Comprehensive modeling of the antioxidant mechanism of ebselen

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.

scholarly journals A Theoretical Study of the Adsorption Process of B-aflatoxins Using Pyracantha koidzumii (Hayata) Rehder Biomasses

Toxins ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 283
Author(s):  
Abraham Méndez-Albores ◽  
René Escobedo-González ◽  
Juan Manuel Aceves-Hernández ◽  
Perla García-Casillas ◽  
María Inés Nicolás-Vázquez ◽  
...  
Keyword(s):  
Functional Groups ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Ph Value ◽  
Theoretical Calculations ◽  
Basis Set ◽  
Hydroxyl Group ◽  
Biosorption Process

Employing theoretical calculations with density functional theory (DFT) using the B3LYP/6-311++G(d,p) functional and basis set, the interaction of the aflatoxin B1 (AFB1) molecule and the functional groups present in the Pyracantha koidzumii biosorbent was investigated. Dissociation free energy and acidity equilibrium constant values were obtained theoretically both in solution (water) and gas phases. Additionally, the molecular electrostatic potential for the protonated molecules was calculated to verify the reactivity. Thus, methanol (hydroxyl group), methylammonium ion (amino group), acetate ion (carboxyl group), and acetone (carbonyl group), were used as representatives of the substrates present in the biomass; these references were considered using the corresponding protonated or unprotonated forms at a pH value of 5. The experimental infrared spectrophotometric data suggested the participation of these functional groups in the AFB1 biosorption process, indicating that the mechanism was dominated by electrostatic interactions between the charged functional groups and the positively charged AFB1 molecule. The theoretical determination indicated that the carboxylate ion provided the highest interaction energy with the AFB1 molecule. Consequently, an enriched biosorbent with compounds containing carboxyl groups could improve the yield of the AFB1 adsorption when using in vitro and in vivo trials.

scholarly journals Insights on forming N,O-coordinated Cu single-atom catalysts for electrochemical reduction CO2 to methane

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yanming Cai ◽  
Jiaju Fu ◽  
Yang Zhou ◽  
Yu-Chung Chang ◽  
Qianhao Min ◽  
...  
Keyword(s):  
Energy Barrier ◽  
Active Sites ◽  
Theoretical Calculations ◽  
High Energy ◽  
Single Atom ◽  
Faradaic Efficiency ◽  
High Energy Barrier ◽  
Catalytic Sites ◽  
Electron Reduction ◽  
First Time

AbstractSingle-atom catalysts (SACs) are promising candidates to catalyze electrochemical CO2 reduction (ECR) due to maximized atomic utilization. However, products are usually limited to CO instead of hydrocarbons or oxygenates due to unfavorable high energy barrier for further electron transfer on synthesized single atom catalytic sites. Here we report a novel partial-carbonization strategy to modify the electronic structures of center atoms on SACs for lowering the overall endothermic energy of key intermediates. A carbon-dots-based SAC margined with unique CuN2O2 sites was synthesized for the first time. The introduction of oxygen ligands brings remarkably high Faradaic efficiency (78%) and selectivity (99% of ECR products) for electrochemical converting CO2 to CH4 with current density of 40 mA·cm-2 in aqueous electrolytes, surpassing most reported SACs which stop at two-electron reduction. Theoretical calculations further revealed that the high selectivity and activity on CuN2O2 active sites are due to the proper elevated CH4 and H2 energy barrier and fine-tuned electronic structure of Cu active sites.

First principle simulation on oxidation mechanism of diethyl ether by nitrogen dioxide

2015 ◽  
Vol 14 (03) ◽  
pp. 1550020 ◽  
Author(s):  
Yuan Yuan ◽  
Wei Hu ◽  
Xuhui Chi ◽  
Cuihua Li ◽  
Dayong Gui ◽  
...  
Keyword(s):  
Diethyl Ether ◽  
Energy Barrier ◽  
Density Functional ◽  
Oxidation Process ◽  
Oxidation Mechanism ◽  
High Energy ◽  
First Principle ◽  
Functional Theory ◽  
The Third ◽  
High Energy Barrier

The oxidation mechanism of diethyl ethers by NO2was carried out using density functional theory (DFT) at the B3LYP/6-31+G (d, p) level. The oxidation process of ether follows four steps. First, the diethyl ether reacts with NO2to produce HNO2and diethyl ether radical with an energy barrier of 20.62 kcal ⋅ mol-1. Then, the diethyl ether radical formed in the first step directly combines with NO2to form CH3CH ( ONO ) OCH2CH3. In the third step, the CH3CH ( ONO ) OCH2CH3was further decomposed into the CH3CH2ONO and CH3CHO with a moderately high energy barrier of 32.87 kcal ⋅ mol-1. Finally, the CH3CH2ONO continues to react with NO2to yield CH3CHO , HNO2and NO with an energy barrier of 28.13 kcal ⋅ mol-1. The calculated oxidation mechanism agrees well with Nishiguchi and Okamoto's experiment and proposal.

scholarly journals 1,3-Di(hetero)aryl-7-substituted Pyrenes—An Undiscovered Area of Important Pyrene Derivatives

Proceedings ◽  
2019 ◽  
Vol 41 (1) ◽  
pp. 28
Author(s):  
Dawid Zych
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Basis Set ◽  
Functional Theory ◽  
Td Dft ◽  
Pyrene Derivatives ◽  
Osmium Complexes ◽  
The Subject ◽  
Theoretical Considerations

In this work, the necessity of synthesis of 1,3-di(hetero)aryl-7-substituted pyrenes is presented based on the results of theoretical calculations by using density functional theory (DFT) and time-dependent density functional theory (TD-DFT) by using Gaussian 09 program with B3LYP exchange-correlation functional and 6-31G** basis set. What is more, the synthetic routes with feasible reagents and conditions are presented. The subject of theoretical considerations are two pyrene derivatives which contain at position 1 and 3 pyrazolyl substituents and at position 7 amine (1) or boron (2) derivative. The theoretical calculations were also performed for the osmium complexes with mentioned ligands (3 and 4). The influence of electron-donating/accepting character of the substituent at position 7 of pyrene on the properties of molecules has been established.

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

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.

Resonance Raman and absorption infrared with density functional theory studies of Fe(III)/Fe(II) and Ni(II) complexes of modified 21-oxaporphyrins

2013 ◽  
Vol 17 (04) ◽  
pp. 289-308 ◽  
Author(s):  
Mateusz Fościak ◽  
Edyta Proniewicz ◽  
Krzysztof Zborowski ◽  
Younkyoo Kim ◽  
Leonard M. Proniewicz
Keyword(s):  
Density Functional ◽  
Theoretical Calculations ◽  
Resonance Raman ◽  
Vibrational Analysis ◽  
Basis Set ◽  
Functional Theory ◽  
B3lyp Level ◽  
Ft Ir ◽  
Optimized Geometries ◽  
Good Agreement

This work presents a complete vibrational analysis of iron [ Fe (II) and Fe (III)] and nickel [ Ni (II)] complexes with 5,10,15,20-tetraphenyl-21-oxaporphyrin [OTPPH] and 5,20-bis(p-tolyl)-10,15-diphenyl-21-oxaporphyrin [ODTDPPH]. In these porphyrins, a furan ring replaces one of the pyrrole rings. The six-coordinate (OTPP) FeIIICl2 and (ODTDPP) FeIIICl2 as well as the five-coordinate (OTPP) FeIICl and (OTPP) NiIICl complexes were investigated using experimental and theoretical methods. The experimental part of this work involved Fourier-transform absorption infrared (FT-IR), resonance Raman (RR), and electron absorption (UV-vis) measurements for all of the investigated complexes. In the theoretical section, optimized geometries and vibrational frequencies for model compounds are provided. The theoretical calculations were performed at the B3LYP level with the LANL2DZ basis set. Good agreement was achieved between the experimental and theoretical vibrational spectra. In addition, charge distributions (GAPT) and geometrical aromaticity indices (Bird's I5 and HOMA) were calculated and discussed.

A THEORETICAL STUDY OF UNSATURATED OLEFIN HYDROGENATION AND ISOMERIZATION ON Pd(111)

2008 ◽  
Vol 15 (03) ◽  
pp. 249-259 ◽  
Author(s):  
PATRICIA G. BELELLI ◽  
NORBERTO J. CASTELLANI
Keyword(s):  
Energy Barrier ◽  
Density Functional ◽  
Theoretical Study ◽  
High Energy ◽  
Slab Model ◽  
Functional Theory ◽  
Hydrogen Addition ◽  
High Energy Barrier ◽  
The Density Functional Theory ◽  
Cis And Trans

The addition of hydrogen to the carbon–carbon double bond of 2-butenes adsorbed on Pd (111) was studied within the density functional theory (DFT) and using a periodic slab model. For that purpose, the Horiuti–Polanyi mechanisms for both complete hydrogenation and isomerization were considered. The hydrogenation of cis and trans-2-butene to produce butane proceeds via the formation of eclipsed and staggered-2-butyl intermediates, respectively. In both cases, a relatively high energy barrier to produce the half-hydrogenated intermediate makes the first hydrogen addition the slowest step of the reaction. The competitive production of trans-2-butene from cis-2-butene requires the conversion from the eclipsed-2-butyl to the staggered-2-butyl isomer. As the corresponding energy barrier is relatively small and because the first of these isomers is less stable than the second, an easy conversion is predicted.

A Combined Experimental and Theoretical Study on the Reaction Mechanism and Molecular Structure of 4-(Diphenylamino)-3-iodo-2(5H)-furanone

2017 ◽  
Vol 70 (7) ◽  
pp. 837
Author(s):  
Xiumei Song ◽  
Fuling Xue ◽  
Zongcai Feng ◽  
Yun Wang ◽  
Zhaoyang Wang ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Density Functional ◽  
Reaction Pathway ◽  
Theoretical Calculations ◽  
Calculation Model ◽  
Basis Set ◽  
Functional Theory ◽  
Evaporation Technique ◽  
Molecular Structure Analysis ◽  
Semi Empirical

The simultaneous α-iodination and Nβ-arylation mechanism of 5-alkyloxy-4-phenylamino-2(5H)-furanone by (diacetoxyiodo)benzene was investigated by means of density functional theory (DFT) with B3LYP/6-31G*//LANL2DZ, selecting 4-(diphenylamino)-5-methyloxy-3-iodo-2(5H)-furanone as the calculation model. In addition, the effect of solvent on the reaction pathway was investigated using the Polarisable Continuum Model (PCM). Good agreement was found between the computational and the experimental results. Furthermore, single crystals of 4-(diphenylamino)-5-ethoxy-3-iodo-2(5H)-furanone were grown by slow evaporation technique. The molecular structure analysis was performed by single crystal X-ray analysis and theoretical calculations using a semi-empirical quantum chemical method and DFT/B3LYP methods with a LANL2DZ as basis set.

New Insight Into Catalytic Mechanism of Glucose-6-Phosphate Dehydrogenase Enzyme: A DFT Study

2020 ◽  
pp. 2140001
Author(s):  
Sadaf Rani ◽  
Fouzia Perveen ◽  
Jerry P Jasinski ◽  
Rehan Zafar Paracha ◽  
Haris Bin Tanveer ◽  
...  
Keyword(s):  
Proton Transfer ◽  
Red Blood Cells ◽  
Blood Cells ◽  
Catalytic Mechanism ◽  
Theoretical Calculations ◽  
High Energy ◽  
Low Energy ◽  
Basis Set ◽  
Sequential Reaction ◽  
Glucose 6 Phosphate Dehydrogenase

The glucose-6-phosphate dehydrogenase (G6PD) enzyme plays a vital role in converting glucose-6-phosphate (G6P) to 6-phosphogluconolactone, as well as in reducing NADP([Formula: see text]) to NADPH. The Asp/His moiety of G6PD acts as a catalytic dyad in the active site of G6PD. This catalytic mechanism describes erythrocyte protection from oxidative stress and prevention of hemolysis; hence their exact understanding is important in the normal functioning of red blood cells. Herein, computational investigations were carried out to describe a plausible mechanism of the G6PD enzyme by using a series of DFT theoretical calculations using the M06-2X/6-31G ([Formula: see text], [Formula: see text]) basis set and performed in the following three discrete steps: (i) Proton transfer from His309 to Asp246, (ii) A subsequent proton transfer from G6P to His309, and (iii) A rate-limiting hydride transfer that reduces NADP([Formula: see text]) to NADPH. The final overall mechanism, therefore, results in the production of phosphogluconolactone and NADPH. The DFT calculations indicate that, in the absence of the His/Asp dyad, the chemical reaction changes from a low-energy sequential mechanism to the proposed concurrent mechanism with a very high energy barrier ([Formula: see text][Formula: see text]kcal[Formula: see text]mol[Formula: see text]). These results show that the Asp246 residue is responsible for transforming a high energy concurrent reaction into a low energy multistep sequential reaction in the G6PD enzyme for the production of NADPH. This work supports the study and design of the mechanism-based inhibitors and provides a detailed understanding of the catalytic mechanism of the enzyme thereby opening new possibilities towards an understanding of controlling detoxification processes due to premature breaking in red blood cells.

A study of experimental and theoretical analysis of N-cyclohexylmethacrylamide monomer based on DFT and HF computations

2016 ◽  
Vol 45 (5) ◽  
pp. 301-307 ◽  
Author(s):  
Feride Akman ◽  
Nevin Çankaya
Keyword(s):  
Density Functional ◽  
Functional Group ◽  
Theoretical Calculations ◽  
Calculated Data ◽  
Basis Set ◽  
Polymer Science ◽  
Content Type ◽  
Hartree Fock ◽  
Good Accord ◽  
Experimental Values

Purpose This paper aims to synthesise and characterise N-cyclohexylmethacrylamide (NCMA) monomer which contains thermosensitive group. The characterisation of monomer was performed both theoretically and experimentally. Design/methodology/approach The monomer was prepared by reacting cyclohexylamine with methacryloyl chloride in the presence of triethylamine at room temperature. The synthesised monomer was characterised by using not only Density Functional Theory (DFT) and Hartree–Fock (HF) with the Gaussian 09 software but also fourier transform infrared (FT–IR), 1H and 13C nuclear magnetic resonance (NMR) spectroscopy. Findings Both the experimental and the theoretical methods demonstrated that the monomer was successfully synthesised. The vibrational frequencies, the molecular structural geometry, such as optimised geometric bond angles, bond lengths and the Mulliken atomic charges of NCMA were investigated by using DFT/B3LYP and HF methods with the 3-21G* basis set. The experimental results were compared with theoretical values. The results revealed that the calculated frequencies were in good accord with the experimental values. Besides, frontier molecular orbitals (FMOs) and molecular electrostatic potential of NCMA were investigated by theoretical calculations at the B3LYP/3–21G* basis set. Research limitations/implications Monomer and polymer containing a thermosensitive functional group have attracted great interest from both industrial and academic fields. Their characterisation can provide great opportunities for polymer science by using DFT and HF methods. Originality/value The monomer containing a thermosensitive functional group and a various polymer may be prepared by using DFT and HF methods described in this paper. The calculated data are greatly important to provide insight into molecular analysis and then used in technological applications.

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