Boosting Graph Neural Networks with Molecular Mechanics: A Case Study of Sigma Profile Prediction

Sigma profiles are quantum-chemistry-derived molecular descriptors that encode the polarity of molecules. They have shown great performance when used as a feature in machine learning applications. To accelerate the development of these models and the construction of large sigma profile databases, this work proposes a graph convolutional network (GCN) architecture to predict sigma profiles from molecule structures. To do so, the usage of molecular mechanics (force field atom types) is explored as a computationally inexpensive node-level featurization technique to encode the local and global chemical environments of atoms in molecules. The GCN models developed in this work accurately predict the sigma profiles of assorted organic and inorganic compounds. The best GCN model here reported, obtained using Merck molecular force field (MMFF) atom types, displayed training and testing set coefficients of determination of 0.98 and 0.96, respectively, which are superior to previous methodologies reported in the literature. This performance boost is shown to be due to both the usage of a convolutional architecture and node-level features based on force field atom types. Finally, to demonstrate their practical applicability, we used GCN-predicted sigma profiles as the input to machine learning models previously developed in the literature that predict boiling temperatures and aqueous solubilities. Using the predicted sigma profiles as input, these models were able to compute both physicochemical properties using significantly less computational resources and displayed only a slight decrease in performance when compared with sigma profiles obtained from quantum chemistry methods.

Exploring the impact of sodium salts on hydrotropic solubilization

Some ionic liquids (ILs) were shown to display a strong ability to enhance the solubility of phenolic compounds through hydrotropy. However, evidence shows that salt ions in hydrotropic aqueous solutions may change the behavior of molecules by promoting possible interactions between the components of the system, thus causing changes in solubility. Herein, we study the impact of sodium salt anions on the hydrotropic dissolution of syringic acid using 1-butyl-3-methylimidazolium chloride ([C4mim]Cl) as a hydrotrope, with a focus on dicyanamide Na[N(CN)2] and thiocyanate Na[SCN] salts. Dynamic light scattering, Raman spectroscopy, and nuclear magnetic resonance spectroscopy were used to investigate how the mixture of IL-salts affects the solvation. The results obtained show that [C4mim]Cl is able to increase the solubility of syringic acid 80-fold. Despite their structural similarities, the presence of Na[N(CN)2] or Na[SCN] in an aqueous solution of [C4mim]Cl induced opposite solubility trends. The addition of Na[N(CN)2] promotes a higher ability to solubilize syringic acid than in the corresponding IL system due to a pH buffering effect, resulting in the deprotonation of the solute. The addition of Na[SCN], on the other hand, induces a relative decrease in syringic acid solubilization at higher concentrations of ILs due to the negative contribution of the NaCl formed by anion-exchange. These results emphasise the often overlooked pH contribution provided by ILs for biomolecule solubilisation whilst providing experimental insights into the structure of aqueous solutions of ionic liquids and the role it plays in the formation of IL-salt aggregates.

Elucidating the Hydrotropic Mechanism of the Antagonistic Salt PPh4Cl

PPh₄Cl is an antagonistic salt that recently showed promise as a hydrotropic agent. Here, we give mechanistic insights into the PPh₄Cl-assisted solubility of a dye molecule using molecular dynamics simulations. Our findings reveal that dye molecules aggregate into a cluster which leads to an accumulation of PPh₄⁺ ions in its vicinity and subsequent exclusion of water molecules from the region. The structural organization is attributed to the preferential interaction of dye molecules and PPh₄Cl. The origin of such preference arises from the difference in π-π and CH-π interaction among the pairs. The hydrodynamic radius of PPh₄Cl indicates a low propensity for cluster formation, which enhances its hydrotropic behavior. The process of dye dissolution is thermodynamically favored and occurs through a cooperative mechanism. Our studies provide molecular insight into experimental observations crucial for the design of novel hydrotropes with enhanced solubilizing properties.

Advanced Fractionation of Kraft Lignin by Aqueous Hydrotropic Solutions

Lignin is an underutilized high-potential biopolymer that has been extensively studied over the past few decades. However, lignin still has drawbacks when compared with well-known petroleum-based equivalents, and the production of tailored lignin fractions is highly in demand. In this work, a new method for the fractionation of Lignoboost Kraft Lignin (LKL) is proposed by using two different hydrotropes: sodium xylenesulfonate (SXS) and sodium cumenesulfonate (SCS). The different fractions are obtained by sequentially decreasing the hydrotropic concentration with the addition of water. Four and three different fractions were retrieved from the use of SXS and SCS, respectively. The LKL and respective fractions were analysed, and compared by GPC, FTIR-ATR, ¹H-NMR, ¹³C-NMR, ³¹P NMR, 2D HSQC and SEM. The fractions showed different molecular weights, polydispersity, and amount of functional groups. Our water-based lignin fractionation platform can potentially be combined with different lignin extraction and processing technologies, with the advantage of hydrotrope recycling.

Progress in the field of hydrotropy: mechanism, applications and green concepts

Sustainability and greenness are the concepts of growing interest in the area of research as well as industries. One of the frequently encountered challenges faced in research and industrial fields is the solubility of the hydrophobic compound. Conventionally organic solvents are used in various applications; however, their contribution to environmental pollution, the huge energy requirement for separation and higher consumption lead to unsustainable practice. We require solvents that curtail the usage of hazardous material, increase the competency of mass and energy and embrace the concept of recyclability or renewability. Hydrotropy is one of the approaches for fulfilling these requirements. The phenomenon of solubilizing hydrophobic compound using hydrotrope is termed hydrotropy. Researchers of various fields are attracted to hydrotropy due to its unique physicochemical properties. In this review article, fundamentals about hydrotropes and various mechanisms involved in hydrotropy have been discussed. Hydrotropes are widely used in separation, heterogeneous chemical reactions, natural product extraction and pharmaceuticals. Applications of hydrotropes in these fields are discussed at length. We have examined the significant outcomes and correlated them with green engineering and green chemistry principles, which could give an overall picture of hydrotropy as a green and sustainable approach for the above applications.

The Impact of Size and Shape in the Performance of Hydrotropes: A Case-Study of Alkanediols

Inspired by the recently proposed cooperative mechanism of hydrotropy, where water molecules mediate the aggregation of hydrotrope around the solute, this work studies the impact of apolar volume and polar...

Assessing the hydrotropic effect in the presence of electrolytes: competition between solute salting-out and salt-induced hydrotrope aggregation

Water solubility enhancement is a long-standing challenge in a multitude of chemistry-related fields. Hydrotropy is a simple and efficient method to improve the solubility of hydrophobic molecules in aqueous media....

Biomass delignification with green solvents towards lignin valorisation: ionic liquids vs deep eutectic solvents

The use of renewable resources as feedstocks to ensure the production of goods and commodities for society has been explored in the last decades to switch off the overexploited and pollutant fossil-based economy. Today there is a strong movement to set bioeconomy as priority, but there are still challenges and technical limitations that must be overcome in the first place, particularly on biomass fractionation. For biomass to be an appellative raw material, an efficient and sustainable separation of its major components must be achieved. On the other hand, the technology development for biomass valorisation must follow green chemistry practices towards eco-friendly processes, otherwise no environmental leverage over traditional petrochemical technologies will be acquired. In this context, the application of green solvents, such as ionic liquids (ILs) and deep eutectic solvents (DES), in biomass fractionation is envisaged as promising technology that encompasses not only efficiency and environmental benefits, but also selectivity, which is a crucial demand to undertake cascade processes at biorefinery level. In particular, this article briefly discusses the disruptive achievements upon the application of ILs and DES in biomass delignification step towards an effective and selective separation of lignin from polysaccharides. The different physicochemical properties of these solvents, their interactions with lignin and their delignification capacity will be scrutinized, while some highlights will be given to the important characteristics of isolated lignin fractions for further valorisation. The advantages and disadvantages between ILs and DES in biomass delignification will be contrasted as well along the article.

Cooperative Sorption on Porous Materials

The functional shape of a sorption isotherm is determined by underlying molecular interactions. However, doubts have been raised on whether the sorption mechanism can be understood in principle from analyzing sorption curves via a range of competing models. We have shown recently that it is possible to translate a sorption isotherm to the underlying molecular interactions via rigorous statistical thermodynamics. The aim of this paper is to fill the gap between the statistical thermodynamic theory and analyzing experimental sorption isotherms, especially of microporous and mesoporous materials. Based on a statistical thermodynamic approach to interfaces, we have derived a cooperative isotherm, as a generalization of the Hill isotherm and our cooperative solubilization model, without the need for assumptions on adsorption sites, layers, and pore geometry. Instead, the statistical characterization of sorbates, such as the sorbate-interface distribution function and the sorbate number distribution, as well as the existence of statistically independent units of the interface, underlies the cooperative sorption isotherm. Our isotherm can be applied directly to literature data to reveal a few key system attributes that control the isotherm: the cooperative number of sorbates and the free energy of transferring sorbates from the saturated vapor to the interface. The sorbate-sorbate interaction is quantified also via the Kirkwood-Buff integral and the excess numbers.

Acid Hydrotropic Fractionation of Lignocelluloses for Sustainable Biorefinery: Advantages, Opportunities, and Research Needs

This Minireview provides a comprehensive discussion on the potential of using acid hydrotropes for sustainably fractionating lignocelluloses for biorefinery applications. Acid hydrotropes are a class of acids that have hydrotrope properties toward lignin, which helps to solubilize lignin in aqueous systems. With the capability of cleaving ether and ester bonds and even lignin-carbohydrate complex (LCC) linkages, these acid hydrotropes can therefore isolate lignin embedded in the plant biomass cell wall and subsequently solubilize the isolated lignin in aqueous systems. Performances of two acid hydrotropes, that is, an aromatic sulfonic acid [p-toluenesulfonic acid (p-TsOH)] and a dicarboxylic acid [maleic acid (MA)], in terms of delignification and dissolution of hemicelluloses, and reducing lignin condensation, were evaluated and compared. The advantages of lignin esterification by MA for producing cellulosic sugars through enzymatic hydrolysis and lignin-containing cellulose nanofibrils (LCNFs) through mechanical fibrillation from the fractionated water insoluble solids (WIS), and for obtaining less condensed lignin with light color, were demonstrated. The excellent enzymatic digestibility of maleic acid hydrotropic fractionation WISs was also demonstrated by comparing with WISs from other fractionation processes. The recyclability and reusability of acid hydrotropes were also reviewed. Finally, perspectives on future research needs to address key technical issues for commercialization were also provided.

Carl Neuberg's hydrotropic appearances (1916)

In his 1916 land-mark paper "Hydrotropic appearances", Carl Neuberg coined the term "hydrotropy", referring to the solubilisation effect of hydrophobic molecules by small, amphiphilic compounds. In this voluminous work he examines 43 different compounds for their hydrotropic effect and touches on many aspects that later became relevant to hydrotrope science (e.g. applications in pharma, green chemistry, pre-ouzo effect, etc.). Given the significance of his work, it is still widely cited today. However, poor availability and a potential language barrier will severely limit the accessibility for international researchers. Therefore, this translation into the English language seeks to provide access to both, his original thoughts as well as his prolific experimental work on this topic.

Novel amorphous solid dispersion based on natural deep eutectic solvent for enhancing delivery of anti-tumor RA-XII by oral administration in rats

At present, oral chemotherapy showing the advantages of non-invasiveness, convenience, and high patient compliance, is gradually replacing traditional intravenous chemotherapy to treat patients with cancer. RA-XII, a unique natural cyclopeptide, exhibits various biological activities, such as anti-tumor, anti-angiogenic, and anti-metastatic activities. Designing an orally available formulation of RA-XII is of great importance in the development of clinically useful anticancer agents. However, RA-XII shows low oral bioavailability in rats due to its poor solubility and low permeability. To overcome these limitations, in this work, a natural deep eutectic solvent (NADES) was designed to efficiently deliver RA-XII by oral administration. A novel NADES composed of betaine and mandelic acid in the molar ratio of 1:1 (Bet-Man NADES) was successfully prepared based on a binary phase diagram of Bet and Man. Acute toxicity studies indicated that Bet-Man NADES was well tolerated with acceptable toxicity. In Bet-Man NADES solutions, the solubility of RA-XII was increased by up to 17.54-fold, and the diffusion and permeability of RA-XII carried out in a Franz cell was also significantly improved 10.35 times. In terms of biopharmaceutical classification this is translated into a change for RA-XII from class IV to class II systems. More importantly, Bet-Man NADES was transferred into the solid formulation by the inclusion of a polymer, and amorphous solid dispersions based on Bet-Man NADES (PVP K30/NADES/RA-XII, ASDs) were successfully prepared to improve uniformity, apparent solubility, dissolution, and cytotoxicity in vitro. Consequently, the oral bioavailability of RA-XII in NADES solutions and ASDs was enhanced by approximately 11.58 and 7.56 times compared with that of pure RA-XII in 0.5% CMCNa. Thus, it can be seen that a natural deep eutectic solvent and its modified amorphous solid dispersions are appropriate novel strategies for improving dissolution rate and bioavailability of poor soluble natural products such as RA-XII.

Role of Hydrotropes in Sparingly Soluble Drug Solubilization: Insight from a Molecular Dynamics Simulation and Experimental Perspectives

Drug molecules' therapeutic efficacy depends on their bioavailability and solubility. But more than 70% of the formulated drug molecules show limited effectiveness due to low water solubility. Thus, the water solubility enhancement technique of drug molecules becomes the need of time. One such way is hydrotropy. The solubilizing agent of a hydrophobic molecule is generally referred to as a hydrotrope, and this phenomenon is termed hydrotropy. This method has high industrial demand, as hydrotropes are noninflammable, readily available, environmentally friendly, quickly recovered, cost-effective, and not involved in solid emulsification. The endless importance of hydrotropes in industry (especially in the pharmaceutical industry) motivated us to prepare a feature article with a clear introduction, detailed mechanistic insights into the hydrotropic solubilization of drug molecules, applications in pharma industries, and some future directions of this technique. Thus, we believe that this feature article will become an adequate manual for the pharmaceutical researchers who want to explore all of the past perspectives of the hydrotropic action of hydrotropes in pharmaceutics.

Cholinium-based ionic liquids as bioinspired hydrotropes to tackle solubility challenges in drug formulation

Hydrotropy is a well-established strategy to enhance the aqueous solubility of hydrophobic drugs, facilitating their formulation for oral and dermal delivery. However, most hydrotropes studied so far possess toxicity issues and are inefficient, with large amounts being needed to achieve significant solubility increases. Inspired by recent developments in the understanding of the mechanism of hydrotropy that reveal ionic liquids as powerful hydrotropes, in the present work the use of cholinium vanillate, cholinium gallate, and cholinium salicylate to enhance the aqueous solubility of two model drugs, ibuprofen and naproxen, is investigated. It is shown that cholinium vanillate and cholinium gallate are able to increase the solubility of ibuprofen up to 500-fold, while all three ionic liquids revealed solubility enhancements up to 600-fold in the case of naproxen. Remarkably, cholinium salicylate increases the solubility of ibuprofen up to 6000-fold. The results obtained reveal the exceptional hydrotropic ability of cholinium-based ionic liquids to increase the solubility of hydrophobic drugs, even at diluted concentrations (below 1 mol·kg^-1), when compared with conventional hydrotropes. These results are especially relevant in the field of drug formulation due to the bio-based nature of these ionic liquids and their low toxicity profiles. Finally, the solubility mechanism in these novel hydrotropes is shown to depend on synergism between both amphiphilic ions.

Cooperativity in micellar solubilization

Sudden onset of solubilization is observed widely around or below the critical micelle concentration (CMC) of surfactants. It has also been reported that micellization is induced by the solutes even below CMC and the solubilized solute increases the aggregation number of the surfactant. These observations suggest enhanced cooperativity in micellization upon solubilization. Recently, we have developed a rigorous statistical thermodynamic theory of cooperative solubilization. Its application to hydrotropy revealed the mechanism of cooperative hydrotropy: hydrotrope self-association enhanced by solutes. Here we generalize our previous cooperative solubilization theory to surfactants. We have shown that the well-known experimental observations, such as the reduction of CMC in the presence of the solutes and the increase of aggregation number, are the manifestations of cooperative solubilization. Thus, the surfactant self-association enhanced by a solute is the driving force of cooperativity and a part of a universal cooperative solubilization mechanism common to hydrotropes and surfactants at low concentrations.

The impact of the counterion in the performance of ionic hydrotropes

The efficiency of an ionic hydrotrope is shown to increase with the hydrophobicity of its counterion, challenging the common view that ionic hydrotropes should possess a small, densely charged counterion such as sodium or chloride.

Chitin Deacetylation Using Deep Eutectic Solvents: Ab Initio-Supported Process Optimization

Chitin is the most abundant marine biopolymer, being recovered during the shell biorefining of crustacean shell waste. In its native form, chitin displays a poor reactivity and solubility in most solvents due to its extensive hydrogen bonding. This can be overcome by deacetylation. However, this process requires a high concentration of acids or bases at high temperatures, forming large amounts of toxic waste. Herein, we report on the first deacetylation with deep eutectic solvents (DESs) as an environmentally friendly alternative, requiring only mild reaction conditions. Biocompatible DESs are efficient in disturbing the native hydrogen-bonding network of chitin, readily dissolving it. First, quantum chemical calculations have been performed to evaluate the feasibility of different DESs to perform chitin deacetylation by studying their mechanism. Comparing these with the calculated barriers for garden-variety alkaline/acidic hydrolysis, which are known to proceed, prospective DESs were identified with barriers around 25 kcal·mol^-1 or lower. Based on density functional theory results, an experimental screening of 10 distinct DESs for chitin deacetylation followed. The most promising DESs were identified as K₂CO₃:glycerol (K₂CO₃:G), choline chloride:acetic acid ([Ch]Cl:AA), and choline chloride:malic acid ([Ch]Cl:MA) and were subjected to further optimization with respect to the water content, process duration, and temperature. Ultimately, [Ch]Cl:MA showed the best results, yielding a degree of deacetylation (DDA) of 40% after 24 h of reaction at 120 °C, which falls slightly behind the threshold value (50%) for chitin to be considered chitosan. Further quantum chemical calculations were performed to elucidate the mechanism. Upon the removal of 40% N-acetyl groups from the chitin structure, its reactivity was considerably improved.

Using coarse-grained molecular dynamics to rationalize biomolecule solubilization mechanisms in ionic liquid-based colloidal systems

Solubilizing agents are widely used to extract poorly soluble compounds from biological matrices. Aqueous solutions of surfactants and hydrotropes are commonly used as solubilizers, however, the underlying mechanism that determines their action is still roughly understood. Among these, ionic liquids (IL) are often used not only for solubilization of a target compound but in liquid-liquid extraction processes. Molecular dynamics simulations can shed light into this issue by providing a microscopic insight of the interactions between solute and solubilising agents. In this work, a new coarse-grained (CG) model was developed under the MARTINI framework for gallic acid (GA) while the CG models of three quaternary ammonium ionic liquids and salts (QAILS) were obtained from literature. Three QAILS were selected bearing in mind their potential solubilising mechanisms: trimethyl-tetradecylammonium chloride ([N1,1,1,14]Cl) as a surfactant, tetrabutylammonium chloride ([N4,4,4,4]Cl) as a hydrotrope, and tributyl-tetradecylammonium chloride ([N4,4,4,14]Cl) as a system combining the characteristics of the other compounds. Throughout this hydrotrope-to-surfactant spectrum and considering the most prevalent GA species across the pH range, the solvation of GA at two concentration levels in aqueous QAILS solutions were studied and discussed. The results of this study indicate that dispersive interactions between the QAILS and GA are generally the driving force in the GA solubilization. However, electrostatic interactions play an increasingly significant role as the GA becomes deprotonated, affecting their placement within the micelle and ultimately the solvation mechanism. The hydrotropic mechanism seen in [N4,4,4,4]Cl corroborates recent models based on the formation of a hydrotrope-solute aggregates driven by dispersive forces. This work contributes to the application of a transferable approach to partition and solubilization studies using molecular dynamics, which could complement experimental assays and quickly screen molecular candidates for these processes.