COSMO-RS Calculations of Partition Coefficients: Different Tools for Conformation Search

Extraction of 5-Hydroxymethylfurfural and Furfural in Aqueous Biphasic Systems: A COSMO-RS Guided Approach to Greener Solvent Selection

5-Hydroxymethylfurfural (HMF) and furfural (Fur) are promising biobased platform chemicals, derived from the dehydration of carbohydrate feedstocks, normally conducted in an aqueous phase. Plagued by side-reactions in such phase, such as the rehydration to levulinic acid (LA) and formic acid (FA) or self-condensation to humins, HMF and Fur necessitates diversification from monophasic aqueous reaction systems toward biphasic systems to mitigate undesired side-reactions. Here, a methodology based on the COnductor-like Screening MOdel for Real Solvents (COSMO-RS) method was used to screen solvent candidates based on the predicted partition coefficients (Ki). Hansen solubility parameters in conjunction with excess thermodynamic quantities determined by COSMO-RS were employed to assess solvent compatibility. Experimental validation of the COSMO-RS values highlighted only minor deviations from the predictions with root-mean-square-error (RMSE) values of HMF and Fur at 0.76 and 5.32, respectively, at 298 K. The combined effort suggested cyclohexanone, isophorone, and methyl isobutyl ketone (MIBK) as the best candidates. Finally, extraction solvent reuse demonstrated cyclohexanone suitability for HMF extraction with KHMF of 3.66 and MIBK for Fur with KFur 7.80 with consistent partitioning across four total runs. Both solvents are classified as recommended by the CHEM21 solvent selection guide, hence adding to the sustainability of the process.

ConfSolv: Prediction of Solute Conformer-Free Energies across a Range of Solvents

Predicting Gibbs free energy of solution is key to understanding the solvent effects on thermodynamics and reaction rates for kinetic modeling. Accurately computing solution free energies requires the enumeration and evaluation of relevant solute conformers in solution. However, even after generation of relevant conformers, determining their free energy of solution requires an expensive workflow consisting of several ab initio computational chemistry calculations. To help address this challenge, we generate a large data set of solution free energies for nearly 44,000 solutes with almost 9 million conformers calculated in 41 different solvents using density functional theory and COSMO-RS and quantify the impact of solute conformers on the solution free energy. We then train a message passing neural network to predict the relative solution free energies of a set of solute conformers, enabling the identification of a small subset of thermodynamically relevant conformers. The model offers substantial computational time savings with predictions usually substantially within 1 kcal/mol of the free energy of the solution calculated by using computational chemical methods.

Intermolecular Interactions as a Measure of Dapsone Solubility in Neat Solvents and Binary Solvent Mixtures

Dapsone is an effective antibacterial drug used to treat a variety of conditions. However, the aqueous solubility of this drug is limited, as is its permeability. This study expands the available solubility data pool for dapsone by measuring its solubility in several pure organic solvents: N-methyl-2-pyrrolidone (CAS: 872-50-4), dimethyl sulfoxide (CAS: 67-68-5), 4-formylmorpholine (CAS: 4394-85-8), tetraethylene pentamine (CAS: 112-57-2), and diethylene glycol bis(3-aminopropyl) ether (CAS: 4246-51-9). Furthermore, the study proposes the use of intermolecular interactions as molecular descriptors to predict the solubility of dapsone in neat solvents and binary mixtures using machine learning models. An ensemble of regressors was used, including support vector machines, random forests, gradient boosting, and neural networks. Affinities of dapsone to solvent molecules were calculated using COSMO-RS and used as input for model training. Due to the polymorphic nature of dapsone, fusion data are not available, which prohibits the direct use of COSMO-RS for solubility calculations. Therefore, a consonance solvent approach was tested, which allows an indirect estimation of the fusion properties. Unfortunately, the resulting accuracy is unsatisfactory. In contrast, the developed regressors showed high predictive potential. This work documents that intermolecular interactions characterized by solute-solvent contacts can be considered valuable molecular descriptors for solubility modeling and that the wealth of encoded information is sufficient for solubility predictions for new systems, including those for which experimental measurements of thermodynamic properties are unavailable.

Recent Advances in Co-Former Screening and Formation Prediction of Multicomponent Solid Forms of Low Molecular Weight Drugs

Multicomponent solid forms of low molecular weight drugs, such as co-crystals, salts, and co-amorphous systems, are a result of the combination of an active pharmaceutical ingredient (API) with a pharmaceutically acceptable co-former. These solid forms can enhance the physicochemical and pharmacokinetic properties of APIs, making them increasingly interesting and important in recent decades. Nevertheless, predicting the formation of API multicomponent solid forms in the early stages of formulation development can be challenging, as it often requires significant time and resources. To address this, empirical and computational methods have been developed to help screen for potential co-formers more efficiently and accurately, thus reducing the number of laboratory experiments needed. This review provides a comprehensive overview of current screening and prediction methods for the formation of API multicomponent solid forms, covering both crystalline states (co-crystals and salts) and amorphous forms (co-amorphous). Furthermore, it discusses recent advances and emerging trends in prediction methods, with a particular focus on artificial intelligence.

New Screening Protocol for Effective Green Solvents Selection of Benzamide, Salicylamide and Ethenzamide

New protocol for screening efficient and environmentally friendly solvents was proposed and experimentally verified. The guidance for solvent selection comes from computed solubility via COSMO-RS approach. Furthermore, solute-solvent affinities computed using advanced quantum chemistry level were used as a rationale for observed solvents ranking. The screening protocol pointed out that 4-formylomorpholine (4FM) is an attractive solubilizer compared to commonly used aprotic solvents such as DMSO and DMF. This was tested experimentally by measuring the solubility of the title compounds in aqueous binary mixtures in the temperature range between 298.15 K and 313.15 K. Additional measurements were also performed for aqueous binary mixtures of DMSO and DMF. It has been found that the solubility of studied aromatic amides is very high and quite similar in all three aprotic solvents. For most aqueous binary mixtures, a significant decrease in solubility with a decrease in the organic fraction is observed, indicating that all systems can be regarded as efficient solvent-anti-solvent pairs. In the case of salicylamide dissolved in aqueous-4FM binary mixtures, a strong synergistic effect has been found leading to the highest solubility for 0.6 mole fraction of 4-FM.

Concentration of Antioxidant Compounds from Calendula officinalis through Sustainable Supercritical Technologies, and Computational Study of Their Permeability in Skin for Cosmetic Use

The growing interest in the cosmetic industry in using compounds of natural and sustainable origin that are safe for humans is encouraging the development of processes that can satisfy these needs. Chlorogenic acid (CHA), caffeic acid (CAF) and ferulic acid (FA) are three compounds widely used within the cosmetic industry due to their functionalities as antioxidants, collagen modifiers or even as radiation protectors. In this work, two advanced separation techniques with supercritical CO2 are used to obtain these three compounds from Calendula officinalis, and these are then evaluated using a computational skin permeability model. This model is encompassed by the COSMO-RS model, the calculations of which make it possible to study the behaviour of the compounds in the epidermis. The results show that both CAF and FA are retained in the stratum corneum, while CHA manages to penetrate to the stratum spinosum. These compounds were concentrated by antisolvent fractionation with super-critical CO2 using a Response Surface Methodology to study the effect of pressure and CO2 flow rate. CHA, CAF and FA were completely retained in the precipitation vessel, with concentrations between 40% and 70% greater than in the original extract. The conditions predicted that the optimal overall yield and enrichment achieved would be 153 bar and 42 g/min.

Resolving unknown isomers of emerging per- and polyfluoroalkyl substances (PFASs) in environmental samples using COSMO-RS-derived retention factor and mass fragmentation patterns

Chromatographic retention factors (k) and mass spectral fragmentation patterns of per- and polyfluoroalkyl substances (PFASs) were determined using the optimized parameters in liquid chromatography with tandem high-resolution mass spectrometry (LC-HRMS) analysis. Characteristic fragment ions obtained at various collision energies (MS² fragmentation) were used to determine the structures of newly discovered (emerging) PFASs detected from industrial effluent and surface water samples. Moreover, COnductor-like Screening MOdel for Realistic Solvents (COSMO-RS) derived octanol-water partition coefficients (K_ow), along with mean isotropic polarizabilities calculated from Density Functional Theory (DFT), of known PFASs were plotted against their experimental k values (k_exp) to obtain a multivariable regression model that can be used to predict k values of unknown PFASs. The k values of different structural isomers of unknown PFASs were calculated and compared to k_exp. The predicted k value for the isomer that matches the MS² fragmentation observed was found to be within 4.2 % of k_exp. This study demonstrates the applicability of an approach that combines the observed MS² fragmentation patterns and k values, together with computationally-derived log K_ow and polarizabilities, in assigning the structures of unknown PFASs at environmentally relevant conditions when no reference standards are available.

Simulation of Deep Eutectic Solvents' Interaction with Membranes of Cancer Cells Using COSMO-RS

Deep eutectic solvent (DES) affinities with cellular membranes structures dictate the degree of cytotoxicity that results from these interactions. The physicochemical properties of choline chloride (ChCl)-DESs suggest non-negligible cytotoxicities that were attested by published researches. In this study, the profiles of novel N,N-diethylammonium chloride (DAC)-based-deep eutectic solvents (DESs) prepared with various hydrogen bond donors (urea, glycerol, ethylene glycol, malonic acid, and zinc chloride) were compared to those of ChCl-DESs by using HelaS3, AGS, MCF-7, and WRL-68 cancer cell lines. The molecular interactions between salts and cellular membranes were investigated to explain the observed cytotoxicity. The results show that ChCl-based DESs (279 ≤ IC₅₀ ≥ 1260 mM) were less toxic than DAC-based DESs (37 ≤ IC₅₀ ≥ 109 mM). COSMO-RS analysis emphasized the importance of salt hydrophobicity with regards to DESs cytotoxicity. Malonic acid increased hydrophobicity and cytotoxicity in general, thus highlighting the potential of ammonium salt-based DESs as anticancer agents.

Use of the normalized hydrophilic-lipophilic-deviation (HLDN) equation for determining the equivalent alkane carbon number (EACN) of oils and the preferred alkane carbon number (PACN) of nonionic surfactants by the fish-tail method (FTM)

The standard HLD (Hydrophilic-Lipophilic-Deviation) equation expressing quantitatively the deviation from the "optimum formulation" of Surfactant/Oil/Water systems is normalized and simplified into a relation including only the three more meaningful formulation variables, namely (i) the "Preferred Alkane Carbon Number" PACN which expresses the amphiphilicity of the surfactant, (ii) the "Equivalent Alkane Carbon Number" EACN which accurately reflects the hydrophobicity of the oil and (iii) the temperature which has a strong influence on ethoxylated surfactants and is thus selected as an effective, continuous and reversible scanning variable. The PACN and EACN values, as well as the "temperature-sensitivity-coefficient"τ of surfactants are determined by reviewing available data in the literature for 17 nonionic n-alkyl polyglycol ether (C_iE_j) surfactants and 125 well-defined oils. The key information used is the so-called "fish-tail-temperature" T* which is a unique data point in true ternary C_iE_j/Oil/Water fish diagrams. The PACNs of C_iE_j surfactants are compared with other descriptors of their amphiphilicity, namely, the cloud point, the HLB number and the PIT-slope value. The EACNs of oils are rationalized by the Effective-Packing-Parameter concept and modelled thanks to the COSMO-RS theory.

Prediction of Lipophilicity of some Quinolone Derivatives by using Quantitative Structure-Activity Relationship

OBJECTIVES

Quantitative structure activity relationship (QSAR) was used to study the partition coefficient of some quinolones and their derivatives.

METHODS

These molecules are broad-spectrum antibiotic pharmaceutics. First, data were divided into two categories of train and test (validation) sets using a random selection method. Second, three approaches, including stepwise selection (STS) (forward), genetic algorithm (GA), and simulated annealing (SA) were used to select the descriptors, to examine the effect feature selection methods. To find the relation between descriptors and partition coefficient, multiple linear regression (MLR), principal component regression (PCR) and partial least squares (PLS) were used.

RESULTS

QSAR study showed that both regression and descriptor selection methods have a vital role in the results. Different statistical metrics showed that the MLR-SA approach with (r2=0.96, q2=0.91, pred_r2=0.95) gives the best outcome.

CONCLUSION

The proposed expression by the MLR-SA approach can be used in the better design of novel quinolones and their derivatives.

COSMOplex: self-consistent simulation of self-organizing inhomogeneous systems based on COSMO-RS

During the past 20 years, the efficient combination of quantum chemical calculations with statistical thermodynamics by the COSMO-RS method has become an important alternative to force-field based simulations for the accurate prediction of free energies of molecules in liquid systems. While it was originally restricted to homogeneous liquids, it later has been extended to the prediction of the free energy of molecules in inhomogeneous systems such as micelles, biomembranes, or liquid interfaces, but these calculations were based on external input about the structure of the inhomogeneous system. Here we report the rigorous extension of COSMO-RS to a self-consistent prediction of the structure and the free energies of molecules in self-organizing inhomogeneous systems. This extends the application range to many new areas, such as the prediction of micellar structures and critical micelle concentrations, finite loading effects in micelles and biomembranes, the free energies and structure of liquid interfaces, microemulsions, and many more related topics, which often are of great practical importance.

Effects of 1-hexanol on C12E10 micelles: a molecular simulations and light scattering study

The micelles of the non-ionic C₁₂E₁₀ surfactant and 1-hexanol as an aqueous solution additives are studied toward the purpose of understanding the role of alcohol additives in tuning the characteristics of alkyl-ethoxylate micellar systems. Our dynamic light scattering and cloud point experiments show that the addition of hexanol induces a response similar to an increase of temperature. We associate the change with increased attraction between the micelles at low to moderate hexanol loadings and a potential increase of the aggregate size at a high hexanol-to-surfactant ratio. Detailed molecular dynamic simulation characterization shows that hexanol solubilizes to a micelle palisade layer when the hexanol-to-C₁₂E₁₀ ratio is less than or equal to 0.5 while swollen micelles, in which a part of hexanol forms an oil core, are present when the ratio increases above approximately 1.5. The simulations indicate that the surface of the micelles is rough. Formation of reverse hexanol structures akin to those found in bulk octanol is observed in the oil core. Molecular simulations associate the increase in attraction between micelles observed via the experiments with decreased chain density in the headgroup region. This density decrease is caused by hexanol molecules solubilized between neighbouring surfactants. Altogether, these findings provide detailed physical characterization of the effect of an archetypal solution additive, hexanol, on an alkyl ethoxylate micelle system. These findings could bear a significance in designing micellar and emulsion based systems with desired solution characteristics or properties for e.g. drug delivery, catalysis, or platforms for green chemistry reactions.

Natural deep eutectic solvents: cytotoxic profile

The purpose of this study was to investigate the cytotoxic profiles of different ternary natural deep eutectic solvents (NADESs) containing water. For this purpose, five different NADESs were prepared using choline chloride as a salt, alongside five hydrogen bond donors (HBD) namely glucose, fructose, sucrose, glycerol, and malonic acid. Water was added as a tertiary component during the eutectics preparation, except for the malonic acid-based mixture. Coincidentally, the latter was found to be more toxic than any of the water-based NADESs. A trend was observed between the cellular requirements of cancer cells, the viscosity of the NADESs, and their cytotoxicity. This study also highlights the first time application of the conductor-like screening model for real solvent (COSMO-RS) software for the analysis of the cytotoxic mechanism of NADESs. COSMO-RS simulation of the interactions between NADESs and cellular membranes' phospholipids suggested that NADESs strongly interacted with cell surfaces and that their accumulation and aggregation possibly defined their cytotoxicity. This reinforced the idea that careful selection of NADESs components is necessary, as it becomes evident that organic acids as HBD highly contribute to the increasing toxicity of these neoteric mixtures. Nevertheless, NADESs in general seem to possess relatively less acute toxicity profiles than their DESs parents. This opens the door for future large scale utilization of these mixtures.

The role of phase behavior in the enzyme catalyzed synthesis of glycerol monolaurate

Partial glycerides such as monoacylglycerides (MAGs) are important functional ingredients with various applications in the cosmetics and food industry.

Solubility prediction, solvate and cocrystal screening as tools for rational crystal engineering

OBJECTIVES

The fact that novel drug candidates are becoming increasingly insoluble is a major problem of current drug development. Computational tools may address this issue by screening for suitable solvents or by identifying potential novel cocrystal formers that increase bioavailability. In contrast to other more specialized methods, the fluid phase thermodynamics approach COSMO-RS (conductor-like screening model for real solvents) allows for a comprehensive treatment of drug solubility, solvate and cocrystal formation and many other thermodynamics properties in liquids. This article gives an overview of recent COSMO-RS developments that are of interest for drug development and contains several new application examples for solubility prediction and solvate/cocrystal screening.

METHODS

For all property predictions COSMO-RS has been used. The basic concept of COSMO-RS consists of using the screening charge density as computed from first principles calculations in combination with fast statistical thermodynamics to compute the chemical potential of a compound in solution.

KEY FINDING

The fast and accurate assessment of drug solubility and the identification of suitable solvents, solvate or cocrystal formers is nowadays possible and may be used to complement modern drug development. Efficiency is increased by avoiding costly quantum-chemical computations using a database of previously computed molecular fragments.

SUMMARY

COSMO-RS theory can be applied to a range of physico-chemical properties, which are of interest in rational crystal engineering. Most notably, in combination with experimental reference data, accurate quantitative solubility predictions in any solvent or solvent mixture are possible. Additionally, COSMO-RS can be extended to the prediction of cocrystal formation, which results in considerable predictive accuracy concerning coformer screening. In a recent variant costly quantum chemical calculations are avoided resulting in a significant speed-up and ease-of-use.

A modeling assessment of the physicochemical properties and environmental fate of emerging and novel per- and polyfluoroalkyl substances

Long-chain perfluoroalkyl carboxylic acids (PFCAs) and perfluoroalkane sulfonic acids (PFSAs) are persistent, bioaccumulative, and toxic contaminants that are globally present in the environment, wildlife and humans. Phase-out actions and use restrictions to reduce the environmental release of long-chain PFCAs, PFSAs and their precursors have been taken since 2000. In particular, long-chain poly- and perfluoroalkyl substances (PFASs) are being replaced with shorter-chain homologues or other fluorinated or non-fluorinated alternatives. A key question is: are these alternatives, particularly the structurally similar fluorinated alternatives, less hazardous to humans and the environment than the substances they replace? Several fluorinated alternatives including perfluoroether carboxylic acids (PFECAs) and perfluoroether sulfonic acids (PFESAs) have been recently identified. However, the scarcity of experimental data prevents hazard and risk assessments for these substances. In this study, we use state-of-the-art in silico tools to estimate key properties of these newly identified fluorinated alternatives. [i] COSMOtherm and SPARC are used to estimate physicochemical properties. The US EPA EPISuite software package is used to predict degradation half-lives in air, water and soil. [ii] In combination with estimated chemical properties, a fugacity-based multimedia mass-balance unit-world model - the OECD Overall Persistence (POV) and Long-Range Transport Potential (LRTP) Screening Tool - is used to assess the likely environmental fate of these alternatives. Even though the fluorinated alternatives contain some structural differences, their physicochemical properties are not significantly different from those of their predecessors. Furthermore, most of the alternatives are estimated to be similarly persistent and mobile in the environment as the long-chain PFASs. The models therefore predict that the fluorinated alternatives will become globally distributed in the environment similar to their predecessors. Although such in silico methods are coupled with uncertainties, this preliminary assessment provides enough cause for concern to warrant experimental work to better determine the properties of these fluorinated alternatives.

Molecular dynamics simulation of SDS and CTAB micellization and prediction of partition equilibria with COSMOmic

Molecular dynamics (MD) simulations of the self-assembly of different ionic surfactants have been performed in order to obtain representative micellar structures. Subsequently, these structures were used to predict the partition behavior of various solutes in these micelles with COSMOmic, an extension of COSMO-RS. This paper includes multiple self-assembled micelles of SDS (sodium dodecyl sulfate, anionic surfactant) and CTAB (cetyltrimethylammoniumbromide, cationic surfactant) at different concentrations. Micellar size, density profiles, and shape (eccentricity) have been investigated. However, the size strongly depends on the functional definition of a micelle. For this reason, we present a method based on the free monomer concentration in aqueous solution as an optimization criterion for the micelle definition. The combination of MD with COSMOmic has the benefit of combining detailed atomistic information from MD with fast calculations of COSMOmic. For the first time the influence of micelle structure on pratition equilibria, predicted with COSMOmic, were investigated. In case of SDS more than 4600 and for CTAB more than 800 single micelles have been studied. The predictions of the partition coefficients with COSMOmic are in good agreement with experimental data. Additionally, the most favorable locations of selected molecules in the micelles as well as probable energy barriers are determined even for complex solutes such as toluene, propanolol, ephedrine, acetone, phenol, lidocaine, syringic acid, coumarin, isovanillin, ferulic acid, and vanillic acid. This method can therefore be applied as a potential screening tool for solutes (e.g., drugs) to find the optimal solute-surfactant combination.

Assessing the accuracy and performance of implicit solvent models for drug molecules: conformational ensemble approaches

The accuracy and performance of implicit solvent methods for solvation free energy calculations were assessed on a set of 20 neutral drug molecules. Molecular dynamics (MD) provided ensembles of conformations in water and water-saturated octanol. The solvation free energies were calculated by popular implicit solvent models based on quantum mechanical (QM) electronic densities (COSMO-RS, MST, SMD) as well as on molecular mechanical (MM) point-charge models (GB, PB). The performance of the implicit models was tested by a comparison with experimental water-octanol transfer free energies (ΔG(ow)) by using single- and multiconformation approaches. MD simulations revealed difficulties in a priori estimation of the flexibility features of the solutes from simple structural descriptors, such as the number of rotatable bonds. An increasing accuracy of the calculated ΔG(ow) was observed in the following order: GB1 ~ PB < GB7 ≪ MST < SMD ~ COSMO-RS with a clear distinction identified between MM- and QM-based models, although for the set excluding three largest molecules, the differences among COSMO-RS, MST, and SMD were negligible. It was shown that the single-conformation approach applied to crystal geometries provides a rather accurate estimate of ΔG(ow) for rigid molecules yet fails completely for the flexible ones. The multiconformation approaches improved the performance, but only when the deformation contribution was ignored. It was revealed that for large-scale calculations on small molecules a recent GB model, GB7, provided a reasonable accuracy/speed ratio. In conclusion, the study contributes to the understanding of solvation free energy calculations for physical and medicinal chemistry applications.

Efficient Combination of Environment Change and Alchemical Perturbation within the Enveloping Distribution Sampling (EDS) Scheme: Twin-System EDS and Application to the Determination of Octanol-Water Partition Coefficients

The methodology of Enveloping Distribution Sampling (EDS) is extended to probe a single-simulation alternative to the thermodynamic cycle that is standardly used for measuring the effect of a modification of a chemical compound, e.g. from a given species to a chemical derivative for a ligand or solute molecule, on the free-enthalpy change associated with a change in environment, e.g. from the unbound state to the bound state for a protein-ligand system or from one solvent to another one for a solute molecule. This alternative approach relies on the coupled simulation of two systems (computational boxes) 1 and 2, and the method is therefore referred to as twin-system EDS. Systems 1 and 2 account for the two choices of environment. The end states of the alchemical perturbation for the twin-system associate the two alternative forms X and Y of the molecule to systems 1 and 2 or 2 and 1, respectively. In this way, the processes of transforming one molecule into the other are carried out simultaneously in opposite directions in the two environments, leading to a change in free enthalpy that is smaller than for the two individual processes and to an energy-difference distribution that is more symmetric. As an illustration, the method is applied to the calculation of octanol-water partition coefficients for C4 to C8 alkanes, 1-hexanol and 1,2-dimethoxyethane. It is shown in particular that the consideration of the residual hydration of octanol leads to calculated partition coefficients that are in better agreement with reported experimental numbers.