Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270110023139/sk3376sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270110023139/sk3376Isup2.hkl |
CCDC reference: 790636
A catalytic quantity of boron trifluoride etherate was added to an ethanol solution containing equimolar quantities of (2E,6E)-2,6-dibenzylidenecyclohexanone and 6-amino-3-methyl-2-(methylthio)pyrimidin-4(3H)-one, and this mixture was then stirred for 3 d at ambient temperature. The resulting solid product was collected by filtration and then recrystallized from an ethanol–dimethylformamide mixture (1:1 v/v), to give yellow crystals of (I) suitable for single-crystal X-ray diffraction [yield 56%, m.p. 490–493 K (decomposition)]. MS (EI) m/z 427 [M+] (6), 350 (100), 302 (8).
All H atoms were located in difference maps. H atoms bonded to C atoms were then treated as riding in geometrically idealized positions, with C—H = 0.95 (aromatic and alkenyl), 0.98 (CH3), 0.99 (CH2) or 1.00 Å (aliphatic CH), and with Uiso(H) = kUeq(C), where k = 1.5 for the methyl groups, which were permitted to rotate but not to tilt, and 1.2 for all other H atoms bonded to C atoms. The H atom bonded to atom N10 was permitted to ride at the position found in a difference map, with Uiso(H) = 1.2Ueq(N), giving an N—H distance of 0.92 Å and a sum of bond angles at atom N10 of 359°. There is a short (1.80 Å) non-bonded intramolecular contact between atoms H10 and H90, but the mutual disposition of the carrier atoms N10 and C90 is determined by the rigidity imposed on this part of the molecular skeleton by the π-system (see first scheme). PLATON (Spek, 2009) reports a void volume of 54.3 Å3 centred at the origin, but none of the maxima in the final difference map is particularly close to the origin, while the SQUEEZE option in PLATON reported only one additional electron per unit cell. We conclude that there is no significant electron density within this void volume.
Data collection: COLLECT (Nonius, 1999); cell refinement: DIRAX/LSQ (Duisenberg et al., 2000); data reduction: EVALCCD (Duisenberg et al., 2003); program(s) used to solve structure: SIR2004 (Burla et al., 2005); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).
C26H25N3OS | Z = 2 |
Mr = 427.55 | F(000) = 452 |
Triclinic, P1 | Dx = 1.326 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 8.382 (2) Å | Cell parameters from 4908 reflections |
b = 10.777 (3) Å | θ = 2.9–27.5° |
c = 12.745 (4) Å | µ = 0.18 mm−1 |
α = 73.18 (3)° | T = 120 K |
β = 85.13 (4)° | Block, yellow |
γ = 76.43 (3)° | 0.27 × 0.20 × 0.10 mm |
V = 1071.1 (5) Å3 |
Bruker Nonius KappaCCD area-detector diffractometer | 3983 independent reflections |
Radiation source: Bruker Nonius FR591 rotating anode | 2998 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.060 |
Detector resolution: 9.091 pixels mm-1 | θmax = 25.5°, θmin = 2.9° |
ϕ and ω scans | h = −10→10 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −13→13 |
Tmin = 0.942, Tmax = 0.983 | l = −15→15 |
22289 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)] = 0.053 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.104 | H-atom parameters constrained |
S = 1.10 | w = 1/[σ2(Fo2) + (0.0261P)2 + 1.055P] where P = (Fo2 + 2Fc2)/3 |
3983 reflections | (Δ/σ)max = 0.001 |
282 parameters | Δρmax = 0.25 e Å−3 |
0 restraints | Δρmin = −0.33 e Å−3 |
C26H25N3OS | γ = 76.43 (3)° |
Mr = 427.55 | V = 1071.1 (5) Å3 |
Triclinic, P1 | Z = 2 |
a = 8.382 (2) Å | Mo Kα radiation |
b = 10.777 (3) Å | µ = 0.18 mm−1 |
c = 12.745 (4) Å | T = 120 K |
α = 73.18 (3)° | 0.27 × 0.20 × 0.10 mm |
β = 85.13 (4)° |
Bruker Nonius KappaCCD area-detector diffractometer | 3983 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | 2998 reflections with I > 2σ(I) |
Tmin = 0.942, Tmax = 0.983 | Rint = 0.060 |
22289 measured reflections |
R[F2 > 2σ(F2)] = 0.053 | 0 restraints |
wR(F2) = 0.104 | H-atom parameters constrained |
S = 1.10 | Δρmax = 0.25 e Å−3 |
3983 reflections | Δρmin = −0.33 e Å−3 |
282 parameters |
x | y | z | Uiso*/Ueq | ||
N1 | 0.7634 (2) | 0.59688 (19) | 0.45936 (15) | 0.0141 (4) | |
C2 | 0.8597 (3) | 0.6404 (2) | 0.37900 (19) | 0.0150 (5) | |
N3 | 0.9623 (2) | 0.56227 (19) | 0.32334 (16) | 0.0154 (4) | |
C4 | 0.9633 (3) | 0.4262 (2) | 0.34686 (19) | 0.0160 (5) | |
C4a | 0.8485 (3) | 0.3808 (2) | 0.42860 (19) | 0.0135 (5) | |
C5 | 0.8262 (3) | 0.2415 (2) | 0.45283 (19) | 0.0130 (5) | |
H5 | 0.9377 | 0.1818 | 0.4552 | 0.016* | |
C5a | 0.7457 (3) | 0.2004 (2) | 0.56387 (18) | 0.0132 (5) | |
C6 | 0.7645 (3) | 0.0543 (2) | 0.6156 (2) | 0.0189 (6) | |
H6A | 0.8722 | 0.0065 | 0.5938 | 0.023* | |
H6B | 0.6777 | 0.0231 | 0.5891 | 0.023* | |
C7 | 0.7527 (3) | 0.0232 (2) | 0.7389 (2) | 0.0201 (6) | |
H7A | 0.8481 | 0.0432 | 0.7664 | 0.024* | |
H7B | 0.7554 | −0.0726 | 0.7710 | 0.024* | |
C8 | 0.5958 (3) | 0.1042 (2) | 0.7744 (2) | 0.0182 (6) | |
H8A | 0.5013 | 0.0738 | 0.7567 | 0.022* | |
H8B | 0.5960 | 0.0883 | 0.8549 | 0.022* | |
C9 | 0.5740 (3) | 0.2513 (2) | 0.72000 (19) | 0.0139 (5) | |
C9a | 0.6628 (3) | 0.2888 (2) | 0.61546 (19) | 0.0137 (5) | |
N10 | 0.6597 (2) | 0.42408 (19) | 0.56882 (15) | 0.0143 (4) | |
H10 | 0.6015 | 0.4874 | 0.6015 | 0.017* | |
C10a | 0.7605 (3) | 0.4659 (2) | 0.48332 (18) | 0.0127 (5) | |
S2 | 0.86063 (8) | 0.80990 (6) | 0.33631 (5) | 0.01852 (17) | |
C21 | 0.7159 (3) | 0.8661 (2) | 0.4327 (2) | 0.0219 (6) | |
H21A | 0.6111 | 0.8435 | 0.4265 | 0.033* | |
H21B | 0.6996 | 0.9627 | 0.4174 | 0.033* | |
H21C | 0.7574 | 0.8230 | 0.5070 | 0.033* | |
C31 | 1.0701 (3) | 0.6163 (3) | 0.2341 (2) | 0.0217 (6) | |
H31A | 1.0086 | 0.6540 | 0.1659 | 0.033* | |
H31B | 1.1628 | 0.5451 | 0.2252 | 0.033* | |
H31C | 1.1113 | 0.6859 | 0.2513 | 0.033* | |
O4 | 1.0596 (2) | 0.35745 (17) | 0.29698 (14) | 0.0203 (4) | |
C51 | 0.7328 (3) | 0.2269 (2) | 0.36100 (19) | 0.0134 (5) | |
C52 | 0.5625 (3) | 0.2602 (2) | 0.3598 (2) | 0.0161 (5) | |
H52 | 0.5031 | 0.2895 | 0.4183 | 0.019* | |
C53 | 0.4782 (3) | 0.2512 (2) | 0.2748 (2) | 0.0220 (6) | |
H53 | 0.3616 | 0.2743 | 0.2750 | 0.026* | |
C54 | 0.5636 (3) | 0.2085 (2) | 0.1893 (2) | 0.0224 (6) | |
H54 | 0.5061 | 0.2021 | 0.1307 | 0.027* | |
C55 | 0.7327 (3) | 0.1754 (2) | 0.1898 (2) | 0.0207 (6) | |
H55 | 0.7917 | 0.1460 | 0.1313 | 0.025* | |
C56 | 0.8167 (3) | 0.1847 (2) | 0.27468 (19) | 0.0164 (5) | |
H56 | 0.9333 | 0.1619 | 0.2740 | 0.020* | |
C90 | 0.4788 (3) | 0.3435 (2) | 0.76298 (19) | 0.0178 (5) | |
H90 | 0.4792 | 0.4325 | 0.7221 | 0.021* | |
C91 | 0.3743 (3) | 0.3313 (2) | 0.8620 (2) | 0.0188 (6) | |
C92 | 0.3073 (3) | 0.2220 (3) | 0.9134 (2) | 0.0206 (6) | |
H92 | 0.3325 | 0.1464 | 0.8859 | 0.025* | |
C93 | 0.2045 (3) | 0.2222 (3) | 1.0041 (2) | 0.0259 (6) | |
H93 | 0.1587 | 0.1471 | 1.0377 | 0.031* | |
C94 | 0.1676 (3) | 0.3294 (3) | 1.0463 (2) | 0.0307 (7) | |
H94 | 0.0989 | 0.3281 | 1.1097 | 0.037* | |
C95 | 0.2315 (4) | 0.4383 (3) | 0.9956 (2) | 0.0360 (8) | |
H95 | 0.2058 | 0.5134 | 1.0237 | 0.043* | |
C96 | 0.3327 (3) | 0.4401 (3) | 0.9042 (2) | 0.0284 (7) | |
H96 | 0.3745 | 0.5170 | 0.8696 | 0.034* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0166 (11) | 0.0134 (10) | 0.0127 (10) | −0.0045 (9) | −0.0006 (9) | −0.0031 (8) |
C2 | 0.0165 (13) | 0.0169 (13) | 0.0121 (12) | −0.0030 (10) | −0.0032 (10) | −0.0045 (10) |
N3 | 0.0153 (11) | 0.0194 (11) | 0.0125 (10) | −0.0075 (9) | 0.0028 (9) | −0.0039 (9) |
C4 | 0.0140 (13) | 0.0199 (13) | 0.0153 (13) | −0.0036 (11) | −0.0027 (10) | −0.0063 (10) |
C4a | 0.0129 (12) | 0.0165 (12) | 0.0110 (12) | −0.0019 (10) | −0.0024 (10) | −0.0041 (10) |
C5 | 0.0111 (12) | 0.0126 (12) | 0.0138 (12) | 0.0015 (10) | 0.0015 (10) | −0.0049 (10) |
C5a | 0.0124 (12) | 0.0160 (12) | 0.0100 (12) | −0.0020 (10) | −0.0017 (10) | −0.0022 (10) |
C6 | 0.0207 (14) | 0.0149 (13) | 0.0187 (14) | −0.0002 (11) | 0.0029 (11) | −0.0048 (10) |
C7 | 0.0248 (14) | 0.0150 (13) | 0.0174 (13) | −0.0025 (11) | 0.0002 (11) | −0.0014 (10) |
C8 | 0.0198 (13) | 0.0192 (13) | 0.0144 (13) | −0.0049 (11) | −0.0005 (11) | −0.0025 (10) |
C9 | 0.0133 (12) | 0.0172 (13) | 0.0113 (12) | −0.0028 (10) | −0.0007 (10) | −0.0042 (10) |
C9a | 0.0132 (12) | 0.0149 (12) | 0.0127 (12) | −0.0039 (10) | −0.0015 (10) | −0.0025 (10) |
N10 | 0.0165 (11) | 0.0115 (10) | 0.0141 (10) | −0.0018 (8) | 0.0064 (9) | −0.0051 (8) |
C10a | 0.0130 (12) | 0.0146 (12) | 0.0099 (12) | −0.0035 (10) | −0.0027 (10) | −0.0013 (10) |
S2 | 0.0219 (3) | 0.0167 (3) | 0.0179 (3) | −0.0086 (3) | 0.0029 (3) | −0.0036 (3) |
C21 | 0.0293 (15) | 0.0172 (13) | 0.0200 (14) | −0.0073 (12) | 0.0053 (12) | −0.0064 (11) |
C31 | 0.0199 (14) | 0.0268 (15) | 0.0179 (14) | −0.0097 (12) | 0.0061 (11) | −0.0036 (11) |
O4 | 0.0185 (9) | 0.0244 (10) | 0.0190 (9) | −0.0035 (8) | 0.0065 (8) | −0.0105 (8) |
C51 | 0.0181 (13) | 0.0072 (11) | 0.0139 (12) | −0.0031 (10) | 0.0007 (10) | −0.0015 (9) |
C52 | 0.0163 (13) | 0.0139 (12) | 0.0170 (13) | −0.0035 (10) | 0.0037 (10) | −0.0039 (10) |
C53 | 0.0199 (14) | 0.0220 (14) | 0.0238 (14) | −0.0069 (11) | −0.0017 (12) | −0.0036 (11) |
C54 | 0.0290 (15) | 0.0216 (14) | 0.0192 (14) | −0.0086 (12) | −0.0049 (12) | −0.0059 (11) |
C55 | 0.0265 (15) | 0.0193 (13) | 0.0170 (13) | −0.0039 (11) | 0.0046 (11) | −0.0084 (11) |
C56 | 0.0143 (12) | 0.0156 (13) | 0.0190 (13) | −0.0014 (10) | 0.0020 (10) | −0.0063 (10) |
C90 | 0.0200 (13) | 0.0179 (13) | 0.0131 (13) | −0.0042 (11) | 0.0021 (11) | −0.0013 (10) |
C91 | 0.0162 (13) | 0.0221 (14) | 0.0134 (13) | 0.0028 (11) | −0.0003 (10) | −0.0033 (10) |
C92 | 0.0173 (13) | 0.0285 (15) | 0.0147 (13) | −0.0028 (12) | −0.0005 (11) | −0.0057 (11) |
C93 | 0.0196 (14) | 0.0375 (17) | 0.0154 (14) | −0.0054 (12) | 0.0012 (11) | −0.0005 (12) |
C94 | 0.0237 (15) | 0.0443 (18) | 0.0143 (14) | 0.0032 (14) | 0.0060 (12) | −0.0037 (13) |
C95 | 0.0438 (19) | 0.0336 (17) | 0.0253 (16) | 0.0038 (14) | 0.0115 (14) | −0.0131 (13) |
C96 | 0.0341 (16) | 0.0227 (15) | 0.0231 (15) | 0.0013 (13) | 0.0099 (13) | −0.0071 (12) |
N1—C2 | 1.296 (3) | C21—H21A | 0.9800 |
C2—N3 | 1.362 (3) | C21—H21B | 0.9800 |
N3—C4 | 1.408 (3) | C21—H21C | 0.9800 |
C4—C4a | 1.417 (3) | C31—H31A | 0.9800 |
C4a—C10a | 1.355 (3) | C31—H31B | 0.9800 |
C10a—N1 | 1.361 (3) | C31—H31C | 0.9800 |
C4—O4 | 1.228 (3) | C51—C56 | 1.386 (3) |
C9—C90 | 1.339 (3) | C51—C52 | 1.388 (3) |
C5a—C9a | 1.341 (3) | C52—C53 | 1.379 (3) |
C9—C9a | 1.467 (3) | C52—H52 | 0.9500 |
C9a—N10 | 1.401 (3) | C53—C54 | 1.384 (4) |
N10—C10a | 1.357 (3) | C53—H53 | 0.9500 |
C2—S2 | 1.750 (2) | C54—C55 | 1.378 (4) |
N3—C31 | 1.462 (3) | C54—H54 | 0.9500 |
C4a—C5 | 1.497 (3) | C55—C56 | 1.378 (3) |
C5—C5a | 1.506 (3) | C55—H55 | 0.9500 |
C5—C51 | 1.525 (3) | C56—H56 | 0.9500 |
C5—H5 | 1.0000 | C90—C91 | 1.465 (3) |
C5a—C6 | 1.496 (3) | C90—H90 | 0.9500 |
C6—C7 | 1.509 (3) | C91—C96 | 1.389 (4) |
C6—H6A | 0.9900 | C91—C92 | 1.391 (4) |
C6—H6B | 0.9900 | C92—C93 | 1.383 (3) |
C7—C8 | 1.511 (3) | C92—H92 | 0.9500 |
C7—H7A | 0.9900 | C93—C94 | 1.372 (4) |
C7—H7B | 0.9900 | C93—H93 | 0.9500 |
C8—C9 | 1.509 (3) | C94—C95 | 1.371 (4) |
C8—H8A | 0.9900 | C94—H94 | 0.9500 |
C8—H8B | 0.9900 | C95—C96 | 1.380 (4) |
N10—H10 | 0.9222 | C95—H95 | 0.9500 |
S2—C21 | 1.783 (3) | C96—H96 | 0.9500 |
C2—N1—C10a | 116.3 (2) | C2—S2—C21 | 99.61 (12) |
N1—C2—N3 | 124.2 (2) | S2—C21—H21A | 109.5 |
N1—C2—S2 | 119.38 (18) | S2—C21—H21B | 109.5 |
N3—C2—S2 | 116.44 (18) | H21A—C21—H21B | 109.5 |
C2—N3—C4 | 120.8 (2) | S2—C21—H21C | 109.5 |
C2—N3—C31 | 121.9 (2) | H21A—C21—H21C | 109.5 |
C4—N3—C31 | 117.2 (2) | H21B—C21—H21C | 109.5 |
O4—C4—N3 | 119.4 (2) | N3—C31—H31A | 109.5 |
O4—C4—C4a | 125.6 (2) | N3—C31—H31B | 109.5 |
N3—C4—C4a | 115.0 (2) | H31A—C31—H31B | 109.5 |
C10a—C4a—C4 | 118.7 (2) | N3—C31—H31C | 109.5 |
C10a—C4a—C5 | 121.4 (2) | H31A—C31—H31C | 109.5 |
C4—C4a—C5 | 119.9 (2) | H31B—C31—H31C | 109.5 |
C4a—C5—C5a | 110.53 (19) | C56—C51—C52 | 118.5 (2) |
C4a—C5—C51 | 110.41 (19) | C56—C51—C5 | 120.5 (2) |
C5a—C5—C51 | 112.90 (19) | C52—C51—C5 | 120.9 (2) |
C4a—C5—H5 | 107.6 | C53—C52—C51 | 120.9 (2) |
C5a—C5—H5 | 107.6 | C53—C52—H52 | 119.5 |
C51—C5—H5 | 107.6 | C51—C52—H52 | 119.5 |
C9a—C5a—C6 | 120.9 (2) | C52—C53—C54 | 119.9 (2) |
C9a—C5a—C5 | 122.5 (2) | C52—C53—H53 | 120.0 |
C6—C5a—C5 | 116.6 (2) | C54—C53—H53 | 120.0 |
C5a—C6—C7 | 111.0 (2) | C55—C54—C53 | 119.5 (2) |
C5a—C6—H6A | 109.4 | C55—C54—H54 | 120.2 |
C7—C6—H6A | 109.4 | C53—C54—H54 | 120.2 |
C5a—C6—H6B | 109.4 | C54—C55—C56 | 120.5 (2) |
C7—C6—H6B | 109.4 | C54—C55—H55 | 119.8 |
H6A—C6—H6B | 108.0 | C56—C55—H55 | 119.8 |
C6—C7—C8 | 110.7 (2) | C55—C56—C51 | 120.6 (2) |
C6—C7—H7A | 109.5 | C55—C56—H56 | 119.7 |
C8—C7—H7A | 109.5 | C51—C56—H56 | 119.7 |
C6—C7—H7B | 109.5 | C9—C90—C91 | 131.3 (2) |
C8—C7—H7B | 109.5 | C9—C90—H90 | 114.3 |
H7A—C7—H7B | 108.1 | C91—C90—H90 | 114.3 |
C9—C8—C7 | 112.9 (2) | C96—C91—C92 | 117.7 (2) |
C9—C8—H8A | 109.0 | C96—C91—C90 | 117.2 (2) |
C7—C8—H8A | 109.0 | C92—C91—C90 | 125.0 (2) |
C9—C8—H8B | 109.0 | C93—C92—C91 | 120.6 (3) |
C7—C8—H8B | 109.0 | C93—C92—H92 | 119.7 |
H8A—C8—H8B | 107.8 | C91—C92—H92 | 119.7 |
C90—C9—C9a | 121.2 (2) | C94—C93—C92 | 120.9 (3) |
C90—C9—C8 | 122.8 (2) | C94—C93—H93 | 119.5 |
C9a—C9—C8 | 116.0 (2) | C92—C93—H93 | 119.5 |
C5a—C9a—N10 | 119.3 (2) | C95—C94—C93 | 119.0 (3) |
C5a—C9a—C9 | 123.3 (2) | C95—C94—H94 | 120.5 |
N10—C9a—C9 | 117.4 (2) | C93—C94—H94 | 120.5 |
C10a—N10—C9a | 121.5 (2) | C94—C95—C96 | 120.7 (3) |
C10a—N10—H10 | 116.6 | C94—C95—H95 | 119.6 |
C9a—N10—H10 | 121.3 | C96—C95—H95 | 119.6 |
C4a—C10a—N10 | 120.9 (2) | C95—C96—C91 | 121.0 (3) |
C4a—C10a—N1 | 124.7 (2) | C95—C96—H96 | 119.5 |
N10—C10a—N1 | 114.4 (2) | C91—C96—H96 | 119.5 |
C10a—N1—C2—N3 | −4.0 (3) | C5a—C9a—N10—C10a | −11.4 (3) |
C10a—N1—C2—S2 | 175.58 (17) | C9—C9a—N10—C10a | 168.3 (2) |
N1—C2—N3—C4 | 3.5 (3) | C4—C4a—C10a—N10 | −174.1 (2) |
S2—C2—N3—C4 | −176.05 (17) | C5—C4a—C10a—N10 | 6.0 (3) |
N1—C2—N3—C31 | −179.2 (2) | C4—C4a—C10a—N1 | 6.0 (4) |
S2—C2—N3—C31 | 1.2 (3) | C5—C4a—C10a—N1 | −173.9 (2) |
C2—N3—C4—O4 | −178.5 (2) | C9a—N10—C10a—C4a | 10.8 (3) |
C31—N3—C4—O4 | 4.1 (3) | C9a—N10—C10a—N1 | −169.3 (2) |
C2—N3—C4—C4a | 1.7 (3) | C2—N1—C10a—C4a | −0.9 (3) |
C31—N3—C4—C4a | −175.7 (2) | C2—N1—C10a—N10 | 179.2 (2) |
O4—C4—C4a—C10a | 174.2 (2) | N1—C2—S2—C21 | 1.6 (2) |
N3—C4—C4a—C10a | −6.0 (3) | N3—C2—S2—C21 | −178.73 (18) |
O4—C4—C4a—C5 | −5.9 (4) | C4a—C5—C51—C56 | 93.1 (3) |
N3—C4—C4a—C5 | 173.91 (19) | C5a—C5—C51—C56 | −142.6 (2) |
C10a—C4a—C5—C5a | −19.3 (3) | C4a—C5—C51—C52 | −84.5 (3) |
C4—C4a—C5—C5a | 160.8 (2) | C5a—C5—C51—C52 | 39.8 (3) |
C10a—C4a—C5—C51 | 106.3 (2) | C56—C51—C52—C53 | 0.1 (3) |
C4—C4a—C5—C51 | −73.6 (3) | C5—C51—C52—C53 | 177.8 (2) |
C4a—C5—C5a—C9a | 18.7 (3) | C51—C52—C53—C54 | 0.0 (4) |
C51—C5—C5a—C9a | −105.5 (3) | C52—C53—C54—C55 | −0.1 (4) |
C4a—C5—C5a—C6 | −160.5 (2) | C53—C54—C55—C56 | −0.1 (4) |
C51—C5—C5a—C6 | 75.3 (3) | C54—C55—C56—C51 | 0.3 (4) |
C9a—C5a—C6—C7 | −25.7 (3) | C52—C51—C56—C55 | −0.3 (3) |
C5—C5a—C6—C7 | 153.5 (2) | C5—C51—C56—C55 | −178.0 (2) |
C5a—C6—C7—C8 | 54.1 (3) | C9a—C9—C90—C91 | 177.1 (2) |
C6—C7—C8—C9 | −53.5 (3) | C8—C9—C90—C91 | −2.4 (4) |
C7—C8—C9—C90 | −157.1 (2) | C9—C90—C91—C96 | 159.7 (3) |
C7—C8—C9—C9a | 23.4 (3) | C9—C90—C91—C92 | −23.7 (4) |
C6—C5a—C9a—N10 | 174.5 (2) | C96—C91—C92—C93 | −0.7 (4) |
C5—C5a—C9a—N10 | −4.7 (3) | C90—C91—C92—C93 | −177.4 (2) |
C6—C5a—C9a—C9 | −5.2 (4) | C91—C92—C93—C94 | −0.7 (4) |
C5—C5a—C9a—C9 | 175.6 (2) | C92—C93—C94—C95 | 1.4 (4) |
C90—C9—C9a—C5a | −173.0 (2) | C93—C94—C95—C96 | −0.6 (4) |
C8—C9—C9a—C5a | 6.5 (3) | C94—C95—C96—C91 | −0.9 (5) |
C90—C9—C9a—N10 | 7.3 (3) | C92—C91—C96—C95 | 1.5 (4) |
C8—C9—C9a—N10 | −173.2 (2) | C90—C91—C96—C95 | 178.4 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
C53—H53···O4i | 0.95 | 2.50 | 3.440 (3) | 170 |
C94—H94···O4ii | 0.95 | 2.48 | 3.325 (3) | 148 |
C54—H54···Cg2iii | 0.95 | 2.93 | 3.772 (3) | 149 |
C96—H96···Cg1iv | 0.95 | 2.89 | 3.765 (3) | 154 |
Symmetry codes: (i) x−1, y, z; (ii) x−1, y, z+1; (iii) x, y, z−1; (iv) −x+1, −y+1, −z+1. |
Experimental details
Crystal data | |
Chemical formula | C26H25N3OS |
Mr | 427.55 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 120 |
a, b, c (Å) | 8.382 (2), 10.777 (3), 12.745 (4) |
α, β, γ (°) | 73.18 (3), 85.13 (4), 76.43 (3) |
V (Å3) | 1071.1 (5) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.18 |
Crystal size (mm) | 0.27 × 0.20 × 0.10 |
Data collection | |
Diffractometer | Bruker Nonius KappaCCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2003) |
Tmin, Tmax | 0.942, 0.983 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 22289, 3983, 2998 |
Rint | 0.060 |
(sin θ/λ)max (Å−1) | 0.606 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.053, 0.104, 1.10 |
No. of reflections | 3983 |
No. of parameters | 282 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.25, −0.33 |
Computer programs: COLLECT (Nonius, 1999), DIRAX/LSQ (Duisenberg et al., 2000), EVALCCD (Duisenberg et al., 2003), SIR2004 (Burla et al., 2005), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).
N1—C2 | 1.296 (3) | C4—O4 | 1.228 (3) |
C2—N3 | 1.362 (3) | C9—C90 | 1.339 (3) |
N3—C4 | 1.408 (3) | C5a—C9a | 1.341 (3) |
C4—C4a | 1.417 (3) | C9—C9a | 1.467 (3) |
C4a—C10a | 1.355 (3) | C9a—N10 | 1.401 (3) |
C10a—N1 | 1.361 (3) | N10—C10a | 1.357 (3) |
N1—C2—S2—C21 | 1.6 (2) | C4a—C5—C51—C52 | −84.5 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
C53—H53···O4i | 0.95 | 2.50 | 3.440 (3) | 170 |
C94—H94···O4ii | 0.95 | 2.48 | 3.325 (3) | 148 |
C54—H54···Cg2iii | 0.95 | 2.93 | 3.772 (3) | 149 |
C96—H96···Cg1iv | 0.95 | 2.89 | 3.765 (3) | 154 |
Symmetry codes: (i) x−1, y, z; (ii) x−1, y, z+1; (iii) x, y, z−1; (iv) −x+1, −y+1, −z+1. |
In our search for new bioactive compounds based on heterocyclic frameworks, pyrimido[4,5-b]quinolines have emerged as interesting targets because of their structural analogy with flavones. Here, we report the molecular and supramolecular structure of the title compound, (I), which was prepared using an acid-catalysed cyclocondensation between (2E,6E)-2,6-dibenzylidenecyclohexanone and 6-amino-3-methyl-2-(methylthio)pyrimidin-4(3H)-one (see first scheme). This synthetic procedure may be contrasted with the synthesis of the related compound, (II) (see second scheme), which employed a multicomponent cyclocondensation reaction under environmentally friendly solvent-free conditions, mediated by microwave radiation (Low, Cobo, Cisneros et al., 2004).
The molecules of (I) contain a stereogenic centre at C5 (Fig. 1) and the reference molecule was selected as one having the R configuration at C5. However, the centrosymmetric space group accommodates equal numbers of the two enantiomorphs. In addition, the two rings which are fused at the C5a—C9a bond (Fig. 1) are both nonplanar. The heterocyclic ring containing atom N10 adopts a boat-type conformation, with atoms C5 and N10 acting as the stem and stern of the boat, respectively. The ring-puckering parameters (Cremer & Pople, 1975) for the atom sequence N10/C9a/C5a/C5/C4a/C10a are Q = 0.205 (2) Å, θ = 103.8 (6)° and ϕ = 2.6 (7), whereas the idealized puckering angles for a boat conformation are θ = 90° and ϕ = 60k°, where k represents an integer. The adjacent carbocyclic ring adopts an envelope conformation, folded across the line C6···C8, with ring-puckering parameters, for the atom sequence C5a/C6–C9/C9a, of Q = 0.481 (3) Å, θ = 58.6 (4)° and ϕ = 117.6 (4)°. The angles may be compared with the idealized values for an envelope conformation of θ = 54.7° and ϕ = 60k°, where k again represents an integer. By contrast, the pyrimidine component of the fused ring system is planar. The remainder of the molecular conformation can be specified in terms of just three torsion angles (Table 1), defining the orientation of the various substituents relative to the adjacent components of the fused ring system. While the C atom of the methylsulfanyl substituent is almost coplanar with the adjacent ring, the aryl ring C51–C56 is nearly orthogonal to the mean plane of the reduced pyridine ring (Table 1), with a dihedral angle between the mean planes of 83.0 (2)°.
Within the fused heterocyclic ring system, the bond distances are fairly similar to those found in the related methylsulfanylpyrimidinone, (III), where the polarized form (IIIa) was deduced to be important (Low, Cobo, Cruz et al., 2004). In particular, in (I), the N10—C10a bond is significantly longer than the N10—C9a bond, while the C4—C4a bond is significantly shorter than the analogous C9—C9a bond, and the C5a—C9a and C9—C90 bonds are localized double bonds. These observations point to a contribution to the electronic structure of (I) from the polarized form (Ia). By contrast, in (II) (Low, Cobo, Cisneros et al., 2004), the polarization of the structure involves the carbonyl unit in the five-membered carbocyclic ring, rather than that in the pyrimidone ring (see second scheme).
The supramolecular aggregation in (I) is determined by two C—H···O hydrogen bonds and two C—H···π(arene) hydrogen bonds (Table 2), but the N—H group in the reduced pyridine ring plays no part in the hydrogen bonding. The only potential acceptor within plausible hydrogen-bonding distance of atom N10 in the reference molecule at (x, y, z) is the corresponding atom N10 in the molecule at (1 - x, 1 - y, 1 - z), but with an N···N distance of 3.163 (2) Å and, more significantly, an N—H···N angle of only 91°.
The two C—H···O hydrogen bonds form a simple sheet. The hydrogen bond having atom C53 as the donor links molecules related by translation into a C(8) (Bernstein et al., 1995) chain running parallel to the [100] direction, while the hydrogen bond having atom C94 as the donor links molecules, again related by translation, into a C(13) chain running parallel to the [101] direction. The combination of these two chain motifs generates a sheet lying parallel to (010) and built from a single type of R43(36) ring (Fig. 2). Of the two C—H···π(arene) hydrogen bonds, that having the longer H···centroid distance lies within the (010) sheet and hence provides a modest reinforcement of the sheet formation, while the shorter of these two interactions weakly links an inversion-related pair of sheets into a bilayer parallel to (010). Aromatic π–π staking interactions, however, are absent from the structure.
It is of interest briefly to compare the supramolecular aggregation in (I) with those in the related compounds, (II) and (III). In (II), which crystallizes as a stoichiometric 1:1 solvate with dimethylformamide (Low, Cobo, Cisneros et al., 2004), inversion-related pairs of pyrimidinedione molecules are linked by pairs of N—H···O hydrogen bonds to form centrosymmetric R22(8) dimers, from which the dimethylformamide molecules are pendent, and these dimers are linked into chains by a single C—H···π(arene) hydrogen bond.
By contrast, (III) crystallizes in a solvent-free form (Low, Cobo, Cruz et al., 2004) and, while the structure contains three hydrogen bonds, one of O—H···O type and two of N—H···O type, two of them are intramolecular. The remaining N—H···O hydrogen bond links molecules related by translation into simple C(9) chains, and antiparallel pairs of these chains are weakly linked by a single π–π stacking interaction involving pyrimidine rings.