Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270108031740/sk3261sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270108031740/sk3261Isup2.hkl |
CCDC reference: 695277
For related literature, see: Allen et al. (1997); Becke (1988); Bessard & Crettaz (2000); Boese & Handy (2001); Boese et al. (2000); Chang et al. (1993); Cremer & Pople (1975); Custelcean (2008); Delly (1996, 1998); Etter (1990); Gale & &Quesada (2006); Gallagher et al. (1999); Hamprecht et al. (1998); Hollingsworth et al. (1994); Kane et al. (1995); Lee et al. (1988); Lyssenko & Antipin (2006); Sun & Zhang (2006); Wu et al. (2006).
A suspension of indole-3-butyric acid (1.02 g, 5 mmol) and dicyclohexyl diimide (1.03 g, 5 mmol) in dry benzene (20 ml) was refluxed for 3 h using a Dean–Stark water separator. Removal of the solvent in vacuo afforded a colorless crystalline solid, which was recrystallized from an acetone/n-hexane mixture (1:1, v/v) to obtain diffraction quality single crystals of the title compound (yield 0.48 g, 23.5%; m.p. 413 K). Analysis found: C 73.38, H 8.55, N 10.30%; calculated for C25H35N3O2: C 73.31, H 8.61, N 10.26%. 1H NMR (δ, CDCl3): 1.23 (m, 11H, –NH—C6H11), 1.74 (m, 11H, –CO—N(C6H11)—CO–), 2.07 (m, 2H, –CH2—CH2—CH2), 2.45 (2H, t, J = 7.2 Hz, –H2C—CH2—CO–), 2.84 (2H, t, J =7.2 Hz, In—CH2—CH2–), 6.78(1H, br s, –CO—NH—C6H11), 7.01 (1H, br s, C2—H), 7.11 (1H, t, J = 7.5 Hz, C6—H), 7.19 (1H, t, J = 7.5 Hz, C5—H), 7.36 (1H, d, J = 8.1 Hz, C7—H), 7.60 (1H, d, J =7.8 Hz, C4—H), 8.02 (1H, br s,-NH).
The NH H-atom positions obtained from a difference Fourier map were refined freely, while the C-bound H atoms were placed in idealized positions using the riding method, with bond distances ranging from 0.93 to 0.98 Å and Uiso(H) set to 1.5Ueq of the parent atoms.
Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2002); data reduction: SAINT (Bruker, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997), CAMERON (Watkin et al., 1993) and DIAMOND (Bergerhoff, 1996); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PARST95 (Nardelli, 1995).
C25H35N3O2 | Z = 2 |
Mr = 409.56 | F(000) = 444 |
Triclinic, P1 | Dx = 1.198 Mg m−3 |
Hall symbol: -P 1 | Melting point: 413 K |
a = 8.4655 (7) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 11.5938 (9) Å | Cell parameters from 3416 reflections |
c = 13.0982 (11) Å | θ = 2.5–26.4° |
α = 68.331 (2)° | µ = 0.08 mm−1 |
β = 86.752 (1)° | T = 100 K |
γ = 72.289 (1)° | Block, colourless |
V = 1135.83 (16) Å3 | 0.50 × 0.46 × 0.40 mm |
Bruker SMART CCD area-detector diffractometer | 3945 independent reflections |
Radiation source: fine-focus sealed tube | 3297 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.029 |
phi and ω scans | θmax = 25.0°, θmin = 1.7° |
Absorption correction: multi-scan (SADABS; Bruker, 2001) | h = −9→10 |
Tmin = 0.964, Tmax = 0.975 | k = −13→12 |
5965 measured reflections | l = −15→15 |
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)] = 0.036 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.100 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.03 | w = 1/[σ2(Fo2) + (0.0586P)2 + 0.0945P] where P = (Fo2 + 2Fc2)/3 |
3945 reflections | (Δ/σ)max < 0.001 |
279 parameters | Δρmax = 0.19 e Å−3 |
0 restraints | Δρmin = −0.19 e Å−3 |
C25H35N3O2 | γ = 72.289 (1)° |
Mr = 409.56 | V = 1135.83 (16) Å3 |
Triclinic, P1 | Z = 2 |
a = 8.4655 (7) Å | Mo Kα radiation |
b = 11.5938 (9) Å | µ = 0.08 mm−1 |
c = 13.0982 (11) Å | T = 100 K |
α = 68.331 (2)° | 0.50 × 0.46 × 0.40 mm |
β = 86.752 (1)° |
Bruker SMART CCD area-detector diffractometer | 3945 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2001) | 3297 reflections with I > 2σ(I) |
Tmin = 0.964, Tmax = 0.975 | Rint = 0.029 |
5965 measured reflections |
R[F2 > 2σ(F2)] = 0.036 | 0 restraints |
wR(F2) = 0.100 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.03 | Δρmax = 0.19 e Å−3 |
3945 reflections | Δρmin = −0.19 e Å−3 |
279 parameters |
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 | ||
O1 | 0.46973 (10) | 0.40938 (8) | 0.39263 (7) | 0.0190 (2) | |
O2 | −0.02179 (11) | 0.65368 (9) | 0.44284 (7) | 0.0244 (2) | |
N1 | 0.46139 (14) | −0.19502 (11) | 0.68548 (9) | 0.0233 (3) | |
H1N | 0.4674 (18) | −0.2477 (15) | 0.6501 (12) | 0.033 (4)* | |
N2 | 0.25303 (12) | 0.56892 (9) | 0.41176 (8) | 0.0168 (2) | |
N3 | 0.17758 (14) | 0.63388 (10) | 0.56127 (8) | 0.0186 (2) | |
H3N | 0.285 (2) | 0.6184 (13) | 0.5732 (11) | 0.029 (4)* | |
C1 | 0.41374 (16) | −0.06108 (12) | 0.63931 (11) | 0.0213 (3) | |
H1 | 0.3766 | −0.0120 | 0.5661 | 0.032* | |
C2 | 0.42848 (15) | −0.01032 (12) | 0.71573 (10) | 0.0191 (3) | |
C3 | 0.49089 (16) | −0.11968 (12) | 0.81649 (10) | 0.0209 (3) | |
C4 | 0.53704 (17) | −0.13317 (13) | 0.92220 (11) | 0.0277 (3) | |
H4 | 0.5270 | −0.0600 | 0.9388 | 0.042* | |
C5 | 0.59779 (19) | −0.25669 (14) | 1.00162 (12) | 0.0339 (4) | |
H5 | 0.6304 | −0.2663 | 1.0717 | 0.051* | |
C6 | 0.61093 (18) | −0.36773 (14) | 0.97821 (12) | 0.0331 (4) | |
H6 | 0.6499 | −0.4497 | 1.0335 | 0.050* | |
C7 | 0.56724 (17) | −0.35793 (13) | 0.87492 (11) | 0.0280 (3) | |
H7 | 0.5761 | −0.4318 | 0.8596 | 0.042* | |
C8 | 0.50929 (16) | −0.23344 (12) | 0.79425 (11) | 0.0223 (3) | |
C9 | 0.38932 (16) | 0.13055 (12) | 0.70050 (10) | 0.0211 (3) | |
H9A | 0.4632 | 0.1379 | 0.7501 | 0.032* | |
H9B | 0.2765 | 0.1611 | 0.7206 | 0.032* | |
C10 | 0.40632 (16) | 0.21821 (11) | 0.58322 (10) | 0.0193 (3) | |
H10A | 0.3329 | 0.2111 | 0.5331 | 0.029* | |
H10B | 0.5194 | 0.1890 | 0.5630 | 0.029* | |
C11 | 0.36375 (15) | 0.36062 (11) | 0.57135 (10) | 0.0179 (3) | |
H11A | 0.2544 | 0.3877 | 0.5977 | 0.027* | |
H11B | 0.4435 | 0.3692 | 0.6163 | 0.027* | |
C12 | 0.36594 (15) | 0.44787 (11) | 0.45302 (10) | 0.0162 (3) | |
C13 | 0.12324 (15) | 0.62092 (11) | 0.47405 (10) | 0.0176 (3) | |
C14 | 0.06160 (15) | 0.68236 (12) | 0.63386 (10) | 0.0197 (3) | |
H14 | −0.0396 | 0.6590 | 0.6310 | 0.030* | |
C15 | 0.13549 (17) | 0.61622 (14) | 0.75174 (10) | 0.0259 (3) | |
H15A | 0.2398 | 0.6333 | 0.7559 | 0.039* | |
H15B | 0.1582 | 0.5227 | 0.7749 | 0.039* | |
C16 | 0.01626 (19) | 0.66619 (16) | 0.82869 (12) | 0.0354 (4) | |
H16A | −0.0832 | 0.6407 | 0.8305 | 0.053* | |
H16B | 0.0683 | 0.6266 | 0.9027 | 0.053* | |
C17 | −0.0311 (2) | 0.81354 (16) | 0.79141 (13) | 0.0428 (4) | |
H17A | 0.0666 | 0.8385 | 0.7969 | 0.064* | |
H17B | −0.1114 | 0.8428 | 0.8394 | 0.064* | |
C18 | −0.10494 (19) | 0.87931 (15) | 0.67327 (13) | 0.0375 (4) | |
H18A | −0.1284 | 0.9729 | 0.6502 | 0.056* | |
H18B | −0.2090 | 0.8618 | 0.6694 | 0.056* | |
C19 | 0.01357 (17) | 0.83041 (13) | 0.59549 (12) | 0.0272 (3) | |
H19A | −0.0394 | 0.8695 | 0.5218 | 0.041* | |
H19B | 0.1128 | 0.8564 | 0.5930 | 0.041* | |
C20 | 0.24072 (16) | 0.64480 (12) | 0.29130 (9) | 0.0187 (3) | |
H20 | 0.3520 | 0.6200 | 0.2649 | 0.028* | |
C21 | 0.19015 (16) | 0.79120 (12) | 0.26508 (10) | 0.0211 (3) | |
H21A | 0.2664 | 0.8106 | 0.3042 | 0.032* | |
H21B | 0.0794 | 0.8203 | 0.2888 | 0.032* | |
C22 | 0.19309 (18) | 0.86252 (13) | 0.14124 (11) | 0.0287 (3) | |
H22A | 0.1584 | 0.9558 | 0.1243 | 0.043* | |
H22B | 0.3056 | 0.8373 | 0.1188 | 0.043* | |
C23 | 0.0780 (2) | 0.83058 (13) | 0.07727 (11) | 0.0337 (4) | |
H23A | −0.0359 | 0.8634 | 0.0944 | 0.051* | |
H23B | 0.0861 | 0.8737 | −0.0010 | 0.051* | |
C24 | 0.12258 (19) | 0.68427 (13) | 0.10549 (11) | 0.0309 (3) | |
H24A | 0.2309 | 0.6535 | 0.0793 | 0.046* | |
H24B | 0.0420 | 0.6667 | 0.0682 | 0.046* | |
C25 | 0.12559 (17) | 0.61045 (13) | 0.22940 (10) | 0.0243 (3) | |
H25A | 0.0141 | 0.6326 | 0.2541 | 0.036* | |
H25B | 0.1635 | 0.5174 | 0.2453 | 0.036* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0197 (5) | 0.0162 (5) | 0.0220 (5) | −0.0042 (4) | 0.0013 (4) | −0.0092 (4) |
O2 | 0.0181 (5) | 0.0285 (5) | 0.0261 (5) | −0.0042 (4) | −0.0016 (4) | −0.0113 (4) |
N1 | 0.0292 (6) | 0.0161 (6) | 0.0271 (6) | −0.0076 (5) | 0.0017 (5) | −0.0105 (5) |
N2 | 0.0195 (5) | 0.0141 (5) | 0.0161 (5) | −0.0033 (4) | 0.0000 (4) | −0.0060 (4) |
N3 | 0.0163 (6) | 0.0192 (6) | 0.0214 (6) | −0.0033 (4) | 0.0004 (4) | −0.0103 (5) |
C1 | 0.0235 (7) | 0.0161 (7) | 0.0227 (7) | −0.0062 (5) | −0.0003 (5) | −0.0049 (5) |
C2 | 0.0202 (7) | 0.0151 (6) | 0.0209 (6) | −0.0050 (5) | 0.0028 (5) | −0.0060 (5) |
C3 | 0.0211 (7) | 0.0179 (7) | 0.0220 (7) | −0.0054 (5) | 0.0057 (5) | −0.0066 (5) |
C4 | 0.0346 (8) | 0.0250 (8) | 0.0224 (7) | −0.0071 (6) | 0.0051 (6) | −0.0097 (6) |
C5 | 0.0386 (9) | 0.0338 (9) | 0.0214 (7) | −0.0071 (7) | 0.0035 (6) | −0.0047 (6) |
C6 | 0.0331 (8) | 0.0219 (8) | 0.0297 (8) | −0.0028 (6) | 0.0047 (6) | 0.0019 (6) |
C7 | 0.0287 (8) | 0.0160 (7) | 0.0338 (8) | −0.0047 (6) | 0.0081 (6) | −0.0058 (6) |
C8 | 0.0220 (7) | 0.0173 (7) | 0.0266 (7) | −0.0060 (5) | 0.0059 (6) | −0.0077 (6) |
C9 | 0.0248 (7) | 0.0171 (7) | 0.0216 (7) | −0.0059 (5) | 0.0019 (5) | −0.0078 (5) |
C10 | 0.0213 (7) | 0.0149 (7) | 0.0215 (7) | −0.0045 (5) | 0.0004 (5) | −0.0073 (5) |
C11 | 0.0178 (6) | 0.0155 (6) | 0.0205 (6) | −0.0038 (5) | −0.0011 (5) | −0.0074 (5) |
C12 | 0.0165 (6) | 0.0144 (6) | 0.0213 (6) | −0.0059 (5) | −0.0018 (5) | −0.0091 (5) |
C13 | 0.0190 (7) | 0.0125 (6) | 0.0198 (6) | −0.0044 (5) | 0.0018 (5) | −0.0047 (5) |
C14 | 0.0187 (7) | 0.0204 (7) | 0.0220 (7) | −0.0059 (5) | 0.0043 (5) | −0.0105 (6) |
C15 | 0.0253 (7) | 0.0302 (8) | 0.0241 (7) | −0.0071 (6) | 0.0016 (6) | −0.0134 (6) |
C16 | 0.0328 (8) | 0.0514 (10) | 0.0282 (8) | −0.0113 (7) | 0.0050 (6) | −0.0234 (7) |
C17 | 0.0368 (9) | 0.0589 (11) | 0.0522 (10) | −0.0137 (8) | 0.0134 (8) | −0.0445 (9) |
C18 | 0.0332 (8) | 0.0284 (8) | 0.0562 (10) | −0.0049 (7) | 0.0117 (7) | −0.0265 (8) |
C19 | 0.0258 (7) | 0.0207 (7) | 0.0364 (8) | −0.0058 (6) | 0.0059 (6) | −0.0134 (6) |
C20 | 0.0235 (7) | 0.0150 (6) | 0.0151 (6) | −0.0032 (5) | −0.0002 (5) | −0.0051 (5) |
C21 | 0.0248 (7) | 0.0159 (7) | 0.0220 (7) | −0.0041 (5) | −0.0013 (5) | −0.0075 (5) |
C22 | 0.0398 (9) | 0.0160 (7) | 0.0235 (7) | −0.0029 (6) | 0.0006 (6) | −0.0040 (6) |
C23 | 0.0485 (9) | 0.0227 (8) | 0.0210 (7) | 0.0001 (7) | −0.0080 (7) | −0.0055 (6) |
C24 | 0.0436 (9) | 0.0248 (8) | 0.0215 (7) | −0.0032 (6) | −0.0082 (6) | −0.0100 (6) |
C25 | 0.0308 (8) | 0.0188 (7) | 0.0235 (7) | −0.0051 (6) | −0.0036 (6) | −0.0092 (6) |
O1—C12 | 1.2409 (14) | C14—C15 | 1.5187 (17) |
O2—C13 | 1.2154 (15) | C14—C19 | 1.5250 (17) |
N1—C8 | 1.3709 (17) | C14—H14 | 0.9800 |
N1—C1 | 1.3758 (16) | C15—C16 | 1.5265 (19) |
N1—H1N | 0.882 (16) | C15—H15A | 0.9700 |
N2—C12 | 1.3629 (15) | C15—H15B | 0.9700 |
N2—C13 | 1.4474 (15) | C16—C17 | 1.519 (2) |
N2—C20 | 1.4874 (15) | C16—H16A | 0.9700 |
N3—C13 | 1.3295 (16) | C16—H16B | 0.9700 |
N3—C14 | 1.4619 (16) | C17—C18 | 1.521 (2) |
N3—H3N | 0.885 (15) | C17—H17A | 0.9700 |
C1—C2 | 1.3630 (18) | C17—H17B | 0.9700 |
C1—H1 | 0.9300 | C18—C19 | 1.5265 (19) |
C2—C3 | 1.4367 (17) | C18—H18A | 0.9700 |
C2—C9 | 1.5016 (16) | C18—H18B | 0.9700 |
C3—C4 | 1.3995 (18) | C19—H19A | 0.9700 |
C3—C8 | 1.4150 (18) | C19—H19B | 0.9700 |
C4—C5 | 1.3819 (19) | C20—C21 | 1.5252 (16) |
C4—H4 | 0.9300 | C20—C25 | 1.5265 (17) |
C5—C6 | 1.401 (2) | C20—H20 | 0.9800 |
C5—H5 | 0.9300 | C21—C22 | 1.5274 (17) |
C6—C7 | 1.378 (2) | C21—H21A | 0.9700 |
C6—H6 | 0.9300 | C21—H21B | 0.9700 |
C7—C8 | 1.3935 (18) | C22—C23 | 1.526 (2) |
C7—H7 | 0.9300 | C22—H22A | 0.9700 |
C9—C10 | 1.5246 (17) | C22—H22B | 0.9700 |
C9—H9A | 0.9700 | C23—C24 | 1.5230 (18) |
C9—H9B | 0.9700 | C23—H23A | 0.9700 |
C10—C11 | 1.5280 (16) | C23—H23B | 0.9700 |
C10—H10A | 0.9700 | C24—C25 | 1.5273 (18) |
C10—H10B | 0.9700 | C24—H24A | 0.9700 |
C11—C12 | 1.5088 (16) | C24—H24B | 0.9700 |
C11—H11A | 0.9700 | C25—H25A | 0.9700 |
C11—H11B | 0.9700 | C25—H25B | 0.9700 |
C8—N1—C1 | 108.57 (11) | C16—C15—H15A | 109.5 |
C8—N1—H1N | 125.4 (10) | C14—C15—H15B | 109.5 |
C1—N1—H1N | 125.8 (10) | C16—C15—H15B | 109.5 |
C12—N2—C13 | 124.00 (10) | H15A—C15—H15B | 108.1 |
C12—N2—C20 | 118.97 (10) | C17—C16—C15 | 111.34 (12) |
C13—N2—C20 | 116.14 (9) | C17—C16—H16A | 109.4 |
C13—N3—C14 | 121.10 (11) | C15—C16—H16A | 109.4 |
C13—N3—H3N | 119.7 (9) | C17—C16—H16B | 109.4 |
C14—N3—H3N | 119.0 (9) | C15—C16—H16B | 109.4 |
C2—C1—N1 | 110.61 (12) | H16A—C16—H16B | 108.0 |
C2—C1—H1 | 124.7 | C16—C17—C18 | 111.05 (12) |
N1—C1—H1 | 124.7 | C16—C17—H17A | 109.4 |
C1—C2—C3 | 106.15 (11) | C18—C17—H17A | 109.4 |
C1—C2—C9 | 128.10 (11) | C16—C17—H17B | 109.4 |
C3—C2—C9 | 125.74 (11) | C18—C17—H17B | 109.4 |
C4—C3—C8 | 118.73 (12) | H17A—C17—H17B | 108.0 |
C4—C3—C2 | 134.23 (12) | C17—C18—C19 | 111.28 (12) |
C8—C3—C2 | 107.00 (11) | C17—C18—H18A | 109.4 |
C5—C4—C3 | 119.14 (13) | C19—C18—H18A | 109.4 |
C5—C4—H4 | 120.4 | C17—C18—H18B | 109.4 |
C3—C4—H4 | 120.4 | C19—C18—H18B | 109.4 |
C4—C5—C6 | 120.99 (13) | H18A—C18—H18B | 108.0 |
C4—C5—H5 | 119.5 | C14—C19—C18 | 110.64 (11) |
C6—C5—H5 | 119.5 | C14—C19—H19A | 109.5 |
C7—C6—C5 | 121.35 (13) | C18—C19—H19A | 109.5 |
C7—C6—H6 | 119.3 | C14—C19—H19B | 109.5 |
C5—C6—H6 | 119.3 | C18—C19—H19B | 109.5 |
C6—C7—C8 | 117.62 (13) | H19A—C19—H19B | 108.1 |
C6—C7—H7 | 121.2 | N2—C20—C21 | 112.03 (9) |
C8—C7—H7 | 121.2 | N2—C20—C25 | 111.79 (10) |
N1—C8—C7 | 130.21 (12) | C21—C20—C25 | 111.43 (10) |
N1—C8—C3 | 107.65 (11) | N2—C20—H20 | 107.1 |
C7—C8—C3 | 122.14 (12) | C21—C20—H20 | 107.1 |
C2—C9—C10 | 113.52 (10) | C25—C20—H20 | 107.1 |
C2—C9—H9A | 108.9 | C20—C21—C22 | 109.36 (10) |
C10—C9—H9A | 108.9 | C20—C21—H21A | 109.8 |
C2—C9—H9B | 108.9 | C22—C21—H21A | 109.8 |
C10—C9—H9B | 108.9 | C20—C21—H21B | 109.8 |
H9A—C9—H9B | 107.7 | C22—C21—H21B | 109.8 |
C9—C10—C11 | 111.69 (10) | H21A—C21—H21B | 108.3 |
C9—C10—H10A | 109.3 | C23—C22—C21 | 111.00 (11) |
C11—C10—H10A | 109.3 | C23—C22—H22A | 109.4 |
C9—C10—H10B | 109.3 | C21—C22—H22A | 109.4 |
C11—C10—H10B | 109.3 | C23—C22—H22B | 109.4 |
H10A—C10—H10B | 107.9 | C21—C22—H22B | 109.4 |
C12—C11—C10 | 111.13 (10) | H22A—C22—H22B | 108.0 |
C12—C11—H11A | 109.4 | C24—C23—C22 | 111.36 (11) |
C10—C11—H11A | 109.4 | C24—C23—H23A | 109.4 |
C12—C11—H11B | 109.4 | C22—C23—H23A | 109.4 |
C10—C11—H11B | 109.4 | C24—C23—H23B | 109.4 |
H11A—C11—H11B | 108.0 | C22—C23—H23B | 109.4 |
O1—C12—N2 | 119.73 (11) | H23A—C23—H23B | 108.0 |
O1—C12—C11 | 120.16 (10) | C23—C24—C25 | 111.49 (11) |
N2—C12—C11 | 120.11 (10) | C23—C24—H24A | 109.3 |
O2—C13—N3 | 125.15 (11) | C25—C24—H24A | 109.3 |
O2—C13—N2 | 120.18 (11) | C23—C24—H24B | 109.3 |
N3—C13—N2 | 114.60 (10) | C25—C24—H24B | 109.3 |
N3—C14—C15 | 109.96 (10) | H24A—C24—H24B | 108.0 |
N3—C14—C19 | 111.25 (10) | C20—C25—C24 | 110.65 (11) |
C15—C14—C19 | 111.73 (11) | C20—C25—H25A | 109.5 |
N3—C14—H14 | 107.9 | C24—C25—H25A | 109.5 |
C15—C14—H14 | 107.9 | C20—C25—H25B | 109.5 |
C19—C14—H14 | 107.9 | C24—C25—H25B | 109.5 |
C14—C15—C16 | 110.68 (11) | H25A—C25—H25B | 108.1 |
C14—C15—H15A | 109.5 | ||
C8—N1—C1—C2 | −0.31 (15) | C10—C11—C12—N2 | 143.14 (11) |
N1—C1—C2—C3 | 0.50 (14) | C14—N3—C13—O2 | 4.45 (18) |
N1—C1—C2—C9 | −179.73 (12) | C14—N3—C13—N2 | −178.61 (10) |
C1—C2—C3—C4 | 177.51 (14) | C12—N2—C13—O2 | −120.32 (13) |
C9—C2—C3—C4 | −2.3 (2) | C20—N2—C13—O2 | 48.75 (15) |
C1—C2—C3—C8 | −0.49 (14) | C12—N2—C13—N3 | 62.58 (14) |
C9—C2—C3—C8 | 179.73 (12) | C20—N2—C13—N3 | −128.35 (11) |
C8—C3—C4—C5 | −0.48 (19) | C13—N3—C14—C15 | 145.83 (11) |
C2—C3—C4—C5 | −178.30 (13) | C13—N3—C14—C19 | −89.84 (13) |
C3—C4—C5—C6 | −1.1 (2) | N3—C14—C15—C16 | 179.74 (10) |
C4—C5—C6—C7 | 1.4 (2) | C19—C14—C15—C16 | 55.68 (14) |
C5—C6—C7—C8 | 0.0 (2) | C14—C15—C16—C17 | −55.71 (15) |
C1—N1—C8—C7 | −179.94 (13) | C15—C16—C17—C18 | 55.99 (16) |
C1—N1—C8—C3 | −0.01 (14) | C16—C17—C18—C19 | −55.91 (16) |
C6—C7—C8—N1 | 178.31 (13) | N3—C14—C19—C18 | −178.94 (11) |
C6—C7—C8—C3 | −1.61 (19) | C15—C14—C19—C18 | −55.61 (14) |
C4—C3—C8—N1 | −178.05 (11) | C17—C18—C19—C14 | 55.43 (16) |
C2—C3—C8—N1 | 0.31 (14) | C12—N2—C20—C21 | −148.53 (11) |
C4—C3—C8—C7 | 1.88 (19) | C13—N2—C20—C21 | 41.82 (13) |
C2—C3—C8—C7 | −179.75 (12) | C12—N2—C20—C25 | 85.57 (13) |
C1—C2—C9—C10 | −27.51 (18) | C13—N2—C20—C25 | −84.08 (12) |
C3—C2—C9—C10 | 152.22 (12) | N2—C20—C21—C22 | 175.58 (10) |
C2—C9—C10—C11 | 179.46 (10) | C25—C20—C21—C22 | −58.32 (14) |
C9—C10—C11—C12 | −174.86 (10) | C20—C21—C22—C23 | 57.75 (14) |
C13—N2—C12—O1 | 177.57 (10) | C21—C22—C23—C24 | −56.38 (16) |
C20—N2—C12—O1 | 8.79 (15) | C22—C23—C24—C25 | 54.40 (16) |
C13—N2—C12—C11 | −1.90 (16) | N2—C20—C25—C24 | −176.96 (10) |
C20—N2—C12—C11 | −170.68 (10) | C21—C20—C25—C24 | 56.81 (14) |
C10—C11—C12—O1 | −36.33 (14) | C23—C24—C25—C20 | −54.30 (15) |
Experimental details
Crystal data | |
Chemical formula | C25H35N3O2 |
Mr | 409.56 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 100 |
a, b, c (Å) | 8.4655 (7), 11.5938 (9), 13.0982 (11) |
α, β, γ (°) | 68.331 (2), 86.752 (1), 72.289 (1) |
V (Å3) | 1135.83 (16) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.08 |
Crystal size (mm) | 0.50 × 0.46 × 0.40 |
Data collection | |
Diffractometer | Bruker SMART CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2001) |
Tmin, Tmax | 0.964, 0.975 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5965, 3945, 3297 |
Rint | 0.029 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.036, 0.100, 1.03 |
No. of reflections | 3945 |
No. of parameters | 279 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.19, −0.19 |
Computer programs: SMART (Bruker, 2001), SAINT (Bruker, 2002), SHELXS97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997), CAMERON (Watkin et al., 1993) and DIAMOND (Bergerhoff, 1996), SHELXL97 (Sheldrick, 2008) and PARST95 (Nardelli, 1995).
X–ray | DFT | |
C1–N1 | 1.3758 (16) | 1.376 |
N1–C8 | 1.3709 (17) | 1.370 |
C12–N2 | 1.3629 (15) | 1.363 |
C20–N2 | 1.4874 (15) | 1.487 |
C13–N2 | 1.4474 (15) | 1.448 |
C13–N3 | 1.3295 (16) | 1.329 |
C13–O2 | 1.2154 (15) | 1.215 |
C14–N3 | 1.4619 (16) | 1.462 |
C8–N1–C1 | 108.57 (11) | 108.6 |
C3–C8–N1 | 107.65 (11) | 107.6 |
C9–C10–C11–C12 | -174.86 (10) | -174.9 |
O2–C13–N3–C14 | 4.45 (18) | 4.5 |
O2–C13–N2–C20 | 48.75 (15) | 48.8 |
D—H···A | D—H | H···A | D···A | D—H···A | |
N3–H3N···O1î^ | X-ray | 0.885 (15) | 2.049 (16) | 2.9326 (14) | 176 (1) |
N3–H3N···O1î^ | Pseudo-Neutron | 1.01 | 1.93 | 2.933 (2) | 176 |
N3–H3N···O1î^ | DFT | 1.10 | 1.83 | 2.933 | 172 |
N1–H1N···O1îi^ | X-ray | 0.882 (16) | 2.06 (2) | 2.914 (1) | 162.7 (14) |
N1–H1N···O1îi^ | Pseudo-Neutron | 1.01 | 1.94 | 2.914 (2) | 162 |
N1–H1N···O1îi^ | DFT | 1.10 | 1.90 | 2.915 | 150 |
C11–H11A···O2îii^ | X-ray | 0.97 | 2.30 | 2.970 (2) | 126 |
C11–H11A···O2îii^ | Pseudo-Neutron | 1.08 | 2.23 | 2.970 (2) | 123 |
C11–H11A···O2îii^ | DFT | 1.14 | 2.19 | 2.969 | 123 |
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) -x+1, -y, -z+1; (iii) -x, -y+1, -z+1. |
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In the molecular recognition and self-assembly process, relatively simple building blocks recognize one another, associate, and form one-, two- and three-dimensional supramolecular frameworks. The phenomenon of specific recognition is facilitated by a combination of different noncovalent interactions, which include electrostatic interactions, hydrogen bonds, hydrophobic interactions and aromatic stacking interactions. The overall combination of various molecular forces, which are quite weak individually, results in the process of self-organization from simple blocks into complex supramolecular structures. In this context, substituted ureas having multiple hydrogen-bonding potential are of considerable current interest (Allen et al., 1997; Gale & Quesada,2006; Custelcean, 2008). Several urea derivatives have been found to contain a one-dimensional α-network, which in turn is linked to form two-dimensional β-sheets through N—H···O hydrogen bonds. Many of these compounds also exhibit a wide range of biological activities as herbicides, pesticides and fungicides (Bessard & Crettaz, 2000; Sun & Zhang, 2006).
As part of an ongoing programme on the synthesis and structural characterization of novel urea derivatives, we synthesized N,N'-dicyclohexyl-N-[4-(3-indolyl)butanoyl]urea, (I), designed for self-complexation, and the crystal structure of (I) was established by single-crystal X-ray analysis. Since the positions of H atoms in molecular systems are usually determined with limited accuracy by an X-ray study, a solid-state density functional theory (DFT) calculation has been performed for a better understanding of the intra- and intermolecular hydrogen-bond geometry in the title compound. The advantage of the DFT method over X-ray structure refinement is that the positions of the H atoms are optimized simultaneously along with the positions of the non-H atoms, thus providing a more reliable hydrogen-bond geometry.
The asymmetric unit of (I) (Fig. 1) consists of a planar indoline group (C1–C8/N1), with an r.m.s. deviation of 0.013 Å, and a dicyclohexylurea unit joined through a butanoyl chain. The two cyclohexyl groups are in a syn–syn conformation with respect to the urea group; the O2—C13—N3—C14 and O2—C13—N2—C20 torsion angles are 4.5 (2) and 48.7 (1)°, respectively. The extended molecular conformation of (I) is indicated by the C9—C10—C11—C12 torsion angle of -174.9 (2)°. Each of the cyclohexyl groups in (I) adopts a chair conformation, with ring-puckering parameters (Cremer & Pople, 1975) Q, θ and ϕ of 0.569 (2) Å, 180.0 (2)° and 344 (53)°, respectively, for the C14—C19 ring, and 0.579 (2) Å, 2.9 (2)° and 54 (3)°, respectively, for the C20–C25 ring. The two carbonyl groups in the N-acylurido unit, are twisted substantially at the central atom N2, with a dihedral angle of 58.3 (1)° between the O1/C12/N2 and N2/C13/O2 planes, which increases the distance between atoms O1 and N3. Therefore, as expected, no intramolecular N3—H3N···O1 hydrogen bond is formed.
The observed bond distances from the X-ray analysis are in accord with the corresponding values reported for other dicyclohexylurea derivaties (Gallagher et al., 1999; Sun & Zhang, 2006; Wu et al., 2006). The shortening of the N3—C13 and N2—C12 bond lengths with the corresponding lengthening of the N2—C13 bond distance (Table 1) can be attributed to π-conjugation in the O1/C12/N2/C13 and O2/C13/N3/C14 fragments of the molecule.
The molecules of (I) are linked by a combination of N—H···O and C—H···O hydrogen bonds (Table 2) into a two-dimensional framework, whose formation is readily analyzed in terms of substructures of lower dimensionality with finite zero-dimensional dimeric units as the building blocks within the structure. A pair of intermolecular N3—H3N···O1 hydrogen bonds with the urea atom N3 in the molecule at (x, y, z) acting as a donor to the butanoyl atom O1 in the molecule at (1 - x, 1 - y, 1 - z) generates a centrosymmetric R22(12) dimeric ring (A) centered at (1/2, 1/2, 1/2). Similarly, a pair of intermolecular N1—H1N···O1 hydrogen bonds in (I) interconnects two molecules at (x, y, z) and (1 - x, -y, 1 - z), producing a centrosymmetric R22(18) dimeric ring (B) centered at (1/2, 0, 1/2). The R22(12) and R22(18) rings are alternately linked into an infinite one-dimensional ABAB··· polymeric chain propagating along the [010] direction (Fig. 2). Adjacent one-dimensional chains are connected via pairs of C11—H11A···O2 hydrogen bonds producing R22(12) motifs, which propagate along the [100] direction. The combination of [010] and [100] chains suffices to generate a continuous two-dimensional framework structure (Fig. 3).
Solid-state DFT calculations have been performed using the Dmol3 code (Delly, 1996, 1998) of the Materials Studio system of programs (Accelrys Inc., Princeton, New Jersey, USA) in the framework of a generalized-gradient approximation. The starting atomic coordinates were taken from the final X-ray refinement cycle. Since the resulting molecular geometry depends on the choice of functionals, theoretical calculations were carried out with the BLYP (Becke, 1988; Lee et al., 1988) and HCTH (Hamprecht et al., 1998; Boese et al., 2000; Boese & Handy, 2001) levels of theory using the numeric DNP basis set. The cell parameters were kept fixed during the DFT calculations. Different functionals describe different classes of molecules with varying degrees of accuracy. Between the two functionals used for the DFT calculation, the results with the HCTH functional agree more closely with the X-ray analysis of the title compound. A comparison of the molecular conformation of (I) as established by the X-ray study and quantum mechanical calculations shows an excellent agreement (Fig. 4); the r.m.s. deviation between the coordinates obtained by geometry optimization and X-ray structure analysis is 0.013 Å. The elongation of the DFT-calculated N2—C13 bond length compared with the N2—C12 and N3—C13 bond distances is consistent with the X-ray analysis of the title compound. The calculated O···H distances (1.831–1.898 Å) in (I) lie in the range of normal N—H···O hydrogen bonds (Lyssenko & Antipin, 2006). The geometries of the hydrogen bonds (Table 2) calculated from the DFT method closely resemble those obtained from the X-ray analysis (X—H bond lengths normalized to neutron distances), with the formation of characteristic R22(12) and R22(18) rings, polymeric chains and finally a two-dimensional supramolecular assembly.
It is of interest to compare briefly the supramolecular structure of (I) with those of other N,N'-disubstituted ureas (Custelcean, 2008). Disubstituted urea derivatives tend to form one-dimensional hydrogen-bonded chains by employing their two NH H-atom donors and the C═O acceptors. The NH H atoms normally adopt an anti conformation with respect to the carbonyl group and form three-center bonds to the urea carbonyl groups. The resulting hydrogen-bonded motif can be described by using the graph set notations (Etter, 1990) as C(4)[R21(6)] (Chang et al., 1993; Hollingsworth et al., 1994). Bulky substituents at the urea N atoms of (I), however, prohibit the formation of short NH···O—C interactions, and consequently the urea planes are twisted relative to one another. The propensity of ureas to form hydrogen-bonded chains and cyclic dimers has been utilized in the design of two-dimensional layered networks (Kane et al., 1995; Wu et al., 2006). In the structure of (I), a two-dimensional supramolecular network based on cyclic R22(12) and R22(18) motifs has been established from NH(urea)···O—C(butanoyl), NH(indonyl)···O—C(butanoyl) and CH(butanoyl)···O—C(urea) interactions.