N-(2-Bromo­phenyl)-2-(4,6-di­methoxy­pyrimidin-2-yl­oxy)­benzyl­amine

Wu, J.; Zhang, P.-Z.; Yu, Q.-S.; Hu, X.-R.; Gu, J.-M.

doi:10.1107/S160053680301852X

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N-(2-Bromophenyl)-2-(4,6-dimethoxypyrimidin-2-yloxy)benzylamine

J. Wu, P.-Z. Zhang, Q.-S. Yu, X.-R. Hu and J.-M. Gu

The title compound, C₁₉H₁₈BrN₃O₃, was synthesized by the reaction of 2-methanesulfonyl-4,6-dimethoxypyrimidine and N-(2-bromophenyl)-2-hydroxybenzylamine in tetrahydrofuran. There are three different planes in the molecule, each of which is conjugated. The dihedral angles between the pyrimidine plane and the planes of the two phenyl rings are 107.85 (4) and 77.38 (2)°, and the dihedral angle between the planes of the two phenyl rings is 103.15 (3)°.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S160053680301852X/om6161sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S160053680301852X/om6161Isup2.hkl Contains datablock I

CCDC reference: 222905

checkCIF report

Key indicators

Single-crystal X-ray study
T = 296 K
Mean (C-C) = 0.006 Å
R factor = 0.048
wR factor = 0.130
Data-to-parameter ratio = 11.0

checkCIF/PLATON results

No syntax errors found



Alert level C
ABSTM02_ALERT_3_C  The ratio of expected to reported Tmax/Tmin(RR) is > 1.10
            Tmin and Tmax reported:      0.678     0.854
            Tmin and Tmax expected:      0.574     0.854
            RR =      1.180
            Please check that your absorption correction is appropriate.
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low .......       0.99
PLAT060_ALERT_3_C Ratio Tmax/Tmin (Exp-to-Rep) (too) Large .......       1.19
PLAT152_ALERT_1_C Supplied and Calc Volume s.u. Inconsistent .....          ?

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   4 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   3 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion

Comment top

4,6-Dimethoxypyrimidines with a phenoxy substituent at the 2-position exhibit marked herbicidal activity (Nezu et al., 1996; Tamaru et al., 1997; Hudson et al., 2002). The new title compound, (I), has shown herbicidal activity against various grass and broadleaf weeds. The present X-ray crystal structure analysis was undertaken in order to improve our understanding of the relationship between structure and activity.

The bond lengths and angles in the pyrimidine moiety are close to those found in related compounds (Hall et al., 1999; Lin et al., 2001), but the N2—C14—N3 angle [129.7 (3)°] deviates significantly from the normal value. The angles in the two benzene rings are close to 120° (Huo et al., 1995), except for the C9—C8—C13 and C2—C1—C6 angles [116.9 (3) and 116.2 (3)°, respectively; Table 1).

The fact that the C9—O1—C14 angle is 119.7 (3)° shows the influence of the pyrimidine and benzene ring on the ether angle (Takashima et al., 1999). The widening of the C1—N1—C7 angle [to 122.5 (3)°] from 108° may be due to steric interaction. The N1—C1 bond distance [1.368 (5) Å] is close to that of a C═N double bond and is probably caused by delocalization of benzene electrons (Table 1).

There is one intramolecular hydrogen bond [N1···Br1=3.065 (3) Å and N1—H5···Br1=122.43°]. The dihedral angles between the pyrimidine plane and the two benzene rings are 107.85 (4) and 77.38 (2)°, and the dihedral angle between the two benzene rings is 103.15 (3)°

Experimental top

To a mixture of N-(2-bromophenyl)-2-hydroxybenzylamine (4.29 g, 5.5 mmol) and potassium carbonate (12.96 g, 46.5 mmol) in tetrahydrofuran (THF; 100 ml), a solution of 2-methanesulfonyl- 4,6-dimethoxypyrimidine (7.50 g, 17.2 mmol) in THF (40 ml) was added dropwise and stirred for 11 h under reflux. The solid was filtered off and the filtrate was evaporated. A single-crystal suitable for X-ray analysis was obtained by recrystallization from ethanol solution. Upon slow evaporation at room temperature for 5 d, a colorless crystalline solid appeared and was collected by filtration.

Computing details top

Data collection: PROCESS-AUTO (Rigaku, 2003); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku, 2003); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: CRYSTALS (Watkin et al., 1996); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: CrystalStructure.

Figures top

Fig. 1. The molecular structure of (I), showing ellipsoids at the 30% probability level.

(I) top

Crystal data top

C₁₉H₁₈BrN₃O₃	Z = 2
M_r = 416.27	F(000) = 424.00
Triclinic, P1	D_x = 1.499 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.7107 Å
a = 8.7821 (5) Å	Cell parameters from 3573 reflections
b = 10.3347 (6) Å	θ = 2.1–27.4°
c = 10.975 (1) Å	µ = 2.26 mm⁻¹
α = 104.779 (5)°	T = 296 K
β = 92.572 (2)°	Platelet, colorless
γ = 105.331 (2)°	0.36 × 0.21 × 0.07 mm
V = 922.1 (1) Å³

Data collection top

Rigaku RAXIS-RAPID diffractometer	2351 reflections with F² > 2.0σ(F²)
Detector resolution: 10.00 pixels mm^-1	R_int = 0.029
ω scans	θ_max = 27.5°
Absorption correction: multi-scan (ABSCOR; Higashi,1995)	h = −9→11
T_min = 0.678, T_max = 0.854	k = −13→13
17152 measured reflections	l = −14→14
4157 independent reflections

Refinement top

Refinement on F²	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.048	w = 1/[0.002F_o² + 1.35σ(F_o²)]/(4F_o²)
wR(F²) = 0.130	(Δ/σ)_max = 0.0001
S = 1.01	Δρ_max = 0.97 e Å⁻³
2788 reflections	Δρ_min = −0.67 e Å⁻³
253 parameters

Crystal data top

C₁₉H₁₈BrN₃O₃	γ = 105.331 (2)°
M_r = 416.27	V = 922.1 (1) Å³
Triclinic, P1	Z = 2
a = 8.7821 (5) Å	Mo Kα radiation
b = 10.3347 (6) Å	µ = 2.26 mm⁻¹
c = 10.975 (1) Å	T = 296 K
α = 104.779 (5)°	0.36 × 0.21 × 0.07 mm
β = 92.572 (2)°

Data collection top

Rigaku RAXIS-RAPID diffractometer	4157 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi,1995)	2351 reflections with F² > 2.0σ(F²)
T_min = 0.678, T_max = 0.854	R_int = 0.029
17152 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.048	253 parameters
wR(F²) = 0.130	H-atom parameters constrained
S = 1.01	Δρ_max = 0.97 e Å⁻³
2788 reflections	Δρ_min = −0.67 e Å⁻³

Special details top

Geometry. ENTER SPECIAL DETAILS OF THE MOLECULAR GEOMETRY

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

	x	y	z	U_iso*/U_eq
Br(1)	0.51346 (7)	−0.03208 (5)	0.29600 (6)	0.0805 (2)
O(1)	0.3026 (3)	0.4381 (2)	−0.0331 (3)	0.0434 (7)
O(2)	0.1436 (3)	0.1535 (3)	−0.4310 (3)	0.0524 (9)
O(3)	−0.1442 (3)	0.0659 (3)	−0.0984 (3)	0.0511 (8)
N(1)	0.4486 (4)	0.2015 (3)	0.1958 (3)	0.0453 (9)
N(2)	0.2240 (4)	0.2997 (3)	−0.2293 (3)	0.0398 (9)
N(3)	0.0771 (3)	0.2555 (3)	−0.0594 (3)	0.0365 (8)
C(1)	0.6000 (4)	0.2376 (3)	0.2557 (3)	0.035 (1)
C(2)	0.6522 (5)	0.1475 (4)	0.3121 (4)	0.043 (1)
C(3)	0.8043 (5)	0.1810 (5)	0.3721 (4)	0.056 (1)
C(4)	0.9089 (5)	0.3069 (5)	0.3774 (5)	0.063 (1)
C(5)	0.8630 (5)	0.3991 (4)	0.3252 (4)	0.056 (1)
C(6)	0.7105 (5)	0.3664 (4)	0.2654 (4)	0.044 (1)
C(7)	0.4026 (5)	0.2749 (4)	0.1092 (4)	0.045 (1)
C(8)	0.3502 (4)	0.4016 (3)	0.1732 (4)	0.034 (1)
C(9)	0.2941 (4)	0.4743 (3)	0.0984 (4)	0.037 (1)
C(10)	0.2439 (5)	0.5894 (4)	0.1510 (5)	0.052 (1)
C(11)	0.2493 (5)	0.6348 (4)	0.2800 (5)	0.054 (1)
C(12)	0.3049 (5)	0.5664 (4)	0.3564 (4)	0.048 (1)
C(13)	0.3547 (4)	0.4513 (4)	0.3024 (4)	0.043 (1)
C(14)	0.1935 (4)	0.3243 (3)	−0.1103 (4)	0.037 (1)
C(15)	0.1204 (4)	0.1869 (4)	−0.3081 (4)	0.039 (1)
C(16)	−0.0061 (4)	0.1044 (4)	−0.2689 (4)	0.045 (1)
C(17)	−0.0232 (4)	0.1429 (4)	−0.1429 (4)	0.038 (1)
C(18)	0.2807 (6)	0.2364 (5)	−0.4681 (4)	0.059 (1)
C(19)	−0.1643 (6)	0.1100 (5)	0.0314 (5)	0.067 (2)
H(1)	0.8376	0.1135	0.4108	0.069*
H(2)	1.0197	0.3320	0.4204	0.069*
H(3)	0.9405	0.4911	0.3300	0.063*
H(4)	0.6781	0.4349	0.2277	0.050*
H(5)	0.3917	0.1127	0.2010	0.054*
H(6)	0.4969	0.3072	0.0653	0.054*
H(7)	0.3137	0.2080	0.0450	0.054*
H(8)	0.2029	0.6387	0.0953	0.063*
H(9)	0.2123	0.7181	0.3187	0.063*
H(10)	0.3107	0.6010	0.4508	0.054*
H(11)	0.3946	0.4019	0.3586	0.051*
H(12)	−0.0819	0.0204	−0.3295	0.050*
H(13)	0.3789	0.2335	−0.4204	0.071*
H(14)	0.2836	0.1996	−0.5613	0.071*
H(15)	0.2754	0.3349	−0.4487	0.071*
H(16)	−0.0664	0.1157	0.0851	0.074*
H(17)	−0.1826	0.2042	0.0498	0.074*
H(18)	−0.2578	0.0422	0.0509	0.074*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Br(1)	0.0822 (4)	0.0505 (3)	0.1143 (6)	0.0123 (2)	−0.0103 (3)	0.0430 (3)
O(1)	0.048 (2)	0.037 (1)	0.037 (2)	−0.004 (1)	−0.009 (1)	0.015 (1)
O(2)	0.057 (2)	0.052 (2)	0.038 (2)	0.003 (1)	0.005 (1)	0.008 (1)
O(3)	0.042 (2)	0.047 (1)	0.048 (2)	−0.005 (1)	0.008 (1)	0.002 (1)
N(1)	0.045 (2)	0.033 (2)	0.056 (2)	0.005 (1)	−0.013 (2)	0.018 (1)
N(2)	0.045 (2)	0.035 (2)	0.038 (2)	0.006 (1)	−0.004 (2)	0.014 (1)
N(3)	0.035 (2)	0.035 (1)	0.036 (2)	0.006 (1)	−0.002 (1)	0.011 (1)
C(1)	0.037 (2)	0.036 (2)	0.032 (2)	0.011 (1)	0.003 (2)	0.008 (1)
C(2)	0.048 (2)	0.038 (2)	0.043 (3)	0.016 (2)	0.002 (2)	0.011 (2)
C(3)	0.058 (3)	0.064 (3)	0.050 (3)	0.034 (2)	−0.007 (2)	0.007 (2)
C(4)	0.037 (2)	0.073 (3)	0.064 (3)	0.016 (2)	−0.008 (2)	−0.007 (2)
C(5)	0.050 (3)	0.047 (2)	0.060 (3)	0.007 (2)	0.007 (2)	0.001 (2)
C(6)	0.048 (2)	0.034 (2)	0.045 (3)	0.006 (2)	0.005 (2)	0.007 (2)
C(7)	0.056 (2)	0.037 (2)	0.042 (2)	0.017 (2)	−0.010 (2)	0.008 (2)
C(8)	0.034 (2)	0.029 (2)	0.036 (2)	0.004 (1)	−0.001 (2)	0.010 (1)
C(9)	0.037 (2)	0.030 (2)	0.036 (2)	−0.000 (1)	−0.006 (2)	0.009 (1)
C(10)	0.052 (2)	0.035 (2)	0.070 (3)	0.010 (2)	−0.002 (2)	0.022 (2)
C(11)	0.050 (3)	0.037 (2)	0.070 (3)	0.013 (2)	0.012 (2)	0.005 (2)
C(12)	0.040 (2)	0.054 (2)	0.041 (3)	0.006 (2)	0.006 (2)	0.002 (2)
C(13)	0.040 (2)	0.048 (2)	0.038 (3)	0.008 (2)	0.003 (2)	0.015 (2)
C(14)	0.040 (2)	0.030 (2)	0.040 (3)	0.007 (1)	−0.009 (2)	0.014 (2)
C(15)	0.044 (2)	0.038 (2)	0.036 (3)	0.015 (2)	−0.001 (2)	0.009 (2)
C(16)	0.042 (2)	0.039 (2)	0.044 (3)	0.003 (2)	−0.002 (2)	0.005 (2)
C(17)	0.028 (2)	0.037 (2)	0.046 (3)	0.008 (1)	−0.001 (2)	0.011 (2)
C(18)	0.074 (3)	0.059 (3)	0.046 (3)	0.011 (2)	0.017 (2)	0.020 (2)
C(19)	0.070 (3)	0.056 (3)	0.060 (3)	0.000 (2)	0.026 (3)	0.006 (2)

Geometric parameters (Å, º) top

Br(1)—C(2)	1.891 (3)	C(6)—H(4)	1.000
O(1)—C(9)	1.406 (5)	C(7)—C(8)	1.516 (5)
O(1)—C(14)	1.357 (3)	C(7)—H(6)	1.000
O(2)—C(15)	1.343 (5)	C(7)—H(7)	1.000
O(2)—C(18)	1.423 (5)	C(8)—C(9)	1.397 (6)
O(3)—C(17)	1.342 (5)	C(8)—C(13)	1.375 (5)
O(3)—C(19)	1.415 (6)	C(9)—C(10)	1.376 (5)
N(1)—C(1)	1.368 (5)	C(10)—C(11)	1.367 (7)
N(1)—C(7)	1.463 (6)	C(10)—H(8)	1.000
N(1)—H(5)	0.939	C(11)—C(12)	1.375 (7)
N(2)—C(14)	1.319 (5)	C(11)—H(9)	1.000
N(2)—C(15)	1.337 (4)	C(12)—C(13)	1.377 (6)
N(3)—C(14)	1.316 (5)	C(12)—H(10)	1.000
N(3)—C(17)	1.346 (4)	C(13)—H(11)	1.000
C(1)—C(2)	1.399 (6)	C(15)—C(16)	1.369 (5)
C(1)—C(6)	1.400 (5)	C(16)—C(17)	1.364 (6)
C(2)—C(3)	1.377 (6)	C(16)—H(12)	1.000
C(3)—C(4)	1.366 (6)	C(18)—H(13)	1.000
C(3)—H(1)	1.000	C(18)—H(14)	1.000
C(4)—C(5)	1.363 (8)	C(18)—H(15)	1.000
C(4)—H(2)	1.000	C(19)—H(16)	1.000
C(5)—C(6)	1.381 (6)	C(19)—H(17)	1.000
C(5)—H(3)	1.000	C(19)—H(18)	1.000

C(9)—O(1)—C(14)	119.7 (3)	O(1)—C(9)—C(8)	119.7 (3)
C(15)—O(2)—C(18)	118.0 (3)	C(11)—C(10)—H(8)	120.4
C(17)—O(3)—C(19)	118.8 (3)	C(11)—C(10)—C(9)	119.4 (5)
C(1)—N(1)—C(7)	122.5 (3)	H(8)—C(10)—C(9)	120.2)
C(1)—N(1)—H(5)	110.0	C(12)—C(11)—H(9)	120.0
C(7)—N(1)—H(5)	125.6	C(12)—C(11)—C(10)	120.3 (4)
C(14)—N(2)—C(15)	114.0 (3)	H(9)—C(11)—C(10)	119.7
C(14)—N(3)—C(17)	113.8 (3)	C(13)—C(12)—H(10)	120.2
C(2)—C(1)—C(6)	116.2 (3)	C(13)—C(12)—C(11)	119.7 (4)
C(2)—C(1)—N(1)	121.4 (3)	H(10)—C(12)—C(11)	120.1
C(6)—C(1)—N(1)	122.4 (4)	H(11)—C(13)—C(8)	118.9
C(3)—C(2)—Br(1)	118.6 (3)	H(11)—C(13)—C(12)	119.2
C(3)—C(2)—C(1)	122.5 (3)	C(8)—C(13)—C(12)	121.9 (4)
Br(1)—C(2)—C(1)	118.8 (3)	O(1)—C(14)—N(2)	112.2 (3)
C(4)—C(3)—H(1)	120.6	O(1)—C(14)—N(3)	118.2 (3)
C(4)—C(3)—C(2)	119.2 (5)	N(2)—C(14)—N(3)	129.7 (3)
H(1)—C(3)—C(2)	120.3	C(16)—C(15)—O(2)	119.1 (3)
C(5)—C(4)—H(2)	119.7	C(16)—C(15)—N(2)	123.1 (4)
C(5)—C(4)—C(3)	120.5 (4)	O(2)—C(15)—N(2)	117.9 (3)
H(2)—C(4)—C(3)	119.8	C(17)—C(16)—H(12)	121.8
C(6)—C(5)—H(3)	119.6	C(17)—C(16)—C(15)	116.5 (3)
C(6)—C(5)—C(4)	120.6 (4)	H(12)—C(16)—C(15)	121.7
H(3)—C(5)—C(4)	119.8	O(3)—C(17)—N(3)	117.6 (3)
H(4)—C(6)—C(1)	119.1	O(3)—C(17)—C(16)	119.4 (3)
H(4)—C(6)—C(5)	119.9	N(3)—C(17)—C(16)	123.0 (3)
C(1)—C(6)—C(5)	121.0 (4)	H(13)—C(18)—H(14)	109.5
C(8)—C(7)—H(6)	107.8	H(13)—C(18)—H(15)	109.5
C(8)—C(7)—H(7)	108.7	H(13)—C(18)—O(2)	109.9
C(8)—C(7)—N(1)	114.5 (3)	H(14)—C(18)—H(15)	109.5
H(6)—C(7)—H(7)	109.5	H(14)—C(18)—O(2)	109.6
H(6)—C(7)—N(1)	107.7	H(15)—C(18)—O(2)	109.0
H(7)—C(7)—N(1)	108.6	H(16)—C(19)—H(17)	109.5
C(9)—C(8)—C(13)	116.9 (3)	H(16)—C(19)—H(18)	109.5
C(9)—C(8)—C(7)	119.2 (3)	H(16)—C(19)—O(3)	109.6
C(13)—C(8)—C(7)	123.9 (4)	H(17)—C(19)—H(18)	109.5
C(10)—C(9)—O(1)	118.3 (4)	H(17)—C(19)—O(3)	109.0
C(10)—C(9)—C(8)	121.8 (4)	H(18)—C(19)—O(3)	109.9

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N(1)—H(5)···Br(1)	0.94	2.45	3.065 (3)	122

Experimental details

Crystal data
Chemical formula	C₁₉H₁₈BrN₃O₃
M_r	416.27
Crystal system, space group	Triclinic, P1
Temperature (K)	296
a, b, c (Å)	8.7821 (5), 10.3347 (6), 10.975 (1)
α, β, γ (°)	104.779 (5), 92.572 (2), 105.331 (2)
V (Å³)	922.1 (1)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	2.26
Crystal size (mm)	0.36 × 0.21 × 0.07

Data collection
Diffractometer	Rigaku RAXIS-RAPID diffractometer
Absorption correction	Multi-scan (ABSCOR; Higashi,1995)
T_min, T_max	0.678, 0.854
No. of measured, independent and observed [F² > 2.0σ(F²)] reflections	17152, 4157, 2351
R_int	0.029
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.048, 0.130, 1.01
No. of reflections	2788
No. of parameters	253
No. of restraints	?
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.97, −0.67

Computer programs: PROCESS-AUTO (Rigaku, 2003), PROCESS-AUTO, CrystalStructure (Rigaku, 2003), SHELXS97 (Sheldrick, 1997), CRYSTALS (Watkin et al., 1996), ORTEP-3 for Windows (Farrugia, 1997), CrystalStructure.

Selected bond angles (º) top

C(9)—O(1)—C(14)	119.7 (3)	C(9)—C(8)—C(13)	116.9 (3)
C(1)—N(1)—C(7)	122.5 (3)	N(2)—C(14)—N(3)	129.7 (3)
C(2)—C(1)—C(6)	116.2 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N(1)—H(5)···Br(1)	0.94	2.45	3.065 (3)	122

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