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

Shi, D.; Qian, D.; Zhang, Q.; Li, J.

doi:10.1107/S1600536809005388

organic compounds

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ISSN: 2056-9890

Volume 65| Part 3| March 2009| Page o615

doi:10.1107/S1600536809005388

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

Daxin Shi,^a Dongfeng Qian,^a Qi Zhang ^a and Jiarong Li ^a ^*

^aSchool of Chemical Engineering and Environment, Beijing Institue of Technology, Beijing 100081, People's Republic of China
^*Correspondence e-mail: shidaxin@bit.edu.cn

(Received 7 January 2009; accepted 15 February 2009; online 28 February 2009)

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 ); Wen et al. (2002 ); For related structures, see: Yu et al. (1992 ); Zhang, Li, Shi et al. (2008 ); Zhang, Li, Yang et al. (2008 ).

Experimental

Crystal data

C₁₂H₁₈N₂O
M_r = 206.28
Monoclinic, P 2₁ /n
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 ) 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[F² > 2σ(F²)] = 0.037
wR(F²) = 0.103
S = 1.13
1862 reflections
144 parameters
2 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.22 e Å⁻³
Δρ_min = −0.22 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O1ⁱ	0.899 (9)	1.993 (9)	2.8832 (14)	169.9 (14)
N2—H2⋯O1ⁱⁱ	0.899 (9)	2.080 (11)	2.9458 (17)	161.3 (15)
Symmetry codes: (i) -x, -y+1, -z; (ii) $[x+{\script{1\over 2}}, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ .

Data collection: CrystalClear (Rigaku/MSC, 2006); cell refinement: CrystalClear; data reduction: CrystalClear; 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 global, I. DOI: 10.1107/S1600536809005388/pk2145sup1.cif

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

checkCIF report

Comment top

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.

Related literature top

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

Experimental top

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.

Computing details top

Data collection: CrystalClear (Rigaku/MSC, 2006); cell refinement: CrystalClear (Rigaku/MSC, 2006); data reduction: CrystalClear (Rigaku/MSC, 2006); 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, drawn with 30% probability ellipsoids.
	Fig. 2. The crystal structure of the title compound, viewed along a axis.

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

Crystal data top

C₁₂H₁₈N₂O	F(000) = 448
M_r = 206.28	D_x = 1.294 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 3035 reflections
a = 10.294 (2) Å	θ = 2.8–27.8°
b = 10.461 (2) Å	µ = 0.08 mm⁻¹
c = 10.659 (2) Å	T = 113 K
β = 112.70 (3)°	Plate, colorless
V = 1059.0 (4) Å³	0.24 × 0.20 × 0.08 mm
Z = 4

Data collection top

Rigaku Saturn diffractometer	1862 independent reflections
Radiation source: rotating anode	1632 reflections with I > 2σ(I)
Confocal multilayer optics monochromator	R_int = 0.034
Detector resolution: 14.63 pixels mm^-1	θ_max = 25.0°, θ_min = 2.8°
ω scans	h = −12→12
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2006)	k = −12→12
T_min = 0.980, T_max = 0.993	l = −12→12
6976 measured reflections

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)] = 0.037	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.103	H atoms treated by a mixture of independent and constrained refinement
S = 1.13	w = 1/[σ²(F_o²) + (0.058P)² + 0.1813P] where P = (F_o² + 2F_c²)/3
1862 reflections	(Δ/σ)_max < 0.001
144 parameters	Δρ_max = 0.22 e Å⁻³
2 restraints	Δρ_min = −0.22 e Å⁻³

Crystal data top

C₁₂H₁₈N₂O	V = 1059.0 (4) Å³
M_r = 206.28	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 10.294 (2) Å	µ = 0.08 mm⁻¹
b = 10.461 (2) Å	T = 113 K
c = 10.659 (2) Å	0.24 × 0.20 × 0.08 mm
β = 112.70 (3)°

Data collection top

Rigaku Saturn diffractometer	1862 independent reflections
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2006)	1632 reflections with I > 2σ(I)
T_min = 0.980, T_max = 0.993	R_int = 0.034
6976 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.037	2 restraints
wR(F²) = 0.103	H atoms treated by a mixture of independent and constrained refinement
S = 1.13	Δρ_max = 0.22 e Å⁻³
1862 reflections	Δρ_min = −0.22 e Å⁻³
144 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
O1	−0.14346 (9)	0.42583 (8)	0.02403 (9)	0.0163 (2)
N1	0.08172 (11)	0.34945 (10)	0.09960 (11)	0.0152 (3)
N2	0.16234 (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	−0.2919	0.2044	0.1147	0.021*
H3B	−0.2364	0.2976	0.2412	0.021*
C4	−0.17249 (14)	0.10798 (13)	0.29541 (15)	0.0219 (3)
H4A	−0.2158	0.1143	0.3614	0.026*
H4B	−0.2031	0.0291	0.2447	0.026*
C5	−0.01109 (13)	0.11111 (13)	0.36688 (14)	0.0196 (3)
H5A	0.0185	0.1558	0.4531	0.023*
H5B	0.0282	0.0255	0.3820	0.023*
C6	0.03058 (13)	0.18298 (11)	0.26602 (13)	0.0152 (3)
C7	0.17877 (12)	0.24061 (11)	0.14698 (13)	0.0142 (3)
C8	0.14163 (13)	0.13822 (12)	0.03476 (14)	0.0165 (3)
H8A	0.0486	0.1045	0.0181	0.020*
H8B	0.1386	0.1776	−0.0487	0.020*
C9	0.24726 (14)	0.02825 (12)	0.07214 (14)	0.0206 (3)
H9A	0.2210	−0.0323	−0.0025	0.025*
H9B	0.2451	−0.0159	0.1513	0.025*
C10	0.39614 (13)	0.07713 (13)	0.10258 (15)	0.0212 (3)
H10A	0.4621	0.0064	0.1303	0.025*
H10B	0.4007	0.1147	0.0212	0.025*
C11	0.43647 (13)	0.17692 (13)	0.21547 (14)	0.0194 (3)
H11A	0.5287	0.2112	0.2298	0.023*
H11B	0.4422	0.1364	0.2993	0.023*
C12	0.32970 (12)	0.28661 (12)	0.18128 (14)	0.0171 (3)
H12A	0.3561	0.3445	0.2582	0.021*
H12B	0.3333	0.3340	0.1045	0.021*
H1	0.1032 (15)	0.4130 (12)	0.0541 (14)	0.025 (4)*
H2	0.2347 (13)	0.1526 (15)	0.3359 (14)	0.034 (5)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0151 (5)	0.0148 (4)	0.0169 (5)	0.0014 (4)	0.0038 (4)	0.0029 (4)
N1	0.0145 (6)	0.0128 (5)	0.0185 (6)	−0.0001 (4)	0.0066 (5)	0.0035 (5)
N2	0.0131 (6)	0.0219 (6)	0.0142 (6)	0.0028 (4)	0.0050 (5)	0.0048 (5)
C1	0.0142 (6)	0.0128 (6)	0.0121 (7)	−0.0016 (5)	0.0030 (5)	−0.0031 (5)
C2	0.0147 (6)	0.0144 (6)	0.0171 (7)	−0.0002 (5)	0.0067 (5)	0.0001 (5)
C3	0.0161 (6)	0.0178 (6)	0.0211 (7)	−0.0003 (5)	0.0087 (5)	0.0006 (6)
C4	0.0209 (7)	0.0242 (7)	0.0239 (8)	−0.0002 (6)	0.0125 (6)	0.0058 (6)
C5	0.0210 (7)	0.0214 (7)	0.0188 (8)	0.0034 (6)	0.0105 (6)	0.0054 (6)
C6	0.0178 (7)	0.0140 (6)	0.0152 (7)	−0.0009 (5)	0.0080 (5)	−0.0017 (5)
C7	0.0134 (6)	0.0146 (6)	0.0144 (7)	0.0003 (5)	0.0052 (5)	0.0021 (5)
C8	0.0161 (7)	0.0167 (6)	0.0157 (7)	−0.0015 (5)	0.0052 (5)	−0.0003 (5)
C9	0.0243 (7)	0.0160 (6)	0.0214 (8)	0.0009 (5)	0.0087 (6)	−0.0021 (5)
C10	0.0208 (7)	0.0234 (7)	0.0219 (8)	0.0052 (6)	0.0110 (6)	0.0003 (6)
C11	0.0134 (6)	0.0256 (7)	0.0197 (7)	0.0017 (5)	0.0068 (5)	−0.0002 (6)
C12	0.0151 (7)	0.0182 (6)	0.0190 (7)	−0.0021 (5)	0.0076 (5)	−0.0026 (5)

Geometric parameters (Å, º) top

O1—C1	1.2612 (15)	C5—H5B	0.9700
N1—C1	1.3623 (16)	C7—C12	1.5299 (17)
N1—C7	1.4698 (16)	C7—C8	1.5399 (18)
N1—H1	0.899 (9)	C8—C9	1.5265 (18)
N2—C6	1.3494 (17)	C8—H8A	0.9700
N2—C7	1.4676 (17)	C8—H8B	0.9700
N2—H2	0.899 (9)	C9—C10	1.5271 (19)
C1—C2	1.4387 (17)	C9—H9A	0.9700
C2—C6	1.3599 (18)	C9—H9B	0.9700
C2—C3	1.5068 (17)	C10—C11	1.5246 (19)
C3—C4	1.5429 (19)	C10—H10A	0.9700
C3—H3A	0.9700	C10—H10B	0.9700
C3—H3B	0.9700	C11—C12	1.5324 (18)
C4—C5	1.5380 (19)	C11—H11A	0.9700
C4—H4A	0.9700	C11—H11B	0.9700
C4—H4B	0.9700	C12—H12A	0.9700
C5—C6	1.5036 (18)	C12—H12B	0.9700
C5—H5A	0.9700

C1—N1—C7	122.29 (10)	N1—C7—C12	109.36 (10)
C1—N1—H1	117.0 (9)	N2—C7—C8	110.53 (10)
C7—N1—H1	118.8 (9)	N1—C7—C8	109.86 (10)
C6—N2—C7	117.35 (11)	C12—C7—C8	109.22 (10)
C6—N2—H2	120.6 (11)	C9—C8—C7	112.53 (11)
C7—N2—H2	121.4 (11)	C9—C8—H8A	109.1
O1—C1—N1	121.07 (11)	C7—C8—H8A	109.1
O1—C1—C2	123.83 (11)	C9—C8—H8B	109.1
N1—C1—C2	114.98 (11)	C7—C8—H8B	109.1
C6—C2—C1	118.79 (11)	H8A—C8—H8B	107.8
C6—C2—C3	111.14 (11)	C8—C9—C10	111.01 (11)
C1—C2—C3	128.16 (11)	C8—C9—H9A	109.4
C2—C3—C4	102.23 (10)	C10—C9—H9A	109.4
C2—C3—H3A	111.3	C8—C9—H9B	109.4
C4—C3—H3A	111.3	C10—C9—H9B	109.4
C2—C3—H3B	111.3	H9A—C9—H9B	108.0
C4—C3—H3B	111.3	C11—C10—C9	110.02 (11)
H3A—C3—H3B	109.2	C11—C10—H10A	109.7
C5—C4—C3	106.03 (10)	C9—C10—H10A	109.7
C5—C4—H4A	110.5	C11—C10—H10B	109.7
C3—C4—H4A	110.5	C9—C10—H10B	109.7
C5—C4—H4B	110.5	H10A—C10—H10B	108.2
C3—C4—H4B	110.5	C10—C11—C12	111.91 (11)
H4A—C4—H4B	108.7	C10—C11—H11A	109.2
C6—C5—C4	102.01 (11)	C12—C11—H11A	109.2
C6—C5—H5A	111.4	C10—C11—H11B	109.2
C4—C5—H5A	111.4	C12—C11—H11B	109.2
C6—C5—H5B	111.4	H11A—C11—H11B	107.9
C4—C5—H5B	111.4	C7—C12—C11	112.98 (10)
H5A—C5—H5B	109.2	C7—C12—H12A	109.0
N2—C6—C2	123.11 (12)	C11—C12—H12A	109.0
N2—C6—C5	125.07 (11)	C7—C12—H12B	109.0
C2—C6—C5	111.77 (11)	C11—C12—H12B	109.0
N2—C7—N1	106.97 (10)	H12A—C12—H12B	107.8
N2—C7—C12	110.86 (11)

C7—N1—C1—O1	−163.93 (11)	C4—C5—C6—C2	16.59 (14)
C7—N1—C1—C2	19.87 (17)	C6—N2—C7—N1	40.32 (14)
O1—C1—C2—C6	−165.34 (12)	C6—N2—C7—C12	159.48 (11)
N1—C1—C2—C6	10.73 (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—C3	173.52 (12)	C1—N1—C7—C12	−164.32 (11)
C6—C2—C3—C4	−15.01 (14)	C1—N1—C7—C8	75.81 (14)
C1—C2—C3—C4	−178.87 (13)	N2—C7—C8—C9	−67.76 (13)
C2—C3—C4—C5	24.67 (14)	N1—C7—C8—C9	174.42 (10)
C3—C4—C5—C6	−25.13 (14)	C12—C7—C8—C9	54.46 (14)
C7—N2—C6—C2	−15.31 (18)	C7—C8—C9—C10	−57.49 (15)
C7—N2—C6—C5	167.51 (12)	C8—C9—C10—C11	56.57 (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—C11	69.13 (14)
C1—C2—C6—C5	164.56 (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—C7	54.85 (15)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1ⁱ	0.90 (1)	1.99 (1)	2.8832 (14)	170 (1)
N2—H2···O1ⁱⁱ	0.90 (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.

Experimental details

Crystal data
Chemical formula	C₁₂H₁₈N₂O
M_r	206.28
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	113
a, b, c (Å)	10.294 (2), 10.461 (2), 10.659 (2)
β (°)	112.70 (3)
V (Å³)	1059.0 (4)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.08
Crystal size (mm)	0.24 × 0.20 × 0.08

Data collection
Diffractometer	Rigaku Saturn diffractometer
Absorption correction	Multi-scan (CrystalClear; Rigaku/MSC, 2006)
T_min, T_max	0.980, 0.993
No. of measured, independent and observed [I > 2σ(I)] reflections	6976, 1862, 1632
R_int	0.034
(sin θ/λ)_max (Å⁻¹)	0.595

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.037, 0.103, 1.13
No. of reflections	1862
No. of parameters	144
No. of restraints	2
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.22, −0.22

Computer programs: CrystalClear (Rigaku/MSC, 2006), 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
N1—H1···O1ⁱ	0.899 (9)	1.993 (9)	2.8832 (14)	169.9 (14)
N2—H2···O1ⁱⁱ	0.899 (9)	2.080 (11)	2.9458 (17)	161.3 (15)

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

Acknowledgements

We thank the Beijing Institute of Technology for financial support.

References

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ISSN: 2056-9890

Volume 65| Part 3| March 2009| Page o615

doi:10.1107/S1600536809005388

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

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

Related literature

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds

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