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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

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.

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.

We report equilibrium and nonequilibrium molecular dynamics (MD) simulations of two nucleosome core particles (NCPs) stacked with their dyad axes oriented in parallel or antiparallel fashion. From the equilibrium trajectories, we determine the bridging behavior of different histone tails and observe that different sets of histone tails play important roles in the two orientations in stabilizing the NCP stack. While the H4 and H2A tails play important intermediary roles in the parallel stack, the H3 and H2B tails are important in the antiparallel stack. We use steered MD simulations to unstack the two NCPs and find a stark difference in their unstacking pathways. While the average rupture force was found to be higher for the parallel stack, the work done for complete unstacking was similar for both orientations. We use Jarzynski equality to determine the PMF profiles along the unstacking pathway, relate our findings to the behavior of NCP mesophases, and derive insights into the enigmatic nucleosomal organization in the chromatin fiber.

It has long been postulated that rare tautomeric or ionized forms of DNA bases may play a role in mispair formation. To investigate the role this phenomenon plays in the mispairing of guanine and to develop a calculation methodology that can be extended to mutagenic DNA damage products, we used first principles quantum mechanics (density functional theory (B3LYP) with the Poisson−Boltzmann continuum−solvation model) to calculate the relative stabilities of tautomers of guanine in various environments and their pK_a values in aqueous solution. This method allows us to calculate site specific pK_a values — information that is experimentally inaccessible — as well as overall pK_a values for each stage, wherein our numbers are in agreement with experimental values. We find that neutral guanine exists in aqueous phase as a mixture of two major keto tautomers, the N_9H form (1) and a N_7H form (3). These keto forms are also major species present in the gas phase, as well as the O_6H enol tautomer (7a). These results show that tautomeric configurations can be drastically different depending on the environment. Here, we discuss the reasons for this environmental variability and suggest some possible implications. Finally, we estimate that the relative population of deprotonated guanine is 0.2−2% in the range of pH 7−8, a significant enough population to potentially play a role in mispair formation.

A new force field (MSXX FF) was developed for barium sulfate (BaSO_4) to reproduce the experimental properties of BaSO_4 crystal (density, lattice energy, compressibility, and vibrational spectrum) and to describe properly the interaction between BaSO_4 and water (binding energies and interatomic distances of Ba(H_2O)_8^(2+) and (SO_4)(H_2O)_6^(2-) clusters determined from ab initio quantum mechanics calculations). Using this FF in combination with F3C FF for water, the surface energies for several surfaces of BaSO_4 were examined both in a vacuum and in the presence of an explicit water bath in contact with them. The same level of FF's are also reported for CaSO_4 and SrSO_4.

In this paper, we use first principles quantum mechanical methods (B3LYP flavor of Density Functional Theory) to examine the mechanism of selective oxidation and ammoxidation of propene by BiMoO_x catalysts. To do this, we use finite clusters chosen to mimic likely sites on the heterogeneous surfaces of the catalysts. We conclude that activation of the propene requires a Bi(V) site, whereas all subsequent reactions involve di-oxo Mo(VI) sites adjacent to the Bi. We find that two such Mo sites are required for the most favorable reactions. These results are compatible with current experimental data. For ammoxidation, we conclude that ammonia activation would be easier on Mo(IV) rather than on Mo(VI). Ammonia would be activated more easily for more reducing condition. Because ammonia and propene are reducing agents, higher partial pressures of them could accelerate the ammonia activation. This is consistent with the kinetic model of ammoxidation proposed by Grasselli and co-workers that imido sites (Mo═NH) are more abundant in higher partial pressures of feed. Our calculations also indicate that allyl groups produced as a result of the hydrogen abstraction from propenes would be adsorbed more easily on imido groups (Mo═NH) than on oxo groups (Mo═O) and that the spectator oxo effect is larger than spectator imido effect. Thus, we propose that the best site for ammoxidation (at least for allyl adsorption) is the imido group of the “oxo-imido” species.