| Literature DB >> 25221868 |
Carlos Z Gómez-Castro1, Itzia I Padilla-Martínez2, Efrén V García-Báez3, José L Castrejón-Flores4, Ana L Peraza-Campos5, Francisco J Martínez-Martínez6.
Abstract
Intramolecular hydrogen bond (HB) formation was analyzed in the model compounds N-(2-benzoylphenyl)acetamide, N-(2-benzoylphenyl)oxalamate and N1,N2-bis(2-benzoylphenyl)oxalamide. The formation of three-center hydrogen bonds in oxalyl derivatives was demonstrated in the solid state by the X-ray diffraction analysis of the geometric parameters associated with the molecular structures. The solvent effect on the chemical shift of H6 [δH6(DMSO-d6)-δH6(CDCl3)] and Δδ(ΝΗ)/ΔT measurements, in DMSO-d6 as solvent, have been used to establish the energetics associated with intramolecular hydrogen bonding. Two center intramolecular HB is not allowed in N-(2-benzoylphenyl)acetamide either in the solid state or in DMSO-d6 solution because of the unfavorable steric effects of the o-benzoyl group. The estimated ΔHº and ΔSº values for the hydrogen bonding disruption by DMSO-d6 of 28.3(0.1) kJ·mol-1 and 69.1(0.4) J·mol-1·K-1 for oxalamide, are in agreement with intramolecular three-center hydrogen bonding in solution. In the solid, the benzoyl group contributes to develop 1-D and 2-D crystal networks, through C-H∙∙∙A (A = O, π) and dipolar C=O∙∙∙A (A = CO, π) interactions, in oxalyl derivatives. To the best of our knowledge, this is the first example where three-center hydrogen bond is claimed to overcome steric constraints.Entities:
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Year: 2014 PMID: 25221868 PMCID: PMC6270700 DOI: 10.3390/molecules190914446
Source DB: PubMed Journal: Molecules ISSN: 1420-3049 Impact factor: 4.411
Figure 1Three-center hydrogen bond.
Figure 2Model compounds.
Figure 3Molecular structure of compound 1. ORTEP at 30% probability level.
Figure 4Molecular structure of compound 2. ORTEP at 30% probability level.
Figure 5Molecular structure of compound 3. ORTEP at 30% probability level.
Selected bond lengths and angles of compounds 1–3.
| 1 | 2 | 3 | |
|---|---|---|---|
| Atoms | Bond Lengths (Å) | ||
| O8–C8 | 1.234(2) | 1.204(3) | 1.211(4) |
| O13–C13 | 1.217(2) | 1.227(2) | 1.223(5) |
| N7–C1 | 1.425(2) | 1.399(2) | 1.402(4) |
| N7–C8 | 1.338(2) | 1.346(2) | 1.350(4) |
| C1–C2 | 1.398(2) | 1.416(3) | 1.407(4) |
| C2–C13 | 1.491(2) | 1.486(2) | 1.483(5) |
| C8–C9(8a) | 1.502(2) | 1.538(3) | 1.548(5) |
| C13–C14 | 1.490(3) | 1.496(2) | 1.495(5) |
| C1–N7–C8 | 123.27(14) | 129.61(16) | 128.9(3) |
| N7–C1–C2 | 121.49(14) | 119.08(16) | 118.8(3) |
| C2–C1–N7–C8 | 52.3(2) | −171.96(18) | −174.7(3) |
| O8–C8–N7–C1 | −3.2(3) | −5.8(3) | −1.2(6) |
| O8–C8–C8a–O8a | 166.7(2) | −180.0(3) | |
| O13–C13–C14–C15 | −135.18(17) | 151.65(18) | −40.2(4) |
| C1–C2–C13–O13 | −145.02(17) | 25.4(3) | 19.14(4) |
Hydrogen bonding geometry.
| Comp. | D–H∙∙∙A | Symmetry Code | D–H (Å) | H∙∙∙A (Å) | D∙∙∙A (Å) | D–H∙∙∙A (°) |
|---|---|---|---|---|---|---|
| N7–H7∙∙∙O8 | −½+x, 1−y, −½+z | 0.88 | 1.91 | 2.7491(19) | 160 | |
| C17–H17∙∙∙O8 | −1+x, y, z | 0.95 | 2.50 | 3.439(2) | 170 | |
| C4–H4∙∙∙
| ½+x, −y, −½+z | 2.54 | 3.4104(19) | 153 | ||
| N7–H7∙∙∙O9 | 0.86 | 2.25 | 2.666(2) | 110 | ||
| N7–H7∙∙∙O13 | 0.86 | 1.97 | 2.662(2) | 136 | ||
| C6–H6∙∙∙O8 | 0.93 | 2.29 | 2.908(3) | 124 | ||
| C17–H17∙∙∙O8 | −1+x, y, −1+z | 0.93 | 2.57 | 3.391(3) | 147 | |
| N7–H7∙∙∙O8a | −x, −y, 1−z | 0.86 | 2.23 | 2.665(4) | 111 | |
| N7–H7∙∙∙O13 | 0.86 | 1.98 | 2.673(4) | 137 | ||
| C6–H6∙∙∙O8 | 0.93 | 2.27 | 2.900(4) | 124 | ||
| C4–H4∙∙∙ | 1−x, −y, −z | 2.81 | 3.612(4) | 145 |
The sum of angles around H7 = 360.0° and 359.0° for compounds 2 and 3, respectively.
Figure 6Supramolecuar structure of compound 1, (a) through N7–H7···O8 and (b) C4–H4∙∙∙Cg(2) interactions.
Figure 7Supramolecuar structure of compound 2, through C13O13∙∙∙C9 and C17–H17∙∙∙O8 interactions.
Figure 8Supramolecuar structure of compound 3, π-stacking and tape formation through (a) C8O8∙∙∙Cg(1) and (b) C4–H4∙∙∙ Cg(2) interactions, respectively.
Summary of 1H- and 13C-NMR data for compounds 1–3 relevant to hydrogen bonding.
| Comp. | (DMSO- | (CDCl3) | ΔδNH b | ΔδH6 c | ||||
|---|---|---|---|---|---|---|---|---|
| δCO | δNH | δH6 | −ΔδNH/ΔT a | δNH | δH6 | |||
| 169.2 | 10.1 | 7.65 | 2.59 | 10.8 | 8.63 | −0.7 | −0.98 | |
| 155.6 | 11.5 | 8.06 | 2.67 | 12.3 | 8.71 | −0.8 | −0.65 | |
| 158.4 | 11.7 | 8.23 | 1.88 | 12.5 | 8.81 | −0.8 | −0.58 | |
a ppb·K−1; b [δNH(DMSO)–δNH(CDCl3)]; c [δH6(DMSO)–δH6(CDCl3)].
Thermodynamic parameters ΔHº and ΔSº (at 298.15 K) of the amide N–H∙∙∙DMSO-d6 HB formation and their standard errors obtained from van’t Hoff plots for compounds 1–3 and reference values for acetanilide, ethyl N-phenyl oxalamate and N,N-bis(2-nitrophenyl)oxalamide.
| Comp. | Δ
| Δ
|
|---|---|---|
| Acetanilide [ | 9.57(0.02) | 16.68(0.07) |
| Ethyl | 11.82(0.08) | 23.2(0.2) |
| 21.1(0.2) | 58.1(0.5) | |
| 6.60(0.03) | 12.9(0.1) | |
| 12.10(0.08) | 23.7(0.2) | |
| 28.3(0.1) | 69.1(0.4) |
Collection and refinement X-ray data of compounds 1–3.
| Compounds | 1 | 2 | 3 |
|---|---|---|---|
| CCDC number | 1013358 | 1013356 | 1013357 |
| Formula | C15H13N1O2 | C17H15N1O4 | C28H20N8O4 |
| M (g·mol−1) | 252.0 | 297.3 | 448.5 |
| Crystal system | Monoclinic | Monoclinic | Monoclinic |
| Space group | P n | P 21/c | P 21/c |
| a (Å) | 8.3679(9) | 9.3796(8) | 6.2377(6) |
| b (Å) | 9.1351(10) | 15.2202(13) | 17.7892(18) |
| c (Å) | 8.9361(9) | 10.6317(9) | 10.8548(9) |
| α (°) | 90 | 90 | 90 |
| β (°) | 115.320(2) | 102.815(1) | 114.429(4) |
| γ (°) | 90 | 90 | 90 |
| V (Å3) | 618.94(7) | 1478.41(4) | 1096.6(2) |
| Z | 2 | 4 | 2 |
| ρcalcd. (g·cm−3) | 1.324 | 1.34 | 1.36 |
| μ (mm−1) | 0.086 | 0.096 | 0.092 |
| F (000) | 252.0 | 623.9 | 467.9 |
| Crystal size (mm) | 0.50 × 0.50 × 0.40 | 0.36 × 0.30 × 0.28 | 0.40 × 0.30 × 0.30 |
| Temp. (K) | 100 (2) | 293(2) | 100(2) |
| θ range (°) | 2.2–26.0 | 2.2–27.6 | 2.3–25.0 |
| Reflections collected | 6206 | 16595 | 9547 |
| Independent reflections | 2419 | 3381 | 1930 |
| Data/restraints/parameters | 2419/2/163 | 3381/0/199 | 1930/0/154 |
| Goof | 1.139 | 1.216 | 1.148 |
| R (int) | 0.030 | 0.029 | 0.068 |
| Final R indices [I > 2σ(I)], R1/wR2 | 0.035/0.090 | 0.066/0.150 | 0.077/0.142 |
| Largest diff. peak/hole (e·Å−3) | 0.284/−0.222 | 0.230/−0.258 | 0.201/−0.185 |