Becke, 3-parameter, Lee-Yang-Parr Research Articles

IDENTIFICATION OF QUINOLONE-TRAIZOLE HYBRIDS AS POTENTIAL INHIBITORS USING IN SILICO APPROACH

Alzheimer’s disease (AD) is a most common form of dementia and results in memory loss, disorientation, impaired thinking and changes in personality as well as mood. The dementia cases mostly turn into the Alzheimer’s disease (AD). Another disease, the Parkinson’s disease (PD), mainly affects dopaminergic neurons in substantia nigra. A series of previously synthesized quinolone-triazole hybrids were investigated and evaluated for their anti-acetyl cholinesterase and against monoamine oxidase reactive properties through in silico characterization. The ground state electronic properties were determined by electron density of the compounds through DFTs (density functional theory) calculation. The geometries of all compounds were optimized using Becke-3-parameter-Lee-Yang-Parr (B3LYP) method and 6-311g basis set. Docking studies were conducted using the AutoDock and Molecular Operating Environment (MOE) software and the results of the potent derivatives found to be encouraging. The data confirmed that all the compounds have drug-like properties and was further confirmed by ADMET (absorption, distribution, metabolism, excretion and toxicity) properties.

Comparative analysis of backbone atom cross-correlation matrices and folding dynamics of amyloid fibril and its complexes with novel biosurfactants isolated from Bacillus strain: a binding free energy calculation (mM-PBSA) and MD simulation approach

In the relentless pursuit of unraveling the intricate pathophysiology of Alzheimer’s disease (AD), amyloid β (Aβ) proteins emerge as focal points due to their pivotal role in disease progression. The pathological hallmark of AD involves the aberrant aggregation of Aβ peptides into amyloid fibrils, precipitating a cascade of neurodegenerative events culminating in cognitive decline and neuronal loss. This study adopts a computational framework to investigate the potential therapeutic efficacy of novel biosurfactants (BS) in mitigating Aβ fibril formation. Initial analyses encompassing sequence alignment, structural elucidation, and functional characterization reveal distinctive attributes of the Aβ peptide and the identified BS candidates. Quantum chemical calculations, using the ORCA Program (v4.0) employed Density Functional Theory (DFT), specifically the Becke 3-parameter Lee-Yang-Parr (B3LYP) method, to investigate the electronic structure and energetics of novel isolates. Molecular docking through AutoDock Vina (version 1.1.2) employing advanced algorithms elucidates the binding affinities and interaction energies between Aβ fibrils and BS molecules. The observed binding energy of −7.0 kcal/mol for BG2A and −6.6 kcal/mol for BG2B, underscoring the robustness and stability of the formed complexes. The binding mechanism of docked complexes was predicted through molecular dynamics (MD) simulations using GROMACS 2021.3 and Charmm36 force field, capture complex dynamics over 100 nanoseconds. Analysis via RMSD, RMSF, Rg, PCA, and SASA offers insights into Aβ-BS complex stability and dynamics. These promising results highlight the potential of BG2A and BG2B as therapeutic candidates against AD. However, rigorous preclinical and clinical validation is crucial to ascertain their safety, efficacy, and translational relevance.

FT-IR, UV–Vis, density functional theory and molecular docking studies on 3,7,11,15-Tetramethyl-2hexadecen-1-ol

The organic molecule of 3,7,11,15-Tetramethyl-2-hexadecen-1-ol is frequently present in plant chlorophyll pigment. The title compound possesses antimicrobial, antibacterial, antioxidant, anti-inflammatory, and anticancer characteristics. The 3TMH molecule are being investigated using Gas Chromatography Mass Spectrometry (GC–MS) analysis, Ultraviolet-Visible (UV–Vis), Fourier Transform Infrared Spectroscopy (FT-IR), and Density Functional Theory (DFT) approach with the Becke,3-parameter, Lee–Yang–Parr (B3LYP) method, 6–311++G (d, p) basis set is used to analyse the geometrical parameters, Highest Occupied Molecular Orbital and the Lowest Unoccupied Molecular Orbital (HOMO-LUMO), and Molecular Electrostatic Potential (MEP) mapping. In the 3TMH molecules, the computed Natural Bond Orbital (NBO) analysis exhibit the high stabilization interaction (intra-inter, hydrogen bonding, and charge delocalization) between the donor and acceptor. The UV–Vis spectra of the maximum absorption correlated with different solvents as determined by Time-Dependent Density Functional Theory (TD-DFT). According to Veda 04, the measured FT-IR spectrum and the theoretical spectra of vibrational assignment with Potential energy distribution (PED%) are in good agreement. The Electron Localization Function (ELF) and Localized Orbital Locator (LOL) mapping has provided an explanation for the chemical bonding within fragments, as well as interactions between the atoms. The strong attraction, strong repulsion, and weak interaction have been estimated Reduced Density Gradient (RDG). Furthermore, the molecular docking examined ligand-protein interaction of least binding energy 6.73 kcal/mol against anti-cancer activity.

Non-covalent interaction, topology, molecular properties, spectral and quantum chemical analysis of 2,5-dinitrophenol

Density functional theory (DFT) using the Becke-3-Parameter-Lee-Yang-Parr (B3LYP) functional and Ab-initio (HF) with the 6–311++G(d,p) basis set were employed to investigate the geometry, electronic structure, and absorption spectra of 2,5-Dinitrophenol(25DNP). The vibrational spectrum was utilized to identify functional groups. The ultraviolet–visible (UV–Vis) spectrum was simulated in the gas phase using TD-DFT to determine the range and percentage of transmission. The computed HOMO and LUMO energies indicate that charge transfer occurs within the molecule. The compound exhibits a molecular first hyperpolarizability (second-order optical nonlinearity) value of 1.690 × 10−30 esu, which is approximately five times greater than that of urea. For hyperpolarizability calculations, the hybrid Hartree-Fock exchange-correlation functional was used in conjunction with the 6–311++G(d,p) basis set. Fukui indices were employed to identify local reactive sites in the chemical system during electrophilic, nucleophilic, radical, and dual descriptor attacks. Docking simulations were performed using the Lamarckian Genetic Algorithm (LGA) and local search approach, ensuring proper establishment of the ligand molecules' starting position, orientation, and torsion. According to the molecular electrostatic potential (MEP) map, positive potential sites are found around hydrogen atoms, while negative potential sites are near electronegative atoms, providing insights into regions where the molecule may interact with other molecules, both internally and externally. Similarly, Mulliken charges and Fukui indices within the organic complex sustain the intermolecular hydrogen bonds.

Benzothiazole-derived Compound with Antitumor Activıiy: Molecular Structure Determination Using Density Functional Theory (Dft) Method

The Gaussian computational chemistry software package was employed to investigate the molecular structure and energetics of benzothiazole, a compound known for its anti-tumor properties. Density functional theory (DFT) calculations were conducted using the Becke, 3-parameter, Lee-Yang-Parr (B3LYP) method, coupled with the LanL2DZ basis set. Molecular structure optimization was carried out to determine the most stable configurations of the benzothiazole compound. Furthermore, thorough analyses of molecular orbital energies, molecular properties, and molecular electrostatic potential surface maps were performed on the optimized molecular system. Our current research suggests that the compound 2-(4-aminophenyl) benzothiazole, containing benzothiazole, maybe a potential drug candidate for free radical species on cells due to its anti-cancer properties.

Experimental and in silico insights: interaction of dimethyl sulphoxide with 1-hexyl-2-methyl imidazolium bromide/1-octyl-2-methyl imidazolium bromide at different temperatures.

Ionic liquids have gained attention as 'designer solvents' since they offer a broad spectrum of properties that can be tuned by altering the constituent ions. In this work, 1-alkyl-2-methyl imidazolium-based ionic liquids with two different alkyl chains (alkyl = hexyl and octyl) have been synthesized and characterized. Since the binary mixture of ionic liquids with molecular solvents can give rise to striking physicochemical properties, the interaction of the synthesized room temperature ionic liquids, 1-hexyl-2-methyl imidazolium bromide [HMIM][Br]/1-octyl-2-methyl imidazolium bromide [OMIM][Br] with DMSO has been examined through density and specific conductance at T = (303.15, 308.15, 313.15 and 318.15) K under atmospheric pressure. The obtained molar volume and excess molar volume are fitted to the Redlich-Kister polynomial equation, and the standard deviation is noted. The positive excess molar volume at elevated temperatures indicates volume expansion due to the mutual loss of dipolar association and differences in the sizes and shapes of the constituent molecules. To have a better understanding of the reactivity and efficacy of 1-hexyl-2-methyl imidazolium bromide and 1-octyl-2-methyl imidazolium bromide with DMSO, the Becke, 3-parameter, Lee-Yang-Parr (B3LYP) correlation function of density functional theory (DFT) has been used. The ORCA Program version 4.0 calculates the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy. The effective reactivities of both the compounds that showed an energy band gap (ΔE), i.e., the difference between ELUMO and EHOMO, are 7.147 and 8.037 kcal mol-1.

Linear and Nonlinear Optical Responses of Nitrobenzofurazan-Sulfide Derivatives: DFT-QTAIM Investigation on Twisted Intramolecular Charge Transfer.

In this study, we report on the green fluorescence exhibited by nitrobenzofurazan-sulfide derivatives (NBD-Si, i = 1-4). The optical responses of these studied compounds in a polar methanol solvent were simulated by the use of time-dependent density functional theory (TD-DFT) employing the Becke-3-Parameter-Lee-Yang-Parr (B3LYP) functional along with the 6-31G(d,p) basis set. The computed energy and oscillator strength (f) results complement the experimental results. The band gap was calculated as the difference between the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO). Additionally, the density of states (DOS) was computed, providing a comprehensive understanding of the fundamental properties of these materials and further corroborating the experimental data. When the experimental data derived from ultraviolet/visible (UV/visible) and fluorescence spectroscopic techniques and those from simulated spectra are analyzed, the extracted values match up adequately. In addition, the NBD-sulfide compounds exhibit a large Stokes shift up to 85 nm in a polar methanol solvent. They are hypothesized to represent a novel paradigm of excited-state intramolecular charge transfer (ICT). To understand the intrinsic optical properties of NBD-Si materials, an ICT was identified, and its direction within the molecule was evaluated using the ratio of βvect and βtotal, values extracted from the computed nonlinear optical (NLO) properties. Moreover, the reduced density gradient (RDG)-based noncovalent interactions (NCIs) were employed to characterize the strength and type of NBD-Si interactions. Furthermore, noncovalent interactions were identified and categorized using the Quantum Theory of Atoms in Molecules (QTAIM) analysis. Ultimately, the combination of Hirshfeld surface analysis and DFT calculations was utilized to enhance the characterization and rationalization of these NCIs.

Design of novel anti-cancer agents targeting COX-2 inhibitors based on computational studies

The overexpression of cyclooxygenase-2 (COX-2) was clearly associated with carcinogenesis, and COX-2 as a possible target has long been exploited for cancer therapy. A group of 29 derivatives of 1, 5-diarylpyrazole was used to study its structural requirements using three-dimensional quantitative structure–activity relationship (3D-QSAR), the density functional theory method, molecular docking, and molecular dynamics. Four 3D-QSAR models were developed, and the predictive capability of the four selected models was also successfully tested using different validation methods. The contribution contours of the comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) models effectively illustrate the relationships between the various chemical characteristics and their biological activities. Using the density functional theory method with the 6-31G (d, p) basis set and the Becke, 3-parameter, Lee-Yang-Parr (B3LYP) function to evaluate chemical reactivity properties, the results obtained from energy gaps of 3.431, 3.446, and 2.727 ev for molecules numbers 21, 22, and 23 indicate that these three molecules have good chemical stability and reactivity and select the most reactive regions in the three molecules studied. Molecular docking results revealed that the active sites of the COX-2 protein (PDB code: 3PGH) were residues ARG222, THR212, HIS386, HIS207, TYR148, and ASP382, in which the most active ligands and now ligands can inhibit the COX-2 enzyme. Based on the various results obtained by molecular modeling, four new compounds (N1, N2, N3, and N4) were proposed with significant predicted activity by different 3D-QSAR models. A molecular docking study and molecular dynamics simulations of the proposed new molecules (N1 and N2) and the most active molecule over 100 ns revealed that all three molecules establish multiple hydrogen interactions with several residues and also exhibit frequent stability throughout the simulation period. As a result, it is strongly recommended to consider the two newly proposed molecules, N1 and N4, as promising candidates for novel anti-cancer agents specifically designed to target COX-2 inhibition.

Robust electrocatalysts decorated three-dimensional laser-induced graphene for selective alkaline OER and HER

Morphological and functional modifications allow graphene to be applied as promising electrode support for improved electrochemical cell performance. Typically, however, modification requires complicated steps with various organic additives, such as binders, which causes low electrochemical stability, especially under harsh pH conditions. Herein, we introduce self-supported and long-term stable water splitting electrodes based on nanoparticles (NPs) decoration on three-dimensional porous laser-induced graphene (3D-LIG). A binder-free, single-step electrochemical process homogeneously decorates the 3D-LIG electrodes with CuO and Pt NPs, referred to CuO-3D-LIG and Pt-3D-LIG electrodes, respectively. These electrodes are individually analyzed for enduring oxygen evolution (OER) and hydrogen evolution (HER) activities. The porous wrinkled morphology of the 3D-LIG offers a large surface area and facilitates electrolyte influx within channels. Whereas strongly anchored CuO and Pt NPs enable highly stable electrochemical performances of the CuO-3D-LIG and the Pt-3D-LIG electrodes. The corresponding OER and HER overpotentials at 10 mA cm−2 (η10) are observed at 251 mV and 455 mV. These electrodes offer excellent electrochemical robustness in operationally challenging alkaline conditions (1 M KOH, pH ∼ 14) for extensive periods. In addition, we confirm the workable electrostatic interactions NPs – graphene via Becke-3-parameter Lee–Yang–Parr (B3LYP) model with 6-31G (d,p) and Stuttgart-Dresden (SDD) basis, which is supposed to be responsible for electrochemical durability and high current density yield of CuO-3D-LIG and Pt-3D-LIG electrodes. This study offers one of a few experiments to utilize decorated 3D-LIG for both OER and HER processes, assuming their substantial industrial potential in overall water splitting.

Experimental and In-Silico investigations on novel bioactive 4-phenyl-2-thioxo-3,4-dihydro-1H-pyrido[1,2-a]pyrimido[4,5-d]pyrimidin-5(2H)-one

In this work, we report an efficient synthesis of pyrimidine fused novel 4-phenyl-2-thioxo-3,4-dihydro-1H-pyrido[1,2-a]pyrimido[4,5-d]pyrimidin-5(2H)-one. The chemical structure of the title compound was ascertained by spectral techniques including UV–Visible, FT-IR, 1H NMR, 13C NMR and HRMS. The molecule was further subjected to quantum chemical calculations at the level of Density Functional Theory method employing B3LYP (Becke 3-parameter, Lee-Yang-Parr) level with 6–311++G(d,p) basis set. The computed characteristics of the molecule were investigated and interpreted comparing with the experimental values. Furthermore, Frontier Molecular Orbital (FMO) analysis was used to predict the energy properties and model the possible charge transfer within the molecule. The reactivity sites were identified by mapping the electron density into Molecular Electrostatic Potential (MEP). The stability of the molecule arising from hyper-conjugative interactions and charge delocalization were analyzed using Natural Bond Orbital (NBO) analysis. All the theoretical values were in good agreement with experimental studies. Docking studies was performed to examine binding sites of the title molecule and bioactivity scores indicated that the ligand's pharmacokinetic and pharmacological properties are sufficiently additive and shows the drug-likeness of the synthesized molecule. The study was validated by i) re-docking the N3-peptide inhibitor and superimposing them onto co-crystallized complex and ii) protein ligand complex. Molecular dynamics simulations were performed for 50 ns to assess the conformational stability and fluctuations of protein-ligand complexes during the simulation.

Pharmacophore Oriented MP2 Characterization of Charge Distribution for Anti-SARS-CoV-2 Inhibitor Nirmatrelvir

Quantum mechanical second order Møller–Plesset (MP2) perturbation theory and density functional theory (DFT) Becke, 3-parameter, Lee-Yang-Parr (B3LYP) and Minnesota 2006 local functional (M06L) calculations were performed to optimize structure of nirmatrelvir and compute the Merz-Kollman electrostatic potential (MK ESP), natural population analysis (NPA), Hirshfeld, charge model 5 (CM5), and mulliken partial charges. The mulliken partial charge distribution of nirmatrelvir exhibits a poor correlation with the MK ESP charges in MP2, B3LYP, and M06L calculations respectively. The NPA, Hirshfeld, and CM5 partial charge scheme of nirmatrelvir indicate a reasonable correlation with MK ESP charge assignments in B3LYP and M06L calculations. The above correlations were not improved by the inclusion of implicit solvation model. The MK ESP and CM5 partial charges show a strong correlation between the results of MP2 and two DFT methods. The three optimized structures present a certain degree of differences from the crystal bioactive conformation of nirmatrelvir, suggesting the nirmatrelvir-enzyme complex is formed in the induced-fit model. The Reactivity of warhead electrophilic nitrile is justified by the relatively weaker strength of π bonds in the MP2 calculations. The nirmatrelvir hydrogen bond acceptors consistently show strong delocalization of lone pair electrons in three calculations, whereas hydrogen bond donors are found to have high polarization on the heavy nitrogen atoms in MP2 computations. This work helps to parametrize the force field of nirmatrelvir and improve accuracy of molecular docking and rational inhibitor design.

A Quinoline-Based Fluorescent Labelling for Zinc Detection and DFT Calculations

8-carboxamidoquinoline derivatives were gradually investigated as zinc's label in resolving weak water solubility, poor membrane permeability, and difficulty measuring free Zn2+ ion in cells quantitatively. The potential of 2-oxo-2-(quinolin-8-ylamino)acid (OQAA) as zinc's label was prepared and characterized spectroscopically. Theoretical and experimental data of OQAA were compared and discussed. The optimized molecular structure, molecular orbital of HOMO-LUMO, energy band gaps, and molecular electrostatic potential (MEP) of OQAA were carried out using the DFT method with Becke-3-Parameter-Lee-Yang-Parr (B3LYP) and 6-31G(d,p) basis set. The intermolecular interaction energy of OQAA-Zn is calculated by using the hybrid method of GEN with a basis set of LANL2DZ for Zn2+ ion and DFT/6-31G(d,p) for OQAA ligand. OQAA exhibited remarkable and excellent fluorescence enhancement selective and qualitatively only for Zn2+ than other metal cations tested (Fe2+, Cu2+, Co2+, Ni2+, Hg2+, Cd2+) under a long wavelength. Job's plot and 1H NMR titrations indicate OQAA-Zn2+ has a binding ratio at 1:1 stoichiometry (M1L1). Substantial shifting of amide N-H proton to higher chemical shift and intensity of the proton peak of N-H amide decrease abruptly implies that Zn2+ is binding to an amide. These changes confirmed interactions among the ligand OQAA and metal Zn2+ ion. As a result of the benefits discussed, OQAA could effectively and selectively optimize and fabricate for Zn2+ sensors.

Investigation of Conformational Analysis of (m-Carbamoylphenyl) Boronic Acid Molecules by Theoretical Methods

In this study, the structural parameters, the electronic energy, the dipole moment (μ), the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy, the polarizability (α), hyperpolarizability (β) and vibrational frequency of (3-Carbamoylphenyl) boronic acid were calculated at Density Functional Theory (DFT) with B3LYP (Becke 3 Parameter Lee-Yang-Parr) model using the 6-311+(2d,p) basis set in gas phase. Also, using the EHOMO and ELUMO energy values of the molecule, the energy gap (Eg = ELUMO -EHOMO), electronegativity (χ), chemical potential (Pi), chemical hardness (η), softness (σ), ionization energy (I), electron affinity (A), electronic chemical potential (µ), global softness (S) values were calculated according to the literature. Equilibrium state (ground state) energy gap value of the molecule were calculated as 5.59 eV. The dipole moment value of the molecule was calculated as 3.41 Debye by the DFT/B3LYP/6-311+G(2d,p) method. The obtained vibrational wave numbers were scaled with appropriate scale factors and the assigning of these vibrational wavenumbers was made according to the potential energy distribution (PED) using the VEDA 4f program. The approximate geometry of the molecules in three dimensions was drawn in the Gauss View 5.0 molecular imaging program, and all theoretical calculations were used with the Gaussian 09W package program.

Theoretical Investigation of Vibration and Electronic Properties of (E)-3-(Benzylideneamino)-4H-1,2,4-Triazol-4-Amine

In this study, the important application areas of triazoles have increased the interest in studies related to them. In this study, the structural parameters, vibrational frequency, the electronic energy, the dipole moment (μ), the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy, the polarizability (α), hyper polarizability (β) and the potential energy curves (PEC) of (E)-3-(benzylideneamino)-4H-1,2,4-triazol-4-amine molecule were calculated at Hartree-Fock (HF) and Density Functional Theory (DFT) with B3LYP (Becke 3 Parameter Lee-Yang-Parr) model using the different basis set in gas phase. The potential energy curves of the studied molecule were performed as a function the θ[C3-N5-C2-N3] torsion angle varying from -180º to 180º at 10º intervals using both B3LYP/6-31+G(d) and HF/6-31+G(d) level of theory. The dipole moment value of the molecule was calculated as 5.43 Debye by the B3LYP/6-311++G(2d,2p) method and as 5.73 Debye by the HF/6-311++G(2d,2p) method, respectively. The obtained vibrational wave numbers were scaled with appropriate scale factors and the assigning of these vibrational wavenumbers was made according to the potential energy distribution (PED) using the VEDA 4f program. Also, by using HOMO-LUMO energies, energy gap values, ionization energy, electron affinity, chemical potential, electronegativity, hardness and softness indices were obtained. The approximate geometry of the molecules in three dimensions was drawn in the Gauss View 5.0 molecular imaging program, and all theoretical calculations were used with the Gaussian 09W package program.

Effect of carboxylic acid and cyanoacrylic acid as anchoring groups on Coumarin 6 dye for dye-sensitized solar cells: DFT and TD-DFT study

Starting with Coumarin-6 dye, two novel D-π-A organic dyes C6X and C6N have been designed by attaching carboxylic acid and cyanoacrylic acid groups as anchoring groups to Coumarn-6 dye, respectively, to understand their potential use in dye-sensitized solar cells (DSSCs). The electronic structure and photophysical and photovoltaic properties of the novel designed dyes were studied using density functional theory DFT and time-dependent density functional theory TD-DFT with the Becke3-Parameter-Lee–Yang–Parr (B3LYP) functional and the 6-31G (d, p) basis set. Optimized structure and electronic properties (highest occupied molecular orbital energy (EHOMO), lowest unoccupied molecular orbital (ELUMO), and energy difference (Eg) between HOMO and LUMO) were calculated showing that C6N has the smallest band gap with the larger absorption region. Density of states (DOS), molecular electrostatic potential (MEP), natural bond orbital (NBO) analysis, non-linear optical (NLO) properties, UV–vis spectra, as well as some crucial parameters affecting the photovoltaic performance of DSSCs, such as light-harvesting efficiency (LHE), electron injection driving force (ΔGinject), dye regeneration driving force(ΔGreg), and the excited state life time(τe), were calculated to study the effect of the anchoring group on the DSSC performance. Additionally, the adsorption of C6X and C6N dyes on the TiO2 anatase (101) surface and the mechanism of electron injection were also investigated using a dye–(TiO2)9 cluster model using TD-B3LYP calculation. The calculated adsorption energies of the dyes suggest a strong adsorption of dyes to a TiO2 surface. The results show that C6N may be theoretically a good candidate as sensitizer of DSSC application.

A New Schiff Base Molecule Prepared from Pyrimidine-2-thione: Synthesis, Spectral Characterization, Cytotoxic Activity, DFT, and Molecular Docking Studies

Schiff base derivatives are some of the most widely used organic compounds for industrial purposes and they exhibit a broad range of biological activities. In this paper, a new Schiff base derivative (2) synthesized from the condensation reaction of 1-amino-5-benzoyl)-4- phenylpyrimidine-2(1H)-thione (1) with 2-chlorobenzaldehyde. The new compound was characterized by 1H, 13C NMR, and FT-IR. The biological activity property of this compound was tested against two different cancer cell lines and a healthy human cell line. The results demonstrate that molecule 2 has antiproliferative activity. In molecular modeling studies, the interaction site was examined using the epidermal growth factor receptor (EGFR) tyrosine kinase domain. Alignment in molecular docking, surface mapping binding, amino acids, and binding energy calculated. Glide score energy was found to be -9.820 kcal/mol and it predicted that the bonding interaction is strong. Theoretical calculations were made to compare the experimental and theoretical data. These calculations were performed on the 6–31 G* basis set using the Density Functional Theory (DFT) method and Becke-3-Parameter-Lee-Yang-Parr (B3LYP). Using this method, various parameters, such as frontier molecular orbitals, HOMO-LUMO energy levels, band gap, and chemical reactivity indices were found and interpreted.

Growth, crystal structure, Hirshfeld surface analysis, DFT studies, physicochemical characterization, and cytotoxicity assays of novel organic triphosphate.

A novel organic-inorganic hybrid compound, named (1-phenylpiperazinium) trihydrogen triphosphate, with the formula (C10H15N2)2H3P3O10 has been obtained by low speed of evaporation of a mixture of an alcoholic solution of 1-phenylpiperazine and triphosphoric acid H5P3O10 at room temperature after using the ion exchange chemical procedure. To carry out a detailed crystallographic structure analysis, single-crystal X-ray diffraction has been reported. In the molecular arrangement, the different entities are held together through N-H…O, O-H…O, and C-H…O hydrogen bonds, building up a three-dimensional packing. Powder X-ray diffraction analysis is acquired to confirm the purity of the product. The nature and the proportion of intermolecular interactions were investigated by Hirshfeld surface analysis. In order to support the experimental results, a density functional theory (DFT) calculation was performed, using the Becke-3-parameter-Lee-Yang-Parr (B3LYP) function with LANL2DZ basis set, and the data indicate much agreement between the experimental and the theoretical results. Thus, the physicochemical properties were studied employing a variety of techniques (FTIR, NMR, UV-visible, and photoluminescence). To get an insight of the possible employment of the present material in biology, cell viability assays were performed.

Electronic and nonlinear optical properties of doped/undoped graphene via coronene based models: a DFT study

Coronene C24H12 can be considered as graphene nanoflakes. This aromatic hydrocarbon allows for detailed calculations and the rapid evaluation of a variety of doped structures while maintaining the periodic aromaticity of graphene. In this study, through density functional theory (DFT) at the B3LYP (BECKE 3-PARAMETER LEE-YANG-PARR) functional with a 6-31G (d) basis set, we have investigated the effects of substituting carbon atoms with B, N, and O on the electronic structure, linear and nonlinear optical properties of graphene. Therefore, we found that the bandgap varies as a function of the considered structure.

Investigation of Conformation, Vibration and Electronic Properties of 2- Methoxythiophene Molecule by Theoretical Methods

In this study, the structural parameters, vibrational frequency, the electronic energy, the dipole moment, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy, the polarizability, hyperpolarizability and the potential energy curves (PEC) of 2-methoxythiophene molecule were calculated at Hartree-Fock (HF) and Density Functional Theory (DFT) with B3LYP (Becke 3 Parameter Lee-Yang-Parr) model using the 6-311++(d,p) basis set in gas phase. The potential energy curves of the molecule were performed as a function the θ[C3-C2-O-C6] torsion angle varying from 0-360º at 10º intervals. The dipole moment value of the molecule was calculated as 1.99 Debye by the DFT/B3LYP/6-311++G(d,p) method and as 2.24 Debye by the HF/6-311++G(d,p) method, respectively. The obtained vibrational wave numbers were scaled with appropriate scale factors and the assigning of these vibrational wavenumbers was made according to the potential energy distribution (PED) using the VEDA 4f program. Also, by using HOMO-LUMO energies, energy gap values, ionization energy, electron affinity, chemical potential, electronegativity, hardness and softness indices were obtained. The approximate geometry of the molecules in three dimensions was drawn in the GaussView 5.0 molecular imaging program, and all theoretical calculations were used with the Gaussian 09W package.

The Role of the Various Solvent Polarities on Piperine Reactivity and Stability

Piperine is a natural cytotoxic agent aware of various therapeutic acts. The aim of this study is to look into the effects of solvent polarity on solvent-free energy, dipole moment, polarizability, and hyper-polarizability of the first order, as well as various molecular properties including chemical hardness and softness, chemical potential, electronegativity, and electrophilicity index, in order to gain a better understanding of its reactivity and stability. The Becke, 3-parameter, Lee-Yang-Parr (B3LYP) level of theory with the cc-pVDZ basis set was used to perform all forms of calculations in both the gas phase and in solution. The Solvation Model on Density (SMD) was used to measure the solvation-free energy, dipole moment, and molecular properties of five solvent systems: water, DMSO, ethanol, cyclohexane, and heptane. As the dielectric constant was reduced, the solving energies gradually decreased, i.e. free energy decreased with declining solvent polarity. Piperine's dipole moment has been found to increase when transitioning from non-polar to polar solvents. The dipole moment of piperine was greater than that of the gas phase in various solvents. PPN's dipole moment and first order hyper-polarizability gradually increased as the solvent polarity increased, while its polarizability decreased. In addition, the hardness, chemical potential and electrophilicity index were decreased from non-polar to polar solvent, but with the rise in solvent polarity for the PPN molecule, softness and electronegativity were increased. The determined free energy solvation, dipole moment, polarizability, hyper-polarizability of the first order, and molecular properties identified in this research may contribute to an understanding of the stability and reactivity of piperine in specific solvent systems.