(4Z,6Z,12Z,14Z)-2,10-Dimethyl-2,8,10,16-tetra­hydro­dipyrazolo[3,4-e:3′,4′-l][1,2,4,8,9,11]hexa­azacyclo­tetra­decine-4,12-diamine

Dolzhenko, A.V.; Pastorin, G.; Dolzhenko, A.V.; Tan, G.K.; Koh, L.L.

doi:10.1107/S1600536809022132

organic compounds

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Volume 65| Part 7| July 2009| Pages o1578-o1579

doi:10.1107/S1600536809022132

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(4Z,6Z,12Z,14Z)-2,10-Dimethyl-2,8,10,16-tetrahydrodipyrazolo[3,4-e:3′,4′-l][1,2,4,8,9,11]hexaazacyclotetradecine-4,12-diamine

Anton V. Dolzhenko,^a ^* Giorgia Pastorin,^a Anna V. Dolzhenko,^a Geok Kheng Tan ^b and Lip Lin Koh ^b

^aDepartment of Pharmacy, Faculty of Science, National University of Singapore, 18 Science Drive 4, Singapore 117543, Singapore, and ^bDepartment of Chemistry, Faculty of Science, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
^*Correspondence e-mail: phada@nus.edu.sg

(Received 3 June 2009; accepted 10 June 2009; online 13 June 2009)

The title compound, C₁₂H₁₆N₁₂, is a centrosymmetric molecule which comprises of a hexaaza[14]annulene macrocyclic ring fused with two pyrazole rings. The macrocyclic ring is essentially planar, with an r.m.s. deviation of 0.0381 Å. The electron pairs of the amino groups are delocalized with the conjugated system of the macrocycle. Strong intramolecular N—H⋯N hydrogen bonds arranged in an S₂²(10) graph-set motif are present in the macrocyclic ring. In the crystal, the amino groups act as donors for intermolecular N—H⋯N interactions with the N atoms of the heterocyclic system, forming a network of two types of extended chains oriented parallel to the [101] and [011] directions. The crystal packing is also stabilized by weak intermolecular C—H⋯N hydrogen bonds formed between pyrazole C—H groups and N atoms of the macrocyclic ring, running in the [10 $[\overline{1}]$ ] direction.

Related literature

The title compound was synthesized according to Dolzhenko et al. (2009 ). For the synthesis and crystal structure studies of related macrocyclic compounds (as nickel complexes), see: Gradinaru et al. (2001 ); Gerbeleu et al. (1991 ); Leovac et al. (1993 ) and references cited therein; Simonov et al. (1988 ). For a review of the graph-set analysis of hydrogen bonding, see: Bernstein et al. (1995 ).

Experimental

Crystal data

C₁₂H₁₆N₁₂
M_r = 328.37
Monoclinic, P 2₁ /n
a = 7.1470 (6) Å
b = 7.5593 (7) Å
c = 13.9174 (13) Å
β = 91.866 (3)°
V = 751.51 (12) Å³
Z = 2
Mo Kα radiation
μ = 0.10 mm⁻¹
T = 223 K
0.22 × 0.08 × 0.06 mm

Data collection

Bruker SMART APEX CCD diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 2001 ) T_min = 0.978, T_max = 0.994
5126 measured reflections
1721 independent reflections
1272 reflections with I > 2σ(I)
R_int = 0.037

Refinement

R[F² > 2σ(F²)] = 0.062
wR(F²) = 0.151
S = 1.06
1721 reflections
122 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.26 e Å⁻³
Δρ_min = −0.17 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3N⋯N4	0.85 (3)	2.09 (3)	2.770 (3)	136 (2)
N5—H5A⋯N1ⁱ	0.88 (3)	2.33 (3)	3.065 (3)	141 (2)
N5—H5B⋯N6ⁱⁱ	0.85 (3)	2.61 (3)	3.466 (3)	174 (2)
C3—H3⋯N6ⁱⁱ	0.94	2.51	3.402 (3)	158
Symmetry codes: (i) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]$ ; (ii) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: SMART (Bruker, 2001 ); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809022132/si2181sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809022132/si2181Isup2.hkl

checkCIF report

Comment top

Macrocyclic compounds, various classes of which have been known for a long time, attract significant attention of the chemists' community due to their unique physico-chemical properties. Several studies on the synthesis and the crystal structure of the planar 1,2,4,8,9,11-hexaaza[14]annulene macrocyclic system have appeared (Gradinaru et al., 2001; Gerbeleu et al., 1991; Leovac et al., 1993; Simonov et al., 1988). However, all of the compounds were prepared and investigated as nickel complexes. Herein, we report the first crystal structure of the ligand with the 1,2,4,8,9,11-hexaaza[14]annulene macrocyclic ring. The title compound is a centrosymmetric molecule, which comprises the hexaaza[14]annulene macrocyclic ring fused with two pyrazole rings. The macrocyclic ring is essentially planar with an r.m.s. deviation of 0.0381 Å. The most outlying from the least-squares plane of the marcocyclic ring are atoms C6 (C6A) and N4 (N4A) with deviations of 0.0654 (17) Å and 0.0577 (18) Å, respectively. The C6—N5 bond distance (1.340 (3) Å) indicates delocalization of the electron pair of the N5 atom, though the amino group adopts a slightly pyramidal geometry with 0.084 (15) Å deviation of N5 from the C6/H5A/H5B mean plane. The strong intramolecular N—H···N hydrogen bonds arranged in a S²₂(10) graph-set motif (Bernstein et al., 1995) are present inside the macrocyclic ring.

In the crystal, the amino groups act as donors for intermolecular N—H···N interaction with the nitrogen atoms N1 (N1A) and N6 (N6A), thereby forming two types of extended chains. The nitrogen atoms N1 (N1A) are acceptors in C(6) chains running parallel to the [101] direction, while the nitrogen atoms N6 (N6A) are acceptors in C(5) chains oriented in the [011] direction. Together, these hydrogen bonds form a centrosymmetric R⁴₄(22) motif. The crystal packing is also stabilized by weak intermolecular C—H···N hydrogen bonds, formed between C3—H (C3A—H) of the pyrazole rings and nitrogen atoms N6 (N6A) of the macrocyclic ring, running in the [101] direction.

Related literature top

The title compound was synthesized according to Dolzhenko et al. (2009). For the synthesis and crystal structure studies of related macrocyclic compounds (as nickel complexes), see: Gradinaru et al. (2001); Gerbeleu et al. (1991); Leovac et al. (1993) and references cited therein; Simonov et al. (1988). For a review of the graph-set analysis of hydrogen bonding, see: Bernstein et al. (1995).

Experimental top

The title compound was synthesized according to Dolzhenko et al. (2009). Single crystals suitable for crystallographic analysis were grown by recrystallization from methanol.

Computing details top

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The molecular structure of the title compound with the atomic numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. Molecular parking in the crystal, viewed along the b axis.

(4Z,6Z,12Z,14Z)-2,10-Dimethyl-2,8,10,16- tetrahydrodipyrazolo[3,4-e:3',4'- l][1,2,4,8,9,11]hexaazacyclotetradecine-4,12-diamine top

Crystal data top

C₁₂H₁₆N₁₂	F(000) = 344
M_r = 328.37	D_x = 1.451 Mg m⁻³
Monoclinic, P2₁/n	Melting point: 537 K
Hall symbol: -P 2yn	Mo Kα radiation, λ = 0.71073 Å
a = 7.1470 (6) Å	Cell parameters from 734 reflections
b = 7.5593 (7) Å	θ = 2.9–21.6°
c = 13.9174 (13) Å	µ = 0.10 mm⁻¹
β = 91.866 (3)°	T = 223 K
V = 751.51 (12) Å³	Block, colourless
Z = 2	0.22 × 0.08 × 0.06 mm

Data collection top

Bruker SMART APEX CCD diffractometer	1721 independent reflections
Radiation source: fine-focus sealed tube	1272 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.037
ϕ and ω scans	θ_max = 27.5°, θ_min = 2.9°
Absorption correction: multi-scan (SADABS; Sheldrick, 2001)	h = −9→8
T_min = 0.978, T_max = 0.994	k = −8→9
5126 measured reflections	l = −18→15

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.062	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.151	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	w = 1/[σ²(F_o²) + (0.0676P)² + 0.2208P] where P = (F_o² + 2F_c²)/3
1721 reflections	(Δ/σ)_max = 0.002
122 parameters	Δρ_max = 0.26 e Å⁻³
0 restraints	Δρ_min = −0.17 e Å⁻³

Crystal data top

C₁₂H₁₆N₁₂	V = 751.51 (12) Å³
M_r = 328.37	Z = 2
Monoclinic, P2₁/n	Mo Kα radiation
a = 7.1470 (6) Å	µ = 0.10 mm⁻¹
b = 7.5593 (7) Å	T = 223 K
c = 13.9174 (13) Å	0.22 × 0.08 × 0.06 mm
β = 91.866 (3)°

Data collection top

Bruker SMART APEX CCD diffractometer	1721 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 2001)	1272 reflections with I > 2σ(I)
T_min = 0.978, T_max = 0.994	R_int = 0.037
5126 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.062	0 restraints
wR(F²) = 0.151	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	Δρ_max = 0.26 e Å⁻³
1721 reflections	Δρ_min = −0.17 e Å⁻³
122 parameters

Special details top

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

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

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

	x	y	z	U_iso*/U_eq
N1	0.5186 (2)	0.7646 (2)	0.56112 (13)	0.0318 (5)
N2	0.6151 (3)	0.6882 (2)	0.48829 (14)	0.0331 (5)
N3	0.2241 (3)	0.9124 (3)	0.56302 (13)	0.0330 (5)
H3N	0.135 (4)	0.945 (3)	0.5254 (18)	0.041 (7)*
N4	0.0731 (2)	0.9323 (2)	0.37750 (13)	0.0329 (5)
N5	0.2238 (4)	0.7748 (3)	0.25680 (16)	0.0483 (6)
H5A	0.125 (4)	0.790 (4)	0.218 (2)	0.050 (8)*
H5B	0.312 (4)	0.702 (3)	0.2455 (19)	0.040 (7)*
N6	−0.0650 (3)	0.9742 (3)	0.30609 (14)	0.0417 (5)
C1	0.3648 (3)	0.8253 (3)	0.51677 (15)	0.0286 (5)
C2	0.3588 (3)	0.7909 (3)	0.41682 (15)	0.0291 (5)
C3	0.5250 (3)	0.7009 (3)	0.40344 (16)	0.0331 (5)
H3	0.5666	0.6566	0.3448	0.040*
C4	0.8014 (3)	0.6185 (3)	0.50829 (19)	0.0416 (6)
H4A	0.8443	0.5566	0.4521	0.062*
H4B	0.7981	0.5372	0.5621	0.062*
H4C	0.8863	0.7151	0.5240	0.062*
C5	0.2062 (3)	0.9460 (3)	0.65708 (17)	0.0381 (6)
H5	0.3035	0.9088	0.6994	0.046*
C6	0.2100 (3)	0.8348 (3)	0.34691 (15)	0.0305 (5)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0292 (10)	0.0340 (10)	0.0322 (10)	−0.0006 (8)	0.0010 (8)	0.0006 (8)
N2	0.0271 (10)	0.0347 (10)	0.0378 (11)	0.0028 (8)	0.0043 (8)	0.0001 (8)
N3	0.0293 (10)	0.0434 (11)	0.0264 (10)	0.0052 (9)	−0.0009 (8)	−0.0012 (9)
N4	0.0288 (10)	0.0427 (10)	0.0272 (9)	0.0007 (8)	0.0014 (8)	0.0031 (8)
N5	0.0422 (14)	0.0694 (16)	0.0330 (12)	0.0178 (12)	−0.0036 (10)	−0.0110 (11)
N6	0.0367 (11)	0.0604 (13)	0.0279 (10)	0.0100 (10)	0.0002 (9)	0.0016 (10)
C1	0.0263 (11)	0.0294 (10)	0.0301 (11)	−0.0045 (9)	0.0009 (9)	0.0016 (9)
C2	0.0294 (11)	0.0293 (10)	0.0288 (11)	−0.0029 (9)	0.0045 (9)	−0.0006 (9)
C3	0.0332 (12)	0.0340 (11)	0.0324 (12)	−0.0010 (10)	0.0064 (10)	−0.0010 (10)
C4	0.0289 (12)	0.0424 (13)	0.0536 (15)	0.0047 (10)	0.0023 (11)	0.0050 (12)
C5	0.0341 (13)	0.0511 (14)	0.0291 (12)	0.0049 (11)	−0.0014 (10)	0.0035 (11)
C6	0.0304 (12)	0.0343 (11)	0.0269 (11)	−0.0038 (9)	0.0035 (9)	0.0003 (9)

Geometric parameters (Å, º) top

N1—C1	1.325 (3)	N5—H5B	0.85 (3)
N1—N2	1.372 (3)	N6—C5ⁱ	1.295 (3)
N2—C3	1.330 (3)	C1—C2	1.414 (3)
N2—C4	1.450 (3)	C2—C3	1.387 (3)
N3—C5	1.344 (3)	C2—C6	1.456 (3)
N3—C1	1.379 (3)	C3—H3	0.9400
N3—H3N	0.85 (3)	C4—H4A	0.9700
N4—C6	1.307 (3)	C4—H4B	0.9700
N4—N6	1.413 (3)	C4—H4C	0.9700
N5—C6	1.340 (3)	C5—N6ⁱ	1.295 (3)
N5—H5A	0.88 (3)	C5—H5	0.9400

C1—N1—N2	103.35 (18)	C1—C2—C6	127.84 (19)
C3—N2—N1	112.65 (18)	N2—C3—C2	108.0 (2)
C3—N2—C4	127.7 (2)	N2—C3—H3	126.0
N1—N2—C4	119.45 (19)	C2—C3—H3	126.0
C5—N3—C1	129.7 (2)	N2—C4—H4A	109.5
C5—N3—H3N	116.9 (17)	N2—C4—H4B	109.5
C1—N3—H3N	113.3 (17)	H4A—C4—H4B	109.5
C6—N4—N6	114.22 (18)	N2—C4—H4C	109.5
C6—N5—H5A	116.4 (17)	H4A—C4—H4C	109.5
C6—N5—H5B	117.8 (18)	H4B—C4—H4C	109.5
H5A—N5—H5B	124 (2)	N6ⁱ—C5—N3	125.0 (2)
C5ⁱ—N6—N4	111.17 (19)	N6ⁱ—C5—H5	117.5
N1—C1—N3	123.7 (2)	N3—C5—H5	117.5
N1—C1—C2	113.13 (19)	N4—C6—N5	125.0 (2)
N3—C1—C2	123.2 (2)	N4—C6—C2	116.68 (19)
C3—C2—C1	102.91 (19)	N5—C6—C2	118.3 (2)
C3—C2—C6	129.2 (2)

Symmetry code: (i) −x, −y+2, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3N···N4	0.85 (3)	2.09 (3)	2.770 (3)	136 (2)
N5—H5A···N1ⁱⁱ	0.88 (3)	2.33 (3)	3.065 (3)	141 (2)
N5—H5B···N6ⁱⁱⁱ	0.85 (3)	2.61 (3)	3.466 (3)	174 (2)
C3—H3···N6ⁱⁱⁱ	0.94	2.51	3.402 (3)	158

Symmetry codes: (ii) x−1/2, −y+3/2, z−1/2; (iii) −x+1/2, y−1/2, −z+1/2.

Experimental details

Crystal data
Chemical formula	C₁₂H₁₆N₁₂
M_r	328.37
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	223
a, b, c (Å)	7.1470 (6), 7.5593 (7), 13.9174 (13)
β (°)	91.866 (3)
V (Å³)	751.51 (12)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.10
Crystal size (mm)	0.22 × 0.08 × 0.06

Data collection
Diffractometer	Bruker SMART APEX CCD diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 2001)
T_min, T_max	0.978, 0.994
No. of measured, independent and observed [I > 2σ(I)] reflections	5126, 1721, 1272
R_int	0.037
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.062, 0.151, 1.06
No. of reflections	1721
No. of parameters	122
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.26, −0.17

Computer programs: SMART (Bruker, 2001), SAINT (Bruker, 2001), SAINT (Bruker, 2001, SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3N···N4	0.85 (3)	2.09 (3)	2.770 (3)	136 (2)
N5—H5A···N1ⁱ	0.88 (3)	2.33 (3)	3.065 (3)	141 (2)
N5—H5B···N6ⁱⁱ	0.85 (3)	2.61 (3)	3.466 (3)	174 (2)
C3—H3···N6ⁱⁱ	0.94	2.51	3.402 (3)	158.3

Symmetry codes: (i) x−1/2, −y+3/2, z−1/2; (ii) −x+1/2, y−1/2, −z+1/2.

Acknowledgements

This work is supported by the National Medical Research Council, Singapore (NMRC/NIG/0020/2008) and the National University of Singapore (R-148–050-091–101/133).

References

Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573. CrossRef CAS Web of Science Google Scholar
Bruker (2001). SMART and SAINT. Bruker AXS GmbH, Karlsruhe, Germany. Google Scholar
Dolzhenko, A. V., Pastorin, G., Dolzhenko, A. V. & Chui, W. K. (2009). Tetrahedron Lett. In the press. Google Scholar
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Gradinaru, J. I., Simonov, Y. A., Arion, V. B., Bourosh, P. N., Popovici, M. A., Bel'skii, V. K. & Gerbeleu, N. V. (2001). Inorg. Chim. Acta, 313, 30–36. Web of Science CSD CrossRef CAS Google Scholar
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doi:10.1107/S1600536809022132

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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

(4Z,6Z,12Z,14Z)-2,10-Di­methyl-2,8,10,16-tetra­hydro­di­pyrazolo[3,4-e:3′,4′-l][1,2,4,8,9,11]hexa­aza­cyclo­tetra­decine-4,12-di­amine

Related literature

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds

(4Z,6Z,12Z,14Z)-2,10-Dimethyl-2,8,10,16-tetrahydrodipyrazolo[3,4-e:3′,4′-l][1,2,4,8,9,11]hexaazacyclotetradecine-4,12-diamine