3.1. Crystal Structure Description of (3E,3′E)-3,3′-((ethane-1,2-diylbis(azanediyl))bis(phenylmethanylylidene))bis(6-phenyl-2H-pyran-2,4(3H)-dione) 1
The crystallographic measurement for compound
1 was performed using was collected on a Rigaku Oxford Diffraction Supernova diffractometer using Cu Kα radiation (see
supplementary information). The topology analyses were performed using Crystal Explorer 17.5 program [
40]. The crystallographic details are summarized in
Table S1 (Supplementary data).
The X-ray structure of 1 is shown in
Figure 2 while the experimental bond distances and angles are listed in
Table S2 (Supplementary data). The compound crystallized in monoclinic crystal system and centrosymmetric C2/c space group with lattice parameters: a = 14.0869(4) Å, b = 20.9041(5) Å, c = 10.1444(2), β = 99.687(2)°. The molecule itself possesses a center of symmetry located at the midpoint of the C19-C19 bond splitting the molecule to two equal halves. The two phenyl rings bonded to C12 showed
cis configuration to one another where such sterically hindered conformation is stabilized by the strong intramolecular N1-H1…O1 hydrogen bonding interactions with a distance of 1.820(2) Å, resulting in a very stable S(6) ring motif (
Figure 3, upper part). The C12-N1 bond distance is found to be 1.324(2) Å, which confirm the single bond character this bond and further revealed the location of the proton H1 at the N1 atomic site rather than O1.
The molecular units in the crystal lattice are packed by two intermolecular hydrogen bonding interactions shown as red dotted lines in
Figure 3 (upper part). The corresponding hydrogen bond parameters are listed in
Table 1. The packed molecules via the N1-H1…O1 and C4-H4…O2 hydrogen bonding interactions with donor-acceptor distances of 2.991(2) and 3.134(2) Å, respectively are shown in
Figure 3 (lower part).
In addition, the molecules are packed by other contacts such as π-π stacking interactions between the pyran-dione moiety from one molecule with another pyran-dione and phenyl moieties from neighboring molecular units (
Figure 4; upper part). The corresponding shortest C…C distances are C9…C9 (3.340 Å) and C2…C8 (3.351 Å), respectively. Another type of contacts which affect the molecular packing is the C-H…π interactions (
Table 2). The upper part of
Figure 4 shows the molecular packing in the crystal structure
via these short C…C and C-H…π contacts.
3.2. Analysis of Molecular Packing
Intermolecular interactions in the solid state structure play very important rule in the crystal stability. In this regard, we employed Hirshfeld surface analysis for decomposing the different intermolecular contacts in the crystal structure the studied systems. The results of the quantitative analysis of all possible intermolecular interactions are shown in
Figure 5 while the complete Hirshfeld surfaces are given in
Figures S1–S6 (Supplementary data).
In the newly presented structure, the molecules are arranged in the crystal via H…H (41.8%), H…C (27.8%), O…H (24.4%) and C…C (3.1%) short contacts. Presentation of the decomposed d
norm maps and fingerprint plots for these interactions are shown in
Figure 6 while list of the most important short contacts are listed in
Table 4.
The shortest O…H contacts are O2…H4, O1…H1 and O1…H19B with contact distances of 2.390, 2.222 and 2.559 Å, respectively. Interestingly, the molecular packing is also controlled by some C-H…π interactions with interaction distances ranging from 2.647 to 2.729 Å. In addition, some π-π stacking interactions were noted with interaction distances of 3.340 Å (C9…C9) and 3.351Å (C2…C8). These short interactions appeared as red regions in the dnorm map with the characteristic features for the short contacts in the fingerprint plot. In contrast, the H…H contacts contributed significantly in the crystal packing by 41.8% from the whole fingerprint area but these interactions have larger distances than the VDWs radii sum of two hydrogen atoms. Similarly, the O…O, C…O and C…N contacts have long interactions distances and small contribution in the fingerprint area.
For compound
2, the molecular packing is controlled by short O…H (21.4%), H…C (26.5%) and C…O (1.6%) contacts in addition to the slightly long C…C (5.1%) interactions (
Figure 7). The shortest contact distances are 2.145 (O3…H2), 2.631 (H20…C8), 3.086 Å (C19…O3) and 3.425 Å (C5…C10), respectively. The latter is longer than the VDWs radii sum of two carbon atoms. The H…H interactions contributed significantly in the molecular packing by 45.0% from the whole fingerprint area. Other intermolecular interactions are shown in
Figure 5 such as N…H interactions are less important.
Similar to
1, the packing in compound
3 is controlled by short O…H (19.1%), H…C (20.2%) and C…C (9.7%) contacts in addition to the common H…H contacts (44.3%) which are found in all compounds presented in this publication (
Figure 8). The H1…C15 (2.712 Å), O2…H2A (1.885 Å) and C2…C5 (3.516 Å) are the shortest. The H…H interactions are generally long and appeared weak so have less importance in the molecular packing of this molecule in the crystal.
In case of compound 4, the percentages of the O…H, H…C, H…H and C…C contacts are 18.2, 21.0, 4.4 and 54.4%, respectively using Hirshfeld calculations. All appeared significant with interaction distances shorter than the VDWs radii sum of the two atoms included in these interactions except the H…H contacts which are slightly longer than the sum of the VDWs radii of two hydrogen atoms (
Figure 9). The shortest interaction distances are O2…H17 (2.431 Å), H22A…C17 (2.623 Å), H16…H22A (2.44 Å) and C2…C10 (3.252 Å), respectively.
In case of compound
5, there are two different molecules per asymmetric unit hence the Hirshfeld surface and fingerprint plots shown in
Figure 10 are presented for the two molecular units in the crystal. The contacts in both molecules are common in both molecular units but showed some differences (
Table 3). The H…H, H…C, O…H and C…C contacts in the crystal of 5 (without letter B in atom label) are in the range of 53.0, 23.8, 18.7 and 1.0, respectively. The corresponding values in 5B (with letter B in atom label) are 53.4, 20.7, 18.3 and 5.8%, respectively. The interactions distances of the different short contacts are listed in
Table 4. The H…C interactions are in the range of 1.986 Å (H17…H20C) to 2.768 Å (H4…C17B) while for O…H contacts, the interactions ranges from 2.280 Å (O1B…H1N) to 2.603 Å (O1…H20C). Two short C…C contacts were detected which are C2B…C10B (3.326 Å) and C11B…C2B (3.390 Å) in this compound.
The X-ray structure of 6 comprised twelve molecular units as symmetric unit as shown in the Hirshfeld d
norm maps presented in
Figure 11. Details regarding all intermolecular interactions and their percentages for the different molecular units are listed in
Table 5. The H…C, H…H and O…H as well as the C…C contacts are the major contacts in the crystal. These contacts are common for all molecular units but differently contributed in the molecular packing. For example the H…C contacts are the minimum (21.4%) in unit 6F while the maximum (23.4%) in 6D. Also, the minimum O…H contacts occurred in unit 6C (22.4%) while it is the maximum in 6I (25.2%). Decomposed fingerprint plots and d
norm Hirshfeld surfaces of the most abundant interactions for one molecular unit are presented in
Figure 12.
3.3. DFT Studies
The optimized geometries of the studied molecules are shown in
Figure 13 along with their overlay with the experimental ones. Generally, there is good structure matching between the optimized and experimental ones. Some variations between the calculated and experimental structures could be attributed to the crystal packing effects (
Tables S3–S8, Supplementary data). Generally, good correlations between the calculated and experimental bond distances and angles (
Figure 14) were obtained.
Natural charge calculations at the different atomic sites are calculated using NBO method and the results are given in
Table S9 (Supplementary data). The pyran-2,4-dione derivatives have electronegative heterocyclic oxygen atom with natural charge ranging from −0.524 e for compound 2 to −0.530 e for compound
6. The two carbonyl oxygen atoms have also negative charge ranging from −0.563 (compound
1) to −0.582 (compound
4) for the carbonyl group at 2-position while ranging from −0.641 e (Compound
4) to −0.649 (compound
4) for the carbonyl group at 4-position. The majority of carbon atoms are also electronegative except those attached to O or N sites. In contrast, all hydrogen atoms are positively charged with maximum natural charges at the OH and NH protons. The natural charges at these hydrogen sites is the maximum for the NH proton in compound
3 (0.462 e) while the least for the OH proton in compound
1 (0.494 e). Due to the presence of differently charged regions, the studied molecules have polar nature with dipole moment ranging from 0.1786 Debye for compound
1 to 3.4590 Debye for compound
6. Presentation of the total electron density mapped with molecular electrostatic potential for the studied molecules showing the positively charge regions in blue colored area while the most negative regions have red color is shown in
Figure 15.
In the same figure, the HOMO and LUMO levels for the studied pyran-2,4-dione are presented. Both molecular orbitals (MOs) are distributed over the π-system of the studied molecules indicating HOMO→LUMO excitaion based mainly on π-π* excitation (
Figure 15). In addition, the energies of these MOs are used to calculate the different reactivity descriptors [
41,
42,
43,
44,
45,
46,
47] such as ionization potential (I), electron affinity (A), hardness (η), electrophilicity index (ω) and chemical potential (μ). The results listed in
Table 6 indicated that
6 has the highest ionization potential, electron affinity, electronegativity and electrophilicity index while the lowest chemical potential. In addition, compound
5 is the hardest among the studied series.
3.5. Conformational Analysis
The presence of more than one possible conformer or tautmer is common in literature in many organic systems [
48,
49]. The X-ray of the pyran-2,4-dione derivatives revealed that their molecular structures stabilized by intramolecular O-H…O or N-H…O hydrogen bonding interactions. In these structures there are two possible isomers for each compound as shown in
Figure 17. Energy and thermodynamic calculations of the two suggested isomers of the studied pyran-2,4-diones were used in order to compare their relative stabilities. The calculations revealed that form
A is the most stable form and has the lowest energy compared to
B (
Table S16). Also, the more negative value of the Gibbs free energy of isomer
A compared to
B indicated that the former is the most stable thermodynamically. Interestingly, the optimization of
15(
B) ended to the same optimized geometry of
15(
A) which further confirm the extrastability of the pyran-2,4-dione (
A) form over the pyran-2-one isomer (
B) which agree with the reported X-ray structure of these compounds [
17].
3.6. AIM Study
Atoms in molecules theory (AIM) [
19,
50] is a popular approach used for describing various inter- and intramolecular interactions efficiently. The AIM topological parameters such as electron density (ρ(r)), kinetic energy density G(r), potential energy density V(r) and total electron energy density (H(r) = V(r) + G(r),) at the bond critical point (BCP) of interaction atoms or fragments [
51,
52,
53] are important for describing the nature and strength of interaction. Generally, the shared interactions have ρ(r) should be ˃10
−1 a.u. while closed-shell interactions have ρ(r) ≈ 10
−2. Hence, ρ(r) is a measure for the degree of covalency in the intermolecular interactions [
21]. In addition, Espinosa [
54] interaction energy (E
int = 1/2 (V
BCP)) is a measure of the strength of intermolecular interactions.
The molecular structures of all systems under investigation are stabilized by intramolecular O…H hydrogen bond. All intramolecular O…H hydrogen bonds have ρ(r) less than 0.1 a.u. which is typical for closed-shell interactions [
55,
56,
57]. As shown in
Table 7, the values of electron density (ρ(r)) of bond critical points are in the range 0.0345–0.0492 a.u. and 0.0228–0.0639 at the X-ray and optimized structure, respectively.
The H-bonding interaction energies (E
int) are generally higher at the optimized geometry than the X-ray one which is attributed to the further relaxation of the donor-hydrogen distance which of course lead to shortening the acceptor (A)…hydrogen (H) distances. The correlation between A…H distances and E
int gave straight lines with high correlation coefficient (R
2 = 0.95–0.998) with negative slope indicating higher E
int for shorter A…H distance (
Figure 18).
In addition, the total energy density (H(r)) [
58] and |
V(
r)|/
G(
r) ratio [
59] are positive and less than 1 for closed-shell interactions while the opposite is true for covalent interactions. The results shown in
Table 7 shed the light on the little covalent character for the studied intramolecular hydrogen bonding interactions.