Synthesis and spectroscopic study of two new pyrazole derivatives with detailed computational evaluation of their reactivity and pharmaceutical potential

Accessing Properties of Molecular Compounds Involved in Cellular Metabolic Processes with Electron Paramagnetic Resonance, Raman Spectroscopy, and Differential Scanning Calorimetry

In this work, we review some physical methods of macroscopic experiments, which have been recently argued to be promising for the acquisition of valuable characteristics of biomolecular structures and interactions. The methods we focused on are electron paramagnetic resonance spectroscopy, Raman spectroscopy, and differential scanning calorimetry. They were chosen since it can be shown that they are able to provide a mutually complementary picture of the composition of cellular envelopes (with special attention paid to mycobacteria), transitions between their molecular patterning, and the response to biologically active substances (reactive oxygen species and their antagonists-antioxidants-as considered in our case study).

DFT investigations and molecular docking as potent inhibitors of SARS-CoV-2 main protease of 4-phenylpyrimidine

In this work, quantum chemical descriptors and a vibrational analysis of 4-Phenylpyrimidine (4-PPy) were also investigated. Through conformational analysis, the most stable conformer can be determined. The geometry of the molecular structure was optimized by using the density functional theory (DFT) at the B3LYP/6-311++G(d,p) level. The theoretically obtained FT-IR and FT-Raman spectral data agree with the experimental results. UV-Vis was done in the gas phase along with different solvents by the TD-DFT method and the PCM solvent model. Molecular electrostatic potential, natural bond orbital analysis, nonlinear optical properties, and global chemical reactivity parameters were described through the DFT method. Besides, the chemical implications of a molecule were explained using an electron localization function and a local orbital locator. We attempted to detect the antiviral activity of the 4-PPy compound by predicting molecular docking into coronavirus 2 (SARS-n-CoV-2) protein structures (6LU7, 6M03, and 6W63), because COVID-19 is known to have serious adverse effects in all areas of human life worldwide, and possible drugs need to be investigated for this. The results of the docking simulation demonstrate good affinities for binding to the receptors.

Quantum computational investigation into structural, spectroscopic, topological and electronic properties of L-histidinium-L-tartrate hemihydrate: Nonlinear optical organic single crystal

For the first time, a systematic investigation of optimization in the geometrical, vibrational, natural bonding orbital (NBO), electronic, linear and nonlinear optical properties, and Hirshfeld surface analysis for the L-histidinium-l-tartrate hemihydrate (HT) crystal is reported by employing the density functional theory (DFT). The geometrical parameters and vibrational frequencies obtained from the B3LYP/6-311++G(d,p) level of theory are in good agreement with the experimental values. The presence of strong hydrogen bonding interactions in the molecule causes an intense absorption peak in the infrared spectrum below 2000 cm^-1. Quantum Theory of Atoms in Molecules (QTAIM) has been used to evaluate the topology of the electron density of a particular molecule to identify the critical points of the system using Multiwfn 3.8. These studies included ELF, LOL, and RDG studies. A time-dependent DFT approach is employed to obtain the excitation energies, oscillator strengths, and UV-Vis spectra for different solvents, such as methanol, ethanol, and water. The NBO analysis of the chosen compound, HT, is performed in terms of atom hybridization and electronic structure. The HOMO-LUMO energies and other associated electronic parameters are also computed. The nucleophilic sites are identified from MEP and Fukui functions analysis. The electrostatic potential and total density of states spectra of HT are discussed in detail. The theoretically obtained polarizability and first order hyperpolarizability values confirm that the grown material HT has NLO efficiency 15.771 times that of urea, and is proposed to be an exceptional nonlinear optical material. In addition, Hirshfeld surface analysis is performed to determine the inter-and intramolecular interactions in the title compound.

In silico Drug Repurposing of Anticancer Drug 5-FU and Analogues Against SARS-CoV-2 Main Protease: Molecular Docking, Molecular Dynamics Simulation, Pharmacokinetics and Chemical Reactivity Studies

Background

Since the last COVID-19 outbreak, several approaches have been given a try to quickly tackle this global calamity. One of the well-established strategies is the drug repurposing, which consists in finding new therapeutic uses for approved drugs. Following the same paradigm, we report in the present study, an investigation of the potential inhibitory activity of 5-FU and nineteen of its analogues against the SARS-CoV-2 main protease (3CLpro).

Material and Methods

Molecular docking calculations were performed to investigate the binding affinity of the ligands within the active site of 3CLpro. The best binding candidates were further considered for molecular dynamics simulations for 100 ns to gain a time-resolved understanding of the behavior of the guest-host complexes. Furthermore, the profile of druggability of the best binding ligands was assessed based on ADMET predictions. Finally, their chemical reactivity was elucidated using different reactivity descriptors, namely the molecular electrostatic potential (MEP), Fukui functions and frontier molecular orbitals.

Results and Discussion

From the calculations performed, four candidates (compounds 14, 15, 16 and 18) show promising results with respect to the binding affinity to the target protease, 3CLpro, the therapeutic profile of druggability and safety. These compounds are maintained inside the active site of 3CLpro thanks to a variety of noncovalent interactions, especially hydrogen bonds, involving important amino acids such as GLU166, HIS163, GLY143, ASN142, HIS172, CYS145. Molecular dynamics simulations suggest that the four ligands are well trapped within the active site of the protein over a time gap of 100 ns, ligand 18 being the most retained.

Conclusion

In line with the findings reported herein, we recommend that further in-vitro and in-vivo investigations are carried out to shed light on the possible mechanism of pharmacological action of the proposed ligands.

Structural and Vibrational Investigation of Benzil-(1,2-Diphenylethane-1,2-Dione): Experimental and Theoretical Studies

Single crystals of benzil commonly known as 1,2-diphenylethane-1,2-dione are grown by the slow evaporation method at room temperature. Gaussian 09 program is applied for theoretical calculations with B3LYP/6-311++G(d,p) basis set. The structure is optimized, and the energy, structural parameters, vibrational frequencies, IR, and Raman intensities are determined. Complete natural bonding orbital (NBO) analysis is carried out to analyze the intramolecular electronic interactions and their stabilization energies. From the second-order perturbation theory analysis of the benzil molecule, it is observed that there exists a hyperconjugative intramolecular stabilization energy between 17.45 and 22.76 KJmol-1. HOMO-LUMO analysis has been performed to identify the charges transferred within the molecule. The energy gap is calculated to be 2.919 eV and thus establishes the soft nature of the molecule. The molecular electrostatic potential (MEP) of the grown crystal was analyzed using the B3LYP method with 6-311++G(d,p) basis set. First-order hyperpolarizability calculations reveal the nonlinear optical microscopic behavior of the benzil molecule with nonzero values. The total value of the first-order hyperpolarizability ( ${\beta }_{\text{tot}}$ ) is of the order of $41.5246\times {10}^{-31}\text{esu}$ , which is found to be 11.135 times that of urea. Hence, benzil can be referred to as a good material for nonlinear optical applications.

Energy and reactivity profile and proton affinity analysis of rimegepant with special reference to its potential activity against SARS-CoV-2 virus proteins using molecular dynamics

Rimegepant is a new medicine developed for the management of chronic headache due to migraine. This manuscript is an attempt to study the various structural, physical, and chemical properties of the molecules. The molecule was optimized using B3LYP functional with 6-311G + (2d,p) basis set. Excited state properties of the compound were studied using CAM-B3LYP functional with same basis sets using IEFPCM model in methanol for the implicit solvent atmosphere. The various electronic descriptors helped to identify the reactivity behavior and stability. The compound is found to possess good nonlinear optical properties in the gas phase. The various intramolecular electronic delocalizations and non-covalent interactions were analyzed and explained. As the compound contain several heterocyclic nitrogen atoms, they have potential proton abstraction features, which was analyzed energetically. The most important result from this study is from the molecular docking analysis which indicates that rimegepant binds irreversibly with three established SARS-CoV-2 proteins with ID 6LU7, 6M03, and 6W63 with docking scores − 9.2988, − 8.3629, and − 9.5421 kcal/mol respectively. Further assessment of docked complexes with molecular dynamics simulations revealed that hydrophobic interactions, water bridges, and π–π interactions play a significant role in stabilizing the ligand within the binding region of respective proteins. MMGBSA-free energies further demonstrated that rimegepant is more stable when complexed with 6LU7 among the selected PDB models. As the pharmacology and pharmacokinetics of this molecule are already established, rimegepant can be considered as an ideal candidate with potential for use in the treatment of COVID patients after clinical studies.

Investigation of Pharmaceutical Importance of 2H-Pyran-2-One Analogues via Computational Approaches

Highly functionalized spirocyclic ketals were synthesized through asymmetric oxidative spirocyclization via carbanion-induced ring transformation of 2H-pyran-2-ones with 1,4-cyclohexandione monoethyleneketal under alkaline conditions. Further acidic-hydrolysis of obtained spirocyclic ketals yields highly substituted 2-tetralone in good yield. Computational analysis based on the DFT calculations and MD simulations has been performed in order to predict and understand global and local reactivity properties of newly synthesized derivatives. DFT calculations covered fundamental reactivity descriptors such as molecular electrostatic potential and average local ionization energies. Nitrogen atom and benzene rings have been recognized as the most important molecular sites from these aspects. Additionally, to predict whether studied compounds are stable towards the autoxidation mechanism, we have also studied the bond dissociation energies for hydrogen abstraction and identified the derivative which might form potentially genotoxic impurities. Interactions with water, including both global and local aspects, have been covered thanks to the MD simulations and calculations of interaction energies with water, counting of formed hydrogen interactions, and radial distribution functions. MD simulations were also used to identify which excipient could be used together with these compounds, and it has been established that the polyvinylpyrrolidone polymer could be highly compatible with these compounds, from the aspect of calculated solubility parameters.

Vibrational spectroscopy, quantum computational and molecular docking studies on 2-chloroquinoline-3-carboxaldehyde

The quantum mechanical density functional theory (DFT) approach was used to analyze vibrational spectroscopy for the title compound 2-chloroquinoline-3-carboxaldehyde, and the observations were compared to experimental results. B3LYP with the 6-311++ G (d, p) basis set produces the optimized molecular structure and vibrational assignments. The charge delocalization and hyper conjugative interactions were studied using NBO analysis. Fukui functions were used to determine the chemical reactivity of the examined molecule. The linear polarizability, first order polarizability, NLO and Thermodynamic properties are calculated. Additionally, Molecular electrostatic potential (MEP) and HOMO-LUMO are reported. Multi wavefunction analysis like ELF (Electron Localization Function) and LOL (Localized Orbital Locator) are analyzed. For the headline compound, drug-likeness properties were examined. Molecular docking analysis on the examined molecule are done to understand the biological functions of the headline molecule and the minimum binding energy, hydrogen bond interactions, are analyzed.

Synthesis and Anti-Proliferative Evaluations of New Heterocyclic Derivatives Using 5,6,8,9-Tetrahydropyrazolo[5,1-b]quinazolin-7(3H)-one Derivatives Derived from Cyclohexa-1,4-dione

BACKGROUND

Recentlty, pyrazoloquinazoline derivatives acquired a special attention due to their wide range of pharmacological activities, especially therapeutic. Through the market, it was found that many pharmacological drugs containing the quinazoline nucleus were known.

OBJECTIVE

The aim of this work is to synthesize target molecules possessing not only anti-tumor activities but also kinase inhibitors. The target molecules were obtained through the synthesis of a series of 5,6,8,9- tetrahydropyrazolo[5,1-b]quinazolin-7(3H)-one derivatives 4a-i using the multi-component reactions of cyclohexane- 1,4-dione (1), the 5-amino-4-(2-arylhydrazono)-4H-pyrazol-3-ol derivatives 2a-c, the aromatic aldehydes 3a-c, respectively. The synthesized compounds were evaluated against c-Met kinase, PC-3 cell line, and different kinds of cancer cell lines together with normal cell line, tyrosine kinases, and Pim-1 kinase.

METHODS

Multi-component reactions were adopted using compound 1 to get different 5,6,8,9- tetrahydropyrazolo[5,1-b]quinazolin-7(3H)-one derivatives which underwent further heterocyclization reactions. The c-Met kinase activity of all compounds was evaluated using Homogeneous Time-Resolved Fluorescence (HTRF) assay, taking foretinib as the positive control. The anti-proliferative activity of all target compounds against the human prostatic cancer PC-3 cell line was measured using MTT assay using SGI-1776 as the reference drug. All the synthesized compounds were assessed for inhibitory activities against A549 (non-small cell lung cancer), H460 (human lung cancer), HT-29 (human colon cancer), and MKN-45 (human gastric cancer) cancer cell lines together with foretinib as the positive control by an MTT assay.

RESULTS

Antiproliferative evaluations and c-Met kinase, Pim-1 kinase inhibitions were performed for the synthesized compounds, where the varieties of substituents through the aryl ring and the thiophene moiety afforded compounds with high activities.

CONCLUSION

The compounds with high antiproliferative activity were tested towards c-Met and the results showed that compounds 4e, 4f, 4g, 4i, 6i, 6k, 6l, 8f, 8i, 10d, 10e, 10f, 10h, 12e, 12f, 12g, 12h, 12i, 14f, 14g, 14h, and 14i were the most potent compounds. A further selection of compounds for the Pim-1 kinase inhibition activity showed that compounds 4f, 6i, 6l, 8h, 8i, 8g, 10d, 12i, and 14f were the most active compounds to inhibit Pim-1.

Excited-state electronic properties, structural studies, noncovalent interactions, and inhibition of the novel severe acute respiratory syndrome coronavirus 2 proteins in Ripretinib by first-principle simulations

Ripretinib is a recently developed drug for the treatment of adults with advanced gastrointestinal stromal tumors. This paper reports an attempt to study this molecule by electronic modeling and molecular mechanics to determine its composition and other specific chemical features via the density-functional theory (DFT), thereby affording sufficient information on the electronic properties and descriptors that can enable the estimation of its molecular bioactivity. We explored most of the physico-chemical properties of the molecule, as well as its stabilization, via the studies of the natural bond orbitals and noncovalent interactions. The electronic excitation, which is a time-dependent process, was examined by the time-dependent DFT with a CAM-B3LYP functional. The molecular docking study indicated that Ripretinib strongly docks with three known novel severe acute respiratory syndrome coronavirus 2 (SARS-n-CoV-2) proteins with a reasonably good docking score.

Structural investigations, quantum mechanical studies on proton and metal affinity and biological activity predictions of selpercatinib

Cancer of the lungs and thyroid is particularly difficult to manage and treat. Notably, selpercatinib has recently been suggested as an effective drug to combat these diseases. The entire world is currently tackling the pandemic caused by the SARS-CoV-19 virus. Numerous pharmaceuticals have been evaluated for the management of the disease caused by SARS-CoV-19 (i.e., COVID-19). In this study, selpercatinib was proposed as a potential inhibitor of different SARS-CoV-19 proteins. Several intriguing effects of the molecule were found during the conducted computational investigations. Selpercatinib could effectively act as a proton sponge and exhibited high proton affinity in solution. Moreover, it was able to form complexes with metal ions in aqueous solutions. Specifically, the compound displayed high affinity towards zinc ions, which are important for the prevention of virus multiplication inside human cells. However, due to their charge, zinc ions are not able to pass the lipid bilayer and enter the cell. Thus, it was determined that selpercatinib could act as an ionophore, effectively transporting active zinc ions into cells. Furthermore, various quantum mechanical analyses, including energy studies, evaluation of the reactivity parameters, examination of the electron localisation and delocalisation properties, as well as assessment of the nonlinear optical (NLO) properties and information entropy, were conducted herein. The performed docking studies (docking scores -9.3169, -9.1002, -8.1853 and -8.1222 kcal mol^-1) demonstrated that selpercatinib strongly bound with four isolated SARS-CoV-2 proteins.

Cocrystals of hydrochlorothiazide with picolinamide, tetramethylpyrazine and piperazine: quantum mechanical studies, docking and modelling of the photovoltaic efficiency for DSSC

Cocrystals are of immense applications in crystal engineering and pharmaceutical chemistry. Hydrochlorothiazide is found to form cocrystals with picolinamide (H1), tetramethylpyrazine (H2) and piperazine (H3). It was characterized using IR spectra, and quantum mechanical calculations for geometry and other properties. Frontier orbital energies are used to predict the energy properties and model the possible charge transfer between the constituents of the cocrystal. The frontier molecular orbital analysis indicates chemical reactivity and bioactivity of the cocrystals. The MEP surface reveals the various reactive surfaces in the cocrystal system, which is very important in deciding various biological activities. The UV-Vis spectra show the possible electronic transitions of the molecules. Simulated electronic spectra using TDDFT method with CAM-B3LYP functional were used to investigate the suitability of the cocrystals to be used in DSSC. Moreover, the molecular docking analysis proves that the cocrystals can act as potential inhibitors and paves the way for developing effective drugs.

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.

Theoretical and Spectroscopic Characterization of API-Related Azoles in Solution and in Solid State

Azoles are a family of five-membered azacyclic compounds with relevant biological and pharmacological activity. Different subclasses of azoles are defined depending on the atomic arrangement and the number of nitrogen atoms present in the ring: pyrazoles, indazoles, imidazoles, benzimidazoles, triazoles, benzotriazoles, tetrazoles and pentazoles. The complete characterization of their structure and the knowledge about their crystal packing and physical and chemical properties are of vital importance for the advancement in the design of new azole-containing drugs. In this review, we report the latest recent contributions to azole chemistry, in particular, those in which theoretical studies have been performed.

Detailed molecular structure (XRD), conformational search, spectroscopic characterization (IR, Raman, UV, fluorescence), quantum mechanical properties and bioactivity prediction of a pyrrole analogue

Pyrroles are an exciting class of organic compounds with immense medicinal activities. This manuscript presents the structural and quantum mechanical studies of 1-(2-aminophenyl) pyrrole using X-Ray diffraction and various spectroscopic methods like Infra-Red, Raman, Ultra-violet and Fluorescence spectroscopy and its comparison with theoretical simulations. The single-crystal X-ray diffraction values and optimized geometry parameters also were within the agreeable range. A fully relaxed potential energy scan revealed the stability of the possible conformers of this molecule. We present the density functional theory results and assignment of the vibrational modes in the infrared spectrum. The experimental and scaled simulated vibrations matched when density functional theory simulations (B3LYP functional with 6–311++G∗∗). The electronic spectrum was simulated using time-dependent density functional theory with CAM-B3LYP functional in dimethylsulphoxide solvent. The fluorescence spectrum of the compound was studied at different excitation wavelengths in the dimethylsulphoxide solvent. The stability of the molecule by intramolecular electron transfer by hyperconjugation was studied with the natural bond orbital analysis. Frontier molecular orbitals and molecular electrostatic potentials of the compound gave an idea about the reactive behaviour of the compounds. Prediction of activity spectral studies followed by docking analysis indicated that the molecule is active against arylacetonitrilase inhibitor.

Spectral characterization, thermochemical studies, periodic SAPT calculations and detailed quantum mechanical profiling various physico-chemical properties of 3,4-dichlorodiuron

A set of experimental and computational techniques have been applied for the understanding of fundamental spectroscopic and reactive properties of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (diuron) compound. Experimental techniques employed in this study encompassed spectroscopic characterization via IR and Raman approaches, while optical properties were studied by measurements of UV/Vis spectra. The thermogravimetric analysis was also studied in order to analyze the stability of diuron. Aside from the determination of reactive properties, DFT calculations on isolated molecules were also used to thoroughly visualize and analyze spectroscopic properties such as IR and UV/Vis. MD simulations were used in order to understand interactions with water, while periodic DFT calculations were used in order to analyze band structure and density of states of the diuron crystal structure. Since the crystal structure of diuron is known, it was used in order to extract the relevant molecular pairs and investigate interactions between them by DFT and symmetry adapted perturbation theory approaches (SAPT).

Detailed quantum mechanical, molecular docking, QSAR prediction, photovoltaic light harvesting efficiency analysis of benzil and its halogenated analogues

The structural, spectroscopic various physico-chemical and biological characteristics of the organic molecule benzil (BZL) and derivatives, 1,2-bis(4-methylphneyl)-1,2-ethanedione (DMB), 4,4′-difluorobenzil (DFB), 4,4′-dichlorobenzil (DCB) and 4,4′-dibromobenzil (DBB) have been studied by various computational methods. The experimental and scaled simulated Raman and IR spectra were compared and found close agreement. Assignments of important peaks are also presented. Detailed information pertaining to the local and global reactivity and other properties like electrophilic and nucleophilic characteristics were analysed. The hyperactive pressure was measured in terms of polarizability and corresponding biological properties were validated to identity reactive sites. Prediction of Activity Spectral Studies (PASS) predicts the biological activity of the compounds and it is found that the candidate molecules can be used as feruloyl esterase inhibitor, bisphosphoglycerate phosphatase inhibitor and Prolylaminopeptidase inhibitor. The crystals structures of those receptors are taken from the protein data bank and docking studies indicates stable complex with the receptors and candidate molecules. Light harvesting efficiency, followed by photovoltaic modelling shows that DMB is the best compound to be used in the DSSC to get the best output.

DFT and molecular docking investigations of oxicam derivatives

The organic molecule tenoxicam and similar derivatives, piroxicam and isoxicam have been studied by quantum chemical theory (DFT), FT-Raman and FT-IR. By FMOs energies the charge transfer inside the molecules are obtained. The UV-Vis spectra of the compounds are simulated to study the electronic transition in the target molecules. By using natural bond orbital (NBO), charge delocalization analyzes arising from hyper conjugative interactions and the stability of the molecules are obtained. First order hyperpolarizability of piroxicam is higher than that of isoxicam and tenoxicam. The reactive areas are thoroughly studied by MEP. Prediction of Activity Spectra gives activities, anti-inflammatory, CYP2C9 substrate and gout treatment. Docked ligands form a stable complex with the receptors.