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Isomorphous crystal structures of chlorodi­acetyl­ene and iododi­acetyl­ene derivatives: simultaneous hydrogen and halogen bonds on carbon­yl

aDépartement de Chimie, Cégep de Sherbrooke, 475 rue du Cégep, Sherbrooke, Québec, J1E 4K1, Canada, bLaboratoire d'Analyses Structurales par Diffraction des Rayons-X, Département de Chimie, Université de Sherbrooke, 2500, boulevard de l'Université, Sherbrooke, Québec, J1K 2R1, Canada, and cLaboratoire de Synthèse Supramoléculaire, Département de Chimie, Institut de Pharmacologie, Université de Sherbrooke, 3001 12e avenue nord, Sherbrooke, QC, J1H 5N4, Canada
*Correspondence e-mail: pierre.baillargeon@usherbrooke.ca

Edited by J. T. Mague, Tulane University, USA (Received 11 June 2017; accepted 7 July 2017; online 17 July 2017)

The crystal structures of tert-butyl (5-chloro­penta-2,4-diyn-1-yl)carbamate, C10H12ClNO2 (II), and tert-butyl (5-iodo­penta-2,4-diyn-1-yl)carbamate, C10H12INO2 (IV), are isomorphous to previously reported structures and accordingly their mol­ecular and supra­molecular structures are similar. In the crystals of (II) and (IV), mol­ecules are linked into very similar two-dimensional wall organizations with anti­parallel carbamate groups involved in a combination of hydrogen and halogen bonds (bifurcated N—H⋯O=C and C≡C—X⋯O=C inter­actions on the same carbonyl group). There is no long-range parallel stacking of diynes, so the topochemical polymerization of di­acetyl­ene is prevented. A Cambridge Structural Database search revealed that C≡C—X⋯O=C contacts shorter than the sum of the van der Waals radii are scarce (only one structure for the C≡C—Cl⋯O=C inter­action and 13 structures for the similar C≡C—I⋯O=C inter­action).

1. Chemical context

Hydrogen bonds (HBs) and halogen bonds (XBs) are considered to be useful noncovalent synthetic tools in crystal engineering (Aakeröy et al., 2015[Aakeröy, C. B., Spartz, C. L., Dembowski, S., Dwyre, S. & Desper, J. (2015). IUCrJ, 2, 498-510.]; Grabowski, 2016[Grabowski, S. J. (2016). Crystals, 6, 59-63.]; Resnati et al., 2015[Resnati, G., Boldyreva, E., Bombicz, P. & Kawano, M. (2015). IUCrJ, 2, 675-690.]; Cinčić et al., 2008[Cinčić, D., Friščić, T. & Jones, W. (2008). Chem. Mater. 20, 6623-6626.]). Indeed, these directional inter­molecular inter­actions facilitate the preparation of the desired solid-state motifs and architectures (Gilday et al., 2015[Gilday, L. C., Robinson, S. W., Barendt, T. A., Langton, M. J., Mullaney, B. R. & Beer, P. D. (2015). Chem. Rev. 115, 7118-7195.]; Cavallo et al., 2016[Cavallo, G., Metrangolo, P., Milani, R., Pilati, T., Priimagi, A., Resnati, G. & Terraneo, G. (2016). Chem. Rev. 116, 2478-2601.]; Priimagi et al., 2013[Priimagi, A., Cavallo, G., Metrangolo, P. & Restani, R. (2013). Acc. Chem. Res. 46, 2686-2695.]; Mukherjee et al., 2014[Mukherjee, A., Tothadi, S. & Desiraju, G. R. (2014). Acc. Chem. Res. 47, 2514-2524.]; Shirman et al., 2015[Shirman, T., Boterashvili, M., Orbach, M., Freeman, D., Shimon, L. J. W., Lahav, M. & van der Boom, M. E. (2015). Cryst. Growth Des. 15, 4756-4759.]; Mukherjee et al., 2017[Mukherjee, A., Teyssandier, J., Hennrich, G., De Feyter, S. & Mali, K. S. (2017). Chem. Sci. 8, 3759-3769.]). For example, using HBs and XBs, the specific organization of terminal di­acetyl­enes (Li et al., 2009[Li, Z., Fowler, F. W. & Lauher, J. W. (2009). J. Am. Chem. Soc. 131, 634-643.]; Ouyang et al., 2003[Ouyang, X., Fowler, F. W. & Lauher, J. W. (2003). J. Am. Chem. Soc. 125, 12400-12401.]), bromodi­acetyl­enes (Jin et al., 2015[Jin, H., Young, C. N., Halada, G. P., Phillips, B. L. & Goroff, N. S. (2015). Angew. Chem. Int. Ed. 54, 14690-14695.]) and iododi­acetyl­enes (Jin et al., 2013[Jin, H., Plonka, A. M., Parise, J. B. & Goroff, N. S. (2013). CrystEngComm, 15, 3106-3110.]; Sun et al., 2006[Sun, A., Lauher, J. W. & Goroff, N. S. (2006). Science, 312, 1030-1034.]) has been obtained to achieve the solid-state topochemical polymerization of di­acetyl­enes. On the other hand, to the best of our knowledge, no chlorodi­acetyl­ene topochemical polymerizations have been reported. Our results show that chlorodi­acetyl­ene (II) is isostructural to iododi­acetyl­ene (IV) and the previously reported bromodi­acetyl­ene (III) and terminal di­acetyl­ene (I) (Baillargeon et al., 2016[Baillargeon, P., Caron-Duval, É., Pellerin, É., Gagné, S. & Dory, Y. L. (2016). Crystals, 6, 37-49.]) (see Scheme[link]). Although the arrangement of diynes in the present article stands no chance of undergoing topochemical polymerization, we suggest that in other systems prone to polymerization, replacing Br, I or H atoms by Cl atoms in their diyne groups might result in successful PolyChloroDi­Acetyl­ene (PCDA) formation as well. This work also contributes to an emerging research theme, namely the concept of orthogonal mol­ecular inter­actions such as HBs and XBs (Kratzer et al., 2015[Kratzer, P., Ramming, B., Römisch, S. & Maas, G. (2015). CrystEngComm, 17, 4486-4494.]; Takemura et al., 2014[Takemura, A., McAllister, L. J., Hart, S., Pridmore, N. E., Karadakov, P. B., Whitwood, A. C. & Bruce, D. W. (2014). Chem. Eur. J. 20, 6721-6732.]; Voth et al., 2009[Voth, A. R., Khuu, P., Oishi, K. & Ho, P. S. (2009). Nat. Chem. 1, 74-79.]), which may find applications in medicinal chemistry and chemical biology (Wilcken et al., 2013[Wilcken, R., Zimmermann, M. O., Lange, A., Joerger, A. C. & Boeckler, F. M. (2013). J. Med. Chem. 56, 1363-1388.]).

[Scheme 1]

2. Structural commentary

The mol­ecular structures of compounds (II) and (IV) are shown in Fig. 1[link]. All bond lengths and angles are within normal ranges. For example, the inter­nal diyne C2—C3 bonds lengths [1.376 (3) Å for (II) and 1.385 (4) Å for (IV)] follow the useful rule of thumb describing a C—C single-bond distance (1.54 Å) decreasing by 0.04 Å each time one of the participating C atoms changes hybridization from sp3 to sp2 or from sp2 to sp (Bent, 1961[Bent, H. A. (1961). Chem. Rev. 61, 275-311.]). Moreover, the observed distances are almost identical to those found recently in the literature for similar halodiynes (Hoheisel et al., 2013[Hoheisel, T. N., Schrettl, S., Marty, R., Todorova, T. K., Corminboeuf, C. & Sienkiewicz, A. (2013). Nat. Chem. 5, 327-334.]; Baillargeon et al., 2016[Baillargeon, P., Caron-Duval, É., Pellerin, É., Gagné, S. & Dory, Y. L. (2016). Crystals, 6, 37-49.]). The relative orientation between the di­acetyl­enic moiety and the carbamate functional group can be established by the absolute value of the torsion angles C4—C5—N1—C6 [111.07 (19)°] for (II) and [103.8 (3)°] for (IV).

[Figure 1]
Figure 1
The mol­ecular structure of (A) compound (II) and (B) compound (IV), showing the atom-labelling schemes. Displacement ellipsoids are drawn at the 50% probability level. H atoms are shown as fixed-size spheres of 0.30 Å.

3. Supra­molecular features

In the crystals of compounds (II) and (IV), mol­ecules are linked via an N—H⋯O=C hydrogen bond between their respective carbamate functionalities [N1—H1⋯O1i (Table 1[link]) and N1—H1⋯O2i (Table 2[link])], generating an anti­parallel stacking pattern which orients the di­acetyl­ene skeleton on each side of the one-dimensional carbamate tape (parts B and D in Fig. 2[link]). For both crystals, the simultaneous presence of halogen and hydrogen bonds with the carbamate O atom have been found. Indeed, additional halogen-bond inter­actions occur with the carbamate O atom [Cl1⋯O1ii for (II) and I1⋯O2ii for (IV)], resulting in an infinite two-dimensional network that can be considered as polar supra­molecular walls. This arrangement is similar to our previous work (Baillargeon et al., 2016[Baillargeon, P., Caron-Duval, É., Pellerin, É., Gagné, S. & Dory, Y. L. (2016). Crystals, 6, 37-49.]) on the terminal di­acetyl­ene (I) (part A in Fig. 2[link]) and the bromodi­acetyl­ene (III) (part C in Fig. 2[link]). In fact, diynes (I)–(IV) (Fig. 2[link]) constitute a complete set of truly isomorphous crystals that can be carefully examined to evaluate the differences and similarities that exist between halogen and hydrogen bonds. Thus, the X⋯O⋯H angle increases as the size of the halogen atom becomes larger. This angle, which is pretty open in the chlorine crystal (II) (Cl1⋯O1⋯H1; part B in Fig. 2[link]; 69°) adopts a near orthogonal geometry with the iodine (I1⋯O2⋯H1; part D in Fig. 2[link]; 83°). It is not a surprise that the bromine crystal (III) represents an inter­mediate case (part C in Fig. 2[link]; 72°). The value for the terminal di­acetyl­ene (I) X = H (part A in Fig. 2[link]; 76°) is closely related to the bromodi­acetyl­ene (Baillargeon et al., 2016[Baillargeon, P., Caron-Duval, É., Pellerin, É., Gagné, S. & Dory, Y. L. (2016). Crystals, 6, 37-49.]).

Table 1
Hydrogen-bond and halogen-bond geometries (Å, °) for (II)[link]

DXA DX XA DA DXA
N1—H1⋯O1i 0.88 2.09 2.934 (2) 162
C1—Cl1⋯O1ii 1.665 (2) 3.127 (2) 4.792 (3) 179.01 (7)
Symmetry codes: (i) [-x+2, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) [-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].

Table 2
Hydrogen-bond and halogen-bond geometries (Å, °) for (IV)[link]

DXA DX XA DA DXA
N1—H1⋯O2i 0.88 2.04 2.881 (2) 160
C1—I1⋯O2ii 1.999 (2) 2.945 (2) 4.919 (3) 168.31 (8)
Symmetry codes: (i) [-x+{\script{3\over 2}}, y+{\script{3\over 2}}, -z+{\script{3\over 2}}]; (ii) [-x+{\script{1\over 2}}, y+{\script{3\over 2}}, -z+{\script{3\over 2}}].
[Figure 2]
Figure 2
Halogen (green lines) and/or hydrogen bonds (blue lines) inside the supra­molecular walls of (A) diyne (I), (B) chloro­diyne (II), (C) bromo­diyne (III) and (D) iodo­diyne (IV). The nonpolar H atoms have been omitted for clarity.

4. Database survey

A survey of the Cambridge Structural Database (Conquest Version 1.19; CSD, Version 5.38, November 2016 plus 3 updates; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) furnished 404 hits of terminal alkynes CC—H having close contacts with carbonyl O=C (shorter than the sum of their van der Waals radii). On the other hand, similar contacts from halogenoalkyne analogs are scarce (1 hit for the chloro­alkyne, 4 hits for the bromo­alkyne and 13 hits for the iodo­alkyne; Table 3[link]). For the iodo­alkyne, results are limited to monovalent iodine and for a structure in which the carbonyl group is not involved in an organometallic complex.

Table 3
CSD data (Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) retrieved for the C≡C—X⋯O=C contacts shorter than the sum of their van der Waals radii

C≡C—X⋯O=C contacts CSD refcode Space group X⋯O distance (Å) C—X⋯O angle (°) Reference
C≡C—Cl⋯O=C NIDWAA P[\overline{1}] 3.111; 3.241 152.59; 158.76 Kawai et al. (2013[Kawai, H., Utamura, T., Motoi, E., Takahashi, T., Sugino, H., Tamura, M., Ohkita, M., Fujiwara, K., Saito, T., Tsuji, T. & Suzuki, T. (2013). Chem. Eur. J. 19, 4513-4524.])
C≡C—Br⋯O=C HEVWAI C2 2.959 158.12 Hoheisel et al. (2013[Hoheisel, T. N., Schrettl, S., Marty, R., Todorova, T. K., Corminboeuf, C. & Sienkiewicz, A. (2013). Nat. Chem. 5, 327-334.])
C≡C—Br⋯O=C HEVWAI01 P212121 2.966 166.70 Hoheisel et al. (2013[Hoheisel, T. N., Schrettl, S., Marty, R., Todorova, T. K., Corminboeuf, C. & Sienkiewicz, A. (2013). Nat. Chem. 5, 327-334.])
C≡C—Br⋯O=C NIDWII P21/n 2.867 171.11 Kawai et al. (2013[Kawai, H., Utamura, T., Motoi, E., Takahashi, T., Sugino, H., Tamura, M., Ohkita, M., Fujiwara, K., Saito, T., Tsuji, T. & Suzuki, T. (2013). Chem. Eur. J. 19, 4513-4524.])
C≡C—Br⋯O=C KAMXII P21/c 3.060 178.26 Baillargeon et al. (2016[Baillargeon, P., Caron-Duval, É., Pellerin, É., Gagné, S. & Dory, Y. L. (2016). Crystals, 6, 37-49.])
C≡C—I⋯O=C COHYUU P[\overline{1}] 3.096 164.55 Luo et al. (2008[Luo, L., Wilhelm, C., Sun, A., Grey, C. P., Lauher, J. W. & Goroff, N. S. (2008). J. Am. Chem. Soc. 130, 7702-7709.])
C≡C—I⋯O=C IYAYUC Pca21 2.861 170.36 Hou et al. (2004[Hou, Z.-K., Ren, Y.-G., Huang, M.-Z., Song, J. & Chen, L.-G. (2004). Acta Cryst. E60, o1336-o1337.])
C≡C—I⋯O=C MASVUZ P21/n 2.834; 2.887 170.72; 172.97 Perkins et al. (2012[Perkins, C., Libri, S., Adams, H. & Brammer, L. (2012). CrystEngComm, 14, 3033-3038.])
C≡C—I⋯O=C TOYPUS P21/c 2.933 175.36 Avtomonov et al. (1997[Avtomonov, E. V., Grüning, R. & Lorberth, J. (1997). Z. Naturforsch. Teil B, 52, 256-258.])
C≡C—I⋯O=C HOWXIC P21/c 2.887 169.51 Dumele et al. (2014[Dumele, O., Wu, D., Trapp, N., Goroff, N. & Diederich, F. (2014). Org. Lett. 16, 4722-4725.])
C≡C—I⋯O=C LUNKOW P2/c 2.791 174.12 Kratzer et al. (2015[Kratzer, P., Ramming, B., Römisch, S. & Maas, G. (2015). CrystEngComm, 17, 4486-4494.])
C≡C—I⋯O=C LUNKUC P21/c 2.754 172.63 Kratzer et al. (2015[Kratzer, P., Ramming, B., Römisch, S. & Maas, G. (2015). CrystEngComm, 17, 4486-4494.])
C≡C—I⋯O=C LUNLAJ P21/c 2.773 173.70 Kratzer et al. (2015[Kratzer, P., Ramming, B., Römisch, S. & Maas, G. (2015). CrystEngComm, 17, 4486-4494.])
C≡C—I⋯O=C LUNLIR Pca21 2.858 170.94 Kratzer et al. (2015[Kratzer, P., Ramming, B., Römisch, S. & Maas, G. (2015). CrystEngComm, 17, 4486-4494.])
C≡C—I⋯O=C LUNLOX C2/c 2.763 175.58 Kratzer et al. (2015[Kratzer, P., Ramming, B., Römisch, S. & Maas, G. (2015). CrystEngComm, 17, 4486-4494.])
C≡C—I⋯O=C IBUYAI P21/m 2.856 177.96 Dumele et al. (2017[Dumele, O., Schreib, B., Warzok, U., Trapp, N., Schalley, C. A. & Diederich, F. (2017). Angew. Chem. Int. Ed. 56, 1152-1157.])
C≡C—I⋯O=C IBUYOW P21/c 2.830 176.52 Dumele et al. (2017[Dumele, O., Schreib, B., Warzok, U., Trapp, N., Schalley, C. A. & Diederich, F. (2017). Angew. Chem. Int. Ed. 56, 1152-1157.])
C≡C—I⋯O=C IBUYUC P[\overline{1}] 2.878 177.89 Dumele et al. (2017[Dumele, O., Schreib, B., Warzok, U., Trapp, N., Schalley, C. A. & Diederich, F. (2017). Angew. Chem. Int. Ed. 56, 1152-1157.])

5. Synthesis and crystallization

5.1. Compound (II)

Tetra-n-butylammonium fluoride (TBAF, 0.437 ml, 1 M in THF, 0.437 mmol), AgNO3 (39 mg, 0.23 mmol) and NCS (190 mg, 1.42 mmol) were added to a solution of BocNHCH2—C≡C—C≡C—TMS (183 mg, 0.728 mmol) in aceto­nitrile (3 ml) at room temperature. The resulting mixture was stirred for 2.5 h under N2 in the absence of light. Purification of the crude product by flash chromatography on silica gel, eluting with mixtures of Hex/DCM/Et2O (gradient from 9:1:1 to 1:1:1), provided compound (II) as a beige solid (yield 72 mg, 46%). Single crystals suitable for X-ray diffraction were prepared by diffusion of pentane into a chloro­form solution of (II) at 263 K. RF = 0.43 (2:1:1 Hex/DCM/Et2O); IR (UATR, ν, cm−1): 3326, 2977, 2920, 2255, 2168, 1673, 1531, 1421, 1368, 1278, 1248, 1222, 1158, 1143, 1042, 1028, 933, 849, 761, 718, 655; 1H NMR (400 MHz, CDCl3): δ 4.72 (br, 1H), 3.99 (d, 2H), 1.45 (s, 9H); HRMS (m/z): calculated for C10H12ClNNaO2 [MNa+]: 236.0449, found: 236.0448.

5.2. Compound (IV)

TBAF (0.437 ml, 1 M in THF, 0.437 mmol), AgNO3 (39 mg, 0.23 mmol) and NIS (328 mg, 1.46 mmol) were added to a solution of BocNHCH2—C≡C—C≡C—TMS (183 mg, 0.728 mmol) in aceto­nitrile (3 ml) at room temperature. The resulting mixture was stirred for 2.5 h under N2 in the absence of light. Purification of the crude product by flash chromatography on silica gel, eluting with mixtures of Hex/DCM/Et2O (gradient from 9:1:1 to 1:1:1) provided compound (IV) as a beige solid (yield 95 mg, 43%). Single crystals suitable for X-ray diffraction were prepared by slow evaporation from a chloro­form solution of (IV) at room temperature. RF = 0.48 (2:1:1 Hex/DCM/Et2O); IR (UATR, ν, cm−1): 3328, 2980, 2933, 2230, 2159, 1661, 1532, 1451, 1420, 1367, 1284, 1250, 1154, 1142, 1042, 1026, 929, 851, 762, 714, 647; 1H NMR (400 MHz, CDCl3): δ 4.73 (br, 1H), 4.02 (d, 2H), 1.44 (s, 9H).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 4[link].

Table 4
Experimental details

  (II) (IV)
Crystal data
Chemical formula C10H12ClNO2 C10H12INO2
Mr 213.66 305.11
Crystal system, space group Monoclinic, P21/c Monoclinic, P21/n
Temperature (K) 173 173
a, b, c (Å) 10.336 (3), 9.171 (3), 11.870 (3) 11.1587 (16), 9.0288 (13), 12.9899 (18)
β (°) 100.656 (5) 108.731 (2)
V3) 1105.8 (5) 1239.4 (3)
Z 4 4
Radiation type Mo Kα Mo Kα
μ (mm−1) 0.32 2.56
Crystal size (mm) 0.34 × 0.22 × 0.02 0.36 × 0.3 × 0.28
 
Data collection
Diffractometer Bruker APEXII Bruker APEXII
Absorption correction Multi-scan (SADABS; Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Multi-scan (SADABS; Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.66, 0.745 0.675, 0.745
No. of measured, independent and observed [I > 2σ(I)] reflections 16132, 2249, 1755 17970, 2532, 2342
Rint 0.045 0.02
(sin θ/λ)max−1) 0.625 0.626
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.036, 0.089, 1.06 0.022, 0.054, 1.08
No. of reflections 2249 2532
No. of parameters 130 130
H-atom treatment H-atom parameters constrained H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.22, −0.21 1.32, −0.69
Computer programs: APEX2 (Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SAINT (Bruker, 2008[Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SORTAV (Blessing, 1995[Blessing, R. H. (1995). Acta Cryst. A51, 33-38.]), SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL2016 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]), Mercury (Macrae et al., 2006[Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453-457.]), WinGX (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Computing details top

For both structures, data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SORTAV (Blessing, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2016 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2006); software used to prepare material for publication: WinGX (Farrugia, 2012) and publCIF (Westrip, 2010).

tert-Butyl (5-chloropenta-2,4-diyn-1-yl)carbamate (II) top
Crystal data top
C10H12ClNO2F(000) = 448
Mr = 213.66Dx = 1.283 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 8841 reflections
a = 10.336 (3) Åθ = 2.8–26.4°
b = 9.171 (3) ŵ = 0.32 mm1
c = 11.870 (3) ÅT = 173 K
β = 100.656 (5)°Plate, orange
V = 1105.8 (5) Å30.34 × 0.22 × 0.02 mm
Z = 4
Data collection top
Bruker APEXII
diffractometer
2249 independent reflections
Radiation source: sealed x-ray tube1755 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.045
φ or ω oscillation scansθmax = 26.4°, θmin = 2.0°
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
h = 1212
Tmin = 0.66, Tmax = 0.745k = 1111
16132 measured reflectionsl = 914
Refinement top
Refinement on F20 constraints
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.036H-atom parameters constrained
wR(F2) = 0.089 w = 1/[σ2(Fo2) + (0.0397P)2 + 0.2863P]
where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max < 0.001
2249 reflectionsΔρmax = 0.22 e Å3
130 parametersΔρmin = 0.21 e Å3
0 restraints
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.40035 (19)0.0211 (2)0.15762 (16)0.0343 (4)
C20.50716 (18)0.0266 (2)0.15615 (16)0.0336 (4)
C30.63096 (19)0.0798 (2)0.15309 (16)0.0336 (4)
C40.73990 (19)0.1223 (2)0.15037 (16)0.0334 (4)
C50.87519 (17)0.1687 (2)0.14761 (17)0.0339 (4)
H5A0.8829350.2748280.162430.041*
H5B0.8943450.1505690.0701250.041*
C61.04144 (17)0.15939 (19)0.32333 (15)0.0271 (4)
C71.22986 (18)0.11065 (19)0.47967 (15)0.0304 (4)
C81.1748 (2)0.1841 (2)0.57483 (17)0.0439 (5)
H8A1.1063640.1223680.5970470.066*
H8B1.2456440.1989550.6411320.066*
H8C1.1369130.2786180.5479230.066*
C91.32333 (19)0.2075 (2)0.42986 (18)0.0408 (5)
H9A1.2787450.2988150.402990.061*
H9B1.4005770.2289710.4889020.061*
H9C1.3512830.157660.3653710.061*
C101.2953 (2)0.0332 (2)0.52078 (19)0.0449 (5)
H10A1.3241360.0827150.4565270.067*
H10B1.3717350.0144140.5813780.067*
H10C1.2323650.0951150.5509160.067*
Cl10.24981 (4)0.08590 (5)0.15756 (4)0.03061 (14)
N10.97160 (14)0.09282 (16)0.23144 (13)0.0314 (4)
H10.9847660.0007390.2215510.038*
O11.03225 (13)0.28874 (13)0.34594 (11)0.0361 (3)
O21.12149 (12)0.06256 (12)0.38708 (11)0.0311 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0342 (11)0.0349 (11)0.0334 (11)0.0009 (9)0.0055 (8)0.0009 (8)
C20.0337 (11)0.0333 (10)0.0323 (11)0.0036 (8)0.0019 (8)0.0007 (8)
C30.0333 (11)0.0300 (10)0.0346 (11)0.0005 (8)0.0011 (8)0.0016 (8)
C40.0339 (11)0.0279 (10)0.0350 (11)0.0023 (8)0.0028 (8)0.0006 (8)
C50.0309 (10)0.0311 (10)0.0368 (11)0.0013 (8)0.0014 (8)0.0030 (8)
C60.0264 (9)0.0222 (9)0.0323 (10)0.0014 (7)0.0045 (7)0.0023 (7)
C70.0311 (10)0.0269 (10)0.0299 (10)0.0017 (8)0.0026 (8)0.0021 (8)
C80.0524 (13)0.0429 (12)0.0369 (12)0.0014 (10)0.0091 (10)0.0049 (9)
C90.0344 (11)0.0415 (12)0.0451 (13)0.0056 (9)0.0037 (9)0.0019 (9)
C100.0468 (13)0.0339 (11)0.0462 (13)0.0041 (10)0.0121 (10)0.0007 (9)
Cl10.0268 (2)0.0320 (3)0.0337 (3)0.00451 (19)0.00733 (18)0.00090 (19)
N10.0303 (8)0.0220 (8)0.0381 (9)0.0024 (7)0.0036 (7)0.0013 (7)
O10.0409 (8)0.0217 (7)0.0427 (8)0.0034 (6)0.0003 (6)0.0014 (6)
O20.0314 (7)0.0220 (7)0.0358 (8)0.0009 (5)0.0049 (6)0.0006 (5)
Geometric parameters (Å, º) top
C1—C21.191 (3)C6—N11.339 (2)
C1—Cl11.666 (2)C6—O21.347 (2)
C2—C31.376 (3)C7—O21.484 (2)
C3—C41.198 (3)C7—C91.511 (3)
C4—C51.468 (3)C7—C81.513 (3)
C5—N11.449 (2)C7—C101.521 (3)
C6—O11.224 (2)
C2—C1—Cl1178.9 (2)O2—C7—C9109.55 (15)
C1—C2—C3179.0 (2)O2—C7—C8110.41 (15)
C4—C3—C2178.2 (2)C9—C7—C8112.70 (16)
C3—C4—C5177.8 (2)O2—C7—C10102.12 (14)
N1—C5—C4112.49 (16)C9—C7—C10110.89 (17)
O1—C6—N1124.66 (17)C8—C7—C10110.67 (17)
O1—C6—O2125.48 (17)C6—N1—C5122.64 (16)
N1—C6—O2109.86 (15)C6—O2—C7121.42 (13)
O1—C6—N1—C50.3 (3)N1—C6—O2—C7166.78 (14)
O2—C6—N1—C5178.98 (15)C9—C7—O2—C659.3 (2)
C4—C5—N1—C6111.1 (2)C8—C7—O2—C665.4 (2)
O1—C6—O2—C713.9 (3)C10—C7—O2—C6176.85 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.882.092.935162
C1—Cl1···O1ii1.673.134.793179
Symmetry codes: (i) x+2, y+1/2, z+1/2; (ii) x+1, y+1/2, z+1/2.
tert-Butyl (5-iodopenta-2,4-diyn-1-yl)carbamate (IV) top
Crystal data top
C10H12INO2F(000) = 592
Mr = 305.11Dx = 1.635 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 9940 reflections
a = 11.1587 (16) Åθ = 2.3–26.4°
b = 9.0288 (13) ŵ = 2.56 mm1
c = 12.9899 (18) ÅT = 173 K
β = 108.731 (2)°Prism, yellow
V = 1239.4 (3) Å30.36 × 0.3 × 0.28 mm
Z = 4
Data collection top
Bruker APEXII
diffractometer
2532 independent reflections
Radiation source: sealed x-ray tube2342 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.02
φ or ω oscillation scansθmax = 26.4°, θmin = 2.1°
Absorption correction: multi-scan
(SADABS; Bruker, 2008)
h = 1213
Tmin = 0.675, Tmax = 0.745k = 1111
17970 measured reflectionsl = 1516
Refinement top
Refinement on F20 constraints
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.022H-atom parameters constrained
wR(F2) = 0.054 w = 1/[σ2(Fo2) + (0.0203P)2 + 1.7447P]
where P = (Fo2 + 2Fc2)/3
S = 1.08(Δ/σ)max = 0.001
2532 reflectionsΔρmax = 1.32 e Å3
130 parametersΔρmin = 0.69 e Å3
0 restraints
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.2157 (2)1.0340 (3)0.3437 (2)0.0328 (6)
C20.3210 (2)1.0012 (3)0.34873 (19)0.0304 (5)
C30.4425 (2)0.9623 (3)0.35280 (19)0.0279 (5)
C40.5465 (2)0.9286 (3)0.35525 (19)0.0275 (5)
C50.6760 (2)0.8938 (3)0.35692 (19)0.0282 (5)
H5A0.7367040.9270890.426910.034*
H5B0.6848330.7850760.3521720.034*
C60.7111 (2)0.8882 (2)0.18051 (19)0.0219 (4)
C70.7579 (3)0.9226 (3)0.0094 (2)0.0344 (6)
C80.7976 (4)1.0622 (3)0.0367 (3)0.0511 (8)
H8A0.7304691.1366250.0498320.077*
H8B0.8123861.0386090.1053070.077*
H8C0.8756161.1012120.0152780.077*
C90.6338 (4)0.8624 (4)0.0654 (3)0.0559 (9)
H9A0.6112520.7723680.0336980.084*
H9B0.6425080.8391130.1363370.084*
H9C0.5671950.9368320.0745870.084*
C100.8637 (3)0.8100 (4)0.0377 (3)0.0506 (8)
H10A0.9364430.8492220.0958070.076*
H10B0.8887030.7894970.026660.076*
H10C0.8346260.7182480.0622970.076*
N10.7077 (2)0.9636 (2)0.26832 (16)0.0263 (4)
H10.7252561.0589130.2724550.032*
O10.73962 (17)0.97953 (18)0.11063 (13)0.0272 (4)
O20.69111 (17)0.75519 (18)0.16743 (14)0.0289 (4)
I10.04221 (2)1.09875 (2)0.33737 (2)0.03907 (7)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0294 (14)0.0398 (14)0.0301 (13)0.0020 (11)0.0106 (10)0.0027 (11)
C20.0333 (14)0.0328 (13)0.0263 (12)0.0012 (11)0.0110 (10)0.0031 (10)
C30.0312 (14)0.0309 (13)0.0250 (11)0.0015 (10)0.0139 (10)0.0011 (10)
C40.0337 (14)0.0284 (12)0.0236 (11)0.0036 (10)0.0135 (10)0.0005 (9)
C50.0298 (13)0.0321 (13)0.0259 (12)0.0007 (10)0.0132 (10)0.0032 (10)
C60.0180 (11)0.0216 (11)0.0271 (11)0.0013 (8)0.0087 (9)0.0020 (9)
C70.0490 (17)0.0323 (13)0.0293 (13)0.0017 (12)0.0229 (12)0.0034 (10)
C80.085 (3)0.0407 (17)0.0437 (17)0.0055 (16)0.0430 (18)0.0016 (13)
C90.067 (2)0.065 (2)0.0325 (15)0.0141 (18)0.0106 (15)0.0046 (15)
C100.065 (2)0.0415 (17)0.063 (2)0.0074 (15)0.0446 (18)0.0051 (15)
N10.0334 (11)0.0215 (10)0.0304 (10)0.0039 (8)0.0191 (9)0.0015 (8)
O10.0396 (10)0.0196 (8)0.0293 (9)0.0004 (7)0.0209 (7)0.0004 (7)
O20.0348 (10)0.0197 (8)0.0352 (9)0.0030 (7)0.0157 (8)0.0001 (7)
I10.02499 (10)0.04928 (12)0.04157 (11)0.00657 (8)0.00878 (7)0.00614 (8)
Geometric parameters (Å, º) top
C1—C21.193 (4)C7—C91.514 (4)
C1—I11.999 (3)C7—C81.521 (4)
C2—C31.385 (4)C8—H8A0.98
C3—C41.191 (4)C8—H8B0.98
C4—C51.472 (3)C8—H8C0.98
C5—N11.452 (3)C9—H9A0.98
C5—H5A0.99C9—H9B0.98
C5—H5B0.99C9—H9C0.98
C6—O21.223 (3)C10—H10A0.98
C6—O11.338 (3)C10—H10B0.98
C6—N11.340 (3)C10—H10C0.98
C7—O11.486 (3)N1—H10.88
C7—C101.512 (4)
C2—C1—I1177.3 (3)H8A—C8—H8B109.5
C1—C2—C3179.1 (3)C7—C8—H8C109.5
C4—C3—C2179.4 (3)H8A—C8—H8C109.5
C3—C4—C5177.4 (3)H8B—C8—H8C109.5
N1—C5—C4112.5 (2)C7—C9—H9A109.5
N1—C5—H5A109.1C7—C9—H9B109.5
C4—C5—H5A109.1H9A—C9—H9B109.5
N1—C5—H5B109.1C7—C9—H9C109.5
C4—C5—H5B109.1H9A—C9—H9C109.5
H5A—C5—H5B107.8H9B—C9—H9C109.5
O2—C6—O1125.7 (2)C7—C10—H10A109.5
O2—C6—N1124.3 (2)C7—C10—H10B109.5
O1—C6—N1110.00 (19)H10A—C10—H10B109.5
O1—C7—C10109.6 (2)C7—C10—H10C109.5
O1—C7—C9109.6 (2)H10A—C10—H10C109.5
C10—C7—C9113.4 (3)H10B—C10—H10C109.5
O1—C7—C8101.7 (2)C6—N1—C5122.3 (2)
C10—C7—C8110.5 (3)C6—N1—H1118.8
C9—C7—C8111.5 (3)C5—N1—H1118.8
C7—C8—H8A109.5C6—O1—C7121.17 (18)
C7—C8—H8B109.5
O2—C6—N1—C51.7 (4)N1—C6—O1—C7175.9 (2)
O1—C6—N1—C5178.5 (2)C10—C7—O1—C658.9 (3)
C4—C5—N1—C6103.9 (3)C9—C7—O1—C666.1 (3)
O2—C6—O1—C73.9 (4)C8—C7—O1—C6175.8 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2i0.882.042.881160
C1—I1···O2ii2.002.954.919168
Symmetry codes: (i) x+3/2, y+3/2, z+3/2; (ii) x+1/2, y+3/2, z+3/2.
CSD data retrieved for the CC—X···OC contacts shorter than the sum of their van der Waals radii top
CC—X···OC contactsCrystal structureSpace groupX···O distance (Å)C—X···O angle (°)Reference
CC—Cl···OCNIDWAAP13.111; 3.241152.59; 158.76Kawai et al. (2013)
CC—Br···OCHEVWAIC22.959158.12Hoheisel et al. (2013)
CC—Br···OCHEVWAI01P2121212.966166.70Hoheisel et al. (2013)
CC—Br···OCNIDWIIP21/n2.867171.11Kawai et al. (2013)
CC—Br···OCKAMXIIP21/c3.060178.26Baillargeon et al. (2016)
CC—I···OCCOHYUUP13.096164.55Luo et al. (2008)
CC—I···OCIYAYUCPca212.861170.36Hou et al. (2004)
CC—I···OCMASVUZP21/n2.834; 2.887170.72; 172.97Perkins et al. (2012)
CC—I···OCTOYPUSP21/c2.933175.36Avtomonov et al. (1997)
CC—I···OCHOWXICP21/c2.887169.51Dumele et al. (2014)
CC—I···OCLUNKOWP2/c2.791174.12Kratzer et al. (2015)
CC—I···OCLUNKUCP21/c2.754172.63Kratzer et al. (2015)
CC—I···OCLUNLAJP21/c2.773173.70Kratzer et al. (2015)
CC—I···OCLUNLIRPca212.858170.94Kratzer et al. (2015)
CC—I···OCLUNLOXC2/c2.763175.58Kratzer et al. (2015)
CC—I···OCIBUYAIP21/m2.856177.96Dumele et al. (2017)
CC—I···OCIBUYOWP21/c2.830176.52Dumele et al. (2017)
CC—I···OCIBUYUCP12.878177.89Dumele et al. (2017)
 

Funding information

Funding for this research was provided by: Fonds de Recherche du Québec – Nature et Technologies (grant No. 2016-CO-194882); Centre d'étude et de recherche transdisciplinaire étudiants-enseignants (CERTEE, Cégep de Sherbrooke); Fondation du Cégep de Sherbrooke.

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