Literature DB >> 22091109

6-Chloro-N-methyl-N-phenyl-pyrimidine-4,5-diamine.

Fuqiang Shi1, Li-Hong Zhu, Long Zhang, Ya-Feng Li.   

Abstract

In the title compound, C(11)H(11)ClN(4), the dihedral angle between the aromatic rings is 66.47 (8)°. In the crystal, mol-ecules 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 pyrim-idine rings also occurs [centroid-centroid separation = 3.7634 (12)Å and slippage = 1.715 Å].

Entities:  

Year:  2011        PMID: 22091109      PMCID: PMC3213532          DOI: 10.1107/S1600536811028303

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


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 = 234.69 Monoclinic, 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[F 2 > 2σ(F 2)] = 0.037 wR(F 2) = 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 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. Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536811028303/hb5937sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811028303/hb5937Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811028303/hb5937Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
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
Rigaku R-AXIS RAPID diffractometer2588 independent reflections
Radiation source: fine-focus sealed tube1983 reflections with I > 2σ(I)
graphiteRint = 0.025
Detector resolution: 10.00 pixels mm-1θmax = 27.5°, θmin = 3.1°
ω scansh = −12→12
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)k = −12→12
Tmin = 0.872, Tmax = 0.905l = −16→16
10835 measured reflections
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 = 1.07w = 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
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.
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)
H60.63370.1773−0.02930.064*
C70.6902 (2)−0.01899 (18)−0.02337 (15)0.0645 (5)
H70.6035−0.0482−0.07770.077*
C80.8007 (2)−0.10947 (17)0.02737 (17)0.0659 (5)
H80.7892−0.19970.00700.079*
C90.9276 (2)−0.0667 (2)0.10786 (17)0.0731 (5)
H91.0029−0.12770.14160.088*
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*
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)
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—C1−178.05 (13)
C3—N2—C2—N1−2.2 (3)C3—N3—C5—C641.5 (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—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—C4−169.80 (17)C5—C6—C7—C8−1.5 (2)
N1—C1—C4—N4171.27 (15)C6—C7—C8—C90.5 (3)
Cl1—C1—C4—N4−6.7 (2)C7—C8—C9—C100.8 (3)
N1—C1—C4—C3−6.8 (2)C8—C9—C10—C5−1.2 (3)
Cl1—C1—C4—C3175.23 (10)C6—C5—C10—C90.3 (2)
N2—C3—C4—N4−170.43 (14)N3—C5—C10—C9−177.38 (14)
D—H···AD—HH···AD···AD—H···A
N4—H4A···N1i0.862.283.0993 (18)159
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N4—H4A⋯N1i0.862.283.0993 (18)159

Symmetry code: (i) .

  2 in total

1.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

2.  Synthesis and biological activity of N(4)-phenylsubstituted-6-(2,4-dichloro phenylmethyl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamines as vascular endothelial growth factor receptor-2 inhibitors and antiangiogenic and antitumor agents.

Authors:  Aleem Gangjee; Sonali Kurup; Michael A Ihnat; Jessica E Thorpe; Satyendra S Shenoy
Journal:  Bioorg Med Chem       Date:  2010-03-27       Impact factor: 3.641

  2 in total
  2 in total

1.  N,N-Dimethyl-5-nitro-N,N-diphenyl-pyrimidine-4,6-diamine.

Authors:  Fuqiang Shi; Li-Hong Zhu; Long Zhang; Ya-Feng Li
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-09-03

2.  6-Chloro-N-methyl-5-nitro-N-phenyl-pyrimidin-4-amine.

Authors:  Fuqiang Shi; Li-Hong Zhu; Li Mu; Long Zhang; Ya-Feng Li
Journal:  Acta Crystallogr Sect E Struct Rep Online       Date:  2011-09-20
  2 in total

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