Julio A. Seijas*,
José Crecente-Campo,
Xesús Feás and
M. Pilar Vázquez-Tato*
Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Santiago de Compostela, Aptdo. 27080, Lugo, Spain. E-mail: julioa.seijas@usc.es; pilar.vazquez.tato@usc.es
First published on 28th March 2014
A novel, fast and efficient method for the synthesis of (3E)-3-(1-aminoethylidene)-6-methyl-3,4-dihydro-2H-pyran-2,4-dione, a natural antiproliferative and cytotoxic product isolated from Fusarium incarnatum (HKI0504), was developed from dehydroacetic acid and urea under solvent-free microwave irradiation. The analysis of the co-crystal structure revealed an asymmetric unit formed by a pair of molecules. Each molecule is joined by two different hydrogen bonds to another two molecules, ordered as four-unit clusters linked by π-stacking, assembled in a brick like layered structure in a set of parallel walls. Besides, the preferred tautomer for crystal structure is the enamine form. This is corroborated by computational NBO analysis, outlining the contribution of enamine resonance and modelling the non-covalent interactions involved by means of Hirshfeld surfaces and G09 counterpoise calculations.
Recently, [(3E-3-(1-aminoethylidene)-6-methyl-3,4-dihydro-2H-pyran-2,4-dione)] (1) has been identified as a natural product which was isolated from the culture broth of Fusarium incarnatum (HKI0504), an endophytic fungus of the mangrove plant Aegiceras corniculatum.2 It showed antiproliferative activity against human umbilical vein endothelial cells (HUVEC), K562 human chronic myeloid leukemia cells (DSM ACC 10) and cytotoxicity against HeLa human cervix carcinoma (DSM ACC 57) cell lines. This endophyte also has been identified as a novel producer of laccase with potential in bioremediation of bisphenol A.3
Compound 1 is an enamine derivative of dehydroacetic acid, (3-acetyl-4-hydroxy-6-methyl-2H-pyran-2-one, 2). Dehydroacetic acid acts as complexing ligand and possesses interesting biological properties such as fungicide and antibacterial activities.4 Its sodium salt is recognized by Food and Agriculture Organization (FAO) and the World Health Organization (WHO) as a safe food preservative, since it has a relatively broad spectrum of antibacterial activity against food-borne pathogens and spoilage organisms. Its enamine derivatives have also been object of wide studies, because of their different biological activities and ability to act as ligands in transition metal complexes.5
The crystallization of the synthetized compound 1 from methanol, rendered a crystal whose structure was resolved resulting in a non-merohedral twin with the twin components related by a 180.0 degree rotation about the [1 0 0] axis. TWINABS was used to apply post-collection corrections. Both twin components were employed in corrections and overlaps in addition to the two components were included in the reflection file. An extra parameter was included on the refinement to properly calculate the twin ratio 0.58(2)/0.42(2). Asymmetric unit (AU, Fig. 2) has two components with slightly different geometries (Table 1).
Molecule II | Å | Molecule I | Å [% II to I] |
---|---|---|---|
O1–C6 | 1.377(6) | O1B–C6B | 1.360 (6) [101.3] |
C3–C30 | 1.420 (7) | C3B–C30B | 1.430 (7) [101.0] |
C3–C4 | 1.448(6) | C3B–C4B | 1.426 (7) [101.5] |
C30–N31 | 1.308 (7) | C30B–N31B | 1.312 (6) [100.3] |
C30–C32 | 1.488 (7) | C30B–C32B | 1.490 (7) [100.1] |
The analysis of the co-crystal10 confirms that the structure of both components in solid state correspond to enamine (1) rather than to imine (3) which agrees with previous studies carried out on this kind of compounds.11 The two molecules in AU are bonded through π-stacking interaction. The value of this interaction (14.18 kcal mol−1) was calculated with Gaussian 09 (MP2/6-311++G(2d,2p) method) with counterpoise correction,12 using the coordinates determined from the co-crystal.
Each molecule of the AU has also π-stacking with a molecule (II′) in the upper face and with another (I′) in the bottom (Fig. 3). The calculated energies for these interactions were 15.01 and 14.93 kcal mol−1 respectively.
Fig. 3 Molecules I and II are inside AU. Molecules I′ (−1 + x, y, z) and II' (1 + x, y, z) belong to different AU's. |
In order to study the slight variation between the two components of the AU, the energy of these molecules was calculated separately (B3LYP/6-311++G(2d,2p)). For one component of the pair (Fig. 3, molecule I) the Hartree–Fock energy was −590.8085 a.u. with a dipole moment of 1.87 D. The other component of the asymmetric unit (Fig. 3, molecule II) rendered HF = −590.8079 a.u. and a dipole moment of 2.00 D. The difference of energy between both is negligible (0.348 kcal mol−1).
Analysis of the co-crystal shows that each molecule is part of a four-molecule cluster joined by hydrogen bonds. Since enamine 1 contains one donor and two different acceptors of hydrogen (Fig. 4a), three types of hydrogen bonding are observed (Fig. 4b): (i) intramolecular bonds N31B⋯O40B and N31⋯O40 (corresponding to molecules II and I respectively), (ii) intermolecular between the amino and the ketone group N31⋯O40B and (iii) intermolecular between the amino group and the lactone N31B⋯O20. The values for intermolecular hydrogen bonds (Table 2), fall inside the category of moderate mostly electrostatic of hydrogen bonds with donor–acceptor as defined by Jeffrey.13
Fig. 4 (a) Acceptor and donor sites in compound 1, (b) (i) intra- and (ii–iii) inter-molecular hydrogen bonds present in four molecules-cluster. |
The calculated total interaction energy of this cluster (MP2/6-311++G(2d,2p)) was 35.49 kcal mol−1 (i.e. 8.87 kcal mol−1 per each pair of molecules). The different types of intermolecular hydrogen bond were studied separately. A couple of molecules joined by COlactone–hydrogen present an interaction of 7.997 kcal mol−1, meanwhile for COketone–hydrogen is 6.568 kcal mol−1. The sum of these energies indicates an additional stabilization of 6.640 kcal mol−1 when the four molecules cluster is considered.
Note that these four molecules have their rings in the same plane and these small clusters are arranged as bricks in a wall, besides all the clusters in a tier have their atoms in the same plane. Thus, two bricks in a tier are bounded by π-stacking (mortar) to one brick (four-molecule cluster) in the upper tier (Fig. 5a), building the wall (Fig. 5b). A plane is separated 3.321 Å from the next parallel plane in the same wall. Planes in vicinal walls are deviated 1.129 Å (Fig. 5c), and the tiers share planes each three walls, showed with a dotted line in Fig. 5d, where is also shown the orientation of the clusters walls inside BFDH predicted morphology of the co-crystal.
The Hirshfeld surface is defined in a crystal as that region around a molecule where the molecule contribution to the crystal electron density exceeds that from all other molecules in the crystal. It allows analyzing how molecules interact with their direct environment.14
When the cluster of four molecules is represented by their corresponding Hirshfeld surfaces with electrostatic potential mapped on it,15 the interactions among them are clearly shown as complimentary, those individual surfaces can be integrated in a four molecules common surface (Fig. 6a and b), being its arrangement in a wall as bricks (Fig. 6c). Fig. 6d shows the disposition of the electrostatic potential mapped on Hirshfeld surfaces of the π-stacked molecules represented in Fig. 2. The dnorm surfaces (Fig. 6e), reveal the close contacts of hydrogen bond donors and acceptors represented in Fig. 4b. The large circular depressions (cyan) are the indicators of hydrogen bonding contacts. The dominant O⋯H–N interactions are evident in the Hirshfeld surface and confirm the nature of the binding forces inside the cluster, π-stacking can also be observed with the upper row of molecules.
Fig. 6 Hirshfeld surfaces mapped with electrostatic potentials (a) individual surfaces in the four molecules cluster, (b) integrated surface for the cluster, (c) surfaces of the clusters in a wall like bricks, (d) individual molecular surfaces showing π-stacking (see Fig. 3), (e) dnorm surface displaying close contacts of hydrogen bonding and π-stacking. |
Natural bond orbital (NBO) analysis of dehydroacetic acid derivatives has proved to be a useful way for understanding the structure of β-enaminones.11 Now, the knowledge of the crystal structure of 1 will allow a better comparison between experimental and calculated data. Thus, the study of the properties in gas phase (b3lyp/6-311++G(2d,2p)) of the more stable component of the AU (molecule I, Fig. 1) was carried out. In this analysis (Table 3), stabilization energy E(2) related to the delocalization trend of electrons from donor to acceptor orbitals, is calculated via perturbation theory. Thus, NBO calculation using Gaussian 09 indicated that the highest interaction correspond to orbitals nN31 → πC3–C30* characteristic of the enamine structure, according to data from X-ray. The next higher energy interactions were πC3–C30 → πC2–O20* and πC3–C30 → πC4–O40* resulting from conjugation of the enamine double bond with both carbonyl groups. The lone pair of the oxygen in the ring is delocalized with the lactone carbonyl and the endocyclic alkene: nO1 → πC2–O20* and nO1 → πC5–C6*. Furthermore, the delocalization πC5–C6 → πC4–O40* supports the β-enaminone structure.
The principal donor–acceptor interactions between NBO orbitals are summarized in Table 3, showing the surfaces whose isovalue represents 95% of the orbital, so the effectiveness of the overlapping can be visualized.
The electronic conjugation in molecules was studied by Wiberg bond indexes,16 the results showed that C3–C30 and C30–N31 bonds have higher values than single bonds as C30–C32 (Fig. 7). So, this structure could be represented as a three centre delocalized bond in C3–C30–N31.
Fig. 7 Wiberg bond indexes for molecules I and II in AU, dashed lines indicate three centre delocalized bonds. |
As it is known, theoretical calculations of magnetic properties can be performed through different methods. The most widely used for this type of calculation is the GIAO method,17 where a source of potential vector of the external magnetic field for each atom is settled independently. Therefore, the coordinates of the structure derived from X-ray data were used to calculate NMR proton shifts (b3lyp/6-311++G(2d,2p)) by this method in the gas phase. The absolute shielding returned by the program was transformed in chemical shifts subtracting the absolute shielding of TMS from the absolute shielding of the molecule. However, the theoretical shifts obtained did not match with the experimental values. GIAO method may include the effect of solvent, and the polarizable continuum model (PCM) is generally used.18 Therefore, the presence of solvent was considered by placing the solute (coordinates from X-ray structure) in a cavity within the solvent reaction field (PCM). The results from this model implemented in Gaussian 09 also showed no accuracy; this could be due to the intermolecular hydrogen bonding present in the crystal. A refined molecular structure was calculated by minimizing the crystal structure with PCM model in chloroform; in this case the shifts (GIAO-PCM) were similar to experimental (Table 4).
Crystal coord. GIAO-(CDCl3) | Crystal coord. GIAO-(CDCl3) | Crystal coord. minimized (CDCl3) | δexp. | ||
---|---|---|---|---|---|
I | 1HNMR δ | II | 1HNMR δ | GIAO-(CDCl3) δ | |
H31B | 9.51 | H31C | 7.99 | 12.95 | 12.56 |
H31A | 3.79 | H31D | 3.46 | 6.22 | 6.96 |
H5 | 3.35 | H5B | 3.46 | 5.97 | 5.70 |
H32A | −1.71 | H32D | −1.75 | 1.71 | 2.65 |
H32B | −0.39 | H32E | −0.57 | 3.04 | 2.65 |
H32C | −0.75 | H32F | −0.64 | 3.04 | 2.65 |
H60A | −1.65 | H60D | −1.75 | 1.94 | 2.13 |
H60B | −1.47 | H60E | −1.39 | 2.26 | 2.13 |
H60C | −1.47 | H60F | −1.48 | 2.26 | 2.13 |
The minimized structure presented a change in the relative positions of H31A, H31B, H31C and H31D (involved in hydrogen bonding). The position of nitrogen was also modified affecting to the length of the hydrogen bonds present (Table 5).
Hydrogen bond | Crystal Xray I | Hydrogen bond | Crystal Xray II | Minimized PCM/CHCl3 |
---|---|---|---|---|
O40B⋯H31C | 1.78(3) | O40⋯H31B | 1.81(4) | 1.75 |
O40B⋯N31B | 2.59(5) | O40⋯N31 | 2.58(5) | 2.58 |
O40B⋯H31D | 3.42(3) | O40⋯H31A | 3.38(5) | 3.49 |
The interaction between O40 and H31B and O40B and H31C can be considered as an example of resonance-assisted hydrogen bond which is a model of synergistic interplay between π-delocalization and hydrogen-bond strengthening (RAHB).19 The interatomic distances (Table 5) from crystal structure and minimized are inside the values found by Gilli for substituted β-enaminones.20 This heteronuclear RAHB is of great chemical and biochemical relevance because chains of H-bonded amide groups determine the secondary structure of proteins. NBO analysis reflects the stabilization gained by donation from two lone pairs of O40 to the acceptor σN10–H20* being 10.68 and 2.12 kcal mol−1 (Table 3, entries 7 and 8). Meanwhile, in the minimized structure the distance between N10 and O40 is shorter, leading to stabilization of 14.92 and 3.42 kcal mol−1, respectively; higher than the observed for crystal, which agrees to a stronger hydrogen bond in the structure in solution.
Crystal data for 1: C16H18N2O6, M = 334.32, a = 6.650(3) Å, b = 8.898(4) Å, c = 13.970(6) Å, α = 92.24(2)°, β = 98.98(2)°, γ = 111.168(19)°, V = 757.3(6) Å3, T = 100(2) K, space group P, Z = 2, μ(MoKα) = 0.113 mm−1, 3506 reflections measured, 3506 independent reflections (Rint = 0.111). The final R1 values were 0.0706 (I > 2σ(I)). The final wR(F2) values were 0.1431 (I > 2σ(I)). The final R1 values were 0.1713 (all data). The final wR(F2) values were 0.1889 (all data). The goodness of fit on F2 was 0.997. In the crystal structure coordinates for hydrogens H31A, H31B, H31C and H31D were positioned by electronic density and refined with a restraint to the length distance of 0.87 Å except H31A which is completely free. For more details on geometry and refinement see ESI.†
Footnote |
† Electronic supplementary information (ESI) available: cif file for compound 1, crystallographic tables, 1H and 13C NMR spectra for compound 1. CCDC 945618. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4ra00582a |
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