PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of actaeInternational Union of Crystallographysearchopen accessarticle submissionjournal home pagethis article
 
Acta Crystallogr Sect E Struct Rep Online. 2008 April 1; 64(Pt 4): o759.
Published online 2008 March 29. doi:  10.1107/S1600536808008003
PMCID: PMC2960917

4-Methyl-6-phenyl­pyrimidin-2-amine

Abstract

The title compound, C11H11N3, was synthesized as part of our research into functionalized pyrimidines. It crystallizes with two independent mol­ecules in the asymmetric unit that differ only in the twist between the two aromatic rings; the torsion angles between the rings are 29.9 (2) and 45.1 (2)°. The crystal packing is dominated by inter­molecular N—H(...)N hydrogen bonds between independent and equivalent mol­ecules, forming an infinite three-dimensional network.

Related literature

For biological activity, see: Zhu & Yang (2005 [triangle]); Sherrington & Taskinen (2001 [triangle]); Ligthart et al. (2005 [triangle]). For a similar structure, see: Fun et al. (2006 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0o759-scheme1.jpg

Experimental

Crystal data

  • C11H11N3
  • M r = 185.23
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o759-efi1.jpg
  • a = 14.0558 (11) Å
  • b = 9.3808 (7) Å
  • c = 18.5227 (12) Å
  • β = 125.950 (4)°
  • V = 1977.1 (2) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.08 mm−1
  • T = 273 (2) K
  • 0.30 × 0.20 × 0.20 mm

Data collection

  • Bruker SMART 1K CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 2004 [triangle]) T min = 0.977, T max = 0.985
  • 17472 measured reflections
  • 3619 independent reflections
  • 2760 reflections with I > 2σ(I)
  • R int = 0.033

Refinement

  • R[F 2 > 2σ(F 2)] = 0.039
  • wR(F 2) = 0.113
  • S = 1.04
  • 3619 reflections
  • 256 parameters
  • H-atom parameters constrained
  • Δρmax = 0.21 e Å−3
  • Δρmin = −0.16 e Å−3

Data collection: SMART (Bruker, 2001 [triangle]); cell refinement: SMART; data reduction: SAINT (Bruker, 2001 [triangle]); program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and local programs.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks h-1, I. DOI: 10.1107/S1600536808008003/fl2182sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808008003/fl2182Isup2.hkl

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

Acknowledgments

The authors thank the Natural Science Foundation of Shandong Province (grant No. Y2005F08).

supplementary crystallographic information

Comment

Pyrimidines are broadly used in the preparation of pesticides and medications (Zhu & Yang, 2005). Functionalized pyrimidines are important for the synthesis of purine- and pteridine-related compounds and also for multiple hydrogen-bonding interactions that play a role in molecular recognition and supramolecular chemistry (Sherrington & Taskinen, 2001; Ligthart et al., 2005). In the title compound, (I), (fig. 1) there are two molecules per asymmetric unit that differ only in the twist between the two aromatic rings with dihedral angles between the phenyl and pyrimidine rings of 29.41 (2)° 46.32 (3)°. Bond lengths and angles for (I) are generally normal (Fun et al., 2006).

In the packing there are intermolecular N—H···N hydrogen bonds that link each independent molecule to related self molecules as well as to the second molecule in the asymmetric unit to create an infinite network of hydrogen bonded molecules (Table 1, Fig. 2).

Experimental

The single crystals of the title compound were obtained by reaction of 1-phenylbutane-1,3-dione(0.2 mmol) with guanidine nitrate(0.2 mmol) by refluxing in DMF(50 ml). The product (yied 89%) was stirred in the DMF and single crystals of the title compound suitable for X-ray measurements were obtained by recrystallization from DMF at room temperature.

Refinement

H atoms were fixed geometrically and allowed to ride on their attached atoms, with N—H=0.86, C—H=0.93 or 0.96 Å, and with Uiso(H) values set at 1.5 Ueq(C)(for CH3) or 1.2 Ueq(C)(for CH2, aromatic CH and NH2).

Figures

Fig. 1.
The molecular structure and atom-labeling scheme for (I), with displacement ellipsoids drawn at the 30% probability level.
Fig. 2.
The packing of (I), showing one layer of molecules connected by N—H···N hydrogen bonds (dashed lines).

Crystal data

C11H11N3F000 = 784
Mr = 185.23Dx = 1.245 Mg m3
Monoclinic, P21/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 512 reflections
a = 14.0558 (11) Åθ = 2–22º
b = 9.3808 (7) ŵ = 0.08 mm1
c = 18.5227 (12) ÅT = 273 (2) K
β = 125.950 (4)ºBlock, colorless
V = 1977.1 (2) Å30.30 × 0.20 × 0.20 mm
Z = 8

Data collection

Bruker SMART 1K CCD area-detector diffractometer3619 independent reflections
Radiation source: fine-focus sealed tube2760 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.033
T = 295(2) Kθmax = 25.4º
thin–slice ω scansθmin = 1.8º
Absorption correction: multi-scan(SADABS; Sheldrick, 2004)h = −14→16
Tmin = 0.977, Tmax = 0.985k = −11→11
17472 measured reflectionsl = −22→20

Refinement

Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.039  w = 1/[σ2(Fo2) + (0.0535P)2 + 0.393P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.113(Δ/σ)max = 0.001
S = 1.04Δρmax = 0.21 e Å3
3619 reflectionsΔρmin = −0.16 e Å3
256 parametersExtinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0088 (13)
Secondary atom site location: difference Fourier map

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.

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

xyzUiso*/Ueq
N11.09631 (12)−0.10203 (14)0.46842 (9)0.0492 (4)
H1A1.0775−0.10720.50490.059*
H1B1.1590−0.14340.48100.059*
N21.06247 (11)−0.02652 (14)0.33737 (9)0.0445 (3)
N30.93111 (10)0.03294 (12)0.37592 (8)0.0371 (3)
C10.69500 (14)0.10273 (16)0.31097 (10)0.0428 (4)
H1C0.72760.02320.34780.051*
C20.59049 (15)0.1585 (2)0.28979 (12)0.0537 (4)
H2B0.55310.11610.31230.064*
C30.54156 (17)0.2762 (2)0.23573 (13)0.0661 (5)
H3B0.47180.31430.22230.079*
C40.59617 (19)0.3378 (2)0.20139 (14)0.0711 (6)
H4A0.56270.41680.16420.085*
C50.70011 (16)0.28266 (19)0.22208 (12)0.0557 (5)
H5A0.73630.32490.19860.067*
C60.75185 (13)0.16463 (15)0.27758 (10)0.0395 (4)
C70.86232 (13)0.10283 (14)0.29811 (10)0.0370 (3)
C80.89113 (14)0.11063 (17)0.23828 (11)0.0462 (4)
H8A0.84350.15980.18470.055*
C91.02765 (13)−0.02917 (15)0.39158 (10)0.0371 (3)
C100.99219 (14)0.04372 (18)0.26026 (11)0.0457 (4)
C111.02670 (19)0.0447 (3)0.19755 (13)0.0730 (6)
H11A1.11080.04760.23110.109*
H11B0.99370.12710.15970.109*
H11C0.9977−0.04000.16160.109*
N40.66133 (12)0.04458 (13)0.54000 (9)0.0466 (4)
H4B0.6190−0.02400.53770.056*
H4C0.73660.03630.57220.056*
N50.49149 (11)0.17062 (13)0.44429 (9)0.0440 (3)
N60.68078 (11)0.26712 (12)0.49771 (8)0.0379 (3)
C120.78707 (15)0.46852 (17)0.44133 (12)0.0494 (4)
H12A0.79970.37410.43390.059*
C130.85244 (17)0.5759 (2)0.43871 (13)0.0597 (5)
H13A0.90800.55330.42850.072*
C140.83596 (17)0.7156 (2)0.45107 (13)0.0644 (5)
H14A0.88090.78710.44990.077*
C150.75362 (19)0.74936 (19)0.46501 (15)0.0683 (6)
H15A0.74290.84380.47400.082*
C160.68603 (17)0.64335 (17)0.46588 (13)0.0566 (5)
H16A0.62860.66740.47380.068*
C170.70284 (13)0.50159 (15)0.45505 (10)0.0404 (4)
C180.62748 (13)0.38817 (15)0.45327 (10)0.0387 (4)
C190.50733 (14)0.40570 (17)0.40489 (11)0.0471 (4)
H19A0.47210.49190.37700.057*
C200.60975 (13)0.16496 (15)0.49325 (10)0.0376 (3)
C210.44081 (14)0.29142 (17)0.39901 (11)0.0475 (4)
C220.30886 (16)0.2934 (2)0.33834 (15)0.0744 (6)
H22A0.27870.22620.35930.112*
H22B0.28230.26810.27900.112*
H22C0.28120.38720.33790.112*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0443 (8)0.0635 (8)0.0430 (8)0.0156 (6)0.0274 (7)0.0176 (7)
N20.0398 (7)0.0573 (8)0.0382 (8)0.0040 (6)0.0239 (7)0.0047 (6)
N30.0349 (7)0.0422 (6)0.0335 (7)0.0002 (5)0.0196 (6)0.0031 (5)
C10.0399 (9)0.0490 (8)0.0359 (9)−0.0024 (7)0.0202 (8)−0.0030 (7)
C20.0455 (10)0.0717 (11)0.0479 (10)−0.0032 (9)0.0296 (9)−0.0102 (9)
C30.0497 (11)0.0876 (14)0.0552 (12)0.0223 (10)0.0275 (10)0.0005 (10)
C40.0712 (13)0.0751 (13)0.0652 (13)0.0330 (11)0.0391 (12)0.0220 (10)
C50.0577 (11)0.0579 (10)0.0533 (11)0.0135 (8)0.0335 (10)0.0141 (8)
C60.0377 (8)0.0430 (8)0.0328 (8)0.0007 (6)0.0179 (7)−0.0014 (6)
C70.0351 (8)0.0379 (7)0.0334 (8)−0.0026 (6)0.0175 (7)0.0012 (6)
C80.0432 (9)0.0582 (9)0.0353 (9)0.0052 (7)0.0220 (8)0.0109 (7)
C90.0345 (8)0.0403 (7)0.0341 (8)−0.0017 (6)0.0187 (7)0.0013 (6)
C100.0414 (9)0.0617 (10)0.0351 (9)0.0007 (7)0.0230 (8)0.0039 (7)
C110.0642 (13)0.1156 (17)0.0521 (12)0.0198 (12)0.0414 (11)0.0190 (11)
N40.0396 (7)0.0426 (7)0.0574 (9)0.0040 (6)0.0284 (7)0.0128 (6)
N50.0377 (7)0.0477 (7)0.0461 (8)0.0007 (6)0.0243 (7)0.0095 (6)
N60.0385 (7)0.0396 (6)0.0385 (7)−0.0002 (5)0.0242 (6)0.0026 (5)
C120.0520 (10)0.0467 (9)0.0570 (11)0.0015 (7)0.0363 (9)0.0049 (7)
C130.0559 (11)0.0681 (11)0.0666 (13)−0.0038 (9)0.0425 (10)0.0081 (9)
C140.0619 (12)0.0561 (11)0.0710 (13)−0.0176 (9)0.0367 (11)0.0032 (9)
C150.0769 (14)0.0424 (9)0.0895 (16)−0.0120 (9)0.0510 (13)−0.0080 (9)
C160.0621 (11)0.0473 (9)0.0710 (12)−0.0024 (8)0.0449 (10)−0.0038 (8)
C170.0416 (8)0.0405 (8)0.0381 (9)−0.0007 (6)0.0229 (7)0.0038 (6)
C180.0429 (9)0.0397 (8)0.0378 (9)0.0014 (6)0.0260 (8)0.0023 (6)
C190.0448 (10)0.0448 (8)0.0519 (10)0.0071 (7)0.0286 (9)0.0139 (7)
C200.0391 (8)0.0406 (7)0.0366 (8)0.0011 (6)0.0243 (7)0.0016 (6)
C210.0399 (9)0.0543 (9)0.0481 (10)0.0049 (7)0.0258 (8)0.0125 (8)
C220.0415 (10)0.0858 (14)0.0792 (15)0.0059 (10)0.0261 (11)0.0336 (12)

Geometric parameters (Å, °)

N1—C91.3459 (19)N4—C201.3467 (19)
N1—H1A0.8600N4—H4B0.8600
N1—H1B0.8600N4—H4C0.8600
N2—C101.339 (2)N5—C211.339 (2)
N2—C91.3509 (19)N5—C201.3484 (19)
N3—C91.3426 (19)N6—C181.3431 (18)
N3—C71.3437 (18)N6—C201.3510 (18)
C1—C21.382 (2)C12—C131.383 (2)
C1—C61.392 (2)C12—C171.384 (2)
C1—H1C0.9300C12—H12A0.9300
C2—C31.374 (3)C13—C141.373 (3)
C2—H2B0.9300C13—H13A0.9300
C3—C41.379 (3)C14—C151.363 (3)
C3—H3B0.9300C14—H14A0.9300
C4—C51.375 (3)C15—C161.382 (2)
C4—H4A0.9300C15—H15A0.9300
C5—C61.391 (2)C16—C171.386 (2)
C5—H5A0.9300C16—H16A0.9300
C6—C71.483 (2)C17—C181.488 (2)
C7—C81.387 (2)C18—C191.380 (2)
C8—C101.378 (2)C19—C211.384 (2)
C8—H8A0.9300C19—H19A0.9300
C10—C111.499 (2)C21—C221.502 (2)
C11—H11A0.9600C22—H22A0.9600
C11—H11B0.9600C22—H22B0.9600
C11—H11C0.9600C22—H22C0.9600
C9—N1—H1A120.0C20—N4—H4B120.0
C9—N1—H1B120.0C20—N4—H4C120.0
H1A—N1—H1B120.0H4B—N4—H4C120.0
C10—N2—C9116.07 (13)C21—N5—C20116.55 (13)
C9—N3—C7116.30 (12)C18—N6—C20115.84 (12)
C2—C1—C6120.52 (15)C13—C12—C17120.02 (16)
C2—C1—H1C119.7C13—C12—H12A120.0
C6—C1—H1C119.7C17—C12—H12A120.0
C3—C2—C1120.35 (17)C14—C13—C12120.58 (17)
C3—C2—H2B119.8C14—C13—H13A119.7
C1—C2—H2B119.8C12—C13—H13A119.7
C2—C3—C4119.81 (17)C15—C14—C13119.89 (16)
C2—C3—H3B120.1C15—C14—H14A120.1
C4—C3—H3B120.1C13—C14—H14A120.1
C5—C4—C3120.12 (18)C14—C15—C16120.07 (17)
C5—C4—H4A119.9C14—C15—H15A120.0
C3—C4—H4A119.9C16—C15—H15A120.0
C4—C5—C6120.95 (18)C15—C16—C17120.81 (17)
C4—C5—H5A119.5C15—C16—H16A119.6
C6—C5—H5A119.5C17—C16—H16A119.6
C5—C6—C1118.24 (15)C12—C17—C16118.59 (15)
C5—C6—C7121.01 (14)C12—C17—C18120.67 (14)
C1—C6—C7120.72 (13)C16—C17—C18120.65 (14)
N3—C7—C8121.26 (14)N6—C18—C19121.89 (13)
N3—C7—C6116.84 (13)N6—C18—C17117.21 (13)
C8—C7—C6121.83 (14)C19—C18—C17120.86 (13)
C10—C8—C7118.27 (14)C18—C19—C21118.12 (14)
C10—C8—H8A120.9C18—C19—H19A120.9
C7—C8—H8A120.9C21—C19—H19A120.9
N3—C9—N1117.08 (13)N4—C20—N5116.82 (13)
N3—C9—N2126.34 (13)N4—C20—N6117.13 (13)
N1—C9—N2116.58 (13)N5—C20—N6126.02 (13)
N2—C10—C8121.75 (14)N5—C21—C19121.31 (14)
N2—C10—C11117.25 (15)N5—C21—C22116.64 (15)
C8—C10—C11120.99 (15)C19—C21—C22121.98 (15)
C10—C11—H11A109.5C21—C22—H22A109.5
C10—C11—H11B109.5C21—C22—H22B109.5
H11A—C11—H11B109.5H22A—C22—H22B109.5
C10—C11—H11C109.5C21—C22—H22C109.5
H11A—C11—H11C109.5H22A—C22—H22C109.5
H11B—C11—H11C109.5H22B—C22—H22C109.5
C6—C1—C2—C3−0.3 (2)C17—C12—C13—C141.1 (3)
C1—C2—C3—C40.9 (3)C12—C13—C14—C15−0.8 (3)
C2—C3—C4—C5−0.8 (3)C13—C14—C15—C16−0.6 (3)
C3—C4—C5—C60.0 (3)C14—C15—C16—C171.7 (3)
C4—C5—C6—C10.7 (3)C13—C12—C17—C160.0 (3)
C4—C5—C6—C7178.44 (17)C13—C12—C17—C18176.76 (16)
C2—C1—C6—C5−0.5 (2)C15—C16—C17—C12−1.4 (3)
C2—C1—C6—C7−178.31 (14)C15—C16—C17—C18−178.14 (17)
C9—N3—C7—C8−0.6 (2)C20—N6—C18—C19−1.1 (2)
C9—N3—C7—C6176.50 (12)C20—N6—C18—C17−178.59 (13)
C5—C6—C7—N3153.34 (15)C12—C17—C18—N645.1 (2)
C1—C6—C7—N3−28.9 (2)C16—C17—C18—N6−138.24 (16)
C5—C6—C7—C8−29.6 (2)C12—C17—C18—C19−132.43 (17)
C1—C6—C7—C8148.13 (15)C16—C17—C18—C1944.2 (2)
N3—C7—C8—C100.5 (2)N6—C18—C19—C21−3.4 (2)
C6—C7—C8—C10−176.46 (14)C17—C18—C19—C21174.05 (15)
C7—N3—C9—N1−178.71 (13)C21—N5—C20—N4179.01 (14)
C7—N3—C9—N20.8 (2)C21—N5—C20—N6−2.9 (2)
C10—N2—C9—N3−0.9 (2)C18—N6—C20—N4−177.49 (13)
C10—N2—C9—N1178.64 (14)C18—N6—C20—N54.5 (2)
C9—N2—C10—C80.7 (2)C20—N5—C21—C19−2.0 (2)
C9—N2—C10—C11−178.21 (16)C20—N5—C21—C22174.92 (16)
C7—C8—C10—N2−0.6 (2)C18—C19—C21—N55.0 (3)
C7—C8—C10—C11178.35 (17)C18—C19—C21—C22−171.76 (18)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1A···N3i0.862.383.1918 (18)157
N1—H1B···N6i0.862.353.2095 (18)175
N4—H4C···N2i0.862.293.1474 (19)176
N4—H4B···N5ii0.862.243.0834 (18)166

Symmetry codes: (i) −x+2, −y, −z+1; (ii) −x+1, −y, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: FL2182).

References

  • Bruker (2001). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Fun, H.-K., Goswami, S., Jana, S. & Chantrapromma, S. (2006). Acta Cryst. E62, o5332–o5334.
  • Ligthart, G. B. W. L., Ohkawa, H., Sijbesma, R. P. & Meijer, E. W. (2005). J. Am. Chem. Soc.127, 810–811. [PubMed]
  • Sheldrick, G. M. (2004). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Sherrington, D. C. & Taskinen, K. A. (2001). Chem. Soc. Rev.30, 83–93.
  • Zhu, W. M. & Yang, A. M. (2005). Appl. Chem. Ind.34, 360–361.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography