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Acta Crystallogr Sect E Struct Rep Online. 2008 September 1; 64(Pt 9): o1846.
Published online 2008 August 30. doi:  10.1107/S160053680802730X
PMCID: PMC2960608

3-Benzyl­oxypyridin-2-amine

Abstract

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 R 2 2(8) ring motif. In addition, there is an intra­molecular N—H(...)O inter­action.

Related literature

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

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Object name is e-64-o1846-scheme1.jpg

Experimental

Crystal data

  • C12H12N2O
  • M r = 200.24
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1846-efi1.jpg
  • 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 [triangle]) 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[F 2 > 2σ(F 2)] = 0.067
  • wR(F 2) = 0.157
  • S = 1.07
  • 2458 reflections
  • 136 parameters
  • H-atom parameters constrained
  • Δρmax = 0.13 e Å−3
  • Δρmin = −0.15 e Å−3

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

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

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

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

supplementary crystallographic information

Comment

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).

Experimental

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.

Refinement

All H atoms attached to C and N atom were fixed geometrically and treated as riding with C—H = 0.93 Å (aromatic) or 0.97 Å (methylene) and N—H = 0.86 Å, and with Uiso(H) =1.2Ueq(C or N).

Figures

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.

Crystal data

C12H12N2OF000 = 848
Mr = 200.24Dx = 1.239 Mg m3
Orthorhombic, PbcaMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 21430 reflections
a = 12.852 (3) Åθ = 3.1–27.5º
b = 7.4068 (15) ŵ = 0.08 mm1
c = 22.561 (4) ÅT = 293 (2) K
V = 2147.6 (8) Å3Block, colourless
Z = 80.15 × 0.10 × 0.07 mm

Data collection

Bruker SMART 1K CCD area-detector diffractometer2458 independent reflections
Radiation source: fine-focus sealed tube1375 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.084
Detector resolution: 8.192 pixels mm-1θmax = 27.5º
T = 293(2) Kθmin = 3.2º
Thin–slice ω scansh = −16→16
Absorption correction: multi-scan(CrystalClear; Rigaku, 2005)k = −9→9
Tmin = 0.982, Tmax = 0.991l = −29→29
19827 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.067H-atom parameters constrained
wR(F2) = 0.157  w = 1/[σ2(Fo2) + (0.0492P)2 + 0.5758P] where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max < 0.001
2458 reflectionsΔρmax = 0.13 e Å3
136 parametersΔρmin = −0.15 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

Special details

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)

xyzUiso*/Ueq
C10.66421 (18)0.4734 (3)−0.00746 (11)0.0624 (7)
H1A0.69250.36090.00120.075*
C20.65962 (19)0.5359 (4)−0.06581 (11)0.0689 (7)
H2A0.68600.4667−0.09670.083*
C30.61591 (19)0.6997 (4)−0.07666 (11)0.0648 (7)
H3A0.61240.7391−0.11570.078*
C40.58293 (17)0.7505 (3)0.02173 (10)0.0501 (6)
C50.62616 (17)0.5814 (3)0.03648 (10)0.0502 (6)
C60.65634 (19)0.3704 (3)0.11541 (11)0.0630 (7)
H6A0.72830.34880.10460.076*
H6B0.61350.27850.09690.076*
C70.64405 (17)0.3635 (3)0.18162 (11)0.0546 (6)
C80.5582 (2)0.4375 (3)0.20964 (11)0.0659 (7)
H8A0.50560.48990.18710.079*
C90.5499 (2)0.4343 (4)0.27071 (12)0.0763 (8)
H9A0.49220.48550.28910.092*
C100.6265 (3)0.3558 (4)0.30437 (13)0.0833 (9)
H10A0.62130.35400.34550.100*
C110.7103 (3)0.2807 (4)0.27693 (13)0.0899 (9)
H11A0.76170.22560.29960.108*
C120.7201 (2)0.2850 (3)0.21579 (12)0.0726 (8)
H12A0.77840.23460.19780.087*
N10.54785 (16)0.8603 (3)0.06572 (8)0.0714 (7)
H1B0.52270.96480.05720.086*
H1C0.55080.82530.10200.086*
N20.57740 (15)0.8083 (3)−0.03408 (8)0.0577 (5)
O10.62485 (13)0.5449 (2)0.09615 (7)0.0628 (5)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0613 (16)0.0619 (15)0.0641 (17)0.0114 (13)−0.0064 (12)−0.0070 (13)
C20.0723 (17)0.0770 (18)0.0575 (17)0.0122 (14)0.0023 (13)−0.0152 (14)
C30.0654 (16)0.0796 (18)0.0494 (14)0.0048 (14)0.0042 (12)−0.0011 (13)
C40.0492 (13)0.0506 (13)0.0506 (13)0.0023 (11)0.0016 (10)0.0002 (11)
C50.0462 (13)0.0560 (14)0.0484 (13)0.0015 (10)−0.0037 (10)−0.0016 (11)
C60.0676 (17)0.0540 (15)0.0673 (17)0.0115 (12)−0.0057 (13)0.0004 (12)
C70.0581 (15)0.0411 (12)0.0645 (15)0.0025 (11)−0.0048 (12)0.0068 (11)
C80.0588 (15)0.0680 (16)0.0709 (17)0.0074 (13)−0.0004 (13)0.0095 (13)
C90.0757 (19)0.0759 (19)0.077 (2)0.0016 (15)0.0155 (15)0.0037 (15)
C100.105 (2)0.079 (2)0.0653 (18)0.0010 (18)0.0042 (17)0.0146 (16)
C110.105 (3)0.091 (2)0.074 (2)0.0223 (19)−0.0172 (18)0.0197 (17)
C120.0774 (19)0.0659 (17)0.0747 (18)0.0221 (14)−0.0066 (14)0.0062 (14)
N10.1049 (18)0.0599 (12)0.0493 (11)0.0246 (12)0.0085 (11)0.0024 (10)
N20.0612 (13)0.0633 (12)0.0486 (11)0.0010 (10)0.0049 (9)0.0027 (10)
O10.0838 (12)0.0531 (10)0.0517 (10)0.0124 (8)−0.0015 (8)0.0041 (8)

Geometric parameters (Å, °)

C1—C51.365 (3)C6—H6B0.9700
C1—C21.397 (3)C7—C121.374 (3)
C1—H1A0.9300C7—C81.384 (3)
C2—C31.359 (3)C8—C91.382 (3)
C2—H2A0.9300C8—H8A0.9300
C3—N21.347 (3)C9—C101.373 (4)
C3—H3A0.9300C9—H9A0.9300
C4—N21.332 (3)C10—C111.361 (4)
C4—N11.360 (3)C10—H10A0.9300
C4—C51.410 (3)C11—C121.386 (4)
C5—O11.373 (3)C11—H11A0.9300
C6—O11.422 (3)C12—H12A0.9300
C6—C71.503 (3)N1—H1B0.8600
C6—H6A0.9700N1—H1C0.8600
C5—C1—C2118.4 (2)C12—C7—C6119.8 (2)
C5—C1—H1A120.8C8—C7—C6121.6 (2)
C2—C1—H1A120.8C9—C8—C7120.7 (2)
C3—C2—C1118.9 (2)C9—C8—H8A119.7
C3—C2—H2A120.5C7—C8—H8A119.7
C1—C2—H2A120.5C10—C9—C8120.2 (3)
N2—C3—C2123.8 (2)C10—C9—H9A119.9
N2—C3—H3A118.1C8—C9—H9A119.9
C2—C3—H3A118.1C11—C10—C9119.3 (3)
N2—C4—N1118.7 (2)C11—C10—H10A120.4
N2—C4—C5122.0 (2)C9—C10—H10A120.4
N1—C4—C5119.3 (2)C10—C11—C12121.1 (3)
C1—C5—O1127.0 (2)C10—C11—H11A119.5
C1—C5—C4119.4 (2)C12—C11—H11A119.5
O1—C5—C4113.67 (19)C7—C12—C11120.2 (3)
O1—C6—C7107.75 (18)C7—C12—H12A119.9
O1—C6—H6A110.2C11—C12—H12A119.9
C7—C6—H6A110.2C4—N1—H1B120.0
O1—C6—H6B110.2C4—N1—H1C120.0
C7—C6—H6B110.2H1B—N1—H1C120.0
H6A—C6—H6B108.5C4—N2—C3117.5 (2)
C12—C7—C8118.6 (2)C5—O1—C6118.36 (18)
C5—C1—C2—C3−1.2 (4)C7—C8—C9—C10−0.6 (4)
C1—C2—C3—N20.9 (4)C8—C9—C10—C11−0.3 (4)
C2—C1—C5—O1−179.2 (2)C9—C10—C11—C121.1 (5)
C2—C1—C5—C40.6 (3)C8—C7—C12—C110.0 (4)
N2—C4—C5—C10.4 (3)C6—C7—C12—C11178.9 (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—C3177.8 (2)
N1—C4—C5—O11.7 (3)C5—C4—N2—C3−0.7 (3)
O1—C6—C7—C12−137.2 (2)C2—C3—N2—C40.0 (4)
O1—C6—C7—C841.6 (3)C1—C5—O1—C6−6.8 (3)
C12—C7—C8—C90.7 (4)C4—C5—O1—C6173.45 (19)
C6—C7—C8—C9−178.1 (2)C7—C6—O1—C5−177.93 (18)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1B···N2i0.862.183.021 (3)166
N1—H1C···O10.862.292.628 (3)104

Symmetry codes: (i) −x+1, −y+2, −z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: AT2616).

References

  • Evans, D. A., Rajapakse, H. A. & Stenkamp, D. (2002). Angew. Chem. Int. Ed.114, 4751–4755.
  • Rigaku (2005). CrystalClear Rigaku Corporation, Tokyo, Japan.
  • Sharma, G. V. M., Prasad, T. R. & Sharma, R. B. S. (2004). Synth. Commun.34, 941–950.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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