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Acta Crystallogr Sect E Struct Rep Online. 2010 September 1; 66(Pt 9): o2301.
Published online 2010 August 18. doi:  10.1107/S1600536810027479
PMCID: PMC3008029

Spiro­[cyclo­pentane-1,2′(1′H)-pyrido[2,3-d]pyrimidin]-4′(3′H)-one

Abstract

The title compound, C11H13N2O, was obtained by cyclo­condensation of 2-amino­pyridine-3-carbonitrile with cyclo­penta­none. The mol­ecule is built up from two fused six-membered rings and one five-membered ring linked through a spiro C atom. Both the pyrimidine and the cyclo­pentane rings adopt envelope conformations. In the crystal structure, mol­ecules are linked by inter­molecular N—H(...)O hydrogen bonds.

Related literature

Many compounds containing the pyrido[2,3-d]pyrimidine scaffold show pharmacological properties such as anti­tumor (Gangjee et al., 1996 [triangle]), analgesic (Cordeu et al., 2007 [triangle]) and anti­bacterial (Robins & Hitchings, 1958 [triangle]) activities. 2-Substituted 2,3-dihydro­pyrido[2,3-d]pyrimidin-4(1H)-one derivatives can be obtained by a Friedlander quinoline condensation, see: Li et al. (2008 [triangle]). For a related structure, see: Zhang et al. (2008 [triangle]). For our previous work, see: Li et al. (2009 [triangle]); Ma et al. (2006 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o2301-scheme1.jpg

Experimental

Crystal data

  • C11H13N3O
  • M r = 203.24
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2301-efi5.jpg
  • a = 10.400 (1) Å
  • b = 12.1650 (15) Å
  • c = 15.370 (2) Å
  • V = 1944.6 (4) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.09 mm−1
  • T = 113 K
  • 0.32 × 0.30 × 0.28 mm

Data collection

  • Rigaku Saturn724 CCD diffractometer
  • Absorption correction: multi-scan (Crystal Clear-SM Expert; Rigaku/MSC, 2009 [triangle]) T min = 0.971, T max = 0.974
  • 21571 measured reflections
  • 2314 independent reflections
  • 2168 reflections with I > 2σ(I)
  • R int = 0.037

Refinement

  • R[F 2 > 2σ(F 2)] = 0.040
  • wR(F 2) = 0.103
  • S = 1.05
  • 2314 reflections
  • 144 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.40 e Å−3
  • Δρmin = −0.20 e Å−3

Data collection: Crystal Clear-SM Expert (Rigaku/MSC, 2009 [triangle]); cell refinement: Crystal Clear-SM Expert; data reduction: Crystal Clear-SM Expert; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: CrystalStructure (Rigaku/MSC, 2009 [triangle]); software used to prepare material for publication: CrystalStructure.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810027479/lx2156sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810027479/lx2156Isup2.hkl

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

Acknowledgments

We thank Beijing Institute of Technology for financial support and Naikai University for the X-ray diffraction analysis.

supplementary crystallographic information

Comment

Many compounds containing pyrido[2,3-d]pyrimidine scaffold show interesting pharmacological properties such as antitumor (Gangjee et al., 1996), analgesic (Cordeu et al., 2007) and antibacterial (Robins et al., 1958) activities. 2-Substituted 2,3-dihydropyrido[2,3-d]pyrimidin-4(1H)-one derivatives can be obtained from the new conversion (PDF) existing in the normal Friedlander quinoline condensation (Li et al., 2008). 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 five-membered ring linked through a spiro C atom. The pyrimidine ring has an envelope conformation with a mean deviation of 0.1321 Å from the plane and N3 at the flap. The five-membered ring also displays an envelope conformation with a mean deviation of 0.1633 Å from the plane and atom C8 at the flap position. The geometry of the fused rings compares well with the related spiro[cyclopentane-1,2'(1'H)-quinazolin-4'(3'H)-one] (Zhang et al., 2008). The crystal packing (Fig. 2) 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).

Experimental

A solution of 2-amino-3-cyanopyridine (2 mmol) and sodium methylate (0.6 mmol) was refluxed in cyclopentanone (3 ml) for 1.5 h. The reaction mixture was cooled to room temperature and then filtered to give the title compound. The product was recrystallizated from a mixed solvent (ethanol:THF/1:1)to give colorless crystalline powder. M.p. 527–528 K. Spectral data: IR (KBr): 3271, 3168, 2922, 1644, 1600, 1420 cm-1; 1H NMR (DMSO,p.p.m.): 1.67–1.83 (8H, s, C4H8), 6.65–3.69 (1H, m, J = 12 Hz, ArH), 7.61 (1H, s, NH), 7.85–7.88 (1H, d, J = 7.2 Hz, ArH), 8.127(1H, s, NH), 8.305 (1H, s, ArH); ESI-MS m/z: [M+H]+ 204.1, [M+Na]+ 226.1; C11H13N3O:calcd. C 65.01, H 6.45, N 20.68; found C 65.06, H 6.47, N 20.50.

Refinement

C—H were included in the riding model approximation with C—H distances 0.95–0.99 Å, and with Uiso(H)=1.2Ueq(C) or 1.5Ueq(C)(methyl). H atoms of NH group were located in difference Fourrier maps with N—H distances 0.891–0.901 Å with Uiso(H)=1.2Ueq(N).

Figures

Fig. 1.
The molecular structure of the title compound with the atom numbering scheme. Displacement ellipsoids are drawn at the 30% probability level. H atoms are presented as a small cycles of arbitrary radius.
Fig. 2.
N—H···O interactions (dotted lines) in the crystal structure of the title compound. [Symmetry codes: (i) - x + 3/2, y +1/2, z; (ii) - x + 1, - y + 1, - z + 1; (iii) - x + 3/2, y - 1/2 , z.]

Crystal data

C11H13N3OF(000) = 864
Mr = 203.24Dx = 1.388 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71075 Å
Hall symbol: -P 2ac 2abCell parameters from 9441 reflections
a = 10.400 (1) Åθ = 1.3–35.6°
b = 12.1650 (15) ŵ = 0.09 mm1
c = 15.370 (2) ÅT = 113 K
V = 1944.6 (4) Å3Block, colorless
Z = 80.32 × 0.30 × 0.28 mm

Data collection

Rigaku Saturn724 CCD diffractometer2314 independent reflections
Radiation source: rotating anode2168 reflections with I > 2σ(I)
graphite multilayerRint = 0.037
Detector resolution: 14.222 pixels mm-1θmax = 27.9°, θmin = 2.7°
ω scansh = −13→13
Absorption correction: multi-scan (CrystalClear-SM Expert; Rigaku/MSC, 2009)k = −16→15
Tmin = 0.971, Tmax = 0.974l = −20→20
21571 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)] = 0.040Hydrogen site location: difference Fourier map
wR(F2) = 0.103H atoms treated by a mixture of independent and constrained refinement
S = 1.05w = 1/[σ2(Fo2) + (0.0569P)2 + 0.6834P] where P = (Fo2 + 2Fc2)/3
2314 reflections(Δ/σ)max < 0.001
144 parametersΔρmax = 0.40 e Å3
0 restraintsΔρmin = −0.20 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
O10.59391 (7)0.42006 (6)0.57792 (5)0.01563 (19)
N10.94264 (9)0.63850 (8)0.68372 (6)0.0171 (2)
N20.80796 (9)0.69549 (8)0.57226 (6)0.0155 (2)
N30.64694 (9)0.58137 (7)0.51402 (6)0.0146 (2)
C10.84778 (10)0.61467 (9)0.62723 (7)0.0137 (2)
C20.78414 (10)0.51204 (9)0.62574 (7)0.0137 (2)
C30.82323 (11)0.43170 (9)0.68436 (7)0.0164 (2)
H30.78180.36210.68550.020*
C40.92347 (11)0.45420 (9)0.74123 (7)0.0185 (2)
H40.95390.40010.78080.022*
C50.97766 (11)0.55837 (9)0.73836 (7)0.0184 (2)
H51.04490.57400.77830.022*
C60.66943 (10)0.49939 (9)0.57020 (7)0.0130 (2)
C70.74197 (10)0.66576 (8)0.49201 (7)0.0134 (2)
C80.83702 (11)0.62728 (9)0.42121 (7)0.0168 (2)
H8A0.90650.58180.44650.020*
H8B0.79240.58450.37550.020*
C90.88986 (11)0.73498 (9)0.38493 (7)0.0193 (2)
H9A0.92650.72420.32610.023*
H9B0.95710.76560.42350.023*
C100.77185 (12)0.81065 (10)0.38176 (8)0.0231 (3)
H10A0.73160.80830.32340.028*
H10B0.79690.88750.39470.028*
C110.67779 (10)0.76755 (9)0.45118 (7)0.0160 (2)
H11A0.59460.74740.42420.019*
H11B0.66200.82440.49600.019*
H10.8471 (15)0.7598 (14)0.5750 (10)0.030 (4)*
H20.5769 (16)0.5770 (12)0.4815 (10)0.024 (4)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0148 (4)0.0129 (4)0.0193 (4)−0.0014 (3)0.0001 (3)0.0009 (3)
N10.0166 (4)0.0201 (5)0.0147 (4)−0.0014 (4)−0.0011 (3)−0.0010 (4)
N20.0177 (5)0.0121 (5)0.0166 (4)−0.0029 (4)−0.0033 (4)0.0003 (3)
N30.0123 (4)0.0140 (4)0.0175 (4)−0.0023 (3)−0.0029 (4)0.0020 (3)
C10.0134 (5)0.0147 (5)0.0131 (5)0.0007 (4)0.0024 (4)−0.0013 (4)
C20.0135 (5)0.0146 (5)0.0130 (5)0.0008 (4)0.0008 (4)−0.0010 (4)
C30.0185 (5)0.0146 (5)0.0161 (5)0.0016 (4)0.0010 (4)−0.0001 (4)
C40.0201 (5)0.0205 (5)0.0147 (5)0.0049 (4)−0.0008 (4)0.0019 (4)
C50.0162 (5)0.0249 (6)0.0142 (5)0.0009 (4)−0.0018 (4)−0.0007 (4)
C60.0130 (5)0.0121 (5)0.0139 (5)0.0016 (4)0.0021 (4)−0.0016 (4)
C70.0129 (5)0.0122 (5)0.0152 (5)−0.0014 (4)−0.0008 (4)0.0011 (4)
C80.0179 (5)0.0153 (5)0.0171 (5)0.0017 (4)0.0006 (4)0.0003 (4)
C90.0182 (5)0.0191 (6)0.0206 (5)0.0000 (4)0.0036 (4)0.0028 (4)
C100.0252 (6)0.0196 (6)0.0246 (6)0.0040 (5)0.0057 (5)0.0082 (5)
C110.0147 (5)0.0138 (5)0.0195 (5)0.0010 (4)−0.0011 (4)0.0030 (4)

Geometric parameters (Å, °)

O1—C61.2500 (13)C4—H40.9500
N1—C51.3372 (14)C5—H50.9500
N1—C11.3458 (14)C7—C111.5404 (14)
N2—C11.3609 (14)C7—C81.5428 (15)
N2—C71.4571 (13)C8—C91.5262 (16)
N2—H10.882 (17)C8—H8A0.9900
N3—C61.3397 (14)C8—H8B0.9900
N3—C71.4646 (13)C9—C101.5349 (16)
N3—H20.885 (16)C9—H9A0.9900
C1—C21.4132 (15)C9—H9B0.9900
C2—C31.3900 (15)C10—C111.5397 (15)
C2—C61.4750 (14)C10—H10A0.9900
C3—C41.3878 (16)C10—H10B0.9900
C3—H30.9500C11—H11A0.9900
C4—C51.3876 (16)C11—H11B0.9900
C5—N1—C1116.60 (10)N2—C7—C8111.75 (9)
C1—N2—C7119.32 (9)N3—C7—C8112.50 (9)
C1—N2—H1118.1 (10)C11—C7—C8103.55 (8)
C7—N2—H1118.5 (10)C9—C8—C7103.17 (9)
C6—N3—C7123.56 (9)C9—C8—H8A111.1
C6—N3—H2117.6 (9)C7—C8—H8A111.1
C7—N3—H2117.8 (9)C9—C8—H8B111.1
N1—C1—N2117.90 (10)C7—C8—H8B111.1
N1—C1—C2122.96 (10)H8A—C8—H8B109.1
N2—C1—C2119.05 (10)C8—C9—C10103.80 (9)
C3—C2—C1118.28 (10)C8—C9—H9A111.0
C3—C2—C6122.57 (10)C10—C9—H9A111.0
C1—C2—C6118.70 (9)C8—C9—H9B111.0
C4—C3—C2119.29 (10)C10—C9—H9B111.0
C4—C3—H3120.4H9A—C9—H9B109.0
C2—C3—H3120.4C9—C10—C11106.36 (9)
C5—C4—C3117.72 (10)C9—C10—H10A110.5
C5—C4—H4121.1C11—C10—H10A110.5
C3—C4—H4121.1C9—C10—H10B110.5
N1—C5—C4125.11 (10)C11—C10—H10B110.5
N1—C5—H5117.4H10A—C10—H10B108.6
C4—C5—H5117.4C10—C11—C7106.30 (9)
O1—C6—N3121.75 (10)C10—C11—H11A110.5
O1—C6—C2122.26 (10)C7—C11—H11A110.5
N3—C6—C2115.89 (9)C10—C11—H11B110.5
N2—C7—N3107.23 (8)C7—C11—H11B110.5
N2—C7—C11110.45 (9)H11A—C11—H11B108.7
N3—C7—C11111.42 (9)
C5—N1—C1—N2178.43 (10)C3—C2—C6—N3−177.04 (10)
C5—N1—C1—C21.72 (16)C1—C2—C6—N310.81 (14)
C7—N2—C1—N1158.25 (10)C1—N2—C7—N344.94 (13)
C7—N2—C1—C2−24.91 (15)C1—N2—C7—C11166.52 (9)
N1—C1—C2—C3−1.20 (16)C1—N2—C7—C8−78.77 (12)
N2—C1—C2—C3−177.86 (10)C6—N3—C7—N2−40.32 (13)
N1—C1—C2—C6171.29 (10)C6—N3—C7—C11−161.29 (10)
N2—C1—C2—C6−5.38 (15)C6—N3—C7—C882.94 (12)
C1—C2—C3—C4−0.71 (16)N2—C7—C8—C9−79.95 (10)
C6—C2—C3—C4−172.89 (10)N3—C7—C8—C9159.36 (9)
C2—C3—C4—C51.92 (16)C11—C7—C8—C938.94 (10)
C1—N1—C5—C4−0.39 (17)C7—C8—C9—C10−39.83 (11)
C3—C4—C5—N1−1.43 (17)C8—C9—C10—C1125.43 (12)
C7—N3—C6—O1−169.27 (9)C9—C10—C11—C7−1.25 (12)
C7—N3—C6—C214.28 (15)N2—C7—C11—C1096.69 (10)
C3—C2—C6—O16.53 (16)N3—C7—C11—C10−144.24 (9)
C1—C2—C6—O1−165.62 (10)C8—C7—C11—C10−23.09 (11)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H1···O1i0.88 (2)2.05 (2)2.918 (1)170 (2)
N3—H2···O1ii0.89 (2)2.00 (2)2.876 (1)172 (1)

Symmetry codes: (i) −x+3/2, y+1/2, z; (ii) −x+1, −y+1, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LX2156).

References

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