The molecule of 3,5-difluoro-4-nitropyridine
N-oxide, C
5H
2F
2N
2O
3, is twisted around the C-NO
2 bond by 38.5 (1)°, while the 3,5-diamino analogue, 3,5-diamino-4-nitropyridine
N-oxide monohydrate, C
5H
6N
4O
3·H
2O, adopts a planar conformation stabilized by intramolecular hydrogen bonds, with a significant redistribution of
electrons.
Supporting information
CCDC references: 146104; 146105
For both compounds, data collection: SMART (Siemens, 1995); cell refinement: SMART; data reduction: SAINT (Siemens, 1995); program(s) used to solve structure: SHELXTL (Bruker, 1997); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.
(I) 3,5-difluoro-4-nitropyridine N-oxide
top
Crystal data top
C5H2F2N2O3 | Dx = 1.820 Mg m−3 |
Mr = 176.09 | Melting point: 124° C K |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
a = 5.479 (2) Å | Cell parameters from 449 reflections |
b = 10.840 (4) Å | θ = 10.0–23.0° |
c = 11.159 (3) Å | µ = 0.19 mm−1 |
β = 104.12 (1)° | T = 295 K |
V = 642.7 (4) Å3 | Block, light yellow |
Z = 4 | 0.35 × 0.25 × 0.20 mm |
F(000) = 352 | |
Data collection top
SMART 1K CCD area-detector diffractometer | 1086 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.032 |
Graphite monochromator | θmax = 27.5°, θmin = 2.7° |
Detector resolution: 8 pixels mm-1 | h = −7→5 |
ω scans | k = −11→14 |
4314 measured reflections | l = −14→14 |
1469 independent reflections | |
Refinement top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.040 | All H-atom parameters refined |
wR(F2) = 0.104 | w = 1/[σ2(Fo2) + (0.030P)2 + 0.2547P] where P = (Fo2 + 2Fc2)/3 |
S = 1.14 | (Δ/σ)max = 0.003 |
1469 reflections | Δρmax = 0.16 e Å−3 |
118 parameters | Δρmin = −0.15 e Å−3 |
0 restraints | Extinction correction: SHELXTL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.054 (5) |
Special details top
Experimental. The data collection nominally covered over a hemisphere of reciprocal space, by
a combination of 4 sets of ω scans; each set at different φ and/or 2θ
angles and each scan (10 sec exposure) covering 0.3° in ω. Crystal decay was
monitored by repeating 50 initial frames at the end of data collection and
comparing 41 duplicate reflections. Crystal to detector distance 4.54 cm. |
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. |
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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1 | 0.6315 (3) | 0.53826 (15) | 0.35891 (14) | 0.0434 (4) | |
C2 | 0.6757 (4) | 0.61027 (19) | 0.46240 (19) | 0.0440 (5) | |
H2 | 0.817 (4) | 0.594 (2) | 0.524 (2) | 0.061 (7)* | |
C3 | 0.5163 (4) | 0.70703 (18) | 0.46799 (17) | 0.0420 (5) | |
C4 | 0.3073 (3) | 0.73343 (17) | 0.37154 (17) | 0.0400 (4) | |
C5 | 0.2711 (3) | 0.65693 (18) | 0.26861 (17) | 0.0418 (5) | |
C6 | 0.4314 (4) | 0.56114 (19) | 0.26238 (19) | 0.0452 (5) | |
H6 | 0.411 (4) | 0.511 (2) | 0.195 (2) | 0.056 (6)* | |
O1 | 0.7806 (3) | 0.44597 (15) | 0.35385 (14) | 0.0640 (5) | |
F3 | 0.5653 (2) | 0.77428 (13) | 0.57141 (11) | 0.0638 (4) | |
N4 | 0.1388 (3) | 0.83620 (16) | 0.37957 (16) | 0.0493 (4) | |
O41 | −0.0870 (3) | 0.81918 (16) | 0.33561 (18) | 0.0714 (5) | |
O42 | 0.2333 (3) | 0.93172 (14) | 0.42902 (16) | 0.0674 (5) | |
F5 | 0.0801 (2) | 0.67666 (12) | 0.17059 (11) | 0.0640 (4) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0450 (9) | 0.0417 (9) | 0.0425 (9) | 0.0058 (7) | 0.0086 (7) | 0.0026 (7) |
C2 | 0.0400 (10) | 0.0500 (11) | 0.0394 (10) | 0.0006 (9) | 0.0045 (8) | 0.0022 (9) |
C3 | 0.0418 (10) | 0.0464 (11) | 0.0373 (10) | −0.0039 (8) | 0.0087 (8) | −0.0033 (8) |
C4 | 0.0369 (10) | 0.0377 (9) | 0.0463 (11) | −0.0017 (8) | 0.0116 (8) | 0.0028 (8) |
C5 | 0.0382 (10) | 0.0417 (10) | 0.0401 (10) | −0.0022 (8) | −0.0011 (8) | 0.0042 (8) |
C6 | 0.0504 (12) | 0.0426 (11) | 0.0395 (10) | 0.0003 (9) | 0.0047 (9) | −0.0021 (9) |
O1 | 0.0658 (10) | 0.0593 (10) | 0.0620 (10) | 0.0265 (8) | 0.0062 (8) | −0.0039 (8) |
F3 | 0.0642 (8) | 0.0720 (9) | 0.0491 (7) | 0.0071 (6) | 0.0017 (6) | −0.0199 (6) |
N4 | 0.0483 (10) | 0.0462 (10) | 0.0556 (11) | 0.0058 (8) | 0.0169 (8) | 0.0066 (8) |
O41 | 0.0436 (9) | 0.0709 (11) | 0.1007 (14) | 0.0100 (8) | 0.0194 (9) | 0.0095 (10) |
O42 | 0.0835 (12) | 0.0447 (9) | 0.0731 (11) | 0.0051 (8) | 0.0175 (9) | −0.0089 (8) |
F5 | 0.0578 (8) | 0.0642 (8) | 0.0554 (8) | 0.0093 (6) | −0.0144 (6) | −0.0037 (6) |
Geometric parameters (Å, º) top
N1—O1 | 1.301 (2) | C4—C5 | 1.391 (3) |
N1—C6 | 1.359 (3) | C4—N4 | 1.464 (2) |
N1—C2 | 1.366 (3) | C5—F5 | 1.334 (2) |
C2—C3 | 1.376 (3) | C5—C6 | 1.372 (3) |
C2—H2 | 0.92 (2) | C6—H6 | 0.91 (2) |
C3—F3 | 1.336 (2) | N4—O42 | 1.227 (2) |
C3—C4 | 1.396 (3) | N4—O41 | 1.228 (2) |
| | | |
O1—N1—C6 | 119.96 (17) | C3—C4—N4 | 121.31 (17) |
O1—N1—C2 | 119.51 (17) | F5—C5—C6 | 117.61 (18) |
C6—N1—C2 | 120.52 (17) | F5—C5—C4 | 120.45 (17) |
N1—C2—C3 | 119.39 (19) | C6—C5—C4 | 121.92 (18) |
N1—C2—H2 | 117.4 (15) | N1—C6—C5 | 120.02 (19) |
C3—C2—H2 | 123.1 (15) | N1—C6—H6 | 117.5 (14) |
F3—C3—C2 | 117.34 (18) | C5—C6—H6 | 122.5 (14) |
F3—C3—C4 | 120.55 (17) | O42—N4—O41 | 125.44 (18) |
C2—C3—C4 | 122.09 (18) | O42—N4—C4 | 117.81 (18) |
C5—C4—C3 | 116.05 (17) | O41—N4—C4 | 116.76 (18) |
C5—C4—N4 | 122.63 (18) | | |
(II) 3,5-diamino-4-nitropyridine N-oxide monohydrate
top
Crystal data top
C5H6N4O3·H2O | Dx = 1.646 Mg m−3 |
Mr = 188.15 | Melting point: >300° C (decomp.) K |
Orthorhombic, Pna21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2c -2n | Cell parameters from 391 reflections |
a = 7.000 (1) Å | θ = 10.4–25.5° |
b = 13.123 (1) Å | µ = 0.14 mm−1 |
c = 8.263 (1) Å | T = 150 K |
V = 759.05 (15) Å3 | Prism, red |
Z = 4 | 0.40 × 0.15 × 0.08 mm |
F(000) = 392 | |
Data collection top
SMART 1K CCD area-detector diffractometer | 837 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.051 |
Graphite monochromator | θmax = 27.5°, θmin = 2.9° |
Detector resolution: 8 pixels mm-1 | h = −9→9 |
ω scans | k = −16→17 |
5153 measured reflections | l = −10→10 |
925 independent reflections | |
Refinement top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.035 | All H-atom parameters refined |
wR(F2) = 0.093 | w = 1/[σ2(Fo2) + (0.0515P)2 + 0.3363P] where P = (Fo2 + 2Fc2)/3 |
S = 1.09 | (Δ/σ)max = 0.003 |
925 reflections | Δρmax = 0.21 e Å−3 |
149 parameters | Δρmin = −0.22 e Å−3 |
1 restraint | Absolute structure: Flack (1983) |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0 (10) |
Special details top
Experimental. The data collection nominally covered over a hemisphere of reciprocal space, by
a combination of 4 sets of ω scans; each set at different φ and/or 2θ
angles and each scan (20 sec exposure) covering 0.3° in ω. Crystal decay was
monitored by repeating 50 initial frames at the end of data collection and
comparing 102 duplicate reflections. Crystal to detector distance 4.54 cm. |
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. The absolute
structure (polarity) could not be determined reliably for the lack of
anomalously scattering atoms. Of 1682 unique reflections measured, 757 Friedel
pairs were merged. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1 | 0.3290 (3) | 0.47510 (15) | 0.2312 (3) | 0.0147 (4) | |
C2 | 0.4014 (4) | 0.4299 (2) | 0.0987 (4) | 0.0156 (6) | |
H2 | 0.444 (5) | 0.473 (3) | 0.011 (5) | 0.025 (9)* | |
C3 | 0.4200 (4) | 0.32302 (18) | 0.0905 (3) | 0.0136 (5) | |
C4 | 0.3529 (4) | 0.26489 (17) | 0.2262 (4) | 0.0129 (5) | |
C5 | 0.2817 (4) | 0.3158 (2) | 0.3684 (3) | 0.0140 (5) | |
C6 | 0.2721 (4) | 0.4232 (2) | 0.3626 (4) | 0.0154 (6) | |
H6 | 0.225 (5) | 0.461 (2) | 0.446 (5) | 0.014 (8)* | |
O1 | 0.3120 (3) | 0.57640 (13) | 0.2305 (3) | 0.0197 (5) | |
O41 | 0.4256 (3) | 0.11343 (14) | 0.0994 (3) | 0.0205 (5) | |
O42 | 0.2907 (3) | 0.10538 (15) | 0.3355 (3) | 0.0226 (5) | |
N3 | 0.4969 (4) | 0.28535 (18) | −0.0446 (3) | 0.0177 (5) | |
H31 | 0.532 (5) | 0.326 (3) | −0.127 (5) | 0.016 (6)* | |
H32 | 0.506 (5) | 0.225 (3) | −0.060 (5) | 0.016 (6)* | |
N4 | 0.3572 (3) | 0.15663 (14) | 0.2199 (3) | 0.0138 (4) | |
N5 | 0.2229 (4) | 0.2695 (2) | 0.5040 (3) | 0.0182 (5) | |
H51 | 0.231 (5) | 0.199 (2) | 0.507 (4) | 0.007 (7)* | |
H52 | 0.190 (5) | 0.306 (3) | 0.584 (5) | 0.021 (9)* | |
O1W | −0.0783 (3) | 0.60634 (15) | 0.2584 (3) | 0.0209 (5) | |
H1W | −0.118 (7) | 0.551 (4) | 0.274 (6) | 0.054 (15)* | |
H2W | 0.047 (7) | 0.593 (3) | 0.242 (7) | 0.057 (14)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0157 (9) | 0.0110 (9) | 0.0173 (11) | −0.0006 (8) | −0.0015 (10) | −0.0039 (11) |
C2 | 0.0167 (13) | 0.0139 (12) | 0.0163 (13) | −0.0017 (10) | 0.0027 (11) | 0.0017 (12) |
C3 | 0.0110 (13) | 0.0133 (11) | 0.0166 (13) | 0.0022 (9) | −0.0014 (11) | −0.0017 (12) |
C4 | 0.0142 (10) | 0.0118 (11) | 0.0128 (12) | 0.0001 (9) | −0.0018 (10) | 0.0015 (13) |
C5 | 0.0122 (12) | 0.0151 (12) | 0.0149 (13) | −0.0012 (10) | −0.0013 (10) | −0.0015 (12) |
C6 | 0.0166 (13) | 0.0158 (12) | 0.0139 (13) | 0.0015 (10) | 0.0028 (11) | −0.0039 (11) |
O1 | 0.0273 (10) | 0.0083 (8) | 0.0234 (11) | 0.0003 (7) | −0.0033 (10) | −0.0012 (9) |
O41 | 0.0311 (12) | 0.0136 (9) | 0.0167 (10) | 0.0015 (8) | 0.0041 (10) | −0.0027 (9) |
O42 | 0.0310 (12) | 0.0132 (9) | 0.0236 (12) | −0.0007 (8) | 0.0100 (10) | 0.0038 (9) |
N3 | 0.0251 (13) | 0.0116 (11) | 0.0163 (13) | 0.0020 (10) | 0.0057 (10) | 0.0003 (11) |
N4 | 0.0126 (9) | 0.0120 (9) | 0.0168 (11) | −0.0002 (8) | 0.0007 (9) | 0.0002 (12) |
N5 | 0.0239 (13) | 0.0146 (12) | 0.0162 (13) | 0.0021 (10) | 0.0067 (11) | 0.0002 (10) |
O1W | 0.0283 (11) | 0.0133 (9) | 0.0212 (11) | 0.0003 (8) | −0.0038 (9) | −0.0010 (9) |
Geometric parameters (Å, º) top
N1—O1 | 1.335 (3) | C5—C6 | 1.411 (4) |
N1—C6 | 1.342 (4) | C6—H6 | 0.91 (4) |
N1—C2 | 1.344 (4) | O41—N4 | 1.242 (3) |
C2—C3 | 1.410 (3) | O42—N4 | 1.258 (3) |
C2—H2 | 0.96 (4) | N3—H31 | 0.90 (4) |
C3—N3 | 1.334 (4) | N3—H32 | 0.80 (3) |
C3—C4 | 1.435 (4) | N5—H51 | 0.92 (3) |
C4—N4 | 1.422 (3) | N5—H52 | 0.85 (4) |
C4—C5 | 1.441 (4) | O1W—H1W | 0.79 (5) |
C5—N5 | 1.339 (4) | O1W—H2W | 0.90 (5) |
| | | |
O1—N1—C6 | 118.9 (2) | C6—C5—C4 | 116.9 (2) |
O1—N1—C2 | 118.0 (2) | N1—C6—C5 | 121.3 (3) |
C6—N1—C2 | 123.1 (2) | N1—C6—H6 | 116 (2) |
N1—C2—C3 | 120.9 (3) | C5—C6—H6 | 122 (2) |
N1—C2—H2 | 118 (2) | C3—N3—H31 | 121 (2) |
C3—C2—H2 | 121 (2) | C3—N3—H32 | 122 (3) |
N3—C3—C2 | 116.5 (3) | H31—N3—H32 | 116 (4) |
N3—C3—C4 | 126.1 (2) | O41—N4—O42 | 120.52 (19) |
C2—C3—C4 | 117.4 (2) | O41—N4—C4 | 119.6 (2) |
N4—C4—C3 | 119.7 (2) | O42—N4—C4 | 119.9 (2) |
N4—C4—C5 | 120.0 (2) | C5—N5—H51 | 117 (2) |
C3—C4—C5 | 120.2 (2) | C5—N5—H52 | 119 (2) |
N5—C5—C6 | 117.8 (2) | H51—N5—H52 | 124 (3) |
N5—C5—C4 | 125.3 (2) | H1W—O1W—H2W | 101 (4) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H31···O1i | 0.90 (4) | 2.05 (4) | 2.922 (3) | 162 (3) |
N3—H32···O41 | 0.80 (3) | 2.05 (4) | 2.599 (3) | 125 (4) |
N3—H32···O1Wii | 0.80 (3) | 2.22 (4) | 2.915 (3) | 145 (4) |
N5—H51···O42 | 0.92 (3) | 1.92 (3) | 2.609 (3) | 130 (3) |
N5—H52···O1Wiii | 0.85 (4) | 2.00 (4) | 2.845 (3) | 172 (4) |
O1W—H1W···O42iv | 0.79 (5) | 2.21 (5) | 2.994 (3) | 175 (5) |
O1W—H2W···O1 | 0.90 (5) | 1.87 (5) | 2.770 (3) | 173 (5) |
Symmetry codes: (i) −x+1, −y+1, z−1/2; (ii) −x+1/2, y−1/2, z−1/2; (iii) −x, −y+1, z+1/2; (iv) x−1/2, −y+1/2, z. |