The global practical implementation of proton exchange membrane fuel cells (PEMFCs) heavily relies on the advancement of highly effective platinum (Pt)-based electrocatalysts for the oxygen reduction reaction (ORR). To achieve high ORR performance, electrocatalysts with highly accessible reactive surfaces are needed to promote the uncovering of active positions for easy mass transportation. In this critical review, we introduce different approaches for the emerging development of effective ORR electrocatalysts, which offer high activity and durability. The strategies, including morphological engineering, geometric configuration modification via supporting materials, alloys regulation, core-shell, and confinement engineering of single atom electrocatalysts (SAEs), are discussed in line with the goals and requirements of ORR performance enhancement. We review the ongoing development of Pt electrocatalysts based on the syntheses, nanoarchitecture, electrochemical performances, and stability. We eventually explore the obstacles and research directions on further developing more effective electrocatalysts.

Ionic liquids (ILs) are a class of salts existing in the liquid state below 100 degrees C, possessing low volatility, high thermal stability as well as many highly attractive solvent and electrochemical capabilities, etc., making them highly tunable for a great variety of applications, such as lubricants, electrolytes, and soft functional materials. In many applications, ILs are first either physi- or chemisorbed on a solid surface to successively create more functional materials. The functions of ILs at solid surfaces can differ considerably from those of bulk ILs, mainly due to distinct interfacial layers with tunable structures resulting in new ionic liquid interface layer properties and enhanced performance. Due to an almost infinite number of possible combinations among the cations and anions to form ILs, the diversity of various solid surfaces, as well as different external conditions and stimuli, a detailed molecular-level understanding of their structure-property relationship is of utmost significance for a judicious design of IL-solid interfaces with appropriate properties for task-specific applications. Many experimental techniques, such as atomic force microscopy, surface force apparatus, and so on, have been used for studying the ion structuring of the IL interface layer. Molecular Dynamics simulations have been widely used to investigate the microscopic behavior of the IL interface layer. To interpret and clarify the IL structure and dynamics as well as to predict their properties, it is always beneficial to combine both experiments and simulations as close as possible. In another theoretical model development to bridge the structure and properties of the IL interface layer with performance, thermodynamic prediction & property modeling has been demonstrated as an effective tool to add the properties and function of the studied nanomaterials. Herein, we present recent findings from applying the multiscale triangle experiment-simulation-thermodynamic modeling in the studies of ion structuring of ILs in the vicinity of solid surfaces, as well as how it qualitatively and quantitatively correlates to the overall ILs properties, performance, and function. We introduce the most common techniques behind experiment-simulation-thermodynamic modeling and how they are applied for studying the IL interface layer structuring, and we highlight the possibilities of the IL interface layer structuring in applications such as lubrication and energy storage. Integrative experiment-simulation-thermodynamic modeling is highly demanded for qualitatively and quantitatively correlating the ionic liquids interface layer structuring to the overall properties, performance, and function.

This work combined gold colloid probe atomic force microscopy (AFM) with a quartz crystal microbalance (QCM) to accurately quantify the molecular interactions of fluorine-free phosphonium-based ionic liquids (ILs) with gold electrode surfaces. First, the interactions of ILs with the gold electrode per unit area (𝐹′_A𝐹, N/m²) were obtained via the force–distance curves measured by gold probe AFM. Second, a QCM was employed to detect the IL amount to acquire the equilibrium number of IL molecules adsorbed onto the gold electrode per unit area (N_IL, Num/m²). Finally, the quantified molecular interactions of ILs with the gold electrode (F₀, nN/Num) were estimated. F₀ is closely related to the IL composition, in which the IL with the same anion but a longer phosphonium cation exhibits a stronger molecular interaction. The changes in the quantified interactions of gold with different ILs are consistent with the interactions predicted by the extended Derjaguin–Landau–Verwey–Overbeek theory, and the van der Waals interaction was identified as the major contribution of the overall interaction. The quantified molecular interaction is expected to enable the direct experimental-derived interaction parameters for molecular simulations and provide the virtual design of novel ILs for energy storage applications.

Natural polyamines play a fundamental role in the cell cycle. Despite being recognized as the most abundant organic counterions of DNA in the cell nucleus, their interactions with DNA have not been fully characterized. In a recent work [S. Perepelytsya, T. Vasiliu, A. Laaksonen, L. Engelbrecht, G. Brancato, and F. Mocci, J. Molec. Liq. 389, 122828 (2023)], we have shown how the interactions between spermidine³⁺ and the DNA double helix induce significant conformational variations in the polyamine molecule. Specifically, we found that DNA induces conformations that are not observed in solution. Following that study, we present here a detailed investigation of the most compact conformation of the polyamine, analyzing its connection to the interaction with the DNA duplex. The analysis reveals that anomalous bent conformations of the spermidine³⁺ molecule result from the interaction of all three amino groups of the polyamine with the DNA phosphate groups on the minor groove side of the double helix. The changes in dihedral angles of the bent spermidine³⁺ molecule can be explained in terms of conformational transformations of six- and seven-membered rings, analogous to cyclohexane and cycloheptane. The analysis of the position of spermidine³⁺ molecule along the DNA surface reveals a sequence specificity of this binding mode with a marked preference for the narrow minor groove of A-tracts. The formation of the anomalous bent conformations of spermidine³⁺ in the complex with the DNA double helix is expected to be of paramount importance in understanding the mechanisms underlying DNA’s biological function.

Natural polyamines play a key role in many biological processes, particularly in the stabilization of DNA double helix structure in the cell nucleus. Among others, the conformational flexibility of polyamines, such as spermidine, is an essential property for the formation of complexes with DNA. Yet, the characterization of the conformational space of polyamines has not been fully elucidated. Using atomistic molecular dynamics (MD) simulations, we present a detailed study of the conformational space of spermidine³⁺ both in solution and in interaction with DNA. We have identified more than 2000 distinct conformations, which can be grouped into seven modes. Notably, the relative population of these modes is highly affected by the interaction of spermidine³⁺ with DNA, thus representing a fingerprint of complex formation. In particular, three of the seven dihedral angles of spermidine³⁺ are predominantly in trans conformation (with or without DNA), while the other four dihedral angles are observed to switch between trans, gauche⁺ and gauche^-. The preference between the latter conformational states was analyzed in terms of the distinct energy contributions composing the potential energy. Overall, our results shed light on the conformational equilibrium and dynamics of spermidine³⁺, which in turn is important for understanding the nature of its interaction with DNA.

SARS-CoV-2 remains a health threat with the continuous emergence of new variants. This work aims to expand the knowledge about the SARS-CoV-2 receptor-binding domain (RBD) interactions with cell receptors and monoclonal antibodies (mAbs). By using constant-pH Monte Carlo simulations, the free energy of interactions between the RBD from different variants and several partners (Angiotensin-Converting Enzyme-2 (ACE2) polymorphisms and various mAbs) were predicted. Computed RBD-ACE2-binding affinities were higher for two ACE2 polymorphisms (rs142984500 and rs4646116) typically found in Europeans which indicates a genetic susceptibility. This is amplified for Omicron (BA.1) and its sublineages BA.2 and BA.3. The antibody landscape was computationally investigated with the largest set of mAbs so far in the literature. From the 32 studied binders, groups of mAbs were identified from weak to strong binding affinities (e.g. S2K146). These mAbs with strong binding capacity and especially their combination are amenable to experimentation and clinical trials because of their high predicted binding affinities and possible neutralization potential for current known virus mutations and a universal coronavirus.

Diffusion-driven rotation in cholesteric liquid crystals has been studied using molecular dynamics simulation. Then a chemical potential gradient parallel to the cholesteric axis induces a torque that rotates the director at a constant rate around this axis, besides driving a mass current. An equimolar mixture of Gay–Berne ellipsoids and Lennard-Jones spheres was used as the molecular model. In order to keep the system homogeneous, the color conductivity algorithm was used to apply a color field instead of a chemical potential gradient to drive a mass current. Then the particles are given a color charge that interacts with a color field in the same way as with an electric field, but these charges do not interact with each other. This algorithm is often used to calculate the mutual diffusion coefficient. In the above liquid crystal model, it was found that the color field induces a torque that rotates the director at a constant rate around the cholesteric axis in addition to driving a mass current. The phenomenon was quantified by calculating the cross-coupling coefficient between the color field and the director angular velocity. The results were cross-checked by using a director rotation algorithm to exert a torque to rotate the director at a constant rate. Besides rotation of the director, this resulted in a mass current parallel to the cholesteric axis. The cross-coupling coefficient between the torque and the mass current was equal to the cross-coupling coefficient between the color field and the director rotation rate within a statistical uncertainty of 10 percent, thus fulfilling the Onsager reciprocity relations. As a further cross-check, these cross-coupling coupling coefficients, the color conductivity, and the twist viscosity were calculated by evaluating the corresponding Green–Kubo relations. Finally, it was noted that the orientation of the cholesteric axis parallel to the color field is the one that minimizes the irreversible energy dissipation rate. This is in accordance with a theorem stating that this quantity is minimal in the linear regime of a nonequilibrium steady state.

The electrical conductivities of the dilute solutions containing ionic liquids (1-hexyl-3-methylimidazolium chloride [Hmim]Cl, 1-hexyl-3-methylimidazolium bromide [Hmim]Br, and 1-hexyl-3-methylimidazolium iodide [Hmim]I) with water and isopropanol were determined in the temperature ranging from 293.15 to 313.15 K. The liquid densities of all binary mixtures were further determined for model parameterization. In theoretical modeling, the limiting molar conductivities Λ⁰(T) were first obtained using the Debye-Hückel-Onsager (DHO) equation, and thereafter the ion association constants K_A(T) were determined using the Shedlovsky equation. The effects of temperature, dielectric constant, and anion size on the values of Λ⁰(T) and K_A(T) were systematically discussed. The Eyring activation enthalpy of charge transport ∆H^* and the Walden values Λ⁰η for all studied binary mixtures were obtained from the temperature-dependent Λ⁰(T).

Intracellular calcium signaling is essential for many cellular processes, including store-operated Ca²⁺ entry (SOCE), which is initiated by stromal interaction molecule 1 (STIM1) detecting endoplasmic reticulum (ER) Ca²⁺ depletion. STIM1 is also activated by temperature independent of ER Ca²⁺ depletion. Here we provide evidence, from advanced molecular dynamics simulations, that EF-SAM may act as a true temperature sensor for STIM1, with the prompt and extended unfolding of the hidden EF-hand subdomain (hEF) even at slightly elevated temperatures, exposing a highly conserved hydrophobic Phe108. Our study also suggests an interplay between Ca²⁺ and temperature sensing, as both, the canonical EF-hand subdomain (cEF) and the hidden EF-hand subdomain (hEF), exhibit much higher thermal stability in the Ca²⁺-loaded form compared to the Ca²⁺-free form. The SAM domain, surprisingly, displays high thermal stability compared to the EF-hands and may act as a stabilizer for the latter. We propose a modular architecture for the EF-hand-SAM domain of STIM1 composed of a thermal sensor (hEF), a Ca²⁺ sensor (cEF), and a stabilizing domain (SAM). Our findings provide important insights into the mechanism of temperature-dependent regulation of STIM1, which has broad implications for understanding the role of temperature in cellular physiology.

A 30% (w/w) [ImCl][EDA]-based deep eutectic solvent (DES) in water has demonstrated superior gravimetric CO2 uptake with desirable kinetics, lower regeneration enthalpy, and lesser degradation than the industrially popular 30% monoethanolamine (MEA) solution.