Glyoxal 2-nitro­phenyl­hydrazone: a hydrogen-bonded chain of R22(12) and R44(24) rings

Wardell, J.L.; Low, J.N.; Glidewell, C.

doi:10.1107/S1600536806016047

organic compounds

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Volume 62| Part 6| June 2006| Pages o2204-o2206

https://doi.org/10.1107/S1600536806016047

Glyoxal 2-nitrophenylhydrazone: a hydrogen-bonded chain of R₂²(12) and R₄⁴(24) rings

James L. Wardell,^a John N. Low ^b and Christopher Glidewell ^c ^*

^aInstituto de Química, Departamento de Química Inorgânica, Universidade Federal do Rio de Janeiro, 21945-970 Rio de Janeiro, RJ, Brazil, ^bDepartment of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen AB24 3UE, Scotland, and ^cSchool of Chemistry, University of St Andrews, Fife KY16 9ST, Scotland
^*Correspondence e-mail: cg@st-andrews.ac.uk

(Received 28 April 2006; accepted 1 May 2006; online 10 May 2006)

Molecules of the title compound, C₈H₇N₃O₃, are effectively planar and are linked into chains of edge-fused R₂²(12) and R₄⁴(24) rings by a combination of N—H⋯O and C—H⋯O hydrogen bonds.

Comment

We report here the molecular and supramolecular structure of the title compound, (I), which completes the series of isomeric glyoxal nitrophenylhydrazones (I)–(III). These three isomers prove to adopt wholly different supramolecular structures. In isomer (II), the molecules are linked into simple C(6) (Bernstein et al., 1995 ) chains by a single N—H⋯O hydrogen bond (Low et al., 2006 ), while in isomer (III), the molecules are linked by N—H⋯O hydrogen bonds to form triply intertwined helices, which are themselves linked by C—H⋯O hydrogen bonds into a three-dimensional channel structure enclosing two types of channel (Glidewell et al., 2005 ).

We have now taken the opportunity to determine the supramolecular structure of compound (I). This isomer forms crystals of rather poor quality, which are subject to non-merohedral twinning. Accordingly, the quality of the structure determination is not high, but the essential features of the supramolecular aggregation are beyond doubt.

The molecules of isomer (I) (Fig. 1) are almost planar, as shown by the key torsion angles (Table 1). There is clear bond fixation in the exocyclic portion of the molecule, and the exocyclic bond angles at C1 and C2 indicate that the short intramolecular H11⋯O21 contact (Table 2) is repulsive in nature.

Two hydrogen bonds (Table 2) link the molecules into a chain of edge-fused centrosymmetric rings running parallel to the [130] direction and generated by inversion. There are R₂²(12) rings centred at ( $[{1\over 2}]$ n, −1 + $[{3\over 2}]$ n, $[{1\over 2}]$ ) (n = zero or integer) and R₄⁴(24) rings centred at ( $[{1\over 4}]$ + $[{1\over 2}]$ n, − $[{1\over 4}]$ + $[{3\over 2}]$ n, $[{1\over 2}]$ ) (n = zero or integer) (Fig. 2). Two chains of this type, related to one another by the action of the twofold rotation axes, pass through each unit cell, but there are no direction-specific interactions between the chains.

We also note here that not only are the supramolecular structures of the isomers (I)–(III) wholly distinct, but they also crystallize in three different space groups (C2/c, Cc and I4₁/a, respectively), with markedly different unit-cell dimensions, having Z = 8, 4, and 16, respectively.

Figure 1
The molecular structure of compound (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 chain of edge-fused R₂²(12) and R₄⁴(24) rings along [130]. For the sake of clarity, H atoms not involved in the motifs shown have been omitted. Atoms marked with an asterisk (*), a hash (#), a dollar sign ($), an ampersand (&) or an `at' sign (@) are at the symmetry positions (1 − x, 1 − y, 1 − z), ( $[{1\over 2}]$ + x, $[{3\over 2}]$ + y, z), (− $[{1\over 2}]$ + x, − $[{3\over 2}]$ + y, z), ( $[{3\over 2}]$ − x, $[{5\over 2}]$ − y, 1 − z) and ( $[{1\over 2}]$ − x, − $[{1\over 2}]$ − y, 1 − z), respectively.

Experimental

Compound (I) was prepared by heating under reflux for 1 h a solution of glyoxal (1 mmol as a 40% aqueous solution) and 2-nitrophenylhydrazine (1 mmol) in methanol (40 ml). The mixture was then cooled to ambient temperature and the solvent was removed under reduced pressure. The residue was recrystallized from ethanol to yield crystals of (I) suitable for single-crystal X-ray diffraction (m.p. 442–444 K).

Crystal data

C₈H₇N₃O₃
M_r = 193.17
Monoclinic, C 2/c
a = 18.670 (4) Å
b = 3.7723 (4) Å
c = 23.896 (5) Å
β = 96.429 (6)°
V = 1672.4 (5) Å³
Z = 8
D_x = 1.534 Mg m⁻³
Mo Kα radiation
μ = 0.12 mm⁻¹
T = 120 (2) K
Needle, orange
0.34 × 0.05 × 0.02 mm

Data collection

Bruker Nonius KappaCCD area-detector diffractometer
φ and ω scans
Absorption correction: multi-scan (SADABS; Sheldrick, 2003 ) T_min = 0.971, T_max = 0.998
6609 measured reflections
1903 independent reflections
975 reflections with I > 2σ(I)
R_int = 0.101
θ_max = 27.6°

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.090
wR(F²) = 0.268
S = 1.09
1903 reflections
128 parameters
H-atom parameters constrained
w = 1/[σ²(F_o²) + (0.1249P)² + 0.4829P] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max < 0.001
Δρ_max = 0.31 e Å⁻³
Δρ_min = −0.30 e Å⁻³

Table 1
Selected geometric parameters (Å, °)

C1—N11	1.382 (5)
N11—N12	1.347 (5)
N12—C11	1.285 (5)
C11—C12	1.447 (6)
C12—O11	1.215 (5)

C2—C1—N11	123.3 (4)
C6—C1—N11	119.9 (4)
C1—C2—N2	122.5 (4)
C3—C2—N2	116.7 (4)

C2—C1—N11—N12	177.4 (4)
C1—N11—N12—C11	−174.3 (4)
N11—N12—C11—C12	177.7 (3)
N12—C11—C12—O11	−172.8 (4)
C1—C2—N2—O21	−7.7 (6)

Table 2
Parameters (Å, °) for hydrogen bonds and short intramolecular contacts

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N11—H11⋯O21	0.88	2.01	2.629 (5)	126
N11—H11⋯O21ⁱ	0.88	2.50	3.327 (5)	157
C4—H4⋯O11ⁱⁱ	0.95	2.50	3.298 (5)	141
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) $[x+{\script{1\over 2}}, y+{\script{3\over 2}}, z]$ .

All H atoms were located in a difference map and then treated as riding atoms, with C—H = 0.95 Å and N—H = 0.88 Å, and with U_iso(H) = 1.2U_eq(C,N). The TwinRotMat option in PLATON (Spek, 2003 ) indicated non-merohedral twinning, and the twin refinement gave twin fractions of 0.302 (5) and 0.698 (5).

Data collection: COLLECT (Nonius, 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/S1600536806016047/lh2061sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536806016047/lh2061Isup2.hkl

Computing details top

Data collection: COLLECT (Nonius, 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).

Glyoxal 2-nitrophenylhydrazone top

Crystal data top

C₈H₇N₃O₃	F(000) = 800
M_r = 193.17	D_x = 1.534 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 1760 reflections
a = 18.670 (4) Å	θ = 2.9–27.5°
b = 3.7723 (4) Å	µ = 0.12 mm⁻¹
c = 23.896 (5) Å	T = 120 K
β = 96.429 (6)°	Needle, orange
V = 1672.4 (5) Å³	0.34 × 0.05 × 0.02 mm
Z = 8

Data collection top

Bruker Nonius KappaCCD area-detector diffractometer	1903 independent reflections
Radiation source: Bruker-Nonius FR591 rotating anode	975 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.101
Detector resolution: 9.091 pixels mm^-1	θ_max = 27.6°, θ_min = 3.4°
φ and ω scans	h = −24→24
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	k = −4→4
T_min = 0.971, T_max = 0.998	l = −24→30
6609 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)] = 0.090	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.268	H-atom parameters constrained
S = 1.09	w = 1/[σ²(F_o²) + (0.1249P)² + 0.4829P] where P = (F_o² + 2F_c²)/3
1903 reflections	(Δ/σ)_max < 0.001
128 parameters	Δρ_max = 0.31 e Å⁻³
0 restraints	Δρ_min = −0.30 e Å⁻³

Special details top

Experimental. IR (KBr disk, ν, cm^-1): 3294, 2832, 1687, 1611, 1584, 1558, 1493, 1426, 1370, 1341, 1302, 1271, 1223, 1156, 1119, 1075,1037, 997, 898, 860, 785, 744, 690, 651, 614, 491.

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

	x	y	z	U_iso*/U_eq
C1	0.5988 (2)	0.9186 (11)	0.61085 (19)	0.0248 (10)
N11	0.53270 (19)	0.7496 (9)	0.60542 (16)	0.0305 (9)
N12	0.49995 (19)	0.6830 (9)	0.65175 (15)	0.0266 (9)
C11	0.4415 (2)	0.5000 (11)	0.6465 (2)	0.0301 (11)
C12	0.4100 (2)	0.4244 (11)	0.6978 (2)	0.0278 (11)
O11	0.35891 (17)	0.2276 (8)	0.70018 (14)	0.0366 (9)
C2	0.6383 (2)	0.9861 (11)	0.56497 (19)	0.0275 (11)
N2	0.6123 (2)	0.8881 (10)	0.50804 (17)	0.0343 (10)
O21	0.55688 (17)	0.7048 (9)	0.49938 (14)	0.0388 (9)
O22	0.6451 (2)	0.9858 (10)	0.46949 (16)	0.0572 (12)
C3	0.7059 (2)	1.1489 (12)	0.5732 (2)	0.0326 (12)
C4	0.7350 (2)	1.2471 (12)	0.6258 (2)	0.0322 (12)
C5	0.6964 (2)	1.1903 (11)	0.6707 (2)	0.0315 (11)
C6	0.6299 (2)	1.0281 (11)	0.6637 (2)	0.0289 (11)
H11	0.5122	0.6861	0.5720	0.037*
H11A	0.4202	0.4188	0.6109	0.036*
H12	0.4304	0.5350	0.7316	0.033*
H3	0.7318	1.1915	0.5419	0.039*
H4	0.7814	1.3534	0.6314	0.039*
H5	0.7159	1.2642	0.7073	0.038*
H6	0.6047	0.9902	0.6955	0.035*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.028 (2)	0.022 (2)	0.024 (3)	0.0001 (18)	0.001 (2)	0.003 (2)
N11	0.032 (2)	0.041 (2)	0.019 (2)	−0.0040 (18)	0.0035 (16)	0.0004 (18)
N12	0.031 (2)	0.033 (2)	0.016 (2)	0.0025 (17)	0.0025 (16)	0.0015 (17)
C11	0.032 (2)	0.031 (2)	0.028 (3)	−0.003 (2)	0.004 (2)	0.001 (2)
C12	0.029 (2)	0.033 (3)	0.022 (3)	−0.001 (2)	0.004 (2)	0.002 (2)
O11	0.0372 (19)	0.047 (2)	0.026 (2)	−0.0079 (17)	0.0051 (15)	0.0017 (15)
C2	0.036 (2)	0.031 (2)	0.015 (3)	−0.004 (2)	0.002 (2)	−0.0004 (19)
N2	0.038 (2)	0.047 (2)	0.018 (2)	−0.007 (2)	0.0057 (18)	−0.0010 (19)
O21	0.0367 (18)	0.059 (2)	0.0205 (19)	−0.0192 (17)	0.0019 (14)	−0.0055 (16)
O22	0.059 (2)	0.089 (3)	0.026 (2)	−0.035 (2)	0.0144 (19)	−0.004 (2)
C3	0.037 (3)	0.039 (2)	0.022 (3)	−0.010 (2)	0.004 (2)	0.001 (2)
C4	0.031 (2)	0.036 (3)	0.029 (3)	−0.009 (2)	−0.001 (2)	0.000 (2)
C5	0.036 (3)	0.029 (2)	0.027 (3)	0.002 (2)	−0.003 (2)	−0.003 (2)
C6	0.038 (3)	0.031 (2)	0.018 (3)	0.003 (2)	0.003 (2)	0.000 (2)

Geometric parameters (Å, º) top

C1—N11	1.382 (5)	C2—N2	1.440 (6)
C1—C6	1.391 (6)	N2—O22	1.219 (5)
C1—C2	1.411 (6)	N2—O21	1.242 (5)
N11—N12	1.347 (5)	C3—C4	1.364 (7)
N11—H11	0.88	C3—H3	0.95
N12—C11	1.285 (5)	C4—C5	1.375 (6)
C11—C12	1.447 (6)	C4—H4	0.95
C11—H11A	0.95	C5—C6	1.378 (6)
C12—O11	1.215 (5)	C5—H5	0.95
C12—H12	0.95	C6—H6	0.95
C2—C3	1.398 (6)

C2—C1—N11	123.3 (4)	O22—N2—O21	121.5 (4)
C6—C1—N11	119.9 (4)	O22—N2—C2	119.4 (4)
C6—C1—C2	116.8 (4)	O21—N2—C2	119.1 (4)
N12—N11—C1	119.4 (4)	C4—C3—C2	120.6 (4)
N12—N11—H11	120.3	C4—C3—H3	119.7
C1—N11—H11	120.3	C2—C3—H3	119.7
C11—N12—N11	118.6 (4)	C3—C4—C5	119.2 (4)
N12—C11—C12	116.4 (4)	C3—C4—H4	120.4
N12—C11—H11A	121.8	C5—C4—H4	120.4
C12—C11—H11A	121.8	C4—C5—C6	121.2 (5)
O11—C12—C11	123.7 (4)	C4—C5—H5	119.4
O11—C12—H12	118.1	C6—C5—H5	119.4
C11—C12—H12	118.1	C5—C6—C1	121.4 (4)
C3—C2—C1	120.8 (4)	C5—C6—H6	119.3
C1—C2—N2	122.5 (4)	C1—C6—H6	119.3
C3—C2—N2	116.7 (4)

C6—C1—N11—N12	−2.0 (6)	C1—C2—N2—O22	172.4 (4)
C2—C1—N11—N12	177.4 (4)	C3—C2—N2—O21	171.3 (4)
C1—N11—N12—C11	−174.3 (4)	C1—C2—N2—O21	−7.7 (6)
N11—N12—C11—C12	177.7 (3)	C1—C2—C3—C4	−0.3 (7)
N12—C11—C12—O11	−172.8 (4)	N2—C2—C3—C4	−179.3 (4)
N11—C1—C2—C3	−178.1 (4)	C2—C3—C4—C5	−1.2 (7)
C6—C1—C2—C3	1.3 (6)	C3—C4—C5—C6	1.7 (7)
N11—C1—C2—N2	0.9 (7)	C4—C5—C6—C1	−0.7 (7)
C6—C1—C2—N2	−179.8 (4)	N11—C1—C6—C5	178.6 (4)
C3—C2—N2—O22	−8.6 (6)	C2—C1—C6—C5	−0.8 (6)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N11—H11···O21	0.88	2.01	2.629 (5)	126
N11—H11···O21ⁱ	0.88	2.50	3.327 (5)	157
C4—H4···O11ⁱⁱ	0.95	2.50	3.298 (5)	141

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

Acknowledgements

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

References

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Volume 62| Part 6| June 2006| Pages o2204-o2206

https://doi.org/10.1107/S1600536806016047

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