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

Baillargeon, P.; Rahem, T.; Caron-Duval, É.; Tremblay, J.; Fortin, C.; Blais, É.; Fan, V.; Fortin, D.; Dory, Y.L.

doi:10.1107/S2056989017010155

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ISSN: 2056-9890

Volume 73| Part 8| August 2017| Pages 1175-1179

https://doi.org/10.1107/S2056989017010155

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

Pierre Baillargeon,^a ^* Tarik Rahem,^a Édouard Caron-Duval,^a Jacob Tremblay,^a Cloé Fortin,^a Étienne Blais,^a Victor Fan,^a Daniel Fortin ^b and Yves L. Dory ^c

^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).

Keywords: crystal structure; halogen bond; hydrogen bond; chlorodiacetylene; iododiacetylene.

CCDC references: 1551031; 1551032

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 ; Grabowski, 2016 ; Resnati et al., 2015 ; Cinčić et al., 2008 ). Indeed, these directional intermolecular interactions facilitate the preparation of the desired solid-state motifs and architectures (Gilday et al., 2015 ; Cavallo et al., 2016 ; Priimagi et al., 2013 ; Mukherjee et al., 2014 ; Shirman et al., 2015 ; Mukherjee et al., 2017 ). For example, using HBs and XBs, the specific organization of terminal diacetylenes (Li et al., 2009 ; Ouyang et al., 2003 ), bromodiacetylenes (Jin et al., 2015 ) and iododiacetylenes (Jin et al., 2013 ; Sun et al., 2006 ) 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 ) (see Scheme). 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 ; Takemura et al., 2014 ; Voth et al., 2009 ), which may find applications in medicinal chemistry and chemical biology (Wilcken et al., 2013 ).

2. Structural commentary

The molecular structures of compounds (II) and (IV) are shown in Fig. 1. 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 ). Moreover, the observed distances are almost identical to those found recently in the literature for similar halodiynes (Hoheisel et al., 2013 ; Baillargeon et al., 2016). 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
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) and N1—H1⋯O2ⁱ (Table 2)], 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). 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) on the terminal diacetylene (I) (part A in Fig. 2) and the bromodiacetylene (III) (part C in Fig. 2). In fact, diynes (I)–(IV) (Fig. 2) 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; 69°) adopts a near orthogonal geometry with the iodine (I1⋯O2⋯H1; part D in Fig. 2; 83°). It is not a surprise that the bromine crystal (III) represents an intermediate case (part C in Fig. 2; 72°). The value for the terminal diacetylene (I) X = H (part A in Fig. 2; 76°) is closely related to the bromodiacetylene (Baillargeon et al., 2016).

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

D—X⋯A	D—X	X⋯A	D⋯A	D—X⋯A
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)

D—X⋯A	D—X	X⋯A	D⋯A	D—X⋯A
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
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 ) 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). 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) 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 )
C≡C—Br⋯O=C	HEVWAI	C2	2.959	158.12	Hoheisel et al. (2013)
C≡C—Br⋯O=C	HEVWAI01	P2₁2₁2₁	2.966	166.70	Hoheisel et al. (2013)
C≡C—Br⋯O=C	NIDWII	P2₁/n	2.867	171.11	Kawai et al. (2013)
C≡C—Br⋯O=C	KAMXII	P2₁/c	3.060	178.26	Baillargeon et al. (2016)
C≡C—I⋯O=C	COHYUU	P $[\overline{1}]$	3.096	164.55	Luo et al. (2008 )
C≡C—I⋯O=C	IYAYUC	Pca2₁	2.861	170.36	Hou et al. (2004 )
C≡C—I⋯O=C	MASVUZ	P2₁/n	2.834; 2.887	170.72; 172.97	Perkins et al. (2012 )
C≡C—I⋯O=C	TOYPUS	P2₁/c	2.933	175.36	Avtomonov et al. (1997 )
C≡C—I⋯O=C	HOWXIC	P2₁/c	2.887	169.51	Dumele et al. (2014 )
C≡C—I⋯O=C	LUNKOW	P2/c	2.791	174.12	Kratzer et al. (2015)
C≡C—I⋯O=C	LUNKUC	P2₁/c	2.754	172.63	Kratzer et al. (2015)
C≡C—I⋯O=C	LUNLAJ	P2₁/c	2.773	173.70	Kratzer et al. (2015)
C≡C—I⋯O=C	LUNLIR	Pca2₁	2.858	170.94	Kratzer et al. (2015)
C≡C—I⋯O=C	LUNLOX	C2/c	2.763	175.58	Kratzer et al. (2015)
C≡C—I⋯O=C	IBUYAI	P2₁/m	2.856	177.96	Dumele et al. (2017 )
C≡C—I⋯O=C	IBUYOW	P2₁/c	2.830	176.52	Dumele et al. (2017)
C≡C—I⋯O=C	IBUYUC	P $[\overline{1}]$	2.878	177.89	Dumele et al. (2017)

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. R_F = 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. R_F = 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.

Table 4
Experimental details

	(II)	(IV)
Crystal data
Chemical formula	C₁₀H₁₂ClNO₂	C₁₀H₁₂INO₂
M_r	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)
V (Å³)	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 )	Multi-scan (SADABS; Bruker, 2008)
T_min, T_max	0.66, 0.745	0.675, 0.745
No. of measured, independent and observed [I > 2σ(I)] reflections	16132, 2249, 1755	17970, 2532, 2342
R_int	0.045	0.02
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	0.22, −0.21	1.32, −0.69
Computer programs: APEX2 (Bruker, 2008), SAINT (Bruker, 2008), SORTAV (Blessing, 1995 ), SHELXS97 (Sheldrick, 2008 ), SHELXL2016 (Sheldrick, 2015 ), ORTEP-3 for Windows (Farrugia, 2012 ), Mercury (Macrae et al., 2006 ), WinGX (Farrugia, 2012) and publCIF (Westrip, 2010 ).

Supporting information

CCDC references: 1551031; 1551032

Crystal structure: contains datablocks global, II, IV. DOI: https://doi.org/10.1107/S2056989017010155/mw2133sup1.cif

Structure factors: contains datablock II. DOI: https://doi.org/10.1107/S2056989017010155/mw2133IIsup2.hkl

Structure factors: contains datablock IV. DOI: https://doi.org/10.1107/S2056989017010155/mw2133IVsup3.hkl

checkCIF report

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

C₁₀H₁₂ClNO₂	F(000) = 448
M_r = 213.66	D_x = 1.283 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 8841 reflections
a = 10.336 (3) Å	θ = 2.8–26.4°
b = 9.171 (3) Å	µ = 0.32 mm⁻¹
c = 11.870 (3) Å	T = 173 K
β = 100.656 (5)°	Plate, orange
V = 1105.8 (5) Å³	0.34 × 0.22 × 0.02 mm
Z = 4

Data collection top

Bruker APEXII diffractometer	2249 independent reflections
Radiation source: sealed x-ray tube	1755 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.045
φ or ω oscillation scans	θ_max = 26.4°, θ_min = 2.0°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −12→12
T_min = 0.66, T_max = 0.745	k = −11→11
16132 measured reflections	l = −9→14

Refinement top

Refinement on F²	0 constraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.036	H-atom parameters constrained
wR(F²) = 0.089	w = 1/[σ²(F_o²) + (0.0397P)² + 0.2863P] where P = (F_o² + 2F_c²)/3
S = 1.06	(Δ/σ)_max < 0.001
2249 reflections	Δρ_max = 0.22 e Å⁻³
130 parameters	Δρ_min = −0.21 e Å⁻³
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

	x	y	z	U_iso*/U_eq
C1	0.40035 (19)	0.0211 (2)	0.15762 (16)	0.0343 (4)
C2	0.50716 (18)	−0.0266 (2)	0.15615 (16)	0.0336 (4)
C3	0.63096 (19)	−0.0798 (2)	0.15309 (16)	0.0336 (4)
C4	0.73990 (19)	−0.1223 (2)	0.15037 (16)	0.0334 (4)
C5	0.87519 (17)	−0.1687 (2)	0.14761 (17)	0.0339 (4)
H5A	0.882935	−0.274828	0.16243	0.041*
H5B	0.894345	−0.150569	0.070125	0.041*
C6	1.04144 (17)	−0.15939 (19)	0.32333 (15)	0.0271 (4)
C7	1.22986 (18)	−0.11065 (19)	0.47967 (15)	0.0304 (4)
C8	1.1748 (2)	−0.1841 (2)	0.57483 (17)	0.0439 (5)
H8A	1.106364	−0.122368	0.597047	0.066*
H8B	1.245644	−0.198955	0.641132	0.066*
H8C	1.136913	−0.278618	0.547923	0.066*
C9	1.32333 (19)	−0.2075 (2)	0.42986 (18)	0.0408 (5)
H9A	1.278745	−0.298815	0.40299	0.061*
H9B	1.400577	−0.228971	0.488902	0.061*
H9C	1.351283	−0.15766	0.365371	0.061*
C10	1.2953 (2)	0.0332 (2)	0.52078 (19)	0.0449 (5)
H10A	1.324136	0.082715	0.456527	0.067*
H10B	1.371735	0.014414	0.581378	0.067*
H10C	1.232365	0.095115	0.550916	0.067*
Cl1	0.24981 (4)	0.08590 (5)	0.15756 (4)	0.03061 (14)
N1	0.97160 (14)	−0.09282 (16)	0.23144 (13)	0.0314 (4)
H1	0.984766	0.000739	0.221551	0.038*
O1	1.03225 (13)	−0.28874 (13)	0.34594 (11)	0.0361 (3)
O2	1.12149 (12)	−0.06256 (12)	0.38708 (11)	0.0311 (3)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0342 (11)	0.0349 (11)	0.0334 (11)	−0.0009 (9)	0.0055 (8)	0.0009 (8)
C2	0.0337 (11)	0.0333 (10)	0.0323 (11)	−0.0036 (8)	0.0019 (8)	0.0007 (8)
C3	0.0333 (11)	0.0300 (10)	0.0346 (11)	−0.0005 (8)	−0.0011 (8)	0.0016 (8)
C4	0.0339 (11)	0.0279 (10)	0.0350 (11)	−0.0023 (8)	−0.0028 (8)	−0.0006 (8)
C5	0.0309 (10)	0.0311 (10)	0.0368 (11)	0.0013 (8)	−0.0014 (8)	−0.0030 (8)
C6	0.0264 (9)	0.0222 (9)	0.0323 (10)	−0.0014 (7)	0.0045 (7)	−0.0023 (7)
C7	0.0311 (10)	0.0269 (10)	0.0299 (10)	0.0017 (8)	−0.0026 (8)	0.0021 (8)
C8	0.0524 (13)	0.0429 (12)	0.0369 (12)	0.0014 (10)	0.0091 (10)	0.0049 (9)
C9	0.0344 (11)	0.0415 (12)	0.0451 (13)	0.0056 (9)	0.0037 (9)	0.0019 (9)
C10	0.0468 (13)	0.0339 (11)	0.0462 (13)	−0.0041 (10)	−0.0121 (10)	−0.0007 (9)
Cl1	0.0268 (2)	0.0320 (3)	0.0337 (3)	0.00451 (19)	0.00733 (18)	0.00090 (19)
N1	0.0303 (8)	0.0220 (8)	0.0381 (9)	−0.0024 (7)	−0.0036 (7)	0.0013 (7)
O1	0.0409 (8)	0.0217 (7)	0.0427 (8)	−0.0034 (6)	0.0003 (6)	0.0014 (6)
O2	0.0314 (7)	0.0220 (7)	0.0358 (8)	−0.0009 (5)	−0.0049 (6)	−0.0006 (5)

Geometric parameters (Å, º) top

C1—C2	1.191 (3)	C6—N1	1.339 (2)
C1—Cl1	1.666 (2)	C6—O2	1.347 (2)
C2—C3	1.376 (3)	C7—O2	1.484 (2)
C3—C4	1.198 (3)	C7—C9	1.511 (3)
C4—C5	1.468 (3)	C7—C8	1.513 (3)
C5—N1	1.449 (2)	C7—C10	1.521 (3)
C6—O1	1.224 (2)

C2—C1—Cl1	178.9 (2)	O2—C7—C9	109.55 (15)
C1—C2—C3	179.0 (2)	O2—C7—C8	110.41 (15)
C4—C3—C2	178.2 (2)	C9—C7—C8	112.70 (16)
C3—C4—C5	177.8 (2)	O2—C7—C10	102.12 (14)
N1—C5—C4	112.49 (16)	C9—C7—C10	110.89 (17)
O1—C6—N1	124.66 (17)	C8—C7—C10	110.67 (17)
O1—C6—O2	125.48 (17)	C6—N1—C5	122.64 (16)
N1—C6—O2	109.86 (15)	C6—O2—C7	121.42 (13)

O1—C6—N1—C5	0.3 (3)	N1—C6—O2—C7	−166.78 (14)
O2—C6—N1—C5	−178.98 (15)	C9—C7—O2—C6	59.3 (2)
C4—C5—N1—C6	111.1 (2)	C8—C7—O2—C6	−65.4 (2)
O1—C6—O2—C7	13.9 (3)	C10—C7—O2—C6	176.85 (16)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1ⁱ	0.88	2.09	2.935	162
C1—Cl1···O1ⁱⁱ	1.67	3.13	4.793	179

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

C₁₀H₁₂INO₂	F(000) = 592
M_r = 305.11	D_x = 1.635 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 9940 reflections
a = 11.1587 (16) Å	θ = 2.3–26.4°
b = 9.0288 (13) Å	µ = 2.56 mm⁻¹
c = 12.9899 (18) Å	T = 173 K
β = 108.731 (2)°	Prism, yellow
V = 1239.4 (3) Å³	0.36 × 0.3 × 0.28 mm
Z = 4

Data collection top

Bruker APEXII diffractometer	2532 independent reflections
Radiation source: sealed x-ray tube	2342 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.02
φ or ω oscillation scans	θ_max = 26.4°, θ_min = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −12→13
T_min = 0.675, T_max = 0.745	k = −11→11
17970 measured reflections	l = −15→16

Refinement top

Refinement on F²	0 constraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.022	H-atom parameters constrained
wR(F²) = 0.054	w = 1/[σ²(F_o²) + (0.0203P)² + 1.7447P] where P = (F_o² + 2F_c²)/3
S = 1.08	(Δ/σ)_max = 0.001
2532 reflections	Δρ_max = 1.32 e Å⁻³
130 parameters	Δρ_min = −0.69 e Å⁻³
0 restraints

Special details top

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
C1	0.2157 (2)	1.0340 (3)	0.3437 (2)	0.0328 (6)
C2	0.3210 (2)	1.0012 (3)	0.34873 (19)	0.0304 (5)
C3	0.4425 (2)	0.9623 (3)	0.35280 (19)	0.0279 (5)
C4	0.5465 (2)	0.9286 (3)	0.35525 (19)	0.0275 (5)
C5	0.6760 (2)	0.8938 (3)	0.35692 (19)	0.0282 (5)
H5A	0.736704	0.927089	0.42691	0.034*
H5B	0.684833	0.785076	0.352172	0.034*
C6	0.7111 (2)	0.8882 (2)	0.18051 (19)	0.0219 (4)
C7	0.7579 (3)	0.9226 (3)	0.0094 (2)	0.0344 (6)
C8	0.7976 (4)	1.0622 (3)	−0.0367 (3)	0.0511 (8)
H8A	0.730469	1.136625	−0.049832	0.077*
H8B	0.812386	1.038609	−0.105307	0.077*
H8C	0.875616	1.101212	0.015278	0.077*
C9	0.6338 (4)	0.8624 (4)	−0.0654 (3)	0.0559 (9)
H9A	0.611252	0.772368	−0.033698	0.084*
H9B	0.642508	0.839113	−0.136337	0.084*
H9C	0.567195	0.936832	−0.074587	0.084*
C10	0.8637 (3)	0.8100 (4)	0.0377 (3)	0.0506 (8)
H10A	0.936443	0.849222	0.095807	0.076*
H10B	0.888703	0.789497	−0.02666	0.076*
H10C	0.834626	0.718248	0.062297	0.076*
N1	0.7077 (2)	0.9636 (2)	0.26832 (16)	0.0263 (4)
H1	0.725256	1.058913	0.272455	0.032*
O1	0.73962 (17)	0.97953 (18)	0.11063 (13)	0.0272 (4)
O2	0.69111 (17)	0.75519 (18)	0.16743 (14)	0.0289 (4)
I1	0.04221 (2)	1.09875 (2)	0.33737 (2)	0.03907 (7)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0294 (14)	0.0398 (14)	0.0301 (13)	0.0020 (11)	0.0106 (10)	0.0027 (11)
C2	0.0333 (14)	0.0328 (13)	0.0263 (12)	−0.0012 (11)	0.0110 (10)	0.0031 (10)
C3	0.0312 (14)	0.0309 (13)	0.0250 (11)	−0.0015 (10)	0.0139 (10)	0.0011 (10)
C4	0.0337 (14)	0.0284 (12)	0.0236 (11)	−0.0036 (10)	0.0135 (10)	0.0005 (9)
C5	0.0298 (13)	0.0321 (13)	0.0259 (12)	0.0007 (10)	0.0132 (10)	0.0032 (10)
C6	0.0180 (11)	0.0216 (11)	0.0271 (11)	0.0013 (8)	0.0087 (9)	0.0020 (9)
C7	0.0490 (17)	0.0323 (13)	0.0293 (13)	−0.0017 (12)	0.0229 (12)	−0.0034 (10)
C8	0.085 (3)	0.0407 (17)	0.0437 (17)	−0.0055 (16)	0.0430 (18)	0.0016 (13)
C9	0.067 (2)	0.065 (2)	0.0325 (15)	−0.0141 (18)	0.0106 (15)	−0.0046 (15)
C10	0.065 (2)	0.0415 (17)	0.063 (2)	0.0074 (15)	0.0446 (18)	−0.0051 (15)
N1	0.0334 (11)	0.0215 (10)	0.0304 (10)	−0.0039 (8)	0.0191 (9)	−0.0015 (8)
O1	0.0396 (10)	0.0196 (8)	0.0293 (9)	0.0004 (7)	0.0209 (7)	0.0004 (7)
O2	0.0348 (10)	0.0197 (8)	0.0352 (9)	−0.0030 (7)	0.0157 (8)	−0.0001 (7)
I1	0.02499 (10)	0.04928 (12)	0.04157 (11)	0.00657 (8)	0.00878 (7)	0.00614 (8)

Geometric parameters (Å, º) top

C1—C2	1.193 (4)	C7—C9	1.514 (4)
C1—I1	1.999 (3)	C7—C8	1.521 (4)
C2—C3	1.385 (4)	C8—H8A	0.98
C3—C4	1.191 (4)	C8—H8B	0.98
C4—C5	1.472 (3)	C8—H8C	0.98
C5—N1	1.452 (3)	C9—H9A	0.98
C5—H5A	0.99	C9—H9B	0.98
C5—H5B	0.99	C9—H9C	0.98
C6—O2	1.223 (3)	C10—H10A	0.98
C6—O1	1.338 (3)	C10—H10B	0.98
C6—N1	1.340 (3)	C10—H10C	0.98
C7—O1	1.486 (3)	N1—H1	0.88
C7—C10	1.512 (4)

C2—C1—I1	177.3 (3)	H8A—C8—H8B	109.5
C1—C2—C3	179.1 (3)	C7—C8—H8C	109.5
C4—C3—C2	179.4 (3)	H8A—C8—H8C	109.5
C3—C4—C5	177.4 (3)	H8B—C8—H8C	109.5
N1—C5—C4	112.5 (2)	C7—C9—H9A	109.5
N1—C5—H5A	109.1	C7—C9—H9B	109.5
C4—C5—H5A	109.1	H9A—C9—H9B	109.5
N1—C5—H5B	109.1	C7—C9—H9C	109.5
C4—C5—H5B	109.1	H9A—C9—H9C	109.5
H5A—C5—H5B	107.8	H9B—C9—H9C	109.5
O2—C6—O1	125.7 (2)	C7—C10—H10A	109.5
O2—C6—N1	124.3 (2)	C7—C10—H10B	109.5
O1—C6—N1	110.00 (19)	H10A—C10—H10B	109.5
O1—C7—C10	109.6 (2)	C7—C10—H10C	109.5
O1—C7—C9	109.6 (2)	H10A—C10—H10C	109.5
C10—C7—C9	113.4 (3)	H10B—C10—H10C	109.5
O1—C7—C8	101.7 (2)	C6—N1—C5	122.3 (2)
C10—C7—C8	110.5 (3)	C6—N1—H1	118.8
C9—C7—C8	111.5 (3)	C5—N1—H1	118.8
C7—C8—H8A	109.5	C6—O1—C7	121.17 (18)
C7—C8—H8B	109.5

O2—C6—N1—C5	−1.7 (4)	N1—C6—O1—C7	175.9 (2)
O1—C6—N1—C5	178.5 (2)	C10—C7—O1—C6	−58.9 (3)
C4—C5—N1—C6	−103.9 (3)	C9—C7—O1—C6	66.1 (3)
O2—C6—O1—C7	−3.9 (4)	C8—C7—O1—C6	−175.8 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2ⁱ	0.88	2.04	2.881	160
C1—I1···O2ⁱⁱ	2.00	2.95	4.919	168

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···O═C contacts shorter than the sum of their van der Waals radii top

CC—X···O═C contacts	Crystal structure	Space group	X···O distance (Å)	C—X···O angle (°)	Reference
CC—Cl···O═C	NIDWAA	P1	3.111; 3.241	152.59; 158.76	Kawai et al. (2013)
CC—Br···O═C	HEVWAI	C2	2.959	158.12	Hoheisel et al. (2013)
CC—Br···O═C	HEVWAI01	P2₁2₁2₁	2.966	166.70	Hoheisel et al. (2013)
CC—Br···O═C	NIDWII	P2₁/n	2.867	171.11	Kawai et al. (2013)
CC—Br···O═C	KAMXII	P2₁/c	3.060	178.26	Baillargeon et al. (2016)
CC—I···O═C	COHYUU	P1	3.096	164.55	Luo et al. (2008)
CC—I···O═C	IYAYUC	Pca2₁	2.861	170.36	Hou et al. (2004)
CC—I···O═C	MASVUZ	P2₁/n	2.834; 2.887	170.72; 172.97	Perkins et al. (2012)
CC—I···O═C	TOYPUS	P2₁/c	2.933	175.36	Avtomonov et al. (1997)
CC—I···O═C	HOWXIC	P2₁/c	2.887	169.51	Dumele et al. (2014)
CC—I···O═C	LUNKOW	P2/c	2.791	174.12	Kratzer et al. (2015)
CC—I···O═C	LUNKUC	P2₁/c	2.754	172.63	Kratzer et al. (2015)
CC—I···O═C	LUNLAJ	P2₁/c	2.773	173.70	Kratzer et al. (2015)
CC—I···O═C	LUNLIR	Pca2₁	2.858	170.94	Kratzer et al. (2015)
CC—I···O═C	LUNLOX	C2/c	2.763	175.58	Kratzer et al. (2015)
CC—I···O═C	IBUYAI	P2₁/m	2.856	177.96	Dumele et al. (2017)
CC—I···O═C	IBUYOW	P2₁/c	2.830	176.52	Dumele et al. (2017)
CC—I···O═C	IBUYUC	P1	2.878	177.89	Dumele 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.

References

Aakeröy, C. B., Spartz, C. L., Dembowski, S., Dwyre, S. & Desper, J. (2015). IUCrJ, 2, 498–510. Web of Science CSD CrossRef PubMed IUCr Journals Google Scholar
Avtomonov, E. V., Grüning, R. & Lorberth, J. (1997). Z. Naturforsch. Teil B, 52, 256–258. CAS Google Scholar
Baillargeon, P., Caron-Duval, É., Pellerin, É., Gagné, S. & Dory, Y. L. (2016). Crystals, 6, 37–49. CSD CrossRef Google Scholar
Bent, H. A. (1961). Chem. Rev. 61, 275–311. CrossRef CAS Web of Science Google Scholar
Blessing, R. H. (1995). Acta Cryst. A51, 33–38. CrossRef CAS Web of Science IUCr Journals Google Scholar
Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Cavallo, G., Metrangolo, P., Milani, R., Pilati, T., Priimagi, A., Resnati, G. & Terraneo, G. (2016). Chem. Rev. 116, 2478–2601. Web of Science CrossRef CAS PubMed Google Scholar
Cinčić, D., Friščić, T. & Jones, W. (2008). Chem. Mater. 20, 6623–6626. Google Scholar
Dumele, O., Schreib, B., Warzok, U., Trapp, N., Schalley, C. A. & Diederich, F. (2017). Angew. Chem. Int. Ed. 56, 1152–1157. CSD CrossRef CAS Google Scholar
Dumele, O., Wu, D., Trapp, N., Goroff, N. & Diederich, F. (2014). Org. Lett. 16, 4722–4725. Web of Science CSD CrossRef CAS PubMed Google Scholar
Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854. Web of Science CrossRef CAS IUCr Journals Google Scholar
Gilday, L. C., Robinson, S. W., Barendt, T. A., Langton, M. J., Mullaney, B. R. & Beer, P. D. (2015). Chem. Rev. 115, 7118–7195. Web of Science CrossRef CAS PubMed Google Scholar
Grabowski, S. J. (2016). Crystals, 6, 59–63. CrossRef Google Scholar
Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. Web of Science CSD CrossRef IUCr Journals Google Scholar
Hoheisel, T. N., Schrettl, S., Marty, R., Todorova, T. K., Corminboeuf, C. & Sienkiewicz, A. (2013). Nat. Chem. 5, 327–334. CSD CrossRef CAS PubMed Google Scholar
Hou, Z.-K., Ren, Y.-G., Huang, M.-Z., Song, J. & Chen, L.-G. (2004). Acta Cryst. E60, o1336–o1337. Web of Science CSD CrossRef IUCr Journals Google Scholar
Jin, H., Plonka, A. M., Parise, J. B. & Goroff, N. S. (2013). CrystEngComm, 15, 3106–3110. Web of Science CSD CrossRef CAS Google Scholar
Jin, H., Young, C. N., Halada, G. P., Phillips, B. L. & Goroff, N. S. (2015). Angew. Chem. Int. Ed. 54, 14690–14695. CSD CrossRef CAS Google Scholar
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. CSD CrossRef CAS PubMed Google Scholar
Kratzer, P., Ramming, B., Römisch, S. & Maas, G. (2015). CrystEngComm, 17, 4486–4494. CSD CrossRef CAS Google Scholar
Li, Z., Fowler, F. W. & Lauher, J. W. (2009). J. Am. Chem. Soc. 131, 634–643. Web of Science CSD CrossRef PubMed CAS Google Scholar
Luo, L., Wilhelm, C., Sun, A., Grey, C. P., Lauher, J. W. & Goroff, N. S. (2008). J. Am. Chem. Soc. 130, 7702–7709. CSD CrossRef PubMed CAS Google Scholar
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. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Mukherjee, A., Teyssandier, J., Hennrich, G., De Feyter, S. & Mali, K. S. (2017). Chem. Sci. 8, 3759–3769. CrossRef CAS PubMed Google Scholar
Mukherjee, A., Tothadi, S. & Desiraju, G. R. (2014). Acc. Chem. Res. 47, 2514–2524. Web of Science CrossRef CAS PubMed Google Scholar
Ouyang, X., Fowler, F. W. & Lauher, J. W. (2003). J. Am. Chem. Soc. 125, 12400–12401. CSD CrossRef PubMed CAS Google Scholar
Perkins, C., Libri, S., Adams, H. & Brammer, L. (2012). CrystEngComm, 14, 3033–3038. Web of Science CSD CrossRef CAS Google Scholar
Priimagi, A., Cavallo, G., Metrangolo, P. & Restani, R. (2013). Acc. Chem. Res. 46, 2686–2695. CrossRef CAS PubMed Google Scholar
Resnati, G., Boldyreva, E., Bombicz, P. & Kawano, M. (2015). IUCrJ, 2, 675–690. Web of Science CrossRef CAS PubMed IUCr Journals Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
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. Web of Science CSD CrossRef CAS Google Scholar
Sun, A., Lauher, J. W. & Goroff, N. S. (2006). Science, 312, 1030–1034. Web of Science CSD CrossRef PubMed CAS Google Scholar
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. Web of Science CSD CrossRef CAS PubMed Google Scholar
Voth, A. R., Khuu, P., Oishi, K. & Ho, P. S. (2009). Nat. Chem. 1, 74–79. Web of Science CrossRef CAS PubMed Google Scholar
Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925. Web of Science CrossRef CAS IUCr Journals Google Scholar
Wilcken, R., Zimmermann, M. O., Lange, A., Joerger, A. C. & Boeckler, F. M. (2013). J. Med. Chem. 56, 1363–1388. Web of Science CrossRef CAS PubMed Google Scholar

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Volume 73| Part 8| August 2017| Pages 1175-1179

https://doi.org/10.1107/S2056989017010155

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research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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

1. Chemical context

2. Structural commentary

3. Supra­molecular features

4. Database survey

5. Synthesis and crystallization

5.1. Compound (II)

5.2. Compound (IV)

6. Refinement

Supporting information

Funding information

References

research communications

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

3. Supramolecular features