Molecular Simulation of the Impact of Defects on Electrolyte Intrusion in Zeolites.

We have investigated through molecular simulation the intrusion of electrolytes in two representative pure-silica zeolites, silicalite-1 and chabazite, in which point defects were introduced in varying amounts. We distinguish between two types of defects, considering either "weak" or "strong" silanol nest defects, resulting in different hydration behaviors. In the presence of weak defects, the hydration process occurs through a homogeneous nucleation process, while with strong defects, we observe an initial adsorption followed by a filling of the nanoporous volume at a higher pressure. However, we show that electrolytes do not penetrate the zeolites, and these defects appear to have only marginal influence on the thermodynamics of electrolyte intrusion. While replacing pure water by the electrolyte solution shifts the intrusion pressure toward higher values because of the drop of water saturation vapor pressure, an increase in hydrophilicity of the framework due to point defects has the opposite effect, showing that controlling the amount of defects in zeolites is crucial for storage energy applications.

Hard-Cation-Soft-Anion Ionic Liquids for PEDOT:PSS Treatment.

A promising conducting polymer poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) experiences significant conductivity enhancement when treated with proper ionic liquids (ILs). Based on the hard-soft-acid-base principle, we propose a combination of a hydrophilic hard cation A+ (instead of the commonly used 1-ethyl-3-methyl imidazolium, EMIM+) and a hydrophobic soft anion X- (such as tetracyanoborate, TCB-) as the best ILs for this purpose. Such ILs would decouple hydrophilic-but-insulating PSS- from conducting-but-hydrophobic PEDOT+ most efficiently by strong interactions with hydrophilic A+ and hydrophobic X-, respectively. Such a favorable ion exchange between PEDOT+:PSS- and A+:X- ILs would allow the growth of conducting PEDOT+ domains decorated by X-, not disturbed by PSS- or A+. Using density functional theory calculations and molecular dynamics simulations, we demonstrate that a protic cation- (aliphatic N-alkyl pyrrolidinium, in particular) combined with the hydrophobic anion TCB- indeed outperforms EMIM+ by promptly leaving hydrophobic TCB- and strongly binding to hydrophilic PSS-.

DNA-assisted assembly of cationic gold nanoparticles: Monte Carlo simulation.

DNA-assisted assembly of ligand-stabilized gold nanoparticles is studied using Monte Carlo simulations with coarse-grained models for DNA and AuNP. Their interaction in a periodic simulation box is described by a combination of electrostatic and pairwise hard core potentials. We first probe the self-assembly of AuNPs resulting in an ordered distribution on a single fixed DNA strand. Subsequently, the effective force calculated between a pair of parallel DNA in the presence of AuNPs shows the attraction between them at short distance associated to a stable equilibrium position. Finally, the osmotic pressure calculated in a compact DNA-AuNP lattice with various amounts of monovalent salt ions shows that an increasing amount of salt prevents aggregate formation.

Protamine-Controlled Reversible DNA Packaging: A Molecular Glue.

Packaging paternal genome into tiny sperm nuclei during spermatogenesis requires 106-fold compaction of DNA, corresponding to a 10-20 times higher compaction than in somatic cells. While such a high level of compaction involves protamine, a small arginine-rich basic protein, the precise mechanism at play is still unclear. Effective pair potential calculations and large-scale molecular dynamics simulations using a simple idealized model incorporating solely electrostatic and steric interactions clearly demonstrate a reversible control on DNA condensates formation by varying the protamine-to-DNA ratio. Microscopic states and condensate structures occurring in semidilute solutions of short DNA fragments are in good agreement with experimental phase diagram and cryoTEM observations. The reversible microscopic mechanisms induced by protamination modulation should provide valuable information to improve a mechanistic understanding of early and intermediate stages of spermatogenesis where an interplay between condensation and liquid-liquid phase separation triggered by protamine expression and post-translational regulation might occur. Moreover, recent vaccines to prevent virus infections and cancers using protamine as a packaging and depackaging agent might be fine-tuned for improved efficiency using a protamination control.

Molecular Dynamics of PEDOT:PSS Treated with Ionic Liquids. Origin of Anion Dependence Leading to Cation Design Principles.

Conductivity enhancement of PEDOT:PSS via the morphological change of PEDOT-rich domains has been achieved by introducing a 1-ethyl-3-methylimidazolium (EMIM)-based ionic liquid (IL) into its aqueous solution, and the degree of such change varies drastically with the anion coupled to the EMIM cation constituting the IL. We carry out a series of molecular dynamics simulations on various simple model systems for the extremely complex mixtures of PEDOT:PSS and EMIM:X IL in water, varying the anion X, the IL concentration, the oligomer model of PEDOT:PSS, and the size of the model systems. The common characteristic found in all simulations is that although planar hydrophobic anions X are the most efficient for ion exchange between PEDOT:PSS and EMIM:X, they tend to bring together planar EMIM cations to PEDOT-rich domains, disrupting PEDOT π-stacks with PEDOT-X-EMIM intercalating layers. Nonplanar hydrophobic anions, which leave most of EMIM cations in water, are efficient for both ion exchange and the formation of extended PEDOT π-stacks, as observed in experiments. Based on such findings, we propose a design principle for new cations replacing EMIM; nonplanar hydrophilic cations combined with hydrophobic anions should improve IL efficiency for PEDOT:PSS treatment.

Ionic Liquid for PEDOT:PSS Treatment. Ion Binding Free Energy in Water Revealing the Importance of Anion Hydrophobicity.

Water solubility of PEDOT:PSS conducting polymer is achieved by PSS at the expense of disturbing the crystallinity and electron mobility of PEDOT. Recently, PEDOT crystallinity and electron mobility have been improved by treating the PEDOT:PSS aqueous solution with 1-ethyl-3-methylimidazolium- (EMIM-) based ionic liquids (IL) EMIM:X. The amount of such improvement varies drastically with the anion X coupled to EMIM cation in the IL. Herein, using umbrella-sampling molecular dynamics simulations on the aqueous solutions of a minimal model of PEDOT:PSS mixed with various EMIM:X ILs, we show that the solvation of each ion in water plays a major role in the free energies of ion binding and exchange. Anions X efficient for the improvement are weakly stabilized by hydration (i.e., hydrophobic) and prefer binding to hydrophobic PEDOT than to hydrophilic EMIM, favoring the ion exchange. In order to fulfill our design principle, a quantitative criterion based on hydration free energy is proposed to select efficient hydrophobic anions X.

Ionic Liquid Designed for PEDOT:PSS Conductivity Enhancement.

Poly-3,4-ethylenedioxythiophene:polystyrenesulfonate (PEDOT:PSS) is a water-processable conducting polymer with promise for use in transparent flexible electrodes and thermoelectric devices, but its conductivity is not satisfactory. Its low conductivity is attributed to the formation of hydrophilic/insulating PSS outer layers encapsulating the conducting/hydrophobic p-doped PEDOT cores. Recently a significant conductivity enhancement has been achieved by adding ionic liquid (IL). It is believed that ion exchange between PEDOT:PSS and IL components helps PEDOT to decouple from PSS and to grow into large-scale conducting domains, but the exact mechanism is still under debate. Here we show through free energy calculations using density functional theory on a minimal model that the most efficient IL pairs are the least tightly bound ones with the lowest binding energies, which would lead to the most efficient ion exchange with PEDOT:PSS. This spontaneous ion exchange followed by nanophase segregation between PEDOT and PSS, with formation of a π-stacked PEDOT aggregate decorated by IL anions, is also supported by molecular dynamics performed on larger PEDOT:PSS models in solution. We also show that the most efficient IL anions would sustain the highest amount of charge carriers uniformly distributed along the PEDOT backbone to further enhance the conductivity, providing that they remain in the PEDOT domain after the ion exchange. Hence, our design principle is that the high-performance IL should induce not only an efficient ion exchange with PEDOT:PSS to improve the PEDOT morphology (to increase mobility) but also a uniform high-level p-doping of PEDOT (to enhance intrinsic conductivity). Based on this principle, a promising (electron-withdrawing, but bulky, soft, and hydrophobic) new IL pair is proposed.