Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270110036218/ln3145sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270110036218/ln3145Isup2.hkl | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270110036218/ln3145IIsup3.hkl |
CCDC references: 798602; 798603
For related literature, see: Bacon (1951); Barnes et al. (1978); Becke (1993); Bonnefous et al. (2005); Cornman et al. (1999); Dasgupta et al. (2008); Ditchfield et al. (1971); Dutta et al. (1999); Frisch et al. (2004); Hunter & Sanders (1990); Janiak (2000); Jiang et al. (2004); Kakuta et al. (2008); Kumar et al. (2007); Morsali et al. (2003); Orpen et al. (1989); Qi, Ma, Li, Zhou, Choi, Chan & Yang (2003); Qi, Yang, Lam, Zhou & Chan (2003); Ray et al. (1997); Zhang et al. (2002, 2006).
Compounds (I) and (II) were synthesized using a literature method (Barnes et al., 1978). X-ray- quality crystals of (I) were grown by slow evaporation of the reaction mixture, while X-ray-quality crystals of (II) were grown by slow evaporation of a saturated solution of (II) in dimethylsulfoxide.
H atoms were refined isotropically without restraints. For compounds (I) and (II) the refined N—H and C—H distances spanned the range 0.86 (2)–0.899 (17) Å and 0.932 (17)–1.014 (19) Å, respectively.
For both compounds, data collection: CrysAlis CCD (Oxford Diffraction, 2008); cell refinement: CrysAlis RED (Oxford Diffraction, 2008); data reduction: CrysAlis RED (Oxford Diffraction, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: WinGX (Farrugia, 1999).
C12H9FN2O | F(000) = 448 |
Mr = 216.21 | Dx = 1.406 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 6230 reflections |
a = 8.2500 (3) Å | θ = 3.0–26.0° |
b = 6.0649 (2) Å | µ = 0.10 mm−1 |
c = 20.5484 (8) Å | T = 296 K |
β = 96.479 (4)° | Rectangular block, colourless |
V = 1021.58 (6) Å3 | 0.60 × 0.45 × 0.35 mm |
Z = 4 |
Oxford Diffraction Xcalibur2 CCD diffractometer | 2005 independent reflections |
Radiation source: Enhance (Mo) X-ray Source | 1593 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.027 |
Detector resolution: 8.4190 pixels mm-1 | θmax = 26.0°, θmin = 3.0° |
ω scans | h = −10→10 |
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2008) | k = −7→7 |
Tmin = 0.960, Tmax = 1.000 | l = −25→25 |
10495 measured reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.049 | All H-atom parameters refined |
wR(F2) = 0.145 | w = 1/[σ2(Fo2) + (0.086P)2 + 0.2055P] where P = (Fo2 + 2Fc2)/3 |
S = 1.03 | (Δ/σ)max < 0.001 |
2005 reflections | Δρmax = 0.18 e Å−3 |
182 parameters | Δρmin = −0.21 e Å−3 |
0 restraints | Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.042 (6) |
C12H9FN2O | V = 1021.58 (6) Å3 |
Mr = 216.21 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 8.2500 (3) Å | µ = 0.10 mm−1 |
b = 6.0649 (2) Å | T = 296 K |
c = 20.5484 (8) Å | 0.60 × 0.45 × 0.35 mm |
β = 96.479 (4)° |
Oxford Diffraction Xcalibur2 CCD diffractometer | 2005 independent reflections |
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2008) | 1593 reflections with I > 2σ(I) |
Tmin = 0.960, Tmax = 1.000 | Rint = 0.027 |
10495 measured reflections |
R[F2 > 2σ(F2)] = 0.049 | 0 restraints |
wR(F2) = 0.145 | All H-atom parameters refined |
S = 1.03 | Δρmax = 0.18 e Å−3 |
2005 reflections | Δρmin = −0.21 e Å−3 |
182 parameters |
Experimental. CrysAlis RED (Oxford Diffraction, 2008). Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm. |
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. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.32637 (17) | 0.5407 (3) | 0.28306 (7) | 0.0429 (4) | |
C2 | 0.2479 (2) | 0.7416 (3) | 0.27325 (9) | 0.0550 (5) | |
C3 | 0.1394 (2) | 0.7772 (3) | 0.21731 (9) | 0.0581 (5) | |
C4 | 0.1131 (2) | 0.6102 (3) | 0.17293 (8) | 0.0533 (4) | |
C5 | 0.1882 (2) | 0.4102 (3) | 0.18130 (8) | 0.0572 (5) | |
C6 | 0.2960 (2) | 0.3736 (3) | 0.23732 (8) | 0.0516 (4) | |
C7 | 0.48262 (19) | 0.3276 (3) | 0.37228 (7) | 0.0459 (4) | |
C8 | 0.60614 (18) | 0.3584 (2) | 0.43165 (7) | 0.0421 (4) | |
C9 | 0.6492 (2) | 0.1784 (3) | 0.47109 (9) | 0.0563 (5) | |
C10 | 0.7559 (2) | 0.2110 (3) | 0.52774 (9) | 0.0624 (5) | |
C11 | 0.8178 (2) | 0.4178 (3) | 0.54068 (9) | 0.0577 (5) | |
C12 | 0.7712 (2) | 0.5864 (3) | 0.49784 (9) | 0.0578 (5) | |
N1 | 0.44150 (16) | 0.5154 (2) | 0.33956 (6) | 0.0478 (4) | |
N2 | 0.66513 (16) | 0.5602 (2) | 0.44373 (7) | 0.0504 (4) | |
O1 | 0.42591 (17) | 0.1465 (2) | 0.35782 (7) | 0.0702 (4) | |
F1 | 0.00806 (16) | 0.6455 (2) | 0.11748 (6) | 0.0823 (5) | |
H2 | 0.270 (2) | 0.857 (3) | 0.3038 (11) | 0.075 (6)* | |
H3 | 0.084 (3) | 0.919 (4) | 0.2095 (11) | 0.079 (6)* | |
H5 | 0.170 (3) | 0.292 (4) | 0.1471 (11) | 0.081 (6)* | |
H6 | 0.349 (3) | 0.236 (4) | 0.2451 (10) | 0.069 (6)* | |
H9 | 0.605 (2) | 0.030 (4) | 0.4605 (10) | 0.075 (6)* | |
H10 | 0.781 (3) | 0.087 (4) | 0.5588 (11) | 0.087 (7)* | |
H11 | 0.892 (3) | 0.452 (3) | 0.5803 (10) | 0.074 (6)* | |
H12 | 0.815 (2) | 0.736 (4) | 0.5053 (9) | 0.065 (5)* | |
H100 | 0.481 (3) | 0.633 (3) | 0.3578 (10) | 0.067 (6)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0378 (7) | 0.0517 (9) | 0.0372 (7) | −0.0069 (6) | −0.0048 (6) | −0.0004 (6) |
C2 | 0.0657 (11) | 0.0471 (9) | 0.0477 (9) | −0.0058 (8) | −0.0128 (7) | −0.0058 (7) |
C3 | 0.0639 (11) | 0.0496 (10) | 0.0563 (10) | 0.0027 (8) | −0.0136 (8) | 0.0027 (8) |
C4 | 0.0493 (9) | 0.0630 (10) | 0.0432 (8) | −0.0049 (7) | −0.0147 (7) | 0.0033 (7) |
C5 | 0.0642 (11) | 0.0617 (11) | 0.0419 (9) | −0.0028 (8) | −0.0108 (7) | −0.0119 (8) |
C6 | 0.0543 (9) | 0.0548 (10) | 0.0430 (8) | 0.0071 (8) | −0.0056 (7) | −0.0068 (7) |
C7 | 0.0436 (8) | 0.0519 (9) | 0.0401 (8) | −0.0060 (7) | −0.0048 (6) | −0.0011 (7) |
C8 | 0.0379 (7) | 0.0476 (8) | 0.0393 (7) | −0.0013 (6) | −0.0025 (6) | −0.0021 (6) |
C9 | 0.0618 (10) | 0.0499 (10) | 0.0532 (10) | −0.0042 (8) | −0.0103 (8) | 0.0023 (8) |
C10 | 0.0708 (12) | 0.0579 (11) | 0.0534 (10) | 0.0075 (9) | −0.0153 (8) | 0.0068 (8) |
C11 | 0.0547 (10) | 0.0635 (11) | 0.0493 (9) | 0.0062 (8) | −0.0183 (7) | −0.0051 (8) |
C12 | 0.0553 (10) | 0.0514 (10) | 0.0607 (10) | −0.0028 (8) | −0.0194 (8) | −0.0053 (8) |
N1 | 0.0478 (7) | 0.0497 (8) | 0.0421 (7) | −0.0078 (6) | −0.0118 (5) | −0.0019 (6) |
N2 | 0.0483 (8) | 0.0488 (8) | 0.0499 (8) | −0.0034 (6) | −0.0128 (6) | 0.0011 (6) |
O1 | 0.0816 (9) | 0.0548 (8) | 0.0664 (8) | −0.0179 (6) | −0.0259 (7) | 0.0006 (6) |
F1 | 0.0825 (8) | 0.0910 (9) | 0.0625 (7) | −0.0005 (7) | −0.0396 (6) | 0.0044 (6) |
C1—C2 | 1.384 (2) | C7—N1 | 1.346 (2) |
C1—C6 | 1.386 (2) | C7—O1 | 1.2178 (19) |
C1—N1 | 1.4230 (18) | C8—C9 | 1.382 (2) |
C2—C3 | 1.392 (2) | C8—N2 | 1.330 (2) |
C2—H2 | 0.94 (2) | C9—C10 | 1.392 (2) |
C3—C4 | 1.364 (3) | C9—H9 | 0.99 (2) |
C3—H3 | 0.98 (2) | C10—C11 | 1.369 (3) |
C4—C5 | 1.364 (3) | C10—H10 | 0.99 (2) |
C4—F1 | 1.3681 (18) | C11—C12 | 1.376 (3) |
C5—C6 | 1.391 (2) | C11—H11 | 0.98 (2) |
C5—H5 | 1.00 (2) | C12—N2 | 1.345 (2) |
C6—H6 | 0.95 (2) | C12—H12 | 0.99 (2) |
C7—C8 | 1.510 (2) | N1—H100 | 0.86 (2) |
C1—C2—C3 | 120.24 (16) | C7—N1—H100 | 115.3 (14) |
C1—C2—H2 | 120.1 (13) | C8—C9—C10 | 118.34 (16) |
C1—C6—C5 | 119.66 (16) | C8—C9—H9 | 121.8 (12) |
C1—C6—H6 | 119.1 (13) | C8—N2—C12 | 116.98 (14) |
C1—N1—H100 | 116.9 (14) | C9—C8—C7 | 118.78 (14) |
C2—C1—C6 | 119.95 (14) | C9—C10—H10 | 119.7 (14) |
C2—C1—N1 | 118.19 (13) | C10—C9—H9 | 119.8 (12) |
C2—C3—H3 | 121.1 (13) | C10—C11—C12 | 119.04 (16) |
C3—C2—H2 | 119.6 (13) | C10—C11—H11 | 122.6 (13) |
C3—C4—C5 | 122.69 (15) | C11—C10—C9 | 118.66 (16) |
C3—C4—F1 | 118.62 (16) | C11—C10—H10 | 121.5 (14) |
C4—C3—C2 | 118.45 (17) | C11—C12—H12 | 121.0 (12) |
C4—C3—H3 | 120.5 (13) | C12—C11—H11 | 118.3 (13) |
C4—C5—C6 | 119.01 (15) | N1—C7—C8 | 114.07 (13) |
C4—C5—H5 | 121.1 (13) | N2—C8—C7 | 117.64 (13) |
C5—C4—F1 | 118.68 (15) | N2—C8—C9 | 123.56 (14) |
C5—C6—H6 | 121.2 (13) | N2—C12—C11 | 123.36 (17) |
C6—C1—N1 | 121.83 (15) | N2—C12—H12 | 115.6 (12) |
C6—C5—H5 | 119.9 (13) | O1—C7—C8 | 120.95 (14) |
C7—N1—C1 | 127.33 (13) | O1—C7—N1 | 124.97 (14) |
C1—C2—C3—C4 | 0.0 (3) | C9—C8—N2—C12 | −0.5 (3) |
C2—C1—C6—C5 | 0.9 (3) | C9—C10—C11—C12 | 0.8 (3) |
C2—C1—N1—C7 | 151.94 (17) | C10—C11—C12—N2 | 1.0 (3) |
C2—C3—C4—C5 | 0.2 (3) | C11—C12—N2—C8 | −1.1 (3) |
C2—C3—C4—F1 | −179.22 (16) | N1—C1—C2—C3 | 177.30 (15) |
C3—C4—C5—C6 | 0.1 (3) | N1—C1—C6—C5 | −176.88 (15) |
C4—C5—C6—C1 | −0.7 (3) | N1—C7—C8—C9 | 176.00 (15) |
C6—C1—C2—C3 | −0.5 (3) | N1—C7—C8—N2 | −2.6 (2) |
C6—C1—N1—C7 | −30.3 (2) | N2—C8—C9—C10 | 2.2 (3) |
C7—C8—C9—C10 | −176.33 (15) | O1—C7—C8—C9 | −2.6 (3) |
C7—C8—N2—C12 | 178.04 (14) | O1—C7—C8—N2 | 178.75 (16) |
C8—C7—N1—C1 | −178.39 (13) | O1—C7—N1—C1 | 0.2 (3) |
C8—C9—C10—C11 | −2.3 (3) | F1—C4—C5—C6 | 179.56 (16) |
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2···O1i | 0.95 (2) | 2.38 (2) | 3.260 (2) | 155 (2) |
C10—H10···F1ii | 1.00 (2) | 2.53 (2) | 3.397 (2) | 145 (2) |
Symmetry codes: (i) x, y+1, z; (ii) x+1, −y+1/2, z+1/2. |
C12H9N3O3 | Z = 2 |
Mr = 243.22 | F(000) = 252 |
Triclinic, P1 | Dx = 1.484 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 6.1490 (3) Å | Cell parameters from 2788 reflections |
b = 7.3055 (3) Å | θ = 3.1–32.0° |
c = 13.6613 (5) Å | µ = 0.11 mm−1 |
α = 100.162 (4)° | T = 295 K |
β = 97.147 (3)° | Plate, colourless |
γ = 112.760 (4)° | 0.60 × 0.45 × 0.05 mm |
V = 544.33 (4) Å3 |
Oxford Diffraction Xcalibur2 CCD diffractometer | 2148 independent reflections |
Radiation source: Enhance (Mo) X-ray Source | 1722 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.016 |
Detector resolution: 8.4190 pixels mm-1 | θmax = 26.0°, θmin = 3.1° |
ω scans | h = −7→7 |
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2008) | k = −5→9 |
Tmin = 0.938, Tmax = 1.000 | l = −16→16 |
4092 measured reflections |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.041 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.124 | All H-atom parameters refined |
S = 1.07 | w = 1/[σ2(Fo2) + (0.0778P)2 + 0.0252P] where P = (Fo2 + 2Fc2)/3 |
2148 reflections | (Δ/σ)max < 0.001 |
199 parameters | Δρmax = 0.13 e Å−3 |
0 restraints | Δρmin = −0.26 e Å−3 |
C12H9N3O3 | γ = 112.760 (4)° |
Mr = 243.22 | V = 544.33 (4) Å3 |
Triclinic, P1 | Z = 2 |
a = 6.1490 (3) Å | Mo Kα radiation |
b = 7.3055 (3) Å | µ = 0.11 mm−1 |
c = 13.6613 (5) Å | T = 295 K |
α = 100.162 (4)° | 0.60 × 0.45 × 0.05 mm |
β = 97.147 (3)° |
Oxford Diffraction Xcalibur2 CCD diffractometer | 2148 independent reflections |
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2008) | 1722 reflections with I > 2σ(I) |
Tmin = 0.938, Tmax = 1.000 | Rint = 0.016 |
4092 measured reflections |
R[F2 > 2σ(F2)] = 0.041 | 0 restraints |
wR(F2) = 0.124 | All H-atom parameters refined |
S = 1.07 | Δρmax = 0.13 e Å−3 |
2148 reflections | Δρmin = −0.26 e Å−3 |
199 parameters |
Experimental. CrysAlis RED (Oxford Diffraction, 2008). Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm. |
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. 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. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. |
x | y | z | Uiso*/Ueq | ||
H3 | 1.536 (3) | 0.836 (2) | 0.7069 (13) | 0.060 (5)* | |
H2 | 1.410 (3) | 0.834 (2) | 0.5340 (13) | 0.054 (4)* | |
H100 | 1.117 (3) | 0.776 (3) | 0.4007 (14) | 0.062 (5)* | |
H12 | 1.171 (4) | 0.826 (3) | 0.1283 (15) | 0.083 (6)* | |
H11 | 0.824 (4) | 0.778 (3) | 0.0123 (15) | 0.072 (5)* | |
H10 | 0.454 (3) | 0.710 (2) | 0.0617 (14) | 0.063 (5)* | |
H9 | 0.444 (3) | 0.685 (2) | 0.2331 (14) | 0.062 (5)* | |
H6 | 0.722 (3) | 0.669 (2) | 0.5757 (13) | 0.055 (4)* | |
H5 | 0.839 (3) | 0.670 (2) | 0.7400 (15) | 0.070 (5)* | |
C12 | 1.0120 (3) | 0.7958 (3) | 0.14864 (11) | 0.0561 (4) | |
C11 | 0.8126 (3) | 0.7685 (3) | 0.07881 (11) | 0.0548 (4) | |
C10 | 0.5975 (3) | 0.7261 (2) | 0.10858 (11) | 0.0521 (4) | |
C9 | 0.5881 (3) | 0.7146 (2) | 0.20833 (10) | 0.0455 (4) | |
C8 | 0.7969 (2) | 0.74383 (18) | 0.27309 (10) | 0.0378 (3) | |
C7 | 0.7905 (2) | 0.73211 (19) | 0.38174 (10) | 0.0386 (3) | |
C1 | 1.0598 (2) | 0.75289 (18) | 0.53927 (9) | 0.0367 (3) | |
C6 | 0.8889 (3) | 0.7021 (2) | 0.59932 (11) | 0.0441 (3) | |
C5 | 0.9591 (3) | 0.7020 (2) | 0.69959 (11) | 0.0456 (4) | |
C4 | 1.1976 (3) | 0.75244 (19) | 0.73875 (9) | 0.0416 (3) | |
C3 | 1.3697 (3) | 0.8015 (2) | 0.68047 (11) | 0.0467 (4) | |
C2 | 1.3002 (3) | 0.8010 (2) | 0.58027 (10) | 0.0435 (3) | |
N2 | 1.0070 (2) | 0.78351 (19) | 0.24510 (9) | 0.0477 (3) | |
N1 | 1.0038 (2) | 0.75641 (17) | 0.43700 (8) | 0.0413 (3) | |
N3 | 1.2710 (3) | 0.75427 (19) | 0.84535 (9) | 0.0537 (4) | |
O1 | 0.60751 (18) | 0.70404 (17) | 0.41444 (8) | 0.0554 (3) | |
O2 | 1.1194 (3) | 0.7113 (2) | 0.89690 (9) | 0.0778 (4) | |
O3 | 1.4842 (3) | 0.7998 (2) | 0.87807 (9) | 0.0827 (4) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C12 | 0.0509 (9) | 0.0893 (11) | 0.0371 (8) | 0.0334 (8) | 0.0172 (7) | 0.0224 (7) |
C11 | 0.0638 (10) | 0.0806 (10) | 0.0288 (7) | 0.0368 (8) | 0.0132 (7) | 0.0172 (7) |
C10 | 0.0521 (9) | 0.0716 (9) | 0.0333 (7) | 0.0289 (8) | 0.0028 (6) | 0.0119 (7) |
C9 | 0.0398 (8) | 0.0599 (8) | 0.0369 (7) | 0.0205 (7) | 0.0083 (6) | 0.0130 (6) |
C8 | 0.0400 (7) | 0.0413 (7) | 0.0305 (7) | 0.0152 (6) | 0.0077 (5) | 0.0088 (5) |
C7 | 0.0392 (7) | 0.0433 (7) | 0.0319 (7) | 0.0149 (5) | 0.0089 (5) | 0.0102 (5) |
C1 | 0.0415 (7) | 0.0408 (7) | 0.0276 (6) | 0.0172 (5) | 0.0080 (5) | 0.0075 (5) |
C6 | 0.0386 (7) | 0.0583 (8) | 0.0353 (7) | 0.0178 (6) | 0.0109 (6) | 0.0147 (6) |
C5 | 0.0476 (8) | 0.0569 (8) | 0.0357 (7) | 0.0207 (7) | 0.0162 (6) | 0.0173 (6) |
C4 | 0.0518 (8) | 0.0461 (7) | 0.0282 (7) | 0.0216 (6) | 0.0082 (6) | 0.0100 (5) |
C3 | 0.0427 (8) | 0.0625 (8) | 0.0363 (7) | 0.0240 (7) | 0.0061 (6) | 0.0124 (6) |
C2 | 0.0408 (8) | 0.0597 (8) | 0.0339 (7) | 0.0225 (6) | 0.0141 (6) | 0.0134 (6) |
N2 | 0.0437 (7) | 0.0700 (8) | 0.0335 (6) | 0.0253 (6) | 0.0113 (5) | 0.0169 (5) |
N1 | 0.0390 (6) | 0.0577 (7) | 0.0284 (6) | 0.0193 (5) | 0.0107 (5) | 0.0134 (5) |
N3 | 0.0668 (9) | 0.0639 (8) | 0.0336 (7) | 0.0301 (7) | 0.0080 (6) | 0.0151 (6) |
O1 | 0.0428 (6) | 0.0891 (8) | 0.0409 (6) | 0.0282 (5) | 0.0159 (5) | 0.0258 (5) |
O2 | 0.0916 (10) | 0.1171 (10) | 0.0393 (6) | 0.0486 (8) | 0.0280 (7) | 0.0339 (7) |
O3 | 0.0702 (9) | 0.1275 (11) | 0.0490 (7) | 0.0384 (8) | −0.0012 (6) | 0.0347 (7) |
C12—N2 | 1.3397 (18) | C1—C2 | 1.394 (2) |
C12—C11 | 1.380 (2) | C1—N1 | 1.4039 (16) |
C12—H12 | 1.00 (2) | C6—C5 | 1.3841 (19) |
C11—C10 | 1.368 (2) | C6—H6 | 0.956 (18) |
C11—H11 | 0.93 (2) | C5—C4 | 1.375 (2) |
C10—C9 | 1.387 (2) | C5—H5 | 0.957 (19) |
C10—H10 | 0.978 (19) | C4—C3 | 1.378 (2) |
C9—C8 | 1.384 (2) | C4—N3 | 1.4662 (17) |
C9—H9 | 0.950 (19) | C3—C2 | 1.3812 (19) |
C8—N2 | 1.3310 (18) | C3—H3 | 0.958 (18) |
C8—C7 | 1.5063 (17) | C2—H2 | 0.973 (17) |
C7—O1 | 1.2193 (17) | N1—H100 | 0.886 (19) |
C7—N1 | 1.3593 (18) | N3—O2 | 1.2158 (18) |
C1—C6 | 1.3910 (18) | N3—O3 | 1.222 (2) |
N2—C12—C11 | 123.40 (14) | C5—C6—H6 | 116.7 (10) |
N2—C12—H12 | 116.4 (12) | C1—C6—H6 | 123.5 (10) |
C11—C12—H12 | 120.2 (12) | C4—C5—C6 | 119.48 (13) |
C10—C11—C12 | 118.93 (14) | C4—C5—H5 | 122.1 (12) |
C10—C11—H11 | 120.4 (12) | C6—C5—H5 | 118.4 (12) |
C12—C11—H11 | 120.7 (12) | C5—C4—C3 | 121.74 (13) |
C11—C10—C9 | 118.82 (14) | C5—C4—N3 | 119.17 (13) |
C11—C10—H10 | 121.1 (11) | C3—C4—N3 | 119.09 (13) |
C9—C10—H10 | 120.0 (11) | C4—C3—C2 | 118.94 (14) |
C8—C9—C10 | 118.30 (14) | C4—C3—H3 | 122.4 (10) |
C8—C9—H9 | 119.2 (11) | C2—C3—H3 | 118.7 (10) |
C10—C9—H9 | 122.5 (11) | C3—C2—C1 | 120.33 (13) |
N2—C8—C9 | 123.61 (13) | C3—C2—H2 | 124.2 (10) |
N2—C8—C7 | 117.25 (12) | C1—C2—H2 | 115.5 (10) |
C9—C8—C7 | 119.13 (12) | C8—N2—C12 | 116.94 (12) |
O1—C7—N1 | 124.87 (12) | C7—N1—C1 | 128.59 (12) |
O1—C7—C8 | 121.32 (12) | C7—N1—H100 | 112.2 (13) |
N1—C7—C8 | 113.81 (12) | C1—N1—H100 | 119.2 (13) |
C6—C1—C2 | 119.69 (12) | O2—N3—O3 | 123.14 (13) |
C6—C1—N1 | 123.42 (12) | O2—N3—C4 | 119.16 (14) |
C2—C1—N1 | 116.88 (12) | O3—N3—C4 | 117.70 (14) |
C5—C6—C1 | 119.81 (14) | ||
N2—C12—C11—C10 | −0.2 (3) | N3—C4—C3—C2 | −179.57 (12) |
C12—C11—C10—C9 | 0.8 (2) | C4—C3—C2—C1 | 0.5 (2) |
C11—C10—C9—C8 | −0.9 (2) | C6—C1—C2—C3 | −1.0 (2) |
C10—C9—C8—N2 | 0.4 (2) | N1—C1—C2—C3 | 179.78 (12) |
C10—C9—C8—C7 | 179.97 (12) | C9—C8—N2—C12 | 0.2 (2) |
N2—C8—C7—O1 | 177.22 (12) | C7—C8—N2—C12 | −179.34 (12) |
C9—C8—C7—O1 | −2.4 (2) | C11—C12—N2—C8 | −0.3 (3) |
N2—C8—C7—N1 | −2.50 (17) | O1—C7—N1—C1 | 0.7 (2) |
C9—C8—C7—N1 | 177.90 (12) | C8—C7—N1—C1 | −179.59 (11) |
C2—C1—C6—C5 | 0.8 (2) | C6—C1—N1—C7 | 6.6 (2) |
N1—C1—C6—C5 | 179.92 (12) | C2—C1—N1—C7 | −174.23 (12) |
C1—C6—C5—C4 | 0.0 (2) | C5—C4—N3—O2 | 0.0 (2) |
C6—C5—C4—C3 | −0.6 (2) | C3—C4—N3—O2 | 179.90 (13) |
C6—C5—C4—N3 | 179.33 (12) | C5—C4—N3—O3 | −179.94 (13) |
C5—C4—C3—C2 | 0.4 (2) | C3—C4—N3—O3 | 0.0 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2···O1i | 0.973 (18) | 2.425 (18) | 3.277 (2) | 145.9 (12) |
Symmetry code: (i) x+1, y, z. |
Experimental details
(I) | (II) | |
Crystal data | ||
Chemical formula | C12H9FN2O | C12H9N3O3 |
Mr | 216.21 | 243.22 |
Crystal system, space group | Monoclinic, P21/c | Triclinic, P1 |
Temperature (K) | 296 | 295 |
a, b, c (Å) | 8.2500 (3), 6.0649 (2), 20.5484 (8) | 6.1490 (3), 7.3055 (3), 13.6613 (5) |
α, β, γ (°) | 90, 96.479 (4), 90 | 100.162 (4), 97.147 (3), 112.760 (4) |
V (Å3) | 1021.58 (6) | 544.33 (4) |
Z | 4 | 2 |
Radiation type | Mo Kα | Mo Kα |
µ (mm−1) | 0.10 | 0.11 |
Crystal size (mm) | 0.60 × 0.45 × 0.35 | 0.60 × 0.45 × 0.05 |
Data collection | ||
Diffractometer | Oxford Diffraction Xcalibur2 CCD diffractometer | Oxford Diffraction Xcalibur2 CCD diffractometer |
Absorption correction | Multi-scan (CrysAlis RED; Oxford Diffraction, 2008) | Multi-scan (CrysAlis RED; Oxford Diffraction, 2008) |
Tmin, Tmax | 0.960, 1.000 | 0.938, 1.000 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 10495, 2005, 1593 | 4092, 2148, 1722 |
Rint | 0.027 | 0.016 |
(sin θ/λ)max (Å−1) | 0.617 | 0.618 |
Refinement | ||
R[F2 > 2σ(F2)], wR(F2), S | 0.049, 0.145, 1.03 | 0.041, 0.124, 1.07 |
No. of reflections | 2005 | 2148 |
No. of parameters | 182 | 199 |
H-atom treatment | All H-atom parameters refined | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.18, −0.21 | 0.13, −0.26 |
Computer programs: CrysAlis CCD (Oxford Diffraction, 2008), CrysAlis RED (Oxford Diffraction, 2008), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), Mercury (Macrae et al., 2008), WinGX (Farrugia, 1999).
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2···O1i | 0.95 (2) | 2.38 (2) | 3.260 (2) | 155 (2) |
C10—H10···F1ii | 1.00 (2) | 2.53 (2) | 3.397 (2) | 145 (2) |
Symmetry codes: (i) x, y+1, z; (ii) x+1, −y+1/2, z+1/2. |
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2···O1i | 0.973 (18) | 2.425 (18) | 3.277 (2) | 145.9 (12) |
Symmetry code: (i) x+1, y, z. |
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Amide functional groups are among the most common and prominent in nature. They are the principal C—N bond type linking amino acids together in proteins, with the latter arguably being the most specialized and versatile of all macromolecules in biology. There are numerous studies of simple carboxamides reporting their biological activity, from antimicrobial agents (Kumar et al., 2007) to potent metabotropic glutamate subtype 5 (mGlu5) receptor antagonists (Bonnefous et al., 2005) and cyclooxygenase-1 selective inhibitors (Kakuta et al., 2008). Furthermore, carboxamide derivatives are ideal molecules for chelating metal ions since deprotonation of the amide N—H group affords a powerful σ-donor group. Coupled with additional functional groups based on N, O or S-donor atoms, polydentate carboxamides may be synthesized with variable arrays of metal-binding sites (Zhang et al., 2002; Dasgupta et al., 2008; Cornman et al., 1999; Jiang et al., 2004).
As part of ongoing work in our laboratory, we have isolated crystals of two previously prepared (Ray et al., 1997; Dutta et al., 1999), but hitherto crystallographically uncharacterized, pyridine-2-carboxamides: N-(4-fluorophenyl)pyridine-2-carboxamide and N-(4-nitrophenyl)pyridine-2-carboxamide, compounds (I) and (II), respectively. In these derivatives, metal binding is possible through the pyridine nitrogen atom, the deprotonated amide nitrogen atom, or the carbonyl oxygen atom. The modes of binding can be controlled in some cases by the reaction conditions. Thus, in a basic medium, the amide N—H group is deprotonated and metal ion coordination occurs through the amide anion (Qi, Ma et al., 2003). However, if the reaction conditions are slightly acidic, binding occurs through the carbonyl oxygen and pyridine nitrogen atoms (Morsali et al., 2003). The molecular and crystal structures of the metal-free carboxamides (I) and (II) are described below. In both cases, a single independent molecule occupies the asymmetric unit.
The pyridine ring and amide moiety of compound (I) are essentially coplanar (Fig. 1), while the p-fluorobenzene ring is twisted out of the pyridyl-amide plane with a C7—N1—C1—C6 torsion angle of 30.3 (2)° and dihedral angle of 31.3 (5)° between the pyridine and benzene ring planes. The out-of-plane twist evident in (I) presumably reflects a balance between three factors. First, a possible conformational adjustment to ameliorate nonbonded steric interactions between the benzene ring ortho-H atoms and neighbouring atoms of the amide functional group. Second, the formation of an extended structure based on unconventional hydrogen bonds (see below). Third, the intrinsic preference for a planar structure in a fully conjugated (resonance-delocalized) aromatic amide system. Noteworthy short intramolecular contacts that at least partly support the first notion are: H6···O1, 2.39 (2) and H2···H100, 2.38 (3) Å. The amide N1—C7 bond measures 1.346 (2) Å, while the C7—O1 bond length is 1.2178 (19) Å, i.e. slightly shorter and longer, respectively, than the typical distances in non-amide systems (Orpen et al., 1989); all other distances are normal.
Inspection of Fig. 2 suggests that unconventional hydrogen bonding is significant in the crystal lattice of (I). Specifically, individual molecules are linked by a two-dimensional network of C—H···O and C—H···F hydrogen bonds (Table 1). The C—H···O hydrogen bond occurs between the aryl hydrogen atom appended to carbon C2 of one molecule and the carbonyl oxygen atom of an adjacent molecule, while the C—H···F hydrogen bond occurs between the para-fluoro atom of the benzene ring and the adjacent molecule's pyridyl hydrogen atom H10 (i.e. para to the pyridyl nitrogen atom).
To better understand the nonplanar conformation of (I), we calculated the gas phase geometry of the compound, starting from the X-ray coordinates, by energy optimization of the molecule using standard DFT [density functional theory?] methods (Frisch et al., 2004) at the B3LYP/6–31G** level of theory (Becke, 1993; Ditchfield et al., 1971). The geometry-optimized conformation was completely planar, in distinct contrast to that of the X-ray crystal structure. No negative eigenvalues were obtained from a frequency calculation on the final planar conformation of the molecule, consistent with location of a true minimum on the potential energy surface. Although we have not conducted a full scan of conformational space for (I), it is highly likely that a planar geometry is preferred on energetic grounds (due to resonance delocalization) for an isolated molecule in the gas phase. The nonplanar conformation of (I) observed in the X-ray structure evidently reflects the principal conformational adjustment that enables formation of the extended one-dimensional hydrogen-bonded structure of (I) in the crystal lattice.
Experimentally significant π-stacking is present between the pyridine rings of adjacent molecules of (I). The interaction has the usual offset anti-parallel geometry with inversion symmetry (Janiak, 2000) in which the nitrogen atom of the first pyridine ring is positioned above the centre of the second ring. The metrics of the interaction, where Cg is the centre of gravity of the pyridine ring, β the angle between the Cg→Cgi vector and the pyridine plane normal, IPS is the interplanar separation (or perpendicular distance of Cg on the partner ring) and LS the lateral shift (or distance between Cg and the perpendicular projection of Cg on the partner ring), are: Cg···Cgi = 3.858 (2) Å, β = 23.7 (2)°, IPS = 3.532 (2) Å and LS = 1.552 (2) Å [symmetry code: (i) 1–x, 1–y, 1–z]. The interplanar separation is slightly longer than the graphite spacing of 3.35 Å (Bacon, 1951), but nevertheless still ideal for π-stacking interactions (Hunter & Sanders, 1990).
In pyridine carboxamide (II), the pyridine ring and the amide moiety are again effectively coplanar, while the p-nitrobenzene ring is slightly twisted out of the amide group plane (Fig. 3). The nonplanarity is markedly less than for (I): the C6—N2—C7—C8 torsion angle is 6.6 (2)° and the dihedral angle between the pyridine and nitrobenzene rings measures 4.1 (2)°. The amide N2—C6 and carbonyl C6—O1 bond distances are 1.3580 (15) and 1.2195 (14) Å, respectively, in agreement with those of (I).
Intermolecular C—H···O hydrogen bonds between the meta-hydrogen atom of the nitrobenzene ring and the carbonyl oxygen atom of a neighbouring molecule leads to the formation of stepped one-dimensional chains of molecules that extend in the [100] direction (Table 2). Furthermore, adjacent one-dimensional chains combine to form sheets that lie parallel to the (0 1 0) plane in the lattice (Fig. 4). One such sheet, for example, lies in the (0 4 0) plane.
Molecules of (II) stack one on top of another as inversion pairs. The π-stacking sequence is defined by the infinite pattern ABA'B'AB··· in which the distance between the molecular mean planes for the structurally distinct inversion pairs AB (or A'B') and BA' (or B'A) measure 3.44 (1) and 3.48 (1) Å, respectively. The π-stacking axis is collinear with the crystallographic b axis leading to an array of inversion-paired π-stacked hydrogen-bonded ribbons in the crystal lattice (Fig. 5). Inspection of the π-stacked molecules running in a direction diagonal to the layers (i.e. the `staircase' axis) highlighted in Fig. 5 indicates that molecules connected by hydrogen bonds exhibit short (ring edge)···(ring edge) nonbonded interactions. The tightest of these occurs between nitrobenzene rings: Cg···Cgi = 4.433 (2) Å, β = 39.9 (2)°, IPS = 3.400 (2) Å and LS = 2.845 (2) Å [symmetry code: (i) 2–x, 1–y, 1–z], where the variables are as defined previously. The staircase-like packing, π-stacking and hydrogen bonding in the crystal lattice of (II) evidently lead to only a minor conformational twist for the experimental structure since the DFT-calculated gas-phase conformation of (II) was completely planar, in accord with the calculated conformation of (I) discussed earlier.
Finally, it is clear that changing the para-substituent on the benzene ring from fluorine in (I) to a nitro group in (II) significantly changes the crystal packing and extended structure of each derivative and thus the observed molecular conformation. In both carboxamides, unconventional hydrogen bonds between amide carbonyl oxygen atoms and aryl C—H donors constitute the primary interaction for the extended solid-state structure. This is augmented by significant π-stacking interactions roughly orthogonal to the planes containing the extended structures in both compounds. Interestingly, the isomorphous para-chloro (Zhang et al., 2006) and para-bromo (Qi, Yang et al., 2003) analogues of (I), which crystallize in space group P1, have (pyridyl)C—H···X (X = Cl, Br) and (aryl)C—H···O(carbonyl) hydrogen-bond networks that lead to two-dimensional hydrogen-bonded sheets somewhat different to those present in monoclinic (I). Specifically, the orientations of the individually planar molecules in the p-Cl and p-Br derivatives are such that all carbonyl groups point in the same direction, in distinct contrast to the orientational preference observed for nonplanar (I), namely rows of oppositely oriented carbonyl groups. Evidently, the presence of a small highly electronegative p-F substituent in (I) appreciably alters the most efficient way in which to pack the carboxamide derivative such that it is not isomorphous with the heavier halogenated congeners in the series.
Deprotonated compounds (I) and (II) are currently being used as anionic ligands for a number of metal ions in our laboratory and their coordination chemistry will be reported elsewhere.