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Chinese Science Bulletin

, Volume 57, Issue 16, pp 1964–1971 | Cite as

Theoretical characterization of electronic structures and properties of C-F···H-C pseudohydrogen bonds

  • Kun YuanEmail author
  • YanZhi Liu
  • LingLing Lü
  • GuoFang Zuo
  • YuanCheng Zhu
  • XiaoNing Dong
Open Access
Article Physical Chemistry

Abstract

The weak intermolecular interactions between 2-F-tetrahydrofuran and imidazole, pyrimidine, adenine, and guanine were studied theoretically using density functional B3LYP/6-311++G** and HF/6-311++G** methods. The results showed that both conventional N...H hydrogen bond and C-F...H-C pseudohydrogen bond (PHB) structures coexist in the four complexes. The weak intermolecular interaction energies indicate that the relative stabilities of the four complexes are in the order guanine...F > imidazole ...F > adenine...F > pyrimidine...F. The characteristics of the four PHBs were determined using geometry optimizations, stretching vibrational frequencies, and natural bond orbital and electron density topological properties calculations. The most important result is that the F group of 2-F-tetrahydrofuran can activate the C-H to accept electrons from another molecule, and C-F...H-C PHB formation is relatively favorable.

Keywords

weak interaction pseudohydrogen bond electronic structure electron density topological property 

References

  1. 1.
    Jiao T F, Liu M H. Supramolecular asemblies and molecular recognition of amphiphilic schiff bases with barbituric acid in organized mMolecular films. J Phys Chem B, 2005, 109: 2532–2539CrossRefGoogle Scholar
  2. 2.
    Jesus V, Surya K D, Chen L H, et al. Development of paramagnetic probes for molecular recognition studies in protein kinases. J Med Chem, 2008, 51: 3460–3465CrossRefGoogle Scholar
  3. 3.
    Xi L, Peng Y H, Ren J S, et al. Carboxyl-modified single-walled carbon nanotubes selectively induce human telomeric i-motif formation. Proc Natl Acad Sci USA, 2006, 103: 19658–19663CrossRefGoogle Scholar
  4. 4.
    Dastidar P. Supramolecular gelling agents: Can they be designed? Chem Soc Rev, 2008, 37: 2699–2715CrossRefGoogle Scholar
  5. 5.
    Lehmann S B C, Spickermann C, Kirchner B. Quantum cluster equilibrium theory applied in hydrogen bond number studies of water. 1. Assessment of the quantum custer equilibrium model for liquid water. J Chem Theory Comput, 2009, 5: 1640–1649CrossRefGoogle Scholar
  6. 6.
    Nguyen T N V, Hughes S R, Peslherbe G H. Microsolvation of the sodium and iodide ions and their ion pair in acetonitrile clusters: A theoretical study. J Phys Chem B, 2008, 112: 621–635CrossRefGoogle Scholar
  7. 7.
    Mohammed G S, Bojan D, Lee J S, et al. Thermodynamics of halogen bonding in solution: Substituent, structural, and solvent effects. J Am Chem Soc, 2010, 132: 1646–1653CrossRefGoogle Scholar
  8. 8.
    Mu Z C, Shu L J, Fuchs H, et al. Two dmensional chiral networks emerging from the aryl-F...H hydrogen-bond-driven self-assembly of partially fluorinated rigid molecular structures. J Am Chem Soc, 2008, 130: 10840–10841CrossRefGoogle Scholar
  9. 9.
    Lv F Z, Peng Z H, Zhang L L, et al. A new type of hydrogen-bonded LBL photoalignment film for liquid crystal (in Chinese). Acta Phy-Chim Sin, 2009, 25: 273–277Google Scholar
  10. 10.
    Howard J A K, Hoy V J, OHagan D, et al. How good is fluorine as a hydrogen bond acceptor? Tetrahedron, 1996, 52: 12613–12622CrossRefGoogle Scholar
  11. 11.
    Dunitz J D. Organic fluorine: Odd man out. ChemBioChem, 2004, 5: 614–621CrossRefGoogle Scholar
  12. 12.
    Pallan P S, Egli M. Pairing geometry of the hydrophobic thymine analogue 2,4-difluorotoluene in duplex DNA as analyzed by X-ray crystallography. J Am Chem Soc, 2009, 131: 12548–12549CrossRefGoogle Scholar
  13. 13.
    Bats J W, Parsch J, Engels J W. 1-deoxy-1-(4-fluorophenyl)-beta-D-ribofuranose, its hemihydrate, and 1-deoxy-1-(2,4-difluorophenyl)-beta-D-ribofuranose: Structural evidence for intermolecular C-H...F-C interactions. Acta Crystallogr Sect C-Cryst Struct Commun, 2000, 56: 201–205CrossRefGoogle Scholar
  14. 14.
    Parsch J, Engels J W. C-F...H-C hydrogen bonds in ribonucleic acids. J Am Chem Soc, 2002, 124: 5664–5672CrossRefGoogle Scholar
  15. 15.
    Frey J A, Leist R, Leutwyler S. Hydrogen bonding of the nucleobase mimic 2-pyridone to fluorobenzenes: An ab initio investigation. J Phys Chem A, 2006, 110: 4188–4195CrossRefGoogle Scholar
  16. 16.
    Sun Z, McLaughlin L W. Probing the nature of three-centered hydrogen bonds in ligand-DNA interactions in the minor groove. J Am Chem Soc, 2007, 129: 12531–12536CrossRefGoogle Scholar
  17. 17.
    Koller A N, Bozilovic J, Engels J W, et al. Aromatic N versus aromatic F: Bioisosterism discovered in RNA base pairing interactions leads to a novel class of universal base analogs. Nucleic Acids Res, 2010, 38: 3133–3146CrossRefGoogle Scholar
  18. 18.
    Bergstrom D E, Swartling D J, Wisor A, et al. Evaluation of thymidine, dideoxythymidine and fluorine substituted deoxyribonucleoside geometry by the Mindo/3 technique: The effect of fluorine substitution on nucleoside geometry and biological activity. Nucleosides Nucleotides, 1991, 10: 693–697CrossRefGoogle Scholar
  19. 19.
    Watts J K, Martin-Pintado N, Gomez-Pinto I, et al. Differential stability of 2′F-ANA*RNA and ANA*RNA hybrid duplexes: Roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility. Nucleic Acids Res, 2010, 38: 2498–2511CrossRefGoogle Scholar
  20. 20.
    Anzahaee M Y, Watts J K, Alla N R, et al. Energetically important C-H...F-C pseudohydrogen bonding in water: Evidence and application to rational design of oligonucleotides with high binding affinity. J Am Chem Soc, 2011, 133: 728–731CrossRefGoogle Scholar
  21. 21.
    Boys S F, Bernardi F. Calculation of small molecular interactions by differences of separate total energies. Some procedures with reduced errors. Mol Phy, 1970, 19: 553–556CrossRefGoogle Scholar
  22. 22.
    King B F, Weinhold F. Structure and spectroscopy of (HCN)n clusters: Cooperative and electronic delocalization effects in C-H...N hydrogen bonding. J Chem Phys, 1995, 103: 333–347CrossRefGoogle Scholar
  23. 23.
    Reed A E, Curtiss L A, Weinhold F. Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chem Rev, 1988, 88: 899–926CrossRefGoogle Scholar
  24. 24.
    Bader R F W. Atoms in Molecules: A Quantum Theory. New York: Clarendon Press, 1990Google Scholar
  25. 25.
    Glendening E D, Badenhoop J K, Reed A E, et al. Natural bond orbital program. Version 5.0. Madison, WI: Theoretical Chemistry Institute, University of Wisconsin, 2001Google Scholar
  26. 26.
    Frisch M J, Trucks G W, Schlegel H B, et al. Gaussian 03 E. 01. Pittsburgh PA: Gaussian Inc, 2004Google Scholar
  27. 27.
    Bader R F W. A quantum theory of molecular structure and its applications. Chem Rev, 1991, 91: 893–928CrossRefGoogle Scholar

Copyright information

© The Author(s) 2012

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Authors and Affiliations

  • Kun Yuan
    • 1
    • 2
    Email author
  • YanZhi Liu
    • 1
    • 2
  • LingLing Lü
    • 1
    • 2
  • GuoFang Zuo
    • 1
    • 2
  • YuanCheng Zhu
    • 1
    • 2
  • XiaoNing Dong
    • 1
    • 2
  1. 1.College of Life-science and ChemistryTianshui Normal UniversityTianshuiChina
  2. 2.Key Laboratory for New Molecular Materials Design and Function of Gansu Education DepartmentTianshuiChina

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