Improvement of anti-inflammatory and anticancer activities of poly(lactic-co-glycolic acid)-sulfasalazine microparticle via density functional theory,molecular docking and ADMET analysis

In the present study, we assessed improvement of anti-inflammatory activity and drug delivery of sulfasalazine (SSZ) by the poly(lactic-co-glycolic acid), (PLGA), in H₂O and dichloromethane (DCM) environments via density functional theory (DFT), ADMET, and molecular docking. Our calculated results based on binding energy and thermodynamic parameter represents that the interaction between SSZ and PLGA in Complex A via double hydrogen bonds is stronger in comparison with Complex B. The analysis of Ultraviolet–visible (UV–VIS) spectra proved the interaction of SSZ with PLGA by time-dependent density functional theory (TDDFT). Infrared (IR) spectra demonstrated that the structure of PLGA was shifted in the presence of the SSZ. The interaction of SSZ with PLGA leads to an increase in dipole moment and higher solubility with more negative Gibbs free solvation energy (ΔG_solv) values and lowering of the energy gap (E_g). The obtained results by Molecular docking demonstrates that the interaction of SSZ via its carboxylate group with PLGA (complex A) had a strong interaction towards the binding pocket of the target and as a potential inhibitor of the COX-2, TNF-α, and IL-1 receptors at the binding site as compared with the complex B.     

Mechanical properties of diboron-porphyrin sheet under strain: A density functional theory study

The mechanical properties of a new two-dimensional semiconductor material named diboron-porphyrin (DP) are studied based on density functional theory. The behavior of DP monolayer under uniaxial and biaxial loadings as well as shear stress is investigated. The in-plane stiffness, Poisson's ratio, bulk and shear moduli of the DP monolayer are found to be close to those of a graphene sheet. It can be concluded that the DP monolayer has stiffness close to the graphene sheet. The difference in magnitude of in-plane stiffness and Poisson's ratio along x- and y-directions shows slightly anisotropic mechanical properties of DP monolayer. It is also observed that DP monolayers can bear high tensile strains before failure. The high stability and hardly deformable structure of DP monolayer are due to its high planar packing density which is comparable with graphene sheet. The fantastic mechanical properties of DP show these materials are desirable for application in nanomechanical devices.     

Host-guest molecular encapsulation of cucurbit[7]uril with dillapiole congeners using docking simulation and density functional theory approaches

Structural Chemistry - Binding affinity and intermolecular interactions are essential characteristics that could be used to comprehend molecular recognition between molecules in supramolecular...     

Conformers,properties, and docking mechanism of the anticancer drug docetaxel: DFT and molecular dynamics studies

The conformational structures and properties of the anticancer drug docetaxel (DTX) are studied theoretically. A total of 3888 trial structures were initially generated by all combinations of internal single‐bond rotamers and screened with the B3LYP/3‐21G* method. A total of 31 unique conformers were further optimized at the B3LYP/6‐311G* method. Their relative energies, dipole moments, rotational constants, and harmonic vibrational frequencies were predicted. Single‐point relative energies were then determined at the M06‐L/6‐311G(2df,p) level. The UV spectrum of the lowest‐lying DTX conformer in methanol was investigated with the TD‐CAM‐B3LYP/6‐311 + G(2df,p) method. The 31 unique DTX structures are mainly docked at three different sites within β‐tubulin. Based on the results of molecular docking and double‐float MD simulations, the lowest‐lying DTX conformer consistently exhibits good docking performance with β‐tubulin. We identified the residues LYS299, ARG215, GLN294, LEU275, THR216, GLU290, PRO274, and THR276 on β‐tubulin as active sites forming a binding pocket responsible for locking DTX within β‐tubulin to make the combination more stable. The RMSD values show that the predicted complexes are favorable, and the SASA analysis shows that the hydrophilic properties of DTX are better than paclitaxel. © 2018 Wiley Periodicals, Inc.     

Theoretical investigation of the molecular structure,vibrational spectra,and molecular docking of tramadol using density functional theory

The optimized molecular structures, harmonic vibrational wavenumbers, and the corresponding vibrational assignments of (1S,2S)-tramadol and (1R,2R)-tramadol are computationally examined using the B3LYP density functional theory method together with the standard 6–311++G(d,p) and def2-TVZP basis sets. The optimized structures show that phenolic rings of both 1R,2R and 1S,2S tramadol adopt planar geometry, which are slightly distorted due to the substitution at the meta-position; and the six-membered cyclohexane adopts a slightly distorted chair conformation. The 1S,2S enantiomer is energetically more favorable than 1R,2R with the energy differences of 1.32 and 1.03 kcal/mol obtained at B3LYP/6–311++G(d,p) and B3LYP/Def2-TVZP levels, respectively. The analysis of the binding pocket in the silico molecular docking with the m-opioid receptor shows that it originated two clusters with the 1S,2S enantiomer and one cluster with the 1R,2R enantiomer of tramadol. The results point to a more stable complex of the m-opioid receptor with the 1R,2R enantiomer of tramadol.     

Optoelectronic properties of benzotrithiophene isomers: A density functional theory study

Benzotrithiophene (BTT) isomers were investigated using density functional theory (DFT) and time‐dependent DFT (TD‐DFT) with the aim to explore their structures, linear optical properties, vertical and adiabatic ionization potentials (IP_v and IP_a), electron affinities (EA_v and EA_a), and reorganization energies (λ). The computed bond lengths and bond angles at the B3LYP/6–311+G (d, p) level of theory are in good agreement with experimental crystal structures of the known BTTs. These molecules are planar with zero dihedral angle, making them an ideal backbone for high charge mobility. The UV–visible spectra of BTT isomers are in the range 280–360 nm. All BTT isomers have low hole/electron reorganization energies, which is the main characteristic of good hole/electron transporting materials, and these isomers in turn have potential applications in the field of organic materials.     

Inhibitor design for 3-hydroxy-3-methyl-glutaryl-CoA reductase enzyme; molecular docking and determination of molecular and electronic properties of ligands by density functional theory method

Designing new inhibitors having less side effects is a need which also could reduce cholesterol levels. To fulfill this aim, we have carried out a molecular docking study toward 3-hydroxy-3-methyl-glutaryl-CoA (HMG-CoA) reductase. A set of designed structural derivatives of statin drugs, eight ligands which are used as HIV-1 integrase inhibitor candidates, a set of terpenoids, and ligands downloaded from Zinc15 database were docked to HMG-CoA reductase enzyme which contains atorvastatin in crystal structure. The analysis of docking studies revealed that statin derivative ligands are more appropriate for inhibition of HMG-CoA reductase. To define the contribution of the molecular properties to the binding of ligands to enzyme structure; the highest occupied molecular orbitals-lowest unoccupied molecular orbitals, hardness, electronegativity, and chemical potential properties of ligands have best score in their sets calculated by quantum mechanical tools.     

Chiroptical properties of artemisinin and artemether investigated using time-dependent density functional theory

Chiroptical properties including electronic circular dichroism(ECD) and optical rotatory dispersion(ORD) of artemisinin and artemether have been fully studied using quantum-chemical calculation based on time-dependent density functional theory.Both theoretical ECD and ORD of these two compounds were in good match with the experimental data.ECD spectrum of artemether could be totally attributed to the peroxide group,and that of artemisinin was an overlay of contribution from δ-lactone and peroxide moieties,which leading to a positive maximum at 260 nm.Our results showed that peroxide group could produce a broad ECD band in the far-UV region originated from electron transitions of HOMO →LUMO,HOMO-1 →LUMO and HOMO-2 →LUMO in the case of artemether.This work provided a theoretical interpretation of the ECD behavior of peroxide bond.     

铁酸锌(311)表面结构的密度泛函理论研究

利用原子层沉积技术（ALD）合成了铁酸锌（ZnFe₂O₄）纳米颗粒。基于密度泛函理论和原子热力学的方法,计算了ZnFe₂O₄的结构、磁性和电子性质,研究了ZnFe₂O₄（311）面六种不同终结面的稳定性与氧化学势和锌化学势的关系。结果表明,ZnFe₂O₄是具有正尖晶石结构的半导体,禁带宽度为1.91 eV,且具有反铁磁性。在ZnFe₂O₄可以稳定存在的化学势范围内,O₁、O₂、Fe₂、Zn₂四种终结面可以稳定存在,且具有不同的稳定区间。在富锌条件下（△μ_Zn=0 eV）,O₁终结面在大部分O化学势范围内最稳定,在贫锌条件下（△μ_Zn=-3.88 eV）,O₂终结面变得最稳定。     

Differential functional theory and molecular docking studies of newly synthesized carbamates

Four new carbamates (RZ1–RZ4) were synthesized from different amine moieties through reported methods. The reaction was monitored using thin layer chromatography and characterization was done using m.p., fourier‐transform infrared spectroscopy (FTIR), and X‐ray diffraction (XRD) techniques. Density functional theory (DFT) studies were carried out using Gaussian 09 software to compare the theoretical and practical parameters of the synthesized compounds. Highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) were also drawn to calculate the energy difference between orbitals. In‐vitro enzyme inhibition potential against acetylcholine esterase (AChE), butyrylcholine esterase (BChE), and protease was checked through standard protocols that suggested moderate inhibition against selected enzymes. Docking studies were also carried out, which depicted that these compounds have ability to bind on the active site of AChE and BChE.     

Adsorption properties and mechanism of sepiolite to graphene oxide in aqueous solution

Graphene oxide (GO) is widely used in various fields such as improving the performance of cement-based materials and making composite materials due to its large specific surface area and abundant oxygen-containing functional groups. However, it has also caused water pollution. To remove GO in aqueous solution, sepiolite (SEP) was used to adsorb it. The effects of pH, adsorbent quality, GO concentration, temperature and adsorption time on the ability of SEP to adsorb GO were investigated. The materials were characterized by SAP and laser particle size analyzer, and the adsorption performance and mechanism of SEP for GO were further analyzed by XRD, FTIR, SEM, TEM, XPS, AFM, and Zeta potential microscopic tests. The results showed that: 1) Under the conditions of temperature 303 K, pH = 3, adsorbent mass 30 mg, and initial concentration of GO 100 mg/L, the adsorption effect was the best, and the adsorption rate reached 94.8 %. 2) The adsorption reached equilibrium at 2160 min, and the adsorption process was more in line with the pseudo-second-order adsorption kinetic equation, and the adsorption behavior was controlled by chemical effects. 3) The adsorption of SEP to GO is more consistent with the Langmuir and Temkin adsorption isotherm model, and the reaction is a spontaneous, endothermic, and entropy-increasing process. Experiments showed that SEP had a strong adsorption capacity for GO, which provides a reference for the treatment of toxic GO in aqueous solution and the realization of water ecological protection.     

A theoretical study on the cyclopropane adsorption onto the copper surfaces by density functional theory and quantum chemical molecular dynamics methods

We report a theoretical study on the cyclopropane adsorption onto Cu(1 1 1) surfaces by density functional theory (DFT) and quantum chemical molecular dynamics methods. The equilibrium geometry of the physisorbed species was obtained using both periodic and cluster models by DFT methods that employ Cambridge serial total energy package (CASTEP), DMol ab initio quantum chemistry software of Accelrys’ materials studio (DMol), and Amsterdam density functional (ADF) program. It was found that the adsorbate molecule was tilted towards the metal surface with one C---C bond (upwards) parallel to the surface and that the physisorption occurred via a third carbon atom pointing (downwards) towards the surface. The electronic distribution and geometrical structure of physisorbed cyclopropane were slightly deviated from its gas phase molecule. The calculated vibrational frequencies and adsorption energies are close to experimental data, confirming the reliability of our DFT results. The adsorption process was simulated using our novel tight-binding quantum chemical molecular dynamics program, ‘Colors’. The calculation results indicated that both the adsorption and desorption processes of cyclopropane took place molecularly. The electron transfer and structural properties of equilibrium position obtained by ‘Colors’ are consistent with those by the first principles DFT methods.     

Calculation of the electronic and optical properties of indium tin oxide by density functional theory

Density functional theory (DFT) was used to calculate the bulk electronic and optical properties of indium tin oxide (ITO). The ITO model was constructed replacing indium atoms with tin atoms in the cubic unit cell of indium oxide. To allow more possibilities for tin atom substitution than afforded by the forty-atom primitive cell of indium oxide all eighty atoms of the unit cell were included in the stoichiometry (In_32−xSn_xO₄₈) using periodic boundary conditions. A number of properties of ITO were calculated including the optical band gap, charge carrier density and plasma frequency. The dependence of the electronic and optical properties of ITO on a variety of parameters such as the tin content, cubic lattice parameter and the distance between adjacent tin atoms was investigated. The electronic and optical properties agreed well with experimental data and allowed insight into the origin of the electronic and optical properties of ITO.     

Gas-phase thermochemical properties of some tri-substituted phenols: A density functional theory study

The study of the energetics of phenolic compounds has a considerable practical interest since this family of compounds includes numerous synthetic and naturally occurring antioxidants. In this work, density functional theory (DFT) has been used to investigate gas-phase thermochemical properties of the following tri-substituted phenols: 2,4,6-trimethylphenol, 2,6-dimethyl-4-tert-butylphenol, 2,6-dimethyl-4-methoxyphenol, 2,4,6-tri-tert-butylphenol, 2,6-di-tert-butyl-4-methylphenol, 2,6-di-tert-butyl-4-methoxyphenol, 2,4,6-trimethoxyphenol, 2,6-dimethoxy-4-methylphenol and 2,6-dimethoxy-4-tert-butylphenol. Molecular structures were computed with the B3LYP and the ωB97X-D functionals and the 6-31G(d) basis set. More accurate energies were obtained from single-point energy calculations with both functionals and the 6-311++G(2df,2pd) basis set. Standard enthalpies of formation of the phenolic molecules and phenoxyl radicals were derived using an appropriate homodesmotic reaction. The OH homolytic bond dissociation enthalpies, gas-phase acidities and adiabatic ionization enthalpies were also calculated. The general good agreement found between the calculated and the few existent experimental gas-phase thermochemical parameters gives confidence to the estimates concerning the phenolic compounds which were not yet experimentally studied.     

The capture of carbonyl sulfide by N-methyldiethanolamine: A systematic density functional theory investigation

In this contribution, the mechanism of carbonyl sulfide (COS) absorption by N-methyldiethanolamine (MDEA) aqueous solution was explored via theoretical computations. Detailed reaction mechanisms were analyzed using density functional theory (DFT) calculations at the B3LYP-D3 level of theory. In total, four different pathways for COS absorption by MDEA have been considered. The most favorable pathway for the removal of COS is a three-step mechanism including the hydrolysis, proton transfer, and dissociation of CO₂, and hydrolysis is the rate-determining step. The mechanisms of the COS absorption by different amines were investigated, and the calculated results suggest that the total energy barrier for the COS absorption by MDEA is comparable to that by monoethanolamine (MEA), diethanolamine (DEA), and diisopropylamine (DIPA), indicating the COS absorption by all the four amines are feasible, while MDEA gives a better performance in terms of thermodynamics.     

Formation mechanism of methane during coal evolution:A density functional theory study

The formation mechanism of methane （CH4） during coal evolution has been investigated by density functional theory （DFT） of quantum chemistry. Thermogenic gas, which is generated during the thermal evolution of medium rank coal, is the main source of coalbed methane （CBM）. Ethylbenzene （A） and 6,7-dimethyl-5,6,7,8-tetrahydro-1-hydroxynaphthalene （B） have been used as model compounds to study the pyrolysis mechanism of highly volatile bituminous coal （R）, according to the similarity of bond orders and bond lengths. All possible paths are designed for each model. It can be concluded that the activation energies for H-assisted paths are lower than others in the process of methane formation; an H radical attacking on β-C to yield CH4 is the dominant path for the formation of CH4 from highly volatile bituminous coal. In addition, the calculated results also reveal that the positions on which H radical attacks and to which intramolecular H migrates have effects on methyl cleavage.     

Formation mechanism of methane during coal evolution: A density functional theory study

The formation mechanism of methane (CH₄) during coal evolution has been investigated by density functional theory (DFT) of quantum chemistry. Thermogenic gas, which is generated during the thermal evolution of medium rank coal, is the main source of coalbed methane (CBM). Ethylbenzene (A) and 6,7-dimethyl-5,6,7,8-tetrahydro-1-hydroxynaphthalene (B) have been used as model compounds to study the pyrolysis mechanism of highly volatile bituminous coal (R), according to the similarity of bond orders and bond lengths. All possible paths are designed for each model. It can be concluded that the activation energies for H-assisted paths are lower than others in the process of methane formation; an H radical attacking on β-C to yield CH₄ is the dominant path for the formation of CH₄ from highly volatile bituminous coal. In addition, the calculated results also reveal that the positions on which H radical attacks and to which intramolecular H migrates have effects on methyl cleavage.     

Structures and properties of metal-free and magnesium tetrathieno[2,3-b]porphyrazine investigated using density functional theory

Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculation were adopted to study the structures and properties of metal-free and magnesium tetrathieno[2,3-b]porphyrazine (TTPPzH₂ and TTPPzMg) using B3LYP method with the 6–31G(d) basis set. A comparison of the geometrical structures, atomic charges, molecular orbitals, UV-vis spectra and infrared (IR) spectra among tetrathieno[2,3-b]porphyrazine (TTPPzH₂), phthalocyanine (H₂Pc) and porphyrazine (H₂Pz) compounds was performed. The substituent effect of the thiophene heterocycle for electron-donating on the structures and properties of these compounds has been discussed. Compared with other atoms, the charge distribution of C_β atoms adjacent to the sulfur atom is significantly influenced by the thiophene heterocycle substituents. The enlargement of the HOMO-LUMO gaps from H₂Pc and MgPc to TTPPzH₂ and TTPPzMg is at the origin of the observed blue shift of the Q band when moving from H₂Pc to TTPPzH₂ compounds. Special emphasis has been devoted to the strongest B bands for TTPPzH₂ compounds which show red shift due to the large destabilization of the lower lying occupied orbitals compared with the corresponding B bands of H₂Pc compounds. With the assistance of animated pictures produced on the basis of the normal coordinates, the significant peaks and vibration modes in the IR spectra of all the compounds were assigned and analyzed.     

Electronic and optical properties of pyrrole and thiophene oligomers: A density functional theory study

The conductive mechanism of pyrrole (Py) and thiophene (Th) oligomers is investigated in the framework of density functional theory. Geometric constructions and electronic structures of neutral n‐Py/n‐Th and oxidized n‐Py^m+/n‐Th^m+ oligomers (6 ≤ n ≤ 48, 2 ≤ m ≤ 18) are reported as a function of oligomer length. The charges in the oxidized oligomers have a localized distribution along the oxidized n‐Py^m+/n‐Th^m+ oligomers, and each set of two positive charges is localized in one area. Therefore, the charge carriers in oxidized n‐Py^m+/n‐Th^m+ oligomers are bipolarons. Furthermore, the nonlinear optical properties of the n‐Py/n‐Th oligomers are investigated, for which the static polarizability α, the first polarizability β, and the second polarizability γ are calculated. When the ratio of m/n is 1/3, the static polarizability <α> and the polarizability anisotropy Δα are maximized. In addition, neutral n‐Py/n‐Th oligomers have maximum <γ> values. The values of β were determined mainly by the dipole of the molecule, while the values of γ were closely related to the aromaticity of the oligomer. The stronger the aromaticity, the bigger the γ value. All calculations indicate that the polarizability and absorption spectrum can be tuned by controlling the oxidation level, making these oligomers applicable as good nonlinear optical materials.     

Structure, spectroscopy, and reactivity properties of porphyrin pincers: a conceptual density functional theory and time-dependent density functional theory study

Porphyrin and pincer complexes are both important categories of compounds in biological and catalytic systems. The idea to combine them is computationally investigated in this work. By employment of density functional theory (DFT), conceptual DFT, and time-dependent DFT approaches, structure, spectroscopy, and reactivity properties of porphyrin pincers are systematically studied for a selection of divalent metal ions. We found that the porphyrin pincers are structurally and spectroscopically different from their precursors and are more reactive in electrophilic and nucleophilic reactions. A few quantitative linear/exponential relationships have been discovered between bonding interactions, charge distributions, and DFT chemical reactivity indices. These results are implicative in chemical modification of hemoproteins and understanding chemical reactivity in heme-containing and other biologically important complexes and cofactors.