Double anomeric effects and a hydrogen-bonded supra­molecular motif in N,N′-bis­(3-nitro­phen­yl)­methane­diamine

In the title compound, C₁₃H₁₂N₄O₄, the mol­ecule lies on a crystallographic twofold axis. Mol­ecules are linked into complex sheets parallel to (100) via one N—H...O and two C—H...O hydrogen bonds. Within the mol­ecule, the 3-nitroanilino fragment is essentially planar, and the C—N—C—N—C fragment assumes a nearly perpendicular/perpendicular conformation, with C—N—C—N torsion angles of 81.18 (18)°, which is controlled by a pair of adjacent anomeric inter­actions. The findings constitute the first demonstration of two anomeric effects existing in one N—C—N unit.

S1. Comment

The reactions (Michael et al., 1997; Layer, 1963) of aliphatic aldehydes with primary amines or ammonia may yield hemiaminals, some of which can be stabilized by electron-withdrawing substituent(s), such as a trichloromethyl group. However, those formed from aliphatic amines subsequently dehydrate to give imines. The imines formed from primary amines are prone to dimerization, polymerization or addition reactions with excess aniline (Michael et al., 1997; Layer, 1963; Zhang, Wang et al., 2007; Zhang, Qin et al., 2007).

Recently, we found that the condensation of formaldehyde with anilines carrying strong electron-withdrawing groups proceeded smoothly to afford N,N'-bisphenylmethanediamines (Kibayashi & Yamazaki, 2007). This suggests that the imines formed from primary amines carrying strong electron-withdrawing substituent(s) are prone to nucleophilic addition reactions with anilines. However, our interest here lies in exploring the anomeric effect(s) in the C—NH—CH₂—NH—C fragment of the title compound, (I).

The anomeric effect plays an important role in controlling the molecular conformation in systems containing geminal heteroatoms (Juaristi & Cuevas, 1992). The term `anomeric effect' generally refers to the preferred torsion angles between the R—X and C—Y bonds in the R—X—CH₂—Y—R' fragments. The conformations increase in energy in the sequence gauche, gauche (1) < anti, gauche (2) < anti, anti (3) (see scheme below). The torsion angle, bond-length variations and bond-angle variations in R—X—CH₂—Y—R' fragments have been rationalized both qualitatively (David et al., 1973; Pinto et al., 1985) and quantitatively (Wolfe et al., 1979) by a perturbational molecular orbital treatment that focuses on the stabilizing orbital interactions between the p-type nonbonding orbitals on X and Y, n(X) and n(Y), with the acceptor orbitals, σ^*(C—X) and σ^*(C—Y), respectively. Whereas both such interactions may operate in (1), symmetry considerations imply that only one such interaction, such as n(X) → σ^*(C—Y), is possible in (2), and neither interaction is possible in (3). These hyperconjugative interactions account for the existence of the anomeric effects.

If we concentrate on the anomeric effect in C—N—C—N—C fragments, crystallographic analyses have confirmed that each such unit adopts a nearly perpendicular, anti conformation (Scheme 1), where one C—N—C—N torsion angle is close to 90° and the other is close to 180°, and that there is only one n(N) → σ^*(C—N) interaction determining the conformation (Zhang, Wang et al., 2009; Zhang, Zhang et al., 2009; Kakanejadifard & Farnia, 1997). While the existence of this conformational effect in N—C—N systems has been widely accepted, the interesting conformational characteristics of the title compound have attracted our attention. We report here the results of our investigation of the anomeric effect and hydrogen-bonded supramolecular structure of (I) (Fig. 1).

The molecule of (I) lies on a crystallographic twofold axis. The 3-nitrophenylamine fragment is essentially planar. The nitro group may be slightly twisted out of the plane of the phenyl ring, but also exhibits significant thermal motion. Interestingly, unlike the reported C—N—C—N—C units with a nearly perpendicular, anti conformation (Zhang, Wang et al., 2009; Zhang, Wang et al., 2009; Kakanejadifard & Farnia, 1997), the C—N—C—N—C fragment here assumes a nearly perpendicular, perpendicular conformation (Fig. 1); the C5—N2—C7—N2ⁱ torsion angle and its symmetry-related counterpart [symmetry code: (i) -x, y, -z + 1/2] is 81.18 (18)°, thus allowing the N2 p-orbital to hyperconjugate with the C7—N2ⁱ σ^* antibonding orbital, with commensurate shortening of the C7—N2 bond. This conformation for the C5—N2—C7—N2ⁱ—C5ⁱ unit is very similar that found in the structures of xxxxx (**please give the full chemical names of the compounds being cited here. Also, the Hanson reference cannot be found at the cited journal/year/page. Please correct. **) (Hanson, 1980; Crisma et al., 2007; Mo et al., 2008). The marked torsion angle preference is just a striking expression of two anomeric effects acting in the N2—C7—N2ⁱ fragment. This can be further confirmed by some correlative geometric parameters (Table 1). In the NH—CH₂—CH₂—NH fragment of N-{2-[(4-nitrophenyl)amino]ethyl}acetamide, (II) (Wang et al., 2004), anomeric interactions are not possible and the N atoms have a similar chemical environment and identical hybridization (sp²) to those of atoms N2 and N2ⁱ of the title compound; in (II), the N—CH₂ bond lengths [1.456 (3) and 1.459 (3) Å] are consistent with the usual values for Nsp²—CH₂ bonds (1.452–1.459 Å; Yonkey et al., 2008; Walczak et al., 2008; Clegg et al., 1999). Thus, for comparison purposes, the N—CH₂ bonds in (II) are considered as following the Nsp²—CH₂ bond model, which does not exhibit anomeric effects. As shown in Table 1, the N2—C7 bond in (I) is much shorter than that for the model N—CH₂ bond. The N2—C7—N2ⁱ angle is also larger than the corresponding value found in a similar anomeric N—CH₂—N unit [112.6 (2)°; Zhang, Zhang et al., 2009]. Therefore, as indicators of the anomeric effects, the nearly perpendicular, perpendicular conformation, the shortening of the N2—C7 bond and the opening of the N2—C7—N2ⁱ angle all point to the conclusion that there are two weak anomeric effects in the same C5—N2—C7—N2ⁱ—C5ⁱ unit, which are best rationalized in terms of n(N2) → σ^*(C7—N2ⁱ) stabilizing interactions. These findings constituted the first demonstration of two anomeric interactions in the same N—C—N fragment.

The supramolecular structure of (I) exhibits some interesting features. The molecules are linked into sheets by two different types of weak hydrogen bonds, one of the N—H···O type and one of the C—H···O type (Table 2). However, the structure can be relatively easily analyzed in terms of a simple one-dimensional chain. In analyzing the chain, for the sake of simplicity, we shall omit any consideration of intermolecular C—H···O interactions involving C4—H4 bonds from the aromatic rings (Table 2), which do not influence the overall supramolecular structure; thus the chain involves only the N—H···O hydrogen bonds. The imine atom N2 at (x, y, z) acts as a hydrogen-bond donor to nitro atom O1 in the molecule at (x, -y + 1, z + 1/2), so generating by propagation along the c-glide plane at y = 1/2 a chain of molecules. This N—H···O interaction can be described by a graph-set motif of C(7) (Bernstein et al., 1995). The twofold symmetry of the molecule means that there is a second series of identical N—H···O interactions running in the opposite direction along the chain of molecules. Thus, the molecules are actually linked into ladders, or chains of rings, where the rings formed by the two N—H···O interactions between pairs of adjacent molecules are centrosymmetric and can be described by the R₂²(18) motif. These rings are centered at (0, 1/2, n/2) (n = zero or integer; Fig. 2). The ladders are laterally linked into a sheet by one type of weak C—H···O hydrogen bond (Table 2). Phenyl atom C6 in the molecule at (x, y, z) acts as a hydrogen-bonded donor to nitro atom O2 in the molecule at (-x, -y + 2, -z), so forming by inversion and the space-group symmetry a corrugated hydrogen-bonded sheet parallel to (100) (Fig. 2). Two such sheets pass through each unit cell in the domains 1/4 > x > -1/4 and 3/4 > x > 1/4, and there are no direction-specific interactions between adjacent sheets.

In conclusion, the crystal structure of (I) has permitted the demonstration for the first time of the existence of two anomeric effects in the C—N—C—N—C fragment, which are best rationalized in terms of n(N) → σ^*(C—N) stabilizing interactions, and that the supramolecular structure exhibits a complex two-dimensional framework formed via two independent weak N—H···O and C—H···O hydrogen bonds.

Related literature

For related literature, see: Bernstein et al. (1995); Clegg et al. (1999); Crisma et al. (2007); David et al. (1973); Hanson (1980); Juaristi & Cuevas (1992); Kakanejadifard & Farnia (1997); Kibayashi & Yamazaki (2007); Layer (1963); Michael et al. (1997); Mo et al. (2008); Pinto et al. (1985); Walczak et al. (2008); Wang et al. (2004); Wolfe et al. (1979); Yonkey et al. (2008); Zhang, Wang, Wang, j & Qu (2007); Zhang, Wang, Zhang & Li (2009); Zhang, Zhang, Zhang & Wang (2009).

S2. Experimental

Into a three-necked round-bottomed flask equipped with a stirrer were introduced 3-nitroaniline (0.1 mol, 13.9 g), aqueous formaldehyde (0.05 mol, 37% 4.0 g) and ethanol (95%, 25 ml). The resulted mixture was refluxed with stirring for ca 10 min, and then the solution was cooled to room temperature. The precipitate was filtered off and washed with cool ethanol (95%). Crystals were obtained by slow cooling of a hot dimethylformamide solution of (I) to ambient temperature. ¹H NMR (dimethyl sulfoxide, 400 MHz) of (I): δ 7.45–7.07 (m, 8H), 7.16 (t, J = 5.6 Hz, 2H), 4.59 (t, J = 5.6 Hz, 2H).

S3. Refinement

All H atoms were placed in idealized positions and allowed to ride on the respective parent atom with C—H distances of 0.93 (aromatic) or 0.97 Å (CH₂) and an N—H distance of 0.86 Å and with U_iso(H) set at 1.2U_eq(C,N). The O atoms of the NO₂ groups have elongated atomic displacement ellipsoids, but a disorder model was not employed, because the ellipsoids of the disordered atoms remained elongated when such a model was considered.

Computing details

Data collection: SMART (Bruker, 1997); cell refinement: SAINT (Bruker, 1997); data reduction: SAINT (Bruker, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures

Fig. 1. The molecular structure of (I), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level. [Symmetry code: (i) -x, y, -z + 1/2.]

Fig. 2. Part of the crystal structure of (I), showing the formation of a C(7) chain of R2^2(18) rings parallel to (001). For the sake of clarity, H atoms not involved in the motif shown have been omitted. Intermolecular interactions are represented by dashed lines. Selected atoms are labelled. [Symmetry codes: (i) -x, y, -z + 1/2; (ii) x, -y + 1, z + 1/2; (iii) -x, -y + 2, -z; (iv) x, -y + 1, z - 1/2; (v) x, -y + 2, z + 1/2.]

N,N'-bis(3-nitrophenyl)methanediamine

Crystal data

C13H12N4O4	F(000) = 600
Mr = 288.36	Dx = 1.507 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
a = 24.517 (6) Å	Cell parameters from 1149 reflections
b = 4.0505 (11) Å	θ = 2.5–26.4°
c = 16.222 (4) Å	µ = 0.12 mm^−1
β = 127.924 (2)°	T = 291 K
V = 1270.7 (6) Å^3	Plate, green
Z = 4	0.43 × 0.24 × 0.15 mm

Data collection

Bruker SMART CCD diffractometer	1167 independent reflections
Radiation source: sealed tube	913 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.023
ϕ and ω scans	θmax = 25.5°, θmin = 2.5°
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	h = −29→29
Tmin = 0.890, Tmax = 0.983	k = −4→4
3715 measured reflections	l = −19→19

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.051	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.148	H-atom parameters constrained
S = 1.04	w = 1/[σ^2(Fo^2) + (0.0765P)^2 + 1.019P] where P = (Fo^2 + 2Fc^2)/3
1167 reflections	(Δ/σ)max < 0.001
96 parameters	Δρmax = 0.21 e Å^−3
0 restraints	Δρmin = −0.19 e Å^−3

Special details

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 > σ(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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
O1	0.13852 (13)	0.4634 (9)	0.05651 (17)	0.1292 (12)
O2	0.05358 (13)	0.7672 (8)	0.00700 (15)	0.1145 (10)
N1	0.10416 (11)	0.6162 (6)	0.07392 (16)	0.0673 (7)
N2	0.06157 (8)	0.8906 (5)	0.32219 (12)	0.0435 (5)
H2D	0.0742	0.8619	0.3843	0.052*
C1	0.12535 (10)	0.6099 (5)	0.18042 (15)	0.0422 (5)
C2	0.18713 (11)	0.4624 (6)	0.25710 (18)	0.0491 (6)
H2	0.2148	0.3662	0.2426	0.059*
C3	0.20635 (11)	0.4637 (6)	0.35729 (18)	0.0529 (6)
H3	0.2480	0.3678	0.4117	0.063*
C4	0.16479 (10)	0.6044 (6)	0.37706 (15)	0.0467 (6)
H4	0.1789	0.6016	0.4450	0.056*
C5	0.10170 (9)	0.7523 (5)	0.29815 (14)	0.0359 (5)
C6	0.08182 (9)	0.7536 (5)	0.19725 (14)	0.0385 (5)
H6	0.0402	0.8489	0.1424	0.046*
C7	0.0000	1.0795 (7)	0.2500	0.0417 (7)
H7A	0.0081	1.2212	0.2103	0.050*	0.50
H7B	−0.0081	1.2212	0.2897	0.050*	0.50

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.1120 (17)	0.226 (3)	0.0798 (15)	0.0437 (19)	0.0744 (15)	−0.0142 (17)
O2	0.1201 (18)	0.186 (3)	0.0547 (11)	0.0660 (19)	0.0622 (13)	0.0366 (14)
N1	0.0654 (13)	0.1015 (18)	0.0544 (12)	0.0020 (12)	0.0467 (11)	−0.0086 (12)
N2	0.0465 (10)	0.0569 (11)	0.0363 (9)	0.0003 (8)	0.0302 (8)	−0.0014 (8)
C1	0.0461 (11)	0.0482 (12)	0.0433 (11)	−0.0064 (9)	0.0330 (9)	−0.0058 (9)
C2	0.0473 (12)	0.0471 (13)	0.0657 (14)	0.0010 (10)	0.0413 (11)	−0.0020 (10)
C3	0.0421 (11)	0.0586 (15)	0.0541 (13)	0.0063 (10)	0.0276 (10)	0.0114 (11)
C4	0.0433 (11)	0.0578 (14)	0.0385 (11)	−0.0015 (10)	0.0248 (9)	0.0046 (9)
C5	0.0393 (10)	0.0359 (11)	0.0371 (9)	−0.0066 (8)	0.0259 (8)	−0.0015 (8)
C6	0.0402 (10)	0.0425 (12)	0.0368 (10)	−0.0004 (8)	0.0256 (8)	0.0011 (8)
C7	0.0535 (16)	0.0389 (16)	0.0516 (16)	0.000	0.0418 (14)	0.000

Geometric parameters (Å, º)

O1—N1	1.210 (3)	C3—C4	1.366 (3)
O2—N1	1.198 (3)	C3—H3	0.9300
N1—C1	1.467 (3)	C4—C5	1.399 (3)
N2—C5	1.380 (2)	C4—H4	0.9300
N2—C7	1.436 (2)	C5—C6	1.391 (3)
N2—H2D	0.8600	C6—H6	0.9300
C1—C2	1.372 (3)	C7—N2	1.436 (2)
C1—C6	1.382 (3)	C7—H7A	0.9700
C2—C3	1.386 (3)	C7—H7B	0.9700
C2—H2	0.9300
O2—N1—O1	122.0 (2)	C3—C4—C5	121.90 (19)
O2—N1—C1	119.74 (19)	C3—C4—H4	119.0
O1—N1—C1	118.2 (2)	C5—C4—H4	119.0
C5—N2—C7	124.08 (13)	N2—C5—C6	122.38 (17)
C5—N2—H2D	118.0	N2—C5—C4	119.65 (16)
C7—N2—H2D	118.0	C6—C5—C4	117.97 (17)
C2—C1—C6	124.09 (18)	C1—C6—C5	118.42 (18)
C2—C1—N1	118.02 (18)	C1—C6—H6	120.8
C6—C1—N1	117.89 (18)	C5—C6—H6	120.8
C1—C2—C3	116.84 (19)	N2—C7—N2^i	115.6 (2)
C1—C2—H2	121.6	N2—C7—H7A	108.4
C3—C2—H2	121.6	N2^i—C7—H7A	108.4
C4—C3—C2	120.8 (2)	N2—C7—H7B	108.4
C4—C3—H3	119.6	N2^i—C7—H7B	108.4
C2—C3—H3	119.6	H7A—C7—H7B	107.4
O2—N1—C1—C2	−173.6 (3)	C7—N2—C5—C4	172.87 (19)
O1—N1—C1—C2	7.2 (4)	C3—C4—C5—N2	179.93 (19)
O2—N1—C1—C6	6.2 (4)	C3—C4—C5—C6	−0.1 (3)
O1—N1—C1—C6	−172.9 (3)	C2—C1—C6—C5	0.6 (3)
C6—C1—C2—C3	−0.7 (3)	N1—C1—C6—C5	−179.32 (18)
N1—C1—C2—C3	179.2 (2)	N2—C5—C6—C1	179.85 (18)
C1—C2—C3—C4	0.5 (3)	C4—C5—C6—C1	−0.1 (3)
C2—C3—C4—C5	−0.1 (3)	C5—N2—C7—N2^i	81.18 (18)
C7—N2—C5—C6	−7.1 (3)

Symmetry code: (i) −x, y, −z+1/2.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2D···O1^ii	0.86	2.57	3.354 (3)	152
C6—H6···O2^iii	0.93	2.59	3.499 (3)	165
C4—H4···O1^ii	0.93	2.55	3.357 (3)	145

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