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Structure determination from X-ray powder diffraction, DFT calculation, and Hirshfeld surface analysis of two fused bicyclic and tricyclic compounds

  • Uday Das (a1) (a2), Tanusri Dey (a1), Paramita Chatterjee (a1) (a3) and Alok K. Mukherjee (a1)

Crystal structures of two fused cyclic systems have been determined from X-ray powder diffraction data and their molecular geometries and intermolecular interactions have been analyzed by solid state DFT calculation and Hirshfeld surface evaluation, respectively.

Crystal structures of two fused cyclic compounds, 4-(methyl(sulfonyl)methoxy-2-vinyl)-2S*,3aR*,4S*,5,7aS*-(hexahydro-1H-indan-3a-yl)methylmethanesulfonate (1) and (1S*,2S*,4S*,7R*)-7-(dimethyl(phenyl)silyl)-4′,5′-dihydro-2′H-spiro[bicyclo[2.2.1]hept[5]ene-2,3′-furan]-2′-one (2), have been solved from laboratory X-ray powder diffraction data using direct space approach and refined following the Rietveld method. In the absence of strong hydrogen bond donating groups, the crystal packing of 1 and 2 exhibits C–H ⋯ O hydrogen bonds and C–H ⋯ π interactions forming two-dimensional (2D) supramolecular network. The nature of intermolecular interactions in 1 and 2 has been analyzed through the Hirshfeld surface and 2D fingerprint plots. The density functional theory optimized molecular geometries in 1 and 2 agree closely with those obtained from the crystallographic study. Hirshfeld surface analysis of 1, 2 and a few related fused carbocyclic and carbooxacyclic systems retrieved from the Cambridge Structural Database indicates that about 85% of Hirshfeld surface area in these compounds are because of H ⋯ H and O ⋯ H interactions.

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Altomare A., Cuocci C., Giacovazzo C., Moliterni A., Rizzi R., Corriero N., and Falcicchio A. (2013). “EXPO 2013: a kit of tools for phasing crystal structures from powder data,” J. Appl. Crystallogr. 46, 12311235.
Arlin J. B., Bhardwaj R. M., Johnston A., Miller G. J., Bardin J., MacDouqall F., Fernandes P., Shankland K., David W. I. F., and Florence A. J. (2014). “Structure and stability of two polymorphs of creatine and its monohydrate,” CrystEngComm 16, 81978204.
Bautista E., Maldonado E., and Ortega A. (2012). “neo-clerodane diterpenes from salvia herbacea,” J. Nat. Prod. 75, 951958.
Becke A. D. (1988). “Density-functional exchange-energy approximation with correct asymptotic behavior,” Phys. Rev. A 38, 30983100.
Bruno I. J., Cole J. C., Kessler M., Luo J., Motherwell W. D. S., Purkis L. H., Smith B. R., Taylor R. R., Cooper I. S., Harris E., and Orpen A. G. (2004). “Retrieval of crystallographically-derived molecular geometry information,” J. Chem. Inf. Comput. Sci. 44, 21332144.
Cremer D. and Pople J. A. (1975). “General definition of ring puckering coordinates,” J. Am. Chem. Soc. 97, 13541358.
Das U., Naskar J., and Mukherjee A. K. (2015). “Conformational analysis of an acyclic tetrapeptide: ab-initio structure determination from X-ray powder diffraction, Hirshfeld surface analysis and electronic structure,” J. Pept. Sci. 21, 845852.
David W. I. F. and Shankland K. (2008). “Structure determination from powder diffraction data,” Acta Crystallogr. A 64, 5264.
Defaut B., Parsons T. B., Spencer N., Male L., Kariuki B. M., and Grainger R. S. (2012). “Synthesis of the trans-hydrindane core of dictyoxetane,” Org. Biomol. Chem. 10, 49264932.
Delley B. (1990). “An all-electron numerical method for solving the local density functional for polyatomic molecules,” J. Chem. Phys. 92, 508517.
Dey T., Chatterjee P., Bhattacharya A., Pal S., and Mukherjee A. K. (2016). “Three nimesulide derivatives: synthesis, ab initio structure determination from powder x-ray diffraction, and quantitative analysis of molecular surface electrostatic potential,” Cryst. Growth Des. 16, 14421452.
Ebner C. and Carreira M. C. (2015). “Pentafulvene for the synthesis of complex natural products: total syntheses of (±)-pallambins A and B,” Angew. Chem. Int. Ed. Engl. 54, 1122711230.
Favre-Nicolin V. and Cerny R. (2002). “ FOX, ‘free objects for crystallography’: a modular approach to ab initio structure determination from powder diffraction,” J. Appl. Crystallogr. 35, 734743.
Favre-Nicolin V. and Cerny R. (2004). “A better FOX: using flexible modelling and maximum likelihood to improve direct-space ab initio structure determination from powder diffraction,” Z. Kristallogr. – Cryst. Mater. 219, 847856.
Findley T. J. K., Sucunza D., Miller L. C., Davies D. T., and Procter D. J. (2008). “A flexible, stereoselective approach to the decorated cis-hydrindane skeleton: synthesis of the proposed structure of faurinone,” Chem. Eur. J. 14, 68626865.
Groom C. R., Bruno I. J., Lightfoot M. P., and Ward S. C. (2016). “The Cambridge Structural Database,” Acta Crystallogr. B 72, 171179.
Harris K. D. M. and Cheung E. Y. (2004). “How to determine structures when single crystals cannot be grown: opportunities for structure determination of molecular materials using powder diffraction data,” Chem. Soc. Rev. 33, 526538.
Harris K. D. M., Tremayne M., and Kariuki B. M. (2001). “Contemporary advances in the use of powder x-ray diffraction for structure determination,” Angew. Chem. Int. Ed. Engl. 40, 16261651.
Hirshfeld F. L. (1977). “Bonded-atom fragments for describing molecular charge densities,” Theor. Chim. Acta 44, 129138.
Hog D. T., Mayer P., and Trauner D. (2012). “A unified approach to trans-hydrindane sesterterpenoids,” J. Org. Chem. 77, 58385843.
Hog D. T., Huber F. M., Mayer P., and Trauner D. (2014). “The total synthesis of (-)- nitidasin,” Angew. Chem. Int. Ed. Engl. 53, 85138517.
Hussain N., Hussain M. M., Carroll P. J., and Walsh P. J. (2013). “Chemo- and diastereoselective tandem dual oxidation of B(pin)-substituted allylicalcohols: synthesis of B(pin)-substituted epoxy alcohols, 2-keto-anti-1,3-diols and dihydroxy-tetrahydrofuran-3-ones,” Chem. Sci. 4, 39463957.
Kotha S., Dipak M. K., and Mobin S. M. (2011). “Serendipitous and acid catalyzed synthesis of spirolactones,” Tetrahedron 67, 46164619.
Larson A. C. and Von Dreele R. B. (2000). General Structure Analysis System (GSAS) (Report LAUR 86-748) (Los Almos National Laboratory, Los Alamos, New Mexico).
Lee C., Yang W., and Parr R. G. (1988). “Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density,” Phys. Rev. B: Condens. Matter Mater. Phys. 37, 785789.
Maity S. (2010). “Synthetic studies on terpenoids”, Ph. D. Thesis, Jadavpur University, Kolkata, India.
Maity S. and Ghosh S. (2009). “A direct route to angularly substituted hydrindanes. Formal synthesis of bakkenolide-A and synthesis of an advanced intermediate to umbellactal,” Tetrahedron 65, 92029210.
Pagola S., Stephens P. W., Bohle D. S., Kosar A. D., and Madsen S. K. (2000). “The structure of malaria pigment beta-haematin,” Nature 404, 307310.
Parkin A., Barr G., Dong W., Gilmore C. J., Jayatilaka D., McKinnon J. J., Spackman M. A., and Wilson C. C. (2007). “Comparing entire crystal structures: structural genetic fingerprinting,” CrystEngComm 9, 648652.
Perdew J. P., Burke K., and Ernzerhof M. (1996). “Generalized gradient approximation made simple,” Phys. Rev. Lett. 77, 38653868.
Rietveld H. M. (1967). “Line profiles of neutron powder-diffraction peaks for structure Refinement,” Acta Crystallogr. 22, 151152.
Seco J. M., Quinoa E., and Riguera R. (2004). “The assignment of absolute configuration by NMR,” Chem. Rev. 104, 17117.
Spackman M. A. and Jayatilaka D. (2009). “Hirshfeld surface analysis,” CrystEngComm 11, 1932.
Spackman M. A. and McKinnon J. J. (2002). “Fingerprinting intermolecular interactions in molecular crystals,” CrystEngComm 4, 378392.
Stewart J. J. (2007). “Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements,” J. Mol. Model. 13, 11731213.
Wagner U. and Kratky C. (2015). “Structure elucidation of natural compounds by x-ray crystallography,” Prog. Chem. Org. Nat. Prod. 100, 175.
Williams P. A., Hughes C. E., and Harris K. D. M. (2015). “L-lysine: exploiting powder x-ray diffraction to complete the set of crystal structures of the 20 directly encoded proteinogenic amino acids,” Angew. Chem. Int. Ed. Engl. 54, 39733977.
Wolff S. K., Grimwood D. J., McKinnon J. J., Turner M. J., Jayatilaka D., and Spackman M. (2012). Crystal Explorer, Version 3.1. (Computer Software) (University of Western Australia, Perth, Australia).
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Powder Diffraction
  • ISSN: 0885-7156
  • EISSN: 1945-7413
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