1,3,5-Tri­fluoro-2,4,6-tri­iodo­benzene–piperazine (2/1)

Hajjar, C.; Ovens, J.S.; Bryce, D.L.

doi:10.1107/S2414314621010440

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 6| Part 10| October 2021| x211044

https://doi.org/10.1107/S2414314621010440

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1,3,5-Trifluoro-2,4,6-triiodobenzene–piperazine (2/1)

Christelle Hajjar,^a Jeffrey S. Ovens ^a and David L. Bryce ^a ^*

^aDepartment of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N6N5, Canada
^*Correspondence e-mail: dbryce@uottawa.ca

Edited by R. J. Butcher, Howard University, USA (Received 1 September 2021; accepted 7 October 2021; online 13 October 2021)

The single-crystal structure of the title compound, C₄H₁₀N₂·2C₆F₃I₃, features a moderately strong halogen bond between one of the three crystallographically distinct iodine atoms and the nitrogen atom. The iodine–nitrogen distance is 2.820 (3) Å, corresponding to 80% of the sum of their van der Waals radii. The C—I⋯N halogen bond angle is 178.0 (1)°, consistent with the linear interaction of nitrogen via a σ-hole opposite the carbon–iodine covalent bond. The other two iodine atoms do not engage in halogen bonding. Some weak C—H⋯F and —H⋯I interactions are also observed. The complete piperazine molecule is generated by symmetry.

Keywords: crystal structure; halogen bonding; stoichiometry; co-crystal.

CCDC reference: 2101749

Structure description

The halogen bond is a moderately strong and directional non-covalent interaction, which has proven very useful in the field of crystal engineering and for the design of co-crystalline materials. Perfluorinated iodobenzenes are commonly used as halogen-bond donors, in part due to their reliable ability to co-crystallize predictably with a range of electron donors (Cavallo, 2016 ). The title compound (Fig. 1), which has a 2:1 1,3,5-trifluoro-2,4,6-triiodobenzene:piperazine (1,4-diazacyclohexane) stoichiometry, features a halogen bond between I1 as the halogen-bond donor and N1 as the halogen-bond acceptor (Fig. 2). The iodine–nitrogen distance is 2.820 (3) Å, which corresponds to 80% of the sum of their van der Waals radii. This is somewhat shorter than the analogous iodine–nitrogen halogen bonds in co-crystals formed from the same halogen-bond donor with acridine (3.022 Å), 1,10-phenanthroline (3.020 and 3.148 Å), or 2,3,5,6-tetramethylpyrazine (2.991 and 2.993 Å), but comparable to those formed with hexamethylenetetramine (2.864 and 2.879 Å) as the electron donor (Szell et al., 2017 ). Comparable distances are also noted in an interesting class of halogen-bonded tubular structures formed from the self-assembly of 1,4-diiodotetrafluorobenzene and piperazine cyclophanes (Raatikainen, 2009 ).

Figure 1
ORTEP plot of the title compound.

Figure 2
Detail of the X-ray crystal structure depicting a halogen bond between iodine and nitrogen, a short contact between iodine and carbon, and a short contact between hydrogen and fluorine. The other two iodine atoms on the aromatic ring do not engage in any halogen bonding or other close contacts.

The C1—I1⋯N1 halogen bond angle in the title compound is 178.0 (1)°, consistent with the linear interaction of nitrogen via a σ-hole opposite the carbon–iodine covalent bond. I1 also shows a short contact with C7 of the piperazine molecule of 3.578 (4) Å; this represents approximately 97% of the sum of their van der Waals radii and is likely a structural consequence of the formation of the adjacent halogen bond rather than a structure-directing element in and of itself. Possible weak hydrogen bonds are also observed between H1 and I2, between H7A and F2, between H7AB and I3, between H8A and I2, and between H8AB and I1 (Table 1). Interestingly, no halogen bonds involving I2 and I3 are observed, despite the fact that they are chemically identical to I1. The structure packs in the triclinic P $[\overline{1}]$ space group and the aromatic molecules lie in layers (Fig. 3). The stoichiometry of the co-crystal is highlighted by noting that pairs of aromatic molecules lying in adjacent layers are connected to each other via halogen bonding to a single common piperazine molecule.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯I2ⁱ	0.86 (2)	3.12 (2)	3.978 (3)	177 (3)
C7—H7A⋯F2ⁱⁱ	0.98	2.40	3.299 (4)	152
C7—H7AB⋯I3ⁱⁱⁱ	0.98	3.23	3.990 (3)	135
C8—H8A⋯I2^iv	0.98	3.19	4.001 (3)	141
C8—H8AB⋯I1^v	0.98	3.26	3.879 (3)	123
Symmetry codes: (i) ; (ii) ; (iii) ; (iv) x, y, z+1; (v) .

Figure 3
View along each of the unit cell axes. (a): along the a axis; (b): along the b axis; (c): along the c axis. Hydrogen atoms not shown.

Synthesis and crystallization

1,3,5-Trifluoro-2,4,6-triiodobenzene was purchased from Alfa Aesar and piperazine was purchased from Sigma–Aldrich. In a typical procedure, the title compound was obtained from the slow evaporation of a solution of the halogen-bond donor (0.025 g in 1 ml of chloroform) and a molar excess of halogen-bond acceptor (0.0412 g in 1 ml of ethanol) at room temperature. The two solutions were prepared independently and stirred. After dissolution, the two solutions were mixed, stirred, and covered to allow for slow evaporation and crystal formation.

Refinement

Crystal data, data collection, and structure refinement details are presented in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₄H₁₀N₂·2C₆F₃I₃
M_r	1105.66
Crystal system, space group	Triclinic, P $[\overline{1}]$
Temperature (K)	203
a, b, c (Å)	8.6450 (5), 9.1660 (5), 9.3403 (5)
α, β, γ (°)	67.433 (1), 72.887 (1), 63.062 (1)
V (Å³)	602.75 (6)
Z	1
Radiation type	Mo Kα
μ (mm⁻¹)	7.78
Crystal size (mm)	0.24 × 0.13 × 0.08

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Krause et al., 2015 )
T_min, T_max	0.537, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections	13748, 3761, 3193
R_int	0.031
(sin θ/λ)_max (Å⁻¹)	0.721

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.025, 0.048, 1.02
No. of reflections	3761
No. of parameters	139
No. of restraints	1
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.56, −0.64
Computer programs: APEX3 and SAINT (Bruker, 2010 ), SHELXT2014/5 (Sheldrick, 2015a ), SHELXL2018/3 (Sheldrick, 2015b ), ShelXle (Hübschle et al., 2011 ) and Mercury (Macrae et al., 2020 ).

Structural data

CCDC reference: 2101749

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314621010440/bv4042sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314621010440/bv4042Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314621010440/bv4042Isup3.cml

checkCIF report

Computing details top

Data collection: APEX3 (Bruker, 2010); cell refinement: SAINT (Bruker, 2010); data reduction: SAINT (Bruker, 2010); program(s) used to solve structure: SHELXT2014/5 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015b) and ShelXle (Hübschle et al., 2011); molecular graphics: Mercury (Macrae et al., 2020).

1,3,5-Trifluoro-2,4,6-triiodobenzene–piperazine (2/1) top

Crystal data top

C₄H₁₀N₂·2C₆F₃I₃	Z = 1
M_r = 1105.66	F(000) = 492
Triclinic, P1	D_x = 3.046 Mg m⁻³
a = 8.6450 (5) Å	Mo Kα radiation, λ = 0.71073 Å
b = 9.1660 (5) Å	Cell parameters from 6804 reflections
c = 9.3403 (5) Å	θ = 2.4–30.7°
α = 67.433 (1)°	µ = 7.78 mm⁻¹
β = 72.887 (1)°	T = 203 K
γ = 63.062 (1)°	Block, colourless
V = 602.75 (6) Å³	0.24 × 0.13 × 0.08 mm

Data collection top

Bruker APEXII CCD diffractometer	3193 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.031
ω and πhi scans	θ_max = 30.8°, θ_min = 2.4°
Absorption correction: multi-scan (SADABS; Krause et al., 2015\bbr00)	h = −12→12
T_min = 0.537, T_max = 0.746	k = −13→13
13748 measured reflections	l = −13→13
3761 independent reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.025	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.048	w = 1/[σ²(F_o²) + (0.0176P)² + 0.1043P] where P = (F_o² + 2F_c²)/3
S = 1.02	(Δ/σ)_max = 0.001
3761 reflections	Δρ_max = 0.56 e Å⁻³
139 parameters	Δρ_min = −0.64 e Å⁻³
1 restraint

Special details top

Experimental. Crystallographic data were collected from single crystals mounted on MiTeGen MicroMounts using parabar oil. Data were collected on a Bruker SMART APEXII single-crystal diffractometer equipped with a sealed tube Mo Kα source (λ= 0.71073 Å), a graphite monochromator, and an APEXII CCD detector. Samples were held at low temperature using a dry compressed air cooling system. Raw data collection and processing were performed with the APEX3 software package from Bruker (2010). Initial unit-cell parameters were determined from 36 data frames from select ω scans. Semi-empirical absorption corrections based on equivalent reflections were applied (Blessing, 1995). Systematic absences in the diffraction data-set and unit-cell parameters were consistent with the assigned space group. The initial structural solutions were determined using SHELXT direct methods (Sheldrick, 2015a) and refined with full-matrix least-squares procedures based on F₂ using SHELXL and ShelXle (Hübschle et al., 2011; Sheldrick, 2015b). Hydrogen atoms were placed geometrically and refined using a riding model.

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.

Refinement. none

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

	x	y	z	U_iso*/U_eq
I1	0.82683 (3)	0.38276 (3)	0.69997 (2)	0.02587 (5)
N1	1.0231 (4)	0.1572 (3)	0.9473 (3)	0.0297 (6)
H1	1.079 (4)	0.212 (4)	0.952 (4)	0.036*
C1	0.6818 (4)	0.5589 (4)	0.5141 (3)	0.0236 (6)
F1	0.8619 (2)	0.3929 (2)	0.3438 (2)	0.0350 (5)
I2	0.70010 (3)	0.60960 (3)	0.02390 (2)	0.03224 (6)
C2	0.7265 (4)	0.5356 (4)	0.3663 (4)	0.0246 (6)
F2	0.4127 (2)	0.9155 (2)	0.1493 (2)	0.0305 (4)
I3	0.22867 (3)	1.04531 (3)	0.44595 (3)	0.03033 (6)
C3	0.6376 (4)	0.6522 (4)	0.2419 (3)	0.0226 (6)
F3	0.4867 (2)	0.7292 (2)	0.6764 (2)	0.0334 (4)
C7	1.1580 (4)	0.0068 (4)	0.8988 (4)	0.0316 (7)
H7A	1.243223	−0.060464	0.972668	0.038*
H7AB	1.220520	0.044203	0.794519	0.038*
C6	0.5381 (4)	0.7041 (4)	0.5336 (3)	0.0235 (6)
C5	0.4444 (4)	0.8275 (4)	0.4131 (3)	0.0218 (6)
C4	0.4991 (4)	0.7972 (4)	0.2689 (3)	0.0225 (6)
C8	0.9301 (4)	0.1016 (4)	1.1043 (4)	0.0315 (7)
H8A	0.841947	0.201779	1.136757	0.038*
H8AB	1.013321	0.034933	1.180012	0.038*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
I1	0.02951 (11)	0.02437 (10)	0.02130 (10)	−0.00916 (8)	−0.00948 (8)	−0.00148 (8)
N1	0.0415 (17)	0.0289 (15)	0.0227 (14)	−0.0176 (13)	−0.0112 (12)	−0.0020 (12)
C1	0.0253 (15)	0.0261 (16)	0.0199 (15)	−0.0109 (12)	−0.0078 (12)	−0.0028 (12)
F1	0.0367 (11)	0.0271 (10)	0.0300 (11)	0.0021 (8)	−0.0089 (8)	−0.0115 (8)
I2	0.04118 (13)	0.03267 (12)	0.02151 (11)	−0.01026 (9)	−0.00498 (9)	−0.01114 (9)
C2	0.0241 (15)	0.0223 (15)	0.0255 (16)	−0.0074 (12)	−0.0017 (12)	−0.0082 (13)
F2	0.0380 (11)	0.0267 (10)	0.0211 (9)	−0.0063 (8)	−0.0141 (8)	−0.0016 (8)
I3	0.02595 (11)	0.02909 (11)	0.02966 (12)	−0.00356 (8)	−0.00403 (8)	−0.01089 (9)
C3	0.0276 (15)	0.0227 (15)	0.0191 (15)	−0.0091 (12)	−0.0049 (12)	−0.0074 (12)
F3	0.0358 (11)	0.0399 (11)	0.0175 (9)	−0.0072 (9)	−0.0039 (8)	−0.0104 (8)
C7	0.0280 (17)	0.0381 (19)	0.0249 (17)	−0.0119 (14)	−0.0076 (13)	−0.0036 (14)
C6	0.0272 (16)	0.0287 (16)	0.0162 (14)	−0.0137 (13)	−0.0017 (11)	−0.0058 (12)
C5	0.0203 (14)	0.0207 (14)	0.0239 (15)	−0.0073 (11)	−0.0039 (11)	−0.0061 (12)
C4	0.0242 (15)	0.0221 (15)	0.0216 (15)	−0.0106 (12)	−0.0103 (12)	0.0002 (12)
C8	0.042 (2)	0.0293 (18)	0.0219 (16)	−0.0107 (15)	−0.0069 (14)	−0.0092 (14)

Geometric parameters (Å, º) top

I1—C1	2.118 (3)	I3—C5	2.078 (3)
N1—C8	1.470 (4)	C3—C4	1.379 (4)
N1—C7	1.475 (4)	F3—C6	1.350 (3)
N1—H1	0.864 (18)	C7—C8ⁱ	1.513 (5)
C1—C6	1.380 (4)	C7—H7A	0.9800
C1—C2	1.392 (4)	C7—H7AB	0.9800
F1—C2	1.343 (3)	C6—C5	1.390 (4)
I2—C3	2.089 (3)	C5—C4	1.381 (4)
C2—C3	1.382 (4)	C8—H8A	0.9800
F2—C4	1.345 (3)	C8—H8AB	0.9800

C8—N1—C7	110.0 (2)	H7A—C7—H7AB	108.3
C8—N1—H1	108 (2)	F3—C6—C1	118.5 (3)
C7—N1—H1	106 (2)	F3—C6—C5	118.1 (3)
C6—C1—C2	116.5 (3)	C1—C6—C5	123.3 (3)
C6—C1—I1	121.3 (2)	C4—C5—C6	116.7 (3)
C2—C1—I1	122.2 (2)	C4—C5—I3	120.8 (2)
F1—C2—C3	118.5 (3)	C6—C5—I3	122.5 (2)
F1—C2—C1	118.4 (3)	F2—C4—C3	118.6 (3)
C3—C2—C1	123.0 (3)	F2—C4—C5	118.1 (3)
C4—C3—C2	117.1 (3)	C3—C4—C5	123.3 (3)
C4—C3—I2	120.5 (2)	N1—C8—C7ⁱ	109.4 (3)
C2—C3—I2	122.4 (2)	N1—C8—H8A	109.8
N1—C7—C8ⁱ	109.0 (3)	C7ⁱ—C8—H8A	109.8
N1—C7—H7A	109.9	N1—C8—H8AB	109.8
C8ⁱ—C7—H7A	109.9	C7ⁱ—C8—H8AB	109.8
N1—C7—H7AB	109.9	H8A—C8—H8AB	108.2
C8ⁱ—C7—H7AB	109.9

C6—C1—C2—F1	−177.8 (3)	F3—C6—C5—C4	−179.3 (3)
I1—C1—C2—F1	2.8 (4)	C1—C6—C5—C4	1.5 (5)
C6—C1—C2—C3	2.0 (5)	F3—C6—C5—I3	−0.7 (4)
I1—C1—C2—C3	−177.5 (2)	C1—C6—C5—I3	−179.9 (2)
F1—C2—C3—C4	179.9 (3)	C2—C3—C4—F2	178.3 (3)
C1—C2—C3—C4	0.1 (5)	I2—C3—C4—F2	−4.3 (4)
F1—C2—C3—I2	2.5 (4)	C2—C3—C4—C5	−1.6 (5)
C1—C2—C3—I2	−177.3 (2)	I2—C3—C4—C5	175.8 (2)
C8—N1—C7—C8ⁱ	60.1 (3)	C6—C5—C4—F2	−179.0 (3)
C2—C1—C6—F3	177.9 (3)	I3—C5—C4—F2	2.4 (4)
I1—C1—C6—F3	−2.6 (4)	C6—C5—C4—C3	0.8 (4)
C2—C1—C6—C5	−2.8 (5)	I3—C5—C4—C3	−177.8 (2)
I1—C1—C6—C5	176.6 (2)	C7—N1—C8—C7ⁱ	−60.3 (4)

Symmetry code: (i) −x+2, −y, −z+2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···I2ⁱⁱ	0.86 (2)	3.12 (2)	3.978 (3)	177 (3)
C7—H7A···F2ⁱⁱⁱ	0.98	2.40	3.299 (4)	152
C7—H7AB···I3^iv	0.98	3.23	3.990 (3)	135
C8—H8A···I2^v	0.98	3.19	4.001 (3)	141
C8—H8AB···I1ⁱ	0.98	3.26	3.879 (3)	123

Symmetry codes: (i) −x+2, −y, −z+2; (ii) −x+2, −y+1, −z+1; (iii) x+1, y−1, z+1; (iv) x+1, y−1, z; (v) x, y, z+1.

Acknowledgements

We thank members of the Bryce lab for assistance and NSERC for funding.

Funding information

Funding for this research was provided by: Natural Sciences and Engineering Research Council of Canada (grant to David L. Bryce).

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