Computational analysis of the effect of [Tea][Ms] and [Tea][H2PO4] ionic liquids on the structure and stability of Aß(17-42) amyloid fibrils.

Experimental studies have reported the possibility of affecting the growth/dissolution of amyloid fibres by the addition of organic salts of the room-temperature ionic-liquid family, raising the tantalizing prospect of controlling these processes under physiological conditions. The effect of [Tea][Ms] and [Tea][H2PO4] at various concentrations on the structure and stability of a simple model of Aß42 fibrils has been investigated by computational means. Free energy computations show that both [Tea][Ms] and [Tea][H2PO4] decrease the stability of fibrils with respect to isolated peptides in solution, and the effect is significantly stronger for [Tea][Ms]. The secondary structure of fibrils is not much affected, but single peptides in solution show a marked decrease in their ß-strand character and an increase in α-propensity, again especially for [Tea][Ms]. These observations, consistent with the experimental picture, can be traced to two primary effects, i.e., the difference in the ionicity of the [Tea][Ms] and [Tea][H2PO4] water solutions and the remarkable affinity of peptides for [Ms]- anions, due to the multiplicity of H-bonds.

The transition from salt-in-water to water-in-salt nanostructures in water solutions of organic ionic liquids relevant for biological applications.

The nanostructure in water solutions of three organic ionic liquids relevant for biological applications has been studied by molecular dynamics simulations based on empirical force fields. The three compounds consisted of two different triethylammonium salts, known to affect the fibrillation kinetics of Aß peptides, and a phosphonium dication, which has been shown to possess a marked bactericidal activity. The structure of solutions spanning a wide concentration range (from 25 to 75 wt%) has been analysed by computing several combinations of partial structure factors, measuring the fluctuation of the ion and water distribution in space. At moderate salt concentration, the results reflect the formation in water of salt-rich domains of nanometric size. With salt concentration increasing beyond 50 wt%, the system enters the so-called water-in-salt regime, in which the aggregation properties of water become relevant, giving origin to water-rich domains in the nearly uniform salt environment. The persistence over a wide concentration range of nearly integer (∼6; ∼4) water-ion coordination numbers suggests the formation of stoichiometric liquid ionic hydrates.

Absorption of Phosphonium Cations and Dications into a Hydrated POPC Phospholipid Bilayer: A Computational Study.

Molecular dynamics (MD) based on an empirical force field is applied to investigate the effect of phosphonium cations ([P6,6,6,6]+) and geminal dications ([DxC10]2+) inserted at T = 300 K into the hydration layer separating planar POPC phospholipid bilayers. Up to high concentration, nearly every added cation and dication becomes absorbed into the lipid phase. Absorption takes place during several microseconds and is virtually irreversible. The neutralizing counterions ([Cl]-, in the present simulation) remain dissolved in water, giving origin to the charge separation and the strong electrostatic double layer at the water/lipid interface. Incorporation of cations and dications changes the properties of the lipid bilayer such as diffusion, viscosity, and the electrostatic pattern. At high ionic concentration, the bilayer acquires a long-wavelength standing undulation, corresponding to a change of phase from fluid planar to ripple. All these changes are potentially able to affect processes relevant in the context of cell biology. The major difference between cations and dications concerns the kinetics of absorption, which takes place nearly two times faster in the [P6,6,6,6]+ case, and for [DxC10]2+ dications displays a marked separation into two-stages, corresponding to the easy absorption of the first phosphonium head of the dication and the somewhat more activated absorption of the second phosphonium head of each dication.

Coarse-Grained Model of Entropy-Driven Demixing.

Entropy-driven demixing transitions play an important role in a variety of phenomena in solution chemistry, in mixtures of ionic liquids, in polymers, and in biosystems. A simple coarse-grained model of a binary (A and B) fluid mixture of Lennard-Jones particles carrying classical harmonic oscillators whose frequency decreases with increasing homo-coordination separates into two nearly pure phases with increasing T, as the entropy gain in lowering the oscillators' frequency overcomes the potential energy and ideal entropy advantage of the homogeneous phase. We characterize features of the demixing transition and outline physical questions that can be addressed by this simple and inexpensive model. Besides and beyond these conceptual points, we provide examples of how the model could be adapted to real systems, aiming at their quantitative description by a coarse-grained model made of particles carrying momentum, energy, and entropy.

Solubility Advantage of Amorphous Ketoprofen. Thermodynamic and Kinetic Aspects by Molecular Dynamics and Free Energy Approaches.

Thermodynamic and kinetic aspects of crystalline (c-KTP) and amorphous (a-KTP) ketoprofen dissolution in water have been investigated by molecular dynamics simulation focusing on free energy properties. Absolute free energies of all relevant species and phases have been determined by thermodynamic integration on a novel path, first connecting the harmonic to the anharmonic system Hamiltonian at low T and then extending the result to the temperature of interest. The free energy required to transfer one ketoprofen molecule from the crystal to the solution is in fair agreement with the experimental value. The absolute free energy of the amorphous form is 19.58 kJ/mol higher than for the crystal, greatly enhancing the ketoprofen concentration in water, although as a metastable species in supersaturated solution. The kinetics of the dissolution process has been analyzed by computing the free energy profile along a reaction coordinate bringing one ketoprofen molecule from the crystal or amorphous phase to the solvated state. This computation confirms that, compared to the crystal form, the dissolution rate is nearly 7 orders of magnitude faster for the amorphous form, providing one further advantage to the latter in terms of bioavailability. The problem of drug solubility, of great practical importance, is used here as a test bed for a refined method to compute absolute free energies, which could be of great interest in biophysics and drug discovery in particular.