Antioxidant Activity of Eugenol And Its Acetyl And Nitroderivatives: A DFT Approach of DPPH Test.

Abstract This work evaluates the antioxidant potential of acetyl and nitro derivatives of eugenol through computational techniques. Structural analysis and Hydrogen Atomic Transfer (HAT) antioxidant mechanism were investigated by density functional theory (DFT). Each molecular structure was optimized by the hybrid functional M06-2X with a basis set 6-31+G(d,p), and the HAT mechanism with HO, HOO, CH3O, DPPH radicals was evaluated. In agreement with experimental data from previous studies, two steps of hydrogen transfer were tested. Thermodynamic data showed the need for two stages of hydrogen transfer, followed by the formation of quinones to make the reaction with DPPH spontaneous. Theoretical kinetic data showed that the preferred antioxidant site depends on the instability of the attacking radical and confirmed the antioxidant profile of eugenol (E1) and 5-allyl-3-nitrobenzene-1,2-diol (E5) in the DPPH test. This study shows that the 4-allyl-2-methoxy-(4-nitrophenol) (E4) structure also has an anti-radical activity that is not seen in the experimental due to chemoselectivity of DPPH.

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DFT Visualization and Experimental Evidence of BHT-Mg-Catalyzed Copolymerization of Lactides, Lactones and Ethylene Phosphates

Polymers ◽

10.3390/polym11101641 ◽

2019 ◽

Vol 11 (10) ◽

pp. 1641 ◽

Cited By ~ 3

Author(s):

Ilya Nifant’ev ◽

Andrey Shlyakhtin ◽

Maxim Kosarev ◽

Dmitry Gavrilov ◽

Stanislav Karchevsky ◽

...

Keyword(s):

Ring Opening ◽

Density Functional ◽

Point Of View ◽

Basis Set ◽

Random Copolymers ◽

Key Factors ◽

Functional Theory ◽

Cyclic Esters ◽

Dft Modeling ◽

Derivatives Of

Catalytic ring-opening polymerization (ROP) of cyclic esters (lactides, lactones) and cyclic ethylene phosphates is an effective way to process materials with regulated hydrophilicity and controlled biodegradability. Random copolymers of cyclic monomers of different chemical nature are highly attractive due to their high variability of characteristics. Aryloxy-alkoxy complexes of non-toxic metals such as derivatives of 2,6-di-tert-butyl-4-methylphenoxy magnesium (BHT-Mg) complexes are effective coordination catalysts for homopolymerization of all types of traditional ROP monomers. In the present paper, we report the results of density functional theory (DFT) modeling of BHT-Mg-catalyzed copolymerization for lactone/lactide, lactone/ethylene phosphate and lactide/ethylene phosphate mixtures. ε-Caprolactone (ε-CL), l-lactide (l-LA) and methyl ethylene phosphate (MeOEP) were used as examples of monomers in DFT simulations by the Gaussian-09 program package with the B3PW91/DGTZVP basis set. Both binuclear and mononuclear reaction mechanistic concepts have been applied for the calculations of the reaction profiles. The results of calculations predict the possibility of the formation of random copolymers based on l-LA/MeOEP, and substantial hindrance of copolymerization for ε-CL/l-LA and ε-CL/MeOEP pairs. From the mechanistic point of view, the formation of highly stable five-membered chelate by the products of l-LA ring-opening and high donor properties of phosphates are the key factors that rule the reactions. The results of DFT modeling have been confirmed by copolymerization experiments.

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In-silico Molecular Docking and ADME/Pharmacokinetic Prediction Studies of Some Novel Carboxamide Derivatives as Anti-tubercular Agents

Chemistry Africa ◽

10.1007/s42250-020-00162-3 ◽

2020 ◽

Vol 3 (4) ◽

pp. 989-1000

Author(s):

Mustapha Abdullahi ◽

Shola Elijah Adeniji

Keyword(s):

Molecular Docking ◽

Binding Affinity ◽

In Silico ◽

Density Functional ◽

Docking Simulation ◽

Basis Set ◽

Hybrid Functional ◽

Standard Drug

AbstractMolecular docking simulation of thirty-five (35) molecules of N-(2-phenoxy)ethyl imidazo[1,2-a]pyridine-3-carboxamide (IPA) with Mycobacterium tuberculosis target (DNA gyrase) was carried out so as to evaluate their theoretical binding affinities. The chemical structure of the molecules was accurately drawn using ChemDraw Ultra software, then optimized at density functional theory (DFT) using Becke’s three-parameter Lee–Yang–Parr hybrid functional (B3LYP/6-311**) basis set in a vacuum of Spartan 14 software. Subsequently, the docking operation was carried out using PyRx virtual screening software. Molecule 35 (M35) with the highest binding affinity of − 7.2 kcal/mol was selected as the lead molecule for structural modification which led to the development of four (4) newly hypothetical molecules D1, D2, D3 and D4. In addition, the D4 molecule with the highest binding affinity value of − 9.4 kcal/mol formed more H-bond interactions signifying better orientation of the ligand in the binding site compared to M35 and isoniazid standard drug. In-silico ADME and drug-likeness prediction of the molecules showed good pharmacokinetic properties having high gastrointestinal absorption, orally bioavailable, and less toxic. The outcome of the present research strengthens the relevance of these compounds as promising lead candidates for the treatment of multidrug-resistant tuberculosis which could help the medicinal chemists and pharmaceutical professionals in further designing and synthesis of more potent drug candidates. Moreover, the research also encouraged the in vivo and in vitro evaluation study for the proposed designed compounds to validate the computational findings.

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Comprehensive modeling of the antioxidant mechanism of ebselen

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633615500534 ◽

2015 ◽

Vol 14 (07) ◽

pp. 1550053

Author(s):

Jun-Hao Jiang ◽

Hui Zhou ◽

Hui-Jie Li ◽

Yu-Chun Wang ◽

Mei Tian ◽

...

Keyword(s):

Energy Barrier ◽

Density Functional ◽

Theoretical Calculations ◽

High Energy ◽

Maximum Energy ◽

Basis Set ◽

Antioxidant Mechanism ◽

Main Pathway ◽

Rate Controlling Step

Three possible catalytic cycles for ebselen have been comprehensively modeled by theoretical calculations using density functional theory (DFT) at a mixed basis set level; the 6-31G(d) basis set for hydrocarbon fragments and the 6-31[Formula: see text]G(d,p) basis set for other atoms. The 2[Formula: see text] cycle is the main pathway in the glutathione peroxidase (GPx) cycle (cycle A), and IM3[Formula: see text]TS3 is the rate controlling process. The 1[Formula: see text]1 cycle is the main pathway for the oxidation cycle (cycle B), and the rate controlling step is the [Formula: see text] step. Ebselen reacts with the selenol 3 to form the diselenide 9, and this is the rate controlling step for cycle C. The extremely high energy barrier for the IM9[Formula: see text]TS9 process indicates that cycle C is unlikely to occur in vivo. Although cycle B is favored based on the energy analysis, with a maximum energy barrier of only 26.68[Formula: see text]kcal/mol at the mixed basis set level, it is generally unlikely to have very high concentrations of peroxides present in vivo. The results indicate that in order to improve the antioxidant activity of ebselen, it would be necessary to suitably modify the molecular structure of ebselen to reduce the energy barrier of the IM3[Formula: see text]TS3 process.

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Protonated heterocyclic derivatives of cyclopropane and cyclopropanone: classical species, alternate sites, and ring fragmentation

Canadian Journal of Chemistry ◽

10.1139/cjc-2015-0029 ◽

2015 ◽

Vol 93 (7) ◽

pp. 708-714 ◽

Cited By ~ 3

Author(s):

Margarida S. Miranda ◽

Darío J.R. Duarte ◽

Joaquim C.G. Esteves da Silva ◽

Joel F. Liebman

Keyword(s):

Density Functional Theory ◽

Gas Phase ◽

Density Functional ◽

Computational Study ◽

Basis Set ◽

Proton Affinities ◽

Functional Theory ◽

Heterocyclic Derivatives ◽

Gas Phase Basicities ◽

Derivatives Of

A computational study has been performed for protonated oxygen- or nitrogen-containing heterocyclic derivatives of cyclopropane and cyclopropanone. We have searched for the most stable conformations of the protonated species using density functional theory with the B3LYP functional and the 6-31G(2df,p) basis set. More accurate enthalpy values were obtained from G4 calculations. Proton affinities and gas-phase basicities were accordingly derived.

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Theoretical investigation of nitro derivatives of tetrazole with density functional theory (DFT)

Journal of Molecular Structure THEOCHEM ◽

10.1016/s0166-1280(98)00316-9 ◽

1999 ◽

Vol 460 (1-3) ◽

pp. 167-173 ◽

Cited By ~ 15

Author(s):

Chen ZhaoXu ◽

Xiao Heming ◽

Song Wenyu

Keyword(s):

Density Functional Theory ◽

Theoretical Investigation ◽

Density Functional ◽

Functional Theory ◽

Nitro Derivatives ◽

Derivatives Of

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THEORETICAL INVESTIGATION OF THE EFFECT OF CONJUATION OF THIOPHENE RINGS ON THE CHARGE TRANSPORT OF THIENOCORONENE DERIVATIVES

Química Nova ◽

10.21577/0100-4042.20170820 ◽

2021 ◽

Author(s):

Ziran Chen ◽

Yujin Zhang ◽

Zhanrong He ◽

Yuan Li ◽

Meihao Xi ◽

...

Keyword(s):

Charge Carrier ◽

Charge Transport ◽

Carrier Mobility ◽

Density Functional ◽

Thiophene Ring ◽

Energy Charge ◽

Charge Carrier Mobility ◽

Basis Set ◽

Basis Sets ◽

Hybrid Functional

Based on density functional theory, quantum chemical calculations of the charge-transport rates were performed for five disc-shaped coronene derivatives with varying numbers of fused thiophene rings, using different basis sets 6-31+G(d) and 6-311++G(d,p), hybrid functionals (B3LYP, M06-2X, CAM-B3LYP, WB97XD, M08-HX), and a dispersion-corrected hybrid functional (M06-2X+D3). Our results indicate that increasing the basis set and adding diffusion and polarisation functions had little effect on the molecular reorganisation energy, charge-transport matrix element t, and charge carrier mobility μ. The charge carrier mobility calculated using B3LYP were relatively large, whereas the results calculated using CAM-B3LYP and WB97XD were similar. Among the five coronene derivatives, molecule b with one thiophene ring could be candidates for a n-type organic semiconductor, and molecule c with two thiophene rings can be designed as a p-type semiconductor.

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Quasi-Relativistic Calculation of EPR g-Tensors with Derivatives of the Decoupling Transformation, Gauge-Including Atomic Orbitals, and Magnetic Balance

10.26434/chemrxiv-2021-32gxb ◽

2021 ◽

Author(s):

Yannick J. Franzke ◽

Jason M. Yu

Keyword(s):

Density Functional ◽

Hyperfine Coupling Constant ◽

Basis Set ◽

Basis Sets ◽

Generalized Gradient ◽

Atomic Orbitals ◽

Experimental Findings ◽

The Impact ◽

Derivatives Of ◽

Magnetic Balance

We present an exact two-component (X2C) ansatz for the EPR g-tensor using gauge-including atomic orbitals (GIAOs) and a magnetically balanced basis set expansion. In contrast to previous X2C and "fully" relativistic ansätze for the g-tensor, this implementation results in a gauge-origin invariant formalism. Furthermore, the derivatives of the relativistic decoupling matrix are considered to form the complete analytical derivative of the X2C Hamiltonian. To reduce the associated computational costs, we apply the diagonal local approximation to the unitary decoupling transformation (DLU) and the (multipole-accelerated) resolution of the identity approximation. The X2C ansatz is compared to Douglas-Kroll-Hess theory and the zeroth-order regular approximation for 11 diatomic molecules. The impact of the relativistic Hamiltonian, the basis set, and the density functional approximation is subsequently assessed for a set of 17 transition-metal complexes to complement our previous work on the hyperfine coupling constant [DOI: 10.33774/chemrxiv-2021-wnz1v-v2]. In total, 24 basis sets and 22 density functional approximations are considered. The quasi-relativistic X2C and DLU-X2C Hamiltonians accurately reproduce the results of the parent "fully" relativistic four-component theory when accounting for two-electron picture-change effects with the modified screened nuclear spin-orbit approximation in the respective one-electron integrals and integral derivatives. Generally, the uncontracted Dyall and segmented-contracted Karlsruhe x2c-type basis sets perform well when compared to large even-tempered basis sets. Moreover, (range-separated) hybrid density functional approximations are needed to match the experimental findings. Here, hybrids based on the meta -generalized gradient approximation are not an a priori improvement. Compared to the other computational parameters, the impact of the GIAOs and the magnetic balance on the actual results in standard calculations is less pronounced. Routine calculations of large molecules are possible with widely available and comparably low- cost hardware as demonstrated for [Pt(C6Cl5)4]− with 3360 basis functions and three spin-(1/2) La(II) and Lu(II) compounds. Both approaches based on a common gauge origin and GIAOs using triple- ζ basis sets lead to a good agreement with the experimental findings. The best agreement is found with hybrid functionals such as PBE0 and ωB97X-D.

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First theoretical probe for alkynyl bridged thiophene modified coumarin nonlinear optical materials with D-π-A and A-π-D-π-A structures

Journal of Nonlinear Optical Physics & Materials ◽

10.1142/s0218863522500084 ◽

2022 ◽

Author(s):

Shanggeng Li ◽

Fanghua Zhu ◽

Yawen Zhou ◽

Jiaming Hu ◽

Jing Li ◽

...

Keyword(s):

Density Functional ◽

Nonlinear Optical ◽

Molecular Design ◽

Energy Levels ◽

Basis Set ◽

Hybrid Functional ◽

Functional Theory ◽

Text Structures ◽

Polar Moment ◽

Vis Spectroscopy

First-principles exploration is very important to molecular design. In this study, geometric structure, intramolecular charge transfer (ICT), energy levels, polar moment, and ultraviolet–visible (UV–Vis) spectroscopy of eight novel and different alkynyl bridged thiophene modified coumarin nonlinear optical molecules with [Formula: see text]-[Formula: see text]-[Formula: see text] and [Formula: see text]-[Formula: see text]-[Formula: see text]-[Formula: see text]-[Formula: see text] structures had been studied by density-functional theory (DFT) calculations within B3LYP hybrid functional using 6-31 [Formula: see text], [Formula: see text] Gaussian type molecular-orbital basis set. This has guiding significance for the design of nonlinear optical molecules and the development of coumarin-based photoelectric molecules.

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Influence of H, H2, O and O2 on Armchair SiGe Nanotubes: A Theoretical Study

Journal of Nanoscience and Nanotechnology ◽

10.1166/jnn.2016.12342 ◽

2016 ◽

Vol 16 (4) ◽

pp. 3447-3456

Author(s):

Prabath Wanaguru ◽

Asok K Ray ◽

Qiming Zhang

Keyword(s):

Molecular Orbital ◽

Density Functional ◽

Energy Gap ◽

Defect Density ◽

Basis Set ◽

Hybrid Functional ◽

Lumo Energy ◽

Adsorption Sites ◽

The Difference ◽

Controlled Adsorption

A systematic, hybrid density functional theory study of interaction between SiGe nanotubes (SiGeNTs) and X (X = H, O, H2 and O2) have been performed using the hybrid functional B3LYP and an all electron 3-21G* basis set implemented in GAUSSIAN 09 suite of software. All possible internal and external adsorption sites were considered, and it was found that H prefers to move onto top of an atom site while O prefers to incorporate into NT wall by breaking the bonds. Adsorption energies for H is ∼2.0 eV and for O it is ∼5.0 eV. Controlled adsorption of atomic H and several molecular O give rises to defect density states in the frontier orbital region. H rich adsorptions predict the difference between highest occupied molecular orbital (HOMO) energy and the lowest unoccupied molecular orbital (LUMO) energy increase while O rich adsorptions predict the decrease in HOMO-LUMO energy gap. O and O2 adsorptions predict definite ionic bonding character while H atomic adsorptions predict covalent bonding. H2 is very neutral towards the adsorption into SiGeNTs and clearly shows the physisorption adsorption. Considering the all adsorptions, the adsorptions happened within the Si vicinity of the SiGeNT shows the most stable and preferred adsorption region.

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Influence of water on the surface of graphene

EPJ Web of Conferences ◽

10.1051/epjconf/201817406002 ◽

2018 ◽

Vol 174 ◽

pp. 06002

Author(s):

Yunus Kaya ◽

Yalçin Kalkan ◽

Rob Veenhof

Keyword(s):

Density Functional Theory ◽

Water Molecule ◽

Density Functional ◽

Theoretical Models ◽

Surface Conductivity ◽

Basis Set ◽

Hybrid Functional ◽

Functional Theory ◽

The Density Functional Theory ◽

Influence Of Water

We have studied how water modifies the surface of graphene and in particular how the surface conductivity of graphene is affected. According to the literature, two types of interactions should be distinguished: physical, where a water molecule remains intact and is located at some distance from the mesh, and chemical, where a water molecule is imbricated in the graphene bond structure. We have developed theoretical models for both types of interactions using the density functional theory (DFT) with the B3LYP hybrid functional combined with the 6-31G(d) basis set. Our calculations show that the surface conductivity of graphene is reduced in the presence of water.

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