Structure and dynamics of the hyaluronan oligosaccharides and their solvation shell in water: organic mixed solvents

Concentration Fluctuation/Microheterogeneity Duality Illustrated with Aqueous 1,4-Dioxane Mixtures

“…In fact, the TIP3P model smears these fundamental differences of the real water model, which are responsible for the typical features of this liquid, such as the hydrophobic effect in particular, which has been initially described as a direct consequence of the existence of microscopic patches of tetrahedrally linked water and disordered water, a model which appears to be still in use. , This smearing may explain why this model is popular in context where the strong self-heterogeneity of water may come as an obstacle in large-scale simulation of complex systems. − …”

“…Further developments into this conjecture would necessitate the development of a mesoscale description of such systems, which means no-coarse graining description where the fluctuation aspect of such self-assembled structure would be irremediably lost. Instead, it would be desirable to build a mesoscale description which would preserve the duality of concentration fluctuation and microsegregation, possibly through field theoretic techniques. , We conjecture that such approaches would allow a theoretical study of complex systems such as those in refs – , which are currently studied by computer simulations using forgiving water models, which are a way to avoid cumbersome water hydrogen bond network problems.…”

“…It is routine nowadays to read papers reporting simulations of complex molecular mixtures, involving mixtures of aqueous and organic solvents, together with ions, co-ions, and with much larger molecules, such as enzymes, and in the perspective of simulating realistic liquids, such as those involved in biological or pharmaceutical systems. , The recent interest in the structure of the solvation shell of hyaluronan oligosaccharides in aqueous organic solvent mixtures is among such modern simulation topics. − On the opposite side of the spectrum in terms of complexity, there are still studies of liquids such as alcohols or binary aqueous mixtures, with a particular focus on their microstructure. The computer simulations of these latter systems reveal appreciable model dependence, which often focuses on minute studies in molecular details.…”

“…In the present paper, we would like to examine closer binary mixtures of aqueous dioxane, which has been used lately as an aqueous organic solvent in the study of more complex mixtures involving hyaluronan and ions. − In particular, we are interested in why these works choose the TIP3P model for water, rather than more modern water models, such as SPC/E, TIP4P, TIP4P-2005, or TIP4P-ew . This question will be answered in the Discussion section below.…”

Solvent effects on carbohydrate transformation: insights into chemical pathway modulation

“…This was attributed to more frequent interactions between HA and Na + cations, resulting in repeated shortening of the chains. 188 Wang et al 189 investigated interactions between the 4-Omethyl glucuronic acid xylan (Gxyl) atoms and DES at various temperatures and HBA/HBD ratios using molecular dynamics simulations. The radial distribution function plot in Fig.…”