organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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

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 ππ 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[Barillari, C., Barlocco, D. & Raveglia, L. (2001). Eur. J. Org. Chem. pp. 4737-4741.]); Gangjee et al. (2010[Gangjee, A., Kurup, S., Ihnat, M., Thorpe, J. & Shenoy, S. (2010). Bioorg. Med. Chem. 18, 3575-3587.]). For slipped ππ stacking inter­actions, see: Glówka et al. (1999[Glówka, M. L., Martynowski, D. & Kozalowska, K. (1999). J. Mol. Struct. 474, 81-89.]).

[Scheme 1]

Experimental

Crystal data
  • C11H11ClN4

  • Mr = 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[Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.872, Tmax = 0.905

  • 10835 measured reflections

  • 2588 independent reflections

  • 1983 reflections with I > 2σ(I)

  • Rint = 0.025

Refinement
  • R[F2 > 2σ(F2)] = 0.037

  • wR(F2) = 0.105

  • S = 1.07

  • 2588 reflections

  • 146 parameters

  • H-atom parameters constrained

  • Δρmax = 0.17 e Å−3

  • Δρmin = −0.34 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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)[Rigaku (1998). PROCESS-AUTO. Rigaku Corporation, Tokyo, Japan.]; cell refinement: PROCESS-AUTO[Rigaku (1998). PROCESS-AUTO. Rigaku Corporation, Tokyo, Japan.]; data reduction: CrystalStructure (Rigaku, 2002)[Rigaku (2002). CrystalStructure. Rigaku Corporation, Tokyo, Japan.]; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: DIAMOND (Brandenburg, 2000[Brandenburg, K. (2000). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: SHELXL97.

Supporting information


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 ππ 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).

Refinement top

All H atoms were located from difference Fourier maps. H atoms attached to C atoms were treated as riding [C-H = 0.93-0.96 Å and Uiso(H) = 1.5Ueq(C) (methyl groups) or 1.2Ueq(C) (other H atoms)]. N-atom of amino group of pyrimidyl ring was treated as sp2 hybridization, and therefore H atoms of amino group were positioned as riding [N-H = 0.86 Å and Uiso(H) = 1.2Ueq(N)].

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
[Figure 1] Fig. 1. The title compound with displacement ellipsoids shown at the 50% probability level.
[Figure 2] Fig. 2. The hydrogen bond of amino group of pyrimidyl ring and the nitrogen of the adjacent pyrimidyl ring and ππ stacking of adjacent pyrimidyl rings.
6-Chloro-N4-methyl-N4-phenylpyrimidine-4,5-diamine top
Crystal data top
C11H11ClN4F(000) = 488
Mr = 234.69Dx = 1.369 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 1000 reflections
a = 9.5887 (19) Åθ = 3.1–27.5°
b = 9.948 (2) ŵ = 0.31 mm1
c = 12.671 (3) ÅT = 293 K
β = 109.63 (3)°Block, colorless
V = 1138.4 (4) Å30.45 × 0.36 × 0.33 mm
Z = 4
Data collection top
Rigaku R-AXIS RAPID
diffractometer
2588 independent reflections
Radiation source: fine-focus sealed tube1983 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.025
Detector resolution: 10.00 pixels mm-1θmax = 27.5°, θmin = 3.1°
ω scansh = 1212
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
k = 1212
Tmin = 0.872, Tmax = 0.905l = 1616
10835 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.105H-atom parameters constrained
S = 1.07 w = 1/[σ2(Fo2) + (0.0596P)2 + 0.0777P]
where P = (Fo2 + 2Fc2)/3
2588 reflections(Δ/σ)max < 0.001
146 parametersΔρmax = 0.17 e Å3
0 restraintsΔρmin = 0.34 e Å3
Crystal data top
C11H11ClN4V = 1138.4 (4) Å3
Mr = 234.69Z = 4
Monoclinic, P21/cMo Kα radiation
a = 9.5887 (19) ŵ = 0.31 mm1
b = 9.948 (2) ÅT = 293 K
c = 12.671 (3) Å0.45 × 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)
Tmin = 0.872, Tmax = 0.905Rint = 0.025
10835 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0370 restraints
wR(F2) = 0.105H-atom parameters constrained
S = 1.07Δρmax = 0.17 e Å3
2588 reflectionsΔρmin = 0.34 e Å3
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
xyzUiso*/Ueq
Cl10.39218 (4)0.36966 (4)0.22870 (4)0.06006 (16)
N10.52906 (15)0.54876 (12)0.14917 (12)0.0536 (3)
N20.74328 (16)0.50645 (12)0.10019 (11)0.0533 (3)
N30.85704 (14)0.29788 (13)0.11914 (11)0.0515 (3)
N40.64945 (17)0.20317 (13)0.22608 (13)0.0607 (4)
H4A0.58610.17940.25710.073*
H4B0.71790.14830.22430.073*
C10.53371 (16)0.42063 (14)0.18003 (12)0.0439 (3)
C20.6380 (2)0.58510 (16)0.11281 (15)0.0590 (4)
H20.64100.67520.09410.071*
C30.74410 (16)0.37803 (13)0.12985 (12)0.0436 (3)
C40.64133 (15)0.32788 (13)0.17980 (11)0.0411 (3)
C50.83458 (16)0.15897 (14)0.08849 (12)0.0443 (3)
C60.70775 (18)0.11594 (16)0.00632 (14)0.0529 (4)
H60.63370.17730.02930.064*
C70.6902 (2)0.01899 (18)0.02337 (15)0.0645 (5)
H70.60350.04820.07770.077*
C80.8007 (2)0.10947 (17)0.02737 (17)0.0659 (5)
H80.78920.19970.00700.079*
C90.9276 (2)0.0667 (2)0.10786 (17)0.0731 (5)
H91.00290.12770.14160.088*
C100.9443 (2)0.06674 (19)0.13924 (15)0.0627 (4)
H101.03020.09480.19500.075*
C110.9716 (2)0.36428 (19)0.0848 (2)0.0854 (7)
H11A0.93280.38420.00610.128*
H11B1.05560.30580.09940.128*
H11C1.00130.44620.12630.128*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0518 (2)0.0508 (2)0.0909 (3)0.00514 (16)0.0415 (2)0.00430 (18)
N10.0596 (8)0.0419 (7)0.0655 (8)0.0004 (6)0.0290 (7)0.0013 (5)
N20.0625 (8)0.0450 (7)0.0612 (8)0.0097 (6)0.0322 (7)0.0021 (5)
N30.0441 (7)0.0521 (7)0.0666 (8)0.0087 (5)0.0294 (6)0.0103 (6)
N40.0722 (9)0.0451 (7)0.0856 (10)0.0066 (6)0.0541 (9)0.0102 (6)
C10.0441 (7)0.0418 (7)0.0507 (8)0.0071 (6)0.0225 (7)0.0064 (6)
C20.0754 (11)0.0386 (7)0.0744 (11)0.0032 (7)0.0400 (10)0.0019 (7)
C30.0439 (7)0.0441 (7)0.0461 (7)0.0073 (6)0.0195 (6)0.0064 (6)
C40.0426 (7)0.0372 (7)0.0457 (7)0.0068 (5)0.0180 (6)0.0057 (5)
C50.0432 (7)0.0482 (8)0.0464 (7)0.0000 (6)0.0215 (6)0.0025 (6)
C60.0468 (8)0.0577 (9)0.0529 (8)0.0021 (7)0.0148 (7)0.0053 (7)
C70.0640 (11)0.0676 (11)0.0659 (11)0.0135 (8)0.0272 (9)0.0210 (8)
C80.0855 (14)0.0476 (9)0.0830 (13)0.0023 (9)0.0525 (12)0.0074 (8)
C90.0815 (13)0.0634 (11)0.0800 (13)0.0262 (10)0.0348 (11)0.0136 (9)
C100.0518 (9)0.0723 (11)0.0595 (10)0.0099 (8)0.0126 (8)0.0002 (8)
C110.0773 (13)0.0696 (12)0.140 (2)0.0238 (10)0.0768 (15)0.0253 (12)
Geometric parameters (Å, º) top
Cl1—C11.7440 (14)C5—C61.377 (2)
N1—C21.326 (2)C5—C101.381 (2)
N1—C11.3296 (19)C6—C71.389 (2)
N2—C21.329 (2)C6—H60.9300
N2—C31.3309 (18)C7—C81.374 (3)
N3—C31.3876 (18)C7—H70.9300
N3—C51.4320 (19)C8—C91.367 (3)
N3—C111.467 (2)C8—H80.9300
N4—C41.3633 (18)C9—C101.379 (3)
N4—H4A0.8600C9—H90.9300
N4—H4B0.8600C10—H100.9300
C1—C41.3850 (19)C11—H11A0.9600
C2—H20.9300C11—H11B0.9600
C3—C41.4282 (18)C11—H11C0.9600
C2—N1—C1114.28 (13)C10—C5—N3119.55 (15)
C2—N2—C3117.64 (12)C5—C6—C7120.07 (16)
C3—N3—C5121.99 (11)C5—C6—H6120.0
C3—N3—C11117.18 (13)C7—C6—H6120.0
C5—N3—C11114.41 (12)C8—C7—C6120.14 (17)
C4—N4—H4A120.0C8—C7—H7119.9
C4—N4—H4B120.0C6—C7—H7119.9
H4A—N4—H4B120.0C9—C8—C7119.88 (16)
N1—C1—C4126.12 (12)C9—C8—H8120.1
N1—C1—Cl1115.43 (10)C7—C8—H8120.1
C4—C1—Cl1118.42 (11)C8—C9—C10120.19 (17)
N1—C2—N2126.91 (14)C8—C9—H9119.9
N1—C2—H2116.5C10—C9—H9119.9
N2—C2—H2116.5C9—C10—C5120.57 (18)
N2—C3—N3117.05 (12)C9—C10—H10119.7
N2—C3—C4121.39 (13)C5—C10—H10119.7
N3—C3—C4121.33 (12)N3—C11—H11A109.5
N4—C4—C1122.70 (12)N3—C11—H11B109.5
N4—C4—C3124.08 (13)H11A—C11—H11B109.5
C1—C4—C3113.19 (12)N3—C11—H11C109.5
C6—C5—C10119.13 (15)H11A—C11—H11C109.5
C6—C5—N3121.28 (14)H11B—C11—H11C109.5
C2—N1—C1—C41.8 (2)N3—C3—C4—N43.9 (2)
C2—N1—C1—Cl1179.82 (12)N2—C3—C4—C17.6 (2)
C1—N1—C2—N23.2 (3)N3—C3—C4—C1178.05 (13)
C3—N2—C2—N12.2 (3)C3—N3—C5—C641.5 (2)
C2—N2—C3—N3178.27 (15)C11—N3—C5—C6109.51 (18)
C2—N2—C3—C43.7 (2)C3—N3—C5—C10140.87 (15)
C5—N3—C3—N2145.53 (14)C11—N3—C5—C1068.1 (2)
C11—N3—C3—N24.8 (2)C10—C5—C6—C71.0 (2)
C5—N3—C3—C439.9 (2)N3—C5—C6—C7178.65 (13)
C11—N3—C3—C4169.80 (17)C5—C6—C7—C81.5 (2)
N1—C1—C4—N4171.27 (15)C6—C7—C8—C90.5 (3)
Cl1—C1—C4—N46.7 (2)C7—C8—C9—C100.8 (3)
N1—C1—C4—C36.8 (2)C8—C9—C10—C51.2 (3)
Cl1—C1—C4—C3175.23 (10)C6—C5—C10—C90.3 (2)
N2—C3—C4—N4170.43 (14)N3—C5—C10—C9177.38 (14)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4A···N1i0.862.283.0993 (18)159
Symmetry code: (i) x+1, y1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC11H11ClN4
Mr234.69
Crystal system, space groupMonoclinic, P21/c
Temperature (K)293
a, b, c (Å)9.5887 (19), 9.948 (2), 12.671 (3)
β (°) 109.63 (3)
V3)1138.4 (4)
Z4
Radiation typeMo Kα
µ (mm1)0.31
Crystal size (mm)0.45 × 0.36 × 0.33
Data collection
DiffractometerRigaku R-AXIS RAPID
diffractometer
Absorption correctionMulti-scan
(ABSCOR; Higashi, 1995)
Tmin, Tmax0.872, 0.905
No. of measured, independent and
observed [I > 2σ(I)] reflections
10835, 2588, 1983
Rint0.025
(sin θ/λ)max1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.037, 0.105, 1.07
No. of reflections2588
No. of parameters146
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
N4—H4A···N1i0.862.283.0993 (18)159
Symmetry code: (i) x+1, y1/2, 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

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

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