organic compounds
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
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).
Experimental
Crystal data
|
Refinement
|
Data collection: RAPID-AUTO (Rigaku, 1998); cell 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).
Supporting information
https://doi.org/10.1107/S1600536811046848/xu5383sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536811046848/xu5383Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S1600536811046848/xu5383Isup3.cml
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%.
Carbon-bound H-atoms were placed in calculated positions (C–H 0.93–0.97 Å) and were included in the
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.There are numerous studies on the
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).
Data collection: RAPID-AUTO (Rigaku, 1998); cell
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).Fig. 1. Thermal ellipsoid plot (Barbour, 2001) of C11H11N3O at the 50% probability level; hydrogen atoms are drawn as spheres of arbitrary radius. |
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 |
Rigaku R-AXIS RAPID IP diffractometer | 2296 independent reflections |
Radiation source: fine-focus sealed tube | 1476 reflections with I > 2σ(I) |
Graphite monochromator | 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 |
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 |
C11H11N3O | V = 1005.92 (12) Å3 |
Mr = 201.23 | Z = 4 |
Monoclinic, P21/n | Mo Kα radiation |
a = 5.8625 (4) Å | µ = 0.09 mm−1 |
b = 9.3610 (7) Å | T = 293 K |
c = 18.4058 (13) Å | 0.22 × 0.17 × 0.15 mm |
β = 95.208 (2)° |
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 = 0.987 | Rint = 0.030 |
9626 measured reflections |
R[F2 > 2σ(F2)] = 0.040 | 2 restraints |
wR(F2) = 0.149 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.12 | Δρmax = 0.14 e Å−3 |
2296 reflections | Δρmin = −0.15 e Å−3 |
144 parameters |
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)* |
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) |
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) |
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) |
Symmetry code: (i) −x+1, −y+1, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C11H11N3O |
Mr | 201.23 |
Crystal system, space group | Monoclinic, P21/n |
Temperature (K) | 293 |
a, b, c (Å) | 5.8625 (4), 9.3610 (7), 18.4058 (13) |
β (°) | 95.208 (2) |
V (Å3) | 1005.92 (12) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.22 × 0.17 × 0.15 |
Data collection | |
Diffractometer | Rigaku R-AXIS RAPID IP |
Absorption correction | Multi-scan (ABSCOR; Higashi, 1995) |
Tmin, Tmax | 0.981, 0.987 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 9626, 2296, 1476 |
Rint | 0.030 |
(sin θ/λ)max (Å−1) | 0.648 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.040, 0.149, 1.12 |
No. of reflections | 2296 |
No. of parameters | 144 |
No. of restraints | 2 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 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).
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) |
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
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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).