Non covalent interactions analysis and spectroscopic characterization combined with molecular docking study of N′-(4-Methoxybenzylidene)-5-phenyl-1H-pyrazole-3-carbohydrazide

3.1 Geometric structure

The optimized structure of MBPPC was simulated by DFT level using B3LYP/6-311+G(2d,p) method. The experimental geometry of the studied molecule was obtained from Cambridge Crystallographic Data Center (CCDC 1437241) (https://www.ccdc.cam.ac.uk). X-ray diffraction evince that the title compound belongs to monoclinic system with a = 10.9734(4) Å, b = 11.8835(5) Å, c = 13.0996 Å cell dimensions. Then, MBPPC crystallizes in space group P2₁/c with four atoms for each unit cell (Z = 4). The stabilization energy and dipole moment value in monomer and dimer geometries are calculated. The SCF energies are-1065.2778 Hartree (monomer) and −2129.9412 Hartree (dimer). The dipole moment values are3.87 and7.35 Debye for monomer and dimer, respectively. The bond lengths and bond angles parameters along with experimental ones are tabulated in Table 1 while the atom labeling scheme is given in Fig. 1. The comparison between computed and experimental bond lengths and angles was established based on RMSD (Root Mean Square Deviation) value. The lower RMSD values calculated for bond lengths 0.0774 (monomer)/0.0784 (dimer) indicate the reasonable correlation between theoretical and experimental parameters. The angle RMSD values of monomeric and dimeric conformation demonstrate a slight difference between experimental and theoretical findings. The deviation between X-ray diffraction and calculated parameters is probably owing to establishment of intermolecular interactions in crystalline structure which resulted by the formation of contacts between proton acceptor and proton donor. The H-bond interactions (N-H…O and C–H…O) formed between the two unit are represented with dashed lines in Fig. S1. The bond lengths and bond angles of these non-covalent contacts range experimentally between 1.91–2.86 Å and 152-157°, respectively. According to the finding results, the hydrogen bonding interactions are considered medium.

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Fig. 1

Optimized structure of N'-(4-Methoxybenzylidene)-5-phenyl-1H-pyrazole-3-carbohydrazide compound.

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3.2 Electron difference density (EDD) analysis

In order to estimate the bonding character between atoms, the EDD technical was conducted. The electron distribution overlapping and electronic density accumulation between atoms display the covalent type of bonding. Whereas, the transfer of electron and the detachment of electronic density distribution show the ionic bonding (Zhang et al., 2018). The EDD surface is also used to understand the electronic charge transition in crystal structure of compound under investigation. The direction of electronic charge transfer is from electron-surplus (nucleophilic sites) areas to electron-deficient (electrophilic sites) areas. To think about the electron reorganization due to the formation of chemical bonds, the EDD map between ground and excited state was drawn in Fig. 2. In intramolecular charge transfer, the nucleophilic region represented on orange correspond to increased electron density. While, the electrophilic regions with increased electron density are shown by blue color. The blue and orange areas contribute to the accumulation and reduction of charge density. As clearly seen from EDD plot, the orange surfaces around oxygen and azote atoms demonstrate the strong electronegativity of these atoms. Therefore, they participate as electron donor in bonding formation. Then, the presence of blue areas at hydrogen atoms of pyrazole and phenyl rings indicate electron density depletion. For benzene ring and carbohydrazide chain, the H atoms with orange surfaces show the accretion of charge density. This fact proves the ability of H-bonding interactions formation in MBPPC crystal arrangement.

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Fig. 2

Electron difference density map of N'-(4-Methoxybenzylidene)-5-phenyl-1H-pyrazole-3-carbohydrazide compound.

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3.3 AIM study

In order to discover the existence of the various interactions in crystalline structure via toplogical analysis, Bader has used the atom in molecule (AIM) theory (Sagaama et al., 2020). Thus, the topological analysis of MBPPC was performed, the AIM graphs generated by Multiwfn program are provided in Fig. 3. The topological parameters at Bond critical point (BCP): electron density ρ(r), Laplacian value Δρ(r), the eigenvalue (λ_1,2,3), Hessian matrix H(r), electrostatic potential V(r) and interaction energy E_int are illustrated in Table 2. In this section we focused on non-covalent interactions present in dimeric structure. Table 2 reveals the existence of five hydrogen bond types. For MBPPC, the density ρ and Laplacian charge density values of these hydrogen bonding interactions ranges respectively between 0.0017 and 0.01 and 0.0075–0.0356 a.u. The positive sign of Laplacian Δρ(r) disclose the electronic load depletion at the level of interatomic path. In addition, the C23-H24…O41 andN5-H39…O41 H-bonds considered the powerful interactions compared to the other ones with 18.11 and 18.90 kJ/mol values, respectively. According to interaction energy value, the increasing order of these H-bonds is C53-H54…O2 < C59-H60…C25 < N3-H40…C66 < C23-H24…O41 < N5-H39…O41. As clearly seen from dimer conformation, the oxygen atom O41 is related to two hydrogen atom (H24 and H39) forming two type of H-bond (N–H…O, C–H…O). From AIM plot, we notice the presence of 3 ring critical points (RCP) in the monomer while in dimer there are 6 RCPs as well as the training of 9 new ring critical points (NRCP). In addition, Fig. 3 show the presence of intra-molecular interaction such as N45-H80…N44 and intermolecular interaction different from H-bond of C-N…N nature.

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Fig. 3

AIM graphs of monomeric and dimeric structures mapped using Multiwfn package.

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3.4 Reduced density gradient analysis

Molecular stability is ensured by inter and intramolecular interactions, reduced density gradient (RDG) analysis was carried out to visualize these non-covalent interactions (NCI). This method can identify the NCI by using the $S=\frac{1}{2(3{\pi }^2)}\frac{\mathrm{\nabla }\rho }{{\rho }^{4/3}}$ function isosurface. The RDG surface of the dimer structure was generated for MBPPC molecule by 0.5 isosurface value, as clearly seen from Fig. S2. Also, VMD plots of non-covalent interactions existing in the monomeric and dimeric conformation were mapped and provided in Fig. 4. The RDG and VMD graphs are coded by a color scale; blue, green and red which correspond respectively to hydrogen bonding interaction (ρ > 0, λ > 0), van der Waals interactions (ρ = 0, λ = 0) and steric effect (ρ > 0, λ < 0). The region associate to steric repulsion effect shows the presence of 4 spikes (Fig. S2) in the ranges 0.005–0.025 a.u. These spikes characterize the repulsion effect in aromatic rings (phenyl, pyrazole, benzyl). The RDG isosurface illustrate the presence of two intensive peaks with sign (λ2)ρ equal to zero. They are certainly matching to van der Waals interactions. The hydrogen bonding interactions are visualized in VMD map by greenish blue areas. In RDG representation, the H-bonds which demonstrating strong attraction effect range between −0.01 and −0.02 a.u. Besides, the VMD plot of monomeric entity demonstrate the presence of intramolecular interaction within MBPPC geometrical structure. The C35-H37…H29 takes place between the methyl group and hydrogen atom of benzene ring. The pyrazole ring interact with phenyl ring form N3-H39…H16 and C7-H8…H20 hydrogen bonds. The C26-H27…N6 was seen between benzene ring and carbohydrazide chain. The N5-H40…N4 intramolecular interaction previously seen in AIM study has been established connecting pyrazole ring and carbohydrazide chain.

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Fig. 4

VMD plots of non covalent interactions existing in the monomer and dimer structures of our molecule.

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3.5 Hirshfeld surface

Hirshfeld surfaces analysis is a practical technical to explore the construction of supramolecular assembly (Ramalingam et al., 2020). The hydrogen bonding interactions and neighboring contacts are discovered by making Hirshfeld surface studies. The non-covalent interactions were estimated using 3D Hirshfeld surfaces and 2D fingerprint plot which mapped by crystal explorer 3. 1 software. These surfaces were plotted starting from the input file CIF (Crystallographic Information File). The 2D dimensional surfaces that have been plotted over d_norm, d_e, d_i, shape index, curvedness are provided in Fig. S3. The d_norm surface was generated over distance range from −0.6182 to 1.4971 Å. The d_i and d_e surface with rescale surface property varies between 0.7313 and 2.7380 Å. The shape index ranging from −1 to 1 Å, whereas the curvedness ranging between −4 and 4 Å. Red-white-blue is the color scale of d_norm map. The red is an indicator of shorter contacts, white color denotes van der Waals interactions while the blue shows the longer intermolecular contacts. The d_i and d_e image make out the hydrogen donors and hydrogen acceptors via red circles. The red triangle illustrated in shape index map as well as the green flat surface limited by blue contour in curvedness surface point to π-π stacking interactions. For clear visualization of intermolecular interactions types, d_norm surface of crystalline molecular arrangement was plotted in Fig. 5. This figure show the presence of six categories of hydrogen bond which are N-H…O, N-H…C, N-H…N, C-H…N, C-H…C and C-H…O. The red spots color intensity gives an idea on intermolecular interaction strength. In this context, the most powerful hydrogen contacts are N-H…O, N-H…C and N-H…N.

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Fig. 5

The intermolecular interactions in crystalline molecular arrangement.

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To identify the directional interaction, the two-dimensional fingerprint plots for reciprocal contacts and their percentage from the total surface. In 2D fingerprint plots, the contours of total print and by element are illustrated respectively by grey and blue regions. As clearly seen from Fig. S4, the O…H/H…O (1.8 Å) interaction appear as symmetrical wings. The H…H (35.6%) and C…H/H…C (33.5%) are the highest interactions due to the presence of abundance hydrogen and carbon atoms on the surface. The weaker contributions are associated to O…N/N…O (0.2%), O…C/C…O (0.8%), N…N (0.5%), N…C/C…N (2%) and finally C…C (0.3%). The other contacts: O…H/H…O and N…H/H…N have percentages equal to 15.2% and 11.7%, respectively.

3.6 HOMO-LUMO and DOS analysis

The highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular (LUMO) considered the most popular frontier orbitals. HOMO represent the nucleophile that gives electron while LUMO is considered as electrophile which accept electron. Energy difference between HOMO-LUMO orbitals determine the energy gap, as illustrated in Fig. S5. The gap energy gives information about chemical reactivity of a molecule (Bhavani et al., 2015). The weaker gap energy value characterizes the strong reactivity of the title compound. The red color represents the positive phase and the negative phase is colored by the green. The E_LUMO = −1.86642 eV; E_HOMO = −6.01916 eV and E_HOMO-LUMO is equal to −4.15274 eV. Starting from HOMO and LUMO energies, the ionization potential, electron affinity, electronegativity, chemical hardness, chemical potential are calculated and listed in Table S1. The gap energy value of dimer (−3.6245 eV) was lower than that of monomer (−4.1527 eV), the dimeric conformation was comparatively more reactive.

To full molecular orbital description, the density of state (DOS) approach was carried out. It gives the orbital population contribution of each entity to the total compound. TDOS, PDOS, OPDOS are respectively the total density of state, partial density of state and overlap density of state. TDOS provide the molecular orbital population of compound under investigation. Whereas, PDOS and OPDOS consists in dividing the compounds into fragments to know the contribution of each group and to predict the nature of interactions between each other. In addition, OPDOS is a helpful tool to discovering the type of contacts between orbitals, atomic groups or atoms. To plot PDOS and OPDOS per fragment, our compound is divided to four groups; methoxybenzylidene (fragment 1), phenyl (fragment2), pyrazole (fragment 3) and carbohydrazide (fragment 4). The Fig. S6 demonstrate the variation of OPDOS (right side) and TDOS as well PDOS (left side) in term of energy (a.u). The vertical dashed line in this figure corresponds to the highest occupied molecular orbital (HOMO) with energy equal to 0.22 a.u. Ranging from −0.35 to −0.50 a.u, the TDOS spectrum show the presence of two intense peaks. According to band intensities of PDOS diagrams, the increasing order of contribution is; pyrazole < carbohydrazide < phenyl < methoxybenzylidene. The methoxybenzylidene groupment predominantly provide to the molecular orbitals. Based on orbital overlap sign, the OPDOS technical classified the interactions on bonding (positive value), anti-bonding (negative value) and non-bonding (zero value) (Muthu et al., 2013). From OPDOS diagram, we can say that the interaction between the four fragments had non-bonding nature. Thus, this spectrum illustrates the non-bonding character of HOMO and LUMO orbitals.

3.7 First and second nonlinear optical properties

Nowadays, the non-linear optical (NLO) compounds are extremely used in optoelectronic and photonic field manufacturing (Govindharajan et al., 2020). They are applied in optical switching and communication as well as information storage. The purpose of this part is to discover the non-linear optical properties of the studied compound. The dipole moments μ, the average polarizability α, the anisotropy of the polarizability Δα, and the first hyperpolarizability β, and the second hyperpolarizability γ of MBPPC are tabulated in Table S2 in comparison to those of urea. The diagram in Fig. S7 shows the nonlinear optical parameters (μ, α, β, and γ) of both systems. The dipole moment of the urea is higher than MBPPC by 0.51 Debye. The component dipole moment μ_y = 1.2 Debye possess the largest contribution to the total electric moment. Then, the isotropic alpha polarisability of MBPPC (44.34 10⁻²⁴esu) was more than eight times larger than urea (5.09 10⁻²⁴esu). The anisotropy of linear polarizability Δα(0;0) of MBPPC and Urea were equal to 50.89, 2.03 10⁻²⁴esu, respectively. Regardless of direction, the α(−w;w) with 1064.6 nm laser pulsation value are 45.71(MBPPC)/ 5.13 10⁻²⁴esu (Urea). The linear polarisability anisotropy of Δα(−w;w) is 54.11 10⁻²⁴esu for compound under investigation and 2.05 10⁻²⁴esu for the compared molecule. Take into account the laser pulsation, the total polarisability and the anisotropy of lineair polarisability values show a little increase compared to parameters without consideration of pulsation. Therefore, the first hyperpolarisability of title molecule is almost 45 times higher than that of urea. The highest first hyperpolarisability value is directly related to intramolecular electronic charge transfer ability emerged from donor to acceptor groups throughout π conjugated contacts (Romani et al., 2020). Under electric field application effect, the first dipole hyperpolarizability β (−w;w,0)|| parallel component to dipole orientation is 3.6 10⁻³⁰esu for MBPPC and 0.02 10⁻³⁰esu for urea. This parameter is a measure of a molecule to act as an electrooptical Pockels effect environment, and the title molecule is a good candidate in this sense. In addition, the second harmonic generation SGH impact allow to rise the first dipole hyperpolarisability β (−2w;w,w)|| which range at 31.99 10⁻³⁰esu (MBPPC) and 0.41 10⁻³⁰esu (urea). The electric field induced SHG augment the second hyperpolarisability value with 40.5 10⁻³⁰esu (MBPPC)/0.20 10⁻³⁰esu (urea) compared to first order β NLO. The second-order NLO γ value of the studied molecule is 52 times higher than that of reference system (urea). Second dipole hyperpolarisability γ(−2w;w,w,0) value with electro-optical Kerr effect (EOKE) are equal to 362.87 and 4.11 10⁻³⁰esu for MBPPC and urea, respectively.

From this analysis, we can deduce that the first and second order NLO parameters are significantly influenced by the application of electric field. Based to calculation results of polarisability also first and second-order hyperpolarisability, the studied compound could be a good candidate for non-linear optical properties.

3.8 Vibrational studies

The MBPPC molecule is formed from 40 atoms, so it possess 114 (3N-6) normal modes. The vibrational assignments of studied compound has been determined using Veda4 program. Table S3 displays the recorded and computed wavenumbers obtained by the hybrid functional B3LYP and 6-311+G(2d,p) basis set. In vibrational theoretical spectrum, there are no imaginary frequencies so the optimized structure of MBPPC possess the lowest potential energy. In Fig. S8 (a), the experimental infrared spectrum of the title compound in solid state was provided ranging from 500 to 4000 cm⁻¹. The theoretical IR and Raman spectra were illustrated in Fig. S8 (b) and S9, respectively. The FT-IR spectra can be divided into two parts: 500–1750 cm⁻¹ and 1750–4000 cm⁻¹. As shown in Fig. S8, a sensible agreement between the experimental and theoretical spectra in the first region (500–1750 cm⁻¹). Whereas, in the second one (1750–4000 cm⁻¹) there are a difference between them. This deviation can be explained by the fact that the calculated and observed spectra were obtained respectively in gas phase and solid state. In the present work, the calculated wavenumbers are scaled, the scaling factors is 0.958 for frequencies higher than 1700 cm-1 while frequencies weaker than 1700 cm⁻¹ are multiplied by 0.983.

3.9 NMR spectral analysis

In order to identify the reactive organic and ionic species, the chemical shifts are habitually employed. NMR spectroscopy has considered as a convenient tool to clarify the molecular structure of compound under investigation. Therefore, structural optimization of the title compound were carried out by B3LYP/6-311G+(2d,p) level. The 1H and 13C isotropic chemical shifts were calculated by using Gauge-independent atomic orbital (GIAO) method with respect to TMS. The recorded and calculated 1H and 13C NMR spectra of MBPPC are illustrated in Fig. S10. The generated 1H and 13C NMR spectra of monomer and dimer conformation were depicted in Fig. S11. The 1H and 13C observed and computed chemical shifts of monomer and dimer are tabulated in Table 3. As plainly seen from this table that the two hydrogen atoms H39 and H40 bonded to the nitrogen atoms N3 and N5 which forms the N–H bond have the largest isotropic shift. For phenyl protons (H16, H14, H12, H10, H8), the chemical shifts observed in the range 7.458–7.830 ppm. While the calculated value are ranging from 7.76 to 8 ppm. The chemical shifts of H20 and H39 of pyrazole ring appear at 7.216 and 13.803 ppm, and computed at 7.31 and 10.02 ppm, respectively. Concerning the carbohydrazide chain, the shifts values of H_24,40 are experimentally founded to be 11.741 and 8.097 ppm and theoretically are equal to 9.95 and 8.19 ppm. The methyl proton (H_36,37,38) possess the weaker chemical shifts, the theoretical values were predicted at 4.06 and 3.84 ppm. Experimentally they were observed in the range 2.482–3.783 ppm. Besides, the 13C chemical shifts are recorded in the range −5–225 ppm. The major deviation between experimental and theoretical 13C shifts is noticed for C31 with −80.37 ppm. The signal predicted and recorded in the interval 168.72–113.83 ppm and 40.203–161.263 ppm, respectively, are assigned to aromatic carbon atoms of phenyl and benzene rings. The peaks occurred at 148.026, 147.272, 39.927 are associated respectively to C21, C18, C19 of pyrazole ring. While, the signals seen at 158.496 and 144.158 ppm correspond to C22 and C23 carbon atoms. Comparing the isotropic chemical sifts of monomer and dimer conformation, there is a lowering of the chemical shifts values especially for the carbon atoms that the protons.

3.10 Molecular docking calculation

3.10.1

3.10.1 MBPPC as anti-microbial agent

Cholera is a contagious epidemic enteric infection caused by a strictly human bacterium “Vibrio cholerae”. This latter is an incurved mobile bacterium inhabited in water has a great resistance to survive in the environment. The intestinal toxi-infection transmitted by ingestion of infected food and water or by direct faecal-oral way. The principal drug used in the treatment of this microbial bacterium is Bactrim. Looking at the sensitivity of certain patients against this type of drug and also in order to have an alternative of Bactrim, molecular docking analysis was carried out. In the current section, we perform a comparative analysis between the useful drug “Bactrim” and the candidate compound “MBPPC” based on binding affinities values. Docking results of both ligands with 5UL7 (Vibrio cholerae) protein were collected in Table S4. This Table display the small difference in binding score between the two ligands which equal to −0.77 kcal/mol. For MBPPC, the interaction energy is equal to −114.11 kcal /mol. The VDW and H-bond interactions are found to be −101.27 and −12.84 kcal/mol, respectively. Concerning Bactrim, the total energy, H-bond and VDW interactions values are found to be respectively −114.88, −81.54 and −33.34 kcal/mol. However, the most stable poses of MBPPC and Bactrim in protein sites are pictured in Fig. 6a. According to this representation, the applicant molecule is located in the protein center while the Bactrim is placed at the edge. Then, Fig. 6b show the interactions established between MBPPC atoms and pocket atoms of residues. There are many categories of interactions indicated with discontinuous lines such as conventional hydrogen bond (green), π-alkyl (purple) and π-anion (mustard yellow). The following residues: Leu 250, Ala 125, Arg 252 forms three π-alkyl interactions with benzene ring. The pyrazole ring works together with Ala 429, Phe 428 and Val 255 to form respectively π-alkyl, conventional hydrogen bond and π-lone pair interaction. Similarly, the π-anion interaction was created among Asp 121 residue and benzene ring. The obtained close binding value between MBPPC and Bactrim along with the numerous weak interactions established among our compound and amino acid residues demonstrate the significant capacity of our compound to be an anti-microbial drug against Vibrio cholerae.

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Fig. 6

Best poses of MBPPC, Bactrim, Rifampicine and Raloxifene in each protein along with the different interactions between ligand atoms and amino residues.

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