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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 8| August 2012| Page o2440
https://doi.org/10.1107/S1600536812030796

1,3-Di­nitro­soimidazolidine

Augusto Rivera,a* Diego Quiroga,a Jaime Ríos-Motta,a Michal Dušekb and Karla Fejfarováb

aUniversidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Departamento de Química, Cra 30 No. 45-03, Bogotá, Código Postal 111321, 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 22 June 2012; accepted 5 July 2012; online 14 July 2012)

The title compound, C3H6N4O2, exhibits partial disorder with the refined occupancy ratios of the two components being 0.582 (5):0.418 (5). In the major component, the nitroso groups have a relative syn spatial arrangement [O=N⋯N=O pseudo-torsion angle = 1.1 (4)°], whereas the other component has an anti disposition [177.6 (1)°]. The N—N=O moieties are almost coplanar with a dihedral angle of 5.3 (3)°, while in the minor occupied set of atoms, this angle is 8 (1)°. In both components, the imidazolidine ring adopts a twisted conformation on the C—C bond and the crystal structure shows the strain of this ring according to the N—CH2—CH2—N torsion angles [25.9 (5) and −23.8 (7)°]. In the crystal, molecules are linked by weak C—H⋯O hydrogen bonds.

Related literature

For a related structure, see: Rivera et al. (2011[Rivera, A., Quiroga, D., Ríos-Motta, J., Fejfarová, K. & Dušek, M. (2011). Acta Cryst. C67, o505-o508.]). For the synthesis of the title compound, see: Rivera et al. (1997[Rivera, A., Gallo, G. I. & Joseph-Nathan, P. (1997). Synth. Commun. 27, 163-168.]). For ring conformations, see Cremer & Pople (1975[Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1358.]). For chemical background on the synthesis and uses of N-nitroso amines, see: Di Salvo et al. (2008[Di Salvo, F., Estrin, D. A., Leitus, G. & Doctorovich, F. (2008). Organometallics, 27, 1985-1995.]).

[Scheme 1]

Experimental

Crystal data

  • C3H6N4O2

  • Mr = 130.1

  • Orthorhombic, P n a 21

  • a = 9.5154 (2) Å

  • b = 5.4338 (1) Å

  • c = 10.7104 (2) Å

  • V = 553.78 (2) Å3

  • Z = 4

  • Cu Kα radiation

  • μ = 1.14 mm−1

  • T = 120 K

  • 0.39 × 0.20 × 0.14 mm
Data collection

  • Agilent Xcalibur diffractometer with an Atlas (Gemini Ultra Cu) detector

  • Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010[Agilent (2010). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England.]) Tmin = 0.636, Tmax = 1

  • 5160 measured reflections

  • 522 independent reflections

  • 514 reflections with I > 3σ(I)

  • Rint = 0.031
Refinement

  • R[F2 > 2σ(F2)] = 0.039

  • wR(F2) = 0.126

  • S = 2.86

  • 522 reflections

  • 87 parameters

  • H-atom parameters constrained

  • Δρmax = 0.12 e Å−3

  • Δρmin = −0.19 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C3y—H3ya⋯O1yi 0.96 1.85 2.681 (12) 143
Symmetry code: (i) x, y+1, z.

Data collection: CrysAlis PRO (Agilent, 2010[Agilent (2010). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SIR2002 (Burla et al., 2003[Burla, M. C., Camalli, M., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Polidori, G. & Spagna, R. (2003). J. Appl. Cryst. 36, 1103.]); program(s) used to refine structure: JANA2006 (Petříček et al., 2006[Petříček, V., Dušek, M. & Palatinus, L. (2006). JANA2006. Institute of Physics, Praha, Czech Republic.]); molecular graphics: DIAMOND (Brandenburg & Putz, 2005[Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact, Bonn, Germany.]); software used to prepare material for publication: JANA2006.

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536812030796/bt5956sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812030796/bt5956Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536812030796/bt5956Isup3.cml

checkCIF report


Comment top

N-nitrosamines are interesting molecules due their strong carcinogenic and mutagenic properties and their utility as synthetic intermediates for the preparation of various N,N-bonded functionalities (Di Salvo et al., 2008). Our group has previously explored the reaction of nitrous acid with cyclic aminals which actually are tertiary amines (Rivera et al., 1997, 2011). Earlier we reported the synthesis and complete characterization by NMR of the title compound 1,3-dinitrosoimidazolidine, obtained by the nitrosation reaction of the cyclic aminal 1,3,6,8-tetraazatricyclo[4.4.1.1.3,8]dodecane (Rivera et al., 1997). NMR experiments of this compound evidenced the existence of a mixture of three isomers: syn-cis, anti, and cis-trans with a ratio of 31:50:19 respectively (Rivera, et al. 1997). However, a recently investigation of (3aRS,7aRS)-1,3-dinitrosooctahydro-1H-benzimidazole, we found that the nitroso groups of this analogous X-ray crystal structure are on a syn-cis disposition (Rivera, et al. 2011). This result suggests that the orientation of the nitroso groups on the imidazolidine ring is largely influenced by their molecular skeletons. To identify the orientation of nitroso groups, we synthesized the title compound and investigated its crystal structure.

X-Ray analysis confirms the molecular structure and atom connectivity as illustrated in Fig. 1. The bond lengths N—C1 and N—NO are normal and comparable to the corresponding values observed in the related structure (Rivera, et al. 2011). The title compound are disordered over two sets of sites [site occupancies = 0.588 (6) and 0.412 (6)]. In both components, the N—N═O moieties are almost coplanar showing dihedral angles of 5.277 (340)° for the major component and 7.81 (97)° for the minor. The nitroso substituents in the major component are on a syn spatial arrangement as can be seen from O1x═N3x···N4═O2 pseudo torsion angle of = 1.119 (410)°, whereas the other component have an anti disposition [pseudo torsion angle O1y═N3y···N4═O2 = 177.662 (129)°] (Figure 2). Both imidazole ring system are twisted on CH2CH2 fragment as seen in the puckering parameters Q(2) = 0.255 (5) Å and φ2 = 122.7 (12)° for major component and Q(2) = 0.236 (8) Å and φ2 = 90.9 (16)° for minor component (Cremer & Pople, 1975). The crystal structure shows the strain of this ring according to the NCH2CH2N torsion angles [N1xC2xC3xN2x = 25.874 (534)° and N1yC2yC3yN2y = -23.808 (735)°].

The crystal packing displays a weak intermolecular C—H···O [C···O = 2.681 (12) Å] non-conventional hydrogen bonding interactions between oxygen atoms in the nitroso moiety and hydrogen atoms in methylene carbons of the heterocyclic ring (Figure 3).

Related literature top

For a related structure, see: Rivera et al. (2011). For the synthesis of the title compound, see: Rivera et al. (1997). For ring conformations, see Cremer & Pople (1975). For chemical background on the synthesis and uses of N-nitroso amines, see: Di Salvo et al. (2008).

Experimental top

For the originally reported synthesis, see: Rivera et al. (1997). Single crystals of the title compound were obtained by recrystallization from EtOH solution (m.p 318 K).

Refinement top

All hydrogen atoms were positioned geometrically and treated as riding on their parent atoms. The isotropic atomic displacement parameters of hydrogen atoms were set to 1.2×Ueq of the parent atom.

The molecule is disordered over two positions with occupancies 0.588 (6):0.412 (6). Selected atoms of both components were refined isotropically as anisotropic refinement lead to unreasonable ADPs.

As the structure contains only light atoms, the Friedel-pairs were merged and the Flack parameter has not been determined.

Structure description top

N-nitrosamines are interesting molecules due their strong carcinogenic and mutagenic properties and their utility as synthetic intermediates for the preparation of various N,N-bonded functionalities (Di Salvo et al., 2008). Our group has previously explored the reaction of nitrous acid with cyclic aminals which actually are tertiary amines (Rivera et al., 1997, 2011). Earlier we reported the synthesis and complete characterization by NMR of the title compound 1,3-dinitrosoimidazolidine, obtained by the nitrosation reaction of the cyclic aminal 1,3,6,8-tetraazatricyclo[4.4.1.1.3,8]dodecane (Rivera et al., 1997). NMR experiments of this compound evidenced the existence of a mixture of three isomers: syn-cis, anti, and cis-trans with a ratio of 31:50:19 respectively (Rivera, et al. 1997). However, a recently investigation of (3aRS,7aRS)-1,3-dinitrosooctahydro-1H-benzimidazole, we found that the nitroso groups of this analogous X-ray crystal structure are on a syn-cis disposition (Rivera, et al. 2011). This result suggests that the orientation of the nitroso groups on the imidazolidine ring is largely influenced by their molecular skeletons. To identify the orientation of nitroso groups, we synthesized the title compound and investigated its crystal structure.

X-Ray analysis confirms the molecular structure and atom connectivity as illustrated in Fig. 1. The bond lengths N—C1 and N—NO are normal and comparable to the corresponding values observed in the related structure (Rivera, et al. 2011). The title compound are disordered over two sets of sites [site occupancies = 0.588 (6) and 0.412 (6)]. In both components, the N—N═O moieties are almost coplanar showing dihedral angles of 5.277 (340)° for the major component and 7.81 (97)° for the minor. The nitroso substituents in the major component are on a syn spatial arrangement as can be seen from O1x═N3x···N4═O2 pseudo torsion angle of = 1.119 (410)°, whereas the other component have an anti disposition [pseudo torsion angle O1y═N3y···N4═O2 = 177.662 (129)°] (Figure 2). Both imidazole ring system are twisted on CH2CH2 fragment as seen in the puckering parameters Q(2) = 0.255 (5) Å and φ2 = 122.7 (12)° for major component and Q(2) = 0.236 (8) Å and φ2 = 90.9 (16)° for minor component (Cremer & Pople, 1975). The crystal structure shows the strain of this ring according to the NCH2CH2N torsion angles [N1xC2xC3xN2x = 25.874 (534)° and N1yC2yC3yN2y = -23.808 (735)°].

The crystal packing displays a weak intermolecular C—H···O [C···O = 2.681 (12) Å] non-conventional hydrogen bonding interactions between oxygen atoms in the nitroso moiety and hydrogen atoms in methylene carbons of the heterocyclic ring (Figure 3).

For a related structure, see: Rivera et al. (2011). For the synthesis of the title compound, see: Rivera et al. (1997). For ring conformations, see Cremer & Pople (1975). For chemical background on the synthesis and uses of N-nitroso amines, see: Di Salvo et al. (2008).

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
[Figure 1] Fig. 1. A view of the title compound with the numbering scheme. Only the major disordered component is shown. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. Overlapped structures of disordered components, showing structural differences.
[Figure 3] Fig. 3. The packing of the title compound, viewed along the a axis. The dashed lines indicate the hydrogen bonds. H atoms not involved in hydrogen bonding have been omitted for clarity.
1,3-Dinitrosoimidazolidine top
Crystal data top
C3H6N4O2F(000) = 272
Mr = 130.1Dx = 1.56 Mg m−3
Orthorhombic, Pna21Cu Kα radiation, λ = 1.5418 Å
Hall symbol: P 2c -2nCell parameters from 4445 reflections
a = 9.5154 (2) Åθ = 4.1–66.8°
b = 5.4338 (1) ŵ = 1.14 mm−1
c = 10.7104 (2) ÅT = 120 K
V = 553.78 (2) Å3Prism, colourless
Z = 40.39 × 0.20 × 0.14 mm
Data collection top
Agilent Xcalibur
diffractometer with an Atlas (Gemini Ultra Cu) detector		522 independent reflections
Radiation source: Enhance Ultra (Cu) X-ray Source514 reflections with I > 3σ(I)
Mirror monochromatorRint = 0.031
Detector resolution: 10.3784 pixels mm-1θmax = 67.0°, θmin = 9.2°
Rotation method data acquisition using ω scansh = −11→11
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2010)		k = −6→6
Tmin = 0.636, Tmax = 1l = −12→12
5160 measured reflections
Refinement top
Refinement on F286 constraints
R[F > 3σ(F)] = 0.039H-atom parameters constrained
wR(F) = 0.126Weighting scheme based on measured s.u.'s w = 1/(σ2(I) + 0.0016I2)
S = 2.86(Δ/σ)max = 0.013
522 reflectionsΔρmax = 0.12 e Å−3
87 parametersΔρmin = −0.19 e Å−3
0 restraints
Crystal data top
C3H6N4O2V = 553.78 (2) Å3
Mr = 130.1Z = 4
Orthorhombic, Pna21Cu Kα radiation
a = 9.5154 (2) ŵ = 1.14 mm−1
b = 5.4338 (1) ÅT = 120 K
c = 10.7104 (2) Å0.39 × 0.20 × 0.14 mm
Data collection top
Agilent Xcalibur
diffractometer with an Atlas (Gemini Ultra Cu) detector		522 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2010)		514 reflections with I > 3σ(I)
Tmin = 0.636, Tmax = 1Rint = 0.031
5160 measured reflections
Refinement top
R[F > 3σ(F)] = 0.0390 restraints
wR(F) = 0.126H-atom parameters constrained
S = 2.86Δρmax = 0.12 e Å−3
522 reflectionsΔρmin = −0.19 e Å−3
87 parameters
Special details top

Experimental. CrysAlisPro (Agilent Technologies, 2010) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

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
xyzUiso*/UeqOcc. (<1)
O1x0.3214 (4)−0.3809 (8)0.2669950.0436 (13)0.582 (5)
O20.0084 (2)0.3676 (5)0.3407 (6)0.0527 (8)
N1x0.2304 (5)−0.1122 (9)0.1438 (8)0.0333 (9)*0.582 (5)
N1y0.2125 (8)−0.1576 (12)0.1559 (9)0.0333 (9)*0.418 (5)
N2x0.0781 (4)0.1899 (8)0.1754 (7)0.0292 (8)*0.582 (5)
N2y0.1109 (6)0.2145 (12)0.1820 (9)0.0292 (8)*0.418 (5)
N3x0.3056 (5)−0.3111 (9)0.1569 (10)0.0342 (15)0.582 (5)
N3y0.2972 (18)−0.338 (3)0.2034 (16)0.063 (5)*0.418 (5)
O1y0.3425 (9)−0.4441 (19)0.1083 (12)0.081 (2)*0.418 (5)
N40.0159 (3)0.3748 (4)0.2258 (6)0.0469 (9)
C10.1576 (2)0.0075 (6)0.2498 (6)0.0348 (8)
C2x0.2145 (5)0.0048 (10)0.0225 (8)0.0369 (11)*0.582 (5)
C2y0.1820 (8)−0.0681 (14)0.0312 (9)0.0369 (11)*0.418 (5)
C3x0.0820 (5)0.1482 (9)0.0410 (8)0.0338 (13)0.582 (5)
C3y0.1527 (8)0.2091 (13)0.0512 (10)0.0338 (13)0.418 (5)
H2xa0.199648−0.11884−0.04010.0443*0.582 (5)
H2xb0.2912440.1161950.0087830.0443*0.582 (5)
H2ya0.098714−0.1469310.0002580.0443*0.418 (5)
H2yb0.263608−0.087618−0.0206010.0443*0.418 (5)
H3xa0.0893870.303307−0.00150.0406*0.582 (5)
H3xb0.002950.0493650.0167930.0406*0.582 (5)
H3ya0.238340.3002370.0407870.0406*0.418 (5)
H3yb0.0749380.258704−0.0000470.0406*0.418 (5)
H1ax0.2252360.0911480.3010890.0417*0.582 (5)
H1bx0.093385−0.1070210.287250.0417*0.582 (5)
H1ay0.2320110.0557140.305250.0417*0.418 (5)
H1by0.079178−0.0684410.290950.0417*0.418 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O1x0.0389 (19)0.053 (2)0.039 (3)0.0103 (15)−0.0008 (19)0.0147 (19)
O20.0448 (12)0.0675 (15)0.0458 (16)0.0025 (10)0.0059 (10)−0.0244 (11)
N3x0.031 (2)0.036 (2)0.036 (3)0.0200 (15)0.008 (2)0.002 (2)
N40.0526 (17)0.0417 (14)0.0463 (17)0.0098 (11)0.0081 (13)−0.0109 (11)
C10.0288 (13)0.0449 (14)0.0306 (14)0.0034 (9)−0.0021 (11)−0.0035 (11)
C3x0.038 (2)0.031 (2)0.033 (2)0.0003 (18)0.007 (2)0.0029 (16)
C3y0.038 (2)0.031 (2)0.033 (2)0.0003 (18)0.007 (2)0.0029 (16)
Geometric parameters (Å, º) top
O1x—N3x1.248 (10)N2y—C11.411 (9)
O2—N41.233 (9)N2y—C3y1.457 (14)
N1x—N3x1.303 (7)N3y—O1y1.25 (2)
N1x—C11.481 (9)C1—H1bx0.96
N1x—C2x1.454 (11)C1—H1ay0.96
N1y—N3y1.366 (17)C1—H1by0.96
N1y—C11.445 (10)C2x—C3x1.495 (7)
N1y—C2y1.451 (13)C2x—H2xa0.96
N2x—N41.285 (6)C2x—H2xb0.96
N2x—C11.480 (7)C2y—C3y1.547 (11)
N2x—C3x1.458 (12)C3x—H3xb0.96
N2y—N41.340 (8)C3y—H3yb0.96
N3x—N1x—C1122.6 (7)N1y—C1—H1ay109.4716
N3x—N1x—C2x121.0 (7)N1y—C1—H1by109.4714
C1—N1x—C2x116.4 (4)N2x—C1—H1bx109.4709
N3y—N1y—C1113.5 (10)N2y—C1—H1ay109.4711
N3y—N1y—C2y134.5 (10)N2y—C1—H1by109.4712
C1—N1y—C2y111.1 (6)N1x—C2x—C3x101.4 (6)
N4—N2x—C1122.2 (7)N1x—C2x—H2xa109.4711
N4—N2x—C3x123.2 (5)N1x—C2x—H2xb109.4713
C1—N2x—C3x114.5 (4)C3x—C2x—H2xa109.4718
N4—N2y—C1123.4 (8)C3x—C2x—H2xb109.4715
N4—N2y—C3y122.3 (7)H2xa—C2x—H2xb116.4713
C1—N2y—C3y113.1 (6)N1y—C2y—C3y103.6 (7)
O1x—N3x—N1x114.8 (8)N2x—C3x—C2x103.4 (6)
N1y—N3y—O1y103.4 (13)N2x—C3x—H3xb109.4711
O2—N4—N2x114.9 (5)C2x—C3x—H3xb109.4711
O2—N4—N2y111.6 (5)N2y—C3y—C2y101.7 (7)
N1x—C1—N2x96.9 (5)N2y—C3y—H3yb109.4711
N1x—C1—H1bx109.4713C2y—C3y—H3yb109.4709
N1y—C1—N2y104.5 (7)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2y—H2ya···O2i0.962.323.177 (10)148
C3y—H3ya···O1yii0.961.852.681 (12)143
Symmetry codes: (i) −x, −y, z−1/2; (ii) x, y+1, z.

Experimental details

Crystal data
Chemical formulaC3H6N4O2
Mr130.1
Crystal system, space groupOrthorhombic, Pna21
Temperature (K)120
a, b, c (Å)9.5154 (2), 5.4338 (1), 10.7104 (2)
V (Å3)553.78 (2)
Z4
Radiation typeCu Kα
µ (mm−1)1.14
Crystal size (mm)0.39 × 0.20 × 0.14
Data collection
DiffractometerAgilent Xcalibur
diffractometer with an Atlas (Gemini Ultra Cu) detector
Absorption correctionMulti-scan
(CrysAlis PRO; Agilent, 2010)
Tmin, Tmax0.636, 1
No. of measured, independent and
observed [I > 3σ(I)] reflections		5160, 522, 514
Rint0.031
(sin θ/λ)max (Å−1)0.597
Refinement
R[F > 3σ(F)], wR(F), S 0.039, 0.126, 2.86
No. of reflections522
No. of parameters87
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.12, −0.19

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

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C3y—H3ya···O1yi0.961.852.681 (12)142.69
Symmetry code: (i) x, y+1, z.
 

Acknowledgements

The authors acknowledge the Dirección de Investigaciones, Sede Bogotá (DIB) de la Universidad Nacional de Colombia for financial support of this work (grant No. 13066) and 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. DQ acknowledges the Vicerrectoría Académica de la Universidad Nacional de Colombia for a fellowship.

References

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 First citationRivera, A., Quiroga, D., Ríos-Motta, J., Fejfarová, K. & Dušek, M. (2011). Acta Cryst. C67, o505–o508.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar

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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 8| August 2012| Page o2440
https://doi.org/10.1107/S1600536812030796
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