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organic compounds
Glyoxal 4-nitrophenylhydrazone: triple helices linked into a three-dimensional channel structure
aSchool of Chemistry, University of St Andrews, Fife KY16 9ST, Scotland, bDepartment of Chemistry, University of Aberdeen, Meston Walk, Old Aberdeen AB24 3UE, Scotland, and cInstituto 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
The molecules of the title compound, C8H7N3O3, which are nearly planar, are linked by an N—H⋯O hydrogen bond into helical chains, three of which are required to define the structure completely. These triply intertwined helices are linked by a C—H⋯O hydrogen bond into a three-dimensional framework enclosing two distinct types of channel, with average cross-sectional areas of 15.0 and 8.2 Å2.
Comment
The title compound, (I), was prepared as part of our continuing study of the supramolecular arrangements of N-(nitrophenyl)imide and -hydrazone derivatives.
The molecules of compound (I) (Fig. 1
) are almost planar, as shown by the leading torsion angles (Table 1
). The side chain between atoms N1 and O1 adopts a planar all-trans conformation, and the nitro group is nearly coplanar with the aryl ring. The bond distances in the 4-nitrophenylhydrazone fragment provide no evidence for the occurrence of the type of quinonoid bond fixation found in 4-nitroaniline (Tonogaki et al., 1993
), which is also typical of simple substituted 4-nitroanilines (Cannon et al., 2001
; Ferguson et al., 2001
; Glidewell et al., 2001
, 2002
, 2004
). There is strong bond fixation in the side chain, with very short N2—C11 and C12—O1 bonds, with no evidence for bond polarization in this fragment.
The supramolecular structure of (I) is three-dimensional and of considerable complexity, but it is constructed using only two hydrogen bonds, one each of the N—H⋯O and C—H⋯O types (Table 2
). The hydrazine atom N1 in the molecule at (x, y, z) acts as hydrogen-bond donor to aldehyde atom O1 in the molecule at (
− y,
+ x, z −
), while atom N1 at (
− y,
+ x, z −
) in turn acts as donor to atom O1 at (
− x, 1 − y, z −
), and thence via the molecule at (y −
,
− x, z −
) to that at (x, y, z − 3). In this way, a C(6) helical chain is formed running parallel to the [001] direction and generated by the 41 screw axis along (
,
, z). One complete turn of this helix spans three unit cells along [001], linking the molecule at (x, y, z) with those at (x, y, n + z) (n = positive or negative integer). Hence, completion of the structure requires three such helical chains, offset by unit translations along [001]. Thus, the effect of the N—H⋯O hydrogen bond is the generation of triply intertwined helices (Fig. 2
). There are no direction-specific interactions between the independent helices in each set of three helices.
The effect of the C—H⋯O hydrogen bond is to link the helices into a three-dimensional framework. Aldehyde atom C12 in the molecule at (x, y, z) acts as hydrogen-bond donor to nitro atom O41 in the molecule at (1 − x, 1 − y, 2 − z), so generating a centrosymmetric R22(22) motif centred at (,
, 1) (Fig. 3
). The two molecules in this motif form parts of helices along (
,
, z) and (
,
, −z), generated by 41 and 43 axes, respectively, and propagation of this dimer motif thus links the reference helix along (
,
, z) to the four adjacent helices along (
,
, −z), (
, 0, −z), (−
,
, −z) and (
, 1, −z), all of which are of opposite hand to the reference helix. In this way, the helices are linked into a three-dimensional framework (Fig. 4
), more strictly described as three interwoven frameworks.
Within the framework there are channels running parallel to the [001] direction and accounting in total for 340.1 Å3 per i.e. some 9.4% of the total volume. This volume is, in fact, partitioned between two types of channel, with four of each type per cell. The larger channels lie along the axes, with an average cross-sectional area of ca 15.0 Å2 and an average diameter of ca 4.4 Å, while the smaller channels lie along the 41 and 43 axes and have an average cross-sectional area of ca 8.2 Å2 and an average diameter of ca 3.2 Å. There is evidence for a very low population of water molecules, possibly disordered and/or mobile, within the larger channels, but no tractable of these guest molecules proved possible. It is not clear whether this residual water is a by-product of the preparation or whether it had been absorbed from the atmosphere after crystallization.
The larger channels in (I) are thus of very similar diameter to those found in piperazine–4,4′-sulfonyldiphenol (1/2) (Coupar et al., 1996
), where the channels of diameter 4.3 Å are entirely unoccupied. In the channel structures formed by N,N′-dithiobisphthalimide (Skakle et al., 2001
; Farrell et al., 2002
; Bowes, Ferguson, Glidewell, Lough et al., 2002
; Bowes, Ferguson, Glidewell, Low & Quesada, 2002
), the channels are a little larger, with average cross-sectional areas of ca 20.4 Å2 and average diameters of ca 5.1 Å. The channels in N,N′-dithiobisphthalimide are always occupied by guest molecules, but the behaviour of the guest can vary from full ordering, as for p-xylene, to intractable disorder of probably mobile molecules for guests such as dichloromethane or tetrahydrofuran.
![]() | Figure 1 The molecule of (I) ![]() |
![]() | Figure 2 A stereoview of part of the crystal structure of (I) ![]() ![]() ![]() |
![]() | Figure 3 Part of the crystal structure of (I) ![]() |
![]() | Figure 4 A space-filling projection, down [001], of part of the crystal structure of (I) ![]() |
Experimental
Compound (I) was prepared by heating under reflux for 1 h a solution of glyoxal (1 mmol as a 40% aqueous solution) and 4-nitrophenylhydrazine (1 mmol) in methanol (40 ml). The mixture was cooled to ambient temperature and the solvent removed under reduced pressure. The residue was crystallized from ethanol to yield crystals of (I)
suitable for single-crystal X-ray diffraction. IR (KBr disk, ν, cm−1): 3263–2850, 1698 (sh), 1686, 1677 (sh), 1538, 1504, 1331, 1272, 1131, 894, 839, 748, 690, 609, 489, 447.
Crystal data
|
Refinement
|
|
|
Crystals of compound (I) are tetragonal. The has a markedly tabular shape, with an axial c/a ratio of only 0.116. The I41/a was uniquely assigned from the and the origin was set to lie at an inversion centre. All H atoms were located from difference maps and then treated as riding atoms, with C—H distances of 0.95 Å and N—H distances of 0.88 Å, and with Uiso(H) = 1.2Ueq(C,N). Examination of the refined structure using PLATON (Spek, 2003
) revealed the presence of void spaces having a total volume of 340.1 Å3 per arranged into a series of channels running parallel to the [001] direction. There was a low residual electron density of 0.9 e Å−3 located on a
axis within the larger of the channels, which is most plausibly ascribed to a partial water molecule. When this density was assigned to an O atom and its site occupancy refined, with Uiso(O) fixed at 0.03 Å2, the occupancy refined to 0.0288 (15), corresponding in total to 0.115 of an O atom. In view of this, the SQUEEZE option in PLATON was applied, and the final utilized data so treated. The final Fo/Fc was produced with the CALC FCF option in PLATON, reporting both the original observed structure factors and calculated structure factors including the disordered solvent contribution.
Data collection: COLLECT (Hooft, 1999); cell 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
10.1107/S0108270105020834/sk1857sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S0108270105020834/sk1857Isup2.hkl
Compound (I) was prepared by heating under reflux for 1 h a solution of glyoxal (1 mmol as a 40% aqueous solution) and 4-nitrophenylhydrazine (1 mmol) in methanol (40 ml). The mixture was cooled to ambient temperature and the solvent removed under reduced pressure. The residue was crystallized from ethanol to yield crystals of (I) suitable for single-crystal X-ray diffraction. IR (KBr disk, ν, cm−1): 3263–2850, 1698 (sh), 1686, 1677 (sh), 1538, 1504, 1331, 1272, 1131, 894, 839, 748, 690, 609, 489, 447.
Crystals of compound (I) are tetragonal. The 4 axis within the larger of the channels, and most plausibly ascribed to a partial water molecule. When this density was assigned to an O atom and its site occupancy refined, with Uiso(O) fixed at 0.03, the occupancy refined to 0.0288 (15), corresponding in total to 0.115 of an O atom. In view of this, the SQUEEZE option in PLATON was applied, and the final utilized data so treated. The final Fo/Fc was produced with the CALC FCF option in PLATON, reporting both the original observed structure factors and calculated structure factors including the disordered solvent contribution.
has a markedly tabular shape, with an axial ratio c/a of only 0.116. The I41/a was uniquely assigned from the and the origin was set to lie at an inversion centre. All H atoms were located from difference maps and then treated as riding atoms, with C—H distances of 0.95 Å and N—H distances of 0.88 Å, and with Uiso(H) = 1.2Ueq(C,N). Examination of the refined structure using PLATON (Spek, 2003) revealed the presence of void spaces having a total volume of 340.1 Å3 per arranged into a series of channels running parallel to the [001] direction. There was a low residual electron density of 0.9 e Å−3 located on aData collection: COLLECT (Hooft, 1999); cell
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).C8H7N3O3 | Dx = 1.417 Mg m−3 |
Mr = 193.17 | Mo Kα radiation, λ = 0.71073 Å |
Tetragonal, I41/a | Cell parameters from 2066 reflections |
Hall symbol: -I 4ad | θ = 4.1–27.5° |
a = 31.4722 (12) Å | µ = 0.11 mm−1 |
c = 3.6560 (1) Å | T = 120 K |
V = 3621.3 (2) Å3 | Rod, red |
Z = 16 | 0.32 × 0.08 × 0.06 mm |
F(000) = 1600 |
Bruker Nonius KappaCCD area-detector diffractometer | 2066 independent reflections |
Radiation source: Bruker Nonius FR91 rotating anode | 1712 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.039 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.5°, θmin = 4.1° |
ϕ and ω scans | h = −27→28 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = 0→40 |
Tmin = 0.974, Tmax = 0.993 | l = 0→4 |
2068 measured reflections |
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)] = 0.037 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.098 | H-atom parameters constrained |
S = 1.06 | w = 1/[σ2(Fo2) + (0.0445P)2 + 2.7428P] where P = (Fo2 + 2Fc2)/3 |
2066 reflections | (Δ/σ)max = 0.001 |
127 parameters | Δρmax = 0.21 e Å−3 |
0 restraints | Δρmin = −0.21 e Å−3 |
C8H7N3O3 | Z = 16 |
Mr = 193.17 | Mo Kα radiation |
Tetragonal, I41/a | µ = 0.11 mm−1 |
a = 31.4722 (12) Å | T = 120 K |
c = 3.6560 (1) Å | 0.32 × 0.08 × 0.06 mm |
V = 3621.3 (2) Å3 |
Bruker Nonius KappaCCD area-detector diffractometer | 2066 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | 1712 reflections with I > 2σ(I) |
Tmin = 0.974, Tmax = 0.993 | Rint = 0.039 |
2068 measured reflections |
R[F2 > 2σ(F2)] = 0.037 | 0 restraints |
wR(F2) = 0.098 | H-atom parameters constrained |
S = 1.06 | Δρmax = 0.21 e Å−3 |
2066 reflections | Δρmin = −0.21 e Å−3 |
127 parameters |
x | y | z | Uiso*/Ueq | ||
O1 | 0.32156 (3) | 0.43155 (3) | 1.0674 (3) | 0.0292 (3) | |
O41 | 0.58550 (3) | 0.60724 (3) | 0.4461 (3) | 0.0293 (3) | |
O42 | 0.55171 (3) | 0.65953 (3) | 0.1969 (3) | 0.0356 (3) | |
N1 | 0.39639 (3) | 0.54756 (3) | 0.6609 (3) | 0.0184 (2) | |
N2 | 0.39389 (3) | 0.50918 (3) | 0.8129 (3) | 0.0186 (2) | |
N4 | 0.55227 (3) | 0.62552 (3) | 0.3606 (3) | 0.0219 (3) | |
C1 | 0.43568 (4) | 0.56610 (4) | 0.5942 (3) | 0.0165 (3) | |
C2 | 0.47373 (4) | 0.54547 (4) | 0.6818 (3) | 0.0175 (3) | |
C3 | 0.51203 (4) | 0.56520 (4) | 0.6087 (3) | 0.0183 (3) | |
C4 | 0.51188 (4) | 0.60533 (4) | 0.4491 (3) | 0.0178 (3) | |
C5 | 0.47447 (4) | 0.62627 (4) | 0.3621 (3) | 0.0186 (3) | |
C6 | 0.43627 (4) | 0.60645 (4) | 0.4337 (3) | 0.0179 (3) | |
C11 | 0.35626 (4) | 0.49273 (4) | 0.8496 (4) | 0.0200 (3) | |
C12 | 0.35452 (4) | 0.45120 (4) | 1.0175 (4) | 0.0216 (3) | |
H1 | 0.3730 | 0.5613 | 0.6022 | 0.022* | |
H2 | 0.4732 | 0.5181 | 0.7909 | 0.021* | |
H3 | 0.5381 | 0.5515 | 0.6665 | 0.022* | |
H5 | 0.4751 | 0.6538 | 0.2551 | 0.022* | |
H6 | 0.4103 | 0.6202 | 0.3739 | 0.022* | |
H11 | 0.3314 | 0.5071 | 0.7707 | 0.024* | |
H12 | 0.3804 | 0.4385 | 1.0933 | 0.026* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0262 (5) | 0.0234 (5) | 0.0378 (6) | −0.0071 (4) | 0.0028 (4) | 0.0058 (4) |
O41 | 0.0168 (5) | 0.0312 (5) | 0.0399 (6) | 0.0000 (4) | −0.0006 (4) | 0.0023 (5) |
O42 | 0.0287 (6) | 0.0286 (5) | 0.0494 (7) | −0.0059 (4) | 0.0046 (5) | 0.0163 (5) |
N1 | 0.0149 (5) | 0.0159 (5) | 0.0243 (6) | 0.0005 (4) | −0.0013 (4) | 0.0045 (4) |
N2 | 0.0204 (5) | 0.0165 (5) | 0.0188 (5) | −0.0011 (4) | 0.0005 (4) | 0.0013 (4) |
N4 | 0.0206 (6) | 0.0220 (6) | 0.0230 (6) | −0.0027 (4) | 0.0021 (4) | −0.0004 (5) |
C1 | 0.0173 (6) | 0.0169 (6) | 0.0153 (6) | −0.0012 (5) | 0.0003 (5) | −0.0013 (5) |
C2 | 0.0204 (6) | 0.0150 (6) | 0.0172 (6) | 0.0003 (5) | −0.0012 (5) | 0.0014 (5) |
C3 | 0.0175 (6) | 0.0191 (6) | 0.0184 (6) | 0.0019 (5) | −0.0020 (5) | −0.0010 (5) |
C4 | 0.0164 (6) | 0.0199 (6) | 0.0170 (6) | −0.0033 (5) | 0.0021 (5) | −0.0012 (5) |
C5 | 0.0227 (6) | 0.0153 (6) | 0.0178 (6) | −0.0003 (5) | 0.0009 (5) | 0.0021 (5) |
C6 | 0.0180 (6) | 0.0175 (6) | 0.0184 (6) | 0.0031 (5) | −0.0010 (5) | 0.0008 (5) |
C11 | 0.0179 (6) | 0.0196 (6) | 0.0226 (7) | −0.0005 (5) | −0.0003 (5) | 0.0012 (5) |
C12 | 0.0222 (6) | 0.0201 (6) | 0.0224 (6) | −0.0011 (5) | 0.0010 (5) | 0.0010 (5) |
C1—N1 | 1.3889 (16) | C2—H2 | 0.95 |
C1—C6 | 1.3991 (17) | C3—C4 | 1.3913 (17) |
C1—C2 | 1.3993 (17) | C3—H3 | 0.95 |
N1—N2 | 1.3319 (14) | C4—C5 | 1.3861 (17) |
N1—H1 | 0.88 | C4—N4 | 1.4575 (16) |
N2—C11 | 1.2995 (16) | N4—O42 | 1.2264 (14) |
C11—C12 | 1.4451 (18) | N4—O41 | 1.2338 (14) |
C11—H11 | 0.95 | C5—C6 | 1.3795 (17) |
C12—O1 | 1.2214 (15) | C5—H5 | 0.95 |
C12—H12 | 0.95 | C6—H6 | 0.95 |
C2—C3 | 1.3821 (17) | ||
N1—C1—C6 | 117.83 (11) | C2—C3—C4 | 119.08 (11) |
N1—C1—C2 | 121.80 (11) | C2—C3—H3 | 120.5 |
C6—C1—C2 | 120.37 (11) | C4—C3—H3 | 120.5 |
N2—N1—C1 | 120.45 (10) | C5—C4—C3 | 122.05 (11) |
N2—N1—H1 | 119.8 | C5—C4—N4 | 118.86 (11) |
C1—N1—H1 | 119.8 | C3—C4—N4 | 119.07 (11) |
C11—N2—N1 | 117.27 (10) | O42—N4—O41 | 122.87 (11) |
N2—C11—C12 | 116.02 (11) | O42—N4—C4 | 118.44 (11) |
N2—C11—H11 | 122.0 | O41—N4—C4 | 118.66 (11) |
C12—C11—H11 | 122.0 | C6—C5—C4 | 118.79 (11) |
O1—C12—C11 | 123.61 (12) | C6—C5—H5 | 120.6 |
O1—C12—H12 | 118.2 | C4—C5—H5 | 120.6 |
C11—C12—H12 | 118.2 | C5—C6—C1 | 120.12 (11) |
C3—C2—C1 | 119.58 (11) | C5—C6—H6 | 119.9 |
C3—C2—H2 | 120.2 | C1—C6—H6 | 119.9 |
C1—C2—H2 | 120.2 | ||
C6—C1—N1—N2 | 179.96 (11) | C3—C4—N4—O41 | −3.42 (18) |
C2—C1—N1—N2 | 0.20 (18) | C3—C4—N4—O42 | 174.96 (12) |
C1—N1—N2—C11 | −176.38 (11) | C5—C4—N4—O41 | 178.35 (12) |
N1—N2—C11—C12 | −179.62 (11) | C5—C4—N4—O42 | −3.27 (18) |
N2—C11—C12—O1 | −179.34 (13) | C3—C4—C5—C6 | −0.53 (19) |
N1—C1—C2—C3 | 179.73 (11) | N4—C4—C5—C6 | 177.64 (11) |
C6—C1—C2—C3 | −0.02 (19) | C4—C5—C6—C1 | 0.55 (19) |
C1—C2—C3—C4 | 0.05 (19) | N1—C1—C6—C5 | 179.95 (11) |
C2—C3—C4—C5 | 0.23 (19) | C2—C1—C6—C5 | −0.29 (19) |
C2—C3—C4—N4 | −177.94 (11) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1i | 0.88 | 2.03 | 2.8574 (14) | 155 |
C12—H12···O41ii | 0.95 | 2.46 | 3.2851 (17) | 145 |
Symmetry codes: (i) −y+3/4, x+1/4, z−3/4; (ii) −x+1, −y+1, −z+2. |
Experimental details
Crystal data | |
Chemical formula | C8H7N3O3 |
Mr | 193.17 |
Crystal system, space group | Tetragonal, I41/a |
Temperature (K) | 120 |
a, c (Å) | 31.4722 (12), 3.6560 (1) |
V (Å3) | 3621.3 (2) |
Z | 16 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.32 × 0.08 × 0.06 |
Data collection | |
Diffractometer | Bruker Nonius KappaCCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2003) |
Tmin, Tmax | 0.974, 0.993 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2068, 2066, 1712 |
Rint | 0.039 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.037, 0.098, 1.06 |
No. of reflections | 2066 |
No. of parameters | 127 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.21, −0.21 |
Computer programs: COLLECT (Hooft, 1999), DENZO (Otwinowski & Minor, 1997) and COLLECT, DENZO and COLLECT, OSCAIL (McArdle, 2003) and SHELXS97 (Sheldrick, 1997), OSCAIL and SHELXL97 (Sheldrick, 1997), PLATON (Spek, 2003), SHELXL97 and PRPKAPPA (Ferguson, 1999).
C1—N1 | 1.3889 (16) | C11—C12 | 1.4451 (18) |
N1—N2 | 1.3319 (14) | C12—O1 | 1.2214 (15) |
N2—C11 | 1.2995 (16) | ||
C2—C1—N1—N2 | 0.20 (18) | C3—C4—N4—O41 | −3.42 (18) |
C1—N1—N2—C11 | −176.38 (11) | C3—C4—N4—O42 | 174.96 (12) |
N1—N2—C11—C12 | −179.62 (11) | C5—C4—N4—O41 | 178.35 (12) |
N2—C11—C12—O1 | −179.34 (13) | C5—C4—N4—O42 | −3.27 (18) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1i | 0.88 | 2.03 | 2.8574 (14) | 155 |
C12—H12···O41ii | 0.95 | 2.46 | 3.2851 (17) | 145 |
Symmetry codes: (i) −y+3/4, x+1/4, z−3/4; (ii) −x+1, −y+1, −z+2. |
Acknowledgements
The X-ray data were collected at the EPSRC X-ray Crystallographic Service, University of Southampton; the authors thank the staff for all their help and advice. JLW thanks CNPq and FAPERJ for financial support.
References
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The title compound, (I), was prepared as part of our continuing study of the supramolecular arrangements of N-(nitrophenyl)imide and -hydrazone derivatives.
The molecules of compound (I) (Fig. 1) are almost planar, as shown by the leading torsion angles (Table 1). The side chain between atoms N1 and O1 adopts a planar all-trans conformation, and the nitro group is nearly coplanar with the aryl ring. The bond distances in the 4-nitrophenylhydrazone fragment provide no evidence for the occurrence of the type of quinonoid bond fixation found in 4-nitroaniline (Tonogaki et al., 1993), which is also typical of simple substituted 4-nitroanilines (Cannon et al., 2001; Ferguson et al., 2001; Glidewell et al., 2001, 2002, 2004). There is strong bond-fixation in the side chain, with very short N2—C11 and C12—O1 bonds, with no evidence for bond polarization in this fragment.
The supramolecular structure of (I) is three-dimensional and of considerable complexity, but it is constructed using only two hydrogen bonds, one each of N—H···O and C—H···O types (Table 2). The hydrazino atom N1 in the molecule at (x, y, z) acts as hydrogen-bond donor to aldehyde atom O1 in the molecule at (3/4 − y, 1/4 + x, z − 3/4), while atom N1 at (3/4 − y, 1/4 + x, z − 3/4) in turn acts as donor to atom O1 at (1/2 − x, 1 − y, z − 3/2), and thence via the molecule at (y − 1/4, 3/4 − x, z − 9/4) to that at (x, y, z − 3). In this way, a C(6) helical chain is formed running parallel to the [001] direction and generated by the 41 screw axis along (1/4, 1/2, z). One complete turn of this helix spans three unit cells along [001], linking the molecule at (x, y, z) with those at (x, y, n + z) (n = positive or negative integer). Hence, completion of the structure requires three such helical chains, offset by unit translations along [001]. Thus, the effect of the N—H···O hydrogen bond is the generation of triply intertwined helices (Fig. 2). There are no direction-specific interactions between the independent helices in each set of three helices.
The effect of the C—H···O hydrogen bond is to link the helices into a three-dimensional framework. The aldehyde atom C12 in the molecule at (x, y, z) acts as hydrogen-bond donor to nitro atom O41 in the molecule at (1 − x, 1 − y, 2 − z), so generating a centrosymmetric R22(22) motif centred at (1/2, 1/2, 1) (Fig. 3). The two molecules in this motif form parts of helices along (1/4, 1/2, z) and (3/4, 1/2, −z), generated by 41 and 43 axes, respectively, and propagation of this dimer motif thus links the reference helix along (1/4, 1/2, z) to the four adjacent helices along (3/4, 1/2, −z), (1/4, 0, −z), (−1/4, 1/2, −z) and (1/4, 1, −z), all of which are of opposite hand to the reference helix. In this way, the helices are linked into a three-dimensional framework (Fig. 4), more strictly described as three interwoven frameworks.
Within the framework there are channels running parallel to the [001] direction and accounting in total for 340.1 Å3 per unit cell, i.e. some 9.4% of the total volume. This volume is, in fact, partitioned between two types of channel, with four of each type per cell. The larger channels lie along the 4 axes, with an average cross-sectional area of ca 15.0 Å2 and average diameter of ca 4.4 Å, while the smaller channels lie along the 41 and 43 axes and have an average cross-sectional area of ca 8.2 Å2 and an average diameter of ca 3.2 Å. There is evidence for a very low population of water molecules, possibly disordered and/or mobile, within the larger channels, but no tractable refinement of these guest molecules proved possible. It is not clear whether this residual water is a by-product of the preparation, or whether it had been absorbed from the atmosphere after crystallization.
The larger channels in (I) are thus of very similar diameter to those found in piperazine–4,4'-sulfonyldiphenol (1/2) (Coupar et al., 1996), where the channels of diameter 4.3 Å are entirely unoccupied. In the channel structures formed by N,N'-dithiobisphthalimide (Skakle et al., 2001; Farrell et al., 2002; Bowes, Ferguson, Glidewell, Lough et al., 2002; Bowes, Ferguson, Glidewell, Low & Quesada, 2002), the channels are a little larger, with average cross-sectional areas of ca 20.4 Å2 and average diameters of ca 5.1 Å. The channels in N,N'-dithiobisphthalimide are always occupied by guest molecules, but the behaviour of the guest can vary from full ordering, as for p-xylene, to intractable disorder of probably mobile molecules, for guests such as dichloromethane or tetrahydrofuran.