A small library of C–H⋯O hydrogen bonds based on supramolecular architectures of 1,5-diketone malonates in the solid state

2.1 Preparation, isolation, and crystallization

1,5-diketone malonates 1a-g were synthesized according to the procedure previously described. (Jiménez-Cruz et al., 1998, 2000) It consists of the C-aroylation of the dimethyl malonate anion (NaH in THF) with the corresponding aroyl chlorides to produce an aroylmalonate. Chemical reagents and solvents were provided by Sigma Aldrich and were used as received. Then, the Michael type addition of the aroylmalonates to methyl vinyl ketone using Triton B or Et₃N in THF affording the 1,5-diketones malonates. ¹H and ¹³C NMR for the unreported 1,5 diketones 1e-g are described here, which were recorded in a Varian Unity Spectrometer at 300 MHz for proton and 75.4 MHz for carbon. The ¹H NMR chemical shifts are expressed in ppm relatives to tetramethylsilane (TMS), and the ¹³C NMR chemical shifts were referenced with the triplet of CDCl₃ (δ = 77 ppm). NMR results and the corresponding spectra are shown in the supplementary section (Figures S1-S6). The characterization for 1a–d was reported elsewhere. (Jiménez-Cruz et al., 1998, 2000) Crystals were grown from 2:1 ethanol–water solutions by slow evaporation for all 1,5-diketone malonates 1a-g.

2.2 X-ray structural determination

The X-ray data for the single crystal of 1,5-diketone dimethyl malonates 1a and 1c-g were collected at 293 K using graphite-monochromated Mo Kα radiation (λ = 0.71073 Å) on a Siemens P4/PC diffractometer. The data collection, (Siemens, 1994) cell refinement and data reduction were carried out using XSCANS. The structure was solved with direct methods and refined by full-matrix least-square methods based on F² using SHELXS97 and SHELXL97 packages. (Sheldrick, 1997, 2008) In addition, 1,5-diketone dimethyl malonate 1b was performed with Cu Kα radiation (λ = 1.54178 Å) at 293 K on a Nicolet P3/F diffractometer; and cell refinement and data reduction were performed with Nicolet P3 Software 1980.

3.1 X-ray crystallographic data for 1,5-diketone malonates 1 a-g

Data for 1,5-diketone malonates 1a-g are shown in Table 1, and geometry parameters such as bond lengths and angles are depicted in Table S1 (Supplementary information).

Crystals suitable for X-ray diffraction were obtained from 1,5-diketone malonates 1a-g; their structural parameters are shown in Table 1. The structure of the compounds 1a-g; is formed by 1,5-diketone and dimethyl malonate, also with substituent groups linked at C1: phenyl, 1,1′-biphenyl, 4-methoxyphenyl, 4-bromophenyl, 1-adamantyl, l-naphthyl and 2-naphthyl, for 1a, 1b, 1c, 1d, 1e, 1f and 1 g, respectively. Fig. 3 shows a drawing displacement ellipsoids of 1,5-diketone malonates 1a-g.

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Fig. 3

View of compounds 1a-g, the displacement ellipsoids are drawn at the 50 % probability level.

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3.2 Structural hierarchy of the small library of hydrogen bonds based on supramolecular architectures of 1,5-diketone malonates 1a-g

From the results obtained on the crystalline structure of these compounds, a structural hierarchy is proposed that allows exploring and tracing a possible route of the elements that constituted their crystallization mechanism leading to the construction of a small library of hydrogen bonds exclusively by C–H⋯O interactions. The crystal structure of the 1,5-diketone malonates 1a-g was analyzed according to the strategy steps: a) Intramolecular hydrogen bonds, b) Intermolecular hydrogen bonds in synthons and macrocycles, and c) Supramolecular architectures.

The strategic sequence of steps for the hierarchy that helps assess the supramolecular architecture in the titled 1,5-diketones is described below.

3.2.1

3.2.1 Intramolecular hydrogen bonds in monomer molecular structure of 1,5-diketones 1a-g

The first approach is to analyze the presence of intramolecular hydrogen bonds observed in the monomer molecular structure of 1,5-diketones 1a-g. Regarding Fig. 4, these bonds generate the kite conformation of each compound and the quasi-perpendicular conformation between the two molecular fragments that constitute the molecule. Thus, the 1,5-diketones and dimethyl malonate moieties resemble two perpendicular molecular axes with a total angle between planes near φ = 90° for the seven molecular structures: the angle between planes(φ) is 90.223, 89.016,90.330, 87.652, 89.845, 93.930 and 89.175° for 1a, 1b, 1c, 1d, 1e, 1f and 1 g, respectively.

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Fig. 4

Intramolecular hydrogen bonds in molecular structures of compounds 1a-g (blue dashed lines) and inspired kite conformation morphology.

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The compounds 1a-g have an average of seven intramolecular hydrogen bonds formed from the carbonyl group of the 1,5-diketones and the functional group –COO in the malonate with the -C–H of the molecule. As a result of this interaction, compounds 1a-g have a kite-like topology given the two perpendicular molecular axes, which are constituted on average by the seven intramolecular hydrogen bonds indicated by blue dashed lines between molecular planes, Fig. 4. Remarkably, C–H⋯O hydrogen bond interactions are key to supporting the kite conformation. Tables 2 show the intramolecular hydrogen bonds in the molecular structure of 1a-g compounds.

Table 2 Distances (Å) and angles (°) of intramolecular hydrogen bonds in the structure of compounds 1a-g, calculated with PLATON (Spek, 2020).

Compound 1a
D─H┄A	H┄A	D┄A	∠D─H┄A
C3─H3A┄O1	2.52(3)	2.851(3)	99.4(17)
C3─H3B┄O5	2.64(3)	2.967(4)	100(2)
C4─H4A┄O2	3.09(3)	3.556(4)	113(2)
C4─H4B┄O6	2.72(3)	3.277(4)	118(2)
C9─H9┄O4	2.42(3)	2.771(4)	102(2)
C13─H13┄O2	2.57(3)	3.325(4)	138(3)
C13─H13┄O6	2.98(3)	3.708(4)	135(2)

Compound 1b
D─H┄A	H┄A	D┄A	∠D─H┄A
C3─H3A┄O2	2.92	3.137(3)	94
C3─H3B┄O6	2.58	2.904(3)	100
C4─H4A┄O5	2.84	3.500(4)	126
C4─H4B┄O1	2.71	3.126(5)	107
C8─H8┄O4	2.44	2.758(4)	100
C12─H12┄O1	3.25	3.966(3)	135
C12─H12┄O5	2.74	3.495(4)	138

Compound 1c
D─H┄A	H┄A	D┄A	∠D─H┄A
C3─H3A┄O2	2.56	2.838(4)	97
C3─H3B┄O6	2.99	3.213(4)	94
C4─H4A┄O5	2.52	3.089(3)	118
C4─H4B┄O1	2.94	3.525(3)	120
C9─H9┄O4	2.51	2.790(4)	98
C13─H13┄O1	2.72	3.362(4)	127
C13─H13┄O5	3.18	3.968(4)	144

Compound 1d
D─H┄A	H┄A	D┄A	∠D─H┄A
C3─H3A┄O6	2.92	3.181(6)	96
C3─H3B┄O2	2.56	2.795(6)	94
C4─H4A┄O1	3.09	3.554(6)	111
C4─H4B┄O5	2.56	3.187(6)	123
C9─H9┄O4	2.45	2.744(7)	99
C13─H13┄O1	2.66	3.346(7)	131
C13─H13┄O5	3.19	3.957(7)	141

Compound 1e
D─H┄A	H┄A	D┄A	∠D─H┄A
C9─H9A┄O2	3.13	3.825(5)	130
C9─H9B┄O6	2.87	3.584(5)	131
C9─H9A┄O1	2.71	3.347(5)	123
C9─H9B┄O5	2.71	3.364(5)	125
C15─H15A┄O5	2.61	3.287(5)	127
C15─H15B┄O4	2.57	2.878(5)	98
C16─H16A┄O4	2.63	2.926(5)	98

Compound 1f
D─H┄A	H┄A	D┄A	∠D─H┄A
C3─H3A┄O5	3.01	3.218(3)	93
C3─H3B┄O1	2.64	2.927(3)	97
C4─H4A┄O2	2.97	3.492(3)	115
C4─H4B┄O6	2.52	3.111(3)	119
C8─H8┄O4	2.42	2.740(3)	100
C10─H10┄O2	2.90	3.609(3)	134
C10─H10┄O6	3.25	3.999(3)	139

Compound 1g
D─H┄A	H┄A	D┄A	∠D─H┄A
C3─H3A┄O1	3.25	3.383(3)	90
C3─H3B┄O5	2.63	2.887(2)	96
C4─H4A┄O6	2.95	3.513(3)	118
C4─H4B┄O2	2.41	3.016(3)	120
C9─H9┄O1	2.67	3.138(3)	112
C9─H9┄O6	2.74	3.378(3)	126
C15─H15┄O4	2.31	2.868(3)	118
C3─H3A┄O1	3.25	3.383(3)	90

3.2.2

3.2.2 Dimers based on synthons and macrocycles by intermolecular hydrogen bonds of 1,5-diketones 1a-g

Hierarchical analysis of the supramolecular structure of 1,5-diketone dimers 1a-g was performed from a synthon and macrocycle approach. A synthon is defined as a representative structural unit that links molecules and crystals and is implicated in all the stages through which molecules progress as they form crystals. (Desiraju, 2013, 1995, 2003) On another side, the motifs generated from intermolecular hydrogen bonds are defined as a type of graph set, such as C (chain), R (ring), D (dimer), and S denotes an intramolecular hydrogen bond. Additionally, the number of donors (d) and acceptors (a) used in motifs are assigned as subscripts and superscripts. In contrast, the size of the motif corresponding to the number of atoms in the repeat unit is indicated in parentheses. (Etter, 1990).

By applying the former concepts, the dimeric structure of compound 1a is formed by the C12-H12┄O4 interaction (Fig. 5), which is a simple hydrogen bond due to the donor interacting with an acceptor. However, because of the long-range hydrogen bonding, a donor may interact with more than one acceptor simultaneously. Also, the 1a dimeric structure presents a bifurcated arrangement of hydrogen bonds (Steiner, 2002) constituted by the C10-H10 donor and the O2 and O6 acceptors. The dimer formed a 16-atom ring with three acceptors and two donors: ${\mathit{R}}_2^3(16)$ . Table 3 shows the distance (Å) and the angle (°) of the intermolecular hydrogen bonds in the structure of dimeric structure 1a.

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Fig. 5

Crystal structure of dimers formed by two supramolecular synthons through the two hydrogen bonds in diketone malonates 1a-g.

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Fig. 5

Crystal structure of dimers formed by two supramolecular synthons through the two hydrogen bonds in diketone malonates 1a-g.

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Table 3 Distances (Å) and angles (°) of intermolecular hydrogen bonds in the structure of compounds 1a-g, calculated with PLATON, (Spek, 2020).

Compound 1a
D─H┄A	H┄A	D┄A	∠D─H┄A
C10─H10┄O2	2.69(3)	3.347(4)	131.6(18)
C10─H10┄O6	2.77(3)	3.586(4)	152.2(19)
C12─H12┄O4	2.63(3)	3.634(4)	174.9(16)

Compound 1b
D─H┄A	H┄A	D┄A	∠D─H┄A
C22─H22┄O5	2.77	3.690(5)	170
C9─H9┄O1	2.41	3.221(4)	145
C6─H6C┄O4	3.01	3.802(8)	140

Compound 1c
D─H┄A	H┄A	D┄A	∠D─H┄A
C10─H10┄O7	2.94	3.480(4)	118

Compound 1d
D─H┄A	H┄A	D┄A	∠D─H┄A
C9─H9┄O4	2.38	3.280(6)	164
C16─H16C┄O1	2.96	3.754(6)	140

Compound 1e
D─H┄A	H┄A	D┄A	∠D─H┄A
C3─H3B┄O5	2.71	3.513(5)	140
C11─H11B┄O2	2.99	3.779(5)	139
C9─H9A┄O6	2.69	3.464(5)	137
C19─H19C┄O2	2.47	3.260(5)	140

Compound 1f
D─H┄A	H┄A	D┄A	∠D─H┄A
C8─H8┄O4	2.59	3.449(3)	154
C14─H14┄O3	2.62	3.431(3)	146
C20─H20B┄O5	2.81	3.485(3)	128
C19─H19B┄O1	2.75	3.598(4)	148

Compound 1g
D─H┄A	H┄A	D┄A	∠D─H┄A
C19─H19B┄O1	2.77	3.601(3)	145
C9─H9┄O6	2.94	3.561(3)	125
C13─H13┄O3	2.61	3.285(3)	130
C11─H11┄O4	2.86	3.678(3)	148

For structure 1b, the supramolecular dimer is formed by three simple intermolecular hydrogen bonds: C6─H6C┄O4, C9─H9┄O1 and C22─H22┄O5. The dimer formed a 20-atom ring with three acceptors and three donors: ${\mathit{R}}_3^3\left(20\right)$ , Fig. 5. Table 3 presents the distance (Å) and angle (°) of the intermolecular hydrogen bonds in structure 1b; the values of distances and bond angles are like those described in the literature. (Sutor,1962, 1963, Steiner, 2002).

The dimeric compound 1c is formed by the interaction C10─H10┄O7. This compound is an example of the role of hydrogen bonds in molecular recognition patterns by structural units called supramolecular synthons, Fig. 5. The synthon constitutes a dimer, an 8-atom ring, with two acceptors and two donors: ${\mathit{R}}_2^2(8)$ . Table 3 presents the distance (Å) and angle (°) of intermolecular hydrogen bonds in the structure of compound 1c. The compound 1d has two dimers formed by two supramolecular synthons through C9─H9┄O4 and C16─H16C┄O1 interactions, Fig. 5. Each of the dimers 1d(a) and 1d(b) formed a 10-atom ring with two acceptors and two donors, ${\mathit{R}}_2^2\left(10\right)$ and ${\mathit{R}}_2^2\left(14\right),$ respectively. Table 3 presents the distance (Å) and angle (°) of the intermolecular hydrogen bonds in compound 1d.

The molecular structure of dimer 1e(a) is formed by the structural unit C3─H3B┄O5, a 10-atom ring with two acceptors and two donors: ${\mathit{R}}_2^2(10)$ . A supramolecular dimer is present in the crystal structure of 1e(b), constituted by three acceptors and three donors: ${\mathit{R}}_3^3\left(16\right),$ a ring with sixteen members. Table 3 presents the distance (Å) and angle (°) of intermolecular hydrogen bonds in the structure of compound 1e.

The molecular structure of 1f(a) has a particular dimer formed by two supramolecular synthons through C8─H8┄O4 and C14─H14┄O3 interactions, with a synthon inside the other. This dimer is formed of two rings, one with 10 atoms and the other with 24 atoms, with two acceptors and two donors in each ring: ${\mathit{R}}_2^2\left(10\right)\mathrm{a}\mathrm{n}\mathrm{d}{\mathit{R}}_2^2\left(24\right),$ respectively; furthermore, two small 1f(b) synthons, each which with a 6-atoms ring $({2\mathit{R}}_2^2\left(6\right))$ by C19─H19B┄O1 and C20─H20B┄O5 interactions are observed. The dimeric compound 1 g(a) with a supramolecular synthon shows the C19─H19B┄O1 interaction, forming a 6-membered ring with two acceptors and two donors: ${\mathit{R}}_2^2\left(6\right)$ , Fig. 5.

The second supramolecular structural unit 1 g(b) is formed by the C9─H9┄O6 interaction that assembles two molecules, the synthon formed by a 14-atom ring with two acceptors and two donors: ${\mathit{R}}_2^2\left(14\right).\mathrm{F}\mathrm{i}\mathrm{n}\mathrm{a}\mathrm{l}\mathrm{l}\mathrm{y},\mathrm{t}$ he third supramolecular structure, 1 g(c), corresponds to a macrocycle with C13─H13┄O3 and C11─H11┄O4 interactions. These interactions comprise a 13-membered ring with two acceptors and two donors: ${\mathit{R}}_2^2(13)$ . Table 3 presents the distance (Å) and angle (°) of intermolecular hydrogen bonds in the structure 1 g.

3.3 Hirshfeld surface analysis of 1,5-diketones

Hirshfeld surface analysis (Wolff et al., 2012) was performed to quantify and visualize the close intermolecular atomic contacts in the crystal structure and the associated fingerprint plots of the molecule showing the significant contributions of the different intermolecular interactions on the Hirshfeld surface. (Spackman & Jayatilaka, 2009) These results show the importance of the intramolecular and the intermolecular C–H⋯O hydrogen-bonds non-covalent interaction in the primary kite-like conformation and the dimer motifs for the 1,5-diketone malonates can be highlighted.

Remarkably H⋯O inside and outside interactions are depicted in the fingerprint plots of the 1,5-diketones 1a–g, Fig. 6. It is noticeable that inside interactions are slightly greater than outside contributions, the first mainly attributed to the carbonyl group of the 1,5-diketones and the functional group –COO in the malonate to the -C–H of the molecule by supporting the kite-like topology. In addition, outside contributions represent C–H⋯O hydrogen bond interactions with intermolecular hydrogen bonds (dimers, synthons and macrocycles). Fig. 7 describs the Hirshfeld surfaces for the diketones, enhancing the inside interactions, Fig. 8 shows the surfaces for dimers synthons.

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Fig. 6

O–H Atom-atom interactions and their contribution to the Hirshfeld fingerprint plot for 1,5-diketones 1a – g.

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Fig. 6

O–H Atom-atom interactions and their contribution to the Hirshfeld fingerprint plot for 1,5-diketones 1a – g.

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Fig. 7

The Hirshfeld surface of 1,5-diketones 1a – g mapped with dnorm.

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Fig. 8

The Hirshfeld surface of 1,5-diketones 1a–g of dimers synthons and macrocycles.

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3.4 Supramolecular architectures

Highlighting the importance of intramolecular c–h⋯o hydrogen bonds in the primary kite-like conformation, the intermolecular C–H⋯O hydrogen bond interactions in dimer motifs for the 1,5-diketone malonates are also important non-covalent interaction at different levels of hierarchy in crystal engineering. (Sutor, 1963, Desiraju, 2003) a small library of supramolecular architectures in diketones 1a-g can be described in the crystal structures in conjunction with the cooperative C–H⋯O hydrogen bonds, Fig. 9.ing the importance of intramolecular C–H⋯O hydrogen bonds in the primary kite-like conformation, the intermolecular C–H⋯O hydrogen bond interactions in dimer motifs for the 1,5-diketone malonates are also important non-covalent interaction at different levels of hierarchy in crystal engineering. (Sutor, 1963, Desiraju, 2003) A small library of supramolecular architectures in diketones 1a-g can be described in the crystal structures in conjunction with the cooperative C–H⋯O hydrogen bonds, Fig. 9.

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Fig. 9

Supramolecular structures through hydrogen bonds of 1,5-diketones 1a-g.

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According to Fig. 9, the motif dimers 1a and 1b with intermolecular hydrogen bonds show a supramolecular chain through 6 hydrogen bond interactions C(6) represented by stick model topology, $\mathbf{C}(6){\mathit{R}}_2^3(16)$ for 1a and $\mathbf{C}(6){\mathit{R}}_3^3(20)$ for 1b. The 1c supramolecular synthon shows a two-dimensional supramolecular structure with three interactions. The 1c synthon is represented by two series of molecules in parallel using the sticks model, ${\mathit{R}}_2^2(8)$ . The compound 1d, with two dimers, generated a supramolecular structure with four C(4) interactions represented by the sticks model, ${\mathbf{C}(4)\mathit{R}}_2^2(10){\mathit{R}}_2^2(14)$ .

The supramolecular structure (with adamantyl moiety) of 1e has a macrocycle in conjunction with the supramolecular synthon. This structural unit has 4 molecules that form a 1D zigzag supramolecular structure with five interactions each, ${\mathit{R}}_2^2\left(10\right),{\mathit{R}}_3^3(16)$ .

For compound 1f, the three synthons generated a 3D supramolecular structure with four interactions represented by the sticks model, ${\mathit{R}}_2^2\left(10\right),{\mathit{R}}_2^2(24){,\mathit{R}}_2^2(6)$ . In the case of 1 g, ${\mathit{R}}_2^2\left(6\right){,\mathit{R}}_2^2\left(14\right),{\mathit{R}}_2^2(13)$ , the interaction of four stick motifs is notable.

CRediT authorship contribution statement

Domingo Salazar-Mendoza: Conceptualization. José Luis García-Gutiérrez: Investigation. Federico Jiménez-Cruz: Conceptualization, Writing – original draft.