DFT Study of L‐Cysteine Fragmentation Route using a Novel Protocol

Oliveira, Carlos Xavier de; Mocellin, Alexandra; Lima, Fabio; Neto, A. M. J. C.; Azevedo, David L.

doi:10.1002/slct.201903453

Cited by 4 publications

(3 citation statements)

References 59 publications

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“…Ligands were selected based on their stability regarding the software used. The 3D structures of the ligands were built in GaussView 6.0 82 and the most stable conformer of each ligand was searched 83 using the density functional theory (DFT) method 84 . The best conformer was chosen and optimized by the density functional theory (DFT) approach with the B3LYP /LANL2DZ method that includes dispersion interactions 85 in Gaussian09 software.…”

Section: Methodsmentioning

confidence: 99%

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: Methodsmentioning

confidence: 99%

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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“…39–43 Isolated cysteine and fragmentation of its cation was theoretically explored by de Oliveira. 44 Experimental studies of the isolated molecule include PEPICO, 45 dissociative electron attachment 46,47 or ion beam irradiation 48 studies. However, it is important to say that studies of isolated cysteine are rather scarce due to difficulty to sublime this thermally delicate compound.…”

Section: Introductionmentioning

confidence: 99%

Non-ergodic fragmentation upon collision-induced activation of cysteine–water cluster cations

Tiefenthaler

Scheier

Erdmann

et al. 2023

Phys. Chem. Chem. Phys.

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“…To connect the theory to the experiment, we calculated the electronic structure of the molecules, using a new protocol [9] applied to benzene (BZ), aniline (ANI), and the nitroanilines (NA) in conformations ortho-, metaand para-(named oNA, mNA, and pNA, respectively) for the neutral and doubly ionized molecules to understand the dynamics of fragmentation of these molecules. But, to achieve this, we evaluate the bond order by Wiberg's bond index to identify the probable places of bonds break [10], and also we had made an analysis of the density of electronics on the bonds by Quantum Theory of Atoms In Molecules (QTAIM) to distinguish the different concentrations of charge in pairs of atoms [11].…”

Section: Introductionmentioning

confidence: 99%

Fragmentation route of doubly ionized benzene, aniline, and nitroanilines monomers using a novel protocol from density functional theory and QTAIM

Oliveira¹,

Costa

Mota

2023

J Mol Model

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The possibility of nding the fragmentation routes by theoretical methods, led us to compare the molecular ions between neutral molecules of benzene, aniline, and o-, m-, and p-nitroaniline, using the Density Functional Theory (DFT), under an aug-cc-pVDZ base set and a B3LYP exchange-correlation functional. After determining the structure and electronic energy of neutral and doubly ionized species, we used a new protocol based on the analysis of Wiberg's binding indexes and the quantum theory of atoms in Bader molecules (QTAIM). Where the charge transfer and electronic distribution in aromatic monomers indicate the possibility of fragment formation in at least two pairs of carbon-carbon (CC) atoms and indicate the possible loss of the -CNH 2 and -NO 2 groups in the aniline and nitroaniline molecules doubly ionized.

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DFT Study of L‐Cysteine Fragmentation Route using a Novel Protocol

Cited by 4 publications

References 59 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

Non-ergodic fragmentation upon collision-induced activation of cysteine–water cluster cations

Fragmentation route of doubly ionized benzene, aniline, and nitroanilines monomers using a novel protocol from density functional theory and QTAIM

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