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Acta Crystallogr Sect E Struct Rep Online. 2009 March 1; 65(Pt 3): o615.
Published online 2009 February 28. doi:  10.1107/S1600536809005388
PMCID: PMC2968495

Cyclo­hexa­nespiro-2′-[2′,3′,6′,7′-tetra­hydro-1′H-cyclo­penta­[d]pyrimidin]-4′(5′H)-one

Abstract

The title compound, C12H18N2O, was synthesized by the reaction of cyclo­hexa­none and 2-amino­cyclo­pent-1-enecarbonitrile. In the mol­ecule of the title compound, the six-carbon ring displays a chair conformation, the six-membered 1,3-diaza ring and the cyclo­pentene ring both assume envelope conformations. Supra­molecular aggregation is achieved by N—H(...)O hydrogen bonds.

Related literature

For general background on the biological activity of pyrimidinones, see: Schramm et al. (1984 [triangle]); Wen et al. (2002 [triangle]); For related structures, see: Yu et al. (1992 [triangle]); Zhang, Li, Shi et al. (2008 [triangle]); Zhang, Li, Yang et al. (2008 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-0o615-scheme1.jpg

Experimental

Crystal data

  • C12H18N2O
  • M r = 206.28
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-0o615-efi1.jpg
  • a = 10.294 (2) Å
  • b = 10.461 (2) Å
  • c = 10.659 (2) Å
  • β = 112.70 (3)°
  • V = 1059.0 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.08 mm−1
  • T = 113 K
  • 0.24 × 0.20 × 0.08 mm

Data collection

  • Rigaku Saturn diffractometer
  • Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2006 [triangle]) T min = 0.980, T max = 0.993
  • 6976 measured reflections
  • 1862 independent reflections
  • 1632 reflections with I > 2σ(I)
  • R int = 0.034

Refinement

  • R[F 2 > 2σ(F 2)] = 0.037
  • wR(F 2) = 0.103
  • S = 1.13
  • 1862 reflections
  • 144 parameters
  • 2 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.22 e Å−3
  • Δρmin = −0.22 e Å−3

Data collection: CrystalClear (Rigaku/MSC, 2006 [triangle]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809005388/pk2145sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809005388/pk2145Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

We thank the Beijing Institute of Technology for financial support.

supplementary crystallographic information

Comment

Pyrimidin-4(5H)-ones are valuable synthetic intermediates, and represent a common structure found in various biologically active compounds Schramm et al., 1984). Functionalization of the pyrimidin-4(5H)-one group offers an attractive method for the generation of derivatives which may constitute interesting medicinal and biological properties. For example, spiro[cyclohexane-1,2'(1'H)-quinazolin]-4'(3'H)-one shows immunosuppressive, antifungal, and antitumor activity (Wen et al., 2002).

Molecules of the title compound (Fig. 1) are linked by N1—H···O1 and N2—H···O1 H-bonds , as shown in Fig. 2 and have a similar conformation as (s)-2-(3-nitrophenyl)-1,2-dihydro-quinazolin-4(3H)-one (Zhang, Li & Shi et al., 2008). The 1,3-diaza ring assumes envelope conformation, similar to that found in 4(3H)-quinazolinone derivatives (Zhang, Li & Yang et al., 2008; Yu et al., 1992). The cyclopentene exists in an envelope formation, and cyclohexane displays a chair conformation.

Experimental

A solution of 2-aminocyclopent-1-enecarbonitrile (10 mmol, 1.08 g) and sodium methanolate (10 mmol, 0.54 g) in cyclohexanone (2 ml), was refluxed for 2 h. The reaction mixture was cooled to 293 K and kept at this temperature for an additional 12 h. The solvent was filtered in vacuo to give 2-cyclohexyl-2,3,6,7-tetrahydro-1H-cyclopenta[d]pyrimidin- 4(5H)-one. The product was recrystallizated from ethanol to give clearless crytals. M.p. 513–514 K; IR (KBr): 3201 (N—H), 3074, 2931 (C—H), 1707 (C=O) cm-1; 1H-NMR(DMSO, p.p.m.): 1.50 (6H, m), 1.74–1.81 (4H, m), 2.28 (2H, t), 2.38 (2H, t), 2.50 (2H, m), 6.57 (1H,s), 6.86 (1H, s). 50 mg of the product was dissolved in ethyl acetate (5 ml) and the solution was kept at room temperature for 4 days to give colorless single crystals.

Refinement

H atoms attached to C were included in calculated positions with a riding model (C—H distance = 0.97 Å), while the N—H hydrogens were refined with N—H distance restraints of 0.90 Å. Uiso values were set to 1.2Ueq of the carrier atom.

Figures

Fig. 1.
The molecular structure of the title compound, drawn with 30% probability ellipsoids.
Fig. 2.
The crystal structure of the title compound, viewed along a axis.

Crystal data

C12H18N2OF(000) = 448
Mr = 206.28Dx = 1.294 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 3035 reflections
a = 10.294 (2) Åθ = 2.8–27.8°
b = 10.461 (2) ŵ = 0.08 mm1
c = 10.659 (2) ÅT = 113 K
β = 112.70 (3)°Plate, colorless
V = 1059.0 (4) Å30.24 × 0.20 × 0.08 mm
Z = 4

Data collection

Rigaku Saturn diffractometer1862 independent reflections
Radiation source: rotating anode1632 reflections with I > 2σ(I)
confocal multilayer opticsRint = 0.034
Detector resolution: 14.63 pixels mm-1θmax = 25.0°, θmin = 2.8°
ω scansh = −12→12
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2006)k = −12→12
Tmin = 0.980, Tmax = 0.993l = −12→12
6976 measured reflections

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.103H atoms treated by a mixture of independent and constrained refinement
S = 1.13w = 1/[σ2(Fo2) + (0.058P)2 + 0.1813P] where P = (Fo2 + 2Fc2)/3
1862 reflections(Δ/σ)max < 0.001
144 parametersΔρmax = 0.22 e Å3
2 restraintsΔρmin = −0.22 e Å3

Special details

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)

xyzUiso*/Ueq
O1−0.14346 (9)0.42583 (8)0.02403 (9)0.0163 (2)
N10.08172 (11)0.34945 (10)0.09960 (11)0.0152 (3)
N20.16234 (11)0.18929 (10)0.26816 (11)0.0165 (3)
C1−0.05332 (13)0.34458 (11)0.09213 (13)0.0137 (3)
C2−0.08039 (13)0.24658 (11)0.17362 (13)0.0152 (3)
C3−0.21300 (13)0.22403 (12)0.19860 (14)0.0179 (3)
H3A−0.29190.20440.11470.021*
H3B−0.23640.29760.24120.021*
C4−0.17249 (14)0.10798 (13)0.29541 (15)0.0219 (3)
H4A−0.21580.11430.36140.026*
H4B−0.20310.02910.24470.026*
C5−0.01109 (13)0.11111 (13)0.36688 (14)0.0196 (3)
H5A0.01850.15580.45310.023*
H5B0.02820.02550.38200.023*
C60.03058 (13)0.18298 (11)0.26602 (13)0.0152 (3)
C70.17877 (12)0.24061 (11)0.14698 (13)0.0142 (3)
C80.14163 (13)0.13822 (12)0.03476 (14)0.0165 (3)
H8A0.04860.10450.01810.020*
H8B0.13860.1776−0.04870.020*
C90.24726 (14)0.02825 (12)0.07214 (14)0.0206 (3)
H9A0.2210−0.0323−0.00250.025*
H9B0.2451−0.01590.15130.025*
C100.39614 (13)0.07713 (13)0.10258 (15)0.0212 (3)
H10A0.46210.00640.13030.025*
H10B0.40070.11470.02120.025*
C110.43647 (13)0.17692 (13)0.21547 (14)0.0194 (3)
H11A0.52870.21120.22980.023*
H11B0.44220.13640.29930.023*
C120.32970 (12)0.28661 (12)0.18128 (14)0.0171 (3)
H12A0.35610.34450.25820.021*
H12B0.33330.33400.10450.021*
H10.1032 (15)0.4130 (12)0.0541 (14)0.025 (4)*
H20.2347 (13)0.1526 (15)0.3359 (14)0.034 (5)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0151 (5)0.0148 (4)0.0169 (5)0.0014 (4)0.0038 (4)0.0029 (4)
N10.0145 (6)0.0128 (5)0.0185 (6)−0.0001 (4)0.0066 (5)0.0035 (5)
N20.0131 (6)0.0219 (6)0.0142 (6)0.0028 (4)0.0050 (5)0.0048 (5)
C10.0142 (6)0.0128 (6)0.0121 (7)−0.0016 (5)0.0030 (5)−0.0031 (5)
C20.0147 (6)0.0144 (6)0.0171 (7)−0.0002 (5)0.0067 (5)0.0001 (5)
C30.0161 (6)0.0178 (6)0.0211 (7)−0.0003 (5)0.0087 (5)0.0006 (6)
C40.0209 (7)0.0242 (7)0.0239 (8)−0.0002 (6)0.0125 (6)0.0058 (6)
C50.0210 (7)0.0214 (7)0.0188 (8)0.0034 (6)0.0105 (6)0.0054 (6)
C60.0178 (7)0.0140 (6)0.0152 (7)−0.0009 (5)0.0080 (5)−0.0017 (5)
C70.0134 (6)0.0146 (6)0.0144 (7)0.0003 (5)0.0052 (5)0.0021 (5)
C80.0161 (7)0.0167 (6)0.0157 (7)−0.0015 (5)0.0052 (5)−0.0003 (5)
C90.0243 (7)0.0160 (6)0.0214 (8)0.0009 (5)0.0087 (6)−0.0021 (5)
C100.0208 (7)0.0234 (7)0.0219 (8)0.0052 (6)0.0110 (6)0.0003 (6)
C110.0134 (6)0.0256 (7)0.0197 (7)0.0017 (5)0.0068 (5)−0.0002 (6)
C120.0151 (7)0.0182 (6)0.0190 (7)−0.0021 (5)0.0076 (5)−0.0026 (5)

Geometric parameters (Å, °)

O1—C11.2612 (15)C5—H5B0.9700
N1—C11.3623 (16)C7—C121.5299 (17)
N1—C71.4698 (16)C7—C81.5399 (18)
N1—H10.899 (9)C8—C91.5265 (18)
N2—C61.3494 (17)C8—H8A0.9700
N2—C71.4676 (17)C8—H8B0.9700
N2—H20.899 (9)C9—C101.5271 (19)
C1—C21.4387 (17)C9—H9A0.9700
C2—C61.3599 (18)C9—H9B0.9700
C2—C31.5068 (17)C10—C111.5246 (19)
C3—C41.5429 (19)C10—H10A0.9700
C3—H3A0.9700C10—H10B0.9700
C3—H3B0.9700C11—C121.5324 (18)
C4—C51.5380 (19)C11—H11A0.9700
C4—H4A0.9700C11—H11B0.9700
C4—H4B0.9700C12—H12A0.9700
C5—C61.5036 (18)C12—H12B0.9700
C5—H5A0.9700
C1—N1—C7122.29 (10)N1—C7—C12109.36 (10)
C1—N1—H1117.0 (9)N2—C7—C8110.53 (10)
C7—N1—H1118.8 (9)N1—C7—C8109.86 (10)
C6—N2—C7117.35 (11)C12—C7—C8109.22 (10)
C6—N2—H2120.6 (11)C9—C8—C7112.53 (11)
C7—N2—H2121.4 (11)C9—C8—H8A109.1
O1—C1—N1121.07 (11)C7—C8—H8A109.1
O1—C1—C2123.83 (11)C9—C8—H8B109.1
N1—C1—C2114.98 (11)C7—C8—H8B109.1
C6—C2—C1118.79 (11)H8A—C8—H8B107.8
C6—C2—C3111.14 (11)C8—C9—C10111.01 (11)
C1—C2—C3128.16 (11)C8—C9—H9A109.4
C2—C3—C4102.23 (10)C10—C9—H9A109.4
C2—C3—H3A111.3C8—C9—H9B109.4
C4—C3—H3A111.3C10—C9—H9B109.4
C2—C3—H3B111.3H9A—C9—H9B108.0
C4—C3—H3B111.3C11—C10—C9110.02 (11)
H3A—C3—H3B109.2C11—C10—H10A109.7
C5—C4—C3106.03 (10)C9—C10—H10A109.7
C5—C4—H4A110.5C11—C10—H10B109.7
C3—C4—H4A110.5C9—C10—H10B109.7
C5—C4—H4B110.5H10A—C10—H10B108.2
C3—C4—H4B110.5C10—C11—C12111.91 (11)
H4A—C4—H4B108.7C10—C11—H11A109.2
C6—C5—C4102.01 (11)C12—C11—H11A109.2
C6—C5—H5A111.4C10—C11—H11B109.2
C4—C5—H5A111.4C12—C11—H11B109.2
C6—C5—H5B111.4H11A—C11—H11B107.9
C4—C5—H5B111.4C7—C12—C11112.98 (10)
H5A—C5—H5B109.2C7—C12—H12A109.0
N2—C6—C2123.11 (12)C11—C12—H12A109.0
N2—C6—C5125.07 (11)C7—C12—H12B109.0
C2—C6—C5111.77 (11)C11—C12—H12B109.0
N2—C7—N1106.97 (10)H12A—C12—H12B107.8
N2—C7—C12110.86 (11)
C7—N1—C1—O1−163.93 (11)C4—C5—C6—C216.59 (14)
C7—N1—C1—C219.87 (17)C6—N2—C7—N140.32 (14)
O1—C1—C2—C6−165.34 (12)C6—N2—C7—C12159.48 (11)
N1—C1—C2—C610.73 (17)C6—N2—C7—C8−79.26 (13)
O1—C1—C2—C3−2.6 (2)C1—N1—C7—N2−44.20 (15)
N1—C1—C2—C3173.52 (12)C1—N1—C7—C12−164.32 (11)
C6—C2—C3—C4−15.01 (14)C1—N1—C7—C875.81 (14)
C1—C2—C3—C4−178.87 (13)N2—C7—C8—C9−67.76 (13)
C2—C3—C4—C524.67 (14)N1—C7—C8—C9174.42 (10)
C3—C4—C5—C6−25.13 (14)C12—C7—C8—C954.46 (14)
C7—N2—C6—C2−15.31 (18)C7—C8—C9—C10−57.49 (15)
C7—N2—C6—C5167.51 (12)C8—C9—C10—C1156.57 (15)
C1—C2—C6—N2−12.96 (19)C9—C10—C11—C12−55.28 (15)
C3—C2—C6—N2−178.51 (11)N2—C7—C12—C1169.13 (14)
C1—C2—C6—C5164.56 (11)N1—C7—C12—C11−173.17 (11)
C3—C2—C6—C5−1.00 (15)C8—C7—C12—C11−52.91 (15)
C4—C5—C6—N2−165.96 (12)C10—C11—C12—C754.85 (15)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.90 (1)1.99 (1)2.8832 (14)170 (1)
N2—H2···O1ii0.90 (1)2.08 (1)2.9458 (17)161 (2)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: PK2145).

References

  • Rigaku/MSC (2006). CrystalClear Rigaku/MSC Inc., The Woodlands, Texas, USA.
  • Schramm, S., Schmitz, E. & Gruengemann, E. (1984). J. Prakt. Chem. (Leipzig), 326, 279–286.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Wen, H. J., Hao, W. Y. & Gong, B. Y. (2002). Zhongguo Kangshengsu ZaZhi, 27, 644–646.
  • Yu, M. J., McCowan, I. R., Mason, N. R., Deeter, J. B. & Mendelsohn, L. G. (1992). J. Med. Chem.35, 2543–2542. [PubMed]
  • Zhang, L., Li, J., Shi, D., Zhang, L. & Fan, Y. (2008). Acta Cryst. E64, o448. [PMC free article] [PubMed]
  • Zhang, L., Li, J., Yang, X., Shi, D. & Chen, J. (2008). Acta Cryst. E64, o450. [PMC free article] [PubMed]

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