2,2′-(1,3-Diazinane-1,3-di­yl)diaceto­nitrile: a second monoclinic polymorph

Rivera, A.; Maldonado, M.; Ríos-Motta, J.; Fejfarová, K.; Dušek, M.

doi:10.1107/S1600536811038013

organic compounds

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Volume 67| Part 10| October 2011| Page o2734

https://doi.org/10.1107/S1600536811038013

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2,2′-(1,3-Diazinane-1,3-diyl)diacetonitrile: a second monoclinic polymorph

Augusto Rivera,^a ^* Mauricio Maldonado,^a Jaime Ríos-Motta,^a Karla Fejfarová ^b and Michal Dušek ^b

^aDepartamento de Química, Universidad Nacional de Colombia, Ciudad Universitaria, Bogotá, Colombia, and ^bInstitute of Physics ASCR, v.v.i., Na Slovance 2, 182 21 Praha 8, Czech Republic
^*Correspondence e-mail: ariverau@unal.edu.co

(Received 15 August 2011; accepted 16 September 2011; online 30 September 2011)

A new monoclinic polymorph of the title compound, C₈H₁₂N₄, in the space group P2₁/n (Z = 4) is reported. The previously known form was also monoclinic, P2₁/c (Z = 4), but the unit-cell parameters and crystal packing were different [Shoja & Saba (1993 ). Acta Cryst. C49, 354–355]. The hexahydropyrimidine ring of the title compound adopts a chair conformation with a diequatorial substitution and with the CH₂-C≡N groups oriented nearly parallel and in the same direction [NC—CH₂⋯CH₂—CN pseudo torsion angle = −6.27 (18)°]. In the crystal, intermolecular C—H⋯ N hydrogen bonds connects the molecules into a chain along the b axis.

Related literature

For the original monoclinic polymorph, see: Shoja & Saba (1993). For the synthesis of the title compound, see: Rivera et al. (2004 ); Katritzky et al. (1990 ). For the use of nitriles in synthesis, see: Prasad & Bhalla (2010 ).

Experimental

Crystal data

C₈H₁₂N₄
M_r = 164.2
Monoclinic, P 2₁ /n
a = 11.1300 (6) Å
b = 6.3501 (3) Å
c = 13.1373 (7) Å
β = 102.066 (6)°
V = 907.99 (8) Å³
Z = 4
Cu Kα radiation
μ = 0.63 mm⁻¹
T = 120 K
0.16 × 0.09 × 0.01 mm

Data collection

Agilent Gemini Ultra diffractometer with an Atlas CCD detector
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010 ) T_min = 0.864, T_max = 1.000
2863 measured reflections
1404 independent reflections
929 reflections with I > 3σ(I)
R_int = 0.027

Refinement

R[F² > 2σ(F²)] = 0.039
wR(F²) = 0.093
S = 1.30
1404 reflections
109 parameters
H-atom parameters constrained
Δρ_max = 0.18 e Å⁻³
Δρ_min = −0.18 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C7—H7B⋯N4ⁱ	0.96	2.59	3.396 (3)	141
Symmetry code: (i) $[-x-{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

Data collection: CrysAlis PRO (Agilent, 2010); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SIR2002 (Burla et al., 2003 ); program(s) used to refine structure: JANA2006 (Petříček et al. 2006 ); molecular graphics: DIAMOND (Brandenburg & Putz, 2005 ); software used to prepare material for publication: JANA2006.

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536811038013/gk2401sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536811038013/gk2401Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536811038013/gk2401Isup3.cml

checkCIF report

Comment top

Nitriles are widely used starting materials and intermediates in organic synthesis. For instance, hydration of nitriles to corresponding carboxamides is an important reaction in nature and organic synthesis (Prasad & Bhalla, 2010). The title compound (I) was synthesized by one-step reaction between the macrocyclic aminal 1,3,7,9,13,15,19,21-octaazapentacyclo- [19.3.1.1^3,7.1^9,13.1^15,19]octacosane and hydrocyanic acid according to a methodology previously published (Rivera, et al. 2004). Single crystals of title compound were obtained by recrystallization from EtOH solution. An alternative synthetic method for the preparation of title compound involves the substitution of benzotriazolyl groups by cyano anion from the key benzotriazolyl intermediate 1,1'-(dihydropyrimidine-1,3(2H,4H)- diyldimethanediyl)-bis(1H-benzotriazole) (Katritzky et al., 1990)

The molecular structure and atom-numbering scheme for (I) are shown in Fig. 1. The cell dimensions of the title modification differ from the cell dimensions of the previously reported monoclinic P2₁/c modification: a = 8.303, b = 8.733, c = 12.998 Å; β = 107.73°, V = 897.7 Å³ (Shoja & Saba 1993). The bond lengths and angles are comparable with the previously reported polymorph.

In the crystal packing (Fig. 2) C—H··· N hydrogen bonds connect the molecules into a chain along the b axis. The C···N distances [3.396 (3) Å] is significantly shorter than the corresponding C···N distances in previously reported polymorph [3.518 (6) Å] (Shoja & Saba 1993), but the N···H distance in the title compound [2.59 Å] is longer than the corresponding N···H in mentionated polymorph [2.547 (18) Å].

Related literature top

For the original monoclinic polymorph, see: Shoja & Saba (1993). For the synthesis of the title compound, see: Rivera et al. (2004); Katritzky et al. (1990). For the use of nitriles in synthesis, see: Prasad & Bhalla (2010).

Experimental top

For the originally reported synthesis, see: Rivera et al. (2004). Single crystals of the title compound were obtained by recrystallization from EtOH solution (m.p. 340 K).

Structure description top

For the original monoclinic polymorph, see: Shoja & Saba (1993). For the synthesis of the title compound, see: Rivera et al. (2004); Katritzky et al. (1990). For the use of nitriles in synthesis, see: Prasad & Bhalla (2010).

Computing details top

Data collection: CrysAlis PRO (Agilent, 2010); cell refinement: CrysAlis PRO (Agilent, 2010); data reduction: CrysAlis PRO (Agilent, 2010); program(s) used to solve structure: SIR2002 (Burla et al., 2003); program(s) used to refine structure: JANA2006 (Petříček et al. 2006); molecular graphics: DIAMOND (Brandenburg & Putz, 2005); software used to prepare material for publication: JANA2006 (Petříček et al., 2006).

Figures top

	Fig. 1. A view of the title molecule. Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. Packing of the molecules of the title compound view along the b axis. Dashed lines represent intermolecular hydrogen bonds.

2,2'-(1,3-Diazinane-1,3-diyl)diacetonitrile top

Crystal data top

C₈H₁₂N₄	F(000) = 352
M_r = 164.2	D_x = 1.201 Mg m⁻³
Monoclinic, P2₁/n	Cu Kα radiation, λ = 1.5418 Å
Hall symbol: -P 2yn	Cell parameters from 1334 reflections
a = 11.1300 (6) Å	θ = 3.4–64.4°
b = 6.3501 (3) Å	µ = 0.63 mm⁻¹
c = 13.1373 (7) Å	T = 120 K
β = 102.066 (6)°	Plate, colourless
V = 907.99 (8) Å³	0.16 × 0.09 × 0.01 mm
Z = 4

Data collection top

Agilent Gemini Ultra diffractometer with an Atlas CCD detector	1404 independent reflections
Radiation source: Enhance Ultra (Cu) X-ray Source	929 reflections with I > 3σ(I)
Mirror monochromator	R_int = 0.027
Detector resolution: 10.3784 pixels mm^-1	θ_max = 64.6°, θ_min = 4.8°
Rotation method data acquisition using ω scans	h = −11→12
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010)	k = −7→3
T_min = 0.864, T_max = 1.000	l = −14→14
2863 measured reflections

Refinement top

Refinement on F²	48 constraints
R[F > 3σ(F)] = 0.039	H-atom parameters constrained
wR(F) = 0.093	Weighting scheme based on measured s.u.'s w = 1/[σ²(I) + 0.0009I²]
S = 1.30	(Δ/σ)_max = 0.001
1404 reflections	Δρ_max = 0.18 e Å⁻³
109 parameters	Δρ_min = −0.18 e Å⁻³
0 restraints

Crystal data top

C₈H₁₂N₄	V = 907.99 (8) Å³
M_r = 164.2	Z = 4
Monoclinic, P2₁/n	Cu Kα radiation
a = 11.1300 (6) Å	µ = 0.63 mm⁻¹
b = 6.3501 (3) Å	T = 120 K
c = 13.1373 (7) Å	0.16 × 0.09 × 0.01 mm
β = 102.066 (6)°

Data collection top

Agilent Gemini Ultra diffractometer with an Atlas CCD detector	1404 independent reflections
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010)	929 reflections with I > 3σ(I)
T_min = 0.864, T_max = 1.000	R_int = 0.027
2863 measured reflections

Refinement top

R[F > 3σ(F)] = 0.039	0 restraints
wR(F) = 0.093	H-atom parameters constrained
S = 1.30	Δρ_max = 0.18 e Å⁻³
1404 reflections	Δρ_min = −0.18 e Å⁻³
109 parameters

Special details top

Refinement. The refinement was carried out against all reflections. The conventional R-factor is always based on F. The goodness of fit as well as the weighted R-factor are based on F and F² for refinement carried out on F and F², respectively. The threshold expression is used only for calculating R-factors etc. and it is not relevant to the choice of reflections for refinement.

The program used for refinement, Jana2006, uses the weighting scheme based on the experimental expectations, see _refine_ls_weighting_details, that does not force S to be one. Therefore the values of S are usually larger than the ones from the SHELX program.

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

	x	y	z	U_iso*/U_eq
N1	0.24013 (14)	0.1540 (2)	0.84921 (11)	0.0221 (5)
N2	0.02686 (14)	0.1567 (2)	0.77670 (12)	0.0227 (5)
N3	0.38363 (17)	−0.2911 (3)	0.97150 (14)	0.0368 (7)
N4	−0.13683 (17)	−0.3109 (3)	0.77144 (15)	0.0432 (7)
C1	0.13764 (16)	0.0291 (3)	0.79354 (14)	0.0219 (6)
C2	0.22087 (19)	0.2149 (3)	0.95257 (15)	0.0283 (7)
C3	0.10159 (19)	0.3355 (3)	0.94117 (15)	0.0314 (7)
C4	−0.00483 (19)	0.2148 (3)	0.87606 (15)	0.0294 (7)
C5	0.35671 (17)	0.0485 (3)	0.85421 (15)	0.0266 (7)
C6	0.37333 (18)	−0.1454 (3)	0.91936 (16)	0.0268 (7)
C7	−0.07465 (18)	0.0560 (3)	0.70529 (16)	0.0276 (7)
C8	−0.11174 (18)	−0.1512 (4)	0.74169 (16)	0.0310 (7)
H1a	0.153761	−0.013785	0.727602	0.0263*
H1b	0.126995	−0.092437	0.834233	0.0263*
H2a	0.287763	0.302129	0.98659	0.034*
H2b	0.217385	0.090842	0.993595	0.034*
H3a	0.109451	0.46939	0.909275	0.0377*
H3b	0.084982	0.362397	1.008806	0.0377*
H4a	−0.019698	0.089559	0.912481	0.0353*
H4b	−0.076841	0.30205	0.86304	0.0353*
H5a	0.422653	0.144787	0.879563	0.0319*
H5b	0.365998	0.014494	0.785061	0.0319*
H7a	−0.053712	0.039324	0.638472	0.0331*
H7b	−0.144222	0.148886	0.692234	0.0331*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0246 (9)	0.0204 (9)	0.0211 (9)	−0.0003 (8)	0.0044 (7)	−0.0017 (7)
N2	0.0234 (9)	0.0233 (9)	0.0218 (9)	0.0035 (8)	0.0057 (7)	0.0005 (7)
N3	0.0429 (12)	0.0326 (11)	0.0332 (10)	0.0053 (9)	0.0042 (9)	0.0033 (9)
N4	0.0343 (11)	0.0396 (12)	0.0549 (13)	−0.0049 (10)	0.0077 (9)	0.0104 (10)
C1	0.0248 (11)	0.0193 (10)	0.0219 (11)	0.0011 (9)	0.0053 (8)	0.0011 (8)
C2	0.0384 (12)	0.0257 (11)	0.0197 (11)	−0.0001 (10)	0.0034 (9)	−0.0023 (9)
C3	0.0442 (13)	0.0262 (11)	0.0248 (11)	0.0079 (11)	0.0093 (9)	−0.0017 (9)
C4	0.0343 (12)	0.0300 (12)	0.0269 (11)	0.0078 (10)	0.0130 (9)	0.0039 (9)
C5	0.0266 (12)	0.0246 (11)	0.0287 (11)	−0.0008 (9)	0.0058 (9)	0.0017 (9)
C6	0.0250 (11)	0.0283 (12)	0.0261 (11)	0.0024 (10)	0.0029 (9)	−0.0041 (10)
C7	0.0270 (11)	0.0280 (11)	0.0268 (11)	−0.0002 (10)	0.0033 (9)	0.0045 (9)
C8	0.0228 (11)	0.0374 (13)	0.0318 (12)	−0.0002 (11)	0.0037 (9)	0.0034 (11)

Geometric parameters (Å, º) top

N1—C1	1.455 (2)	C2—H2b	0.96
N1—C2	1.470 (3)	C3—C4	1.516 (3)
N1—C5	1.450 (2)	C3—H3a	0.96
N2—C1	1.453 (2)	C3—H3b	0.96
N2—C4	1.469 (3)	C4—H4a	0.96
N2—C7	1.457 (2)	C4—H4b	0.96
N3—C6	1.143 (3)	C5—C6	1.489 (3)
N4—C8	1.142 (3)	C5—H5a	0.96
C1—H1a	0.96	C5—H5b	0.96
C1—H1b	0.96	C7—C8	1.487 (3)
C2—C3	1.513 (3)	C7—H7a	0.96
C2—H2a	0.96	C7—H7b	0.96

C1—N1—C2	110.95 (15)	C4—C3—H3b	109.4713
C1—N1—C5	111.79 (14)	H3a—C3—H3b	107.3996
C2—N1—C5	112.44 (14)	N2—C4—C3	108.91 (17)
C1—N2—C4	111.01 (14)	N2—C4—H4a	109.471
C1—N2—C7	111.87 (15)	N2—C4—H4b	109.4718
C4—N2—C7	112.62 (16)	C3—C4—H4a	109.4714
N1—C1—N2	108.89 (15)	C3—C4—H4b	109.4711
N1—C1—H1a	109.4708	H4a—C4—H4b	110.0256
N1—C1—H1b	109.4715	N1—C5—C6	114.25 (17)
N2—C1—H1a	109.4709	N1—C5—H5a	109.4711
N2—C1—H1b	109.472	N1—C5—H5b	109.4716
H1a—C1—H1b	110.0468	C6—C5—H5a	109.4711
N1—C2—C3	109.65 (15)	C6—C5—H5b	109.4712
N1—C2—H2a	109.4713	H5a—C5—H5b	104.2272
N1—C2—H2b	109.4713	N3—C6—C5	177.6 (2)
C3—C2—H2a	109.4712	N2—C7—C8	114.28 (16)
C3—C2—H2b	109.4706	N2—C7—H7a	109.4703
H2a—C2—H2b	109.2966	N2—C7—H7b	109.4712
C2—C3—C4	111.47 (17)	C8—C7—H7a	109.4713
C2—C3—H3a	109.4714	C8—C7—H7b	109.4717
C2—C3—H3b	109.4712	H7a—C7—H7b	104.193
C4—C3—H3a	109.471	N4—C8—C7	178.0 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C7—H7B···N4ⁱ	0.96	2.59	3.396 (3)	141

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

Experimental details

Crystal data
Chemical formula	C₈H₁₂N₄
M_r	164.2
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	120
a, b, c (Å)	11.1300 (6), 6.3501 (3), 13.1373 (7)
β (°)	102.066 (6)
V (Å³)	907.99 (8)
Z	4
Radiation type	Cu Kα
µ (mm⁻¹)	0.63
Crystal size (mm)	0.16 × 0.09 × 0.01

Data collection
Diffractometer	Agilent Gemini Ultra diffractometer with an Atlas CCD detector
Absorption correction	Multi-scan (CrysAlis PRO; Agilent, 2010)
T_min, T_max	0.864, 1.000
No. of measured, independent and observed [I > 3σ(I)] reflections	2863, 1404, 929
R_int	0.027
(sin θ/λ)_max (Å⁻¹)	0.586

Refinement
R[F > 3σ(F)], wR(F), S	0.039, 0.093, 1.30
No. of reflections	1404
No. of parameters	109
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.18, −0.18

Computer programs: CrysAlis PRO (Agilent, 2010), SIR2002 (Burla et al., 2003), JANA2006 (Petříček et al. 2006), DIAMOND (Brandenburg & Putz, 2005), JANA2006 (Petříček et al., 2006).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C7—H7B···N4ⁱ	0.96	2.59	3.396 (3)	141

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

Acknowledgements

We acknowledge the Dirección de Investigaciones, Sede Bogotá (DIB) de la Universidad Nacional de Colombia, for financial support of this work, as well as the Institutional research plan No. AVOZ10100521 of the Institute of Physics and the Praemium Academiae project of the Academy of Sciences of the Czech Republic.

References

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