CRYSTAL GROWTH & DESIGN
Weak Csp3-H‚‚‚F-C Interaction Overshadows the Strong CtC-H‚‚‚OdC Hydrogen Bond: Structure of Pentafluorophenyl Prop-2-ynyl Carbonate
2007 VOL. 7, NO. 5 844-846
Angshuman R. Choudhury,† Ramakrishna G. Bhat,‡ Tayur N. Guru Row,*,† and Srinivasan Chandrasekaran*,‡ Solid State and Structural Chemistry Unit and Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, Karnataka, India ReceiVed July 25, 2006; ReVised Manuscript ReceiVed February 20, 2007
ABSTRACT: Weak Csp3-H‚‚‚F-C interaction overshadows the strong CtC-H‚‚‚OdC in the structure of pentafluorophenyl prop-2ynyl carbonate as seen by singe crystal X-ray studies at 90 and 290 K. The study of intermolecular interactions involving organic fluorine has been a field of interest in the past.1-4 A number of reports in the literature subscribe to the conclusion that organic fluorine hardly accepts hydrogen bonds and does not contribute to the crystal packing.1,2 It was claimed that fluorine, being the most electronegative element, does not participate in the formation of the C-H‚‚‚F-C hydrogen bond in generating a crystal lattice.2 Shimoni and Glusker, however, pointed out that although C-H‚‚‚F-C interactions are weak as compared to C-H‚‚‚O-C interactions, their contribution cannot be ignored in determining the modes of molecular packing in complexes and in crystals.3 A number of studies have been carried out in this area in recent years to explore the different modes of interactions involving the C-F group.5 We have been involved in the investigation and evaluation of the interactions offered by organic fluorine in different chemical environments and demonstrated that fluorine provides different types (C-F‚‚‚F, C-H‚‚‚F, and C-F‚‚‚π) of directional interactions to build crystal lattices in a number of organic compounds.6,7 We have elucidated that in the presence of an acceptor like CdO, fluorine interactions remain silent and the removal of the CdO group from a similar chemical environment activates interactions involving fluorine. All of these results suggest that fluorine can generate different types of packing motifs via C-F‚‚‚F, C-H‚‚‚F, and C-F‚‚‚π interactions, especially in the absence of strong hydrogen bond donors and/or acceptors such as N-H, O-H, CdO, etc. Herein, we report the preference of Csp3-H‚‚‚F-C interactions over an accessible and highly favorable tC-H‚‚‚OdC hydrogen bond in the case of pentafluorophenyl prop-2-ynyl carbonate (PocOPfp, 1) (Figure 1). A search in the Cambridge Structural Database of crystal structures points out that the molecules, which contain both a CdO acceptor and a tC-H donor, pack in the crystal lattice via tC-H‚‚‚OdC hydrogen bonds.8 PocOPfp, although, contains both a CdO acceptor and a tC-H donor, along with five C-F groups, and it uniquely crystallizes utilizing a pair of significant C-H‚‚‚F-C interactions! Database analysis in this context reveals that there are reports of four such cases (see the Supporting Information) where the preference moves over to C-H‚‚‚F-C rather than tC-H‚‚‚OdC contacts. In connection with our work on peptide synthesis, propargyloxycarbonyl chloride (Poc-Cl) was treated with pentaflurorophenol under alkaline conditions to give PocOPfp (1) as a white crystalline solid in almost quantitative yield (Scheme 1). The reagent Poc-Cl was prepared by the reaction of propargyl alcohol with diphosgene in anhydrous ether in good yield.9 Compound 1 was crystallized as rods from a solution in cyclohexane. Single-crystal data sets were * To whom correspondence should be addressed. Tel: 91-80-22932404. Fax:91 80 2360 0529. E-mail:
[email protected]. † Solid State and Structural Chemistry Unit. ‡ Department of Organic Chemistry.
Figure 1. Molecular structure of 1; displace.
Figure 2. Packing diagram of the molecule viewed down the c-axis; intermolecular C-H‚‚‚F interactions are shown as dotted lines.
Scheme 1
recorded on a Bruker AXS single-crystal X-ray diffractometer equipped with a Smart Apex CCD area detector at 293(2) and 90.0(2) K. The crystal data collected at 293 K indicated that the novel packing features of this molecule and hence another set of data were collected at 90.0(2) K to evaluate the intermolecular interactions. The crystal structures at both temperatures were solved in the monoclinic P21/n space group.10 The ORTEP and packing diagrams of the compound at 90 K are shown in Figures 1 and 2, respectively. The molecule, in the solid state at both temperatures, adopts a unique conformation with the carbonyl group pointing upward from the plane of the phenyl ring, and C7 and O2 are at distances of 0.951(1) and 1.933(1) Å, respectively, from the plane of phenyl ring. The angle between the least-squares planes passing through O1, O2, O3, and C7 and C8, C9, C10, and H3 of 74(2)° indicates that the carbonyl group and the -CtC-H group are significantly
10.1021/cg060489t CCC: $37.00 © 2007 American Chemical Society Published on Web 04/11/2007
Communications
Crystal Growth & Design, Vol. 7, No. 5, 2007 845
Figure 3. Molecular chain via C-H‚‚‚F interactions involving atoms H1 and F3.
Figure 4. Molecular dimer via C-H‚‚‚F interactions involving atoms H2 and F2. Table 1 interaction H···F (Å) C···F (Å) ∠C-H···F (Å)
temp (K)
C8-H1···F3
C8-H2···F2
C10-H3···F1
90 293 90 293 90 293
2.35(2) 2.44(2) 3.269(2) 3.356(2) 158(1) 157(2)
2.57(2) 2.63(2) 3.373(2) 3.497(3) 144(1) 143(2)
2.62(2) 2.73(2) 3.208(2) 3.295(3) 123(1) 125(2)
away from one another in the molecule. This, in turn, is expected to facilitate the formation of an intermolecular tC-H‚‚‚OdC hydrogen bond with the CdO group of another molecule. Surprisingly, in the crystal structure, it has been observed that the two hydrogens on sp3-carbon, C8 participate in the intermoleular C-H‚‚‚F-C interactions and build the lattice. Neither the -CdO group nor the acidic acetylenic hydrogen (-CtC-H) offer any intermolecular interaction of any significance; the shortest H‚‚‚O distance observed in the structure is 2.89(2) Å (at 90 K), which is much longer than the sum of their van der Waals radii (2.6 Å). Compound 1 forms cooperative molecular chains involving H1 and F3 (Figure 3) and head to tail dimers involving H2 and F2 (Figure 4) via C-H‚‚‚F interactions at both temperatures (Table 1). The molecular structure determination of 1, at two different temperatures, has shed light on the crystal packing. Although the overall molecular conformation and packing in the lattice at both 293 and 90 K remain the same, careful examination of the orientations of neighboring -CtC-H groups reveals that the spacing between them is unequal at 90 K (Figure 5a), while they are identical at 293 K (Figure 5b). We have also carried out a search in the database for the stacking of the -CtC-H group in different structures and found that 68 structures reported in the CCDC with C‚‚‚C distances from 2 to 4 Å and ∠C‚‚‚CtC between 45 and 135° show such stacking. In a majority of the cases (60 hits), we find that the groups remain parallel to each other.11 This study also shows that the acetylenic stack is quite rare and is unusual. To find out the nature of this stacking interaction, this infrequently observed feature needs to be studied in detail in the future. The observation of an interesting and apparently stronger Csp3-H‚‚‚F interaction in the molecular structure of PocOPfp (1), which has overshadowed the anticipated and very likely tC-H‚‚‚OdC hydrogen bond, supports that when the molecules can align the less preferred contacts can dominate. In our recent study,12 C-H‚‚‚F-C has been quantified via charge density studies
Figure 5. Disposition of the molecules across the -CtC-H group at 90 (a) and 293 K (b).
to belong to the hierarchy of hydrogen bonds. It appears as though the directionalities offered by the crystal lattice attain superiority in such cases. Acknowledgment. We thank DST, New Delhi, for the support of the CCD facility at IISc, Bangalore. Supporting Information Available: CIF files for rgb1_m and rgb90k_m, Cambridge structural database search results, ORTEP diagrams, tables of crystal data and torsion angles, and search overviews. This material is available free of charge via the Internet at http://pubs.acs.org.
References (1) Howard, J. A. K.; Hoy, V. J.; O’Hagan, D.; Smith, G. T. Tetrahedron 1996, 52, 12613. (2) Dunitz, J. D.; Taylor, R. Chem. Eur. J. 1997, 3, 89. (3) Shimoni, L.; Glusker, J. P. Struct. Chem. 1994, 5, 383. (4) Thalladi, V. R.; Weiss, H.-C.; Bla¨ser, D.; Boese, R.; Nangia, A.; Desiraju, G. R. J. Am. Chem. Soc. 1998, 120, 8702. (5) (a) Vangala, V. R.; Nangia, A.; Lynch, V. M. Chem. Commun. 2002, 1304. (b) Nangia, A. New J. Chem. 2000, 24, 1049. (c) van den Berg, J.-A.; Seddon, K. R. Cryst. Growth Des. 2003, 3, 643. (d) Thallapally, P. K.; Nangia, A. CrystEngComm 2001, 3, 1; Nangia, A. CrystEngComm 2002, 4, 93; Reichenba¨cher, K.; Su¨ss, H. I.; Hulliger, J. Chem. Soc. ReV. 2005, 34, 22. (6) (a) Prasanna, M. D.; Guru Row, T. N. CrystEngComm 2000, 2, 134. (b) Prasanna, M. D.; Guru Row, T. N. J. Mol. Struct. 2001, 562, 55. (c) Prasanna, M. D.; Guru Row, T. N. J. Mol. Struct. 2001, 559, 255. (d) Prasanna, M. D.; Guru Row, T. N. Cryst. Eng. 2000, 3, 135. (7) (a) Choudhury, A. R.; Urs, U. K.; Nagarajan, K.; Guru Row, T. N. J. Mol. Struct. 2002, 605, 71. (b) Choudhury, A. R.; Guru Row, T. N. Cryst. Growth Des. 2004, 4, 47. (c) Choudhury, A. R.; Nagarajan, K.; Guru Row, T. N. Acta Crystallogr. 2004, C60, 644. (d) Choudhury, A. R.; Nagarajan, K.; Guru Row, T. N. Acta. Crystallogr. 2004, C60, 219. (e) Choudhury, A. R.; Guru Row, T. N. Acta Crystallogr. 2004, E60, 1595. (8) (a) Allen, F. H.; Howard, J. A. K.; Hoy, V. J.; Desiraju, G. R.; Reddy, D. S.; Wilson, C. C. J. Am. Chem. Soc. 1996, 118, 4081. (b) Boryczka, S.; Rozenberg, M. S.; Schreurs, A. M. M.; Kroon, J.; Strikov, E. B.; Steiner, T. New J. Chem. 2001, 25, 1111. (9) Bhat, R. G.; Kerouredan, E.; Porhiel, E.; Chandrasekaran, S. Tetrahedron Lett. 2002, 43, 2467.
846 Crystal Growth & Design, Vol. 7, No. 5, 2007 (10) C10H3O3F5; M ) 266.1; monoclinic; a ) 7.3166(11) Å; b ) 17.7688(28) Å; c ) 7.4574(12) Å; β ) 98.305(2)°; V ) 959.35(4) Å3; T ) 90.0(2) K; space group, P21/n; Z ) 4; Fcalcd ) 1.84 g cm-3; µ(Mo KR) ) 0.197 mm-1; refln meaured, 6981; unique refln, 1753; no. of parameters ) 175; Robs ) 0.028; wR2obs ) 0.072; ∆Fmin,max ) -0.258, 0.211; g.o.f. ) 1.068.
Communications (11) Representative scatterograms and the details of the data base search are reported in the Supporting Information. (12) Chopra, D.; Cameron, T. S.; Ferrara, R. D.; Guru Row, T. N. J. Phys. Chem. A 2006, 110, 10465.
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