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

Xu, J.; Gao, S.; Ng, S.W.

doi:10.1107/S1600536811046848

organic compounds

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Volume 67| Part 12| December 2011| Page o3258

https://doi.org/10.1107/S1600536811046848

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

Jing Xu,^a Shan Gao ^a and Seik Weng Ng ^b,^c ^*

^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 ); Issa et al. (2011 ); Shalabi & Abdel-Ghani (1990 ). For a related structure, see: Xu et al. (2011 ).

Experimental

Crystal data

C₁₁H₁₁N₃O
M_r = 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 ) 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[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
Δρ_max = 0.14 e Å⁻³
Δρ_min = −0.15 e Å⁻³

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)
Symmetry code: (i) -x+1, -y+1, -z+1.

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 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536811046848/xu5383sup1.cif

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

checkCIF report

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%.

Structure description 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).

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

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

C₁₁H₁₁N₃O	F(000) = 424
M_r = 201.23	D_x = 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

Data collection top

Rigaku R-AXIS RAPID IP diffractometer	2296 independent reflections
Radiation source: fine-focus sealed tube	1476 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.030
ω scan	θ_max = 27.4°, θ_min = 3.1°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −7→6
T_min = 0.981, T_max = 0.987	k = −12→12
9626 measured reflections	l = −23→23

Refinement top

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(F_o²) + (0.0796P)² + 0.034P] where P = (F_o² + 2F_c²)/3
2296 reflections	(Δ/σ)_max = 0.001
144 parameters	Δρ_max = 0.14 e Å⁻³
2 restraints	Δρ_min = −0.15 e Å⁻³

Crystal data top

C₁₁H₁₁N₃O	V = 1005.92 (12) Å³
M_r = 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)°

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)
T_min = 0.981, T_max = 0.987	R_int = 0.030
9626 measured reflections

Refinement top

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	Δρ_max = 0.14 e Å⁻³
2296 reflections	Δρ_min = −0.15 e Å⁻³
144 parameters

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

	x	y	z	U_iso*/U_eq
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)*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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
M_r	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)
T_min, T_max	0.981, 0.987
No. of measured, independent and observed [I > 2σ(I)] reflections	9626, 2296, 1476
R_int	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
Δρ_max, Δρ_min (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).

Hydrogen-bond geometry (Å, º) top

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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