Research Articles

X-ray crystal structure of N-benzyl-2-(4,6-diaminopyrimidin-2-ylthio)-acetamide

Vol. 1 No. 2 (2014) 28-32 Published July 28, 2014

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Abstract

N-benzyl-2-(4,6-diaminopyrimidin-2-ylthio)-acetamide, was synthesized by the reaction of 4,6-diamino-pyrimidine-2-thiol with 2-chloro-N-benzyl acetamide in the presence of potassium hydroxide under reflux conditions and crystallized. X-ray diffraction intensity data were collected at room temperature (293k) on a Bruker axs SMART APEXII single crystal X-ray diffractometer equipped with graphite monochromatic Mo K? (?=0.71073 radiation and CCD detector. The compound crystallizes in the monoclinic P21/n space group with four molecules in the unit cell (a=8.5657(5) b=9.3203(5) c=18.2134(10) ?=90, ?=91.540(4) , ?=90 and Z=4). The three dimensional molecular structure of this compound was determined by X-ray crystallography using SHELXS97 and later refined by SHELXL97 to a final R-value 4.3%. In the crystal, the molecular structure is stabilized by intramolecular NH...S, CH...N and CH...O hydrogen bonds and the packing is stabilized by intermolecular NH...N and NHO hydrogen bonds.

References

  1. Xu, L. B.; Sun, W.; Liu, H. Y.; Wang, L. L.; Xiao, J. H.; Yang, X. H.; Li, S., Synthesis of 5-substituted benzyl-2,4-diamino pyrimidine derivatives as c-Fms kinase inhibitors. Chinese Chem Lett 2010, 21, 1318-1321.
  2. http://dx.doi.org/10.1016/j.cclet.2010.06.023 DOI: https://doi.org/10.1016/j.cclet.2010.06.023
  3. Blumenkopf, T. A.; Mueller, E. E.; Roskamp, E. J. Preparation of 2,4-diaminopyrimidines as immunosuppressants. US20030191307A1, 2003.
  4. Cowart, M. D.; Altenbach, R. J.; Liu, H.; Hsieh, G. C.; Drizin, I.; Milicic, I.; Miller, T. R.; Witte, D. G.; Wishart, N.; Fix-Stenzel, S. R., Rotationally constrained 2, 4-diamino-5, 6-disubstituted pyrimidines: a new class of histamine H4 receptor antagonists with improved druglikeness and in vivo efficacy in pain and inflammation models. J Med Chem 2008, 51, 6547-6557.
  5. http://dx.doi.org/10.1021/jm800670r DOI: https://doi.org/10.1021/jm800670r
  6. Mahe, Y.; Michelet, J.-F.; Pichaud, P.; Galey, J.-B., Pyrimidine 3-oxide compounds for inducing/stimulating hair growth and/or retarding hair loss. Google Patents: 2003.
  7. Kandeel, M.; El-Meligie, S.; Omar, R.; Roshdy, S.; Youssef, K., Synthesis of certain 1, 2, 3-selenadiazole, 1, 2, 3-thiadiazole and 1, 2-oxazoline derivatives of anticipated antibacterial activity. J Pharm Sci 1994, 3, 197-205.
  8. Holla, B. S.; Mahalinga, M.; Karthikeyan, M. S.; Akberali, P. M.; Shetty, N. S., Synthesis of some novel pyrazolo [3, 4-< i> d] pyrimidine derivatives as potential antimicrobial agents. Bioorg Med Chem 2006, 14, 2040-2047.
  9. http://dx.doi.org/10.1016/j.bmc.2005.10.053 DOI: https://doi.org/10.1016/j.bmc.2005.10.053
  10. Nogueras, M.; Snchez, A.; Melguizo, M.; Quijano, M. L.; Melgarejo, M., Synthesis of 5-glycosylamino pyrimidines. A new class of compounds with potential anti-aids activity. Bioorg Med Chem Lett 1993, 3, 601-606.
  11. http://dx.doi.org/10.1016/S0960-894X(01)81237-3 DOI: https://doi.org/10.1016/S0960-894X(01)81237-3
  12. Hockov, D.; Hol, A.; Masojdkov, M.; Andrei, G.; Snoeck, R.; De Clercq, E.; Balzarini, J., 5-Substituted-2, 4-diamino-6-[2-(phosphonomethoxy) ethoxy] pyrimidines Acyclic Nucleoside Phosphonate Analogues with Antiviral Activity. J Med Chem 2003, 46, 5064-5073.
  13. http://dx.doi.org/10.1021/jm030932o DOI: https://doi.org/10.1021/jm030932o
  14. Bayrakdarian, M.; Butterworth, J.; Hu, Y.-J.; Santhakumar, V.; Tomaszewski, M. J., Development of 2, 4-diaminopyrimidine derivatives as novel SNSR4 antagonists. Bioorg Med Chem 2011, 21, 2102-2105.
  15. http://dx.doi.org/10.1016/j.bmcl.2011.01.138 DOI: https://doi.org/10.1016/j.bmcl.2011.01.138
  16. Hockov, D.; Hol, A. n.; Masojdkov, M.; Andrei, G.; Snoeck, R.; De Clercq, E.; Balzarini, J., Synthesis and antiviral activity of 2,4-diamino-5-cyano-6-[2-(phosphonomethoxy)ethoxy]pyrimidine and related compounds. Bioorg Med Chem 2004, 12, 3197-3202.
  17. http://dx.doi.org/10.1016/j.bmc.2004.04.002 DOI: https://doi.org/10.1016/j.bmc.2004.04.002
  18. Perales, J. B.; Freeman, J.; Bacchi, C. J.; Bowling, T.; Don, R.; Gaukel, E.; Mercer, L.; Moore Iii, J. A.; Nare, B.; Nguyen, T. M.; Noe, R. A.; Randolph, R.; Rewerts, C.; Wring, S. A.; Yarlett, N.; Jacobs, R. T., SAR of 2-amino and 2,4-diamino pyrimidines with in vivo efficacy against Trypanosoma brucei. Bioorg Med Chem Lett 2011, 21, 2816-2819.
  19. http://dx.doi.org/10.1016/j.bmcl.2011.03.097 DOI: https://doi.org/10.1016/j.bmcl.2011.03.097
  20. Gangjee, A.; Adair, O.; Queener, S. F., Synthesis of 2,4-Diamino-6-(thioarylmethyl)pyrido[2,3-d]pyrimidines as dihydrofolate reductase inhibitors. Bioorg Med Chem 2001, 9, 2929-2935.
  21. http://dx.doi.org/10.1016/S0968-0896(01)00223-1 DOI: https://doi.org/10.1016/S0968-0896(01)00223-1
  22. Algul, O.; Paulsen, J. L.; Anderson, A. C., 2,4-Diamino-5-(2?-arylpropargyl)pyrimidine derivatives as new nonclassical antifolates for human dihydrofolate reductase inhibition. J Mol Graph Model 2011, 29, 608-613.
  23. http://dx.doi.org/10.1016/j.jmgm.2010.11.004 DOI: https://doi.org/10.1016/j.jmgm.2010.11.004
  24. Gangjee, A.; Yang, J.; McGuire, J. J.; Kisliuk, R. L., Synthesis and evaluation of a classical 2,4-diamino-5-substituted-furo[2,3-d]pyrimidine and a 2-amino-4-oxo-6-substituted-pyrrolo[2,3-d]pyrimidine as antifolates. Bioorg Med Chem 2006, 14, 8590-8598.
  25. http://dx.doi.org/10.1016/j.bmc.2006.08.029 DOI: https://doi.org/10.1016/j.bmc.2006.08.029
  26. Farrugia, L. J., WinGX and ORTEP for Windows: an update. J Appl Crystallogr 2012, 45, 849-854.
  27. http://dx.doi.org/10.1107/S0021889812029111 DOI: https://doi.org/10.1107/S0021889812029111
  28. Bruker, A., APEX2-Software Suite for Crystallographic Programs. Bruker AXS, Inc., Madison, WI, USA 2009.
  29. Sheldrick, G., A short history of SHELX. Acta Crystallogr A 2008, 64, 112-122.
  30. http://dx.doi.org/10.1107/S0108767307043930 DOI: https://doi.org/10.1107/S0108767307043930
  31. Nardelli, M., PARST95 an update to PARST: a system of Fortran routines for calculating molecular structure parameters from the results of crystal structure analyses. J Appl Crystallogr 1995, 28, 659-659.
  32. http://dx.doi.org/10.1107/S0021889895007138 DOI: https://doi.org/10.1107/S0021889895007138
  33. Spek, A., Structure validation in chemical crystallography. Acta Crystallogr D 2009, 65, 148-155.
  34. http://dx.doi.org/10.1107/S090744490804362X DOI: https://doi.org/10.1107/S090744490804362X

Author information

  • Ajay Kumar Timiri

    BIRLA INSTITUTE OF TECHNOLOGY - MESRA

  • Subasri S

    Madras University, Chennai

  • Vishwanathan Vijayan

    University of Madras, Chennai

  • Velmurugan Devadasan

    University of Madras, Chennai

  • Barij Nayan Sinha

    Birla Institute of Technology, Mesra image/svg+xml

  • Manish Kesherwani

    University of Madras image/svg+xml

  • Venkatesan Jayaprakash

    BIT, Mesra

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Timiri, A. K.; S, S.; Vijayan, V.; Devadasan, V.; Sinha, B. N.; Kesherwani, M.; Jayaprakash, V. X-Ray Crystal Structure of N-Benzyl-2-(4,6-Diaminopyrimidin-2-Ylthio)-Acetamide. J Pharm Chem 2014, 1 (2), 28-32. https://doi.org/10.14805/jphchem.2014.art9.
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Received
March 15, 2014
Published
July 28, 2014
Section
Research Articles
Pages
28-32

Keywords

  • Acetamide
  • crystal structure
  • 4
  • 6-diamino pyrimidine
  • hydrogen bond
  • molecular dynamics

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