Application of quantum chemical approximations to environmental problems: prediction of water solubility for nitro compounds

COSMO Models for the Pharmaceutical Development of Parenteral Drug Formulations

The aqueous solubility of active pharmaceutical ingredients is one of the most important features to be considered during the development of parenteral formulations in the pharmaceutical industry. Computational modelling has become in the last years an integral part of pharmaceutical development. In this context, ab initio computational models, such as COnductor-like Screening MOdel (COSMO), have been proposed as promising tools for the prediction of results without the effective use of resources. Nevertheless, despite the clear evaluation of computational resources, some authors had not achieved satisfying results and new calculations and algorithms have been proposed over the years to improve the outcomes. In the development and production of aqueous parenteral formulations, the solubility of Active Pharmaceutical Ingredients (APIs) in an aqueous and biocompatible vehicle is a decisive step. This work aims to study the hypothesis that COSMO models could be useful in the development of new parenteral formulations, mainly aqueous ones.

Simplex representation of molecular structure as universal QSAR/QSPR tool

We review the development and application of the Simplex approach for the solution of various QSAR/QSPR problems. The general concept of the simplex method and its varieties are described. The advantages of utilizing this methodology, especially for the interpretation of QSAR/QSPR models, are presented in comparison to other fragmentary methods of molecular structure representation. The utility of SiRMS is demonstrated not only in the standard QSAR/QSPR applications, but also for mixtures, polymers, materials, and other complex systems. In addition to many different types of biological activity (antiviral, antimicrobial, antitumor, psychotropic, analgesic, etc.), toxicity and bioavailability, the review examines the simulation of important properties, such as water solubility, lipophilicity, as well as luminescence, and thermodynamic properties (melting and boiling temperatures, critical parameters, etc.). This review focuses on the stereochemical description of molecules within the simplex approach and details the possibilities of universal molecular stereo-analysis and stereochemical configuration description, along with stereo-isomerization mechanism and molecular fragment "topography" identification.

Artificial intelligence in drug design: algorithms, applications, challenges and ethics

The discovery paradigm of drugs is rapidly growing due to advances in machine learning (ML) and artificial intelligence (AI). This review covers myriad faces of AI and ML in drug design. There is a plethora of AI algorithms, the most common of which are summarized in this review. In addition, AI is fraught with challenges that are highlighted along with plausible solutions to them. Examples are provided to illustrate the use of AI and ML in drug discovery and in predicting drug properties such as binding affinities and interactions, solubility, toxicology, blood–brain barrier permeability and chemical properties. The review also includes examples depicting the implementation of AI and ML in tackling intractable diseases such as COVID-19, cancer and Alzheimer’s disease. Ethical considerations and future perspectives of AI are also covered in this review.

QSPR modeling of octanol-water partition coefficient and organic carbon normalized sorption coefficient of diverse organic chemicals using Extended Topochemical Atom (ETA) indices

Octanol-water partition coefficient (logK_ow) and soil organic carbon content normalized sorption coefficient (logK_oc) values are two important physicochemical properties in the context of bioaccumulation and environmental fate of organic compounds and their environmental risk assessment. Simple, interpretable and easy-to-derive extended topochemical atom (ETA) indices obtained from 2D structural representation of compounds were used for quantitative structure-property relationship (QSPR) modeling of these two endpoints. Linear regression based models developed using only ETA indices show encouraging statistical and validation results. Based on the information obtained from developed QSPR models, we may conclude that molecular volume, branching pattern, presence of hydrophobic Cl atoms, cyclicity/fusion, polar environment, electron density, unsaturation content, hydrogen bonding propensity or hydrogen bond donor atoms, local topology, presence of heteroatoms and aromaticity are crucial factors in controlling the logK_ow and logK_oc values of the compounds. The suggested explanatory features for different classes of chemicals or the whole diverse set can help in safer designing of chemicals, which is one of the primary agenda of the "Green Chemistry" program.

Adsorption of nitrogen-containing compounds on hydroxylated α-quartz surfaces

Adsorption energies of various nitrogen-containing compounds (specifically, 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), 2,4-dinitroanisole (DNAn), and 3-nitro-1,2,4-triazole-5-one (NTO)) on the hydroxylated (001) and (100) α-quartz surfaces are computed. Different density functionals are utilized and both periodic as well as cluster approaches are applied. From the adsorption energies, partition coefficients on the considered α-quartz surfaces are derived. While TNT and DNT are preferably adsorbed on the (001) surface of α-quartz, NTO is rather located on both α-quartz surfaces.

Adsorption energies of different nitrogen-containing compounds on two hydroxylated (001) and (100) quartz surfaces are computed.

QSPR modeling of the logKow and logKoc of polymethoxylated, polyhydroxylated diphenyl ethers and methoxylated-, hydroxylated-polychlorinated diphenyl ethers

In the present study, the structural parameters of 209 types of polymethoxylated diphenyl ethers (PMeODEs), 209 types of polyhydroxylated diphenyl ethers (PHODEs), seven types of methoxylated-polychlorinated diphenyl ethers (MeO-PCDEs) and seven types of hydroxylated-polychlorinated diphenyl ethers (HO-PCDEs) were calculated using the Gaussian 09 program at the B3LYP/6-311G** level. Using structural and positional parameters as descriptors, quantitative structure-property relationships (QSPR) models for the prediction of n-octanol/water partition coefficient (logK_ow) and soil sorption coefficient normalized to organic carbon (logK_oc) were established and verified. The position parameters N₂₍₆₎, N₃₍₅₎ and N₄ were the main positional factors influencing logK_ow and logK_oc of PMeODEs and PHODEs. The molecular polarizability α was entered into the QSPR models of the logK_ow and logK_oc of PMeODEs, PHODEs and MeO/HO-PCDEs, indicating that the molecular volume could influence the two environment-related properties of DEs significantly. All of the established QSPR models showed good goodness-of-fit, robustness, and predictive ability. The two models for all of the tested DEs are slightly inferior compared with the models for only a class of compounds. In addition, application domain analysis indicated that the models reliably predicted the logK_ow and logK_oc of the mon- to hexa-DEs.

Light-triggered Supramolecular Isomerism in a Self-catenated Zn(II)-organic Framework: Dynamic Photo-switching CO2 Uptake and Detection of Nitroaromatics

A self-catenated Zn(II)-organic framework formulated as [Zn₂(3,3′-bpeab)(oba)₂]·DMF (1) exhibiting a six-connected 4⁴·6¹⁰·8 topology has been successfully synthesized through the mixed-ligand of kinked 3,3′-bis[2-(4-pyridyl)ethenyl]azobenzene (3,3′-bpeab) and 4,4′-oxybis-benzoic acid (H₂oba) under solvothermal condition. UV light triggers isomerization of complex 1 in a single-crystal-to-single-crystal (SCSC) manner, giving rise to a conformational supramolecular isomer 1_UV through the pedal motion of photoresponsive double bonds. Dynamic photo-switching in the obtained light-responsive supramolecular isomers leads to instantly reversible CO₂ uptake. Furthermore, the ligand originated fluorescence emission of water-resistant complex 1 is selectively sensitive to 4-nitrotoluene (4-NT) owing to a higher quenching efficiency of the perilous explosive over other structurally similar nitroaromatics, prefiguring the potentials of 1 as a fluorescence sensor towards 4-NT in aquatic media.

Novel enhanced applications of QSPR models: Temperature dependence of aqueous solubility

A model developed to predict aqueous solubility at different temperatures has been proposed based on quantitative structure-property relationships (QSPR) methodology. The prediction consists of two steps. The first one predicts the value of k parameter in the linear equation lgSw=kT+c, where Sw is the value of solubility and T is the value of temperature. The second step uses Random Forest technique to create high-efficiency QSPR model. The performance of the model is assessed using cross-validation and external test set prediction. Predictive capacity of developed model is compared with COSMO-RS approximation, which has quantum chemical and thermodynamic foundations. The comparison shows slightly better prediction ability for the QSPR model presented in this publication. © 2016 Wiley Periodicals, Inc.

Experimental and computational study of membrane affinity for selected energetic compounds

The affinity of various energetic compounds for a biological membrane was investigated using experimental and computational techniques. We measured octanol-water (log(Kow)) and liposome-water (log(Klipw)) partition coefficients for the following chemicals: trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), 2,6-dinitrotoluene (2,6-DNT), 2,4-dinitroanisole (DNAN), 2methoxy-5-nitrophenol (2M5NP), 2,4,6-trinitrobenzene (TNB), and 2,4-dinitrophenol (2,4-DNP). In order to determine log(Klipw) experimentally, we used artificial solid supported lipid liposomes produced under trade mark TRANSIL. Log(Kow) value were predicted with several program packages including the COSMOthermX software. Log(Klipw) were estimated with COSMOmic as implemented in the COSMOthermX program package. In order to verify accuracy of our experimentally obtained results, we performed basic statistical analysis of data taken from the literature. We concluded that compounds considered in this study possess a moderate ability to penetrate into membranes. Comparison of both coefficients has shown that in general, the log(Kow) values are slightly smaller than log(Klipw).

Experimental investigation on the soil sorption properties and hydrophobicity of polymethoxylated, polyhydroxylated diphenyl ethers and methoxylated-, hydroxylated-polychlorinated diphenyl ethers

In the present study, twenty-six types of polymethoxylated diphenyl ethers (PMeODEs), twenty types of polyhydroxylated diphenyl ethers (PHODEs), seven types of methoxylated-polychlorinated diphenyl ethers (MeO-PCDEs) and seven types of hydroxylated-polychlorinated diphenyl ethers (HO-PCDEs) were synthesized. The logKow and logKoc values of all of the synthesized compounds were then determined using HPLC. The soil sorption properties of five types of selected substituted diphenyl ethers (DEs) were investigated. Sorption behavior studies suggested that rapid sorption played a primary role in the sorption process of the selected DEs and their sorption isotherms were fitted the Freundlich logarithmic model. For PMeODEs and PHODEs, with the increase in the number of substituents, both logKow and logKoc values exhibited linearly decreasing trends. Unlike PMeODEs and PHODEs, both logKow and logKoc values of MeO/HO-PCDEs were decreased linearly with the increasing number of chlorine atoms. The reason maybe that both methoxy and hydroxyl are hydrophilic groups, whereas the chlorine atom is hydrophobic group. Linear relationships were observed for the logKow and logKoc of all studied DEs. Moreover, the logKow of PMeODEs, PHODEs, MeO- and HO-PCDEs and their corresponding PCDEs showed good linearity.

Synthesis and QSPR study on environment-related properties of polychlorinated diphenyl sulfides (PCDPSs)

Twenty-nine congeners of polychlorinated diphenyl sulfide (PCDPS) theoretically possible were synthesized and purified, and their octanol-water partition coefficients (logK(ow)) and high performance liquid chromatography capacity factors (HPLC-logk') were determined. Then the constitutional and structural descriptors were obtained respectively to establish 2D models and comparative molecular similarity indices analysis (CoMSIA) method was used to establish 3D models. All the models were robust and predictive, indicating that the electrostatic effect may be the primary factor influencing the two properties of PCDPS. The logK(ow) and logk' values of all PCDPS congeners were predicted based on these models. The establishment of linear equation on logK(ow) between PCDPS and chlorinated or brominated diphenyl ether (PCDE, PBDE) was attempted, and the hydrophobic differences were considered to relate with the size of the molecules.

Environment-related properties of polyhydroxylated dibenzo-p-dioxins

Polyhydroxylated dibenzo-p-dioxins (PHODDs) are important metabolic and synthetic products of polychlorinated dibenzo-p-dioxins (PCDDs). Two types of hydrogen bonds exist in PHODD molecules: one between a hydroxyl group (HO) and an oxygen atom of the ether bond, and the other between two ortho hydroxyls of a benzene ring. By fully optimized calculation with density functional theory (DFT), their bond energies were ascertained to be approximately 9-14 kJ/mol and 15-19 kJ/mol respectively by the comparison of standard Gibbs energy of formation (Δ(f)G(θ)) between different molecules, which was experimentally verified. The two types of hydrogen bonds affect the hydrophilicity and stability of the molecules. The torsional potential of hydroxyls and the orientation making the congener most stable were obtained. The octanol-water partition coefficients (logK(ow)s) were calculated based on the group contribution method, and the standard state entropy (S(θ)), standard enthalpy (Δ(f)H(θ)) of formation and Δ(f)G(θ) were obtained from the combination of DFT calculation and isodesmic reaction for the stable PHODD congeners. The number and position of hydroxyl substitution (N(PHOS)) were employed as descriptors to establish quantitative structure-property relationship (QSPR) models. Although the hydrophilicity of PHODDs increases with the number of hydroxyl groups, it is impaired by the intramolecular hydrogen bonds. The logK(ow)s of PHODDs are much smaller than those of PCDDs, and the variation trend with the number of substituents is different. In addition, the relative stability order of PHODD congeners was theoretically proposed, which is quite different from that of PCDDs. Considering the ionization in water, first-order ionization constants of PHODDs were calculated according to the results of SMD method of Self-Consistent Reaction Field Theory (SCRF), and they were influenced by the hydrogen bonds.

Evaluation of the dependence of aqueous solubility of nitro compounds on temperature and salinity: a COSMO-RS simulation

The solubility in pure and saline water at various temperatures was calculated for selected nitro compounds (nitrobenzene, 1,3,5-trinitrobenzene, 2-nitrotoluene, 3-nitrotoluene, 4-nitrotoluene, 2,4-dinitrotoluene, 2,6-dinitrotoluene, 2,3-dinitrotoluene, 3,4-dinitrotoluene, 2,4,6-trinitrotoluene) using the Conductor-like Screening model for Real Solvents (COSMO-RS). The results obtained were compared with experimental values. The COSMO-RS predictions have shown high accuracy in reproducing the trends of aqueous solubilities for both temperature and salinity. The proposed methodology was then applied to predict the aqueous solubilities of 19 nitro compounds in the temperature range of 5-50°C in saline solutions. The salting-out parameters of the Setschenow equation were also calculated. The predicted salting-out parameters were overestimated when compared to the measured values, but these parameters can still be used for qualitative estimation of the trends.

New QSPR equations for prediction of aqueous solubility for military compounds

The development of a new quantitative structure-property relationship (QSPR) model to predict aqueous solubility (S(w)) accurately for compounds of military interest is presented. The ability of the new model to predict solubility is assessed and compared to available experimental data. A large set of structurally diverse organic compounds was used in this analysis. SiRMS methodology was employed to develop PLS models based on 135 training compounds and predictive accuracy was tested for 155 compounds selected for that purpose. The use of descriptors calculated only from the 2D level of representation of molecular structure produces a well-fitted and robust QSPR model (R(2)=0.90; Q(2)=0.87). Predictive ability for the model produced in this study on external test set (R(test)(2)=0.81) is comparable to the predictive ability of EPI Suite 4.0. Consensus solubility predictions using SiRMS and EPI models for 25 compounds of military interest (not included into the training set) have been completed.