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Journal of Molecular Modeling

, Volume 19, Issue 10, pp 4073–4077 | Cite as

Entropy versus aromaticity in the conformational dynamics of aromatic rings

  • Oleg V. Shishkin
  • Przemyslaw Dopieralski
  • Irina V. Omelchenko
  • Leonid Gorb
  • Zdzislaw Latajka
  • Jerzy Leszczynski
Original Paper

Abstract

Comparison of the results of Car-Parrinello molecular dynamics simulations of isolated benzene, pyrimidine and 1,2,4-triazine molecules reveals that the unusually low population of planar geometry of the benzene ring is caused by entropy effects despite its high aromaticity. The decrease in symmetry of the molecule results in smaller changes in entropy and Gibbs free energy due to out-of-plane deformations of the ring, leading to an increase in the population of planar geometry of the ring. This leads to differences in the topology of potential energy and Gibbs free energy surfaces.

Figure

Entropy vs aromaticity in conformational dynamics of aromatic rings

Keywords

Benzene Aromaticity Conformational flexibility Car-Parrinello molecular dynamics Entropy 

Notes

Acknowledgments

The authors gratefully acknowledge the Wroclaw Supercomputer Center (WCSS), the Galera-ACTION Cluster and the Academic Computer Center in Gdansk (CI TASK) for providing computer time.

References

  1. 1.
    Allcock HR (1972) Chem Rev 72:315–356, and references thereinCrossRefGoogle Scholar
  2. 2.
    Spackman MA (1992) Chem Rev 92:1769–1797, and references thereinCrossRefGoogle Scholar
  3. 3.
    Krygowski TM, Cyranski MK (2001) Chem Rev 101:1385–1419CrossRefGoogle Scholar
  4. 4.
    Shishkin OV, Dopieralski P, Omelchenko IV, Gorb L, Latajka Z, Leszczynski J (2011) J Phys Chem Lett 2:2881–2884CrossRefGoogle Scholar
  5. 5.
    Berger R, Fischer C, Klessinger M (1998) J Phys Chem A 102:7157–7167CrossRefGoogle Scholar
  6. 6.
    Bernhardsson A, Forsberg N, Malmqvist P-A, Roos BO, Serrano-Andres L (2000) J Chem Phys 112:2798–2809CrossRefGoogle Scholar
  7. 7.
    Li J, Lin C-K, Li XY, Zhu CY, Lin SH (2010) Phys Chem Chem Phys 12:14967–14976CrossRefGoogle Scholar
  8. 8.
    Isayev O, Furmanchuk A, Gorb L, Shishkin OV, Leszczynski J (2007) J Phys Chem B 111:3476–3480CrossRefGoogle Scholar
  9. 9.
    Shishkin OV, Pichugin KY, Gorb L, Leszczynski J (2002) J Mol Struct 616:159–166CrossRefGoogle Scholar
  10. 10.
    Omelchenko IV, Shishkin OV, Gorb L, Leszczynski J, Fias S, Bultinck P (2011) Phys Chem Chem Phys 13:20536–20548CrossRefGoogle Scholar
  11. 11.
    Shishkin OV, Omelchenko IV, Krasovska MV, Zubatyuk RI, Gorb L, Leszczynski J (2006) J Mol Struct 791:158–164CrossRefGoogle Scholar
  12. 12.
    Car R, Parrinello M (1985) Phys Rev Lett 55:2471–2474CrossRefGoogle Scholar
  13. 13.
    Marx D, Hutter J (2009) Ab initio molecular dynamics: basic theory and advanced methods. Cambridge University Press, Cambridge, UK, pp 1–578Google Scholar
  14. 14.
    CPMD Program Package; see http://www.cpmd.org.
  15. 15.
    Troullier N, Martins JL (1991) Phys Rev B 43:1993–2006CrossRefGoogle Scholar
  16. 16.
    Perdew JP, Burke K, Ernzerhof M (1996) Phys Rev Lett 77:3865–3868CrossRefGoogle Scholar
  17. 17.
    Nose S (1984) Mol Phys 52:255–268CrossRefGoogle Scholar
  18. 18.
    Martyna GJ, Tuckerman ME, Klein ML (1992) J Chem Phys 97:2635–2643CrossRefGoogle Scholar
  19. 19.
    Hockney RW (1970) Methods Comput Phys 9:136–211Google Scholar
  20. 20.
    Mŏller C, Plesset MS (1934) Phys Rev 46:618–622CrossRefGoogle Scholar
  21. 21.
    Kendall RA, Dunning TH Jr, Harrison RJ (1992) J Chem Phys 96:6796–6806CrossRefGoogle Scholar
  22. 22.
    Bird CW (1992) Tetrahedron 48:335–340CrossRefGoogle Scholar
  23. 23.
    Schleyer PR, Maerker C, Dransfeld A, Jiao H, van Eikema Hommes NJR (1996) J Am Chem Soc 118:6317–6318CrossRefGoogle Scholar
  24. 24.
    Raczynska ED, Hallman M, Kolczynska K, Stepniewski TM (2010) Symmetry 2:1485–1509CrossRefGoogle Scholar
  25. 25.
    Gordy WJ (1947) J Chem Phys 15:305–310CrossRefGoogle Scholar
  26. 26.
    Fallah-Bagher-Shaidaei H, Wannere CS, Corminboeuf C, Puchta R, Schleyer PR (2006) Org Lett 8:863–866CrossRefGoogle Scholar
  27. 27.
    Ditchfield R (1974) Mol Phys 27:789–807CrossRefGoogle Scholar
  28. 28.
    Frisch MJ, Trucks GW, Schlegel HB et al (2004) Gaussian 03, revision C.01. Gaussian, Inc, Wallingford CTGoogle Scholar
  29. 29.
    Zefirov NS, Palyulin VA, Dashevskaya EE (1990) J Phys Org Chem 3:147–158CrossRefGoogle Scholar
  30. 30.
    Berezin KV, Kosterina EK (1998) J Appl Spectrosc 65:196–200CrossRefGoogle Scholar
  31. 31.
    Billes F, Mikosch H (1995) J Mol Struct 349:409–412CrossRefGoogle Scholar
  32. 32.
    Thastum Bach D, Hegelund F, Beukes JA, Nicolaisen FM, Palmer MH (1999) J Mol Spectrosc 198:77–93CrossRefGoogle Scholar
  33. 33.
    Furmanchuk A, Shishkin OV, Isayev O, Gorb L, Leszczynski J (2010) Phys Chem Chem Phys 12:9945–9954CrossRefGoogle Scholar
  34. 34.
    Wannier GH (1987) Statistical physics. Dover, New York, pp 1–532Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Oleg V. Shishkin
    • 1
    • 2
  • Przemyslaw Dopieralski
    • 3
  • Irina V. Omelchenko
    • 1
  • Leonid Gorb
    • 4
    • 5
  • Zdzislaw Latajka
    • 3
  • Jerzy Leszczynski
    • 4
  1. 1.Department of X-Ray Diffraction Studies and Quantum Chemistry, SSI “Institute for Single Crystals”National Academy of Science of UkraineKharkivUkraine
  2. 2.Department of Inorganic ChemistryV. N. Karazin Kharkiv National UniversityKharkivUkraine
  3. 3.Faculty of ChemistryUniversity of WroclawWroclawPoland
  4. 4.Department of Chemistry, Interdisciplinary Center for NanotoxicityJackson State UniversityJacksonUSA
  5. 5.Department of Molecular Biophysics, Institute of Molecular Biology and Genetics, Key State Laboratory in Molecular and Cell BiologyNational Academy of Sciences of UkraineKyivUkraine

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