Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer

The description of peptides and the use of molecular dynamics simulations to refine structures and investigate the dynamics on an atomistic scale are well developed. Through a consensus in this community over multiple decades, parameters were developed for molecular interactions that only require the sequence of amino-acids and an initial guess for the three-dimensional structure. The recent discovery of peptoids will require a retooling of the currently available interaction potentials in order to have the same level of confidence in the predicted structures and pathways as there is presently in the peptide counterparts. Here we present modeling of peptoids using a combination of ab initio molecular dynamics (AIMD) and atomistic resolution classical force field (FF) to span the relevant time and length scales. To properly account for the dominant forces that stabilize ordered structures of peptoids, namely steric-, electrostatic, and hydrophobic interactions mediated through side chain–side chain interactions in the FF model, those have to be first mapped out using high fidelity atomistic representations. A key feature here is not only to use gas phase quantum chemistry tools, but also account for solvation effects in the condensed phase through AIMD. One major challenge is to elucidate ion binding to charged or polar regions of the peptoid and its concomitant role in the creation of local order. Here, similar to proteins, a specific ion effect is observed suggesting that both the net charge and the precise chemical nature of the ion will need to be described

Quantifying the Molecular-Scale Aqueous Response to the Mica Surface

Modeling assembly at surfaces requires an understanding of the interactions between solutes, solvents, and surfaces at multiple scales. We investigated the solvent response (water structure and orientation) to a dielectric surface (mica) using density functional theory. A different water structure is engendered by replacing naturally occurring surface ions (K⁺) with H₃O⁺. We also validate classical models for the mica surface (CLAYFF) against DFT predictions. The detailed microscopic response of water to mica can be used as input into continuum models for the total interactions between two mica surfaces supporting a strong correlation between physicochemical phenomena at different scales

Peptoid Backbone Flexibilility Dictates Its Interaction with Water and Surfaces: A Molecular Dynamics Investigation

Peptoids are peptide-mimetic biopolymers that are easy to synthesize and adaptable for use in drugs, chemical scaffolds, and coatings. However, there is insufficient information about their structural preferences and interactions with the environment in various applications. We conducted a study to understand the fundamental differences between peptides and peptoids using molecular dynamics simulations with semiempirical (PM6) and empirical (AMBER) potentials, in conjunction with metadynamics enhanced sampling. From studies of single molecules in water and on surfaces, we found that sarcosine (model peptoid) is much more flexible than alanine (model peptide) in different environments. However, the sarcosine and alanine interact similarly with a hydrophobic or a hydrophilic. Finally, this study highlights the conformational landscape of peptoids and the dominant interactions that drive peptoids toward these conformations

Marcus Theory of Ion-Pairing

We present a theory for ion pair dissociation and association, motivated by the concepts of Marcus theory of electron transfer. Despite the extensive research on ion-pairing in many chemical and biological processes, much can be learned from the exploration of collective reaction coordinates. To this end, we explore two reaction coordinates, ion pair distance and coordination number. The study of the correlation between these reaction coordinates provides a new insight into the mechanism and kinetics of ion pair dissociation and association in water. The potential of mean force on these 2D surfaces computed from molecular dynamics simulations of different monovalent ion pairs reveal a Marcus-like mechanism for ion-pairing: Water molecules rearrange forming an activated coordination state prior to ion pair dissociation or association, followed by relaxation of the coordination state due to further water rearrangement. Like Marcus theory, we find the existence of an inverted region where the transition rates are slower with increasing exergonicity. This study provides a new perspective for the future investigations of ion-pairing and transport

Mixed Molecular and Dissociative Water Adsorption on Hydroxylated TiO₂(110): An Infrared Spectroscopy and Ab Initio Molecular Dynamics Study

We have investigated the structure and dynamics of water (D2O) adsorbed on TiO2(110) for coverages between 0 and 1 monolayer (ML) with infrared reflection absorption spectroscopy and ab initio molecular dynamics (AIMD) simulations. For D2O coverages as low as 0.4 ML on a hydroxylated surface, IR spectra typical of hydrogen-bonded chains of water molecules are observed. However, for D2O coverages ≥0.3 ML, a sharp, high-frequency peak is also observed in the p-polarized spectra that is red-shifted relative to the bridging hydroxyl peak. This new peak is not observed for water adsorbed on an oxidized surface. Based on the AIMD simulations and comparisons with previous IR spectra for TiO2 nanoparticles, the new peak is assigned to terminal hydroxyl groups produced by dissociative adsorption of some of the water on TiO2(110). The simulations indicate that water dissociation is related to the presence of defect electrons in the system, but not due to direct interactions between adsorbed water and bridging hydroxyls

Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics

Understanding specific ion effects on proteins remains a considerable challenge. <i>N</i>-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkaline earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the infrared (IR) shifts corresponding to the binding of either sodium or calcium to aqueous <i>N</i>-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous <i>N</i>-methylacetamide with different affinities and in different geometries. Because sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to <i>N</i>-methylacetamide in pure water

Ab Initio Molecular Dynamics Simulation of Proton Hopping in a Model Polymer Membrane

We report the results of ab initio molecular dynamics simulations of a model Nafion polymer membrane initially equilibrated using classical molecular dynamics simulations. We studied three hydration levels (λ) of 3, 9, and 15 H₂O/SO₃^– corresponding to dry, hydrated, and saturated fuel cell membrane, respectively. The barrier for proton transfer from the SO₃^––H₃O⁺ contact ion pair to a solvent-separated ion pair decreased from 2.3 kcal/mol for λ = 3 to 0.8 kcal/mol for λ = 15. The barrier for proton transfer between two water molecules was in the range from 0.7 to 0.8 kcal/mol for the λ values studied. The number of proton shuttling events between a pair of water molecules is an order of magnitude more than the number of proton hops across three distinct water molecules. The proton diffusion coefficient at λ = 15 is about 0.9 × 10^–5 cm²/s, which is in good agreement with experiment and our previous quantum hopping molecular dynamics simulations

Electrochemical Surface Potential Due to Classical Point Charge Models Drives Anion Adsorption to the Air–Water Interface

We demonstrate that the driving forces for ion adsorption to the air–water interface for point charge models result from both cavitation and a term that is of the form of a negative electrochemical surface potential. We carefully characterize the role of the free energy due to the <i>electrochemical</i> surface potential computed from simple empirical models and its role in ionic adsorption within the context of dielectric continuum theory. Our research suggests that the electrochemical surface potential due to point charge models provides anions with a significant driving force for adsoprtion to the air–water interface. This is contrary to the results of ab initio simulations that indicate that the <i>average electrostatic</i> surface potential should favor the desorption of anions at the air–water interface. The results have profound implications for the studies of ionic distributions in the vicinity of hydrophobic surfaces and proteins

The Role of Broken Symmetry in Solvation of a Spherical Cavity in Classical and Quantum Water Models

Insertion of a hard sphere cavity in liquid water breaks translational symmetry and generates an electrostatic potential difference between the region near the cavity and the bulk. Here, we clarify the physical interpretation of this potential and its calculation. We also show that the electrostatic potential in the center of small, medium, and large cavities depends very sensitively on the form of the assumed molecular interactions for different classical simple point-charge models and quantum mechanical DFT-based interaction potentials, as reflected in their description of donor and acceptor hydrogen bonds near the cavity. These differences can significantly affect the magnitude of the scalar electrostatic potential. We argue that the result of these studies will have direct consequences toward our understanding of the thermodynamics of ion solvation through the cavity charging process

Data_Sheet_1_Algal Colonization of Young Arctic Sea Ice in Spring.pdf

<p>The importance of newly formed sea ice in spring is likely to increase with formation of leads in a more dynamic Arctic icescape. We followed the ice algal species succession in young ice (≤ 0.27 m) in spring at high temporal resolution (sampling every second day for 1 month in May–June 2015) in the Arctic Ocean north of Svalbard. We document the early development of the ice algal community based on species abundance and chemotaxonomic marker pigments, and relate the young-ice algal community to the communities in the under-ice water column and the surrounding older ice. The seeding source seemed to vary between algal groups. Dinoflagellates were concluded to originate from the water column and diatoms from the surrounding older ice, which emphasizes the importance of older ice as a seeding source over deep oceanic regions and in early spring when algal abundance in the water column is low. In total, 120 taxa (80 identified to species or genus level) were recorded in the young ice. The protist community developed over the study period from a ciliate, flagellate, and dinoflagellate dominated community to one dominated by pennate diatoms. Environmental variables such as light were not a strong driver for the community composition, based on statistical analysis and comparison to the surrounding thicker ice with low light transmission. The photoprotective carotenoids to Chl a ratio increased over time to levels found in other high-light habitats, which shows that the algae were able to acclimate to the light levels of the thin ice. The development into a pennate diatom-dominated community, similar to the older ice, suggests that successional patterns tend toward ice-associated algae fairly independent of environmental conditions like light availability, season or ice type, and that biological traits, including morphological and physiological specialization to the sea ice habitat, play an important role in colonization of the sea ice environment. However, recruitment of ice-associated algae could be negatively affected by the ongoing loss of older ice, which acts as a seeding repository.</p