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

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ISSN: 2056-9890

6′-Bromo-1′H-spiro­[cyclo­hexane-1,2′-pyrido[2,3-d]pyrimidin]-4′(3′H)-one

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

(Received 31 October 2011; accepted 4 December 2011; online 21 December 2011)

The title compound, C12H14BrN3O, is built up from two fused six-membered rings and one six-membered ring linked through a spiro C atom. The hydro­pyrimidine ring has an envelope conformation and the cyclo­hexane ring is in a chair conformation. In the crystal, mol­ecules are linked by N—H⋯O and N—H⋯N hydrogen bonds, forming a mol­ecular tape along the b axis.

Related literature

For medicinal and biological properties of 2,3-dihydro­pyrido[2,3-d]-pyrimidin-4(1H)-one derivatives, see: Parish et al. (1982[Parish, H. A. Jr, Gilliom, R. D., Purcell, W. P., Browne, R. K., Spirk, R. F. & White, H. D. (1982). J. Med. Chem. 25, 98-102.]); Narayana et al. (2009[Narayana, B., Rao, A. R. & Rao, P. S. (2009). Eur. J. Med. Chem. 44, 1369-1376.]). For related structures, see: Shi et al. (2010[Shi, D., Yang, L., Tang, J., Wang, X. & Li, J. (2010). Acta Cryst. E66, o2301.]); Ling et al. (2009[Ling, Z., Shi, D., Yanqiu, F., Wei, X. & Li, J. (2009). Acta Cryst. E65, o1097.]).

[Scheme 1]

Experimental

Crystal data
  • C12H14BrN3O

  • Mr = 296.17

  • Monoclinic, P 21 /c

  • a = 10.591 (3) Å

  • b = 12.359 (3) Å

  • c = 9.116 (3) Å

  • β = 97.951 (4)°

  • V = 1181.7 (6) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 3.47 mm−1

  • T = 153 K

  • 0.40 × 0.24 × 0.09 mm

Data collection
  • Rigaku AFC10/Saturn724+ diffractometer

  • Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2009[Rigaku/MSC (2009). CrystalClear and CrystalStructure. Rigaku/MSC, The Woodlands, Texas, USA.]) Tmin = 0.324, Tmax = 0.732

  • 10128 measured reflections

  • 3160 independent reflections

  • 2283 reflections with I > 2σ(I)

  • Rint = 0.046

Refinement
  • R[F2 > 2σ(F2)] = 0.035

  • wR(F2) = 0.074

  • S = 1.00

  • 3160 reflections

  • 162 parameters

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

  • Δρmax = 0.55 e Å−3

  • Δρmin = −0.66 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1N⋯N3i 0.83 (2) 2.52 (2) 3.337 (2) 169 (2)
N2—H2N⋯O1ii 0.83 (2) 1.98 (2) 2.807 (2) 175 (2)
Symmetry codes: (i) [-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) [-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].

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-Dihydropyrido[2,3-d]-pyrimidin-4(1H)-ones are a class of fused heterocycles which possess diuretic (Parish et al., 1982) and anti-bacterial activity (Narayana et al., 2009). 2-Substituted 2,3-dihydropyrido [2,3-d]pyrimidin-4(1H)-one derivatives can be obtained from the cyclocondensation of 2-amino-3-cyanopyridine with cyclopentanone (Shi et al., 2010). Here, we report the crystal structure of the title compound (Fig. 1). The molecular structure is built up with two fused six-membered ring and one six-membered ring linked through a spiro C atom. The pyrimidine ring has an envelope 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). Cyclohexane ring has a similar chair conformation as cyclohexanespiro-2'-[2',3',6',7'-tetrahydro-1'H- cyclopenta[d]pyrimidin]-4'(5'H)-one (Ling et al., 2009). The crystal packing (Fig. 2) is stabilized by intermolecular N—H···O and N—H···N hydrogen bonds (Table 1).

Related literature top

For medicinal and biological properties of 2,3-dihydropyrido[2,3-d]-pyrimidin-4(1H)-one derivatives, see: Parish et al. (1982); Narayana et al. (2009). For related structures, see: Shi et al. (2010); Ling et al. (2009).

Experimental top

A solution of 5-Br-2-amino-3-cyanopyridine (2 mmol) and sodium methylate (0.6 mmol) was refluxed in cyclohexanone (3 ml) for 10 min. The reaction mixture was cooled to room temperature and then filtered to give the title compound. The product was recrystallizated from THF to give light yellow crystalline powder (m.p. 531–532 K). 1H–NMR(DMSO, p.p.m.):1.30–1.73 (10H, m, C5H10), 7.79 (1H, s, NH), 7.92 (1H, d, J = 2.4 Hz, Pyridine-H), 8.24 (1H, d, J = 2.4 Hz, Pyridine-H), 8.35 (1H, s, NH); ESI-MS m/z: [M+H]+ 296.1; C12H14BrN3O: calcd. C 48.67, H 4.76, N 14.19; found C 48.88, H 4.787, N 14.06.

Refinement top

C-bounf H atoms were included in the riding model approximation, with C—H = 0.95–0.99 Å, and with Uiso(H) = 1.2Ueq(C) or 1.5Ueq(methyl C), while the N-bound H atoms were refined freely [N—H = 0.83 (2) Å].

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 30% probability level.
[Figure 2] Fig. 2. A packing diagram, showing N—H···O and N—H···N interactions (dotted lines) in the crystal structure of the title compound.
6'-Bromo-1'H-spiro[cyclohexane-1,2'-pyrido[2,3- d]pyrimidin]-4'(3'H)-one top
Crystal data top
C12H14BrN3OF(000) = 600
Mr = 296.17Dx = 1.665 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3621 reflections
a = 10.591 (3) Åθ = 2.6–29.1°
b = 12.359 (3) ŵ = 3.47 mm1
c = 9.116 (3) ÅT = 153 K
β = 97.951 (4)°Platelet, colourless
V = 1181.7 (6) Å30.40 × 0.24 × 0.09 mm
Z = 4
Data collection top
Rigaku AFC10/Saturn724+
diffractometer
3160 independent reflections
Radiation source: Rotating Anode2283 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.046
Detector resolution: 28.5714 pixels mm-1θmax = 29.1°, θmin = 2.6°
ϕ and ω scansh = 1412
Absorption correction: multi-scan
(CrystalClear; Rigaku/MSC, 2009)
k = 1616
Tmin = 0.324, Tmax = 0.732l = 1212
10128 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.074H atoms treated by a mixture of independent and constrained refinement
S = 1.00 w = 1/[σ2(Fo2) + (0.0295P)2 + 0.126P]
where P = (Fo2 + 2Fc2)/3
3160 reflections(Δ/σ)max = 0.001
162 parametersΔρmax = 0.55 e Å3
0 restraintsΔρmin = 0.66 e Å3
Crystal data top
C12H14BrN3OV = 1181.7 (6) Å3
Mr = 296.17Z = 4
Monoclinic, P21/cMo Kα radiation
a = 10.591 (3) ŵ = 3.47 mm1
b = 12.359 (3) ÅT = 153 K
c = 9.116 (3) Å0.40 × 0.24 × 0.09 mm
β = 97.951 (4)°
Data collection top
Rigaku AFC10/Saturn724+
diffractometer
3160 independent reflections
Absorption correction: multi-scan
(CrystalClear; Rigaku/MSC, 2009)
2283 reflections with I > 2σ(I)
Tmin = 0.324, Tmax = 0.732Rint = 0.046
10128 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0350 restraints
wR(F2) = 0.074H atoms treated by a mixture of independent and constrained refinement
S = 1.00Δρmax = 0.55 e Å3
3160 reflectionsΔρmin = 0.66 e Å3
162 parameters
Special details top

Experimental. Spectral data: IR (KBr): 3274, 3175, 2927, 1677, 1610, 1422 cm-1.

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
Br10.99820 (2)0.65490 (2)0.61599 (3)0.03640 (10)
O10.58435 (14)0.40734 (11)0.39085 (16)0.0171 (3)
N10.45035 (17)0.52063 (14)0.2500 (2)0.0151 (4)
N20.49356 (17)0.71034 (14)0.2458 (2)0.0188 (4)
N30.68151 (16)0.78374 (13)0.3597 (2)0.0176 (4)
C10.2735 (2)0.64979 (16)0.2411 (2)0.0150 (4)
H1A0.28140.64180.35010.018*
H1B0.24960.72570.21640.018*
C20.1676 (2)0.57477 (17)0.1687 (2)0.0179 (5)
H2A0.18650.49940.20150.021*
H2B0.08550.59600.20050.021*
C30.1565 (2)0.58081 (18)0.0002 (2)0.0194 (5)
H3A0.09020.52960.04480.023*
H3B0.13030.65470.03360.023*
C40.2831 (2)0.55308 (17)0.0524 (2)0.0172 (5)
H4A0.27510.56170.16130.021*
H4B0.30460.47650.02850.021*
C50.3902 (2)0.62565 (16)0.0209 (2)0.0160 (4)
H5A0.37430.70060.01520.019*
H5B0.47170.60140.00980.019*
C60.40340 (19)0.62564 (15)0.1905 (2)0.0129 (4)
C70.55747 (19)0.49967 (15)0.3433 (2)0.0127 (4)
C80.64262 (19)0.59204 (16)0.3832 (2)0.0125 (4)
C90.6063 (2)0.69577 (16)0.3293 (2)0.0139 (4)
C100.7594 (2)0.57798 (17)0.4683 (2)0.0174 (5)
H100.78630.50860.50510.021*
C110.8365 (2)0.66793 (17)0.4987 (3)0.0203 (5)
C120.7942 (2)0.76778 (17)0.4435 (3)0.0203 (5)
H120.84820.82860.46650.024*
H1N0.408 (2)0.4668 (17)0.220 (2)0.015 (6)*
H2N0.474 (2)0.7700 (19)0.208 (3)0.026 (7)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Br10.02057 (13)0.02781 (14)0.05373 (19)0.00860 (11)0.01997 (11)0.01191 (13)
O10.0199 (8)0.0096 (7)0.0194 (8)0.0000 (6)0.0054 (6)0.0021 (6)
N10.0143 (9)0.0080 (8)0.0209 (10)0.0027 (7)0.0049 (7)0.0002 (7)
N20.0163 (10)0.0070 (9)0.0298 (11)0.0006 (7)0.0085 (8)0.0047 (8)
N30.0143 (10)0.0111 (9)0.0259 (11)0.0045 (7)0.0027 (8)0.0016 (8)
C10.0165 (11)0.0128 (10)0.0153 (10)0.0017 (9)0.0011 (8)0.0012 (8)
C20.0133 (11)0.0189 (11)0.0216 (12)0.0025 (9)0.0031 (9)0.0022 (9)
C30.0130 (11)0.0208 (11)0.0227 (12)0.0036 (9)0.0029 (9)0.0027 (10)
C40.0194 (11)0.0184 (10)0.0131 (10)0.0000 (9)0.0003 (8)0.0017 (9)
C50.0167 (11)0.0145 (10)0.0175 (11)0.0032 (8)0.0050 (9)0.0026 (9)
C60.0117 (10)0.0070 (9)0.0182 (11)0.0004 (8)0.0042 (8)0.0004 (8)
C70.0135 (10)0.0112 (10)0.0132 (10)0.0009 (8)0.0013 (8)0.0005 (8)
C80.0129 (10)0.0113 (10)0.0130 (10)0.0002 (8)0.0006 (8)0.0005 (8)
C90.0137 (10)0.0111 (9)0.0165 (11)0.0006 (8)0.0010 (8)0.0003 (8)
C100.0153 (11)0.0151 (10)0.0204 (11)0.0008 (9)0.0020 (9)0.0041 (9)
C110.0120 (10)0.0200 (11)0.0262 (12)0.0040 (9)0.0064 (9)0.0027 (10)
C120.0161 (11)0.0148 (10)0.0281 (13)0.0052 (9)0.0034 (9)0.0019 (10)
Geometric parameters (Å, º) top
Br1—C111.896 (2)C3—C41.523 (3)
O1—C71.240 (2)C3—H3A0.9900
N1—C71.346 (2)C3—H3B0.9900
N1—C61.467 (2)C4—C51.525 (3)
N1—H1N0.83 (2)C4—H4A0.9900
N2—C91.336 (3)C4—H4B0.9900
N2—C61.459 (3)C5—C61.533 (3)
N2—H2N0.83 (2)C5—H5A0.9900
N3—C121.339 (3)C5—H5B0.9900
N3—C91.354 (3)C7—C81.469 (3)
C1—C21.533 (3)C8—C101.377 (3)
C1—C61.539 (3)C8—C91.407 (3)
C1—H1A0.9900C10—C111.384 (3)
C1—H1B0.9900C10—H100.9500
C2—C31.530 (3)C11—C121.384 (3)
C2—H2A0.9900C12—H120.9500
C2—H2B0.9900
C7—N1—C6128.11 (17)C4—C5—C6113.60 (18)
C7—N1—H1N115.1 (15)C4—C5—H5A108.8
C6—N1—H1N116.7 (15)C6—C5—H5A108.8
C9—N2—C6126.21 (17)C4—C5—H5B108.8
C9—N2—H2N120.3 (17)C6—C5—H5B108.8
C6—N2—H2N112.6 (17)H5A—C5—H5B107.7
C12—N3—C9116.82 (17)N2—C6—N1109.55 (16)
C2—C1—C6112.62 (16)N2—C6—C5108.24 (17)
C2—C1—H1A109.1N1—C6—C5110.62 (17)
C6—C1—H1A109.1N2—C6—C1109.04 (16)
C2—C1—H1B109.1N1—C6—C1109.38 (17)
C6—C1—H1B109.1C5—C6—C1109.98 (16)
H1A—C1—H1B107.8O1—C7—N1122.07 (18)
C3—C2—C1110.73 (17)O1—C7—C8121.69 (18)
C3—C2—H2A109.5N1—C7—C8116.22 (17)
C1—C2—H2A109.5C10—C8—C9119.49 (18)
C3—C2—H2B109.5C10—C8—C7120.94 (18)
C1—C2—H2B109.5C9—C8—C7119.53 (18)
H2A—C2—H2B108.1N2—C9—N3117.56 (18)
C4—C3—C2110.80 (17)N2—C9—C8120.06 (18)
C4—C3—H3A109.5N3—C9—C8122.37 (18)
C2—C3—H3A109.5C8—C10—C11118.05 (19)
C4—C3—H3B109.5C8—C10—H10121.0
C2—C3—H3B109.5C11—C10—H10121.0
H3A—C3—H3B108.1C12—C11—C10119.4 (2)
C3—C4—C5111.35 (17)C12—C11—Br1120.17 (16)
C3—C4—H4A109.4C10—C11—Br1120.42 (16)
C5—C4—H4A109.4N3—C12—C11123.84 (19)
C3—C4—H4B109.4N3—C12—H12118.1
C5—C4—H4B109.4C11—C12—H12118.1
H4A—C4—H4B108.0
C6—C1—C2—C356.1 (2)N1—C7—C8—C10174.77 (19)
C1—C2—C3—C456.8 (2)O1—C7—C8—C9178.41 (19)
C2—C3—C4—C555.7 (2)N1—C7—C8—C93.0 (3)
C3—C4—C5—C654.2 (2)C6—N2—C9—N3174.7 (2)
C9—N2—C6—N14.4 (3)C6—N2—C9—C85.9 (3)
C9—N2—C6—C5116.3 (2)C12—N3—C9—N2180.0 (2)
C9—N2—C6—C1124.1 (2)C12—N3—C9—C80.6 (3)
C7—N1—C6—N21.1 (3)C10—C8—C9—N2179.6 (2)
C7—N1—C6—C5120.3 (2)C7—C8—C9—N21.8 (3)
C7—N1—C6—C1118.4 (2)C10—C8—C9—N31.0 (3)
C4—C5—C6—N2170.86 (16)C7—C8—C9—N3178.8 (2)
C4—C5—C6—N169.1 (2)C9—C8—C10—C110.6 (3)
C4—C5—C6—C151.8 (2)C7—C8—C10—C11178.3 (2)
C2—C1—C6—N2171.29 (17)C8—C10—C11—C120.2 (3)
C2—C1—C6—N168.9 (2)C8—C10—C11—Br1179.67 (16)
C2—C1—C6—C552.7 (2)C9—N3—C12—C110.3 (3)
C6—N1—C7—O1176.9 (2)C10—C11—C12—N30.6 (4)
C6—N1—C7—C84.5 (3)Br1—C11—C12—N3179.88 (18)
O1—C7—C8—C103.8 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1N···N3i0.83 (2)2.52 (2)3.337 (2)169 (2)
N2—H2N···O1ii0.83 (2)1.98 (2)2.807 (2)175 (2)
Symmetry codes: (i) x+1, y1/2, z+1/2; (ii) x+1, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC12H14BrN3O
Mr296.17
Crystal system, space groupMonoclinic, P21/c
Temperature (K)153
a, b, c (Å)10.591 (3), 12.359 (3), 9.116 (3)
β (°) 97.951 (4)
V3)1181.7 (6)
Z4
Radiation typeMo Kα
µ (mm1)3.47
Crystal size (mm)0.40 × 0.24 × 0.09
Data collection
DiffractometerRigaku AFC10/Saturn724+
diffractometer
Absorption correctionMulti-scan
(CrystalClear; Rigaku/MSC, 2009)
Tmin, Tmax0.324, 0.732
No. of measured, independent and
observed [I > 2σ(I)] reflections
10128, 3160, 2283
Rint0.046
(sin θ/λ)max1)0.684
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.035, 0.074, 1.00
No. of reflections3160
No. of parameters162
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.55, 0.66

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···N3i0.83 (2)2.52 (2)3.337 (2)169 (2)
N2—H2N···O1ii0.83 (2)1.98 (2)2.807 (2)175 (2)
Symmetry codes: (i) x+1, y1/2, z+1/2; (ii) x+1, y+1/2, z+1/2.
 

Acknowledgements

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

References

First citationNarayana, B., Rao, A. R. & Rao, P. S. (2009). Eur. J. Med. Chem. 44, 1369–1376.  PubMed
First citationLing, Z., Shi, D., Yanqiu, F., Wei, X. & Li, J. (2009). Acta Cryst. E65, o1097.  Web of Science CSD CrossRef IUCr Journals
First citationParish, H. A. Jr, Gilliom, R. D., Purcell, W. P., Browne, R. K., Spirk, R. F. & White, H. D. (1982). J. Med. Chem. 25, 98–102.  CrossRef CAS PubMed Web of Science
First citationRigaku/MSC (2009). CrystalClear and CrystalStructure. Rigaku/MSC, The Woodlands, Texas, USA.
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals
First citationShi, D., Yang, L., Tang, J., Wang, X. & Li, J. (2010). Acta Cryst. E66, o2301.  Web of Science CSD CrossRef IUCr Journals

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