5-Chloro-2-nitro­benzaldehyde isonicotinoylhydrazone: a three-dimensional framework built from N—H⋯N and C—H⋯O hydrogen bonds

Wardell, S.M.S.V.; Souza, M.V.N. de; Wardell, J.L.; Low, J.N.; Glidewell, C.

doi:10.1107/S1600536806026420

organic compounds

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ISSN: 2056-9890

Volume 62| Part 8| August 2006| Pages o3361-o3363

https://doi.org/10.1107/S1600536806026420

5-Chloro-2-nitrobenzaldehyde isonicotinoylhydrazone: a three-dimensional framework built from N—H⋯N and C—H⋯O hydrogen bonds

Solange M. S. V. Wardell,^a Marcus V. N. de Souza,^a James L. Wardell,^b John N. Low ^c and Christopher Glidewell ^d ^*

^aInstituto de Tecnologia em Fármacos, Far-Manguinhos, FIOCRUZ, 21041-250 Rio de Janeiro, RJ, Brazil, ^bInstituto de Química, Departamento de Química Inorgânica, Universidade Federal do Rio de Janeiro, CP 68563, 21945-970 Rio de Janeiro, RJ, Brazil, ^cDepartment of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen AB24 3UE, Scotland, and ^dSchool of Chemistry, University of St Andrews, Fife KY16 9ST, Scotland
^*Correspondence e-mail: cg@st-andrews.ac.uk

(Received 7 July 2006; accepted 7 July 2006; online 14 July 2006)

In the title compound, C₁₃H₉ClN₄O₃, the molecules are linked into a three-dimensional framework by one N—H⋯N hydrogen bond and three C—H⋯O hydrogen bonds.

Comment

We report here the molecular and supramolecular structure of the title compound, (I) (Fig. 1), originally synthesized as a potential antimycobacterial agent (Junior et al., 2005 ).

The coordination of the hydrazine atom N1 is planar and the central spacer unit between C1 and C21 is nearly planar, as shown by the leading torsion angles (Table 1); however, the two rings are significantly twisted out of this plane, although the two rings remain nearly parallel.

The molecules of (I) are linked by a combination of N—H⋯N and C—H⋯O hydrogen bonds (Table 2) into a three-dimensional framework structure, whose formation is readily analysed in terms of a number of very simple one-dimensional substructures, each formed by the action of a single hydrogen bond.

Amino atom N1 in the molecule at (x, y, z) acts as hydrogen-bond donor to pyridyl atom N4 in the molecule at (−x, − $[{1\over 2}]$ + y, $[{3\over 2}]$ − z), so forming a C(7) (Bernstein et al., 1995 ) chain running parallel to the [010] direction and generated by the 2₁ screw axis along (0, y, $[{3\over 4}]$ ) (Fig. 2). Atoms C3 and C24 in the molecule at (x, y, z) act as hydrogen-bond donors, respectively, to carbonyl atom O7 in the molecule at (x, $[{3\over 2}]$ − y, $[{1\over 2}]$ + z), and nitro atom O221 in the molecule at (x, $[{1\over 2}]$ − y, − $[{1\over 2}]$ + z), so forming two distinct C(6) chains running parallel to the [001] direction and generated respectively by the c-glide planes at y = 0.75 (Fig. 3) and y = 0.25 (Fig. 4). Finally, atom C5 in the molecule at (x, y, z) acts as hydrogen-bond donor to nitro atom O222 in the molecule at (−1 + x, 1 + y, z), so generating by translation a C(12) chain running parallel to the [1 $[\overline{1}]$ 0] direction (Fig. 5).

The combination of the [010], [001] and [1 $[\overline{1}]$ 0] chains generates a single three-dimensional framework structure: it is notable that all three O atoms act as hydrogen-bond acceptors.

Figure 1
The molecular structure of (I)

, showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level.

Figure 2
Part of the crystal structure of compound (I)

, showing the formation of a C(7) chain along [010] built from N—H⋯N hydrogen bonds. For the sake of clarity, H atoms bonded to C atoms have been omitted. Atoms marked with an asterisk (*) or a hash (#) are at the symmetry positions (−x, − $[{1\over 2}]$ + y, $[{3\over 2}]$ − z) and (−x, $[{1\over 2}]$ + y, $[{3\over 2}]$ − z), respectively.

Figure 3
Part of the crystal structure of compound (I)

, showing the formation of a C(6) chain along [001] built from C—H⋯O(carbonyl) hydrogen bonds. For the sake of clarity, H atoms not involved in the motif shown have been omitted. Atoms marked with an asterisk (*) or a hash (#) are at the symmetry positions (x, $[{3\over 2}]$ − y, $[{1\over 2}]$ + z) and (x, $[{3\over 2}]$ − y, − $[{1\over 2}]$ + z), respectively.

Figure 4
Part of the crystal structure of compound (I)

, showing the formation of a C(6) chain along [001] built from C—H⋯O(nitro) hydrogen bonds. For the sake of clarity, H atoms not involved in the motif shown have been omitted. Atoms marked with an asterisk (*) or a hash (#) are at the symmetry positions (x, $[{1\over 2}]$ − y, − $[{1\over 2}]$ + z) and (x, $[{1\over 2}]$ − y, $[{1\over 2}]$ + z), respectively.

Figure 5
Part of the crystal structure of compound (I)

, showing the formation of a C(12) chain along [1 $[\overline{1}]$ 0] built from C—H⋯O(nitro) hydrogen bonds. For the sake of clarity, H atoms not involved in the motif shown have been omitted. Atoms marked with an asterisk (*) or a hash (#) are at the symmetry positions (−1 + x, 1 + y, z) and (1 + x, −1 + y, z), respectively.

Experimental

Crystals of the title compound were prepared according to a published procedure (Junior et al., 2005).

Crystal data

C₁₃H₉ClN₄O₃
M_r = 304.69
Monoclinic, P 2₁ /c
a = 8.0597 (2) Å
b = 10.4797 (4) Å
c = 15.4798 (6) Å
β = 97.383 (2)°
V = 1296.63 (8) Å³
Z = 4
D_x = 1.561 Mg m⁻³
Mo Kα radiation
μ = 0.31 mm⁻¹
T = 120 (2) K
Lath, colourless
0.34 × 0.16 × 0.08 mm

Data collection

Bruker–Nonius KappaCCD diffractometer
φ and ω scans
Absorption correction: multi-scan (SADABS; Sheldrick, 2003 ) T_min = 0.916, T_max = 0.976
17385 measured reflections
2980 independent reflections
2132 reflections with I > 2σ(I)
R_int = 0.053
θ_max = 27.5°

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.040
wR(F²) = 0.143
S = 1.09
2980 reflections
190 parameters
H-atom parameters constrained
w = 1/[σ²(F_o²) + (0.0817P)² + 0.135P] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max < 0.001
Δρ_max = 0.36 e Å⁻³
Δρ_min = −0.36 e Å⁻³

Table 1
Selected torsion angles (°)

C2—C1—C7—N1	24.3 (3)
C1—C7—N1—N2	−174.60 (17)
C7—N1—N2—C27	175.55 (18)
N1—N2—C27—C21	179.18 (16)
N2—C27—C21—C22	163.1 (2)
C21—C22—N22—O221	−29.5 (3)

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯N4ⁱ	0.88	2.14	3.002 (3)	168
C3—H3⋯O7ⁱⁱ	0.95	2.46	3.371 (3)	161
C5—H5⋯O222ⁱⁱⁱ	0.95	2.35	3.175 (3)	145
C24—H24⋯O221^iv	0.95	2.47	3.327 (3)	151
Symmetry codes: (i) $[-x, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (ii) $[x, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]$ ; (iii) x-1, y+1, z; (iv) $[x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

All H atoms were located in difference maps, and then treated as riding atoms, with C—H = 0.95 Å, N—H = 0.88 Å and U_iso(H) = 1.2U_eq(C,N).

Data collection: COLLECT (Hooft, 1999 ); cell refinement: DENZO (Otwinowski & Minor, 1997 ) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: OSCAIL (McArdle, 2003 ) and SHELXS97 (Sheldrick, 1997 ); program(s) used to refine structure: OSCAIL and SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003 ); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536806026420/lh2127sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536806026420/lh2127Isup2.hkl

Computing details top

Data collection: COLLECT (Hooft, 1999); cell refinement: DENZO (Otwinowski & Minor, 1997) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: OSCAIL (McArdle, 2003) and SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: OSCAIL and SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).

5-Chloro-2-nitrobenzaldehyde isonicotinoylhydrazone top

Crystal data top

C₁₃H₉ClN₄O₃	F(000) = 624
M_r = 304.69	D_x = 1.561 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 2980 reflections
a = 8.0597 (2) Å	θ = 2.4–27.5°
b = 10.4797 (4) Å	µ = 0.31 mm⁻¹
c = 15.4798 (6) Å	T = 120 K
β = 97.383 (2)°	Lath, colourless
V = 1296.63 (8) Å³	0.34 × 0.16 × 0.08 mm
Z = 4

Data collection top

Bruker–Nonius KappaCCD diffractometer	2980 independent reflections
Radiation source: Bruker-Nonius FR591 rotating anode	2132 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.053
Detector resolution: 9.091 pixels mm^-1	θ_max = 27.5°, θ_min = 2.4°
φ and ω scans	h = −10→10
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	k = −12→13
T_min = 0.916, T_max = 0.976	l = −20→20
17385 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)] = 0.040	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.143	H-atom parameters constrained
S = 1.09	w = 1/[σ²(F_o²) + (0.0817P)² + 0.135P] where P = (F_o² + 2F_c²)/3
2980 reflections	(Δ/σ)_max < 0.001
190 parameters	Δρ_max = 0.36 e Å⁻³
0 restraints	Δρ_min = −0.36 e Å⁻³

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
C1	0.0301 (3)	0.7986 (2)	0.63712 (13)	0.0170 (5)
C2	0.0839 (3)	0.7718 (2)	0.72369 (13)	0.0182 (5)
C3	0.0234 (3)	0.8436 (2)	0.78804 (14)	0.0201 (5)
N4	−0.0852 (2)	0.93930 (19)	0.77059 (12)	0.0212 (4)
C5	−0.1344 (3)	0.9650 (2)	0.68648 (15)	0.0237 (5)
C6	−0.0799 (3)	0.8991 (2)	0.61819 (14)	0.0206 (5)
C7	0.0889 (3)	0.7284 (2)	0.56203 (13)	0.0188 (5)
O7	0.0865 (2)	0.77907 (16)	0.49088 (10)	0.0298 (4)
N1	0.1468 (2)	0.60745 (16)	0.57975 (11)	0.0179 (4)
N2	0.2145 (2)	0.54538 (17)	0.51433 (11)	0.0186 (4)
C27	0.2790 (2)	0.4353 (2)	0.53226 (13)	0.0184 (5)
C21	0.3495 (2)	0.3683 (2)	0.46136 (13)	0.0162 (4)
C22	0.4603 (3)	0.2650 (2)	0.47262 (13)	0.0174 (5)
N22	0.5337 (2)	0.22436 (19)	0.56006 (12)	0.0222 (4)
O221	0.55542 (19)	0.30530 (16)	0.61789 (10)	0.0272 (4)
O222	0.5726 (2)	0.11140 (16)	0.57015 (11)	0.0324 (4)
C23	0.5128 (3)	0.1994 (2)	0.40315 (14)	0.0200 (5)
C24	0.4612 (3)	0.2393 (2)	0.31871 (14)	0.0208 (5)
C25	0.3551 (2)	0.3436 (2)	0.30634 (13)	0.0192 (5)
Cl25	0.28646 (7)	0.39720 (6)	0.20175 (3)	0.0280 (2)
C26	0.2974 (3)	0.4059 (2)	0.37533 (13)	0.0178 (5)
H2	0.1616	0.7048	0.7389	0.022*
H3	0.0609	0.8239	0.8472	0.024*
H5	−0.2116	1.0328	0.6729	0.028*
H6	−0.1171	0.9223	0.5596	0.025*
H1	0.1352	0.5678	0.6287	0.022*
H27	0.2814	0.3985	0.5885	0.022*
H23	0.5839	0.1272	0.4135	0.024*
H24	0.4976	0.1964	0.2705	0.025*
H26	0.2214	0.4750	0.3643	0.021*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0200 (10)	0.0147 (11)	0.0167 (11)	−0.0042 (9)	0.0039 (8)	−0.0017 (8)
C2	0.0241 (11)	0.0135 (11)	0.0172 (11)	−0.0003 (9)	0.0025 (9)	0.0003 (9)
C3	0.0263 (11)	0.0186 (12)	0.0152 (10)	−0.0041 (10)	0.0017 (9)	0.0000 (9)
N4	0.0221 (9)	0.0224 (10)	0.0190 (10)	−0.0006 (8)	0.0022 (7)	−0.0066 (8)
C5	0.0239 (11)	0.0231 (13)	0.0227 (12)	0.0051 (10)	−0.0028 (9)	−0.0062 (10)
C6	0.0226 (11)	0.0205 (12)	0.0173 (11)	−0.0010 (9)	−0.0025 (9)	−0.0027 (9)
C7	0.0217 (11)	0.0186 (12)	0.0157 (11)	−0.0025 (9)	0.0011 (8)	−0.0007 (9)
O7	0.0481 (11)	0.0256 (9)	0.0169 (8)	0.0077 (8)	0.0085 (7)	0.0031 (7)
N1	0.0230 (9)	0.0185 (10)	0.0133 (9)	0.0005 (8)	0.0058 (7)	−0.0006 (7)
N2	0.0208 (9)	0.0190 (10)	0.0165 (9)	−0.0006 (8)	0.0049 (7)	−0.0043 (8)
C27	0.0205 (11)	0.0206 (12)	0.0146 (10)	−0.0028 (9)	0.0035 (8)	−0.0010 (9)
C21	0.0167 (10)	0.0162 (11)	0.0158 (10)	−0.0027 (9)	0.0023 (8)	−0.0009 (8)
C22	0.0185 (10)	0.0184 (11)	0.0150 (10)	−0.0031 (9)	0.0009 (8)	0.0015 (9)
N22	0.0203 (9)	0.0286 (12)	0.0180 (9)	0.0000 (8)	0.0034 (8)	0.0035 (9)
O221	0.0276 (9)	0.0361 (10)	0.0174 (8)	−0.0046 (7)	0.0013 (7)	−0.0014 (7)
O222	0.0414 (10)	0.0277 (10)	0.0281 (10)	0.0133 (8)	0.0039 (8)	0.0102 (7)
C23	0.0193 (11)	0.0182 (12)	0.0227 (12)	0.0018 (9)	0.0034 (9)	−0.0017 (9)
C24	0.0226 (11)	0.0234 (12)	0.0170 (11)	0.0015 (9)	0.0052 (9)	−0.0031 (9)
C25	0.0198 (11)	0.0225 (12)	0.0150 (10)	−0.0019 (9)	0.0012 (8)	0.0015 (9)
Cl25	0.0349 (3)	0.0344 (4)	0.0150 (3)	0.0088 (3)	0.0045 (2)	0.0037 (2)
C26	0.0180 (10)	0.0170 (12)	0.0183 (11)	0.0012 (9)	0.0023 (8)	0.0006 (9)

Geometric parameters (Å, º) top

C1—C2	1.383 (3)	C27—C21	1.477 (3)
C1—C6	1.384 (3)	C27—H27	0.95
C1—C7	1.503 (3)	C21—C22	1.400 (3)
C2—C3	1.386 (3)	C21—C26	1.400 (3)
C2—H2	0.95	C22—C23	1.387 (3)
C3—N4	1.336 (3)	C22—N22	1.469 (3)
C3—H3	0.95	N22—O221	1.229 (2)
N4—C5	1.339 (3)	N22—O222	1.229 (2)
C5—C6	1.380 (3)	C23—C24	1.385 (3)
C5—H5	0.95	C23—H23	0.95
C6—H6	0.95	C24—C25	1.386 (3)
C7—O7	1.221 (3)	C24—H24	0.95
C7—N1	1.366 (3)	C25—C26	1.382 (3)
N1—N2	1.374 (2)	C25—Cl25	1.736 (2)
N1—H1	0.88	C26—H26	0.95
N2—C27	1.281 (3)

C2—C1—C6	118.19 (19)	N2—C27—H27	121.6
C2—C1—C7	123.99 (19)	C21—C27—H27	121.6
C6—C1—C7	117.77 (19)	C22—C21—C26	116.40 (19)
C1—C2—C3	119.4 (2)	C22—C21—C27	125.13 (19)
C1—C2—H2	120.3	C26—C21—C27	118.42 (18)
C3—C2—H2	120.3	C23—C22—C21	122.67 (19)
N4—C3—C2	123.0 (2)	C23—C22—N22	116.36 (18)
N4—C3—H3	118.5	C21—C22—N22	120.91 (18)
C2—C3—H3	118.5	O221—N22—O222	124.18 (19)
C3—N4—C5	116.87 (18)	O221—N22—C22	118.29 (18)
N4—C5—C6	124.1 (2)	O222—N22—C22	117.52 (19)
N4—C5—H5	117.9	C24—C23—C22	119.8 (2)
C6—C5—H5	117.9	C24—C23—H23	120.1
C5—C6—C1	118.4 (2)	C22—C23—H23	120.1
C5—C6—H6	120.8	C23—C24—C25	118.30 (19)
C1—C6—H6	120.8	C23—C24—H24	120.9
O7—C7—N1	123.4 (2)	C25—C24—H24	120.9
O7—C7—C1	121.0 (2)	C26—C25—C24	121.9 (2)
N1—C7—C1	115.62 (18)	C26—C25—Cl25	117.99 (17)
C7—N1—N2	116.68 (17)	C24—C25—Cl25	120.07 (16)
C7—N1—H1	122.6	C25—C26—C21	120.81 (19)
N2—N1—H1	120.5	C25—C26—H26	119.6
C27—N2—N1	117.08 (18)	C21—C26—H26	119.6
N2—C27—C21	116.84 (19)

C6—C1—C2—C3	1.6 (3)	C26—C21—C22—C23	−2.1 (3)
C7—C1—C2—C3	179.1 (2)	C27—C21—C22—C23	175.0 (2)
C1—C2—C3—N4	−0.3 (3)	C26—C21—C22—N22	174.93 (18)
C2—C3—N4—C5	−0.5 (3)	C27—C21—C22—N22	−8.0 (3)
C3—N4—C5—C6	0.0 (3)	C23—C22—N22—O221	147.72 (19)
N4—C5—C6—C1	1.2 (3)	C21—C22—N22—O221	−29.5 (3)
C2—C1—C6—C5	−2.0 (3)	C23—C22—N22—O222	−30.9 (3)
C7—C1—C6—C5	−179.66 (19)	C21—C22—N22—O222	151.9 (2)
C2—C1—C7—O7	−154.4 (2)	C21—C22—C23—C24	3.0 (3)
C6—C1—C7—O7	23.1 (3)	N22—C22—C23—C24	−174.15 (19)
C2—C1—C7—N1	24.3 (3)	C22—C23—C24—C25	−1.2 (3)
C1—C7—N1—N2	−174.60 (17)	C23—C24—C25—C26	−1.5 (3)
C7—N1—N2—C27	175.55 (18)	C23—C24—C25—Cl25	−179.84 (16)
N1—N2—C27—C21	179.18 (16)	C24—C25—C26—C21	2.4 (3)
N2—C27—C21—C22	163.1 (2)	Cl25—C25—C26—C21	−179.24 (16)
C6—C1—C7—N1	−158.12 (18)	C22—C21—C26—C25	−0.6 (3)
O7—C7—N1—N2	4.2 (3)	C27—C21—C26—C25	−177.83 (19)
N2—C27—C21—C26	−19.9 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···N4ⁱ	0.88	2.14	3.002 (3)	168
C3—H3···O7ⁱⁱ	0.95	2.46	3.371 (3)	161
C5—H5···O222ⁱⁱⁱ	0.95	2.35	3.175 (3)	145
C24—H24···O221^iv	0.95	2.47	3.327 (3)	151

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

Acknowledgements

X-ray data were collected at the EPSRC National Crystallography Service, University of Southampton, England. The authors thank the staff of the Service for all their help and advice. JLW thanks CNPq for financial support.

References

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