Experimental (electrochemistry) and theoretical (ab initio and Density Functional Theory) studies of hydrogen and sulfide adsorption on palladium (100) surface

The adsorption of H and S2- species on Pd (100) has been studied with ab initio, density-functional calculations and electrochemical methods. A cluster of five Pd atoms with a frozen geometry described the surface. The computational calculations were performed through the GAUSSIAN94 program, and the basis functions adapted to a pseudo-potential obtained by using the Generator Coordinate Method adapted to the this program. Using the cyclic voltammetry technique through a Model 283 Potentiostat/Galvanostat E.G.&G-PAR obtained the electrochemical results. The calculated chemisorption geometry has a Pd-H distance of 1.55Å, and the potential energy surface was calculated using the Becke3P86//(GCM/DFT/SBK) methodology. The adsorption of S2- ions on Pd surface obtained both through comparison between the experimental and theoretical results, at MP2 level, suggest a S2- absorption into the metallic cluster. The produced Pd-(S2-) system was show to be very stable under the employed experimental conditions. The paper has shows the powerful aid of computational methods to interpret adsorption experimental data.473479Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação para o Desenvolvimento da UNESP (FUNDUNESP

Photobiomodulation reduces the cytokine storm syndrome associated with Covid-19 in the zebrafish model

Although the exact mechanism of the pathogenesis of COVID-19 is not fully understood, oxidative stress and the release of pro-inflammatory cytokines have been highlighted as playing a vital role in the pathogenesis of the disease. In this sense, alternative treatments are needed to reduce the inflammation caused by COVID-19. Therefore, this study aimed to investigate the potential effect of red PBM as an attractive therapy to downregulate the cytokine storm caused by COVID-19 from a zebrafish model. RT-PCR analyses and protein-protein interaction prediction among SARS-CoV-2 and Danio rerio proteins showed that rSpike was responsible for generating systemic inflammatory processes with significantly increased pro-inflammatory (il1b, il6, tnfa, and nfkbiab), oxidative stress (romo1) and energy metabolism (slc2a1a, coa1) mRNA markers, with a pattern like those observed in COVID-19 cases in humans. On the other hand, PBM treatment decreased the mRNA levels of these pro-inflammatory and oxidative stress markers compared with rSpike in various tissues, promoting an anti-inflammatory response. Conversely, PBM promotes cellular and tissue repair of injured tissues and significantly increases the survival rate of rSpike-inoculated individuals. Additionally, metabolomics analysis showed that the most impacted metabolic pathways between PBM and the rSpike-treated groups were related to steroid metabolism, immune system, and lipids metabolism. Together, our findings suggest that the inflammatory process is an incisive feature of COVID-19, and red PBM can be used as a novel therapeutic agent for COVID-19 by regulating the inflammatory response. Nevertheless, the need for more clinical trials remains, and there is a significant gap to overcome before clinical trials.publishedVersio

Theoretical Study Of Molecular And Electronic Structures Of 5(1) Knot Systems: Two-layered Oniom Calculations

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)In this study we examine the electronic and molecular structures of the [5(1) knot center dot center dot center dot(PF6)(10)](+) pentafoil knot system and report calculated interaction energies that result from halides (X = F, Cl, Br, and I) localized at the center of the [5(1) knot center dot center dot center dot(PF6)(9)]X molecular structure. The equilibrium geometries were fully optimized at the ONIOM(M06/6-31G(2d,p):PM6) level of theory, starting from an initial geometry for the pentafoil knot obtained from experimental X-ray data. The molecular systems were divided into two layers, for which the M06/6-31G(2d, p) level of theory was used to describe the high layer ([C4H6](5)X-structure) and the PM6 semiempirical method was employed for the low layer. The calculated electronic energies show that the interaction between the fluorine anion and the pentafoil knot produces the most stable structure, whereas an unfavorable interaction is observed for iodide due to the diffuse character of its electronic cloud. Using basis set superposition error (BSSE) correction techniques, the observed values of the interaction are -0.201 hartrees for the fluoride ion and -0.100 hartrees for iodide.26510281033Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Theoretical Study of Molecular and Electronic Structures of 5 1

In this study we examine the electronic and molecular structures of the [5(1) knot center dot center dot center dot(PF6)(10)](+) pentafoil knot system and report calculated interaction energies that result from halides (X = F, Cl, Br, and I) localized at the center of the [5(1) knot center dot center dot center dot(PF6)(9)]X molecular structure. The equilibrium geometries were fully optimized at the ONIOM(M06/6-31G(2d,p):PM6) level of theory, starting from an initial geometry for the pentafoil knot obtained from experimental X-ray data. The molecular systems were divided into two layers, for which the M06/6-31G(2d, p) level of theory was used to describe the high layer ([C4H6](5)X-structure) and the PM6 semiempirical method was employed for the low layer. The calculated electronic energies show that the interaction between the fluorine anion and the pentafoil knot produces the most stable structure, whereas an unfavorable interaction is observed for iodide due to the diffuse character of its electronic cloud. Using basis set superposition error (BSSE) correction techniques, the observed values of the interaction are -0.201 hartrees for the fluoride ion and -0.100 hartrees for iodide

Solvent Effects in the Regioselective N-Functionalization of Tautomerizable Heterocycles Catalyzed by Methyl Trifluoromethanesulfonate: A Density Functional Theory Study with Implicit Solvent Model

Methyl trifluoromethanesulfonate was found to catalyze the reaction of the nucleophilic substitution of the hydroxyl group of alcohols by N-heterocycles followed by X- to N- alkyl group migration (X = O, S) to obtain N-functionalized benzoxazolone, benzothiazolethione, indoline, benzoimidazolethione and pyridinone derivatives. A high degree of solvent dependency on the yield of the products was observed during optimization of the reaction parameters. The yield of the product was found to be 0%, 48% and 70% in acetonitrile, 1,2-dichloroethane and chloroform, respectively. The mechanism of the reaction was established through experiments as well as DFT calculations. The functional B3LYP and 6-311++G(d) basis function sets were used to optimize the molecular geometries. D3 Grimme empiric dispersion with Becke–Johnson dumping was employed, and harmonic vibrational frequencies were calculated to characterize the stationary points on the potential energy surface. To ensure that all the stationary points were smoothly connected to each other, intrinsic reaction coordinate (IRC) analyses were performed. The influence of solvents was considered using the solvation model based on density (SMD). The free energy profiles of the mechanisms were obtained with vibrational unscaled zero-point vibrational energy (ZPE), thermal, enthalpy, entropic and solvent corrections

Solvent Effects in the Regioselective N-Functionalization of Tautomerizable Heterocycles Catalyzed by Methyl Trifluoromethanesulfonate: A Density Functional Theory Study with Implicit Solvent Model

Methyl trifluoromethanesulfonate was found to catalyze the reaction of the nucleophilic substitution of the hydroxyl group of alcohols by N-heterocycles followed by X- to N- alkyl group migration (X = O, S) to obtain N-functionalized benzoxazolone, benzothiazolethione, indoline, benzoimidazolethione and pyridinone derivatives. A high degree of solvent dependency on the yield of the products was observed during optimization of the reaction parameters. The yield of the product was found to be 0%, 48% and 70% in acetonitrile, 1,2-dichloroethane and chloroform, respectively. The mechanism of the reaction was established through experiments as well as DFT calculations. The functional B3LYP and 6-311++G(d) basis function sets were used to optimize the molecular geometries. D3 Grimme empiric dispersion with Becke–Johnson dumping was employed, and harmonic vibrational frequencies were calculated to characterize the stationary points on the potential energy surface. To ensure that all the stationary points were smoothly connected to each other, intrinsic reaction coordinate (IRC) analyses were performed. The influence of solvents was considered using the solvation model based on density (SMD). The free energy profiles of the mechanisms were obtained with vibrational unscaled zero-point vibrational energy (ZPE), thermal, enthalpy, entropic and solvent corrections

Estudo da adsorção de hidrogênio e sulfeto na superfície de paládio: aspectos experimentais (eletroquímica) e teóricos (ab initio e Teoria do Funcional da Densidade)

The adsorption of H and S2- species on Pd (100) has been studied with ab initio, density-functional calculations and electrochemical methods. A cluster of five Pd atoms with a frozen geometry described the surface. The computational calculations were performed through the GAUSSIAN94 program, and the basis functions adapted to a pseudo-potential obtained by using the Generator Coordinate Method adapted to the this program. Using the cyclic voltammetry technique through a Model 283 Potentiostat/Galvanostat E.G.&G-PAR obtained the electrochemical results. The calculated chemisorption geometry has a Pd-H distance of 1.55Å, and the potential energy surface was calculated using the Becke3P86//(GCM/DFT/SBK) methodology. The adsorption of S2- ions on Pd surface obtained both through comparison between the experimental and theoretical results, at MP2 level, suggest a S2- absorption into the metallic cluster. The produced Pd-(S2-) system was show to be very stable under the employed experimental conditions. The paper has shows the powerful aid of computational methods to interpret adsorption experimental data

All electron fully relativistic Dirac-Fock calculation for darmstadtium carbide using prolapse free basis set

For the first time, ab inito all electron fully relativistic and correlated Dirac-Fock calculations with prolapse free basis set are reported for a Super Heavy Element. We investigated the relativistic effects on bonding and on some spectroscopic constants for the darmstadtium carbide and our results at DF/CCSD(T) with a prolapse free basis set suggest for R-e, omega(e) and D-e the values of 174 pm, 1114 cm(-1) and 7.29 eV, respectively. These values are very similar to the values for PtC found on literature. It was also found that prolapse free basis set may be important to estimate the dissociation energy using Relativistic 4-components correlated methods. (c) 2007 ELsevier B.V. All rights reserved