Water as an Active Constituent in Cell Biology

Pathway Selection in Temporal Evolution of Supramolecular Polymers of Ionic π-Systems: Amphiphilic Organic Solvent Dictates the Fate of Water

Understanding solvent-solute interactions is essential to designing and synthesising soft materials with tailor-made functions. Although the interaction of the solute with the solvent mixture is more complex than the single solvent medium, solvent mixtures are exciting to unfold several unforeseen phenomena in supramolecular chemistry. Here, we report two unforeseen pathways observed during the hierarchical assembly of cationic perylene diimides (cPDIs) in water and amphiphilic organic solvent (AOS) mixtures. When the aqueous supramolecular polymers (SPs) of cPDIs are injected into AOS, initially kinetically trapped short SPs are formed, which gradually transform into thermodynamically stable high aspect ratio SP networks. Using various experimental and theoretical investigations, we found that this temporal evolution follows two distinct pathways depending on the nature of the water-AOS interactions. If the AOS is isopropanol (IPA), water is released from cPDIs into bulk IPA due to strong hydrogen bonding interactions, which further decreases the monomer concentration of cPDIs (Pathway-1). In the case of dioxane AOS, cPDI monomer concentration further increases as water is retained among cPDIs (Pathway-2) due to relatively weak interactions between dioxane and water. Interestingly, these two pathways are accelerated by external stimuli such as heat and mechanical agitation.

Weakly Hydrated Solute of Mixed Hydrophobic-Hydrophilic Nature

Infrared (IR) spectroscopy is a commonly used and invaluable tool in studies of solvation phenomena in aqueous solutions. Concurrently, density functional theory calculations and ab initio molecular dynamics simulations deliver the solvation shell picture at the molecular detail level. The mentioned techniques allowed us to gain insights into the structure and energy of the hydrogen bonding network of water molecules around methylsulfonylmethane (MSM). In the hydration sphere of MSM, there are two types of populations of water molecules: a significant share of water molecules weakly bonded to the sulfone group and a smaller share of water molecules strongly bonded to each other around the methyl groups of MSM. The very weak hydrogen bond of water molecules with the hydrophilic group causes the extended network of water hydrogen bonds to be not "anchored" on the sulfone group, and consequently, the MSM hydration shell is labile.

Modeling of the Hydrogen Bond-Induced Frequency Shifts of the HOH and HOD Bending Modes of Water

The intramolecular bending mode of water is a possible useful probe of the hydrogen-bond situations in aqueous systems, but the behavior of its frequency and intensity should be further elucidated for better understanding on its nature and, hence, for its better utilization as a probe. Here, an analysis toward this goal is conducted by doing theoretical calculations on molecular clusters of normal isotopic and deuterated species of water and examining the correlations among the vibrational, structural, and electrostatic properties. It is shown that electrostatic interactions, particularly both of the in-plane components of the electric field along the OH bond and perpendicular to it, play a major role in controlling the hydrogen bond-induced shifts of the force constant, but additional factors, including the intermolecular structural and/or charge-transfer properties, are also important. Models of the hydrogen bond-induced shifts of the force constant are presented in a form that may be combined with classical molecular dynamics. With regard to the infrared intensity changes, it is shown on the basis of the electron density analysis that the intermolecular charge flux and polarization effect play an important role, depending on the angular characteristics of the hydrogen bond.

Probing the structure of water in individual living cells

Water regulates or even governs a wide range of biological processes. Despite its fundamental importance, surprisingly little is known about the structure of intracellular water. Herein we employ a Raman micro-spectroscopy technique to uncover the composition, abundance and vibrational spectra of intracellular water in individual living cells. In three different cell types, we show a small but consistent population (~3%) of non-bulk-like water. It exhibits a weakened hydrogen-bonded network and a more disordered tetrahedral structure. We attribute this population to biointerfacial water located in the vicinity of biomolecules. Moreover, our whole-cell modeling suggests that all soluble (globular) proteins inside cells are surrounded by, on average, one full molecular layer (about 2.6 Angstrom) of biointerfacial water. Furthermore, relative invariance of biointerfacial water is observed among different single cells. Overall, our study not only opens up experimental possibilities of interrogating water structure in vivo but also provides insights into water in life.

MANUSCRIPT Local Crowd, Local Probe: Strengths and Drawbacks of Azidohomoalanine as a Site-Specific Crowding Probe

Every residue on a protein can be characterized by its interaction with water, in lack or in excess, as water is the matrix of biological systems. Infrared spectroscopy and the implementation of local azidohomoalanine (AHA) probes allow us to move beyond an ensemble or surface-driven conceptualization of water behavior and toward a granular, site-specific picture. In this paper, we examined the role of crowding in modulating both global and local behavior on the β-hairpin, TrpZip2 using a combination of Fourier-transform infrared spectroscopy (FTIR) spectroscopy, two-dimensional infrared (2D IR) spectroscopy, and molecular dynamics simulations. We found that, at the amino acid level, crowding drove dehydration of both sheet and turn peptide sites as well as free AHA. However, the subpicosecond dynamics showed highly individualized responses based on the local environment. Interestingly, while steady-state FTIR measurements revealed similar responses at the amino-acid level to hard versus soft crowding (dehydration), we found that PEG and glucose had opposite stabilizing and destabilizing effects on the protein secondary structure, emphasizing an important distinction in understanding the impact of crowding on protein structure as well as the role of crowding across length scales.

The Dependence of Hydrophobic Interactions on the Shape of Solute Surface

According to our recent studies on hydrophobicity, this work is aimed at understanding the dependence of hydrophobic interactions on the shape of a solute's surface. It has been observed that dissolved solutes primarily affect the structure of interfacial water, which refers to the top layer of water at the interface between the solute and water. As solutes aggregate in a solution, hydrophobic interactions become closely related to the transition of water molecules from the interfacial region to the bulk water. It is inferred that hydrophobic interactions may depend on the shape of the solute surface. To enhance the strength of hydrophobic interactions, the solutes tend to aggregate, thereby minimizing their surface area-to-volume ratio. This also suggests that hydrophobic interactions may exhibit directional characteristics. Moreover, this phenomenon can be supported by calculated potential mean forces (PMFs) using molecular dynamics (MD) simulations, where different surfaces, such as convex, flat, or concave, are associated with a sphere. Furthermore, this concept can be extended to comprehend the molecular packing parameter, commonly utilized in studying the self-assembly behavior of amphiphilic molecules in aqueous solutions.

Nuclear quantum effects on the vibrational dynamics of the water-air interface

We have applied path-integral molecular dynamics simulations to investigate the impact of nuclear quantum effects on the vibrational dynamics of water molecules at the water-air interface. The instantaneous fluctuations in the frequencies of the O-H stretch modes are calculated using the wavelet method of time series analysis, while the time scales of vibrational spectral diffusion are determined from frequency-time correlation functions and joint probability distributions. We find that the inclusion of nuclear quantum effects leads not only to a redshift in the vibrational frequency distribution by about 120 cm-1 for both the bulk and interfacial water molecules but also to an acceleration of the vibrational dynamics at the water-air interface by as much as 35%. In addition, a blueshift of about 45 cm-1 is seen in the vibrational frequency distribution of interfacial water molecules compared to that of the bulk. Furthermore, the dynamics of water molecules beyond the topmost molecular layer was found to be rather similar to that of bulk water.

Spontaneous Curvature Induction in an Artificial Bilayer Membrane

Maintaining lipid asymmetry across membrane leaflets is critical for functions like vesicular traffic and organelle homeostasis. However, a lack of molecular-level understanding of the mechanisms underlying membrane fission and fusion processes in synthetic systems precludes their development as artificial analogs. Here, we report asymmetry induction of a bilayer membrane formed by an extended π-conjugated molecule with oxyalkylene side chains bearing terminal tertiary amine moieties (BA1) in water. Autogenous protonation of the tertiary amines in the periphery of the bilayer by water induces anisotropic curvature, resulting in membrane fission to form vesicles and can be monitored using time-dependent spectroscopy and microscopy. Interestingly, upon loss of the induced asymmetry by extensive protonation using an organic acid restored bilayer membrane. The mechanism leading to the compositional asymmetry in the leaflet and curvature induction in the membrane is validated by density functional theory (DFT) calculations. Studies extended to control molecules having changes in hydrophilic (BA2) and hydrophobic (BA3) segments provide insight into the delicate nature of molecular scale interactions in the dynamic transformation of supramolecular structures. The synergic effect of hydrophobic interaction and the hydrated state of BA1 aggregates provide dynamicity and unusual stability. Our study unveils mechanistic insight into the dynamic transformation of bilayer membranes into vesicles.

Hydration of N-Hydroxyurea from Ab Initio Molecular Dynamics Simulations

N-Hydroxyurea (HU) is an important chemotherapeutic agent used as a first-line treatment in conditions such as sickle cell disease and β-thalassemia, among others. To date, its properties as a hydrated molecule in the blood plasma or cytoplasm are dramatically understudied, although they may be crucial to the binding of HU to the radical catalytic site of ribonucleotide reductase, its molecular target. The purpose of this work is the comprehensive exploration of HU hydration. The topic is studied using ab initio molecular dynamic (AIMD) simulations that apply a first principles representation of the electron density of the system. This allows for the calculation of infrared spectra, which may be decomposed spatially to better capture the spectral signatures of solute-solvent interactions. The studied molecule is found to be strongly hydrated and tightly bound to the first shell water molecules. The analysis of the distance-dependent spectra of HU shows that the E and Z conformers spectrally affect, on average, 3.4 and 2.5 of the closest H2O molecules, respectively, in spheres of radii of 3.7 Å and 3.5 Å, respectively. The distance-dependent spectra corresponding to these cutoff radii show increased absorbance in the red-shifted part of the water OH stretching vibration band, indicating local enhancement of the solvent's hydrogen bond network. The radially resolved IR spectra also demonstrate that HU effortlessly incorporates into the hydrogen bond network of water and has an enhancing effect on this network. Metadynamics simulations based on AIMD methodology provide a picture of the conformational equilibria of HU in solution. Contrary to previous investigations of an isolated HU molecule in the gas phase, the Z conformer of HU is found here to be more stable by 17.4 kJ·mol-1 than the E conformer, pointing at the crucial role that hydration plays in determining the conformational stability of solutes. The potential energy surface for the OH group rotation in HU indicates that there is no intramolecular hydrogen bond in Z-HU in water, in stark contrast to the isolated solute in the gas phase. Instead, the preferred orientation of the hydroxyl group is perpendicular to the molecular plane of the solute. In view of the known chaotropic effect of urea and its N-alkyl-substituted derivatives, N-hydroxyurea emerges as a unique urea derivative that exhibits a kosmotropic ordering of nearby water. This property may be of crucial importance for its binding to the catalytic site of ribonucleotide reductase with a concomitant displacement of a water molecule.

Adaptive Response to Solvation in Flexible Molecules: Oligo Hydrates of 4-Hydroxy-2-butanone

Structural changes induced by water play a pivotal role in chemistry and biology but remain challenging to predict, measure, and control at molecular level. Here we explore size-governed gas-phase water aggregation in the flexible molecule 4-hydroxy-2-butanone, modeling the conformational adaptability of flexible substrates to host water scaffolds and the preference for sequential droplet growth. The experiment was conducted using broadband rotational spectroscopy, rationalized with quantum chemical calculations. Two different isomers were observed experimentally from the di- to the pentahydrates (4-hydroxy-2-butanone-(H2O)n=2-5), including the 18O isotopologues for the di- and trihydrates. Interestingly, to accommodate water molecules effectively, the heavy atom skeleton of 4-hydroxy-2-butanone reshapes in every observed isomer and does not correspond to the stable conformer of the free monomer. All solvates initiate from the alcohol group (proton donor) but retain the carbonyl group as secondary binding point. The water scaffolds closely resemble those found in the pure water clusters, balancing between the capability of 4-hydroxy-2-butanone for steering the orientation and position of the water molecules and the ability of water to modulate the monomer's conformation. The present work thus provides an accurate molecular description on how torsionally flexible molecules dynamically adapt to water along progressing solvation.

Influence of H+, OH- and salts on hydrophobic self-assembly

In spite of the ubiquity of acid/base ions and salts in biological systems, their influence on hydrophobic self-assembly remains an open question. Here we use a combined experimental and theoretical strategy to quantify the influence of H+ and OH-, as well as salts containing Li+, Na+, Cl- and Br-, on the hydrophobic self-assembly of micelles composed of neutral oily 1,2-hexanediol surfactants. The distributions of aggregate sizes, both below and above the critical micelle concentration (CMC), are determined using Raman multivariate curve resolution (Raman-MCR) spectroscopy to quantify the multi-aggregation chemical potential surface (MCPS) that drives self-assembly. The results reveal that ions have little influence on the formation of hydrophobic contact dimers but can significantly drive high-order self assembly. Moreover, the hydration-shells of oily solutes are found to expel the above salt ions and OH-, but to attract H+, with wide-ranging implications.

Water will Find Its Way: Transport through Narrow Tunnels in Hydrolases

An aqueous environment is vital for life as we know it, and water is essential for nearly all biochemical processes at the molecular level. Proteins utilize water molecules in various ways. Consequently, proteins must transport water molecules across their internal network of tunnels to reach the desired action sites, either within them or by functioning as molecular pipes to control cellular osmotic pressure. Despite water playing a crucial role in enzymatic activity and stability, its transport has been largely overlooked, with studies primarily focusing on water transport across membrane proteins. The transport of molecules through a protein's tunnel network is challenging to study experimentally, making molecular dynamics simulations the most popular approach for investigating such events. In this study, we focused on the transport of water molecules across three different α/β-hydrolases: haloalkane dehalogenase, epoxide hydrolase, and lipase. Using a 5 μs adaptive simulation per system, we observed that only a few tunnels were responsible for the majority of water transport in dehalogenase, in contrast to a higher diversity of tunnels in other enzymes. Interestingly, water molecules could traverse narrow tunnels with subangstrom bottlenecks, which is surprising given the commonly accepted water molecule radius of 1.4 Å. Our analysis of the transport events in such narrow tunnels revealed a markedly increased number of hydrogen bonds formed between the water molecules and protein, likely compensating for the steric penalty of the process. Overall, these commonly disregarded narrow tunnels accounted for ∼20% of the total water transport observed, emphasizing the need to surpass the standard geometrical limits on the functional tunnels to properly account for the relevant transport processes. Finally, we demonstrated how the obtained insights could be applied to explain the differences in a mutant of the human soluble epoxide hydrolase associated with a higher incidence of ischemic stroke.

Formation of H-bonding networks in the solid state structure of a trinuclear cobalt(iii/ii/iii) complex with N2O2 donor Schiff base ligand and glutaric acid as bridging co-ligand: synthesis, structure and DFT study

A trinuclear linear mixed-valence centrosymmetric cobalt(iii)-cobalt(ii)-cobalt(iii) complex, [CoII{(μ-L)(μ-Hglu)CoIII(OH2)}2](ClO4)2·6H2O has been synthesized during tetradentate N2O2 donor 'Schiff base' ligand, H2L {N,N'-bis(salicylidene)-1,3-diaminopropane} and glutaric acid (H2glu) as anionic co-ligand. The complex has been characterized by spectroscopic measurements and its solid state structure has been determined by single crystal X-ray diffraction analysis. The supra-molecular assembly formed by the hydrogen bonding interactions in the solid state of the complex has been analysed using DFT calculations.

Electron videography of a lipid-protein tango

Biological phenomena, from enzymatic catalysis to synaptic transmission, originate in the structural transformations of biomolecules and biomolecular assemblies in liquid water. However, directly imaging these nanoscopic dynamics without probes or labels has been a fundamental methodological challenge. Here, we developed an approach for "electron videography"-combining liquid phase electron microscopy with molecular modeling-with which we filmed the nanoscale structural fluctuations of individual, suspended, and unlabeled membrane protein nanodiscs in liquid. Systematic comparisons with biochemical data and simulation indicate the graphene encapsulation involved can afford sufficiently reduced effects of the illuminating electron beam for these observations to yield quantitative fingerprints of nanoscale lipid-protein interactions. Our results suggest that lipid-protein interactions delineate dynamically modified membrane domains across unexpectedly long ranges. Moreover, they contribute to the molecular mechanics of the nanodisc as a whole in a manner specific to the protein within. Overall, this work illustrates an experimental approach to film, quantify, and understand biomolecular dynamics at the nanometer scale.

Entropy Tug-of-War Determines Solvent Effects in the Liquid-Liquid Phase Separation of a Globular Protein

Liquid-liquid phase separation (LLPS) plays a key role in the compartmentalization of cells via the formation of biomolecular condensates. Here, we combined atomistic molecular dynamics (MD) simulations and terahertz (THz) spectroscopy to determine the solvent entropy contribution to the formation of condensates of the human eye lens protein γD-Crystallin. The MD simulations reveal an entropy tug-of-war between water molecules that are released from the protein droplets and those that are retained within the condensates, two categories of water molecules that were also assigned spectroscopically. A recently developed THz-calorimetry method enables quantitative comparison of the experimental and computational entropy changes of the released water molecules. The strong correlation mutually validates the two approaches and opens the way to a detailed atomic-level understanding of the different driving forces underlying the LLPS.

Dynamics of Water Clusters Confined in Ionic Liquid at an Elevated Pressure

Over the years, numerous experimental and theoretical efforts have been dedicated to investigating the mysteries of water and determining its new unexplored physical properties. Despite this, high-pressure studies of water and aqueous mixtures close to the glass transition still represent an unknown area of research. Herein, we address a fundamental issue: the validity of the density scaling concept for fast water dynamics. For this purpose, we performed ambient and high-pressure dielectric measurements of a supercooled equimolar aqueous mixture of an acidic ionic liquid. All isothermal and isobaric relaxation data describing the time scale of charge transport (τσ) and fast dynamics within the water clusters (τν) reveal visual evidence of a liquid-glass transition. Furthermore, both relaxation processes satisfy the ργ/T scaling concept with a single exponent γ = 0.58. Thus, the scaling exponent is a state-point-independent parameter for the dynamics of water clusters confined in ionic liquid investigated in the pressure range up to 300 MPa.

Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder

The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, with a special focus on the performance of all the later generation Minnesota functionals. Findings are contextualized within the current knowledge on DFT for describing bulk water under ambient conditions and compared to experimental data. We find that, contrary to the prevalent idea that local and semilocal functionals overstructure water and underestimate dynamical properties, M06-L, revM06-L, and M11-L understructure water, while MN12-L and MN15-L overdistance water molecules due to weak cohesive effects. This can be attributed to a weakening of the hydrogen bond network, which leads to dynamical fingerprints that are over fast. While most of the hybrid Minnesota functionals (M06, M08-HX, M08-SO, M11, MN12-SX, and MN15) also yield understructured water, their dynamical properties generally improve over their semilocal counterparts. It emerges that exact exchange is a crucial component for accurately describing hydrogen bonds, which ultimately leads to corrections in both the dynamical and structural properties. However, an excessive amount of exact exchange strengthens hydrogen bonds and causes overstructuring and slow dynamics (M06-HF). As a compromise, M06-2X is the best performing Minnesota functional for water, and its D3 corrected variant shows very good structural agreement. From previous studies considering nuclear quantum effects (NQEs), the hybrid revPBE0-D3, and the rung-5 RPA (RPA@PBE) have been identified as the only two approximations that closely agree with experiments. Our results suggest that the M06-2X(-D3) functionals have the potential to further improve the reproduction of experimental properties when incorporating NQEs through path integral approaches. This work provides further proof that accurate modeling of water interactions requires the inclusion of both exact exchange and balanced (non-local) correlation, highlighting the need for higher rungs on Jacob's ladder to achieve predictive simulations of complex biological systems in aqueous environments.

Tuning the low-temperature phase behavior of aqueous ionic liquids

Water's anomalous behavior is often explained using a two-liquid model, where two types of water, high-density liquid (HDL) and low-density liquid (LDL), can be separated via a liquid-liquid phase transition (LLPT) at low temperature. Mixtures of water and the ionic liquid hydrazinium trifluoroacetate were suggested to also show an LLPT but with the advantage that there is no rapid ice crystallization hampering its observation. It remains controversial whether these solutions exhibit an LLPT or are instead associated with complex phase separation phenomena. We here show detailed low-temperature calorimetry and diffraction experiments on aqueous solutions containing hydrazinium trifluoroacetate and other similar ionic liquids, all at a solute mole fraction of x = 0.175. Hydrazinium trifluoroacetate, ammonium trifluoroacetate, ethylammonium trifluoroacetate and hydrazinium pentafluoropropionate all boast exothermic transitions unrelated to crystallization as well as remarkable structural changes upon cooling into the glassy state. We propose a model inspired by micelle formation and decomposition in surfactant solutions, which is complemented by MD simulations and allows rationalizing the rich phase behavior of our mixtures during cooling. The fundamental aspect of the model is the hydrophobic nature of fluorinated anions that enables aggregation, which is reversed upon cooling and culminates in the remarkable exothermic first-order transition observed at low temperature. That is, we assign the first-order transition not to an LLPT but to phase-separations similar to the ones when falling below the Krafft temperature. All other solutions merely show simple vitrification behavior. Still, they exhibit distinct differences in liquid fragility, which is decreased continuously with decreasing hydrophobicity of the anions. This might enable the systematic tuning of ionic liquids with the goal of designing aqueous solutions of specific fragility.

Wetting Behavior of Kerogen Surfaces: Insights from Molecular Dynamics

In this study, the wettability of a kerogen surface, a key component of shale reservoirs, is investigated by using molecular dynamics simulations. Specifically, we examined the impact of droplet size and morphology as well as surface roughness on the water contact angles. The findings highlighted that the contact angle dependency on the droplet size intensifies with increased rigidity of the surface. Conversely, as the surface becomes more flexible and rougher, it gains hydrophilicity. The higher hydrophilicity stems from the ability of water molecules to penetrate the kerogen corrugations and form more hydrogen bonds with heteroatoms, particularly oxygen. Notably, the contact angle of kerogen hovers between 65 and 75°, thereby crossing the transition from an underoil hydrophilic to an underoil hydrophobic state. Consequently, minor alterations in the kerogen nanostructure can dramatically alter the wetting preference between water and oil. This insight is of paramount significance for refining strategies in managing fluid interactions in shale reservoirs such as geological carbon storage or oil extraction.

The dawn of hydrogen and halogen bonds and their crucial role in collisional processes probing long-range intermolecular interactions

This perspective review focuses on the results of an internally consistent study developed in the Perugia laboratory, centered on the fundamental interaction components that, at large intermolecular distances, determine the formation of weak intermolecular hydrogen (HB) and halogen (XB) bonds. This investigation exploits old and novel molecular beam scattering experiments involving several gaseous prototypical systems. In particular, we focus on the kinetic energy dependence of the total (elastic + inelastic) integral cross-sections. Of particular interest is the measure of quantum interference patterns in the energy dependence of cross-sections of targeted systems and their shift compared to that of known reference systems. We interpreted these findings as interaction energy stabilization components, such as charge transfer, σ-hole, and polar flattening, that emerge at intermediate separation distance ranges and selectively manifest for specific geometries of collision complexes. Another significant observable we discuss is the absolute value of the cross-section and its dependence on permanent multipole moments of the collisional partners. Specifically, we show how the spontaneous orientation of rotationally cold and polar molecules, due to the electric field gradient associated with the interaction between permanent multipole moments, can significantly modify the magnitude of the total cross-section, even at high values of the impact parameter. We are confident that the present results can help extend the force field formulation to various interacting systems and carry out molecular dynamics simulations under conditions of application interest.

Prebiotically plausible chemoselective pantetheine synthesis in water

Coenzyme A (CoA) is essential to all life on Earth, and its functional subunit, pantetheine, is important in many origin-of-life scenarios, but how pantetheine emerged on the early Earth remains a mystery. Earlier attempts to selectively synthesize pantetheine failed, leading to suggestions that "simpler" thiols must have preceded pantetheine at the origin of life. In this work, we report high-yielding and selective prebiotic syntheses of pantetheine in water. Chemoselective multicomponent aldol, iminolactone, and aminonitrile reactions delivered spontaneous differentiation of pantoic acid and proteinogenic amino acid syntheses, as well as the dihydroxyl, gem-dimethyl, and β-alanine-amide moieties of pantetheine in dilute water. Our results are consistent with a role for canonical pantetheine at the outset of life on Earth.

Modulation of Gold Nanoparticle Ligand Structure-Dynamic Relationships Probed Using Solution NMR

Ligand dynamics plays a critical role in the chemical and biological properties of gold nanoparticles (AuNPs). In this study, ligands featuring hydrophobic alkanethiol interiors and hydrophilic shells were used to systematically examine the effects of ligand headgroups on the ligand dynamics. Solution nuclear magnetic resonance (NMR) spectroscopy provided quantitative insight into the monolayer ligand dynamics. Notably, the introduction of hydrophobic moieties to the cationic headgroups significantly decreased ligand conformational mobility; however, variations in hydrophobicity among these moieties had a limited effect on this reduction. Further examination of ligand dynamics under various physiological conditions, including ionic strength and temperature, showed that ligands bound to the AuNP surface become less conformationally mobile with an increase in ionic strength or decreasing temperature. This exploration of ligand dynamics provides insight into designing nanoparticles tailored to specific biological applications.

Molecular Crowding: Physiologic Sensing and Control

The cytoplasm is densely packed with molecules that contribute to its nonideal behavior. Cytosolic crowding influences chemical reaction rates, intracellular water mobility, and macromolecular complex formation. Overcrowding is potentially catastrophic; to counteract this problem, cells have evolved acute and chronic homeostatic mechanisms that optimize cellular crowdedness. Here, we provide a physiology-focused overview of molecular crowding, highlighting contemporary advances in our understanding of its sensing and control. Long hypothesized as a form of crowding-induced microcompartmentation, phase separation allows cells to detect and respond to intracellular crowding through the action of biomolecular condensates, as indicated by recent studies. Growing evidence indicates that crowding is closely tied to cell size and fluid volume, homeostatic responses to physical compression and desiccation, tissue architecture, circadian rhythm, aging, transepithelial transport, and total body electrolyte and water balance. Thus, molecular crowding is a fundamental physiologic parameter that impacts diverse functions extending from molecule to organism.

Hyaluronic Acid Unveiled: Exploring the Nanomechanics and Water Retention Properties at the Single-Molecule Level

Hyaluronic acid (HA), a vital glycosaminoglycan in living organisms, possesses remarkable mechanical and viscoelastic properties that have garnered significant attention in therapeutic, biomedical, and cosmetic applications. However, a comprehensive picture of the physicochemical and biocharacterization of HA at the single-molecule level remains elusive. In this work, atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) and molecular dynamics (MD) simulation were used to investigate the nanomechanics and water retention properties of HA at the single-molecule level. The present study aims to unravel the intricate details of the influence of molecular structure on HA behavior and shed light on its unique attributes. According to the force measurements, the energy used to stretch a HA chain in water is 8.45 kJ/mol, significantly surpassing that of Curdlan (3.45 kJ/mol) and chitin (2.23 kJ/mol), both of which possess molecular structures partially similar to that of HA. Intriguingly, the strength of the intrachain interaction of HA (5.54 kJ/mol) was considerably weaker compared to Curdlan (11.06 kJ/mol) and chitin (or cellulose, 10.76 kJ/mol). This result indicates that HA exhibits a preference for interacting with water rather than with itself, thereby showing enhanced water affinity. Moreover, the force measurements demonstrated that changing the glycosidic bond from β-(1-3) (Curdlan) or β-(1-4) (chitin or cellulose) to β-(1-3) + β-(1-4) (HA) resulted in polysaccharides displaying improved water affinity and more extended conformation. These conclusions were further verified by molecular dynamics (MD) simulations. Overall, our work sheds new light on the nanomechanics and water retention properties of HA at the single-molecule level, offering valuable insights for future research in this field.

Curli Amyloid Fibers in Escherichia coli Biofilms: The Influence of Water Availability on their Structure and Functional Properties

Escherichia coli biofilms consist of bacteria embedded in a self-produced matrix mainly made of protein fibers and polysaccharides. The curli amyloid fibers found in the biofilm matrix are promising versatile building blocks to design sustainable bio-sourced materials. To exploit this potential, it is crucial to understand i) how environmental cues during biofilm growth influence the molecular structure of these amyloid fibers, and ii) how this translates at higher length scales. To explore these questions, the effect of water availability during biofilm growth on the conformation and functions of curli is studied. Microscopy and spectroscopy are used to characterize the amyloid fibers purified from biofilms grown on nutritive substrates with different water contents, and micro-indentation to measure the rigidity of the respective biofilms. The purified curli amyloid fibers present differences in the yield, structure, and functional properties upon biofilm growth conditions. Fiber packing and β-sheets content correlate with their hydrophobicity and chemical stability, and with the rigidity of the biofilms. This study highlights how E. coli biofilm growth conditions impact curli structure and functions contributing to macroscopic materials properties. These fundamental findings infer an alternative strategy to tune curli structure, which will ultimately benefit engineering hierarchical and functional curli-based materials.

Hydrodynamic Control of Alzheimer Aβ Fibrillation with Glucosaminic Acid Containing Click-Cyclized β-Bodies

It is well established that the dynamic hydration shell plays a vital role in macromolecular functions such as protein-ligand, protein-protein, protein-DNA, and protein-lipid interactions. Here we investigate how the water modality affects conformational changes, solubility, and motion of fibrillar proteins. The hypothesis is that the introduction of a poly hydroxyl amino acid would increase solvation of the fibril forming peptides, preventing their misfolding and aggregation. For the amyloid β (Aβ) peptide, which is considered to be connected with nervous system diseases, including dementia and cognitive decline in Alzheimer's disease, the formation of β-sheet fibrils always occurs with a conformational change and a decrease in the dynamic hydration shell around Aβ(1-42). We present novel cyclic d-amino acid peptides that effectively inhibit fibrillation through affecting the dynamic hydration shell of Aβ(1-42) in vitro. Using de novo design within the software Molecular Operating Environment (MOE), five different peptides that recognize Alzheimer's fibrils were designed and synthesized. Three of them were cyclic all-d-amino acid peptides incorporating the same polyhydroxy building block derived from d-glucosaminic acid (GA). One peptide was the parent cyclic all d-amino acid inhibitor with no GA incorporated, and another was an all l-amino acid linear fibrillation inhibitor. The GA-containing peptides were found to show significantly improved inhibition of Aβ(1-42) aggregation. The inhibition was dramatically improved by the synergistic application of two GA peptides targeting each end of the growing fibril. The present study may facilitate future developments of intervention strategies for Alzheimer's disease and similar neurodegenerative diseases.

Water inside the Selectivity Filter of a K+ Ion Channel: Structural Heterogeneity, Picosecond Dynamics, and Hydrogen Bonding

Water inside biological ion channels regulates the key properties of these proteins, such as selectivity, ion conductance, and gating. In this article, we measure the picosecond spectral diffusion of amide I vibrations of an isotope-labeled KcsA potassium channel using two-dimensional infrared (2D IR) spectroscopy. By combining waiting time (100-2000 fs) 2D IR measurements of the KcsA channel including 13C18O isotope-labeled Val76 and Gly77 residues with molecular dynamics simulations, we elucidated the site-specific dynamics of water and K+ ions inside the selectivity filter of KcsA. We observe inhomogeneous 2D line shapes with extremely slow spectral diffusion. Our simulations quantitatively reproduce the experiments and show that water is the only component with any appreciable dynamics, whereas K+ ions and the protein are essentially static on a picosecond timescale. By analyzing simulated and experimental vibrational frequencies, we find that water in the selectivity filter can be oriented to form hydrogen bonds with adjacent or nonadjacent carbonyl groups with the reorientation timescales being three times slower and comparable to that of water molecules in liquid, respectively. Water molecules can reside in the cavity sufficiently far from carbonyls and behave essentially like "free" gas-phase-like water with fast reorientation times. Remarkably, no interconversion between these configurations was observed on a picosecond timescale. These dynamics are in stark contrast with liquid water, which remains highly dynamic even in the presence of ions at high concentrations.

Ice-Like Dynamics of Water Clusters

Understanding certain behaviors of water, e.g., its dynamics, is extremely important in various fields. Recently, using 1H nuclear magnetic resonance spectroscopy, we have identified a metastable state of water molecules, i.e., water clusters, in hydrophobic solvents in addition to dissolved water molecules and a small bulk water domain. However, the low abundance of water clusters made observing their dynamics challenging. In this study, the dynamics of water clusters in benzene-d6 were investigated by quasi-elastic neutron scattering measurements using the AGNES time-of-flight spectrometer of the Japan Research Reactor JRR-3. The diffusion dynamics of the hydrogen atoms were much slower than those of bulk water (with a self-diffusion coefficient of 1.15 × 10-9 m2/s at 273 K) and even slower than the upper-limit dynamics at the observable scale (10-10 m2/s). The dynamics of water clusters are slow, "like ice", even at 283-303 K, which is above the freezing point of water (273 K).

Understanding the intricacy of protein in hydrated deep eutectic solvent: Solvation dynamics, conformational fluctuation dynamics, and stability

Deep eutectic solvents (DESs) are potential biocatalytic media due to their easy preparation, fine-tuneability, biocompatibility, and most importantly, due to their ability to keep protein stable and active. However, there are many unanswered questions and gaps in our knowledge about how proteins behave in these alternate media. Herein, we investigated solvation dynamics, conformational fluctuation dynamics, and stability of human serum albumin (HSA) in 0.5 Acetamide/0.3 Urea/0.2 Sorbitol (0.5Ac/0.3Ur/0.2Sor) DES of varying concentrations to understand the intricacy of protein behaviour in DES. Our result revealed a gradual decrease in the side-chain flexibility and thermal stability of HSA beyond 30 % DES. On the other hand, the associated water dynamics around domain-I of HSA decelerate only marginally with increasing DES content, although viscosity rises considerably. We propose that even though macroscopic solvent properties are altered, a protein feels only an aqueous type of environment in the presence of DES. This is probably the first experimental study to delineate the role of the associated water structure of the enzyme for maintaining its stability inside DES. Although considerable effort is necessary to generalize such claims, it might serve as the basis for understanding why proteins remain stable and active in DES.

Ultrafast Spectroscopy Reveals Slow Water Dynamics in Biocondensates

Cells achieve high spatiotemporal control over biochemical processes through compartmentalization to membrane-bound as well as membraneless organelles that assemble by liquid-liquid phase separation. Characterizing the balance of forces within these environments is essential to understanding their stability and function, and water is an integral part of the condensate, playing an important role in mediating electrostatic and hydrogen-bonding interactions. Here, we investigate the ultrafast, picosecond hydrogen-bond dynamics of a model biocondensate consisting of a peptide poly-l-arginine (Poly-R) and the nucleic acid adenosine monophosphate (AMP) using coherent two-dimensional infrared (2D IR) spectroscopy. We investigated three vibrational modes: the arginine side-chain C═N stretches, an AMP ring mode, and the amide backbone carbonyl stretching modes. Dynamics slow considerably between the dilute phase and the condensate phase for each vibrational probe. For example, the arginine side-chain C═N modes slow from 0.38 to 2.26 ps due to strong electrostatic interactions. All-atom molecular dynamics simulations provide an atomistic interpretation of the H-bond network disruption resulting from electrostatic contributions as well as collapse within the condensate. Simulations predict that a fraction of water molecules are highly constrained within the condensate, explaining the observed slowdown in the H-bond dynamics.

Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data

Biological macromolecules in solution are surrounded by a hydration shell, whose structure differs from the structure of bulk solvent. While the importance of the hydration shell for numerous biological functions is widely acknowledged, it remains unknown how the hydration shell is regulated by macromolecular shape and surface composition, mainly because a quantitative probe of the hydration shell structure has been missing. We show that small-angle scattering in solution using X-rays (SAXS) or neutrons (SANS) provide a protein-specific probe of the protein hydration shell that enables quantitative comparison with molecular simulations. Using explicit-solvent SAXS/SANS predictions, we derived the effect of the hydration shell on the radii of gyration Rg of five proteins using 18 combinations of protein force field and water model. By comparing computed Rg values from SAXS relative to SANS in D2O with consensus SAXS/SANS data from a recent worldwide community effort, we found that several but not all force fields yield a hydration shell contrast in remarkable agreement with experiments. The hydration shell contrast captured by Rg values depends strongly on protein charge and geometric shape, thus providing a protein-specific footprint of protein-water interactions and a novel observable for scrutinizing atomistic hydration shell models against experimental data.

Femtosecond Electron-Transfer Dynamics across the D2O/Cs+/Cu(111) Interface: The Impact of Hydrogen Bonding

Hydrogen bonding is essential in electron-transfer processes at water-electrode interfaces. We study the impact of the H-bonding of water as a solvent molecule on real-time electron-transfer dynamics across a Cs+-Cu(111) ion-metal interface using femtosecond time-resolved two-photon photoelectron spectroscopy. We distinguish in the formed water-alkali aggregates two regimes below and above two water molecules per ion. Upon crossing the boundary of these regimes, the lifetime of the excess electron localized transiently at the Cs+ ion increases from 40 to 60 fs, which indicates a reduced alkali-metal interaction. Furthermore, the energy transferred to a dynamic structural rearrangement due to hydration is reduced from 0.3 to 0.2 eV concomitantly. These effects are a consequence of H-bonding in the water-water interaction and the beginning formation of a nanoscale water network. This finding is supported by real-space imaging of the solvatomers and vibrational frequency shifts of the OH stretching and bending modes calculated for these specific interfaces.

Dehydration of biological membranes in a non-condensing environment

The study of the dehydration process in a cell membrane allows a better understanding of how water is bound to it. While in prior studies, cell dehydration was commonly analyzed under osmotic stress conditions, in the present work, we focus on the dehydration driven by evaporation in a restricted condensing environment. Using a thermogravimetry method, we studied the dehydration of Escherichia coli through isothermal evaporation in the presence of a gas flux. To figure out the loss of mass in this situation, we first evaluated the dynamics of water evaporation of a suspension of multilamellar liposomes. We found that the evaporation of liposomal suspensions composed of individual lipids is constant, although slightly restricted by the presence of liposomes, while the evaporation of liposomal suspensions composed of a mixture of different lipids follows an exponential decay. This is explained considering that the internal pressure at the air-water interface is proportional to the amount of bound water. The evaporation of water from a biomass sample follows this latter behaviour.

Osmolyte induced protein stabilization: modulation of associated water dynamics might be a key factor

The mechanism of protein stabilization by osmolytes remains one of the most important and long-standing puzzles. The traditional explanation of osmolyte-induced stability through the preferential exclusion of osmolytes from the protein surface has been seriously challenged by the observations like the concentration-dependent reversal of osmolyte-induced stabilization/destabilization. The more modern explanation of protein stabilization/destabilization by osmolytes considers an indirect effect due to osmolyte-induced distortion of the water structure. It provides a general mechanism, but there are numerous examples of protein-specific effects, i.e., a particular osmolyte might stabilize one protein, but destabilize the other, that could not be rationalized through such an explanation. Herein, we hypothesized that osmolyte-induced modulation of associated water might be a critical factor in controlling protein stability in such a medium. Taking different osmolytes and papain as a protein, we proved that our proposal could explain protein stability in osmolyte media. Stabilizing osmolytes rigidify associated water structures around the protein, whereas destabilizing osmolytes make them flexible. The strong correlation between the stability and the associated water dynamics, and the fact that such dynamics are very much protein specific, established the importance of considering the modulation of associated water structures in explaining the osmolyte-induced stabilization/destabilization of proteins. More interestingly, we took another protein, bromelain, for which a traditionally stabilizing osmolyte, sucrose, acts as a stabilizer at higher concentrations but as a destabilizer at lower concentrations. Our proposal successfully explains such observations, which is probably impossible by any known mechanisms. We believe this report will trigger much research in this area.

Chirality-Selected Coacervate by Chiral Gemini Surfactant

Chiral surfactants present opportunities to self-assemble into supramolecules with a chiral trait; however, the effects of stereochemistry on the formation of simple coacervates remain unclear. Here, we investigate the chirality-selected phase behavior in mixtures of chiral gemini surfactant 1,4-bis(dodecyl-N,N-dimethylammonium bromide)-2,3-butanediol (12-4(OH)2-12) with an oppositely charged chiral mandelic acid (MA). It demonstrates that altering the chirality of surfactants yields a heightened ability to regulate the phase behavior, leading to the formation of three different network-like structures, i.e., wormlike micelle, coacervate, and hydrogel, in the racemate, enantiomer, and mesomer, respectively. The different aggregate structures arise from the intermolecular and intramolecular hydrogen-bond interactions of the two hydroxyl groups located at stereogenic centers. Intriguingly, although they contain similar microstructures, the solid-like hydrogel and liquid-like wormlike micelle show similar low hydration ability and have no encapsulation capability, whereas only coacervate formed by the enantiomers of 12-4(OH)2-12 displays liquid-like characteristics, strong capacity to sequester diverse solutes, and high affinity for tightly bound water simultaneously. These findings further highlight the unique and advantageous properties of coacervates as a promising model for exploring the biological process and understanding how chirality plays a crucial role in early life scenarios and cell evolution at the molecular level.

Temperature-dependent dielectric relaxation and hydrophobicity of aqueous alanine using time domain reflectometry

Physical, chemical and microbiological stability of the materials is affected by the rotational and translational mobility of free and hydrated water. The role of water in areas such as protein hydration and enzyme activity, food technology, lyophilization and polymers hydration is, therefore, important and can be well understood in terms of dielectric relaxation spectroscopy. Concentration and temperature-dependent hydrophobicity of amino acid is reflected in their tendencies to appear in appropriate positions in proteins. Therefore, to gain more insights on the temperature and concentration dependence of hydrophobicity and structural properties of amino acid, dielectric relaxation of aqueous alanine have been studied in the temperature region 303.15 K to 278.15 K. Time domain spectroscopy have been used in the frequency range of 10 MHz to 30 GHz and in the concentration range 0.18708 ≤ c/M ≤ 0.74831. Two relaxation processes namely the low-frequency relaxation (l) and the high-frequency relaxation (h) has been detected for the aqueous alanine. Dielectric parameters such as static dielectric constant (εj), relaxation time (τj) dipole moments (û) and correlation factor (g) have been studied to investigate molecular interaction between alanine and water. The number of water molecules irrotationally bond by the solute molecules (Zib) was also determined to examine the hydrophobicity of alanine which was found more hydrophobic towards low temperatures and concentrations. Thermodynamic parameters calculated are also supported well for the hydrophobic behaviour of alanine towards low temperatures and concentrations.Communicated by Ramaswamy H. Sarma.

The Role H-Bonding and Supramolecular Structures in Homogeneous and Enzymatic Catalysis

The article analyzes the role of hydrogen bonds and supramolecular structures in enzyme catalysis and model systems. Hydrogen bonds play a crucial role in many enzymatic reactions. However, scientists have only recently attempted to harness the power of hydrogen bonds in homogeneous catalytic systems. One of the newest directions is associated with attempts to control the properties of catalysts by influencing the "second coordination sphere" of metal complexes. The role H-bonding, and the building of stable supramolecular nanostructures due to intermolecular H-bonds, based on catalytic active heteroligand iron (Fe) or nickel (Ni) complexes formed during hydrocarbon oxidations were assessed via the AFM (Atomic-force microscopy) method, which was proposed and applied by authors of this manuscript. Th is article also discusses the roles of hydrogen bonds and supramolecular structures in oxidation reactions catalyzed by heteroligand Ni and Fe complexes, which are not only effective homogeneous catalysts but also structural and functional models of Oxygenases.

Unravelling the structural features of monosaccharide glyceraldehyde upon mono-hydration by quantum chemistry and rotational spectroscopy

Water is a fundamental molecule for life, and investigating its interaction with monosaccharides is of great interest in order to understand its influence on their conformational behavior. In this study, we report on the conformational landscape of monosaccharide glyceraldehyde, the simplest aldose sugar, in the presence of a single water molecule in the gas phase. This investigation was performed using a combination of Fourier transform microwave spectroscopy and theoretical calculations. Out of the nine calculated conformers, only the lowest energy conformer was experimentally observed and characterized. Interestingly, the presence of water was found to induce structural features in the lowest energy conformer of the glyceraldehyde monomer, with water positioned between the alcohol groups. To analyze this interaction further, non-covalent interaction plots were employed to map the intermolecular interactions in the observed species. Additionally, natural bond orbital analysis was conducted to study the effects of charge transfer in the monohydrate system. Furthermore, topological analysis based on Bader's Atoms in Molecules theory was performed to gain insights into the observed complex. The results of all three analyses consistently showed the formation of relatively strong hydrogen bonds between water and glyceraldehyde, leading to the formation of a seven-member ring network.

Water molecule ordering on the surface of an intrinsically disordered protein

The dynamics and local structure of the hydration water on surfaces of folded proteins have been extensively investigated. However, our knowledge of the hydration of intrinsically disordered proteins (IDPs) is more limited. Here, we compare the local structure of water molecules hydrating a globular protein, lysozyme, and the intrinsically disordered N-terminal of c-Src kinase (SH4UD) using molecular dynamics simulation. The radial distributions from the protein surface of the first and the second hydration shells are similar for the folded protein and the IDP. However, water molecules in the first hydration shell of both the folded protein and the IDP are perturbed from the bulk. This perturbation involves a loss of tetrahedrality, which is, however, significantly more marked for the folded protein than the IDP. This difference arises from an increase in the first hydration shell of the IDP of the fraction of hydration water molecules interacting with oxygen. The water ordering is independent of the compactness of the IDP. In contrast, the lifetimes of water molecules in the first hydration shell increase with IDP compactness, indicating a significant impact of IDP configuration on water surface pocket kinetics, which here is linked to differential pocket volumes and polarities.

Temperature-dependent hydration behavior of aqueous lysine: an approach towards protein binding through dielectric spectroscopy

Present work reports interaction between water and amino acid lysine for understanding the physicochemical properties that will be useful in the structure formation of protein. The dielectric relaxation of aqueous lysine was systematically investigated over a temperature range spanning from 298.15 K to 278.15 K, encompassing frequencies ranging from 10 MHz to 30 GHz, and across a concentration range of 0.152 M to 0.610 M. Within this study, aqueous lysine revealed the presence of two distinct relaxation modes. The low-frequency relaxation process (l-process) is primarily associated with the relaxation of lysine molecules, whereas the high-frequency relaxation process (h-process) is attributed to water molecules interacting with lysine. Several key dielectric parameters, including static dielectric constant (εj), relaxation time (τj), dipole moment (μj), correlation factor (gj), and the number of water molecules rotationally bonded by solute molecules (Zib), were meticulously determined. These parameters were interpreted in terms of molecular interactions, hydrogen bonding, hydrophobicity, and Lys-Lys binding. Additionally, various thermodynamic parameters such as molar enthalpy (ΔHj), molar entropy (ΔSj), and molar free energy (ΔFj) were calculated to provide further insights into the system's characteristics and behavior.Communicated by Ramaswamy H. Sarma.

Water inside the selectivity filter of a K+ ion channel: structural heterogeneity, picosecond dynamics, and hydrogen-bonding

Water inside biological ion channels regulates the key properties of these proteins such as selectivity, ion conductance, and gating. In this Article we measure the picosecond spectral diffusion of amide I vibrations of an isotope labeled KcsA potassium channel using two-dimensional infrared (2D IR) spectroscopy. By combining waiting time (100 - 2000 fs) 2D IR measurements of the KcsA channel including 13C18O isotope labeled Val76 and Gly77 residues with molecular dynamics simulations, we elucidated the site-specific dynamics of water and K+ ions inside the selectivity filter of KcsA. We observe inhomogeneous 2D lineshapes with extremely slow spectral diffusion. Our simulations quantitatively reproduce the experiments and show that water is the only component with any appreciable dynamics, whereas K+ ions and the protein are essentially static on a picosecond timescale. By analyzing simulated and experimental vibrational frequencies, we find that water in the selectivity filter can be oriented to form hydrogen bonds with adjacent, or non-adjacent carbonyl groups with the reorientation timescales being three times slower and comparable to that of water molecules in liquid, respectively. Water molecules can reside in the cavity sufficiently far from carbonyls and behave essentially like "free" gas-phase-like water with fast reorientation times. Remarkably, no interconversion between these configurations were observed on a picosecond timescale. These dynamics are in stark contrast with liquid water that remains highly dynamic even in the presence of ions at high concentrations.

Terahertz Spectroscopy of Aqueous Solutions of Sodium Halides (NaX): Self- and Cross-Correlation Contributions of Ions and Hydration Shell Water for X- = F-, Cl-, Br-, and I. J Phys Chem B 2023;127:9323-9335. [PMID: 37871257 DOI: 10.1021/acs.jpcb.3c05228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

We investigated the terahertz (THz) absorption spectra of aqueous sodium halide solutions through molecular dynamics simulations using polarizable models of both water and ions. Specifically, we have considered aqueous solutions (∼1 M) of NaF, NaCl, NaBr, and NaI and calculated the difference THz spectrum of these solutions by subtracting the corresponding pure water contribution from the total THz spectrum of an ionic solution. The difference absorption spectrum of a given solution is then dissected into contributions from ion and ion-water correlations and also modifications of water-water correlations in the presence of the ions. The different components are further decomposed into induced dipole and permanent charge/dipole components and also into self- and cross-correlation components. The ion-water cross-correlation components are subsequently decomposed into contributions coming from different solvation shells through radially resolved calculations of such ion-water cross-correlations. Through all of these dissections, we could investigate the origin of different parts of the difference THz spectra of the sodium halide solutions studied here. It is found that while features below or around 100 cm-1 and also around 200 cm-1 arise mainly from ion and ion-water motion, that at the librational region above 600 cm-1 primarily originates from changes in water librational motion influenced by the ions. The variations of intensities of different components are also linked to the size and charge density of the anions in the solutions.

Solvation of Nanoions in Aqueous Solutions

In recent years it has been increasingly recognized that different classes of large ions with multiple valency have effects conceptually similar to weakly solvated ions in the Hofmeister series, also labeled by the term chaotropic. The term "superchaotropic effect" has been coined because these effects are much more strongly pronounced for nanometer-sized ions, whose adsorption properties often resemble typical surfactants. Despite this growing interest in these nanometer-sized ions, a simple conceptual extension of the Hofmeister series toward nanoions has not been achieved because an extrapolation of the one-dimensional surface charge density scale does not lead to the superchaotropic regime. In this work, we discuss a generic model that is broadly applicable to ions of nearly spherical shape and thus includes polyoxometalates and boron clusters. We present a qualitative classification scheme in which the ion size appears as a second dimension. Ions of different sizes but the same charge density differ in their bulk solvation free energy. As the ions grow bigger at constant surface charge density, they become more stable in solution, but the adsorption behavior is still governed by the surface charge density. A detailed molecular dynamics simulation study of large ions that is based on a shifted Lennard-Jones potential is presented that supports the presented classification scheme.

Terahertz spectroscopy as a method for investigation of hydration shells of biomolecules

The hydration of biomolecules is one of the fundamental processes underlying the construction of living matter. The formation of the native conformation of most biomolecules is possible only in an aqueous environment. At the same time, not only water affects the structure of biomolecules, but also biomolecules affect the structure of water, forming hydration shells. However, the study of the structure of biomolecules is given much more attention than their hydration shells. A real breakthrough in the study of hydration occurred with the development of the THz spectroscopy method, which showed that the hydration shell of biomolecules is not limited to 1-2 layers of strongly bound water, but also includes more distant areas of hydration with altered molecular dynamics. This review examines the fundamental features of the THz frequency range as a source of information about the structural and dynamic characteristics of water that change during hydration. The applied approaches to the study of hydration shells of biomolecules based on THz spectroscopy are described. The data on the hydration of biomolecules of all main types obtained from the beginning of the application of THz spectroscopy to the present are summarized. The emphasis is placed on the possible participation of extended hydration shells in the realization of the biological functions of biomolecules and at the same time on the insufficient knowledge of their structural and dynamic characteristics.

Eggs of the mosquito Aedes aegypti survive desiccation by rewiring their polyamine and lipid metabolism

Upon water loss, some organisms pause their life cycles and escape death. While widespread in microbes, this is less common in animals. Aedes mosquitoes are vectors for viral diseases. Aedes eggs can survive dry environments, but molecular and cellular principles enabling egg survival through desiccation remain unknown. In this report, we find that Aedes aegypti eggs, in contrast to Anopheles stephensi, survive desiccation by acquiring desiccation tolerance at a late developmental stage. We uncover unique proteome and metabolic state changes in Aedes embryos during desiccation that reflect reduced central carbon metabolism, rewiring towards polyamine production, and enhanced lipid utilisation for energy and polyamine synthesis. Using inhibitors targeting these processes in blood-fed mosquitoes that lay eggs, we infer a two-step process of desiccation tolerance in Aedes eggs. The metabolic rewiring towards lipid breakdown and dependent polyamine accumulation confers resistance to desiccation. Furthermore, rapid lipid breakdown is required to fuel energetic requirements upon water reentry to enable larval hatching and survival upon rehydration. This study is fundamental to understanding Aedes embryo survival and in controlling the spread of these mosquitoes.

Insights into the Rearrangement of the Molecular Assembly Structure of 6-Aminonicotinic Acid in Its Hydrated Environment

Water, as a ubiquitous and essential component of life, is known to have a significant impact on the structure and function of organic molecules. In this study, we investigate the role of water in the phase transition of organic molecular assembly structures by scanning tunneling microscopy at room temperature. The results show that the -O-H···O hydrogen induced by water molecules can lead to a significant structural transition in the molecular assembly, specifically through selective weakening of -C-H···O between 6-aminonicotinic acid and the formation of new -O-H···O bonds between 6-aminonicotinic acid and water molecules. Subsequent thermal treatment of these molecular assembly structures reveals that the formation of -N-H···O hydrogen bonds induced by water molecules has created a different pathway for the phase transition of the molecular assembly structure. This knowledge has important implications for the design of organic molecules with specific nanostructures that can be controlled through hydration.

Diffusiophoresis of Weakly Charged Fluid Droplets in a General Electrolyte Solution: An Analytical Theory

Owing to the importance of analytical results for electrokinetics of colloidal entities, we performed a mathematical analysis to determine the closed form analytical results for the diffusiophoretic velocity of a hydrophobic and polarizable fluid droplet. A comprehensive mathematical model is developed for diffusiophoresis, considering the background aqueous medium as general electrolytes (e.g., binary valence-symmetric/asymmetric electrolytes and a mixed solution of binary electrolytes). We performed our analysis under a weak concentration gradient, and the analytical results for diffusiophoretic velocity are calculated within the Debye-Hückel electrostatic framework. The exact form of the diffusiophoretic velocity is further approximated with negligible error, and the approximate form is found to be free from any of the cumbersome exponential integrals and thus very convenient for practical use. The present theory also covers the diffusiophoresis of perfectly dielectric as well as perfectly conducting droplets as its limiting case. In addition, we have further derived a number of closed form expressions for diffusiophoretic velocity pertaining to several particular cases, and we observed that the derived limit correctly recovers the available existing analytical results for diffusiophoretic velocity. Thus, the present analytical theory for diffusiophoresis can be applied to a wide class of fluidic droplets, e.g., hydrophobic and dielectric oil/conducting mercury droplets, air bubbles, nanoemulsions, as well as any polarizable and hydrophobic fluidic droplet suspended in a solution of general electrolytes.

Impact of hierarchical water dipole orderings on the dynamics of aqueous salt solutions

Ions exhibit highly ion-specific complex behaviours when solvated in water, which remains a mystery despite the fundamental importance of ion solvation in nature, science, and technology. Here we explain these ion-specific properties by the ion-induced hierarchical dipolar, translational, and bond-orientational orderings of ion hydration shell under the competition between ion-water electrostatic interactions and inter-water hydrogen bonding. We first characterise this competition by a new length λHB(q), explaining the ion-specific effects on solution dynamics. Then, by continuously tuning ion size and charge, we find that the bond-orientational order of the ion hydration shell highly develops for specific ion size and charge combinations. This ordering drastically stabilises the hydration shell; its degree changes the water residence time around ions by 11 orders of magnitude for main-group ions. These findings are fundamental to ionic processes in aqueous solutions, providing a physical principle for electrolyte design and application.

A new apparatus and the relevant method to retrieve IR spectra of solutes from the corresponding aqueous solutions

An apparatus and relevant approach to obtaining IR spectra of solutes from the corresponding aqueous solution were developed. In the experiment, aqueous solutions were converted into aerosols using an ultrasonic or a pneumatic device. Subsequently, water in the nebulized solution is completely gasified under a high-speed flow and low vacuum environment. Via this process, the aqueous solution changes into a mixture of a solute or solutes and gaseous water, whose single-beam IR spectra are collected. Then, the newly developed RMF (retrieving moisture-free IR spectrum) method and the relevant approach described in our recent papers have been adopted to treat the resultant single-beam sample spectrum. As a result, the spectral contribution of the vibrational-rotational peaks of gaseous water can be removed or significantly attenuated, and IR spectra of solutes can be obtained. The approach shows an obvious advantage in retrieving the IR spectrum of volatile solutes from its aqueous solution. This capability is showcased by obtaining IR spectra of isopropanol and ethyl acetate successfully. IR spectra of these compounds can be retrieved even if the concentration of the solute is below 10 wt%. Moreover, atomization via ultrasonic/pneumatic methods offers a mild way to gasify solutes whose boiling points are remarkably higher than that of water. This advantage is manifested by acquiring IR spectra of 1-butanol and 1,2-propanediol in the gaseous phase under ambient conditions.

Solvation thermodynamics from cavity shapes of amino acids

According to common physical chemistry wisdom, the solvent cavities hosting a solute are tightly sewn around it, practically coinciding with its van der Waals surface. Solvation entropy is primarily determined by the surface and the volume of the cavity while enthalpy is determined by the solute-solvent interaction. In this work, we challenge this picture, demonstrating by molecular dynamics simulations that the cavities surrounding the 20 amino acids deviate significantly from the molecular surface. Strikingly, the shape of the cavity alone can be used to predict the solvation free energy, entropy, enthalpy, and hydrophobicity. Solute-solvent interactions involving the different chemical moieties of the amino acid, determine indirectly the cavity shape, and the properties of the branches but do not have to be taken explicitly into account in the prediction model.