3.1. Structural geometry
The optimized geometrical parameters of the title molecule were calculated by the DFT method with B3LYP and CAM-B3LYP function levels at 6-311 + + G(d,p) basis set and the atom numbering molecular structure is shown in Fig. 1. The theoretical values of total energy are calculated to be -522.6270 and − 522.3791 a.u., respectively. As shown in Table 1, the computed structural parameters of the title molecule according to the above mentioned theory are found to be in good agreement with the X-ray data. The bond distances and bond angles in the pyrimidine rings substituted by the NH2 group are found in the regular range. The magnitude of the bond lengths C6-N11, N10-H14, N10-H15, N11-H17 and N11-H16 show significant differences from the experimental values 1.286, 1.097, 1.108, 1.040 and 1.000 (Å) degrees to the corresponding calculated values 1.000/1.001, 1.003/1.004, 1.001/1.002 and 1.000/1.004 (Å) degrees respectively. Bond lengths C2-N3, C4-N5 and C6-N7 show that both possess double bond characteristics, which are in excellent agreement with the observed results. The calculated bond angle value of N1-C9-C8 at 136.07/135.91 Å is slightly longer than the observed value of 135.03 Å due to the electron withdrawing group. The pyrimidine ring substituted amino groups are H16-N11-H17 optimized bond length is slightly shorter than the H14-N10-H15 atoms as a difference of 2.26 Å (X-ray). Furthermore, the bond angles of N5-C6-N7, N5-C6-N11, C9-C8-N10, N1-C9-C8 and C8-N10-H15 in the range of 126.61/126.27o, 117.47/117.78o, 124.69/124.51o, 136.07/135.91o and 117.46/117.35o with B3LYP/CAM-B3LYP method and 124.22o, 117.56o, 124.54o, 135.03o and 117.06o with XRD analysis and the geometrical parameters are listed in Table 1.
Table 1
Observed and calculated structural parameters (bond (Å) lengths, angles (°)) and dihedral angles (in degree) for DAP.
| Structural parameters | B3LYP | CAM-B3LYP | Experimental |
| Bond lengths (Å) |
| N1-C2 | 1.374 | 1.382 | 1.360 |
| N1-C9 | 1.396 | 1.401 | 1.419 |
| N1-H12 | 1.001 | 1.003 | - |
| C2-N3 | 1.316 | 1.324 | 1.333 |
| C2-H13 | 1.074 | 1.074 | 1.045 |
| N3-C4 | 1.394 | 1.400 | 1.371 |
| C4-N5 | 1.345 | 1.349 | 1.354 |
| C4-C9 | 1.399 | 1.410 | 1.344 |
| N5-C6 | 1.340 | 1.351 | 1.359 |
| C6-N7 | 1.365 | 1.370 | 1.353 |
| C6-N11 | 1.358 | 1.363 | 1.286 |
| N7-C8 | 1.337 | 1.347 | 1.290 |
| C8-C9 | 1.402 | 1.406 | 1.326 |
| C8-N10 | 1.364 | 1.369 | 1.283 |
| N10-H14 | 1.000 | 1.001 | 1.097 |
| N10-H15 | 1.003 | 1.004 | 1.108 |
| N11-H16 | 1.001 | 1.002 | 1.040 |
| N11-H17 | 1.000 | 1.004 | 1.000 |
| Bond Angles (°) |
| C2-N1-C9 | 106.28 | 106.13 | 103.67 |
| C2-N1-H12 | 125.76 | 125.76 | - |
| C9-N1-H12 | 127.95 | 128.09 | - |
| N1-C2-N3 | 113.25 | 113.24 | 113.82 |
| N1-C2-H13 | 122.00 | 122.09 | 120.09 |
| N3-C2-H13 | 124.74 | 124.66 | 124.61 |
| C2-N3-C4 | 105.10 | 105.21 | 104.59 |
| N3-C4-N5 | 126.38 | 126.61 | 124.03 |
| N3-C4-C9 | 109.94 | 109.83 | 108.02 |
| N5-C4-C9 | 123.67 | 123.55 | 121.54 |
| C4-N5-C6 | 113.87 | 114.17 | 112.39 |
| N5-C6-N7 | 126.61 | 126.27 | 124.22 |
| N5-C6-N11 | 117.47 | 117.78 | 117.56 |
| N7-C6-N11 | 115.91 | 115.93 | 115.82 |
| C6-N7-C8 | 119.02 | 119.29 | 118.71 |
| N7-C8-C9 | 118.30 | 118.20 | 118.58 |
| N7-C8-N10 | 117.00 | 117.28 | 117.04 |
| C9-C8-N10 | 124.69 | 124.51 | 124.54 |
| N1-C9-C4 | 105.41 | 105.57 | 102.58 |
| N1-C9-C8 | 136.07 | 135.91 | 135.03 |
| C4-C9-C8 | 118.50 | 118.50 | 118.50 |
| C8-N10-H14 | 123.23 | 123.25 | 123.82 |
| C8-N10-H15 | 117.46 | 117.35 | 117.06 |
| H14-N10-H15 | 119.29 | 119.39 | 119.65 |
| C6-N11-H16 | 118.91 | 118.83 | 117.30 |
| C6-N11-H17 | 119.72 | 119.62 | 119.94 |
| H16-N11-H17 | 121.36 | 121.54 | 121.91 |
3.2. HOMO-LUMO analysis
The MO theory and their properties are the most widely used for physicists and chemists. This is also used in electron densities for predicting the most reactive position in largest π-conjugated electron systems, which is play an significant role in the optical and biological activity [10]. FMOs energies are present important chemical descriptors that can use it to determine the electron donating ability and electron accepting ability of the chemical structure. Furthermore, the frontier orbital energy level is very useful quantities in the chemical compound stability and reactivity [11–13]; it is a measure of the intramolecular charge transfer (ICT). Mostly, molecules with a small value of HOMO-LUMO energy gap are directly related with a high chemical stability and low reactivity and vice versa. The pictorial representation of HOMO-LUMO electron density map and their energy values were calculated and it is shown in Fig. 2. From the plot, the HOMO orbital of the π-nature of the compound is mainly contained over the carbonyl group and slightly over the oxygen group within their structure, and the empty LUMO orbital is located on the aromatic benzene rings of the bioactive compound. The value of the energy separation between the frontier energy level is -4.8308 eV. The results suggest that the ICT from the electron-donating groups and electron-accepting groups through conjugated systems improves the bioactivity of the DAP compound.
3.3. Chemical relativities
The HOMO-LUMO energy gap determines electrical transport properties in metal free organic and inorganic molecules. The chemical reactivity of title molecule such as ionization potential (IP),electron affinity (EA), chemical potential(µ), (S), electrophilicity index(ω) and electronegativity(χ) chemical hardness and softness, as well as local descriptors can be calculated and are obtained in terms of the frontier orbital energy values and chemical hardness than the B3LYP method are presented in Table 2. The values of chemical hardness (ƞ), global softness (S) and local reactivity descriptors, electron affinity (EA), ionization potential (IP), specifically Fukui function and have been stimulated justified within the background of quantum chemical calculation. The HSAB (Hard-Soft Acid-Base) theory fundamentally measures the resistance to deformation or change of the ions radius, atoms under small perturbations of the charge cloud during physical and chemical reactivity. Generally, a high value EHOMO-ELUMO energy gap means a hard acids and bases molecule and low value EHOMO-ELUMO energy gap means a soft acids and bases molecule.
Table 2
Calculated energy values of DAP by CAM-B3LYP/6-311 + + G (d,p) method
| Energies (eV) |
| Frontier orbitals |
| HOMO (eV) | -6.6857 |
| LUMO (eV) | -1.8549 |
| Energy gap (eV) | -4.8308 |
| Global Descriptors |
| Ionization potential (IP) a.u. | 6.6857 |
| Electron affinity (EA) a.u. | 1.8549 |
| Chemical hardness (ƞ) a.u. | 2.4154 |
| Chemical softness (S) a.u. | 0.4042 |
| Chemical potential (µ) a.u. | -2.4154 |
| Electronegativity (χ) a.u. | 4.2703 |
| Electrophilicity index (ω) a.u. | -1.0034 |
3.4. MESP surface
The molecular structure (MEP) [14] simultaneously displays molecular electrostatic potential regions (positive, negative and neutral) total density map, spin density, alpha and beta charge analysis as given in supporting information Figure S1. The MEP surface map has been used to determine the molecular system with its physicochemical properties and biological activities. The mapped isodensity surface values are characterized by chemical reactivity and different color coding of the molecule are represented by potential V(r) increases in the order blue green yellow orange red, i.e., the red color area represents the more electronegative molecular surface that is associated with nucleophilic attacks, while the blue color area denotes the more positive regions that are associated with electrophilic attacks, and green regions represent regions of zero potential. The information thus obtained from the charge distribution of the potential surface can be used to understand the hydrogen bonding and dipole-dipole interactions. As shown in Fig. 3, the surface ranges from − 6.230e-2 to + 6.230e-2 a.u of title compounds, where the dark blue color part indicates the poor electron regions and the red color area indicates the rich electron regions. The red regions with a most electronegative potential were determined on N2, N3 and C8 atoms while blue regions with a positive potential were determined at N2 atom, respectively. The MEP surface maps are in understanding to the simulated atomic charges inside the considered frameworks and show that an unsymmetrical charge distribution in the compounds may have suggestions on their biological properties.
3.5. NLO properties
The organic NLO materials that possess properties of compound 6DCP, for example, such as electric dipole moments, molecular polarizability and hyperpolarizability, have been computed by using the present methods [15–17]. The value of the dipole moment is calculated at 6.3119/6.4387 Debye in the gas phase. This value of the dipole moment implies the presence of strong dipole-dipole interactions and electronegativity of the title compound. Molecular polarizability and hyperpolarizability are the most important geometrical descriptors for the optical behavior of the molecule. Furthermore, the first order polarizability is directly related to the binding affinity and ability of the target molecule; highly polarizable sites make it possible to bind more strongly to hydrogen-bonding interactions with the target as compared to weakly polarizable sites. The polarizability and the hyperpolarizability were determined to be α = 68.37/68.42×10− 23, Δα = 144.26/144.53×10− 24, and βtot = 2.36/2.52×10− 32 e.s.u., respectively (see Table 3). These results showed a hyperactive mechanism for the biological activity of the DAP molecule. These high polarizability values clearly show that the biological activity was induced in good order.
Table 3
Total static dipole moment (µ), the mean polarizability (α0), the anisotropy of the polarizability (Δα), and the mean first order hyperpolarizability (β) for DAP.
| Parameters | µ (Debye) | α0 | αtot (esu) | βtot (esu) |
| B3LYP | 6.3119 | 68.37 | 144.26 | 2.36 |
| CAM-B3LYP | 6.4387 | 68.42 | 144.53 | 2.52 |
3.6. NBO analysis
The NBO orbital analysis is a powerful technique for examining intra and intermolecular charge transfer interaction among bonds, and also provides a suitable basis for studying ICT in molecular system or conjugative interaction in molecular methods. There are three classes of NBOs analysis is carried [18] out by considering all possible interactions of electron density between occupied (i) Lewis-type orbitals (σ and π bonding), (ii) empty non-Lewis orbitals (acceptors formally unfilled) and (iii) Rydberg or antibond NBO orbitals, which create from orbitals external the atomic valence shell. For each Lewis-type (i) and non-Lewis acceptor (j) orbitals, the stabilization energy E (2) value associated with electron delocalization between electron donors-acceptors is estimated as
$${E}^{\left(2\right)}={q}_{i}\frac{{F}^{2} (i,j)}{{?}_{i}-{?}_{j}}$$
Where q_ithe orbital occupancy, i and j are the energies of the donor/acceptor orbitals and F(i,j) is the off diagonal NBO Fock matrix elements. The most significant interactions between the bonding/antibonding and Lewis/non-Lewis orbitals are responsible for charge transfer interactions and the characteristics of biological activity of the molecule. The delocalization of intermolecular interaction between the donor and acceptor interactions of the entire molecular system is related to the stabilization energy E(2) values. Electron delocalization or hyper conjugation is an important interaction between occupied and unoccupied NBO-typed Lewis structures of NBO orbitals (one-centre Rydberg or two-centre anti-bonding) corresponding to the strongest i and j interactions. The stabilizing interactions formed by the hybrid orbitals overlap between the bonding ((C-C)) and anti-bonding (*(C-C)) orbitals indicate strong ICT interactions in the hyperconjugation. The most significant interactions between localized and delocalization orbitals with N and C lone pairs, where the primary hyperconjugative interaction between the nLP N11 atoms interacted with the anti-bonding orbital σ*N1→C2 with a corresponding stabilization energy of 82.02 kcal mol− 1. The other lone pair species such as nLP N7, nLP N1, nLP N3, nLP N9, nLP N10, nLP N11 and the bonding orbitals σ* C2→N3, σ* C2→N11, σ* N3→C4, σ* C4→C5, σ* N7→C8, σ* N1→C6, σ* C8→N9, σ* C2→N3 and the stabilization energies are 14.82, 3.79, 12.58, 21.64, 18.95, 10.65, 10.29 and 10.03 kcal/mol (see Supplementary Table S1). The anti-bonding orbital interaction energy between σ*N1 - C2→π*C4, σ* N3 - C4→ σ* C5 - C6 and σ* C5 - C6→ π* C5 leads to a large stabilization energy of 37.24, 74.07 and 63.44 kcal/mol respectively. Relatively high energy values of electron density transfer interactions point out that the strong ICT interactions leading to delocalization energy of the molecule.
3.7. Mulliken charge analysis
The atomic charge distribution has a major effect on the vibrational band of a molecule reported in this study, and the bar chart representing the charge distribution is displayed in Fig. 4. Hence, the mulliken population analysis of DAP was also obtained by the DFT method in order to explain the atomic charges. These atomic charge techniques play a vital role in the chemical application of calculations in computational chemistry, including vibrational spectroscopy, electronic structure, non-linear optical, and a lot of properties of molecular structures [19, 20]. From Supplementary Table S2, it can be seen that the atomic charge distribution of the N1, N3, N5, N7 and N11 atoms for DAP ligand, which indicates that the intermolecular charge transfer from the purine rings. The previous values of negatively charged electrons are observed for the nitrogen atoms N1, N3, N5, N7 and N11, respectively. The most positively charged H15 atom is at 0.339622/0.347076e, which is involved in the intramolecular charge transfer (ICT) process in a molecular system. All the H atoms display a positive electrical charge from the additional un-neutralized protons. This result also suggests that the N10, N11 and N1 atoms has a higher negative value, which means the high electron density of the atom can easily interact with the positive charge part of the chemical compound. Finally, we can conclude that the atomic charge analysis prove that the antibonding bonding interaction of the molecular systems.
3.8. Fukui Function
The ab initio calculation is an effective tool for studying the local reactivity descriptor and site selectivity. The Fukui functions are measured in order to get information about the chemical and local site reactivity within a molecule [21–23]. There are three types of condensed or atomic Fukui function on the kth atomic local site on the molecule, viz., and, which are related to nucleophilic, electrophilic and free radical attack. As shown in supporting information Figure S2, the values of condensed or atomic Fukui functions values for the following atoms: C7, C8, C10, C11, N1, N2, N3, N4 and N5. The calculated Fukui function for C7,C10, N2 and N5 show that possible electrophilic attacks whereas the condensed Fukui function for C8, C4, N1 and N3 atoms as sites for possible nucleophilic attacks and the Fukui function values suggest to C11, N4 atoms predict possible free radical attacks of DAP are listed in Supplementary Table S3. These results permit us to know which are the most potential reactive sites Fukui functions , and
3.9. Analysis of charge density topologies: A Quantum theory of atoms in molecule (QTAIMs) analysis rationalization
Generally, the values of the topological properties of the molecule provide us additional helpful information about the intra-molecular hydrogen bond interactions, such as the strong/weak covalent bond interactions in terms of molecular electron density (ED) ρBCP at the bond critical points, the values of the ED and its associated Laplacian ∇2ρ (rBCP) at the eigenvalues of the hessian matrix ED (λ1, λ2, λ3) and the λ1/ λ2 is negative ratio were calculated in the ring critical points (RCPs) theory [24]. More QTAIM study information allows us to determine the presence of cycles in chemical bonding and the structure of a molecular system. According to Rozas et al. reported [25] three standard criteria points for classifying H-bonds: (i) the strong intramolecular hydrogen bonds ∇2ρ (rBCP) < 0, HBCP < 0 and (ii) the weak intramolecular hydrogen bonds ∇2ρ (rBCP) > 0, H (rBCP) > 0 and (iii) the covalent or ionic in medium intramolecular hydrogen bonds ∇2ρ (rBCP) > 0, H (rBCP) < 0. The presence of a hessian matrix and the ring critical point confirms the cyclic character of an atomic chain and the specific molecule. This study shows two types of hydrogen critical points (HBCPs) of the electron density Δρ in real space: N12-H14 and N9-H8 interactions observed only for DAP were performed by using the AIM calculations. The charge density space is (3,-1) HBCPs and (3,-3) nuclear attractor critical point (nacp) while the latter is bonding characterized by a signature of 1and a rank of 3 (Fig. 5). The AIM method also allows us to ascertain the electron density to Lewis structure in our compound. The graphical representations of the AIM analysis and the BCPs (red dots) between the hydrogen interacting atoms of the title ligand are shown in Fig. 6, and the optimized as well as topological properties of Laplacian at these CPs and the theoretical values of the electron density are given in Table 4.
Table 4
Topological properties of the critical points for intramolecular H-bonds.
| Molecule | Interaction | G(r) | K(r) | V(r) | E(r) or H(r) | ELF |
| DAP | N12—H14 | 0.143 | 0.611 | -0.612 | -0.611 | 0.999 |
| N9—H8 | 0.567 | 0.644 | -0.645 | -0.644 | 0.999 |
| LOL | RDG | LP | Hessian matrix |
| λ1 | λ2 | λ3 |
| 0.979 | 0.100 | -0.244 | -0.818 | 0.541 | -0.517 |
| 0.992 | 0.289 | -0.257 | -0.810 | -0.135 | 0.148 |
| G(r) →Lagrangian kinetic energy, K(r) →Hamiltonian kinetic energy, V(r) →Potential energy density, E(r) or H(r) →Energy density, ELF →Electron localization function, LOL →Localized orbital locator, RDG →Reduced density gradient, LP →Laplacian of electron density. |
3.9.1 Reduced charge density gradient (RDG) vs. sign (λ2) ρ plot analysis
Development of the reduced density gradient plot and isosurfaces density based AIM approach, was introduced using the non-bonded interactions initially proposed by Johnson [26] and co-workers [27, 28]. The presence of weak chemical interaction between two atomic basins in a binary complex can be represented by RDG’s and NCI that depends on the normalized is given by the following equation
Accordingly, a 2D and 3D plot between reduced density gradient (s) and sign Δρ will result in three dimensional fingerprint maps in the reduced ED and gradient isosurface shows that bonded and nonbonded strong repulsion interactions. For the improve understanding of RDG isosurface colors indicates the character of the interaction: blue and green colors represent the strong interactions or steric effects and red RDG surface indicating nonbonded repulsions or steric clashes. Figure 7 shows the values of the sign isosurface value (2) 0.541a.u. range, followed by the critical point crossing to understand the correspond to the tail regions of the reduced density gradient for the bonded and non-bonded repulsion interactions.
3.10. Hirshfeld surface (HS) analysis
The 3D Hirshfeld surface (HS) projections and their respective 2D fingerprint (FP) plots were used to explore quantitative information associated with the nature of these interactions and to study the different types of non-covalent interactions in the crystal structure. Molecular surface counters and fingerprint plots were done using the program Crystal Explorer version 17.5 [29, 30]. The HS was mapped with the (a) d norm (e), (b) d norm (i), (c) di and (d) of crystalline forms is given in Fig. 8, which reveals that the most important information about the H-H interactions of the crystal packing. The dominant interactions succeed in the 3D crystal structure through the strong H-bonding networks of contacts like C-C, C-H, C-N and N-H, which can be seen mapped as red spots on the crystal. Form Fig. 9 illustrates the two-dimensional fingerprint plots (FP) are decomposed to highlight the nature of intermolecular contacts. The bifurcated long and sharp spikes denote N-C bonds, which are the largest contributor (40.95%) and are characterized by strong interactions. Moreover, the small spike region labelled red color in Fig. 9 denotes C-C, C-H and C-N interactions, which are important in the dnorm maps. The HS surface inter-contacts increase in the order C-C, C-H and C-N. The left side 2D FP plots represent the outer interactions (regions) of the crystal.
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Drug Transport Properties
The structural-based biological and chemical properties of DAP ligand were done by using the Molinspiration web (http://www.molinspiration.com/) software. The Lipinski’s rule of five (RO5) which is evaluate drug-likeness or determine the chemical substance and also to determine their pharmacological or bioactivity score such as miLogP value, TPSA, natoms, nviolation, volume, nrotb, enzyme inhibitor, kinase inhibitor, nuclear receptor, protease inhibitor, ion channel modulator and GPCR ligand are listed in Supplementary Table S3 and a graph of calculated logP vs. experimental logP is shown in Fig. 10. Molecules from the world drug index were used for this procedure.
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Molecular Docking studies
The docking approach has been playing an increasingly significant role in computer aided drug design and development for the treatment of several diseases. This computational method provides insight into possible binding interactions between the ligand-receptor complexes, which can confirm the experimental result. The Quantitative Structure-activity relationships (QSAR) have become an efficient tools to the study the medicinal chemistry methods, including biological activity and pharmaceutical properties of synthesized analogues towards pathogens. The MD studies of the title compound were performed by surflex2.0 software [31]. The MD results are analyzed by H-bonding distance between the residues of binding pose and also calculated the binding interaction free energies. The 3D model of 1UOM and 1SAO proteins was downloaded from structural Bioinformatics Protein Data Bank (http://www.rcsb.org/pdb/home/home.do). The hydrogen binding site of ligand-protein interaction was obtained by PYMOL software and using Discovery studio visualiser DS 2.0 [32].
In the presence of the DAP ligand, molecular docking studies were carried out to determine the potential H-bonding interactions on estrogen receptor-α (1UOM) and anti-inflammatory (1SA0) agent targeted receptors. The visual representation of possible binding sites and amino acid residues interacting of title compound with target proteins are shown in Figs. 11 and 12. In 1UOM protein, the benzene and 2H-imidazole groups of the title compound were placed within the hydrophobic pocket enclosed with namely GLN 408, ARG 329, LYS 252, GLU 257, GLY 378, ALA 382 and the amino acids (1SA0) of protein residues that interacted with DAP were ASN 101, GLN 11, LEU 248, LSY 254, GTP 600, forming π-π interactions with the pyrimidine and 2H-imidazole rings, which were involved in the binding of the compound and yielded a binding affinity of -6.7 and − 6.2 kcal/mol respectively. The 2H-imidazole served as a hydrogen bond acceptor to LYS 252, LUE 248 NH and oxygen group. The cut-off of 2 to 3 Å reduced distance or H-bond interactions between the donor and acceptor of the molecular system. The results are shown in Table 5 and will be discussed on the hydrogen bonds distance and protein-ligand interactions. The higher binding energy shows the estrogen receptor-α (ERα) is properly bound with DAP is associated with the treatment of breast cancer.
Table 5
Binding free energy (ΔG binding), Bond distance, Interacting residues and Torsional Free Energy (kcal/mol) of ligands.
| protein | Binding free energy(ΔG binding) | Torsional Free Energy(kcal/mol) | Interacting residues | Bond distance |
| 1UOM | -6.7 | 2.03 | GLN 408, ARG 329, LYS 252, GLU 257, GLY 378, ALA 382 | 2.74, 2.98 |
| 1SA0 | -6.2 | 1.76 | ASN 101, GLN 11, LEU 248, LSY 254, GTP 600 | 2.67, 2.49 |