organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2414-3146

6-Nitro-1,10-phenanthrolin-5-amine

aDepartment of Chemistry, Unversity of the Free State, PO Box 339, Bloemfontein, 9301, South Africa
*Correspondence e-mail: visserhg@ufs.ac.za

Edited by W. T. A. Harrison, University of Aberdeen, Scotland (Received 31 May 2019; accepted 16 July 2019; online 19 July 2019)

In the title compound, C12H8N4O2, the dihedral angle between the phenanthroline ring system and the nitro group is 23.75 (14)°. The mol­ecule features intra­molecular N—H⋯O and C—H⋯O hydrogen bonds. In the crystal, N—H⋯(N,N), C—H⋯N and C—H⋯O hydrogen bonds link the mol­ecules into [100] chains.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

When 1,10-phenanthroline coordinates to transition metals, it forms thermally and chemically stable complexes. The combination of electronic transitions of the metal and the conjugated π- electron system of 1,10-phenanthroline leads to complexes with inter­esting photophysical, photochemical and electrochemical properties. To expand this chemistry, the synthesis of 1,10-phenanthroline derivatives with substituents on positions 3 to 8 is necessary (Khimich et al., 2006[Khimich, N. N., Obrezkov, N. P. & Koptelova, L. A. (2006). Russ. J. Org. Chem. 42, 555-557.]). The title compound is formed by the amination of 5-nitro-1,10-phenanthroline using ethanol and dioxane. The use of phendi­amine (1,10-phenanthroline-5,6-di­amine) as an N,N′-bidentate ligand was one of the main aims in the study. Phendi­amine can be coordinated to two metal centres and can act as a bridging ligand. 5-Amino-6-nitro-1,10-phenanthroline is comparable to phendione (1,10-phenanthroline-5,6-dione) and 5-nitro-1,10-phenanthroline.

The title compound crystallizes in space group Pbca with one mol­ecule in the asymmetric unit (Fig. 1[link]). The nitro group is twisted from the rest of the mol­ecule by 23.75 (14)°. The O atoms of the nitro group accept intra­molecular hydrogen bonds from the adjacent NH and CH groups (Table 1[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N3—H4A⋯N1i 0.89 (3) 2.34 (3) 3.092 (4) 143 (3)
N3—H4A⋯N2i 0.89 (3) 2.55 (3) 3.111 (4) 122 (2)
N3—H4B⋯O1 0.93 (4) 1.90 (4) 2.571 (4) 127 (3)
C3—H3⋯N1i 0.95 2.61 3.438 (4) 145
C8—H6⋯O2 0.95 2.12 2.716 (4) 119
C9—H7⋯O1ii 0.95 2.46 3.395 (4) 167
Symmetry codes: (i) [x-{\script{1\over 2}}, y, -z+{\script{1\over 2}}]; (ii) [x+{\script{1\over 2}}, -y+{\script{3\over 2}}, -z+1].
[Figure 1]
Figure 1
The mol­ecular structure of the title compound showing 50% displacement ellipsoids.

In the extended structure, there are no ππ stacking inter­actions but infinite chains are observed propagating along the a-axis direction via N3—H4A⋯(N1,N2), C3—H3⋯N1 and C9—H7⋯O1 inter­actions (Table 1[link], Fig. 2[link]). Adjacent mol­ecules in the chain are rotated by approximately 90° with respect to each other (Fig. 3[link]).

[Figure 2]
Figure 2
Illustration of the hydrogen-bonding inter­actions observed in 5-amino-6-nitro-1,10-phenanthroline. Inter­molecular inter­actions are illustrated in green dashed lines while intra­molecular inter­actions are illustrated by purple dashed lines.
[Figure 3]
Figure 3
Representation of the packing of 5-amino-6-nitro-1,10-phenanthroline along the a axis.

A search of the Cambridge Structural Database (Version 5.32, update Feb 2011, Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) for 1,10-phenanthroline derivatives with nitro­gen atoms on positions 5 and 6 gave 136 hits, with a variety of substituents on the nitro­gen atoms. One of these structures, N′′,N′′′-1,10-phenanthroline-5,6-diylbis (N,N,N′,N′-tetra­methyl­guanidine) reported by Ortmeyer et al., (2017[Ortmeyer, J., Vukadinovic, Y., Neuba, A., Egold, H., Flörke, U. & Henkel, G. (2017). Eur. J. Org. Chem. pp. 6085-6095.]) (refcode ZEQREV) has similar bond distances and angles to those in the title compound.

Synthesis and crystallization

The synthesis of the title compound was achieved according to the literature method of Bolger et al. (1996[Bolger, J., Gourdon, A., Ishow, E. & Launay, J. (1996). Inorg. Chem. 35, 2937-2944.]). 5-Nitro-1,10-phenanthroline (3.49 g, 15.5 mmol) was dissolved in a mixture of 100 ml of ethanol/dioxane (3:2) and heated to 60°C until all the solids were dissolved. It was rapidly cooled to 4°C and formed a fine suspension. Powdered hydroxyl amine hydro­chloride (6.84 g, 9.84 mmol) was added, followed by the dropwise addition of KOH (7.27 g, 129.5 mmol) in methanol (100 ml). The solution was stirred at 4°C for one hour and then heated to 60°C for another hour. The solution was poured onto ice and resulted in the formation of a yellow precipitate, which was washed with water and methanol after filtration. Yellow single crystals suitable for X-ray diffraction were obtained in chloro­form at room temperature. Yield: 0.5441 g (14%). IR (ATR, cm−1): 1626, 1523, 1486, 1433, 1383, 1302, 1260, 1172, 1095, 827, 796, 734, 670. 1H NMR (300 MHz, DMSO-d6): δ 9.2 (dd, J = 1.35, 4.26 Hz, 1H), 9.1 (dd, J = 1.36, 8.44 Hz, 1H), 8.8 (dd, J = 1.47, 4.27 Hz, 1H), 8.7 (dd, J = 1.48, 8.58 Hz, 1H), 8.6 (s, 2H), 7.9 (dd, J = 4.27, 8.46 Hz, 1H) and 7.7 (dd, J = 4.15, 8.46 Hz, 1H). 13C NMR (600 MHz, DMSO-d6): δ 154, 148, 147, 144, 140, 137, 134, 131, 125, 124, 123, 121. UV/Vis: (λmax = 419 nm) = 19985 M−1 cm−1.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link].

Table 2
Experimental details

Crystal data
Chemical formula C12H8N4O2
Mr 240.22
Crystal system, space group Orthorhombic, Pbca
Temperature (K) 100
a, b, c (Å) 14.265 (8), 8.060 (4), 17.564 (9)
V3) 2019.4 (19)
Z 8
Radiation type Mo Kα
μ (mm−1) 0.11
Crystal size (mm) 0.37 × 0.12 × 0.09
 
Data collection
Diffractometer Bruker APEXII CCD
Absorption correction Multi-scan (SADABS; Bruker, 2012[Bruker (2012). APEX2, SAINT and SADABS. Bruker AXS Inc, Madison, Wisconsin, USA.])
Tmin, Tmax 0.984, 0.99
No. of measured, independent and observed [I > 2σ(I)] reflections 13477, 2426, 1204
Rint 0.093
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.058, 0.176, 1.03
No. of reflections 2426
No. of parameters 172
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.36, −0.39
Computer programs: APEX2 and SAINT (Bruker, 2012[Bruker (2012). APEX2, SAINT and SADABS. Bruker AXS Inc, Madison, Wisconsin, USA.]), SIR92 (Altomare et al., 1994[Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435.]), SHELXL2018/3 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), DIAMOND (Brandenburg, 2006[Brandenburg, K. (2006). DIAMOND. Crystal Impact GbR, Bonn, Germany.]) and OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]).

Structural data


Computing details top

Data collection: APEX2 (Bruker, 2012); cell refinement: SAINT (Bruker, 2012); data reduction: SAINT (Bruker, 2012); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015); molecular graphics: DIAMOND (Brandenburg, 2006); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

6-Nitro-1,10-phenanthrolin-5-amine top
Crystal data top
C12H8N4O2F(000) = 992
Mr = 240.22Dx = 1.58 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 1396 reflections
a = 14.265 (8) Åθ = 3.7–23.4°
b = 8.060 (4) ŵ = 0.11 mm1
c = 17.564 (9) ÅT = 100 K
V = 2019.4 (19) Å3Cuboid, yellow
Z = 80.37 × 0.12 × 0.09 mm
Data collection top
Bruker APEXII CCD
diffractometer
1204 reflections with I > 2σ(I)
φ and ω scansRint = 0.093
Absorption correction: multi-scan
(SADABS; Bruker, 2012)
θmax = 28.0°, θmin = 4.0°
Tmin = 0.984, Tmax = 0.99h = 1818
13477 measured reflectionsk = 710
2426 independent reflectionsl = 2223
Refinement top
Refinement on F2Hydrogen site location: mixed
Least-squares matrix: fullH atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.058 w = 1/[σ2(Fo2) + (0.0669P)2 + 0.4998P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.176(Δ/σ)max < 0.001
S = 1.03Δρmax = 0.36 e Å3
2426 reflectionsΔρmin = 0.39 e Å3
172 parametersExtinction correction: SHELXL-2018/3 (Sheldrick 2015)
0 restraintsExtinction coefficient: 0.0047 (14)
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. Aromatic H atoms were positioned geometrically with a C—H distance of 0.95 Å and constrained to ride on their parent atoms with Uiso (H) = 1.2 Ueq(C).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
N10.40826 (14)0.4435 (3)0.33237 (13)0.0383 (6)
C120.26583 (16)0.3587 (3)0.27163 (14)0.0286 (6)
C60.15781 (17)0.5134 (3)0.38771 (14)0.0309 (6)
C70.25963 (17)0.5190 (3)0.39240 (14)0.0300 (6)
C110.31313 (17)0.4415 (3)0.33443 (15)0.0305 (6)
C40.16718 (16)0.3585 (3)0.26734 (14)0.0284 (6)
N20.32090 (15)0.2864 (3)0.21825 (13)0.0356 (6)
N30.01725 (16)0.4325 (3)0.31972 (18)0.0445 (7)
C50.11029 (17)0.4399 (3)0.32623 (15)0.0311 (6)
O10.02003 (14)0.6244 (3)0.43663 (12)0.0562 (7)
N40.10335 (16)0.5857 (3)0.44757 (14)0.0421 (6)
C90.40771 (19)0.6088 (4)0.44486 (17)0.0458 (8)
H70.4425750.667990.4820970.055*
C80.31192 (19)0.6052 (4)0.44809 (16)0.0404 (7)
H60.2802660.6610660.4881660.048*
C10.27861 (19)0.2137 (4)0.15956 (15)0.0393 (7)
H10.3166260.1640690.1214160.047*
C30.12573 (19)0.2785 (3)0.20499 (15)0.0364 (7)
H30.0594290.2743570.2002540.044*
C20.18162 (19)0.2063 (4)0.15100 (16)0.0383 (7)
H20.1546550.1519060.1082960.046*
C100.4533 (2)0.5254 (4)0.38678 (18)0.0471 (8)
H80.519870.5268780.3857990.057*
O20.13845 (16)0.6016 (4)0.51179 (13)0.0786 (9)
H4A0.009 (2)0.385 (4)0.2794 (19)0.062 (11)*
H4B0.020 (3)0.483 (5)0.356 (2)0.089 (13)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0250 (12)0.0449 (14)0.0449 (15)0.0012 (10)0.0059 (10)0.0005 (11)
C120.0267 (13)0.0276 (13)0.0316 (15)0.0004 (10)0.0020 (11)0.0042 (11)
C60.0295 (14)0.0318 (15)0.0314 (16)0.0029 (11)0.0023 (11)0.0023 (11)
C70.0311 (13)0.0289 (13)0.0299 (15)0.0011 (10)0.0031 (11)0.0039 (11)
C110.0241 (13)0.0319 (14)0.0357 (17)0.0018 (10)0.0045 (11)0.0059 (12)
C40.0250 (13)0.0297 (13)0.0305 (15)0.0010 (11)0.0015 (11)0.0049 (11)
N20.0286 (12)0.0423 (14)0.0359 (14)0.0018 (10)0.0011 (10)0.0001 (11)
N30.0244 (12)0.0594 (17)0.0496 (18)0.0033 (11)0.0012 (12)0.0095 (14)
C50.0249 (13)0.0335 (14)0.0349 (16)0.0005 (10)0.0005 (11)0.0040 (12)
O10.0419 (12)0.0726 (16)0.0540 (15)0.0196 (11)0.0072 (10)0.0093 (11)
N40.0380 (14)0.0534 (16)0.0349 (15)0.0023 (12)0.0047 (12)0.0033 (11)
C90.0395 (17)0.0499 (19)0.048 (2)0.0064 (14)0.0132 (14)0.0088 (15)
C80.0392 (16)0.0405 (16)0.0415 (18)0.0008 (13)0.0048 (13)0.0052 (13)
C10.0400 (16)0.0447 (17)0.0331 (17)0.0039 (13)0.0041 (13)0.0003 (13)
C30.0293 (14)0.0395 (16)0.0405 (17)0.0023 (12)0.0049 (12)0.0011 (13)
C20.0392 (15)0.0423 (17)0.0333 (17)0.0042 (13)0.0035 (12)0.0008 (13)
C100.0269 (14)0.0532 (19)0.061 (2)0.0059 (13)0.0116 (14)0.0047 (16)
O20.0519 (15)0.142 (3)0.0419 (15)0.0144 (15)0.0048 (12)0.0285 (14)
Geometric parameters (Å, º) top
N1—C101.327 (3)N3—H4A0.89 (3)
N1—C111.358 (3)N3—H4B0.93 (4)
C12—N21.355 (3)O1—N41.244 (3)
C12—C41.409 (3)N4—O21.241 (3)
C12—C111.455 (3)C9—C81.368 (4)
C6—C51.406 (4)C9—C101.384 (4)
C6—N41.431 (3)C9—H70.95
C6—C71.456 (3)C8—H60.95
C7—C81.413 (4)C1—C21.393 (4)
C7—C111.418 (4)C1—H10.95
C4—C31.402 (4)C3—C21.369 (4)
C4—C51.469 (4)C3—H30.95
N2—C11.331 (3)C2—H20.95
N3—C51.333 (3)C10—H80.95
C10—N1—C11118.1 (2)C6—C5—C4117.5 (2)
N2—C12—C4122.8 (2)O2—N4—O1120.0 (2)
N2—C12—C11116.9 (2)O2—N4—C6119.4 (2)
C4—C12—C11120.3 (2)O1—N4—C6120.5 (2)
C5—C6—N4118.3 (2)C8—C9—C10119.3 (3)
C5—C6—C7122.5 (2)C8—C9—H7120.4
N4—C6—C7119.2 (2)C10—C9—H7120.4
C8—C7—C11115.5 (2)C9—C8—C7120.6 (3)
C8—C7—C6125.6 (2)C9—C8—H6119.7
C11—C7—C6118.9 (2)C7—C8—H6119.7
N1—C11—C7123.5 (2)N2—C1—C2123.6 (3)
N1—C11—C12116.7 (2)N2—C1—H1118.2
C7—C11—C12119.8 (2)C2—C1—H1118.2
C3—C4—C12117.6 (2)C2—C3—C4119.4 (2)
C3—C4—C5121.5 (2)C2—C3—H3120.3
C12—C4—C5120.9 (2)C4—C3—H3120.3
C1—N2—C12117.6 (2)C3—C2—C1119.1 (3)
C5—N3—H4A121 (2)C3—C2—H2120.5
C5—N3—H4B119 (2)C1—C2—H2120.5
H4A—N3—H4B120 (3)N1—C10—C9123.0 (3)
N3—C5—C6124.4 (3)N1—C10—H8118.5
N3—C5—C4118.0 (3)C9—C10—H8118.5
C5—C6—C7—C8173.1 (3)C7—C6—C5—N3179.8 (2)
N4—C6—C7—C86.7 (4)N4—C6—C5—C4176.8 (2)
C5—C6—C7—C112.7 (4)C7—C6—C5—C43.4 (4)
N4—C6—C7—C11177.5 (2)C3—C4—C5—N31.4 (4)
C10—N1—C11—C71.4 (4)C12—C4—C5—N3178.7 (2)
C10—N1—C11—C12176.6 (2)C3—C4—C5—C6178.4 (2)
C8—C7—C11—N11.9 (4)C12—C4—C5—C61.7 (4)
C6—C7—C11—N1178.2 (2)C5—C6—N4—O2156.5 (3)
C8—C7—C11—C12176.0 (2)C7—C6—N4—O223.7 (4)
C6—C7—C11—C120.2 (3)C5—C6—N4—O119.7 (4)
N2—C12—C11—N12.2 (3)C7—C6—N4—O1160.1 (3)
C4—C12—C11—N1176.7 (2)C10—C9—C8—C70.7 (4)
N2—C12—C11—C7179.7 (2)C11—C7—C8—C90.8 (4)
C4—C12—C11—C71.4 (4)C6—C7—C8—C9176.7 (3)
N2—C12—C4—C30.4 (4)C12—N2—C1—C21.0 (4)
C11—C12—C4—C3179.2 (2)C12—C4—C3—C20.7 (4)
N2—C12—C4—C5179.4 (2)C5—C4—C3—C2179.1 (2)
C11—C12—C4—C50.6 (4)C4—C3—C2—C10.2 (4)
C4—C12—N2—C10.4 (4)N2—C1—C2—C30.6 (4)
C11—C12—N2—C1178.4 (2)C11—N1—C10—C90.3 (4)
N4—C6—C5—N30.1 (4)C8—C9—C10—N11.4 (5)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H4A···N1i0.89 (3)2.34 (3)3.092 (4)143 (3)
N3—H4A···N2i0.89 (3)2.55 (3)3.111 (4)122 (2)
N3—H4B···O10.93 (4)1.90 (4)2.571 (4)127 (3)
C3—H3···N1i0.952.613.438 (4)145
C8—H6···O20.952.122.716 (4)119
C9—H7···O1ii0.952.463.395 (4)167
Symmetry codes: (i) x1/2, y, z+1/2; (ii) x+1/2, y+3/2, z+1.
 

Funding information

This research was supported by the Central Research Fund (CRF) of the University of the Free State for 2018.

References

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First citationDolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationGroom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179.  Web of Science CrossRef IUCr Journals Google Scholar
First citationKhimich, N. N., Obrezkov, N. P. & Koptelova, L. A. (2006). Russ. J. Org. Chem. 42, 555–557.  CrossRef CAS Google Scholar
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First citationSheldrick, G. M. (2015). Acta Cryst. C71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar

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