Ion aggregation in high salt solutions. IV. Graph-theoretical analyses of ion aggregate structure and water hydrogen bonding network

Molecular Aggregation Behavior and Microscopic Heterogeneity in Binary Osmolyte-Water Solutions

Osmolytes, small organic compounds, play a key role in modulating the protein stability in aqueous solutions, but the operating mechanism of the osmolyte remains inconclusive. Here, we attempt to clarify the mode of osmolyte action by quantitatively estimating the microheterogeneity of osmolyte-water mixtures with the aid of molecular dynamics simulation, graph theoretical analysis, and spatial distribution measurement in the four osmolyte solutions of trimethylamine-N-oxide (TMAO), tetramethylurea (TMU), dimethyl sulfoxide, and urea. TMAO, acting as a protecting osmolyte, tends to remain isolated with no formation of osmolyte aggregates while preferentially interacting with water, but there is a strong aggregation propensity in the denaturant TMU solution, characterized by favored hydrophobic interactions between TMU molecules. Taken together, the mechanism of osmolyte action on protein stability is proposed as a comprehensive one that encompasses the direct interactions between osmolytes and proteins and indirect interactions through the regulation of water properties in the osmolyte-water mixtures.

Molecular heterogeneity in aqueous cosolvent systems

Aqueous cosolvent systems (ACoSs) are mixtures of small polar molecules such as amides, alcohols, dimethyl sulfoxide, or ions in water. These liquids have been the focus of fundamental studies due to their complex intermolecular interactions as well as their broad applications in chemistry, medicine, and materials science. ACoSs are fully miscible at the macroscopic level but exhibit nanometer-scale spatial heterogeneity. ACoSs have recently received renewed attention within the chemical physics community as model systems to explore the relationship between intermolecular interactions and microscopic liquid-liquid phase separation. In this perspective, we provide an overview of ACoS spatial segregation, dynamic heterogeneity, and multiscale relaxation dynamics. We describe emerging approaches to characterize liquid microstructure, H-bond networks, and dynamics using modern experimental tools combined with molecular dynamics simulations and network-based analysis techniques.

Insights into the hydrogen bond network topology of phosphoric acid and water systems

Phosphoric acid and its mixtures with water are some of the best proton conducting materials known to science. Although the proton conductivity in pure phosphoric acid decreases upon external doping with excess H+ or OH-, the addition of water improves it substantially. A number of experimental and theoretical studies indicate that these systems form a very special case of hydrogen bond networks which not only facilitate fast proton transport but also show a number of other interesting properties such as glass forming ability. In this work, we present the molecular dynamics simulation results of the H3PO4-H2O system over the entire concentration range. The hydrogen bond networks were analyzed in terms of conventional microscopic as well as topological properties based on graph and network theory. The results show that the hydrogen bond network of H3PO4 is fundamentally different from that of H2O. On average, each phosphoric acid molecule tends to form more and stronger hydrogen bonds than water which leads to a much more connected and clustered network showing small-world properties which are absent in pure water. Moreover, these hydrogen bond network properties persist in the H3PO4-H2O mixtures as well, even at relatively high water contents. Finally, many of the physical properties such as molecular diffusion coefficients seem to be also intimately related to the network topological properties and follow similar trends with respect to system content. These results strongly indicate that many important properties such as proton transport in phosphoric acid and its aqueous systems are fundamentally related to their hydrogen bond network topology and might hold the key for their ultimate molecular understanding.

Understanding alcohol aggregates and the water hydrogen bond network towards miscibility in alcohol solutions: graph theoretical analysis

Under ambient conditions, methanol and ethanol are miscible in water at all concentrations, while n-butanol is partially miscible. This is the first study to quantitatively examine the miscibility of butanol and compare with miscible alcohols by employing molecular dynamics simulations and graph theoretical analysis of three water-alcohol mixtures at various concentrations. We show how distinct alcohol aggregates are formed, thereby affecting the water structure, which established the relationship between the morphological structure of the aggregates and the miscibility of the alcohol in aqueous solution. The aggregates of methanol and ethanol in highly concentrated solutions form an extended H-bond network that intertwines well with the H-bond network of water. n-Butanol tends to self-associate and form large aggregates, while such aggregates are segregated from water. Graph theoretical analysis revealed that the alcohol aggregates of methanol and ethanol solutions have a morphological structure different from that of n-butanol, although there is no significant difference in morphology between the three pure alcohols. These two distinct alcohol aggregates are classified as water-compatible and water-incompatible depending upon their interaction with the water H-bond network, and their effect on the water structure was investigated. Our study reveals that the water-compatible network of alcohol aggregates in methanol and ethanol solutions disrupts the water H-bond networks, while the water-incompatible network of n-butanol aggregates does not considerably alter the water structure, which is consistent with the experimental results. Furthermore, we propose that miscible alcohols form water-compatible networks in binary aqueous systems while partially miscible alcohols form water-incompatible networks. The bifurcating hypothesis on the alcohol aggregation behavior in liquid water is of critical use to understand the fundamental issues such as solubility and phase separation in solution systems.

Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis

It has long been observed that trimethylamine N-oxide (TMAO) and urea demonstrate dramatically different properties in a protein folding process. Even with the enormous theoretical and experimental research work on these two osmolytes, various aspects of their underlying mechanisms still remain largely elusive. In this paper, we propose to use the weighted persistent homology to systematically study the osmolytes molecular aggregation and their hydrogen-bonding network from a local topological perspective. We consider two weighted models, i.e., localized persistent homology (LPH) and interactive persistent homology (IPH). Boltzmann persistent entropy (BPE) is proposed to quantitatively characterize the topological features from LPH and IPH, together with persistent Betti number (PBN). More specifically, from the localized persistent homology models, we have found that TMAO and urea have very different local topology. TMAO is found to exhibit a local network structure. With the concentration increase, the circle elements in these networks show a clear increase in their total numbers and a decrease in their relative sizes. In contrast, urea shows two types of local topological patterns, i.e., local clusters around 6 Å and a few global circle elements at around 12 Å. From the interactive persistent homology models, it has been found that our persistent radial distribution function (PRDF) from the global-scale IPH has same physical properties as the traditional radial distribution function. Moreover, PRDFs from the local-scale IPH can also be generated and used to characterize the local interaction information. Other than the clear difference of the first peak value of PRDFs at filtration size 4 Å, TMAO and urea also shows very different behaviors at the second peak region from filtration size 5 Å to 10 Å. These differences are also reflected in the PBNs and BPEs of the local-scale IPH. These localized topological information has never been revealed before. Since graphs can be transferred into simplicial complexes by the clique complex, our weighted persistent homology models can be used in the analysis of various networks and graphs from any molecular structures and aggregation systems.

GCIceNet: a graph convolutional network for accurate classification of water phases

We develop GCIceNet, which automatically generates machine-based order parameters for classifying the phases of water molecules via supervised and unsupervised learning with graph convolutional networks.

Persistent homology analysis of osmolyte molecular aggregation and their hydrogen-bonding networks

Dramatically different patterns can be observed in the topological fingerprints for hydrogen-bonding networks from two types of osmolyte systems.

Graph-Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions

All-atom molecular dynamics simulations combined with graph-theoretic analysis reveal that clustering of monomethyl phosphate dianion (MMP^2-) is strongly influenced by the types and combinations of cations in the aqueous solution. Although Ca²⁺ promotes the formation of stable and large MMP^2- clusters, K⁺ alone does not. Nonetheless, clusters are larger and their link lifetimes are longer in mixtures of K⁺ and Ca²⁺. This "synergistic" effect depends sensitively on the Lennard-Jones interaction parameters between Ca²⁺ and the phosphorus oxygen and correlates with the hydration of the clusters. The pronounced MMP^2- clustering effect of Ca²⁺ in the presence of K⁺ is confirmed by Fourier transform infrared spectroscopy. The characterization of the cation-dependent clustering of MMP^2- provides a starting point for understanding cation-dependent clustering of phosphoinositides in cell membranes.

Dynamic heterogeneity in aqueous ionic solutions

It is well known that supercooled liquids have heterogeneous dynamics, but it is still unclear whether dynamic heterogeneity also exists in aqueous ionic solutions at room or even higher temperatures.