The title compound, C
18H
16N
6O
2, can be crystallized in two polymorphic forms,
viz. orthorhombic, described here, and triclinic. In the orthorhombic polymorph, both 2-pyridylmethyl moieties lie out of the plane of the pyrazine ring by
ca 80°. One amide moiety lies in the plane of the pyrazine ring, while the other is almost perpendicular to the pyrazine ring. This structure contrasts with that of the triclinic polymorph, which is L-shaped, with one of the (2-pyridylmethyl)amide substituents lying almost in the plane of the pyrazine ring because of the presence of a bifurcated (N—H
N,N′) intramolecular hydrogen bond.
Supporting information
CCDC reference: 234869
Key indicators
- Single-crystal X-ray study
- T = 153 K
- Mean (C-C) = 0.002 Å
- R factor = 0.032
- wR factor = 0.079
- Data-to-parameter ratio = 10.1
checkCIF/PLATON results
No syntax errors found
Alert level C
PLAT230_ALERT_2_C Hirshfeld Test Diff for O2 - C12 = 5.30 su
0 ALERT level A = In general: serious problem
0 ALERT level B = Potentially serious problem
1 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
0 ALERT type 3 Indicator that the structure quality may be low
0 ALERT type 4 Improvement, methodology, query or suggestion
Data collection: X-AREA (Stoe & Cie, 2003); cell refinement: X-AREA; data reduction: X-RED32 Stoe & Cie, 2003); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: PLATON (Spek, 1990); software used to prepare material for publication: SHELXL97.
Crystal data top
C18H16N6O2 | F(000) = 1456 |
Mr = 348.37 | Dx = 1.401 Mg m−3 |
Orthorhombic, Pbca | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ac 2ab | Cell parameters from 15934 reflections |
a = 8.5131 (6) Å | θ = 1.3–25.6° |
b = 31.862 (2) Å | µ = 0.10 mm−1 |
c = 12.1757 (6) Å | T = 153 K |
V = 3302.6 (4) Å3 | Block, colourless |
Z = 8 | 0.50 × 0.50 × 0.40 mm |
Data collection top
Stoe IPDS-II diffractometer | 2456 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.045 |
Graphite monochromator | θmax = 25.5°, θmin = 1.3° |
ω scans | h = −10→7 |
18389 measured reflections | k = −38→38 |
3034 independent reflections | l = −14→14 |
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)] = 0.032 | All H-atom parameters refined |
wR(F2) = 0.079 | w = 1/[σ2(Fo2) + (0.0478P)2 + 0.1168P] where P = (Fo2 + 2Fc2)/3 |
S = 1.03 | (Δ/σ)max = 0.001 |
3034 reflections | Δρmax = 0.17 e Å−3 |
300 parameters | Δρmin = −0.14 e Å−3 |
0 restraints | Extinction correction: shelxl97, FC*=KFC[1+0.001XFC2Λ3/SIN(2Θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0087 (9) |
Special details top
Geometry. Bond distances, angles etc. have been calculated using the rounded
fractional coordinates. All su's are estimated from the variances of the
(full) variance-covariance matrix. The cell e.s.d.'s are taken into account in
the estimation of distances, angles and torsion angles |
Refinement. Refinement on F2 for ALL reflections except those flagged by the user
for potential systematic errors. Weighted R-factors wR
and all goodnesses of fit S are based on F2,
conventional R-factors R are based on F, with F
set to zero for negative F2. The observed criterion of F2 >
σ(F2) is used only for calculating -R-factor-obs
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 | |
O1 | 0.48512 (11) | 0.11895 (3) | 0.67140 (7) | 0.0331 (3) | |
O2 | 0.66545 (11) | 0.11705 (3) | 0.44520 (8) | 0.0328 (3) | |
N1 | 0.15489 (13) | 0.14818 (3) | 0.51065 (9) | 0.0316 (3) | |
N2 | 0.33433 (14) | 0.11150 (3) | 0.34397 (9) | 0.0347 (4) | |
N3 | 0.27131 (14) | 0.15786 (3) | 0.71466 (9) | 0.0318 (3) | |
N4 | 0.47626 (15) | 0.22332 (3) | 0.76079 (11) | 0.0393 (4) | |
N5 | 0.55206 (13) | 0.05570 (3) | 0.49747 (9) | 0.0280 (3) | |
N6 | 0.76169 (13) | −0.02198 (3) | 0.42001 (9) | 0.0291 (3) | |
C1 | 0.29800 (15) | 0.13237 (3) | 0.53071 (10) | 0.0264 (3) | |
C2 | 0.38618 (15) | 0.11353 (3) | 0.44781 (10) | 0.0272 (4) | |
C3 | 0.19148 (18) | 0.12732 (4) | 0.32535 (12) | 0.0372 (4) | |
C4 | 0.10223 (17) | 0.14503 (4) | 0.40816 (12) | 0.0363 (4) | |
C5 | 0.36065 (15) | 0.13594 (3) | 0.64586 (10) | 0.0265 (3) | |
C6 | 0.31589 (17) | 0.16569 (4) | 0.82746 (11) | 0.0345 (4) | |
C7 | 0.39115 (15) | 0.20801 (4) | 0.84357 (11) | 0.0307 (4) | |
C8 | 0.37539 (19) | 0.22895 (4) | 0.94271 (12) | 0.0400 (5) | |
C9 | 0.4489 (2) | 0.26717 (4) | 0.95676 (15) | 0.0507 (5) | |
C10 | 0.5344 (2) | 0.28365 (4) | 0.87083 (15) | 0.0501 (5) | |
C11 | 0.5456 (2) | 0.26067 (4) | 0.77576 (16) | 0.0478 (5) | |
C12 | 0.54885 (15) | 0.09581 (4) | 0.46547 (10) | 0.0272 (4) | |
C13 | 0.70008 (16) | 0.03740 (4) | 0.53576 (11) | 0.0297 (4) | |
C14 | 0.79668 (15) | 0.01783 (3) | 0.44534 (10) | 0.0260 (3) | |
C15 | 0.91649 (16) | 0.03958 (4) | 0.39401 (11) | 0.0340 (4) | |
C16 | 1.00657 (17) | 0.01966 (4) | 0.31531 (12) | 0.0360 (4) | |
C17 | 0.97450 (16) | −0.02165 (4) | 0.29072 (11) | 0.0311 (4) | |
C18 | 0.85102 (15) | −0.04081 (4) | 0.34334 (11) | 0.0305 (4) | |
H3 | 0.157 (2) | 0.1258 (5) | 0.2487 (16) | 0.051 (4)* | |
H3N | 0.182 (2) | 0.1687 (5) | 0.6879 (14) | 0.051 (5)* | |
H4 | −0.002 (2) | 0.1566 (5) | 0.3932 (13) | 0.044 (4)* | |
H5N | 0.456 (2) | 0.0453 (4) | 0.5211 (13) | 0.042 (4)* | |
H6A | 0.221 (2) | 0.1630 (4) | 0.8713 (13) | 0.046 (4)* | |
H6B | 0.3944 (19) | 0.1431 (4) | 0.8504 (12) | 0.038 (4)* | |
H8 | 0.313 (2) | 0.2173 (5) | 0.9989 (15) | 0.049 (5)* | |
H9 | 0.442 (2) | 0.2812 (6) | 1.0290 (16) | 0.064 (5)* | |
H10 | 0.592 (2) | 0.3114 (5) | 0.8761 (14) | 0.058 (5)* | |
H11 | 0.608 (2) | 0.2717 (5) | 0.7115 (15) | 0.058 (5)* | |
H13A | 0.7658 (19) | 0.0597 (4) | 0.5710 (12) | 0.035 (4)* | |
H13B | 0.6723 (17) | 0.0151 (4) | 0.5890 (12) | 0.029 (3)* | |
H15 | 0.9327 (19) | 0.0685 (5) | 0.4141 (12) | 0.038 (4)* | |
H16 | 1.093 (2) | 0.0350 (5) | 0.2808 (14) | 0.048 (4)* | |
H17 | 1.0368 (19) | −0.0376 (4) | 0.2376 (13) | 0.037 (4)* | |
H18 | 0.8215 (18) | −0.0698 (5) | 0.3263 (12) | 0.038 (4)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0301 (5) | 0.0389 (5) | 0.0304 (5) | 0.0065 (4) | −0.0037 (4) | −0.0014 (4) |
O2 | 0.0300 (5) | 0.0349 (4) | 0.0336 (5) | −0.0025 (4) | 0.0040 (4) | 0.0027 (4) |
N1 | 0.0278 (6) | 0.0318 (5) | 0.0352 (6) | 0.0033 (4) | −0.0035 (5) | −0.0004 (4) |
N2 | 0.0395 (7) | 0.0370 (6) | 0.0275 (6) | 0.0030 (5) | −0.0036 (5) | −0.0007 (4) |
N3 | 0.0264 (6) | 0.0393 (6) | 0.0297 (6) | 0.0019 (5) | −0.0001 (5) | −0.0068 (4) |
N4 | 0.0409 (7) | 0.0341 (5) | 0.0428 (7) | −0.0011 (5) | 0.0080 (6) | −0.0040 (5) |
N5 | 0.0251 (6) | 0.0287 (5) | 0.0303 (6) | 0.0034 (4) | 0.0033 (5) | −0.0007 (4) |
N6 | 0.0266 (6) | 0.0317 (5) | 0.0290 (6) | 0.0011 (4) | 0.0016 (5) | −0.0004 (4) |
C1 | 0.0256 (6) | 0.0240 (5) | 0.0297 (7) | −0.0005 (4) | 0.0002 (5) | 0.0010 (4) |
C2 | 0.0301 (7) | 0.0250 (5) | 0.0265 (7) | −0.0010 (5) | −0.0005 (5) | 0.0008 (4) |
C3 | 0.0404 (8) | 0.0402 (7) | 0.0311 (8) | 0.0030 (6) | −0.0094 (7) | 0.0007 (5) |
C4 | 0.0332 (8) | 0.0379 (7) | 0.0378 (8) | 0.0047 (6) | −0.0093 (6) | 0.0007 (5) |
C5 | 0.0255 (6) | 0.0255 (5) | 0.0285 (7) | −0.0026 (5) | 0.0006 (5) | 0.0003 (4) |
C6 | 0.0332 (7) | 0.0445 (7) | 0.0257 (7) | −0.0062 (6) | 0.0051 (6) | −0.0047 (5) |
C7 | 0.0262 (7) | 0.0358 (6) | 0.0300 (7) | 0.0060 (5) | −0.0004 (6) | −0.0042 (5) |
C8 | 0.0429 (9) | 0.0441 (7) | 0.0329 (8) | 0.0091 (6) | −0.0017 (7) | −0.0075 (6) |
C9 | 0.0636 (11) | 0.0402 (7) | 0.0483 (10) | 0.0137 (7) | −0.0163 (9) | −0.0153 (7) |
C10 | 0.0543 (10) | 0.0300 (7) | 0.0661 (11) | 0.0038 (6) | −0.0142 (9) | −0.0062 (7) |
C11 | 0.0486 (9) | 0.0338 (7) | 0.0610 (11) | −0.0017 (6) | 0.0050 (8) | 0.0003 (7) |
C12 | 0.0301 (7) | 0.0307 (6) | 0.0207 (6) | 0.0022 (5) | 0.0023 (5) | −0.0028 (4) |
C13 | 0.0296 (7) | 0.0324 (6) | 0.0272 (7) | 0.0050 (5) | 0.0003 (5) | 0.0001 (5) |
C14 | 0.0235 (6) | 0.0298 (6) | 0.0246 (6) | 0.0038 (5) | −0.0018 (5) | 0.0021 (4) |
C15 | 0.0336 (7) | 0.0295 (6) | 0.0390 (8) | −0.0005 (5) | 0.0051 (6) | −0.0002 (5) |
C16 | 0.0301 (7) | 0.0424 (7) | 0.0356 (8) | −0.0026 (6) | 0.0082 (6) | 0.0040 (5) |
C17 | 0.0264 (7) | 0.0409 (6) | 0.0259 (7) | 0.0066 (5) | −0.0001 (5) | −0.0018 (5) |
C18 | 0.0287 (7) | 0.0329 (6) | 0.0299 (7) | 0.0009 (5) | 0.0006 (6) | −0.0040 (5) |
Geometric parameters (Å, º) top
O1—C5 | 1.2299 (15) | C8—C9 | 1.3798 (19) |
O2—C12 | 1.2265 (16) | C9—C10 | 1.379 (2) |
N1—C1 | 1.3408 (16) | C10—C11 | 1.373 (2) |
N1—C4 | 1.3298 (18) | C13—C14 | 1.5090 (18) |
N2—C2 | 1.3407 (17) | C14—C15 | 1.3824 (18) |
N2—C3 | 1.3358 (19) | C15—C16 | 1.382 (2) |
N3—C5 | 1.3297 (16) | C16—C17 | 1.3772 (18) |
N3—C6 | 1.4466 (17) | C17—C18 | 1.3741 (19) |
N4—C7 | 1.3337 (18) | C3—H3 | 0.980 (19) |
N4—C11 | 1.3409 (17) | C4—H4 | 0.978 (17) |
N5—C12 | 1.3363 (16) | C6—H6A | 0.972 (17) |
N5—C13 | 1.4647 (17) | C6—H6B | 1.021 (15) |
N6—C14 | 1.3389 (14) | C8—H8 | 0.942 (18) |
N6—C18 | 1.3453 (17) | C9—H9 | 0.99 (2) |
N3—H3N | 0.896 (17) | C10—H10 | 1.013 (16) |
N5—H5N | 0.928 (16) | C11—H11 | 1.009 (18) |
C1—C2 | 1.3938 (17) | C13—H13A | 1.001 (14) |
C1—C5 | 1.5044 (17) | C13—H13B | 0.990 (14) |
C2—C12 | 1.5109 (18) | C15—H15 | 0.963 (16) |
C3—C4 | 1.383 (2) | C16—H16 | 0.978 (17) |
C6—C7 | 1.5057 (18) | C17—H17 | 0.979 (15) |
C7—C8 | 1.3857 (19) | C18—H18 | 0.980 (16) |
| | | |
C1—N1—C4 | 116.68 (11) | C13—C14—C15 | 121.65 (10) |
C2—N2—C3 | 116.20 (11) | C14—C15—C16 | 119.52 (12) |
C5—N3—C6 | 122.59 (11) | C15—C16—C17 | 118.67 (13) |
C7—N4—C11 | 117.46 (13) | C16—C17—C18 | 118.35 (12) |
C12—N5—C13 | 119.41 (11) | N6—C18—C17 | 123.91 (12) |
C14—N6—C18 | 117.17 (11) | N2—C3—H3 | 114.6 (10) |
C6—N3—H3N | 120.1 (11) | C4—C3—H3 | 123.4 (10) |
C5—N3—H3N | 117.3 (11) | N1—C4—H4 | 116.9 (9) |
C13—N5—H5N | 121.2 (9) | C3—C4—H4 | 121.1 (9) |
C12—N5—H5N | 114.5 (9) | N3—C6—H6A | 106.8 (10) |
C2—C1—C5 | 121.10 (11) | N3—C6—H6B | 108.1 (8) |
N1—C1—C5 | 117.61 (11) | C7—C6—H6A | 111.2 (8) |
N1—C1—C2 | 121.28 (11) | C7—C6—H6B | 108.5 (8) |
N2—C2—C12 | 114.71 (11) | H6A—C6—H6B | 109.4 (12) |
C1—C2—C12 | 123.47 (11) | C7—C8—H8 | 119.8 (10) |
N2—C2—C1 | 121.76 (11) | C9—C8—H8 | 120.9 (10) |
N2—C3—C4 | 122.04 (13) | C8—C9—H9 | 118.9 (11) |
N1—C4—C3 | 121.99 (13) | C10—C9—H9 | 122.3 (11) |
O1—C5—N3 | 124.38 (12) | C9—C10—H10 | 122.7 (10) |
O1—C5—C1 | 120.52 (11) | C11—C10—H10 | 119.0 (10) |
N3—C5—C1 | 115.09 (11) | N4—C11—H11 | 115.8 (10) |
N3—C6—C7 | 112.94 (11) | C10—C11—H11 | 120.3 (10) |
N4—C7—C8 | 122.33 (12) | N5—C13—H13A | 109.6 (8) |
C6—C7—C8 | 120.23 (12) | N5—C13—H13B | 106.8 (8) |
N4—C7—C6 | 117.40 (12) | C14—C13—H13A | 107.5 (9) |
C7—C8—C9 | 119.28 (14) | C14—C13—H13B | 108.1 (8) |
C8—C9—C10 | 118.79 (15) | H13A—C13—H13B | 111.2 (12) |
C9—C10—C11 | 118.26 (13) | C14—C15—H15 | 118.1 (9) |
N4—C11—C10 | 123.87 (16) | C16—C15—H15 | 122.4 (9) |
O2—C12—C2 | 120.46 (11) | C15—C16—H16 | 119.1 (10) |
N5—C12—C2 | 114.68 (11) | C17—C16—H16 | 122.2 (10) |
O2—C12—N5 | 124.74 (12) | C16—C17—H17 | 122.2 (8) |
N5—C13—C14 | 113.65 (11) | C18—C17—H17 | 119.5 (8) |
N6—C14—C13 | 115.99 (11) | N6—C18—H18 | 115.0 (9) |
N6—C14—C15 | 122.34 (11) | C17—C18—H18 | 121.1 (9) |
| | | |
C4—N1—C1—C2 | −0.16 (16) | C2—C1—C5—N3 | 174.20 (10) |
C4—N1—C1—C5 | 179.44 (10) | N1—C1—C5—O1 | 173.85 (10) |
C1—N1—C4—C3 | −1.57 (18) | N1—C1—C5—N3 | −5.40 (14) |
C3—N2—C2—C1 | −2.09 (16) | C1—C2—C12—O2 | −95.14 (15) |
C3—N2—C2—C12 | −179.31 (10) | N2—C2—C12—O2 | 82.03 (14) |
C2—N2—C3—C4 | 0.37 (18) | N2—C2—C12—N5 | −94.24 (13) |
C6—N3—C5—O1 | 2.93 (18) | C1—C2—C12—N5 | 88.60 (14) |
C6—N3—C5—C1 | −177.86 (10) | N2—C3—C4—N1 | 1.5 (2) |
C5—N3—C6—C7 | 97.34 (13) | N3—C6—C7—N4 | −32.27 (17) |
C11—N4—C7—C6 | −178.86 (13) | N3—C6—C7—C8 | 149.91 (13) |
C11—N4—C7—C8 | −1.1 (2) | C6—C7—C8—C9 | 178.23 (14) |
C7—N4—C11—C10 | 0.3 (2) | N4—C7—C8—C9 | 0.5 (2) |
C13—N5—C12—O2 | 14.69 (19) | C7—C8—C9—C10 | 0.8 (2) |
C13—N5—C12—C2 | −169.22 (11) | C8—C9—C10—C11 | −1.6 (2) |
C12—N5—C13—C14 | −89.76 (13) | C9—C10—C11—N4 | 1.0 (3) |
C18—N6—C14—C13 | −176.90 (11) | N5—C13—C14—N6 | −85.59 (13) |
C18—N6—C14—C15 | 1.56 (18) | N5—C13—C14—C15 | 95.95 (14) |
C14—N6—C18—C17 | 0.15 (19) | C13—C14—C15—C16 | 176.92 (12) |
N1—C1—C2—N2 | 2.08 (16) | N6—C14—C15—C16 | −1.5 (2) |
C5—C1—C2—C12 | −0.54 (16) | C14—C15—C16—C17 | −0.4 (2) |
N1—C1—C2—C12 | 179.05 (10) | C15—C16—C17—C18 | 1.9 (2) |
C5—C1—C2—N2 | −177.51 (10) | C16—C17—C18—N6 | −1.9 (2) |
C2—C1—C5—O1 | −6.56 (16) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3N···N1 | 0.896 (17) | 2.267 (17) | 2.6921 (16) | 108.7 (13) |
N3—H3N···N4i | 0.896 (17) | 2.547 (17) | 3.2785 (16) | 139.2 (14) |
N5—H5N···N6ii | 0.928 (16) | 2.122 (16) | 3.0493 (16) | 178.3 (13) |
C3—H3···O2iii | 0.980 (19) | 2.378 (19) | 3.3178 (18) | 160.5 (14) |
C6—H6A···O1i | 0.972 (17) | 2.505 (16) | 3.1855 (17) | 127.0 (11) |
C6—H6B···O1 | 1.021 (15) | 2.437 (15) | 2.8114 (16) | 100.7 (9) |
C10—H10···O2iv | 1.013 (16) | 2.509 (16) | 3.4749 (17) | 159.2 (13) |
Symmetry codes: (i) x−1/2, y, −z+3/2; (ii) −x+1, −y, −z+1; (iii) x−1/2, y, −z+1/2; (iv) x, −y+1/2, z+1/2. |
Notes: dihedral angles between various aromatic rings in the orthorhombic
and triclinic polymorphs of (I); Plane A = pyrazine ring; Plane B = pyridine
ring (containing N4); Plane C = pyridine ring (containing N6). topPolymorph | Plane–Plane | Angle (°) | Polymorph | Plane–Plane | Angle (°) |
orthorhombic | A–B | 81.5 (1) | triclinic | A–B | 17.8 (2) |
| A–C | 80.7 (1) | | A–C | 60.5 (2) |
| B–C | 25.1 (1) | | B–C | 74.1 (2) |