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Molecules 2014, 19(9), 14446-14460; doi:10.3390/molecules190914446

Article
Solid State Structure and Solution Thermodynamics of Three-Centered Hydrogen Bonds (O∙∙∙H∙∙∙O) Using N-(2-Benzoyl-phenyl) Oxalyl Derivatives as Model Compounds
Carlos Z. Gómez-Castro 1, Itzia I. Padilla-Martínez 1,*, Efrén V. García-Báez 1, José L. Castrejón-Flores 1, Ana L. Peraza-Campos 2 and Francisco J. Martínez-Martínez 2,*
1
Departamento de Ciencias Básicas, Unidad Profesional Interdisciplinaria de Biotecnología del Instituto Politécnico Nacional, Av. Acueducto s/n Barrio la Laguna Ticomán, México D.F. 07340, Mexico
2
Laboratorio de Posgrado, Facultad de Ciencias Químicas, Universidad de Colima, Km 9 Carretera Colima-Coquimatlán, Colima 28400, Mexico
*
Authors to whom correspondence should be addressed; Tel.: +52-555-7296000 (ext. 56324) (I.I.P.-M.); Fax: +52-555-7296000 (ext. 56305) (I.I.P.-M.); Tel./Fax: +52-312-3161163 (F.J.M.-M.).
Received: 27 August 2014 / Accepted: 9 September 2014 / Published: 12 September 2014

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 Δ and Δ 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.
Keywords:
three-center hydrogen bond; oxalamide; oxalamate; steric effect; solvent effect; proton mobility; cooperativity

1. Introduction

Non-covalent interactions have been considered as the driving forces involved in molecular recognition processes. Among them, hydrogen bonding is probably the most important in biological systems [1,2]. Oxalamate and oxalamide moieties, in contrast to amides, are not found in biomolecules, but they have been employed as pseudopeptide templates in bioorganic and medicinal chemistry [3,4]. Bis-oxalamides exhibit gelation properties, and such ability is a consequence of strong and directional intermolecular hydrogen bonding [5].

The three-centered hydrogen bond (THB), or bifurcated hydrogen bond, classified as non-classical hydrogen bonding, is responsible for the biological activity of peptides, proteins, DNA, and other bioactive molecules [6,7,8]. One acceptor and two donor groups (H∙∙∙A∙∙∙H) or one donor and two acceptor groups (A∙∙∙H∙∙∙A) can form two structurally different THBs (Figure 1) [9,10], known as three-center acceptor (bifurcated acceptor) and three-center donor (bifurcated donor) hydrogen bonds, respectively. In addition, they can be composed of intermolecular, intramolecular or both components. The energetic superiority of two-centered or regular HB over a bifurcated acceptor THB in non- aromatic systems has been demonstrated [11,12], but over a bifurcated donor THB is still in a matter of debate [13,14,15].

Figure 1. Three-center hydrogen bond.
Figure 1. Three-center hydrogen bond.
Molecules 19 14446 g001 1024

From a supramolecular point of view, intermolecular H∙∙∙A∙∙∙H THBs have been exploited to form multicomponent crystals [16,17,18], they have been associated with the properties of amyloid fibrils [19] and their reversible formation has been induced by high pressure phase transition in organic crystals [20]. On the other hand, intramolecular A∙∙∙H∙∙∙A THBs have been successfully used to rigidify the backbones of macrocyclic precursors [21] as well as for promoting the formation of stable dimeric complexes in solution [22]. A complete description of the effect of THB formation on the properties of several materials has been compiled elsewhere [23].

In this contribution, N-(2-benzoylphenyl)acetamide (1) has been chosen as a model compound for a two centered or regular hydrogen bond (HB), ethyl N-(2-benzoylphenyl)oxalamate (2) for a three-centered hydrogen bond (THB) and N1,N2-bis(2-benzoylphenyl)oxalamide (3) as a model compound for cooperativity effects associated with THB formation (Figure 2). It is worth mentioning that in a previous publication [24], we have used an analogous approach to study the thermodynamic properties and cooperativity involvement in THB formation in solution. Herein, the model compounds present important steric effects exerted by the benzoyl group not included before in the study of THBs.

Figure 2. Model compounds.
Figure 2. Model compounds.
Molecules 19 14446 g002 1024

Compound 1 has been used as a model compound of ATPasa binding [25], and as starting material for the synthesis of more complex compounds such as quinazolines [26,27], indole derivatives [28,29,30], 4-phenylquinolin-2(1H)-one derivatives [31], azabenzopyrylium perchlorates [32] and COX inhibitors [33]. Compounds 2 and 3 have been used as starting materials for the synthesis of indole derivatives [34,35], while compound 3 has been additionally used to form complexing ligands for several metals [36,37,38]. Surprisingly, despite the wide use of these compounds their X-ray structures have not been reported yet. Therefore, the aims of this contribution were to establish the molecular structure of the model compounds in the solid state by X-ray diffraction analysis and to estimate the thermodynamic properties associated with hydrogen bonding in solution by NMR.

2. Results and Discussion

2.1. Molecular Structure of 13 in the Solid State

The molecular structures and atom numbering of acetamide 1, oxalamate 2 and oxalamide 3 are shown in Figure 3, Figure 4 and Figure 5, respectively. A summary of bond lengths and angles is listed in Table 1. The bond lengths N7–C1 and N7–C8, around the benzamide group, are very similar between the three compounds, and the mean values are very close to the ones measured for acetanilide [1.413(3) Å and 1.354(3), respectively] [39,40,41]. The amide group in compound 1 is out of the plane of the phenyl ring, whereas the ethyloxalamate group in compound 2 and oxalamide group in compound 3 are almost in the same plane as the phenyl ring, as shown by the C2–C1–N7–C8 torsion angles. It is worthy of mention that the structurally analogous compounds N-(2-acetylphenyl)acetamide [42] and N1,N2-bis(2-acetylphenyl)oxalamide [43,44] adopt a planar conformation forming two- and three-centered hydrogen bonds in the solid state.

The two carbonyl groups of the oxalyl moiety in compounds 2 and 3 are antiperiplanar, with O8=C8–C9(8a)=O9(8a) torsion angles near to 180°, in accord with the most frequently adopted conformation seen in open systems. In spite of the planarity exhibited by the oxalamate and oxalamide groups, the CO–CO bond length values for 2 and 3 are close to the value for Csp3–Csp3 single bond [45], indicating the absence of π conjugation.

Figure 3. Molecular structure of compound 1. ORTEP at 30% probability level.
Figure 3. Molecular structure of compound 1. ORTEP at 30% probability level.
Molecules 19 14446 g003 1024
Figure 4. Molecular structure of compound 2. ORTEP at 30% probability level.
Figure 4. Molecular structure of compound 2. ORTEP at 30% probability level.
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Figure 5. Molecular structure of compound 3. ORTEP at 30% probability level.
Figure 5. Molecular structure of compound 3. ORTEP at 30% probability level.
Molecules 19 14446 g005 1024
Table 1. Selected bond lengths and angles of compounds 13.
Table 1. Selected bond lengths and angles of compounds 13.
123
AtomsBond Lengths (Å)
O8–C81.234(2)1.204(3)1.211(4)
O13–C131.217(2)1.227(2)1.223(5)
N7–C11.425(2)1.399(2)1.402(4)
N7–C81.338(2)1.346(2)1.350(4)
C1–C21.398(2)1.416(3)1.407(4)
C2–C131.491(2)1.486(2)1.483(5)
C8–C9(8a)1.502(2)1.538(3)1.548(5)
C13–C141.490(3)1.496(2)1.495(5)
Bond and Torsion Angles (°)
C1–N7–C8123.27(14)129.61(16)128.9(3)
N7–C1–C2121.49(14)119.08(16)118.8(3)
C2–C1–N7–C852.3(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)

Most benzamides bearing hydrogen bonding acceptor groups in the ortho position form intramolecular hydrogen bonds with the amide NH [46]. In this case, however, the carbonyl moiety of the 2-benzoyl pendant group is almost opposite the NH, [C1–C2–C13–O13 = −145.21(16)°] avoiding intramolecular hydrogen bonding in amide 1, but instead, allowing intermolecular hydrogen bonding (vide infra) and intermolecular dipolar carbonyl-carbonyl interactions (C8O8∙∙∙C13 distance of 2.826(2) Å, C8–O8∙∙∙C13 angle of 91.8(2)°). This conformational preference can be explained by the steric effect of the 2-benzoyl group that restricts the free rotation around the C2–CO bond. In contrast to the result obtained for amide 1, the 2-benzoyl pendant group points towards the NH in both oxalamate 2 and oxalamide 3, with small C1–C2–C13–O13 torsion angles, forming an intramolecular hydrogen bond. The gradual narrowing of the N7–C1–C2 angle is the results of the conformation exhibited by each compound. In fact, the NH becomes engaged with two carbonyl acceptors, forming an intramolecular three centered hydrogen bonding motif S(6) type [47], whose geometric parameters are listed in Table 2. In addition, the secondary soft H-bonding interaction C6–H6∙∙∙O8 completes the H-bonding pattern as an S(6)S(5)S(6) and [S(6)S(5)S(6)]2 motifs for 2 and 3, respectively. In oxalamate and bis-oxalamide systems, the participation of C6–H6∙∙∙O8 hydrogen bonding as a cooperative interaction in THB formation, has not been noticed in either solution or the solid state [48,49].

The whole H-bonding system forms a plane defined by the O13C13C2C1C6N7C8O8C9(8a)O9(8a) group of atoms of which the maximum deviation is exhibited by O13 and O9 [−0.3240 (13) and 0.2808 (17) Å, respectively], in compound 2, and C13 and O13 [−0.1804 (33) and 0.1356 (26) Å, respectively], in compound 3. These results suggest that the formation of the intramolecular three-centered hydrogen bond O9(8a)∙∙∙H7∙∙∙O13, in compounds 2 and 3, is strongly favored over an intermolecular one, as observed in compound 1.

Table 2. Hydrogen bonding geometry.
Table 2. Hydrogen bonding geometry.
Comp.D–H∙∙∙ASymmetry CodeD–H (Å)H∙∙∙A (Å)D∙∙∙A (Å)D–H∙∙∙A (°)
1N7–H7∙∙∙O8−½+x, 1−y, −½+z0.881.912.7491(19)160
C17–H17∙∙∙O8−1+x, y, z0.952.503.439(2)170
C4–H4∙∙∙ Cg(2)½+x, −y, −½+z 2.543.4104(19)153
2N7–H7∙∙∙O9 0.862.252.666(2)110
N7–H7∙∙∙O13 0.861.972.662(2)136
C6–H6∙∙∙O8 0.932.292.908(3)124
C17–H17∙∙∙O8−1+x, y, −1+z0.932.573.391(3)147
3N7–H7∙∙∙O8a−x, −y, 1−z0.862.232.665(4)111
N7–H7∙∙∙O13 0.861.982.673(4)137
C6–H6∙∙∙O8 0.932.272.900(4)124
C4–H4∙∙∙Cg(2)1−x, −y, −z 2.813.612(4)145

The sum of angles around H7 = 360.0° and 359.0° for compounds 2 and 3, respectively.

2.2. Supramolecular Structure of 13 in Solid State

The supramolecular structure of amide 1 is achieved by a combination of strong and weak hydrogen bonding interactions, whose geometric parameters are listed in Table 2. The amide NH is involved in strong H-bonding interactions with the amide carbonyl from a neighboring molecule, N7–H7···O8, developing a C(4) chain along the [1 0 −1] direction (Figure 6a). The second dimension is accomplished by C4–H4∙∙∙Cg(2) weak interactions (Cg(2) is the centroid of the C14–C19 ring) along the [1 0 1] direction (Figure 6b).

Figure 6. Supramolecuar structure of compound 1, (a) through N7–H7···O8 and (b) C4–H4∙∙∙Cg(2) interactions.
Figure 6. Supramolecuar structure of compound 1, (a) through N7–H7···O8 and (b) C4–H4∙∙∙Cg(2) interactions.
Molecules 19 14446 g006 1024

Because the N7–H7, the best H-donor, is involved in intramolecular hydrogen bonding, the supramolecular structure is governed by soft C–H∙∙∙A (A = O, π) [50] and dipolar C=O∙∙∙A (A = CO, π) interactions [51] for 2 and 3, and the hydrogen bonding geometric parameters are listed in Table 2. In the case of oxalamate 2, the C13–O13∙∙∙C9 dipolar interaction between ketone and ester carbonyls (C13O13∙∙∙C9 distance of 2.973(3) Å; C13–O13∙∙∙C9 angle of 112.5(2)°; symmetry code: −x, 1−y, 1−z), forms centrosymmetric dimers interlinked by C17–H17∙∙∙O8 interactions to form ribbons that propagate along the [1 7 −1] direction (Figure 7).

Figure 7. Supramolecuar structure of compound 2, through C13O13∙∙∙C9 and C17–H17∙∙∙O8 interactions.
Figure 7. Supramolecuar structure of compound 2, through C13O13∙∙∙C9 and C17–H17∙∙∙O8 interactions.
Molecules 19 14446 g007 1024

Molecules of oxalamide 3 π-stack along the [0 2 3] direction through C8–O8∙∙∙Cg(1) interactions [O8∙∙∙Cg(1) distance of 3.321(3) Å; C8–O8∙∙∙Cg(1) angle of 86.12(19); symmetry code: 1−x, −y, 1−z; Cg(1) is the centroid of the benzamide (C1–C6) ring] (Figure 8a). The stacked columns are joined together through C4–H4∙∙∙Cg(2) interactions along the [2 7 2] direction (Figure 8b).

Figure 8. Supramolecuar structure of compound 3, π-stacking and tape formation through (a) C8O8∙∙∙Cg(1) and (b) C4–H4∙∙∙ Cg(2) interactions, respectively.
Figure 8. Supramolecuar structure of compound 3, π-stacking and tape formation through (a) C8O8∙∙∙Cg(1) and (b) C4–H4∙∙∙ Cg(2) interactions, respectively.
Molecules 19 14446 g008 1024

2.3. Molecular Structure of 13 in Solution

Compounds 13, were characterized by 1H- and 13C-NMR; nOe experiments on the NH proton were used to unequivocally assign H6. A summary of data concerning HB is given in Table 3. The NHCO carbon atom of amide 1 appears at higher frequency when compared with compounds 2 and 3. These results suggest the gradual increase of electronic delocalization of the nitrogen lone pair into the adjacent carbonyl group in going from 1 to 3, in agreement with the smaller N7–C8 distance than the N7–C1 one observed by X-ray diffraction (vide supra). The conformation observed in the solid state seems to be the same in DMSO-d6 solution for each compound, and the chemical shift of H6 is very sensitive to the field effects caused by the neighboring amide carbonyl group. In DMSO-d6 solution, the δH6 is shifted to high frequencies by the local deshielding effect of the amide carbonyl group. This effect has been known for a long time for o-substituted anilides [52]. Thus, the amide CO is found most of the time in the nearby of H6, in exo conformation, in oxalamide 3 followed by oxalamate 2 and amide 1. On the other hand, the chemical shift of the NH also appears to higher frequency, indicating a progressive engagement in HB in the compounds in the order 3 > 2 > 1.

Table 3. Summary of 1H- and 13C-NMR data for compounds 13 relevant to hydrogen bonding.
Table 3. Summary of 1H- and 13C-NMR data for compounds 13 relevant to hydrogen bonding.
Comp.(DMSO-d6)(CDCl3)ΔδNH bΔδH6 c
δCOδNHδH6−ΔδNH/ΔT aδNHδH6
1169.210.17.652.5910.88.63−0.7−0.98
2155.611.58.062.6712.38.71−0.8−0.65
3158.411.78.231.8812.58.81−0.8−0.58

a ppb·K−1; b [δNH(DMSO)–δNH(CDCl3)]; c [δH6(DMSO)–δH6(CDCl3)].

The solvent effect on the NH chemical shift has been accepted as a general test for proton mobility [53]. Thus, the 1H-NMR spectra of compounds 13 were recorded in CDCl3 solution and compared with those recorded in DMSO-d6 solution, and the results are shown in Table 3 for NH and H6. In general, both δNH and δH6 signals, in CDCl3 solutions, are shifted to higher frequencies relative to DMSO solutions. Small and similar ΔδNH values [δNH(DMSO)–δNH(CDCl3)] were observed for compounds 13. This result suggests that the δNH is not sensitive to solvent effects, probably due to the steric protection effect exerted by the benzoyl group. Additionally, the δH6, in CDCl3 solutions, is shifted to high frequencies in the three compounds with values of ΔδH6 decreasing in the following order: 1 > 2 > 3. These results indicate that the conformation exo, of the amide carbonyl, is favored in less polar solvents and the effect is smaller for strongly hydrogen bonded systems. Moreover, in chloroform solutions the three model compounds are in a full hydrogen bonding state.

A more reliable criterion to judge the strength of HB is the temperature gradient of the amide proton chemical shift. Smaller ΔδNH/ΔT values are associated with strong intramolecular HB particularly those values smaller than −2.0 ppb·K−1 that correspond with three centered HB systems [54]. Thus, the measured values for compounds 13, shown in Table 3, are in agreement with the formation of a regular hydrogen bond in 1 and 2 and with the presence of a three centered hydrogen bond in compound 3 in DMSO-d6 solution.

Furthermore, the Δδ(ΝΗ)/ΔT measurements, using DMSO-d6 as solvent, have been used to establish the energetics associated with intramolecular hydrogen bonding [24,55]. The method is based on a nonlinear fitting (NLF) procedure, followed by van't Hoff data treatment which is applied to the equilibrium established between an intramolecular hydrogen bonding at the initial state and the association with the solvent at the final state of the NH proton, at increasing temperatures. The results are listed in Table 4 as well as the corresponding values for acetanilide, ethyl N-phenyloxalamate and N1,N2-bis(2-nitrophenyl)oxalamide, as reference compounds [24]. In each case both enthalpy and entropy changes are positive, in agreement with the energy required to disrupt intramolecular hydrogen bonding and to reach a more disordered final state by association with the solvent. Both Δ and Δ values for amide 1 are in the range for non-hydrogen bonding state, but they are smaller than those predicted for acetanilide. In the case of compound 2, the similarity of its Δ and Δ values with those previously reported for ethyl N-phenyloxalamate suggests the same HB scheme characterized by the absence of of intramolecular HB with the o-carbonyl moiety. The predicted Δ and Δ values, for compound 3, suggest a full three centered hydrogen bonding scheme which is stronger than the one found in N1,N2-bis(2-nitrophenyl)oxalamide.

For reference purposes, the estimated Δ and Δ values for oxalamates, 18.7(1.0) kJ·mol−1 and 42.0(4.7) J·mol−1·K−1 and oxalamides, 24.4(1.7) kJ·mol−1 and 61.9(11) J·mol−1·K−1, are given. These values represent the energy required to break a full three-centered hydrogen bond (A∙∙∙H∙∙∙O=C) [24].

Table 4. Thermodynamic parameters Δ and Δ (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 13 and reference values for acetanilide, ethyl N-phenyl oxalamate and N1,N2-bis(2-nitrophenyl)oxalamide.
Table 4. Thermodynamic parameters Δ and Δ (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 13 and reference values for acetanilide, ethyl N-phenyl oxalamate and N1,N2-bis(2-nitrophenyl)oxalamide.
Comp.Δ /kJ·mol−1Δ /J·mol−1·K−1
Acetanilide [24]9.57(0.02)16.68(0.07)
Ethyl N-phenyl oxalamate [24]11.82(0.08)23.2(0.2)
N1,N2-bis(2-nitrophenyl)oxalamide [24]21.1(0.2)58.1(0.5)
16.60(0.03)12.9(0.1)
212.10(0.08)23.7(0.2)
328.3(0.1)69.1(0.4)

3. Experimental Section

3.1. Instruments

Melting points were measured on an Electrothermal IA apparatus and are uncorrected. IR spectra were recorded at 25 °C using a Varian 3100 FT-IR with ATR system Excalibur Series spectrophotometer. 1H- and 13C-NMR spectra was recorded on a Varian Mercury 300 MHz (1H, 300.08; 13C, 75.46 MHz) in DMSO-d6. The spectra was measured with tetramethylsilane as internal reference following standard techniques. Standard HETCOR and nOe experiments were performed to properly assign H6. Variable temperature experiments were performed using a temperature controller that maintained the temperature constant within 0.2 °C and increased the temperature automatically by 10 °C increments, from 20 to 120 °C, with a delay of 5 min for the temperature stabilization. Each spectrum was obtained with 32 scans. Samples concentration was maintained at 5 mg/0.4 mL or less in DMSO-d6 solutions. Temperature controller was calibrated using standard techniques given by the manufacturer. General procedure for NLF and van’t Hoff data treatments were performed as reported [21,51].

General Crystallographic data (excluding structure factors) for the structures in this paper have been deposited in the Cambridge Crystallographic Data Centre as supplementary publication numbers CCDC 1 (1013358), 2 (1013356) and 3 (1013357). A summary of collection and refinement of the X-ray data is listed in Table 5. H atoms were treated as riding atoms, with C–H distances in the range of 0.93–0.96 Å and N–H distances in the range of 0.86–0.88 Å. X-ray diffraction cell refinement and data collection: BRUKER APEX II Diffractometer with Mo radiation (kα, λ = 0.71073 Å) and SAINT [56], programs used to solve structures: SHELXS-97 [57], software used to prepare material for publication: PLATON [58], WinGX [59] and Mercury [60].

Table 5. Collection and refinement X-ray data of compounds 13.
Table 5. Collection and refinement X-ray data of compounds 13.
Compounds123
CCDC number101335810133561013357
FormulaC15H13N1O2C17H15N1O4C28H20N8O4
M (g·mol−1)252.0297.3448.5
Crystal systemMonoclinicMonoclinicMonoclinic
Space groupP nP 21/cP 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 (°)909090
β (°)115.320(2)102.815(1)114.429(4)
γ (°)909090
V (Å3)618.94(7)1478.41(4)1096.6(2)
Z242
ρcalcd. (g·cm−3)1.3241.341.36
μ (mm−1)0.0860.0960.092
F (000)252.0623.9467.9
Crystal size (mm)0.50 × 0.50 × 0.400.36 × 0.30 × 0.280.40 × 0.30 × 0.30
Temp. (K)100 (2)293(2)100(2)
θ range (°)2.2–26.02.2–27.62.3–25.0
Reflections collected6206165959547
Independent reflections241933811930
Data/restraints/parameters2419/2/1633381/0/1991930/0/154
Goof1.1391.2161.148
R (int)0.0300.0290.068
Final R indices [I > 2σ(I)], R1/wR20.035/0.0900.066/0.1500.077/0.142
Largest diff. peak/hole (e·Å−3)0.284/−0.2220.230/−0.2580.201/−0.185

3.2. Synthesis of Compounds

Compounds 13 are known. They were synthetized starting from commercial 2-aminobenzophenone and the corresponding acid chlorides (acetyl chloride (1), monoethyl oxalyl chloride (2) or oxalyl chloride (3)) in equimolar quantities following reported procedures [48]. All of the compounds were crystallized from CHCl3 solutions.

4. Conclusions

The formation of two- and three-center hydrogen bonds in the solid state was demonstrated by the analysis of the geometric parameters associated with the molecular structure by X-ray diffraction. The combined effects of N–H∙∙∙O=CPh, C6–H∙∙∙O=C and N–H∙∙∙O=C interactions form THBs and have a global effect resulting in the flattening of the molecular structure. Thus, the two center intramolecular HB is not allowed in N-(2-benzoylphenyl)acetamide neither in the solid state nor in DMSO-d6 solution, and this effect is attributed to the unfavorable steric effects of o-benzoyl group.

The syn-disposition between the NH and ester carbonyl in ethyl N-(2-benzoylphenyl)oxalamate promotes the alignment of the NH, facilitating the hydrogen bonding engagement with the carbonyl moiety of the benzoyl group in the solid state but not in DMSO solution. Cooperative stabilizing effects are necessary to overcome the steric constraints imposed by the benzoyl group allowing the formation of THB in N1,N2-bis(2-benzoylphenyl)oxalamide in either solid state and in DMSO solution. Extensive intramolecular hydrogen bonding, when at least six adjacent rings [S(6)S(5)S(6)]2 are formed, are required to yield the steric constraints imposed by the benzoyl group in solution, whereas in the solid the formation of intermolecular hydrogen bonding system S(6)S(5)S(6) is sufficient.

Due to the steric restrictions, the effect of the solvent as a test for proton mobility on the NH chemical shift analysis is not accurate. However, the compounds showed intramolecularly hydrogen bonding in chloroform solutions in agreement with the solvent effect observed on the aromatic proton H6 of ca 1.0 ppm.

The estimated Δ and Δ values for the hydrogen bonding disruption in DMSO-d6 are 28.3(0.1) kJ·mol−1 and 69.1(0.4) J·mol−1·K−1 for oxalamide 3, which correlates with the energy of the intramolecular three-center hydrogen bonding in solution demonstrating that it is thermodynamically favored.

The benzoyl group contributes to develop 1-D and 2-D crystal networks, in compounds 2 and 3, built by the concurrence C–H∙∙∙A (A = O, π) and dipolar C=O∙∙∙A (A = CO, π) interactions. In contrast, most ortho-substituted oxalamides are characterized by their lack of supramolecular structure.

Acknowledgments

This work was supported by CONACYT grant 83378, SIP-IPN (Secretaria de Investigación y Postgrado del Instituto Politécnico Nacional), CGIC-UdeC (Coordinación General de Investigación Científíca de la Universidad de Colima).

Author Contributions

(C.Z.G.-C.) Synthesis of compounds and the analysis of NMR data. (I.I.P.-M.) Collection and analysis of NMR data; design and conduction of the study; manuscript writing. (E.V.G.-B.) Collection and resolution of X-ray diffraction data. (J.L.C.-F.) Manuscript writing. (A.L.P.-C.) Crystallization of compounds. (F.J.M.-M.) Synthesis of compounds, analysis of NMR data; design and conduction of the study.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Jeffrey, G.A. Introduction to Hydrogen Bonding; Oxford University Press: New York, NY, USA, 1997. [Google Scholar]
  2. Desiraju, G.R.; Steiner, T. The weak hydrogen bond. In Structural Chemistry and Biology; Monographs on Crystallography, 9th ed.; International Union of Crystallography; Oxford University Press: Oxford, UK, 1999. [Google Scholar]
  3. Levin, S.; Nowick, J.S. A new artificial β-sheet that dimerizes through parallel β-sheet interactions. Org. Lett. 2009, 11, 1003–1006. [Google Scholar] [CrossRef]
  4. Khakshoor, O.; Nowick, J.S. Use of disulfide “staples” to stabilize β-sheet quaternary structure. Org. Lett. 2009, 11, 3000–3003. [Google Scholar] [CrossRef]
  5. Frkanec, L.; Žinić, M. Chiral bis(amino acid)- and bis(amino alcohol)-oxalamide gelators. Gelation properties, self-assembly motifs and chirality effects. Chem. Commun. 2010, 46, 522–537. [Google Scholar]
  6. Preissner, R.; Egner, U.; Saenger, W. Occurrence of bifurcated three-center hydrogen bonds in proteins. FEBS Lett. 1991, 288, 192–196. [Google Scholar] [CrossRef]
  7. Fritsch, V.; Westhof, E. Three-center hydrogen bonds in DNA: Molecular dynamics of poly(dA).cntdot.poly(dT). J. Am. Chem. Soc. 1991, 113, 8271–8277. [Google Scholar]
  8. Liu, A.; Lu, Z.; Wang, J.; Yao, L.; Li, Y.; Yan, H. NMR detection of bifurcated hydrogen bonds in large proteins. J. Am. Chem. Soc. 2008, 130, 2428–2429. [Google Scholar] [CrossRef]
  9. Taylor, R.; Kennard, O.; Versichel, W. Geometry of the nitrogen-hydrogen∙∙∙oxygen-carbon (N–H∙∙∙O=C) hydrogen bond. 2. Three-center (bifurcated) and four-center (trifurcated) bonds. J. Am. Chem. Soc. 1984, 106, 244–248. [Google Scholar]
  10. Jeffrey, G.A.; Maluszynska, H. A survey of the geometry of hydrogen bonds in the crystal structures of barbiturates, purines and pyrimidines. J. Mol. Struct. 1986, 147, 127–142. [Google Scholar] [CrossRef]
  11. Yang, J.; Christianson, L.A.; Gellman, S.H. Comparison of an HXH three-center hydrogen bond with alternative two-center hydrogen bonds in a model system. Org. Lett. 1999, 1, 11–13. [Google Scholar] [CrossRef]
  12. Parra, R.D.; Zeng, H.; Zhu, J.; Zheng, C.; Zeng, X.C.; Gong, B. Stable three-center hydrogen bonding in a partially rigidified structure. Chem. Eur. J. 2001, 7, 4352–4357. [Google Scholar] [CrossRef]
  13. Parra, R.D.; Olsen, J. Cooperativity in intramolecular bifurcated hydrogen bonds: An ab initio study. J. Phys. Chem. 2008, 112, 3492–3498. [Google Scholar] [CrossRef]
  14. Adcock, W.; Graton, J.; Laurence, C.; Luçon, C.; Trout, N. Three-centre hydrogen bonding in the complexes of syn-2,4-difluoroadamantane with 4-fluorophenol and hydrogen fluoride. J. Phys. Org. Chem. 2005, 18, 227–234. [Google Scholar] [CrossRef]
  15. Parra, R.D.; Furukawa, M.; Gong, B.; Zeng, X.C. Energetics and cooperativity in three-center hydrogen bonding interactions. I. Diacetamide-X dimers (X = HCN, CH3OH). J. Chem. Phys. 2001, 115, 6030–6035. [Google Scholar]
  16. Eppel, S.; Bernstein, J. Statistics-based design of multicomponent molecular crystals with the three-center hydrogen bond. Cryst. Growth Des. 2009, 9, 1683–1691. [Google Scholar] [CrossRef]
  17. Rudzevich, Y.; Rudzevich, V.; Schollmeyer, D.; Thondorfc, I.K.; Bohmer, V. Hydrogen bonding in dimers of tritolyl and tritosylurea derivatives of triphenylmethanes. Org. Biomol. Chem. 2006, 4, 3938–3944. [Google Scholar] [CrossRef]
  18. González-González, J.S.; Martínez-Martínez, F.J.; García-Báez, E.V.; Cruz, A.; Morín-Sánchez, L.M.; Rojas-Lima, S.; Padilla-Martínez, I.I. Molecular complexes of diethyl N,N-1,3-phenyldioxalamate and resorcinols: Conformational switching through intramolecular three-centered hydrogen-bonding. Cryst. Growth Des. 2014, 14, 628–642. [Google Scholar]
  19. Fulara, A.; Dzwolak, W. Bifurcated hydrogen bonds stabilize fibrils of poly(l-glutamic) acid. J. Phys. Chem. B 2010, 114, 8278–8283. [Google Scholar] [CrossRef]
  20. Wang, K.; Liu, J.; Yang, K.; Liu, B.; Zou, B. High-pressure-induced reversible phase transition in sulfamide. J. Phys. Chem. C 2014, 118, 18640–18645. [Google Scholar] [CrossRef]
  21. Feng, W.; Yamato, K.; Yang, L.; Ferguson, J.S.; Zhong, L.; Zou, S.; Yuan, L.; Zeng, X.-C.; Gong, B. Efficient kinetic macrocyclization. J. Am. Chem. Soc. 2009, 131, 2629–263. [Google Scholar] [CrossRef]
  22. Li, X.; Fang, Y.; Deng, P.; Hu, J.; Li, T.; Feng, W.; Yuan, L. Self-complementary quadruply hydrogen-bonded duplexes based on imide and urea units. Org. Lett. 2011, 13, 4628–4631. [Google Scholar] [CrossRef]
  23. Parra, R.D.; Streu, K. Cooperative effects in regular and bifurcated intramolecular OH∙∙∙O=C interactions: A computational study. Comput. Theor. Chem. 2011, 977, 181–187. [Google Scholar] [CrossRef]
  24. Gómez-Castro, C.Z.; Padilla-Martínez, I.I.; Martínez-Martínez, F.J.; García-Báez, E.V. Thermodynamic characterization of three centered hydrogen bond using o-aromatic amides, oxalamates and bis-oxalamides as model compounds. ARKIVOC 2008, 227, 244. [Google Scholar]
  25. Swann, S.L.; Song, D.; Sun, C.; Hajduk, P.J.; Petros, A.M. Labeled ligand displacement: Extending NMR-based screening of protein targets. ACS Med. Chem. Lett. 2010, 1, 295–299. [Google Scholar] [CrossRef]
  26. Patterson, S.; Alphey, M.S.; Jones, D.C.; Shanks, E.J.; Street, I.P.; Frearson, J.A.; Wyatt, P.G.; Gilbert, I.H.; Fairlamb, A.H. Dihydroquinazolines as a novel class of trypanosoma brucei trypanothione reductase inhibitors: Discovery, synthesis, and characterization of their binding mode by protein crystallography. J. Med. Chem. 2011, 54, 6514–6530. [Google Scholar] [CrossRef]
  27. Sayed, A.A. An efficient synthesis of 4-phenyl-2-aminoquinolines. Synth. Comm. 1991, 21, 749–756. [Google Scholar] [CrossRef]
  28. Fuerstner, A.; Jumbam, D.N. Titanium-induced syntheses of furans, benzofurans and indoles. Tetrahedron 1992, 48, 5991–6010. [Google Scholar] [CrossRef]
  29. Fan, X.; Zhang, Y. SmI2 mediated synthesis of 2,3-disubstituted indole derivatives. Tetrahedron 2003, 59, 1917–1923. [Google Scholar] [CrossRef]
  30. Fan, X.; Zhang, X. Facile preparation of 2,3-disubstituted indole derivatives through low-valent titanium induced intramolecular reductive coupling reactions of acylamid. J. Chem. Res. Synopses 2003, 11, 696–697. [Google Scholar] [CrossRef]
  31. Park, K.K.; Lee, J.J. Facile synthesis of 4-phenylquinolin-2(1H)-one derivatives from N-acyl-o-aminobenzophenones. Tetrahedron 2004, 60, 2993–2999. [Google Scholar] [CrossRef]
  32. Dulenko, V.I.; Alekseev, N.N.; Golyak, V.M.; Nikolyukin, Y.A. 4-Aza-2-benzopyrylium salts. Chem. Heterocycl. Compd. 1976, 12, 1067. [Google Scholar] [CrossRef]
  33. Dannhardt, G.; Fiebich, B.L.; Schweppenhauser, J. COX-1/COX-2 inhibitors based on the methanone moiety. Eur. J. Med. Chem. 2002, 37, 147–161. [Google Scholar] [CrossRef]
  34. Fuerstner, A.; Ptock, A.; Weintritt, H.; Goddard, R.; Krueger, C. Titanium-induced zipper reactions. Angew. Chem. Int. Ed. Engl. 1995, 34, 678–681. [Google Scholar] [CrossRef]
  35. Fuerstner, A.; Hupperts, A.; Seidel, G. Ethyl 5-chloro-3-phenylindole-2-carboxylate. Org. Synth. 1999, 76, 142–150. [Google Scholar] [CrossRef]
  36. Zhang, Y.-H.; Wang, Q.-L.; Yang, G.-M. Synthesis, crystal structures and spectroscopic properties of two novel oxamido-bridged trinuclear complexes [Cu2M] (M = Cu, Zn). Transit. Metal. Chem. 2006, 31, 856–859. [Google Scholar] [CrossRef]
  37. Zhang, Y.-H.; Yu, M.; Wang, Q.-L.; Xu, G.-F.; Hu, M.; Yang, G.-M.; Liao, D.-Z. A macrocyclic oxamido vanadium(IV)-oxo ligand and its derivative VOIV 2MII (M = Cu, Mn) trinuclear complexes: Synthesis, structures and magnetic properties. Polyhedron 2008, 27, 3371–3376. [Google Scholar] [CrossRef]
  38. Black, D.S.C.; Vanderzalm, C.H.B.; Wong, L.C.H. Metal template reactions. XIV. Synthesis of macrocyclic metal complexes from 2,2'-(oxalyldiimino)bisbenzaldehyde and related oxamido aldehydes and ketones. Aust. J. Chem. 1982, 35, 2435–2443. [Google Scholar]
  39. Brown, C.J.; Cobridge, D.E. The crystal structure of acetanilide. Acta Crystallogr. 1954, 7, 711–715. [Google Scholar] [CrossRef]
  40. Brown, C.J. Further refinement of the crystal structure of acetanilide. Acta Crystallogr. 1966, 21, 442–445. [Google Scholar] [CrossRef]
  41. Wasserman, H.J.; Ryan, R.R.; Layne, S.P. Structure of acetanilide (C8H9NO) at 113 K. Acta Crystallogr. Sect. C: Cryst. Struct. Commun. 1985, 41, 783–785. [Google Scholar]
  42. Slater, H.L.; Rozynski, H.; Crundwell, G.; Glagovich, N.M. N-(2-Acetylphenyl)acetamide. Acta Crystallogr. Sect. E: Struct. Rep. 2006, 62, o1957–o1958. [Google Scholar]
  43. Brewer, G.A.; Jasinski, J.P.; Butcher, R.J.; Scheidt, W.R. N,N'-Bis(2-acetylphenyl)ethanediamide, a second polymorph. Acta Crystallogr. Sect. E: Struct. Rep. 2007, 63, o4889. [Google Scholar]
  44. Brewer, G.A.; Jasinski, J.P.; Butcher, R.J.; Scheidt, W.R. N,N'-Bis(2-acetylphenyl)ethanediamide. Acta Crystallogr. Sect. E: Struct. Rep. 2007, 63, o4887–o4888. [Google Scholar]
  45. Dewar, M.J.S.; Schmeizing, H.N. Resonance and conjugation—II. Factors determining bond lengths and heats of formation. Tetrahedron 1968, 11, 96–120. [Google Scholar]
  46. Dugave, C.; Demange, L. Cis-trans isomerization of organic molecules and biomolecules: Implications and applications. Chem. Rev. 2003, 103, 2475–2532. [Google Scholar] [CrossRef]
  47. Bernstein, J.; Davis, R.E.; Shimoni, L.; Chang, N.-L. Patterns in hydrogen bonding: Functionality and graph set analysis in crystals. Angew. Chem. Int. Ed. Engl. 1995, 34, 1555–1573. [Google Scholar] [CrossRef]
  48. Martínez-Martínez, F.J.; Padilla-Martínez, I.I.; Brito, M.A.; Geniz, E.D.; Rojas, R.C.; Saavedra, J.B.; Höpfl, H.; Tlahuextl, M.; Contreras, R. Three-center intramolecular hydrogen bonding in oxamide derivatives. NMR and X-ray diffraction study. J. Chem. Soc. Perkin Trans. 2 1998, 2, 401–406. [Google Scholar]
  49. Padilla-Martínez, I.I.; Martínez-Martínez, F.J.; García-Báez, E.V.; Torres-Valencia, J.M.; Rojas-Lima, S.; Höpfl, H. Further insight into three center hydrogen bonding. Participation in tautomeric equilibria of heterocyclic amides. J. Chem. Soc. Perkin Trans. 2 2001, 9, 1817–1823. [Google Scholar]
  50. Nishio, M. CH/π Hydrogen bonds in crystals. CrystEngComm 2004, 6, 130–158. [Google Scholar] [CrossRef]
  51. Allen, F.H.; Baalham, C.A.; Lommerse, J.P.M.; Raithby, P.R. Carbonyl-carbonyl interactions can be competitive with hydrogen bonds. Acta Crystallogr. Sect. B: Struct. Sci. 1998, 54, 320–329. [Google Scholar]
  52. Hibbert, F.; Mills, J.F.; Nyburg, S.C.; Parkins, A.W. Hydrogen bonding and structure of 2-hydroxy-N-acylanilines in the solid state and in solution. J. Chem. Soc. Perkin Trans. 2 1998, 3, 629–634. [Google Scholar] [CrossRef]
  53. Parra, R.D.; Gong, B.; Zeng, X.C. Energetics and cooperativity in three-center hydrogen bonding interactions. II. Intramolecular hydrogen bonding systems. J. Chem. Phys. 2001, 115, 6036–6041. [Google Scholar]
  54. Kessler, H. Conformation and biological activity of cyclic peptides. Angew. Chem. Int. Ed. 1982, 21, 512–523. [Google Scholar] [CrossRef]
  55. Llor, J.; Muñoz, L. Tautomeric equilibrium of pyridoxine in water. Thermodynamic characterization by 13C and 15N Nuclear Magnetic Resonance. J. Org. Chem. 2000, 65, 2716–2722. [Google Scholar]
  56. Bruker. APEX II, SAINT, SADABS and SHELXTL; Bruker AXS Inc: Madison, WI, USA, 2004. [Google Scholar]
  57. Sheldrick, G.M. SHELXS97 and SHELXL97; University of Göttingen: Göttingen, Germany, 1997. [Google Scholar]
  58. Spek, A.L. PLATON, Version of March 2002; University of Utrecht: Heidelberglaan, The Netherlands, 2002. [Google Scholar]
  59. Farrugia, L.J. WinGX suite for small molecule single crystal crystallography. J. Appl. Crystallogr. 1999, 32, 837–838. [Google Scholar] [CrossRef]
  60. Macrae, C.F.; Edgington, P.R.; McCabe, P.; Pidcock, E.; Shields, G.P.; Taylor, R.; Towler, M.; van de Streek, J. Mercury: Visualization and analysis of crystal structures. J. Appl. Crystallogr. 2006, 39, 453–457. [Google Scholar] [CrossRef]
  • Sample Availability: Samples of the compounds 13 are available from the authors.
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