A Comprehensive Study of N-Butyl-1H-Benzimidazole

Imidazole derivatives have found wide application in organic and medicinal chemistry. In particular, benzimidazoles have proven biological activity as antiviral, antimicrobial, and antitumor agents. In this work, we experimentally and theoretically investigated N-Butyl-1H-benzimidazole. It has been shown that the presence of a butyl substituent in the N position does not significantly affect the conjugation and structural organization of benzimidazole. The optimized molecular parameters were performed by the DFT/B3LYP method with 6-311++G(d,p) basis set. This level of theory shows excellent concurrence with the experimental data. The non-covalent interactions that existed within our compound N-Butyl-1H-benzimidazole were also analyzed by the AIM, RDG, ELF, and LOL topological methods. The color shades of the ELF and LOL maps confirm the presence of bonding and non-bonding electrons in N-Butyl-1H-benzimidazole. From DFT calculations, various methods such as molecular electrostatic potential (MEP), Fukui functions, Mulliken atomic charges, and frontier molecular orbital (HOMO-LUMO) were characterized. Furthermore, UV-Vis absorption and natural bond orbital (NBO) analysis were calculated. It is shown that the experimental and theoretical spectra of N-Butyl-1H-benzimidazole have a peak at 248 nm; in addition, the experimental spectrum has a peak near 295 nm. The NBO method shows that the delocalization of the aσ-electron from σ (C1–C2) is distributed into antibonding σ* (C1–C6), σ* (C1–N26), and σ* (C6–H11), which leads to stabilization energies of 4.63, 0.86, and 2.42 KJ/mol, respectively. Spectroscopic investigations of N-Butyl-1H-benzimidazole were carried out experimentally and theoretically to find FTIR vibrational spectra. © 2022 by the authors

Synthesis, X-ray crystal structure, Hirshfeld surface analysis, DFT, AIM, ELF, RDG and molecular docking studies of bis[4-(dimethylamino)pyridinium]di-mu-chlorido-bis[dichloridomercurate(II)]

International audienceBis[4-(dimethylamino)pyridinium]di-mu-chlorido-bis[dichloridomercurate(II)] has been achieved from a mixture of mercury(II) chloride in water with an aqueous HCl solution containing 4-dimethylaminopyridine by the slow evaporation technique. The structure of this compound has been determined by single-crystal X-ray diffraction. This compound crystallizes in the triclinic space group P1 over bar with the following lattice parameters: a = 7.5505(7) angstrom, b = 11.8684(12), c = 13.4777(12) angstrom, alpha = 82.836(3), beta = 76.516(3), gamma = 76.355(3) angstrom, Z = 2 and V = 1138.22(19) angstrom(3). The structure of the compound can be described as organic-inorganic layers stacked along the b and c-axes which are connected by weak N-H center dot center dot center dot Cl and C-H center dot center dot center dot Cl hydrogen bonds forming a three-dimensional network. The IR spectra confirmed the presence of organic cations and the thermal stability of the compound was measured by thermal analysis DSC/TG. Hirshfeld surface analysis and the associated two-dimensional fingerprint plots were used to explore and quantify the intermolecular interactions in the crystal. The geometrical optimization, electronic, topological and biological properties of the compound were theoretically studied using DFT. The HOMO/LUMO analysis was used to determine the charge transfer within the structure. Good consistency was found between the calculated results and the experimental structure and IR spectra. Furthermore, thermodynamic functions for the compound revealed significant evolution with temperature and the potential biological activities were investigated by using molecular docking analysis

Study of a new piperidone as an anti-Alzheimer agent : molecular docking, electronic and intermolecular interaction investigations by DFT method

In this work, experimental spectroscopic and theoretical methods as quantum chemical calculation were performed for 3-chloro-r(2),c(6)-bis(4-fluorophenyl)-3-methylpiperidin-4-one (abbreviated as CFMP). The CFMP was synthesized and analysed using FT-IR, 1H NMR, 13C NMR, and UV–Vis spectroscopy. Standard functional B3LYP/6–311++G(d,p) density functional theory (DFT) calculations were utilized for the CFMP compound. Molecular electrostatic potential, non-linear optical, and natural bond orbital studies were performed. The charge transfer inside the molecule was demonstrated using HOMO-LUMO energy calculations and Mulliken atomic charges. The vibrational frequency was computed using the DFT/B3LYP/6–311++G(d,p) method. The non-covalent interactions were investigated using the Hirshfeld surface analysis. Furthermore, molecular docking was studied to discover novel inhibitors and drugs in treating Alzheimer's diseases. Further, docking studies were performed to predict and describe the interactions of four proteins with the ligand. This result demonstrates that the CFMP has an inhibitor effect against Alzheimer's diseases

3-Chloro-3-methyl-2,6-diarylpiperidin-4-ones as Anti-Cancer Agents: Synthesis, Biological Evaluation, Molecular Docking, and In Silico ADMET Prediction

10.3390/biom12081093BIOMOLECULES12

Impact of non-covalent interactions on FT-IR spectrum and properties of 4-methylbenzylammonium nitrate : a DFT and molecular docking study

In this research, the impact of non-covalent interactions on the FT-IR spectrum and structural, electronic, topological and vibrational properties of hybrid 4-methylbenzylammonium nitrate (4MBN) have been studied combining B3LYP/CC-PVTZ calculations with molecular docking. 4MBN was synthesized and characterized by using the FT-IR spectrum while the optimized structures in gas phase and in ethanol and aqueous solutions have evidenced monodentate coordination between the nitrate and methylbenzylammonium groups, in agreement with that experimental determined for this species by X-ray diffraction. Here, non-covalent interactions were deeply analyzed in terms of topological parameters (AIM), electron localization function (ELF), localized orbital locator (LOL), Hirshfeld surface and reduced density gradient (RDG) method. Weak interactions such as H-bonds, VDW and steric effect in 4MBN were visualized and quantified by the independent gradient density (IGM) based on the promolecular density. The hyper-conjugative and the delocalization of charge in 4MBN have been elucidated by natural bonding orbital (NBO) while its chemical reactivity was studied and discussed by using molecular electrostatic potential surface (MESP), frontier molecular orbital (FMOs), density of state (DOS) and partial density of state (PDOS). The complete vibrational assignments of 69 vibration modes expected for 4MBN are reported together with the scaled force constants while the electronic transitions were evaluated by TD-DFT calculations in ethanol solution. Thermal analysis (DTA and DSC) was also determined. Molecular docking calculations have suggested that 4MBN presents biological activity and could act as a good inhibitor against schizophrenia disease

Molecular modeling and biological activity analysis of new organic-inorganic hybrid : 2-(3,4-dihydroxyphenyl) ethanaminium nitrate

In this paper, experimental and theoretical results of 2-(3, 4-dihydroxyphenyl) ethanaminium nitrate (2DOPN) have been investigated. From DFT calculations, molecular geometry and optimized parameters of 2-(3, 4-dihydroxyphenyl) ethanaminium nitrate have been obtained at B3LYP/ 6–311 ++ G(d, p) level of theory and compared with the available X-ray data. The non covalent interactions of the crystal structure were investigated by QTAIM analysis, ELF, LOL and Hirsfeld surfaces. In addition to study the weak interaction, a visualized approach known as RDG has been carried out. Mulliken atomic charge has been used to describe the process of electronegativity equalization and charge transfer in chemical reactions. NBO analysis was also performed to find the charge transfer within the molecule and their stabilization energy. Electronic proprieties such as MEP, ESP and the frontier molecular orbital analysis HOMO-LUMO of molecule were studied. The dipole moment (µ) and the first hyperpolarisability (β0) have been calculated and found that our compound is a potential NLO material. Thermal behavior (TGA and DTA) of C8H12NO2 (NO3) have also been undertaken and reported. The biological activity of 2DOPN through ligand and proteins interactions has been confirmed theoretically for the treatment of Parkinson disease with respect to chosen proteins. The activities of our molecule with divers proteins were studied in accordance with literature survey and the results were presented here

Investigations on the non-covalent interactions, drug-likeness, molecular docking and chemical properties of 1,1,4,7,7- pentamethyldiethylenetriammonium trinitrate by density-functional theory

An advanced organic–inorganic hybrid compound 1,1,4,7,7-pentamethyldiethylenetriammonium trinitrate (PMDT) has been synthesized and characterized by X-ray diffractometry. The title molecule is abbreviated as PMDT has been investigated using experimental and computational techniques. The quantum chemical study was carried out using DFT calculation with B3LYP/6–31++G(d, p) basis set. Different methods have been performed to quantify the non covalent interactions within the title molecule. Atoms In Molecules (AIM) approach at bond critical points BCP's of the hydrogen bonds (C–H…O and N–H…O) in PMDT have been applied. Electron localization Function (ELF) and Local Orbital Locator (LOL) methods were studied in order to detect the electron density at bonding and anti-bonding sites of the title compound. The Hirshfeld surface analysis exposes important information on the inter and intramolecular interactions present in the crystal structure. Further characterization of the non covalent interactions has been shown by reduced Density of Gradient (RDG) and Independent Gradient Model (IGM). In addition, to map and analyze the weak-interaction regions, the interaction region indicators (IRI) have been used. The effect of polar solvents for the electrophilic and nucleophilic sites has been investigated. The ChELPG and Mulliken population analyses have been carried out. Frontier molecular orbital's (HOMO-LUMO) was discussed to afford the information about the reactivity of the PMDT molecule in gas, water and DMSO solvation. The temperature behavior and conductivity of the title molecule have been analyzed. Finally, in order to estimate the antibacterial mechanism of the PMDT compound action, molecular docking calculations were carried out on the active sites of various proteins

Deciphering non-covalent interactions of 1,3-Benzenedimethanaminium bis(trioxonitrate): Synthesis, empirical and computational study

International audience1,3-Benzenedimethanaminium bis(trioxonitrate), denoted by BD(NO3)(2) was prepared and its structure determined by X-ray crystallography. This compound solidifies into the triclinic system and the P2(1)/c space group with the lattice parameters a = 21.4308 (7) angstrom, b = 5.7255 (2) angstrom, c = 20.4476 (5) angstrom, beta = 108.502 (1) degrees, V = 2379.28 (13) angstrom(3), Z = 8, R = 0.047 and Rw = 0.129. In the crystal, the ions are allied by a huge number of N-H center dot center dot center dot O hydrogen bonds, creating layers parallel to (100). These layers are associated by hydrogen bonding type C-H center dot center dot center dot O, endorsing consequently a 3D arrangement. B3LYP/6-311 ++G**calculations were carried out to analyze the structure and properties of BD(NO3)(2). Intermolecular contacts involved in the selection and packaging of the crystalline structure of BD(NO3)(2) were investigated using fingerprint traces of the Hirshfeld surface. HOMO and LUMO analyses explain the charge transfers within the molecule. Topological analysis, RDG, molecular electrostatic potential (MEP) have been processed to calculate the intermolecular H-bonds interactions in detail. Thermal fusion and decomposition were investigated using TG, DTA and DSC measurements. Ionic conduction (H+) has been intentional in the temperature range 323 to 393 K, indicating semiconductor behavior of the material produced. Complete assignments of bands observed in the FTIR spectrum were reported together with the main force constants. The presence of dimeric species is important to explain why the intense bands predicted for the monomer due to N-H center dot center dot center dot O-N interactions are not observed in the experimental IR spectrum. The biological activity of BD(NO3)(2) was accomplished in silico to investigate their antibacterial activity

Bonding and noncovalent interactions effects in 2,6-dimethylpiperazine-1,4-diium oxalate oxalic acid: DFT calculation, topological analysis, NMR and molecular docking studies

International audienceThe pharmaceutical proprieties of the 2,6-dimethylpiperazine-1,4-diium oxalate oxalic acid compound have been studied and the relevant drug design has been considered. The investigated organic compound with formula (2,6-(CH3)C4H10N2)2(C2O4)2·H2C2O4 (2DPOA) has been synthesized by slow evaporation technique at room temperature of a molar ratio 3:2 mix of oxalic acid and 2,6-dimethylpiperazine. Then 2DPOA has been characterized by IR, 13C NMR, UV–visible and the DFT calculation at the B3LYP level of theory has been made. The molecular structure and parameters (bond angles and lengths) of the molecule have been optimized using the Gaussian 09 software and compared with the XRD data. The atoms-in-molecules (AIM), electron localization function (ELF), and localized orbital locator (LOL) methods have been utilized to determine the types and nature of noncovalent interactions present within the 2DPOA molecule. These methods offer insights into the characteristics and behavior of these interactions. Furthermore, the presence of these interactions has been confirmed through the Hirshfeld Surface (HS) and reduced density gradient (RDG) analysis. The NBO analysis is employed to assess the charge exchange occurring within the studied compound. The molecular reactive sites have been examined using the molecular potential surface and Mulliken atomic charges. The energy gap between HOMO–LUMO and chemical properties of 2DPOA have been determined within the frontier molecular orbital theory. The UV–Vis spectrum of the 2DPOA molecule has been recorded and examined. The calculated and experimental infrared absorption and nuclear magnetic resonance spectra of 2DPOA molecule have been investigated. Finally, the molecular docking simulation has been used to find novel inhibitors and drugs for the cancer and epilepsy disease treatment