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Acta Crystallographica Section E: Structure Reports Online logoLink to Acta Crystallographica Section E: Structure Reports Online
. 2011 Nov 12;67(Pt 12):o3258. doi: 10.1107/S1600536811046848

2-[(Pyrimidin-2-yl­amino)­meth­yl]phenol

Jing Xu a, Shan Gao a, Seik Weng Ng b,c,*
PMCID: PMC3238918  PMID: 22199767

Abstract

In the title compound, C11H11N3O, the aromatic rings at either ends of the –CH2–NH– link are twisted by 72.58 (8)°; the hy­droxy substituent is a hydrogen-bond donor to an N atom of the pyrimidine ring. The other N atom of the pyrimidine ring is a hydrogen-bond acceptor to the amino group of an inversion-related mol­ecule.

Related literature

For the N-salicyl­idene-2-amino­pyrimidine precursor, see: El-Haty et al. (1990 ▶); Issa et al. (2011 ▶); Shalabi & Abdel-Ghani (1990 ▶). For a related structure, see: Xu et al. (2011 ▶).graphic file with name e-67-o3258-scheme1.jpg

Experimental

Crystal data

  • C11H11N3O

  • M r = 201.23

  • Monoclinic, Inline graphic

  • a = 5.8625 (4) Å

  • b = 9.3610 (7) Å

  • c = 18.4058 (13) Å

  • β = 95.208 (2)°

  • V = 1005.92 (12) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 293 K

  • 0.22 × 0.17 × 0.15 mm

Data collection

  • Rigaku R-AXIS RAPID IP diffractometer

  • Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ▶) T min = 0.981, T max = 0.987

  • 9626 measured reflections

  • 2296 independent reflections

  • 1476 reflections with I > 2σ(I)

  • R int = 0.030

Refinement

  • R[F 2 > 2σ(F 2)] = 0.040

  • wR(F 2) = 0.149

  • S = 1.12

  • 2296 reflections

  • 144 parameters

  • 2 restraints

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.14 e Å−3

  • Δρmin = −0.15 e Å−3

Data collection: RAPID-AUTO (Rigaku, 1998 ▶); cell refinement: RAPID-AUTO; data reduction: CrystalClear (Rigaku/MSC, 2002 ▶); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: X-SEED (Barbour, 2001 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶).

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536811046848/xu5383sup1.cif

e-67-o3258-sup1.cif (14.5KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811046848/xu5383Isup2.hkl

e-67-o3258-Isup2.hkl (112.9KB, hkl)

Supplementary material file. DOI: 10.1107/S1600536811046848/xu5383Isup3.cml

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

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A D⋯A D—H⋯A
O1—H1o⋯N2 0.86 (1) 1.92 (1) 2.761 (2) 164 (2)
N1—H1n⋯N3i 0.88 (1) 2.15 (1) 3.023 (2) 176 (2)
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Symmetry code: (i) Inline graphic.

Acknowledgments

This work was supported by the Key Project of the Natural Science Foundation of Heilongjiang Province (No. ZD200903), the Key Project of the Education Bureau of Heilongjiang Province (No. 12511z023), Heilongjiang University (Hdtd2010–04) and the University of Malaya.

supplementary crystallographic information

Comment

There are numerous studies on the Schiff bases derived by condensing salicyldehyde and an aromatic amine. In this study, the azomethine double-bond of N-salicylidene-2-aminopyrimidine (El-Haty et al., 1990; Issa et al., 2011; Shalabi & Abdel-Ghani, 1990) is reduced by sodium borohydride to yield the title secondary amine (Scheme I). The two aromatic rings at either ends of the –CH2–NH– link of C11H11N3O are twisted by 72.58 (8)°; the hydroxy substituent is hydrogen-bond donor to anone N atom of the pyrimidyl ring (Fig. 1). The other N atom of the pyrimidyl ring is hydrogen-bond acceptor to the amino group of an inversion-related molecule (Table 1).

Experimental

A solution of 2-aminopyrimidine (1 mmol) and salicylaldehyde (1 mmol) in toluene (50 ml) was heated for 10 h. The solvent was removed under vacuum, and the residue was reduced in absolute methanol by sodium borohydride. Colorless crystals were obtained by recrystallization from methanol; yield 80%.

Refinement

Carbon-bound H-atoms were placed in calculated positions (C–H 0.93–0.97 Å) and were included in the refinement in the riding model approximation, with Uiso(H) = 1.2Ueq(C). The amino and hydroxy H-atoms were located in a difference Fourier map, and were refined with distance restraints N–H 0.88±0.01 Å and O–H 0.84±0.01 Å; their temperature factors were refined.

Figures

Fig. 1.

Fig. 1.

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Thermal ellipsoid plot (Barbour, 2001) of C11H11N3O at the 50% probability level; hydrogen atoms are drawn as spheres of arbitrary radius.

Crystal data

C11H11N3O F(000) = 424
Mr = 201.23 Dx = 1.329 Mg m−3
Monoclinic, P21/n Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn Cell parameters from 6005 reflections
a = 5.8625 (4) Å θ = 3.1–27.4°
b = 9.3610 (7) Å µ = 0.09 mm−1
c = 18.4058 (13) Å T = 293 K
β = 95.208 (2)° Prism, colorless
V = 1005.92 (12) Å3 0.22 × 0.17 × 0.15 mm
Z = 4
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Data collection

Rigaku R-AXIS RAPID IP diffractometer 2296 independent reflections
Radiation source: fine-focus sealed tube 1476 reflections with I > 2σ(I)
graphite Rint = 0.030
ω scan θmax = 27.4°, θmin = 3.1°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995) h = −7→6
Tmin = 0.981, Tmax = 0.987 k = −12→12
9626 measured reflections l = −23→23
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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)] = 0.040 Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.149 H atoms treated by a mixture of independent and constrained refinement
S = 1.12 w = 1/[σ2(Fo2) + (0.0796P)2 + 0.034P] where P = (Fo2 + 2Fc2)/3
2296 reflections (Δ/σ)max = 0.001
144 parameters Δρmax = 0.14 e Å−3
2 restraints Δρmin = −0.15 e Å−3
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Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

x y z Uiso*/Ueq
O1 1.0476 (2) 0.91985 (13) 0.62203 (7) 0.0630 (4)
N1 0.5979 (2) 0.67826 (16) 0.53868 (8) 0.0571 (4)
N2 0.9251 (2) 0.77099 (14) 0.49494 (7) 0.0534 (4)
N3 0.7438 (2) 0.55875 (14) 0.44465 (7) 0.0517 (4)
C1 0.9836 (3) 0.82174 (16) 0.67131 (9) 0.0488 (4)
C2 1.1341 (3) 0.79323 (18) 0.73237 (9) 0.0554 (4)
H2 1.2718 0.8428 0.7393 0.066*
C3 1.0819 (3) 0.69305 (19) 0.78229 (10) 0.0622 (5)
H3 1.1850 0.6737 0.8225 0.075*
C4 0.8756 (3) 0.62029 (19) 0.77307 (10) 0.0646 (5)
H4 0.8405 0.5512 0.8066 0.078*
C5 0.7224 (3) 0.65110 (18) 0.71357 (10) 0.0581 (4)
H5 0.5827 0.6034 0.7081 0.070*
C6 0.7718 (2) 0.75136 (16) 0.66180 (9) 0.0500 (4)
C7 0.5997 (3) 0.78265 (19) 0.59729 (9) 0.0580 (4)
H7A 0.4480 0.7868 0.6143 0.070*
H7B 0.6329 0.8760 0.5779 0.070*
C8 0.7604 (2) 0.66981 (16) 0.49207 (8) 0.0478 (4)
C9 1.0801 (3) 0.75831 (19) 0.44642 (10) 0.0574 (4)
H9 1.1954 0.8266 0.4466 0.069*
C10 1.0780 (3) 0.65013 (19) 0.39651 (9) 0.0593 (5)
H10 1.1880 0.6432 0.3633 0.071*
C11 0.9034 (3) 0.55172 (19) 0.39818 (9) 0.0550 (4)
H11 0.8973 0.4766 0.3650 0.066*
H1O 1.000 (4) 0.889 (3) 0.5791 (8) 0.117 (9)*
H1N 0.501 (3) 0.6073 (14) 0.5417 (10) 0.062 (5)*
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Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
O1 0.0674 (8) 0.0543 (7) 0.0667 (8) −0.0114 (5) 0.0032 (6) 0.0017 (6)
N1 0.0425 (7) 0.0658 (9) 0.0629 (8) −0.0070 (6) 0.0040 (6) −0.0127 (7)
N2 0.0488 (7) 0.0504 (8) 0.0601 (8) −0.0022 (6) 0.0006 (6) 0.0040 (6)
N3 0.0495 (7) 0.0547 (8) 0.0500 (7) 0.0018 (6) 0.0006 (6) −0.0008 (6)
C1 0.0492 (8) 0.0404 (8) 0.0572 (9) 0.0000 (6) 0.0070 (7) −0.0069 (7)
C2 0.0488 (8) 0.0575 (10) 0.0590 (10) −0.0035 (7) −0.0001 (8) −0.0112 (8)
C3 0.0656 (11) 0.0631 (11) 0.0563 (10) 0.0039 (8) −0.0026 (8) −0.0032 (8)
C4 0.0772 (12) 0.0569 (10) 0.0611 (10) −0.0049 (9) 0.0134 (9) 0.0010 (8)
C5 0.0504 (9) 0.0557 (10) 0.0694 (11) −0.0077 (7) 0.0120 (8) −0.0116 (8)
C6 0.0427 (8) 0.0484 (9) 0.0591 (10) 0.0026 (6) 0.0064 (7) −0.0118 (7)
C7 0.0446 (8) 0.0635 (10) 0.0652 (10) 0.0062 (7) 0.0016 (8) −0.0130 (8)
C8 0.0426 (8) 0.0499 (9) 0.0494 (8) 0.0026 (6) −0.0039 (7) 0.0025 (7)
C9 0.0523 (9) 0.0568 (10) 0.0629 (10) −0.0025 (7) 0.0042 (8) 0.0124 (8)
C10 0.0572 (10) 0.0637 (11) 0.0581 (10) 0.0031 (8) 0.0100 (8) 0.0067 (8)
C11 0.0581 (9) 0.0561 (10) 0.0503 (9) 0.0067 (8) 0.0019 (8) 0.0012 (7)
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Geometric parameters (Å, °)

O1—C1 1.367 (2) C3—H3 0.9300
O1—H1O 0.863 (10) C4—C5 1.382 (3)
N1—C8 1.341 (2) C4—H4 0.9300
N1—C7 1.455 (2) C5—C6 1.387 (2)
N1—H1N 0.878 (9) C5—H5 0.9300
N2—C9 1.336 (2) C6—C7 1.515 (2)
N2—C8 1.350 (2) C7—H7A 0.9700
N3—C11 1.325 (2) C7—H7B 0.9700
N3—C8 1.3552 (19) C9—C10 1.367 (2)
C1—C2 1.390 (2) C9—H9 0.9300
C1—C6 1.402 (2) C10—C11 1.380 (2)
C2—C3 1.367 (2) C10—H10 0.9300
C2—H2 0.9300 C11—H11 0.9300
C3—C4 1.385 (3)
C1—O1—H1O 107.4 (18) C5—C6—C1 118.05 (15)
C8—N1—C7 123.78 (14) C5—C6—C7 120.21 (15)
C8—N1—H1N 119.7 (12) C1—C6—C7 121.74 (15)
C7—N1—H1N 115.0 (12) N1—C7—C6 114.25 (13)
C9—N2—C8 116.03 (14) N1—C7—H7A 108.7
C11—N3—C8 116.12 (14) C6—C7—H7A 108.7
O1—C1—C2 118.23 (14) N1—C7—H7B 108.7
O1—C1—C6 121.74 (14) C6—C7—H7B 108.7
C2—C1—C6 120.03 (15) H7A—C7—H7B 107.6
C3—C2—C1 120.70 (15) N1—C8—N2 118.73 (14)
C3—C2—H2 119.7 N1—C8—N3 116.33 (14)
C1—C2—H2 119.7 N2—C8—N3 124.93 (15)
C2—C3—C4 120.10 (16) N2—C9—C10 123.37 (16)
C2—C3—H3 120.0 N2—C9—H9 118.3
C4—C3—H3 120.0 C10—C9—H9 118.3
C5—C4—C3 119.47 (17) C9—C10—C11 116.19 (16)
C5—C4—H4 120.3 C9—C10—H10 121.9
C3—C4—H4 120.3 C11—C10—H10 121.9
C4—C5—C6 121.60 (16) N3—C11—C10 123.36 (16)
C4—C5—H5 119.2 N3—C11—H11 118.3
C6—C5—H5 119.2 C10—C11—H11 118.3
O1—C1—C2—C3 −178.05 (15) C5—C6—C7—N1 −79.8 (2)
C6—C1—C2—C3 2.4 (2) C1—C6—C7—N1 100.33 (18)
C1—C2—C3—C4 −1.1 (3) C7—N1—C8—N2 −6.1 (2)
C2—C3—C4—C5 −0.8 (3) C7—N1—C8—N3 174.43 (14)
C3—C4—C5—C6 1.4 (3) C9—N2—C8—N1 −178.93 (13)
C4—C5—C6—C1 0.0 (2) C9—N2—C8—N3 0.4 (2)
C4—C5—C6—C7 −179.92 (15) C11—N3—C8—N1 179.28 (13)
O1—C1—C6—C5 178.65 (14) C11—N3—C8—N2 −0.1 (2)
C2—C1—C6—C5 −1.8 (2) C8—N2—C9—C10 −0.5 (2)
O1—C1—C6—C7 −1.5 (2) N2—C9—C10—C11 0.2 (2)
C2—C1—C6—C7 178.06 (14) C8—N3—C11—C10 −0.2 (2)
C8—N1—C7—C6 −74.7 (2) C9—C10—C11—N3 0.2 (2)
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Hydrogen-bond geometry (Å, °)

D—H···A D—H H···A D···A D—H···A
O1—H1o···N2 0.86 (1) 1.92 (1) 2.761 (2) 164 (2)
N1—H1n···N3i 0.88 (1) 2.15 (1) 3.023 (2) 176 (2)
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Symmetry codes: (i) −x+1, −y+1, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: XU5383).

References

  1. Barbour, L. J. (2001). J. Supramol. Chem. 1, 189–191.
  2. El-Haty, M. T., Mohamed, A. E., Adam, F. A. & Gabr, A. A. (1990). Spectrochim. Acta Part A, 46, 1743–1749.
  3. Higashi, T. (1995). ABSCOR Rigaku Corporation, Tokyo, Japan.
  4. Issa, Y. M., El Ansary, A. L., Sherif, O. E. & Hassib, H. B. (2011). Spectrochim. Acta Part A, 79, 513–521. [DOI] [PubMed]
  5. Rigaku (1998). RAPID-AUTO Rigaku Corporation, Tokyo, Japan.
  6. Rigaku/MSC (2002). CrystalClear Rigaku/MSC Inc., The Woodlands, Texas, USA.
  7. Shalabi, A. S. & Abdel-Ghani, N. T. (1990). Egypt. J. Chem. 33, 345–357.
  8. Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [DOI] [PubMed]
  9. Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.
  10. Xu, J., Gao, S. & Ng, S. W. (2011). Acta Cryst. E67, o3259. [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) global, I. DOI: 10.1107/S1600536811046848/xu5383sup1.cif

e-67-o3258-sup1.cif (14.5KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811046848/xu5383Isup2.hkl

e-67-o3258-Isup2.hkl (112.9KB, hkl)

Supplementary material file. DOI: 10.1107/S1600536811046848/xu5383Isup3.cml

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

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

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