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Analysis of Small Molecule X-Ray Crystal Structures: Chemical Crystallography with Undergraduate Students in a Teaching Laboratory

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Abstract

The molecular structures of six small molecule organic compounds have been studied by X-ray diffraction in collaboration with undergraduate students enrolled in an advanced integrated laboratory course. The structures of 3-chloro-2-fluorobenzonitrile (1) [orthorhombic, P212121, a = 3.7679(13) Å, b = 12.546(4) Å, c = 13.780(5) Å], 5-chloro-2-fluorobenzonitrile (2) [monoclinic, P21/c, a = 3.7909(7) Å, b = 14.265(3) Å, c = 12.171(2) Å, β = 92.314(3)°], 2-bromo-3′-hydroxyacetophenone (3) [triclinic, P-1, a = 7.7081(3) Å, b = 9.8840(3) Å, c = 10.7320(4) Å, α = 98.4345(4)°, β = 90.6184(4)°, γ = 105.9259(4)°], 3-chlorobenzoylacetonitrile (4) [monoclinic, Cc, a = 4.8086(6) Å, b = 32.929(4) Å, c = 10.5855(13) Å, β = 97.665(1)°], 4-bromo-1-indanone (5) [triclinic, P-1, a = 7.3731(4) Å, b = 7.5419(4) Å, c = 8.2370(4) Å, α = 62.927(1)°, β = 71.160(1)°, γ = 71.521(1)°], and 4-bromo-1-indanol (6) [monoclinic, P21/c, a = 12.7914(9) Å, b = 4.6949(4) Å, c = 27.864(2) Å, β = 94.707(1)°] reveal several different types of intermolecular interactions, such as hydrogen bonding, π-stacking, halogen–halogen interactions, and C–H···X (X = O, N, halogen) interactions.

Graphical Abstract

The molecular structures of six small molecule organic compounds have been studied by X-ray diffraction in collaboration with undergraduate students enrolled in an advanced integrated laboratory course. The structures reveal several different types of intermolecular interactions, such as hydrogen bonding, π-stacking, halogen–halogen interactions, and C–H···X (X = O, N, halogen) interactions.

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References

  1. Sheldrick GM (2008) Acta Crystallogr A64:112–122

    Article  Google Scholar 

  2. Macrae CF, Edgington PR, McCabe P, Pidcock E, Shields GP, Taylor R, Towler M, van de Streek J (2006) J Appl Crystallogr 39:453–457

    Article  CAS  Google Scholar 

  3. Dolomanov OV, Bourhis LJ, Gildea RJ, Howard JAK, Puschmann H (2009) J Appl Crystallogr 42:339–341

    Article  CAS  Google Scholar 

  4. Rossi M, Berman HM (1988) J Chem Educ 65:472–473

    Article  Google Scholar 

  5. Kantardjieff KA, Lind C, Ngd J, Santarsiero BD (2010) J Appl Crystallogr 43:1181–1188

    Article  CAS  Google Scholar 

  6. Crundwell G, Phan J, Kantardjieff KA (1999) J Chem Educ 76:1242–1245

    Article  CAS  Google Scholar 

  7. Kantardjieff KA (2010) J Appl Crystallogr 43:1276–1282

    Article  CAS  Google Scholar 

  8. Ortiz AL, Sanchez-Bajo F, Cumbrera FL, Guiberteau F (2013) J Appl Crystallogr 46:242–247

    Article  CAS  Google Scholar 

  9. Wilson CC, Parkin A, Thomas LH (2012) J Chem Educ 89:34–37

    Article  CAS  Google Scholar 

  10. Pett VB (2010) J Appl Crystallogr 43:1139–1143

    Article  CAS  Google Scholar 

  11. Battle GM, Ferrence GM, Allen FH (2010) J Appl Crystallogr 43:1208–1223

    Article  CAS  Google Scholar 

  12. Sun H, DiMagno SG (2006) Angew Chem Int Ed 45:2720–2725

    Article  CAS  Google Scholar 

  13. Saczewski F, Kornicka A, Hudson AL, Laird S, Scheinin M, Laurila JM, Rybczynska A, Boblewski K, Lehmann A, Gdaniec M (2011) Bioorg Med Chem 19:321–329

    Article  CAS  Google Scholar 

  14. Fauvet PG, Massaux M, Chevalier R (1978) Acta Crystallogr B34:1376–1378

    Article  CAS  Google Scholar 

  15. Salonen LM, Ellermann M, Diederich F (2011) Angew Chem Int Ed 50:4808–4842

    Article  CAS  Google Scholar 

  16. Lueckheide M, Rothman N, Ko B, Tanski JM (2013) Polyhedron 58:79–84

    Article  CAS  Google Scholar 

  17. Pedireddi VR, Reddy DS, Goud BS, Craig DC, Rae AD, Desiraju GR (1994) J Chem Soc Perkin Trans 11:2353–2360

    Article  Google Scholar 

  18. Ding H, Zhang Y (2009) Huaxue Gongye Yu Gongcheng Jishu 30:18–20

    CAS  Google Scholar 

  19. Clark JH, Nightingale DJ (1996) J Fluor Chem 78:91–93

    Article  CAS  Google Scholar 

  20. Buettelmann B, Ballard TM, Gasser R, Fischer H, Hernandez M-C, Knoflach F, Knust H, Stadler H, Thomas AW, Trube G (2009) Bioorg Med Chem Lett 19:5958–5961

    Article  CAS  Google Scholar 

  21. Savall BM, Gomez L, Chavez F, Curtis M, Meduna SP, Kearney A, Dunford P, Cowden J, Thurmond RL, Grice C, Edwards JP (2011) Bioorg Med Chem Lett 21:6577–6581

    Article  CAS  Google Scholar 

  22. Cox PJ (2001) Acta Crystallogr E57:o1203–o1205

    Google Scholar 

  23. Saha BK, Nangia A (2007) Heteroat Chem 18:185–194

    Article  CAS  Google Scholar 

  24. Martin R (1997) Handbook of hydroxyacetophenone: preparation and physical properties. Kluwer, Dordrecht

    Book  Google Scholar 

  25. Nefzi A, Arutyunyan S (2010) Tetrahedron Lett 51:4797–4800

    Article  CAS  Google Scholar 

  26. Bhandari SV, Parikh JK, Bothara KG, Chitre TS, Lokwani DK, Devale TL, Modhave NS, Pawar VS, Panda S (2010) J Enzym Inhib Med Chem 25:520–530

    Article  CAS  Google Scholar 

  27. Qing W-X, Zhang W (2009) Acta Crystallogr E65:o2837

    Google Scholar 

  28. Pyo A, Park A, Jung HM, Lee S (2012) Synthesis 44:2885–2888

    Article  CAS  Google Scholar 

  29. van der Klein PAM, Kourounakis AP, Ijzerman AP (1999) J Med Chem 42:3629–3635

    Article  Google Scholar 

  30. Norman MH, Chen N, Chen Z, Fotsch C, Hale C, Han N, Hurt R, Jenkins T, Kincaid J, Liu L, Lu Y, Moreno O, Santora VJ, Sonnenberg JD, Karbon W (2000) J Med Chem 43:4288–4312

    Article  CAS  Google Scholar 

  31. Hu Y, Xia Q, Shangguan S, Liu X, Hu Y, Sheng R (2012) Molecules 17:9683–9696

    Article  CAS  Google Scholar 

  32. Gomez-Lor B, de Frutos O, Ceballos PA, Granier T, Echavarren AM (2001) Eur J Org Chem 2001:2107–2114

    Article  Google Scholar 

  33. Geitmann M, Elinder M, Seeger C, Brandt P, de Esch IJP, Danielson UH (2011) J Med Chem 54:699–708

    Article  CAS  Google Scholar 

  34. Cui H, Akhmedov NG, Petersen JL, Wang KK (2010) J Org Chem 75:2050–2056

    Article  CAS  Google Scholar 

  35. Celik I, Akkurt M, Yilmaz M, Tutar A, Erenler R, Garcia-Granda S (2012) Acta Crystallogr E68:o833

    Google Scholar 

  36. Sugai T, Kuwahara S, Hoshino C, Matsuo N, Mori K (1982) Agric Biol Chem 46:2579–2585

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The authors gratefully acknowledge support for the X-ray diffraction facilities at Vassar College from the National Science Foundation under Grant No. 0521237 (J.M.T. P.I.).

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  1. Department of Chemistry, Vassar College, Poughkeepsie, NY, 12604, USA

    Hannah Aldeborgh, Kaylene George, Morgan Howe, Heili Lowman, Holger Moustakas, Nora Strunsky & Joseph M. Tanski

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  1. Hannah Aldeborgh
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  2. Kaylene George
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Correspondence to Joseph M. Tanski.

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Aldeborgh, H., George, K., Howe, M. et al. Analysis of Small Molecule X-Ray Crystal Structures: Chemical Crystallography with Undergraduate Students in a Teaching Laboratory. J Chem Crystallogr 44, 70–81 (2014). https://doi.org/10.1007/s10870-013-0485-z

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