6-Chloro-N4-methyl-N4-phenyl­pyrimidine-4,5-diamine

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

doi:10.1107/S1600536811028303

organic compounds

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ISSN: 2056-9890

Volume 67| Part 8| August 2011| Page o2089

doi:10.1107/S1600536811028303

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6-Chloro-N⁴-methyl-N⁴-phenylpyrimidine-4,5-diamine

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

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

(Received 30 June 2011; accepted 14 July 2011; online 23 July 2011)

In the title compound, C₁₁H₁₁ClN₄, the dihedral angle between the aromatic rings is 66.47 (8)°. In the crystal, molecules are linked by N—H⋯N hydrogen bonds, generating C(5) chains propagating in [010]. Slipped aromatic π–π stacking between centrosymmetrically related pairs of pyrimidine rings also occurs [centroid–centroid separation = 3.7634 (12)Å and slippage = 1.715 Å].

Related literature

For background to pyrimidines, see: Barillari et al. (2001 ); Gangjee et al. (2010 ). For slipped π–π stacking interactions, see: Glówka et al. (1999 ).

Experimental

Crystal data

C₁₁H₁₁ClN₄
M_r = 234.69
Monoclinic, P 2₁ /c
a = 9.5887 (19) Å
b = 9.948 (2) Å
c = 12.671 (3) Å
β = 109.63 (3)°
V = 1138.4 (4) Å³
Z = 4
Mo Kα radiation
μ = 0.31 mm⁻¹
T = 293 K
0.45 × 0.36 × 0.33 mm

Data collection

Rigaku R-AXIS RAPID diffractometer
Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ) T_min = 0.872, T_max = 0.905
10835 measured reflections
2588 independent reflections
1983 reflections with I > 2σ(I)
R_int = 0.025

Refinement

R[F² > 2σ(F²)] = 0.037
wR(F²) = 0.105
S = 1.07
2588 reflections
146 parameters
H-atom parameters constrained
Δρ_max = 0.17 e Å⁻³
Δρ_min = −0.34 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N4—H4A⋯N1ⁱ	0.86	2.28	3.0993 (18)	159
Symmetry code: (i) $[-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: PROCESS-AUTO (Rigaku, 1998); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku, 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: 10.1107/S1600536811028303/hb5937sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811028303/hb5937Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811028303/hb5937Isup3.cml

checkCIF report

Comment top

Pyrimidine diamines exhibit a wide range of biological activities (Barillari, et al., 2001; Gangjee et al.,2010). Here, the crystal structure of the title compound, (I), is determined by X-ray single crystal diffraction.

In the structure of (I) (Fig. 1), N-methyl group links pyrimidyl and phenyl rings of which the dihedral angle is 66.62 (5)°. Two chloropyrimidyl rings of two adjacent molecules point to the opposite directions with π-π conjugation, in which stacking h (center-plane) is in 3.3411 Å, d(center-center) in 3.7633 Å and shift r (displacement of two centers) in 1.7319 Å (Glówka, et al., 1999). The H-bond betwen amino group of pyrimidyl ring and the nitrogen of the adjacent pyrimidyl ring (N4—H4A···N1ⁱ) results in the formation of infinite chain (Fig. 2).

Related literature top

For background to pyrimidines, see: Barillari et al. (2001); Gangjee et al. (2010). For slipped π–π stacking interactions, see: Glówka et al. (1999).

Experimental top

4,6-Dichloro-5-nitro-pyrimidine (5.20 g, 27 mmol), N-methylbenzenamine (3.2 mL, 32 mmol) and triethylamine (7.6 mL, 54 mmol) were dissolved in anhydrous THF (20 mL). The reaction mixture was stirred at room temperature overnight, concentrated in vacuo, diluted with water, and extracted with EtOAc. The organic phase was washed with 1mol/L HCl and brine, dried over anhydrous MgSO₄, and concentrated in vacuo to give rise to the solid crude product. The recrystallization of crude product from methanol provided the desired pure product of 6-chloro-N-methyl-5-nitro-N- phenylpyrimidin-4-amine (yellow solid, 5.7g, 80% yield, m.p. 133.5-135.5 °C). 6-Chloro-N-methyl-5-nitro-N-phenylpyrimidin-4-amine (4.36g, 16.5 mmol) was dissolved in a mixture of ethanol (59.0 mL) and water (17.0 mL). Iron powder (2.8 g, 50mmol) and NH₄Cl (0.56 g, 10.0 mmol) were added to it. The mixture was then stirred in reflux for 5 h, cooled to room temperature, and filtered through a pad of celite. The filtrate was concentrated in vacuo. The residue was extracted with EtOAc. The organic extract was washed with saturated NaHCO₃, water, and brine and dried over anhydrous MgSO₄. It was then filtered and concentrated in vacuo to the crude product which was purified by flash chromatography (elution with 9% EtOAc in petroleum ether followed by 20% EtOAc in petroleum ether) to give 6-chloro-N⁴-methyl-N⁴-phenylpyrimidine-4,5-diamine (white solid, 3.1g, 80% yield, m.p. 81.0-83.0 °C).

Computing details top

Data collection: PROCESS-AUTO (Rigaku, 1998); cell refinement: PROCESS-AUTO (Rigaku, 1998); data reduction: CrystalStructure (Rigaku, 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 with displacement ellipsoids shown at the 50% probability level.
	Fig. 2. The hydrogen bond of amino group of pyrimidyl ring and the nitrogen of the adjacent pyrimidyl ring and π–π stacking of adjacent pyrimidyl rings.

6-Chloro-N⁴-methyl-N⁴-phenylpyrimidine-4,5-diamine top

Crystal data top

C₁₁H₁₁ClN₄	F(000) = 488
M_r = 234.69	D_x = 1.369 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 1000 reflections
a = 9.5887 (19) Å	θ = 3.1–27.5°
b = 9.948 (2) Å	µ = 0.31 mm⁻¹
c = 12.671 (3) Å	T = 293 K
β = 109.63 (3)°	Block, colorless
V = 1138.4 (4) Å³	0.45 × 0.36 × 0.33 mm
Z = 4

Data collection top

Rigaku R-AXIS RAPID diffractometer	2588 independent reflections
Radiation source: fine-focus sealed tube	1983 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.025
Detector resolution: 10.00 pixels mm^-1	θ_max = 27.5°, θ_min = 3.1°
ω scans	h = −12→12
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	k = −12→12
T_min = 0.872, T_max = 0.905	l = −16→16
10835 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)] = 0.037	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.105	H-atom parameters constrained
S = 1.07	w = 1/[σ²(F_o²) + (0.0596P)² + 0.0777P] where P = (F_o² + 2F_c²)/3
2588 reflections	(Δ/σ)_max < 0.001
146 parameters	Δρ_max = 0.17 e Å⁻³
0 restraints	Δρ_min = −0.34 e Å⁻³

Crystal data top

C₁₁H₁₁ClN₄	V = 1138.4 (4) Å³
M_r = 234.69	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 9.5887 (19) Å	µ = 0.31 mm⁻¹
b = 9.948 (2) Å	T = 293 K
c = 12.671 (3) Å	0.45 × 0.36 × 0.33 mm
β = 109.63 (3)°

Data collection top

Rigaku R-AXIS RAPID diffractometer	2588 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	1983 reflections with I > 2σ(I)
T_min = 0.872, T_max = 0.905	R_int = 0.025
10835 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.037	0 restraints
wR(F²) = 0.105	H-atom parameters constrained
S = 1.07	Δρ_max = 0.17 e Å⁻³
2588 reflections	Δρ_min = −0.34 e Å⁻³
146 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	0.39218 (4)	0.36966 (4)	0.22870 (4)	0.06006 (16)
N1	0.52906 (15)	0.54876 (12)	0.14917 (12)	0.0536 (3)
N2	0.74328 (16)	0.50645 (12)	0.10019 (11)	0.0533 (3)
N3	0.85704 (14)	0.29788 (13)	0.11914 (11)	0.0515 (3)
N4	0.64945 (17)	0.20317 (13)	0.22608 (13)	0.0607 (4)
H4A	0.5861	0.1794	0.2571	0.073*
H4B	0.7179	0.1483	0.2243	0.073*
C1	0.53371 (16)	0.42063 (14)	0.18003 (12)	0.0439 (3)
C2	0.6380 (2)	0.58510 (16)	0.11281 (15)	0.0590 (4)
H2	0.6410	0.6752	0.0941	0.071*
C3	0.74410 (16)	0.37803 (13)	0.12985 (12)	0.0436 (3)
C4	0.64133 (15)	0.32788 (13)	0.17980 (11)	0.0411 (3)
C5	0.83458 (16)	0.15897 (14)	0.08849 (12)	0.0443 (3)
C6	0.70775 (18)	0.11594 (16)	0.00632 (14)	0.0529 (4)
H6	0.6337	0.1773	−0.0293	0.064*
C7	0.6902 (2)	−0.01899 (18)	−0.02337 (15)	0.0645 (5)
H7	0.6035	−0.0482	−0.0777	0.077*
C8	0.8007 (2)	−0.10947 (17)	0.02737 (17)	0.0659 (5)
H8	0.7892	−0.1997	0.0070	0.079*
C9	0.9276 (2)	−0.0667 (2)	0.10786 (17)	0.0731 (5)
H9	1.0029	−0.1277	0.1416	0.088*
C10	0.9443 (2)	0.06674 (19)	0.13924 (15)	0.0627 (4)
H10	1.0302	0.0948	0.1950	0.075*
C11	0.9716 (2)	0.36428 (19)	0.0848 (2)	0.0854 (7)
H11A	0.9328	0.3842	0.0061	0.128*
H11B	1.0556	0.3058	0.0994	0.128*
H11C	1.0013	0.4462	0.1263	0.128*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0518 (2)	0.0508 (2)	0.0909 (3)	−0.00514 (16)	0.0415 (2)	−0.00430 (18)
N1	0.0596 (8)	0.0419 (7)	0.0655 (8)	0.0004 (6)	0.0290 (7)	−0.0013 (5)
N2	0.0625 (8)	0.0450 (7)	0.0612 (8)	−0.0097 (6)	0.0322 (7)	−0.0021 (5)
N3	0.0441 (7)	0.0521 (7)	0.0666 (8)	−0.0087 (5)	0.0294 (6)	−0.0103 (6)
N4	0.0722 (9)	0.0451 (7)	0.0856 (10)	0.0066 (6)	0.0541 (9)	0.0102 (6)
C1	0.0441 (7)	0.0418 (7)	0.0507 (8)	−0.0071 (6)	0.0225 (7)	−0.0064 (6)
C2	0.0754 (11)	0.0386 (7)	0.0744 (11)	−0.0032 (7)	0.0400 (10)	0.0019 (7)
C3	0.0439 (7)	0.0441 (7)	0.0461 (7)	−0.0073 (6)	0.0195 (6)	−0.0064 (6)
C4	0.0426 (7)	0.0372 (7)	0.0457 (7)	−0.0068 (5)	0.0180 (6)	−0.0057 (5)
C5	0.0432 (7)	0.0482 (8)	0.0464 (7)	0.0000 (6)	0.0215 (6)	−0.0025 (6)
C6	0.0468 (8)	0.0577 (9)	0.0529 (8)	0.0021 (7)	0.0148 (7)	−0.0053 (7)
C7	0.0640 (11)	0.0676 (11)	0.0659 (11)	−0.0135 (8)	0.0272 (9)	−0.0210 (8)
C8	0.0855 (14)	0.0476 (9)	0.0830 (13)	−0.0023 (9)	0.0525 (12)	−0.0074 (8)
C9	0.0815 (13)	0.0634 (11)	0.0800 (13)	0.0262 (10)	0.0348 (11)	0.0136 (9)
C10	0.0518 (9)	0.0723 (11)	0.0595 (10)	0.0099 (8)	0.0126 (8)	0.0002 (8)
C11	0.0773 (13)	0.0696 (12)	0.140 (2)	−0.0238 (10)	0.0768 (15)	−0.0253 (12)

Geometric parameters (Å, º) top

Cl1—C1	1.7440 (14)	C5—C6	1.377 (2)
N1—C2	1.326 (2)	C5—C10	1.381 (2)
N1—C1	1.3296 (19)	C6—C7	1.389 (2)
N2—C2	1.329 (2)	C6—H6	0.9300
N2—C3	1.3309 (18)	C7—C8	1.374 (3)
N3—C3	1.3876 (18)	C7—H7	0.9300
N3—C5	1.4320 (19)	C8—C9	1.367 (3)
N3—C11	1.467 (2)	C8—H8	0.9300
N4—C4	1.3633 (18)	C9—C10	1.379 (3)
N4—H4A	0.8600	C9—H9	0.9300
N4—H4B	0.8600	C10—H10	0.9300
C1—C4	1.3850 (19)	C11—H11A	0.9600
C2—H2	0.9300	C11—H11B	0.9600
C3—C4	1.4282 (18)	C11—H11C	0.9600

C2—N1—C1	114.28 (13)	C10—C5—N3	119.55 (15)
C2—N2—C3	117.64 (12)	C5—C6—C7	120.07 (16)
C3—N3—C5	121.99 (11)	C5—C6—H6	120.0
C3—N3—C11	117.18 (13)	C7—C6—H6	120.0
C5—N3—C11	114.41 (12)	C8—C7—C6	120.14 (17)
C4—N4—H4A	120.0	C8—C7—H7	119.9
C4—N4—H4B	120.0	C6—C7—H7	119.9
H4A—N4—H4B	120.0	C9—C8—C7	119.88 (16)
N1—C1—C4	126.12 (12)	C9—C8—H8	120.1
N1—C1—Cl1	115.43 (10)	C7—C8—H8	120.1
C4—C1—Cl1	118.42 (11)	C8—C9—C10	120.19 (17)
N1—C2—N2	126.91 (14)	C8—C9—H9	119.9
N1—C2—H2	116.5	C10—C9—H9	119.9
N2—C2—H2	116.5	C9—C10—C5	120.57 (18)
N2—C3—N3	117.05 (12)	C9—C10—H10	119.7
N2—C3—C4	121.39 (13)	C5—C10—H10	119.7
N3—C3—C4	121.33 (12)	N3—C11—H11A	109.5
N4—C4—C1	122.70 (12)	N3—C11—H11B	109.5
N4—C4—C3	124.08 (13)	H11A—C11—H11B	109.5
C1—C4—C3	113.19 (12)	N3—C11—H11C	109.5
C6—C5—C10	119.13 (15)	H11A—C11—H11C	109.5
C6—C5—N3	121.28 (14)	H11B—C11—H11C	109.5

C2—N1—C1—C4	1.8 (2)	N3—C3—C4—N4	3.9 (2)
C2—N1—C1—Cl1	179.82 (12)	N2—C3—C4—C1	7.6 (2)
C1—N1—C2—N2	3.2 (3)	N3—C3—C4—C1	−178.05 (13)
C3—N2—C2—N1	−2.2 (3)	C3—N3—C5—C6	41.5 (2)
C2—N2—C3—N3	−178.27 (15)	C11—N3—C5—C6	−109.51 (18)
C2—N2—C3—C4	−3.7 (2)	C3—N3—C5—C10	−140.87 (15)
C5—N3—C3—N2	−145.53 (14)	C11—N3—C5—C10	68.1 (2)
C11—N3—C3—N2	4.8 (2)	C10—C5—C6—C7	1.0 (2)
C5—N3—C3—C4	39.9 (2)	N3—C5—C6—C7	178.65 (13)
C11—N3—C3—C4	−169.80 (17)	C5—C6—C7—C8	−1.5 (2)
N1—C1—C4—N4	171.27 (15)	C6—C7—C8—C9	0.5 (3)
Cl1—C1—C4—N4	−6.7 (2)	C7—C8—C9—C10	0.8 (3)
N1—C1—C4—C3	−6.8 (2)	C8—C9—C10—C5	−1.2 (3)
Cl1—C1—C4—C3	175.23 (10)	C6—C5—C10—C9	0.3 (2)
N2—C3—C4—N4	−170.43 (14)	N3—C5—C10—C9	−177.38 (14)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N4—H4A···N1ⁱ	0.86	2.28	3.0993 (18)	159

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

Experimental details

Crystal data
Chemical formula	C₁₁H₁₁ClN₄
M_r	234.69
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	9.5887 (19), 9.948 (2), 12.671 (3)
β (°)	109.63 (3)
V (Å³)	1138.4 (4)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.31
Crystal size (mm)	0.45 × 0.36 × 0.33

Data collection
Diffractometer	Rigaku R-AXIS RAPID diffractometer
Absorption correction	Multi-scan (ABSCOR; Higashi, 1995)
T_min, T_max	0.872, 0.905
No. of measured, independent and observed [I > 2σ(I)] reflections	10835, 2588, 1983
R_int	0.025
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.037, 0.105, 1.07
No. of reflections	2588
No. of parameters	146
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.17, −0.34

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

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N4—H4A···N1ⁱ	0.86	2.28	3.0993 (18)	159

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

Acknowledgements

This project was sponsored by the Scientific Research Foundation for Returned Overseas Chinese Scholars, State Education Ministry (20071108) and the Scientific Research Foundation for the Returned Overseas Team, Chinese Education Ministry.

References

Barillari, C., Barlocco, D. & Raveglia, L. (2001). Eur. J. Org. Chem. pp. 4737–4741. CrossRef Google Scholar
Brandenburg, K. (2000). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Gangjee, A., Kurup, S., Ihnat, M., Thorpe, J. & Shenoy, S. (2010). Bioorg. Med. Chem. 18, 3575–3587. Web of Science CrossRef CAS PubMed Google Scholar
Glówka, M. L., Martynowski, D. & Kozalowska, K. (1999). J. Mol. Struct. 474, 81–89. Google Scholar
Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan. Google Scholar
Rigaku (1998). PROCESS-AUTO. Rigaku Corporation, Tokyo, Japan. Google Scholar
Rigaku (2002). CrystalStructure. Rigaku Corporation, Tokyo, Japan. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar