3-Benzyl­oxypyridin-2-amine

Lin, D.-J.; Sun, Y.; Li, Z.-S.; Sun, B.-W.

doi:10.1107/S160053680802730X

organic compounds

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Volume 64| Part 9| September 2008| Page o1846

doi:10.1107/S160053680802730X

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3-Benzyloxypyridin-2-amine

De-Jun Lin,^a Yu Sun,^a ^* Zhong-Shu Li ^a and Bai-Wang Sun ^a

^aOrdered Matter Science Research Center, College of Chemistry and Chemical, Engineering, Southeast University, Nanjing 210096, People's Republic of China
^*Correspondence e-mail: chmsunbw@seu.edu.cn

(Received 15 August 2008; accepted 25 August 2008; online 30 August 2008)

In the title compound, C₁₂H₁₂N₂O, the dihedral angle between the planes of the pyridine and phenyl rings plane is 35.94 (12)°. In the crystal structure, centrosymmetrically related molecules are linked by a pair of N—H⋯N hydrogen bonds, forming a dimer with an R₂²(8) ring motif. In addition, there is an intramolecular N—H⋯O interaction.

Related literature

For background, see: Sharma et al. (2004 ); Evans et al. (2002 ).

Experimental

Crystal data

C₁₂H₁₂N₂O
M_r = 200.24
Orthorhombic, P b c a
a = 12.852 (3) Å
b = 7.4068 (15) Å
c = 22.561 (4) Å
V = 2147.6 (8) Å³
Z = 8
Mo Kα radiation
μ = 0.08 mm⁻¹
T = 293 (2) K
0.15 × 0.10 × 0.07 mm

Data collection

Bruker SMART 1K CCD area-detector diffractometer
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005 ) T_min = 0.982, T_max = 0.991
19827 measured reflections
2458 independent reflections
1375 reflections with I > 2σ(I)
R_int = 0.084

Refinement

R[F² > 2σ(F²)] = 0.067
wR(F²) = 0.157
S = 1.07
2458 reflections
136 parameters
H-atom parameters constrained
Δρ_max = 0.13 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
N1—H1B⋯N2ⁱ	0.86	2.18	3.021 (3)	166
N1—H1C⋯O1	0.86	2.29	2.628 (3)	104
Symmetry code: (i) -x+1, -y+2, -z.

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053680802730X/at2616sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S160053680802730X/at2616Isup2.hkl

checkCIF report

Comment top

Benzyl ethers and their derivatives are used as protecting group (Sharma et al., 2004) for alcohols and phenols in the synthesis of natural products (Evans et al., 2002). Here we report the synthesis and structure of the title compound, namely 3-(benzyloxy)pyridin-2-amine (I).

In the title compound (I) (Fig.1), the dihedral angle between the pyridine ring plane and benzene ring plane is 35.94 (12)°. In the crystal structure, centrosymmetrically related molecules are linked by a pair of N—H···N hydrogen bonds to form a dimer with an R₂²(8) ring motif (Fig. 2). In addition, there is an intramolecular N—H···O interaction (Table 1).

Related literature top

For background, see: Sharma et al. (2004); Evans et al. (2002).

Experimental top

3-(Benzyloxy)pyridin-2-amine (0.020 g, 0.1 mmol) was added to a solution containing ethanol (8 ml) and ether (4 ml). The mixture was stirred at room temperature for 10 min and then filtered off. After a few days, colourless single crystals were obtained.

Computing details top

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The molecular structure of the title molecule, with the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level. The intramolecular N—H···O contact is shown as a dashed line.
	Fig. 2. View of the packing and hydrogen bonding of the compound (I), down along the b axis. Hydrogen bonds are shown as dashed lines. H atoms not involved in hydrogen bonding have been omitted for clarity.

3-Benzyloxypyridin-2-amine top

Crystal data top

C₁₂H₁₂N₂O	F(000) = 848
M_r = 200.24	D_x = 1.239 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 21430 reflections
a = 12.852 (3) Å	θ = 3.1–27.5°
b = 7.4068 (15) Å	µ = 0.08 mm⁻¹
c = 22.561 (4) Å	T = 293 K
V = 2147.6 (8) Å³	Block, colourless
Z = 8	0.15 × 0.10 × 0.07 mm

Data collection top

Bruker SMART 1K CCD area-detector diffractometer	2458 independent reflections
Radiation source: fine-focus sealed tube	1375 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.084
Detector resolution: 8.192 pixels mm^-1	θ_max = 27.5°, θ_min = 3.2°
Thin–slice ω scans	h = −16→16
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	k = −9→9
T_min = 0.982, T_max = 0.991	l = −29→29
19827 measured reflections

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)] = 0.067	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.157	H-atom parameters constrained
S = 1.07	w = 1/[σ²(F_o²) + (0.0492P)² + 0.5758P] where P = (F_o² + 2F_c²)/3
2458 reflections	(Δ/σ)_max < 0.001
136 parameters	Δρ_max = 0.13 e Å⁻³
0 restraints	Δρ_min = −0.15 e Å⁻³

Crystal data top

C₁₂H₁₂N₂O	V = 2147.6 (8) Å³
M_r = 200.24	Z = 8
Orthorhombic, Pbca	Mo Kα radiation
a = 12.852 (3) Å	µ = 0.08 mm⁻¹
b = 7.4068 (15) Å	T = 293 K
c = 22.561 (4) Å	0.15 × 0.10 × 0.07 mm

Data collection top

Bruker SMART 1K CCD area-detector diffractometer	2458 independent reflections
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005)	1375 reflections with I > 2σ(I)
T_min = 0.982, T_max = 0.991	R_int = 0.084
19827 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.067	0 restraints
wR(F²) = 0.157	H-atom parameters constrained
S = 1.07	Δρ_max = 0.13 e Å⁻³
2458 reflections	Δρ_min = −0.15 e Å⁻³
136 parameters

Special details top

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) top

	x	y	z	U_iso*/U_eq
C1	0.66421 (18)	0.4734 (3)	−0.00746 (11)	0.0624 (7)
H1A	0.6925	0.3609	0.0012	0.075*
C2	0.65962 (19)	0.5359 (4)	−0.06581 (11)	0.0689 (7)
H2A	0.6860	0.4667	−0.0967	0.083*
C3	0.61591 (19)	0.6997 (4)	−0.07666 (11)	0.0648 (7)
H3A	0.6124	0.7391	−0.1157	0.078*
C4	0.58293 (17)	0.7505 (3)	0.02173 (10)	0.0501 (6)
C5	0.62616 (17)	0.5814 (3)	0.03648 (10)	0.0502 (6)
C6	0.65634 (19)	0.3704 (3)	0.11541 (11)	0.0630 (7)
H6A	0.7283	0.3488	0.1046	0.076*
H6B	0.6135	0.2785	0.0969	0.076*
C7	0.64405 (17)	0.3635 (3)	0.18162 (11)	0.0546 (6)
C8	0.5582 (2)	0.4375 (3)	0.20964 (11)	0.0659 (7)
H8A	0.5056	0.4899	0.1871	0.079*
C9	0.5499 (2)	0.4343 (4)	0.27071 (12)	0.0763 (8)
H9A	0.4922	0.4855	0.2891	0.092*
C10	0.6265 (3)	0.3558 (4)	0.30437 (13)	0.0833 (9)
H10A	0.6213	0.3540	0.3455	0.100*
C11	0.7103 (3)	0.2807 (4)	0.27693 (13)	0.0899 (9)
H11A	0.7617	0.2256	0.2996	0.108*
C12	0.7201 (2)	0.2850 (3)	0.21579 (12)	0.0726 (8)
H12A	0.7784	0.2346	0.1978	0.087*
N1	0.54785 (16)	0.8603 (3)	0.06572 (8)	0.0714 (7)
H1B	0.5227	0.9648	0.0572	0.086*
H1C	0.5508	0.8253	0.1020	0.086*
N2	0.57740 (15)	0.8083 (3)	−0.03408 (8)	0.0577 (5)
O1	0.62485 (13)	0.5449 (2)	0.09615 (7)	0.0628 (5)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0613 (16)	0.0619 (15)	0.0641 (17)	0.0114 (13)	−0.0064 (12)	−0.0070 (13)
C2	0.0723 (17)	0.0770 (18)	0.0575 (17)	0.0122 (14)	0.0023 (13)	−0.0152 (14)
C3	0.0654 (16)	0.0796 (18)	0.0494 (14)	0.0048 (14)	0.0042 (12)	−0.0011 (13)
C4	0.0492 (13)	0.0506 (13)	0.0506 (13)	0.0023 (11)	0.0016 (10)	0.0002 (11)
C5	0.0462 (13)	0.0560 (14)	0.0484 (13)	0.0015 (10)	−0.0037 (10)	−0.0016 (11)
C6	0.0676 (17)	0.0540 (15)	0.0673 (17)	0.0115 (12)	−0.0057 (13)	0.0004 (12)
C7	0.0581 (15)	0.0411 (12)	0.0645 (15)	0.0025 (11)	−0.0048 (12)	0.0068 (11)
C8	0.0588 (15)	0.0680 (16)	0.0709 (17)	0.0074 (13)	−0.0004 (13)	0.0095 (13)
C9	0.0757 (19)	0.0759 (19)	0.077 (2)	0.0016 (15)	0.0155 (15)	0.0037 (15)
C10	0.105 (2)	0.079 (2)	0.0653 (18)	0.0010 (18)	0.0042 (17)	0.0146 (16)
C11	0.105 (3)	0.091 (2)	0.074 (2)	0.0223 (19)	−0.0172 (18)	0.0197 (17)
C12	0.0774 (19)	0.0659 (17)	0.0747 (18)	0.0221 (14)	−0.0066 (14)	0.0062 (14)
N1	0.1049 (18)	0.0599 (12)	0.0493 (11)	0.0246 (12)	0.0085 (11)	0.0024 (10)
N2	0.0612 (13)	0.0633 (12)	0.0486 (11)	0.0010 (10)	0.0049 (9)	0.0027 (10)
O1	0.0838 (12)	0.0531 (10)	0.0517 (10)	0.0124 (8)	−0.0015 (8)	0.0041 (8)

Geometric parameters (Å, º) top

C1—C5	1.365 (3)	C6—H6B	0.9700
C1—C2	1.397 (3)	C7—C12	1.374 (3)
C1—H1A	0.9300	C7—C8	1.384 (3)
C2—C3	1.359 (3)	C8—C9	1.382 (3)
C2—H2A	0.9300	C8—H8A	0.9300
C3—N2	1.347 (3)	C9—C10	1.373 (4)
C3—H3A	0.9300	C9—H9A	0.9300
C4—N2	1.332 (3)	C10—C11	1.361 (4)
C4—N1	1.360 (3)	C10—H10A	0.9300
C4—C5	1.410 (3)	C11—C12	1.386 (4)
C5—O1	1.373 (3)	C11—H11A	0.9300
C6—O1	1.422 (3)	C12—H12A	0.9300
C6—C7	1.503 (3)	N1—H1B	0.8600
C6—H6A	0.9700	N1—H1C	0.8600

C5—C1—C2	118.4 (2)	C12—C7—C6	119.8 (2)
C5—C1—H1A	120.8	C8—C7—C6	121.6 (2)
C2—C1—H1A	120.8	C9—C8—C7	120.7 (2)
C3—C2—C1	118.9 (2)	C9—C8—H8A	119.7
C3—C2—H2A	120.5	C7—C8—H8A	119.7
C1—C2—H2A	120.5	C10—C9—C8	120.2 (3)
N2—C3—C2	123.8 (2)	C10—C9—H9A	119.9
N2—C3—H3A	118.1	C8—C9—H9A	119.9
C2—C3—H3A	118.1	C11—C10—C9	119.3 (3)
N2—C4—N1	118.7 (2)	C11—C10—H10A	120.4
N2—C4—C5	122.0 (2)	C9—C10—H10A	120.4
N1—C4—C5	119.3 (2)	C10—C11—C12	121.1 (3)
C1—C5—O1	127.0 (2)	C10—C11—H11A	119.5
C1—C5—C4	119.4 (2)	C12—C11—H11A	119.5
O1—C5—C4	113.67 (19)	C7—C12—C11	120.2 (3)
O1—C6—C7	107.75 (18)	C7—C12—H12A	119.9
O1—C6—H6A	110.2	C11—C12—H12A	119.9
C7—C6—H6A	110.2	C4—N1—H1B	120.0
O1—C6—H6B	110.2	C4—N1—H1C	120.0
C7—C6—H6B	110.2	H1B—N1—H1C	120.0
H6A—C6—H6B	108.5	C4—N2—C3	117.5 (2)
C12—C7—C8	118.6 (2)	C5—O1—C6	118.36 (18)

C5—C1—C2—C3	−1.2 (4)	C7—C8—C9—C10	−0.6 (4)
C1—C2—C3—N2	0.9 (4)	C8—C9—C10—C11	−0.3 (4)
C2—C1—C5—O1	−179.2 (2)	C9—C10—C11—C12	1.1 (5)
C2—C1—C5—C4	0.6 (3)	C8—C7—C12—C11	0.0 (4)
N2—C4—C5—C1	0.4 (3)	C6—C7—C12—C11	178.9 (2)
N1—C4—C5—C1	−178.1 (2)	C10—C11—C12—C7	−1.0 (5)
N2—C4—C5—O1	−179.8 (2)	N1—C4—N2—C3	177.8 (2)
N1—C4—C5—O1	1.7 (3)	C5—C4—N2—C3	−0.7 (3)
O1—C6—C7—C12	−137.2 (2)	C2—C3—N2—C4	0.0 (4)
O1—C6—C7—C8	41.6 (3)	C1—C5—O1—C6	−6.8 (3)
C12—C7—C8—C9	0.7 (4)	C4—C5—O1—C6	173.45 (19)
C6—C7—C8—C9	−178.1 (2)	C7—C6—O1—C5	−177.93 (18)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1B···N2ⁱ	0.86	2.18	3.021 (3)	166
N1—H1C···O1	0.86	2.29	2.628 (3)	104

Symmetry code: (i) −x+1, −y+2, −z.

Experimental details

Crystal data
Chemical formula	C₁₂H₁₂N₂O
M_r	200.24
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	293
a, b, c (Å)	12.852 (3), 7.4068 (15), 22.561 (4)
V (Å³)	2147.6 (8)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.08
Crystal size (mm)	0.15 × 0.10 × 0.07

Data collection
Diffractometer	Bruker SMART 1K CCD area-detector diffractometer
Absorption correction	Multi-scan (CrystalClear; Rigaku, 2005)
T_min, T_max	0.982, 0.991
No. of measured, independent and observed [I > 2σ(I)] reflections	19827, 2458, 1375
R_int	0.084
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.067, 0.157, 1.07
No. of reflections	2458
No. of parameters	136
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.13, −0.15

Computer programs: CrystalClear (Rigaku, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1B···N2ⁱ	0.86	2.18	3.021 (3)	166
N1—H1C···O1	0.86	2.29	2.628 (3)	104

Symmetry code: (i) −x+1, −y+2, −z.

References

Evans, D. A., Rajapakse, H. A. & Stenkamp, D. (2002). Angew. Chem. Int. Ed. 114, 4751–4755. CrossRef Google Scholar
Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan. Google Scholar
Sharma, G. V. M., Prasad, T. R. & Sharma, R. B. S. (2004). Synth. Commun. 34, 941–950. Web of Science CrossRef CAS Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar

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CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 64| Part 9| September 2008| Page o1846

doi:10.1107/S160053680802730X

Open

access