General AMBER Force Field Parameters for Diphenyl Diselenides and Diphenyl Ditellurides

Torsello, Mauro; Pimenta, António; Wolters, Lando P.; Moreira, Irina S.; Orian, Laura; Polimeno, Antonino

doi:10.1021/acs.jpca.6b02250

Cited by 26 publications

(38 citation statements)

References 77 publications

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“…It is observed that the stable equilibrium structures differ mainly in spatial orientation of two phenyl rings in case of (PhSe) 2 and similar to (PhS) 2 system discussed earlier. Such observations are also reported in the literature for diphenylchalcogen systems including (PhTe) 2 based on conformation analysis . It is interesting to mention that for (PhSe) 2 system, it is possible to calculate chemical shift in the NMR spectra accurately from only these two equilibrium structures .…”

Section: Resultssupporting

confidence: 76%

“…Such observations are also reported in the literature for diphenylchalcogen systems including (PhTe) 2 based on conformation analysis . It is interesting to mention that for (PhSe) 2 system, it is possible to calculate chemical shift in the NMR spectra accurately from only these two equilibrium structures . This certainly demonstrates that such methods have predictive ability and can be very useful to interpret experimental results and to provide better insights.…”

Section: Resultssupporting

confidence: 73%

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Effect of excess electron on structure, bonding, and spectral properties of sulfur/selenium based dichalcogen systems

Kumar

Maity

2018

Int J of Quantum Chemistry

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First principle based quantum chemical methods are employed to characterize structure, bonding, and spectral properties of sulfur and selenium based dichalcogen systems in presence of an excess electron. Inter molecular two-center three-electron (2c-3e) bonding between two chalcogen (X) atoms is described in the systems of the type (R-X) 2•-(R = Ph, PhCH 2 X = S, Se). In addition, effect of electron withdrawing (-NO 2 ) and electron donating (-CH 3 ) groups in phenyl ring on the stability of these 2c-3e bonded systems is also studied in water medium applying a macroscopic hydration model. Molecular parameters and binding energy of the neutral, (R-X) 2 and reduced, (R-X) 2 •dichalcogen systems are compared. Search for minimum energy structures of these open shell doublet systems are carried out applying various density functionals with dispersion corrections and MP2 method considering 6-311++G (d,p) set of basis functions for all atoms. Effect of water medium is introduced through a macroscopic solvation model based on density (SMD). Frontier molecular orbitals based analysis is carried out for showing the definite presence of 2c-3e bond between two chalcogen atoms in these radical anions of sulfur and selenium based aromatic dichalcogen systems. Excited state calculations are performed on all these systems using Time Dependent Density Functional Theory (TDDFT). UV-Vis spectra are simulated and effect of solvent water on the absorption maximum of these radical anions is discussed. This study illustrates that the combination of electronic effect and geometrical flexibility decides the strength of two-center three-electron bond in these systems. K E Y W O R D S 2c-3e bond, antioxidant, chalcogen, density functional theory, excess electron, hemi bond, radical anion, selenium, sulfur 1 | INTRODUCTIONSulfur and selenium are present in amino acids, peptides, and proteins, essential for various biological redox reactions. Selenocystine and selenomethonine systems can act as an antioxidant by killing harmful peroxides in organisms, and these are also responsible for protection against inflammation and cancer. [1][2][3] Sulfur and selenium based diaryl dichalcogenes are eco-friendly oxidizing agents and demanding drugs in pharmaceutical chemistry mainly for their antioxidant properties. [4] One electron reduction of neutral disulfides and diselenides may lead to the formation of two-center three-electron (2c-3e) bonded radical anion systems. [5][6][7][8][9][10][11][12][13] The extra electron in such systems is accommodated in the lowest unoccupied molecular orbital which is often an antibonding sigma orbital. Due to the presence of this electron in a repulsive antibonding orbital, such three electron bonded species are not very stable and may dissociate easily. Having two electrons in the highest bonding sigma orbital and one electron in the lowest antibonding sigma orbital results in the formation of a half bond (bond order = 0.5) and hence these 2c-3e bond is also known as hemi bond or half bond. The typical symbol for s...

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Section: Resultssupporting

confidence: 76%

Section: Resultssupporting

confidence: 73%

Effect of excess electron on structure, bonding, and spectral properties of sulfur/selenium based dichalcogen systems

Kumar

Maity

2018

Int J of Quantum Chemistry

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“…On the other hand, for the Sec‐ and Tec‐based enzymes, no suitable parameters were available. Thus, we chose to derive the missing parameters for these residues by using a protocol and tools recently employed by some of us to derive GAFF (General AMBER Force Field) parameters for a series of organochalcogen compounds …”

Section: Methodsmentioning

confidence: 99%

“…For Lennard–Jones σ and ϵ parameters, we used 2.1200 Å and 0.2910 kcal mol −1 for Se and 2.2600 Å and 0.3980 kcal mol −1 for tellurium, consistent with previous work . During the simulation, they were combined according to the Lorentz–Berthelot mixing rules.…”

Section: Methodsmentioning

confidence: 99%

Role of the Chalcogen (S, Se, Te) in the Oxidation Mechanism of the Glutathione Peroxidase Active Site

Bortoli

Torsello²,

Bickelhaupt

et al. 2017

ChemPhysChem

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The oxidation by H O of the human phospholipid hydroperoxide glutathione peroxidase (GPx4), used as a model peroxidase selenoenzyme, as well as that of its cysteine (Cys) and tellurocysteine (Tec) mutants, was investigated in silico through a combined classic and quantum mechanics approach to assess the role of the different chalcogens. To perform this analysis, new parameters for selenocysteine (Sec) and tellurocysteine (Tec) were accurately derived for the AMBER ff14SB force field. The oxidation represents the initial step of the antioxidant activity of GPx, which catalyzes the reduction of H O and organic hydroperoxides by glutathione (GSH). A mechanism involving a charge-separation intermediate is feasible for the Cys and Sec enzymes, leading from the initial thiol/selenol form to sulfenic/selenenic acid, whereas for the Tec mutant a direct oxidation pathway is proposed. Activation strain analyses, performed for Cys-GPx and Sec-GPx, provided insight into the rate-accelerating effect of selenium as compared to sulfur and the role of specific amino acids other than Cys/Sec that are typically conserved in the catalytic pocket.

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“…For a more extensive discussion on this conformational flexibility and its significant effect on the 77 Se chemical shift, the curious reader is referred to a recently published paper by some of us, [45] as well as others.…”

Section: Oxidation Of Phsesephmentioning

confidence: 99%

Mechanistic Insight into the Oxidation of Organic Phenylselenides by H₂O₂

Ribaudo

Bellanda

Menegazzo

et al. 2017

Chemistry A European J

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The oxidation of organic phenylselenides by H O is investigated in model compounds, namely, n-butyl phenyl selenide (PhSe(nBu)), bis(phenylselanyl)methane (PhSeMeSePh), diphenyl diselenide (PhSeSePh), and 1,2-bis(phenylselanyl)ethane (PhSeEtSePh). Through a combined experimental ( H and Se NMR) and computational approach, we characterize the direct oxidation of monoselenide to selenoxide, the stepwise double oxidation of PhSeMeSePh that leads to different diastereomeric diselenoxides, the complete oxidation of the diphenyldiselenide that leads to selenium-selenium bond cleavage, and the subsequent formation of the phenylseleninic product. The oxidation of PhSeEtSePh also results in the formation of phenylseleninic acid along with 1-(vinylseleninyl)benzene, which is derived from a side elimination reaction. The evidence of a direct mechanism, in addition to an autocatalytic mechanism that emerges from kinetic studies, is discussed. By considering our observations of diselenides with chalcogen atoms that are separated by alkyl spacers of different length, a rationale for the advantage of diselenide versus monoselenide catalysts is presented.

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General AMBER Force Field Parameters for Diphenyl Diselenides and Diphenyl Ditellurides

Cited by 26 publications

References 77 publications

Effect of excess electron on structure, bonding, and spectral properties of sulfur/selenium based dichalcogen systems

Effect of excess electron on structure, bonding, and spectral properties of sulfur/selenium based dichalcogen systems

Role of the Chalcogen (S, Se, Te) in the Oxidation Mechanism of the Glutathione Peroxidase Active Site

Mechanistic Insight into the Oxidation of Organic Phenylselenides by H₂O₂

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General AMBER Force Field Parameters for Diphenyl Diselenides and Diphenyl Ditellurides

Cited by 26 publications

References 77 publications

Effect of excess electron on structure, bonding, and spectral properties of sulfur/selenium based dichalcogen systems

Effect of excess electron on structure, bonding, and spectral properties of sulfur/selenium based dichalcogen systems

Role of the Chalcogen (S, Se, Te) in the Oxidation Mechanism of the Glutathione Peroxidase Active Site

Mechanistic Insight into the Oxidation of Organic Phenylselenides by H2O2

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Mechanistic Insight into the Oxidation of Organic Phenylselenides by H₂O₂