N 4,N 6-Dimethyl-5-nitro-N 4,N 6-diphenyl­pyrimidine-4,6-diamine

Fuqiang Shi; Li-Hong Zhu; Long Zhang; Ya-Feng Li

doi:10.1107/S1600536811035094

. 2011 Sep 3;67(Pt 10):o2559. doi: 10.1107/S1600536811035094

N ⁴,N ⁶-Dimethyl-5-nitro-N ⁴,N ⁶-diphenylpyrimidine-4,6-diamine

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

PMCID: PMC3201557 PMID: 22058732

Abstract

In the title compound, C₁₈H₁₇N₅O₂, the pyrimidine ring makes dihedral angles of 66.09 (12), 71.39 (13) and 56.7 (3)° with two phenyl rings and the nitro group, respectively. The dihedral angle between the two phenyl rings is 44.05 (14)°.

Related literature

For applications of pyrimidine diamines, see: Barillari et al. (2001 ▶); Che et al. (2008 ▶); Itoh et al. (2004 ▶); Koppel & Robins (1958 ▶); Shi et al. (2011 ▶).

Experimental

Crystal data

C₁₈H₁₇N₅O₂
M _r = 335.37
Monoclinic,
a = 10.794 (2) Å
b = 7.0019 (14) Å
c = 23.650 (6) Å
β = 109.02 (3)°
V = 1689.8 (6) Å³
Z = 4
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 293 K
0.50 × 0.12 × 0.10 mm

Data collection

Rigaku R-AXIS RAPID diffractometer
Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ▶) T _min = 0.956, T _max = 0.991
15784 measured reflections
3843 independent reflections
2018 reflections with I > 2σ(I)
R _int = 0.108

Refinement

R[F ² > 2σ(F ²)] = 0.074
wR(F ²) = 0.146
S = 1.05
3843 reflections
228 parameters
H-atom parameters constrained
Δρ_max = 0.17 e Å⁻³
Δρ_min = −0.20 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.

Supplementary Material

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536811035094/is2768sup1.cif

e-67-o2559-sup1.cif^{(17.2KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811035094/is2768Isup2.hkl

e-67-o2559-Isup2.hkl^{(188.4KB, hkl)}

Supplementary material file. DOI: 10.1107/S1600536811035094/is2768Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

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.

supplementary crystallographic information

Comment

Pyrimidine diamines, important intermediate products (Koppel et al., 1958; Itoh et al., 2004; Che et al., 2008; Shi et al., 2011), exhibit a wide range of biological activities (Barillari et al., 2001). Here, the crystal structure of N⁴,N⁶- dimethyl-5-nitro-N⁴, N⁶-diphenylpyrimidine-4,6-diamine is determined by X-ray single crystal diffraction.

In the structure of the title compound (Fig. 1), the dihedral angles between pyrimidyl and two phenyl rings and between two phenyl rings are 66.09 (12), 71.39 (13) and 44.05 (14)°, respectively.

Experimental

4,6-Dichloro-5-nitro-pyrimidine (192 mg, 1 mmol), N-methylbenzenamine (0.33 mL, 3 mmol) and triethylamine (0.22 mL, 2 mmol) were dissolved in anhydrous THF (10 mL). The reaction mixture was stirred in reflux overnight. The product was concentrated in vacuo, diluted with water, and extracted with EtOAc. The organic phase was washed with 1mol/L HCl, brine, and dried over anhydrous MgSO₄. The crude product was purified by flash chromatography (elution with 15% EtOAc in petroleum ether) to give N⁴,N⁶-dimethyl-5-nitro-N⁴, N⁶-diphenylpyrimidine- 4,6-diamine (yellow solid, 256 mg, 76.4%, 166.4-168.6 °C). ¹H NMR (CDCl₃, 400 Hz), δ: 8.46 (s, 1H), 7.23-7.19(m, 4H), 7.13-7.11(m, 2H), 7.02-6.99(m, 4H), 3.50 (s, 6H); ¹³C NMR (CDCl₃, 100 Hz), δ: 156.0, 155.7, 144.2, 129.2, 126.6, 125.1, 121.0, 42.0; ES-MS: 336.1 [(M + H⁺)].

Figures

Fig. 1. — The molecular structure of the title compound, with the atom-labelling scheme. Displacement ellipsoid are shown at the 50% probability level.

Crystal data

C₁₈H₁₇N₅O₂	F(000) = 704
M_r = 335.37	D_x = 1.318 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 500 reflections
a = 10.794 (2) Å	θ = 3.1–27.5°
b = 7.0019 (14) Å	µ = 0.09 mm⁻¹
c = 23.650 (6) Å	T = 293 K
β = 109.02 (3)°	Block, colorless
V = 1689.8 (6) Å³	0.50 × 0.12 × 0.10 mm
Z = 4

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Data collection

Rigaku R-AXIS RAPID diffractometer	3843 independent reflections
Radiation source: fine-focus sealed tube	2018 reflections with I > 2σ(I)
graphite	R_int = 0.108
Detector resolution: 10.00 pixels mm^-1	θ_max = 27.5°, θ_min = 3.1°
ω scans	h = −14→13
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	k = −9→9
T_min = 0.956, T_max = 0.991	l = −30→30
15784 measured reflections

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Refinement

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)] = 0.074	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.146	H-atom parameters constrained
S = 1.05	w = 1/[σ²(F_o²) + (0.0524P)² + 0.0764P] where P = (F_o² + 2F_c²)/3
3843 reflections	(Δ/σ)_max < 0.001
228 parameters	Δρ_max = 0.17 e Å⁻³
0 restraints	Δρ_min = −0.20 e Å⁻³

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Special details

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.

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

	x	y	z	U_iso*/U_eq
O1	0.84317 (18)	0.0703 (3)	0.35192 (9)	0.0577 (6)
O2	0.85674 (17)	0.2808 (3)	0.42079 (8)	0.0586 (6)
N1	0.5774 (2)	0.2175 (3)	0.41820 (9)	0.0435 (6)
N2	0.45045 (19)	0.3519 (3)	0.32882 (10)	0.0434 (6)
N3	0.52690 (19)	0.3954 (3)	0.24557 (9)	0.0412 (5)
N4	0.7997 (2)	0.2043 (3)	0.37282 (10)	0.0424 (6)
N5	0.74616 (19)	0.3627 (3)	0.25459 (9)	0.0393 (5)
C1	0.7275 (3)	−0.2635 (4)	0.44234 (13)	0.0553 (8)
H1	0.7216	−0.3782	0.4218	0.066*
C2	0.8135 (3)	−0.2471 (5)	0.49962 (14)	0.0639 (9)
H2	0.8663	−0.3498	0.5176	0.077*
C3	0.8210 (3)	−0.0796 (5)	0.53010 (13)	0.0678 (10)
H3	0.8784	−0.0692	0.5690	0.081*
C4	0.6587 (2)	0.0578 (4)	0.44551 (10)	0.0387 (6)
C5	0.6500 (3)	−0.1108 (4)	0.41512 (11)	0.0446 (7)
H5	0.5921	−0.1224	0.3763	0.054*
C6	0.7441 (3)	0.0745 (4)	0.50349 (12)	0.0562 (8)
H6	0.7496	0.1885	0.5243	0.067*
C7	0.4741 (3)	0.2699 (5)	0.44293 (13)	0.0705 (10)
H7A	0.4531	0.4028	0.4354	0.085*
H7B	0.5041	0.2470	0.4853	0.085*
H7C	0.3975	0.1943	0.4243	0.085*
C8	0.6703 (2)	0.2779 (3)	0.33805 (10)	0.0338 (6)
C9	0.5681 (2)	0.2799 (3)	0.36205 (11)	0.0362 (6)
C10	0.6494 (2)	0.3447 (3)	0.27970 (11)	0.0359 (6)
C11	0.4380 (2)	0.3965 (4)	0.27283 (13)	0.0456 (7)
H11	0.3545	0.4341	0.2493	0.055*
C12	0.8912 (3)	0.5770 (4)	0.32865 (12)	0.0461 (7)
H12	0.8181	0.6442	0.3303	0.055*
C13	0.9840 (3)	0.3278 (4)	0.28633 (12)	0.0474 (7)
H13	0.9742	0.2256	0.2601	0.057*
C14	1.0143 (3)	0.6310 (4)	0.36414 (13)	0.0573 (8)
H14	1.0246	0.7332	0.3904	0.069*
C15	1.1078 (3)	0.3861 (4)	0.32153 (13)	0.0573 (8)
H15	1.1815	0.3241	0.3184	0.069*
C16	1.1223 (3)	0.5339 (5)	0.36078 (13)	0.0604 (9)
H16	1.2056	0.5690	0.3853	0.072*
C17	0.8759 (2)	0.4228 (3)	0.29054 (10)	0.0365 (6)
C18	0.7094 (3)	0.3940 (4)	0.19040 (10)	0.0503 (7)
H18A	0.6509	0.2945	0.1697	0.060*
H18B	0.7865	0.3927	0.1786	0.060*
H18C	0.6664	0.5154	0.1805	0.060*

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Atomic displacement parameters (Å²)

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0466 (12)	0.0511 (12)	0.0785 (14)	0.0176 (10)	0.0247 (11)	0.0139 (11)
O2	0.0418 (11)	0.0717 (14)	0.0505 (11)	−0.0089 (10)	−0.0010 (9)	0.0050 (11)
N1	0.0423 (12)	0.0468 (13)	0.0451 (12)	0.0077 (11)	0.0194 (10)	0.0064 (11)
N2	0.0315 (12)	0.0430 (13)	0.0557 (14)	0.0047 (10)	0.0143 (10)	0.0090 (11)
N3	0.0313 (12)	0.0410 (12)	0.0469 (12)	0.0030 (10)	0.0066 (10)	0.0064 (10)
N4	0.0323 (12)	0.0434 (14)	0.0507 (14)	0.0013 (11)	0.0126 (11)	0.0124 (12)
N5	0.0314 (11)	0.0470 (13)	0.0389 (12)	0.0007 (10)	0.0108 (10)	0.0015 (10)
C1	0.065 (2)	0.0434 (16)	0.0620 (18)	0.0039 (15)	0.0270 (16)	0.0043 (15)
C2	0.059 (2)	0.064 (2)	0.066 (2)	0.0128 (17)	0.0162 (16)	0.0262 (18)
C3	0.058 (2)	0.084 (2)	0.0471 (17)	−0.0004 (19)	−0.0025 (15)	0.0157 (18)
C4	0.0346 (14)	0.0434 (15)	0.0364 (13)	−0.0024 (12)	0.0091 (11)	0.0021 (12)
C5	0.0439 (15)	0.0456 (17)	0.0420 (14)	−0.0041 (13)	0.0107 (12)	0.0034 (13)
C6	0.0603 (19)	0.0576 (19)	0.0424 (15)	−0.0027 (15)	0.0054 (14)	−0.0024 (14)
C7	0.069 (2)	0.092 (2)	0.0630 (19)	0.0289 (19)	0.0377 (17)	0.0118 (18)
C8	0.0234 (12)	0.0313 (13)	0.0417 (14)	0.0007 (10)	0.0037 (11)	0.0031 (11)
C9	0.0312 (13)	0.0316 (13)	0.0450 (14)	0.0009 (11)	0.0112 (12)	−0.0002 (12)
C10	0.0302 (13)	0.0311 (13)	0.0424 (14)	−0.0017 (11)	0.0063 (12)	−0.0019 (11)
C11	0.0287 (14)	0.0426 (16)	0.0610 (18)	0.0040 (12)	0.0087 (13)	0.0123 (14)
C12	0.0433 (16)	0.0426 (15)	0.0566 (16)	−0.0036 (13)	0.0219 (13)	−0.0039 (14)
C13	0.0416 (15)	0.0460 (16)	0.0568 (16)	0.0059 (13)	0.0188 (13)	−0.0010 (13)
C14	0.059 (2)	0.0513 (17)	0.0600 (18)	−0.0148 (16)	0.0176 (15)	−0.0084 (15)
C15	0.0347 (15)	0.064 (2)	0.073 (2)	0.0080 (15)	0.0174 (15)	0.0161 (17)
C16	0.0452 (18)	0.068 (2)	0.0580 (18)	−0.0170 (17)	0.0033 (15)	0.0101 (17)
C17	0.0321 (13)	0.0390 (14)	0.0393 (13)	−0.0003 (12)	0.0129 (11)	0.0038 (12)
C18	0.0465 (16)	0.0653 (19)	0.0403 (15)	0.0101 (15)	0.0157 (13)	0.0026 (14)

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Geometric parameters (Å, °)

O1—N4	1.223 (3)	C5—H5	0.9300
O2—N4	1.224 (3)	C6—H6	0.9300
N1—C9	1.370 (3)	C7—H7A	0.9600
N1—C4	1.438 (3)	C7—H7B	0.9600
N1—C7	1.464 (3)	C7—H7C	0.9600
N2—C11	1.324 (3)	C8—C9	1.395 (3)
N2—C9	1.355 (3)	C8—C10	1.404 (3)
N3—C11	1.319 (3)	C11—H11	0.9300
N3—C10	1.353 (3)	C12—C14	1.374 (4)
N4—C8	1.464 (3)	C12—C17	1.382 (3)
N5—C10	1.366 (3)	C12—H12	0.9300
N5—C17	1.444 (3)	C13—C17	1.375 (4)
N5—C18	1.455 (3)	C13—C15	1.385 (4)
C1—C2	1.375 (4)	C13—H13	0.9300
C1—C5	1.381 (4)	C14—C16	1.374 (4)
C1—H1	0.9300	C14—H14	0.9300
C2—C3	1.365 (4)	C15—C16	1.365 (4)
C2—H2	0.9300	C15—H15	0.9300
C3—C6	1.382 (4)	C16—H16	0.9300
C3—H3	0.9300	C18—H18A	0.9600
C4—C5	1.369 (3)	C18—H18B	0.9600
C4—C6	1.386 (3)	C18—H18C	0.9600

C9—N1—C4	121.6 (2)	C9—C8—N4	120.7 (2)
C9—N1—C7	118.9 (2)	C10—C8—N4	119.2 (2)
C4—N1—C7	116.6 (2)	N2—C9—N1	116.1 (2)
C11—N2—C9	116.0 (2)	N2—C9—C8	118.9 (2)
C11—N3—C10	115.8 (2)	N1—C9—C8	125.0 (2)
O1—N4—O2	124.5 (2)	N3—C10—N5	117.0 (2)
O1—N4—C8	117.7 (2)	N3—C10—C8	119.1 (2)
O2—N4—C8	117.8 (2)	N5—C10—C8	123.9 (2)
C10—N5—C17	120.2 (2)	N3—C11—N2	129.4 (2)
C10—N5—C18	118.7 (2)	N3—C11—H11	115.3
C17—N5—C18	116.9 (2)	N2—C11—H11	115.3
C2—C1—C5	120.4 (3)	C14—C12—C17	120.0 (3)
C2—C1—H1	119.8	C14—C12—H12	120.0
C5—C1—H1	119.8	C17—C12—H12	120.0
C3—C2—C1	119.8 (3)	C17—C13—C15	119.3 (3)
C3—C2—H2	120.1	C17—C13—H13	120.4
C1—C2—H2	120.1	C15—C13—H13	120.4
C2—C3—C6	120.5 (3)	C16—C14—C12	119.9 (3)
C2—C3—H3	119.8	C16—C14—H14	120.0
C6—C3—H3	119.8	C12—C14—H14	120.0
C5—C4—C6	120.1 (2)	C16—C15—C13	120.5 (3)
C5—C4—N1	120.5 (2)	C16—C15—H15	119.8
C6—C4—N1	119.4 (2)	C13—C15—H15	119.8
C4—C5—C1	119.7 (2)	C15—C16—C14	120.2 (3)
C4—C5—H5	120.1	C15—C16—H16	119.9
C1—C5—H5	120.1	C14—C16—H16	119.9
C3—C6—C4	119.5 (3)	C13—C17—C12	120.1 (2)
C3—C6—H6	120.3	C13—C17—N5	120.0 (2)
C4—C6—H6	120.3	C12—C17—N5	119.9 (2)
N1—C7—H7A	109.5	N5—C18—H18A	109.5
N1—C7—H7B	109.5	N5—C18—H18B	109.5
H7A—C7—H7B	109.5	H18A—C18—H18B	109.5
N1—C7—H7C	109.5	N5—C18—H18C	109.5
H7A—C7—H7C	109.5	H18A—C18—H18C	109.5
H7B—C7—H7C	109.5	H18B—C18—H18C	109.5
C9—C8—C10	120.1 (2)

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Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: IS2768).

References

Barillari, C., Barlocco, D. & Raveglia, L. (2001). Eur. J. Org. Chem. pp. 4737–4741.
Brandenburg, K. (2000). DIAMOND Crystal Impact GbR, Bonn, Germany.
Che, X., Zheng, L., Dang, Q. & Bai, X. (2008). J. Org. Chem. 73, 1147–1149. [DOI] [PubMed]
Higashi, T. (1995). ABSCOR Rigaku Corporation, Tokyo, Japan.
Itoh, T., Sato, K. & Mase, T. (2004). Adv. Synth. Catal. 346, 1859–1867.
Koppel, H. & Robins, R. (1958). J. Org. Chem. 23, 1457–1460.
Rigaku (1998). PROCESS-AUTO Rigaku Corporation, Tokyo, Japan.
Rigaku/MSC (2002). CrystalStructure Rigaku/MSC Inc., The Woodlands, Texas, USA.
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [DOI] [PubMed]
Shi, F., Zhu, L.-H., Zhang, L. & Li, Y.-F. (2011). Acta Cryst. E67, o2089. [DOI] [PMC free article] [PubMed]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536811035094/is2768sup1.cif

e-67-o2559-sup1.cif^{(17.2KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811035094/is2768Isup2.hkl

e-67-o2559-Isup2.hkl^{(188.4KB, hkl)}

Supplementary material file. DOI: 10.1107/S1600536811035094/is2768Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

[bb1] Barillari, C., Barlocco, D. & Raveglia, L. (2001). Eur. J. Org. Chem. pp. 4737–4741.

[bb2] Brandenburg, K. (2000). DIAMOND Crystal Impact GbR, Bonn, Germany.

[bb3] Che, X., Zheng, L., Dang, Q. & Bai, X. (2008). J. Org. Chem. 73, 1147–1149. [DOI] [PubMed]

[bb4] Higashi, T. (1995). ABSCOR Rigaku Corporation, Tokyo, Japan.

[bb5] Itoh, T., Sato, K. & Mase, T. (2004). Adv. Synth. Catal. 346, 1859–1867.

[bb6] Koppel, H. & Robins, R. (1958). J. Org. Chem. 23, 1457–1460.

[bb7] Rigaku (1998). PROCESS-AUTO Rigaku Corporation, Tokyo, Japan.

[bb8] Rigaku/MSC (2002). CrystalStructure Rigaku/MSC Inc., The Woodlands, Texas, USA.

[bb9] Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [DOI] [PubMed]

[bb10] Shi, F., Zhu, L.-H., Zhang, L. & Li, Y.-F. (2011). Acta Cryst. E67, o2089. [DOI] [PMC free article] [PubMed]

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N ⁴,N ⁶-Dimethyl-5-nitro-N ⁴,N ⁶-diphenylpyrimidine-4,6-diamine

Fuqiang Shi

Li-Hong Zhu

Long Zhang

Ya-Feng Li

Abstract

Related literature

Experimental

Crystal data

Data collection

Refinement

Supplementary Material

Acknowledgments

supplementary crystallographic information

Comment

Experimental

Refinement

Figures

Fig. 1.

Crystal data

Data collection

Refinement

Special details

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

Atomic displacement parameters (Å²)

Geometric parameters (Å, °)

Footnotes

References

Associated Data

Supplementary Materials

ACTIONS

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PERMALINK

N 4,N 6-Dimethyl-5-nitro-N 4,N 6-diphenyl­pyrimidine-4,6-diamine

Fuqiang Shi

Li-Hong Zhu

Long Zhang

Ya-Feng Li

Abstract

Related literature

Experimental

Crystal data

Data collection

Refinement

Supplementary Material

Acknowledgments

supplementary crystallographic information

Comment

Experimental

Refinement

Figures

Fig. 1.

Crystal data

Data collection

Refinement

Special details

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

Atomic displacement parameters (Å2)

Geometric parameters (Å, °)

Footnotes

References

Associated Data

Supplementary Materials

ACTIONS

PERMALINK

RESOURCES

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N ⁴,N ⁶-Dimethyl-5-nitro-N ⁴,N ⁶-diphenylpyrimidine-4,6-diamine

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

Atomic displacement parameters (Å²)