Water as an Active Constituent in Cell Biology

Thermal inactivation scaling applied for SARS-CoV-2

Based on a model of protein denaturation rate limited by an entropy-related barrier, we derive a simple formula for virus inactivation time as a function of temperature. Loss of protein structure is described by two reaction coordinates: conformational disorder of the polymer and wetting by the solvent. These establish a competition between conformational entropy and hydrophobic interaction favoring random coil or globular states, respectively. Based on the Landau theory of phase transition, the resulting free energy barrier is found to decrease linearly with the temperature difference T - Tm, and the inactivation rate should scale as U to the power of T - Tm. This form recalls an accepted model of thermal damage to cells in hyperthermia. For SARS-CoV-2 the value of U in Celsius units is found to be 1.32. Although the fitting of the model to measured data is practically indistinguishable from Arrhenius law with an activation energy, the entropy barrier mechanism is more suitable and could explain the pronounced sensitivity of SARS-CoV-2 to thermal damage. Accordingly, we predict the efficacy of mild fever over a period of ∼24 h in inactivating the virus.

Rotational dynamics of proteins in nanochannels: role of solvent's local viscosity

Viscosity variation of solvent in local regions near a solid surface, be it a biological surface of a protein or an engineered surface of a nanoconfinement, is a direct consequence of intermolecular interactions between the solid body and the solvent. The current coarse-grained molecular dynamics study takes advantage of this phenomenon to investigate the anomaly in a solvated protein's rotational dynamics confined using a representative solid matrix. The concept of persistence time, the characteristic time of structural reordering in liquids, is used to compute the solvent's local viscosity. With an increase in the degree of confinement, the confining matrix significantly influences the solvent molecule's local viscosity present in the protein hydration layer through intermolecular interactions. This effect contributes to the enhanced drag force on protein motion, causing a reduction in the rotational diffusion coefficient. Simulation results suggest that the direct matrix-protein non-bonded interaction is responsible for the occasional jump and discontinuity in orientational motion when the protein is in very tight confinement.

Supramolecular Depolymerization in the Mixture of Two Poor Solvents: Mechanistic Insights and Modulation of Supramolecular Polymerization of Ionic π-Systems

Solvents are fundamentally essential for the synthesis and processing of soft materials. Supramolecular polymers (SPs), an emerging class of soft materials, are usually stable in single and mixtures of poor solvents. In contrast to these preconceived notions, here we report the depolymerization of SPs in the mixture of two poor solvents. This surprising behavior was observed for well-known cationic perylene diimides (cPDIs) in the mixtures of water and amphiphilic organic solvents such as isopropanol (IPA). cPDIs form stable SPs in water and IPA but readily depolymerize into monomers in 50-70 vol% IPA containing water. This is due to the selective solvation of the π-surface of cPDIs by alkyl chains of IPA and ionic side chains by water, as evidenced by molecular dynamic simulations. Moreover, by systematically changing the ratio between water and amphiphilic organic solvent, we could achieve an unprecedented supramolecular polymerization both by increasing and decreasing the solvent polarity.

Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network

Assessing the hydropathy properties of molecules, like proteins and chemical compounds, has a crucial role in many fields of computational biology, such as drug design, biomolecular interaction, and folding prediction. Over the past decades, many descriptors were devised to evaluate the hydrophobicity of side chains. In this field, recently we likewise have developed a computational method, based on molecular dynamics data, for the investigation of the hydrophilicity and hydrophobicity features of the 20 natural amino acids, analyzing the changes occurring in the hydrogen bond network of water molecules surrounding each given compound. The local environment of each residue is complex and depends on the chemical nature of the side chain and the location in the protein. Here, we characterize the solvation properties of each amino acid side chain in the protein environment by considering its spatial reorganization in the protein local structure, so that the computational evaluation of differences in terms of hydropathy profiles in different structural and dynamical conditions can be brought to bear. A set of atomistic molecular dynamics simulations have been used to characterize the dynamic hydrogen bond network at the interface between protein and solvent, from which we map out the local hydrophobicity and hydrophilicity of amino acid residues.

Effective Debye relaxation models for binary solutions of polar liquids at terahertz frequencies

There are many effective medium models that accurately describe the dielectric properties of mixtures. However, these models assume that the components are non-interacting. This assumption is not valid for solutions of polar liquids, resulting in significant deviations between the measured and theoretically predicted values of the complex index of refraction of the mixtures. We present three effective medium theories by expanding the well-known Debye relaxation model for solutions of polar liquids in the terahertz (THz) regime. The new effective medium models proposed in this paper predict the individual relaxation Debye parameters based on the cooperative motion dynamics and self-associative properties of each mixture, and therefore explain the deviation of the dielectric functions of the solutions from the traditional effective medium models. These models are verified through reflection measurements of four alcohol-water solutions acquired through THz time-domain spectroscopy (THz-TDS). Compared to the current mixed medium models, the new effective Debye theorem predicts the dielectric properties of polar solutions more accurately and has the potential to explain inter-species mixing schemes and interactions.

Modifying conformational distribution of chiral tetrahydro-2-furoic acid through its interaction with water: a rotational spectroscopic and theoretical investigation

Rotational spectrum of a binary complex formed between tetrahydro-2-furoic acid (THFA) and water was measured using a chirped pulse Fourier transform microwave spectrometer. A comprehensive theoretical conformational search procedure was carried out using CREST, a conformational searching tool, and DFT calculations to aid the spectral assignment and interpretation. The final conformer ensemble is classified into two structural groups: Type 1 conformers showing a classic carboxylic acid monohydrate structure with two strong hydrogen-bonds formed between the COOH group of cis-THFA and water, and the much less stable Type 2 conformers with trans-THFA and weaker intermolecular interactions with water. The 'cis-' and 'trans-' labels refer to the configurations where the carboxylic C[double bond, length as m-dash]O and OH functional groups are on the same or opposite side, respectively. Only the two most stable Type 2 conformers containing trans-THFA I and II were observed experimentally in a neon jet expansion with an abundance ratio of 1 : 1. This relative abundance observation differs greatly from that of the THFA monomer, i.e. with trans-THFA I : trans-THFA II : cis-THFA III of 10 : 1 : 1 in a neon jet expansion, reported previously. The observation indicates a kinetically controlled formation process of different types of the monohydrates in a jet expansion, whereas a thermodynamically controlled process dominates within each type of structures. The relative stability of the THFA ring conformations is altered by interaction with water, showing a noticeable water induced conformational preference.

Evaluation of biological activities, structural and conformational properties of bovine beta- and alpha-trypsin isoforms in aqueous-organic media

The study of the biological activity of trypsin isoforms in aqueous-organic media is of great interest to various fields of knowledge and biochemistry applications. Thus enzymatic, structural, and energetic properties of bovine β- and α-trypsin isoforms were compared in aqueous-organic media using 30 mg of each isoform. The results showed that the changes induced on the structure and activity of the same trypsin isoform occur at different concentrations. Better results for activity (ionic strength of 0.11 mol·L^-1, at 37 °C and pH 8.0) were found in 0-40% of ethanolic media in which the activity for β-trypsin was about 60% higher than ɑ-trypsin. The ethanolic system does not cause significant changes in the level of secondary structure but the β-trypsin isoform undergoes a major rearrangement. The use of until 60% (v/v) ethanol showed that β-trypsin presents a denaturation process 17% more cooperative. The organic solvent causes redistribution in the supramolecular arrangement of both isoforms: all concentrations used induced the β-trypsin molecules to rearrange into agglomerates. The ɑ-trypsin rearranges into agglomerates up to 60% (v/v) of ethanol and aggregates at 80% (v/v) of ethanol. Both isoforms keep the enzymatic activity up to 60% (v/v) of ethanol.

Towards molecular movies with X-ray photon correlation spectroscopy

In this perspective article we highlight research opportunities and challenges in probing structural dynamics of molecular systems using X-ray Photon Correlation Spectroscopy (XPCS). The development of new X-ray sources, such as 4th generation storage rings and X-ray free-electron lasers (XFELs), provides promising new insights into molecular motion. Employing XPCS at these sources allows to capture a very broad range of timescales and lengthscales, spanning from femtoseconds to minutes and atomic scales to the mesoscale. Here, we discuss the scientific questions that can be addressed with these novel tools for two prominent examples: the dynamics of proteins in biomolecular condensates and the dynamics of supercooled water. Finally, we provide practical tips for designing and estimating feasibility of XPCS experiments as well as on detecting and mitigating radiation damage.

The melibiose-derived glycation product mimics a unique epitope present in human and animal tissues

Non-enzymatic modification of proteins by carbohydrates, known as glycation, leads to generation of advanced glycation end-products (AGEs). In our study we used in vitro generated AGEs to model glycation in vivo. We discovered in vivo analogs of unusual melibiose-adducts designated MAGEs (mel-derived AGEs) synthesized in vitro under anhydrous conditions with bovine serum albumin and myoglobin. Using nuclear magnetic resonance spectroscopy we have identified MAGEs as a set of isomers, with open-chain and cyclic structures, of the fructosamine moiety. We generated a mouse anti-MAGE monoclonal antibody and show for the first time that the native and previously undescribed analogous glycation product exists in living organisms and is naturally present in tissues of both invertebrates and vertebrates, including humans. We also report MAGE cross-reactive auto-antibodies in patients with diabetes. We anticipate our approach for modeling glycation in vivo will be a foundational methodology in cell biology. Further studies relevant to the discovery of MAGE may contribute to clarifying disease mechanisms and to the development of novel therapeutic options for diabetic complications, neuropathology, and cancer.

Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo

Water molecules can be found interacting with the surface and within cavities in proteins. However, water exchange between bulk and buried hydration sites can be slow compared to simulation timescales, thus leading to the inefficient sampling of the locations of water. This can pose problems for free energy calculations for computer-aided drug design. Here, we apply a hybrid method that combines nonequilibrium candidate Monte Carlo (NCMC) simulations and molecular dynamics (MD) to enhance sampling of water in specific areas of a system, such as the binding site of a protein. Our approach uses NCMC to gradually remove interactions between a selected water molecule and its environment, then translates the water to a new region, before turning the interactions back on. This approach of gradual removal of interactions, followed by a move and then reintroduction of interactions, allows the environment to relax in response to the proposed water translation, improving acceptance of moves and thereby accelerating water exchange and sampling. We validate this approach on several test systems including the ligand-bound MUP-1 and HSP90 proteins with buried crystallographic waters removed. We show that our BLUES (NCMC/MD) method enhances water sampling relative to normal MD when applied to these systems. Thus, this approach provides a strategy to improve water sampling in molecular simulations which may be useful in practical applications in drug discovery and biomolecular design.

Water-Mediated Interactions Determine Helix Formation of Peptides in Open Nanotubes

Water-mediated interactions (WMIs) play diverse roles in molecular biology. They are particularly relevant in geometrically confined spaces such as the interior of the chaperonin, at the interface between ligands and their binding partners, and in the ribosome tunnel. Inspired in part by the geometry of the ribosome tunnel, we consider confinement effects on the stability of peptides. We describe results from replica exchange molecular dynamics simulations of a system containing a 23-alanine or 23-serine polypeptide confined to nonpolar and polar nanotubes in the gas phase and when open to a water reservoir. We quantify the effect of water in determining the preferred conformational states of these polypeptides by calculating the difference in the solvation free energy for the helix and coil states in the open nanotube in the two phases. Our simulations reveal several possibilities. We find that nanoscopic confinement preferentially stabilizes the helical state of polypeptides with hydrophobic side chains, which is explained by the entropic stabilization mechanism proposed on the basis of polymer physics. Polypeptide chains with hydrophilic side chains can adopt helical structures within nanotubes, but helix formation is sensitive to the nature of the nanotube due to WMIs. We elaborate on the potential implications of our findings to the stability of peptides in the ribosome tunnel.

Hydration and dynamics of L-glutamate ion in aqueous solution

Aqueous solutions of sodium l-glutamate (NaGlu) in the concentration range 0 < c/M ≤ 1.90 at 25 °C were investigated by dielectric relaxation spectroscopy (DRS) and statistical mechanics (1D-RISM and 3D-RISM calculations) to study the hydration and dynamics of the l-glutamate (Glu-) anion. Although at c → 0 water molecules beyond the first hydration shell are dynamically affected, Glu- hydration is rather fragile and for c ⪆ 0.3 M apparently restricted to H2O molecules hydrogen bonding to the carboxylate groups. These hydrating dipoles are roughly parallel to the anion moment, leading to a significantly enhanced effective dipole moment of Glu-. However, l-glutamate dynamics is determined by the rotational diffusion of individual anions under hydrodynamic slip boundary conditions. Thus, the lifetime of the hydrate complexes, as well as of possibly formed [Na+Glu-]0 ionpairs and l-glutamate aggregates, cannot exceed the characteristic timescale for Glu- rotation.

Moisture Content of Bacterial Cells Determines Thermal Resistance of Salmonella enterica Serotype Enteritidis PT 30

Salmonella spp. are resilient bacterial pathogens in low-moisture foods. There has been a general lack of understanding of critical factors contributing to the enhanced thermal tolerance of Salmonella spp. in dry environments. In this study, we hypothesized that the moisture content (X_W ) of bacterial cells is a critical intrinsic factor influencing the resistance of Salmonella spp. to thermal inactivation. We selected Salmonella enterica serotype Enteritidis PT 30 to test this hypothesis. We first produced viable freeze-dried S. Enteritidis PT 30, conditioned the bacterial cells to different X_W s (7.7, 9.2, 12.4, and 15.7 g water/100 g dry solids), and determined the thermal inactivation kinetics of those cells at 80°C. The results show that the D-value (the time required to achieve a 1-log reduction) decreased exponentially with increasing X_W We further measured the water activities (a_w) of the freeze-dried S. Enteritidis PT 30 as influenced by temperatures between 20 and 80°C. By using those data, we estimated the X_W of S. Enteritidis PT 30 from the published papers that related the D-values of the same bacterial strain at 80°C with the a_w of five different food and silicon dioxide matrices. We discovered that the logarithmic D-values of S. Enteritidis PT 30 in all those matrices also decreased linearly with increasing X_W of the bacterial cells. The findings suggest that the amount of moisture in S. Enteritidis PT 30 is a determining factor of its ability to resist thermal inactivation. Our results may help future research into fundamental mechanisms for thermal inactivation of bacterial pathogens in dry environments.IMPORTANCE This study established a logarithmic relationship between the thermal death time (D-value) of S. Enteritidis PT 30 and the moisture content (X_W ) of the bacterial cells by conducting thermal inactivation tests on freeze-dried S Enteritidis PT 30. We further verified this relationship using literature data for S. Enteritidis PT 30 in five low-moisture matrices. The findings suggest that the X_W of S. Enteritidis PT 30, which is rapidly adjusted by microenvironmental a_w, or relative humidity, during heat treatments, is the key intrinsic factor determining the thermal resistance of the bacterium. The quantitative relationships reported in this study may help guide future designs of industrial thermal processes for the control of S. Enteritidis PT 30 or other Salmonella strains in low-moisture foods. Our findings highlight a need for further fundamental investigation into the role of water in protein denaturation and the accumulation of compatible solutes during thermal inactivation of bacterial pathogens in dry environments.

Investigating states of gas in water encapsulated between graphene layers

Conventionally, only two states are assumed to exist in water: well-dispersed gas monomers and gas bubbles. Rarely is this paradigm explored experimentally. To close this gap, here we used transmission electron microscopy (TEM) to study degassed water, deionized water, and gas-supersaturated water encapsulated in graphene liquid cells. While neither degassed water nor deionized water yielded specific features, two major microscopic structures were evident in gas-supersaturated water: (1) polycrystalline nanoparticles formed of gas molecules and (2) a high density of tiny cells. Dark-field TEM imaging revealed that water molecules surrounding each cell form crystalline structures-a surprising discovery of a clathrate state in gas-supersaturated water that may help resolve several long-standing puzzles. Overall, this study suggests that water may form a matrix that actively interacts with gas molecules in complex and subtle ways.

Unravelling the microhydration frameworks of prototype PAH by infrared spectroscopy: naphthalene–(water)1–3

Microhydration structures of the prototypical PAH, naphthalene, are probed by IR spectroscopy in helium droplets. The sequential water addition produces an extended hydrogen-bonded hydration network bound via π hydrogen bond to the aromatic ring.

The transition from salt-in-water to water-in-salt nanostructures in water solutions of organic ionic liquids relevant for biological applications

Computer simulations show how nano-structural motifs in organic salts/water solutions change with salt content increasing from dilute to highly concentrated.

Mapping solvation heterogeneity in live cells by hyperspectral stimulated Raman scattering microscopy

Water provides a dynamic matrix in which all biochemical processes occur in living organisms. The structure and dynamics of intracellular water constitute the cornerstone for understanding all aspects of cellular function. Fundamentally, direct visualization of subcellular solvation heterogeneity is essential but remains challenging with commonly used nuclear magnetic resonance methods due to poor spatial resolution. To explore this question, we demonstrate a vibrational-shift imaging approach by combining the spectral-focusing hyperspectral stimulated Raman scattering technique with an environmentally sensitive nitrile probe. The sensing ability of a near-infrared nitrile-containing molecule is validated in the solution phase, microscopic droplets, and cellular environments. Finally, we quantitatively measure the subcellular solvation variance between the cytoplasm (29.5%, S.E. 1.8%) and the nucleus (57.3%, S.E. 1.0%), which is in good agreement with previous studies. This work sheds light on heterogeneous solvation in live systems using coherent Raman microscopy and opens up new avenues to explore environmental variance in complex systems with high spatiotemporal resolution.

Molecular Mechanism of Acceleration and Retardation of Collective Orientation Relaxation of Water Molecules in Aqueous Solutions

The collective orientation relaxation (COR) of water molecules in aqueous solutions is faster or slower with an increase in the concentration of the solutions than that in pure water; for example, acceleration (deceleration) of the COR is observed in a solution of sodium chloride (tetramethylammonium chloride) with increasing concentration. However, the molecular mechanism of the solution and concentration dependence of the relaxation time of the COR has not yet been clarified. We theoretically investigate the concentration dependence of the COR of water molecules in solutions of tetramethylammonium chloride (TMACl), guanidinium chloride (GdmCl), and sodium chloride (NaCl). Based on the Mori-Zwanzig equation, we identify two opposing factors that determine the COR of water molecules in any aqueous solution: the correlation of dipole moments and the single-molecule orientation relaxation. We reveal the molecular mechanism of the concentration dependence of the relaxation time of the COR in the TMACl, GdmCl, and NaCl solutions in terms of these two factors.

Three-Dimensional Molecular Mapping of Ionic Liquids at Electrified Interfaces

Electric double layers (EDLs), occurring ubiquitously at solid-liquid interfaces, are critical for electrochemical energy conversion and storage processes such as capacitive charging and redox reactions. However, to date the molecular-scale structure of EDLs remains elusive. Here we report an advanced technique, electrochemical three-dimensional atomic force microscopy (EC-3D-AFM), and use it to directly image the molecular-scale EDL structure of an ionic liquid under different electrode potentials. We observe not only multiple discrete ionic layers in the EDL on a graphite electrode but also a quasi-periodic molecular density distribution within each layer. Furthermore, we find pronounced 3D reconfiguration of the EDL at different voltages, especially in the first layer. Combining the experimental results with molecular dynamics simulations, we find potential-dependent molecular redistribution and reorientation in the innermost EDL layer, both of which are critical to EDL capacitive charging. We expect this mechanistic understanding to have profound impacts on the rational design of electrode-electrolyte interfaces for energy conversion and storage.

Decoupling between the translation and rotation of water in the proximity of a protein molecule

The interaction between water and biomacromolecules is of fundamental interest in biophysics, biochemistry and physical chemistry. By combining neutron scattering and molecular dynamics simulations on a perdeuterated protein at a series of hydration levels, we demonstrated that the translational motion of water is slowed down more significantly than its rotation, when water molecules approach the protein molecule. Further analysis of the simulation trajectories reveals that the observed decoupling results from the fact that the translational motion of water is more correlated over space and more retarded by the charged/polar residues and spatial confinement on the protein surface, than the rotation. Moreover, around the stable protein residues (with smaller atomic fluctuations), water exhibits more decoupled dynamics, indicating a connection between the observed translation-rotation decoupling in hydration water and the local stability of the protein molecule.

Solute-Solvent Interactions in Modern Physical Organic Chemistry: Supramolecular Polymers as a Muse

Interactions between solvents and solutes are a cornerstone of physical organic chemistry and have been the subject of investigations over the last century. In recent years, a renewed interest in fundamental aspects of solute-solvent interactions has been sparked in the field of supramolecular chemistry in general and that of supramolecular polymers in particular. Although solvent effects in supramolecular chemistry have been recognized for a long time, the unique opportunities that supramolecular polymers offer to gain insight into solute-solvent interactions have become clear relatively recently. The multiple interactions that hold the supramolecular polymeric structure together are similar in strength to those between solute and solvent. The cooperativity found in ordered supramolecular polymers leads to the possibility of amplifying these solute-solvent effects and will shed light on extremely subtle solvation phenomena. As a result, many exciting effects of solute-solvent interactions in modern physical organic chemistry can be studied using supramolecular polymers. Our aim is to put the recent progress into a historical context and provide avenues toward a more comprehensive understanding of solvents in multicomponent supramolecular systems.

Chemical Synthesis of an Erythropoietin Glycoform Having a Triantennary N-Glycan: Significant Change of Biological Activity of Glycoprotein by Addition of a Small Molecular Weight Trisaccharide

The glycosylation of proteins contributes to the modulation of the structure and biological activity of glycoproteins. Asparagine-linked glycans (N-glycans) of glycoproteins naturally exhibit diverse antennary patterns, such as bi-, tri-, and tetra-antennary forms. However, there are no chemical or biological methods to obtain homogeneous glycoproteins via the intentional alteration of the antennary form of N-glycans. Thus, the functions of the individual antennary form of N-glycan at a molecular level remain unclear. Herein, we report the chemical synthesis of an erythropoietin (EPO) glycoform having a triantennary sialylglycan at position 83, as well as two biantennary sialylglycans at both positions 24 and 38. We demonstrated efficient liquid-phase condensation reactions to prepare a sialylglycopeptide having a triantennary N-glycan prepared by the addition of a Neu5Ac-α-2,6-Gal-β-1,4-GlcNAc element to the biantennary glycan under semisynthetic conditions. The molecular weight of the newly added antennary element was ∼3% of the EPO glycoform, and the introduced position was the most distant from the bioactive protein. However, in vivo assays using mice revealed that the additional antennary element at position 83 dramatically increased the hematopoietic activity compared to a commercially available native EPO. These unprecedented data clearly indicate that the antennary pattern of N-glycans inherently plays a critical role in the modulation of protein functions.

The Dynamism of Intrinsically Disordered Proteins: Binding-Induced Folding, Amyloid Formation, and Phase Separation

Intrinsically disordered proteins (IDPs) or natively unfolded proteins do not undergo autonomous folding into a well-defined 3-D structure and challenge the conventional structure-function paradigm. They are involved in a multitude of critical physiological functions by adopting various structural states via order-to-disorder transitions or by maintaining their disordered characteristics in functional complexes. In recent times, there has been a burgeoning interest in the investigation of intriguing behavior of IDPs using highly multidisciplinary and complementary approaches due to the pivotal role of this unique class of protein chameleons in physiology and disease. Over the past decade or so, our laboratory has been actively investigating the unique physicochemical properties of this class of highly dynamic, flexible, rapidly interconverting proteins. We have utilized a diverse array of existing and emerging tools involving steady-state and time-resolved fluorescence, Raman spectroscopy, circular dichroism, light scattering, fluorescence microscopy, and atomic force microscopy coupled with site-directed mutagenesis and other biochemical and biophysical tools to study a variety of interesting and important aspects of IDPs. In this Feature Article, I describe our work on the conformational characteristics, solvation dynamics, binding-induced folding, amyloid formation, and liquid-liquid phase separation of a number of amyloidogenic IDPs. A series of these studies described here captures the role of conformational plasticity and dynamics in directing binding, folding, assembly, aggregation, and phase transitions implicated in physiology and pathology.

Reorientation-induced relaxation of free OH at the air/water interface revealed by ultrafast heterodyne-detected nonlinear spectroscopy

The uniqueness of water originates from its three-dimensional hydrogen-bond network, but this hydrogen-bond network is suddenly truncated at the interface and non-hydrogen-bonded OH (free OH) appears. Although this free OH is the most characteristic feature of interfacial water, the molecular-level understanding of its dynamic property is still limited due to the technical difficulty. We study ultrafast vibrational relaxation dynamics of the free OH at the air/water interface using time-resolved heterodyne-detected vibrational sum frequency generation (TR-HD-VSFG) spectroscopy. With the use of singular value decomposition (SVD) analysis, the vibrational relaxation (T₁) times of the free OH at the neat H₂O and isotopically-diluted water interfaces are determined to be 0.87 ± 0.06 ps (neat H₂O), 0.84 ± 0.09 ps (H₂O/HOD/D₂O = 1/2/1), and 0.88 ± 0.16 ps (H₂O/HOD/D₂O = 1/8/16). The absence of the isotope effect on the T₁ time indicates that the main mechanism of the vibrational relaxation of the free OH is reorientation of the topmost water molecules. The determined sub-picosecond T₁ time also suggests that the free OH reorients diffusively without the switching of the hydrogen-bond partner by the topmost water molecule.

Water’s hydrogen-bond network is truncated at hydrophobic interfaces and the dynamics of the resulting free OH groups is not well understood. The authors experimentally show that the main vibrational relaxation mechanism for free OH at the air-water interface is a diffusive molecular reorientation, rather than intramolecular energy transfer.

First-passage fingerprints of water diffusion near glutamine surfaces

The extent to which biological interfaces affect the dynamics of water plays a key role in the exchange of matter and chemical interactions that are essential for life. The density and the mobility of water molecules depend on their proximity to biological interfaces and can play an important role in processes such as protein folding and aggregation. In this work, we study the dynamics of water near glutamine surfaces-a system of interest in studies of neurodegenerative diseases. Combining molecular-dynamics simulations and stochastic modelling, we study how the mean first-passage time and related statistics of water molecules escaping subnanometer-sized regions vary from the interface to the bulk. Our analysis reveals a dynamical complexity that reflects underlying chemical and geometrical properties of the glutamine surfaces. From the first-passage time statistics of water molecules, we infer their space-dependent diffusion coefficient in directions normal to the surfaces. Interestingly, our results suggest that the mobility of water varies over a longer length scale than the chemical potential associated with the water-protein interactions. The synergy of molecular dynamics and first-passage techniques opens the possibility for extracting space-dependent diffusion coefficients in more complex, inhomogeneous environments that are commonplace in living matter.

A minimum quantum chemistry CCSD(T)/CBS dataset of dimeric interaction energies for small organic functional groups

We have performed a quantum chemistry study on the bonding patterns and interaction energies for 31 dimers of small organic functional groups (dubbed the SOFG-31 dataset), including the alkane-alkene-alkyne (6 + 4 + 4 = 14, AAA) groups, alcohol-aldehyde-ketone (4 + 4 + 3 = 11, AAK) groups, and carboxylic acid-amide (3 + 3 = 6, CAA) groups. The basis set superposition error corrected super-molecule approach using the second order Møller-Plesset perturbation theory (MP2) with the Dunning's aug-cc-pVXZ (X = D, T, Q) basis sets has been employed in the geometry optimization and energy calculations. To calibrate the MP2 calculated interaction energies for these dimeric complexes, we perform single-point calculations with the coupled cluster with single, double, and perturbative triple excitations method at the complete basis set limit [CCSD(T)/CBS] using the well-tested extrapolation methods. In order to gain more physical insights, we also perform a parallel series of energy decomposition calculations based on the symmetry adapted perturbation theory (SAPT). The collection of these CCSD(T)/CBS interaction energy values can serve as a minimum quantum chemistry dataset for testing or training less accurate but more efficient calculation methods. As an application, we further propose a segmental SAPT model based on chemically recognizable segments in a specific functional group. These model interactions can be used to construct coarse-grained force fields for larger molecular systems.

Intrinsic Contributions of 2'-Hydroxyl to the Hydration of Nucleosides at the Monomeric Level

Although many reports have revealed structural differences between DNA and RNA at the polymeric level, there are no comparative studies with 2'-deoxyribonucleoside and ribonucleoside to explore the role of the 2'-OH group at the monomeric level under the same conditions. Inspired by this, herein, the intrinsic contributions of the 2'-OH group in the nucleoside have been systematically investigated by directly solving the single-crystal structures of 2'-deoxy-2-aminoadenosine (1), 2-aminoadenosine (2), and 2-aminoarabinofuranosyladenine (3) in water. The 2'-OH group not only influenced the conformation and base-pair pattern of the single-nucleoside molecule, but also played a fundamental role in the entire supramolecular structure. Interestingly, compound 1, which did not contain the 2'-OH group, displayed strong hydration, whereas 2 and 3 (with the 2'-OH group in the opposite direction) exhibited no hydration, which was completely different from that observed in nucleic acids. Meanwhile, compound 1 trapped water molecules to form unique trihydrol moieties, which further served as the backbone to construct the simplest double-chain DNA-like structures. To this end, to investigate the effect of the biological environment on these unique structures, the solvent was changed from water to phosphate-buffered saline (PBS). Surprisingly, such a subtle adjustment led to entirely different superstructures, consisting of 2D lamellar structures in water and 3D porous structures in PBS. These large morphological differences could be attributed to delicate ion hydration, which was also confirmed through variable-temperature X-ray analysis, SEM, and intermolecular interaction energy calculations. In summary, this study comprehensively investigated the intrinsic contributions of 2'-hydroxyl to the hydration of nucleosides at the monomeric level; this is helpful to further understand the differences in DNA/RNA and the impact of their surrounding environment.

Fast increase of nanofluidic slip in supercooled water: the key role of dynamics

Nanofluidics is an emerging field offering innovative solutions for energy harvesting and desalination. The efficiency of these applications depends strongly on liquid-solid slip, arising from a favorable ratio between viscosity and interfacial friction. Using molecular dynamics simulations, we show that wall slip increases strongly when water is cooled below its melting point. For water on graphene, the slip length is multiplied by up to a factor of five and reaches 230 nm at the lowest simulated temperature, T ∼ 225 K; experiments in nanopores can reach much lower temperatures and could reveal even more drastic changes. The predicted fast increase in water slip can also be detected at supercoolings reached experimentally in bulk water, as well as in droplets flowing on anti-icing surfaces. We explain the anomalous slip behavior in the supercooled regime by a decoupling between viscosity and bulk density relaxation dynamics, and we rationalize the wall-type dependence of the enhancement in terms of interfacial density relaxation dynamics. While providing fundamental insights on the molecular mechanisms of hydrodynamic transport in both interfacial and bulk water in the supercooled regime, this study is relevant to the design of anti-icing surfaces, could help explain the subtle phase and dynamical behaviors of supercooled confined water, and paves the way to explore new behaviors in supercooled nanofluidic systems.

The Bending Mode of Water: A Powerful Probe for Hydrogen Bond Structure of Aqueous Systems

Insights into the microscopic structure and dynamics of the water's hydrogen-bonded network are crucial to understand the role of water in biology, atmospheric and geochemical processes, and chemical reactions in aqueous systems. Vibrational spectroscopy of water has provided many such insights, in particular using the O-H stretch mode. In this Perspective, we summarize our recent studies that have revealed that the H-O-H bending mode can be an equally powerful reporter for the microscopic structure of water and provides more direct access to the hydrogen-bonded network than the conventionally studied O-H stretch mode. We discuss the fundamental vibrational properties of the water bending mode, such as the intermolecular vibrational coupling, and its effects on the spectral lineshapes and vibrational dynamics. Several examples of static and ultrafast bending mode spectroscopy illustrate how the water bending mode provides an excellent window on the microscopic structure of both bulk and interfacial water.

Spatial localization of charged molecules by salt ions in oil-confined water microdroplets

Cells contain more than 100 mM salt ions that are typically confined to dimensions of 5 to 10 micrometers by a hydrophobic cellular membrane. We found that in aqueous microdroplets having the same size as cells and that are confined in hydrocarbon oil, negatively charged molecules were distributed rather uniformly over the interior of the microdroplet, whereas positively charged molecules were localized at and near the surface. However, the addition of salt (NaCl) to the microdroplet caused all charged molecules to be localized near the oil-water interface. This salt-induced relocalization required less salt concentration in microdroplets compared to bulk water. Moreover, the localization became more prominent as the size of the microdroplet was reduced. The relocatization also critically depended on the type of oil. Our results imply that salt ions and different hydrophobic interfaces together may govern the local distribution of charged biomolecules in confined intracellular environments.

Dynamic behaviors of interfacial water on the self-assembly monolayer (SAM) heterogeneous surface

Dynamic behaviors of water molecules near the surface with mixed hydrophobic and hydrophilic areas are studied by molecular dynamics simulation. More specifically, the diffusion coefficient and hydrogen bond lifetime of interfacial water on the self-assembly monolayer composed of hydrophobic and hydrophilic groups and their dependence on the mixing ratio are studied. The diffusion dramatically slows down, and the hydrogen bond lifetime considerably increases when a few hydrophilic groups are added to the hydrophobic surface. When the percentage of hydrophilic groups increases to 25%, the behavior of interfacial water is similar to the case of the pure hydrophilic surface. The sensitivity to the hydrophilic group can be attributed to the fact that the grafted hydrophilic groups can not only retard the directly bound water molecules but also affect indirectly bound water by stabilizing hydrogen bonds among interfacial water molecules.

Confinement Effects on Glass-Forming Aqueous Dimethyl Sulfoxide Solutions

Combining broadband dielectric spectroscopy and nuclear magnetic resonance studies, we analyze the reorientation dynamics and the translational diffusion associated with the glassy slowdown of the eutectic aqueous dimethyl sulfoxide solution in nano-sized confinements, explicitly, in silica pores with different diameters and in ficoll and lysozyme matrices at different concentrations. We observe that both rotational and diffusive dynamics are slower and more heterogeneous in the confinements than in the bulk but the degree of these effects depends on the properties of the confinement and differs for the components of the solution. For the hard and the soft matrices, the slowdown and the heterogeneity become more prominent when the size of the confinement is reduced. In addition, the dynamics are more retarded for dimethyl sulfoxide than for water, implying specific guest-host interactions. Moreover, we find that the temperature dependence of the reorientation dynamics and of the translational diffusion differs in severe confinements, indicating a breakdown of the Stokes–Einstein–Debye relation. It is discussed to what extent these confinement effects can be rationalized in the framework of core-shell models, which assume bulk-like and slowed-down motions in central and interfacial confinement regions, respectively.

Occurrence and stability of lone pair-π and OH-π interactions between water and nucleobases in functional RNAs

We identified over 1000 instances of water-nucleobase stacking contacts in a variety of RNA molecules from a non-redundant set of crystal structures with resolution ≤3.0 Å. Such contacts may be of either the lone pair-π (lp-π) or the OH-π type, in nature. The distribution of the distances of the water oxygen from the nucleobase plane peaks at 3.5 Å for A, G and C, and approximately at 3.1-3.2 Å for U. Quantum mechanics (QM) calculations confirm, as expected, that the optimal energy is reached at a shorter distance for the lp-π interaction as compared to the OH-π one (3.0 versus 3.5 Å). The preference of each nucleobase for either type of interaction closely correlates with its electrostatic potential map. Furthermore, QM calculations show that for all the nucleobases a favorable interaction, of either the lp-π or the OH-π type, can be established at virtually any position of the water molecule above the nucleobase skeleton, which is consistent with the uniform projection of the OW atoms over the nucleobases ring we observed in the experimental occurrences. Finally, molecular dynamics simulations of a model system for the characterization of water-nucleobase stacking contacts confirm the stability of these interactions also under dynamic conditions.

Hydration Shell Changes in Surfactant Aggregate Transitions Revealed by Raman-MCR Spectroscopy

Hydration states of many self-assemblies directly relate to their structures and functions. Here, we use Raman multivariate curve resolution (Raman-MCR) assisted by differential scanning calorimetry and nuclear magnetic resonance to explore the hydration properties of aggregates formed by three cationic ammonium surfactants, trimethylene-1,3-bis(dodecyldimethylammonium bromide) (12-3-12(Br)₂), didodecyldimethylammonium bromide (DDAB), and dodecyltrimethylammonium bromide (DTAB). For 12-3-12(Br)₂, the transitions from spherical to rodlike and wormlike micelles lead to about 20% and 60% dehydration and gradually weaken water tetrahedral order and H-bond in hydration shells for both headgroup and hydrophobic chain. As to DDAB, unilamellar vesicles contain two kinds of hydration water species, but multicompartment vesicles exhibit decreased water order and weaker H-bond. DTAB only forms spherical micelles and its hydration structure is similar to that of the 12-3-12(Br)₂ spherical micelles. This work provides a basis to explore the hydration states of complex biological self-assemblies.

Anomalous sub-diffusion of water in biosystems: From hydrated protein powders to concentrated protein solution to living cells

Water is essential to life and its translational motion in living systems mediates various biological processes, including transportation of function-required ingredients and facilitating the interaction between biomacromolecules. By combining neutron scattering and isotopic labeling, the present work characterizes translational motion of water on a biomolecular surface, in a range of systems: a hydrated protein powder, a concentrated protein solution, and in living Escherichia coli (E. coli) cells. Anomalous sub-diffusion of water is observed in all samples, which is alleviated upon increasing the water content. Complementary molecular dynamics simulations and coarse-grained numerical modeling demonstrated that the sub-diffusive behavior results from the heterogeneous distribution of microscopic translational mobility of interfacial water. Moreover, by comparing the experimental results measured on E. coli cells with those from a concentrated protein solution with the same amount of water, we show that water in the two samples has a similar average mobility, however the underlying distribution of motion is more heterogeneous in the living cell.