Unraveling the Influence of Osmolytes on Water Hydrogen-Bond Network: From Local Structure to Graph Theory Analysis

Application of Density Functional Theory to Molecular Engineering of Pharmaceutical Formulations

This review systematically examines the pivotal applications of the Density Functional Theory (DFT) in drug formulation design, emphasizing its capability to elucidate molecular interaction mechanisms through quantum mechanical calculations. By solving the Kohn-Sham equations with precision up to 0.1 kcal/mol, DFT enables accurate electronic structure reconstruction, providing theoretical guidance for optimizing drug-excipient composite systems. In solid dosage forms, DFT clarifies the electronic driving forces governing active pharmaceutical ingredient (API)-excipient co-crystallization, predicting reactive sites and guiding stability-oriented co-crystal design. For nanodelivery systems, DFT optimizes carrier surface charge distribution through van der Waals interactions and π-π stacking energy calculations, thereby enhancing targeting efficiency. Furthermore, DFT combined with solvation models (e.g., COSMO) quantitatively evaluates polar environmental effects on drug release kinetics, delivering critical thermodynamic parameters (e.g., ΔG) for controlled-release formulation development. Notably, DFT-driven co-crystal thermodynamic analysis and pH-responsive release mechanism modeling substantially reduce experimental validation cycles. While DFT faces challenges in dynamic simulations of complex solvent environments, its integration with molecular mechanics and multiscale frameworks has achieved computational breakthroughs. This work offers interdisciplinary methodology support for accelerating data-driven formulation design.

Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions

Water dynamics are investigated in binary osmolyte-water mixtures, exhibiting a microscopic heterogeneity driven by molecular aggregation, on the basis of molecular dynamics (MD) simulation studies. The protecting osmolyte TMAO molecules in solution are evenly dispersed without the formation of noticeable osmolyte aggregates, while the denaturant TMU molecules aggregate readily, generating microscopic heterogeneity in the spatial distribution of component molecules in TMU-water mixtures. A combined study of MD simulation with graph theoretical analysis and spatial inhomogeneity measurement with h-values in the two osmolyte solutions revealed that the translational and rotational motions of water in the microheterogeneous environment of TMU-water mixtures are less hindered than those in the homogeneous media of TMAO-water mixtures. The analysis of the osmolyte-water H-bond lifetime in the binary solutions shows that destabilizing osmolyte TMU makes relatively weak osmolyte-water interaction, compared to that in protecting osmolyte TMAO, enabling the interplay of TMU-TMU or TMU-protein as well as TMU-water interaction. Taken together, the complementary contributions of the two hypotheses are proposed to elucidate the operating mechanism of the osmolyte on protein stability, encompassing a direct mechanism for the preferential interaction between the osmolyte and protein and an indirect mechanism for the modulation of the water structure and dynamics in the osmolyte solutions.

Ultrasonic-assisted plasma-activated water extraction of polysaccharide from Hemerocallis citrina Baroni: Structural characterization and antioxidant mechanism in vitro

Natural polysaccharides derived from Hemerocallis citrina Baroni exhibit significant biological activity. To enhance extraction efficiency and antioxidant activity, ultrasonic-assised plasma-activated water (PAW) was utilized to extract polysaccharides from Hemerocallis citrina Baroni. PAW demonstrated enhanced permeability and diffusion capabilities due to a reduced percentage of fully hydrogen-bonded structures, along with optimal pH (3.4) and conductivity (157.20 μS/cm). Compared to other methods, PAW significantly improved the extraction efficiency of polysaccharides to 38.24 %. Hemerocallis citrina Baroni polysaccharides predominantly consisted of α-pyranose sugars with sugar uronic acids, and ultrasound-assisted PAW did not alter their major functional groups. The extracted Hemerocallis citrina Baroni polysaccharides exhibited a semi-rigid triple-helical structure. Importantly, these polysaccharides displayed strong antioxidant activity, with ABTS+, DPPH, and O2- radical scavenging rates of 66.31 %, 65.98 %, and 47.73 % respectively. This study provides an effective method for extracting natural plant polysaccharides and offers valuable insights into their potential applications in the food industry and beyond.

Osmolyte-induced protein stability changes explained by graph theory

Enhanced stabilization of protein structures via the presence of inert osmolytes is a key mechanism adopted both by physiological systems and in biotechnological applications. While the intrinsic stability of proteins is ultimately fixed by their amino acid composition and organization, the interactions between osmolytes and proteins together with their concentrations introduce an additional layer of complexity and in turn, a method of modulating protein stability. Here, we combined experimental measurements with molecular dynamics simulations and graph-theory-based analyses to predict the stabilizing/destabilizing effects of different kinds of osmolytes on proteins during heat-mediated denaturation. We found that (i) proteins in solution with stability-enhancing osmolytes tend to have more compact interaction networks than those assumed in the presence of destabilizing osmolytes; (ii) a strong negative correlation (R = -0.85) characterizes the relationship between the melting temperatureT m and the preferential interaction coefficient defined by the radial distribution functions of osmolytes and water around the protein and (iii) a positive correlation exists between osmolyte-osmolyte clustering and the extent of preferential exclusion from the local domain of the protein, suggesting that exclusion may be driven by enhanced steric hindrance of aggregated osmolytes.

Structure and Dynamics of Water in Polysaccharide (Alginate) Solutions and Gels Explained by the Core-Shell Model

In both biological and engineered systems, polysaccharides offer a means of establishing structural stiffness without altering the availability of water. Notable examples include the extracellular matrix of prokaryotes and eukaryotes, artificial skin grafts, drug delivery materials, and gels for water harvesting. Proper design and modeling of these systems require detailed understanding of the behavior of water confined in pores narrower than about 1 nm. We use molecular dynamics simulations to investigate the properties of water in solutions and gels of the polysaccharide alginate as a function of the water content and polymer cross-linking. We find that a detailed understanding of the nanoscale dynamics of water in alginate solutions and gels requires consideration of the discrete nature of water. However, we also find that the trends in tortuosity, permeability, dielectric constant, and shear viscosity can be adequately represented using the "core-shell" conceptual model that considers the confined fluid as a continuum.

Unraveling the interplay of temperature with molecular aggregation and miscibility in TEA-water mixtures

In the phase diagram of binary liquid mixtures, a miscibility gap is found with the concomitant liquid-liquid phase separation, wherein temperature is a key parameter in modulating the phase behavior. This includes critical temperatures such as the lower critical solution temperature (LCST) and upper critical solution temperature (UCST). Using a comprehensive approach including molecular dynamics (MD) simulation, graph theoretical analysis and spatial inhomogeneity measurement in an LCST-type mixture, we attempt to establish the relationship between the molecular aggregation pattern and phase behavior in TEA-water mixtures. At lower temperatures of binary liquid mixtures, TEA molecules tend to aggregate while simultaneously interacting with water forming a homogeneous solution. As the temperature increases, these TEA aggregates tend to self-associate by minimizing the interaction with water, which facilitates formation of two distinct liquid phases in the binary liquid. The spatial distribution analysis also reveals that the TEA aggregates compatible with water promote uniform distribution of water molecules, maintaining a homogeneous solution, while the water-incompatible ones generate isolation of water H-bond aggregates, leading to liquid-liquid phase separation in the binary system. This current study on temperature-induced molecular aggregation behavior is anticipated to contribute to a critical understanding of the phase behavior in binary liquid mixtures, including UCST, LCST, and reentrant phase behavior.

The counteracting influence of 2-hydroxypropyl substitution and the presence of a guest molecule on the shape and size of the β-cyclodextrin cavity

The aqueous solubility of β-cyclodextrin (β-CD), a cyclic carbohydrate comprising seven α-D-glucose molecules, is enhanced by 2-hydroxypropyl (2-HP) substitution of the hydroxyl groups at the CD rims. Our thorough analysis of the structural and solvation properties with different degrees of 2-hydroxypropyl substitution on β-CD using molecular dynamics simulations reveals that the solubility is enhanced at the cost of the structural distortion of the CD cyclic structure. Substitution at the secondary rim predominantly enhances the favourable interactions between CD and water by decreasing CD-CD hydrogen bonding and promoting CD-water hydrogen bonding. However, the effect of substitution at the primary rim on the CD-water interactions is minimal; the hydrogen bonds between water and the primary hydroxyl group in native CD merely get replaced by those between water and 2-HP, since the substitution makes the primary hydroxyl oxygen (O6 atom) inaccessible to water. In contrast, substitution at the primary rim maintains the structural integrity of CD, while substitution at the secondary rim results in structural distortion due to the disruption of the intramolecular hydrogen bond belt, even leading to cavity closure. Certain strategic substitutions of the primary hydroxyl groups can help in the reduction of structural distortion, depending upon the degree of substitution at the secondary hydroxyl rim. A detailed inspection of the simulation trajectory revealed that the tilting of glucose units with the primary hydroxyl oxygen (O6) pointing inward is the primary driver for cavity closure. Even though the dynamics of glucose tilting can influence the kinetics of host-guest complex formation, once the guest is well incorporated into the cavity, glucose tilting is inhibited and the cavity opens up as in native β-CD.

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.

Synergistic effect of lecithin and alginate, CMC, or PVP in stabilizing curcumin and its potential mechanism

This work aims to advance the understanding of the synergistic mechanism of lecithin and polymers (alginate, CMC, and PVP) in stabilizing curcumin, with a major focus on understanding the nanocomplex formation process and the main binding energy between molecules. It is demonstrated that lecithin and polymers have a synergistic effect in increasing the thermal acid, light, and digestion stability of curcumin. The potential mechanism is that the hydrophobic parts of curcumin molecules are first anchored at the region of the hydrophobic cavity of lecithin by van der Waals, while the hydrophilic parts are outward and are further encapsulated by hydrophilic polymers by van der Waals and electrostatic interaction to form a protective shell. This study contributes to our understanding of the synergistic mechanism of lecithin, polymers, and hydrophobic compounds, which can promote the synergistic use of lecithin and polymers to prepare nanocomplexes as an important tool for delivering bioactive compounds.

Probing the Conformational Preference to β-Strand during Peptide Self-Assembly

Alanine-rich tetrapeptides like A₃K dominantly exist as polyproline II helices in dilute aqueous solutions. However, during self-assembly, based on the free energy calculation in implicit solvent for various peptide conformations, only the peptides in the β-strand conformation can be packed closely. This necessitates the conformational transition to the β-strand commonly observed during peptide self-assembly such as in amyloid fibril formation. In fact, the closest interpeptide distance of 4.8 Å is consistent with the interstrand distance determined from the X-ray diffraction pattern of many amyloid fibrils. The position of free energy minimum obtained from implicit solvent calculation matches exactly with the explicit solvent simulation through umbrella sampling when the peptide conformations are restrained, demonstrating the applicability of the former for rapid screening of peptide configurations favorable for self-assembly. The barrier in the free energy profile in the presence of water arises out of the entropic restriction on the interstitial water molecules while satisfying the hydrogen bonding of both the peptides by forming water mediated hydrogen bond bridge. Further, the high energy barrier observed for the β-strand suggests that peptides initially tend to self-assemble in the polyproline II structure to mitigate the desolvation energy cost; the transition to the β-strand would happen only in the later stage after crossing the barrier. The umbrella sampling simulations with peptides allowed to change conformations, relative to each other, confirm the dynamic conformational transition during the course of the self-assembly supporting the "dock and lock" mechanism suggested for amyloid fibrillar growth.

Molecular Dynamics Simulation of Drug Solubilization Behavior in Surfactant and Cosolvent Injections

Surfactants and cosolvents are often combined to solubilize insoluble drugs in commercially available intravenous formulations to achieve better solubilization. In this study, six marketed parenteral formulations with surfactants and cosolvents were investigated on the aggregation processes of micelles, the structural characterization of micelles, and the properties of solvent using molecular dynamics simulations. The addition of cosolvents resulted in better hydration of the core and palisade regions of micelles and an increase in both radius of gyration (Rg) and the solvent accessible surface area (SASA), causing a rise in critical micelle concentration (CMC), which hindered the phase separation of micelles. At the same time, the presence of cosolvents disrupted the hydrogen bonding structure of water in solution, increasing the solubility of insoluble medicines. Therefore, the solubilization mechanism of the cosolvent and surfactant mixtures was successfully analyzed by molecular dynamics simulation, which will benefit future formulation development for drug delivery.

The ability of trimethylamine N-oxide to resist pressure induced perturbations to water structure

Trimethylamine N-oxide (TMAO) protects organisms from the damaging effects of high pressure. At the molecular level both TMAO and pressure perturb water structure but it is not understood how they act in combination. Here, we use neutron scattering coupled with computational modelling to provide atomistic insight into the structure of water under pressure at 4 kbar in the presence and absence of TMAO. The data reveal that TMAO resists pressure-induced perturbation to water structure, particularly in retaining a clear second solvation shell, enhanced hydrogen bonding between water molecules and strong TMAO - water hydrogen bonds. We calculate an 'osmolyte protection' ratio at which pressure and TMAO-induced energy changes effectively cancel out. Remarkably this ratio translates across scales to the organism level, matching the observed concentration dependence of TMAO in the muscle tissue of organisms as a function of depth. Osmolyte protection may therefore offer a molecular mechanism for the macroscale survival of life in extreme environments.

Balancing the Equation: A Natural History of Trimethylamine and Trimethylamine-N-oxide

Trimethylamine (TMA) and its N-oxide (TMAO) are ubiquitous in prokaryote and eukaryote organisms as well as in the environment, reflecting their fundamental importance in evolutionary biology, and their diverse biochemical functions. Both metabolites have multiple biological roles including cell-signaling. Much attention has focused on the significance of serum and urinary TMAO in cardiovascular disease risk, yet this is only one of the many facets of a deeper TMA-TMAO partnership that reflects the significance of these metabolites in multiple biological processes spanning animals, plants, bacteria, and fungi. We report on analytical methods for measuring TMA and TMAO and attempt to critically synthesize and map the global functions of TMA and TMAO in a systems biology framework.

Water Activity Prediction in Sugar and Polyol Systems Using Theoretical Molecular Descriptors

Water activity is a key factor in the development of pharmaceutical, cosmetic, and food products. In aqueous solutions of nonelectrolytes, the Norrish model provides a simple and effective way to evaluate this quantity. However, it contains a parameter, known as the Norrish constant, that must be estimated from experimental data. In this study, a new strategy is proposed for the prediction of water activity in the absence of experimental information, based on the use of theoretical molecular descriptors for characterizing the effects of a solute. This approach was applied to the evaluation of water activity in the presence of sugars (glucose, fructose, xylose, sucrose) and polyols (sorbitol, xylitol, glycerol, erythritol). The use of two descriptors related to the constitutional and connectivity properties of the solutes was first investigated. Subsequently, a new theoretical descriptor, named the global information index (G), was developed. By using this index, the water activity curves in the binary systems were reconstructed. The positive results obtained support the proposed strategy, as well as the possibility of including, in a single information index, the main molecular features of a solute that determine its effects on water activity.