Insights into the contrasting effects of sulfidation on dechlorination of chlorinated aliphatic hydrocarbons by zero-valent iron.

Contrasting effects of sulfidation on contaminants reduction by zero-valent iron (ZVI) has been reported in literature but the underlying mechanisms remain unclear. Here, under well-controlled conditions, we compared the performance of ZVI and sulfidated ZVI (S-ZVI) toward a series of chlorinated compounds. Results revealed that, although S-ZVI was more reactive than ZVI toward hexachloroethane, pentachloroethane, tetrachloroethylene, and trichloroethene, sulfidation hindered the dechlorination of the other ten tested chlorinated aliphatics by a factor of 1.5-125. Moreover, S-ZVI may lead to an accumulation of toxic partially-dechlorinated products. Analogous to its effects on ZVI reactivity, sulfidation also exerted positive, negligible, or negative effects on the electron efficiency of ZVI. Solvent kinetic isotope effect analysis suggested that direct electron transfer rather than reaction with atomic hydrogen was the dominant reduction mechanism in S-ZVI system. Hence, the sulfidation enhancing effects could be expected only when direct electron transfer is the preferred reduction route for target contaminants. Furthermore, linear free energy relationships analysis indicated one-electron reduction potential could be used to predict the transformation of chlorinated ethanes by S-ZVI, whereas for chlorinated ethenes, their adsorption properties on S-ZVI determined the dechlorination process. All these findings may offer guidance for the decision-making regarding the application of S-ZVI.

The Mechanism of Folding of Human Frataxin in Comparison to the Yeast Homologue - Broad Energy Barriers and the General Properties of the Transition State.

The funneled energy landscape theory suggests that the folding pathway of homologous proteins should converge at the late stages of folding. In this respect, proteins displaying a broad energy landscape for folding are particularly instructive, allowing inferring both the early, intermediate and late stages of folding. In this paper we explore the folding mechanisms of human frataxin, an essential mitochondrial protein linked to the neurodegenerative disorder Friedreich's ataxia. Building upon previous studies on the yeast homologue, the folding pathway of human frataxin is thoroughly examined, revealing a mechanism implying the presence of a broad energy barrier, reminiscent of the yeast counterpart. Through an extensive site-directed mutagenesis, we employed a Φ -value analysis to map native-like contacts in the folding transition state. The presence of a broad energy barrier facilitated the exploration of such contacts in both early and late folding events. We compared results from yeast and human frataxin providing insights into the impact of native topology on the folding mechanism and elucidating the properties of the underlying free energy landscape. The findings are discussed in the context of the funneled energy landscape theory of protein folding.

Nucleophilicity of 4-(Alkylthio)-3-imidazoline Derived Enamines.

Imidazolidine-4-thiones (ITOs) are cyclic, secondary amines that were considered as potential prebiotic organocatalysts for light-driven α-alkylations of aldehydes by bromoacetonitrile (BAN). Recent studies showed that the initially supplied ITOs represent the pre-catalyst because they undergo S-alkylation with BAN to give 4-(alkylthio)-3-imidazolines (TIMs). Given that the same reagent mix that undergoes light-driven α-alkylations is also effective in the dark, we synthesized ten ITO- or TIM-derived enamines of aldehydes and characterized their nucleophilic reactivities by kinetic studies in acetonitrile. The experimental second-order rate constants k2 for reactions of enamines with benzhydrylium ions (reference electrophiles) were evaluated by the Mayr-Patz equation, lg k2 (20 °C)=sN (N+E). The determined nucleophilicities N (and sN ) reveal the reactivity profiles of these enamines under prebiotically relevant conditions as well as their potential for use in organocatalytic synthesis.

Distinguishing between concerted, sequential and barrierless conformational changes: Folding versus allostery.

Characterization of transition and intermediate states of reactions provides insights into their mechanisms and is often achieved through analysis of linear free energy relationships. Such an approach has been used extensively in protein folding studies but less so for analyzing allosteric transitions. Here, we point out analogies in ways to characterize pathways and intermediates in folding and allosteric transitions. Achieving an understanding of the mechanisms by which proteins undergo allosteric switching is important in many cases for obtaining insights into how they function.

The effect of descriptor database selection on the physicochemical characterization and prediction of water-air, octanol-air and octanol-water partition constants using the solvation parameter model.

The distribution of neutral compounds in biphasic separation systems can be described by the solvation parameter model using six solute properties, or descriptors. These descriptors (McGowan's characteristic volume, excess molar refraction, dipolarity/polarizability, hydrogen-bond acidity and basicity, and the gas-liquid partition constant on n-hexadecane at 298.15 K) are curated in two publicly accessible databases for hundreds (WSU compound descriptor database) or thousands (Abraham compound descriptor database). These databases were developed independently using different approaches resulting in descriptor values that vary for many compounds. Previously, it was shown that the two descriptor databases are not interchangeable, and the WSU descriptor database consistently demonstrated improved model performance for chromatographic systems where the uncertainty in the dependent variable was minimized by suitable quality control and calibration procedures. In this report we wish to evaluate whether the same conclusions are true for models with a dependent variable containing significant measurement uncertainty. To evaluate this hypothesis, we assembled databases for water-air, octanol-air, and octanol-water partition constants reported by multiple laboratories using various measurement methods. It was found that database selection has little effect on model quality or model predictive capability but significantly affects the assignment of the contribution of individual intermolecular interactions to the dependent variable. The latter information is database specific, and a quantitative comparison of system constants should be restricted to models using the same compound descriptor database.

Reactivity of electrophilic cyclopropanes.

Cyclopropanes that carry an electron-accepting group react as electrophiles in polar, ring-opening reactions. Analogous reactions at cyclopropanes with additional C2 substituents allow one to access difunctionalized products. Consequently, functionalized cyclopropanes are frequently used building blocks in organic synthesis. The polarization of the C1-C2 bond in 1-acceptor-2-donor-substituted cyclopropanes not only favorably enhances reactivity toward nucleophiles but also directs the nucleophilic attack toward the already substituted C2 position. Monitoring the kinetics of non-catalytic ring-opening reactions with a series of thiophenolates and other strong nucleophiles, such as azide ions, in DMSO provided the inherent SN2 reactivity of electrophilic cyclopropanes. The experimentally determined second-order rate constants k 2 for cyclopropane ring-opening reactions were then compared to those of related Michael additions. Interestingly, cyclopropanes with aryl substituents at the C2 position reacted faster than their unsubstituted analogues. Variation of the electronic properties of the aryl groups at C2 gave rise to parabolic Hammett relationships.

The influence of descriptor database selection on the solvation parameter model for separation processes.

The distribution of neutral compounds in biphasic separation systems can be described by the solvation parameter model using six solute properties, or descriptors. These descriptors characterize the size (McGowan's characteristic volume), V, excess molar refraction, E, dipolarity/polarizability, S, hydrogen-bond acidity and basicity, A and B, and the gas-liquid partition constant on n-hexadecane at 298.15 K, L. McGowan's characteristic volume and the excess molar refraction for liquids are available by calculation (E requires and experimental refractive index). The other descriptors and excess molar refraction for solids are experimental quantities and subject to greater variation or are estimated using computational or empirical models. Solute descriptors for several thousand compounds are available in the Abraham descriptor database and for several hundred compounds in the WSU descriptor database. These publicly accessible databases were developed independently using different approaches and for many compounds provide different descriptor values. In this report we evaluate the effect of mixing descriptors from the two databases on modeling chromatographic retention factors and liquid-liquid partition constants. It is shown that the two descriptor databases are not interchangeable. The WSU descriptor database consistently demonstrates improved model quality as determined by statistical parameters. Model system constants exhibit a general dependence on database selection with an approximately linear trend as a function of the fraction of compounds assigned descriptors from either database. There is no general model performance advantage to using mixed descriptor datasets and no real cause for concern for relatively large datasets containing < 15 % of compounds with descriptors assigned from the other database. For small datasets, descriptor quality is an important variable for adequate model performance.

Structure-Reactivity Insights on the Alkaline Hydrolysis of Organophosphates: Non-Leaving and Leaving Group Effects in a Bilinear Brønsted-Like Relationship.

The high toxicity of organophosphates, along with its wide use as agrochemicals and chemical warfare, urges efficient degradation methods. Alkaline hydrolysis stands out, which is strongly structure-dependent. The alkaline hydrolysis of various organophosphates is described using a bilinear variation of the Brønsted equation, which evaluates concomitantly the effect of the leaving and non-leaving groups. Over 50 reactions were successfully correlated linearly and the contribution of the usually underestimated non-leaving group seems to be as important as the leaving group. The hetero atom effect (P=O and P=S) seems to vary the contribution of these groups. This concise understanding of the structure-reactivity relationship allows to predict optimal neutralization processes and is key for chemical security, saving time, resources and avoiding unnecessary manipulation of toxic chemicals.

Recent advances for estimating environmental properties for small molecules from chromatographic measurements and the solvation parameter model.

The transfer of neutral compounds between immiscible phases in chromatographic or environmental systems can be described by six solute properties (solute descriptors) using the solvation parameter model. The solute descriptors are size (McGowan's characteristic volume), V, excess molar refraction, E, dipolarity/polarizability, S, hydrogen-bond acidity and basicity, A and B, and the gas-liquid partition constant on n-hexadecane at 298.15 K, L. V and E for liquids are accessible by calculation but the other descriptors and E for solids are determined experimentally by chromatographic, liquid-liquid partition, and solubility measurements. These solute descriptors are available for several thousand compounds in the Abraham solute descriptor databases and for several hundred compounds in the WSU experimental solute descriptor database. In the first part of this review, we highlight features important in defining each descriptor, their experimental determination, compare descriptor quality for the two organized descriptor databases, and methods for estimating Abraham solute descriptors. In the second part we focus on recent applications of the solvation parameter model to characterize environmental systems and its use for the identification of surrogate chromatographic models for estimating environmental properties.

Some aspects of additives effects on retention in supercritical fluid chromatography studied by linear free energy relationships method.

This work is dedicated to the investigation of additives effects on retention mechanisms in supercritical fluid chromatography. Additives are compounds which are added to the mobile phase in small quantities and greatly affect retention factors, peak shape, separation selectivity and other chromatographic parameters. Linear free energy relationship (LFER) method with an expanded set of descriptors including the ones taking ionic interactions into account was used to probe the effect of four types of additive: trifluoroacetic acid, diethylamine, ammonium acetate and water - on retention on four polar stationary phase bearing different functional groups: bare silica, cyano, 2-ethylpyridine and zwitter-ionic sulfobetaine. Effects of all additives were shown to be complex, involving different intermolecular interactions and not uniform. The direction and magnitude of retention change depends not only on additive concentration, but on all other component of a chromatography system: type of a stationary phase, mobile phase composition and the nature of the solute. Various subtle effects were registered, the most peculiar among them being the fact that diethylamine and ammonium acetate provide identical changes of LFER constants. We hypothesize that this is caused by the convergence of diethylamine into a methylcarbamate via reaction with carbon dioxide and methanol, which then behaves as a salt additive.

Thermodynamics-Based Model Construction for the Accurate Prediction of Molecular Properties From Partition Coefficients.

Developing models for predicting molecular properties of organic compounds is imperative for drug development and environmental safety; however, development of such models that have high predictive power and are independent of the compounds used is challenging. To overcome the challenges, we used a thermodynamics-based theoretical derivation to construct models for accurately predicting molecular properties. The free energy change that determines a property equals the sum of the free energy changes (ΔGFs) caused by the factors affecting the property. By developing or selecting molecular descriptors that are directly proportional to ΔGFs, we built a general linear free energy relationship (LFER) for predicting the property with the molecular descriptors as predictive variables. The LFER can be used to construct models for predicting various specific properties from partition coefficients. Validations show that the models constructed according to the LFER have high predictive power and their performance is independent of the compounds used, including the models for the properties having little correlation with partition coefficients. The findings in this study are highly useful for applications in drug development and environmental safety.

Inherent Reactivity of Spiro-Activated Electrophilic Cyclopropanes.

The kinetics of the ring-opening reactions of thiophenolates with geminal bis(acceptor)-substituted cyclopropanes in DMSO at 20 °C was monitored by photometric methods. The determined second-order rate constants of the SN 2 reactions followed linear relationships with Mayr nucleophilicity parameters (N/sN ) and Brønsted basicities (pKaH ) of the thiophenolates as well as with Hammett substituent parameters (σ) for groups attached to the thiophenolates. Phenyl-substituted cyclopropanes reacted by up to a factor of 15 faster than their unsubstituted analogues, in accord with the known activating effect of adjacent π-systems in SN 2 reactions. Variation of the electronic properties of substituents at the phenyl groups of the cyclopropanes gave rise to parabolic Hammett relationships. Thus, the inherent SN 2 reactivity of electrophilic cyclopropanes is activated by electron-rich π-systems because of the more advanced C1-C2 bond polarization in the transition state. On the other hand, electron-poor π-systems also lower the energetic barriers for the attack of anionic nucleophiles owing to attractive electrostatic interactions.

Mechanistic Insight into the Reactivities of Aqueous-Phase Singlet Oxygen with Organic Compounds.

Singlet oxygen (1O2) is a selective reactive oxygen species that plays a key role for the fate of various organic compounds in the aquatic environment under sunlight irradiation, engineered water oxidation systems, atmospheric water droplets, and biomedical systems. While the initial rate-determining charge-transfer reaction mechanisms and kinetics of 1O2 have been studied extensively, no comprehensive studies have been performed to elucidate the reaction mechanisms with organic compounds that have various functional groups. In this study, we use density functional theory calculations to determine elementary reaction mechanisms with a wide variety of organic compounds. The theoretically calculated aqueous-phase free energies of activation of single electron transfer and 1O2 addition reactions are compared to the experimentally determined rate constants in the literature to determine linear free-energy relationships. The theoretically calculated free energies of activation for the groups of phenolates and phenols show excellent correlations with the Hammett constants that accept electron densities by through-resonance. The dominant elementary reaction mechanism is discussed for each group of compounds. As a practical implication, we demonstrate the fate of environmentally relevant organic compounds induced by photochemically produced intermediate species at different pH and evaluate the impact of predicting rate constants to the half-life.

Nucleophilicities and Nucleofugalities of Thio- and Selenoethers.

Rate constants for the reactions of dialkyl chalcogenides with laser flash photolytically generated benzhydrylium ions have been measured photometrically to integrate them into the comprehensive benzhydrylium-based nucleophilicity scale. Combining these rate constants with the previously reported equilibrium constants for the same reactions provided the corresponding Marcus intrinsic barriers and made it possible to quantify the leaving group abilities (nucleofugalities) of dialkyl sulfides and dimethyl selenide. Due to the low intrinsic barriers, dialkyl chalcogenides are fairly strong nucleophiles (comparable to pyridine and N-methylimidazole) as well as good nucleofuges; this makes them useful group-transfer reagents.

Experimental Quantum Chemistry: A Hammett-inspired Fingerprinting of Substituent Effects.

The quantum mechanically calculable Q descriptor is shown to be a potent quantifier of chemical reactivity in complex molecules - it shows a strong correlation to experimentally derived field effects in non-aromatic substrates and Hammett σm and σp parameters. Models for predicting substituent effects from Q are presented and applied, including on the elusive pentazolyl substituent. The presented approach enables fast computational estimation of substituent effects, and, in extension, medium-throughput screening of molecules and compound design. An experimental dataset is suggested as a candidate benchmark for aiding the general development and comparison of electronic structure analyses. It is here used to evaluate the experimental quantum chemistry (EQC) framework for chemical bonding analysis in larger molecules.

Lewis Acidic Boranes, Lewis Bases, and Equilibrium Constants: A Reliable Scaffold for a Quantitative Lewis Acidity/Basicity Scale.

A quantitative Lewis acidity/basicity scale toward boron-centered Lewis acids has been developed based on a set of 90 experimental equilibrium constants for the reactions of triarylboranes with various O-, N-, S-, and P-centered Lewis bases in dichloromethane at 20 °C. Analysis with the linear free energy relationship log KB =LAB +LBB allows equilibrium constants, KB , to be calculated for any type of borane/Lewis base combination through the sum of two descriptors, one for Lewis acidity (LAB ) and one for Lewis basicity (LBB ). The resulting Lewis acidity/basicity scale is independent of fixed reference acids/bases and valid for various types of trivalent boron-centered Lewis acids. It is demonstrated that the newly developed Lewis acidity/basicity scale is easily extendable through linear relationships with quantum-chemically calculated or common physical-organic descriptors and known thermodynamic data (ΔH BF 3 ). Furthermore, this experimental platform can be utilized for the rational development of borane-catalyzed reactions.

Linear free energy relationship models for the retention of partially ionized acid-base compounds in reversed-phase liquid chromatography.

The LFER model of Abraham is applied to the retention of the neutral and ionic forms of 94 solutes in a C18 column and 40% v/v acetonitrile/water mobile phase. The results show that polarizability and cavity formation interactions increase retention, whereas dipole and hydrogen bonding interactions favours partition to the mobile phase and thus, they decrease retention. The coefficients of the ionic descriptors measure the effect of the electrostatic interactions and their contribution to partition of the cation or anion between the two mobile and stationary chromatographic phases. A new LFER model for application to the retention of partially dissociated acids and bases is derived averaging the descriptors of the neutral and ionic forms according to their degrees of ionization in the mobile phase. This new LFER model is satisfactorily compared to other literature modified Abraham models for a set of 498 retention data of partially dissociated acids and bases. All tested models require the calculation of the ionization degrees of the compounds at the measuring pH. Calculation of the ionization degrees in the chromatographic mobile phase (i.e. from pH and pKa in the eluent) give good correlations for all tested models. However, estimation of these ionization degrees from pH - pKa data in pure water gives biased estimations of the retention of the partially ionized solutes.

Yolk-Water Partitioning of Neutral Organic Compounds in the Model Organism Danio rerio.

Yolk is the most important temporary biological compartment of the early life stages of fish embryos. The sorption strength of a chemical to yolk components may significantly influence the distribution of that chemical in the fish embryo. We determined yolk-water partition coefficients (Kyolk/water , in liters of water per kilogram of yolk, normalized to dry wt) for 70 neutral organic chemicals. The log Kyolk/water values range from 0.76 to 6.56. On the basis of these values, we developed polyparameter linear free energy relationship models to predict yolk-water partitioning for a broad range of neutral organic chemicals with a root mean squared error of 0.37 and r2 of 0.919. These models can be applied for the prediction of internal concentrations at equilibrium (neglecting biotransformation and active transport) in the zebrafish embryo test system. Environ Toxicol Chem 2020;39:1506-1516. © 2020 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Evaluation of temperature and pressure effects on retention in supercritical fluid chromatography on polar stationary phases.

Four polar stationary phases (ethylene-bridged hybrid silica, cyanopropyl, 2-ethylpyridine, and zwitterionic sulfobetaine) have been characterized in supercritical fluid chromatography (SFC) by linear free energy relationships (LFER) method with an extended set of Abraham's descriptors. Temperature (25-55 °C) and pressure (110-180 bar) effects on analyte retention, separation selectivity and LFER-coefficients of chromatographic systems have been studied using the 89 test compounds of various chemical classes and carbon dioxide - methanol (9:1 v/v) binary solvent as a mobile phase. It was found that for the selected stationary phases temperature and pressure had only moderate effects on selectivity. The retention times of all analytes decrease, as can be expected, if the pressure rises at the isothermal conditions due to the increase of the fluid density and its eluting power. The effect of temperature on retention is complicated and depends both on the chemical class of analyzed compounds and the stationary phase type. Temperature and pressure variations lead to small changes in the LFER-coefficients, and general trends observed do not depend much on the stationary phase type. It may be difficult to interpret the LFER-analysis results because of the evident, more significant chromatographic phenomena.

Descriptors for terpene esters from chromatographic and partition measurements: Estimation of human odor detection thresholds.

We have used gas chromatographic retention data together with other data to obtain Abraham descriptors for 30 terpene esters. These include the air-water partition coefficient, as log Kw, for which no experimental values are available for any terpene ester. The other descriptors are the ester dipolarity, S, the hydrogen bond basicity, B, (the ester hydrogen bond acidity is zero for the esters studied), and L the logarithm of the air-hexadecane partition coefficient. Both S and B are larger than those for simple aliphatic esters, as expected from the terpene ester structures that include ring systems and ethylenic double bonds. These descriptors can then be used to obtain a large number of physicochemical and environmental properties of terpene esters. We have analyzed experimental results on human odor detection thresholds and have constructed another equation for the calculation of these thresholds, to go with a previous equation that we have reported. Then the descriptors for terpene esters can be used to estimate the important odor detection thresholds.