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Influence of hydrogen bonds on edge-to-face interactions between pyridine molecules

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Abstract

Edge-to-face interactions between two pyridine molecules and the influence of simultaneous hydrogen bonding of one or both of the pyridines to water on those interactions were studied by analyzing data from ab initio calculations. The results show that the edge-to-face interactions of pyridine dimers that are hydrogen bonded to water are generally stronger than those of non-H-bonded pyridine dimers, especially when the donor pyridine forms a hydrogen bond. The binding energy of the most stable edge-to-face interacting H-bonded pyridine dimer is −5.05 kcal/mol, while that for the most stable edge-to-face interacting non-H-bonded pyridine dimer is −3.64 kcal/mol. The interaction energy data obtained in this study cannot be explained solely by the differences in electrostatic potential between pyridine and the pyridine–water dimer. However, the calculated cooperative effect can be predicted using electrostatic potential maps.

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References

  1. Meyer EA, Castellano RK, Diederich F (2003) Interactions with aromatic rings in chemical and biological recognition. Angew Chem Int Ed 42:1210–1250

  2. Salonen LM, Ellermann M, Diederich F (2011) Aromatic rings in chemical and biological recognition: energetics and structures. Angew Chem Int Ed 50:4808–4842

  3. Bissantz C, Kuhn B, Stahl M (2010) A medicinal chemist’s guide to molecular interactions. J Med Chem 53:5061–5084

  4. Burley SK, Petsko GA (1985) Aromatic–aromatic interaction: a mechanism of protein structure stabilization. Science 229:23–28

  5. Hunter CA, Sanders JKM (1990) The nature of π–π interactions. J Am Chem Soc 112:5525–5534

  6. Chakrabarti P, Samanta U (1995) CH/pi interaction in the packing of the adenine ring in protein structures. J Mol Biol 251:9–14

  7. Chakrabarti P, Bhattacharyya R (2007) Geometry of nonbonded interactions involving planar groups in proteins. Prog Biophys Mol Biol 95:83–137

  8. Saha RP et al (2007) Interaction geometry involving planar groups in protein interfaces. Proteins 67:84–97

  9. Chourasia M et al (2011) Aromatic–aromatic interactions database, a(2)ID: an analysis of aromatic pi-networks in proteins. Int J Biol Macromol 48:540–552

  10. Samanta U, Chakrabarti P (2001) Assessing the role of tryptophan residues in the binding site. Protein Eng 14:7–15

  11. Chelli R, Gervasio FL, Procacci P, Schettino V (2002) Stacking and T-shape competition in aromatic-aromatic amino acid interactions. J Am Chem Soc 124:6133–6143

  12. Gsponer J, Haberthür U, Caflisch A (2003) The role of side-chain interactions in the early steps of aggregation: molecular dynamics simulations of an amyloid-forming peptide from the yeast Prion Sup35. PNAS 100:5154–5159

  13. Aravinda S, Shamala N, Das C, Sriranjini A, Karle IL, Balaram P (2003) Aromatic−aromatic interactions in crystal structures of helical peptide scaffolds containing projecting phenylalanine residues. J Am Chem Soc 125:5308–5315

  14. Makwana KM, Mahalakshmi R (2014) Comparative analysis of cross strand aromatic–Phe interactions in designed peptide β-hairpins. Org Biomol Chem 12:2053–2061

  15. Geronimo I, Lee EC, Singh NJ, Kim KS (2010) How different are electron-rich and electron-deficient interactions? J Chem Theory Comput 6:1931–1934

  16. Schweizer WB, Dunitz JD (2006) Quantum mechanical calculations for benzene dimer energies: present problems and future challenges. J Chem Theory Comput 2:288–291

  17. Rezač J, Hobza P (2008) Benzene dimer: dynamic structure and thermodynamics derived from on-the-fly ab initio DFT-D molecular dynamic simulations. J Chem Theory Comput 4:1835–1840

  18. Pitonak M, Neogrady P, Rezac J, Jurecka P, Urban M, Hobza P (2008) Benzene dimer: high-level wave function and density functional theory calculations. J Chem Theory Comput 4:1829–1834

  19. Bludský O, Rubeš M, Soldán P, Nachtigall P (2008) Investigation of the benzene-dimer potential energy surface: DFT/CCSD(T) correction scheme. J Chem Phys 128:114102/1–114102/8

  20. Janowski T, Pulay P (2007) High accuracy benchmark calculations on the benzene dimer potential energy surface. Chem Phys Lett 447:27–32

  21. Bettinger HF, Kar T, Sanchez-Garcia E (2009) Borazine and benzene homo- and heterodimers. J Phys Chem A 113:3353–3359

  22. Sherrill CD, Takatani T, Hohenstein EG (2009) An assessment of theoretical methods for nonbonded interactions: comparison to complete basis set limit coupled-cluster potential energy curves for the benzene dimer, the methane dimer, benzene-methane, and benzene-H2S. J Phys Chem A113:10146–10159

  23. Ninković DB, Janjić GV, Veljković DŽ, Sredojević DN, Zarić SD (2011) What are the preferred horizontal displacements in parallel aromatic–aromatic interactions? Significant interactions at large displacements. ChemPhysChem 12:3511–3514

  24. Lee EC, Kim D, Jurečka P, Tarakeshwar P, Hobza P, Kim KS (2007) Understanding of assembly phenomena by aromatic–aromatic interactions: benzene dimer and the substituted systems. J. Phys Chem A 111:3446–3457

  25. Chakraborty S, Omidyan R, Alata I, Nielsen IB, Dedonder C, Broquier M, Jouvet C (2009) Protonated benzene dimer: an experimental and ab initio study. J Am Chem Soc 31:11091–11097

  26. Wen XD, Hoffmann R, Ashcroft NW (2011) Benzene under high pressure: a story of molecular crystals transforming to saturated networks, with a possible intermediate metallic phase. J Am Chem Soc 23:9023–9035

  27. Hohenstein EG, Duan J, Sherrill CD (2011) Origin of the surprising enhancement of electrostatic energies by electron-donating substituents in substituted sandwich benzene dimers. J Am Chem Soc 34:13244–13247

  28. Wheeler SE, Houk KN (2008) Substituent effects in the benzene dimer are due to direct interactions of the substituents with the unsubstituted benzene. J Am Chem Soc 33:10854–10855

  29. Ninković DB, Andrić JM, Malkov SN, Zarić SD (2014) What are the preferred horizontal displacements of aromatic–aromatic interactions in proteins? Comparison with the calculated benzene–benzene potential energy surface. Phys Chem Chem Phys 16:11173–11177

  30. Malenov DP, Ninković DB, Sredojević DN, Zarić SD (2014) Stacking of benzene with metal chelates: calculated CCSD(T)/CBS interaction energies and potential-energy curves. ChemPhysChem 15:2458–2461

  31. Malenov DP, JLj D, Janjić GV (2016) Coordinating benzenes stack stronger than noncoordinating benzenes, even at large horizontal displacements. Cryst Growth Des 16:4169–4172

  32. Hohenstein EG, Sherrill CD (2009) Effects of heteroatoms on aromatic π–π interactions: benzene–pyridine and pyridine dimer. J Phys Chem A 113:878–886

  33. Mignon P, Loverix S, Proft FD, Geerlings P (2004) Influence of stacking on hydrogen bonding: quantum chemical study on pyridine−benzene model complexes. J Phys Chem A 108:6038–6044

  34. Mishra BK, Sathyamurthy N (2005) Pi–pi interaction in pyridine. J Phys Chem A 109:6–8

  35. Mishra BK, Arey JS, Sathyamurthy NJ (2010) Stacking and spreading interaction in N-heteroaromatic systems. J Phys Chem A 114:9606–9616

  36. Piacenza M, Grimme S (2005) Van der Waals interactions in aromatic systems: structure and energetics of dimers and trimers of pyridine. ChemPhysChem 6:1554–1558

  37. Ninković DB, Janjić GV, Zarić SD (2012) Crystallographic and ab initio study of pyridine stacking interactions. Local nature of hydrogen bond effect in stacking interactions. Cryst Growth Des 12:1060–1063

  38. Janjić GV, Ninković DB, Zarić SD (2013) Influence of supramolecular structures in crystals on parallel stacking interactions between pyridine molecules. Acta Cryst B69:389–394

  39. Escudero D, Estarellas C, Frontera A, Quiñonero D, Deyà PM (2009) Theoretical and crystallographic study of edge-to-face aromatic interactions between pyridine moieties and benzene. Chem Phys Lett 468:280–285

  40. Ninković DB, Andric JM, Zarić SD (2013) Parallel interactions at large horizontal displacement in pyridine–pyridine and benzene–pyridine dimers. ChemPhysChem 14:237–243

  41. Janjić GV, Veljković DŽ, Zarić SD (2011) Water/aromatic parallel alignment interactions. Significant interactions at large horizontal displacements. Cryst Growth Des 11:2680–2683

  42. Frisch MJ et al (2009) Gaussian 09, revision A.1. Gaussian, Inc., Wallingford

  43. 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

  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

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Acknowledgments

This work was supported by the Serbian Ministry of Education, Science, and Technological Development (grant no. 172065).

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Authors and Affiliations

  1. Innovation Center of the Faculty of Chemistry, Studentski trg 12-16, Belgrade, Serbia

    Jelena M. Andrić

  2. Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade, Serbia

    Ivana S. Antonijević & Goran V. Janjić

  3. Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade, Serbia

    Snežana D. Zarić

  4. Department of Chemistry, Texas A & M University at Qatar, P.O. Box 23874, Doha, Qatar

    Snežana D. Zarić

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  1. Jelena M. Andrić
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  2. Ivana S. Antonijević
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Correspondence to Snežana D. Zarić.

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This paper belongs to Topical Collection P. Politzer 80th Birthday Festschrift

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Andrić, J.M., Antonijević, I.S., Janjić, G.V. et al. Influence of hydrogen bonds on edge-to-face interactions between pyridine molecules. J Mol Model 24, 60 (2018). https://doi.org/10.1007/s00894-017-3570-y

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  • DOI: https://doi.org/10.1007/s00894-017-3570-y

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