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

Elgemeie, G.H.; Jones, P.G.

doi:10.1107/S2056989016012196

research communications

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Volume 72| Part 9| September 2016| Pages 1239-1241

https://doi.org/10.1107/S2056989016012196

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

Galal H. Elgemeie ^a and Peter G. Jones ^b ^*

^aChemistry Department, Faculty of Science, Helwan University, Cairo, Egypt, and ^bInstitut für Anorganische und Analytische Chemie, Technische Universität Braunschweig, Postfach 3329, D-38023 Braunschweig, Germany
^*Correspondence e-mail: p.jones@tu-bs.de

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 25 July 2016; accepted 27 July 2016; online 2 August 2016)

In the title compound, C₁₁H₁₃N₃O, 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.

Keywords: crystal structure; cyclohepta[b]pyridine; carbonitrile; N—NH₂ group; tautomer; N—H⋯O hydrogen bonding.

CCDC reference: 1496294

1. Chemical context

We have recently described various novel approaches for the synthesis of a new class of N-substituted amino derivatives of pyridines and pyrimidines (Elgemeie, Salah et al., 2015 ; Elgemeie et al., 2016 ). These compounds are important as pyrimidine ring systems that are not nucleoside analogs, and are interesting as antimetabolic agents (Elgemeie & Hamed, 2014 ; Elgemeie & Abd Elaziz, 2015 ). They have a greater selectivity for a broader range of human tumors, hence our interest in this class of compounds (Elgemeie, Abou-Zeid et al., 2015 ; Elgemeie, Mohamed et al., 2015 ).

We report here a novel one-step synthesis of a cycloheptane-ring-fused N-amino-2-pyridone derivative by reaction of the sodium salt of 2-(hydroxymethylene)-1-cycloheptanone (1) with a cyanoacetohydrazide (2). Thus, (1) reacted with (2) in piperidine acetate to give a product of molecular formula C₁₁H₁₃N₃O (M⁺ = 203), for which two isomeric structures, (3) and (4), seemed possible, corresponding to two possible modes of cyclization. Spectroscopic data cannot differentiate between these structures, and therefore the crystal structure was determined, confirming the exclusive presence of tautomer (3) in the solid state. The formation of (3) from the reaction of (1) and (2) is assumed to proceed via initial addition of the active methylene carbon atom of (2) to the formyl group of (1) to give the favoured, kinetically controlled product (3). The ¹H NMR spectra of the product revealed the presence of an N—NH₂ group at δ = 6.4 p.p.m. and a pyridine H-4 at 7.8 p.p.m. in solution.

2. Structural commentary

The structure of the title compound is shown in Fig. 1 and confirms the presence of tautomer (3) in the solid state. Molecular dimensions [e.g. the hydrazinic N1—N2 bond length of 1.4201 (15) Å] may be regarded as normal; an extensive structural investigation of alkyl-substituted 3-cyano-2-pyridones (with an unsubstituted NH function in the ring) was published by Fischer et al. (2004 ). The seven-membered ring adopts a conformation such that all three atoms C6, C7 and C8 lie to the same side of the plane formed by the pyridone ring together with C5 and C9; the respective deviations from this plane are 1.480 (2), 1.616 (3) and 1.470 (2) Å.

Figure 1
The molecular structure of the title compound, with atom labelling. Displacement ellipsoids are drawn at the 50% probability level. The intramolecular N—H⋯O hydrogen bond is shown as a dashed line (see Table 1

)

3. Supramolecular features

The classical hydrogen-bond donor N1—H01 is only involved in intramolecular hydrogen bonding (Fig. 1 and Table 1). The second such donor N1—H02 forms a classical hydrogen bond to the acceptor O1 of a neighbouring molecule related by the 2₁ screw axis. Additionally, the `weak' but quite short hydrogen bond C4—H4⋯O1 links molecules related by the c glide plane. The overall effect is to build up double layers of molecules (Fig. 2 and Table 1) parallel to the bc plane, in which the top and bottom molecules of the layer are related by inversion.

Table 1
Hydrogen-bond geometry (Å, °)

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⋯O1ⁱ	0.91 (2)	2.16 (2)	3.0225 (15)	158.2 (17)
C4—H4⋯O1ⁱⁱ	0.95	2.45	3.2105 (16)	137
C9—H9A⋯O1ⁱ	0.99	2.63	3.4903 (16)	146
Symmetry codes: (i) $[-x, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) $[x, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]$ .

Figure 2
Crystal packing of the title compound, viewed approximately normal to the bc plane. Dashed lines indicate the hydrogen bonds (see Table 1

), and for clarity H atoms not involved in hydrogen bonding have been omitted.

4. Database survey

A search of the Cambridge Structural Database (CSD, Version 5.37, last update May 2016; Groom et al., 2016 ) revealed four other examples of the cyclohepta[b]pyridin-2-one ring system: refcodes AHEQAF (Elgemeie et al., 2002 ), ATUYAP and IBATUB (Albov et al., 2004a ,b ) and QAHLOB (Fischer et al., 2004).

5. Synthesis and crystallization

A solution of the sodium salt of 2-(hydroxymethylene)-1-cycloheptanone [(1); 1.60 g, 0.01 mol], N-cyanoacetohydrazide [(2); 0.09 g, 0.01 mol] and piperidine acetate (1 ml) in water (30 ml) and ethanol (30 ml) was refluxed for 10 min. Acetic acid (1.5 ml) was added to the hot solution. The precipitated solid was collected by filtration and crystallized from ethanol, giving colourless plate-like crystals (yield 85%, m.p. 508 K).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. The NH hydrogens were located in a difference Fourier map and freely refined. The C-bound H atoms were included using a riding model starting from calculated positions: C—H = 0.95–0.99 Å with U_iso(H) = 1.2U_eq(C).

Table 2
Experimental details

Crystal data
Chemical formula	C₁₁H₁₃N₃O
M_r	203.24
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	100
a, b, c (Å)	8.5680 (4), 10.0475 (4), 11.6778 (5)
β (°)	103.272 (4)
V (Å³)	978.46 (7)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	0.74
Crystal size (mm)	0.10 × 0.10 × 0.05

Data collection
Diffractometer	Oxford Diffraction Xcalibur Atlas Nova
Absorption correction	Multi-scan (CrysAlis PRO; Agilent, 2010 )
T_min, T_max	0.795, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	19833, 2046, 1674
R_int	0.062
(sin θ/λ)_max (Å⁻¹)	0.630

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.109, 1.06
No. of reflections	2046
No. of parameters	144
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.28, −0.30
Computer programs: (CrysAlis PRO; Agilent, 2010), SHELXS97 and SHELXL97 (Sheldrick, 2008 ) and XP (Siemens, 1994 ).

Supporting information

CCDC reference: 1496294

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S2056989016012196/su5315sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989016012196/su5315Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989016012196/su5315Isup3.cml

checkCIF report

Computing details top

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 top

Crystal data top

C₁₁H₁₃N₃O	F(000) = 432
M_r = 203.24	D_x = 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) Å³	0.10 × 0.10 × 0.05 mm
Z = 4

Data collection top

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	R_int = 0.062
Detector resolution: 10.3543 pixels mm^-1	θ_max = 76.1°, θ_min = 5.3°
ω–scan	h = −10→10
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010)	k = −12→12
T_min = 0.795, T_max = 1.000	l = −14→14
19833 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)] = 0.039	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.109	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	w = 1/[σ²(F_o²) + (0.0602P)² + 0.2053P] where P = (F_o² + 2F_c²)/3
2046 reflections	(Δ/σ)_max < 0.001
144 parameters	Δρ_max = 0.28 e Å⁻³
0 restraints	Δρ_min = −0.30 e Å⁻³

Special details top

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 (Å²) top

	x	y	z	U_iso*/U_eq
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 (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
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) top

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) top

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···O1ⁱ	0.91 (2)	2.16 (2)	3.0225 (15)	158.2 (17)
C4—H4···O1ⁱⁱ	0.95	2.45	3.2105 (16)	137
C9—H9A···O1ⁱ	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.

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