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

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

aKey Laboratory of Functional Inorganic Material Chemistry, Ministry of Education, Heilongjiang University, Harbin 150080, People's Republic of China, bDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia, and cChemistry Department, Faculty of Science, King Abdulaziz University, PO Box 80203 Jeddah, Saudi Arabia
*Correspondence e-mail: seikweng@um.edu.my

(Received 4 November 2011; accepted 7 November 2011; online 12 November 2011)

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[El-Haty, M. T., Mohamed, A. E., Adam, F. A. & Gabr, A. A. (1990). Spectrochim. Acta Part A, 46, 1743-1749.]); Issa et al. (2011[Issa, Y. M., El Ansary, A. L., Sherif, O. E. & Hassib, H. B. (2011). Spectrochim. Acta Part A, 79, 513-521.]); Shalabi & Abdel-Ghani (1990[Shalabi, A. S. & Abdel-Ghani, N. T. (1990). Egypt. J. Chem. 33, 345-357.]). For a related structure, see: Xu et al. (2011[Xu, J., Gao, S. & Ng, S. W. (2011). Acta Cryst. E67, o3259.]).

[Scheme 1]

Experimental

Crystal data
  • C11H11N3O

  • Mr = 201.23

  • Monoclinic, P 21 /n

  • 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[Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.981, Tmax = 0.987

  • 9626 measured reflections

  • 2296 independent reflections

  • 1476 reflections with I > 2σ(I)

  • Rint = 0.030

Refinement
  • R[F2 > 2σ(F2)] = 0.040

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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)
Symmetry code: (i) -x+1, -y+1, -z+1.

Data collection: RAPID-AUTO (Rigaku, 1998[Rigaku (1998). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan.]); cell refinement: RAPID-AUTO; data reduction: CrystalClear (Rigaku/MSC, 2002[Rigaku/MSC (2002). CrystalClear. Rigaku/MSC Inc., The Woodlands, Texas, USA.]); 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: X-SEED (Barbour, 2001[Barbour, L. J. (2001). J. Supramol. Chem. 1, 189-191.]); software used to prepare material for publication: publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Comment top

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).

Related literature top

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).

Experimental top

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 top

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.

Structure description top

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).

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).

Computing details top

Data collection: RAPID-AUTO (Rigaku, 1998); cell refinement: RAPID-AUTO (Rigaku, 1998); 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).

Figures top
[Figure 1] Fig. 1. Thermal ellipsoid plot (Barbour, 2001) of C11H11N3O at the 50% probability level; hydrogen atoms are drawn as spheres of arbitrary radius.
2-[(Pyrimidin-2-ylamino)methyl]phenol top
Crystal data top
C11H11N3OF(000) = 424
Mr = 201.23Dx = 1.329 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 6005 reflections
a = 5.8625 (4) Åθ = 3.1–27.4°
b = 9.3610 (7) ŵ = 0.09 mm1
c = 18.4058 (13) ÅT = 293 K
β = 95.208 (2)°Prism, colorless
V = 1005.92 (12) Å30.22 × 0.17 × 0.15 mm
Z = 4
Data collection top
Rigaku R-AXIS RAPID IP
diffractometer
2296 independent reflections
Radiation source: fine-focus sealed tube1476 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.030
ω scanθmax = 27.4°, θmin = 3.1°
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
h = 76
Tmin = 0.981, Tmax = 0.987k = 1212
9626 measured reflectionsl = 2323
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)] = 0.040Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.149H 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 parametersΔρmax = 0.14 e Å3
2 restraintsΔρmin = 0.15 e Å3
Crystal data top
C11H11N3OV = 1005.92 (12) Å3
Mr = 201.23Z = 4
Monoclinic, P21/nMo Kα radiation
a = 5.8625 (4) ŵ = 0.09 mm1
b = 9.3610 (7) ÅT = 293 K
c = 18.4058 (13) Å0.22 × 0.17 × 0.15 mm
β = 95.208 (2)°
Data collection top
Rigaku R-AXIS RAPID IP
diffractometer
2296 independent reflections
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
1476 reflections with I > 2σ(I)
Tmin = 0.981, Tmax = 0.987Rint = 0.030
9626 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0402 restraints
wR(F2) = 0.149H atoms treated by a mixture of independent and constrained refinement
S = 1.12Δρmax = 0.14 e Å3
2296 reflectionsΔρmin = 0.15 e Å3
144 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O11.0476 (2)0.91985 (13)0.62203 (7)0.0630 (4)
N10.5979 (2)0.67826 (16)0.53868 (8)0.0571 (4)
N20.9251 (2)0.77099 (14)0.49494 (7)0.0534 (4)
N30.7438 (2)0.55875 (14)0.44465 (7)0.0517 (4)
C10.9836 (3)0.82174 (16)0.67131 (9)0.0488 (4)
C21.1341 (3)0.79323 (18)0.73237 (9)0.0554 (4)
H21.27180.84280.73930.066*
C31.0819 (3)0.69305 (19)0.78229 (10)0.0622 (5)
H31.18500.67370.82250.075*
C40.8756 (3)0.62029 (19)0.77307 (10)0.0646 (5)
H40.84050.55120.80660.078*
C50.7224 (3)0.65110 (18)0.71357 (10)0.0581 (4)
H50.58270.60340.70810.070*
C60.7718 (2)0.75136 (16)0.66180 (9)0.0500 (4)
C70.5997 (3)0.78265 (19)0.59729 (9)0.0580 (4)
H7A0.44800.78680.61430.070*
H7B0.63290.87600.57790.070*
C80.7604 (2)0.66981 (16)0.49207 (8)0.0478 (4)
C91.0801 (3)0.75831 (19)0.44642 (10)0.0574 (4)
H91.19540.82660.44660.069*
C101.0780 (3)0.65013 (19)0.39651 (9)0.0593 (5)
H101.18800.64320.36330.071*
C110.9034 (3)0.55172 (19)0.39818 (9)0.0550 (4)
H110.89730.47660.36500.066*
H1O1.000 (4)0.889 (3)0.5791 (8)0.117 (9)*
H1N0.501 (3)0.6073 (14)0.5417 (10)0.062 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0674 (8)0.0543 (7)0.0667 (8)0.0114 (5)0.0032 (6)0.0017 (6)
N10.0425 (7)0.0658 (9)0.0629 (8)0.0070 (6)0.0040 (6)0.0127 (7)
N20.0488 (7)0.0504 (8)0.0601 (8)0.0022 (6)0.0006 (6)0.0040 (6)
N30.0495 (7)0.0547 (8)0.0500 (7)0.0018 (6)0.0006 (6)0.0008 (6)
C10.0492 (8)0.0404 (8)0.0572 (9)0.0000 (6)0.0070 (7)0.0069 (7)
C20.0488 (8)0.0575 (10)0.0590 (10)0.0035 (7)0.0001 (8)0.0112 (8)
C30.0656 (11)0.0631 (11)0.0563 (10)0.0039 (8)0.0026 (8)0.0032 (8)
C40.0772 (12)0.0569 (10)0.0611 (10)0.0049 (9)0.0134 (9)0.0010 (8)
C50.0504 (9)0.0557 (10)0.0694 (11)0.0077 (7)0.0120 (8)0.0116 (8)
C60.0427 (8)0.0484 (9)0.0591 (10)0.0026 (6)0.0064 (7)0.0118 (7)
C70.0446 (8)0.0635 (10)0.0652 (10)0.0062 (7)0.0016 (8)0.0130 (8)
C80.0426 (8)0.0499 (9)0.0494 (8)0.0026 (6)0.0039 (7)0.0025 (7)
C90.0523 (9)0.0568 (10)0.0629 (10)0.0025 (7)0.0042 (8)0.0124 (8)
C100.0572 (10)0.0637 (11)0.0581 (10)0.0031 (8)0.0100 (8)0.0067 (8)
C110.0581 (9)0.0561 (10)0.0503 (9)0.0067 (8)0.0019 (8)0.0012 (7)
Geometric parameters (Å, º) top
O1—C11.367 (2)C3—H30.9300
O1—H1O0.863 (10)C4—C51.382 (3)
N1—C81.341 (2)C4—H40.9300
N1—C71.455 (2)C5—C61.387 (2)
N1—H1N0.878 (9)C5—H50.9300
N2—C91.336 (2)C6—C71.515 (2)
N2—C81.350 (2)C7—H7A0.9700
N3—C111.325 (2)C7—H7B0.9700
N3—C81.3552 (19)C9—C101.367 (2)
C1—C21.390 (2)C9—H90.9300
C1—C61.402 (2)C10—C111.380 (2)
C2—C31.367 (2)C10—H100.9300
C2—H20.9300C11—H110.9300
C3—C41.385 (3)
C1—O1—H1O107.4 (18)C5—C6—C1118.05 (15)
C8—N1—C7123.78 (14)C5—C6—C7120.21 (15)
C8—N1—H1N119.7 (12)C1—C6—C7121.74 (15)
C7—N1—H1N115.0 (12)N1—C7—C6114.25 (13)
C9—N2—C8116.03 (14)N1—C7—H7A108.7
C11—N3—C8116.12 (14)C6—C7—H7A108.7
O1—C1—C2118.23 (14)N1—C7—H7B108.7
O1—C1—C6121.74 (14)C6—C7—H7B108.7
C2—C1—C6120.03 (15)H7A—C7—H7B107.6
C3—C2—C1120.70 (15)N1—C8—N2118.73 (14)
C3—C2—H2119.7N1—C8—N3116.33 (14)
C1—C2—H2119.7N2—C8—N3124.93 (15)
C2—C3—C4120.10 (16)N2—C9—C10123.37 (16)
C2—C3—H3120.0N2—C9—H9118.3
C4—C3—H3120.0C10—C9—H9118.3
C5—C4—C3119.47 (17)C9—C10—C11116.19 (16)
C5—C4—H4120.3C9—C10—H10121.9
C3—C4—H4120.3C11—C10—H10121.9
C4—C5—C6121.60 (16)N3—C11—C10123.36 (16)
C4—C5—H5119.2N3—C11—H11118.3
C6—C5—H5119.2C10—C11—H11118.3
O1—C1—C2—C3178.05 (15)C5—C6—C7—N179.8 (2)
C6—C1—C2—C32.4 (2)C1—C6—C7—N1100.33 (18)
C1—C2—C3—C41.1 (3)C7—N1—C8—N26.1 (2)
C2—C3—C4—C50.8 (3)C7—N1—C8—N3174.43 (14)
C3—C4—C5—C61.4 (3)C9—N2—C8—N1178.93 (13)
C4—C5—C6—C10.0 (2)C9—N2—C8—N30.4 (2)
C4—C5—C6—C7179.92 (15)C11—N3—C8—N1179.28 (13)
O1—C1—C6—C5178.65 (14)C11—N3—C8—N20.1 (2)
C2—C1—C6—C51.8 (2)C8—N2—C9—C100.5 (2)
O1—C1—C6—C71.5 (2)N2—C9—C10—C110.2 (2)
C2—C1—C6—C7178.06 (14)C8—N3—C11—C100.2 (2)
C8—N1—C7—C674.7 (2)C9—C10—C11—N30.2 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1o···N20.86 (1)1.92 (1)2.761 (2)164 (2)
N1—H1n···N3i0.88 (1)2.15 (1)3.023 (2)176 (2)
Symmetry code: (i) x+1, y+1, z+1.

Experimental details

Crystal data
Chemical formulaC11H11N3O
Mr201.23
Crystal system, space groupMonoclinic, P21/n
Temperature (K)293
a, b, c (Å)5.8625 (4), 9.3610 (7), 18.4058 (13)
β (°) 95.208 (2)
V3)1005.92 (12)
Z4
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.22 × 0.17 × 0.15
Data collection
DiffractometerRigaku R-AXIS RAPID IP
Absorption correctionMulti-scan
(ABSCOR; Higashi, 1995)
Tmin, Tmax0.981, 0.987
No. of measured, independent and
observed [I > 2σ(I)] reflections
9626, 2296, 1476
Rint0.030
(sin θ/λ)max1)0.648
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.040, 0.149, 1.12
No. of reflections2296
No. of parameters144
No. of restraints2
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.14, 0.15

Computer programs: RAPID-AUTO (Rigaku, 1998), CrystalClear (Rigaku/MSC, 2002), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), X-SEED (Barbour, 2001), publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1o···N20.86 (1)1.92 (1)2.761 (2)164 (2)
N1—H1n···N3i0.88 (1)2.15 (1)3.023 (2)176 (2)
Symmetry code: (i) x+1, y+1, z+1.
 

Acknowledgements

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.

References

First citationBarbour, L. J. (2001). J. Supramol. Chem. 1, 189–191.  CrossRef CAS Google Scholar
First citationEl-Haty, M. T., Mohamed, A. E., Adam, F. A. & Gabr, A. A. (1990). Spectrochim. Acta Part A, 46, 1743–1749.  Google Scholar
First citationHigashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.  Google Scholar
First citationIssa, Y. M., El Ansary, A. L., Sherif, O. E. & Hassib, H. B. (2011). Spectrochim. Acta Part A, 79, 513–521.  CrossRef CAS Google Scholar
First citationRigaku (1998). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan.  Google Scholar
First citationRigaku/MSC (2002). CrystalClear. Rigaku/MSC Inc., The Woodlands, Texas, USA.  Google Scholar
First citationShalabi, A. S. & Abdel-Ghani, N. T. (1990). Egypt. J. Chem. 33, 345–357.  CAS Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationWestrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationXu, J., Gao, S. & Ng, S. W. (2011). Acta Cryst. E67, o3259.  Web of Science CSD CrossRef IUCr Journals Google Scholar

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ISSN: 2056-9890
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