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Themed collection QSARs and computational chemistry methods in environmental chemical sciences

32 items
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Contents list

Editorial

QSARs and computational chemistry methods in environmental chemical sciences

Guest editors Kathrin Fenner and Paul Tratnyek introduce the themed issue on “QSARs and computational chemistry methods in environmental chemical sciences” of Environmental Science: Processes & Impacts.

Graphical abstract: QSARs and computational chemistry methods in environmental chemical sciences
Open Access Perspective

In silico environmental chemical science: properties and processes from statistical and computational modelling

Theoretical and statistical approaches to calculation of properties that determine the environmental fate and effects of substances are summarized, with emphasis on their integration into “in silico environmental chemical science”.

Graphical abstract: In silico environmental chemical science: properties and processes from statistical and computational modelling
Perspective

History of EPI Suite™ and future perspectives on chemical property estimation in US Toxic Substances Control Act new chemical risk assessments

A discussion of the past developments, current practices, and future opportunities in QSAR modeling for new chemical risk assessments.

Graphical abstract: History of EPI Suite™ and future perspectives on chemical property estimation in US Toxic Substances Control Act new chemical risk assessments
Perspective

(Q)SARs to predict environmental toxicities: current status and future needs

An assessment of (Q)SARs to predict acute and chronic ecotoxicity.

Graphical abstract: (Q)SARs to predict environmental toxicities: current status and future needs
Critical Review

A review of quantitative structure–property relationships for the fate of ionizable organic chemicals in water matrices and identification of knowledge gaps

QSPR prediction models for chemical fate and exposure are critically reviewed so that knowledge gaps may be filled in subsequent study.

Graphical abstract: A review of quantitative structure–property relationships for the fate of ionizable organic chemicals in water matrices and identification of knowledge gaps
Critical Review

Virulence factor activity relationships (VFARs): a bioinformatics perspective

Virulence factor activity relationships (VFARs) – a concept loosely based on quantitative structure–activity relationships (QSARs) for chemicals was proposed as a predictive tool for ranking risks due to microorganisms relevant to water safety.

Graphical abstract: Virulence factor activity relationships (VFARs): a bioinformatics perspective
Paper

Ranking REACH registered neutral, ionizable and ionic organic chemicals based on their aquatic persistency and mobility

REACH registered neutral, ionizable and ionic organic chemicals were evaluated for their potential to present a hazard to drinking water sources.

Graphical abstract: Ranking REACH registered neutral, ionizable and ionic organic chemicals based on their aquatic persistency and mobility
Paper

Baseline toxicity and ion-trapping models to describe the pH-dependence of bacterial toxicity of pharmaceuticals

The pH-dependence of cytotoxicity of diverse acidic, basic and multiprotic pharmaceuticals could be explained by baseline toxicity after invoking mixture effects of all species and delayed uptake of charged species.

Graphical abstract: Baseline toxicity and ion-trapping models to describe the pH-dependence of bacterial toxicity of pharmaceuticals
Paper

Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data

Eawag-Soil offers an extensive collection of data on pesticide soil degradation pathways and half-lives for diverse uses, including QSBR development.

Graphical abstract: Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data
Paper

Development of a QSAR model for predicting aqueous reaction rate constants of organic chemicals with hydroxyl radicals

This study provides a QSAR model for predicting the aqueous reaction rate constants of organic chemicals with hydroxyl radicals.

Graphical abstract: Development of a QSAR model for predicting aqueous reaction rate constants of organic chemicals with hydroxyl radicals
Paper

Prediction of acute toxicity of emerging contaminants on the water flea Daphnia magna by Ant Colony Optimization–Support Vector Machine QSTR models

Prediction of acute toxicity towards Daphnia magna using Ant Colony Optimization–Support Vector Machine QSTR models.

Graphical abstract: Prediction of acute toxicity of emerging contaminants on the water flea Daphnia magna by Ant Colony Optimization–Support Vector Machine QSTR models
Paper

General baseline toxicity QSAR for nonpolar, polar and ionisable chemicals and their mixtures in the bioluminescence inhibition assay with Aliivibrio fischeri

A general QSAR model for the Microtox assay with the ionisation-corrected liposome–water distribution ratio is applicable to diverse chemicals including acids and bases.

Graphical abstract: General baseline toxicity QSAR for nonpolar, polar and ionisable chemicals and their mixtures in the bioluminescence inhibition assay with Aliivibrio fischeri
Paper

Sulfate radical oxidation of aromatic contaminants: a detailed assessment of density functional theory and high-level quantum chemical methods

DFT and high-level quantum methods are utilized to explore sulfate radical-driven oxidation.

Graphical abstract: Sulfate radical oxidation of aromatic contaminants: a detailed assessment of density functional theory and high-level quantum chemical methods
Open Access Paper

Oxidation potentials of phenols and anilines: correlation analysis of electrochemical and theoretical values

New experimental and theoretical oxidation potentials for substituted phenols and anilines give improved correlations to kinetic data with manganese oxides.

Graphical abstract: Oxidation potentials of phenols and anilines: correlation analysis of electrochemical and theoretical values
Paper

Classification of baseline toxicants for QSAR predictions to replace fish acute toxicity studies

Classification of baseline and excess toxicants to replace 50% of fish acute toxicity testing with reliable QSAR predictions.

Graphical abstract: Classification of baseline toxicants for QSAR predictions to replace fish acute toxicity studies
Paper

Diverging effects of isotopic fractionation upon molecular diffusion of noble gases in water: mechanistic insights through ab initio molecular dynamics simulations

Simulation snapshot of a dissolved krypton atom within a typical water cavity responsible for the size dependent diffusion behavior of noble gases.

Graphical abstract: Diverging effects of isotopic fractionation upon molecular diffusion of noble gases in water: mechanistic insights through ab initio molecular dynamics simulations
Paper

The degradation mechanism of sulfamethoxazole under ozonation: a DFT study

Sulfamethoxazole (SMX), a kind of antibiotic, remains in the environment and threatens public health.

Graphical abstract: The degradation mechanism of sulfamethoxazole under ozonation: a DFT study
Paper

Predicting the phospholipophilicity of monoprotic positively charged amines

The sorption affinity of eighty-six charged amine structures to phospholipid monolayers (log KIAM) was determined using immobilized artificial membrane high-performance liquid chromatography (IAM-HPLC).

Graphical abstract: Predicting the phospholipophilicity of monoprotic positively charged amines
Paper

Linear free energy relationships for the adsorption of volatile organic compounds onto multiwalled carbon nanotubes at different relative humidities: comparison with organoclays and activated carbon

Adsorption behavior of volatile organic compounds (VOCs) on carbon nanotubes is critical for developing effective assessment and treatments for nanomaterial-bound contaminants.

Graphical abstract: Linear free energy relationships for the adsorption of volatile organic compounds onto multiwalled carbon nanotubes at different relative humidities: comparison with organoclays and activated carbon
Paper

Quantifying the equilibrium partitioning of substituted polycyclic aromatic hydrocarbons in aerosols and clouds using COSMOtherm

Functional groups attached to polycyclic aromatic hydrocarbons (PAHs) can significantly modify the environmental fate of the parent compound.

Graphical abstract: Quantifying the equilibrium partitioning of substituted polycyclic aromatic hydrocarbons in aerosols and clouds using COSMOtherm
Paper

A computer-based prediction platform for the reaction of ozone with organic compounds in aqueous solution: kinetics and mechanisms

A computer-based prediction platform for predicting kinetics and pathways for the reaction of ozone with micropollutants was developed.

Graphical abstract: A computer-based prediction platform for the reaction of ozone with organic compounds in aqueous solution: kinetics and mechanisms
Paper

Development of polyparameter linear free energy relationship models for octanol–air partition coefficients of diverse chemicals

This study develops pp-LFER models to predict octanol–air partition coefficients at different temperatures for diverse chemicals.

Graphical abstract: Development of polyparameter linear free energy relationship models for octanol–air partition coefficients of diverse chemicals
Paper

In silico kinetics of alkaline hydrolysis of 1,3,5-trinitro-1,3,5-triazinane (RDX): M06-2X investigation

The kinetics of alkaline hydrolysis of 1,3,5-trinitro-1,3,5-triazinane were predicted under different conditions.

Graphical abstract: In silico kinetics of alkaline hydrolysis of 1,3,5-trinitro-1,3,5-triazinane (RDX): M06-2X investigation
Paper

3D-QSAR predictions for bovine serum albumin–water partition coefficients of organic anions using quantum mechanically based descriptors

The 3D-QSAR model predicts the bovine serum albumin–water partition coefficients for neutral and anionic chemicals influenced by steric effects.

Graphical abstract: 3D-QSAR predictions for bovine serum albumin–water partition coefficients of organic anions using quantum mechanically based descriptors
Paper

QSARs for phenols and phenolates: oxidation potential as a predictor of reaction rate constants with photochemically produced oxidants

One electron oxidation potential predicts the reactivity of phenol and phenolate compounds in a single correlation.

Graphical abstract: QSARs for phenols and phenolates: oxidation potential as a predictor of reaction rate constants with photochemically produced oxidants
Open Access Paper

Atmospheric oxidation of halogenated aromatics: comparative analysis of reaction mechanisms and reaction kinetics

This study provides valuable insight into the mechanism of tropospheric degradation and fate of halogenated aromatic systems.

Graphical abstract: Atmospheric oxidation of halogenated aromatics: comparative analysis of reaction mechanisms and reaction kinetics
Paper

Ferrate(VI) initiated oxidative degradation mechanisms clarified by DFT calculations: a case for sulfamethoxazole

Ferrate(VI) is an efficient and environmentally friendly oxidant for the degradation of organic micropollutants.

Graphical abstract: Ferrate(vi) initiated oxidative degradation mechanisms clarified by DFT calculations: a case for sulfamethoxazole
Paper

Oligomeric models for estimation of polydimethylsiloxane–water partition ratios with COSMO-RS theory: impact of the combinatorial term on absolute error

PDMS passive sampling media effectively modelled with small oligomers using COSMO-RS.

Graphical abstract: Oligomeric models for estimation of polydimethylsiloxane–water partition ratios with COSMO-RS theory: impact of the combinatorial term on absolute error
32 items

About this collection

Quantitative structure-activity relationships (QSARs) have long been used in environmental sciences. More recently, molecular modeling and chemoinformatic methods have become widespread. These methods have the potential to expand and accelerate advances in environmental chemistry because they complement observational and experimental data with “in silico” results and analysis.  

To encourage these advances, the guest editors of this themed issue, Paul Tratnyek (OHSU) and Kathrin Fenner (Eawag), recruited papers from among the best practitioners of in silico environmental science. Authors were selected to represent the diversity of this community, including disciplinary perspectives and intended applications.

The specific topics covered in this issue range from detailed studies of specific processes using advanced molecular methods—such as the diffusion of noble gases in water, or the mechanism of antibiotic oxidation by ozone—to more general applications of statistical and “big data” approaches—such as data mining for new transformation pathways and multi-dimensional metrics for ecological risk assessment.

The resulting collection of perspectives, critical reviews and research papers provides a comprehensive and balanced perspective on the whole range of “in silico” methods in environmental science at this time. Hopefully, it also will encourage and expand the opportunities that computational approaches offer for further advances in environmental chemistry, ecotoxicology, risk assessment, and related aspects of environmental science.

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