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ISSN: 2056-9890

4-Chloro-7-hydr­­oxy-6-methyl-1,7-naphthyridin-8(7H)-one

aPfizer Global Research and Development, La Jolla Labs, 10770 Science Center Drive, San Diego, CA 92121, USA, and bDepartment of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
*Correspondence e-mail: alex.yanovsky@pfizer.com

(Received 16 November 2009; accepted 23 November 2009; online 28 November 2009)

The title compound, C9H7ClN2O2, was prepared by reaction of methyl 4-chloro-3-(prop-1-yn­yl)picolinate with hydroxy­l­amine in MeOH/KOH solution. The two essentially planar mol­ecules which make up the asymmetric unit have almost identical geometries and and are linked into dimeric aggregates via pairs of O—H⋯O hydrogen bonds. These aggregates have almost perfect inversion symmetry; however, quite unusually, the inversion center of the dimer does not coincide with the crystallographic inversion center.

Related literature

For the synthesis, see: Knight et al. (2002[ Knight, D. W., Lewis, P. B. M., Abdul Malik, K. M., Mshvidobadze, E. V. & Vasilevsky, S. G. (2002). Tetrahedron Lett. 43, 9187-9189.]). For the structures of related compounds with a similar bicyclic framework, see: Ikeura et al. (1998[ Ikeura, Y., Ishichi, Y., Tanaka, T., Fujishima, A., Murabayashi, M., Kawada, M., Ishimaru, T., Kamo, I., Doi, T. & Natsugari, H. (1998). J. Med. Chem. 41, 4232-4239.]); Natsugari et al. (1995[ Natsugari, H., Ikeura, Y., Kiyota, Y., Ishichi, Y., Ishimaru, T., Saga, O., Shirafuji, H., Tanaka, T., Kamo, I., Doi, T. & Otsuka, M. (1995). J. Med. Chem. 38, 3106-3120.]). For structural analysis, see: Spek (2009[ Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

[Scheme 1]

Experimental

Crystal data
  • C9H7ClN2O2

  • Mr = 210.62

  • Monoclinic, P 21 /c

  • a = 9.3983 (4) Å

  • b = 13.8786 (5) Å

  • c = 13.5643 (5) Å

  • β = 107.663 (3)°

  • V = 1685.86 (11) Å3

  • Z = 8

  • Cu Kα radiation

  • μ = 3.80 mm−1

  • T = 100 K

  • 0.14 × 0.12 × 0.08 mm

Data collection
  • Bruker APEXII CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2001[ Bruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.618, Tmax = 0.751

  • 12070 measured reflections

  • 3061 independent reflections

  • 2420 reflections with I > 2σ(I)

  • Rint = 0.032

Refinement
  • R[F2 > 2σ(F2)] = 0.042

  • wR(F2) = 0.115

  • S = 1.05

  • 3061 reflections

  • 255 parameters

  • H-atom parameters constrained

  • Δρmax = 0.50 e Å−3

  • Δρmin = −0.41 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O11—H11C⋯O22 0.84 2.02 2.675 (2) 134
O21—H21C⋯O12 0.84 2.09 2.677 (2) 127

Data collection: APEX2 (Bruker, 2007[ Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2007[ Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; 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: SHELXTL (Sheldrick, 2008[ Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

The title compound was obtained using the reaction of of methyl 4-chloro-3-(prop-1-ynyl)picolinate with hydroxylamine in MeOH/KOH solution (Knight et al., 2002). The structural formula of the product was confirmed by the present study (Fig. 1).

There are two independent molecules in the structure, which show almost identical geometry. The molecules are essentially planar (with the exception of methyl H atoms) and their parameters are quite similar to those found in related structures with analogous carbon-nitrogen bicyclic framework (Ikeura et al., 1998; Natsugari et al., 1995). To the best of our knowledge, however, this is the first structurally characterized system of this kind with the O-substitution at the N atom next to C=O group.

The molecules in the asymmetric unit of the title compound are linked into dimeric aggregates via H-bonds (Table 1). These aggregates have almost ideal inversion symmetry, however, quite unusually, the inversion center of the dimer does not coincide with the crystallographic inversion center.

Related literature top

For the synthesis, see: Knight et al. (2002). For the structures of related compounds with a similar bicyclic framework, see: Ikeura et al. (1998); Natsugari et al. (1995). For structural analysis, see: Spek (2009).

Experimental top

Warm solutions (50°C) of hydroxylamine hydrochloride (199.0 mg, 2.86 mmol, 6 eq) in methanol (2.0 M, 1.43 ml) and potassium hydroxide (241.0 mg, 4.29 mmol, 9 eq) in methanol (4.0 M, 1.07 ml) were mixed; the resulting solution was cooled to below 40°C and potassium chloride precipitated out. The precipitate was filtered and the filtrate was added to a vial containing methyl 4-chloro-3-(prop-1-ynyl)picolinate (100.0 mg, 0.4770 mmol); the flask containing the filtrate was rinsed with an additional 1 ml of MeOH and added to the reaction vial. The resulting mixture was then heated to reflux. A precipitate formed within 20 minutes. The reaction was monitored by LCMS; after consumption of starting material (about 75 min), the mixture was removed from heat and cooled to room temperature, diluted with ether and the precipitate was collected. To the precipitate was added minimal amount of acetic acid to quench the mixture. The mixture was then triturated in ethyl acetate and filtered. The filtrate was collected, concentrated and the solid dried to give 26 mg (26%) of the title compound. A small sample was dissolved in methanol:dichloromethane (1:1) and heated at 50°C to dryness to obtain crystals of sufficient quality for X-ray diffraction experiment. LC—MS m/z (% relative intensity, ion): 211.0 (100.0%), 213.0 (32.0%), 212.0 (9.9%), 214.0 (3.2%). 1H NMR (400 MHz, DMSO-d6) δ p.p.m. 2.46 (s, 3H) 6.67 (br. s., 1H) 7.88 (br. s., 1H) 8.65 (br. s., 1H) 11.62 (br. s., 1H).

Refinement top

All H atoms were placed in geometrically calculated positions (C—H 0.98 Å and 0.95 Å for methyl and aromatic CH-groups; O—H 0.84 Å) and included in the refinement in riding motion approximation. The Uiso(H) were set to 1.2Ueq of the carrying atom (1.5Ueq for methyl and hydroxyl H atoms).

Two independent molecules in the structure of the title compound are related by almost ideal non-crystallographic inversion center, which prompted us to perform additional checks on the presence of higher genuine symmetry by careful inspection of atomic coordinates as well as by using ADDSYM option in PLATON (Spek, 2009). Nevertheless, no unaccounted crystallographic symmetry was detected.

Computing details top

Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); 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
[Figure 1] Fig. 1. Molecular structure of the title compound, showing 50% probability displacement ellipsoids and atom numbering scheme. H atoms are drawn as circles with arbitrary small radius. H-bonds are shown as dashed lines.
4-Chloro-7-hydroxy-6-methyl-1,7-naphthyridin-8(7H)-one top
Crystal data top
C9H7ClN2O2F(000) = 864
Mr = 210.62Dx = 1.660 Mg m3
Monoclinic, P21/cCu Kα radiation, λ = 1.54178 Å
Hall symbol: -P 2ybcCell parameters from 4820 reflections
a = 9.3983 (4) Åθ = 4.7–67.9°
b = 13.8786 (5) ŵ = 3.80 mm1
c = 13.5643 (5) ÅT = 100 K
β = 107.663 (3)°Block, light yellow
V = 1685.86 (11) Å30.14 × 0.12 × 0.08 mm
Z = 8
Data collection top
Bruker APEXII CCD area-detector
diffractometer
3061 independent reflections
Radiation source: fine-focus sealed tube2420 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.032
phi and ω scansθmax = 68.1°, θmin = 4.7°
Absorption correction: multi-scan
(SADABS; Bruker, 2001)
h = 1111
Tmin = 0.618, Tmax = 0.751k = 1316
12070 measured reflectionsl = 1616
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)] = 0.042Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.115H-atom parameters constrained
S = 1.05 w = 1/[σ2(Fo2) + (0.0643P)2 + 0.6521P]
where P = (Fo2 + 2Fc2)/3
3061 reflections(Δ/σ)max < 0.001
255 parametersΔρmax = 0.50 e Å3
0 restraintsΔρmin = 0.41 e Å3
Crystal data top
C9H7ClN2O2V = 1685.86 (11) Å3
Mr = 210.62Z = 8
Monoclinic, P21/cCu Kα radiation
a = 9.3983 (4) ŵ = 3.80 mm1
b = 13.8786 (5) ÅT = 100 K
c = 13.5643 (5) Å0.14 × 0.12 × 0.08 mm
β = 107.663 (3)°
Data collection top
Bruker APEXII CCD area-detector
diffractometer
3061 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2001)
2420 reflections with I > 2σ(I)
Tmin = 0.618, Tmax = 0.751Rint = 0.032
12070 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0420 restraints
wR(F2) = 0.115H-atom parameters constrained
S = 1.05Δρmax = 0.50 e Å3
3061 reflectionsΔρmin = 0.41 e Å3
255 parameters
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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
Cl110.07931 (6)0.29765 (4)0.57976 (4)0.02505 (17)
O110.62329 (17)0.16036 (11)0.68417 (13)0.0229 (4)
H11C0.69500.19930.69680.034*
O120.62280 (17)0.34923 (11)0.68384 (12)0.0220 (4)
N110.3605 (2)0.45541 (13)0.64550 (14)0.0199 (4)
N120.4903 (2)0.21085 (13)0.66186 (14)0.0175 (4)
C110.2323 (2)0.50128 (17)0.63118 (17)0.0213 (5)
H11A0.23430.56970.63370.026*
C120.0938 (3)0.45514 (17)0.61247 (16)0.0210 (5)
H12A0.00510.49120.60450.025*
C130.0903 (2)0.35705 (17)0.60603 (16)0.0186 (5)
C140.2232 (2)0.30333 (16)0.62197 (16)0.0171 (5)
C150.2303 (2)0.20137 (16)0.61942 (16)0.0179 (5)
H15A0.14060.16490.60330.021*
C160.3631 (2)0.15509 (16)0.63963 (16)0.0171 (5)
C170.4990 (2)0.30963 (16)0.66367 (16)0.0174 (5)
C180.3550 (2)0.35808 (16)0.64246 (16)0.0166 (5)
C190.3820 (3)0.04884 (15)0.63766 (17)0.0204 (5)
H19A0.28370.01790.61650.031*
H19B0.43900.02630.70680.031*
H19C0.43580.03230.58840.031*
Cl211.58399 (6)0.29188 (4)0.92532 (4)0.02425 (17)
O210.87294 (17)0.40291 (12)0.82957 (13)0.0275 (4)
H21C0.80440.36160.81760.041*
O220.88743 (17)0.21429 (11)0.81342 (12)0.0228 (4)
N211.1594 (2)0.11748 (14)0.85899 (14)0.0202 (4)
N221.0090 (2)0.35700 (13)0.84478 (14)0.0187 (4)
C211.2917 (3)0.07633 (17)0.87918 (17)0.0213 (5)
H21A1.29600.00790.87890.026*
C221.4260 (3)0.12739 (17)0.90091 (17)0.0221 (5)
H22A1.51860.09440.91530.026*
C231.4211 (2)0.22576 (17)0.90105 (16)0.0188 (5)
C241.2824 (2)0.27445 (16)0.88048 (16)0.0163 (5)
C251.2672 (2)0.37650 (16)0.88112 (16)0.0175 (5)
H25A1.35310.41610.89290.021*
C261.1319 (3)0.41747 (16)0.86517 (17)0.0180 (5)
C271.0071 (2)0.25806 (16)0.83737 (17)0.0184 (5)
C281.1554 (2)0.21492 (16)0.86006 (16)0.0167 (5)
C291.1054 (3)0.52295 (16)0.86981 (18)0.0225 (5)
H29A1.20030.55750.88250.034*
H29B1.06290.53640.92600.034*
H29C1.03570.54430.80390.034*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl110.0151 (3)0.0280 (3)0.0313 (3)0.0015 (2)0.0058 (2)0.0012 (2)
O110.0132 (8)0.0163 (8)0.0371 (9)0.0040 (6)0.0046 (7)0.0022 (7)
O120.0165 (8)0.0176 (8)0.0311 (9)0.0031 (7)0.0061 (7)0.0023 (7)
N110.0227 (10)0.0143 (9)0.0217 (10)0.0003 (8)0.0052 (8)0.0002 (8)
N120.0155 (10)0.0133 (9)0.0238 (10)0.0022 (7)0.0059 (8)0.0011 (8)
C110.0249 (12)0.0154 (11)0.0222 (11)0.0031 (10)0.0050 (9)0.0002 (9)
C120.0209 (12)0.0219 (12)0.0201 (11)0.0072 (10)0.0059 (9)0.0002 (9)
C130.0173 (11)0.0207 (12)0.0172 (11)0.0007 (9)0.0041 (9)0.0005 (9)
C140.0190 (12)0.0173 (11)0.0163 (11)0.0008 (9)0.0070 (9)0.0007 (9)
C150.0171 (11)0.0174 (11)0.0189 (11)0.0040 (9)0.0050 (9)0.0010 (9)
C160.0199 (11)0.0154 (11)0.0156 (10)0.0022 (9)0.0048 (9)0.0007 (9)
C170.0188 (11)0.0163 (11)0.0177 (11)0.0012 (9)0.0062 (9)0.0019 (9)
C180.0189 (12)0.0139 (11)0.0167 (11)0.0002 (9)0.0051 (9)0.0001 (9)
C190.0230 (11)0.0133 (11)0.0223 (11)0.0006 (9)0.0033 (9)0.0001 (9)
Cl210.0159 (3)0.0256 (3)0.0303 (3)0.0007 (2)0.0057 (2)0.0016 (2)
O210.0126 (8)0.0200 (8)0.0473 (11)0.0039 (7)0.0053 (7)0.0038 (8)
O220.0171 (8)0.0211 (8)0.0297 (9)0.0029 (7)0.0063 (7)0.0010 (7)
N210.0248 (10)0.0143 (9)0.0217 (10)0.0000 (8)0.0074 (8)0.0010 (8)
N220.0150 (9)0.0149 (10)0.0255 (10)0.0037 (8)0.0051 (8)0.0004 (8)
C210.0255 (12)0.0147 (11)0.0234 (12)0.0033 (10)0.0069 (10)0.0004 (9)
C220.0231 (12)0.0199 (12)0.0244 (12)0.0065 (10)0.0089 (10)0.0018 (10)
C230.0172 (11)0.0221 (12)0.0167 (11)0.0000 (9)0.0045 (9)0.0000 (9)
C240.0188 (12)0.0163 (11)0.0138 (11)0.0012 (9)0.0050 (9)0.0009 (9)
C250.0184 (11)0.0164 (11)0.0174 (11)0.0018 (9)0.0047 (9)0.0005 (9)
C260.0204 (11)0.0149 (11)0.0191 (11)0.0014 (9)0.0065 (9)0.0012 (9)
C270.0191 (12)0.0170 (11)0.0190 (11)0.0000 (9)0.0057 (9)0.0017 (9)
C280.0182 (12)0.0161 (11)0.0166 (11)0.0014 (9)0.0061 (9)0.0010 (9)
C290.0236 (12)0.0155 (12)0.0268 (12)0.0013 (10)0.0053 (10)0.0001 (10)
Geometric parameters (Å, º) top
Cl11—C131.733 (2)Cl21—C231.729 (2)
O11—N121.384 (2)O21—N221.387 (2)
O11—H11C0.8400O21—H21C0.8405
O12—C171.240 (3)O22—C271.232 (3)
N11—C111.323 (3)N21—C211.320 (3)
N11—C181.352 (3)N21—C281.353 (3)
N12—C171.373 (3)N22—C271.377 (3)
N12—C161.378 (3)N22—C261.386 (3)
C11—C121.403 (3)C21—C221.399 (3)
C11—H11A0.9500C21—H21A0.9500
C12—C131.364 (3)C22—C231.366 (3)
C12—H12A0.9500C22—H22A0.9500
C13—C141.414 (3)C23—C241.419 (3)
C14—C181.407 (3)C24—C281.408 (3)
C14—C151.418 (3)C24—C251.424 (3)
C15—C161.356 (3)C25—C261.349 (3)
C15—H15A0.9500C25—H25A0.9500
C16—C191.486 (3)C26—C291.489 (3)
C17—C181.459 (3)C27—C281.462 (3)
C19—H19A0.9800C29—H29A0.9800
C19—H19B0.9800C29—H29B0.9800
C19—H19C0.9800C29—H29C0.9800
N12—O11—H11C109.5N22—O21—H21C109.5
C11—N11—C18116.9 (2)C21—N21—C28117.2 (2)
C17—N12—C16127.42 (19)C27—N22—C26127.62 (19)
C17—N12—O11117.17 (18)C27—N22—O21117.13 (18)
C16—N12—O11115.41 (17)C26—N22—O21115.25 (17)
N11—C11—C12124.1 (2)N21—C21—C22123.9 (2)
N11—C11—H11A118.0N21—C21—H21A118.0
C12—C11—H11A118.0C22—C21—H21A118.0
C13—C12—C11118.1 (2)C23—C22—C21118.5 (2)
C13—C12—H12A121.0C23—C22—H22A120.7
C11—C12—H12A121.0C21—C22—H22A120.7
C12—C13—C14120.9 (2)C22—C23—C24120.4 (2)
C12—C13—Cl11119.42 (18)C22—C23—Cl21120.15 (18)
C14—C13—Cl11119.71 (18)C24—C23—Cl21119.49 (18)
C18—C14—C13115.4 (2)C28—C24—C23115.6 (2)
C18—C14—C15119.9 (2)C28—C24—C25120.3 (2)
C13—C14—C15124.6 (2)C23—C24—C25124.1 (2)
C16—C15—C14121.0 (2)C26—C25—C24120.7 (2)
C16—C15—H15A119.5C26—C25—H25A119.7
C14—C15—H15A119.5C24—C25—H25A119.7
C15—C16—N12117.5 (2)C25—C26—N22117.7 (2)
C15—C16—C19125.0 (2)C25—C26—C29124.7 (2)
N12—C16—C19117.43 (19)N22—C26—C29117.6 (2)
O12—C17—N12119.6 (2)O22—C27—N22120.1 (2)
O12—C17—C18126.2 (2)O22—C27—C28126.1 (2)
N12—C17—C18114.20 (19)N22—C27—C28113.74 (19)
N11—C18—C14124.6 (2)N21—C28—C24124.4 (2)
N11—C18—C17115.49 (19)N21—C28—C27115.7 (2)
C14—C18—C17119.9 (2)C24—C28—C27119.9 (2)
C16—C19—H19A109.5C26—C29—H29A109.5
C16—C19—H19B109.5C26—C29—H29B109.5
H19A—C19—H19B109.5H29A—C29—H29B109.5
C16—C19—H19C109.5C26—C29—H29C109.5
H19A—C19—H19C109.5H29A—C29—H29C109.5
H19B—C19—H19C109.5H29B—C29—H29C109.5
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O11—H11C···O220.842.022.675 (2)134
O21—H21C···O120.842.092.677 (2)127

Experimental details

Crystal data
Chemical formulaC9H7ClN2O2
Mr210.62
Crystal system, space groupMonoclinic, P21/c
Temperature (K)100
a, b, c (Å)9.3983 (4), 13.8786 (5), 13.5643 (5)
β (°) 107.663 (3)
V3)1685.86 (11)
Z8
Radiation typeCu Kα
µ (mm1)3.80
Crystal size (mm)0.14 × 0.12 × 0.08
Data collection
DiffractometerBruker APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2001)
Tmin, Tmax0.618, 0.751
No. of measured, independent and
observed [I > 2σ(I)] reflections
12070, 3061, 2420
Rint0.032
(sin θ/λ)max1)0.602
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.115, 1.05
No. of reflections3061
No. of parameters255
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.50, 0.41

Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O11—H11C···O220.842.022.675 (2)134
O21—H21C···O120.842.092.677 (2)127
 

References

First citation Bruker (2001). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citation Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
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