Hybrid Functional Analysis of Electronic Properties of Transition-Metal Phthalocyanines

Klysko, Yu. V.; Syrotyuk, S. V.

doi:10.15407/ujpe66.1.55

Cited by 3 publications

(5 citation statements)

References 53 publications

(32 reference statements)

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“…CoPc presents a greater possibility of interaction between CuPc and NoPc, for the three proteins considered in this study. This result may be related to the significant differences in the hybridization of the 3d states of Co and Cu transition elements with the states in the valence and conduction bands, as observed in the study of KLYSKO and SYROTYUK (2021) 140 . To assess docking results, it is conventional to use the lowest docking score which can create a better binding between the ligand and the protein.…”

Section: Resultsmentioning

confidence: 93%

Interactions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics

Alencar

Arouche

Neto

et al. 2022

Sci Rep

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The new coronavirus, SARS-CoV-2, caused the COVID-19 pandemic, characterized by its high rate of contamination, propagation capacity, and lethality rate. In this work, we approach the use of phthalocyanines as an inhibitor of SARS-CoV-2, as they present several interactive properties of the phthalocyanines (Pc) of Cobalt (CoPc), Copper (CuPc) and without a metal group (NoPc) can interact with SARS-CoV-2, showing potential be used as filtering by adsorption on paints on walls, masks, clothes, and air conditioning filters. Molecular modeling techniques through Molecular Docking and Molecular Dynamics were used, where the target was the external structures of the virus, but specifically the envelope protein, main protease, and Spike glycoprotein proteases. Using the g_MM-GBSA module and with it, the molecular docking studies show that the ligands have interaction characteristics capable of adsorbing the structures. Molecular dynamics provided information on the root-mean-square deviation of the atomic positions provided values between 1 and 2.5. The generalized Born implicit solvation model, Gibbs free energy, and solvent accessible surface area approach were used. Among the results obtained through molecular dynamics, it was noticed that interactions occur since Pc could bind to residues of the active site of macromolecules, demonstrating good interactions; in particular with CoPc. Molecular couplings and free energy showed that S-gly active site residues interacted strongly with phthalocyanines with values of − 182.443 kJ/mol (CoPc), 158.954 kJ/mol (CuPc), and − 129.963 kJ/mol (NoPc). The interactions of Pc's with SARS-CoV-2 may predict some promising candidates for antagonists to the virus, which if confirmed through experimental approaches, may contribute to resolving the global crisis of the COVID-19 pandemic.

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Section: Resultsmentioning

confidence: 93%

Interactions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics

Alencar

Arouche

Neto

et al. 2022

Sci Rep

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“…It was found that realistic band gaps, wave functions, and crystal potentials obtained with PBE0 hybrid functional [4] for the exchange-correlation energy al-lowed to obtain an electronic structure in nanostructures [5,6] that shows good comparison with the experiment. The use of the PBE0 hybrid functional made it possible to compare well the parameters of the electronic energy spectrum in a solid solution of CdMnTe [7] with the measured values [8].…”

Section: Introductionmentioning

confidence: 95%

“…The recommended value of the mixing factor  is equal to 0.25. In formula (5), the exchange energy, in which the SIE of 3d electrons is the largest, is partially subtracted. In fact, these electrons move in narrow energy bands with a high density of states (DOS).…”

Section: Calculationmentioning

confidence: 99%

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Electronic Structure of ZnS Crystal Doped with One or Two Transition Metal Atoms (Cr, Fe)

Syrotyuk¹

2021

J. Nano- Electron. Phys.

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“… is important for describing materials containing d (f) electrons. In particular, it has been successfully used to study nanostructures containing transition 3d elements [13,14]. Energy band structure peculiarities and luminescent parameters of CeX 3 (X = Cl, Br, I) crystals were revealed and shown good comparison with experiment [15].…”

mentioning

confidence: 99%

The Effect of Hydrostatic Pressure and Cationic Vacancy on the Electronic and Magnetic Properties of the ZnSe:T Crystals (T = Ti, V, Cr, Mn, Fe, Co, Ni)

Syrotyuk

2021

EEJP

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The parameters of the spin-polarized electronic energy spectrum of ZnSe:T crystals (T = Ti, V, Cr, Mn, Fe, Co, Ni) are studied on the basis of a 2 × 2 × 2 supercell built on the basis of a ZnSe unit cell with a sphalerite structure. The supercell contains 64 atoms, with one Zn atom replaced by one transition 3d element T. The first stage of this study is to calculate in the ideal material ZnTSe parameters of electronic energy bands, dependent on the external hydrostatic pressure. At the second stage, the effect of pressure on the parameters of the electronic energy spectrum in the ZnTSe materials is investigated, taking into account the Zn vacancy. The calculations were performed using the Abinit program. For a better description of strongly correlated 3d electrons of the element T, a hybrid exchange-correlation functional PBE0 with an admixture of the Hartree-Fock exchange potential was used, in which the self-interaction error of these electrons is removed. Based on the obtained spin-polarized electron densities of states, the magnetic moments of the supercells were also determined. A significant effect of pressure on the parameters of electronic energy zones was revealed. So, the ideal ZnTiSe material at zero pressure is a metal for both spin values, but under pressure it becomes a semiconductor. The same material with a point defect, i.e. a vacancy at the site of the Zn atom, exhibits semiconductor properties for both spin orientations at zero pressure. It was found that vacancies radically change the parameters of electronic energy bands. The magnetic moments of the supercell, as integral values of the spin-polarized densities of electronic states, also reflect these changes. Thus, in ZnTiSe material without defects, the magnetic moments of the supercell are 1.92, 2.0 and 2.0, at pressures 0, 21 and 50 GPa, respectively, while in the same material with a vacancy, the corresponding values are 0.39, 0.02 and 0.36. The ideal ZnVSe material at zero pressure is also a metal for both values of the spin moment, but in the presence of a cationic vacancy it is characterized by a pseudogap because the Fermi level is localized in the upper part of the valence band. Ideal ZnFeSe and ZnNiSe crystals are characterized by similar dependences of the electronic energy parameters on the pressure, for both spins. However, the same materials with a cationic vacancy are characterized by the Fermi level immersed in the valence band for a spin up.

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Hybrid Functional Analysis of Electronic Properties of Transition-Metal Phthalocyanines

Cited by 3 publications

References 53 publications

Interactions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics

Interactions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics

Electronic Structure of ZnS Crystal Doped with One or Two Transition Metal Atoms (Cr, Fe)

The Effect of Hydrostatic Pressure and Cationic Vacancy on the Electronic and Magnetic Properties of the ZnSe:T Crystals (T = Ti, V, Cr, Mn, Fe, Co, Ni)

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