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ISSN: 2414-3146

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

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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.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

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[Cavallo, G., Metrangolo, P., Milani, R., Pilati, T., Priimagi, A., Resnati, G. & Terraneo, G. (2016). Chem. Rev. 116, 2478-2601.]). The title compound (Fig. 1[link]), 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[link]). 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[Szell, P. M. J., Gabriel, S. A., Gill, R. D. D., Wan, S. Y. H., Gabidullin, B. & Bryce, D. L. (2017). Acta Cryst. C73, 157-167.]). 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[Raatikainen, K., Huuskonen, J., Lahtinen, M., Metrangolo, P. & Rissanen, K. (2009). Chem. Commun. pp. 2160-2162.]).

[Figure 1]
Figure 1
ORTEP plot of the title compound.
[Figure 2]
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[link]). 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[link]). 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 DA 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⋯I2iv 0.98 3.19 4.001 (3) 141
C8—H8AB⋯I1v 0.98 3.26 3.879 (3) 123
Symmetry codes: (i) [-x+2, -y+1, -z+1]; (ii) [x+1, y-1, z+1]; (iii) [x+1, y-1, z]; (iv) x, y, z+1; (v) [-x+2, -y, -z+2].
[Figure 3]
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[link].

Table 2
Experimental details

Crystal data
Chemical formula C4H10N2·2C6F3I3
Mr 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)
V3) 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[Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3-10.])
Tmin, Tmax 0.537, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections 13748, 3761, 3193
Rint 0.031
(sin θ/λ)max−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
Δρmax, Δρmin (e Å−3) 0.56, −0.64
Computer programs: APEX3 and SAINT (Bruker, 2010[Bruker (2010). APEX3 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT2014/5 (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2018/3 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), ShelXle (Hübschle et al., 2011[Hübschle, C. B., Sheldrick, G. M. & Dittrich, B. (2011). J. Appl. Cryst. 44, 1281-1284.]) and Mercury (Macrae et al., 2020[Macrae, C. F., Sovago, I., Cottrell, S. J., Galek, P. T. A., McCabe, P., Pidcock, E., Platings, M., Shields, G. P., Stevens, J. S., Towler, M. & Wood, P. A. (2020). J. Appl. Cryst. 53, 226-235.]).

Structural data


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
C4H10N2·2C6F3I3Z = 1
Mr = 1105.66F(000) = 492
Triclinic, P1Dx = 3.046 Mg m3
a = 8.6450 (5) ÅMo Kα radiation, λ = 0.71073 Å
b = 9.1660 (5) ÅCell parameters from 6804 reflections
c = 9.3403 (5) Åθ = 2.4–30.7°
α = 67.433 (1)°µ = 7.78 mm1
β = 72.887 (1)°T = 203 K
γ = 63.062 (1)°Block, colourless
V = 602.75 (6) Å30.24 × 0.13 × 0.08 mm
Data collection top
Bruker APEXII CCD
diffractometer
3193 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.031
ω and πhi scansθmax = 30.8°, θmin = 2.4°
Absorption correction: multi-scan
(SADABS; Krause et al., 2015\bbr00)
h = 1212
Tmin = 0.537, Tmax = 0.746k = 1313
13748 measured reflectionsl = 1313
3761 independent reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.025H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.048 w = 1/[σ2(Fo2) + (0.0176P)2 + 0.1043P]
where P = (Fo2 + 2Fc2)/3
S = 1.02(Δ/σ)max = 0.001
3761 reflectionsΔρmax = 0.56 e Å3
139 parametersΔρmin = 0.64 e Å3
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
xyzUiso*/Ueq
I10.82683 (3)0.38276 (3)0.69997 (2)0.02587 (5)
N11.0231 (4)0.1572 (3)0.9473 (3)0.0297 (6)
H11.079 (4)0.212 (4)0.952 (4)0.036*
C10.6818 (4)0.5589 (4)0.5141 (3)0.0236 (6)
F10.8619 (2)0.3929 (2)0.3438 (2)0.0350 (5)
I20.70010 (3)0.60960 (3)0.02390 (2)0.03224 (6)
C20.7265 (4)0.5356 (4)0.3663 (4)0.0246 (6)
F20.4127 (2)0.9155 (2)0.1493 (2)0.0305 (4)
I30.22867 (3)1.04531 (3)0.44595 (3)0.03033 (6)
C30.6376 (4)0.6522 (4)0.2419 (3)0.0226 (6)
F30.4867 (2)0.7292 (2)0.6764 (2)0.0334 (4)
C71.1580 (4)0.0068 (4)0.8988 (4)0.0316 (7)
H7A1.2432230.0604640.9726680.038*
H7AB1.2205200.0442030.7945190.038*
C60.5381 (4)0.7041 (4)0.5336 (3)0.0235 (6)
C50.4444 (4)0.8275 (4)0.4131 (3)0.0218 (6)
C40.4991 (4)0.7972 (4)0.2689 (3)0.0225 (6)
C80.9301 (4)0.1016 (4)1.1043 (4)0.0315 (7)
H8A0.8419470.2017791.1367570.038*
H8AB1.0133210.0349331.1800120.038*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
I10.02951 (11)0.02437 (10)0.02130 (10)0.00916 (8)0.00948 (8)0.00148 (8)
N10.0415 (17)0.0289 (15)0.0227 (14)0.0176 (13)0.0112 (12)0.0020 (12)
C10.0253 (15)0.0261 (16)0.0199 (15)0.0109 (12)0.0078 (12)0.0028 (12)
F10.0367 (11)0.0271 (10)0.0300 (11)0.0021 (8)0.0089 (8)0.0115 (8)
I20.04118 (13)0.03267 (12)0.02151 (11)0.01026 (9)0.00498 (9)0.01114 (9)
C20.0241 (15)0.0223 (15)0.0255 (16)0.0074 (12)0.0017 (12)0.0082 (13)
F20.0380 (11)0.0267 (10)0.0211 (9)0.0063 (8)0.0141 (8)0.0016 (8)
I30.02595 (11)0.02909 (11)0.02966 (12)0.00356 (8)0.00403 (8)0.01089 (9)
C30.0276 (15)0.0227 (15)0.0191 (15)0.0091 (12)0.0049 (12)0.0074 (12)
F30.0358 (11)0.0399 (11)0.0175 (9)0.0072 (9)0.0039 (8)0.0104 (8)
C70.0280 (17)0.0381 (19)0.0249 (17)0.0119 (14)0.0076 (13)0.0036 (14)
C60.0272 (16)0.0287 (16)0.0162 (14)0.0137 (13)0.0017 (11)0.0058 (12)
C50.0203 (14)0.0207 (14)0.0239 (15)0.0073 (11)0.0039 (11)0.0061 (12)
C40.0242 (15)0.0221 (15)0.0216 (15)0.0106 (12)0.0103 (12)0.0002 (12)
C80.042 (2)0.0293 (18)0.0219 (16)0.0107 (15)0.0069 (14)0.0092 (14)
Geometric parameters (Å, º) top
I1—C12.118 (3)I3—C52.078 (3)
N1—C81.470 (4)C3—C41.379 (4)
N1—C71.475 (4)F3—C61.350 (3)
N1—H10.864 (18)C7—C8i1.513 (5)
C1—C61.380 (4)C7—H7A0.9800
C1—C21.392 (4)C7—H7AB0.9800
F1—C21.343 (3)C6—C51.390 (4)
I2—C32.089 (3)C5—C41.381 (4)
C2—C31.382 (4)C8—H8A0.9800
F2—C41.345 (3)C8—H8AB0.9800
C8—N1—C7110.0 (2)H7A—C7—H7AB108.3
C8—N1—H1108 (2)F3—C6—C1118.5 (3)
C7—N1—H1106 (2)F3—C6—C5118.1 (3)
C6—C1—C2116.5 (3)C1—C6—C5123.3 (3)
C6—C1—I1121.3 (2)C4—C5—C6116.7 (3)
C2—C1—I1122.2 (2)C4—C5—I3120.8 (2)
F1—C2—C3118.5 (3)C6—C5—I3122.5 (2)
F1—C2—C1118.4 (3)F2—C4—C3118.6 (3)
C3—C2—C1123.0 (3)F2—C4—C5118.1 (3)
C4—C3—C2117.1 (3)C3—C4—C5123.3 (3)
C4—C3—I2120.5 (2)N1—C8—C7i109.4 (3)
C2—C3—I2122.4 (2)N1—C8—H8A109.8
N1—C7—C8i109.0 (3)C7i—C8—H8A109.8
N1—C7—H7A109.9N1—C8—H8AB109.8
C8i—C7—H7A109.9C7i—C8—H8AB109.8
N1—C7—H7AB109.9H8A—C8—H8AB108.2
C8i—C7—H7AB109.9
C6—C1—C2—F1177.8 (3)F3—C6—C5—C4179.3 (3)
I1—C1—C2—F12.8 (4)C1—C6—C5—C41.5 (5)
C6—C1—C2—C32.0 (5)F3—C6—C5—I30.7 (4)
I1—C1—C2—C3177.5 (2)C1—C6—C5—I3179.9 (2)
F1—C2—C3—C4179.9 (3)C2—C3—C4—F2178.3 (3)
C1—C2—C3—C40.1 (5)I2—C3—C4—F24.3 (4)
F1—C2—C3—I22.5 (4)C2—C3—C4—C51.6 (5)
C1—C2—C3—I2177.3 (2)I2—C3—C4—C5175.8 (2)
C8—N1—C7—C8i60.1 (3)C6—C5—C4—F2179.0 (3)
C2—C1—C6—F3177.9 (3)I3—C5—C4—F22.4 (4)
I1—C1—C6—F32.6 (4)C6—C5—C4—C30.8 (4)
C2—C1—C6—C52.8 (5)I3—C5—C4—C3177.8 (2)
I1—C1—C6—C5176.6 (2)C7—N1—C8—C7i60.3 (4)
Symmetry code: (i) x+2, y, z+2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···I2ii0.86 (2)3.12 (2)3.978 (3)177 (3)
C7—H7A···F2iii0.982.403.299 (4)152
C7—H7AB···I3iv0.983.233.990 (3)135
C8—H8A···I2v0.983.194.001 (3)141
C8—H8AB···I1i0.983.263.879 (3)123
Symmetry codes: (i) x+2, y, z+2; (ii) x+2, y+1, z+1; (iii) x+1, y1, z+1; (iv) x+1, y1, 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).

References

First citationBruker (2010). APEX3 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationCavallo, 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
First citationHübschle, C. B., Sheldrick, G. M. & Dittrich, B. (2011). J. Appl. Cryst. 44, 1281–1284.  Web of Science CrossRef IUCr Journals Google Scholar
First citationKrause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3–10.  Web of Science CSD CrossRef ICSD CAS IUCr Journals Google Scholar
First citationMacrae, C. F., Sovago, I., Cottrell, S. J., Galek, P. T. A., McCabe, P., Pidcock, E., Platings, M., Shields, G. P., Stevens, J. S., Towler, M. & Wood, P. A. (2020). J. Appl. Cryst. 53, 226–235.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationRaatikainen, K., Huuskonen, J., Lahtinen, M., Metrangolo, P. & Rissanen, K. (2009). Chem. Commun. pp. 2160–2162.  Web of Science CSD CrossRef Google Scholar
First citationSheldrick, G. M. (2015a). Acta Cryst. A71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSheldrick, G. M. (2015b). Acta Cryst. C71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSzell, P. M. J., Gabriel, S. A., Gill, R. D. D., Wan, S. Y. H., Gabidullin, B. & Bryce, D. L. (2017). Acta Cryst. C73, 157–167.  Web of Science CSD CrossRef IUCr Journals Google Scholar

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