N-(5-Nitro-pyridin-2-yl)-5H-dibenzo[d,f][1,3]diazepine-6-carboxamide.

The title compound, C(19)H(13)N(5)O(3), can be obtained from the corresponding α-amido-α-amino-nitrone in a reaction with biphenyl-2,2'-diamine. The amido-amidine core has distinctive geometrical parameters including: an outstandingly long Csp(2)-Csp(2) single bond of 1.5276 (13) Å and an amidine N-C-N angle of 130.55 (9)°. Intra-molecular N-H⋯O, N-H⋯N and C-H⋯O hydrogen bonds occur. In the crystal, mol-ecules form layers parallel to (001) via weak inter-molecular C-H⋯N inter-actions. The layers are linked via N-H⋯O hydrogen bonds and π-π inter-actions along [001] [benzene-pyridine centroid-centroid distance = 3.672 (2) Å].

Related literature

For the synthesis of the title compound, see: Trzewik et al. (2008 ▶). For the reaction mechanism, see: Trzewik et al. (2010 ▶). For similar structures, see: Zaleska et al. (2007 ▶); Hodorowicz et al. (2007 ▶). For hydrogen bond graph-set analysis, see: Bernstein et al. (1995 ▶).

Experimental

Crystal data

C19H13N5O3

M = 359.34

Monoclinic,

a = 12.9702 (2) Å

b = 9.2104 (1) Å

c = 13.4145 (2) Å

β = 100.692 (1)°

V = 1574.68 (3) Å3

Z = 4

Mo Kα radiation

μ = 0.11 mm−1

T = 110 K

0.30 × 0.20 × 0.15 mm

Data collection

Oxford Diffraction SuperNova Dual Cu at zero Atlas diffractometer

Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009 ▶) T min = 0.969, T max = 0.984

127481 measured reflections

4577 independent reflections

3784 reflections with I > 2σ(I)

R int = 0.052

Refinement

R[F 2 > 2σ(F 2)] = 0.036

wR(F 2) = 0.110

S = 1.06

4577 reflections

250 parameters

2 restraints

H atoms treated by a mixture of independent and constrained refinement

Δρmax = 0.39 e Å−3

Δρmin = −0.21 e Å−3

Data collection: CrysAlis PRO (Oxford Diffraction, 2009 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SIR92 (Altomare et al., 1994 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: Mercury (Macrae et al., 2006 ▶) and ORTEP-3 (Farrugia, 1997 ▶); software used to prepare material for publication: SHELXL97, PARST (Nardelli, 1995 ▶) and WinGX (Farrugia, 1999 ▶).

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811018629/vm2095sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536811018629/vm2095Isup2.hkl

Supplementary material file. DOI: 10.1107/S1600536811018629/vm2095Isup3.cml

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

C19H13N5O3	F(000) = 744
Mr = 359.34	Dx = 1.516 Mg m−3
Monoclinic, P21/c	Melting point = 477–478 K
Hall symbol: -P 2ybc	Mo Kα radiation, λ = 0.71073 Å
a = 12.9702 (2) Å	Cell parameters from 34515 reflections
b = 9.2104 (1) Å	θ = 3.0–44.5°
c = 13.4145 (2) Å	µ = 0.11 mm−1
β = 100.692 (1)°	T = 110 K
V = 1574.68 (3) Å3	Block, orange
Z = 4	0.30 × 0.20 × 0.15 mm

Oxford Diffraction SuperNova Dual Cu at zero Atlas diffractometer	4577 independent reflections
Radiation source: Oxford Diffraction SuperNova (Mo) X-ray Source	3784 reflections with I > 2σ(I)
mirror	Rint = 0.052
Detector resolution: 10.3756 pixels mm-1	θmax = 30.0°, θmin = 3.0°
ω scans	h = −18→17
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009)	k = 0→12
Tmin = 0.969, Tmax = 0.984	l = 0→18
127481 measured reflections

Refinement on F2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.036	H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.110	w = 1/[σ2(Fo2) + (0.0729P)2 + 0.1623P] where P = (Fo2 + 2Fc2)/3
S = 1.06	(Δ/σ)max < 0.001
4577 reflections	Δρmax = 0.39 e Å−3
250 parameters	Δρmin = −0.21 e Å−3
2 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008)
0 constraints	Extinction coefficient: 0
Primary atom site location: structure-invariant direct methods

Experimental. CrysAlisPro, Oxford Diffraction Ltd., Version 1.171.33.66. Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm (Oxford Diffraction, 2009).

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 > 2σ(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.

	x	y	z	Uiso*/Ueq
N2	0.15616 (7)	0.02467 (9)	0.92909 (6)	0.01621 (17)
H2	0.1014 (9)	−0.0115 (14)	0.9524 (9)	0.019*
C3	0.14265 (7)	0.16642 (10)	0.90162 (7)	0.01300 (18)
N3	0.20711 (6)	0.25840 (9)	0.87513 (6)	0.01359 (16)
C4	0.03385 (7)	0.22423 (10)	0.90872 (7)	0.01420 (18)
O4	−0.03207 (5)	0.14658 (8)	0.93589 (6)	0.02028 (17)
N5	0.02224 (6)	0.36682 (9)	0.88352 (6)	0.01523 (17)
H5	0.0796 (9)	0.4033 (13)	0.8674 (9)	0.018*
C21	0.31624 (7)	0.23319 (10)	0.88312 (7)	0.01323 (18)
C22	0.37511 (8)	0.36134 (11)	0.89410 (7)	0.0173 (2)
H22	0.3397	0.4520	0.8913	0.021*
C23	0.48377 (8)	0.35967 (12)	0.90890 (8)	0.0207 (2)
H23	0.5223	0.4479	0.9161	0.025*
C24	0.53540 (8)	0.22716 (12)	0.91305 (8)	0.0202 (2)
H24	0.6099	0.2239	0.9260	0.024*
C25	0.47790 (7)	0.09954 (11)	0.89823 (7)	0.0172 (2)
H25	0.5143	0.0098	0.8995	0.021*
C26	0.36771 (7)	0.09835 (10)	0.88136 (7)	0.01375 (18)
C31	0.21410 (7)	−0.07550 (10)	0.88061 (7)	0.01417 (18)
C32	0.16781 (8)	−0.21063 (11)	0.85663 (8)	0.0187 (2)
H32	0.1011	−0.2310	0.8730	0.022*
C33	0.21824 (9)	−0.31577 (11)	0.80897 (8)	0.0219 (2)
H33	0.1863	−0.4078	0.7930	0.026*
C34	0.31554 (9)	−0.28566 (11)	0.78484 (8)	0.0218 (2)
H34	0.3509	−0.3571	0.7527	0.026*
C35	0.36072 (8)	−0.15065 (11)	0.80807 (8)	0.0181 (2)
H35	0.4267	−0.1305	0.7900	0.022*
C36	0.31255 (7)	−0.04244 (10)	0.85732 (7)	0.01404 (18)
N51	−0.04575 (6)	0.59431 (9)	0.85591 (6)	0.01663 (18)
C52	−0.12294 (8)	0.69109 (11)	0.85240 (7)	0.01701 (19)
H52	−0.1109	0.7889	0.8352	0.020*
C53	−0.21986 (8)	0.65325 (11)	0.87304 (7)	0.01609 (19)
C54	−0.23889 (8)	0.51174 (11)	0.90003 (8)	0.0181 (2)
H54	−0.3054	0.4849	0.9143	0.022*
C55	−0.15953 (7)	0.41067 (11)	0.90574 (8)	0.01687 (19)
H55	−0.1691	0.3131	0.9251	0.020*
C56	−0.06433 (7)	0.45741 (10)	0.88190 (7)	0.01390 (18)
N57	−0.30275 (7)	0.76288 (10)	0.86450 (7)	0.02042 (19)
O58	−0.39181 (6)	0.72147 (10)	0.86834 (7)	0.0296 (2)
O59	−0.27849 (7)	0.89005 (9)	0.85351 (7)	0.02897 (19)

	U11	U22	U33	U12	U13	U23
N2	0.0173 (4)	0.0141 (4)	0.0190 (4)	0.0005 (3)	0.0079 (3)	0.0029 (3)
C3	0.0147 (4)	0.0141 (4)	0.0099 (4)	0.0007 (3)	0.0014 (3)	0.0000 (3)
N3	0.0138 (4)	0.0149 (4)	0.0119 (4)	−0.0002 (3)	0.0020 (3)	−0.0001 (3)
C4	0.0150 (4)	0.0153 (4)	0.0119 (4)	0.0004 (3)	0.0014 (3)	0.0005 (3)
O4	0.0173 (3)	0.0184 (3)	0.0263 (4)	−0.0001 (3)	0.0073 (3)	0.0053 (3)
N5	0.0124 (4)	0.0150 (4)	0.0187 (4)	−0.0001 (3)	0.0039 (3)	0.0016 (3)
C21	0.0137 (4)	0.0162 (4)	0.0096 (4)	−0.0006 (3)	0.0015 (3)	0.0010 (3)
C22	0.0191 (5)	0.0161 (4)	0.0173 (5)	−0.0019 (3)	0.0049 (4)	−0.0011 (4)
C23	0.0189 (5)	0.0223 (5)	0.0217 (5)	−0.0066 (4)	0.0055 (4)	−0.0032 (4)
C24	0.0138 (4)	0.0281 (5)	0.0186 (5)	−0.0021 (4)	0.0024 (4)	0.0007 (4)
C25	0.0154 (4)	0.0212 (5)	0.0152 (4)	0.0021 (4)	0.0030 (3)	0.0035 (4)
C26	0.0156 (4)	0.0159 (4)	0.0097 (4)	0.0004 (3)	0.0021 (3)	0.0023 (3)
C31	0.0161 (4)	0.0135 (4)	0.0130 (4)	0.0018 (3)	0.0028 (3)	0.0028 (3)
C32	0.0199 (5)	0.0153 (4)	0.0211 (5)	−0.0014 (4)	0.0041 (4)	0.0028 (4)
C33	0.0280 (5)	0.0139 (4)	0.0239 (5)	−0.0009 (4)	0.0054 (4)	0.0021 (4)
C34	0.0294 (5)	0.0156 (5)	0.0222 (5)	0.0044 (4)	0.0093 (4)	0.0017 (4)
C35	0.0197 (4)	0.0170 (4)	0.0184 (5)	0.0039 (4)	0.0057 (4)	0.0035 (4)
C36	0.0155 (4)	0.0134 (4)	0.0128 (4)	0.0015 (3)	0.0014 (3)	0.0037 (3)
N51	0.0172 (4)	0.0150 (4)	0.0171 (4)	0.0001 (3)	0.0017 (3)	0.0015 (3)
C52	0.0201 (4)	0.0158 (4)	0.0139 (4)	0.0010 (4)	−0.0001 (3)	0.0002 (3)
C53	0.0168 (4)	0.0192 (5)	0.0109 (4)	0.0048 (3)	−0.0012 (3)	−0.0018 (3)
C54	0.0146 (4)	0.0223 (5)	0.0173 (5)	0.0006 (4)	0.0024 (3)	−0.0004 (4)
C55	0.0151 (4)	0.0174 (4)	0.0180 (5)	−0.0011 (3)	0.0028 (4)	0.0010 (4)
C56	0.0142 (4)	0.0148 (4)	0.0118 (4)	0.0006 (3)	0.0001 (3)	0.0000 (3)
N57	0.0221 (4)	0.0247 (4)	0.0131 (4)	0.0081 (3)	−0.0003 (3)	−0.0017 (3)
O58	0.0187 (4)	0.0389 (5)	0.0316 (5)	0.0099 (3)	0.0057 (3)	0.0046 (4)
O59	0.0345 (5)	0.0193 (4)	0.0306 (5)	0.0084 (3)	−0.0002 (3)	−0.0015 (3)

N2—C3	1.3591 (12)	C31—C36	1.4031 (13)
N2—C31	1.4213 (12)	C32—C33	1.3891 (14)
N2—H2	0.892 (11)	C32—H32	0.9500
C3—N3	1.2858 (12)	C33—C34	1.3878 (15)
C3—C4	1.5276 (13)	C33—H33	0.9500
N3—C21	1.4186 (12)	C34—C35	1.3853 (15)
C4—O4	1.2211 (11)	C34—H34	0.9500
C4—N5	1.3575 (12)	C35—C36	1.4048 (13)
N5—C56	1.3958 (12)	C35—H35	0.9500
N5—H5	0.879 (11)	N51—C52	1.3348 (13)
C21—C22	1.3987 (13)	N51—C56	1.3419 (12)
C21—C26	1.4122 (13)	C52—C53	1.3812 (14)
C22—C23	1.3864 (14)	C52—H52	0.9500
C22—H22	0.9500	C53—C54	1.3870 (14)
C23—C24	1.3883 (15)	C53—N57	1.4639 (13)
C23—H23	0.9500	C54—C55	1.3794 (13)
C24—C25	1.3864 (14)	C54—H54	0.9500
C24—H24	0.9500	C55—C56	1.3996 (13)
C25—C26	1.4050 (13)	C55—H55	0.9500
C25—H25	0.9500	N57—O58	1.2265 (12)
C26—C36	1.4872 (13)	N57—O59	1.2288 (13)
C31—C32	1.3933 (13)
C3—N2—C31	123.51 (8)	C33—C32—C31	120.63 (9)
C3—N2—H2	112.5 (8)	C33—C32—H32	119.7
C31—N2—H2	116.2 (8)	C31—C32—H32	119.7
N3—C3—N2	130.55 (9)	C34—C33—C32	119.62 (10)
N3—C3—C4	116.30 (8)	C34—C33—H33	120.2
N2—C3—C4	113.09 (8)	C32—C33—H33	120.2
C3—N3—C21	124.20 (8)	C35—C34—C33	119.47 (9)
O4—C4—N5	126.12 (9)	C35—C34—H34	120.3
O4—C4—C3	121.37 (8)	C33—C34—H34	120.3
N5—C4—C3	112.50 (8)	C34—C35—C36	122.42 (9)
C4—N5—C56	129.34 (8)	C34—C35—H35	118.8
C4—N5—H5	111.8 (8)	C36—C35—H35	118.8
C56—N5—H5	118.9 (8)	C31—C36—C35	116.95 (9)
C22—C21—C26	119.56 (8)	C31—C36—C26	124.20 (8)
C22—C21—N3	112.79 (8)	C35—C36—C26	118.85 (8)
C26—C21—N3	127.65 (8)	C52—N51—C56	117.84 (8)
C23—C22—C21	121.75 (9)	N51—C52—C53	121.94 (9)
C23—C22—H22	119.1	N51—C52—H52	119.0
C21—C22—H22	119.1	C53—C52—H52	119.0
C22—C23—C24	119.05 (9)	C52—C53—C54	120.14 (9)
C22—C23—H23	120.5	C52—C53—N57	119.53 (9)
C24—C23—H23	120.5	C54—C53—N57	120.33 (9)
C25—C24—C23	119.80 (9)	C55—C54—C53	118.79 (9)
C25—C24—H24	120.1	C55—C54—H54	120.6
C23—C24—H24	120.1	C53—C54—H54	120.6
C24—C25—C26	122.26 (9)	C54—C55—C56	117.43 (9)
C24—C25—H25	118.9	C54—C55—H55	121.3
C26—C25—H25	118.9	C56—C55—H55	121.3
C25—C26—C21	117.41 (9)	N51—C56—N5	112.52 (8)
C25—C26—C36	118.41 (8)	N51—C56—C55	123.85 (9)
C21—C26—C36	124.09 (8)	N5—C56—C55	123.63 (9)
C32—C31—C36	120.89 (9)	O58—N57—O59	124.44 (9)
C32—C31—N2	116.34 (8)	O58—N57—C53	117.77 (9)
C36—C31—N2	122.77 (9)	O59—N57—C53	117.79 (9)
C31—N2—C3—N3	−40.22 (16)	C32—C33—C34—C35	−0.43 (16)
C31—N2—C3—C4	142.83 (9)	C33—C34—C35—C36	1.23 (16)
N2—C3—N3—C21	−9.51 (16)	C32—C31—C36—C35	0.77 (14)
C4—C3—N3—C21	167.36 (8)	N2—C31—C36—C35	−179.14 (9)
N3—C3—C4—O4	−177.99 (9)	C32—C31—C36—C26	−179.29 (9)
N2—C3—C4—O4	−0.58 (13)	N2—C31—C36—C26	0.80 (14)
N3—C3—C4—N5	1.05 (12)	C34—C35—C36—C31	−1.38 (14)
N2—C3—C4—N5	178.47 (8)	C34—C35—C36—C26	178.68 (9)
O4—C4—N5—C56	−0.22 (17)	C25—C26—C36—C31	151.43 (9)
C3—C4—N5—C56	−179.21 (9)	C21—C26—C36—C31	−32.08 (14)
C3—N3—C21—C22	−153.01 (9)	C25—C26—C36—C35	−28.63 (13)
C3—N3—C21—C26	26.82 (15)	C21—C26—C36—C35	147.86 (9)
C26—C21—C22—C23	−3.56 (15)	C56—N51—C52—C53	−0.98 (14)
N3—C21—C22—C23	176.28 (9)	N51—C52—C53—C54	1.09 (15)
C21—C22—C23—C24	−0.09 (15)	N51—C52—C53—N57	−177.84 (9)
C22—C23—C24—C25	2.66 (15)	C52—C53—C54—C55	0.01 (15)
C23—C24—C25—C26	−1.61 (15)	N57—C53—C54—C55	178.94 (9)
C24—C25—C26—C21	−1.98 (14)	C53—C54—C55—C56	−1.11 (14)
C24—C25—C26—C36	174.74 (9)	C52—N51—C56—N5	−179.63 (8)
C22—C21—C26—C25	4.48 (13)	C52—N51—C56—C55	−0.22 (15)
N3—C21—C26—C25	−175.34 (9)	C4—N5—C56—N51	177.97 (9)
C22—C21—C26—C36	−172.04 (9)	C4—N5—C56—C55	−1.44 (16)
N3—C21—C26—C36	8.14 (15)	C54—C55—C56—N51	1.27 (15)
C3—N2—C31—C32	−134.33 (10)	C54—C55—C56—N5	−179.39 (9)
C3—N2—C31—C36	45.58 (14)	C52—C53—N57—O58	169.30 (9)
C36—C31—C32—C33	−0.04 (15)	C54—C53—N57—O58	−9.64 (14)
N2—C31—C32—C33	179.87 (10)	C52—C53—N57—O59	−10.38 (14)
C31—C32—C33—C34	−0.14 (16)	C54—C53—N57—O59	170.68 (9)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···O4	0.89 (1)	2.24 (1)	2.7041 (11)	112 (1)
N2—H2···O4i	0.89 (1)	2.26 (1)	3.0725 (11)	152 (1)
N5—H5···N3	0.88 (1)	2.11 (1)	2.6191 (11)	116 (1)
C55—H55···O4	0.95	2.33	2.9266 (12)	120
C32—H32···N51ii	0.95	2.47	3.3000 (13)	146

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2⋯O4	0.89 (1)	2.24 (1)	2.7041 (11)	112 (1)
N2—H2⋯O4i	0.89 (1)	2.26 (1)	3.0725 (11)	152 (1)
N5—H5⋯N3	0.88 (1)	2.11 (1)	2.6191 (11)	116 (1)
C55—H55⋯O4	0.95	2.33	2.9266 (12)	120
C32—H32⋯N51ii	0.95	2.47	3.3000 (13)	146

Symmetry codes: (i) ; (ii) .