6-Chloro-N-methyl-5-nitro-N-phenyl­pyrimidin-4-amine

Shi, F.; Zhu, L.-H.; Mu, L.; Zhang, L.; Li, Y.-F.

doi:10.1107/S1600536811037664

organic compounds

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ISSN: 2056-9890

Volume 67| Part 10| October 2011| Page o2689

https://doi.org/10.1107/S1600536811037664

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6-Chloro-N-methyl-5-nitro-N-phenylpyrimidin-4-amine

Fuqiang Shi,^a Li-Hong Zhu,^a Li Mu,^b Long Zhang ^a and Ya-Feng Li ^a ^*

^aSchool of Chemical Engineering, Changchun University of Technology, Changchun 130012, People's Republic of China, and ^bSchool of Bioscience and Technology, Changchun University, Changchun 130022, People's Republic of China
^*Correspondence e-mail: fly012345@sohu.com

(Received 14 September 2011; accepted 15 September 2011; online 20 September 2011)

In the title compound, C₁₁H₉ClN₄O₂, the dihedral angle between the aromatic rings is 79.67 (8)°. π–π stacking between centrosymmetrically related pairs of pyrimidine rings occurs along [100] [centroid–centroid separations = 3.4572 (8) and 3.5433 (7) Å].

Related literature

For a related structure, see: Shi et al. (2011 ).

Experimental

Crystal data

C₁₁H₉ClN₄O₂
M_r = 264.67
Triclinic, $[P \overline 1]$
a = 6.8980 (14) Å
b = 8.9282 (18) Å
c = 11.427 (2) Å
α = 73.76 (3)°
β = 86.80 (3)°
γ = 84.21 (3)°
V = 672.0 (2) Å³
Z = 2
Mo Kα radiation
μ = 0.28 mm⁻¹
T = 293 K
0.44 × 0.38 × 0.13 mm

Data collection

Rigaku R-AXIS RAPID diffractometer
Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ) T_min = 0.885, T_max = 0.964
5925 measured reflections
2730 independent reflections
1742 reflections with I > 2σ(I)
R_int = 0.030

Refinement

R[F² > 2σ(F²)] = 0.049
wR(F²) = 0.154
S = 1.07
2730 reflections
164 parameters
H-atom parameters constrained
Δρ_max = 0.25 e Å⁻³
Δρ_min = −0.19 e Å⁻³

Data collection: PROCESS-AUTO (Rigaku, 1998 ); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002 ); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2000 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536811037664/ng5229sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536811037664/ng5229Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536811037664/ng5229Isup3.cml

checkCIF report

Comment top

Here, the crystal structure of 6-chloro-N-methyl-5-nitro-N-phenylpyrimidin-4-amine, the precursor of 6-chloro-N-methyl-N-phenylpyrimidine-4,5-diamine (Shi et al., 2011) is determined by X-ray single crystal diffraction.

In the structure of (I) (Fig. 1), the dihedral angle between the aromatic rings is 79.667 (81)°. Uninterrupted aromatic π-π stacking between centrosymmetrically related pairs of pyrimidine rings occurs along with [100] direction [centroid – centroid separation = 3.4572 (8)Å or 3.5433 (7)Å].

Related literature top

For a related structure, see: Shi et al. (2011).

Experimental top

To a solution of 4,6-dichloro-5-nitro-pyrimidine (2.08 g, 10.8 mmol), and triethylamine (13.0 mL, 0.55 mmol) in anhydrous THF (25 mL) was added a solution of N-methylbenzylamine (0.85 mL, 10.8 mmol) in anhydrous THF (15 mL) slowly. The reaction mixture was stirred at room temperature overnight. The reaction mixture was concentrated in vacuo, diluted with water, and extracted with EtOAc. The organic phase was washed with 1N HCl, brine, dried over anhydrous MgSO₄, and concentrated in vacuo to yield the crude product as a solid. Purification by recrystallization from methanol provided the desired pure product, 6-chloro-N-methyl-5-nitro-N-phenylpyrimidin-4-amine (yellow solid, 1.85g, 64.7%, 130.3-131.4 °C). ¹H NMR (CDCl₃, 400 Hz), δ: 8.51 (s, 1H), 7.393-7.37(m, 3H), 7.17-7.15(m, 2H), 3.57 (s, 3H); ¹³C NMR (CDCl₃, 100 Hz), δ: 156.6, 153.9, 152.4, 142.2, 129.8, 128.6, 126.3, 41.7. ES-MS: 265.0 [(M + H⁺)].

Structure description top

For a related structure, see: Shi et al. (2011).

Computing details top

Data collection: PROCESS-AUTO (Rigaku, 1998); cell refinement: PROCESS-AUTO (Rigaku, 1998); data reduction: CrystalStructure (Rigaku/MSC, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2000); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. The title compound, C₁₁H₉ClN₄O₂, with the atom-labelling scheme. Displacement ellipsoid are shown at the 50% probability level.
	Fig. 2. Aromatic π-π stacking between centrosymmetrically related pairs of pyrimidine rings along 100].

6-Chloro-N-methyl-5-nitro-N-phenylpyrimidin-4-amine top

Crystal data top

C₁₁H₉ClN₄O₂	Z = 2
M_r = 264.67	F(000) = 272
Triclinic, P1	D_x = 1.308 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 6.8980 (14) Å	Cell parameters from 500 reflections
b = 8.9282 (18) Å	θ = 3.4–27.5°
c = 11.427 (2) Å	µ = 0.28 mm⁻¹
α = 73.76 (3)°	T = 293 K
β = 86.80 (3)°	Block, colorless
γ = 84.21 (3)°	0.44 × 0.38 × 0.13 mm
V = 672.0 (2) Å³

Data collection top

Rigaku R-AXIS RAPID diffractometer	2730 independent reflections
Radiation source: fine-focus sealed tube	1742 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.030
Detector resolution: 10.00 pixels mm^-1	θ_max = 27.5°, θ_min = 3.4°
ω scans	h = −8→7
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	k = −10→10
T_min = 0.885, T_max = 0.964	l = −14→14
5925 measured reflections

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)] = 0.049	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.154	H-atom parameters constrained
S = 1.07	w = 1/[σ²(F_o²) + (0.0827P)² + 0.0097P] where P = (F_o² + 2F_c²)/3
2730 reflections	(Δ/σ)_max < 0.001
164 parameters	Δρ_max = 0.25 e Å⁻³
0 restraints	Δρ_min = −0.19 e Å⁻³

Crystal data top

C₁₁H₉ClN₄O₂	γ = 84.21 (3)°
M_r = 264.67	V = 672.0 (2) Å³
Triclinic, P1	Z = 2
a = 6.8980 (14) Å	Mo Kα radiation
b = 8.9282 (18) Å	µ = 0.28 mm⁻¹
c = 11.427 (2) Å	T = 293 K
α = 73.76 (3)°	0.44 × 0.38 × 0.13 mm
β = 86.80 (3)°

Data collection top

Rigaku R-AXIS RAPID diffractometer	2730 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	1742 reflections with I > 2σ(I)
T_min = 0.885, T_max = 0.964	R_int = 0.030
5925 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.049	0 restraints
wR(F²) = 0.154	H-atom parameters constrained
S = 1.07	Δρ_max = 0.25 e Å⁻³
2730 reflections	Δρ_min = −0.19 e Å⁻³
164 parameters

Special details top

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

	x	y	z	U_iso*/U_eq
Cl1	0.27001 (12)	0.38397 (9)	0.55435 (6)	0.0897 (3)
C1	0.2612 (3)	0.1851 (3)	0.52481 (19)	0.0585 (5)
C2	0.2496 (3)	0.1772 (2)	0.40780 (17)	0.0483 (5)
C3	0.2386 (3)	0.0133 (2)	0.38625 (17)	0.0485 (5)
C4	0.2470 (3)	−0.1014 (3)	0.59315 (19)	0.0655 (6)
H4	0.2468	−0.1895	0.6599	0.079*
N1	0.2346 (3)	−0.1270 (2)	0.48527 (16)	0.0600 (5)
N2	0.2610 (3)	0.0465 (3)	0.62119 (16)	0.0694 (6)
C5	0.2510 (3)	0.1072 (2)	0.16239 (18)	0.0544 (5)
C6	0.4329 (4)	0.1522 (3)	0.1186 (2)	0.0716 (7)
H6	0.5428	0.1063	0.1631	0.086*
C7	0.4528 (5)	0.2692 (4)	0.0051 (3)	0.0954 (9)
H7	0.5759	0.3000	−0.0227	0.114*
C8	0.2935 (6)	0.3371 (4)	−0.0638 (2)	0.1037 (11)
H8	0.3077	0.4122	−0.1381	0.124*
C9	0.1135 (6)	0.2917 (4)	−0.0205 (3)	0.1034 (11)
H9	0.0043	0.3376	−0.0656	0.124*
C10	0.0897 (4)	0.1749 (3)	0.0930 (2)	0.0817 (8)
H10	−0.0337	0.1445	0.1202	0.098*
C11	0.2102 (5)	−0.1969 (3)	0.2719 (3)	0.0965 (10)
H11A	0.3338	−0.2570	0.2895	0.145*
H11B	0.1728	−0.1948	0.1917	0.145*
H11C	0.1136	−0.2440	0.3307	0.145*
N4	0.2395 (3)	0.3422 (2)	0.31108 (16)	0.0611 (5)
N3	0.2279 (3)	−0.0184 (2)	0.27815 (15)	0.0610 (5)
O1	0.0799 (3)	0.4051 (2)	0.27365 (17)	0.0885 (6)
O2	0.3903 (3)	0.4091 (2)	0.27659 (17)	0.0889 (6)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.1161 (6)	0.1002 (6)	0.0686 (4)	−0.0261 (4)	0.0009 (4)	−0.0440 (4)
C1	0.0513 (12)	0.0778 (15)	0.0475 (11)	−0.0073 (9)	−0.0013 (9)	−0.0187 (10)
C2	0.0444 (10)	0.0555 (12)	0.0418 (10)	−0.0054 (8)	0.0014 (8)	−0.0081 (9)
C3	0.0462 (11)	0.0536 (12)	0.0419 (10)	−0.0013 (8)	0.0020 (8)	−0.0082 (9)
C4	0.0575 (13)	0.0777 (16)	0.0451 (12)	0.0008 (10)	−0.0005 (9)	0.0073 (11)
N1	0.0608 (11)	0.0606 (11)	0.0494 (10)	−0.0012 (8)	0.0025 (8)	−0.0022 (8)
N2	0.0645 (12)	0.0960 (15)	0.0422 (10)	−0.0040 (10)	−0.0054 (8)	−0.0101 (10)
C5	0.0695 (14)	0.0575 (12)	0.0366 (10)	−0.0065 (9)	0.0008 (9)	−0.0137 (9)
C6	0.0695 (16)	0.0932 (18)	0.0524 (13)	−0.0116 (12)	0.0033 (11)	−0.0199 (12)
C7	0.103 (2)	0.123 (2)	0.0616 (16)	−0.0383 (18)	0.0260 (16)	−0.0237 (16)
C8	0.158 (3)	0.105 (2)	0.0433 (14)	−0.033 (2)	0.0002 (18)	−0.0056 (14)
C9	0.129 (3)	0.107 (2)	0.0651 (17)	−0.0076 (19)	−0.0391 (19)	−0.0022 (16)
C10	0.0740 (17)	0.102 (2)	0.0656 (15)	−0.0096 (13)	−0.0142 (13)	−0.0141 (14)
C11	0.170 (3)	0.0617 (16)	0.0635 (16)	−0.0234 (16)	0.0113 (17)	−0.0244 (12)
N4	0.0828 (14)	0.0553 (11)	0.0452 (10)	−0.0049 (9)	0.0051 (9)	−0.0154 (8)
N3	0.0842 (13)	0.0542 (11)	0.0436 (9)	−0.0103 (8)	0.0035 (8)	−0.0115 (8)
O1	0.0992 (14)	0.0837 (13)	0.0688 (11)	0.0162 (10)	−0.0197 (10)	−0.0035 (9)
O2	0.1063 (15)	0.0742 (12)	0.0829 (13)	−0.0353 (10)	0.0259 (11)	−0.0125 (9)

Geometric parameters (Å, º) top

Cl1—C1	1.905 (2)	C6—H6	0.9300
C1—C2	1.366 (3)	C7—C8	1.375 (5)
C1—N2	1.408 (3)	C7—H7	0.9300
C2—C3	1.560 (3)	C8—C9	1.368 (4)
C2—N4	1.573 (3)	C8—H8	0.9300
C3—N3	1.349 (3)	C9—C10	1.431 (4)
C3—N1	1.436 (2)	C9—H9	0.9300
C4—N1	1.324 (3)	C10—H10	0.9300
C4—N2	1.456 (3)	C11—N3	1.633 (3)
C4—H4	0.9300	C11—H11A	0.9600
C5—C6	1.380 (3)	C11—H11B	0.9600
C5—C10	1.388 (3)	C11—H11C	0.9600
C5—N3	1.488 (3)	N4—O1	1.226 (2)
C6—C7	1.430 (4)	N4—O2	1.242 (3)

C2—C1—N2	119.2 (2)	C6—C7—H7	119.4
C2—C1—Cl1	119.29 (17)	C9—C8—C7	118.4 (2)
N2—C1—Cl1	121.46 (16)	C9—C8—H8	120.8
C1—C2—C3	118.29 (17)	C7—C8—H8	120.8
C1—C2—N4	113.29 (18)	C8—C9—C10	121.4 (3)
C3—C2—N4	128.35 (16)	C8—C9—H9	119.3
N3—C3—N1	110.90 (18)	C10—C9—H9	119.3
N3—C3—C2	127.02 (16)	C5—C10—C9	120.0 (3)
N1—C3—C2	122.06 (17)	C5—C10—H10	120.0
N1—C4—N2	128.60 (19)	C9—C10—H10	120.0
N1—C4—H4	115.7	N3—C11—H11A	109.5
N2—C4—H4	115.7	N3—C11—H11B	109.5
C4—N1—C3	112.86 (19)	H11A—C11—H11B	109.5
C1—N2—C4	118.93 (18)	N3—C11—H11C	109.5
C6—C5—C10	118.8 (2)	H11A—C11—H11C	109.5
C6—C5—N3	121.0 (2)	H11B—C11—H11C	109.5
C10—C5—N3	120.1 (2)	O1—N4—O2	120.9 (2)
C5—C6—C7	120.2 (2)	O1—N4—C2	118.81 (18)
C5—C6—H6	119.9	O2—N4—C2	120.25 (19)
C7—C6—H6	119.9	C3—N3—C5	120.02 (17)
C8—C7—C6	121.2 (3)	C3—N3—C11	120.80 (17)
C8—C7—H7	119.4	C5—N3—C11	118.93 (17)

Experimental details

Crystal data
Chemical formula	C₁₁H₉ClN₄O₂
M_r	264.67
Crystal system, space group	Triclinic, P1
Temperature (K)	293
a, b, c (Å)	6.8980 (14), 8.9282 (18), 11.427 (2)
α, β, γ (°)	73.76 (3), 86.80 (3), 84.21 (3)
V (Å³)	672.0 (2)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	0.28
Crystal size (mm)	0.44 × 0.38 × 0.13

Data collection
Diffractometer	Rigaku R-AXIS RAPID
Absorption correction	Multi-scan (ABSCOR; Higashi, 1995)
T_min, T_max	0.885, 0.964
No. of measured, independent and observed [I > 2σ(I)] reflections	5925, 2730, 1742
R_int	0.030
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.049, 0.154, 1.07
No. of reflections	2730
No. of parameters	164
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.25, −0.19

Computer programs: PROCESS-AUTO (Rigaku, 1998), CrystalStructure (Rigaku/MSC, 2002), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2000).

Acknowledgements

This project is sponsored by the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry (grant No. 20071108) and the Scientific Research Foundation for the Returned Overseas Team, Chinese Education Ministry.

References

Brandenburg, K. (2000). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan. Google Scholar
Rigaku (1998). PROCESS-AUTO. Rigaku Corporation, Tokyo, Japan. Google Scholar
Rigaku/MSC (2002). CrystalStructure. Rigaku/MSC, The Woodlands, Texas, USA. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Shi, F., Zhu, L.-H., Zhang, L. & Li, Y.-F. (2011). Acta Cryst. E67, o2089. Web of Science CSD CrossRef IUCr Journals Google Scholar