Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270110008474/fg3158sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270110008474/fg3158IIsup2.hkl |
CCDC reference: 774906
Polymorph (II) of benzene-1,2-diamine was formed during co-crystallization in a 1:1 molar ratio of benzene-1,2-diamine (6 mg) with phenazine (10 mg). The two components were dissolved in a methanol–diethyl ether (6 ml, 1:1 v/v) solvent mixture and the solution was slowly evaporated. As only one relatively large crystal of form (II) (2 × 1 × 0.5 mm) was found in the crystallization vial, it was cut into small pieces, one of which was used for structure determination. Unfortunately, our attempts to produce more crystals of form (II) by repeating the crystallization conditions were unsuccessful. Crystallization of benzene-1,2-diamine carried out under a wide range of different sets of conditions (different solvents, different co-solute molecules) led systematically to polymorph (I).
All H atoms were identified in difference Fourier maps but for refinement all C-bound H atoms were placed in calculated positions, with C—H = 0.93 Å, and refined as riding on their carrier atoms, with Uiso(H) = 1.2Ueq(C). All N-bound H atoms were freely refined (coordinates and isotropic displacement parameters). [Range of N—H distances?]
Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell refinement: CrysAlis PRO (Oxford Diffraction, 2009); data reduction: CrysAlis PRO (Oxford Diffraction, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997) and Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).
C6H8N2 | F(000) = 464 |
Mr = 108.14 | Dx = 1.211 Mg m−3 |
Orthorhombic, Pbca | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ac 2ab | Cell parameters from 1955 reflections |
a = 7.5330 (17) Å | θ = 2.9–28.8° |
b = 7.8350 (15) Å | µ = 0.08 mm−1 |
c = 20.098 (4) Å | T = 293 K |
V = 1186.2 (4) Å3 | Block, pale-pink |
Z = 8 | 0.5 × 0.25 × 0.1 mm |
Oxford XcaliburE CCD area-detector diffractometer | 1204 independent reflections |
Radiation source: fine-focus sealed tube | 817 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.029 |
ω scans | θmax = 26.4°, θmin = 4.3° |
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009) | h = −9→8 |
Tmin = 0.776, Tmax = 1.000 | k = −9→9 |
6421 measured reflections | l = −25→25 |
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)] = 0.036 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.088 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.94 | w = 1/[σ2(Fo2) + (0.054P)2] where P = (Fo2 + 2Fc2)/3 |
1204 reflections | (Δ/σ)max < 0.001 |
89 parameters | Δρmax = 0.11 e Å−3 |
0 restraints | Δρmin = −0.20 e Å−3 |
C6H8N2 | V = 1186.2 (4) Å3 |
Mr = 108.14 | Z = 8 |
Orthorhombic, Pbca | Mo Kα radiation |
a = 7.5330 (17) Å | µ = 0.08 mm−1 |
b = 7.8350 (15) Å | T = 293 K |
c = 20.098 (4) Å | 0.5 × 0.25 × 0.1 mm |
Oxford XcaliburE CCD area-detector diffractometer | 1204 independent reflections |
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009) | 817 reflections with I > 2σ(I) |
Tmin = 0.776, Tmax = 1.000 | Rint = 0.029 |
6421 measured reflections |
R[F2 > 2σ(F2)] = 0.036 | 0 restraints |
wR(F2) = 0.088 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.94 | Δρmax = 0.11 e Å−3 |
1204 reflections | Δρmin = −0.20 e Å−3 |
89 parameters |
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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. |
x | y | z | Uiso*/Ueq | ||
N1 | 0.54191 (17) | 0.26495 (14) | 0.49593 (5) | 0.0443 (3) | |
H11 | 0.6074 (18) | 0.1881 (17) | 0.5225 (6) | 0.053 (4)* | |
H12 | 0.440 (2) | 0.2877 (18) | 0.5127 (7) | 0.067 (5)* | |
N2 | 0.30911 (16) | 0.42760 (13) | 0.41182 (6) | 0.0463 (3) | |
H21 | 0.361 (2) | 0.4984 (18) | 0.4408 (7) | 0.064 (4)* | |
H22 | 0.253 (2) | 0.4824 (18) | 0.3806 (7) | 0.067 (4)* | |
C1 | 0.53540 (15) | 0.21377 (13) | 0.42921 (6) | 0.0346 (3) | |
C2 | 0.42111 (15) | 0.30052 (13) | 0.38596 (5) | 0.0352 (3) | |
C3 | 0.41203 (18) | 0.24953 (15) | 0.32035 (6) | 0.0457 (4) | |
H3 | 0.3335 | 0.3038 | 0.2916 | 0.055* | |
C4 | 0.5182 (2) | 0.11875 (18) | 0.29683 (6) | 0.0566 (4) | |
H4 | 0.5110 | 0.0861 | 0.2524 | 0.068* | |
C5 | 0.6342 (2) | 0.03709 (17) | 0.33868 (6) | 0.0556 (4) | |
H5 | 0.7070 | −0.0495 | 0.3227 | 0.067* | |
C6 | 0.64204 (16) | 0.08434 (14) | 0.40470 (6) | 0.0435 (3) | |
H6 | 0.7201 | 0.0285 | 0.4332 | 0.052* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0459 (8) | 0.0443 (6) | 0.0427 (6) | 0.0065 (6) | −0.0047 (6) | −0.0011 (5) |
N2 | 0.0476 (8) | 0.0395 (6) | 0.0518 (7) | 0.0092 (5) | −0.0031 (5) | 0.0042 (5) |
C1 | 0.0335 (7) | 0.0292 (6) | 0.0410 (6) | −0.0051 (5) | 0.0004 (5) | 0.0001 (4) |
C2 | 0.0336 (7) | 0.0298 (6) | 0.0423 (6) | −0.0051 (5) | 0.0028 (5) | 0.0050 (5) |
C3 | 0.0507 (9) | 0.0452 (7) | 0.0412 (7) | −0.0053 (6) | −0.0032 (6) | 0.0079 (6) |
C4 | 0.0690 (10) | 0.0596 (8) | 0.0411 (7) | −0.0037 (8) | 0.0053 (7) | −0.0081 (6) |
C5 | 0.0538 (10) | 0.0545 (8) | 0.0584 (8) | 0.0062 (7) | 0.0064 (7) | −0.0150 (6) |
C6 | 0.0377 (7) | 0.0388 (7) | 0.0541 (7) | 0.0028 (6) | −0.0037 (6) | −0.0017 (5) |
N1—C1 | 1.4004 (16) | C2—C3 | 1.3795 (16) |
N1—H11 | 0.944 (14) | C3—C4 | 1.3833 (18) |
N1—H12 | 0.855 (15) | C3—H3 | 0.9300 |
N2—C2 | 1.4047 (15) | C4—C5 | 1.3711 (18) |
N2—H21 | 0.893 (15) | C4—H4 | 0.9300 |
N2—H22 | 0.868 (15) | C5—C6 | 1.3788 (17) |
C1—C6 | 1.3843 (15) | C5—H5 | 0.9300 |
C1—C2 | 1.3996 (16) | C6—H6 | 0.9300 |
C1—N1—H11 | 112.2 (8) | C2—C3—C4 | 120.83 (12) |
C1—N1—H12 | 113.9 (10) | C2—C3—H3 | 119.6 |
H11—N1—H12 | 112.2 (13) | C4—C3—H3 | 119.6 |
C2—N2—H21 | 114.8 (10) | C5—C4—C3 | 120.29 (11) |
C2—N2—H22 | 112.0 (10) | C5—C4—H4 | 119.9 |
H21—N2—H22 | 111.9 (14) | C3—C4—H4 | 119.9 |
C6—C1—C2 | 119.46 (11) | C4—C5—C6 | 119.50 (12) |
C6—C1—N1 | 122.01 (11) | C4—C5—H5 | 120.3 |
C2—C1—N1 | 118.50 (11) | C6—C5—H5 | 120.3 |
C3—C2—C1 | 118.92 (11) | C5—C6—C1 | 120.95 (12) |
C3—C2—N2 | 121.95 (11) | C5—C6—H6 | 119.5 |
C1—C2—N2 | 118.94 (11) | C1—C6—H6 | 119.5 |
C6—C1—C2—C3 | 2.82 (16) | C2—C3—C4—C5 | 0.2 (2) |
N1—C1—C2—C3 | −179.13 (11) | C3—C4—C5—C6 | 1.1 (2) |
C6—C1—C2—N2 | 177.82 (9) | C4—C5—C6—C1 | −0.4 (2) |
N1—C1—C2—N2 | −4.13 (16) | C2—C1—C6—C5 | −1.53 (17) |
C1—C2—C3—C4 | −2.20 (18) | N1—C1—C6—C5 | −179.50 (12) |
N2—C2—C3—C4 | −177.05 (11) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H11···N2i | 0.944 (14) | 2.207 (14) | 3.1250 (16) | 163.8 (11) |
N2—H21···N1ii | 0.893 (15) | 2.365 (15) | 3.2404 (16) | 166.6 (13) |
Symmetry codes: (i) x+1/2, −y+1/2, −z+1; (ii) −x+1, −y+1, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C6H8N2 |
Mr | 108.14 |
Crystal system, space group | Orthorhombic, Pbca |
Temperature (K) | 293 |
a, b, c (Å) | 7.5330 (17), 7.8350 (15), 20.098 (4) |
V (Å3) | 1186.2 (4) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 0.08 |
Crystal size (mm) | 0.5 × 0.25 × 0.1 |
Data collection | |
Diffractometer | Oxford XcaliburE CCD area-detector diffractometer |
Absorption correction | Multi-scan (CrysAlis PRO; Oxford Diffraction, 2009) |
Tmin, Tmax | 0.776, 1.000 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6421, 1204, 817 |
Rint | 0.029 |
(sin θ/λ)max (Å−1) | 0.625 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.036, 0.088, 0.94 |
No. of reflections | 1204 |
No. of parameters | 89 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.11, −0.20 |
Computer programs: CrysAlis PRO (Oxford Diffraction, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997) and Mercury (Macrae et al., 2006).
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H11···N2i | 0.944 (14) | 2.207 (14) | 3.1250 (16) | 163.8 (11) |
N2—H21···N1ii | 0.893 (15) | 2.365 (15) | 3.2404 (16) | 166.6 (13) |
Symmetry codes: (i) x+1/2, −y+1/2, −z+1; (ii) −x+1, −y+1, −z+1. |
Increased interest in co-crystals has resulted in several recent reports of the serendipitous formation of a new polymorph by one of the substrates during attempted co-crystallization experiments (Callear & Hursthouse, 2009; Dey et al., 2006; Rafilovich & Bernstein, 2006; Wenger & Bernstein, 2007), with the most famous case represented by a new polymorph of aspirin (Vishweshwar et al., 2005; Bond et al., 2007). Our attempts to prepare new co-crystals have already resulted in obtaining the elusive β form of phenazine (Herbstein & Schmidt, 1955; Jankowski & Gdaniec, 2002) and the hydrated form of 1,4-benzenediamine (Czapik et al., 2010). Crystal structures of all three benzenediamine isomers are known (Betz et al., 2008; Poveteva et al., 1975; Stalhandske, 1981) and polymorphism has not been observed for any of these compounds so far. Recently, we have shown that unstable 1,4-benzamine dihydrate converts on dehydration to its known anhydrous form (Czapik et al., 2010). Polymorphism and hydrate formation are rather exceptional among aromatic amines, as shown by our survey of the Cambridge Structural Database (CSD, Version 5.31; Allen, 2002), which gave 48 structures of aromatic amines of the general formula [CnHm(NH2)x] with at least one primary amino group attached to the aromatic ring and with only C and H atoms in the remaining part of the molecule. Among these amines only benzidine has been shown to exhibit polymorphism, with four polymorphic forms characterized so far (Rafilovich & Bernstein, 2006). Another aspect that emerged from this CSD search was the unusually high percentage of structures with Z' ≠ 1. Out of the 48 structures analysed, 15 had Z' > 1, 21 had Z' = 1 and 12 had Z' < 1.
In this paper, we report the crystal structure of a new polymorph, (II), of benzene-1,2-diamine with Z' = 1, produced unexpectedly during an attempt to synthesize co-crystals of phenazine with benzene-1,2-diamine. This new form was obtained from a 1:1 mixture of the above two components dissolved in methanol–diethyl ether (1:1 v/v). Slow evaporation of the solution resulted in precipitation of two types of crystals, yellow needles (subsequently identified as the 2:1 phenazine–benzene-1,2-diamine complex) and a pale-pink tabloid crystal which has been shown to be a new orthorhombic form, (II), of benzene-1,2-diamine. The known form, (I), of benzene-1,2-diamine is monoclinic in space group P21/c and crystallizes with one molecule in the asymmetric unit (Stalhandske, 1981; CSD Refcode BAGFIY).
The molecular structure of (II), with the atom-numbering scheme, is shown in Fig. 1. In the two polymorphs the molecules have very similar geometries and exhibit non-crystallographic C2 symmetry, with both amino N atoms sp3 hybridized and one of the N—H bonds of each NH2 group virtually in the plane of the benzene ring, resulting in two short intramolecular H···N contacts of 2.508 (14) and 2.538 (14) Å between the ortho-situated amino substituents. The C—N bond lengths of 1.4004 (16) and 1.4047 (15) Å are consistent with the N hybridization state, and the endocyclic bond angles at C1 and C2, both smaller than 120°, are consistent with the electron-donating character of the amine groups (Domenicano et al., 1975).
A projection of the crystal structure of (II) along the a axis is shown in Fig. 2(a). This crystal structure can be seen as constructed from bilayers (centred at z = 0, 1/2, 1.0 etc.) that are parallel to (001) and have the polar amino groups directed to the inside and the aromatic groups, which have a herringbone arrangement, directed to the outside. The amino groups, each acting as a single donor and a single acceptor, are involved in two weak intermolecular N—H···N hydrogen bonds (Table 1, Fig. 3) operating between monolayers. Additionally, one of the amino groups forms an N2—H22···π interaction [H22···Cgiii = 2.59 Å and N2—H22···Cgiii = 141°, where Cg is the centroid of the aromatic ring; symmetry code: (iii) 1/2 - x, 1/2 + y, z] with the aromatic ring of the b-glide-related molecule within the same monolayer (Fig. 3). A closer look at the structure of form (I) (Stalhandske, 1981; Fig. 2b) reveals that the two polymorphs of benzene-1,2-diamine exhibit two-dimensional isostructurality (Fábián & Kálmán, 2004) because they are constructed from virtually identical bilayers with similar metric parameters [b = 7.544(s.u.?) Å, c = 7.716(s.u.?) Å and α = 90° in (I), and a = 7.533 (2) Å, b = 7.835 (2) Å and γ = 90° in (II)] and the same layer group symmetry [p121/c1 in (I) and p21/b11 in (II)]. The two polymorphs differ in the stacking arrangement of the bilayers: in form (I), neighbouring bilayers are generated by a unit translation along the a axis, whereas in form (II) they are generated by a c-glide. In both crystalline forms the interactions between the bilayer surface atoms are only of the van der Waals type, with all interlayer contacts being longer than the sum of the van der Waals radii of the appropriate atoms.
The melting temperatures measured for both polymorphs using a Boetius apparatus were 368–370 K for (I) (reference value 375.5 K; CRC Handbook of Chemistry and Physics, 1998) and 366–368 K for (II), and no phase changes were observed under a polarizing microscope when the crystals were heated from room temperature to the m.p. Interestingly, the two forms also have very similar volumes for a single diamine molecule [147.9 and 148.3 Å3 for (I) and (II), respectively] and thus also similar crystal densities, 1.214 and 1.211 Mg m-3 for forms (I) and (II), respectively. However, simulated powder diffractograms show that the two forms can be easily discerned from their diffraction patterns (Fig. 4)
Since one (N1—H12) of the N—H groups in (II) is not involved in any specific intermolecular interactions, we decided to check whether the monohydroxy congener of benzene-1,2-diamine, 1,2-aminophenol, formed a similar structure. Aminophenols have been extensively studied (Allen et al., 1997; Dey et al., 2005, 2006) in the context of the saturated hydrogen-bond principle introduced by Ermer & Eling (1994) and in relation to crystal structure prediction using the supramolecular synthon approach. Indeed, the structure for form (II) reported here for benzene-1,2-diamine is essentially isomorphous with the only known orthorhombic form of 1,2-aminophenol (Ashfaquzzaman & Pant, 1979, CSD Refcode AMPHOM10; Korp et al., 1981, CSD Refcode AMPHOM02; Allen et al., 1997, CSD Refcode AMPHOM03) and very similar in structure to 2-amino-4-methylphenol (Kashino et al., 1988; Dey et al., 2005), which has the unit-cell parameter c elongated by ca 2.8 Å compared with (II) due to the presence of the methyl substituents on the bilayer surface. Moreover, the monoclinic polymorph, (I), closely resembles, in a similar manner, the structure of the monoclinic compounds 2-amino-4-chlorophenol (Ashfaquzzaman & Pant, 1979) and 2-amino-4-ethylphenol (Dey et al., 2006). These examples show that ortho-aminophenols and aromatic ortho-diamines show extensive similarities in their crystal packing. However, these similarities do not extend to the meta and para isomers of these compounds