On the Role of Tetramethylammonium Cation and Effects of Solvent Dynamics on the Stability of the Cage-like Silicates Si6O156-and Si8O208-in Aqueous Solution. A Molecular Dynamics Study

2006 ◽  
Vol 128 (2) ◽  
pp. 596-606 ◽  
Author(s):  
Stavros Caratzoulas ◽  
Dionisis G. Vlachos ◽  
Michael Tsapatsis
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Solvent Dynamics ◽  
The Stability

scholarly journals Simulating Absorption Spectra of Flavonoids in Aqueous Solution: A Polarizable QM/MM Study

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5853
Author(s):  
Sulejman Skoko ◽  
Matteo Ambrosetti ◽  
Tommaso Giovannini ◽  
Chiara Cappelli
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Hydrogen Bonding ◽  
Force Field ◽  
Absorption Spectra ◽  
Computational Study ◽  
Md Simulations ◽  
Quantum Mechanical ◽  
Hydrogen Bonding Interactions

We present a detailed computational study of the UV/Vis spectra of four relevant flavonoids in aqueous solution, namely luteolin, kaempferol, quercetin, and myricetin. The absorption spectra are simulated by exploiting a fully polarizable quantum mechanical (QM)/molecular mechanics (MM) model, based on the fluctuating charge (FQ) force field. Such a model is coupled with configurational sampling obtained by performing classical molecular dynamics (MD) simulations. The calculated QM/FQ spectra are compared with the experiments. We show that an accurate reproduction of the UV/Vis spectra of the selected flavonoids can be obtained by appropriately taking into account the role of configurational sampling, polarization, and hydrogen bonding interactions.

scholarly journals The Role of Endogenous Proteins on the Emulsification of Silicone Oils Used in Vitreoretinal Surgery

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Irene Nepita ◽  
Rodolfo Repetto ◽  
Jan O. Pralits ◽  
Mario R. Romano ◽  
Francesca Ravera ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Serum Proteins ◽  
Vitreous Body ◽  
Vitreoretinal Surgery ◽  
It Value ◽  
Silicone Oils ◽  
Dilational Viscoelasticity ◽  
Endogenous Proteins ◽  
The Stability

The present work is aimed at investigating the chemicophysical properties of the interface between silicone oils (SOs) used in vitreoretinal surgery and aqueous solutions, in the presence of surfactant biomolecules. Such molecules are thought to play an important role in the formation of SO emulsions in vitrectomised eyes, in which the natural vitreous body has been replaced with a SO. In particular, we have measured the interfacial tension (IT) and the interfacial dilational viscoelasticity (DV) of the interface between SO (Siluron 1000) and serum proteins (albumin and γ-globulins) at various concentrations in a Dulbecco alkaline buffer. The equilibrium IT value is relevant for the onset of emulsification, and the DV influences the stability of an emulsion, once formed. The study is complemented by preliminary emulsification tests. The experimental results show that, when proteins are dissolved in the aqueous solution, the rheological properties of the interface change. The IT decreases significantly for physiological protein concentrations, and the DV modulus achieves high values, even for small protein concentrations. The emulsification tests confirm that, in the presence of proteins, emulsions are stable on the time scale of months. We conclude that the measured values of IT in the presence of serum proteins are compatible with the promotion of droplet formation, which, in addition, are expected to be stable against coalescence. Adsorption of biomolecules at the interface with the SO is, therefore, likely to play an important role in the generation of an emulsion in eyes subjected to vitrectomy. These findings are relevant to identify strategies to avoid or control the formation of emulsions in eyes.

scholarly journals Forever Young: Structural Stability of Telomeric Guanine-Quadruplexes in Presence of Oxidative DNA Lesions

2020 ◽  
Author(s):  
Tom Miclot ◽  
Camille Corbier ◽  
Alessio Terenzi ◽  
Cécilia Hognon ◽  
Stéphanie Grandemange ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Molecular Dynamics ◽  
Structural Stability ◽  
Md Simulations ◽  
Dna Lesions ◽  
Computational Investigation ◽  
Telomeric Dna ◽  
G Quadruplex ◽  
The Stability

AbstractHuman telomeric DNA (h-Telo), in G-quadruplex (G4) conformation, is characterized by a remarkable structural stability that confers it the capacity to resist to oxidative stress producing one or even clustered 8-oxoguanine lesions. We present a combined experimental/computational investigation, by using circular dichroism in aqueous solutions, cellular immunofluorescence assays and molecular dynamics (MD) simulations, that identifies the crucial role of the stability of G4s to oxidative lesions, related also to their biological role as inhibitors of telomerase, an enzyme overexpressed in most cancers associated to oxidative stress.

Impact of inorganic buffering ions on the stability of Fe(vi) in aqueous solution: role of the carbonate ion

2016 ◽  
Vol 18 (6) ◽  
pp. 4415-4422 ◽  
Author(s):  
Michal Kolář ◽  
Petr Novák ◽  
Karolína M. Šišková ◽  
Libor Machala ◽  
Ondřej Malina ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Carbonate Ion ◽  
The Stability ◽  
Ph Range

The study presents a systematic kinetics investigation of the decay of ferrate(vi) in the presence of inorganic buffering ions (borate, phosphate, and carbonate) at a pH range from 6.0 to 9.0.

scholarly journals Structure and stability of aquotetrafluorouranyl(VI) in the solid state — Density functional study of [UO2F4(H2O)][NMe4]2·2H2O,

2009 ◽  
Vol 87 (7) ◽  
pp. 818-823 ◽  
Author(s):  
Michael Bühl
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Density Functional ◽  
State Density ◽  
Functional Study ◽  
X Ray ◽  
X Ray Crystallography ◽  
Coordinated Water ◽  
Density Functional Computations

Periodic density functional computations have been performed for solid [UO2F4(H2O)][NMe4]2·2H2O at the BLYP level. A model with disordered fluoro and aquo ligands in the uranyl anion is significantly lower in energy than one with a symmetrical assignment of these sites, which was favored in the original X-ray crystallography study. According to optimized energies and Car–Parrinello molecular dynamics (CPMD) simulations, the [UO2F4(H2O)]2− ion in the solid is stable with respect to loss of the coordinated water molecule. In contrast, CPMD simulations had found this ligand to be unbound in aqueous solution. The role of the counterions in stabilizing the higher coordination number in the crystal is discussed.

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