A hydrogen-bonded chain of edge-fused rings in 5-nitro­isatin

Glidewell, C.; Low, J.N.; Skakle, J.M.S.; Wardell, J.L.

doi:10.1107/S1600536806037627

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 62| Part 10| October 2006| Pages o4572-o4574

https://doi.org/10.1107/S1600536806037627

A hydrogen-bonded chain of edge-fused rings in 5-nitroisatin

Christopher Glidewell,^a ^* John N. Low,^b Janet M. S. Skakle ^c and James L. Wardell ^d

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

(Received 15 September 2006; accepted 15 September 2006; online 22 September 2006)

The title compound, C₈H₄N₂O₄, crystallizes with Z′ = 2. The molecules are linked by a combination of N—H⋯O and C—H⋯O hydrogen bonds into chains of edge-fused R₄⁴(16) and R₄⁴(26) rings.

Comment

We report here the molecular and supramolecular structure of 5-nitroisatin (I), whose behaviour is briefly compared with that of 5-iodoisatin (II), which we reported recently (Garden et al., 2006 ).

Compound (I) crystallizes with Z′ = 2 in the space group P $[\overline{1}]$ (Fig. 1), and the two molecules have very similar dimensions. Both exhibit long bonds, C11—C12 and C21—C22, between the two carbonyl groups (Table 1), as typically found in isatins (Palenik et al., 1990 ; Garden et al., 2006), while the dihedral angles between the nitro groups and the adjacent aryl rings are 10.4 (2)° in molecule 1 and 7.4 (2)° in molecule 2.

The molecules are linked into chains of edge-fused rings by a combination of N—H⋯O and C—H⋯O hydrogen bonds (Table 2). The N—H⋯O hydrogen bonds link groups of four molecules, two of each type, into centrosymmetric R₄⁴(16) rings (Bernstein et al., 1995 ) (Fig. 2), and these tetramolecular aggregates are linked by a single C—H⋯O hydrogen bond into a chain of edge-fused rings along [001], with R₄⁴(16) rings centred at (½, ½, n + ½) (n = zero or integer) alternating with R₄⁴(26) rings centred at (½, ½, n) (n = zero or integer) (Fig. 3).

These chain of rings are weakly linked by a sheared, parallel (type III, Allen et al., 1998 ) carbonyl–carbonyl interaction. Atom O11 in the molecule at (x, y, z), which lies in the chain along (½, ½, z), makes a short dipolar contact with atom C22 in the molecule at (−x, 1 − y, 1 − z), which is part of the chain along (0, ½, z); the key dimensions are O11⋯·C22ⁱ = 2.835 (4) Å, O11⋯O22ⁱ = 3.266 (3) Å, C11—O11⋯C22ⁱ = 145.8 (2)° and C11—O11⋯O22ⁱ = 163.9 (2)° [symmetry code: (i) −x, 1 − y, 1 − z]. Propagation by inversion of this interaction links the chains into sheets parallel to (010).

In 5-iodoisatin, (II), by contrast, which crystallizes with Z′ = 1, the molecules are linked by a combination of one N—H⋯O hydrogen bond, one C—H⋯O hydrogen bond and one iodo–carbonyl interaction into sheets containing alternating columns of R₂²(9) and R₄³(16) rings, while in isatin itself, the molecules are linked by paired N—H⋯O hydrogen bonds into R₂²(8) dimers which are themselves linked into sheets by aromatic π–π stacking interactions (Garden et al., 2006).

Figure 1
The two independent molecules of compound (I)

, showing the atom-labelling scheme and the hydrogen-bond (dashed line) within the selected asymmetric unit. Displacement ellipsoids are drawn at the 30% probability level.

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

, showing the formation of a centrosymmetric tetramolecular aggregate built from N—H⋯O hydrogen bonds. For the sake of clarity, H atoms bonded to C atoms have been omitted. Atoms marked with an asterisk (*) are at the symmetry position (1 − x, 1 − y, 1 − z), and hydrogen bonds are shown as dashed lines

Figure 3
A stereoscopic view of part of the crystal structure of compound (I)

, showing the formation of a chain of edge-fused R₄⁴(16) and R₄⁴(26) rings along [001]. Hydrogen bonds are shown as dashed lines, and for the sake of clarity, H atoms not involved in the motifs shown have been omitted.

Experimental

A commercial sample (Aldrich) of 5-nitroisatin was recrystallized from ethanol.

Crystal data

C₈H₄N₂O₄
M_r = 192.13
Triclinic, $[P \overline 1]$
a = 5.5595 (6) Å
b = 12.0772 (13) Å
c = 12.2795 (14) Å
α = 87.322 (3)°
β = 87.355 (3)°
γ = 83.049 (3)°
V = 816.85 (16) Å³
Z = 4
D_x = 1.562 Mg m⁻³
Mo Kα radiation
μ = 0.13 mm⁻¹
T = 291 (2) K
Thick plate, colourless
0.28 × 0.12 × 0.07 mm

Data collection

Bruker SMART 1000 CCD area-detector diffractometer
φ and ω scans
Absorption correction: multi-scan (SADABS; Bruker, 2000 ) T_min = 0.954, T_max = 0.991
6130 measured reflections
4096 independent reflections
1331 reflections with I > 2σ(I)
R_int = 0.040
θ_max = 28.5°

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.061
wR(F²) = 0.109
S = 1.00
4096 reflections
253 parameters
H-atom parameters constrained
w = 1/[σ²(F_o²) + (0.0209P)²] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max < 0.001
Δρ_max = 0.47 e Å⁻³
Δρ_min = −0.17 e Å⁻³

Table 1
Selected geometric parameters (Å, °)

C11—C12	1.558 (4)
C21—C22	1.552 (4)

C14—C15—N15—O151	−11.5 (5)
C14—C15—N15—O152	169.8 (3)
C24—C25—N25—O251	8.0 (6)
C24—C25—N25—O252	−173.5 (4)

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N11—H11⋯O21	0.86	2.11	2.888 (3)	151
N21—H21⋯O11ⁱ	0.86	2.03	2.875 (3)	168
C27—H27⋯O152ⁱⁱ	0.93	2.43	3.272 (4)	151
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) x, y, z-1.

All H atoms were located in difference maps and then treated as riding atoms, with C—H = 0.93 Å, N—H = 0.86 Å and U_iso(H) = 1.2U_eq(C,N).

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997 ); program(s) used to refine structure: 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/S1600536806037627/gg2007sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536806037627/gg2007Isup2.hkl

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 and PRPKAPPA (Ferguson, 1999).

5-nitroisatin top

Crystal data top

C₈H₄N₂O₄	Z = 4
M_r = 192.13	F(000) = 392
Triclinic, P1	D_x = 1.562 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 5.5595 (6) Å	Cell parameters from 4096 reflections
b = 12.0772 (13) Å	θ = 2.3–28.5°
c = 12.2795 (14) Å	µ = 0.13 mm⁻¹
α = 87.322 (3)°	T = 291 K
β = 87.355 (3)°	Plate, colourless
γ = 83.049 (3)°	0.28 × 0.12 × 0.07 mm
V = 816.85 (16) Å³

Data collection top

Bruker SMART 1000 CCD area-detector diffractometer	4096 independent reflections
Radiation source: fine-focus sealed X-ray tube	1331 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.040
φ and ω scans	θ_max = 28.5°, θ_min = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2000)	h = −7→7
T_min = 0.954, T_max = 0.991	k = −9→16
6130 measured reflections	l = −16→16

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)] = 0.061	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.109	H-atom parameters constrained
S = 1.00	w = 1/[σ²(F_o²) + (0.0209P)²] where P = (F_o² + 2F_c²)/3
4096 reflections	(Δ/σ)_max < 0.001
253 parameters	Δρ_max = 0.47 e Å⁻³
0 restraints	Δρ_min = −0.17 e Å⁻³

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

	x	y	z	U_iso*/U_eq
N11	0.3270 (4)	0.52765 (19)	0.6854 (2)	0.0572 (7)
C11	0.5305 (5)	0.4543 (3)	0.6734 (3)	0.0540 (9)
O11	0.5875 (3)	0.39001 (17)	0.60197 (17)	0.0665 (6)
C12	0.6815 (6)	0.4705 (3)	0.7740 (3)	0.0601 (9)
O12	0.8707 (4)	0.41752 (17)	0.79350 (18)	0.0800 (7)
C13	0.5357 (5)	0.5591 (2)	0.8353 (2)	0.0502 (8)
C14	0.5719 (5)	0.6104 (3)	0.9294 (2)	0.0596 (9)
C15	0.3956 (6)	0.6924 (3)	0.9633 (3)	0.0604 (9)
N15	0.4302 (7)	0.7516 (3)	1.0631 (3)	0.0870 (10)
O151	0.5978 (6)	0.7118 (2)	1.1205 (2)	0.1182 (11)
O152	0.2903 (5)	0.8343 (2)	1.0838 (2)	0.1104 (10)
C16	0.1877 (6)	0.7245 (3)	0.9071 (3)	0.0639 (9)
C17	0.1489 (5)	0.6716 (2)	0.8130 (3)	0.0625 (9)
C18	0.3247 (5)	0.5898 (2)	0.7790 (2)	0.0504 (8)
N21	−0.0737 (4)	0.71675 (19)	0.4343 (2)	0.0621 (8)
C21	−0.1946 (6)	0.6865 (3)	0.5280 (3)	0.0621 (9)
O21	−0.1308 (4)	0.61082 (18)	0.59215 (18)	0.0763 (7)
C22	−0.4299 (6)	0.7701 (3)	0.5318 (3)	0.0698 (10)
O22	−0.5799 (5)	0.7723 (2)	0.6023 (2)	0.1049 (9)
C23	−0.4190 (5)	0.8428 (2)	0.4307 (2)	0.0549 (8)
C24	−0.5712 (6)	0.9294 (3)	0.3880 (3)	0.0731 (10)
C25	−0.5048 (7)	0.9777 (3)	0.2914 (4)	0.0791 (11)
N25	−0.6688 (8)	1.0689 (3)	0.2399 (4)	0.1154 (15)
O251	−0.8492 (6)	1.1031 (3)	0.2982 (3)	0.1604 (17)
O252	−0.6190 (6)	1.1048 (3)	0.1501 (3)	0.1631 (17)
C26	−0.2895 (7)	0.9444 (3)	0.2369 (3)	0.0812 (11)
C27	−0.1306 (6)	0.8572 (3)	0.2793 (3)	0.0706 (10)
C28	−0.2009 (5)	0.8062 (2)	0.3768 (3)	0.0557 (8)
H11	0.2117	0.5352	0.6403	0.069*
H14	0.7106	0.5903	0.9688	0.072*
H16	0.0742	0.7815	0.9323	0.077*
H17	0.0088	0.6909	0.7744	0.075*
H21	0.0656	0.6843	0.4129	0.075*
H24	−0.7167	0.9545	0.4243	0.088*
H26	−0.2496	0.9804	0.1711	0.097*
H27	0.0169	0.8341	0.2437	0.085*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N11	0.0482 (17)	0.0578 (17)	0.0646 (19)	0.0037 (13)	−0.0135 (13)	−0.0073 (14)
C11	0.053 (2)	0.046 (2)	0.064 (2)	−0.0084 (16)	−0.0050 (18)	−0.0027 (17)
O11	0.0613 (15)	0.0629 (15)	0.0755 (17)	0.0028 (11)	−0.0079 (12)	−0.0256 (12)
C12	0.048 (2)	0.061 (2)	0.071 (2)	−0.0081 (17)	−0.0072 (18)	0.0146 (18)
O12	0.0617 (15)	0.0758 (16)	0.0988 (19)	0.0089 (12)	−0.0162 (13)	0.0053 (13)
C13	0.050 (2)	0.049 (2)	0.051 (2)	−0.0031 (15)	−0.0012 (17)	−0.0018 (16)
C14	0.053 (2)	0.067 (2)	0.059 (2)	−0.0110 (17)	−0.0023 (18)	0.0049 (18)
C15	0.070 (2)	0.065 (2)	0.051 (2)	−0.0243 (19)	0.0047 (19)	−0.0083 (18)
N15	0.098 (3)	0.092 (3)	0.077 (3)	−0.032 (2)	0.007 (2)	−0.019 (2)
O151	0.131 (3)	0.134 (3)	0.099 (2)	−0.029 (2)	−0.035 (2)	−0.0329 (18)
O152	0.118 (2)	0.116 (2)	0.101 (2)	−0.0201 (18)	0.0192 (18)	−0.0535 (18)
C16	0.065 (2)	0.055 (2)	0.071 (3)	−0.0070 (17)	0.008 (2)	−0.0085 (18)
C17	0.055 (2)	0.062 (2)	0.068 (3)	0.0018 (17)	−0.0009 (18)	−0.0056 (18)
C18	0.050 (2)	0.055 (2)	0.046 (2)	−0.0057 (16)	0.0025 (16)	−0.0014 (16)
N21	0.0507 (17)	0.0605 (18)	0.072 (2)	0.0061 (13)	−0.0037 (15)	−0.0008 (15)
C21	0.057 (2)	0.061 (2)	0.070 (3)	−0.0070 (18)	−0.0160 (19)	−0.0118 (19)
O21	0.0721 (16)	0.0747 (17)	0.0816 (18)	−0.0048 (12)	−0.0245 (13)	0.0130 (13)
C22	0.058 (2)	0.084 (3)	0.070 (3)	−0.0134 (19)	0.0164 (19)	−0.038 (2)
O22	0.115 (2)	0.102 (2)	0.097 (2)	−0.0168 (16)	0.0296 (17)	−0.0162 (15)
C23	0.057 (2)	0.049 (2)	0.058 (2)	−0.0044 (16)	−0.0006 (17)	−0.0028 (17)
C24	0.056 (2)	0.051 (2)	0.112 (3)	−0.0058 (18)	−0.003 (2)	−0.008 (2)
C25	0.075 (3)	0.054 (2)	0.110 (4)	−0.009 (2)	−0.033 (2)	0.009 (2)
N25	0.098 (3)	0.071 (3)	0.180 (5)	−0.027 (2)	−0.047 (3)	0.040 (3)
O251	0.098 (3)	0.097 (3)	0.278 (5)	0.005 (2)	−0.036 (3)	0.057 (3)
O252	0.188 (4)	0.120 (3)	0.188 (4)	−0.049 (2)	−0.085 (3)	0.085 (3)
C26	0.107 (3)	0.066 (3)	0.076 (3)	−0.032 (2)	−0.018 (2)	0.013 (2)
C27	0.068 (2)	0.070 (3)	0.075 (3)	−0.0117 (19)	0.007 (2)	−0.008 (2)
C28	0.055 (2)	0.053 (2)	0.061 (2)	−0.0076 (17)	−0.0075 (18)	−0.0078 (17)

Geometric parameters (Å, º) top

N11—C11	1.357 (3)	N21—C21	1.363 (4)
N11—C18	1.401 (3)	N21—C28	1.399 (3)
N11—H11	0.86	N21—H21	0.86
C11—O11	1.205 (3)	C21—O21	1.209 (3)
C11—C12	1.558 (4)	C21—C22	1.552 (4)
C12—O12	1.191 (3)	C22—O22	1.173 (3)
C12—C13	1.476 (4)	C22—C23	1.489 (4)
C13—C14	1.371 (4)	C23—C24	1.363 (4)
C13—C18	1.392 (4)	C23—C28	1.388 (4)
C14—C15	1.371 (4)	C24—C25	1.353 (4)
C14—H14	0.93	C24—H24	0.93
C15—C16	1.380 (4)	C25—C26	1.370 (4)
C15—N15	1.479 (4)	C25—N25	1.479 (4)
N15—O152	1.218 (3)	N25—O252	1.200 (4)
N15—O151	1.232 (3)	N25—O251	1.245 (4)
C16—C17	1.384 (4)	C26—C27	1.388 (4)
C16—H16	0.93	C26—H26	0.93
C17—C18	1.368 (3)	C27—C28	1.383 (4)
C17—H17	0.93	C27—H27	0.93

C11—N11—C18	112.8 (3)	C21—N21—C28	112.6 (3)
C11—N11—H11	123.6	C21—N21—H21	123.7
C18—N11—H11	123.6	C28—N21—H21	123.7
O11—C11—N11	129.0 (3)	O21—C21—N21	127.0 (3)
O11—C11—C12	126.2 (3)	O21—C21—C22	128.7 (3)
N11—C11—C12	104.7 (3)	N21—C21—C22	104.3 (3)
O12—C12—C13	130.5 (3)	O22—C22—C23	129.2 (3)
O12—C12—C11	124.4 (3)	O22—C22—C21	124.8 (4)
C13—C12—C11	105.1 (2)	C23—C22—C21	106.0 (3)
C14—C13—C18	120.0 (3)	C24—C23—C28	120.7 (3)
C14—C13—C12	132.9 (3)	C24—C23—C22	133.6 (3)
C18—C13—C12	107.1 (3)	C28—C23—C22	105.7 (2)
C13—C14—C15	117.4 (3)	C25—C24—C23	118.2 (3)
C13—C14—H14	121.3	C25—C24—H24	120.9
C15—C14—H14	121.3	C23—C24—H24	120.9
C14—C15—C16	123.0 (3)	C24—C25—C26	122.4 (3)
C14—C15—N15	119.1 (3)	C24—C25—N25	120.0 (4)
C16—C15—N15	117.9 (3)	C26—C25—N25	117.5 (4)
O152—N15—O151	124.8 (4)	O252—N25—O251	125.8 (4)
O152—N15—C15	118.4 (4)	O252—N25—C25	119.7 (5)
O151—N15—C15	116.9 (4)	O251—N25—C25	114.4 (5)
C15—C16—C17	119.7 (3)	C25—C26—C27	120.4 (3)
C15—C16—H16	120.2	C25—C26—H26	119.8
C17—C16—H16	120.2	C27—C26—H26	119.8
C18—C17—C16	117.4 (3)	C28—C27—C26	117.2 (3)
C18—C17—H17	121.3	C28—C27—H27	121.4
C16—C17—H17	121.3	C26—C27—H27	121.4
C17—C18—C13	122.5 (3)	C27—C28—C23	121.1 (3)
C17—C18—N11	127.2 (3)	C27—C28—N21	127.5 (3)
C13—C18—N11	110.2 (3)	C23—C28—N21	111.4 (3)

C18—N11—C11—O11	−179.5 (3)	C28—N21—C21—O21	178.2 (3)
C18—N11—C11—C12	0.4 (3)	C28—N21—C21—C22	−1.2 (3)
O11—C11—C12—O12	−2.4 (5)	O21—C21—C22—O22	2.3 (6)
N11—C11—C12—O12	177.6 (3)	N21—C21—C22—O22	−178.4 (3)
O11—C11—C12—C13	179.2 (3)	O21—C21—C22—C23	−178.1 (3)
N11—C11—C12—C13	−0.8 (3)	N21—C21—C22—C23	1.3 (3)
O12—C12—C13—C14	2.4 (6)	O22—C22—C23—C24	−1.2 (7)
C11—C12—C13—C14	−179.4 (3)	C21—C22—C23—C24	179.1 (4)
O12—C12—C13—C18	−177.5 (3)	O22—C22—C23—C28	178.7 (4)
C11—C12—C13—C18	0.8 (3)	C21—C22—C23—C28	−0.9 (4)
C18—C13—C14—C15	−0.9 (4)	C28—C23—C24—C25	0.6 (5)
C12—C13—C14—C15	179.3 (3)	C22—C23—C24—C25	−179.4 (4)
C13—C14—C15—C16	−0.1 (5)	C23—C24—C25—C26	−1.4 (6)
C13—C14—C15—N15	−178.6 (3)	C23—C24—C25—N25	177.6 (3)
C14—C15—N15—O151	−11.5 (5)	C24—C25—N25—O251	8.0 (6)
C14—C15—N15—O152	169.8 (3)	C24—C25—N25—O252	−173.5 (4)
C16—C15—N15—O152	−8.7 (4)	C26—C25—N25—O252	5.5 (6)
C16—C15—N15—O151	169.9 (3)	C26—C25—N25—O251	−172.9 (4)
C14—C15—C16—C17	1.2 (5)	C24—C25—C26—C27	0.8 (6)
N15—C15—C16—C17	179.7 (3)	N25—C25—C26—C27	−178.2 (3)
C15—C16—C17—C18	−1.2 (4)	C25—C26—C27—C28	0.6 (5)
C16—C17—C18—C13	0.2 (4)	C26—C27—C28—C23	−1.4 (5)
C16—C17—C18—N11	−178.3 (3)	C26—C27—C28—N21	179.3 (3)
C14—C13—C18—C17	0.9 (4)	C24—C23—C28—C27	0.8 (5)
C12—C13—C18—C17	−179.3 (3)	C22—C23—C28—C27	−179.1 (3)
C14—C13—C18—N11	179.6 (2)	C24—C23—C28—N21	−179.8 (3)
C12—C13—C18—N11	−0.6 (3)	C22—C23—C28—N21	0.3 (4)
C11—N11—C18—C17	178.7 (3)	C21—N21—C28—C27	180.0 (3)
C11—N11—C18—C13	0.1 (3)	C21—N21—C28—C23	0.6 (4)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N11—H11···O21	0.86	2.11	2.888 (3)	151
N21—H21···O11ⁱ	0.86	2.03	2.875 (3)	168
C27—H27···O152ⁱⁱ	0.93	2.43	3.272 (4)	151

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

Acknowledgements

X-ray data were collected at the University of Aberdeen; the authors thank the University of Aberdeen for funding the purchase of the diffractometer. JLW thanks CNPq and FAPERJ for financial support.

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