Natural Bond Orbital Analysis Research Articles

DFT Study of Nanotubes as the Drug Delivery Vehicles for an Anticancer Drug

Abstract: Chemicals and poisons in the body interfere with the cell cycle and inhibit the growth of cancer cells. In this way, the function of chemicals in the body is controlled by taking anti-cancer drugs. Due to the degradability and compatibility of carbon nanotubes and boron nitride with the environment, they can act as suitable drug carriers for the transfer of anticancer drugs and deliver the drugs to the target cells. In the current work, the encapsulation of Formestane (FMS) anticancer drug into the carbon (CNT) and boron nitride (BNNT) (8,8) nanotubes was investigated for the first time using the density functional theory: B3LYP/3-21G* and the natural bond orbital analysis in the gas phase. Using natural bond orbital analysis, the charge transfer between FMS drug and CNT and BNNT nanotubes (8,8)/ FMS (BNNT/FMS) complexes were explored. Based on the results obtained from the calculation of encapsulation energy, it was found that the adsorption process was favorable. The interaction effects of FMS drug and CNT and BNNT (8,8) nanotubes on the natural bond orbital charge, the chemical shift parameters, and electronic properties were also evaluated. This study revealed that CNT and BNNT (8,8) nanotubes can be a suitable carrier for FMS drug delivery. The ultraviolet-visible spectra of the FMS drug, the CNT and BNNT (8,8), and the BNNT/FMS complexes were computed using time-dependent density functional theory (DFT: B3LYP) calculations.

Spectroscopic characterization and quantum chemical calculations on Favipiravir-Guanine biomolecular complex

Favipiravir, a medication, has drawn a lot of interest recently as a possible therapeutic option for viral illnesses such as the COVID-19 pandemic. In the current work, Favipiravir + Guanine combination is being spectroscopically characterized using Fourier Transformed Infrared Spectroscopy, Raman, and Surface-Enhanced Raman Spectroscopy tools. Density functional theory along with the Becke 3-Parameter, Lee-Yang-Parr method and the basis set 6-311++ G(d,p) is used to explore the molecular interactions between the monomers of Guanine and Favipiravir. The stability of the complex resulting from the charge delocalization is thoroughly examined by natural bond orbital analysis that demonstrates the C=O∙∙∙H intermolecular hydrogen bond formation. The nature of the intermolecular hydrogen bond is described using atoms in molecules analysis. Molecular electrostatic potential mapping depicts various regions of electrostatic potential for the molecules, characterizing their reactive nature. The complex’s frontier molecular orbital gap of 2.39 eV indicates a higher possibility of electronic charge transfer, which in turn enhances the chemical reactivity of the complex. An analysis of the complex’s hyperpolarizability reveals a good non-linear optical response. The antiviral activity of the Favipiravir + Guanine complex is demonstrated by its molecular docking against the 6LU7 receptor (−5.61 kcal/mol).

Cycloaddition reaction of methylidyne radical with dipyrromethanol: quantum chemical insights into the formation of di(pyridin-2-yl)methanol

Density functional theory was employed to investigate methylidyne radical reaction on to the unsaturation of dipyrromethanol moiety through cycloaddition forming a six membered di(pyridin-2-yl)methanol followed by H-elimination via ring expansion. Time-dependent density functional theory (TD-DFT) simulations were performed to figure out the ultraviolet–visible spectrum of dipyrromethanol and di(pyridin-2-yl)methanol. Ultraviolet–visible spectrum of dipyrromethanol and di(pyridin-2-yl)methanol shows that two sharp absorption peaks were obtained at λ max = 161 nm and 206 nm for the reactant dipyrromethanol while a sharp peak was observed for the product di(pyridin-2-yl)methanol at shorter wavelength (λ max = 170 nm). The theoretical IR spectrum of dipyrromethanol and di(pyridin-2-yl)methanol shows that a significant red shift of 129 cm−1 was observed in the case of di(pyridin-2-yl)methanol due to presence of two strong intra-molecular hydrogen bonds, which indicates its higher stability than the dipyrromethanol. HOMO–LUMO energy gap calculations and natural bond orbital (NBO) analysis endorse the type of electronic transition for the desired product di(pyridin-2-yl)methanol is π–π*. The global reactivity analysis shows the electron donor and acceptor nature of dipyrromethanol and methylidyne radical, respectively. A potential energy surface is constructed via methylidyne radical addition, ring expansion, and hydrogen elimination transition states. Thermodynamics study and potential energy surface of the title reaction indicates its highly exothermicity and spontaneous in nature.

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.

Regiodivergent Synthesis of 4- and 5-Sulfenyl Oxazoles from Alkynyl Thioethers.

The regiodivergent synthesis of 4- and 5-sulfenyl oxazoles from 1,4,2-dioxazoles and alkynyl thioethers has been achieved. Gold-catalysed conditions are used to favour the formation of 5-sulfenyl oxazoles via β-selective attack of the nitrenoid relative to the sulfenyl group. In contrast, 4-sulfenyl oxazoles are formed by α-selective reaction under Brønsted acid conditions from the same substrates. The nature of stabilising gold-sulfur interactions have been investigated by natural bond orbital analysis, showing that the S→Au interactions are significantly stronger in the intermediate that favours the 5-sulfenyl oxazoles. A kinetic survey identifies catalyst inhibition processes. This study into the regiodivergent methods includes the development of telescoped annulation-oxidation protocols for regioselective access to oxazole sulfoxides and sulfones.

Computational Evaluation of the Structural, Topological, and Solvent Effects on the Nonlinear Optical Properties of 1-Methylurea Butanedioic Acid Crystal

In silico investigation of the effects of a molecule’s framework and surroundings on its nonlinear optical (NLO) response is still an active topic of study in the fields of photonics and optoelectronics. NLO materials play a crucial role in modern photonics and optoelectronic technologies. Presented here is a comprehensive theoretical analysis of the structural, topological, and NLO features of 1-methylurea butanedioic acid (MUBA) alongside solvent effects (water, DMSO, and benzene) using the DFT method at the B3LYP(D4)/6–311++G(d,p) level. Geometric and infrared parameters were calculated and compared with experimental values. The analysis using atoms in molecules (AIM) and the independent gradient model (IGM) reveals the presence of two noncovalent intermolecular interactions: N4–H16⋯O12 and O6–H25⋯O3, which stabilize the crystal structure. The natural bond orbital (NBO) analysis reveals that the LP(1)N4 ⟶ π∗(C2-O3) interaction is the most stabilizing and is enhanced in solvent environments. NLO data show that the first (βtot) and second (γ) hyperpolarizability values of MUBA are approximately 0.6–1.1 and 8.3–17.0 times higher than those of urea. In addition, the quadratic and cubic responses of MUBA are significantly reduced and increased, respectively, in solvent environments. Based on its NLO susceptibilities, MUBA exhibits SHG, EOPE, OKE, and EFISHG properties, suggesting its potential application in the production of optoelectronic devices and optical limiting. This study enhances our understanding of the factors influencing the NLO behaviour of organic crystals, providing valuable insights for designing materials with enhanced NLO characteristics. The implications extend to industries such as telecommunications and computing, where faster data transmission rates are in high demand.

Molecular Hydrogen Acts as a Hydrogen Bond Proton Acceptor: From Protonated Betaine Tagging to the Weakest Hydrogen Bond.

In an attempt to gain further insights into the intermolecular interactions implied by Rizzo's group's cautionary tale related to molecular tagging in infrared multiple photon dissociation (IRMPD) spectroscopy with molecular messengers [Masson, A. . J. Chem. Phys. 2015, 143, 104313], in the present study, we provide an in-depth analysis of the noncovalent interaction between the molecular hydrogen and protonated betaine molecule in the gas phase. We aim to shed some new light on the fundamental issues concerning the wide diapason of hydrogen-bonding-type intermolecular interactions, with a wide variety of proton acceptors. We demonstrate that in the course of tagging the protonated betaine with molecular hydrogen from the OH group side, it is the σ bond of molecular hydrogen that plays the role of hydrogen-bonding proton acceptor. The tagging thus induces a small yet significant red shift of the protonated betaine O-H stretching mode. We investigate the performance of a wide range of density functional theory (DFT) functionals for the calculation of anharmonic vibrational frequency shifts of the studied system, which are essential for the correct interpretation of the experimental IRMPD data. For an accurate prediction of the OH stretching frequency shifts, specifically designed functionals such as Handy's group HCTH/407 should be applied. The empirical dispersion correction enhances the systematic overestimation of the anharmonic frequency shift, characteristic of the most widely used DFT functionals. Combining the full-wave function approach with the charge field perturbation and natural bond orbital (NBO) deletion analyses, we demonstrate that the frequency shift in the OH-tagged structure is governed by the σHH → σ*OH intermolecular charge transfer. This interaction stabilizes the OH-tagged dimer as well, in contrast to the dipole-quadrupole electrostatic interaction energy term. Topological analysis of the electron density reveals the presence of an intermolecular bond critical point with a positive value of the density Laplacian very close to the lower limit for hydrogen bonds. NCI analyses demonstrate that the OH···H2 interaction is weaker than the intramolecular CH···O one within the protonated betaine molecule, with the through of reduced density gradient appearing at less negative sign(λ2)·ρ values. Analyzing the O-H stretching vibrational potential with the second-generation absolutely localized molecular orbitals energy decomposition analysis (ALMO-EDA 2) revealed that in the case of betaineH(+) tagged from the OH group side, the permanent electrostatics (ΔEelec), polarization (ΔEpol), and charge-transfer (ΔEct) contributions to the total intermolecular interaction energy contribute favorably to the weak hydrogen bond formation and to the red shift of the fundamental O-H stretching frequency, the ΔEct contribution being the most significant in the last context. The Pauli repulsion term, on the other hand, favors an O-H stretching frequency blue shift as a consequence of the vibrational confinement effects.

DFT investigation of M2F superalkali doped dodecafluorophenylene (C13H10F12) derivatives with remarkable static and dynamic NLO response

Herein, based on density functional theory (DFT) simulations, the static and dynamic hyperpolarizabilities of the superalkalides based on Janus molecules have been explored. The designed superalkalides M2F(F)-DDFP-M2F(H) contain Janus based Dodecafluorophenylene (DDFP) molecule doped with superalkalis on both sides acting as both electron acceptors and donors. Thermodynamic stabilities are evident from the negative values of interaction energies, which are observed in the range of −2.96 eV to −3.63 eV. The maximum interaction energy (Eint) obtained is −3.63 eV for Li2F(F)-DDFP-Li2F(H) complex. The NBO (natural bond orbital) and FMO (frontier molecular orbital) analyses confirm the true superalkalide nature of the designed complexes. FMO analysis further reveals the reduction in energy gap E(H-L) from 10.43 eV (for bare DDFP) to 3.17 eV for the designed superalkalis. Furthermore, NLO response of the studied complexes reveals that the maximum values of polarizability (617 au) and hyperpolarizability are seen for Na2F(F)-DDFP-K2F(H) (4.25 × 104 au) complex, which confirms the remarkable NLO response of newly designed superalkalides. Moreover, frequency dependent analysis indicates that the maximum values of simple harmonic generation (SHG), electro-optical pockel effect (EOPE) and hyper Rayleigh scattering are 7.79 × 106, 2.75 × 106 and 4.45 × 106 au, respectively. The EOKE and EFISHG values are 6.79 × 107 and 7.68 × 1010 at 1339 nm suggesting significant increase in the NLO response of the reported complexes. These results manifest that our designed complexes might provide new paths towards the exceptionally high performance NLO materials. Moreover, we expect that the present work will provide guidance for designing and synthesis of superalkali based NLO materials in future.

Electronic structure and optical spectral analysis of the MnO42- anion with consideration of site and Jahn-Teller distortion.

The ground state of 3d1 MnO42- was studied by density functional theory (DFT) and complete active space self-consistent field (CASSCF) methods in terms of a variety of molecular point group structures to ascertain the site and Jahn-Teller (JT) distortion effect. Modeling results from UB3LYP/6-31+G(d) calculations with natural bond orbital analysis show the four Mn-O bonds are coordinate covalent. The one-electron matrix elements from CASSCF(AILFT) (abinitio ligand field theory) with a second order perturbation treatment were used to calculate the parameters of the angular overlap model. These allowed the calculation of JT stabilization energies and first and second order JT coupling constants for MnO42- with C2v and D2d symmetry. Absorption spectra and excited state transition energies were calculated assuming the lattice distorted geometry was C2v with time-dependent DFT (TDDFT) using the unrestricted coulomb-attenuating UCAM-B3LYP density functional and with the spin-adapted spin-flip DFT using the UBH&HLYP density functional, both with the AUG-CC-PVTZ basis set. The mean absolute deviation of the calculations from experimental excited states for the ligand field and ligand-to-metal charge transfer (LMCT) bands was better than 0.1eV. Several new assignments for LMCT excited states were made on the basis of the TDDFT excitation results.

Expanding chalcogen bonds in thiophenes to interactions with halogens.

Compounds containing the thiophene moiety find several applications in physics and chemistry, such as electrical conduction, which depends on specific conformations to properly exhibiting the desired properties. In turn, chalcogen bonding has found to modulate the conformation of some N-thiophen-2-ylfomamides. Since halogens participate in a kin interaction (halogen bonding) and are abundant in agrochemicals, pharmaceuticals, and materials, we have quantum-chemically explored the interaction between organic halogen and thiophene as a conformational modulator in some model compounds. Although such interaction indeed appears, as demonstrated by atoms in molecules and natural bond orbital analysis, it is inefficient to control the conformational equilibrium. An energy decomposition analysis scheme demonstrated that halomethane and thiophene tend to move away from one another due to a core component (Pauli repulsion and exchange), which is mainly due to a deformation term. Therefore, chalcogen bonds with halogens appear weaker than with other chalcogens.

Studies on the synthesis, growth, and characterization of 2-cyanopyridinium salicylate single crystals for nonlinear optical applications

By employing methanol as the solvent in slow solvent evaporation method, a new nonlinear optical organic single crystal of 2-cyanopyridinium salicylate (2-CPSC) was grown. The lattice parameters of the 2-CPSC crystals were found out to be a = 7.7764(9) Å, b = 12.3938(17) Å, c = 12.3685(18) Å, and β = 94.44º using single crystal X-ray diffraction (SCXRD) analysis. The confirmation of crystalline nature was done by powder XRD analysis. The 2-CPSC crystal's chemical composition and functional groups were confirmed by Fourier transform infrared (FTIR) spectral analysis. The optical study was done by ultraviolet-visible-near infrared (UV–Vis-NIR) spectral analysis showing a cutoff wavelength of 338 nm. Studies on the grown 2-CPSC crystal's dielectric and Vicker's microhardness were also conducted. The linear dependence of photocurrent with the applied electric field was revealed for the grown crystals. The 2-CPSC crystal's third-order nonlinearity was investigated by the single-beam Z-scan technique using a continuous He-Ne laser. The open aperture Z-scan reveals the two-photo absorption mechanism and the closed aperture Z-scan study reveals the positive nonlinearity of the 2-CPSC crystals with third order susceptibility value of χ3=2.6763×10−6(esu). The density functional theory (DFT) method of B3LYP level with the 6–31++G(d,p) basis set was used for different quantum chemical calculations like geometry optimization, natural bond orbital (NBO) analysis, mulliken atomic charge, and molecular electrostatic potential (MEP). The higher nonlinearity of the 2-CPSC can be a potential alternative for commercially available potassium dihydrogen phosphate (KDP) and candidate for its application in nonlinear optical devices like optical limiting and optical switching.

Identification of cholesterol in different media by using the FT-IR, FT-Raman and UV–visible spectra combined with DFT calculations

In this investigation, the experimental FT-IR and FT-Raman spectra of cholesterol in the solid phase and in ethanol solution have been combined with the B3LYP/6–311++G** calculations and the scaled quantum mechanical force field (SQMFF) methodology, normal internal coordinates and transferable scaling factors to obtain the complete vibrational assignments of 216 vibration modes expected. Hence, complete vibrational assignments for that steroid of greatest biological importance are reported for first time in gas phase and ethanol solution together with its scaled force constants. Changes in the positions of some bands and in force constants values are observed in the different media due to the predicted intra-molecular interactions between CH3/CH3, CH3/CH2 and CH2/CH2 groups by atoms in molecules (AIM) calculations. The 1H- and 13C NMR chemical shifts of normal and deuterated cholesterol in aqueous solution confirm that the H atom of OH group is involved in the formation of H bonds in solution. Studies of experimental electronic spectra of cholesterol in different concentrations of ethanol revealed that the positions of peaks maxima increase conform increase the solution concentration. The natural bond orbital (NBO) analyses reveal that the polar OH group and the four fused rings play important roles in the stability and properties of cholesterol than the large hydrophobic moiety. Frontier orbitals predicted low reactivity of cholesterol in ethanol probably due to its high ω value in this medium.

Computational study of charge transfer iso-surface in first three excited states, electron-hole transition effects, chemical nature and bond order analysis investigations of chrysogine

This work presents the theoretical DFT (Density Functional Theory) studies and the biological application of chrysogine, a marine alkaloid. Energy minimisation and additional DFT evaluations were performed for vacuum and solvent media. It has been observed that solvation with polar solvents has resulted in a slight variation in the molecule’s properties. The Multiwfn software was employed to carry out various topological analyses. Among these, the charge transfer studies show that the second and third excited states are the most significant. From the reactivity analysis, the least energy gap (4.9624 eV) is obtained in water, indicating that chrysogine is most reactive in aqueous media. Theoretical UV studies show that the trends in λmax values correspond to n -->π* and n -->σ* electronic transitions within the molecule. An increase in medium polarity has demonstrated in the MEP (Molecular Electrostatic Potential) maps an increase in the potential range from −6.619 × 10−2 a.u. to 6.619 × 10−2 a.u. in the gas phase, to a sharp rise to −8.036 × 10−2 a.u. to 8.036 × 10−2 a.u. in ethanol, −8.098 × 10−2 a.u. to 8.098 × 10−2 a.u. in methanol, −8.130 × 10−2 a.u. to 8.130 × 10−2 a.u. in DMSO, and −8.127 × 10-2 a.u. to 8.127 × 10−2 a.u. in water. The most significant transition contributing to molecular stability from NBO (Natural Bond Orbital) analysis is: (O2-C9) π* → π* (C7-C8) with the energy of 258.13 kcal mol−1. The ADMET profile for the molecule was assimilated with the help of online servers. The molecule was docked against lung cancer target proteins (PDB ID: 1NTK, 3QFB) using software such as AutoDock Tools and PyMOL. The respective illustrations and data were visualised using Discovery Studio Visualizer. Good binding affinities (−5.69 kcal mol−1 for 1NTK and −6.64 kcal mol−1 for 3QFB proteins) and interactions were achieved with the selected targets.

Antibacterial [Zn(nicotinamide)2Cl2] complex for the treatment of skin conditions: An experimental-theoretical study of physicochemical, microbiological and in silico pharmacokinetic properties

A dichlorobis(nicotinamide)zinc(II) complex, [Zn(nicotinamide)2Cl2], was crystallized through the slow evaporation method, and its vibrational, electronic, structural, and thermal properties have been characterized. Density functional theory (DFT) was used for the accurate analysis of intramolecular vibrational modes, obtaining chemical reactivity indices and comparative studies of geometric and electronic parameters, including solvation effects in methanol, ethanol, and water, as well as in vacuum. Additionally, the nature and strength of the bonds associated with the coordination sphere (Cl–Zn and N–Zn) were elucidated from the quantum theory of atoms in molecules and natural bond orbital analyses. Powder X-ray diffraction showed that the coordination compound belongs to a monoclinic symmetry with P21/a (C2h5) space group. Thermal analyses revealed that the material is stable up to 200 °C. From DFT calculations, the complex is chemically more stable in solvents compared to vacuum conditions, with the aqueous medium offering greater stability. The chemical stability was also analyzed by infrared and Raman spectroscopy, with the results showing spectral changes mainly for the vibrational spectra obtained in methanol, ethanol, and water against those obtained in vacuum. Biological experiments showed the complex antibacterial activity against Gram-positive and Gram-negative bacteria, mainly against the Cutibacterium acnes ATCC 6919 strain. A computational study of the absorption, distribution, metabolism, excretion (ADME), and drug-likeness were calculated to support the experimental data.

Evaluating the efficacy of newly synthesized amino acid derivatives as corrosion inhibitors in acidic solutions

Three benzimidazole derivatives, with tryptophan (BIT), tyrosine (BIY), and histidine (BIH) amino acid units, have remarkable protective properties as eco-friendly corrosion inhibitors for steel under severe acidic conditions. At a temperature of 303 K, the corrosion inhibition efficiency of BIT, BIY, and BIH at a concentration of 10 mM is 90.09 %, 92.53 %, and 93.43 %, respectively. Electrochemical tests indicate that the adsorption of these substances on the substrate leads to an increase in charge transfer resistance and interfacial electric double layer thickness. This effectively hinders the dissolution of metal and the evolution of hydrogen. The analysis of the surface structure and appearance using SEM-EDS indicates that the inhibitors have the ability to create a protective coating through both chemical and physical bonding, effectively protecting the metal from corrosive substances. Theoretical calculations, such as Density Functional Theory (DFT) and Natural Bond Orbital (NBO) analysis, along with FUKUI analysis, help identify active sites and adsorption configuration. This enhances our understanding of the corrosion mitigation mechanism. These findings align with the experimental conclusion that the formation of a stable protective film contributes to superior inhibition performance against acidic corrosion conditions.

Self-assembled crown ether (15CR5) with alkaline earth metals to stimulate nonlinear optical properties: The comprehensive study by silico technique

Crown Ether (15CR5) molecule is a worthwhile organic material exhibiting excellent NLO properties and characteristics. In this research, density functional theory (DFT) was extensively employed to study the nonlinear optical (NLO) properties of alkaline earth metal doped 15CR5 by using WB97XD/6-31G+(d, p). Binding energies, interaction energies, vertical ionization energies and reactivity parameters unveiled the thermodynamic stability of these systems. These molecules show a lower value of HUMO-LUMO energy gap indicating their superior electronic properties. Moreover, these complexes possess high oscillator strength and lower excitation energies displaying their better electrical and optical characteristics than pure 15CR5. Non-covalent analysis was carried out for all the designed systems forecasted the van der wall interactions between 15CR5 and dopants. These complexes in the visible region have excess electrons that are highly absorbed in the range of 405.73 to 608.27 compared to 15CR5. The Hyperpolarizability (βtot) of these designed materials was in the range of 9097.21–21627.85 au which is significantly higher than its pure counterpart. Results based on the density of state (DOS), natural bond orbital analysis (NBO) and transition density matrix (TDM) were also strongly supported the enhancement of the NLO properties of these systems. These newly designed alkaline earth metal doped 15CR5 systems with promising NLO characteristics can be used for optoelectronic applications.

GeSe nanoclusters as potential drug delivery agent for anti-cancer drugs: First-principles study

For effective drug delivery, a drug carrier that is biocompatible, antitoxic, and appropriate for drug loading/release is required. Here, GeSe nanoclusters are investigated as potential drug delivery for anti-cancer drugs using density functional theory (DFT) calculations. They are dynamically and energetically stable with abundant active sites that facilitate binding with drugs. The anti-cancer drugs, adrucil and hydroxyurea, are successfully loaded on the nanoclusters with adsorption energy ∼ -0.7 eV. Interestingly, no chemical bonds were formed between the drug and the nanocluster highlighting the robust non-covalent interactions (NCI). These slight changes in the electronic properties after drug adsorption are confirmed by the partial density of states, natural bond orbital (NBO) and NCI analysis, and UV–vis spectra. This moderate adsorption without notable changes in the electronic structure facilitates the drug release at the infected tissue. Therefore, GeSe nanoclusters with appropriate electronic and drug adsorption/release properties represent a viable drug delivery agent.

Fluoride-Ion Donor Properties of AsF5

Fluoride-Ion Donor Properties of AsF₅

Comparison of Cu3, Cu5, and Cu7 clusters as potential antioxidants: A theoretical quest.

Herein, we compare and contrast the dual roles of Cun clusters (n = 3, 5, and 7 atoms) in scavenging or generating RO• free radicals from ROH at the theoretical levels (where R = H, methyl, ethyl, n-propyl, i-propyl, n-butyl, t-butyl, and phenyl). This investigation is performed in water media to mimic the actual environment in the biological system. In the presence of the Cun clusters, bond dissociation energy (BDE) of RO-H and R-OH is reduced. This is clear evidence for the increased possibility of both the RO-H and R-OH bonds breakage and scavenging of RO• radicals. The nature of anchoring bonds responsible for the interaction of Cun clusters with ROH and RO• are interpreted using the quantum theory of atoms in molecules (QTAIM) and the natural bond orbital (NBO) analysis. The DFT results indicate that the O•⋅⋅⋅•Cu bond is stronger and has more covalent character in RO•⋅⋅⋅•Cun radical complexes than in ROH⋅⋅⋅•Cun. Therefore, the interactions of Cun clusters with RO• radicals (antioxidant) are more pronounced than their interactions with ROH non-radicals (pro-oxidant). The GAMESS software package was utilized in this paper. The B3LYP and M06 functions with the 6-311 + + G(d,p), and LANL2DZ/SDD basis sets was used to perform the important geometrical parameters of RO•⋅⋅⋅•Cun and ROH⋅⋅⋅•Cun, binding energy (Eb), and bond dissociation energy (BDE).

In silico rationalization of piperidin-4-one analogs as anaplastic lymphoma kinase inhibitors: Integration of density functional theory, topological descriptor, molecular docking and pharmacological feature profiling

Anaplastic lymphoma kinase (ALK) was involved in the development of various cancer types. Although several ALK inhibitors have been advanced to clinical trials, the emergence of drug resistance has limited the clinical application of them. Hence, developing new ALK inhibitors which can overcome resistance is essential. Here, we designed a novel ALK inhibitor Piperidin-4-One based on the structure of the second-generation ALK inhibitor ceritinib. The target compound 1-(cyclopropanecarbonyl)-2,6-bis(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-3-methylpiperidin-4-one (CDMP) was computed using density functional theory (DFT) method. The stability and charge delocalization of the molecule was also studied by natural bond orbital (NBO) analysis. The HOMO-LUMO energies describe the charge transfer takes place within the molecule. Molecular electrostatic potential has been analyzed. The reported molecule used as a potential NLO material since it has high µβ0 value. Additionally, statistical analyses were conducted to clarify the connections between ADMET properties of CDMP and molecular descriptors based on degree, neighborhood degree, degree entropy and neighborhood degree entropy. This thorough examination seeks to uncover the complex interactions between Density Functional Theory and molecular descriptors, offering valuable insights into the relationships among CDMP drug properties. The binding mode mechanism of the title compound was investigated through molecular docking studies, focusing on cancer-related proteins such as 4TT7, 5FTO and 3AOX. Furthermore, an assessment of Drug-likeness and ADMET properties revealed favorable pharmacokinetic profiles for the compound, with no indications of toxicity observed.