organic compounds
1,3-Dinitrosoimidazolidine
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
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 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). 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 see: Di Salvo et al. (2008).
Experimental
Crystal data
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Refinement
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Data collection: CrysAlis PRO (Agilent, 2010); cell 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
https://doi.org/10.1107/S1600536812030796/bt5956sup1.cif
contains datablocks global, I. DOI: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
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).
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
lead to unreasonable ADPs.As the structure contains only light atoms, the Friedel-pairs were merged and the
has not been determined.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
which actually are tertiary (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 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 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
see: Di Salvo et al. (2008).Data collection: CrysAlis PRO (Agilent, 2010); cell
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).C3H6N4O2 | F(000) = 272 |
Mr = 130.1 | Dx = 1.56 Mg m−3 |
Orthorhombic, Pna21 | Cu Kα radiation, λ = 1.5418 Å |
Hall symbol: P 2c -2n | Cell parameters from 4445 reflections |
a = 9.5154 (2) Å | θ = 4.1–66.8° |
b = 5.4338 (1) Å | µ = 1.14 mm−1 |
c = 10.7104 (2) Å | T = 120 K |
V = 553.78 (2) Å3 | Prism, colourless |
Z = 4 | 0.39 × 0.20 × 0.14 mm |
Agilent Xcalibur diffractometer with an Atlas (Gemini Ultra Cu) detector | 522 independent reflections |
Radiation source: Enhance Ultra (Cu) X-ray Source | 514 reflections with I > 3σ(I) |
Mirror monochromator | Rint = 0.031 |
Detector resolution: 10.3784 pixels mm-1 | θmax = 67.0°, θmin = 9.2° |
Rotation method data acquisition using ω scans | h = −11→11 |
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010) | k = −6→6 |
Tmin = 0.636, Tmax = 1 | l = −12→12 |
5160 measured reflections |
Refinement on F2 | 86 constraints |
R[F > 3σ(F)] = 0.039 | H-atom parameters constrained |
wR(F) = 0.126 | Weighting scheme based on measured s.u.'s w = 1/(σ2(I) + 0.0016I2) |
S = 2.86 | (Δ/σ)max = 0.013 |
522 reflections | Δρmax = 0.12 e Å−3 |
87 parameters | Δρmin = −0.19 e Å−3 |
0 restraints |
C3H6N4O2 | V = 553.78 (2) Å3 |
Mr = 130.1 | Z = 4 |
Orthorhombic, Pna21 | Cu Kα radiation |
a = 9.5154 (2) Å | µ = 1.14 mm−1 |
b = 5.4338 (1) Å | T = 120 K |
c = 10.7104 (2) Å | 0.39 × 0.20 × 0.14 mm |
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 = 1 | Rint = 0.031 |
5160 measured reflections |
R[F > 3σ(F)] = 0.039 | 0 restraints |
wR(F) = 0.126 | H-atom parameters constrained |
S = 2.86 | Δρmax = 0.12 e Å−3 |
522 reflections | Δρmin = −0.19 e Å−3 |
87 parameters |
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. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
O1x | 0.3214 (4) | −0.3809 (8) | 0.266995 | 0.0436 (13) | 0.582 (5) |
O2 | 0.0084 (2) | 0.3676 (5) | 0.3407 (6) | 0.0527 (8) | |
N1x | 0.2304 (5) | −0.1122 (9) | 0.1438 (8) | 0.0333 (9)* | 0.582 (5) |
N1y | 0.2125 (8) | −0.1576 (12) | 0.1559 (9) | 0.0333 (9)* | 0.418 (5) |
N2x | 0.0781 (4) | 0.1899 (8) | 0.1754 (7) | 0.0292 (8)* | 0.582 (5) |
N2y | 0.1109 (6) | 0.2145 (12) | 0.1820 (9) | 0.0292 (8)* | 0.418 (5) |
N3x | 0.3056 (5) | −0.3111 (9) | 0.1569 (10) | 0.0342 (15) | 0.582 (5) |
N3y | 0.2972 (18) | −0.338 (3) | 0.2034 (16) | 0.063 (5)* | 0.418 (5) |
O1y | 0.3425 (9) | −0.4441 (19) | 0.1083 (12) | 0.081 (2)* | 0.418 (5) |
N4 | 0.0159 (3) | 0.3748 (4) | 0.2258 (6) | 0.0469 (9) | |
C1 | 0.1576 (2) | 0.0075 (6) | 0.2498 (6) | 0.0348 (8) | |
C2x | 0.2145 (5) | 0.0048 (10) | 0.0225 (8) | 0.0369 (11)* | 0.582 (5) |
C2y | 0.1820 (8) | −0.0681 (14) | 0.0312 (9) | 0.0369 (11)* | 0.418 (5) |
C3x | 0.0820 (5) | 0.1482 (9) | 0.0410 (8) | 0.0338 (13) | 0.582 (5) |
C3y | 0.1527 (8) | 0.2091 (13) | 0.0512 (10) | 0.0338 (13) | 0.418 (5) |
H2xa | 0.199648 | −0.11884 | −0.0401 | 0.0443* | 0.582 (5) |
H2xb | 0.291244 | 0.116195 | 0.008783 | 0.0443* | 0.582 (5) |
H2ya | 0.098714 | −0.146931 | 0.000258 | 0.0443* | 0.418 (5) |
H2yb | 0.263608 | −0.087618 | −0.020601 | 0.0443* | 0.418 (5) |
H3xa | 0.089387 | 0.303307 | −0.0015 | 0.0406* | 0.582 (5) |
H3xb | 0.00295 | 0.049365 | 0.016793 | 0.0406* | 0.582 (5) |
H3ya | 0.23834 | 0.300237 | 0.040787 | 0.0406* | 0.418 (5) |
H3yb | 0.074938 | 0.258704 | −0.000047 | 0.0406* | 0.418 (5) |
H1ax | 0.225236 | 0.091148 | 0.301089 | 0.0417* | 0.582 (5) |
H1bx | 0.093385 | −0.107021 | 0.28725 | 0.0417* | 0.582 (5) |
H1ay | 0.232011 | 0.055714 | 0.30525 | 0.0417* | 0.418 (5) |
H1by | 0.079178 | −0.068441 | 0.29095 | 0.0417* | 0.418 (5) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1x | 0.0389 (19) | 0.053 (2) | 0.039 (3) | 0.0103 (15) | −0.0008 (19) | 0.0147 (19) |
O2 | 0.0448 (12) | 0.0675 (15) | 0.0458 (16) | 0.0025 (10) | 0.0059 (10) | −0.0244 (11) |
N3x | 0.031 (2) | 0.036 (2) | 0.036 (3) | 0.0200 (15) | 0.008 (2) | 0.002 (2) |
N4 | 0.0526 (17) | 0.0417 (14) | 0.0463 (17) | 0.0098 (11) | 0.0081 (13) | −0.0109 (11) |
C1 | 0.0288 (13) | 0.0449 (14) | 0.0306 (14) | 0.0034 (9) | −0.0021 (11) | −0.0035 (11) |
C3x | 0.038 (2) | 0.031 (2) | 0.033 (2) | 0.0003 (18) | 0.007 (2) | 0.0029 (16) |
C3y | 0.038 (2) | 0.031 (2) | 0.033 (2) | 0.0003 (18) | 0.007 (2) | 0.0029 (16) |
O1x—N3x | 1.248 (10) | N2y—C1 | 1.411 (9) |
O2—N4 | 1.233 (9) | N2y—C3y | 1.457 (14) |
N1x—N3x | 1.303 (7) | N3y—O1y | 1.25 (2) |
N1x—C1 | 1.481 (9) | C1—H1bx | 0.96 |
N1x—C2x | 1.454 (11) | C1—H1ay | 0.96 |
N1y—N3y | 1.366 (17) | C1—H1by | 0.96 |
N1y—C1 | 1.445 (10) | C2x—C3x | 1.495 (7) |
N1y—C2y | 1.451 (13) | C2x—H2xa | 0.96 |
N2x—N4 | 1.285 (6) | C2x—H2xb | 0.96 |
N2x—C1 | 1.480 (7) | C2y—C3y | 1.547 (11) |
N2x—C3x | 1.458 (12) | C3x—H3xb | 0.96 |
N2y—N4 | 1.340 (8) | C3y—H3yb | 0.96 |
N3x—N1x—C1 | 122.6 (7) | N1y—C1—H1ay | 109.4716 |
N3x—N1x—C2x | 121.0 (7) | N1y—C1—H1by | 109.4714 |
C1—N1x—C2x | 116.4 (4) | N2x—C1—H1bx | 109.4709 |
N3y—N1y—C1 | 113.5 (10) | N2y—C1—H1ay | 109.4711 |
N3y—N1y—C2y | 134.5 (10) | N2y—C1—H1by | 109.4712 |
C1—N1y—C2y | 111.1 (6) | N1x—C2x—C3x | 101.4 (6) |
N4—N2x—C1 | 122.2 (7) | N1x—C2x—H2xa | 109.4711 |
N4—N2x—C3x | 123.2 (5) | N1x—C2x—H2xb | 109.4713 |
C1—N2x—C3x | 114.5 (4) | C3x—C2x—H2xa | 109.4718 |
N4—N2y—C1 | 123.4 (8) | C3x—C2x—H2xb | 109.4715 |
N4—N2y—C3y | 122.3 (7) | H2xa—C2x—H2xb | 116.4713 |
C1—N2y—C3y | 113.1 (6) | N1y—C2y—C3y | 103.6 (7) |
O1x—N3x—N1x | 114.8 (8) | N2x—C3x—C2x | 103.4 (6) |
N1y—N3y—O1y | 103.4 (13) | N2x—C3x—H3xb | 109.4711 |
O2—N4—N2x | 114.9 (5) | C2x—C3x—H3xb | 109.4711 |
O2—N4—N2y | 111.6 (5) | N2y—C3y—C2y | 101.7 (7) |
N1x—C1—N2x | 96.9 (5) | N2y—C3y—H3yb | 109.4711 |
N1x—C1—H1bx | 109.4713 | C2y—C3y—H3yb | 109.4709 |
N1y—C1—N2y | 104.5 (7) |
D—H···A | D—H | H···A | D···A | D—H···A |
C2y—H2ya···O2i | 0.96 | 2.32 | 3.177 (10) | 148 |
C3y—H3ya···O1yii | 0.96 | 1.85 | 2.681 (12) | 143 |
Symmetry codes: (i) −x, −y, z−1/2; (ii) x, y+1, z. |
Experimental details
Crystal data | |
Chemical formula | C3H6N4O2 |
Mr | 130.1 |
Crystal system, space group | Orthorhombic, Pna21 |
Temperature (K) | 120 |
a, b, c (Å) | 9.5154 (2), 5.4338 (1), 10.7104 (2) |
V (Å3) | 553.78 (2) |
Z | 4 |
Radiation type | Cu Kα |
µ (mm−1) | 1.14 |
Crystal size (mm) | 0.39 × 0.20 × 0.14 |
Data collection | |
Diffractometer | Agilent Xcalibur diffractometer with an Atlas (Gemini Ultra Cu) detector |
Absorption correction | Multi-scan (CrysAlis PRO; Agilent, 2010) |
Tmin, Tmax | 0.636, 1 |
No. of measured, independent and observed [I > 3σ(I)] reflections | 5160, 522, 514 |
Rint | 0.031 |
(sin θ/λ)max (Å−1) | 0.597 |
Refinement | |
R[F > 3σ(F)], wR(F), S | 0.039, 0.126, 2.86 |
No. of reflections | 522 |
No. of parameters | 87 |
H-atom treatment | H-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).
D—H···A | D—H | H···A | D···A | D—H···A |
C3y—H3ya···O1yi | 0.96 | 1.85 | 2.681 (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
Agilent (2010). CrysAlis PRO. Agilent Technologies, Yarnton, Oxfordshire, England. Google Scholar
Brandenburg, K. & Putz, H. (2005). DIAMOND. Crystal Impact, Bonn, Germany. Google Scholar
Burla, M. C., Camalli, M., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Polidori, G. & Spagna, R. (2003). J. Appl. Cryst. 36, 1103. CrossRef IUCr Journals Google Scholar
Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354–1358. CrossRef CAS Web of Science Google Scholar
Di Salvo, F., Estrin, D. A., Leitus, G. & Doctorovich, F. (2008). Organometallics, 27, 1985–1995. Web of Science CSD CrossRef CAS Google Scholar
Petříček, V., Dušek, M. & Palatinus, L. (2006). JANA2006. Institute of Physics, Praha, Czech Republic. Google Scholar
Rivera, A., Gallo, G. I. & Joseph-Nathan, P. (1997). Synth. Commun. 27, 163–168. CrossRef CAS Web of Science Google Scholar
Rivera, 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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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).