Elucidating the Role of Interfacial Hydrogen Bonds on Glass Transition Temperature Change in a Poly(Vinyl Alcohol)/SiO2 Polymer-Nanocomposite by Noncovalent Interaction Characterization and Atomistic Molecular Dynamics Simulations.

A thorough experimental investigation of polymer-glass transition temperature (Tg ) is performed on poly(vinyl alcohol) (PVA) and fumed silica nanoparticle (SiNP) composite. This is done together with atomistic molecular dynamics simulations of PVA systems in contact with bare and fully hydroxylated silica. Experimentally, PVA-SiNP composites are prepared by simple solution casting from aqueous solutions followed by its characterization using Fourier-transform infrared spectroscopy (FTIR), dynamic mechanical analysis (DMA), and dynamic scanning calorimetry (DSC). Both theoretical and experimentally deduced Tg are correlated with the presence of hydrogen bonding interactions involving OH functionality present on the surface of SiNP and along PVA polymer backbone. Further deconvolution of FTIR data show that inter-molecular hydrogen bonding present between PVA and SiNP surface is directly responsible for the increase in Tg . SiNP filler and PVA matrix ratio is also optimized for a desired Tg increase. An optimal loading of SiNP exists, in order to yield the maximum Tg increase arising from the competition between hydrogen bonding and crowding effect of SiNP.

On the Stability of Proteins Solvated in Imidazolium-Based Ionic Liquids Studied with Replica Exchange Molecular Dynamics.

The stability of two small proteins, one composed of three α-helices (α-peptide) and another composed of a ß-sheet (ß-peptide) solvated in five different ionic liquids (ILs), is analyzed using replica exchange molecular dynamics (REMD) simulations. ILs are composed of 1-butyl-3-methylimidazolium (BMIM) cations, paired with five different anions of varying hydrophilicity and size, namely, Cl-, NO3-, BF4-, PF6-, and NTf2-. REMD simulations greatly improve structure sampling and mitigate bias toward the initial folded peptide structure, thereby providing more adequate simulations to study protein stability. Cluster analysis, DSSP analysis and derivation of radius of gyration, interaction energies, and hydrogen bonding are used to quantify structural peptide changes in a large temperature range from 250 to 650 K. α-Peptides are least stable in ILs that contain small anions with localized negative charge, such as in BMIM-Cl and BMIM-NO3. Destabilization is caused by direct electrostatic interactions of anions with α-helices that are exposed to the solvent. This destabilization is characterized not by unfolded but instead by compact misfolded structures. Also, ß-peptides retain compact structures up to at least 400 K, below which unfolding hardly occurs. However, intrapeptide hydrogen bonds that constitute the ß-sheet are not exposed to the solvent. Therefore, ß-peptides are generally more stable than α-peptides in all considered ILs. Moreover, on contrary to α-peptides, ß-peptides are least stable in less polar ILs, such as BMIM-PF6 and BMIM-NTf2, because dissolving ß-sheets requires large structural changes of the peptide. Such transitions are energetically less opposed in ILs with weaker mutual ion coordination. A large interaction density within ILs, for example, in BMIM-Cl, is thus kinetically trapping ß-peptides in the original folded state. Additionally, in BMIM-BF4, interactions with ß-peptides are so weak, compared to an aqueous solvent, resulting in stronger interactions within the peptide, which extend ß-sheets, hence causing misfolding of a different kind. The results reveal how direct ion-peptide interactions and solvent reorganization energy in ILs are both crucial in determining protein stability. These insights could translate into guidelines for the design of new IL solvents with improved protein stability.

How the spontaneous insertion of amphiphilic imidazolium-based cations changes biological membranes: a molecular simulation study.

The insertion of 1-octyl-3-methylimidazolium cations (OMIM(+)) from a diluted aqueous ionic liquid (IL) solution into a model of a bacterial cell membrane is investigated. Subsequently, the mutual interactions of cations inside the membrane and their combined effect on membrane properties are derived. The ionic liquid solution and the membrane model are simulated using molecular dynamics in combination with empirical force fields. A high propensity of OMIM(+) for membrane insertion is observed, with a cation concentration at equilibrium inside the membrane 47 times larger than in the solvent. Once inserted, cations exhibit a weak effective attraction inside the membrane at a distance of 1.3 nm. At this free energy minimum, negatively charged phosphates of the phospholipids are sandwiched between two OMIM(+) to form energetically favorable OMIM(+)-phosphate-OMIM(+) types of coordination. The cation-cation association free energy is 5.9 kJ mol(-1), whereas the activation barrier for dissociation is 10.1 kJ mol(-1). Subsequently, OMIM(+) are inserted into the leaflet of the membrane bilayer that represents the extracellular side. The cations are evenly distributed with mutual cation distances according to the found optimum distance of 1.3 nm. Because of the short length of the cation alkyl chains compared to lipid fatty acids, voids are generated in the hydrophobic core of the membrane. These voids disorder the fatty acids, because they enable fatty acids to curl into these empty spaces and also cause a thinning of the membrane by 0.6 nm. Additionally, the membrane density increases at its center. The presence of OMIM(+) in the membrane facilitates the permeation of small molecules such as ammonia through the membrane, which is chosen as a model case for small polar solutes. The permeability coefficient of the membrane with respect to ammonia increases substantially by a factor of seven. This increase is caused by a reduction of the involved free energy barriers, which is effected by the cations through the thinning of the membrane and favorable interactions of the delocalized OMIM(+) charge with ammonia inside the membrane. Overall, the results indicate the antimicrobial effect of amphiphilic imidazolium-based cations that are found in various common ILs. This effect is caused by an alteration of the permeability of the bacterial membrane and other property changes.

Protein-like dynamics of polycarbonate polymers in water.

The dynamics of amphiphilic peptide-mimicking polycarbonate polymers are investigated, considering variations in polymer length, monomer sequence, and monomer modification. The polymers are simulated in aqueous solution with atomistic molecular dynamics simulations and an empirical force field. Various structural polymer properties, interaction strengths, and solvation free energies are derived. It is found that water is a less favorable solvent for these polymers than for peptides. Moreover, polymers readily adopt irreversibly a compact state that consists of a variety of distinct compact conformations that are adopted through frequent transitions. Furthermore, the polymers exhibit a strong propensity to form large aggregates. The driving forces for these processes appear to be a hydrophobic effect and more favorable polymer-solvent interactions of aggregates that overcome the otherwise strong mutual repulsion between the positively charged polymers. Replacing hydrophobic residues with polar side chains destabilizes the compact conformations of the polymers. Our results also indicate that the monomer sequence has little effect on the overall solvation properties of the polymer molecule. However, the sequence influences flexibility and compactness of the monomer in solution. Overall, the results of this work confirm the protein-like characteristics of these polymers and elucidate the role of single residues in influencing the structure and aggregation in aqueous solution.

Impact of ionic liquids in aqueous solution on bacterial plasma membranes studied with molecular dynamics simulations.

The impact of five different imidazolium-based ionic liquids (ILs) diluted in water on the properties of a bacterial plasma membrane is investigated using molecular dynamics (MD) simulations. Cations considered are 1-octyl-3-methylimidazolium (OMIM), 1-octyloxymethyl-3-methylimidazolium (OXMIM), and 1-tetradecyl-3-methylimidazolium (TDMIM), as well as the anions chloride and lactate. The atomistic model of the membrane bilayer is designed to reproduce the lipid composition of the plasma membrane of Gram-negative Escherichia coli. Spontaneous insertion of cations into the membrane is observed in all ILs. Substantially more insertions of OMIM than of OXMIM occur and the presence of chloride reduces cation insertions compared to lactate. In contrast, anions do not adsorb onto the membrane surface nor diffuse into the bilayer. Once inserted, cations are oriented in parallel to membrane lipids with cation alkyl tails embedded into the hydrophobic membrane core, while the imidazolium-ring remains mostly exposed to the solvent. Such inserted cations are strongly associated with one to two phospholipids in the membrane. The overall order of lipids decreased after OMIM and OXMIM insertions, while on the contrary the order of lipids in the vicinity of TDMIM increased. The short alkyl tails of OMIM and OXMIM generate voids in the bilayer that are filled by curling lipids. This cation induced lipid disorder also reduces the average membrane thickness. This effect is not observed after TDMIM insertions due to the similar length of cation alkyl chain and the fatty acids of the lipids. This lipid-mimicking behavior of inserted TDMIM indicates a high membrane affinity of this cation that could lead to an enhanced accumulation of cations in the membrane over time. Overall, the simulations reveal how cations are inserted into the bacterial membrane and how such insertions change its properties. Moreover, the different roles of cations and anions are highlighted and the fundamental importance of cation alkyl chain length and its functionalization is demonstrated.

How ion properties determine the stability of a lipase enzyme in ionic liquids: a molecular dynamics study.

The influence of eight different ionic liquid (IL) solvents on the stability of the lipase Candida antarctica lipase B (CAL-B) is investigated with molecular dynamics (MD) simulations. Considered ILs contain cations that are based either on imidazolium or guanidinium as well as nitrate, tetrafluoroborate or hexafluorophosphate anions. Partial unfolding of CAL-B is observed during high-temperature MD simulations and related changes of CAL-B regarding its radius of gyration, surface area, secondary structure, amount of solvent close to the backbone and interaction strength with the ILs are evaluated. CAL-B stability is influenced primarily by anions in the order NO(3)(-)≪ BF(4)(-) < PF(6)(-) of increasing stability, which agrees with experiments. Cations influence protein stability less than anions but still substantially. Long decyl side chains, polar methoxy groups and guanidinium-based cations destabilize CAL-B more than short methyl groups, other non-polar groups and imidazolium-based cations, respectively. Two distinct causes for CAL-B destabilization are identified: a destabilization of the protein surface is facilitated mostly by strong Coulomb interactions of CAL-B with anions that exhibit a localized charge and strong polarization as well as with polar cation groups. Surface instability is characterized by an unraveling of α-helices and an increase of surface area, radius of gyration and protein-IL total interaction strength of CAL-B, all of which describe a destabilization of the folded protein state. On the other hand, a destabilization of the protein core is facilitated when direct core-IL interactions are feasible. This is the case when long alkyl chains are involved or when particularly hydrophobic ILs induce major conformational changes that enable ILs direct access to the protein core. This core instability is characterized by a disintegration of ß-sheets, diffusion of ions into CAL-B and increasing protein-IL van der Waals interactions. This process describes a stabilization of the unfolded protein state. Both of these processes reduce the folding free energy and thus destabilize CAL-B. The results of this work clarify the impact of ions on CAL-B stabilization. An extrapolation of the observed trends enables proposing novel ILs in which protein stability could be enhanced further.

On the different roles of anions and cations in the solvation of enzymes in ionic liquids.

The solvation of the enzyme Candida antarctica lipase B (CAL-B) was studied in eight different ionic liquids (ILs). The influence of enzyme-ion interactions on the solvation of CAL-B and the structure of the enzyme-IL interface are analyzed. CAL-B and ILs are described with molecular dynamics (MD) simulations in combination with an atomistic empirical force field. The considered cations are based on imidazolium or guanidinium that are paired with nitrate, tetrafluoroborate or hexafluorophosphate anions. The interactions of CAL-B with ILs are dominated by Coulomb interactions with anions, while the second largest contribution stems from van der Waals interactions with cations. The enzyme-ion interaction strength is determined by the ion size and the magnitude of the ion surface charge. The solvation of CAL-B in ILs is unfavorable compared to water because of large formation energies for the CAL-B solute cages in ILs. The internal energy in the IL and of CAL-B increases linearly with the enzyme-ion interaction strength. The average electrostatic potential on the surface of CAL-B is larger in ILs than in water, due to a weaker screening of charged enzyme residues. Ion densities increased moderately in the vicinity of charged residues and decreased close to non-polar residues. An aggregation of long alkyl chains close to non-polar regions and the active site entrance of CAL-B are observed in one IL that involved long non-polar decyl groups. In ILs that contain 1-butyl-3-methylimidazolium cations, the diffusion of one or two cations into the active site of CAL-B occurs during MD simulations. This suggests a possible obstruction of the active site in these ILs. Overall, the results indicate that small ions lead to a stronger electrostatic screening within the solvent and stronger interactions with the enzyme. Also a large ion surface charge, when more hydrophilic ions are used, increases enzyme-IL interactions. An increase of these interactions destabilizes the enzyme and impedes enzyme solvation due to an increase in solute cage formation energies.