The planar electron-rich heterocyclic diamine 2,3-diaminophenazine (DAP), C12H10N4, is of particular interest to both chemists and biochemists because of its rich organic chemistry and intense luminescence. In this paper, we report the first structure of DAP in its non-protonated form and describe the intriguing crystal packing, which features π–π, hydrogen- and T-bonded interactions.
Supporting information
CCDC reference: 158272
2,3-Diaminophenazine was prepared by addition of a stoichiometric quantity of
copper(II) hydroxide to an aqueous suspension of 1,2-phenylenediamine·The
resultant brown precipitate was collected by filtration and subsequently
crystallized by slow diffusion of acetonitrile vapour into a methanolic
solution of the title compound.
H atoms were placed geometrically with C'-H and N—H distances of 0.93 and 0.86 Å, respectively, and Uiso(H) = 1.2Ueq(C', N).
Data collection: SMART (Bruker, 1999); cell refinement: SAINT (Bruker, 1999); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 1997); program(s) used to refine structure: SHELXTL; molecular graphics: ORTEP-32 for Windows (Farrugia, 1998).
Phenazine-2,3-diamine
top
Crystal data top
C12H10N4 | Dx = 1.442 Mg m−3 |
Mr = 210.24 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, P212121 | Cell parameters from 1452 reflections |
a = 4.8355 (8) Å | θ = 2.1–26.4° |
b = 11.583 (2) Å | µ = 0.09 mm−1 |
c = 17.304 (3) Å | T = 293 K |
V = 969.2 (3) Å3 | Trigonal prism, brown |
Z = 4 | 0.3 × 0.25 × 0.2 mm |
F(000) = 440 | |
Data collection top
Bruker AXS SMART CCD area detector diffractometer | 985 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.032 |
Graphite monochromator | θmax = 26.4°, θmin = 2.1° |
ω–2θ scans | h = −4→6 |
3272 measured reflections | k = −14→13 |
1182 independent reflections | l = −21→8 |
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)] = 0.041 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.115 | H-atom parameters constrained |
S = 1.05 | w = 1/[σ2(Fo2) + (0.0785P)2 + 0.0252P] where P = (Fo2 + 2Fc2)/3 |
1182 reflections | (Δ/σ)max < 0.001 |
145 parameters | Δρmax = 0.19 e Å−3 |
0 restraints | Δρmin = −0.19 e Å−3 |
Crystal data top
C12H10N4 | V = 969.2 (3) Å3 |
Mr = 210.24 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 4.8355 (8) Å | µ = 0.09 mm−1 |
b = 11.583 (2) Å | T = 293 K |
c = 17.304 (3) Å | 0.3 × 0.25 × 0.2 mm |
Data collection top
Bruker AXS SMART CCD area detector diffractometer | 985 reflections with I > 2σ(I) |
3272 measured reflections | Rint = 0.032 |
1182 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.041 | 0 restraints |
wR(F2) = 0.115 | H-atom parameters constrained |
S = 1.05 | Δρmax = 0.19 e Å−3 |
1182 reflections | Δρmin = −0.19 e Å−3 |
145 parameters | |
Special details top
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) top | x | y | z | Uiso*/Ueq | |
N1 | −0.6437 (5) | 0.40416 (18) | 0.61117 (11) | 0.0326 (6) | |
H1A | −0.6772 | 0.3312 | 0.6109 | 0.039* | |
H1B | −0.7240 | 0.4481 | 0.6444 | 0.039* | |
C2 | −0.4623 (5) | 0.45044 (19) | 0.55864 (13) | 0.0225 (5) | |
C3 | −0.3303 (5) | 0.38408 (18) | 0.50493 (12) | 0.0235 (5) | |
H3 | −0.3727 | 0.3059 | 0.5020 | 0.028* | |
C4 | −0.1325 (5) | 0.42995 (18) | 0.45394 (12) | 0.0215 (5) | |
N5 | −0.0064 (4) | 0.36121 (15) | 0.40245 (11) | 0.0233 (5) | |
C6 | 0.1894 (5) | 0.4090 (2) | 0.35679 (12) | 0.0227 (5) | |
C7 | 0.3380 (5) | 0.3399 (2) | 0.30386 (13) | 0.0276 (6) | |
H7 | 0.2976 | 0.2616 | 0.3001 | 0.033* | |
C8 | 0.5403 (5) | 0.3862 (2) | 0.25808 (14) | 0.0301 (6) | |
H8 | 0.6373 | 0.3391 | 0.2240 | 0.036* | |
C9 | 0.6025 (5) | 0.5054 (2) | 0.26237 (13) | 0.0294 (6) | |
H9 | 0.7396 | 0.5364 | 0.2309 | 0.035* | |
C10 | 0.4629 (5) | 0.5750 (2) | 0.31218 (13) | 0.0276 (6) | |
H10 | 0.5060 | 0.6531 | 0.3143 | 0.033* | |
C11 | 0.2523 (5) | 0.53033 (19) | 0.36109 (13) | 0.0237 (5) | |
N12 | 0.1178 (4) | 0.60103 (16) | 0.41102 (10) | 0.0243 (5) | |
C13 | −0.0689 (5) | 0.55304 (18) | 0.45788 (12) | 0.0213 (5) | |
C14 | −0.2120 (5) | 0.62085 (18) | 0.51267 (13) | 0.0240 (5) | |
H14 | −0.1745 | 0.6995 | 0.5155 | 0.029* | |
C15 | −0.4038 (5) | 0.57448 (18) | 0.56162 (12) | 0.0226 (5) | |
N16 | −0.5416 (5) | 0.64086 (16) | 0.61467 (11) | 0.0295 (5) | |
H16A | −0.5082 | 0.7136 | 0.6177 | 0.035* | |
H16B | −0.6616 | 0.6097 | 0.6449 | 0.035* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0369 (13) | 0.0217 (10) | 0.0391 (11) | −0.0029 (11) | 0.0099 (11) | −0.0002 (9) |
C2 | 0.0197 (12) | 0.0202 (11) | 0.0276 (11) | −0.0006 (11) | −0.0048 (10) | 0.0026 (9) |
C3 | 0.0239 (12) | 0.0161 (10) | 0.0304 (11) | −0.0015 (11) | −0.0023 (11) | 0.0032 (9) |
C4 | 0.0214 (12) | 0.0161 (10) | 0.0268 (11) | −0.0003 (11) | −0.0064 (11) | 0.0009 (9) |
N5 | 0.0236 (11) | 0.0186 (9) | 0.0277 (9) | 0.0005 (10) | −0.0017 (9) | 0.0009 (8) |
C6 | 0.0212 (12) | 0.0227 (11) | 0.0240 (11) | −0.0006 (11) | −0.0055 (10) | 0.0028 (9) |
C7 | 0.0277 (13) | 0.0218 (11) | 0.0332 (12) | −0.0016 (11) | −0.0019 (12) | −0.0038 (10) |
C8 | 0.0271 (13) | 0.0319 (12) | 0.0313 (12) | 0.0020 (12) | 0.0019 (11) | −0.0040 (11) |
C9 | 0.0254 (13) | 0.0322 (13) | 0.0306 (12) | −0.0013 (11) | 0.0015 (12) | 0.0073 (10) |
C10 | 0.0287 (13) | 0.0243 (11) | 0.0299 (12) | −0.0029 (12) | 0.0003 (11) | 0.0041 (10) |
C11 | 0.0235 (13) | 0.0193 (11) | 0.0283 (11) | 0.0027 (11) | −0.0053 (11) | 0.0012 (9) |
N12 | 0.0250 (11) | 0.0187 (9) | 0.0290 (10) | 0.0000 (10) | −0.0017 (9) | 0.0010 (8) |
C13 | 0.0201 (13) | 0.0163 (10) | 0.0275 (11) | 0.0001 (10) | −0.0022 (10) | 0.0025 (9) |
C14 | 0.0241 (12) | 0.0151 (10) | 0.0328 (11) | −0.0001 (11) | −0.0047 (11) | −0.0006 (9) |
C15 | 0.0229 (12) | 0.0192 (11) | 0.0255 (11) | 0.0027 (11) | −0.0037 (11) | 0.0011 (9) |
N16 | 0.0343 (12) | 0.0201 (10) | 0.0342 (11) | 0.0011 (10) | 0.0059 (10) | −0.0012 (8) |
Geometric parameters (Å, º) top
N1—C2 | 1.372 (3) | C7—C8 | 1.368 (3) |
C2—C3 | 1.365 (3) | C8—C9 | 1.415 (3) |
C2—C15 | 1.465 (3) | C9—C10 | 1.359 (3) |
C3—C4 | 1.406 (3) | C10—C11 | 1.421 (3) |
C4—N5 | 1.342 (3) | C11—N12 | 1.357 (3) |
C4—C13 | 1.460 (3) | N12—C13 | 1.335 (3) |
N5—C6 | 1.352 (3) | C13—C14 | 1.412 (3) |
C6—C7 | 1.413 (3) | C14—C15 | 1.366 (3) |
C6—C11 | 1.439 (3) | C15—N16 | 1.371 (3) |
| | | |
C3—C2—N1 | 122.0 (2) | C10—C9—C8 | 120.4 (2) |
C3—C2—C15 | 119.1 (2) | C9—C10—C11 | 121.2 (2) |
N1—C2—C15 | 118.9 (2) | N12—C11—C10 | 120.2 (2) |
C2—C3—C4 | 122.2 (2) | N12—C11—C6 | 121.4 (2) |
N5—C4—C3 | 120.12 (19) | C10—C11—C6 | 118.4 (2) |
N5—C4—C13 | 121.0 (2) | C13—N12—C11 | 117.37 (19) |
C3—C4—C13 | 118.9 (2) | N12—C13—C14 | 120.50 (19) |
C4—N5—C6 | 117.59 (18) | N12—C13—C4 | 121.4 (2) |
N5—C6—C7 | 120.2 (2) | C14—C13—C4 | 118.1 (2) |
N5—C6—C11 | 121.2 (2) | C15—C14—C13 | 122.02 (19) |
C7—C6—C11 | 118.6 (2) | C14—C15—N16 | 121.7 (2) |
C8—C7—C6 | 121.1 (2) | C14—C15—C2 | 119.7 (2) |
C7—C8—C9 | 120.3 (2) | N16—C15—C2 | 118.7 (2) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···N5i | 0.86 | 2.39 | 3.154 (3) | 148 |
N1—H1B···C9ii | 0.86 | 2.79 | 3.586 (3) | 154 |
N16—H16A···N12iii | 0.86 | 2.29 | 3.119 (3) | 163 |
N16—H16B···C8ii | 0.86 | 2.68 | 3.474 (3) | 154 |
C3—H3···N5i | 0.93 | 2.63 | 3.371 (3) | 137 |
C14—H14···N12iii | 0.93 | 2.82 | 3.578 (3) | 139 |
Symmetry codes: (i) x−1/2, −y+1/2, −z+1; (ii) −x−1/2, −y+1, z+1/2; (iii) x−1/2, −y+3/2, −z+1. |
Experimental details
Crystal data |
Chemical formula | C12H10N4 |
Mr | 210.24 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 293 |
a, b, c (Å) | 4.8355 (8), 11.583 (2), 17.304 (3) |
V (Å3) | 969.2 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.3 × 0.25 × 0.2 |
|
Data collection |
Diffractometer | Bruker AXS SMART CCD area detector diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3272, 1182, 985 |
Rint | 0.032 |
(sin θ/λ)max (Å−1) | 0.625 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.041, 0.115, 1.05 |
No. of reflections | 1182 |
No. of parameters | 145 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.19, −0.19 |
Absolute structure parameter | not determined |
Selected geometric parameters (Å, º) topN1—C2 | 1.372 (3) | C11—N12 | 1.357 (3) |
C4—N5 | 1.342 (3) | N12—C13 | 1.335 (3) |
N5—C6 | 1.352 (3) | C15—N16 | 1.371 (3) |
| | | |
C3—C2—N1 | 122.0 (2) | C13—N12—C11 | 117.37 (19) |
N1—C2—C15 | 118.9 (2) | C14—C15—N16 | 121.7 (2) |
C4—N5—C6 | 117.59 (18) | N16—C15—C2 | 118.7 (2) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1A···N5i | 0.86 | 2.39 | 3.154 (3) | 148 |
N1—H1B···C9ii | 0.86 | 2.79 | 3.586 (3) | 154 |
N16—H16A···N12iii | 0.86 | 2.29 | 3.119 (3) | 163 |
N16—H16B···C8ii | 0.86 | 2.68 | 3.474 (3) | 154 |
C3—H3···N5i | 0.93 | 2.63 | 3.371 (3) | 137 |
C14—H14···N12iii | 0.93 | 2.82 | 3.578 (3) | 139 |
Symmetry codes: (i) x−1/2, −y+1/2, −z+1; (ii) −x−1/2, −y+1, z+1/2; (iii) x−1/2, −y+3/2, −z+1. |
The planar electron-rich heterocyclic diamine 2,3-diaminophenazine (DAP) is a compound which has long been of interest initially because of its chemical and physical properties and more recently because of its mutagenic and genotoxic behaviour. The fact that DAP has a rich and varied chemistry is demonstrated by the vast number of organic transformations that have been published in the literature. In addition, the compound has been well characterized spectroscopically by NMR, absorption and most notably by emission techniques, where the remarkable luminescence of DAP has been intensively studied and exploited in analytical and biochemical applications. \sch
DAP is known to luminesce strongly both in strongly polar organic solvents (Zheng et al., 1997) and in aqueous buffer solution especially when embedded within a micelle structure (Mekler & Bystryak, 1992). Indeed, it is the luminescence of DAP that sparked our interest in the molecule, especially as probes-containing phenazine have shown potential in the exploration of nucleic acid structure. Further, DAP has been shown to damage DNA (Watanabe et al., 1996) and so may have some role to play as a chemotherapeutic agent. The compound has found useful application in analytical chemistry as a catalymetric analyte, where it is used as a marker in fluorimetric determinations of laccose activity (Huang et al., 1998) and in immunoassay determination of enzyme-catalysed reactions such as the oxidation of 1,2-phenylenediamine (o-PD) by horseradish peroxidase (Jiao et al., 1998).
Synthetically, DAP is prepared by the catalysed, autosensitized or photochemical oxidation cyclization of o-PD. The oxidation has been catalysed by various oxidants, including silver oxide, lead(IV) oxide, ferric chloride, cupric chloride and perchlorate and by cobalt perchlorate (Crank & Makin, 1989). The oxidation takes place in two one-electron transfer steps - a mechanism which may have relevance when studying the biological functions of metal-containing proteins (Loveless et al., 1981). The fact that the heterocycle is produced in high yield in neutral or acid conditions, but not in basic conditions, perhaps explains why only structures of the protonated molecule (as its chloride or perchlorate salts) have been previously published (Brownstein & Enright, 1995; Peng & Liaw, 1986). These studies have shown that the heterocycle protonates at the phenazine nitrogen although spectroscopic evidence suggests that the more basic amine nitrogen atoms are protonated in solution. When one of the phenazine nitrogen atoms is protonated the cation may exist in six resonance forms which, when the individual π bond strengths are considered, explains the lack of symmetry of the bond lengths in the structures of protonated DAP. In contrast, the structure of DAP (Fig. 1.) shows a high degree of symmetry both in bond lengths and angles on each side of the molecular C2 axis (Table 1). In the solid state, the structure of DAP is essentially planar, however a small degree of bending is discernable. This curvature may be attributed to the geometry of the central pyrazine ring which displays some distortions from that of an ideal aromatic ring (Table 1).
The crystal packing of DAP (Fig. 2) is particularly interesting and as the molecule is replete with numerous π-bonding and hydrogen-bond donor and acceptor sites it may be expected that it can act as a particularly versatile supramolecular tecton. Indeed, it is found that DAP forms infinite π-π stacks in the x and z directions, a feature which is a consequence of the orthorhombic crystal system. The average arene-arene non-bonded distance is 3.64 Å. The infinite π stacks are connected in three dimensions by way of intermolecular hydrogen bonds (Table 2). The hydrogen bonds connect the amine H1A and H16A and the aromatic H3 and H14 protons of one molecule and the pyrazine nitrogen atoms (N5 and N12) of its nearest neighbour. In addition, there are T-bonded interactions which feature the terminal benzene ring (C6 to C11) of one molecule and the amine protons (H1B and H16B) of its nearest neighbour. The typical NH—π distance is 2.71 Å. The cumulative effect of these intermolecular interactions is to create a particularly attractive three dimensional supramolecular network.