Synthesis and structure of push–pull merocyanines based on barbituric and thiobarbituric acid

The synthesis and crystal structures of 1,3-diethyl-5-{(2E,4E)-6-[(E)-1,3,3-trimethylindolin-2-ylidene]hexa-2,4-dien-1-ylidene}pyrimidine-2,4,6(1H,3H,5H)-trione or TMI, C25H29N3O3, and 1,3-diethyl-2-sulfanylidene-5-[2-(1,3,3-trimethylindolin-2-ylidene)ethylidene]dihydropyrimidine-4,6(1H,5H)-dione or DTB, C21H25N3O2S, are described. These compounds contain the same indole derivative donor group and differ in their acceptor groups (in TMI it contains oxygen in the para position, and in DTB sulfur) and the length of the π-bridge.


Structural commentary
Both title compounds have the same donor 2,3-dihydro-1,3,3trimethyl-1H-indole moiety with different acceptors: 1,3-diethyl-2-oxobarbituric acid in TMI (Fig. 1a) and 1,3-diethyl-2thiobarbituric acid in DTB (Fig. 1b). The double and single bonds in the TMI -bridge vary in length from 1.372 (2) to 1.410 (2) Å , the difference between the single and double bonds getting smaller closer to the acceptor, indicating a higher degree of conjugation in this region. The dihedral angles between donor group and the bridge and between the bridge and the acceptor group are 9.10 (12) and 7.44 (12) , respectively. All three fragments of the TMI structure are slightly distorted from a planar configuration, as shown by the r.m.s. deviations of 0.022 and 0.039 Å , respectively, for atoms in the donor and acceptor groups.
Comparing DTB to TMI, it is observed that DTB possesses a more planar and rigid structure, consistent with previously reported results for studies of push-pull chromophores with different -bridge lengths (Tillotson et al., 2019). The dihedral angles between the three fragments are smaller, 3.21 (14) between the donor group and the bridge and 1.04 (14) between the bridge and the acceptor group. The r.m.s. deviations of atoms in DTB are also smaller, being 0.014 and 0.020 Å for the donor and acceptor groups, respectively.
In both structures, the -bridge has an almost planar structure with insignificant r.m.s. deviations of atoms from planarity of 0.007 and 0.009 Å for TMI and DTB, respectively. In DTB, the bond-length distribution in the central fragment does not correspond to that in the scheme. According to the observed bond lengths [C8-C12 1.403 (1), C12-C13 1.386 (1), C13-C14 1.404 (1) Å ], the central fragment can be presented as C8-C12 C13-C14, which indicates that the contribution of the zwitterionic form in the molecular structure of DTB. It should be mentioned that measurements of the first molecular hyperpolarizability, , have positive values for dyes with hexamethine bridges, such as TMI, while dyes with a dimethine bridge have negative values (Ortiz et al., 1994). The authors connect this effect with the high polarization and zwitterionic form of molecule DTB, which has a short conjugated bridge.
For push-pull molecules be applied in the form of nonlinear crystalline materials, they should exhibit a non-centrosymmetric type of packing. TMI and DTB both crystallize in the centrosymmetric space group P2 1 /c. According to the bond order alternation pattern in these structures (see the supporting information), we suggest that they have the potential to be used as non-linear optical materials, but for this application they should be either be embedded in a polymer matrix or recrystallized under different conditions to attain an acentric packing mode.

Database survey
The Cambridge Structural Database (CSD version 5.40, last update November 2018; Groom et al., 2016) was searched three times: for the donor group, which is the same for both studied structures, and separately for each acceptor group. A search for the full structures gave zero hits. The dependence of the first hyperpolarizability on polarization and the length of the -bridge that comprises donor or acceptors of studied molecules is described in several publications [KIYTOC and KOFMAU, Kulinich et al., 2007;GUBDAK, Liess et al., 2015 (Fig. 4); POLZEV, Ortiz et al., 1994;WIMHAD and 1308 Bogdanov et al. The molecular packing in the crystals of compounds (a) TMI and (b) DTB.

Figure 4
The moleculular structure of a compound with a similar structure to DTB (PAQYEM; Song et al., 2005). WIMHEH, Klikar et al., 2013;WEVMUF, Bourhill et al., 1994]. In addition, the acceptor group of the TMI structure has been studied separately and the results were published (DETBAR10; Bideau et al., 1976). The acceptor group of DTB was studied as an independent molecule (DETSBR10; Bideau et al., 1976), as a part of several chromophore molecules (GUDWEH, Adamson et al., 1999;GUDWEH01, Naik et al., 2017;WEVMUF, Bourhill et al., 1994) and also as an anion in complexes with different cations (HUKMAD, HUKMEH, HUKMIL and HUKMOR; Molokeev et al., 2015). We found several publications in which the molecules are similar to our donor and acceptors, for instance PAQYEM (Song et al., 2005) is similar to TMI, but with a methyl group instead of an oxygen atom in the ortho position of the acceptor ring, and a cyano group in the meta position instead of an ethyl group (Fig. 4). Two structures of the separately crystallized acceptor group (DETSBR01, Bideau et al., 1977;DETSBR11, Padgett et al., 2007) are very close to that of the acceptor of DTB, but with hydroxy groups in the ortho positions instead of carbonyl oxygen atoms (Fig. 5).

Synthesis and crystallization
The synthesis of TMI was described by Ortiz et al. (1994), and this material was kindly presented to our group for structural studies by Professor Marderr's group. A scheme for the synthesis of DTB is shown in Fig. 6.
2-(1,3,3-Trimethylindolin-2-ylidene)acetaldehyde (0.25 g, 1.2 mmol) and diethylthiobarbituric acid (0.25 g, 1.24 mmol) were dissolved in about 35 mL of absolute ethanol with stirring and sonication. After stirring for 1 h at room temperature, the product was precipitated by adding distilled water. The   Synthesis Single crystals of both DTB and TMI were grown by vapour diffusion using chloroform as the solvent and cyclohexane as the antisolvent. Crystallization took place over a three week period to give DTB crystals of suitable size and quality.

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 3. The hydrogen atoms on the aromatic ring of the donor group and the -bridge in both structures were positioned geometrically, C-H = 0.95 Å . Other hydrogens were positioned with idealized geometries C-H = 0.98-0.99 Å . All H atoms were refined using a riding model with U iso (H) = 1.2U eq (C) or 1.5U eq (C-methyl). Special details Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.