Modeling the conformational preference, spectroscopic properties, UV light harvesting efficiency, biological receptor inhibitory ability and other physico-chemical properties of five imidazole derivatives using quantum mechanical and molecular mechanics tools

Discovery of natural multi-targets neuraminidase inhibitor glycosides compounds against influenza A virus through network pharmacology, virtual screening, molecular dynamics simulation, and in vitro experiment

Influenza virus continually challenges both human and animal health. Moreover, influenza viruses are easy to mutate. In a certain degree, vaccines may not catch up with rapid mutant paces of viruses. Anti-influenza drugs NIs (neuraminidase inhibitors) are one of the best choices. Therefore, based on ADMET properties, eight optimal natural multi-targets NIs glycosides compounds (IC50  = 0.094-97.275 μM) are found from radix glycyrrhizae, flos sophorae, caulis spatholobi, radix astragali, radix glycyrrhizae, semen astragali complanati, and common fenugreek seed through network pharmacology, molecular docking, dynamics simulation, quantum chemistry, and in vitro experiment. Moreover, mechanism research illustrates these natural compounds treat influenza A virus through key targets TLR4, TNF, and IL6 (high fever, acute respiratory distress syndrome), MAPK1, and MAPK3 (MAPK signaling pathway, viral RNP export, and viral protein expression), IL1B (NOD-like receptor signaling pathway, suppressed maturation of pro-IL-1β and pro-IL-18), CASP3 (apoptosis), AKT1 (inhibited premature apoptosis), and EP300 (viral myocarditis, chemoattraction of monocytes and macrophages, T-cell activation antibody response).

Porphyrin and phthalocyanine heavy metal removal: overview of theoretical investigation for heterojunction organic solar cell applications

CONTEXT

Heavy metals are highly noxious, and their presence can cause diverse effects on living organisms and the environment. Crown ether porphyrins and phthalocyanines are known to effectively extract these pollutants and are also used in photovoltaic devices. This study aims to evaluate various factors that govern intramolecular charge transfer (ICT) and photo-injection processes, including maximum absorption wavelength (λ_max), density of states (DOS), charge transfer dipole (μ_CT), light harvesting efficiency (LHE), open-circuit voltage (V_oc), and free energy change of electron injection (ΔG_inj) in order to investigate the performance of different compounds designed from metalloporphyrins for bulk-heterojunction organic solar cell (BHJ-OSC) applications. The porphyrin complex showed the best optoelectronic properties, with remarkable LHE values and CT amounts compared to phthalocyanine derivatives. The central metal played a significant role in optimizing the optical properties of the materials for use in solar cells. HgPr4O and CdPr4O were found to have optimal V_oc values, resulting in effective injection, high electron, and hole mobilities, making them ideal materials for highly efficient BHJ-OSC devices.

METHODS

Density functional theory (DFT) approach was employed with the B3LYP functional and the def2TZVP basis set as implemented in the Gaussian 16 revision C.01 program to investigate the designed complexes and to compute geometrical parameters, frontier molecular orbitals (FMOs), and natural bond orbital (NBO). Furthermore, the time-dependent density functional theory (TD-DFT) method was used to analyze the optical properties and photovoltaic characteristics of selected metalloporphyrins by examining the UV-Vis spectra. In summary, the study presents a thorough description of the structural and electronic properties of the investigated complexes and provides insights into their potential use in photovoltaic applications.

Schiff Bases from α-ionone with Adenine, Cytosine, and l-leucine Biomolecules: Synthesis, Structural Features, Electronic Structure, and Medicinal Activities

Tea is a very important source of the terepenoid [Formula: see text]-ionone, which is much appreciated as a medicinal beverage. Schiff bases are a very important class of organic compounds usually formed by the condensation of carbonyl compounds with amines. [Formula: see text]-ionone is a carbonyl terpenoid obtained from Schiff bases on condensation with nucleobases like adenine and cytosine and the amino acid [Formula: see text]-leucine. We synthesized these three Schiff bases and characterized them using UV, FTIR, and H1 and C13-NMR spectra. The molecules were optimized using B3LYP/6-311+G(2d,p) level followed by the simulation of FT-IR spectra, of which the simulated and experimental spectra showed complete agreement. The UV spectra were simulated using TD-DFT, and the electronic excitations were carefully analyzed. Natural bond orbitals provided an analysis of the stability of the compound, which is supplemented by the data from frontier molecular orbital analysis. Detailed wavefunction analysis is reported which predicts the active centers, reactivity profile, and the extent of non-covalent interactions. PASS indicated that compounds show antieczemic properties and antiarthritic properties, which is confirmed with the help of molecular docking results.

Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-based Drug Design and Discovery

Quantum mechanics (QM) is physics based theory which explains the physical properties of nature at the level of atoms and sub-atoms. Molecular mechanics (MM) construct molecular systems through the use of classical mechanics. So, hybrid quantum mechanics and molecular mechanics (QM/MM) when combined together can act as computer-based methods which can be used to calculate structure and property data of molecular structures. Hybrid QM/MM combines the strengths of QM with accuracy and MM with speed. QM/MM simulation can also be applied for the study of chemical process in solutions as well as in the proteins, and has a great scope in structure-based drug design (CADD) and discovery. Hybrid QM/MM also applied to HTS, to derive QSAR models and due to availability of many protein crystal structures; it has a great role in computational chemistry, especially in structure- and fragment-based drug design. Fused QM/MM simulations have been developed as a widespread method to explore chemical reactions in condensed phases. In QM/MM simulations, the quantum chemistry theory is used to treat the space in which the chemical reactions occur; however the rest is defined through molecular mechanics force field (MMFF). In this review, we have extensively reviewed recent literature pertaining to the use and applications of hybrid QM/MM simulations for ligand and structure-based computational methods for the design and discovery of therapeutic agents.

Exploring the charge injection aptitude in pyrazol and oxazole derivatives by the first-principles approach

Azole derived products acquired significant consideration in everyday life based on their improved biological potential to the semiconducting substances. The research focused in-depth within pyrazol, and oxazole compounds 1–4 concerning charge transport, structural, optical as well as electronic properties. The density functional theory (DFT) along with time-dependent DFT were used for the optimization of their ground state geometries and excitation energies. We also investigated the molecule’s electron coupling constants (|V RP|) as well as electron injection (ΔG inject) values. For better understanding, charge transport and electronic characteristics were performed through quantum chemical computations. The |V RP| and ΔG inject values of pyrazole, as well as oxazole molecules, exhibited that these compounds could be competent for dye-sensitized solar cell applications. The pyrazole higher diagonal band gap enlightening these might have enhanced fill factor (FF) along with short-circuit current density (J sc ). We have also explored the electron injection, energy level offset, dissociation of excitons, and band alignment of studied compounds to shed light on the functionality of these compounds for photovoltaic and semiconductor device applications.

Experimental and computational studies of an antiplasmodial derivative of allantoin; antimycobacterial essential oil from Cordia batesii WERNHAM (Boraginaceae)

Background

Chemical and pharmacological investigations were performed on the stems of Cordia batesii (Boraginaeae); chemical studies included quantum calculations applied on a newly described compound.

Results

A new derivative of allantoin (1) named batesiin (2) was characterized. Thirteen other known compounds involving allantoin (1) were either isolated or identified. GC–MS enabled the identification of six compounds from a fraction containing essential oil. MeOH extract and some isolated compounds were tested in vitro against Pf7G8 CQS and Pf Dd2 CQR strains of Plasmodium falciparum; extract disclosed a moderate antiplasmodial activity (IC₅₀ = 50 μg mL⁻¹). Meantime, the CH₂Cl₂ extract and essential oil fraction were tested on a resistant mycobacterial strain of Mycobacterium tuberculosis; a potent antimycobacterial activity with a MIC = 9.52 μg mL⁻¹ was deduced from essential oil. Density functional theory (DFT) calculations were carried on batesiin (2). Calculated chemical shifts at B3LYP/6-31G(d,p) and MPW1PW91/6-31G+(d,p) showed much better correlations with the experimental data. Time dependent DFT at B3LYP/6-31G+(d,p) displayed a major absorption band 3.01 nm higher than the experimental value.

Conclusion

Cordia batesii can be considered as promising in search of compounds with antimalarial and antitubercular properties. DFT studies are very helpful when trying to learn more about the spectroscopic insights of a derivative of allantoin (1).

Conformational analysis and quantum descriptors of two new imidazole derivatives by experimental, DFT, AIM, molecular docking studies and adsorption activity on graphene

1-[2-(2-hydroxy-3-methoxy-5-(4-methoxyphenylazo)benzaldeneamino)ethyl]-3-methyl-3H-imidazole (HMY) and 1-[2-(2-hydroxy-3-methoxy-5-(4-methylphenylazo)benzaldene amino)ethyl]-3-methyl-3H-imidazole (HMM) were synthesized and characterized using spectral analysis. Conformational analysis has been achieved using potential energy scan for different rotable bonds for obtaining the lowest energy conformer. Conformer with minimum energy is obtained along the dihedral angle N30-C31-C34-N37. QTAIM analysis gives nature and strength of hydrogen bonding interactions. UV-Vis, electrostatic potential and chemical descriptors are analyzed. Interaction of HMY and HMM with graphene is analyzed in terms of SERS activity. Chemical reactivity descriptors were investigated for graphene-drug systems. NLO activity of parent drugs and its graphene complexes show good activity. The wavenumber downshift of different modes is noted. Title molecules exhibit inhibitory activity against cytochrome C peroxidase. Interactions with graphene sheets are theoretically predicted for the title compounds.

Structural and physico-chemical evaluation of melatonin and its solution-state excited properties, with emphasis on its binding with novel coronavirus proteins

Melatonin is a natural hormone from the pineal gland that regulates the sleep-wake cycle. We examined the structure and physico-chemical properties of melatonin using electronic structure methods and molecular-mechanics tools. Density functional theory (DFT) was used to optimise the ground-state geometry of the molecule from frontier molecular orbitals, which were analysed using the B3LYP functional. As its electrons interacted with electromagnetic radiation, electronic excitations between different energy levels were analysed in detail using time-dependent DFT with CAM-B3LYP orbitals. The results provide a wealth of information about melatonin's electronic properties, which will enable the prediction of its bioactivity. Molecular docking studies predict the biological activity of the molecules against the coronavirus2 protein. Excellent docking scores of −7.28, −7.20, and −7.06 kcal/mol indicate that melatonin can help to defend against the viral load in vulnerable populations. Hence it can be investigated as a candidate drug for the management of COVID.

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Detailed quantum mechanical studies of the sleep regulating hormone melatonin

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Analysed the intramolecular stabilisation and nonlinear properties

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Excited state properties using TD-DFT formalism

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Compound active binds to three known novel coronavirus 2019 proteins.