Novel synthetic ester of Brassicasterol, DFT investigation including NBO, NLO response, reactivity descriptor and its intramolecular interactions analyzed by AIM theory

Theoretical study by DFT and TD-DFT of NLO-active push-pull molecules composed of conjugated bridges based on cyclic rings: Titanol, Ferrol, Nickelol and Zinkol

CONTEXT

This research is based on the theoretical study of seven push-pull molecules composed of conjugated bridges based on two different organometallic rings, these bridges are linked at their ends by acceptor groups (-NO2) and donor groups (-N(CH3)2) on the α position of the rings mentioned above. The location of the donor and acceptor groups revealed that the addition of the acceptor groups near the rings (Titanol, Ferrol and Nickelol) improves the NLO response in comparison with the grafting of these groups on the Zinkol ring and also influences the positioning of the π electrons at the level of the chromophores studied. The molecule 2B gave the highest values ​​of static first hyperpolarisabilitiy (βtot) and static second hyperpolarisabilitiy (γav), knowing that: βtot (2B) = 135.79 * 10-30 esu and γav (2B) = 135.79 * 10-35 esu. The highest values ​​of dynamic firstβ ‖ λ - 2 ω ; ω , ω and secondγ ‖ λ - 2 ω ; ω , ω , 0 hyperpolarisabilities are assigned to the molecule 1C with the following values:γ ‖ λ - 2 ω ; ω , ω , 0 =1,218,310.00 * 10-30 esu andγ ‖ λ - 2 ω ; ω , ω , 0 =1,324,520,000 * 10-35 esu. The metal Zn is considered as an acceptor group and the remaining metals (Ti, Fe and Ni) are considered as donor groups. The specific solvents for the seven molecules are water, ethanol and acetonitrile. The maximum wavelengths recorded for all molecules in combination with all solvents are in the range of 421.39 to 765.28 nm. λ METHOD: The calculations were performed using Gaussian 16 software to perform DFT calculations with B3LYP functional. The LanL2DZ basis-set was used for transition metals, while the 6-31 +  + G(d,p) basis-set was used for nonmetal atoms. The functionals used are: CAM-B3LYP, LC-wPBE, LC-BLYP, M11, wB97X, M08-HX, M06-2X, MN12SX, MN15, and M06HF. The basis-sets used are: 6-31G(d,p), 6-31 +  + G(d,p), cc-pVDZ, aug-cc-pVDZ, 6-311G(d,p), 6-311 +  + G(d,p), cc-pVTZ, and aug-cc-pVTZ. The Natural Bond Orbital (NBO) calculations are performed by the NBO program incorporated by default in the Gaussian 16 program. The solvation models studied are the CPCM model (conductor polarizable continuum model) and the SMD model (Solvation Model Density). Excited states calculations are calculated by the time-dependent DFT method (TD-DFT).

Determining the Factors Accounting for Reaction Selectivity: A Relative Energy Gradient - Interacting Quantum Atoms and Natural Bonding Orbitals Study

Identifying the main physicochemical properties accounting for the course of a reaction is of utmost importance to rationalize chemical syntheses. To this aim, the relative energy gradient (REG) method is an appealing approach because it is an unbiased and automatic process to extract the most relevant pieces of energy information. Initially formulated within the interacting quantum atoms (IQA) framework for a single reaction, here we extend the REG method to natural bond orbitals (NBO) analysis and to the case of two competitive processes. This development enables the determination of the driving forces of any chemical selectivity. We illustrate the extended REG method on the case study of ring opening in cyclobutenes, which is an important instance of the so-called torquoselectivity.

Structural, computational and in silico studies of 4-bromo-3-flurobenzonitrile as anti-Alzheimer and anti-Parkinson agents

A novel dimer of the 4-bromo-3-fluorobenzonitrile was crystallized and studied using a spectroscopic method such as the scanning electron microscope method. The computational simulations substantiated the structural analysis findings. The Hirshfeld surface analysis has been performed for visualizing, exploring and quantifying the intra and inter-molecular interactions that stabilize the crystal packing of the compound. The NBO and QTAIM analyses were applied to study the nature and origin of the attractive forces involved in the crystal structure. Further, the pharmacokinetic properties of the compound were evaluated, indicating good brain-blood barrier and central nervous system penetration capability. Hence, in silico studies was carried out to explore the binding pattern of the titled compound against acetylcholinesterase and butyrylcholinesterase, and tumor necrosis factor-alpha converting enzyme proteins using molecular docking and molecular dynamics simulations approach. Further, the titled compound is compared with standard drugs through molecular docking studies. The in silico studies finally predicts that the compound under investigation may act as a good inhibitor for treating Alzheimer's disease and further in vitro and in vivo studies may provide its therapeutic potential.Communicated by Ramaswamy H. Sarma.

Synthesis, characterization, in vitro antimycobacterial and cytotoxicity evaluation, DFT calculations, molecular docking and ADME studies of new isomeric benzimidazole-1,2,3-triazole-quinoline hybrid mixtures

New benzimidazole-1,2,3-triazole-quinoline hybrids and their intermediates, differing in substitutions at the C-2 and/or C6 positions of the benzimidazole ring, were successfully synthesized in 55---80 % yields, with the C6-substituted ones forming as inseparable tautomeric mixtures. The synthesized compounds were fully characterised by FT-IR, 1D- and 2D-NMR, and HRMS. In-depth NMR analysis and DFT molecular calculations showed that the tautomeric mixtures formed in a ratio of almost 1:1 ratio (cis and trans), except for 5 g, where the ratio is 1:2. In vitro antimycobacterial activity evaluation against the H37Rv strain of Mycobacterial tuberculosis was undertaken on all synthesized compounds, and a selected number were further screened for their cytotoxicity on TZM-bl cell lines. Hybrid compounds showed excellent MIC90 activities ranging from 1.07 to 8.66 μM and were all more efficacious than the first-line reference drug, ethambutol (MIC90 = 9.54 μM). In particular, hybrid compounds 5b (MIC90 = 1.54 μM, CC50 = 58.89 μM and % cell viability = 14.07), 5d (MIC90 = 2.08 μM, CC50 = 0.27 μM, and % cell viability = 149.50 %) and 5 g (MIC90 = 1.49 μM, CC50 = 4.62 μM and % cell viability = 44.03) were the most promising. Significantly, 5b and 5 g were over six times more efficacious than ethambutol but exhibited cytotoxicity towards TZM-bl cell-lines compared to 5d, which was over four times more active than ethambutol. The physical combination (mimicking combination therapy) of individual pharmacophoric components making up 5 g were less active, indicating the synergistic effect of hybridization. In addition, more than 60 % of all the synthesized hybrids showed better activity than their respective pharmacophoric components. In silico ADME studies of the hybrids revealed favourable physico-chemical properties, while molecular modeling studies suggested binding interactions with Val 61, Gly 62, Glu 65, Ala 66, and Phe 69 amino acid in a reported similar manner to bedaquiline, an approved quinoline-based anti-TB drug.

Characteristics of new pyrrolic derivatives and their oligomers using DFT and TD-DFT calculations

CONTEXT

This article is based on the study of pyrrolic derivatives and their oligomers. Knowing that, pyrrolic derivatives are widely studied on an industrial scale. The aim of this work is to find pyrrolic derivatives having the same physicochemical characteristics such as the pyrrolic edifice. Six derivatives were studied by substituting the hydrogens in the β position of the pyrroles with the following radicals: -CHO, -Cl, -CN, -NO, and -OH. The study was carried out theoretically using ab initio and density functional of theory (DFT) methods. In the first step, molecules of four units were taken into consideration in order to make the comparison between them. This comparison showed that the majority of molecules exhibited high intramolecular charge transfer (ICT) compared to the molecule composed of four pyrrolic units (OP4), and also exhibited strong nucleophilic and electrophilic characteristics. Natural bond orbital (NBO) analysis has shown continuous ICT mechanisms for certain molecules. The studied derivatives showed good solvation in several solvents compared to OP4. The molecules substituted by the radicals -CHO, -CN, -OH, and -NO generated several peaks in the excited states, which is the opposite case for the other molecules with a single peak. The effects of chain elongation revealed exponential equations generated by the two parameters energy gaps (ΔEH-L) and maximum wavelengths (λmax) as a function of the number of units (n). These equations were used to predict the maximum and minimum values of the above parameters for more elongated oligomers.

METHOD

The software used to make the calculations is Gaussian 16. All geometries were calculated by B3LYP functional and 6-31++G(d,p) basis set. The electronic parameters ΔEH-L were calculated by the following functionals: B3LYP, CAM-B3LYP, LC-wPBE, LC-BLYP, wB97X, M062X, M06HF, and M11 in addition to the second-order Møller-Plesset method (MP2) while always keeping the basis set mentioned before. An effect of basis set variation was studied by the optimal functional in combination with the following basis sets: 6-31G(d,p), 6-31++G(d,p), cc-pVDZ, AUG-cc-pVDZ, 6-311G(d,p), 6-311++G(d,p), cc-pVTZ, and AUG-cc-pVTZ. The NBO study was carried out with the M06HF/6-31++G(d,p) functional using the NBO method. The solvation parameters were calculated by M06HF/6-31++G(d,p) in the presence of the implicit solvation model Solvation Model based on Density (SMD). The excited states were calculated by M06HF/6-31++G(d,p) by the implicit solvation model Conductor Polarizable Continuum Model (CPCM).

Study of nonlinear optical responses of phytochemicals of Clitoria ternatea by quantum mechanical approach and investigation of their anti-Alzheimer activity with in silico approach

Clitoria ternatea is a flowering plant with promising medicinal plants with a wide variety of active phytochemicals. The present study aimed at the computational investigation of the nonlinear optical (NLO) responses of the active phytochemicals of the Clitoria ternatea. The computational investigation of the NLO features was done by using the density functional theory (DFT) by B3LYP/6-311G + + (d, p) basis set. The structural parameters, mulliken charge distribution, and molecular electrostatic potential (MEP) surface clearly show the intramolecular charge transfer within Clitorin. The NLO properties were identified by computing the polarizability parameters. As the plant has high medicinal characteristics, the inhibiting properties of its phytochemicals were also investigated to combat Alzheimer disease (AD). The systematic in silico study identifies Clitorin as the most active and inhibiting phytochemicals of the plant. The results obtained from molecular dynamics (MD) simulation tell the stability of the complex and make it a fair selection as a drug-like molecule against AD. The cardio-toxicity analysis done for the Clitorin molecule verifies that it is harmless for the heart.

Supplementary information

The online version contains supplementary material available at 10.1007/s11224-022-01981-5.

Computational and Experimental Investigations of 7-(4-nitrophenyl)benzo[6,7]chromeno[3,2-e]pyrido[1,2-a]pyrimidin-6(7h)-one

Acstract:

In-silico studies are used for the prediction of the properties of several novel materials using computer simulation technique. The present study describes the complete description of the molecular vibrations and electronic feature of the title compound by this technique. 7-(4-nitrophenyl)benzo[6,7]chromeno[3,2-e]pyrido[1,2-a]pyrimidin-6(7H)-one was prepared by the multicomponent reaction of 2H-pyrido[1,2-a]pyrimidine-2,4(3H)-dione, 2-naphthol and p-nitrobenzaldehyde. The structure of the compound was confirmed by UV, IR, NMR (1H, 13C) and mass spectroscopic studies. The compound was further subjected to quantum chemical calculations at the level of Hartee-Fock (HF) method using Lan2DZ basis set to compute polarizability, hyperpolarizabilities, AIM approach, Natural bond orbital analysis, complete vibrational assignments, Mulliken charges, spectral analysis and HOMO-LUMO energies

Theoretical study of new push–pull molecules based on transition metals for NLO applications and determination of ICT mechanisms by DFT calculations

This study is based on the valuation of a few model molecules. The objective of this research is focussed on the nonlinear optical (NLO) improvement of four organometallic molecules and one organic molecule. These molecules have been subjected to several calculations by different functionals: CAM–B3LYP, LC–BLYP, LC–wPBE, wB97X, M11, M06–2X, M08–HX and M08–SO. These functionals gave three orders of classification of the [Formula: see text] parameters. The CAM–B3LYP functional recorded very good agreement between [Formula: see text] parameters and gaps ([Formula: see text]. Significant first hyperpolarizabilities ([Formula: see text] have been obtained around 880 * 10[Formula: see text][Formula: see text]esu. The mechanisms of intramolecular charge transfer (ICT) have shown energetic passages from donor groups to acceptors and vice versa. The substitution of metals influences the location of [Formula: see text] electrons at the level of the chromophores. Finally, the lengthening of the aromatic chains between the acceptor and donor groups shows significant NLO improvements. The first and second hyperpolarizabilities ([Formula: see text] and ([Formula: see text] for a chain of several benzene rings are of the order of 21,663.16 * 10[Formula: see text][Formula: see text]esu and 16,464.65 * 10[Formula: see text][Formula: see text]esu, respectively.

Synthesis, spectroscopic investigation, molecular docking and DFT studies of novel (2Z,4Z)-2,4-bis(4-chlorobenzylidene)-5-oxo-1-phenylpyrrolidine-3-carboxylic acid (BCOPCA)

The synthesized compound (2Z,4Z)-2,4-bis(4-chlorobenzylidene)-5-oxo-1-phenylpyrrolidine-3-carboxylic acid (BCOPCA) was characterised by Ultraviolet, FT-Infra Red, ¹H, ¹³C Nuclear Magnetic Resonance and mass spectroscopy. The compound was further subjected to quantum chemical calculations at the level of density functional theory (DFT) using 6-31G (d,p) basis sets method with B3LYP and CAM-B3LYP hybrid functionals. The intramolecular interactions, polarizability, hyperpolarizability and nonlinear optical properties of the title compound were also incorporated in the study. The total first static hyperpolarizability (β₀ = 19.477 × 10⁻³⁰ and 16.924 × 10⁻³⁰ esu) value was also computed and indicated the title molecule as an interesting forthcoming NLO material. The other thermodynamic properties (entropy, heat capacity and zero vibrational energy) were also discussed. The study also includes NBO computations, complete vibrational assignments, Mulliken charges, UV–Visible spectral analysis and HOMO–LUMO energies. The regions of low and high electron density were obtained from MESP and ESP maps. The calculated parameters for BCOPCA using aforementioned functions are harmonious with the experimental findings. The in-vitro antimicrobial activity and molecular docking studies of BCOPCA were also done and showed a good correlation.

Inhibition mechanism of L,D-transpeptidase 5 in presence of the β-lactams using ONIOM method

Tuberculosis (TB) is one of the world's deadliest diseases resulting from infection by the bacterium, Mycobacterium tuberculosis (M.tb). The L,D-transpeptidase enzymes catalyze the synthesis of 3 → 3 transpeptide linkages which are predominant in the peptidoglycan of the M.tb cell wall. Carbapenems is class of β-lactams that inactivate L,D-transpeptidases by acylation, although differences in antibiotic side chains modulate drug binding and acylation rates. Herein, we used a two-layered our Own N-layer integrated Molecular Mechanics ONIOM method to investigate the catalytic mechanism of L,D-transpeptidase 5 (Ldt_Mt5) by β-lactam derivatives. Ldt_Mt5 complexes with six β-lactams, ZINC03788344 (1), ZINC02462884 (2), ZINC03791246 (3), ZINC03808351 (4), ZINC03784242 (5) and ZINC02475683 (6) were simulated. The QM region (high-level) comprises the β-lactam, one water molecule and the Cys360 catalytic residue, while the rest of the Ldt_Mt5 residues were treated with AMBER force field. The activation energies (ΔG^#) were calculated with B3LYP, M06-2X and ωB97X density functionals with 6-311++G(2d, 2p) basis set. The ΔG^# for the acylation of Ldt_Mt5 by the selected β-lactams were obtained as 13.67, 20.90, 22.88, 24.29, 27.86 and 28.26 kcal mol^-1respectively. Several of the compounds showed an improved ΔG^# when compared to the previously calculated energies for imipenem and meropenem for the acylation step for Ldt_Mt5. This model provides further validation of the catalytic inhibition mechanism of LDTs with atomistic detail.