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ISSN: 2056-9890

7′-Amino-1′H-spiro­[cyclo­heptane-1,2′-pyrimido[4,5-d]pyrimidin]-4′(3′H)-one

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

(Received 26 June 2012; accepted 10 July 2012; online 25 July 2012)

The title compound, C12H17N5O, was obtained by cyclo­condensation of 2,4-diamino­pyrimidine-5-carbonitrile with cyclo­hepta­none. The tetra­hydro­pyrimidine ring has a dis­torted boat conformation and the cyclo­heptane ring adopts a chair conformation. In the crystal, molecules are linked via N—H⋯O and N—H⋯N hydrogen bonds generating a three-dimensional network.

Related literature

For medicinal and biological properties of 2,3-dihydro­pyrimido[4,5-d]pyrimidin-4(1H)-one derivatives, see: Gebauer et al. (2003[Gebauer, M. G., Mckinlat, C. & Gready, J. E. (2003). Eur. J. Med. Chem. 38, 719-728.]); McDermott et al. (2006[McDermott, L. A., et al. (2006). Bioorg. Med. Chem. Lett. 16, 1950-1953.]). For a related structure, see: Shi et al. (2010[Shi, D., Yang, L., Tang, J., Wang, X. & Li, J. (2010). Acta Cryst. E66, o2301.]).

[Scheme 1]

Experimental

Crystal data
  • C12H17N5O

  • Mr = 247.31

  • Monoclinic, P 21 /n

  • a = 10.798 (3) Å

  • b = 10.365 (3) Å

  • c = 11.341 (3) Å

  • β = 110.287 (4)°

  • V = 1190.5 (6) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 153 K

  • 0.39 × 0.35 × 0.26 mm

Data collection
  • Rigaku AFC10/Saturn724+ diffractometer

  • 9163 measured reflections

  • 3450 independent reflections

  • 3237 reflections with I > 2σ(I)

  • Rint = 0.036

Refinement
  • R[F2 > 2σ(F2)] = 0.054

  • wR(F2) = 0.129

  • S = 1.00

  • 3450 reflections

  • 180 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.35 e Å−3

  • Δρmin = −0.22 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1N⋯O1i 0.88 (2) 2.05 (2) 2.9176 (16) 167 (2)
N2—H2N⋯O1ii 0.87 (2) 2.30 (2) 3.1587 (16) 168.3 (17)
N5—H0B⋯O1iii 0.84 (2) 2.22 (2) 2.9234 (17) 141.4 (19)
N5—H0A⋯N3iv 0.87 (2) 2.11 (2) 2.9826 (18) 172.5 (17)
Symmetry codes: (i) -x+1, -y, -z+1; (ii) [x+{\script{1\over 2}}, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]; (iii) [-x+{\script{3\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]; (iv) -x+2, -y+1, -z+1.

Data collection: CrystalClear (Rigaku/MSC, 2009[Rigaku/MSC (2009). CrystalClear and CrystalStructure. Rigaku/MSC, The Woodlands, Texas, USA.]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: CrystalStructure (Rigaku/MSC, 2009[Rigaku/MSC (2009). CrystalClear and CrystalStructure. Rigaku/MSC, The Woodlands, Texas, USA.]); software used to prepare material for publication: CrystalStructure.

Supporting information


Comment top

2,3-Dihydropyrimido[4,5-d]pyrimidin-4(1H)-ones constitute a class of fused heterocycles which possess anti-cancer (McDermott et al., 2006) and anti-bacterial activity (Gebauer et al., 2003). 2-Substituted 2,3-dihydropyrimido[4,5-d]pyrimidin-4(1H)-one derivatives can be obtained from the cyclocondensation of 2,4-diaminopyrimidine-5-carbonitrile with cycloheptanone. Here, we report the crystal structure of the title compound (Fig. 1).

The molecular structure (Fig. 1) is built up with two fused six-membered ring and one seven-membered ring linked through a spiro C atom. The hydropyrimidine ring has a distorted bath conformation, similar to that found in Spiro{cyclopentane-1,2'(1'H)pyrido [2',3'-d]pyrimidin-4'(3'H)-one} (Shi et al., 2010). The crystal packing is stabilized by intermolecular N–H···O hydrogen bonds between the two N–H groups and the ketone O atoms of the neighbouring molecules (Table 1).

Related literature top

For medicinal and biological properties of 2,3-dihydropyrimido[4,5-d]pyrimidin-4(1H)-one derivatives, see: Gebauer et al. (2003); McDermott et al. (2006). For a related structure, see: Shi et al. (2010).

Experimental top

A solution of 2,4-diaminopyrimidine-5-carbonitrile (2 mmol) and sodium methylate (2 mmol) was refluxed in cycloheptanone (3 ml) for 6 h. The reaction mixture was cooled to room temperature and then filtered to give the title compound. The product was recrystallizated from methanol to give light yellow crystalline powder.

Spectral data: IR (KBr): 3413, 3339, 3173, 2933, 1659, 1624, 1600, 1473, 1408 cm-1; 1H-NMR(DMSO,p.p.m.):1.57 (8H, s,CH), 1.79-1.90 (4H, m, CH), 6.60 (2H, s, NH2), 7.856 (1H, s, pyrimidine-NH), 7.865 (1H, s, pyrimidine-H), 8.168 (1H, s, NH-CO); ESI-MS m/z: [M+H]+ 248.1.

Structure description top

2,3-Dihydropyrimido[4,5-d]pyrimidin-4(1H)-ones constitute a class of fused heterocycles which possess anti-cancer (McDermott et al., 2006) and anti-bacterial activity (Gebauer et al., 2003). 2-Substituted 2,3-dihydropyrimido[4,5-d]pyrimidin-4(1H)-one derivatives can be obtained from the cyclocondensation of 2,4-diaminopyrimidine-5-carbonitrile with cycloheptanone. Here, we report the crystal structure of the title compound (Fig. 1).

The molecular structure (Fig. 1) is built up with two fused six-membered ring and one seven-membered ring linked through a spiro C atom. The hydropyrimidine ring has a distorted bath conformation, similar to that found in Spiro{cyclopentane-1,2'(1'H)pyrido [2',3'-d]pyrimidin-4'(3'H)-one} (Shi et al., 2010). The crystal packing is stabilized by intermolecular N–H···O hydrogen bonds between the two N–H groups and the ketone O atoms of the neighbouring molecules (Table 1).

For medicinal and biological properties of 2,3-dihydropyrimido[4,5-d]pyrimidin-4(1H)-one derivatives, see: Gebauer et al. (2003); McDermott et al. (2006). For a related structure, see: Shi et al. (2010).

Computing details top

Data collection: CrystalClear (Rigaku/MSC, 2009); cell refinement: CrystalClear (Rigaku/MSC, 2009); data reduction: CrystalClear (Rigaku/MSC, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: CrystalStructure (Rigaku/MSC, 2009); software used to prepare material for publication: CrystalStructure (Rigaku/MSC, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound with the atom numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.
7'-Amino-1'H-spiro[cycloheptane-1,2'-pyrimido[4,5-d]pyrimidin]- 4'(3'H)-one top
Crystal data top
C12H17N5OF(000) = 528
Mr = 247.31Dx = 1.380 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 10.798 (3) ÅCell parameters from 4105 reflections
b = 10.365 (3) Åθ = 2.0–30.0°
c = 11.341 (3) ŵ = 0.09 mm1
β = 110.287 (4)°T = 153 K
V = 1190.5 (6) Å3Block, colourless
Z = 40.39 × 0.35 × 0.26 mm
Data collection top
Rigaku AFC10/Saturn724+
diffractometer
3237 reflections with I > 2σ(I)
Radiation source: Rotating AnodeRint = 0.036
Graphite monochromatorθmax = 30.0°, θmin = 2.2°
Detector resolution: 28.5714 pixels mm-1h = 1515
phi and ω scansk = 1410
9163 measured reflectionsl = 915
3450 independent reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.054H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.129 w = 1/[σ2(Fo2) + (0.0495P)2 + 0.960P]
where P = (Fo2 + 2Fc2)/3
S = 1.00(Δ/σ)max < 0.001
3450 reflectionsΔρmax = 0.35 e Å3
180 parametersΔρmin = 0.21 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008)
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0058 (19)
Crystal data top
C12H17N5OV = 1190.5 (6) Å3
Mr = 247.31Z = 4
Monoclinic, P21/nMo Kα radiation
a = 10.798 (3) ŵ = 0.09 mm1
b = 10.365 (3) ÅT = 153 K
c = 11.341 (3) Å0.39 × 0.35 × 0.26 mm
β = 110.287 (4)°
Data collection top
Rigaku AFC10/Saturn724+
diffractometer
3237 reflections with I > 2σ(I)
9163 measured reflectionsRint = 0.036
3450 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0540 restraints
wR(F2) = 0.129H atoms treated by a mixture of independent and constrained refinement
S = 1.00Δρmax = 0.35 e Å3
3450 reflectionsΔρmin = 0.21 e Å3
180 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
xyzUiso*/Ueq
O10.50270 (10)0.09029 (10)0.36576 (9)0.0190 (2)
N10.59501 (11)0.15243 (11)0.56975 (10)0.0168 (2)
N20.76803 (11)0.30528 (12)0.63161 (10)0.0180 (2)
N30.83812 (11)0.40875 (11)0.48490 (10)0.0175 (2)
N40.71560 (11)0.38221 (12)0.26293 (10)0.0190 (2)
N50.90263 (12)0.50418 (13)0.33343 (12)0.0217 (3)
C10.55839 (13)0.36082 (13)0.65798 (12)0.0190 (3)
H1A0.60870.43800.69960.023*
H1B0.51150.38320.56870.023*
C20.45569 (14)0.33082 (16)0.71849 (13)0.0235 (3)
H2A0.43610.23720.71060.028*
H2B0.37300.37740.67230.028*
C30.50040 (16)0.36863 (18)0.85753 (14)0.0302 (4)
H3A0.52700.46050.86520.036*
H3B0.42390.36080.88610.036*
C40.61375 (15)0.29004 (18)0.94541 (13)0.0281 (3)
H4A0.58030.20280.95360.034*
H4B0.64210.33071.02960.034*
C50.73471 (14)0.27534 (16)0.90615 (12)0.0235 (3)
H5A0.80850.24030.97790.028*
H5B0.76150.36170.88620.028*
C60.71173 (14)0.18714 (14)0.79249 (12)0.0198 (3)
H6A0.64950.11820.79580.024*
H6B0.79660.14520.80020.024*
C70.65745 (12)0.25199 (13)0.66346 (11)0.0150 (2)
C80.57409 (12)0.16677 (13)0.44658 (12)0.0153 (2)
C90.64680 (12)0.27115 (13)0.41465 (12)0.0158 (2)
C100.75182 (12)0.33111 (13)0.51061 (12)0.0154 (2)
C110.81680 (12)0.42899 (13)0.36179 (12)0.0167 (3)
C120.63510 (13)0.30267 (13)0.29228 (12)0.0177 (3)
H120.56500.26480.22560.021*
H2N0.8326 (19)0.3443 (19)0.6896 (18)0.026 (5)*
H0A0.9754 (19)0.5290 (18)0.3921 (18)0.023 (4)*
H0B0.893 (2)0.514 (2)0.257 (2)0.033 (5)*
H1N0.557 (2)0.087 (2)0.593 (2)0.035 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0220 (5)0.0204 (5)0.0161 (4)0.0067 (4)0.0087 (4)0.0042 (3)
N10.0218 (5)0.0164 (5)0.0142 (5)0.0044 (4)0.0089 (4)0.0008 (4)
N20.0165 (5)0.0254 (6)0.0122 (5)0.0068 (4)0.0050 (4)0.0011 (4)
N30.0180 (5)0.0208 (6)0.0151 (5)0.0047 (4)0.0075 (4)0.0006 (4)
N40.0220 (5)0.0207 (6)0.0147 (5)0.0036 (4)0.0066 (4)0.0003 (4)
N50.0217 (6)0.0278 (6)0.0166 (5)0.0085 (5)0.0077 (4)0.0009 (5)
C10.0207 (6)0.0194 (6)0.0166 (6)0.0011 (5)0.0062 (5)0.0008 (5)
C20.0193 (6)0.0331 (8)0.0189 (6)0.0024 (5)0.0076 (5)0.0015 (5)
C30.0295 (7)0.0423 (10)0.0217 (7)0.0034 (7)0.0127 (6)0.0065 (6)
C40.0288 (7)0.0405 (9)0.0162 (6)0.0032 (6)0.0091 (5)0.0045 (6)
C50.0209 (6)0.0346 (8)0.0129 (6)0.0037 (5)0.0033 (5)0.0000 (5)
C60.0217 (6)0.0234 (7)0.0151 (6)0.0022 (5)0.0074 (5)0.0044 (5)
C70.0157 (5)0.0180 (6)0.0121 (5)0.0026 (4)0.0057 (4)0.0007 (4)
C80.0158 (5)0.0166 (6)0.0151 (5)0.0011 (4)0.0073 (4)0.0017 (4)
C90.0173 (5)0.0171 (6)0.0137 (5)0.0029 (4)0.0064 (4)0.0009 (4)
C100.0162 (5)0.0171 (6)0.0140 (5)0.0006 (4)0.0065 (4)0.0001 (4)
C110.0181 (6)0.0174 (6)0.0163 (6)0.0011 (4)0.0080 (5)0.0004 (4)
C120.0190 (6)0.0196 (6)0.0142 (5)0.0026 (5)0.0054 (4)0.0012 (4)
Geometric parameters (Å, º) top
O1—C81.2541 (16)C2—H2A0.9900
N1—C81.3437 (17)C2—H2B0.9900
N1—C71.4670 (16)C3—C41.520 (2)
N1—H1N0.88 (2)C3—H3A0.9900
N2—C101.3488 (17)C3—H3B0.9900
N2—C71.4698 (16)C4—C51.527 (2)
N2—H2N0.87 (2)C4—H4A0.9900
N3—C101.3376 (16)C4—H4B0.9900
N3—C111.3505 (17)C5—C61.529 (2)
N4—C121.3215 (17)C5—H5A0.9900
N4—C111.3552 (17)C5—H5B0.9900
N5—C111.3328 (17)C6—C71.5304 (18)
N5—H0A0.87 (2)C6—H6A0.9900
N5—H0B0.84 (2)C6—H6B0.9900
C1—C21.525 (2)C8—C91.4543 (18)
C1—C71.5408 (19)C9—C121.3883 (18)
C1—H1A0.9900C9—C101.4144 (17)
C1—H1B0.9900C12—H120.9500
C2—C31.531 (2)
C8—N1—C7123.01 (11)H4A—C4—H4B107.4
C8—N1—H1N118.1 (14)C4—C5—C6113.60 (12)
C7—N1—H1N118.0 (14)C4—C5—H5A108.8
C10—N2—C7119.65 (10)C6—C5—H5A108.8
C10—N2—H2N117.5 (13)C4—C5—H5B108.8
C7—N2—H2N119.5 (13)C6—C5—H5B108.8
C10—N3—C11115.90 (11)H5A—C5—H5B107.7
C12—N4—C11115.27 (11)C5—C6—C7116.11 (12)
C11—N5—H0A120.4 (12)C5—C6—H6A108.3
C11—N5—H0B118.1 (14)C7—C6—H6A108.3
H0A—N5—H0B120.3 (19)C5—C6—H6B108.3
C2—C1—C7115.82 (12)C7—C6—H6B108.3
C2—C1—H1A108.3H6A—C6—H6B107.4
C7—C1—H1A108.3N1—C7—N2107.14 (10)
C2—C1—H1B108.3N1—C7—C6108.14 (11)
C7—C1—H1B108.3N2—C7—C6109.00 (10)
H1A—C1—H1B107.4N1—C7—C1110.33 (10)
C1—C2—C3113.10 (12)N2—C7—C1109.07 (11)
C1—C2—H2A109.0C6—C7—C1112.98 (11)
C3—C2—H2A109.0O1—C8—N1121.95 (12)
C1—C2—H2B109.0O1—C8—C9122.43 (12)
C3—C2—H2B109.0N1—C8—C9115.49 (11)
H2A—C2—H2B107.8C12—C9—C10115.88 (12)
C4—C3—C2115.65 (13)C12—C9—C8123.65 (11)
C4—C3—H3A108.4C10—C9—C8119.55 (11)
C2—C3—H3A108.4N3—C10—N2119.12 (11)
C4—C3—H3B108.4N3—C10—C9122.00 (12)
C2—C3—H3B108.4N2—C10—C9118.83 (12)
H3A—C3—H3B107.4N5—C11—N3117.18 (12)
C3—C4—C5115.99 (13)N5—C11—N4115.99 (12)
C3—C4—H4A108.3N3—C11—N4126.82 (12)
C5—C4—H4A108.3N4—C12—C9123.97 (12)
C3—C4—H4B108.3N4—C12—H12118.0
C5—C4—H4B108.3C9—C12—H12118.0
C7—C1—C2—C390.57 (16)O1—C8—C9—C125.9 (2)
C1—C2—C3—C467.94 (19)N1—C8—C9—C12178.21 (12)
C2—C3—C4—C550.1 (2)O1—C8—C9—C10162.74 (13)
C3—C4—C5—C671.13 (19)N1—C8—C9—C1013.19 (18)
C4—C5—C6—C788.34 (16)C11—N3—C10—N2179.16 (12)
C8—N1—C7—N241.57 (16)C11—N3—C10—C91.64 (19)
C8—N1—C7—C6158.93 (12)C7—N2—C10—N3162.87 (12)
C8—N1—C7—C177.05 (15)C7—N2—C10—C919.52 (19)
C10—N2—C7—N142.90 (16)C12—C9—C10—N32.94 (19)
C10—N2—C7—C6159.69 (12)C8—C9—C10—N3166.53 (12)
C10—N2—C7—C176.53 (15)C12—C9—C10—N2179.53 (12)
C5—C6—C7—N1158.50 (11)C8—C9—C10—N211.01 (19)
C5—C6—C7—N285.34 (14)C10—N3—C11—N5178.86 (12)
C5—C6—C7—C136.09 (16)C10—N3—C11—N42.2 (2)
C2—C1—C7—N176.85 (14)C12—N4—C11—N5176.75 (13)
C2—C1—C7—N2165.72 (11)C12—N4—C11—N34.3 (2)
C2—C1—C7—C644.33 (15)C11—N4—C12—C92.6 (2)
C7—N1—C8—O1168.59 (12)C10—C9—C12—N40.7 (2)
C7—N1—C8—C915.46 (18)C8—C9—C12—N4168.33 (13)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N···O1i0.88 (2)2.05 (2)2.9176 (16)167 (2)
N2—H2N···O1ii0.87 (2)2.30 (2)3.1587 (16)168.3 (17)
N5—H0B···O1iii0.84 (2)2.22 (2)2.9234 (17)141.4 (19)
N5—H0A···N3iv0.87 (2)2.11 (2)2.9826 (18)172.5 (17)
Symmetry codes: (i) x+1, y, z+1; (ii) x+1/2, y+1/2, z+1/2; (iii) x+3/2, y+1/2, z+1/2; (iv) x+2, y+1, z+1.

Experimental details

Crystal data
Chemical formulaC12H17N5O
Mr247.31
Crystal system, space groupMonoclinic, P21/n
Temperature (K)153
a, b, c (Å)10.798 (3), 10.365 (3), 11.341 (3)
β (°) 110.287 (4)
V3)1190.5 (6)
Z4
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.39 × 0.35 × 0.26
Data collection
DiffractometerRigaku AFC10/Saturn724+
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
9163, 3450, 3237
Rint0.036
(sin θ/λ)max1)0.704
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.054, 0.129, 1.00
No. of reflections3450
No. of parameters180
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.35, 0.21

Computer programs: CrystalClear (Rigaku/MSC, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), CrystalStructure (Rigaku/MSC, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N···O1i0.88 (2)2.05 (2)2.9176 (16)167 (2)
N2—H2N···O1ii0.87 (2)2.30 (2)3.1587 (16)168.3 (17)
N5—H0B···O1iii0.84 (2)2.22 (2)2.9234 (17)141.4 (19)
N5—H0A···N3iv0.87 (2)2.11 (2)2.9826 (18)172.5 (17)
Symmetry codes: (i) x+1, y, z+1; (ii) x+1/2, y+1/2, z+1/2; (iii) x+3/2, y+1/2, z+1/2; (iv) x+2, y+1, z+1.
 

Acknowledgements

The authors thank Beijing Institute of Technology for the X-ray diffraction analysis.

References

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