Bases and Dimension of Vector Spaces Over Lattices

Marenich, E. E.; Marenich, V. E.

doi:10.1007/s10958-016-2712-6

Cited by 3 publications

(2 citation statements)

References 4 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The calculated ionization potential (I) value was used as a control and compared with the experimental I value of melatonin, 7.70 eV [32]. To simulate aqueous and lipid environments, we use the continuum solvation model based on density (SMD) [33], used to simulate solvent effects (water, ε = 78.36 and pentyl ethanoate as a model for lipidic ones, ε = 4.73).…”

Section: Computational Methodologymentioning

confidence: 99%

DFT and Molecular Docking Studies of Melatonin and Some Analogues Interaction with Xanthine Oxidase as a Possible Antiradical Mechanism

Manzanilla,

Martinez-Alfaro,

Robles

2024

J. Mex. Chem. Soc.

View full text Add to dashboard Cite

Melatonin (Mel) and some of its active metabolites such as N1-acetyl-5-methoxykynuramine (AMK), N1-acetyl-N2-formyl-5-methoxykynuramine (AFMK), 6-hydroxymelatonin (6OHM), and the analogues Ir and It recently designed by Galano's group, have been studied within density functional theory (DFT). The purpose is to evaluate some plausible mechanisms of action of melatonin's metabolites and analogues with the free radicals (FR): OH ̇, NO ̇2, HOO ̇, and CH3O͘ . We calculated global chemical reactivity descriptors from conceptual DFT to evaluate their antiradical properties. We used water and pentyl ethanoate as solvents to simulate the physiological conditions, modeled via the continuum solvation model based on density (SMD). We assess the following plausible mechanisms: single electrons transfer (SET), hydrogen atom transfer (HAT) and xanthine oxidase (XO) inhibition. We performed our calculations at the M06-2X/6-31+G* level of theory. The results indicate that Mel, AMK, AFMK, 6OHM, It, and Ir are good antiradicals towards the FRs: NO ̇2 and CH3O , while It and Ir could be suitable XO inhibitors. Keywords: Antiradical properties; Density Functional Theory; melatonin; xanthine oxidase; molecular docking. Resumen. La melatonina (Mel) y algunos de sus metabolitos activos como N1-acetil-5-metoxiquinuramina (AMK), N1-acetil-N2-formil-5-metoxiquinuramina (AFMK), 6-hidroximelatonina (6OHM) y los análogos Ir e It, diseñados recientemente por el grupo de Galano, han sido estudiados con la teoría de funcionales de la densidad (DFT). El propósito es evaluar algunos mecanismos de acción plausibles de los metabolitos y análogos de la melatonina con los radicales libres (FR):OH ̇, NO ̇2, HOO ̇ y CH3O ̇. Calculamos los descriptores de reactividad química global a partir de DFT conceptual para evaluar sus propiedades antirradicales. Usamos agua y etanoato de pentilo como solventes para simular las condiciones fisiológicas, modeladas a través del modelo continuo de solvatación basado en la densidad (SMD). Evaluamos los siguientes mecanismos plausibles: transferencia de electrones individuales (SET), transferencia de átomos de hidrógeno (HAT) e inhibición de la xantina oxidasa (XO). Realizamos nuestros cálculos al nivel de teoría M06-2X/6-31+G*. Los resultados indican que Mel, AMK, AFMK, 6OHM, It e Ir son buenos antirradicales frente a los FRs: NO ̇2 y CH3O ̇, mientras que It e Ir podrían ser inhibidores adecuados de XO.

show abstract

Section: Computational Methodologymentioning

confidence: 99%

DFT and Molecular Docking Studies of Melatonin and Some Analogues Interaction with Xanthine Oxidase as a Possible Antiradical Mechanism

Manzanilla,

Martinez-Alfaro,

Robles

2024

J. Mex. Chem. Soc.

View full text Add to dashboard Cite

show abstract

“…We then generated 110 configurations with the water molecule located at varying distances from the μ3-OH, μ3-O and Olinker interaction sites for which the interaction energies were calculated at the DFT level of theory and corrected for the basis set superposition error (BSSE) using the counterpoise method. 65,66 Finally, the partial charges of the atoms in the metal node and organic linkers were calculated using the Charge Model 5 (CM5) 67 as implemented in Gaussian 16 68 with the same DFT functional and basis set used for the single point energy refinements.…”

Section: Force Fieldmentioning

confidence: 99%

Computational Insights into the Interaction of Water with the UiO-66 Metal-Organic Framework and Its Functionalized Derivatives

Zhang

Paesani

Lessio

2023

Preprint

View full text Add to dashboard Cite

The UiO-66 metal-organic framework (MOF) has been identified as a promising hydrophilic material for water harvesting. Recent studies show that its water uptake ability at low relative humidity (RH) can be improved by incorporating hydrophilic functional groups into the framework. In this work, we provide computational insights into the adsorption of water in UiO-66 and its functionalized derivatives to reveal the role played by different adsorption sites and functional groups in the adsorption mechanism. We started by developing molecular models for UiO-66, UiO-66-NH2, UiO-66-OH, and UiO-66-(OH)2 compatible with the MB-pol data-driven many-body potential of water. We then benchmarked these models against ab initio data. We used these models to perform molecular dynamics simulations and calculate radial distribution functions, IR spectra, and two-dimensional density distribution maps for water in the MOFs. These results consistently show that the μ3-OH sites are the preferential interaction sites for water in UiO-66 and all its variants, and the formation of localised water clusters inside the octahedral pores is responsible for the abrupt step in the experimental adsorption isotherms. Furthermore, the presence of functional groups in the framework allows water to cluster in the octahedral pores at lower RH, thus making the MOF a more efficient water harvester. Overall, this study provides molecular-level insights into the pore filling process of UiO-66 and its functionalized derivatives, which are needed for the design of efficient water harvesting materials based on MOFs.

show abstract