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Acta Crystallogr C. 2009 September 15; 65(Pt 9): o438–o440.
Published online 2009 August 8. doi:  10.1107/S0108270109029618
PMCID: PMC2737422

5-Nitro-N 4,N 6-diphenyl­pyrimidine-4,6-diamine: polarized mol­ecules linked into π-stacked chains via three-centre C—H(...)(O)2 hydrogen bonds


Mol­ecules of the title compound, C16H13N5O2, have no inter­nal symmetry despite the symmetric pattern of substitution in the pyrimidine ring. The intra­molecular distances indicate polarization of the electronic structure. There are two intra­molecular N—H(...)O hydrogen bonds and mol­ecules are linked into centrosymmetric dimers by pairs of three-centre C—H(...)(O)2 hydrogen bonds. These dimers are linked into chains by means of a π–π stacking inter­action.


We report here the mol­ecular and supra­molecular structure of the title compound, (I) (Fig. 1 [triangle]), which we compare with the related compounds (II)–(V) (Makarov et al., 1997 [triangle]; Quesada et al., 2003 [triangle]; Glidewell et al., 2003 [triangle]; Quesada et al., 2004 [triangle], respectively).

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Object name is c-65-0o438-scheme1.jpg

Figure 1
The mol­ecular structure of (I), showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level.

Despite the presence of three adjacent substituents in the pyrimidine ring in (I), this ring is planar within experimental uncertainty; the maximum deviation from the mean plane of the ring is seen for atom N3 [0.007 (2) Å; Fig. 1 [triangle]]. This behaviour may be contrasted with that of the close analogue (II) [Cambridge Structural Database (Allen, 2002 [triangle]) refcode RENTUZ; Makarov et al., 1997 [triangle]], where the pyrimidine ring adopts a boat conformation. The maximum deviation from the mean ring plane in (II) is shown by the C atom corresponding to atom C5 in (I) [0.167 (2) Å], while the nitro N atom is displaced by 1.028 (2) Å to one side of the mean ring plane and the two N atoms of the dimethyl­amine groups are displaced by 0.411 (2) and 0.443 (2) Å, respectively, to the other side of the ring plane. Similarly, in the cation of (III) (Quesada et al., 2003 [triangle]), where the pyrimidine ring adopts a twist-boat conformation, the N atom of the nitro group is displaced by 1.273 (3) Å to one side of the mean plane of the ring, while the N atoms of the two piperidine substituents are displaced by 0.111 (3) and 0.257 (3) Å to the opposite side of the mean plane. Significant distortion from planarity is, in fact, quite commonly but not invariably observed in highly substituted pyrimidines, particularly in those carrying three adjacent substituents at positions 4, 5 and 6 (Low et al., 2007 [triangle]; Melguizo et al., 2003 [triangle]; Quesada et al., 2003 [triangle], 2004 [triangle]; Trilleras et al., 2007 [triangle], 2009 [triangle]; Cobo et al., 2008 [triangle]).

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Object name is c-65-0o438-scheme2.jpg

The mol­ecular conformation in (I) can be defined in terms of a small number of torsion angles (Table 1 [triangle]), which indicate that, while the nitro group and one of the phenyl rings (C61–C66) are essentially coplanar with the pyrimidine ring, the other phenyl ring (C41–C46) is markedly displaced from this plane. Thus, the dihedral angles between the plane of the pyrimidine ring and those of the C41–C46 and C61–C66 rings, respectively, are 60.9 (2) and 1.8 (2)°. Accordingly, the mol­ecule has no inter­nal symmetry, even though the pattern of substituents on the pyrimidine ring permits C 2v (mm2) mol­ecular symmetry, or either of its subgroups, C 2 or Cs. The fact that the C61–C66 ring is effectively coplanar with the py­rim­i­dine ring indicates that there are no intra­molecular factors preventing the adoption of the full mol­ecular symmetry in the crystal. Thus, (I) is an example of a crystal structure in which the mol­ecules exhibit far less than the full mol­ecular symmetry. Perhaps the most familiar example of this phenomenon is benzene, where the unperturbed mol­ecule in the gas phase has D 6h (6/mmm) symmetry (Kimura & Kubo, 1960 [triangle]), but only a centre of inversion is retained in the crystalline state for both ortho­rhom­bic (Cox et al., 1958 [triangle]; Bacon et al., 1964 [triangle]) and monoclinic (Fourme et al., 1971 [triangle]) polymorphs.

Table 1
Selected geometric parameters (Å, °)

The mol­ecule of dimethoxy­nitro­pyrimidine (IV) (Glidewell et al., 2003 [triangle]) exhibits no crystallographic symmetry, but the non-H atoms are effectively coplanar, apart from the nitro group, which is twisted out of the ring plane by some 30°, so that this mol­ecule exhibits approximate but noncrystallographic C 2 rotational symmetry. The deviation of the nitro group from the ring plane in (IV) is best attributed to nonbonded electronic repulsions between the O atoms of the nitro group and those of the meth­oxy groups, in contrast to the attractive N—H(...)O hydrogen bonds in (I), where the nitro group is effectively coplanar with the pyrimidine ring.

Within the mol­ecule of (I), the C5—N5 bond (Table 1 [triangle]) is very short for its type [mean value (Allen et al., 1987 [triangle]) = 1.468 Å and lower quartile value = 1.460 Å], while the N—O distances are both long (mean value = 1.217 Å and upper quartile value = 1.225 Å); similarly, the C4—N4 and C6—N6 bonds are short for their type (mean value = 1.353 Å and lower quartile value = 1.347 Å), while the C4—C5 and C5—C6 bonds are both long (mean value in pyrimidines = 1.387 Å and upper quartile value = 1.400 Å). These values indicate that polarized forms such as (Ia) and (Ib) are significant contributors to the overall electronic structure in addition to the delocalized aromatic form (I). The corresponding distances in (II) exhibit an exactly analogous pattern of behaviour, showing firstly that the development of polarized forms involving electronic delocalization from amine groups to nitro groups does not depend upon the presence of a planar mol­ecular skeleton, and secondly that the energy cost of evading steric clashes between adjacent substituents by rotation of the amine and nitro groups about the exocyclic C—N bonds, with concomitant loss of the delocalization, exceeds that of distorting the formally aromatic ring. Compound (V) (Quesada et al., 2004 [triangle]) is another close analogue of (I), containing two primary amine substituents, but with a nitroso group rather than a nitro group, so that only one intra­molecular N—H(...)O hydrogen bond is present; again the electronic structure is markedly polarized, with extensive delocalization involving all three amine substituents.

Each of the two independent N—H bonds participates in an intra­molecular hydrogen bond (Table 2 [triangle]), forming two edge-fused S(6) motifs (Bernstein et al., 1995 [triangle]), but the N—H bonds play no role in the inter­molecular aggregation. Instead, pairs of mol­ecules are linked into centrosymmetric dimers by means of an asymmetric, but effectively planar, three-centre C—H(...)(O)2 hydrogen bond, in which the O51i(...)H66(...)O52i [symmetry code: (i) −x, −y + 2, −z + 1] angle is 51°, giving a sum of angles at H66 of 359°. The dimer thus contains two concentric and centrosymmetric An external file that holds a picture, illustration, etc.
Object name is c-65-0o438-efi1.jpg(16) motifs together with two symmetry-related An external file that holds a picture, illustration, etc.
Object name is c-65-0o438-efi2.jpg(4) rings (Fig. 2 [triangle]). These hydrogen-bonded dimers are linked into a chain by a single π–π stacking inter­action. The planes of the pyrimidine ring in the mol­ecule at (x, y, z) and the C61–C66 aryl ring in the mol­ecule at (−x + 1, −y + 1, −z + 1) make a dihedral angle of 1.8 (2)°, with an inter­planar spacing of ca 3.36 Å. The corresponding ring-centroid separation is 3.6500 (15) Å, with a ring-centroid offset of ca 1.426 Å. Propagation of this inter­action by inversion thus links the hydrogen-bonded dimers centred at (n, 1 − n, An external file that holds a picture, illustration, etc.
Object name is c-65-0o438-efi3.jpg), where n represents an integer, into a chain running parallel to the [1An external file that holds a picture, illustration, etc.
Object name is c-65-0o438-efi4.jpg0] direction (Fig. 2 [triangle]), where pairs of mol­ecules centred across (An external file that holds a picture, illustration, etc.
Object name is c-65-0o438-efi3.jpg + n, An external file that holds a picture, illustration, etc.
Object name is c-65-0o438-efi3.jpgn, An external file that holds a picture, illustration, etc.
Object name is c-65-0o438-efi3.jpg), where n again represents an integer, participate in π–π stacking inter­actions. Two chains of this type, related to one another by the translational symmetry operations, pass through each unit cell, but there are no direction-specific inter­actions between the chains; in particular, C—H(...)π hydrogen bonds are absent.

Figure 2
A stereoview of part of the crystal structure of (I), showing the formation of a chain along [1An external file that holds a picture, illustration, etc.
Object name is c-65-0o438-efi4.jpg0] built by the π stacking of hydrogen-bonded dimers. For the sake of clarity, H atoms not involved in the motifs shown have been omitted.
Table 2
Hydrogen-bond geometry (Å, °)

It is of inter­est briefly to compare the one-dimensional supra­molecular aggregation in (I) with the corresponding behaviour in the related compounds (II)–(V). In (II) (Makarov et al., 1997 [triangle]), there are no significant direction-specific inter­actions between the mol­ecules; the closest inter­molecular contacts involve methyl C—H bonds. By contrast, in the hydrated salt (III) (Quesada et al., 2003 [triangle]), a combination of three O—H(...)O hydrogen bonds and three N—H(...)O hydrogen bonds link the components into a continuous three-dimensional structure, but the anion and solvent components play a dominant role here. Two hydrogen bonds, one each of the N—H(...)O and N—H(...)N types, link the mol­ecules of (IV) into sheets built from alternating An external file that holds a picture, illustration, etc.
Object name is c-65-0o438-efi1.jpg(8) and An external file that holds a picture, illustration, etc.
Object name is c-65-0o438-efi9.jpg(32) rings (Glidewell et al., 2003 [triangle]). Finally, in (V) (Quesada et al., 2004 [triangle]), two N—H(...)N hydrogen bonds generate chains of rings, which are linked into sheets by an N—H(...)O hydrogen bond; these sheets are themselves linked by a C—H(...)O hydrogen bond to form a three-dimensional structure. Thus, in the simple unsolvated compounds (II), (I), (IV) and (V), the supra­molecular structures can be regarded as, respectively, zero-, one-, two- and three-dimensional.


Aniline (2 mmol) was added dropwise to a solution of 4,6-dichloro-5-nitro­pyrimidine (1 mmol) in tetra­hydro­furan (10 ml) containing triethyl­amine (0.5 ml), and the resulting reaction mixture was stirred at ambient temperature for 4 h. The mixture was concentrated under reduced pressure, diluted with water and exhaustively extracted with ethyl acetate. The combined organic extracts were washed firstly with aqueous hydro­chloric acid (1 mol dm3) and then with brine, and finally dried over anhydrous magnesium sulfate. The solvent was removed under reduced pressure to yield the product as a yellow solid (yield 98%, m.p. 441–443 K). Crystals suitable for single-crystal X-ray diffraction were obtained from a solution in dimethyl sulfoxide.

Crystal data

  • C16H13N5O2
  • M r = 307.31
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is c-65-0o438-efi10.jpg
  • a = 7.9112 (11) Å
  • b = 5.5582 (6) Å
  • c = 30.665 (3) Å
  • β = 94.541 (10)°
  • V = 1344.2 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.11 mm−1
  • T = 120 K
  • 0.43 × 0.21 × 0.05 mm

Data collection

  • Bruker–Nonius KappaCCD diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 2003 [triangle]) T min = 0.931, T max = 0.995
  • 20376 measured reflections
  • 3094 independent reflections
  • 1658 reflections with I > 2σ(I)
  • R int = 0.084


  • R[F 2 > 2σ(F 2)] = 0.057
  • wR(F 2) = 0.153
  • S = 1.08
  • 3094 reflections
  • 208 parameters
  • H-atom parameters constrained
  • Δρmax = 0.34 e Å−3
  • Δρmin = −0.38 e Å−3

All H atoms were located in difference maps and then treated as riding atoms in geometrically idealized positions, with C—H distances of 0.95 Å and N—H distances of 0.88 Å, and with U iso(H) values of 1.2U eq(carrier).

Data collection: COLLECT (Hooft, 1999 [triangle]); cell refinement: DIRAX/LSQ (Duisenberg et al., 2000 [triangle]); data reduction: EVALCCD (Duisenberg et al., 2003 [triangle]); program(s) used to solve structure: SIR2004 (Burla et al., 2005 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: PLATON (Spek, 2009 [triangle]); software used to prepare material for publication: SHELXL97 and PLATON.

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S0108270109029618/gg3208sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S0108270109029618/gg3208Isup2.hkl


The authors thank ‘Servicios Técnicos de Investigación of Universidad de Jaén’ and the staff for the data collection. JC and MN thank the Consejería de Innovación, Ciencia y Empresa (Junta de Andalucía, Spain), the Universidad de Jaén (project reference UJA_07_16_33) and Ministerio de Ciencia e Innovación (project reference SAF2008-04685-C02-02) for financial support. RR thanks COLCIENCIAS and Universidad Nacional for financial support, and Fundación Carolina for a fellowship to carry out postgraduate studies at the Universidad de Jaén.


Supplementary data for this paper are available from the IUCr electronic archives (Reference: GG3208). Services for accessing these data are described at the back of the journal.


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