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Acta Crystallogr Sect E Struct Rep Online. 2010 February 1; 66(Pt 2): o401.
Published online 2010 January 20. doi:  10.1107/S160053681000098X
PMCID: PMC2979870

Benzyl N-(4-pyrid­yl)carbamate

Abstract

The title compound, C13H12N2O2, was obtained by the reaction of 4-amino­pyridine and benzyl chloro­formate in tetra­hydro­furan. The crystal structure contains N—H(...)N hydrogen bonds between two unique mol­ecules within layers and anti­parallel C—O(...)O—C inter­actions [O(...)O = 3.06 (3) Å] between the two mol­ecules of the asymmetric unit.

Related literature

The title compound was synthesized in order to investigate the nature of its reversion tetrodotoxin-induced cardiorespiratory depression, see: Chang et al. (1997 [triangle]). For a related structure, see: Zheng et al. (2005 [triangle]).

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Object name is e-66-0o401-scheme1.jpg

Experimental

Crystal data

  • C13H12N2O2
  • M r = 228.25
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o401-efi1.jpg
  • a = 11.9439 (5) Å
  • b = 13.2120 (6) Å
  • c = 14.6574 (7) Å
  • β = 98.418 (4)°
  • V = 2288.06 (18) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.09 mm−1
  • T = 293 K
  • 0.30 × 0.22 × 0.18 mm

Data collection

  • Bruker SMART APEX area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2001 [triangle]) T min = 0.973, T max = 0.984
  • 11332 measured reflections
  • 4028 independent reflections
  • 2831 reflections with I > 2σ(I)
  • R int = 0.039

Refinement

  • R[F 2 > 2σ(F 2)] = 0.036
  • wR(F 2) = 0.070
  • S = 1.05
  • 4028 reflections
  • 307 parameters
  • H-atom parameters constrained
  • Δρmax = 0.17 e Å−3
  • Δρmin = −0.17 e Å−3

Data collection: SMART (Bruker, 2001 [triangle]); cell refinement: SAINT (Bruker, 2001 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]) and PLATON (Spek, 2009 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053681000098X/jh2125sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053681000098X/jh2125Isup2.hkl

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

Acknowledgments

This work was supported by the Science and Technology Program of the Oceans and Fisheries Bureau of Xiamen (grant No. 200911) and the Natural Science Foundation of Fujian Province of China (grant No. 2009 J05099).

supplementary crystallographic information

Comment

The title compound, (I), a 4-aminopyridine analog, was synthesized for investigation of the nature of its reversion tetrodotoxin-induced cardiorespiratorydepression (Chang et al., 1997). The crystal packing is stabilized by stronger N-H···N hydrogen bonds between molecules within layers and antiparallel C-O ··· O-C interactions between the two molecules of the asymmetric unit, and bond lengths and angles are in agreement with values reported for a similar compound (Zheng et al., 2005). The dihedral angle between the planes of the phenzene ring and pyridine ring systems is 66.2 (3) °.

Experimental

A solution of dry tetrahydrofuran (15 ml) containing 4-aminopyridine (5 mmol, 0.47 g) and triethylamine (0.70 ml) was added dropwise to the solution of tetrahydrofuran (15 ml) containing the benzyl chloroformate (5 mmol, 0.85 g). The reaction mixture was stirred for 6 h in ice bath and the solvent was then removed under reduced pressure to give a residue, which was extracted with ethyl acetate (3 × 15 ml). The solution was dried over anhydrous MgSO4 and concentrated under vacuum to obtain a slurry residue, which was purified by silica gel column chromatography (petroleum ether/ethyl acetate = 2:1) to give products I as colorless amorphous solids. Single crystals of (I) suitable for X-ray analysis were obtained by slow evaporation of a petroleum ether /dichloromethane solution (1:1 v/v).

Refinement

All H atoms were placed in geometrically idealized positions and treated as riding on their parent atoms, with C—H = 0.93 (aromatic), 0.97 (CH2), N—H = 0.86 Å and Uiso(H) = 1.2Ueq (aromatic C, CH2 and N).

Figures

Fig. 1.
ORTEPII (Farrugia, 1997) plot of the title molecule with displacement ellipsoids srawn at the 30% probability level. H atoms are drawn as spheres of arbitrary radii.
Fig. 2.
The formation of the title compound.

Crystal data

C13H12N2O2F(000) = 960
Mr = 228.25Dx = 1.325 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2895 reflections
a = 11.9439 (5) Åθ = 2.1–26.4°
b = 13.2120 (6) ŵ = 0.09 mm1
c = 14.6574 (7) ÅT = 293 K
β = 98.418 (4)°Chunk, colorless
V = 2288.06 (18) Å30.30 × 0.22 × 0.18 mm
Z = 8

Data collection

Bruker APEX area-detector diffractometer4028 independent reflections
Radiation source: fine-focus sealed tube2831 reflections with I > 2σ(I)
graphiteRint = 0.039
[var phi] and ω scanθmax = 25.0°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2001)h = −14→12
Tmin = 0.973, Tmax = 0.984k = −15→15
11332 measured reflectionsl = −17→17

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.036Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.070H-atom parameters constrained
S = 1.05w = 1/[σ2(Fo2) + (0.0229P)2 + 0.110P] where P = (Fo2 + 2Fc2)/3
4028 reflections(Δ/σ)max < 0.001
307 parametersΔρmax = 0.17 e Å3
0 restraintsΔρmin = −0.17 e Å3

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
N2'0.16150 (9)0.18181 (9)−0.00328 (9)0.0227 (3)
H2'C0.21400.1458−0.02160.027*
O10.42587 (8)0.17805 (9)0.26686 (8)0.0335 (3)
O20.24197 (8)0.13329 (8)0.22775 (8)0.0330 (3)
O1'0.13791 (8)0.32072 (8)0.08678 (8)0.0301 (3)
O2'0.30953 (8)0.27290 (8)0.05366 (8)0.0288 (3)
N20.36888 (9)0.04846 (9)0.16579 (9)0.0240 (3)
H2C0.30880.01790.14030.029*
C10.35408 (12)0.12531 (12)0.22453 (11)0.0241 (4)
N1'−0.16725 (10)0.07480 (10)−0.09588 (10)0.0297 (3)
C90.47128 (11)0.01402 (12)0.14254 (10)0.0217 (4)
C3'0.48132 (13)0.36576 (11)0.08454 (12)0.0269 (4)
C130.57368 (12)0.06602 (13)0.16021 (12)0.0292 (4)
H13A0.57890.12780.19090.035*
C100.47072 (12)−0.07770 (12)0.09719 (11)0.0254 (4)
H10A0.4040−0.11470.08440.031*
C1'0.19585 (12)0.26347 (12)0.04966 (11)0.0229 (4)
C9'0.05051 (12)0.14969 (11)−0.03138 (11)0.0200 (4)
C10'0.03345 (12)0.07278 (12)−0.09590 (11)0.0244 (4)
H10B0.09480.0447−0.11930.029*
C13'−0.04470 (12)0.18983 (12)0.00023 (11)0.0257 (4)
H13B−0.03820.24210.04320.031*
N10.66870 (10)−0.06576 (10)0.08657 (9)0.0290 (3)
C11'−0.07391 (12)0.03782 (12)−0.12545 (12)0.0281 (4)
H11A−0.0827−0.0144−0.16840.034*
C30.09174 (12)0.16792 (12)0.31022 (11)0.0243 (4)
C110.56904 (12)−0.11411 (12)0.07098 (12)0.0283 (4)
H11B0.5662−0.17600.04060.034*
C2'0.36095 (12)0.36077 (12)0.10249 (12)0.0333 (4)
H2'A0.35850.35430.16810.040*
H2'B0.32060.42180.08040.040*
C120.66733 (12)0.02252 (13)0.13053 (12)0.0328 (4)
H12A0.73520.05790.14220.039*
C8−0.00463 (13)0.21433 (13)0.26577 (12)0.0320 (4)
H8A0.00150.27120.22940.038*
C40.08082 (15)0.08481 (13)0.36471 (12)0.0367 (4)
H4A0.14540.05420.39610.044*
C20.20694 (13)0.20348 (13)0.29487 (12)0.0348 (5)
H2A0.20340.27210.27110.042*
H2B0.25940.20170.35200.042*
C4'0.50592 (14)0.36917 (12)−0.00500 (13)0.0351 (4)
H4'A0.44720.3691−0.05430.042*
C8'0.56941 (14)0.36833 (13)0.15684 (13)0.0388 (5)
H8'A0.55450.36530.21730.047*
C12'−0.14897 (12)0.14942 (12)−0.03432 (12)0.0309 (4)
H12B−0.21190.1767−0.01270.037*
C5'0.61669 (16)0.37268 (13)−0.02173 (15)0.0465 (5)
H5'A0.63220.3726−0.08210.056*
C6−0.12000 (16)0.09262 (18)0.32858 (15)0.0521 (6)
H6A−0.19110.06710.33450.063*
C7−0.11059 (14)0.17636 (16)0.27524 (14)0.0453 (5)
H7A−0.17540.20790.24530.054*
C7'0.68094 (15)0.37554 (14)0.13934 (17)0.0522 (6)
H7'A0.74000.37990.18820.063*
C6'0.70368 (16)0.37628 (14)0.05031 (18)0.0524 (6)
H6'A0.77820.37920.03880.063*
C5−0.02418 (18)0.04609 (15)0.37357 (14)0.0495 (6)
H5A−0.0304−0.01100.40960.059*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N2'0.0176 (7)0.0229 (7)0.0278 (8)0.0018 (5)0.0046 (6)−0.0046 (7)
O10.0266 (6)0.0403 (7)0.0339 (7)−0.0061 (5)0.0051 (6)−0.0154 (6)
O20.0215 (6)0.0421 (7)0.0365 (7)0.0007 (5)0.0081 (5)−0.0205 (6)
O1'0.0277 (6)0.0280 (7)0.0356 (7)0.0020 (5)0.0078 (5)−0.0092 (6)
O2'0.0214 (6)0.0273 (7)0.0383 (7)−0.0062 (4)0.0065 (5)−0.0115 (6)
N20.0162 (7)0.0282 (8)0.0276 (8)−0.0019 (5)0.0028 (6)−0.0090 (7)
C10.0233 (9)0.0283 (10)0.0212 (9)0.0012 (7)0.0051 (7)−0.0013 (8)
N1'0.0224 (7)0.0310 (9)0.0357 (9)−0.0012 (6)0.0043 (6)−0.0044 (7)
C90.0185 (8)0.0276 (10)0.0191 (9)0.0019 (6)0.0030 (7)0.0019 (8)
C3'0.0293 (9)0.0198 (9)0.0318 (11)−0.0058 (7)0.0054 (8)−0.0060 (8)
C130.0241 (9)0.0307 (10)0.0330 (11)−0.0027 (7)0.0048 (8)−0.0103 (9)
C100.0205 (8)0.0269 (10)0.0295 (10)−0.0034 (7)0.0055 (7)−0.0029 (8)
C1'0.0242 (9)0.0223 (9)0.0221 (9)−0.0004 (7)0.0033 (7)0.0016 (8)
C9'0.0192 (8)0.0202 (9)0.0206 (9)−0.0012 (6)0.0028 (7)0.0039 (7)
C10'0.0203 (8)0.0265 (9)0.0271 (10)0.0009 (7)0.0061 (7)−0.0019 (8)
C13'0.0239 (9)0.0262 (10)0.0271 (10)0.0012 (7)0.0044 (7)−0.0036 (8)
N10.0222 (7)0.0331 (9)0.0317 (9)0.0007 (6)0.0047 (6)−0.0040 (7)
C11'0.0271 (9)0.0271 (10)0.0305 (10)−0.0019 (7)0.0055 (8)−0.0047 (8)
C30.0266 (9)0.0256 (9)0.0213 (10)0.0015 (7)0.0056 (7)−0.0087 (8)
C110.0258 (9)0.0263 (10)0.0331 (11)0.0001 (7)0.0055 (8)−0.0047 (8)
C2'0.0333 (10)0.0257 (10)0.0416 (12)−0.0096 (7)0.0083 (9)−0.0127 (9)
C120.0205 (9)0.0409 (12)0.0370 (11)−0.0067 (7)0.0044 (8)−0.0096 (9)
C80.0373 (10)0.0330 (11)0.0258 (10)0.0034 (8)0.0051 (8)−0.0031 (8)
C40.0448 (11)0.0343 (11)0.0298 (11)0.0040 (8)0.0019 (9)−0.0028 (9)
C20.0327 (10)0.0393 (11)0.0347 (11)−0.0014 (8)0.0120 (8)−0.0194 (9)
C4'0.0386 (10)0.0310 (10)0.0357 (11)−0.0110 (8)0.0058 (9)−0.0024 (9)
C8'0.0431 (11)0.0353 (11)0.0357 (12)−0.0068 (8)−0.0021 (9)−0.0078 (9)
C12'0.0213 (9)0.0340 (11)0.0387 (11)0.0033 (7)0.0088 (8)−0.0030 (9)
C5'0.0514 (13)0.0368 (12)0.0574 (14)−0.0174 (9)0.0287 (11)−0.0123 (10)
C60.0404 (12)0.0747 (16)0.0449 (14)−0.0236 (11)0.0189 (11)−0.0234 (12)
C70.0291 (10)0.0607 (14)0.0442 (13)0.0035 (9)−0.0009 (9)−0.0149 (12)
C7'0.0303 (11)0.0444 (13)0.0755 (17)−0.0052 (8)−0.0141 (11)−0.0119 (12)
C6'0.0327 (11)0.0376 (12)0.090 (2)−0.0091 (9)0.0212 (13)−0.0203 (12)
C50.0732 (15)0.0442 (13)0.0340 (12)−0.0213 (11)0.0174 (11)−0.0027 (10)

Geometric parameters (Å, °)

N2'—C1'1.3569 (19)N1—C111.3407 (19)
N2'—C9'1.3954 (17)C11'—H11A0.9300
N2'—H2'C0.8600C3—C41.375 (2)
O1—C11.2042 (18)C3—C81.380 (2)
O2—C11.3509 (16)C3—C21.502 (2)
O2—C21.4572 (17)C11—H11B0.9300
O1'—C1'1.2072 (17)C2'—H2'A0.9700
O2'—C1'1.3561 (16)C2'—H2'B0.9700
O2'—C2'1.4520 (17)C12—H12A0.9300
N2—C11.3595 (19)C8—C71.387 (2)
N2—C91.3932 (17)C8—H8A0.9300
N2—H2C0.8600C4—C51.378 (2)
N1'—C12'1.333 (2)C4—H4A0.9300
N1'—C11'1.3457 (18)C2—H2A0.9700
C9—C101.382 (2)C2—H2B0.9700
C9—C131.394 (2)C4'—C5'1.381 (2)
C3'—C4'1.387 (2)C4'—H4'A0.9300
C3'—C8'1.380 (2)C8'—C7'1.396 (2)
C3'—C2'1.500 (2)C8'—H8'A0.9300
C13—C121.383 (2)C12'—H12B0.9300
C13—H13A0.9300C5'—C6'1.369 (3)
C10—C111.3749 (19)C5'—H5'A0.9300
C10—H10A0.9300C6—C71.369 (3)
C9'—C10'1.383 (2)C6—C51.379 (3)
C9'—C13'1.3940 (19)C6—H6A0.9300
C10'—C11'1.372 (2)C7—H7A0.9300
C10'—H10B0.9300C7'—C6'1.371 (3)
C13'—C12'1.381 (2)C7'—H7'A0.9300
C13'—H13B0.9300C6'—H6'A0.9300
N1—C121.334 (2)C5—H5A0.9300
C1'—N2'—C9'127.25 (12)O2'—C2'—H2'A110.3
C1'—N2'—H2'C116.4C3'—C2'—H2'A110.3
C9'—N2'—H2'C116.4O2'—C2'—H2'B110.3
C1—O2—C2117.22 (12)C3'—C2'—H2'B110.3
C1'—O2'—C2'116.32 (11)H2'A—C2'—H2'B108.5
C1—N2—C9126.80 (13)N1—C12—C13125.66 (14)
C1—N2—H2C116.6N1—C12—H12A117.2
C9—N2—H2C116.6C13—C12—H12A117.2
O1—C1—O2124.86 (14)C7—C8—C3120.14 (17)
O1—C1—N2127.57 (13)C7—C8—H8A119.9
O2—C1—N2107.58 (13)C3—C8—H8A119.9
C12'—N1'—C11'115.17 (13)C3—C4—C5121.07 (18)
C10—C9—N2117.48 (13)C3—C4—H4A119.5
C10—C9—C13117.66 (13)C5—C4—H4A119.5
N2—C9—C13124.85 (14)O2—C2—C3105.19 (12)
C4'—C3'—C8'118.84 (15)O2—C2—H2A110.7
C4'—C3'—C2'120.56 (16)C3—C2—H2A110.7
C8'—C3'—C2'120.59 (15)O2—C2—H2B110.7
C12—C13—C9117.70 (15)C3—C2—H2B110.7
C12—C13—H13A121.2H2A—C2—H2B108.8
C9—C13—H13A121.2C3'—C4'—C5'120.68 (18)
C9—C10—C11119.81 (14)C3'—C4'—H4'A119.7
C9—C10—H10A120.1C5'—C4'—H4'A119.7
C11—C10—H10A120.1C3'—C8'—C7'120.08 (18)
O1'—C1'—O2'124.01 (14)C3'—C8'—H8'A120.0
O1'—C1'—N2'127.63 (14)C7'—C8'—H8'A120.0
O2'—C1'—N2'108.35 (12)N1'—C12'—C13'125.71 (14)
C10'—C9'—N2'117.64 (12)N1'—C12'—H12B117.1
C10'—C9'—C13'117.46 (14)C13'—C12'—H12B117.1
N2'—C9'—C13'124.90 (14)C6'—C5'—C4'120.17 (19)
C9'—C10'—C11'120.04 (13)C6'—C5'—H5'A119.9
C9'—C10'—H10B120.0C4'—C5'—H5'A119.9
C11'—C10'—H10B120.0C7—C6—C5120.11 (17)
C12'—C13'—C9'117.82 (15)C7—C6—H6A119.9
C12'—C13'—H13B121.1C5—C6—H6A119.9
C9'—C13'—H13B121.1C6—C7—C8120.13 (18)
C12—N1—C11115.19 (12)C6—C7—H7A119.9
N1'—C11'—C10'123.78 (16)C8—C7—H7A119.9
N1'—C11'—H11A118.1C6'—C7'—C8'120.2 (2)
C10'—C11'—H11A118.1C6'—C7'—H7'A119.9
C4—C3—C8119.03 (15)C8'—C7'—H7'A119.9
C4—C3—C2120.24 (15)C5'—C6'—C7'119.99 (17)
C8—C3—C2120.62 (16)C5'—C6'—H6'A120.0
N1—C11—C10123.99 (15)C7'—C6'—H6'A120.0
N1—C11—H11B118.0C6—C5—C4119.50 (19)
C10—C11—H11B118.0C6—C5—H5A120.2
O2'—C2'—C3'107.20 (12)C4—C5—H5A120.2
C2—O2—C1—O1−7.0 (2)C4'—C3'—C2'—O2'56.18 (19)
C2—O2—C1—N2173.09 (13)C8'—C3'—C2'—O2'−124.65 (17)
C9—N2—C1—O10.4 (3)C11—N1—C12—C130.1 (3)
C9—N2—C1—O2−179.66 (14)C9—C13—C12—N1−0.4 (3)
C1—N2—C9—C10166.73 (15)C4—C3—C8—C7−0.9 (2)
C1—N2—C9—C13−14.4 (2)C2—C3—C8—C7175.37 (15)
C10—C9—C13—C120.5 (2)C8—C3—C4—C51.6 (2)
N2—C9—C13—C12−178.37 (15)C2—C3—C4—C5−174.66 (15)
N2—C9—C10—C11178.65 (15)C1—O2—C2—C3−157.99 (14)
C13—C9—C10—C11−0.3 (2)C4—C3—C2—O277.04 (18)
C2'—O2'—C1'—O1'−3.0 (2)C8—C3—C2—O2−99.19 (16)
C2'—O2'—C1'—N2'175.94 (13)C8'—C3'—C4'—C5'1.5 (2)
C9'—N2'—C1'—O1'4.4 (3)C2'—C3'—C4'—C5'−179.31 (14)
C9'—N2'—C1'—O2'−174.45 (13)C4'—C3'—C8'—C7'0.8 (3)
C1'—N2'—C9'—C10'171.04 (15)C2'—C3'—C8'—C7'−178.39 (15)
C1'—N2'—C9'—C13'−8.5 (2)C11'—N1'—C12'—C13'−0.2 (2)
N2'—C9'—C10'—C11'179.55 (14)C9'—C13'—C12'—N1'−0.1 (2)
C13'—C9'—C10'—C11'−0.9 (2)C3'—C4'—C5'—C6'−2.2 (3)
C10'—C9'—C13'—C12'0.6 (2)C5—C6—C7—C80.4 (3)
N2'—C9'—C13'—C12'−179.87 (14)C3—C8—C7—C6−0.1 (3)
C12'—N1'—C11'—C10'−0.1 (2)C3'—C8'—C7'—C6'−2.4 (3)
C9'—C10'—C11'—N1'0.7 (2)C4'—C5'—C6'—C7'0.5 (3)
C12—N1—C11—C100.1 (2)C8'—C7'—C6'—C5'1.8 (3)
C9—C10—C11—N10.0 (3)C7—C6—C5—C40.3 (3)
C1'—O2'—C2'—C3'−170.42 (13)C3—C4—C5—C6−1.3 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2'—H2'C···N1i0.862.092.9460 (16)171
N2—H2C···N1'ii0.862.112.9630 (18)170

Symmetry codes: (i) −x+1, −y, −z; (ii) −x, −y, −z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: JH2125).

References

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