaphthalenes: dominance of polar/π over charge-transfer effects. Pure Appl Chem 67:683–689CrossRefGoogle Scholar
  13. 13.
    Wheeler SE, Bloom JWG (2014) Toward a more complete understanding of noncovalent interactions involving aromatic rings. J Phys Chem A 118:6133–6147PubMedCrossRefPubMedCentralGoogle Scholar
  14. 14.
    Kollman PA (1977) In: Schaefer III HF (ed) Applications of electronic structure theory, vol 4. Plenum, New YorkGoogle Scholar
  15. 15.
    Alkorta I, Rozas I, Elguero J (1998) Non-conventional hydrogen bonds. Chem Soc Rev 27:163–170CrossRefGoogle Scholar
  16. 16.
    Solimannejad M, Ghafari S (2013) Ab initio study of ternary radical–molecule complexes between HCN(HNC) and HO(HS) species. Struct Chem 24:1493–1498CrossRefGoogle Scholar
  17. 17.
    Rutledge LR, Wetmore SD (2011) Modeling the chemical step utilized by human alkyladenine DNA glycosylase: a concerted mechanism AIDS in selectively excising damaged purines. J Am Chem Soc 133:16258–16269PubMedCrossRefPubMedCentralGoogle Scholar
  18. 18.
    Biot C, Wintjens R, Rooman M (2004) Stair motifs at protein−DNA interfaces: nonadditivity of H-bond, stacking, and cation−π interactions. J Am Chem Soc 126:6220–6221PubMedCrossRefPubMedCentralGoogle Scholar
  19. 19.
    Ji B, Wang W, Deng D, Zhang Y (2011) Symmetrical bifurcated halogen bond: design and synthesis. Cryst Growth Des 11:3622–3628CrossRefGoogle Scholar
  20. 20.
    Robertazzi A, Platts JA (2006) Gas-phase DNA oligonucleotide structures. A QM/MM and Atoms in Molecules Study. J Phys Chem A 110:3992–4000PubMedCrossRefPubMedCentralGoogle Scholar
  21. 21.
    Quiñonero D, Frontera A, Escudero D, Ballester P, Costa A, Dey PM (2008) MP2 Study of synergistic effects between X–H/π (X = C,N,O) and π–π interactions. Theor Chem Accounts 120:385–393CrossRefGoogle Scholar
  22. 22.
    Gholipour A, Saydi H, Neiband MS, Neyband RS (2012) Simultaneous interactions of pyridine with substituted benzene ring and H–F in X-ben⊥pyr···H–F complexes: a cooperative study. Struct Chem 23:367–373CrossRefGoogle Scholar
  23. 23.
    Saha S, Sastry GN (2015) Cooperative or anticooperative: how noncovalent interactions influence each other. J Phys Chem B 119:11121–11135PubMedCrossRefPubMedCentralGoogle Scholar
  24. 24.
    Wolfe J, Nemeth D, Costero A, Rebek J (1988) Convergent functional groups: catalysis of hemiacetal cleavage in a synthetic molecular cleft. J Am Chem Soc 110:983–984CrossRefGoogle Scholar
  25. 25.
    Voss F, Vogt F, Herdtweck E, Bach T (2011) Synthesis of catalytically active ruthenium complexes with a remote chiral lactam as hydrogen-bonding motif. Synthesis 6:961–971Google Scholar
  26. 26.
    Wintner EA, Conn MM, Rebek J (1994) Self-replicating molecules: a second generation. J Am Chem Soc 116:8877–8884CrossRefGoogle Scholar
  27. 27.
    Tjivikua T, Ballester P, Rebek J (1990) Self-replicating system. J Am Chem Soc 112:1249–1250CrossRefGoogle Scholar
  28. 28.
    Rebek J, Askew B, Ballester P, Buhr C, Jones S, Nemeth D, Williams K (1987) Molecular recognition: hydrogen bonding and stacking interactions stabilize a model for nucleic acid structure. J Am Chem Soc 109:5033–5035CrossRefGoogle Scholar
  29. 29.
    Rebek J (1990) Molecular recognition and biophysical organic chemistry. Acc Chem Res 23:399–404CrossRefGoogle Scholar
  30. 30.
    Faraoni R, Blanzat M, Kubicek S, Braun C, Bernd Schweizer W, Gramlich V, Diederich F (2004) New Rebek imide-type receptors for adenine featuring acetylene-linked π-stacking platforms. Org Biomol Chem 2:1962–1964PubMedCrossRefPubMedCentralGoogle Scholar
  31. 31.
    Faraoni R, Castellano RK, Gramlichc V, Diederich F (2004) H-Bonded complexes of adenine with Rebek imide receptors are stabilised by cation–π interactions and destabilised by stacking with perfluoroaromatics. Chem Commun 4:370–371CrossRefGoogle Scholar
  32. 32.
    Riwar L, Trapp N, Kuhn B, Diederich F (2017) Substituent effects in parallel-displaced π-π stacking interactions: distance matters. Angew Chem Int Ed 56:11252–11257CrossRefGoogle Scholar
  33. 33.
    Dumele O, Trapp N, Diederich F (2015) Halogen bonding molecular capsules. Angew Chem Int Ed 54:12339–12344CrossRefGoogle Scholar
  34. 34.
    Harder M, Carnero Corrales MA, Trapp N, Kuhn B, Diederich F (2015) Rebek imide platforms as model systems for the investigation of weak intermolecular interactions. Chem Eur J 21:8455–8463PubMedCrossRefPubMedCentralGoogle Scholar
  35. 35.
    Salonen LM, Ellermann M, Diederich F (2011) Aromatic rings in chemical and biological recognition: energetics and structures. Angew Chem Int Ed 50:4808–4842CrossRefGoogle Scholar
  36. 36.
    Riwar LJ, Trapp N, Kuhn B, Diederich F (2017) Substituent effects in parallel-displaced stacking interactions: distance matters. Angew Chem Int Ed 56:11252–11257CrossRefGoogle Scholar
  37. 37.
    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, Peralta Jr JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, 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 O, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2003) Gaussian 03, Revision C.02. GAUSSIAN, Inc, Wallingford CTGoogle Scholar
  38. 38.
    Boys SB, Bernardi F (1970) The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol Phys 19:553–566CrossRefGoogle Scholar
  39. 39.
    BieglerKonig FW, Schonbohm J, Bayles D (2001) Software News and Updates AIM2000- a program to analyze and visualize atoms in molecules. J Comput Chem 22:545–559CrossRefGoogle Scholar
  40. 40.
    Schmidt MW, Baldridge KK, Boat 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 14:1347–1363CrossRefGoogle Scholar
  41. 41.
    Zhu W, Tan X, Shen J, Luo X, Cheng F, Mok PC, Ji R, Chen K, Jiang H (2003) Differentiation of cation−π bonding from cation−π intermolecular interactions: a quantum chemistry study using density-functional theory and Morokuma decomposition methods. J Phys Chem A 107:2296–2303CrossRefGoogle Scholar
  42. 42.
    Ebrahimi A, Habibi M, Neyband RS, Gholipour AR (2009) Cooperativity of pi-stacking and hydrogen bonding interactions and substituent effects on X-ben//pyr...H-F complexes. Phys Chem Chem Phys 11:11424–11431PubMedCrossRefPubMedCentralGoogle Scholar
  43. 43.
    Ghafari NikooJooneghani S, Gholipour A (2019) Mutual cooperation of π-π stacking and pnicogen bond interactions of substituted monomeric Lawesson’s reagent and pyridine rings: Theoretical insight into Pyr||X-PhPS2⊥pyr complexes. Chem Phys Lett 721:91–98CrossRefGoogle Scholar
  44. 44.
    Ghafari S, Gholipour A (2015) Simultaneous interactions of pyrimidine ring with BeF2 and BF3 in BeF2 center dot center dot center dot X-Pyr center dot center dot center dot BF3 complexes: non-cooperativity. J Mol Model 21:1–7CrossRefGoogle Scholar
  45. 45.
    Rozas I, Alkorta I, Elguero J (2000) Behavior of Ylides Containing N, O, and C atoms as hydrogen bond acceptors. J Am Chem Soc 122:11154–11161CrossRefGoogle Scholar

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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Chemistry, Payame Noor UniversityTehranIran
  2. 2.Department of Chemistry, Faculty of ScienceVali-e-Asr University of RafsanjanRafsanjanIran

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