Crystal structure of 1-amino-2-oxo-2,5,6,7,8,9-hexa­hydro-1H-cyclo­hepta­[b]pyridine-3-carbo­nitrile

In the title compound the seven-membered ring adopts a conformation such that the three atoms not involved in the aromatic plane lie on the same side of that plane. One hydrazinic H atom forms an intra­molecular hydrogen bond to the O atom; the other forms a classical inter­molecular hydrogen bond N—H...O, which combines with a `weak' H_ar...O inter­action to build up double layers of mol­ecules parallel to the bc plane.

Key indicators

• Single-crystal X-ray study
• T = 100 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.039
• wR factor = 0.109
• Data-to-parameter ratio = 14.2

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT480_ALERT_4_C Long H...A H-Bond Reported H9A    ..  O1      ..       2.63 Ang.

Alert level G
PLAT005_ALERT_5_G No Embedded Refinement Details found  in the CIF     Please Do !
PLAT230_ALERT_2_G Hirshfeld Test Diff for    C3     --  C10     ..        5.9 s.u.
PLAT720_ALERT_4_G Number of Unusual/Non-Standard Labels ..........          2 Note
PLAT899_ALERT_4_G SHELXL97   is Deprecated and Succeeded by SHELXL       2014 Note
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600          4 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density           9 Note

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
   1 ALERT level C = Check. Ensure it is not caused by an omission or oversight
   6 ALERT level G = General information/check it is not something unexpected

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   4 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

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Computing details

Data collection: (CrysAlis PRO; Agilent, 2010); cell refinement: (CrysAlis PRO; Agilent, 2010); data reduction: (CrysAlis PRO; Agilent, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP (Siemens, 1994); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

1-Amino-2-oxo-2,5,6,7,8,9-hexahydro-1H-cyclohepta[b]pyridine-3-carbonitrile

Crystal data

C11H13N3O	F(000) = 432
Mr = 203.24	Dx = 1.380 Mg m^−3
Monoclinic, P21/c	Cu Kα radiation, λ = 1.54184 Å
Hall symbol: -P 2ybc	Cell parameters from 6583 reflections
a = 8.5680 (4) Å	θ = 3.9–76.1°
b = 10.0475 (4) Å	µ = 0.74 mm^−1
c = 11.6778 (5) Å	T = 100 K
β = 103.272 (4)°	Plate, colourless
V = 978.46 (7) Å^3	0.10 × 0.10 × 0.05 mm
Z = 4

Data collection

Oxford Diffraction Xcalibur Atlas Nova diffractometer	2046 independent reflections
Radiation source: sealed X-ray tube, Nova (Cu) X-ray Source	1674 reflections with I > 2σ(I)
Mirror monochromator	Rint = 0.062
Detector resolution: 10.3543 pixels mm^-1	θmax = 76.1°, θmin = 5.3°
ω–scan	h = −10→10
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010)	k = −12→12
Tmin = 0.795, Tmax = 1.000	l = −14→14
19833 measured reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.039	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.109	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	w = 1/[σ^2(Fo^2) + (0.0602P)^2 + 0.2053P] where P = (Fo^2 + 2Fc^2)/3
2046 reflections	(Δ/σ)max < 0.001
144 parameters	Δρmax = 0.28 e Å^−3
0 restraints	Δρmin = −0.30 e Å^−3

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Least-squares planes (x,y,z in crystal coordinates) and deviations from them (* indicates atom used to define plane)

8.5275 (0.0007) x + 0.7466 (0.0052) y - 3.3783 (0.0058) z = 0.3993 (0.0040)

* -0.0117 (0.0008) N1 * 0.0031 (0.0009) C2 * 0.0072 (0.0009) C3 * -0.0090 (0.0009) C4 * 0.0007 (0.0009) C4A * 0.0097 (0.0009) C9A 1.4803 (0.0024) C6 1.6155 (0.0026) C7 1.4700 (0.0023) C8

Rms deviation of fitted atoms = 0.0079

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 > 2sigma(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 (Ų)

	x	y	z	Uiso*/Ueq
N1	0.14967 (13)	0.49677 (10)	0.37289 (9)	0.0161 (3)
C2	0.13750 (15)	0.63589 (13)	0.36852 (11)	0.0168 (3)
C3	0.17684 (15)	0.69947 (13)	0.48064 (12)	0.0168 (3)
C4	0.22210 (15)	0.62730 (13)	0.58375 (11)	0.0173 (3)
H4	0.2451	0.6727	0.6571	0.021*
C4A	0.23457 (16)	0.48899 (13)	0.58178 (11)	0.0169 (3)
C5	0.29860 (17)	0.41294 (13)	0.69430 (11)	0.0197 (3)
H5A	0.2243	0.3391	0.7000	0.024*
H5B	0.3025	0.4729	0.7622	0.024*
C6	0.46697 (17)	0.35590 (14)	0.70100 (12)	0.0218 (3)
H6A	0.5315	0.4231	0.6703	0.026*
H6B	0.5197	0.3395	0.7845	0.026*
C7	0.46682 (17)	0.22636 (14)	0.63197 (12)	0.0212 (3)
H7A	0.5787	0.1942	0.6447	0.025*
H7B	0.4055	0.1587	0.6651	0.025*
C8	0.39649 (16)	0.23537 (13)	0.49953 (12)	0.0199 (3)
H8A	0.4085	0.1478	0.4637	0.024*
H8B	0.4596	0.3008	0.4656	0.024*
C9	0.21817 (16)	0.27618 (13)	0.46552 (12)	0.0186 (3)
H9A	0.1708	0.2467	0.3841	0.022*
H9B	0.1597	0.2312	0.5185	0.022*
C9A	0.19855 (15)	0.42414 (13)	0.47385 (11)	0.0159 (3)
C10	0.17377 (16)	0.84204 (14)	0.48160 (12)	0.0200 (3)
N2	0.12201 (15)	0.43233 (12)	0.26182 (10)	0.0207 (3)
H01	0.090 (2)	0.500 (2)	0.2110 (18)	0.036 (5)*
H02	0.037 (2)	0.376 (2)	0.2551 (16)	0.030 (5)*
N3	0.17469 (17)	0.95620 (12)	0.48127 (12)	0.0298 (3)
O1	0.09637 (12)	0.69230 (9)	0.27097 (8)	0.0208 (2)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
N1	0.0174 (6)	0.0137 (5)	0.0162 (5)	−0.0004 (4)	0.0016 (4)	−0.0012 (4)
C2	0.0134 (6)	0.0151 (6)	0.0214 (7)	0.0001 (4)	0.0028 (5)	0.0014 (5)
C3	0.0150 (6)	0.0129 (6)	0.0223 (6)	−0.0009 (4)	0.0037 (5)	−0.0012 (5)
C4	0.0154 (6)	0.0171 (6)	0.0199 (6)	−0.0005 (5)	0.0047 (5)	−0.0024 (5)
C4A	0.0153 (6)	0.0162 (6)	0.0192 (6)	0.0000 (5)	0.0036 (5)	0.0012 (5)
C5	0.0240 (7)	0.0182 (6)	0.0170 (6)	0.0015 (5)	0.0051 (5)	0.0018 (5)
C6	0.0212 (7)	0.0241 (7)	0.0182 (6)	0.0018 (5)	0.0006 (5)	0.0020 (5)
C7	0.0197 (7)	0.0204 (7)	0.0229 (7)	0.0036 (5)	0.0037 (5)	0.0044 (5)
C8	0.0199 (7)	0.0182 (6)	0.0215 (6)	0.0026 (5)	0.0048 (5)	0.0005 (5)
C9	0.0193 (7)	0.0137 (6)	0.0218 (6)	−0.0002 (5)	0.0026 (5)	−0.0003 (5)
C9A	0.0133 (6)	0.0145 (6)	0.0195 (6)	−0.0006 (4)	0.0030 (5)	0.0008 (4)
C10	0.0183 (6)	0.0182 (7)	0.0227 (6)	0.0002 (5)	0.0033 (5)	−0.0007 (5)
N2	0.0272 (7)	0.0176 (6)	0.0154 (5)	−0.0018 (5)	0.0006 (5)	−0.0033 (4)
N3	0.0340 (8)	0.0182 (6)	0.0366 (7)	0.0000 (5)	0.0068 (6)	−0.0004 (5)
O1	0.0237 (5)	0.0170 (4)	0.0199 (5)	0.0012 (4)	0.0012 (4)	0.0039 (4)

Geometric parameters (Å, º)

N1—C9A	1.3680 (16)	C10—N3	1.1471 (19)
N1—C2	1.4017 (16)	C4—H4	0.9500
N1—N2	1.4201 (15)	C5—H5A	0.9900
C2—O1	1.2486 (16)	C5—H5B	0.9900
C2—C3	1.4260 (18)	C6—H6A	0.9900
C3—C4	1.3826 (18)	C6—H6B	0.9900
C3—C10	1.4328 (18)	C7—H7A	0.9900
C4—C4A	1.3943 (18)	C7—H7B	0.9900
C4A—C9A	1.3892 (18)	C8—H8A	0.9900
C4A—C5	1.5101 (17)	C8—H8B	0.9900
C5—C6	1.5375 (19)	C9—H9A	0.9900
C6—C7	1.5308 (19)	C9—H9B	0.9900
C7—C8	1.5283 (18)	N2—H01	0.90 (2)
C8—C9	1.5432 (18)	N2—H02	0.91 (2)
C9—C9A	1.5018 (17)
C9A—N1—C2	124.66 (11)	C4A—C5—H5B	109.1
C9A—N1—N2	119.86 (10)	C6—C5—H5B	109.1
C2—N1—N2	115.22 (10)	H5A—C5—H5B	107.8
O1—C2—N1	119.27 (11)	C7—C6—H6A	108.8
O1—C2—C3	126.31 (12)	C5—C6—H6A	108.8
N1—C2—C3	114.42 (11)	C7—C6—H6B	108.8
C4—C3—C2	121.64 (12)	C5—C6—H6B	108.8
C4—C3—C10	121.30 (12)	H6A—C6—H6B	107.7
C2—C3—C10	117.01 (12)	C8—C7—H7A	108.3
C3—C4—C4A	121.04 (12)	C6—C7—H7A	108.3
C9A—C4A—C4	118.72 (12)	C8—C7—H7B	108.3
C9A—C4A—C5	120.85 (12)	C6—C7—H7B	108.3
C4—C4A—C5	120.26 (12)	H7A—C7—H7B	107.4
C4A—C5—C6	112.46 (11)	C7—C8—H8A	108.7
C7—C6—C5	113.75 (11)	C9—C8—H8A	108.7
C8—C7—C6	115.79 (11)	C7—C8—H8B	108.7
C7—C8—C9	114.41 (11)	C9—C8—H8B	108.7
C9A—C9—C8	111.42 (11)	H8A—C8—H8B	107.6
N1—C9A—C4A	119.48 (12)	C9A—C9—H9A	109.3
N1—C9A—C9	119.26 (11)	C8—C9—H9A	109.3
C4A—C9A—C9	121.22 (12)	C9A—C9—H9B	109.3
N3—C10—C3	178.28 (16)	C8—C9—H9B	109.3
C3—C4—H4	119.5	H9A—C9—H9B	108.0
C4A—C4—H4	119.5	N1—N2—H01	102.6 (13)
C4A—C5—H5A	109.1	N1—N2—H02	108.8 (12)
C6—C5—H5A	109.1	H01—N2—H02	107.1 (17)
C9A—N1—C2—O1	177.72 (12)	C4A—C5—C6—C7	−80.60 (15)
N2—N1—C2—O1	3.59 (17)	C5—C6—C7—C8	61.27 (16)
C9A—N1—C2—C3	−1.60 (18)	C6—C7—C8—C9	−61.68 (16)
N2—N1—C2—C3	−175.73 (11)	C7—C8—C9—C9A	80.91 (14)
O1—C2—C3—C4	−179.57 (13)	C2—N1—C9A—C4A	2.30 (19)
N1—C2—C3—C4	−0.30 (18)	N2—N1—C9A—C4A	176.17 (12)
O1—C2—C3—C10	−2.1 (2)	C2—N1—C9A—C9	−175.43 (12)
N1—C2—C3—C10	177.22 (11)	N2—N1—C9A—C9	−1.55 (18)
C2—C3—C4—C4A	1.5 (2)	C4—C4A—C9A—N1	−0.99 (18)
C10—C3—C4—C4A	−175.93 (13)	C5—C4A—C9A—N1	−176.19 (12)
C3—C4—C4A—C9A	−0.82 (19)	C4—C4A—C9A—C9	176.68 (12)
C3—C4—C4A—C5	174.41 (12)	C5—C4A—C9A—C9	1.48 (19)
C9A—C4A—C5—C6	66.67 (16)	C8—C9—C9A—N1	109.73 (13)
C4—C4A—C5—C6	−108.45 (14)	C8—C9—C9A—C4A	−67.96 (16)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H01···O1	0.90 (2)	2.05 (2)	2.6255 (15)	120.4 (16)
N2—H02···O1^i	0.91 (2)	2.16 (2)	3.0225 (15)	158.2 (17)
C4—H4···O1^ii	0.95	2.45	3.2105 (16)	137
C9—H9A···O1^i	0.99	2.63	3.4903 (16)	146

Symmetry codes: (i) −x, y−1/2, −z+1/2; (ii) x, −y+3/2, z+1/2.