Photophysics of a nucleic acid-protein crosslinking model strongly depends on solvation dynamics: an experimental and theoretical study.

We present a combined experimental and theoretical study of the photophysics of 5-benzyluracil (5BU) in methanol, which is a model system for interactions between nucleic acids and proteins. A molecular dynamics study of 5BU in solution through efficient DFT-based hybrid ab initio potentials revealed a remarkable conformational flexibility - allowing the population of two main conformers - as well as specific solute-solvent interactions, which both appear as relevant factors for the observed 5BU optical absorption properties. The simulated absorption spectrum, calculated on such an ensemble, enabled a molecular interpretation of the experimental UV-Vis lowest energy band, which is also involved in the induced photo-reactivity upon irradiation. In particular, the first two excited states (mainly involving the uracil moiety) both contribute to the 5BU lowest energy absorption. Moreover, as a key finding, the nature and brightness of such electronic transitions are strongly influenced by 5BU conformation and the microsolvation of its heteroatoms.

A new insight into the surface adsorption in the solution phase: A modification of the Langmuir isotherm.

The Langmuir isotherm, originally developed to study the adsorption of gases, has been modified in this research to investigate the adsorption of solutes in the solution phase. The modification considers the adsorption of solvent molecules and the interactions between adsorbed particles and the species in the solution. Three equations have been obtained to calculate the contribution of these additional effects on the Gibbs free energy, enthalpy, and entropy of solute adsorption based on the new isotherm. The study evaluated the efficiency of the new isotherm in the adsorption of some metal ions in an aqueous solution and found that it is more accurate than the Langmuir isotherm and provides a deeper insight into the adsorption process in the solution phase. PRACTITIONER POINTS: Modification of the Langmuir isotherm for adsorption in solution. Comparison of the efficiency of the Langmuir and modified Langmuir isotherms. Accurate determination of ∆ H ads o $$ \Delta {H}_{ads}^o $$ and ∆ S ads o $$ \Delta {S}_{ads}^o $$ for Pb(II), Cd(II), and Ni(II) adsorption.

Liquid-liquid biopolymers aqueous solution segregative phase separation in food: From fundamentals to applications-A review.

As a result of the spontaneous movement of molecules, liquid-liquid biopolymer segregative phase separation takes place in an aqueous solution. The efficacy of this type of separation can be optimized under conditions where variables such as pH, temperature, and molecular concentrations have minimal impact on its dynamics. Recently, interest in the applications of biopolymers and their segregative phase separation-associated molecular stratification has increased, particularly in the food industry, where these methods permit the purification of specific particles and the embedding of microcapsules. The present review offers a comprehensive examination of the theoretical mechanisms that regulate the liquid-liquid biopolymers aqueous solution segregative phase separation, the factors that may exert an impact on this procedure, and the importance of this particular separation method in the context of food science. These discussion points also address existing difficulties and future possibilities related to the use of segregative phase separation in food applications. This highlights the potential for the design of novel functional foods and the enhancement of food properties.

Osmotic Pressure and Its Biological Implications.

Gaining insight into osmotic pressure and its biological implications is pivotal for revealing mechanisms underlying numerous fundamental biological processes across scales and will contribute to the biomedical and pharmaceutical fields. This review aims to provide an overview of the current understanding, focusing on two central issues: (i) how to determine theoretically osmotic pressure and (ii) how osmotic pressure affects important biological activities. More specifically, we discuss the representative theoretical equations and models for different solutions, emphasizing their applicability and limitations, and summarize the effect of osmotic pressure on lipid phase separation, cell division, and differentiation, focusing on the mechanisms underlying the osmotic pressure dependence of these biological processes. We highlight that new theory of osmotic pressure applicable for all experimentally feasible temperatures and solute concentrations needs to be developed, and further studies regarding the role of osmotic pressure in other biological processes should also be carried out to improve our comprehensive and in-depth understanding. Moreover, we point out the importance and challenges of developing techniques for the in vivo measurement of osmotic pressure.

The search for novel proline analogs for viscosity reduction and stabilization of highly concentrated monoclonal antibody solutions.

Administration of monoclonal antibodies (mAbs) is currently focused on subcutaneous injection associated with increased patient adherence and reduced treatment cost, leading to sustainable healthcare. The main bottleneck is low volume that can be injected, requiring highly concentrated mAb solutions. The latter results in increased solution viscosity with pronounced mAb aggregation propensity because of intensive protein-protein interactions. Small molecule excipients have been proposed to restrict the protein-protein interactions, contributing to reduced viscosity. The aim of the study was to discover novel compounds that reduce the viscosity of highly concentrated mAb solution. First, the chemical space of proline analogs was explored and 35 compounds were determined. Viscosity measurements revealed that 18 proline analogs reduced the mAb solution viscosity similar to or more than proline. The compounds forming both electrostatic and hydrophobic interactions with mAb reduced the viscosity of the formulation more efficiently without detrimentally effecting mAb physical stability. A correlation between the level of interaction and viscosity-reducing effect was confirmed with molecular dynamic simulations. Structure rigidity of the compounds and aromaticity contributed to their viscosity-reducing effect, dependent on molecule size. The study results highlight the novel proline analogs as an effective approach in viscosity reduction in development of biopharmaceuticals for subcutaneous administration.

Molecular dynamics simulations as a guide for modulating small molecule aggregation.

Small colloidally aggregating molecules (SCAMs) can be problematic for biological assays in drug discovery campaigns. However, the self-associating properties of SCAMs have potential applications in drug delivery and analytical biochemistry. Consequently, the ability to predict the aggregation propensity of a small organic molecule is of considerable interest. Chemoinformatics-based filters such as ChemAGG and Aggregator Advisor offer rapid assessment but are limited by the assay quality and structural diversity of their training set data. Complementary to these tools, we explore here the ability of molecular dynamics (MD) simulations as a physics-based method capable of predicting the aggregation propensity of diverse chemical structures. For a set of 32 molecules, using simulations of 100 ns in explicit solvent, we find a success rate of 97% (one molecule misclassified) as opposed to 75% by Aggregator Advisor and 72% by ChemAGG. These short timescale MD simulations are representative of longer microsecond trajectories and yield an informative spectrum of aggregation propensities across the set of solutes, capturing the dynamic behaviour of weakly aggregating compounds. Implicit solvent simulations using the generalized Born model were less successful in predicting aggregation propensity. MD simulations were also performed to explore structure-aggregation relationships for selected molecules, identifying chemical modifications that reversed the predicted behaviour of a given aggregator/non-aggregator compound. While lower throughput than rapid cheminformatics-based SCAM filters, MD-based prediction of aggregation has potential to be deployed on the scale of focused subsets of moderate size, and, depending on the target application, provide guidance on removing or optimizing a compound's aggregation propensity.

Volumetric and taste behavior of D(+)-glucose and D(-)-fructose in aqueous solutions of ethanolammoium acetate.

The hydration and taste behaviour of glucose and fructose in aqueous ethanolammonium acetate solutions were investigated by measuring volumetric properties. Density and speed of sound were measured at four different temperatures. Apparent and partial molar volumes, apparent specific compressibility, apparent specific volume, transfer volumes, and hydration numbers were determined from the measured density and speed of sound data. Positive transfer properties of saccharides from water to aqueous ethanolammonium acetate solutions suggested the dominance of hydrophilic-ionic interactions. However, such interactions weakened with incremental concentrations of ethanolammonium acetate. The transfer properties increased in the order: glucose > fructose, indicating stronger interactions between glucose and ethanolammonium acetate. The apparent specific volume and apparent specific isentropic compressibility values for monosaccharides in water and in aqueous ethanolammonium acetate were found to fall within the sweet taste modality.

Dissolution and regeneration of starch in hydroxyl-functionalized ionic liquid aqueous solution.

There have been continuous quests for suitable solvents for starch, given the importance of effective starch dissolution in its modification and subsequent materials production. In light of this, the potential of hydroxyl-functionalized ionic liquid (IL) as a promising solvent for starch was investigated. Within this study, a hydroxyl-functionalized IL 1-(2,3-dihydroxypropyl)-3-methylimidazole chloride ([Dhpmim][Cl]) was synthesized, and the dissolution of starch in this IL and its aqueous solutions was examined. Starch (5.35 wt%) was completely dissolved in [Dhpmim][Cl] within 2 h at 100 °C. The solubility of starch in [Dhpmim][Cl]-water mixtures initially increased and then decreased with rising water content. The optimal ratio was found to be 1:9 (wt/wt) water:[Dhpmim][Cl], achieving the highest solubility at 9.28 wt%. Density functional theory (DFT) simulations elucidated the possible interactions between starch and solvents. After dissolution and regeneration in the 1:9 water:[Dhpmim][Cl] mixture, starch showed no discernible change in the molecular structure, with no derivatization reaction observed. Regenerated starch exhibited a transformation in crystalline structure from A-type to V-type, and its relative crystallinity (12.4 %) was lower than that of native starch (25.2 %), resulting in decreased thermal stability. This study suggests that the hydroxyl-functionalized IL, [Dhpmim][Cl], and its aqueous solutions serve as effective solvents for starch dissolution.

Interaction between Sophorolipids and ß-glucan in Aqueous Solutions.

Skin disorders, including acne vulgaris, atopic dermatitis, and rosacea, are characterized by the presence of biofilms, which are communities of microorganisms. The mechanical stability of biofilms is attributed to one of their constituents-polysaccharides-which are secreted by microorganisms. Sophorolipids are biosurfactants with biofilm disruption and removal abilities and are expected to become alternatives for classical petrochemical-based surfactants in cosmetics. In this study, we investigated the influence of sophorolipids on ß-glucan such as dispersion status, interaction mechanism, and configuration change as a model polysaccharide of biofilm in aqueous solution. Dynamic light scattering measurements showed that sophorolipids interfere with the aggregation of ß- glucan in aqueous solutions. In contrast, sodium dodecyl sulfate (SDS), which is used as a typical surfactant reference, promotes the aggregation of ß-glucan. The interaction between sophorolipids and ß-glucan were investigated using surface tension measurements and isothermal titration calorimetry (ITC). Surface tension increased only near critical micelle concentration (CMC) region of sophorolipids in the presence of ß-glucan. This suggests that the interaction occurred in the solution rather than at the air-liquid interface. Moreover, the results of ITC indicate that hydrophobic interactions were involved in this interaction. In addition, the results of optical rotation measurements indicate that sophorolipids did not unfold the triple helical structure of ß-glucan. ß-glucan dispersion was expected to be caused steric hindrance and electrostatic repulsion when sophorolipids interacted with ß-glucan via hydrophobic interactions owing to the unique molecular structure of sophorolipids attributed by a bulky sugar moiety and a carboxyl functional group. These results demonstrated unique performances of sophorolipids on ß-glucan and provided more insights on the efficacy of sophorolipids as good anti-biofilms.

Adsorption behavior of Mo(VI) from aqueous solutions using tungstate-modified magnetic nanoparticle.

A new magnetic nanoparticle modified with sodium tungstate (Mnp-Si-W) was synthesized and employed for the sorption of molybdenum from aqueous solutions. The prepared nanoparticles (Mnp-Si-W) were characterized by different advanced techniques. Different parameters that influenced the adsorption percent of Mo(VI) were investigated using a batch process. Based on a systematic investigation of the adsorption isotherms and kinetics models, Mo(VI) adsorption follows the Langmuir model and pseudo-second-order kinetics. According to the Langmuir isotherm model, the Mnp-Si-W nanoparticles exhibited a maximum adsorption capacity of 182.03 mg g-1 for Mo(VI) at pH 2.0. The effect of competing ions showed that the prepared nanoparticles have a high selectivity for the sorption of molybdenum. Moreover, the effect of some interfering anions on Mo(VI) ion sorption is found in the following order: phosphate < sulfate < chromate. Finally, the nanoparticle (Mnp-Si-W) can be successfully reused five times.

Close-Up Look at Electronic Spectroscopic Signatures of Common Pharmaceuticals in Solution.

Simulating electronic properties and spectral signals requires robust computational approaches that need tuning with the system's peculiarities. In this paper, we test implicit and fully atomistic solvation models for the calculation of UV-vis and electronic circular dichroism (ECD) spectra of two pharmaceutically relevant molecules, namely, (2S)-captopril and (S)-naproxen, dissolved in aqueous solution. Room temperature molecular dynamics simulations reveal that these two drugs establish strong contacts with the surrounding solvent molecules via hydrogen bonds. Such specific interactions, which play a major role in the spectral response and are neglected in implicit approaches, are further characterized and quantified with natural bond orbital methods. Our calculations show that simulated spectra, and especially ECD, are in good agreement with experiments solely when conformational and configurational dynamics, mutual polarization, and solute-solvent repulsion effects are considered.

The investigation of sorption-desorption performance and mechanism of copper by surfactant-modified zeolite in aqueous solutions.

As the most common filler in stormwater treatment, zeolite (NZ-Y) has good cation exchange capability and stabilization potential for the removal of heavy metal from aqueous solutions. In this study, sodium dodecyl sulfate (SDS) and NZ-Y were selected to preparing new adsorbent (SDS-NZ) by using a simple hydrothermal method. The sorption-desorption performance and mechanism of Cu(II) onto SDS-NZ were investigated. The results showed that the sorption of Cu(II) on SDS-NZ was in accordance with the pseudo-second-order kinetic model with an equilibrium time of 4 h. The sorption behavior fitted Langmuir isotherm with a saturation sorption capability of 9.03 mg/g, which was three times higher than that of NZ-Y. The modification of SDS increases the average pore size of NZ-Y by 3.96 nm, which results in a richer internal pore structure and more useful sorption sites for Cu(II) sorption. There was a positive correlation between solution pH values and sorption capability of Cu(II) in the range of 3.0-6.0. With the ionic strength increased, the sorption capability of Cu(II) onto SDS-NZ first decreased and then increased, which may be attributed to competitive sorption and compression of the electronic layer. The desorption of Cu(II) on SDS-NZ was favored by the increase in SDS concentration and ionic strength and decrease in solution pH values. The application of SDS-NZ in runoff improved the leaching risk of Cu(II). After several cycles, the ability of reused SDS-NZ to efficiently adsorb most heavy metals was verified with removal rates above 99%.

Removal of strontium by nanofiltration: Role of complexation and speciation of strontium with organic matter.

Strontium (Sr) removal from water is required because excessive naturally occurring Sr exposure is hazardous to human health. Climate and seasonal changes cause water quality variations, in particular quality and quantity of organic matter (OM) and pH, and such variations affect Sr removal by nanofiltration (NF). The mechanisms for such variations are not clear and thus OM complexation and speciation require attention. Sr removal by NF was investigated with emphasis on the role of OM (type and concentration) and pH (2-12) on possible removal mechanisms, specifically size and/or charge exclusion as well as solute-solute interactions. The filtration results show that the addition of various OM (10 types) and an increase of OM concentration (2-100 mgC.L-1) increased Sr removal by 10-15%. The Sr-OM interaction was enhanced with increasing OM concentration, implying enhanced size exclusion via Sr-OM interaction as the main mechanism. Such interactions were quantified by asymmetric flow field-flow fractionation (FFFF) coupled with an inductively coupled plasma mass spectrometer (ICP-MS). Both extremely low and high pH increased Sr removal due to the enhanced charge exclusion and Sr-OM interactions. This work elucidated and verified the mechanism of OM and pH on Sr removal by NF membranes.

Concentration Dependence of Elastic and Viscoelastic Properties of Aqueous Solutions of Ficoll and Bovine Serum Albumin by Brillouin Light Scattering Spectroscopy.

The cellular environment is crowded with macromolecules of different shapes and sizes. The effect of this macromolecular crowding has been studied in a variety of synthetic crowding environments: two popular examples are the compact colloid-like Ficoll macromolecule and the globular protein bovine serum albumin (BSA). Recent studies have indicated that a significant component of bound or surface-associated water in these crowders reduces the available free volume. In this work, Brillouin light scattering experiments were performed on aqueous solutions of Ficoll 70 and Ficoll 400 with concentrations ranging from 1 to 35 wt % and BSA with concentrations of 1 to 27 wt %. From the dependence of spectral peak parameters on polymer concentration, we determined fundamental solution properties: hypersound velocity, adiabatic bulk modulus and compressibility, apparent viscosity, and hypersound attenuation. The existing theory that ignores intermolecular interactions can capture only the observed linear trends in the frequency shift up to a threshold concentration, beyond which a quadratic term accounting for intermolecular interactions is necessary. This likely indicates a transition from the dilute to semidilute regime. In the Ficoll solutions (but not BSA), we see evidence for a central mode, which is indicative of relaxation in the hydration shell of Ficoll.

A Smart Skin for Hydrogels That Enables Switchable Solute Release.

Many applications of hydrogels rely on their ability to deliver encapsulated solutes, such as drugs; however, small hydrophilic solutes rapidly leak out of gels by diffusion. A need exists for a way to regulate solute release out of gels─to ensure zero release until a desired time (the OFF state) and thereafter for the release to be switched ON at a high rate. This should ideally be a repeatable switch; i.e., the gel should be cyclable repeatedly between the ON and OFF states. Such perfect, cyclical ON-OFF release of solutes from gels is demonstrated for the first time through a "smart skin" that is synthesized rapidly (in ∼10 min) around an entire gel. The thin (∼100 µm) and transparent polymer skin is endowed with redox-responsive properties through the use of urethane and acrylate monomers, one of which contains a thioether group. Initially, the skin is hydrophobic (water contact angle 102°), and it completely prevents hydrophilic solutes from leaking out of the gel. When contacted with oxidants such as hydrogen peroxide (H2O2), the thioethers are converted to sulfoxides, making the skin hydrophilic (water contact angle 42°) and thereby turning ON the release of solutes. Conversely, solute release can be turned OFF subsequently by adding a reducing agent such as vitamin C that reverts the sulfoxides to thioethers and thus returns the skin to its hydrophobic state. The release rate in the ON state can be tuned via the skin thickness as well as the oxidant concentration. The ability to regulate solute delivery from gels using smart skins is likely to prove significant in areas ranging from separations to agriculture and drug delivery.

Solvent polarity and hydrophobicity of solutes are two sides of the same coin.

The hydrophobicity of solutes measures the intensity of a solute's interaction with aqueous environment. The aqueous environment may change with its composition, leading to changes in its solvent properties largely characterized by polarity. As a result, the relative hydrophobicity of a solute is a function of the solute structure and the properties of the water-based solvent determined by the total composition of the aqueous phase. This aspect is commonly ignored by medicinal chemists even though it is essential for drug distribution between different biological tissues. Partitioning of solutes in aqueous two-phase systems provides the relative hydrophobicity estimates for any water-soluble compounds that can be used to improve predictions of the toxicity and other biological effects of these compounds.

Quantifying Protein Shape to Elucidate Its Influence on Solution Viscosity in High-Concentration Electrolyte Solutions.

Therapeutic proteins with a high concentration and low viscosity are highly desirable for subcutaneous and certain local injections. The shape of a protein is known to influence solution viscosity; however, the precise quantification of protein shape and its relative impact compared to other factors like charge-charge interactions remains unclear. In this study, we utilized seven model proteins of varying shapes and experimentally determined their shape factors (v) based on Einstein's viscosity theory, which correlate strongly with the ratios of the proteins' surface area to the 2/3 power of their respective volumes, based on protein crystal structures resolved experimentally or predicted by AlphaFold. This finding confirms the feasibility of computationally estimating protein shape factors from amino acid sequences alone. Furthermore, our results demonstrated that, in high-concentration electrolyte solutions, a more spherical protein shape increases the protein's critical concentration (C*), the transition concentration beyond which protein viscosity increases exponentially relative to concentration increases. In summary, our work elucidates protein shape as a key determinant of solution viscosity through quantitative analysis and comparison with other contributing factors. This provides insights into molecular engineering strategies to optimize the molecular design of therapeutic proteins, thus optimizing their viscosity.

Charged Biological Membranes Repel Large Neutral Molecules by Surface Dielectrophoresis and Counterion Pressure.

Macromolecular crowding is the usual condition of cells. The implications of the crowded cellular environment for protein stability and folding, protein-protein interactions, and intracellular transport drive a growing interest in quantifying the effects of crowding. While the properties of crowded solutions have been extensively studied, less attention has been paid to the interaction of crowders with the cellular boundaries, i.e., membranes. However, membranes are key components of cells and most subcellular organelles, playing a central role in regulating protein channel and receptor functions by recruiting and binding charged and neutral solutes. While membrane interactions with charged solutes are dominated by electrostatic forces, here we show that significant charge-induced forces also exist between membranes and neutral solutes. Using neutron reflectometry measurements and molecular dynamics simulations of poly(ethylene glycol) (PEG) polymers of different molecular weights near charged and neutral membranes, we demonstrate the roles of surface dielectrophoresis and counterion pressure in repelling PEG from charged membrane surfaces. The resulting depletion zone is expected to have consequences for drug design and delivery, the activity of proteins near membrane surfaces, and the transport of small molecules along the membrane surface.

Synthesis of organic-solvent-soluble cellulose and preparation of fluorescent polyurethanes for the detection and removal of Hg+ ions.

Modifying cellulose to obtain materials with favorable processing properties and functions is highly significant, especially, for the detection and removal of heavy metal ions. In this study, fluorescent cellulose-based polyurethane (PU) films containing naphthalimide fluorophore were synthesized and could use for the convenient detection and removal of Hg+ ions. Firstly, the microcrystalline cellulose was treated with SOCl2 to convert some -OH groups into -Cl. Simultaneously, a naphthalimide derivative (NAN) with -NH- groups was synthesized. Subsequently, a fluorescent cellulose-based probe (Cel-NAN) was prepared by utilizing the substitution reaction between -Cl on cellulose and -NH- on NAN. Finally, two cellulose-based fluorescent PU films (Cel-NAN-PU1 and Cel-NAN-PU2) were successfully synthesized by reacting the unreacted -OH groups on Cel-NAN with PEG-1000 and HDI/IPDI. These as-prepared PU films could serve as portable fluorescence test papers to Hg+ ions in aqueous solutions. Upon contact with Hg+ ions, the fluorescence was quenched, acting as a "turn-off" probe. Simultaneously, these films could serve as adsorbents for the removal of Hg+ ions from aqueous systems. Cel-NAN-PU1 film exhibited a removal efficiency over 80 % and an adsorption capacity of 8.4 mg·cm-2 for Hg+. These cellulose-based fluorescent PU films possess promising potential in the field of mercury pollution control.

Acid insoluble lignin material production by chemical activation of olive endocarps for an efficient furfural adsorption-removal from aqueous solutions.

The present work describes a protocol of chemical activation, with acid catalyst, of olive endocarps to obtain acid insoluble lignin-rich materials with high capacities for the adsorption of furfural present in aqueous media. During biomass activation, factors such as acid concentration, reaction time and temperature, solid/liquid ratio and the presence of water extractives strongly affected both the surface characteristics of the treated bioadsorbents and their capacities for furfural retention (percentage increase close to 600% with respect to the crude biomass). Once a treated solid with good adsorbent properties was obtained, the optimal conditions for adsorption were found: stirring speed 80 rpm, temperature 303 K and adsorbent load 7.5 g solid/50 cm3. Kinetic study indicated the pseudo-second order model provided the best fit of the experimental data. At 303 K, the equilibrium adsorption capacities values ranged from 2.27 mg g-1 to 29.29 mg g-1, for initial furfural concentrations between 0.49 g dm-3 and 12.88 g dm-3. Freundlich model presented the best isotherm (R2 = 0.996 and SE = 4.7%) providing KF and n values of 0.115 (mg g-1) (mg dm-3)-n and 0.610, respectively. Since physical interactions predominate in the adsorption of furfural on chemically activated olive endocarps, the furfural removal process could have occurred reversibly on the heterogeneous surface of the bioadsorbents.