Crystal structure of the co-crystalline adduct 1,3,6,8-tetra-aza-tri-cyclo-[4.4.1.13,8]dodecane (TATD)-4-iodo-phenol (1/2): supra-molecular assembly mediated by halogen and hydrogen bonding.

The asymmetric unit of the title co-crystalline adduct, 1,3,6,8-tetra-aza-tri-cyclo[4.4.1.13,8]dodecane (TATD)-4-iodo-phenol (1/2), C8H16N4·2C6H5IO, comprises a half mol-ecule of the aminal cage polyamine plus a 4-iodo-phenol mol-ecule. A twofold rotation axis generates the other half of the adduct. The components are linked by two inter-molecular O-H⋯N hydrogen bonds. The adducts are further linked into a three-dimensional framework structure by a combination of N⋯I halogen bonds and weak non-conventional C-H⋯O and C-H⋯I hydrogen bonds.

Chemical context

Halogenoorganic compounds are able to play a role in organic supra­molecular assemblies as electrophilic species, and have been used as models in the construction of self-assembled architectures. Non-covalent bonds such as hydrogen bonds (HB) and halogen bonds (XB) attract inter­est in crystal engineering because they have clear directional properties (Umezono & Okuno, 2017 ▸). Hydrogen bonds have been used successfully to construct supra­molecular architectures as a result of their high directionality, which also results in high selectivity. Halogen bonds exhibit similar directionality and strength to hydrogen bonds and can offer a new approach to the control of supra­molecular assemblies (Jin et al., 2014 ▸). XB also play important roles in natural systems, and have been effectively applied in various fields including crystal engineering, solid-state mol­ecular recognition, materials with optical properties and supra­molecular liquid crystals (Li et al., 2017 ▸). The strength of the inter­actions involving halogens increases on going from chlorine to bromine to iodine. Although hydrogen bonds are likely to be more effective, XB also are also important in crystal packing (Aakeröy et al., 2015 ▸; Geboes et al., 2017 ▸). In view of the analogies between halogen and hydrogen bonding, we think that the 4-iodo­phenol mol­ecule offers inter­esting possibilities for exploring the effect of halogen-bonding inter­actions on supra­molecular assemblies of phenols with polyamines. Following our previous work on acid–base adducts based on macrocyclic aminals and phenols, we report herein the synthesis and crystal structure of the title compound, a supra­molecular complex assembled through non-covalent HB and XB inter­actions between 4-iodo­phenol and 1,3,6,8-tetra­aza­tri­cyclo­[4.4.1.13,8]dodecane (TATD).

Structural commentary

The title compound is isostructural with 1,3,6,8-tetra­aza­tri­cyclo­[4.4.1.13,8]dodecane (TATD)–4-bromo­phenol (Rivera, Uribe et al., 2015 ▸): both crystallize in the space group Fdd2, and the differences between the unit-cell parameters (a, b, c) are < 7%. The asymmetric unit comprises one half of a 1,3,6,8-tetra­aza­tri­cyclo­[4.4.1.13,8]dodecane (TATD) mol­ecule and one iodo­phenol mol­ecule held together by inter­molecular O—H⋯N hydrogen bonds [O⋯N 2.741 (6) Å; O—H⋯N 154 (7)°; Table 1 ▸]. The complete adduct is generated by a crystallographic twofold rotation axis, (Fig. 1 ▸).

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯N1	0.84 (1)	1.96 (4)	2.741 (6)	154 (7)
C5—H5B⋯I1i	0.99	3.03	3.961 (7)	158
C13—H13⋯O1ii	0.95	2.53	3.455 (6)	165

Symmetry codes: (i) ; (ii) .

Figure 1

A view of the mol­ecular structure of the title compound, showing the atom-labelling scheme, with displacement ellipsoids drawn at the 50% probability. H atoms bonded to C atoms are omitted for clarity. Hydrogen bonds are drawn as dashed lines. Atoms labelled with the suffix A are generated using the symmetry operator (−x + 1, −y + 1, z).

Apart from the C—I/Br bond-length differences and some of the bond angles in the benzene ring, the mol­ecules have similar geometric data (bond lengths and angles). The C14—I1 bond length [2.106 (5) Å] is in good agreement with the value reported for 4-iodo­phenol itself [2.104 (5) Å; Merz, 2006 ▸]. The overall mol­ecular conformation of TATD observed here is very close to that of TATD in the related bromo­phenol adduct (Rivera, Uribe et al., 2015 ▸).

Supra­molecular features

In the crystal, the three independent mol­ecules are linked via two inter­molecular O1—H1⋯N1 hydrogen bonds (Table 1 ▸ and Fig. 1 ▸). These supra­molecular units are then linked by direction-specific inter­molecular inter­actions, including both non-conventional hydrogen bonds and halogen bonds, C—H⋯O and C—H⋯I hydrogen bonds, forming slabs lying parallel to the bc plane (Table 1 ▸ and Fig. 2 ▸). However, considering the donor–acceptor bond lengths of 3.961 (7) Å [C5—H5B⋯I1] and 3.455 (6) Å [C13—H13⋯O1], which exceed the sum of the corresponding van der Waals radii (0.281 and 0.255 Å, respectively), the strength of the these non-conventional hydrogen bonds can be classified as very weak (Steiner, 2003 ▸).

Figure 2

A view of the crystal packing of the title compound, showing the O—H⋯N hydrogen bonds; and C—H⋯O and C—H⋯hydrogen bonds (dashed lines).

In addition, as indicated by a PLATON analysis (Spek, 2009 ▸), the iodine atom is involved, as an electron-density acceptor, in two short contacts with N2 and C3, seemingly forming a bifurcated halogen bond, where the I⋯N [3.351 (5) Å] and I⋯C distances [3.519 (5) Å] are 0.18 and 0.16 Å, respectively, less than the sum of the corresponding van der Waals radii (Alvarez, 2013 ▸). The I⋯N distance corresponds to 90% of the sum of the van der Waals radii (3.70 Å) and the C14—I1⋯N2iii angle of 173.11 (2)° is close to being linear [symmetry code: (iii) x + , −y + , z + ]. Taking into account these geometrical parameters, the I1⋯N2 contacts can formally be considered as halogen bonds. It appears that this contact imposes the relatively close, but significantly longer I⋯C contact. Unsurprisingly, this pattern is repeated with the isostructural bromo analogue (Rivera, Uribe et al., 2015 ▸) with Br⋯N = 3.292 (4) and C⋯Br = 3.477 (4) Å. There is also a Cl⋯N halogen bond in the related 4-chloro-3,5-di­methyl­phenol analogue (Rivera, Rojas, et al., 2015 ▸) with Cl⋯N = 3.1680 (16); the C⋯Cl contact has extended to 3.5828 (19) Å and can be disregarded.

Database survey

The structure of 1,3,6,8-tetra­aza­tri­cyclo­[4.4.1.13,8]dodecane has already been determined (Murray-Rust, 1974 ▸; Rivera et al., 2014 ▸). Since the mol­ecule is rigid, it is not surprising that it compares very closely with the TATD mol­ecule in the title compound. The structure of 1,3,6,8-tetra­aza­tri­cyclo[4.4.1.13,8]dodecane hydro­quinone (Rivera et al., 2007 ▸) shows two O—H⋯N hydrogen bonds of similar geometry to that of the title compound. Inter­estingly, this pattern is repeated with 4-bromo­phenol 1,3,6,8-tetra­aza­tri­cyclo­[4.4.1.13,8]dodecane (Rivera, Uribe et al., 2015 ▸), which is isostructural with the title compound. In contrast, 4-chloro-3,5-di­methyl­phenol 1,3,6,8-tetra­aza­tri­cyclo­[4.4.1.13,8]dodecane (Rivera, Rojas et al., 2015 ▸) only forms one O—H⋯N hydrogen bond, nonetheless with similar geometric parameters to those in the title compound. Similarly, in the supra­molecular complex with a 2:1 ratio of 4-iodo­phenol to the aza-donor 1,4-di­aza­bicyclo[2.2.2]octane (Nayak & Pedireddi, 2017 ▸), the mol­ecules are again connected through O—H⋯N hydrogen bonds but with no halogen-bond inter­action involving the iodo substituent.

Synthesis and crystallization

A mixture of 1,3,6,8-tetra­aza­tri­cyclo­[4.4.1.13,8]dodecane (TATD) (0.168g, 1 mmol) and 4-iodo­phenol (0.440g, 2 mmol) was ground at room temperature with a pestle in a mortar for 15 min., as required to complete the reaction (TLC). The mixture was recrystallized from a mixture of n-hexane with a few drops of ethanol to obtain crystals suitable for X-ray analysis, m.p. = 391 K. (yield: 56%).

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. All H atoms were located in a difference electron-density map. The hydroxyl H atom was refined freely, while C-bound H atoms were fixed geometrically (C—H = 0.95 or 0.99 Å) and refined using a riding-model approximation, with U iso(H) set to 1.2U eq of the parent atom

Table 2

Experimental details

Crystal data
Chemical formula	C8H16N4·2C6H5IO
M r	608.25
Crystal system, space group	Orthorhombic, F d d2
Temperature (K)	173
a, b, c (Å)	20.8869 (16), 22.4197 (13), 9.6352 (6)
V (Å3)	4512.0 (5)
Z	8
Radiation type	Mo Kα
μ (mm−1)	2.81
Crystal size (mm)	0.24 × 0.23 × 0.23
Data collection
Diffractometer	Stoe IPDS II two-circle
Absorption correction	Multi-scan (X-AREA; Stoe & Cie, 2001 ▸)
T min, T max	0.548, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	7213, 2102, 2079
R int	0.029
(sin θ/λ)max (Å−1)	0.606
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S	0.025, 0.065, 1.06
No. of reflections	2102
No. of parameters	132
No. of restraints	2
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)	0.25, −0.67
Absolute structure	Classical Flack (1983 ▸) method preferred over Parsons because s.u. lower
Absolute structure parameter	−0.03 (4)

Computer programs: X-AREA (Stoe & Cie, 2001 ▸), XP in SHELXTL-Plus and SHELXS2016 (Sheldrick, 2008 ▸) and SHELXL2016 (Sheldrick, 2015 ▸).

Crystal structure: contains datablock(s) I. DOI: 10.1107/S2056989017014943/sj5537sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989017014943/sj5537Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S2056989017014943/sj5537Isup3.cml

CCDC reference: 1580038

Additional supporting information: crystallographic information; 3D view; checkCIF report

C8H16N4·2C6H5IO	Dx = 1.791 Mg m−3
Mr = 608.25	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Fdd2	Cell parameters from 15571 reflections
a = 20.8869 (16) Å	θ = 3.6–25.9°
b = 22.4197 (13) Å	µ = 2.81 mm−1
c = 9.6352 (6) Å	T = 173 K
V = 4512.0 (5) Å3	Block, yellow
Z = 8	0.24 × 0.23 × 0.23 mm
F(000) = 2368

Stoe IPDS II two-circle diffractometer	2079 reflections with I > 2σ(I)
Radiation source: Genix 3D IµS microfocus X-ray source	Rint = 0.029
ω scans	θmax = 25.5°, θmin = 3.6°
Absorption correction: multi-scan (X-AREA; Stoe & Cie, 2001)	h = −24→25
Tmin = 0.548, Tmax = 1.000	k = −26→27
7213 measured reflections	l = −11→11
2102 independent reflections

Refinement on F2	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.025	w = 1/[σ2(Fo2) + (0.0495P)2 + 5.1297P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.065	(Δ/σ)max = 0.002
S = 1.06	Δρmax = 0.25 e Å−3
2102 reflections	Δρmin = −0.67 e Å−3
132 parameters	Absolute structure: Classical Flack (1983) method preferred over Parsons because s.u. lower
2 restraints	Absolute structure parameter: −0.03 (4)

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.

	x	y	z	Uiso*/Ueq	Occ. (<1)
N1	0.5189 (2)	0.55327 (17)	0.2785 (4)	0.0293 (9)
N2	0.4501 (2)	0.5309 (2)	0.0695 (5)	0.0335 (9)
C1	0.500000	0.500000	0.3551 (8)	0.0350 (16)
H1A	0.463825	0.511142	0.416230	0.042*	0.5
H1B	0.536176	0.488858	0.416229	0.042*	0.5
C2	0.4734 (3)	0.5730 (3)	0.1705 (6)	0.0413 (13)
H2A	0.435585	0.589927	0.218543	0.050*
H2B	0.493847	0.606119	0.119081	0.050*
C3	0.500000	0.500000	−0.0073 (9)	0.0383 (16)
H3A	0.521109	0.529565	−0.068331	0.046*	0.5
H3B	0.478891	0.470437	−0.068336	0.046*	0.5
C4	0.3977 (3)	0.4922 (3)	0.1176 (7)	0.0439 (13)
H4A	0.381691	0.469170	0.037109	0.053*
H4B	0.362214	0.517973	0.149924	0.053*
C5	0.4138 (3)	0.4485 (3)	0.2331 (7)	0.0456 (14)
H5A	0.386853	0.458252	0.314539	0.055*
H5B	0.401546	0.407971	0.201822	0.055*
I1	0.63999 (2)	0.68958 (2)	1.00445 (6)	0.03902 (14)
O1	0.5030 (2)	0.65445 (17)	0.4344 (4)	0.0364 (8)
H1	0.518 (3)	0.623 (2)	0.402 (7)	0.05 (2)*
C11	0.5320 (2)	0.6593 (2)	0.5604 (6)	0.0293 (10)
C12	0.5220 (3)	0.7116 (2)	0.6361 (6)	0.0352 (11)
H12	0.494289	0.741464	0.600328	0.042*
C13	0.5518 (2)	0.72031 (19)	0.7624 (7)	0.0330 (10)
H13	0.544963	0.756109	0.813067	0.040*
C14	0.5920 (2)	0.6759 (2)	0.8149 (6)	0.0293 (10)
C15	0.6015 (2)	0.6234 (2)	0.7428 (7)	0.0312 (9)
H15	0.628314	0.593158	0.780345	0.037*
C16	0.5715 (2)	0.6147 (2)	0.6143 (6)	0.0309 (10)
H16	0.578032	0.578773	0.564169	0.037*

	U11	U22	U33	U12	U13	U23
N1	0.038 (2)	0.028 (2)	0.022 (2)	−0.0009 (16)	−0.0024 (17)	0.0024 (16)
N2	0.031 (2)	0.045 (2)	0.025 (2)	0.0090 (19)	0.0002 (17)	0.0008 (18)
C1	0.047 (4)	0.035 (4)	0.023 (3)	−0.008 (3)	0.000	0.000
C2	0.050 (3)	0.038 (3)	0.036 (3)	0.015 (3)	−0.006 (2)	0.004 (2)
C3	0.032 (3)	0.061 (4)	0.022 (3)	0.011 (3)	0.000	0.000
C4	0.026 (2)	0.067 (4)	0.038 (3)	0.007 (2)	−0.003 (2)	0.002 (3)
C5	0.039 (3)	0.050 (3)	0.048 (4)	−0.007 (2)	−0.001 (3)	0.002 (3)
I1	0.0425 (2)	0.03403 (19)	0.0405 (2)	−0.00169 (13)	−0.00853 (15)	−0.00435 (16)
O1	0.044 (2)	0.0297 (18)	0.0355 (19)	0.0035 (16)	−0.0077 (17)	−0.0043 (16)
C11	0.024 (2)	0.030 (2)	0.034 (2)	−0.0028 (18)	0.0035 (19)	0.0018 (19)
C12	0.035 (3)	0.029 (2)	0.041 (3)	0.005 (2)	0.001 (2)	0.000 (2)
C13	0.037 (2)	0.0255 (19)	0.036 (3)	0.0028 (18)	0.007 (2)	−0.005 (3)
C14	0.027 (2)	0.032 (2)	0.030 (2)	−0.0029 (19)	0.003 (2)	0.000 (2)
C15	0.030 (2)	0.027 (2)	0.036 (3)	0.0023 (16)	0.001 (2)	0.001 (2)
C16	0.033 (2)	0.024 (2)	0.036 (2)	−0.0012 (18)	0.002 (2)	−0.002 (2)

N1—C1	1.458 (5)	C5—H5A	0.9900
N1—C5i	1.474 (7)	C5—H5B	0.9900
N1—C2	1.478 (7)	I1—C14	2.106 (5)
N2—C2	1.440 (8)	O1—C11	1.361 (6)
N2—C3	1.453 (6)	O1—H1	0.838 (14)
N2—C4	1.472 (8)	C11—C16	1.395 (7)
C1—H1A	0.9900	C11—C12	1.397 (8)
C1—H1B	0.9900	C12—C13	1.381 (9)
C2—H2A	0.9900	C12—H12	0.9500
C2—H2B	0.9900	C13—C14	1.398 (8)
C3—H3A	0.9900	C13—H13	0.9500
C3—H3B	0.9900	C14—C15	1.382 (7)
C4—C5	1.520 (9)	C15—C16	1.401 (8)
C4—H4A	0.9900	C15—H15	0.9500
C4—H4B	0.9900	C16—H16	0.9500
C1—N1—C5i	112.8 (4)	C5—C4—H4B	108.2
C1—N1—C2	115.3 (4)	H4A—C4—H4B	107.3
C5i—N1—C2	114.4 (5)	N1i—C5—C4	116.4 (5)
C2—N2—C3	114.5 (4)	N1i—C5—H5A	108.2
C2—N2—C4	115.1 (5)	C4—C5—H5A	108.2
C3—N2—C4	114.4 (4)	N1i—C5—H5B	108.2
N1—C1—N1i	119.2 (6)	C4—C5—H5B	108.2
N1—C1—H1A	107.5	H5A—C5—H5B	107.3
N1i—C1—H1A	107.5	C11—O1—H1	103 (5)
N1—C1—H1B	107.5	O1—C11—C16	122.6 (5)
N1i—C1—H1B	107.5	O1—C11—C12	117.7 (5)
H1A—C1—H1B	107.0	C16—C11—C12	119.6 (5)
N2—C2—N1	119.8 (4)	C13—C12—C11	120.8 (5)
N2—C2—H2A	107.4	C13—C12—H12	119.6
N1—C2—H2A	107.4	C11—C12—H12	119.6
N2—C2—H2B	107.4	C12—C13—C14	119.3 (5)
N1—C2—H2B	107.4	C12—C13—H13	120.4
H2A—C2—H2B	106.9	C14—C13—H13	120.4
N2—C3—N2i	118.8 (7)	C15—C14—C13	120.8 (5)
N2—C3—H3A	107.6	C15—C14—I1	119.5 (4)
N2i—C3—H3A	107.6	C13—C14—I1	119.8 (4)
N2—C3—H3B	107.6	C14—C15—C16	119.8 (5)
N2i—C3—H3B	107.6	C14—C15—H15	120.1
H3A—C3—H3B	107.0	C16—C15—H15	120.1
N2—C4—C5	116.5 (5)	C11—C16—C15	119.7 (5)
N2—C4—H4A	108.2	C11—C16—H16	120.2
C5—C4—H4A	108.2	C15—C16—H16	120.2
N2—C4—H4B	108.2
C5i—N1—C1—N1i	−82.7 (4)	O1—C11—C12—C13	−177.7 (5)
C2—N1—C1—N1i	51.3 (3)	C16—C11—C12—C13	1.5 (8)
C3—N2—C2—N1	−55.1 (7)	C11—C12—C13—C14	−0.5 (8)
C4—N2—C2—N1	80.5 (7)	C12—C13—C14—C15	−0.9 (8)
C1—N1—C2—N2	−50.6 (7)	C12—C13—C14—I1	178.2 (4)
C5i—N1—C2—N2	82.6 (7)	C13—C14—C15—C16	1.3 (8)
C2—N2—C3—N2i	53.6 (4)	I1—C14—C15—C16	−177.8 (4)
C4—N2—C3—N2i	−82.3 (4)	O1—C11—C16—C15	178.1 (5)
C2—N2—C4—C5	−65.6 (7)	C12—C11—C16—C15	−1.1 (8)
C3—N2—C4—C5	70.1 (7)	C14—C15—C16—C11	−0.3 (8)
N2—C4—C5—N1i	−3.8 (8)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···N1	0.84 (1)	1.96 (4)	2.741 (6)	154 (7)
C5—H5B···I1ii	0.99	3.03	3.961 (7)	158
C13—H13···O1iii	0.95	2.53	3.455 (6)	165