Aqueous ionic liquids and their influence on peptide conformations: denaturation and dehydration mechanisms.

Low concentrated aqueous ionic liquids (ILs) and their influence on protein structures have attracted a lot of interest over the last few years. This can be mostly attributed to the fact that aqueous ILs, depending on the ion species involved, can be used as protein protectants or protein denaturants. Atomistic molecular dynamics (MD) simulations are performed in order to study the influence of different aprotic ILs on the properties of a short hairpin peptide.

ForConX: A forcefield conversion tool based on XML.

The force field conversion from one MD program to another one is exhausting and error-prone. Although single conversion tools from one MD program to another exist not every combination and both directions of conversion are available for the favorite MD programs Amber, Charmm, Dl-Poly, Gromacs, and Lammps. We present here a general tool for the force field conversion on the basis of an XML document.

Imidazolium-Based Lipid Analogues and Their Interaction with Phosphatidylcholine Membranes.

4,5-Dialkylated imidazolium lipid salts are a new class of lipid analogues showing distinct biological activities. The potential effects of the imidazolium lipids on artificial lipid membranes and the corresponding membrane interactions was analyzed. Therefore, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) was employed to create an established lipid monolayer model and a bilayer membrane.

Molecular dynamics analysis of the effect of electronic polarization on the structure and single-particle dynamics of mixtures of ionic liquids and lithium salts.

We report a molecular dynamics study on the effect of electronic polarization on the structure and single-particle dynamics of mixtures of the aprotic ionic liquid 1-ethyl-3-methylimidazolium bis-(trifluoromethylsulfonyl)-imide ([EMIM][TFSI]) doped with a lithium salt with the same anion at 298 K and 1 bar. In particular, we analyze the effect of electron density fluctuations on radial distribution functions, velocity autocorrelation functions, cage correlation functions, mean-squared displacements, and vibrational densities of states, comparing the predictions of the quantum-chemistry-based Atomistic Polarizable Potential for Liquids, Electrolytes, & Polymers (APPLE&P) with those of its nonpolarizable version and those of the standard non-polarizable Optimized Potentials for Liquid Simulations-All Atom (OPLS-AA). We found that the structure of the mixture is scarcely modified by the fluctuations in electron charge of their constituents, but their transport properties are indeed quite drastically changed, with larger mobilities being predicted for the different species in the bulk mixtures with the polarizable force field.

Atomistic insights into deep eutectic electrolytes: the influence of urea on the electrolyte salt LiTFSI in view of electrochemical applications.

The influence of urea on the conducting salt lithium bis-(trifluoromethanesulfonyl)-imide (LiTFSI) in terms of lithium ion coordination numbers and lithium ion transport properties is studied via atomistic molecular dynamics simulations. Our results indicate that the presence of urea favors the formation of a deep eutectic electrolyte with pronounced ion conductivities which can be explained by a competition between urea and TFSI in occupying the first coordination shell around lithium ions. All simulation findings verify that high urea concentrations lead to a significant increase of ionic diffusivities and an occurrence of relatively high lithium transference numbers in good agreement with experimental results.

Properties of Apolar Solutes in Alkyl Imidazolium-Based Ionic Liquids: The Importance of Local Interactions.

The solvation and the dynamic properties of apolar model solutes in alkyl imidazolium-based ionic liquids (IL) are studied by using all-atom molecular dynamics simulations. In regards to specific IL effects, we focused on the often used 1-ethyl-3-methyl imidazolium cation in combination with the anions tetrafluoroborate, acetate, and bis(trifluoromethanesulfonyl)imide. Our findings reveal that the size of the anion crucially influences the accumulation behavior of the cations, which results in modified IL solvation properties.

The influence of cations on lithium ion coordination and transport in ionic liquid electrolytes: a MD simulation study.

The dynamical and structural properties in two ionic liquid electrolytes (ILEs) based on 1-ethyl-3-methylimidazolium bis-(trifluoromethanesulfonyl)-imide ([emim][TFSI]) and N-methyl-N-propylpyrrolidinium bis-(trifluoromethanesulfonyl)imide([pyr13][TFSI]) were compared as a function of lithium bis-(trifluoromethanesulfonyl)-imide (LiTFSI) salt concentrations using atomistic molecular dynamics (MD) simulations. The many-body polarizable APPLE&P force field has been utilized. The influence of anion polarization on the structure of the first coordination shell of Li(+) was examined.

Peptides in the presence of aqueous ionic liquids: tunable co-solutes as denaturants or protectants?

We studied the stability of a small β-hairpin peptide under the influence of an aqueous 1-ethyl-3-methylimidazolium acetate ([EMIM](+)[ACE](-)) solution via all-atom molecular dynamics simulations in combination with metadynamics. Our free energy results indicate a denaturation of the peptide structure in the presence of the ionic liquid which is validated by a significant broadening of the end-to-end distance. The radial distribution functions between the ions and the peptide were used for the calculation of the preferential binding coefficients in terms of the Kirkwood-Buff theory.

Solvent effects of 1-ethyl-3-methylimidazolium acetate: solvation and dynamic behavior of polar and apolar solutes.

We study the solvation properties of the ionic liquid 1-ethyl-3-methylimidazolium acetate ([EMIM](+)[ACE](-)) and the resulting dynamic behavior for differently charged model solutes at room temperature via atomistic molecular dynamics (MD) simulations of 300 ns length and 200 ns equilibration time. The solutes are simple model spheres which are either positively or negatively charged with a valency of one, or uncharged. The numerical findings indicate a distinct solvation behavior with the occurrence of well-pronounced solvation shells whose composition significantly depends on the charge of the solute.

Comparing induced point-dipoles and Drude oscillators.

Classical Molecular Dynamics simulations describing electrostatic interactions only by point charges can be augmented by the inclusion of atomic polarisabilities modelling charge flexibility. Two widely used models, Drude oscillators and induced point-dipoles, are compared in a systematic study using their respective implementations in CHARMM and AMBER. The question of necessity and importance of polarisable hydrogen atoms is raised and two implementations, in an implicit or explicit manner, are compared to the case of non-polarisable hydrogen atoms.

A combined theoretical and experimental study of the influence of different anion ratios on lithium ion dynamics in ionic liquids.

In this paper, we investigate via experimental and simulation techniques the transport properties, in terms of total ionic conductivity and ion diffusion coefficients, of ionic liquids doped with lithium salts. They are composed of two anions, bis(fluorosulfonyl)imide (FSI) and bis(trifluoromethanesulfonyl)imide (TFSI), and two cations, N-ethyl-N-methylimidazolium (emim) and lithium ions. The comparison of the experimental results with the simulations shows very good agreement over a wide temperature range and a broad range of compositions.