Structure and hydrogen bond dynamics of water–dimethyl sulfoxide mixtures by computer simulations

Nanostructure and interfacial mechanical properties of PEG/cellulose nanocomposites studied with molecular dynamics

Our starting hypothesis is that Polyethylene glycol (PEG) can be utilized to mix with the biopolymers for consolidating fiber-reinforced composites without deteriorating their hygro-mechanical properties. The effect of PEG on the shear strength during pull-out of crystalline cellulose (CC) fiber out of an amorphous cellulose matrix is simulated with molecular dynamics. The interfacial shear stress shows a stick-slip behavior and is weakened with increasing moisture content. Shear strength increases at low moisture content, manifesting a slight strengthening of interfacial mechanical property due to cohesive forces exerted by the water molecules. At higher moisture content, shear strength is reduced due to breakage of the hydrogen bonds between CC and matrix by water molecules. When adding PEG, amorphous cellulose around the crystalline fiber is replaced by PEG, forming a mixture with amorphous cellulose. It is found that PEG-treated CC-AC composite maintains its shear strength and the presence of PEG does not deteriorate the dependence of the shear strength on moisture content. A shear strength model based on the number of hydrogen bonds between the fiber and the matrix is developed, which validates our initial hypothesis by unraveling the fundamental mechanisms at play. The model reveals that, although the shear strength per hydrogen bond between the fiber and PEG is lower than the shear strength per hydrogen bond between the fiber and amorphous cellulose, the final shear strength is partly compensated by an increase in the total number of hydrogen bonds with increasing PEG ratio. Since PEG reduces the moisture content in the composite at low relative humidity, PEG treated wood in museum conditions will show enhanced shear strength. The framework is a basis for further investigation of realistic archaeological wood with PEG-treatment.

Assessing the impact of different Urushiol primer solvents on dentin remineralization and bond strength

OBJECTIVES

To investigate urushiol's potential as a dentin cross-linking agent, promoting remineralization of etched dentin and preventing activation of endogenous proteases causing collagen degradation within the hybrid layer. The goal is to improve bond strength and durability at the resin-dentin interface.

METHODS

Urushiol primers with varying concentrations were prepared using ethanol and dimethyl sulfoxide (DMSO) as solvents. Dentin from healthy molars underwent grinding and acid etching for 15 s, followed by a 1min application of urushiol primer. After 14 and 28 days of remineralization incubation and remineralization were used to assess by Attenuated Total Reflection Fourier Transform Infrared spectroscopy (ATR-FTIR), Micro-Raman spectroscopy, X-ray Diffraction (XRD), Atomic Force Microscopy (AFM), Vickers Hardness, Scanning Electron Microscopy (SEM), and Energy X-ray dispersive spectroscopy (EDS). The overall performance of urushiol primers as dentin adhesives was observed by microtensile bond strength (μTBS) testing and nanoleakage assessment. Investigated the inhibitory properties of the urushiol primers on endogenous metalloproteinases (MMPs) utilizing in situ zymography, and the cytotoxicity of the primers was tested.

RESULTS

Based on ATR-FTIR, Raman, XRD, EM-EDS and Vickers hardness analyses, the 0.7%-Ethanol group significantly enhanced dentin mineral content and improved mechanical properties the most. Pretreatment notably increased the μTBS of restorations, promoted the stability of the mixed layer, and reduced nanoleakage and MMPs activity after 28 days.

SIGNIFICANCE

The urushiol primer facilitates remineralization in demineralized dentin, enhancing remineralization in etched dentin, effectively improving the bonding interface stability, with optimal performance observed at a 0.7 wt% concentration of the urushiol primer.

Conformational Landscape of NADH and Ion Binding in Water/DMSO Mixtures via 31P NMR Spectroscopy

This study reports on the conformational states of nicotinamide adenine dinucleotide (NADH) in water/DMSO mixtures and examines the influence of ion binding. We observe evidence of conformational changes through a series of NMR techniques, including 31P NMR relaxation (R1 and R2), chemical exchange saturation transfer (CEST), and diffusion-ordered spectroscopy (DOSY) experiments. The observed variation of the conformational states is indicative of the solvent's influence on NADH's structural flexibility. The experimental findings, in combination with viscosity data, are shown to be in line with findings from earlier molecular dynamics studies. The reported observations emphasize the critical role of the solvent environment in determining the conformational states of NADH and similar molecules with relevance for the biophysiological context. The results found herein can help in studying the biophysical behavior of NADH and similar biomolecules and their associated metabolic pathways under various solvent conditions.

Unraveling relationship between complex lifetimes and microscopic diffusion in deep eutectic solvents

Aqueous mixtures of deep eutectic solvents (DESs) have emerged as a subject of interest in recent years for their tailored physicochemical properties. However, a comprehensive understanding of water's multifaceted influence on the microscopic dynamics, including its impact on improved transport properties of the DES, remains elusive. Additionally, the diffusion mechanisms within DESs manifest heterogeneous behavior, intricately tied to the formation and dissociation kinetics of complexes and hydrogen bonds. Therefore, it is imperative to explore the intricate interplay between bond kinetics, diffusion mechanism, and dynamical heterogeneity. This work employs water as an agent to explore their relationships by studying various relaxation phenomena in a DES based on acetamide and lithium perchlorate over a wide range of water concentrations. Notably, acetamide exhibits Fickian yet non-Gaussian diffusion across all water concentrations with Fickian (τf) and Gaussian (τg) timescales following a power-law relationship, τg∝τfγ, γ ∼ 1.4. The strength of coupling between bond kinetics and different diffusion timescales is estimated through various power-law relationships. Notably, acetamide-water hydrogen bond lifetime is linked to diffusive timescales through a single power-law over the entire water concentration studied. However, the relationship between diffusive timescales and the lifetime of acetamide-lithium complexes shows a sharp transition in behavior at 20 wt. % water, reflecting a change from vehicular diffusion below this concentration to structural diffusion above it. Our findings emphasize the critical importance of understanding bond dynamics within DESs, as they closely correlate with and regulate the molecular diffusion processes within these systems.

Nonlinear composition dependence of hydrogen bond lifetime in water-DMSO binary mixtures: The role of hydrophobic interaction

The lifetime of a hydrogen bond between water and dimethyl sulfoxide (DMSO) is found to be considerably longer than that between two water molecules in neat water. This is counter-intuitive because the charge on the oxygen in DMSO is considerably less than that in water. Additionally, the strength of the water-dimethyl sulfoxide (w-D) hydrogen bond is found to be strongly composition dependent; the lifetime of the hydrogen bond is ten times larger at 30% than at very low concentrations. Using computer simulations, we perform microscopic structural and dynamic analysis to find that these anomalies arise at least partly from an "action-at-a-distance" effect where the attraction between the hydrophobic methyl groups results in the self-aggregation of DMSO molecules that "cages" both the rotational and linear motions of the molecules involved. This is reflected in the observed strong correlation of the lifetime with the local coordination number of the associated methyl groups. The elongated w-D h-bond lifetime causes a slowdown of collective dynamics and affects the lifetime of the w-w h-bond. This nonlinear feedback mechanism explains the strong composition dependence of viscosity and is anticipated to play a dominant role in many self-assemblies. Furthermore, the w-D hydrogen bond breaking mechanism changes from low to high DMSO concentration, a phenomenon not anticipated a priori. We introduce a new order parameter-based free energy surface of the bond breaking pathway. A two-dimensional transition state rate theory calculation is performed for the lifetime of the w-D h-bond that is found to be semi-quantitatively accurate.

Wettability behavior of DTMS modified SiO2: Experimental and molecular dynamics study

In this research, the wetting behavior of SiO2 modified with dodecyltrimethoxysilane (DTMS) was explored using both experimental and molecular dynamics (MD) simulation approaches. The experimental results reveal that DTMS can chemically bond to the SiO2 surface, and the contact angle (CA) reaches the maximum value of 157.7° when the mass of DTMS is twice that of SiO2. The different wetting behaviors caused by DTMS grafting were analyzed by CA fitting, ionic pairs, concentration distribution, molecule orientation, and interfacial interaction energy. The results demonstrate that a 25 % DTMS grafting rate resulted in a maximum CA of 158.2°, which is ascribed to the disruption of interfacial hydrogen bonding and changes in the hydration structure caused by DTMS grafting. Moreover, the above hydrophobic SiO2 model shows a slight decrease in CA as the water temperature increases, which is consistent with the experimental findings. In contrast, an opposite change was observed for the pristine SiO2 model. Although the higher water temperature enhances the diffusion capacity of water molecules in both models, the difference in interfacial interactions is responsible for the change in CA. We hope this finding will contribute to a deeper understanding of the wetting adjustment of SiO2.

Solvation Structures and Transport Mechanisms of Cations in Water-in-Bisalt Electrolytes for High-Concentration Lithium-Ion Batteries Revealed by Molecular Dynamics Simulations

The development of safe and cost-effective electrolytes for rechargeable batteries is currently underway. While water-based electrolytes hold promise, their restricted electrochemical stability window poses a challenge. Combining multiple ionic species emerges as a promising strategy to broaden this stability window and optimize Li-ion battery performance. This study focuses on dual-cation electrolytes, which blend lithium and potassium acetates to enhance the electrochemical characteristics of the solution at high concentrations. We investigated the solvation structure of each ion and its interactions on a molecular level. Our analysis reveals that ion clusters and aggregates are formed through shared acetate and water molecules at high salt concentrations. Furthermore, the residence time analyses of atom pairs indicate that cations diffuse in vehicular mode at low concentrations. In contrast, they switch to a structural mode at high concentrations due to diminishing water content. This study offers a comprehensive model for exploring diverse solvation structures of cations and gaining insights into their diffusion mechanisms within water-in-bisalt electrolytes for aqueous Li-ion batteries.

Computation of Overhauser dynamic nuclear polarization processes reveals fundamental correlation between water dynamics, structure, and solvent restructuring entropy

Hydration water dynamics, structure, and thermodynamics are crucially important to understand and predict water-mediated properties at molecular interfaces. Yet experimentally and directly quantifying water behavior locally near interfaces at the sub-nanometer scale is challenging, especially at interfaces submerged in biological solutions. Overhauser dynamic nuclear polarization (ODNP) experiments measure equilibrium hydration water dynamics within 8-15 angstroms of a nitroxide spin probe on instantaneous timescales (10 picoseconds to nanoseconds), making ODNP a powerful tool for probing local water dynamics in the vicinity of the spin probe. As with other spectroscopic techniques, concurrent computational analysis is necessary to gain access to detailed molecular level information about the dynamic, structural, and thermodynamic properties of water from experimental ODNP data. We chose a model system that can systematically tune the dynamics of water, a water-glycerol mixture with compositions ranging from 0 to 0.3 mole fraction glycerol. We demonstrate the ability of molecular dynamics (MD) simulations to compute ODNP spectroscopic quantities, and show that translational, rotational, and hydrogen bonding dynamics of hydration water align strongly with spectroscopic ODNP parameters. Moreover, MD simulations show tight correlations between the dynamic properties of water that ODNP captures and the structural and thermodynamic behavior of water. Hence, experimental ODNP readouts of varying water dynamics suggest changes in local structural and thermodynamic hydration water properties.

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

The structural properties of aqueous 1-4 dioxane mixtures are studied by computer simulations of different water and dioxane force field models, from the perspective of illustrating the link between structural properties at the molecular level and measurable properties such as radiation scattering intensities and Kirkwood-Buff integrals (KBIs). A strategy to consistently correct the KBI obtained from simulations is proposed, which allows us to obtain the genuine KBI corresponding to a given pair of molecular species, in the entire concentration range, and without necessitating excessively large system sizes. The application of this method to the aqueous dioxane mixtures, with an all-atom CHARMM dioxane model and 2 water models, namely, SPC/E and TIP3P, allows one to understand the differences in the structure of the corresponding mixtures at the molecular level, particularly concerning the role of the water aggregates and its model dependence. This study allows us to characterize the dual role played by the concentration fluctuations and the domain segregation, particularly in what concerns the calculated X-ray spectra.

Controlling Interfacial Hydrogen Bonding at a Gold Surface: The Effect of Organic Cosolvents

Water often serves as both a reactant and solvent in electrocatalytic reactions. Interfacial water networks can affect the transport and kinetics of these reactions, e.g., hydrogen evolution reaction and CO2 reduction reaction. Adding cosolvents that influence the hydrogen-bonding (H-bonding) environment, such as dimethyl sulfoxide (DMSO), has the potential to tune the reactivity of these important electrocatalytic reactions by regulating the interfacial local environment and water network. We investigate interfacial H-bonding networks in water-DMSO cosolvent mixtures on gold surfaces by using surface-enhanced infrared absorption spectroscopy and molecular dynamics simulations. Experiments and simulations show that the gold surface is enriched with dehydrated DMSO molecules and the mixture phase-separates to form water clusters. Simulations show a "buckled" water conformation at the surface, further constraining interfacial H-bonding. The small size of these water clusters and the energetically unfavorable H-bond conformations might inhibit H-bonding with bulk water, suppressing the proton diffusion required for efficient hydrogen evolution reaction processes.

Bridging the Gap in Cryopreservation Mechanism: Unraveling the Interplay between Structure, Dynamics, and Thermodynamics in Cryoprotectant Aqueous Solutions

Cryoprotectants play a crucial role in preserving biological material, ensuring their viability during storage and facilitating crucial applications such as the conservation of medical compounds, tissues, and organs for transplantation. However, the precise mechanism by which cryoprotectants modulate the thermodynamic properties of water to impede the formation and growth of ice crystals, thus preventing long-term damage, remains elusive. This is evident in the use of empirically optimized recipes for mixtures that typically contain DMSO, glycerol, and various sugar constituents. Here, we use terahertz calorimetry, Overhauser nuclear polarization, and molecular dynamics simulations to show that DMSO exhibits a robust structuring effect on water around its methyl groups, reaching a maximum at a DMSO mole fraction of XDMSO = 0.33. In contrast, glycerol exerts a smaller water-structuring effect, even at higher concentrations (Scheme 1). These results potentially suggest that the wrapped water around DMSO's methyl group, which can be evicted upon ligand binding, may render DMSO a more surface-active cryoprotectant than glycerol, while glycerol may participate more as a viscogen that acts on the entire sample. These findings shed light on the molecular intricacies of cryoprotectant solvation behavior and have potentially significant implications for optimizing cryopreservation protocols.

Deswelling Mechanisms of PNIPAM Grafted in Nanochannels: A Molecular Dynamics Simulation Study

Porous thermosensitive hydrogels exhibit a more flexible strategy for freshwater capture compared to conventional hydrogels. This study employs molecular dynamics (MD) simulation to investigate the deswelling behavior of poly(N-isopropylacrylamide) (PNIPAM) grafted within the nanochannel, aiming to elucidate the deswelling elimination process at various temperatures. Notably, a distinct phase separation is observed at specific temperatures above the lower solution temperature (LCST). Furthermore, this study takes the effect of heat flux into account, wherein distinct heat fluxes lead to varying levels of phase separation between water and the polymer. Specifically, the number of hydrogen bonds, volume of polymer chains, and density distribution of water molecules are statistically analyzed to reveal the mechanism of phase separation in a thermosensitive hydrogel. These findings provide insight into the accelerated deswelling kinetics of the PNIPAM polymer chain, which has guiding significance for the field of water harvesting by the enhancement of the water release capacity in thermosensitive hydrogels.

Ion diffusion captures composition-dependent anomalies in water-DMSO binary mixtures

Aqueous dimethyl sulfoxide (Aq-DMSO) binary mixture exhibits many fascinating composition-dependent anomalies that are explained by using the peculiarities of the water-DMSO hydrogen bond. Ions can couple strongly to these composition-dependent anomalies to produce exotic dynamics of their own. We carry out theoretical studies using computer simulations to understand the structural and dynamical aspects of rigid monovalent cations (Li+, Na+, K+, Rb+, and Cs+) in aqueous DMSO solutions, with chloride as the counterion. We uncover a number of composition-dependent ion diffusion anomalies, which can be traced back to the interplay between the size-dependent charge density of the ion and the resulting difference in interactions of the ion with water and DMSO molecules. Size and composition dependence of the diffusion coefficients of the five ions exhibit fascinating variations that can be explained partially.

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.

Measuring the Capacitance of Carbon in Ionic Liquids: From Graphite to Graphene

The physical electrochemistry of the carbon/ionic liquids interface underpins the processes occurring in a vast range of applications spanning electrochemical energy storage, iontronic devices, and lubrication. Elucidating the charge storage mechanisms at the carbon/electrolyte interface will lead to a better understanding of the operational principles of such systems. Herein, we probe the charge stored at the electrochemical double layer formed between model carbon systems, ranging from single-layer graphene to graphite and the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EMIM-TFSI). The effect of the number of graphene layers on the overall capacitance of the interface is investigated. We demonstrate that in pure EMIM-TFSI and at moderate potential biases, the electronic properties of graphene and graphite govern the overall capacitance of the interface, while the electrolyte contribution to the latter is less significant. In mixtures of EMIM-TFSI with solvents of varying relative permittivity, the complex interplay between electrolyte ions and solvent molecules is shown to influence the charge stored at the interface, which under certain conditions overcomes the effects of relative permittivity. This work provides additional experimental insights into the continuously advancing topic of electrochemical double-layer structure at the interface between room temperature ionic liquids and carbon materials.

Identification of local structures in water from supercooled to ambient conditions

Studies of water thermodynamics have long been tied to the identification of two distinct families of local structures, whose competition could explain the origin of the many thermodynamic anomalies and the hypothesized liquid-liquid critical point in water. Despite the many successes and insights gained, the structural indicators proposed throughout the years were not able to unequivocally identify these two families over a wide range of conditions. We show that a recently introduced indicator, Ψ, which exploits information on the hydrogen bond network connectivity, can reliably identify these two distinct local environments over a wide range of thermodynamic conditions (188-300 K and 0-13 kbar) and that close to the liquid-liquid critical point, the spatial correlations of density fluctuations are identical to those of the Ψ indicator. Our results strongly support the idea that water thermodynamic properties arise from the competition between two distinct and identifiable local environments.

Effects of different cryopreservation parameters on the differences between trypan blue and fluorescent SYTO 13/GelRed assays

Post-thaw cell viability assessment is very important in cryopreservation because it is the main assessment method used to optimize the cryopreservation protocols for each cell type; hence, having standardized accurate, quick, and reliable assays for post-thaw cell viability measurements is of utmost importance. The trypan blue exclusion assay and nucleic-acid-binding fluorescence-based assays are two different methods for cell viability assessment. Both assays identify cells with damaged membranes by whether they let a compound enter the cell. In this study, these two assays are compared in the context of cryopreservation and the impacts of important cryopreservation parameters on the differences in measurements are investigated. H9c2 myoblasts were cryopreserved with different freezing protocols. Cell membrane integrities were measured immediately after thaw as well as after cryoprotectant removal by a hemocytometer-based trypan blue dye exclusion assay and a dual fluorometric SYTO 13/GelRed assay; and the results were compared. This study quantifies how i) the absence or presence of different cryoprotectants, ii) different cell-cryoprotectant incubation conditions, and iii) the presence or removal of cryoprotectants after thaw affect the differences between these two viability assays.

Liquid-Liquid Crossover in Water Model: Local Structure vs Kinetics of Hydrogen Bonds

In equilibrium and supercooled liquids, polymorphism is manifested by thermodynamic regions defined in the phase diagram, which are predominantly of different short- and medium-range order (local structure). It is found that on the phase diagram of the water model, the thermodynamic region corresponding to the equilibrium liquid phase is divided by a line of the smooth liquid-liquid crossover. In the case of the water model TIP4P/2005, this crossover is revealed by various local order parameters and corresponds to pressures on the order of 3150 ± 350 atm at ambient temperature. In the vicinity of the crossover, the dynamics of water molecules change significantly, which is reflected, in particular, in the fact that the self-diffusion coefficient reaches its maximum values. In addition, changes in the structure also manifest themselves in changes in the kinetics of hydrogen bonding, which are captured by values of such quantities as the average lifetime of hydrogen bonding, the average lifetimes of different local coordination numbers, and the frequencies of changes in different local coordination numbers. An interpretation of the hydrogen bond kinetics in terms of the free energy landscape concept in the space of possible coordination numbers is proposed.

Human Natural Killer Cells Cryopreserved without DMSO Sustain Robust Effector Responses

Natural killer (NK) cell-based immunotherapy has benefitted from the multiple strengths that NK cells offer in adoptive transfer settings, not the least of which is their safety and potential for allogeneic use. Such use, however, necessitates the cryopreservation of NK cell-based therapy products to support logistical efforts in deploying these cells in different locations, decentralized from the point of collection or manufacturing. DMSO, the most commonly used cryoprotective agent (CPA), has been effective in protecting immune cells during freezing and thawing, but its ability to induce molecular and genetic changes to immune cells as well as its toxicity has stimulated interest in alternative CPAs. However, replacing DMSO's ability to act intracellularly has been difficult, and the sensitivity of human peripheral blood-derived NK cells to freezing and thawing-induced damage has meant that investigations into the potential of replacing DMSO are lacking. As a first step toward establishing the feasibility of cryopreserving human NK cells with CPAs' alternative to DMSO, we investigate the potential of using noncell-penetrating and cell-penetrating CPAs to recover NK cells post-thaw without DMSO. Here, we find that cryoprotection using cell-penetrating CPAs can retain the viability of human peripheral blood-derived NK cells to a comparable degree to DMSO. In addition, non-DMSO-cryopreserved human NK cells were as cytotoxic as those cryopreserved with DMSO and displayed a comparable level of surface markers of activation. In summary, we present the first example of the potential of developing non-DMSO CPA formulations that could be deployed in future cell therapy regimens.

Nanoscale Insights into CO2 Enhanced Shale Gas Recovery in Gas-Water Coexisting Kerogen Nanopores

The presence of water clusters in kerogen nanopores reduces the occurrence and migration of methane (CH4) and thus affects shale gas extraction. CO2 injection, as an effective approach to enhance shale gas recovery, still presents challenges in its ability to mitigate the impact of immobile water clusters within the kerogen. In this work, molecular dynamics simulations were employed to investigate the microscopic transport process of water clusters and CH4 following CO2 injection in the gas-water coexisting kerogen nanopores. The results demonstrate that CO2 can desorb irreducible water clusters to dredge the pores while extracting CH4, enhancing gas-water mobility, and shale gas recovery by transitioning the wettability of the kerogen nanopore surface from weakly water-wet to CO2-wet. The impact of CO2 on the wettability of kerogen surfaces is primarily manifested in two aspects: CO2 can intrude the interface between water clusters and kerogen to reduce the number of hydrogen bonds between them, resulting in the detachment of water clusters; and the surface of kerogen nanopores can form a layer of CO2 gas film, which prevents desorbed water clusters and CH4 from readsorbing onto the wall surface. This study provides important insights in enhancing the understanding of the microscopic mechanisms in nanoscale flow, as well as for the development of an unconventional gas reservoir.

Liquid-Vapor Interface of Aqueous Ethylene Glycol Solutions: A Molecular Dynamics Study

While the organic constituent in an aqueous binary solution enriches its liquid-vapor (l-v) interface, the extent of enrichment can depend nonlinearly on its mole fraction. A microscopic quantification and rationalization of this behavior are crucial to understand the dependence of properties such as surface tension and evaporation rate of the solution on its composition. Extensive all-atom molecular dynamics simulations of aqueous ethylene glycol (EG) solutions show that the composition of the solution at the l-v interface deviates the most from that in the bulk solution at an EG mole fraction of 0.3. The population of EG molecules with their central C-C dihedral in the gauche conformation was found to be higher at the l-v interface than that in the bulk solution to facilitate the orientation of its hydrophobic methyl groups toward the vapor phase. Free energy calculations reveal that in dilute EG solutions, an EG molecule is most stable at the l-v interface. The behavior of vapor pressure in aqueous EG solutions is ideal and follows Raoult's law, while in contrast, the aqueous solution of dimethyl sulfoxide does not. A rationale for the same is provided through the orientational distribution of interfacial water molecules in the respective solutions.

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

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

The rigidity of a structural bridge on HLA-I binding groove explains its differential outcome in cancer immune response

The tremendous success of immune checkpoint blockade (ICB) therapy has raised the great demand for the development of predictive biomarkers. A recent cancer genomic study suggested that human leukocyte antigen (HLA)-B*44:02 and HLA-B*15:01 alleles may act as potential biomarkers for ICB therapies, however, the underlying molecular mechanisms remain largely elusive. Here, we investigated the molecular origins of differential responses to ICB therapies for four representative HLA alleles: HLA-B*44:02, HLA-B*15:01, HLA-B*07:02, and HLA-B*53:01, using extensive all-atom molecular dynamics simulations. We first demonstrated that the relatively more rigid peptide-binding groove of HLA-B*15:01, than those in the other three HLA alleles, may result in challenges in its recognition with T-cell receptors. Specifically, the "bridge" structure in HLA-B*15:01 is stabilized through both intramolecular electrostatic interactions between the HLA residues and intermolecular interactions between the HLA and the antigenic peptide. These observations were further confirmed by in silico mutagenesis studies, as well as simulations of several other HLA-B*15:01-peptide complexes. By contrast, the "bridge" structure is either completely absent in HLA-B*44:02 or easily perturbed in HLA-B*07:02 and HLA-B*53:01. Our findings provide detailed structural and mechanistic insights into how HLA genotype influences ICB responses and may have important implications for developing immune markers.

Micro-Solvation of Propofol in Propylene Glycol-Water Binary Mixtures: Molecular Dynamics Simulation Studies

The water microstructure around propofol plays a crucial role in controlling their solubility in the binary mixture. The unusual nature of such a water microstructure can influence both translational and reorientational dynamics, as well as the water hydrogen bond network near propofol. We have carried out all-atom molecular dynamics simulations of five different compositions of the propylene glycol (PG)/water binary mixture containing propofol (PFL) molecules to investigate the differential behavior of water microsolvation shells around propofol, which is likely to control the propofol solubility. It is evident from the simulation snapshots for various compositions that the PG at high molecular ratio favors the water cluster and extended chainlike network that percolates within the PG matrix, where the propofol is in the dispersed state. We estimated that the radial distribution function indicates higher ordered water microstructure around propofol for high PG content, as compared to the lower PG content in the PG/water mixture. So, the hydrophilic PG regulates the stability of the water micronetwork around propofol and its solubility in the binary mixture. We observed that the translational and rotational mobility of water belonging to the propofol microsolvation shell is hindered for high PG content and relaxed toward the low PG molecular ratio in the PG/water mixture. It has been noticed that the structural relaxation of the hydrogen bond formed between the propofol and the water molecules present in the propofol microsolvation shell for all five compositions is found to be slower for high PG content and becomes faster on the way to low PG content in the mixture. Simultaneously, we calculated the intermittent residence time correlation function of the water molecules belonging to the microsolvation shell around the propofol for five different compositions and found a faster short time decay followed up with long time components. Again, the origin of such long time decay is primarily from the structural relaxation of the microsolvation shell around the propofol, where the high PG content shows the slower structural relaxation that turns faster as the PG content approaches to the other end of the compositions. So, our studies showed that the slower structural relaxation of the microsolvation shell around propofol for a high PG molecular ratio in the PG/water mixture correlate well with the extensive ordering of the water microstructure and restricted water mobility and facilitates the dissolution process of propofol in the binary mixture.

Improvement of Temperature Distribution Uniformity of Ready-to-Eat Rice during Microwave Reheating via Optimizing Packaging Structure

The taste quality of ready-to-eat rice is influenced by the uniformity of temperature distribution during microwave reheating. The temperature distribution uniformity of ready-to-eat rice loaded in a rectangular lunch box is investigated under microwave reheating. The results show that with a 10-80 °C temperature increase in the ready-to-eat rice, the thermal conductivity increases, dielectric constant, and specific heat increase and then decrease, while the dielectric loss factor decreases and then slightly increases. The microwave-heating process of ready-to-eat rice exhibits a clear 'corner effect', and the observed 'hot spot' results in poor temperature uniformity in ready-to-eat rice. A metalized packaging structure design is subsequently proposed to ameliorate the temperature non-uniformity. According to comparative results of four metalized packaging forms, the spray film volume and film thickness corresponding to film volume are developed as 3.5×10-4 mL/mm2, 0.30 mm, respectively, which levels off the difference in temperature to improve the temperature distribution uniformity of ready-to-eat rice by microwave reheating.

Molecular Dynamics Studies of the Ho(III) Aqua-tris(dibenzoylmethane) Complex: Role of Water Dynamics

The seven-coordinate Ho(III) aqua-tris(dibenzoylmethane)(DBM) complex, referred to as Ho-(DBM)₃·H₂O, was first reported in the late 1960s. It has a threefold symmetric structure, with Ho at the center of three dibenzoylmethane ligands and hydrogen-bonded water to ligands. It is considered that the hydrogen bonds between the water molecule and the ligands surrounding Ho play an important role in the formation of its symmetrical structure. In this work, we developed new force-field parameters for classical molecular dynamics (CMD) simulations to theoretically elucidate the structure and dynamics of Ho-(DBM)₃·H₂O. To develop the force field, structural optimization and molecular dynamics were performed on the basis of ab initio calculations using the plane-wave pseudopotential method. The force-field parameters for CMD were then optimized to reproduce the data obtained from ab initio calculations. Validation of the developed force field showed good agreement with the experimental crystalline structure and ab initio data. The vibrational properties of water in Ho-(DBM)₃·H₂O were investigated by comparison with bulk liquid water. The vibrational motion of water was found to have a characteristic mode originating from stationary rotational motion along the c-axis of Ho(III) aqua-tris(dibenzoylmethane). Contrary to expectations, the hydrogen-bond dynamics of water in Ho-(DBM)₃·H₂O were found to be almost equivalent to those of bulk liquid water except for librational motion. This development route for force-field parameters for CMD and the establishment of water dynamics can advance the understanding of water-coordinated metal complexes with high coordination numbers such as Ho-(DBM)₃·H₂O.

Local solvation structures govern the mixing thermodynamics of glycerol-water solutions

Glycerol is a major cryoprotective agent and is widely used to promote protein stabilization. By a combined experimental and theoretical study, we show that global thermodynamic mixing properties of glycerol and water are dictated by local solvation motifs. We identify three hydration water populations, i.e., bulk water, bound water (water hydrogen bonded to the hydrophilic groups of glycerol) and cavity wrap water (water hydrating the hydrophobic moieties). Here, we show that for glycerol experimental observables in the THz regime allow quantification of the abundance of bound water and its partial contribution to the mixing thermodynamics. Specifically, we uncover a 1 : 1 connection between the population of bound waters and the mixing enthalpy, which is further corroborated by the simulation results. Therefore, the changes in global thermodynamic quantity - mixing enthalpy - are rationalized at the molecular level in terms of changes in the local hydrophilic hydration population as a function of glycerol mole fraction in the full miscibility range. This offers opportunities to rationally design polyol water, as well as other aqueous mixtures to optimize technological applications by tuning mixing enthalpy and entropy based on spectroscopic screening.

Microwave Sensor for the Determination of DMSO Concentration in Water-DMSO Binary Mixture

This research aims to develop a microwave sensor to accurately measure the concentration of dimethyl sulfoxide (DMSO) in water-DMSO binary mixtures. The proposed sensor will utilize microwave frequency measurements to determine the DMSO concentration, providing a non-invasive and efficient method for analyzing DMSO solutions. The research will involve the design, fabrication, and testing of the sensor, as well as the development of an appropriate calibration model. The outcomes of this study will contribute to improved monitoring and quality control in various fields, including pharmaceuticals, chemical synthesis, and biomedical research. The binary mixtures of dimethyl sulfoxide (DMSO) and water with varying concentrations were investigated in the frequency range of 1 GHz to 5 GHz at room temperature using a microwave sensor. The proposed microwave sensor design was based on an interdigital capacitor (IDC) microstrip antenna loaded with a hexagonal complementary ring resonator (HCRR). The performance of the sensor, fabricated using the print circuit board (PCB) technique, was validated through simulations and experiments. The reflection coefficient (S₁₁) and resonance frequency (F_r) of binary mixtures of DMSO and water solutions were recorded and analyzed for DMSO concentrations ranging from 0% v/v to 75% v/v. Mathematical models were developed to analyze the data, and laboratory tests showed that the sensor can detect levels of DMSO/water binary mixtures. The sensor is capable of detecting DMSO concentrations ranging from 0% v/v to 75% v/v, with a maximum sensitivity of 0.138 dB/% for S₁₁ and ΔS₁₁ and 0.2 MHz/% for F_r and ΔF_r at a concentration of 50% v/v. The developed microwave sensor can serve as an alternative for detecting DMSO concentrations in water using a simple and cost-effective technique. This method can effectively analyze a wide range of concentrations, including highly concentrated solutions, quickly and easily.

Emerging Trends of Computational Chemistry and Molecular Modeling in Froth Flotation: A Review

Froth flotation is the most versatile process in mineral beneficiation, extensively used to concentrate a wide range of minerals. This process comprises mixtures of more or less liberated minerals, water, air, and various chemical reagents, involving a series of intermingled multiphase physical and chemical phenomena in the aqueous environment. Today's main challenge facing the froth flotation process is to gain atomic-level insights into the properties of its inherent phenomena governing the process performance. While it is often challenging to determine these phenomena via trial-and-error experimentations, molecular modeling approaches not only elicit a deeper understanding of froth flotation but can also assist experimental studies in saving time and budget. Thanks to the rapid development of computer science and advances in high-performance computing (HPC) infrastructures, theoretical/computational chemistry has now matured enough to successfully and gainfully apply to tackle the challenges of complex systems. In mineral processing, however, advanced applications of computational chemistry are increasingly gaining ground and demonstrating merit in addressing these challenges. Accordingly, this contribution aims to encourage mineral scientists, especially those interested in rational reagent design, to become familiarized with the necessary concepts of molecular modeling and to apply similar strategies when studying and tailoring properties at the molecular level. This review also strives to deliver the state-of-the-art integration and application of molecular modeling in froth flotation studies to assist either active researchers in this field to disclose new directions for future research or newcomers to the field to initiate innovative works.

Ultrafast Water H-Bond Rearrangement in a Metal-Organic Framework Probed by Femtosecond Time-Resolved Infrared Spectroscopy

We investigated the water H-bond network and its dynamics in Ni₂Cl₂BTDD, a prototypical MOF for atmospheric water harvesting, using linear and ultrafast IR spectroscopy. Utilizing isotopic labeling and infrared spectroscopy, we found that water forms an extensive H-bonding network in Ni₂Cl₂BTDD. Further investigation with ultrafast spectroscopy revealed that water can reorient in a confined cone up to ∼50° within 1.3 ps. This large angle reorientation indicates H-bond rearrangement, similar to bulk water. Thus, although the water H-bond network is confined in Ni₂Cl₂BTDD, different from other confined systems, H-bond rearrangement is not hindered. The picosecond H-bond rearrangement in Ni₂Cl₂BTDD corroborates its reversibility with minimal hysteresis in water sorption.

Molecular dynamics study of low molecular weight gel forming salt-triggered dipeptide

Molecular dynamics simulation method was used to study the aggregation of Na and Ca salts in different concentrations of Naphthalene-dipeptide (2NapFF) solutions. The results show that high-valence Ca2+ triggers the formation of a gel at a certain dipeptide concentration, and the low-valence Na+ system follows the aggregation law of general surfactants. The results also show that hydrophobic and electrostatic forces are the main driving forces for the formation of dipeptide aggregates, and that hydrogen bonds do not play a major role in the formation of dipeptide solution aggregates. Hydrophobic and electrostatic effects are the main driving forces for the formation of gels in dipeptide solutions triggered by Ca2+. Electrostatic attraction drives Ca2+ to form a weak coordination with four oxygen atoms on two carboxyl groups, which causes the dipeptide molecules to form a gel with a branched network structure.

One-Pot Synthesis, E-/Z-Equilibrium in Solution of 3-Hetarylaminomethylidenefuran-2(3H)-ones and the Way to Selective Synthesis of the E-Enamines

We describe a method to synthesize a new class of hetarylaminomethylidene derivatives of furan-2(3H)-ones. The method uses 5-(4-chlorophenyl)furan-2(3H)-one, triethyl orthoformate, and heterocyclic amines with different ring sizes and heteroatoms under refluxing in absolute isopropyl alcohol. The obtained enamines exist in an equilibrium of E- and Z-isomers, whose configurations relative to the double exocyclic C=C bond were confirmed with a set of NMR spectroscopy data. The E-/Z-equilibrium of the synthesized compounds is affected by the configuration of the intermediate, the volume of its substituents, the site of enolate attack, the presence of intramolecular interactions of amino components, the time of the transformation, the order of mixing of the initial reagents, and the use of polar solvents in the NMR experiment. The advantages of the method are that the reaction time is short, the product yield is high, and product purification is easy.

Wettability of net C, net W and net Y: a molecular dynamics simulation study

The experimental synthesis of biphenylene, a two-dimensional carbon allotrope, theoretically predicted in 1997, took place in 2021. Biphenylene is also called net C. Two close relatives of this structure, known as net W and net Y, have not yet been experimentally synthesized. In this article, the wettability properties of these three carbon allotropes are investigated, using molecular dynamics simulation. The electronic and mechanical properties of these allotropes have been extensively studied, but their wettability properties are unknown. The chemical structure of the three allotropes is similar and contain four, six, and eight carbon membered rings. The results of molecular dynamics calculations with reactive potential show that net C, net W and net Y are hydrophobic substrates with contact angles of 122.3° ± 1.3°, 126.2° ± 1.3° and 127.8° ± 1.2°, respectively. The droplets on the above-mentioned substrates have a completely layered structure. That is, the water molecules inside the droplet are completely placed in certain layers. Calculating the order parameter for water molecules shows that the degree of water molecules' tetrahedrality on all three substrates is exactly the same. In terms of hydrogen bonding at the interface, the three substrates act identically and show almost the same effect. The droplet displacement is the highest on net W and the lowest on net Y. Furthermore, the van der Waals potential on all three substrates has been scanned. It is demonstrated that the amount of droplet displacement on the surface is inversely related to the surface density of the potential peaks.

Supramolecular Protein Stabilization with Zwitterionic Polypeptide-Cucurbit[7]uril Conjugates

Protein aggregation is an obstacle for the development of new biopharmaceuticals, presenting challenges in shipping and storage of vital therapies. Though a variety of materials and methods have been explored, the need remains for a simple material that is biodegradable, nontoxic, and highly efficient at stabilizing protein therapeutics. In this work, we investigated zwitterionic polypeptides prepared using a rapid and scalable polymerization technique and conjugated to a supramolecular macrocycle host, cucurbit[7]uril, for the ability to inhibit aggregation of model protein therapeutics insulin and calcitonin. The polypeptides are based on the natural amino acid methionine, and zwitterion sulfonium modifications were compared to analogous cationic and neutral structures. Each polymer was end-modified with a single cucurbit[7]uril macrocycle to afford supramolecular recognition and binding to terminal aromatic amino acids on proteins. Only conjugates prepared from zwitterionic structures of sufficient chain lengths were efficient inhibitors of insulin aggregation and could also inhibit aggregation of calcitonin. This polypeptide exhibited no cytotoxicity in human cells even at concentrations that were five-fold of the intended therapeutic regime. We explored treatment of the zwitterionic polypeptides with a panel of natural proteases and found steady biodegradation as expected, supporting eventual clearance when used as a protein formulation additive.

Infrared spectroscopic analysis of hydrogen-bonding interactions in cryopreservation solutions

BACKGROUND

In this study we investigated hydrogen bonding interactions in hydrated and frozen solutions of different cryoprotective agents (CPAs) including dimethyl sulfoxide, glycerol, ethylene glycol, propylene glycol, and trehalose. We also investigated the effect of CPAs on ice crystal growth during storage and correlated this with storage stability of liposomes.

METHODS

FTIR spectroscopy was used to study hydrogen bonding interactions in CPA solutions in H₂O and D₂O, and their thermal response was analyzed using van 't Hoff analysis. The effect of CPAs on ice crystal growth during storage was investigated by microscopy and correlated with storage stability of liposomes encapsulated with a fluorescent dye.

RESULTS

Principal component analyses demonstrated that different CPAs can be recognized based on the shape of the OD band region only. Chemically similar molecules such as glycerol and ethylene glycol closely group together in a principal component score plot, whereas trehalose and DMSO appear as condensed separated clusters. The OH/OD band of CPA solutions exhibits an overall shift to higher wavenumbers with increasing temperature and changed fractions of weak and strong hydrogen interactions. CPAs diminish ice crystal formation in frozen samples during storage and minimize liposome leakage during freezing but cannot prevent leakage during frozen storage.

CONCLUSIONS

CPAs can be distinguished from one another based on the hydrogen bonding network that is formed in solution. DMSO-water mixtures behave anomalous compared to other CPAs that have OH groups. CPAs modulate ice crystal formation during frozen storage but cannot prevent liposome leakage during frozen storage.

Dehydration does not affect lipid-based hydration lubrication

Phosphatidylcholine (PC) lipid bilayers at surfaces massively reduce sliding friction, via the hydration lubrication mechanism acting at their highly-hydrated phosphocholine headgroups, a central paradigm of biological lubrication, particularly at articular cartilage surfaces where low friction is crucial for joint well-being. Nanotribological measurements probed the effect on such lubrication of dehydration by dimethyl sulfoxide (DMSO), known to strongly dehydrate the phosphocholine headgroups of such PC bilayers, i.e. reduce the thickness of the inter-bilayer water layer, and thus expected to substantially degrade the hydration lubrication. Remarkably, and unexpectedly, we found that the dehydration has little effect on the friction. We used several approaches, including atomic force microscopy, small- and wide-angle X-ray scattering and all-atom molecular dynamics simulations to elucidate this. Our results show that while DMSO clearly removes hydration water from the lipid head-groups, this is offset by both higher areal head-group density and by rigidity-enhancement of the lipid bilayers, both of which act to reduce frictional dissipation. This sheds strong light on the robustness of lipid-based hydration lubrication in biological systems, despite the ubiquitous presence of bio-osmolytes which compete for hydration water.

Hydrogen Bond Thermodynamics in Aqueous Acid Solutions: A Combined DFT and Classical Force-Field Approach

The thermodynamics of hydrogen bonds in aqueous and acidic solutions significantly impacts the kinetics and thermodynamics of acid reaction chemistry. We utilize in this work a multiscale approach, combining density functional theory (DFT) with classical molecular dynamics (MD) to model hydrogen bond thermodynamics in an acidic solution. Using thermodynamic cycles, we split the solution phase free energy into its gas phase counterpart plus solvation free energies. We validate this DFT/MD approach by calculating the aqueous phase hydrogen bond free energy between two water molecules (H₂O-···-H₂O), the free energy to transform an H₃O⁺ cation into an H₅O₂⁺ cation, and the hydrogen bond free energy of protonated water clusters (H₃O⁺-···-H₂O and H₅O₂⁺-···-H₂O). The computed equilibrium hydrogen bond free energy of H₂O-···-H₂O is remarkably accurate, especially considering the large individual contributions to the thermodynamic cycle. Turning to cations, we find the ion to be more stable than H₃O⁺ by roughly 1-2 k_BT. This small free energy difference allows for thermal fluctuation between the two idealized motifs, consistent with spectroscopic and simulation studies. Lastly, hydrogen bonding free energies between either H⁺ cation and H₂O in solution were found to be stronger than between two H₂O, though much less so than in vacuum because of dielectric screening in solution. Altogether, our results suggest the DFT/MD approach is promising for application in modeling hydrogen bonding and proton transfer thermodynamics in condensed phases.

Distinctly different solvation behaviors of poly(N,N-diethylacrylamide) gels in water/acetone and water/DMSO mixtures

The solvation behaviors and intermolecular interactions of a poly(N,N-diethylacrylamide) (PDEA) gel network in water/DMSO and water/acetone mixtures have been investigated by variable-temperature high-resolution ¹H MAS NMR. Unlike decreasing volume phase transition temperature (VPTT) of the typical thermosensitive poly(N-isopropylacrylamide) (PNIPAM) gel induced by both acetone and DMSO in a water-rich region, distinct phase transition behaviors are revealed for the PDEA gel. That is, acetone is found to increase the VPTT of PDEA directly in the water-rich region while DMSO is also found to increase the VPTT of PDEA at a very low concentration but then decrease the VPTT as the concentration further increases. The above distinctly different VPTT shifts of PDEA are attributed to the different polymer-cosolvent interactions in water/acetone and water/DMSO systems. DMSO molecules with a strong water affinity are preferentially excluded by the PDEA gel network, and can promote the volume phase transition by favoring the collapse of the PDEA gel network, while acetone molecules preferentially adsorbed on the polymer interact with PDEA via non-specific van der Waals interaction, which favors the swollen state of the PDEA gel.

Non-monotonic composition dependence of the breakdown of Stokes-Einstein relation for water in aqueous solutions of ethanol and 1-propanol: explanation using translational jump-diffusion approach

A series of experimental and simulation studies examined the validity of the Stokes-Einstein relationship (SER) of water in binary water/alcohol mixtures of different mixture compositions. These studies revealed a strong non-monotonic composition dependence of the SER with maxima at the specific alcohol mole fraction where the non-idealities of the thermodynamic and transport properties are observed. The translational jump-diffusion (TJD) approach elucidated the breakdown of the SER in pure supercooled water as caused by the jump translation of molecules. The breakdown of SER in the supercooled water/methanol binary mixture was successfully explained using the same TJD approach. To further generalize the picture, here we focus on the non-monotonic composition dependence of SER breakdown of water in two water/alcohol mixtures (water/ethanol and water/propanol) for a broad temperature range. In agreement with previous studies, maximum breakdown of SER is observed for the mixture with alcohol mole fraction x = 0.2. Diffusion of the water molecules at the maximum SER breakdown point is largely contributed by jump-diffusion. The residual-diffusion, obtained by subtracting the jump-diffusion from the total diffusion, approximately follows the SER for different compositions and temperatures. We also performed hydrogen (H-)bond dynamics and observed that the contribution of jump-diffusion is proportional to the total free energy of activation of breaking all H-bonds that exist around a molecule. This study, therefore, suggests that the more a molecule is trapped by H-bonding, the more likely it is to diffuse through the jump-diffusion mechanism, eventually leading to an increasing degree of SER breakdown.

The Journey of 1-Keto-1,2,3,4-Tetrahydrocarbazole Based Fluorophores: From Inception to Implementation

Carbazole is a unique template associated with several biological activities. It is due to the diverse and versatile biological properties of carbazole derivatives that they are of immense interest to the research community. 1-keto-1,2,3,4-tetrahydrocarbazoles are important synthetic intermediates to obtain carbazole derivatives. Several members of this family emit fluorescence on photoexcitation. In the context of biochemical and biophysical research, designing and characterising small molecule environment sensitive fluorophores is extremely significant. This article aims to be a state of the art review with synthetic and photophysical details of a variety of fluorophores based on 1-keto-1,2,3,4-tetrahydrocarbazole skeleton.

Exploring Heterogeneous Dynamical Environment around an Ensemble of Aβ42 Peptide Monomer Conformations

Exploring the conformational properties of amyloid β (Aβ) peptides and the role of solvent (water) in guiding the dynamical environment at their interfaces is crucial for microscopic understanding of Aβ misfolding, which is involved in causing the most common neurodegenerative disorder, i.e., Alzheimer's disease. While numerous studies in the past have emphasized examining the conformational states of Aβ peptides, the role of water has not received much attention. Here, we have performed all-atom molecular dynamics simulations of several full-length Aβ₄₂ peptide monomers with different initial configurations. Our efforts are directed toward probing the origin of the heterogeneous dynamics of water around various segments of the Aβ peptide, identified as the two terminal segments (N-term and C-term) and the two hydrophobic segments (hp1 and hp2), along with the central turn region interconnecting hp1 and hp2. Our results revealed that water hydrating hp1, hp2, and turn (nonterminal segments) and C-term segments exhibit nonuniformly restricted translational as well as rotational motions. The degree of such restriction has been found to be correlated with the hydrogen bond relaxation time scales at the interface. Importantly, it is revealed that the water molecules around hp1 and, to some extent, around hp2, form relatively rigid hydration layers, compared to that around the other segments. Such rigid hydration layers arise due to relatively more solid-like caging motions resulting in relatively lesser hydration entropy. As hp1 and hp2 have been demonstrated to play a central role in Aβ aggregation, we believe that distinct water dynamics in the vicinity of these two segments, as outlined in this study, can provide vital information in understanding the early stages of the onset of the aggregation process of such peptides at higher concentration that can further aid toward advances in AD therapeutics.

On-Off Infrared Absorption of the S═O Vibrational Probe of Dimethyl Sulfoxide

Dimethyl sulfoxide (DMSO), a polar solvent molecule, is used in a wide range of therapeutic and pharmacological applications. Different intermolecular interactions, such as dimerization and hydrogen bonding with water, are crucial to understanding the role of DMSO in applications. Herein, we study DMSO in various solvation environments to decipher the environment-dependent dimerization and hydrogen-bonding propensity. We use a combination of infrared spectroscopy, quantum mechanical calculations, and molecular dynamics simulations to reach our conclusions. Although DMSO can exist in a dynamic equilibrium between monomers and dimers, our results show that the relative intensity of the S═O stretch and the CH₃ rocking modes is a spectroscopic indicator of the extent of DMSO dimerization in solution. The dimerization (self-association) is seen to be maximum in neat DMSO. When dissolved in different solvents, the dimerization propensity decreases with increasing solvent polarity. In the presence of a protic solvent, such as water, DMSO forms a hydrogen bond with the solvent molecules, thereby reducing the extent of dimerization. Further, we estimate the hydrogen-bond occupancy of DMSO. Our results show that DMSO predominantly exists as doubly hydrogen-bonded in water.

Adsorption characteristics of peptides on ω-functionalized self-assembled monolayers: a molecular dynamics study

Molecular dynamics simulations were employed to investigate the adsorption behavior of a variety of amino-acid side-chain analogs (SCAs) and a β-hairpin (HP7) peptide on a series of liquid-like self-assembled monolayers (SAMs) with terminal functional groups of -OH, -OCH₃, -CH₃, and -CF₃. The relationships between the adsorption free energy of the SCAs and the interfacial properties of water on the SAMs were examined to determine the acute predictors of protein adsorption on the SAM surfaces. The structural changes of HP7 on the SAM surfaces were also investigated to understand the relationship between the surface nature and protein denaturation. It was found that the adsorption free energy of the SCAs was linearly related to the surface hydrophobicity, which was computed as the free energy of cavity formation near the SAM-water interfaces. In addition, the hydrophobic -CH₃ and -CF₃ SAMs produced substantial conformational changes in HP7 because of the strong hydrophobic attractions to the nonpolar side chains. The hydrophilic surface terminated by -OH also promoted structural changes in HP7 resulting from the formation of hydrogen bonds between the hydrophilic tail and HP7. Consequently, the moderate amphiphilic surface terminated by -OCH₃ avoided the denaturation of HP7 most efficiently, thus improving the biocompatibility of the surface. In conclusion, these results provide a deep understanding of protein adsorption for a wide range of polymeric surfaces, and they can potentially aid the design of appropriate biocompatible coatings for medical applications.