The crystal structures of two symmetrical pyridine-2-carboxamides, namely
N,
N′-(propane-1,3-diyl)bis(pyridine-2-carboxamide), C
15H
16N
4O
2, (I), and
N,
N′-(butane-1,4-diyl)bis(pyridine-2-carboxamide), C
16H
18N
4O
2, (II), exhibit extended hydrogen-bonded sequences involving their amide groups. In (I), conventional bifurcated amide–carbonyl (N—H)
O hydrogen bonding favours the formation of one-dimensional chains, the axes of which run parallel to [001]. Unconventional bifurcated pyridine–carbonyl C—H
O hydrogen bonding links adjacent one-dimensional chains to form a `porous' three-dimensional lattice with interconnected, yet unfilled, voids of 60.6 (2) Å
3 which combine into channels that run parallel to, and include, [001]. 4% of the unit-cell volume of (I) is vacant. Compound (II) adopts a Z-shaped conformation with inversion symmetry, and exhibits an extended structure comprising one-dimensional hydrogen-bonded chains along [100] in which individual molecules are linked by complementary pairs of amide N—H
O hydrogen bonds. These hydrogen-bonded chains interlock
via π–π interactions between pyridine rings of neighbouring molecules to form sheets parallel with (010); each sheet is one Z-shaped molecule thick and separated from the next sheet by the
b-axis dimension [7.2734 (4) Å].
Supporting information
CCDC references: 804123; 804124
Compounds (I) and (II) were synthesized according to the literature method
(Barnes et al., 1978). X-ray quality crystals of (I) were
obtained by
the slow evaporation of a saturated solution of (I) in a chloroform–diethyl
ether mixture (1:6 v/v). X-ray quality crystals of (II) formed
upon slow evaporation of a saturated solution of (II) in a
dichloromethane–hexane mixture (1:6 v/v).
H atoms attached to amide N atoms were located by difference Fourier synthesis
and refined isotropically. The remaining H atoms were positioned geometrically
and refined using a riding model, with C—H = 0.97 Å and Uiso(H) =
1.2Ueq(C) for methylene H atoms, and C—H = 0.93 Å and
Uiso(H) = 1.2Ueq(C) for aromatic H atoms.
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 (CSD 2.0 Version; Macrae et al., 2008); software used to prepare material for publication: WinGX (Farrugia, 1999).
(I)
N,
N'-(propane-1,3-diyl)bis(pyridine-2-carboxamide)
top
Crystal data top
C15H16N4O2 | F(000) = 600 |
Mr = 284.32 | Dx = 1.239 Mg m−3 |
Monoclinic, Cc | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: C -2yc | Cell parameters from 3923 reflections |
a = 16.7558 (15) Å | θ = 2.8–32.0° |
b = 9.9188 (7) Å | µ = 0.09 mm−1 |
c = 9.7665 (6) Å | T = 296 K |
β = 110.140 (8)° | Plate, colourless |
V = 1523.9 (2) Å3 | 0.65 × 0.40 × 0.15 mm |
Z = 4 | |
Data collection top
Oxford Xcalibur 2 CCD area-detector diffractometer | 2452 independent reflections |
Radiation source: fine-focus sealed tube | 1882 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.023 |
Detector resolution: 8.4190 pixels mm-1 | θmax = 32.0°, θmin = 3.0° |
ω scans | h = −24→24 |
Absorption correction: multi-scan [CrysAlis RED (Oxford Diffraction, 2008); empirical (using intensity measurements) absorption
correction
using spherical harmonics, implemented in the SCALE3 ABSPACK scaling algorithm] | k = −14→14 |
Tmin = 0.947, Tmax = 0.987 | l = −13→10 |
7542 measured reflections | |
Refinement top
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)] = 0.037 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.101 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.98 | w = 1/[σ2(Fo2) + (0.0661P)2] where P = (Fo2 + 2Fc2)/3 |
2452 reflections | (Δ/σ)max < 0.001 |
198 parameters | Δρmax = 0.11 e Å−3 |
2 restraints | Δρmin = −0.17 e Å−3 |
Crystal data top
C15H16N4O2 | V = 1523.9 (2) Å3 |
Mr = 284.32 | Z = 4 |
Monoclinic, Cc | Mo Kα radiation |
a = 16.7558 (15) Å | µ = 0.09 mm−1 |
b = 9.9188 (7) Å | T = 296 K |
c = 9.7665 (6) Å | 0.65 × 0.40 × 0.15 mm |
β = 110.140 (8)° | |
Data collection top
Oxford Xcalibur 2 CCD area-detector diffractometer | 2452 independent reflections |
Absorption correction: multi-scan [CrysAlis RED (Oxford Diffraction, 2008); empirical (using intensity measurements) absorption
correction
using spherical harmonics, implemented in the SCALE3 ABSPACK scaling algorithm] | 1882 reflections with I > 2σ(I) |
Tmin = 0.947, Tmax = 0.987 | Rint = 0.023 |
7542 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.037 | 2 restraints |
wR(F2) = 0.101 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.98 | Δρmax = 0.11 e Å−3 |
2452 reflections | Δρmin = −0.17 e Å−3 |
198 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. |
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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
C1 | −0.17348 (17) | 0.7986 (3) | −0.0231 (3) | 0.0741 (6) | |
H1 | −0.1954 | 0.7927 | 0.0521 | 0.089* | |
C2 | −0.17990 (18) | 0.9194 (3) | −0.0950 (3) | 0.0804 (7) | |
H2A | −0.2047 | 0.9938 | −0.0677 | 0.097* | |
C3 | −0.14934 (19) | 0.9282 (3) | −0.2066 (3) | 0.0776 (7) | |
H3A | −0.1528 | 1.0091 | −0.2565 | 0.093* | |
C4 | −0.11290 (13) | 0.8155 (2) | −0.2457 (2) | 0.0622 (5) | |
H4 | −0.0924 | 0.8186 | −0.3229 | 0.075* | |
C5 | −0.10814 (10) | 0.69896 (18) | −0.16657 (16) | 0.0462 (3) | |
C6 | −0.06680 (9) | 0.57519 (18) | −0.20077 (15) | 0.0421 (3) | |
C7 | −0.01312 (14) | 0.34915 (19) | −0.1169 (2) | 0.0574 (4) | |
H7A | −0.0361 | 0.3169 | −0.2166 | 0.069* | |
H7B | −0.0260 | 0.2824 | −0.0550 | 0.069* | |
C8 | 0.08334 (13) | 0.3623 (2) | −0.0731 (2) | 0.0608 (5) | |
H8A | 0.1072 | 0.2732 | −0.0730 | 0.073* | |
H8B | 0.0960 | 0.4156 | −0.1463 | 0.073* | |
C9 | 0.12664 (12) | 0.4264 (2) | 0.0747 (2) | 0.0560 (4) | |
H9A | 0.1858 | 0.4425 | 0.0872 | 0.067* | |
H9B | 0.1004 | 0.5131 | 0.0771 | 0.067* | |
C10 | 0.18819 (10) | 0.27292 (16) | 0.28139 (17) | 0.0452 (3) | |
C11 | 0.17313 (10) | 0.20021 (17) | 0.40577 (17) | 0.0460 (3) | |
C12 | 0.23058 (12) | 0.1048 (2) | 0.4837 (2) | 0.0583 (4) | |
H12 | 0.2791 | 0.0858 | 0.4614 | 0.070* | |
C13 | 0.21475 (15) | 0.0381 (3) | 0.5956 (3) | 0.0734 (6) | |
H13 | 0.2519 | −0.0278 | 0.6494 | 0.088* | |
C14 | 0.14317 (18) | 0.0709 (3) | 0.6257 (3) | 0.0880 (8) | |
H14 | 0.1310 | 0.0276 | 0.7006 | 0.106* | |
C15 | 0.08952 (19) | 0.1686 (4) | 0.5439 (3) | 0.0966 (10) | |
H15 | 0.0417 | 0.1911 | 0.5667 | 0.116* | |
N1 | −0.13726 (10) | 0.68912 (17) | −0.05605 (16) | 0.0566 (4) | |
N2 | −0.05466 (9) | 0.47532 (15) | −0.10567 (15) | 0.0466 (3) | |
N3 | 0.12243 (10) | 0.34503 (16) | 0.19586 (16) | 0.0522 (3) | |
N4 | 0.10263 (12) | 0.2327 (2) | 0.4338 (2) | 0.0716 (5) | |
O1 | −0.04648 (8) | 0.57020 (14) | −0.31106 (12) | 0.0532 (3) | |
O2 | 0.25671 (8) | 0.26360 (15) | 0.26290 (16) | 0.0624 (3) | |
H2 | −0.0697 (15) | 0.490 (2) | −0.025 (3) | 0.060 (6)* | |
H3 | 0.0807 (17) | 0.350 (2) | 0.226 (3) | 0.059 (6)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
C1 | 0.0862 (14) | 0.0869 (15) | 0.0620 (12) | 0.0303 (12) | 0.0420 (11) | 0.0086 (11) |
C2 | 0.0983 (17) | 0.0771 (15) | 0.0740 (14) | 0.0384 (13) | 0.0400 (13) | 0.0125 (12) |
C3 | 0.0933 (16) | 0.0719 (14) | 0.0727 (15) | 0.0224 (12) | 0.0353 (12) | 0.0217 (11) |
C4 | 0.0722 (12) | 0.0700 (11) | 0.0511 (10) | 0.0081 (9) | 0.0299 (9) | 0.0134 (9) |
C5 | 0.0433 (7) | 0.0638 (9) | 0.0333 (7) | 0.0021 (7) | 0.0155 (6) | 0.0018 (6) |
C6 | 0.0382 (7) | 0.0591 (9) | 0.0306 (7) | −0.0047 (6) | 0.0140 (5) | −0.0030 (6) |
C7 | 0.0759 (12) | 0.0549 (9) | 0.0439 (9) | 0.0024 (8) | 0.0240 (8) | −0.0051 (7) |
C8 | 0.0749 (12) | 0.0688 (11) | 0.0501 (9) | 0.0216 (9) | 0.0360 (8) | 0.0101 (8) |
C9 | 0.0536 (9) | 0.0627 (10) | 0.0561 (10) | 0.0060 (8) | 0.0247 (8) | 0.0129 (8) |
C10 | 0.0476 (8) | 0.0425 (7) | 0.0454 (8) | 0.0018 (6) | 0.0159 (6) | −0.0059 (6) |
C11 | 0.0479 (8) | 0.0441 (7) | 0.0419 (8) | 0.0009 (6) | 0.0101 (6) | −0.0037 (6) |
C12 | 0.0532 (9) | 0.0527 (9) | 0.0597 (11) | 0.0061 (7) | 0.0075 (8) | 0.0014 (8) |
C13 | 0.0666 (13) | 0.0654 (12) | 0.0708 (13) | 0.0025 (9) | 0.0012 (10) | 0.0215 (10) |
C14 | 0.0852 (16) | 0.1065 (19) | 0.0689 (15) | 0.0072 (14) | 0.0221 (13) | 0.0416 (14) |
C15 | 0.0873 (16) | 0.138 (3) | 0.0777 (16) | 0.0361 (17) | 0.0446 (13) | 0.0539 (17) |
N1 | 0.0609 (8) | 0.0720 (10) | 0.0465 (8) | 0.0140 (7) | 0.0310 (7) | 0.0073 (7) |
N2 | 0.0529 (7) | 0.0573 (8) | 0.0355 (6) | 0.0023 (6) | 0.0226 (6) | −0.0005 (6) |
N3 | 0.0499 (7) | 0.0649 (9) | 0.0463 (7) | 0.0115 (6) | 0.0222 (6) | 0.0108 (7) |
N4 | 0.0689 (10) | 0.0931 (13) | 0.0612 (10) | 0.0276 (9) | 0.0331 (8) | 0.0327 (9) |
O1 | 0.0592 (7) | 0.0730 (8) | 0.0346 (5) | −0.0045 (6) | 0.0255 (5) | −0.0047 (5) |
O2 | 0.0519 (7) | 0.0652 (8) | 0.0757 (9) | 0.0097 (5) | 0.0292 (6) | 0.0063 (6) |
Geometric parameters (Å, º) top
C1—N1 | 1.336 (3) | C8—H8B | 0.9700 |
C1—C2 | 1.374 (4) | C9—N3 | 1.454 (2) |
C1—H1 | 0.9300 | C9—H9A | 0.9700 |
C2—C3 | 1.357 (3) | C9—H9B | 0.9700 |
C2—H2A | 0.9300 | C10—O2 | 1.226 (2) |
C3—C4 | 1.389 (3) | C10—N3 | 1.338 (2) |
C3—H3A | 0.9300 | C10—C11 | 1.507 (2) |
C4—C5 | 1.377 (3) | C11—N4 | 1.340 (2) |
C4—H4 | 0.9300 | C11—C12 | 1.377 (2) |
C5—N1 | 1.3325 (19) | C12—C13 | 1.379 (3) |
C5—C6 | 1.503 (2) | C12—H12 | 0.9300 |
C6—O1 | 1.2374 (17) | C13—C14 | 1.369 (4) |
C6—N2 | 1.325 (2) | C13—H13 | 0.9300 |
C7—N2 | 1.454 (2) | C14—C15 | 1.375 (4) |
C7—C8 | 1.528 (3) | C14—H14 | 0.9300 |
C7—H7A | 0.9700 | C15—N4 | 1.332 (3) |
C7—H7B | 0.9700 | C15—H15 | 0.9300 |
C8—C9 | 1.514 (3) | N2—H2 | 0.92 (3) |
C8—H8A | 0.9700 | N3—H3 | 0.85 (3) |
| | | |
N1—C1—C2 | 123.2 (2) | N3—C9—H9A | 108.8 |
N1—C1—H1 | 118.4 | C8—C9—H9A | 108.8 |
C2—C1—H1 | 118.4 | N3—C9—H9B | 108.8 |
C3—C2—C1 | 118.8 (2) | C8—C9—H9B | 108.8 |
C3—C2—H2A | 120.6 | H9A—C9—H9B | 107.7 |
C1—C2—H2A | 120.6 | O2—C10—N3 | 124.08 (16) |
C2—C3—C4 | 119.5 (2) | O2—C10—C11 | 120.53 (15) |
C2—C3—H3A | 120.3 | N3—C10—C11 | 115.39 (14) |
C4—C3—H3A | 120.3 | N4—C11—C12 | 123.37 (17) |
C5—C4—C3 | 117.83 (18) | N4—C11—C10 | 116.94 (14) |
C5—C4—H4 | 121.1 | C12—C11—C10 | 119.69 (16) |
C3—C4—H4 | 121.1 | C11—C12—C13 | 118.64 (19) |
N1—C5—C4 | 123.34 (16) | C11—C12—H12 | 120.7 |
N1—C5—C6 | 116.47 (15) | C13—C12—H12 | 120.7 |
C4—C5—C6 | 120.18 (14) | C14—C13—C12 | 118.53 (19) |
O1—C6—N2 | 123.95 (16) | C14—C13—H13 | 120.7 |
O1—C6—C5 | 120.82 (15) | C12—C13—H13 | 120.7 |
N2—C6—C5 | 115.24 (12) | C13—C14—C15 | 119.3 (2) |
N2—C7—C8 | 113.13 (16) | C13—C14—H14 | 120.4 |
N2—C7—H7A | 109.0 | C15—C14—H14 | 120.4 |
C8—C7—H7A | 109.0 | N4—C15—C14 | 123.3 (2) |
N2—C7—H7B | 109.0 | N4—C15—H15 | 118.3 |
C8—C7—H7B | 109.0 | C14—C15—H15 | 118.3 |
H7A—C7—H7B | 107.8 | C5—N1—C1 | 117.31 (18) |
C9—C8—C7 | 114.58 (15) | C6—N2—C7 | 123.53 (14) |
C9—C8—H8A | 108.6 | C6—N2—H2 | 117.7 (15) |
C7—C8—H8A | 108.6 | C7—N2—H2 | 118.6 (15) |
C9—C8—H8B | 108.6 | C10—N3—C9 | 123.00 (15) |
C7—C8—H8B | 108.6 | C10—N3—H3 | 114.2 (16) |
H8A—C8—H8B | 107.6 | C9—N3—H3 | 122.1 (16) |
N3—C9—C8 | 113.67 (17) | C15—N4—C11 | 116.87 (19) |
| | | |
N1—C1—C2—C3 | 1.1 (5) | C10—C11—C12—C13 | −178.99 (18) |
C1—C2—C3—C4 | 0.3 (4) | C11—C12—C13—C14 | −0.9 (3) |
C2—C3—C4—C5 | −1.1 (4) | C12—C13—C14—C15 | 0.1 (4) |
C3—C4—C5—N1 | 0.6 (3) | C13—C14—C15—N4 | 1.1 (6) |
C3—C4—C5—C6 | −178.0 (2) | C4—C5—N1—C1 | 0.7 (3) |
N1—C5—C6—O1 | 171.93 (16) | C6—C5—N1—C1 | 179.36 (18) |
C4—C5—C6—O1 | −9.4 (2) | C2—C1—N1—C5 | −1.6 (4) |
N1—C5—C6—N2 | −8.0 (2) | O1—C6—N2—C7 | 2.2 (3) |
C4—C5—C6—N2 | 170.74 (17) | C5—C6—N2—C7 | −177.88 (15) |
N2—C7—C8—C9 | 52.3 (2) | C8—C7—N2—C6 | 75.5 (2) |
C7—C8—C9—N3 | 66.7 (2) | O2—C10—N3—C9 | −3.2 (3) |
O2—C10—C11—N4 | 169.13 (19) | C11—C10—N3—C9 | 177.22 (15) |
N3—C10—C11—N4 | −11.2 (2) | C8—C9—N3—C10 | 103.1 (2) |
O2—C10—C11—C12 | −11.2 (2) | C14—C15—N4—C11 | −1.4 (5) |
N3—C10—C11—C12 | 168.40 (16) | C12—C11—N4—C15 | 0.5 (4) |
N4—C11—C12—C13 | 0.6 (3) | C10—C11—N4—C15 | −179.8 (2) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O1i | 0.92 (3) | 2.08 (3) | 2.8688 (18) | 144 (2) |
N3—H3···O1i | 0.85 (3) | 2.18 (3) | 2.931 (2) | 147 (2) |
C1—H1···O2ii | 0.93 | 2.47 | 3.397 (3) | 175 |
C13—H13···O2iii | 0.93 | 2.58 | 3.366 (3) | 143 |
Symmetry codes: (i) x, −y+1, z+1/2; (ii) x−1/2, y+1/2, z; (iii) x, −y, z+1/2. |
(II)
N,
N'-(butane-1,4-diyl)bis(pyridine-2-carboxamide)
top
Crystal data top
C16H18N4O2 | Z = 1 |
Mr = 298.34 | F(000) = 158 |
Triclinic, P1 | Dx = 1.360 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 5.3215 (2) Å | Cell parameters from 2485 reflections |
b = 7.2734 (4) Å | θ = 2.8–32.1° |
c = 9.7993 (5) Å | µ = 0.09 mm−1 |
α = 83.509 (4)° | T = 296 K |
β = 77.256 (4)° | Block, colourless |
γ = 81.005 (4)° | 0.4 × 0.4 × 0.4 mm |
V = 364.18 (3) Å3 | |
Data collection top
Oxford Diffraction Xcalibur 2 CCD diffractometer | 2246 independent reflections |
Radiation source: fine-focus sealed tube | 1810 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.015 |
Detector resolution: 8.4190 pixels mm-1 | θmax = 32.1°, θmin = 2.8° |
ω scans | h = −4→7 |
Absorption correction: multi-scan [CrysAlis RED (Oxford Diffraction, 2008); empirical (using intensity measurements) absorption
correction
using spherical harmonics, implemented in the SCALE3 ABSPACK scaling algorithm] | k = −10→10 |
Tmin = 0.584, Tmax = 1.000 | l = −14→14 |
3732 measured reflections | |
Refinement top
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)] = 0.044 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.136 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.11 | w = 1/[σ2(Fo2) + (0.085P)2 + 0.0083P] where P = (Fo2 + 2Fc2)/3 |
2246 reflections | (Δ/σ)max < 0.001 |
104 parameters | Δρmax = 0.21 e Å−3 |
0 restraints | Δρmin = −0.28 e Å−3 |
Crystal data top
C16H18N4O2 | γ = 81.005 (4)° |
Mr = 298.34 | V = 364.18 (3) Å3 |
Triclinic, P1 | Z = 1 |
a = 5.3215 (2) Å | Mo Kα radiation |
b = 7.2734 (4) Å | µ = 0.09 mm−1 |
c = 9.7993 (5) Å | T = 296 K |
α = 83.509 (4)° | 0.4 × 0.4 × 0.4 mm |
β = 77.256 (4)° | |
Data collection top
Oxford Diffraction Xcalibur 2 CCD diffractometer | 2246 independent reflections |
Absorption correction: multi-scan [CrysAlis RED (Oxford Diffraction, 2008); empirical (using intensity measurements) absorption
correction
using spherical harmonics, implemented in the SCALE3 ABSPACK scaling algorithm] | 1810 reflections with I > 2σ(I) |
Tmin = 0.584, Tmax = 1.000 | Rint = 0.015 |
3732 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.044 | 0 restraints |
wR(F2) = 0.136 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.11 | Δρmax = 0.21 e Å−3 |
2246 reflections | Δρmin = −0.28 e Å−3 |
104 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. |
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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
C1 | 0.20233 (19) | 0.65575 (14) | 0.59376 (10) | 0.0424 (2) | |
H1 | 0.3406 | 0.5927 | 0.6315 | 0.051* | |
C2 | −0.0219 (2) | 0.72579 (14) | 0.68544 (10) | 0.0438 (2) | |
H2A | −0.0308 | 0.7137 | 0.7818 | 0.053* | |
C3 | −0.23104 (19) | 0.81372 (14) | 0.63037 (11) | 0.0426 (2) | |
H3 | −0.3834 | 0.8630 | 0.6889 | 0.051* | |
C4 | −0.20975 (17) | 0.82716 (13) | 0.48621 (10) | 0.0385 (2) | |
H4 | −0.3496 | 0.8814 | 0.4463 | 0.046* | |
C5 | 0.02448 (16) | 0.75804 (11) | 0.40274 (9) | 0.0325 (2) | |
C6 | 0.05511 (17) | 0.77626 (13) | 0.24526 (10) | 0.0366 (2) | |
C7 | 0.3730 (2) | 0.76471 (14) | 0.02148 (10) | 0.0416 (2) | |
H7A | 0.5376 | 0.8131 | −0.0117 | 0.050* | |
H7B | 0.2425 | 0.8471 | −0.0195 | 0.050* | |
C8 | 0.39718 (18) | 0.56986 (13) | −0.02760 (9) | 0.0379 (2) | |
H8A | 0.2304 | 0.5241 | 0.0027 | 0.045* | |
H8B | 0.4394 | 0.5782 | −0.1294 | 0.045* | |
N1 | 0.22975 (14) | 0.67428 (11) | 0.45417 (8) | 0.0379 (2) | |
N2 | 0.30155 (16) | 0.76497 (12) | 0.17383 (8) | 0.0398 (2) | |
H2 | 0.420 (2) | 0.7414 (18) | 0.2243 (14) | 0.050 (3)* | |
O1 | −0.13525 (15) | 0.80127 (13) | 0.19031 (8) | 0.0562 (2) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
C1 | 0.0414 (5) | 0.0462 (5) | 0.0397 (5) | −0.0037 (4) | −0.0126 (4) | 0.0011 (4) |
C2 | 0.0497 (5) | 0.0486 (5) | 0.0330 (4) | −0.0112 (4) | −0.0060 (4) | −0.0019 (4) |
C3 | 0.0397 (5) | 0.0439 (5) | 0.0407 (5) | −0.0041 (4) | 0.0006 (4) | −0.0090 (4) |
C4 | 0.0332 (4) | 0.0395 (5) | 0.0411 (5) | 0.0004 (3) | −0.0062 (3) | −0.0062 (4) |
C5 | 0.0321 (4) | 0.0304 (4) | 0.0354 (4) | −0.0035 (3) | −0.0071 (3) | −0.0056 (3) |
C6 | 0.0366 (4) | 0.0378 (4) | 0.0361 (4) | −0.0024 (3) | −0.0091 (3) | −0.0062 (3) |
C7 | 0.0484 (5) | 0.0422 (5) | 0.0318 (4) | −0.0033 (4) | −0.0047 (4) | −0.0034 (3) |
C8 | 0.0418 (5) | 0.0452 (5) | 0.0275 (4) | −0.0044 (4) | −0.0089 (3) | −0.0050 (3) |
N1 | 0.0338 (4) | 0.0406 (4) | 0.0383 (4) | −0.0002 (3) | −0.0084 (3) | −0.0037 (3) |
N2 | 0.0374 (4) | 0.0491 (5) | 0.0329 (4) | −0.0015 (3) | −0.0062 (3) | −0.0117 (3) |
O1 | 0.0425 (4) | 0.0851 (6) | 0.0436 (4) | −0.0075 (4) | −0.0166 (3) | −0.0022 (4) |
Geometric parameters (Å, º) top
C1—N1 | 1.3368 (12) | C6—O1 | 1.2289 (11) |
C1—C2 | 1.3896 (14) | C6—N2 | 1.3382 (12) |
C1—H1 | 0.9300 | C7—N2 | 1.4572 (12) |
C2—C3 | 1.3795 (15) | C7—C8 | 1.5252 (13) |
C2—H2A | 0.9300 | C7—H7A | 0.9700 |
C3—C4 | 1.3856 (14) | C7—H7B | 0.9700 |
C3—H3 | 0.9300 | C8—C8i | 1.5205 (18) |
C4—C5 | 1.3866 (12) | C8—H8A | 0.9700 |
C4—H4 | 0.9300 | C8—H8B | 0.9700 |
C5—N1 | 1.3355 (11) | N2—H2 | 0.871 (13) |
C5—C6 | 1.5083 (12) | | |
| | | |
N1—C1—C2 | 123.45 (9) | N2—C6—C5 | 114.60 (8) |
N1—C1—H1 | 118.3 | N2—C7—C8 | 112.26 (8) |
C2—C1—H1 | 118.3 | N2—C7—H7A | 109.2 |
C3—C2—C1 | 118.56 (9) | C8—C7—H7A | 109.2 |
C3—C2—H2A | 120.7 | N2—C7—H7B | 109.2 |
C1—C2—H2A | 120.7 | C8—C7—H7B | 109.2 |
C2—C3—C4 | 118.71 (8) | H7A—C7—H7B | 107.9 |
C2—C3—H3 | 120.6 | C8i—C8—C7 | 113.53 (9) |
C4—C3—H3 | 120.6 | C8i—C8—H8A | 108.9 |
C3—C4—C5 | 118.62 (8) | C7—C8—H8A | 108.9 |
C3—C4—H4 | 120.7 | C8i—C8—H8B | 108.9 |
C5—C4—H4 | 120.7 | C7—C8—H8B | 108.9 |
N1—C5—C4 | 123.43 (8) | H8A—C8—H8B | 107.7 |
N1—C5—C6 | 116.96 (8) | C5—N1—C1 | 117.14 (8) |
C4—C5—C6 | 119.61 (8) | C6—N2—C7 | 123.00 (8) |
O1—C6—N2 | 124.23 (8) | C6—N2—H2 | 115.9 (8) |
O1—C6—C5 | 121.17 (8) | C7—N2—H2 | 120.6 (9) |
| | | |
N1—C1—C2—C3 | 2.26 (16) | C4—C5—C6—N2 | 158.63 (9) |
C1—C2—C3—C4 | 0.54 (15) | N2—C7—C8—C8i | −60.39 (13) |
C2—C3—C4—C5 | −2.45 (15) | C4—C5—N1—C1 | 0.82 (14) |
C3—C4—C5—N1 | 1.84 (14) | C6—C5—N1—C1 | −179.18 (7) |
C3—C4—C5—C6 | −178.16 (8) | C2—C1—N1—C5 | −2.91 (15) |
N1—C5—C6—O1 | 159.32 (9) | O1—C6—N2—C7 | −5.62 (16) |
C4—C5—C6—O1 | −20.68 (14) | C5—C6—N2—C7 | 175.10 (8) |
N1—C5—C6—N2 | −21.38 (12) | C8—C7—N2—C6 | −85.15 (11) |
Symmetry code: (i) −x+1, −y+1, −z. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O1ii | 0.874 (12) | 2.412 (11) | 3.0901 (12) | 134.8 (11) |
Symmetry code: (ii) x+1, y, z. |
Experimental details
| (I) | (II) |
Crystal data |
Chemical formula | C15H16N4O2 | C16H18N4O2 |
Mr | 284.32 | 298.34 |
Crystal system, space group | Monoclinic, Cc | Triclinic, P1 |
Temperature (K) | 296 | 296 |
a, b, c (Å) | 16.7558 (15), 9.9188 (7), 9.7665 (6) | 5.3215 (2), 7.2734 (4), 9.7993 (5) |
α, β, γ (°) | 90, 110.140 (8), 90 | 83.509 (4), 77.256 (4), 81.005 (4) |
V (Å3) | 1523.9 (2) | 364.18 (3) |
Z | 4 | 1 |
Radiation type | Mo Kα | Mo Kα |
µ (mm−1) | 0.09 | 0.09 |
Crystal size (mm) | 0.65 × 0.40 × 0.15 | 0.4 × 0.4 × 0.4 |
|
Data collection |
Diffractometer | Oxford Xcalibur 2 CCD area-detector diffractometer | Oxford Diffraction Xcalibur 2 CCD diffractometer |
Absorption correction | Multi-scan [CrysAlis RED (Oxford Diffraction, 2008); empirical (using intensity measurements) absorption
correction
using spherical harmonics, implemented in the SCALE3 ABSPACK scaling algorithm] | Multi-scan [CrysAlis RED (Oxford Diffraction, 2008); empirical (using intensity measurements) absorption
correction
using spherical harmonics, implemented in the SCALE3 ABSPACK scaling algorithm] |
Tmin, Tmax | 0.947, 0.987 | 0.584, 1.000 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 7542, 2452, 1882 | 3732, 2246, 1810 |
Rint | 0.023 | 0.015 |
(sin θ/λ)max (Å−1) | 0.746 | 0.748 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.037, 0.101, 0.98 | 0.044, 0.136, 1.11 |
No. of reflections | 2452 | 2246 |
No. of parameters | 198 | 104 |
No. of restraints | 2 | 0 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.11, −0.17 | 0.21, −0.28 |
Hydrogen-bond geometry (Å, º) for (I) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O1i | 0.92 (3) | 2.08 (3) | 2.8688 (18) | 144 (2) |
N3—H3···O1i | 0.85 (3) | 2.18 (3) | 2.931 (2) | 147 (2) |
C1—H1···O2ii | 0.93 | 2.47 | 3.397 (3) | 175 |
C13—H13···O2iii | 0.93 | 2.58 | 3.366 (3) | 143 |
Symmetry codes: (i) x, −y+1, z+1/2; (ii) x−1/2, y+1/2, z; (iii) x, −y, z+1/2. |
Hydrogen-bond geometry (Å, º) for (II) top
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···O1i | 0.874 (12) | 2.412 (11) | 3.0901 (12) | 134.8 (11) |
Symmetry code: (i) x+1, y, z. |
Bis(pyridine-amide) and bis(quinoline-amide) derivatives comprise a large group of organic compounds that are ideal for the mono- or dinuclear chelation of metal ions (Tsuboyama et al., 1984; Chan et al., 1998; Cornman et al., 1999), as well as the formation of coordination polymers (Kajikawa et al., 1998; van der Horst et al., 2008). The basic structural features of these compounds allow them to function as multidentate N,N'-donor ligands, or as mixed N,O-donor ligands in situations where the carbonyl O atoms are used for binding. When coordinated as N,N'-donor ligands, these deprotonated diamide derivatives are typically capable of stabilizing metal ions in both high and mid-to-low oxidation states (Havranek et al., 1999; Lee et al., 2002). The deprotonated amide N atoms ostensibly function as hard σ-donors and such ligands exhibit a thermodynamic preference for the coordination of hard metal ions, in accord with the general principles of the HSAB (hard-soft-acid-base) theory (Pearson, 1963).
Metal-free pyridine-amides are inherently interesting from the standpoint of chemical biology. Thus, mono(pyridine-amide) analogues have well documented biological activities (Kumar et al., 2007; Bonnefous et al., 2005; Kakuta et al., 2008). On the other hand, structural and biological studies of the analogous metal-free bis(pyridine-amides) are lacking. Notwithstanding this, and consistent with the primary function of bis(pyridine-amides) as tetradentate ligands for metal ions, Che reported significant anticancer and anti-HIV activity for several gold(III) chelates of the basic bis(pyridine-amide) ligand system in a recent patent (Che, 2004). Furthermore, ruthenium(III) nitrosyl derivatives of bis(pyridine-amides) have been studied as photoactive anticancer compounds (Patra et al., 2004; Rose et al., 2007, 2008). Growing interest in biological studies of the metal chelates of this class of compounds is also exemplified by reports of the interactions of vanadium(III) and oxovanadium(IV) complexes of the bis(pyridine-amide) system with proteins (Vlahos et al., 2000). As part of ongoing work in our laboratory, we have isolated crystals of two previously prepared (Barnes et al., 1978), but hitherto crystallographically uncharacterized, bis(pyridine-amide) ligands, namely N,N'-(propane-1,3-diyl)bis(pyridine-2-carboxamide), (I), and N,N'-(butane-1,4-diyl)bis(pyridine-2-carboxamide), (II). For the single-crystal X-ray structures of (I) and (II) reported here, the asymmetric units comprise single and half-molecules, respectively.
The structure of (I) lacks symmetry and is located at a general position in the unit cell. The two pyridine-amide moieties, although not confined to the same plane in the crystal lattice, individually exhibit the expected near-planar geometry for a resonance-delocalized amide system (Fig. 1). The amide N—C bonds average 1.332 (9) Å, while the mean carbonyl C—O bond length measures 1.232 (8) Å. These distances are slightly shorter and longer, respectively, than the typical distances found in non-amide systems (Orpen et al., 1989). All other distances are normal. The amide groups are rotated slightly out of the plane of the pyridine rings, as evidenced by the dihedral angles N1—C5—C6—O1 and N4—C11—C10—O2, which deviate slightly from 180°, having values of 171.93 (16) and 169.13 (19)°, respectively. The dihedral angle between the two pyridine ring planes measures 34.09 (16)°, with the ring centroids separated by 9.383 (2) Å.
The conformation of the propyl bridge linking the two pyridine-amide groups in (I) is not the normal staggered arrangement for an aliphatic chain. From Fig. 1, it is clear that the bridging group adopts a more twisted conformation, which allows the two amide N—H groups to point in roughly the same direction [the N—H vectors are oriented at an angle of 19 (2)° to one another]. This conformation directly reflects the extended structure of the compound (Table 1), since the two N—H groups serve as hydrogen-bond donors to one of the carbonyl O atoms, specifically O1i [symmetry code: (i) x, -y + 1, z + 1/2], of a neighbouring molecule. As shown in Fig. 2, this bifurcated hydrogen-bonding pattern repeats to create a one-dimensional hydrogen-bonded chain parallel to [001]. The extended structure of (I) is made more intricate by a second, unconventional, bifurcated hydrogen bond involving carbonyl atom O2 (Table 1). In this three-centred interaction, the two hydrogen-bond donors are pyridine C—H groups of two neighbouring molecules. The combined effect of these hydrogen bonds and the conventional hydrogen bonds involving the N—H groups is the assembly of a rather open three-dimensional network structure with a pattern akin to a diamond mesh when viewed down [001]. As shown in Fig. 3, open channels run parallel to [001] at the four unit-cell corners and down the unit-cell centre. These continuous channels contain solvent-accessible voids of 60.6 (1) Å3 (when mapped with a 1.2 Å probe radius and a grid spacing of 0.2 Å). In principle, small molecules the size of hydrogen-bonded water (40 Å3) could fit into voids with such dimensions. The crystals of (I) were, however, isolated as an unsolvated lattice, with ca 4% of the unit-cell volume unoccupied. The three-dimensional network structure of (I) is presumably facilitated by (i) the flexible propyl bridge and (ii) the combination of hydrogen-bond donors/acceptors that are available. Bridge flexibility appears to be critical, since rigid aromatic bridges in bis(pyridine-amide) derivatives do not typically enable the formation of similar network structures (Fun et al., 1999; Jain et al., 2004). There is no evidence for π-stacking of the pyridine rings in the structure of (I), despite the expectation that such interactions might occur, given their abundance in heteroaromatic systems (Janiak, 2000).
Compound (II) lies about an inversion centre (Fig. 4) which is at the mid-point of the C8—C8i bond [symmetry code: (i) 1 - x, 1 - y, -z] of the butyl bridge (i.e. the C4H8 chain). The symmetry-unique amide N—C and C—O distances measure 1.3382 (12) and 1.2289 (11) Å, respectively, consistent with those of (I). Interestingly, the symmetry-unique pyridine ring and amide group are not coplanar, as evidenced by the non-zero N1—C5—C6—N2 torsion angle [-21.38 (12)°]. The out-of-plane tilt of the pyridine ring (relative to the amide group) is roughly double the average observed for the two pyridine rings in (I) and reflects a combination of two factors: (i) the formation of hydrogen bonds (N—H···O) between the amide groups of neighbouring molecules (Table 2), which leads to infinite one-dimensional chains (see below), and (ii) alleviation of unfavourable steric interactions between the closely juxtaposed pyridine rings of each monomer unit within the one-dimensional hydrogen-bonded chain, presumably as a consequence of hydrogen-bond formation. The latter notion was straightforwardly confirmed by calculating the structure of the Ci symmetry monomer of (II) in the gas-phase using density functional theory (DFT) at the B3LYP/6-31G** level of theory (Frisch et al., 2004; Becke, 1993; Ditchfield et al., 1971). The DFT-calculated structure of (II) has a similar butyl-chain conformation to the X-ray structure. However, the pyridine ring and amide functional groups are exactly coplanar, due to the absence of intermolecular interactions in the gas-phase structure.
The one-dimensional hydrogen-bonded chains in (II) run parallel to (010) with the chain axis collinear with [100], as shown in Fig. 5. The C8—C8' bond mid-points of the assembled molecules, where atom C8' is related to atom C8 by inversion, are all located in the (020) plane, such that this plane defines the spatial arrangement (one pyridine-amide unit above the plane and one below it) and directionality of the hydrogen-bonded polymer chains. Each one-dimensional chain has a distinct Z shape and interlocks with a neighbouring chain via intermolecular π–π interactions involving the pyridine rings (Fig. 6). Because of the layered packing of the molecules, each pyridine ring is sandwiched between two π-stacked partners. Both interactions have the usual offset antiparallel geometry with inversion symmetry (Janiak, 2000). The metrics of the interactions, where Cg is the centre of gravity of the pyridine ring, β the angle between the Cg→Cgi,ii vector and the pyridine plane normal, IPS the interplanar separation (or perpendicular distance between Cg and the mean plane passing through Cgi,ii ) and LS the lateral shift (or distance between Cg and the perpendicular projection of Cg on the partner ring) are: (i) Cg···Cgi = 3.7099 (6) Å, β = 23.0 (2)°, IPS = 3.4163 (4) Å and LS = 1.447 (2) Å [symmetry code: (i) -x, 1 - y, 1 - z] for the first partner ring, and (ii) Cg···Cgii = 3.7452 (6) Å, β = 23.6 (2)°, IPS = 3.4313 (4) Å and LS = 1.501 (2) Å [symmetry code: (ii) -x, 2 - y, 1 - z] for the second ring. In both cases, the interplanar separation is slightly greater than the graphite spacing of 3.35 Å (Bacon, 1951), but is nevertheless fully consistent with well defined π-stacking interactions (Hunter & Sanders, 1990).
Finally, altering the length of the carbon bridge between the amide groups in the present compounds not only permits changes in the molecular conformation, but also facilitates different crystal packing architectures for each derivative. In both (I) and (II), traditional amide N—H···O hydrogen bonding is clearly the dominant interaction responsible for the extended solid-state structures. This is accompanied by unconventional C—H···O hydrogen bonding in (I) and significant pyridine···pyridine π–π stacking interactions in (II). Interestingly, the previously reported (Stephens & Vagg, 1988) ethyl-bridged bis(pyridine-amide) analogue of (I) and (II) exhibits crystallographically required inversion symmetry (space group Pccn) and a Z-shaped conformation akin to that of (II). Furthermore, similar sheets of N—H···O hydrogen-bonded units dominate the extended structure of the ethyl-bridged congener. The key difference, however, is that intermolecular pyridine···amide π–π interactions are favoured in the ethyl derivative because of the shorter bridge length, and each molecule thus forms hydrogen bonds with four neighbours rather than two. This establishes repeating two-dimensional N—H···O hydrogen-bond networks, or hydrogen-bonded sheets, parallel to (and including) the (010) plane. Since the individual molecules within a hydrogen-bonded sheet are oriented at 74.8° relative to those in an adjacent sheet, a herringbone packing pattern is both distinctly evident and unique to the ethyl derivative. Deprotonated (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.