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Annular tautomerism: experimental observations and quantum mechanics calculations

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Abstract

The use of MP2 level quantum mechanical (QM) calculations on isolated heteroaromatic ring systems for the prediction of the tautomeric propensities of whole molecules in a crystalline environment was examined. A Polarisable Continuum Model was used in the calculations to account for environment effects on the tautomeric relative stabilities. The calculated relative energies of tautomers were compared to relative abundances within the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB). The work was focussed on 84 annular tautomeric forms of 34 common ring systems. Good agreement was found between the calculations and the experimental data even if the quantity of these data was limited in many cases. The QM results were compared to those produced by much faster semiempirical calculations. In a search for other sources of the useful experimental data, the relative numbers of known compounds in which prototropic positions were often substituted by heavy atoms were also analysed. A scheme which groups all annular tautomeric transformations into 10 classes was developed. The scheme was designed to encompass a comprehensive set of known and theoretically possible tautomeric ring systems generated as part of a previous study. General trends across analogous ring systems were detected as a result. The calculations and statistics collected on crystallographic data as well as the general trends observed should be useful for the better modelling of annular tautomerism in the applications such as computer-aided drug design, small molecule crystal structure prediction, the naming of compounds and the interpretation of protein—small molecule crystal structures.

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References

  1. Katritzky AR, Lagowski JM (1963) Prototropic Tautomerism of Heteroaromatic compounds: I. General discussion and methods of study. Adv Heterocycl Chem 1:311–338

    Article  CAS  Google Scholar 

  2. Katritzky AR, Lagowski JM (1963) Prototropic Tautomerism of Heteroaromatic compounds: II. Six-membered rings. Adv Heterocycl Chem 1:339–437

    Article  CAS  Google Scholar 

  3. Katritzky AR, Lagowski JM (1963) Prototropic Tautomerism of Heteroaromatic compounds: III. Five-membered rings and one hetero atom. Adv Heterocycl Chem 2:1–26

    Article  CAS  Google Scholar 

  4. Katritzky AR, Lagowski JM (1963) Prototropic Tautomerism of Heteroaromatic compounds: IV. Five-membered rings with two or more hetero atoms. Adv Heterocycl Chem 2:27–81

    Article  CAS  Google Scholar 

  5. Minkin V, Garnovsk A, Elguero J, Katritzky A, Denisko O (2000) The Tautomerism of Heterocycles: Five-membered rings with two or more heteroatoms. Adv Heterocycl Chem 76:157–323

    Article  CAS  Google Scholar 

  6. Stanovnik B, Tiler M, Katritzky A, Denisko O (2001) The Tautomerism of Heterocycles. Six-membered heterocycles: Part 1, Annular Tautomerism. Adv Heterocycl Chem 81:253–303

    Article  CAS  Google Scholar 

  7. Stanovnik B, Tisler M, Katritzky A, Denisko O (2006) The Tautomerism of Heterocycles: substituent Tautomerism of six-membered ring Heterocycles. Adv Heterocycl Chem 91:1–134

    Article  CAS  Google Scholar 

  8. Elguero J, Katritzky A, Denisko O (2000) Prototropic Tautomerism of Heterocycles: Heteroaromatic tautomerism. General overview and methodology. Adv Heterocycl Chem 76:1–84

    Article  CAS  Google Scholar 

  9. Shcherbakova I, Elguero J, Katritzky A (2000) Tautomerism of Heterocycles: condensed five-six, five-five, and six-six ring systems with heteroatoms in both rings. Adv Heterocycl Chem 77:51–113

    Article  CAS  Google Scholar 

  10. Martin YC (2009) Let’s not forget tautomers. J Comput Aided Mol Des 23:693–704

    Article  CAS  Google Scholar 

  11. Alkorta I, Blanco F, Elguero J (2008) Application of Free-Wilson matrices to the analysis of the tautomerism and aromaticity of azapentalenes: a DFT study. Tetrahedron 64:3826–3836

    Article  CAS  Google Scholar 

  12. Alkorta I, Blanco F, Elguero J (2008) Heteropentalenes aromaticity: a theoretical study. J Mol Struct THEOCHEM 851:75–83

    Article  CAS  Google Scholar 

  13. Alkorta I, Elguero J, Liebman J (2006) The Annular Tautomerism of imidazoles and pyrazoles: the possible existence of nonaromatic forms. Struct Chem 17:439–444

    Article  CAS  Google Scholar 

  14. Allen F (2002) The cambridge structural database: a quarter of a million crystal structures and rising. Acta Crystallogr B 58:380–388

    Article  Google Scholar 

  15. Berman H, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov I, Bourne P (2000) The Protein Data Bank. Nucl Acids Res 28:235–242

    Article  CAS  Google Scholar 

  16. Hao MH, Haq O, Muegge I (2007) Torsion angle preference and energetics of small-molecule ligands bound to proteins. J Chem Inf Model 47:2242–2252

    Article  CAS  Google Scholar 

  17. Pitt W, Parry D, Perry B, Groom C (2009) Heteroaromatic rings of the future. J Med Chem 52:2952–2963

    Article  CAS  Google Scholar 

  18. Platonov MO, Samijlenko SP, Sudakov OO, Kondratyuk IV, Hovorun DM (2005) To what extent can methyl derivatives be regarded as stabilized tautomers of xanthine? Spectrochim Acta Part A Mol Biomol Spectrosc 62:112–114

    Article  CAS  Google Scholar 

  19. Alkorta I, Goya P, Elguero J, Singh SP (2007) A simple approach to the tautomerism of aromatic heterocycles. Natl Acad Sci Letts 30:139–159

    CAS  Google Scholar 

  20. Bruno I, Cole J, Edgington P, Kessler M, Macrae C, McCabe P, Pearson J, Taylor R (2002) New software for searching the Cambridge structural database and visualizing crystal structures. Acta Crystallogr B 58:389–397

    Article  Google Scholar 

  21. James CA, Weininger D, Delay J SMARTS. http://www.daylight.com/dayhtml/doc/theory/index.html

  22. Schreyer A, Blundell T (2009) CREDO: a protein–ligand interaction database for drug discovery. Chem Biol Drug Des 73:157–167

    Article  CAS  Google Scholar 

  23. Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536–540

    CAS  Google Scholar 

  24. Dalby A, Nourse J, Hounshell D, Gushurst A, Grier D, Leland B, Laufer J (1992) Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited. J Chem Inf Comput Sci 32:244–255

    CAS  Google Scholar 

  25. Weininger D (1988) SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J Chem Inf Comput Sci 28:31–36

    CAS  Google Scholar 

  26. Idrissi MS, Senechal M, Sauvaitre H, Cotrait M, Garrigou-Lagrange C (1980) J Chim Phys 77:195

    Google Scholar 

  27. Claramunt RM, Lopez C, Garcia MA, Otero MD, Torres MR, Pinilla E, Alarcon SM, Alkorta I, Elguero J (2001) Untitled. New J Chem 25:1061–1068

    Article  CAS  Google Scholar 

  28. Bairoch A, Apweiler R, Wu C, Barker W, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin M, Natale D, O’Donovan C, Redaschi N, Yeh LS (2005) The universal protein resource (UniProt). Nucl Acids Res 33:D154–D159

    Article  CAS  Google Scholar 

  29. Alkorta I, Elguero J (2005) Theoretical estimation of the Annular Tautomerism of Indazoles. J Phys Org Chem 18:719–724

    Article  CAS  Google Scholar 

Download references

Acknowledgments

AJCC thanks the Pfizer Institute for Pharmaceutical Materials Sciences for funding. WRP thanks UCB Celltech for funding his secondment to Professor Tom Blundell’s group. Thanks also to Dr Yvonne Martin for her encouragement and invitation to submit a paper in this subject area

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Correspondence to William R. Pitt.

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Cruz-Cabeza, A.J., Schreyer, A. & Pitt, W.R. Annular tautomerism: experimental observations and quantum mechanics calculations. J Comput Aided Mol Des 24, 575–586 (2010). https://doi.org/10.1007/s10822-010-9345-5

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  • DOI: https://doi.org/10.1007/s10822-010-9345-5

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