Free energy calculations of small molecules in dense amorphous polymers. Effect on the initial guess configuration in molecular dynamics studies

The excess free energy of small molecules in the amorphous polymers poly(ethylene) and poly(dimethylsiloxane) was calculated, using the test-particle-insertion method. The method was applied to polymer configurations obtained from molecular dynamics simulations with differently prepared initial guess configurations. It was found that the calculated solubility coefficients strongly depend on the quality of the initial guess configuration. Slow compression of dilute systems, during which process only the repulsive parts of the nonbonded Lennard-Jones potentials are taken into account, yields polymer melts which are better relaxed, and which offer lower solubilities for guest molecules compared with polymer melts generated at the experimental density or prepared by compressing boxes with soft-core nonbonded potentials. For the last two methods initial stresses relax by straining the internal modes (bond angles, torsion angles) of the chain

Water-Mediated Ion Pairing: Occurrence and Relevance

We present an overview of the studies of ion pairing in aqueous media of the past decade. In these studies, interactions between ions, and between ions and water, are investigated with relatively novel approaches, including dielectric relaxation spectroscopy, far-infrared (terahertz) absorption spectroscopy, femtosecond mid-infrared spectroscopy, and X-ray spectroscopy and scattering, as well as molecular dynamics simulation methods. With these methods, it is found that ion pairing is not a rare phenomenon only occurring for very particular, strongly interacting cations and anions. Instead, for many salt solutions and their interfaces, the measured and calculated structure and dynamics reveal the presence of a distinct concentration of contact ion pairs (CIPs), solvent shared ion pairs (SIPs), and solvent-separated ion pairs (2SIPs). We discuss the importance of specific ion-pairing interactions between cations like Li+ and Na+ and anionic carboxylate and phosphate groups for the structure and functioning of large (bio)molecular systems

Ag-functionalized carbon molecular-sieve membranes based on polyelectrolyte/polyimide blend precursors

We prepared dense flat-sheet Ag-functionalized carbon molecular-sieve (CMS) membranes from blends of P84 co-polyimide and a sulfonated poly(ether ether ketone) with a Ag+ counterion (AgSPEEK). These blends offer the possibility of producing new functionalized precursor structures, which were previously not possible, such as integrally skinned asymmetric hollow fibers. Membranes prepared at a pyrolysis end temperature of 800 °C showed a maximum permeability for all tested gases at a Ag content of approximately 2.5 wt.-% (He permeability PHe = 465 Barrer (1 Barrer = 7.5 × 10-18 m2 s-1 Pa-1), PCO2 = 366 Barrer, PO2 = 91.8 Barrer, PN2 = 10.3 Barrer). The maximum achieved selectivity for O2 over N2 with CMS membranes based on these blends was O2/N2 = 13.5 (Ag content: 4.5 wt.-%, PO2 = 52.7 Barrer). The CO2 over N2 selectivity reached a value of 48.9 (Ag content: 4.5 wt.-%, PCO2 = 191 Barrer). These observations are explained by the formation of selective bypasses around Ag nanoclusters in the CMS matrix.\u

Assymetric bipolar membranes in acid-base electrodialysis

In this experimental study, the influence of asymmetric bipolar membranes on the salt impurities in the acid and base product is investigated. The thickness of one, the other, or both ion-permeable layers of a bipolar membrane is increased. With increased layer thickness, the current-voltage curves of the electrodialysis repeat unit recorded in a pilot-scale module show a reduced limiting current density, and thus they indicate an overall higher selectivity of these arrangements. Furthermore, these curves indicate water transport limitations for some membrane arrangements. Electrodialysis experiments with the same module at a high current density confirm the overall salt ion flux reduction. Moreover, these acid-base electrodialysis experiments directly reveal an increased asymmetry of the salt ion fluxes which can be utilized to design custom-made bipolar membranes with very high purity of either the produced acid or the base while keeping the bipolar membrane functioning without water transport limitations. The presented experiments also show that the bipolar membrane behavior can be characterized in situ, i.e., as a part of a electrodialysis repeat unit mounted in a pilot-scale electrodialysis module

Novel gas separation membranes containing covalently bonded fullerenes

In this work, we report superior mass transport properties of polymers prepared by the covalent coupling of supermolecular carbon cages (e.g., fullerenes, bucky balls) to a poly(2,6-dimethyl-1,4-phenylene oxide) (PPO) polymer. Dispersing the bucky balls into the polymer reduces gas permeability, whereas covalent bonding enhances permeability up to 80% in comparison to the pure PPO. Gas pair selectivity, however, is not compromised and stays constant

Intrinsic Conformational Preferences and Interactions in α-Synuclein Fibrils: Insights from Molecular Dynamics Simulations

Amyloid formation by the intrinsically disordered α-synuclein protein is the hallmark of Parkinson's disease. We present atomistic Molecular Dynamics simulations of the core of α-synuclein using enhanced sampling techniques to describe the conformational and binding free energy landscapes of fragments implicated in fibril stabilization. The theoretical framework is derived to combine the free energy profiles of the fragments into the reaction free energy of a protein binding to a fibril. Our study shows that individual fragments in solution have a propensity toward attaining non-β conformations, indicating that in a fibril β-strands are stabilized by interactions with other strands. We show that most dimers of hydrogen-bonded fragments are unstable in solution, while hydrogen bonding stabilizes the collective binding of five fragments to the end of a fibril. Hydrophobic effects make further contributions to the stability of fibrils. This study is the first of its kind where structural and binding preferences of the five major fragments of the hydrophobic core of α-synuclein have been investigated. This approach improves sampling of intrinsically disordered proteins, provides information on the binding mechanism between the core sequences of α-synuclein, and enables the parametrization of coarse grained models