Visualization of Self-Assembly and Hydration of a β-Hairpin through Integrated Small and Wide-Angle Neutron Scattering

Fundamental understanding of the structure and assembly of nanoscale building blocks is crucial for the development of novel biomaterials with defined architectures and function. However, accessing self-consistent structural information across multiple length scales is challenging. This limits opportunities to exploit atomic scale interactions to achieve emergent macroscale properties. In this work we present an integrative small- and wide-angle neutron scattering approach coupled with computational modeling to reveal the multiscale structure of hierarchically self-assembled β hairpins in aqueous solution across 4 orders of magnitude in length scale from 0.1 Å to 300 nm. Our results demonstrate the power of this self-consistent cross-length scale approach and allows us to model both the large-scale self-assembly and small-scale hairpin hydration of the model β hairpin CLN025. Using this combination of techniques, we map the hydrophobic/hydrophilic character of this model self-assembled biomolecular surface with atomic resolution. These results have important implications for the multiscale investigation of aqueous peptides and proteins, for the prediction of ligand binding and molecular associations for drug design, and for understanding the self-assembly of peptides and proteins for functional biomaterials.

Quantification and Distribution of Three Types of Hydrogen Bonds in Mixtures of an Ionic Liquid with the Hydrogen-Bond-Accepting Molecular Solvent DMSO Explored by Neutron Diffraction and Molecular Dynamics Simulations

The concept of hydrogen bonding is celebrating its 100th birthday. Hydrogen bonds (H-bonds) play a key role in the structure and function of biological molecules, the strength of materials, and molecular binding. Herein, we study H-bonding in mixtures of a hydroxyl-functionalized ionic liquid with the neutral, H-bond-accepting molecular liquid dimethylsulfoxide (DMSO) using neutron diffraction experiments and molecular dynamics simulations. We report the geometry, strength, and distribution of three different types of H-bond OH···O, formed between the hydroxyl group of the cation and either the oxygen atom of another cation, the counteranion, or the neutral molecule. Such a variety of different strengths and distributions of H-bonds in one single mixture could hold the promise of providing solvents with potential applications in H-bond-related chemistry, for example, to alter the natural selectivity patterns of catalytic reactions or the conformation of catalysts.

Bridging Structure, Dynamics, and Thermodynamics: An Example Study on Aqueous Potassium Halides

Aqueous salt systems are ubiquitous in all areas of life. The ions in these solutions impose important structural and dynamic perturbations to water. In this study, we employ a combined neutron scattering, nuclear magnetic resonance, and computational modeling approach to deconstruct ion-specific perturbations to water structure and dynamics and shed light on the molecular origins of bulk thermodynamic properties of the solutions. Our approach uses the atomistic scale resolution offered to us by neutron scattering and computational modeling to investigate how the properties of particular short-ranged microenvironments within aqueous systems can be related to bulk properties of the system. We find that by considering only the water molecules in the first hydration shell of the ions that the enthalpy of hydration can be determined. We also quantify the range over which ions perturb water structure by calculating the average enthalpic interaction between a central halide anion and the surrounding water molecules as a function of distance and find that the favorable anion-water enthalpic interactions only extend to ∼4 Å. We further validate this by showing that ions induce structure in their solvating water molecules by examining the distribution of dipole angles in the first hydration shell of the ions but that this perturbation does not extend into the bulk water. We then use these structural findings to justify mathematical models that allow us to examine perturbations to rotational and diffusive dynamics in the first hydration shell around the potassium halide ions from NMR measurements. This shows that as one moves down the halide series from fluorine to iodine, and ionic charge density is therefore reduced, that the enthalpy of hydration becomes less negative. The first hydration shell also becomes less well structured, and rotational and diffusive motions of the hydrating water molecules are increased. This reduction in structure and increase in dynamics are likely the origin of the previously observed increased entropy of hydration as one moves down the halide series. These results also suggest that simple monovalent potassium halide ions induce mostly local perturbations to water structure and dynamics.

The Double-Faced Nature of Hydrogen Bonding in Hydroxy-Functionalized Ionic Liquids Shown by Neutron Diffraction and Molecular Dynamics Simulations

We characterize the double-faced nature of hydrogen bonding in hydroxy-functionalized ionic liquids by means of neutron diffraction with isotopic substitution (NDIS), molecular dynamics (MD) simulations, and quantum chemical calculations. NDIS data are fit using the empirical potential structure refinement technique (EPSR) to elucidate the nearest neighbor H⋅⋅⋅O and O⋅⋅⋅O pair distribution functions for hydrogen bonds between ions of opposite charge and the same charge. Despite the presence of repulsive Coulomb forces, the cation-cation interaction is stronger than the cation-anion interaction. We compare the hydrogen-bond geometries of both "doubly charged hydrogen bonds" with those reported for molecular liquids, such as water and alcohols. In combination, the NDIS measurements and MD simulations reveal the subtle balance between the two types of hydrogen bonds: The small transition enthalpy suggests that the elusive like-charge attraction is almost competitive with conventional ion-pair formation.

Theoretical Calculation of the Thermodynamic Properties of 20 Amino Acid Ionic Liquids

The thermodynamic properties of gas-phase amino acid ionic liquids (AAILs) containing 20 amino acids ([AA]^-) and 1-ethyl-3-methylimidazolium ([Emim]⁺) are studied using a combination of the ab initio method, molecular dynamics simulations, Born-Haber (BH) cycle analysis, and isodesmic reactions. The M06-2X/TZVP method is used to explore the structure and dissociation enthalpies of [Emim][AA] by considering dispersion interaction, and the MP2/Aug-cc-pVTZ method is used to correct these enthalpies. The vaporization enthalpies of all 20 AAILs are calculated by molecular dynamics simulations, and the gas-phase formation enthalpies (Δ_f H) of the 20 [AA]^- anions and [Emim]⁺ cation are calculated by the density functional theory/M06-2X method and isodesmic reaction approaches. To obtain the Δ_f H of the AAILs, interconnections in the corresponding BH cycles are evaluated. A systematic study of the 20 [Emim][AA] ion pairs provides some initial factors contributing to the thermodynamic properties of AAILs: including length of the alkyl chain, interatomic electronic effects, steric repulsion from the cyclic group, and H-bonds formed by functional groups. Generally speaking, the results of this work provide insights into the structure-property relationships of not only ILs but also any ionic or molecular substance.

Solvation Structure of Uracil in Ionic Liquids

The local solvation environment of uracil dissolved in the ionic liquid 1-ethyl-3-methylimidazolium acetate has been studied using neutron diffraction techniques. At solvent:solute (ionic liquid:uracil) ratios of 3:1 and 2:1, little perturbation of the ion-ion correlations compared to those of the neat ionic liquid are observed. We find that solvation of the uracil is driven predominantly by the acetate anion of the solvent. While short distance correlations exist between uracil and the imidazolium cation, the geometry of these contacts suggest that they cannot be considered as hydrogen bonds, in contrast to other studies by Araújo et al. (J. M. Araújo, A. B. Pereiro, J. N. Canongia-Lopes, L. P. Rebelo, I. M. Marrucho, J. Phys. Chem. B 2013, 117, 4109-4120). Nevertheless, this combination of interactions of the solute with both the cation and anion components of the solvents helps explain the high solubility of the nucleobase in this media. In addition, favourable uracil-uracil contacts are observed, of similar magnitude to those between cation and uracil, and are also likely to aid dissolution.

Micro- and mesoscopic structural features of a bio-based choline-amino acid ionic liquid

The structure of bio-based choline–norleucine ionic liquid has been explored by means of combined x-ray diffraction and MD simulations.