4-Amino-2-phenoxy­pyrimidine

Shah Bakhtiar, N.; Abdullah, Z.; Ng, S.W.

doi:10.1107/S1600536809026580

organic compounds

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Volume 65| Part 8| August 2009| Page o1858

doi:10.1107/S1600536809026580

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4-Amino-2-phenoxypyrimidine

Nasir Shah Bakhtiar,^a Zanariah Abdullah ^a and Seik Weng Ng ^a ^*

^aDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
^*Correspondence e-mail: seikweng@um.edu.my

(Received 7 July 2009; accepted 8 July 2009; online 15 July 2009)

In the title compound, C₁₀H₉N₃O, the organic rings linked to the ether O atom make a dihedral angle of 76.8 (1)° and the C—O—C angle is widened to 119.07 (15)°. In the crystal, adjacent molecules are connected by an N—H⋯N hydrogen bond, generating a chain running parallel to the b axis. The crystal is a non-merohedral twin with a ratio of twin components of 0.508 (3):0.492 (3).

Related literature

For 2-phenoxypyrimidine, see: Shah Bakhtiar et al. (2009 ). For the procedure to cope with twinned diffraction data, see: Spek (2003 ).

Experimental

Crystal data

C₁₀H₉N₃O
M_r = 187.20
Monoclinic, P 2₁ /n
a = 8.8443 (3) Å
b = 12.1214 (3) Å
c = 9.0415 (2) Å
β = 96.751 (2)°
V = 962.58 (5) Å³
Z = 4
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 120 K
0.40 × 0.20 × 0.10 mm

Data collection

Bruker SMART APEX diffractometer
Absorption correction: none
6375 measured reflections
2178 independent reflections
1694 reflections with I > 2σ(I)
R_int = 0.028

Refinement

R[F² > 2σ(F²)] = 0.055
wR(F²) = 0.163
S = 1.10
2178 reflections
136 parameters
2 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.43 e Å⁻³
Δρ_min = −0.32 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H1⋯N1ⁱ	0.88 (1)	2.12 (1)	2.992 (2)	173 (2)
Symmetry code: (i) $[-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: APEX2 (Bruker, 2008 ); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001 ); software used to prepare material for publication: publCIF (Westrip, 2009 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809026580/bt2994sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809026580/bt2994Isup2.hkl

checkCIF report

Related literature top

For 2-phenoxypyrimidine, see: Shah Bakhtiar et al. (2009). For the procedure to cope with twinned diffraction data, see: Spek (2003).

Experimental top

Phenol (1.88 g, 20 mmol) and sodium hydroxide (0.80 g, 20 mmol) were dissolved in water (50 ml) and to the solution was added 4-amino-2-chloropyridimidine (2.60 g, 20 mmol) dissolved in THF (50 ml). The mixture was heated for 4 h. Water was added and the organic phase was extracted with chloroform. The chloroform solution was dried over sodium sulfate; slow evaporation led to the formation of colorless crystals.

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: publCIF (Westrip, 2009).

Figures top

Fig. 1. Anisotropic displacement ellipsoid plot (Barbour, 2001) of C₁₀H₉N₃O at the 70% probability level; hydrogen atoms are drawn as spheres of arbitrary radius.

4-Amino-2-phenoxypyrimidine top

Crystal data top

C₁₀H₉N₃O	F(000) = 392
M_r = 187.20	D_x = 1.292 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 2238 reflections
a = 8.8443 (3) Å	θ = 2.3–27.9°
b = 12.1214 (3) Å	µ = 0.09 mm⁻¹
c = 9.0415 (2) Å	T = 120 K
β = 96.751 (2)°	Block, colorless
V = 962.58 (5) Å³	0.40 × 0.20 × 0.10 mm
Z = 4

Data collection top

Bruker SMART APEX diffractometer	1694 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.028
Graphite monochromator	θ_max = 27.5°, θ_min = 2.8°
ω scans	h = −10→11
6375 measured reflections	k = −15→15
2178 independent reflections	l = −10→11

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)] = 0.055	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.163	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	w = 1/[σ²(F_o²) + (0.0791P)² + 0.3378P] where P = (F_o² + 2F_c²)/3
2178 reflections	(Δ/σ)_max = 0.001
136 parameters	Δρ_max = 0.43 e Å⁻³
2 restraints	Δρ_min = −0.32 e Å⁻³

Crystal data top

C₁₀H₉N₃O	V = 962.58 (5) Å³
M_r = 187.20	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 8.8443 (3) Å	µ = 0.09 mm⁻¹
b = 12.1214 (3) Å	T = 120 K
c = 9.0415 (2) Å	0.40 × 0.20 × 0.10 mm
β = 96.751 (2)°

Data collection top

Bruker SMART APEX diffractometer	1694 reflections with I > 2σ(I)
6375 measured reflections	R_int = 0.028
2178 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.055	2 restraints
wR(F²) = 0.163	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	Δρ_max = 0.43 e Å⁻³
2178 reflections	Δρ_min = −0.32 e Å⁻³
136 parameters

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.2422 (2)	0.48867 (12)	−0.00659 (16)	0.0317 (4)
N1	0.2790 (2)	0.36872 (13)	0.19209 (18)	0.0235 (4)
N2	0.2591 (2)	0.56448 (13)	0.21860 (17)	0.0213 (4)
N3	0.2755 (3)	0.64646 (15)	0.4479 (2)	0.0348 (5)
H1	0.252 (3)	0.7092 (13)	0.402 (2)	0.030 (7)*
H2	0.284 (3)	0.641 (2)	0.5458 (11)	0.037 (7)*
C1	0.2551 (3)	0.39941 (16)	−0.1029 (2)	0.0220 (5)
C2	0.3964 (3)	0.35937 (18)	−0.1237 (2)	0.0264 (5)
H2A	0.4857	0.3889	−0.0693	0.032*
C3	0.4063 (3)	0.27495 (19)	−0.2257 (2)	0.0339 (6)
H3	0.5030	0.2460	−0.2410	0.041*
C4	0.2763 (4)	0.23278 (18)	−0.3052 (2)	0.0369 (7)
H4	0.2836	0.1744	−0.3741	0.044*
C5	0.1354 (3)	0.2756 (2)	−0.2843 (2)	0.0374 (6)
H5	0.0461	0.2475	−0.3403	0.045*
C6	0.1240 (3)	0.35942 (19)	−0.1819 (2)	0.0307 (5)
H6	0.0274	0.3887	−0.1665	0.037*
C7	0.2617 (2)	0.47102 (16)	0.1428 (2)	0.0197 (4)
C8	0.2997 (3)	0.36125 (17)	0.3429 (2)	0.0283 (5)
H8	0.3133	0.2900	0.3862	0.034*
C9	0.3022 (3)	0.44951 (17)	0.4354 (2)	0.0296 (5)
H9	0.3190	0.4413	0.5405	0.036*
C10	0.2785 (3)	0.55438 (16)	0.3677 (2)	0.0236 (5)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0606 (12)	0.0159 (7)	0.0178 (7)	0.0050 (7)	0.0018 (7)	0.0013 (5)
N1	0.0341 (11)	0.0165 (8)	0.0197 (8)	0.0014 (7)	0.0032 (7)	0.0007 (6)
N2	0.0281 (10)	0.0149 (8)	0.0212 (8)	0.0028 (7)	0.0038 (7)	0.0003 (6)
N3	0.0665 (16)	0.0182 (9)	0.0204 (9)	0.0070 (9)	0.0083 (9)	−0.0008 (7)
C1	0.0351 (13)	0.0156 (9)	0.0151 (9)	0.0006 (8)	0.0018 (8)	0.0031 (7)
C2	0.0301 (12)	0.0255 (10)	0.0229 (10)	−0.0038 (9)	0.0005 (9)	0.0044 (8)
C3	0.0476 (15)	0.0264 (11)	0.0310 (11)	0.0084 (11)	0.0186 (11)	0.0062 (9)
C4	0.073 (2)	0.0193 (10)	0.0198 (10)	−0.0061 (12)	0.0127 (11)	−0.0026 (8)
C5	0.0511 (17)	0.0348 (12)	0.0238 (11)	−0.0161 (12)	−0.0058 (11)	0.0001 (9)
C6	0.0311 (13)	0.0319 (12)	0.0284 (11)	0.0006 (10)	0.0013 (10)	0.0036 (9)
C7	0.0217 (11)	0.0186 (9)	0.0185 (9)	0.0015 (8)	0.0012 (8)	0.0019 (7)
C8	0.0455 (14)	0.0174 (9)	0.0221 (10)	0.0044 (9)	0.0046 (9)	0.0046 (7)
C9	0.0482 (15)	0.0216 (10)	0.0194 (9)	0.0028 (10)	0.0057 (9)	0.0027 (7)
C10	0.0312 (12)	0.0181 (9)	0.0223 (9)	0.0008 (8)	0.0062 (9)	−0.0007 (7)

Geometric parameters (Å, º) top

O1—C7	1.359 (2)	C2—H2A	0.9500
O1—C1	1.402 (2)	C3—C4	1.380 (4)
N1—C7	1.320 (2)	C3—H3	0.9500
N1—C8	1.357 (3)	C4—C5	1.384 (4)
N2—C7	1.326 (2)	C4—H4	0.9500
N2—C10	1.344 (2)	C5—C6	1.386 (3)
N3—C10	1.333 (3)	C5—H5	0.9500
N3—H1	0.880 (10)	C6—H6	0.9500
N3—H2	0.882 (10)	C8—C9	1.356 (3)
C1—C2	1.375 (3)	C8—H8	0.9500
C1—C6	1.376 (3)	C9—C10	1.416 (3)
C2—C3	1.387 (3)	C9—H9	0.9500

C7—O1—C1	119.07 (15)	C4—C5—C6	120.2 (2)
C7—N1—C8	113.46 (17)	C4—C5—H5	119.9
C7—N2—C10	115.63 (16)	C6—C5—H5	119.9
C10—N3—H1	119.1 (16)	C1—C6—C5	118.8 (2)
C10—N3—H2	118.5 (18)	C1—C6—H6	120.6
H1—N3—H2	122 (2)	C5—C6—H6	120.6
C2—C1—C6	121.9 (2)	N1—C7—N2	129.54 (18)
C2—C1—O1	120.0 (2)	N1—C7—O1	118.65 (17)
C6—C1—O1	118.0 (2)	N2—C7—O1	111.80 (16)
C1—C2—C3	118.7 (2)	C9—C8—N1	123.86 (18)
C1—C2—H2A	120.6	C9—C8—H8	118.1
C3—C2—H2A	120.6	N1—C8—H8	118.1
C4—C3—C2	120.4 (2)	C8—C9—C10	116.79 (18)
C4—C3—H3	119.8	C8—C9—H9	121.6
C2—C3—H3	119.8	C10—C9—H9	121.6
C3—C4—C5	119.9 (2)	N3—C10—N2	117.46 (18)
C3—C4—H4	120.0	N3—C10—C9	121.85 (18)
C5—C4—H4	120.0	N2—C10—C9	120.69 (18)

C7—O1—C1—C2	−76.8 (2)	C8—N1—C7—O1	179.1 (2)
C7—O1—C1—C6	107.6 (2)	C10—N2—C7—N1	0.8 (3)
C6—C1—C2—C3	−1.1 (3)	C10—N2—C7—O1	−179.63 (19)
O1—C1—C2—C3	−176.53 (17)	C1—O1—C7—N1	−5.8 (3)
C1—C2—C3—C4	0.4 (3)	C1—O1—C7—N2	174.56 (18)
C2—C3—C4—C5	0.7 (3)	C7—N1—C8—C9	0.2 (4)
C3—C4—C5—C6	−1.2 (3)	N1—C8—C9—C10	1.3 (4)
C2—C1—C6—C5	0.6 (3)	C7—N2—C10—N3	−179.5 (2)
O1—C1—C6—C5	176.15 (18)	C7—N2—C10—C9	0.9 (3)
C4—C5—C6—C1	0.5 (3)	C8—C9—C10—N3	178.6 (2)
C8—N1—C7—N2	−1.3 (3)	C8—C9—C10—N2	−1.8 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H1···N1ⁱ	0.88 (1)	2.12 (1)	2.992 (2)	173 (2)

Symmetry code: (i) −x+1/2, y+1/2, −z+1/2.

Experimental details

Crystal data
Chemical formula	C₁₀H₉N₃O
M_r	187.20
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	120
a, b, c (Å)	8.8443 (3), 12.1214 (3), 9.0415 (2)
β (°)	96.751 (2)
V (Å³)	962.58 (5)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.40 × 0.20 × 0.10

Data collection
Diffractometer	Bruker SMART APEX diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	6375, 2178, 1694
R_int	0.028
(sin θ/λ)_max (Å⁻¹)	0.650

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.055, 0.163, 1.10
No. of reflections	2178
No. of parameters	136
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)	0.43, −0.32

Computer programs: APEX2 (Bruker, 2008), SAINT (Bruker, 2008), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), X-SEED (Barbour, 2001), publCIF (Westrip, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H1···N1ⁱ	0.88 (1)	2.12 (1)	2.992 (2)	173 (2)

Symmetry code: (i) −x+1/2, y+1/2, −z+1/2.

Acknowledgements

We thank the University of Malaya (FP047/2008 C, RG027/09AFR) for supporting this study.

References

Barbour, L. J. (2001). J. Supramol. Chem. 1, 189–191. CrossRef CAS Google Scholar
Bruker (2008). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Shah Bakhtiar, N., Abdullah, Z. & Ng, S. W. (2009). Acta Cryst. E65, o114. Web of Science CSD CrossRef IUCr Journals Google Scholar
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Westrip, S. P. (2009). publCIF. In preparation. Google Scholar