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Acta Crystallogr Sect E Struct Rep Online. 2009 December 1; 65(Pt 12): o3177.
Published online 2009 November 21. doi:  10.1107/S1600536809049009
PMCID: PMC2972038

Phenazine–naphthalene-1,5-diamine–water (1/1/2)

Abstract

The asymmetric unit of the title compound, C12H8N2·C10H10N2·2H2O, contains one half-mol­ecule of phenazine, one half-mol­ecule of naphthalene-1,5-diamine and one water mol­ecule. The phenazine and naphthalene-1,5-diamine mol­ecules are located on inversion centers. The water mol­ecules serve as bridges between the naphthalene-1,5-diamine mol­ecules and also between the naphthalene-1,5-diamine and phenazine mol­ecules. The naphthalene-1,5-diamine and water mol­ecules are connected via N—H(...)O and O—H(...)N hydrogen bonds, forming a T4(2) motif. They are arranged into a two-dimensional polymeric structure parallel to (10An external file that holds a picture, illustration, etc.
Object name is e-65-o3177-efi1.jpg) in which the water mol­ecule is a single donor and a double acceptor, whereas the amino group is a double donor and a single acceptor in the hydrogen bonding. These two-dimensional assemblies alternate with the layers of phenazine mol­ecules arranged into a herringbone motif. Each phenazine mol­ecule is hydrogen bonded to two water mol­ecules and thus a three-dimensional framework of hydrogen-bonded mol­ecules is generated.

Related literature

For the structures of co-crystals of aromatic diaza­heterocycles with small aromatic mol­ecules, see: Thalladi et al. (2000 [triangle]); Kadzewski & Gdaniec (2006 [triangle]); Czapik & Gdaniec (2008 [triangle]). For structures with similar T4(2) hydrogen-bond motifs, see: Anthony et al. (2007 [triangle]); Neely et al. (2007 [triangle]). For symbols of hydrogen-bond motifs, see: Infantes et al. (2003 [triangle]). For a description of the Cambridge Structural Database, see: Allen (2002 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o3177-scheme1.jpg

Experimental

Crystal data

  • C12H8N2·C10H10N2·2H2O
  • M r = 374.44
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o3177-efi2.jpg
  • a = 13.0395 (10) Å
  • b = 4.9266 (2) Å
  • c = 15.7211 (12) Å
  • β = 112.508 (9)°
  • V = 933.00 (11) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.09 mm−1
  • T = 130 K
  • 0.25 × 0.25 × 0.25 mm

Data collection

  • Kuma KM-4-CCD κ-geometry diffractometer
  • Absorption correction: none
  • 5251 measured reflections
  • 1643 independent reflections
  • 1357 reflections with I > 2σ(I)
  • R int = 0.022

Refinement

  • R[F 2 > 2σ(F 2)] = 0.047
  • wR(F 2) = 0.140
  • S = 1.08
  • 1643 reflections
  • 143 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.22 e Å−3
  • Δρmin = −0.23 e Å−3

Data collection: CrysAlis CCD (Oxford Diffraction, 2007 [triangle]); cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2007 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 [triangle]) and Mercury (Macrae et al., 2006 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809049009/rz2392sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809049009/rz2392Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

supplementary crystallographic information

Comment

The title compound has been obtained unintentionally during our attempts to co-crystallize phenazine with naphthalene-1,5-diamine. Heterocycles like phenazine and quinoxaline are known to form a robust host framework with one-dimensional channels filled with small aromatic guest molecules (Thalladi et al., 2000; Kadzewski & Gdaniec; 2006). Inclusion of water molecules have however a significant impact on arrangement of molecules in these co-crystals (Czapik & Gdaniec, 2008).

Crystal packing of the title compound is shown in Fig. 2. Phenazine and naphthalene-1,5-diamine molecules are situated around inversion centers and are arranged into stacks along [010] by π–π stacking interactions. The molecules of naphthalene-1,5-diamine and water are connected via N—H···O and O—H···N hydrogen bonds that form the T4(2) motif (Table 1, Fig. 3). These hydrogen bonds connect molecules into a two-dimensional polymeric structure parallel to (1 0 - 1) in which the water molecule is a single donor and a double acceptor whereas the amino group plays a role a double donor and a single acceptor (Fig. 3). The layers of naphthalene-1,5-diamine and water molecules alternate with the layers of phenazine in which these aromatic molecules show a herringbone arrangement (Fig. 4). The phenazine molecules are hydrogen bonded to two water molecules and thus a three-dimensional framework of hydrogen-bonded molecules is generated (Fig. 2).

The Cambridge Structural Database (Allen, 2002) was searched for the structures containing C—NH2 groups and water molecules to look for the frequency of the T4(2) motif (Infantes et al., 2003) generated by primary amino groups and water molecules. The search was limited to organic compounds with polymeric and ionic structures excluded and gave only two structures with the CSD refcodes DISNEZ, (Anthony et al., 2007) and MIMWAH01 (Neely et al., 2007). In both cases the donor and acceptor functions of the amino group and water molecule were analogous to those in the title compound.

Experimental

The title compound was obtained by dissolving phenazine (0.100 g, 0.55 mmol) and naphthalene-1,5-diamine (0.088 g, 0.55 mmol) in 5 ml of acetone. Slow evaporation of the solution yielded red cuboid crystals.

Refinement

All H atoms were located in electron-density difference maps. C-bonded H atoms were placed at calculated positions, with C—H = 0.93 Å, and were refined as riding on their carrier C atoms, with Uĩso(H) = 1.2Ueq(C). The H atoms of the OH and NH groups were freely refined (coordinates and isotropic displacement parameters).

Figures

Fig. 1.
: The molecular structure of the title compound with displacement ellipsoids shown at the 50% probability level. Hydrogen bonds are shown as dashed lines and only atoms from the asymmetric unit are labelled.
Fig. 2.
: Crystal packing viewed down the y axis. Hydrogen bonds are shown with dashed lines.
Fig. 3.
Hydrogen-bonded water molecule and aromatic amine generating the T4(2) motif.
Fig. 4.
The herringbone arrangement of phenazine molecules parallel to (1 0 - 1)

Crystal data

C12H8N2·C10H10N2·2H2OF(000) = 396
Mr = 374.44Dx = 1.333 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 3369 reflections
a = 13.0395 (10) Åθ = 2.6–27.9°
b = 4.9266 (2) ŵ = 0.09 mm1
c = 15.7211 (12) ÅT = 130 K
β = 112.508 (9)°Cube, red
V = 933.00 (11) Å30.25 × 0.25 × 0.25 mm
Z = 2

Data collection

Kuma KM-4-CCD κ-geometry diffractometer1357 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.022
graphiteθmax = 25.0°, θmin = 4.4°
ω scansh = −15→15
5251 measured reflectionsk = −5→5
1643 independent reflectionsl = −18→18

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.047Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.140H atoms treated by a mixture of independent and constrained refinement
S = 1.08w = 1/[σ2(Fo2) + (0.0606P)2 + 1.1003P] where P = (Fo2 + 2Fc2)/3
1643 reflections(Δ/σ)max < 0.001
143 parametersΔρmax = 0.22 e Å3
0 restraintsΔρmin = −0.23 e Å3

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 (Å2)

xyzUiso*/Ueq
N1A0.12558 (17)0.2658 (5)0.18906 (13)0.0249 (5)
H1N0.116 (3)0.419 (8)0.218 (2)0.054 (10)*
H2N0.198 (3)0.258 (6)0.1847 (19)0.038 (8)*
C1A0.03659 (18)0.2272 (5)0.10357 (15)0.0220 (5)
C2A−0.05954 (19)0.3753 (5)0.08078 (15)0.0245 (5)
H2A−0.06550.50560.12140.029*
C3A−0.14918 (19)0.3314 (5)−0.00367 (16)0.0248 (5)
H3A−0.21350.4343−0.01850.030*
C4A0.14256 (19)−0.1391 (5)0.06406 (16)0.0243 (5)
H4A0.2021−0.11340.11970.029*
C5A0.04549 (18)0.0218 (5)0.04242 (15)0.0223 (5)
N1B0.05503 (15)0.9466 (4)0.43964 (12)0.0220 (5)
C2B0.08133 (18)0.8115 (5)0.51930 (15)0.0211 (5)
C3B0.16597 (18)0.6111 (5)0.54398 (16)0.0252 (5)
H3B0.20310.57530.50510.030*
C4B0.19301 (19)0.4712 (5)0.62413 (17)0.0279 (6)
H4B0.24890.34110.63990.033*
C5B−0.02539 (18)1.1344 (5)0.41932 (15)0.0217 (5)
C6B−0.0560 (2)1.2869 (5)0.33626 (15)0.0258 (6)
H6B−0.02061.25530.29590.031*
C7B−0.1367 (2)1.4781 (5)0.31585 (16)0.0290 (6)
H7B−0.15551.57780.26170.035*
O1W0.12857 (15)0.7813 (4)0.29145 (12)0.0297 (5)
H1W0.137 (3)0.932 (10)0.269 (3)0.074 (13)*
H2W0.107 (2)0.819 (6)0.337 (2)0.035 (8)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N1A0.0267 (11)0.0260 (12)0.0211 (10)−0.0033 (9)0.0081 (8)−0.0025 (9)
C1A0.0246 (12)0.0221 (12)0.0212 (11)−0.0043 (10)0.0108 (9)0.0018 (9)
C2A0.0294 (12)0.0227 (12)0.0247 (12)−0.0004 (10)0.0138 (10)0.0008 (10)
C3A0.0222 (11)0.0244 (13)0.0292 (12)0.0022 (10)0.0114 (10)0.0043 (10)
C4A0.0223 (11)0.0243 (13)0.0261 (12)−0.0029 (10)0.0089 (9)0.0011 (10)
C5A0.0261 (11)0.0201 (12)0.0240 (11)−0.0036 (9)0.0132 (10)0.0020 (9)
N1B0.0252 (10)0.0201 (10)0.0230 (10)−0.0026 (8)0.0119 (8)−0.0032 (8)
C2B0.0226 (11)0.0181 (12)0.0247 (11)−0.0044 (9)0.0114 (9)−0.0038 (9)
C3B0.0245 (12)0.0240 (12)0.0302 (12)−0.0001 (10)0.0139 (10)−0.0017 (10)
C4B0.0250 (12)0.0216 (13)0.0346 (13)0.0027 (10)0.0085 (10)−0.0008 (10)
C5B0.0228 (11)0.0196 (12)0.0246 (12)−0.0039 (9)0.0111 (9)−0.0040 (9)
C6B0.0312 (12)0.0262 (13)0.0220 (12)−0.0006 (11)0.0124 (10)−0.0005 (10)
C7B0.0355 (13)0.0237 (13)0.0257 (12)−0.0014 (11)0.0094 (10)0.0021 (10)
O1W0.0405 (10)0.0279 (11)0.0257 (9)0.0042 (8)0.0182 (8)−0.0001 (8)

Geometric parameters (Å, °)

N1A—C1A1.412 (3)N1B—C5B1.342 (3)
N1A—H1N0.91 (4)C2B—C3B1.420 (3)
N1A—H2N0.97 (3)C2B—C5Bii1.440 (3)
C1A—C2A1.374 (3)C3B—C4B1.359 (3)
C1A—C5A1.431 (3)C3B—H3B0.9300
C2A—C3A1.410 (3)C4B—C7Bii1.422 (4)
C2A—H2A0.9300C4B—H4B0.9300
C3A—C4Ai1.367 (3)C5B—C6B1.425 (3)
C3A—H3A0.9300C6B—C7B1.356 (3)
C4A—C3Ai1.367 (3)C6B—H6B0.9300
C4A—C5A1.420 (3)C7B—H7B0.9300
C4A—H4A0.9300O1W—H1W0.85 (5)
C5A—C5Ai1.422 (4)O1W—H2W0.89 (3)
N1B—C2B1.341 (3)
C1A—N1A—H1N111 (2)N1B—C2B—C3B119.61 (19)
C1A—N1A—H2N113.2 (16)N1B—C2B—C5Bii121.3 (2)
H1N—N1A—H2N113 (3)C3B—C2B—C5Bii119.1 (2)
C2A—C1A—N1A120.8 (2)C4B—C3B—C2B120.3 (2)
C2A—C1A—C5A120.1 (2)C4B—C3B—H3B119.8
N1A—C1A—C5A119.1 (2)C2B—C3B—H3B119.8
C1A—C2A—C3A120.6 (2)C3B—C4B—C7Bii120.7 (2)
C1A—C2A—H2A119.7C3B—C4B—H4B119.7
C3A—C2A—H2A119.7C7Bii—C4B—H4B119.7
C4Ai—C3A—C2A120.7 (2)N1B—C5B—C6B120.1 (2)
C4Ai—C3A—H3A119.7N1B—C5B—C2Bii121.2 (2)
C2A—C3A—H3A119.7C6B—C5B—C2Bii118.7 (2)
C3Ai—C4A—C5A120.5 (2)C7B—C6B—C5B120.2 (2)
C3Ai—C4A—H4A119.7C7B—C6B—H6B119.9
C5A—C4A—H4A119.7C5B—C6B—H6B119.9
C4A—C5A—C5Ai119.2 (3)C6B—C7B—C4Bii121.0 (2)
C4A—C5A—C1A121.9 (2)C6B—C7B—H7B119.5
C5Ai—C5A—C1A118.9 (3)C4Bii—C7B—H7B119.5
C2B—N1B—C5B117.47 (18)H1W—O1W—H2W107 (3)

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

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1A—H1N···O1W0.91 (4)2.10 (4)2.999 (3)169 (3)
N1A—H2N···O1Wiii0.97 (3)2.15 (3)3.102 (3)166 (2)
O1W—H1W···N1Aiv0.85 (5)2.04 (5)2.871 (3)167 (4)
O1W—H2W···N1B0.89 (3)2.07 (3)2.953 (3)174 (3)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: RZ2392).

References

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