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

Oosthuizen, U.; Schutte-Smith, M.; Visser, H.G.

doi:10.1107/S2414314619010162

organic compounds

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ISSN: 2414-3146

Volume 4| Part 7| July 2019| x191016

https://doi.org/10.1107/S2414314619010162

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

U. Oosthuizen,^a M. Schutte-Smith ^a and Hendrik G. Visser ^a ^*

^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.

Keywords: crystal structure; phenanthroline; functionalization; bidentate ligands.

CCDC reference: 1940842

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 ). 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). 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).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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
The molecular structure of the title compound showing 50% displacement ellipsoids.

In the extended structure, there are no π–π 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, Fig. 2). Adjacent molecules in the chain are rotated by approximately 90° with respect to each other (Fig. 3).

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
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 ) 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 ) (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 ). 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: ∊ (λ_max = 419 nm) = 19985 M⁻¹ cm⁻¹.

Refinement

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

Table 2
Experimental details

Crystal data
Chemical formula	C₁₂H₈N₄O₂
M_r	240.22
Crystal system, space group	Orthorhombic, Pbca
Temperature (K)	100
a, b, c (Å)	14.265 (8), 8.060 (4), 17.564 (9)
V (Å³)	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 )
T_min, T_max	0.984, 0.99
No. of measured, independent and observed [I > 2σ(I)] reflections	13477, 2426, 1204
R_int	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
Δρ_max, Δρ_min (e Å⁻³)	0.36, −0.39
Computer programs: APEX2 and SAINT (Bruker, 2012), SIR92 (Altomare et al., 1994 ), SHELXL2018/3 (Sheldrick, 2015 ), DIAMOND (Brandenburg, 2006 ) and OLEX2 (Dolomanov et al., 2009 ).

Structural data

CCDC reference: 1940842

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314619010162/hb4300sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314619010162/hb4300Isup2.hkl

checkCIF report

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

C₁₂H₈N₄O₂	F(000) = 992
M_r = 240.22	D_x = 1.58 Mg m⁻³
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 1396 reflections
a = 14.265 (8) Å	θ = 3.7–23.4°
b = 8.060 (4) Å	µ = 0.11 mm⁻¹
c = 17.564 (9) Å	T = 100 K
V = 2019.4 (19) Å³	Cuboid, yellow
Z = 8	0.37 × 0.12 × 0.09 mm

Data collection top

Bruker APEXII CCD diffractometer	1204 reflections with I > 2σ(I)
φ and ω scans	R_int = 0.093
Absorption correction: multi-scan (SADABS; Bruker, 2012)	θ_max = 28.0°, θ_min = 4.0°
T_min = 0.984, T_max = 0.99	h = −18→18
13477 measured reflections	k = −7→10
2426 independent reflections	l = −22→23

Refinement top

Refinement on F²	Hydrogen site location: mixed
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.058	w = 1/[σ²(F_o²) + (0.0669P)² + 0.4998P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.176	(Δ/σ)_max < 0.001
S = 1.03	Δρ_max = 0.36 e Å⁻³
2426 reflections	Δρ_min = −0.39 e Å⁻³
172 parameters	Extinction correction: SHELXL-2018/3 (Sheldrick 2015)
0 restraints	Extinction 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 U_iso (H) = 1.2 U_eq(C).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
N1	0.40826 (14)	0.4435 (3)	0.33237 (13)	0.0383 (6)
C12	0.26583 (16)	0.3587 (3)	0.27163 (14)	0.0286 (6)
C6	0.15781 (17)	0.5134 (3)	0.38771 (14)	0.0309 (6)
C7	0.25963 (17)	0.5190 (3)	0.39240 (14)	0.0300 (6)
C11	0.31313 (17)	0.4415 (3)	0.33443 (15)	0.0305 (6)
C4	0.16718 (16)	0.3585 (3)	0.26734 (14)	0.0284 (6)
N2	0.32090 (15)	0.2864 (3)	0.21825 (13)	0.0356 (6)
N3	0.01725 (16)	0.4325 (3)	0.31972 (18)	0.0445 (7)
C5	0.11029 (17)	0.4399 (3)	0.32623 (15)	0.0311 (6)
O1	0.02003 (14)	0.6244 (3)	0.43663 (12)	0.0562 (7)
N4	0.10335 (16)	0.5857 (3)	0.44757 (14)	0.0421 (6)
C9	0.40771 (19)	0.6088 (4)	0.44486 (17)	0.0458 (8)
H7	0.442575	0.66799	0.482097	0.055*
C8	0.31192 (19)	0.6052 (4)	0.44809 (16)	0.0404 (7)
H6	0.280266	0.661066	0.488166	0.048*
C1	0.27861 (19)	0.2137 (4)	0.15956 (15)	0.0393 (7)
H1	0.316626	0.164069	0.121416	0.047*
C3	0.12573 (19)	0.2785 (3)	0.20499 (15)	0.0364 (7)
H3	0.059429	0.274357	0.200254	0.044*
C2	0.18162 (19)	0.2063 (4)	0.15100 (16)	0.0383 (7)
H2	0.154655	0.151906	0.108296	0.046*
C10	0.4533 (2)	0.5254 (4)	0.38678 (18)	0.0471 (8)
H8	0.51987	0.526878	0.385799	0.057*
O2	0.13845 (16)	0.6016 (4)	0.51179 (13)	0.0786 (9)
H4A	−0.009 (2)	0.385 (4)	0.2794 (19)	0.062 (11)*
H4B	−0.020 (3)	0.483 (5)	0.356 (2)	0.089 (13)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0250 (12)	0.0449 (14)	0.0449 (15)	−0.0012 (10)	−0.0059 (10)	−0.0005 (11)
C12	0.0267 (13)	0.0276 (13)	0.0316 (15)	0.0004 (10)	−0.0020 (11)	0.0042 (11)
C6	0.0295 (14)	0.0318 (15)	0.0314 (16)	0.0029 (11)	0.0023 (11)	0.0023 (11)
C7	0.0311 (13)	0.0289 (13)	0.0299 (15)	0.0011 (10)	−0.0031 (11)	0.0039 (11)
C11	0.0241 (13)	0.0319 (14)	0.0357 (17)	−0.0018 (10)	−0.0045 (11)	0.0059 (12)
C4	0.0250 (13)	0.0297 (13)	0.0305 (15)	−0.0010 (11)	−0.0015 (11)	0.0049 (11)
N2	0.0286 (12)	0.0423 (14)	0.0359 (14)	0.0018 (10)	0.0011 (10)	−0.0001 (11)
N3	0.0244 (12)	0.0594 (17)	0.0496 (18)	0.0033 (11)	−0.0012 (12)	−0.0095 (14)
C5	0.0249 (13)	0.0335 (14)	0.0349 (16)	−0.0005 (10)	0.0005 (11)	0.0040 (12)
O1	0.0419 (12)	0.0726 (16)	0.0540 (15)	0.0196 (11)	0.0072 (10)	−0.0093 (11)
N4	0.0380 (14)	0.0534 (16)	0.0349 (15)	−0.0023 (12)	0.0047 (12)	−0.0033 (11)
C9	0.0395 (17)	0.0499 (19)	0.048 (2)	−0.0064 (14)	−0.0132 (14)	−0.0088 (15)
C8	0.0392 (16)	0.0405 (16)	0.0415 (18)	−0.0008 (13)	−0.0048 (13)	−0.0052 (13)
C1	0.0400 (16)	0.0447 (17)	0.0331 (17)	0.0039 (13)	0.0041 (13)	0.0003 (13)
C3	0.0293 (14)	0.0395 (16)	0.0405 (17)	−0.0023 (12)	−0.0049 (12)	0.0011 (13)
C2	0.0392 (15)	0.0423 (17)	0.0333 (17)	−0.0042 (13)	−0.0035 (12)	−0.0008 (13)
C10	0.0269 (14)	0.0532 (19)	0.061 (2)	−0.0059 (13)	−0.0116 (14)	−0.0047 (16)
O2	0.0519 (15)	0.142 (3)	0.0419 (15)	−0.0144 (15)	0.0048 (12)	−0.0285 (14)

Geometric parameters (Å, º) top

N1—C10	1.327 (3)	N3—H4A	0.89 (3)
N1—C11	1.358 (3)	N3—H4B	0.93 (4)
C12—N2	1.355 (3)	O1—N4	1.244 (3)
C12—C4	1.409 (3)	N4—O2	1.241 (3)
C12—C11	1.455 (3)	C9—C8	1.368 (4)
C6—C5	1.406 (4)	C9—C10	1.384 (4)
C6—N4	1.431 (3)	C9—H7	0.95
C6—C7	1.456 (3)	C8—H6	0.95
C7—C8	1.413 (4)	C1—C2	1.393 (4)
C7—C11	1.418 (4)	C1—H1	0.95
C4—C3	1.402 (4)	C3—C2	1.369 (4)
C4—C5	1.469 (4)	C3—H3	0.95
N2—C1	1.331 (3)	C2—H2	0.95
N3—C5	1.333 (3)	C10—H8	0.95

C10—N1—C11	118.1 (2)	C6—C5—C4	117.5 (2)
N2—C12—C4	122.8 (2)	O2—N4—O1	120.0 (2)
N2—C12—C11	116.9 (2)	O2—N4—C6	119.4 (2)
C4—C12—C11	120.3 (2)	O1—N4—C6	120.5 (2)
C5—C6—N4	118.3 (2)	C8—C9—C10	119.3 (3)
C5—C6—C7	122.5 (2)	C8—C9—H7	120.4
N4—C6—C7	119.2 (2)	C10—C9—H7	120.4
C8—C7—C11	115.5 (2)	C9—C8—C7	120.6 (3)
C8—C7—C6	125.6 (2)	C9—C8—H6	119.7
C11—C7—C6	118.9 (2)	C7—C8—H6	119.7
N1—C11—C7	123.5 (2)	N2—C1—C2	123.6 (3)
N1—C11—C12	116.7 (2)	N2—C1—H1	118.2
C7—C11—C12	119.8 (2)	C2—C1—H1	118.2
C3—C4—C12	117.6 (2)	C2—C3—C4	119.4 (2)
C3—C4—C5	121.5 (2)	C2—C3—H3	120.3
C12—C4—C5	120.9 (2)	C4—C3—H3	120.3
C1—N2—C12	117.6 (2)	C3—C2—C1	119.1 (3)
C5—N3—H4A	121 (2)	C3—C2—H2	120.5
C5—N3—H4B	119 (2)	C1—C2—H2	120.5
H4A—N3—H4B	120 (3)	N1—C10—C9	123.0 (3)
N3—C5—C6	124.4 (3)	N1—C10—H8	118.5
N3—C5—C4	118.0 (3)	C9—C10—H8	118.5

C5—C6—C7—C8	173.1 (3)	C7—C6—C5—N3	−179.8 (2)
N4—C6—C7—C8	−6.7 (4)	N4—C6—C5—C4	−176.8 (2)
C5—C6—C7—C11	−2.7 (4)	C7—C6—C5—C4	3.4 (4)
N4—C6—C7—C11	177.5 (2)	C3—C4—C5—N3	1.4 (4)
C10—N1—C11—C7	−1.4 (4)	C12—C4—C5—N3	−178.7 (2)
C10—N1—C11—C12	176.6 (2)	C3—C4—C5—C6	178.4 (2)
C8—C7—C11—N1	1.9 (4)	C12—C4—C5—C6	−1.7 (4)
C6—C7—C11—N1	178.2 (2)	C5—C6—N4—O2	156.5 (3)
C8—C7—C11—C12	−176.0 (2)	C7—C6—N4—O2	−23.7 (4)
C6—C7—C11—C12	0.2 (3)	C5—C6—N4—O1	−19.7 (4)
N2—C12—C11—N1	2.2 (3)	C7—C6—N4—O1	160.1 (3)
C4—C12—C11—N1	−176.7 (2)	C10—C9—C8—C7	−0.7 (4)
N2—C12—C11—C7	−179.7 (2)	C11—C7—C8—C9	−0.8 (4)
C4—C12—C11—C7	1.4 (4)	C6—C7—C8—C9	−176.7 (3)
N2—C12—C4—C3	0.4 (4)	C12—N2—C1—C2	−1.0 (4)
C11—C12—C4—C3	179.2 (2)	C12—C4—C3—C2	−0.7 (4)
N2—C12—C4—C5	−179.4 (2)	C5—C4—C3—C2	179.1 (2)
C11—C12—C4—C5	−0.6 (4)	C4—C3—C2—C1	0.2 (4)
C4—C12—N2—C1	0.4 (4)	N2—C1—C2—C3	0.6 (4)
C11—C12—N2—C1	−178.4 (2)	C11—N1—C10—C9	−0.3 (4)
N4—C6—C5—N3	−0.1 (4)	C8—C9—C10—N1	1.4 (5)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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−1/2, 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

Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435. CrossRef Web of Science IUCr Journals Google Scholar
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6-Nitro-1,10-phenanthrolin-5-amine

Structure description

Synthesis and crystallization

Refinement

Structural data

Funding information

References

organic compounds