Ionic diffusion and proton transfer of MgCl2 and CaCl2 aqueous solutions: an ab initio study under electric field

Electromagnetic bioeffects: a multiscale molecular simulation perspective

Electromagnetic bioeffects remain an enigma from both the experimental and theoretical perspectives despite the ubiquitous presence of related technologies in contemporary life. Multiscale computational modelling can provide valuable insights into biochemical systems and predict how they will be perturbed by external stimuli. At a microscopic level, it can be used to determine what (sub)molecular scale reactions various stimuli might induce; at a macroscopic level, it can be used to examine how these changes affect dynamic behaviour of essential molecules within the crowded biomolecular milieu in living tissues. In this review, we summarise and evaluate recent computational studies that examined the impact of externally applied electric and electromagnetic fields on biologically relevant molecular systems. First, we briefly outline the various methodological approaches that have been employed to study static and oscillating field effects across different time and length scales. The practical value of such modelling is then illustrated through representative case-studies that showcase the diverse effects of electric and electromagnetic field on the main physiological solvent - water, and the essential biomolecules - DNA, proteins, lipids, as well as some novel biomedically relevant nanomaterials. The implications and relevance of the theoretical multiscale modelling to practical applications in therapeutic medicine are also discussed. Finally, we summarise ongoing challenges and potential opportunities for theoretical modelling to advance the current understanding of electromagnetic bioeffects for their modulation and/or beneficial exploitation in biomedicine and industry.

Water-Assisted Chemical Route Towards the Oxygen Evolution Reaction at the Hydrated (110) Ruthenium Oxide Surface: Heterogeneous Catalysis via DFT-MD and Metadynamics Simulations

Notwithstanding that RuO₂ is a promising catalyst for the oxygen evolution reaction (OER), a plethora of fundamental details on its catalytic properties are still elusive, severely limiting its large‐scale deployment. It is also established experimentally that corrosion and wettability of metal oxides can, in fact, enhance the catalytic activity for OER owing to the formation of a hydrated surface layer. However, the mechanistic interplay between surface wettability, interfacial water dynamics and OER across RuO₂, and what degree these processes are correlated are still debated. Herein, spin‐polarized Density Functional Theory Molecular Dynamics (DFT‐MD) simulations, coupled with advanced enhanced sampling methods in the well‐tempered metadynamics framework, are applied to gain a global understanding of RuO₂ aqueous interface (explicit water solvent) in catalyzing the OER, and hence possibly help in the design of novel catalysts in the context of photochemical water oxidation. The present study quantitatively assesses the free‐energy barriers behind the OER at the (110)‐RuO₂ catalyst surface revealing plausible pathways composing the reaction network of the O₂ evolution. In particular, OER is investigated at room temperature when such a surface is exposed to both gas‐phase and liquid‐phase water. Albeit a unique efficient pathway has been identified in the gas‐phase OER, a surprisingly lowest‐free‐energy‐requiring reaction route is possible when (110)‐RuO₂ is in contact with explicit liquid water. By estimating the free‐energy surfaces associated to these processes, we reveal a noticeable water‐assisted OER mechanism which involves a crucial proton‐transfer‐step assisted by the local water environment. These findings pave the way toward the systematic usage of DFT‐MD coupled with metadynamics techniques for the fine assessment of the activity of catalysts, considering finite‐temperature and explicit‐solvent effects.

Enhanced conductivity of water at the electrified air–water interface: a DFT-MD characterization

DFT-based molecular dynamics simulations of the electrified air–liquid water interface are presented, where a homogeneous field is applied parallel to the surface plane (i.e. parallel to the 2D-HBonded-Network/2DN).

Interactions between cyclic nucleotides and common cations: an ab initio molecular dynamics study

We present the first, to the best of our knowledge, ab initio molecular dynamics (AIMD) investigation on three aqueous solutions where an abasic cyclic nucleotide model is solvated in the presence of distinct cations (i.e., Na⁺, K⁺ and Mg²⁺). We elucidate the typical modalities of interaction between those ionic species and the nucleotide moiety by first-principles numerical simulations, starting from an inner-shell binding configuration on a time scale of 100 ps (total simulation time of ∼600 ps). Whereas the strong "structure-maker" Mg²⁺ is permanently bound to one of the two oxygen atoms of the phosphate group of the nucleotide model, Na⁺ and K⁺ show binding times τ_b of 65 ps and 10-15 ps, respectively, thus reflecting their chemical nature in aqueous solutions. Furthermore, we qualitatively relate these findings to approximate free-energy barriers of the cations' unbinding obtained by means of exploratory well-tempered metadynamics. With the aim of shedding light on the features of commonly employed force-fields (FFs), classical MD simulations (almost 200 trajectories with a total simulation time of ∼18 μs) using the biomolecular AMBER FF are also reported. By choosing several combinations of the parametrization for the water environment (i.e., TIP3P, SPC/E and OPC) and cations (i.e., Joung-Cheatham, Li-Merz 12-6 and Li-Merz 12-6-4), we found significant differences in the radial distribution functions and residence times compared to the ab initio results. The Na⁺ and K⁺ ions wrongly show quasi-identical radial distribution functions and the Li & Merz 12-6-4 Lennard-Jones parameters for Mg²⁺ were found to be essential in quickly reaching the binding state consistent with AIMD.