Ions’ motion in water

Abstract

Over the decades, a great deal of attention has been focused on the solvation and transport properties of small rigid monatomic ions such as Na + , K + , Li + , Cl − , and Br − due to their importance in physical chemistry. Much less attention has been devoted to polyatomic ions although many polyatomic ions (such as nitrate, acetate, sulfate, and ammonium) are of great importance in biological and chemical processes. While the translational diffusion of smaller rigid ions shows the remarkable nonmonotonic dependence on inverse ion size (known as the "breakdown of Walden product"), the intermediate-to large-sized polyatomic ions (such as nitrate, acetate, and sulfate) exhibit different anomalies pointed out only recently. In this Perspective article, we provide an overview of how rotational diffusion and translational diffusion of these ions themselves are coupled to translational and rotational motions of water molecules. We discuss how diffusion of polyatomic ions is different from that of monatomic ions due to the rotational self-motion of the former that enhances diffusion in specific cases because of symmetry. While a continuum hydrodynamic model fails to describe the motion of polyatomic ions, we discuss how a mode-coupling theory approach can capture many aspects of this coupling between the solute ion and solvent water. We discuss how ionic mobility in water and other dipolar solvents are intimately connected to the dipolar solvation dynamics, in particular to its ultrafast component. We point out how the usual thinking on the relation between the diffusion and entropy needs to be modified in the case of ion diffusion.

Insulin dissociates by diverse mechanisms of coupled unfolding and unbinding

“…The monomers rotate relative to each other in opposite ways along the two limiting paths. Previous studies 30,31 reported rotation of the interfacial β strands relative to each other, as characterized by a pseudodihedral angle (here denoted Φ β ) defined by the C α atoms of Tyr B26 , Phe B24 , Tyr B 26 , and Phe B 24 , where the primes distinguish one monomer from the other. In addition to Φ β , we calculate the pseudodihedral angle (Φ α ) between the geometric centers of the backbone atoms of the residues that define the dimeric interfacial alpha helices: Ser B9 -Leu B11 , Leu B17 -Cys B19 , Leu B 17 -Cys B 19 , and Ser B 9 -Leu B 11 .…”

“…In particular, Figure 8 of ref. 31 indicates a path which begins with a slight increase in Φ β coupled to an increase in β from approximately 0.6 to 1.1 nm. This initial step is followed by a 30 • decrease in Φ β coupled to a return to a dimer-like β (near 0.6 nm) as the dissociation progresses.…”

“…Recently, Bagchi and coworkers used metadynamics to compute the free energy as a function of the monomer-monomer center-of-mass distance and the number of intermolecular contacts, subject to restraints on the radii of gyration of the monomers. [30][31][32] They identified a single major pathway of dissociation in which the number of intermolecular contacts was first observed to markedly decrease before the center-of mass distance increased. Through additional collective variables, they also characterized the protein-protein and protein-solvent interactions of Phe B24 and Tyr B26 , indicating that conformational rearrangement and intramonomeric unfolding are both coupled to the dissociation.…”

Hydration Structure and Dynamics of the Favipiravir Antiviral Drug: A Molecular Modelling Approach

“…Therefore, rotational dynamics can be very important from the study of pharmacokinetics, although they are often neglected and attention is primarily paid on the translational dynamics. In the case of solutes dissolved in water, the rotational dynamics is strongly affected by their local environment and particularly the HB network around them 50 . Translational diffusion of these solutes is often coupled to their rotational dynamics which in turn are coupled to similar motions of the surrounding water molecules 50 .…”

“…In the case of solutes dissolved in water, the rotational dynamics is strongly affected by their local environment and particularly the HB network around them 50 . Translational diffusion of these solutes is often coupled to their rotational dynamics which in turn are coupled to similar motions of the surrounding water molecules 50 . The reorientational dynamics of the Favipiravir in the present study was also studied in terms of the Legendre reorientational time correlation functions for specific intramolecular vectors of the cation:…”