The title compound, C
6H
4N
4O
2, is a potential nucleobase surrogate. In the crystal structure, molecules are linked by intermolecular N—H
N hydrogen bonds [H
N = 1.88 (3) Å] to form one-dimensional chains in the
b-axis direction.
Supporting information
CCDC reference: 296614
Key indicators
- Single-crystal X-ray study
- T = 298 K
- Mean (C-C) = 0.004 Å
- R factor = 0.053
- wR factor = 0.099
- Data-to-parameter ratio = 11.9
checkCIF/PLATON results
No syntax errors found
Alert level C
PLAT026_ALERT_3_C Ratio Observed / Unique Reflections too Low .... 49 Perc.
PLAT230_ALERT_2_C Hirshfeld Test Diff for N6 - C6 .. 5.48 su
0 ALERT level A = In general: serious problem
0 ALERT level B = Potentially serious problem
2 ALERT level C = Check and explain
0 ALERT level G = General alerts; check
0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
1 ALERT type 2 Indicator that the structure model may be wrong or deficient
1 ALERT type 3 Indicator that the structure quality may be low
0 ALERT type 4 Improvement, methodology, query or suggestion
The title compound was synthesized according to published protocols (Cristalli et al., 1987) and recrystallized from water. It gave a satisfactory elemental analysis: calculated for C6H4N4O2: C 43.9, H 2.5, N 34.1%; found: C 43.6, H 2.4, N 34.8%. The calculations were performed using the ADF programme (te Velde et al., 2001; Fonseca Guerra et al., 1998; ADF2005.01, SCM, Theoretical Chemistry, Vrije Universiteit, Amsterdam, The Netherlands, https://www.scm.com/). Calculations were carried out as described in the literature (Fonseca Guerra et al., 2000). The determination of the pKa value was performed as described in the literature (Müller, Polonius & Roitzsch, 2005 or Müller, Böhme et al., 2005?).
All H atoms were found in a difference Fourier map and refined isotropically [C—H = 0.92 (2)–0.99 (3) Å].
Data collection: KappaCCD Software (Nonius, 1998); cell refinement: DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL-Plus (Sheldrick, 1990); software used to prepare material for publication: SHELXL97.
6-Nitro-1-deazapurine
top
Crystal data top
C6H4N4O2 | F(000) = 336 |
Mr = 164.13 | Dx = 1.512 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 6291 reflections |
a = 11.684 (2) Å | θ = 3–27.5° |
b = 9.5750 (19) Å | µ = 0.12 mm−1 |
c = 7.2052 (14) Å | T = 298 K |
β = 116.53 (3)° | Block, yellow |
V = 721.2 (3) Å3 | 0.2 × 0.05 × 0.05 mm |
Z = 4 | |
Data collection top
Bruker–Nonius KappaCCD diffractometer | Rint = 0.082 |
157 frames via ω–rotation (Δω2°) and 400s per frame scans | θmax = 26.5°, θmin = 3.6° |
6047 measured reflections | h = −14→14 |
1483 independent reflections | k = −12→10 |
728 reflections with I > 2σ(I) | l = −9→6 |
Refinement top
Refinement on F2 | 0 restraints |
Least-squares matrix: full | All H-atom parameters refined |
R[F2 > 2σ(F2)] = 0.053 | w = 1/[σ2(Fo2) + (0.0304P)2 + 0.1392P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.099 | (Δ/σ)max < 0.001 |
S = 1.01 | Δρmax = 0.19 e Å−3 |
1483 reflections | Δρmin = −0.22 e Å−3 |
125 parameters | |
Crystal data top
C6H4N4O2 | V = 721.2 (3) Å3 |
Mr = 164.13 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 11.684 (2) Å | µ = 0.12 mm−1 |
b = 9.5750 (19) Å | T = 298 K |
c = 7.2052 (14) Å | 0.2 × 0.05 × 0.05 mm |
β = 116.53 (3)° | |
Data collection top
Bruker–Nonius KappaCCD diffractometer | 728 reflections with I > 2σ(I) |
6047 measured reflections | Rint = 0.082 |
1483 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.053 | 0 restraints |
wR(F2) = 0.099 | All H-atom parameters refined |
S = 1.01 | Δρmax = 0.19 e Å−3 |
1483 reflections | Δρmin = −0.22 e Å−3 |
125 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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O1 | 0.2563 (2) | 0.6124 (2) | 0.2776 (4) | 0.0996 (9) | |
O2 | 0.4285 (2) | 0.5426 (2) | 0.2698 (3) | 0.0812 (7) | |
N3 | 0.2151 (2) | 0.0968 (2) | 0.2911 (3) | 0.0497 (6) | |
N6 | 0.3280 (2) | 0.5216 (3) | 0.2780 (3) | 0.0605 (7) | |
N7 | 0.06591 (19) | 0.4195 (2) | 0.2507 (3) | 0.0425 (6) | |
N9 | 0.01668 (19) | 0.19438 (19) | 0.2543 (3) | 0.0444 (6) | |
C1 | 0.3713 (3) | 0.2669 (3) | 0.3058 (4) | 0.0529 (7) | |
C2 | 0.3300 (3) | 0.1313 (3) | 0.3075 (4) | 0.0536 (8) | |
C4 | 0.1393 (2) | 0.2058 (3) | 0.2733 (3) | 0.0394 (6) | |
C5 | 0.1713 (2) | 0.3468 (2) | 0.2711 (3) | 0.0385 (6) | |
C6 | 0.2901 (2) | 0.3766 (3) | 0.2857 (4) | 0.0435 (7) | |
C8 | −0.0210 (3) | 0.3236 (3) | 0.2426 (4) | 0.0449 (7) | |
H2 | 0.386 (2) | 0.051 (3) | 0.317 (4) | 0.068 (8)* | |
H8 | −0.099 (2) | 0.353 (2) | 0.230 (3) | 0.033 (6)* | |
H7 | 0.052 (3) | 0.516 (3) | 0.252 (4) | 0.090 (10)* | |
H1 | 0.455 (2) | 0.289 (2) | 0.317 (4) | 0.061 (8)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0917 (17) | 0.0530 (14) | 0.181 (3) | −0.0107 (13) | 0.0848 (17) | −0.0068 (14) |
O2 | 0.0641 (13) | 0.0926 (16) | 0.0992 (17) | −0.0282 (12) | 0.0474 (12) | −0.0053 (12) |
N3 | 0.0498 (14) | 0.0459 (13) | 0.0588 (15) | 0.0049 (12) | 0.0292 (11) | 0.0015 (10) |
N6 | 0.0493 (16) | 0.0672 (18) | 0.0700 (17) | −0.0189 (14) | 0.0313 (13) | −0.0065 (13) |
N7 | 0.0421 (13) | 0.0348 (12) | 0.0552 (14) | −0.0009 (11) | 0.0259 (10) | 0.0005 (10) |
N9 | 0.0425 (14) | 0.0328 (13) | 0.0628 (15) | 0.0022 (9) | 0.0279 (11) | 0.0032 (10) |
C1 | 0.0375 (17) | 0.074 (2) | 0.0506 (17) | −0.0011 (16) | 0.0227 (13) | 0.0011 (15) |
C2 | 0.0521 (19) | 0.056 (2) | 0.0574 (19) | 0.0109 (17) | 0.0286 (15) | 0.0013 (15) |
C4 | 0.0375 (16) | 0.0383 (15) | 0.0456 (16) | 0.0037 (12) | 0.0214 (12) | 0.0008 (11) |
C5 | 0.0362 (15) | 0.0393 (14) | 0.0419 (15) | −0.0011 (12) | 0.0193 (12) | 0.0014 (11) |
C6 | 0.0439 (16) | 0.0459 (16) | 0.0433 (16) | −0.0058 (13) | 0.0217 (12) | −0.0011 (12) |
C8 | 0.0374 (17) | 0.0417 (17) | 0.0618 (19) | 0.0016 (14) | 0.0276 (14) | 0.0024 (13) |
Geometric parameters (Å, º) top
O1—N6 | 1.207 (3) | N9—C4 | 1.381 (3) |
O2—N6 | 1.218 (3) | C1—C6 | 1.379 (3) |
N3—C2 | 1.335 (3) | C1—C2 | 1.387 (4) |
N3—C4 | 1.337 (3) | C1—H1 | 0.97 (2) |
N6—C6 | 1.465 (3) | C2—H2 | 0.99 (3) |
N7—C8 | 1.352 (3) | C4—C5 | 1.403 (3) |
N7—C5 | 1.365 (3) | C5—C6 | 1.374 (3) |
N7—H7 | 0.94 (3) | C8—H8 | 0.92 (2) |
N9—C8 | 1.303 (3) | | |
| | | |
C2—N3—C4 | 114.3 (2) | C1—C2—H2 | 120.6 (14) |
O1—N6—O2 | 124.3 (3) | N3—C4—N9 | 124.1 (2) |
O1—N6—C6 | 117.5 (2) | N3—C4—C5 | 125.7 (2) |
O2—N6—C6 | 118.2 (2) | N9—C4—C5 | 110.2 (2) |
C8—N7—C5 | 106.4 (2) | N7—C5—C6 | 137.3 (2) |
C8—N7—H7 | 122.5 (18) | N7—C5—C4 | 105.1 (2) |
C5—N7—H7 | 130.9 (18) | C6—C5—C4 | 117.7 (2) |
C8—N9—C4 | 103.7 (2) | C5—C6—C1 | 118.3 (2) |
C6—C1—C2 | 119.2 (3) | C5—C6—N6 | 120.4 (2) |
C6—C1—H1 | 117.7 (14) | C1—C6—N6 | 121.3 (2) |
C2—C1—H1 | 123.1 (14) | N9—C8—N7 | 114.6 (2) |
N3—C2—C1 | 124.8 (3) | N9—C8—H8 | 125.9 (14) |
N3—C2—H2 | 114.6 (14) | N7—C8—H8 | 119.5 (13) |
| | | |
C4—N3—C2—C1 | −0.4 (4) | C4—N9—C8—N7 | 0.5 (3) |
C2—N3—C4—N9 | 179.9 (2) | C2—C1—C6—C5 | 0.9 (4) |
C2—N3—C4—C5 | −0.1 (3) | C6—C1—C2—N3 | −0.1 (4) |
O1—N6—C6—C1 | −174.0 (3) | C2—C1—C6—N6 | −178.5 (2) |
O1—N6—C6—C5 | 6.6 (3) | N3—C4—C5—N7 | −179.9 (2) |
O2—N6—C6—C1 | 6.9 (3) | N3—C4—C5—C6 | 0.9 (3) |
O2—N6—C6—C5 | −172.5 (2) | N9—C4—C5—N7 | 0.1 (2) |
C8—N7—C5—C4 | 0.2 (2) | N9—C4—C5—C6 | −179.1 (2) |
C8—N7—C5—C6 | 179.1 (3) | N7—C5—C6—N6 | −0.7 (4) |
C5—N7—C8—N9 | −0.4 (3) | N7—C5—C6—C1 | 179.9 (2) |
C8—N9—C4—N3 | 179.7 (2) | C4—C5—C6—N6 | 178.2 (2) |
C8—N9—C4—C5 | −0.3 (2) | C4—C5—C6—C1 | −1.3 (3) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N7—H7···O1 | 0.94 (3) | 2.49 (4) | 2.830 (3) | 102 (3) |
N7—H7···N9i | 0.94 (3) | 1.88 (3) | 2.797 (3) | 166 (3) |
C2—H2···O2ii | 0.99 (3) | 2.51 (3) | 3.224 (4) | 129 (2) |
Symmetry codes: (i) −x, y+1/2, −z+1/2; (ii) −x+1, y−1/2, −z+1/2. |
Experimental details
Crystal data |
Chemical formula | C6H4N4O2 |
Mr | 164.13 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 298 |
a, b, c (Å) | 11.684 (2), 9.5750 (19), 7.2052 (14) |
β (°) | 116.53 (3) |
V (Å3) | 721.2 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.2 × 0.05 × 0.05 |
|
Data collection |
Diffractometer | Bruker–Nonius KappaCCD diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6047, 1483, 728 |
Rint | 0.082 |
(sin θ/λ)max (Å−1) | 0.628 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.053, 0.099, 1.01 |
No. of reflections | 1483 |
No. of parameters | 125 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.19, −0.22 |
Selected geometric parameters (Å, º) topN3—C2 | 1.335 (3) | N9—C4 | 1.381 (3) |
N3—C4 | 1.337 (3) | C1—C6 | 1.379 (3) |
N6—C6 | 1.465 (3) | C1—C2 | 1.387 (4) |
N7—C8 | 1.352 (3) | C4—C5 | 1.403 (3) |
N7—C5 | 1.365 (3) | C5—C6 | 1.374 (3) |
N9—C8 | 1.303 (3) | | |
| | | |
C2—N3—C4 | 114.3 (2) | N7—C5—C6 | 137.3 (2) |
C8—N7—C5 | 106.4 (2) | N7—C5—C4 | 105.1 (2) |
C8—N9—C4 | 103.7 (2) | C6—C5—C4 | 117.7 (2) |
C6—C1—C2 | 119.2 (3) | C5—C6—C1 | 118.3 (2) |
N3—C2—C1 | 124.8 (3) | C5—C6—N6 | 120.4 (2) |
N3—C4—N9 | 124.1 (2) | C1—C6—N6 | 121.3 (2) |
N3—C4—C5 | 125.7 (2) | N9—C8—N7 | 114.6 (2) |
N9—C4—C5 | 110.2 (2) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N7—H7···N9i | 0.94 (3) | 1.88 (3) | 2.797 (3) | 166 (3) |
C2—H2···O2ii | 0.99 (3) | 2.51 (3) | 3.224 (4) | 129 (2) |
Symmetry codes: (i) −x, y+1/2, −z+1/2; (ii) −x+1, y−1/2, −z+1/2. |
The title purine derivative, (I), was synthesized in the course of our studies of potential ligands for metal-mediated base pairs and models thereof (Müller, Polonius & Roitzsch, 2005; Müller, Böhme et al., 2005). The ultimately resulting metal ion-containing oligonucleotides represent promising synthetic targets as they are expected to show interesting physical properties that are difficult to obtain with other compounds (Wagenknecht, 2003).
The title compound is essentially planar (Fig. 1), with only the exocyclic nitro group deviating slightly from the least-squares best plane of the purine ring system [7.18 (17)°]. All bond lengths and angles are in the expected range. An interesting feature observed in purine and its derivatives is the N7—H versus N9—H tautomerism. For example, in the structure of purine (Watson et al., 1965) the same N atom as in the title compound is protonated, but in solution a solvent-dependent equilibrium between the two tautomers is observed (Gonella or Gonnella & Roberts, 1982). The present study shows that in the solid state 6-nitro-1-deazapurine exists in the N7—H tautomeric form. As in the crystal structure of purine, molecules of (I) are linked by intermolecular N—H···N hydrogen bonds to form one-dimensional chains (Table 2 and Fig. 2). The assignment as the N7—H tautomer is based not only on the fact that the proton could be found in the difference Fourier map but also on the values of the angles C8—N9—C4 and C8—N7—C5, which are 103.7 (2) and 106.4 (2)°, respectively. A comparison with 91 other solid-state structures of purine derivatives (nine of which are reported as N7—H tautomers) as retrieved from the Cambridge Structural Database (Version 5.26; Allen, 2002) shows that the respective angle involving the protonated N atom is typically larger by about 3°. In fact, the average values for these angles in the above-mentioned nine N7—H tautomers are coincidentally identical to the values observed in the title structure (103.7 and 106.4°). For comparison, the respective average angles in the N9—H tautomers are 106.3 and 103.3°. In addition, the C8—N7 and C8—N9 bond lengths of 1.352 (3) and 1.303 (3) Å agree well with the sequence of the single and double bonds as given in the chemical scheme. A theoretical calculation performed with the ADF programme (te Velde et al., 2001; Fonseca Guerra et al., 1998; ADF2005.01] further supports these findings by showing that in the gas phase the N7—H tautomer is more stable by 14.1 kJ mol−1 than the N9—H form. The pKa value of the N7—H proton as determined by pD-dependent 1H NMR spectroscopy is 1.4 (1).