Dissociation of molecular aggregates under high hydrostatic pressure: the influence of water structure on Benzene cluster solubility

Abstract

Em condições críticas, a água pode solvatar moléculas hidrofóbicas, tornando-se um solvente poderoso para agentes apolares. Para discutir o efeito da pressão em agregados de benzeno em água, foram executadas seis simulações consecutivas de 5000 ps (picossegundos) por modelagem e dinâmica molecular de moléculas de benzeno inseridas em caixas d´água cúbicas em diferentes condições de pressão, de 1 bar a 5 kbar. O raio de giro, o coeficiente de difusão, a função de distribuição radial, o número de ligações hidrogênio entre as moléculas de água e a área acessível ao solvente, foram monitorados. Os resultados mostraram que acima de 3 kbar, a estrutura da segunda camada de solvatação desaparece e os agregados de benzeno desmembram-se gradualmente. Até 2 kbar, a solubilidade e a difusão das moléculas de benzeno são inversamente proporcionais ao aumento da pressão e acima de 3 kbar o comportamento é o inverso.In some critical conditions water can solvate hydrophobic molecules, becoming a powerful solvent for nonpolar agents. To discuss the pressure effect on hydrated benzene clusters we carried out six consecutive 5000 ps (pico seconds) molecular dynamics simulations of benzene molecules in water cubic boxes at different pressure conditions, ranging from 1 bar to 5 kbar. Radius of gyration, diffusion coefficient, radial atomic pair distribution functions, number of hydrogen bonds between water molecules and the solvent accessible surface were monitored. Results showed that above 3 kbar the second hydration layer structure vanishes and the benzene clusters start to break up gradually. Up to 2 kbar, the solubility and diffusion of benzene molecules are inversely proportional to the increase of the pressure and above 3 kbar this behavior is inverted.

Role of Mutual Diffusion in the Dissolution Behavior of One Primary Bulk Gas Nanobubble in Liquid: A Molecular Dynamics Study

“…Figure a,b depicts the mutual diffusion coefficient at the interface as a function of the inner pressure and the nondimensional radius, respectively, throughout the BNB’s whole life, where the typical results obtained from the S–E equation ( D = k B T / C πη r h , where C , η, and r h are boundary condition constant, viscosity, and hydrodynamic radius of a rigid, spherical solute particle, respectively) and the empirical results fitted by the Arrhenius equation (as shown in eq ) are exhibited as benchmarks; meanwhile, similar diffusion coefficient results of oxygen or water from the papers − are shown for comparison. Obviously, the mutual diffusion coefficient at the interface decreases with the contraction of the primary bulk gas NB in liquid, and its value sharply reduces lower than the diffusion coefficients reported by other authors, which might be caused by the unstable equilibrium at the initial stage of phase transition.…”

“…Mutual diffusion coefficient at the interface as a function of (a) the logarithmic inner pressure and (b) the nondimensional radius of the primary bulk gas nanobubble, where thick lines denote the results calculated from eq , hollow circles show the results resolved from the S–E equation, dashed lines denote the empirical results fitted by the Arrhenius equation (as eq shows), and solid five-pointed stars represent the results reported by Bett and Cappi, Shimizu and Kushiro, Gonçalves et al, and Yasui et al …”

Modelling of noble anaesthetic gases and high hydrostatic pressure effects in lipid bilayers

“…24 The bond length is expressed by this means as a function of uniform hydrostatic pressure and of a scaling parameter that changes the attractive component of the LJ solvent-solute interaction. 25,26 The Berendsen weak coupling method does not correspond to any known statistical mechanical ensemble and may lead to artefacts in isolated molecules; however, it is common practice to apply Berendsen rescaling for relatively large biomolecules in explicit solvent, assuming that the approximation produces satisfactory data for statistically evaluated properties. 27 Simple LJ systems reveal many of the complex features observed experimentally for which the bond length changes are inferred by Raman peak shis upon an applied uniform pressure in the 1 kbar range.…”

Molecular modeling and NMR studies of benzyl substituted mannosyl trisaccharide binding to two mannose‐specific lectins: Allium sativam agglutinin I and Concanavalin A

“…The calculated vacuum molecular energy surfaces for the α(1→3) and α(1→6) linkages as a function of glycosidic torsional angles are displayed within Figure 3, using energy contours at 1 kcal/mol intervals above the observed minimum. Simulations were performed by building the trimannoside from lowest minima obtained from the disaccharide maps using the molecular modeling package GROMACS40 with most current carbohydrate force‐field parameters in OPLS‐AA41–46 in explicit SPC47 water. This modeling protocol for oligosaccharides has been shown to give accurate torsional properties for glycosidic linkages incorporating the experimental constraints 48, 49.…”

“…All MD simulations were performed under periodic boundary condition using the package GROMACS v 3.3.1 40. The benzyl‐substituted trimannoside was modeled using parameters of OPLS‐AA force field for the benzene/benzyl moiety and for the carbohydrate from earlier reports 41–46…”