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Research paper thumbnail of FINAL GOAL of CADASTER to exemplify the integration of information, models and strategies for carrying out hazard and risk assessments for four classes of emerging pollutants: • Perfluorinated Compounds • Triazoles / benzotriazoles Prioritization of emerging pollutants on the basis of chemical st...

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Research paper thumbnail of ChemInform Abstract: SYNTHESIS OF ESTRAGOLE, A GENERAL ROUTE TO ALLYLPHENOLS FROM PROPENYLPHENOLS

Chemischer Informationsdienst, 1974

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Research paper thumbnail of QSARINS ‐Chem standalone version: A new platform‐independent software to profile chemicals for physico‐chemical properties, fate, and toxicity

Journal of Computational Chemistry, 2021

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Research paper thumbnail of QSARINS model 2 for log Koc

Research paper thumbnail of QSARINS model for hydroxyl-mediated tropospheric degradation using online descriptors

Research paper thumbnail of Physico-Chemical Property prediction of emerging pollutants:PFCs and (B)TAZs for environmental distribution

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Research paper thumbnail of QSARINS model 1 for log Koc

2.1.Date of QMRF: 30/01/2015 2.2.QMRF author(s) and contact details: [1]Paola Gramatica Insubria ... more 2.1.Date of QMRF: 30/01/2015 2.2.QMRF author(s) and contact details: [1]Paola Gramatica Insubria University, Department of Theoretical and Applied Sciences (DiSTA), via J.H. Dunant 3, 21100 Varese (Italy) +390332421573 paola.gramatica@uninsubria.it http://www.qsar.it/ [2]Stefano Cassani Insubria University, Department of Theoretical and Applied Sciences (DiSTA), via J.H. Dunant 3, 21100 Varese (Italy) +390332421439 stefano.cassani@uninsubria.it http://www.qsar.it/ 2.3.Date of QMRF update(s): 2.4.QMRF update(s): 2.5.Model developer(s) and contact details: [1]Stefano Cassani Insubria University, Department of Theoretical and Applied Sciences (DiSTA), via J.H. Dunant 3, 21100 Varese (Italy) +390332421439 stefano.cassani@uninsubria.it http://www.qsar.it/ [2]Paola Gramatica Insubria University, Department of Theoretical and Applied Sciences (DiSTA), via J.H. Dunant 3, 21100 Varese (Italy) +390332421573 paola.gramatica@uninsubria.it http://www.qsar.it/ 2.6.Date of model development and/or...

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Research paper thumbnail of Modelling Of POP Environmental Persistence And Long Range Transport By QSAR And Chemometric Approaches

The Long Range Transport (LRT) potential of chemicals is due to the combination of their persiste... more The Long Range Transport (LRT) potential of chemicals is due to the combination of their persistence in the environment and their inherent tendency towards mobility, and is an undesirable property of POPs (Persistent Organic Pollutants). Finding the best combination of chemical properties to minimize LRT is a multicriteria problem that can be approached by MultiCriteria Decision-Making (MCDM) techniques. Utility functions have been applied to two proposed indexes, the “global persistence index” and the “mobility index”, allowing a ranking of the studied chemicals according to their LRT potential. The “global persistence index” was obtained by linear combination, by Principal Component Analysis of the half-life data in various environmental compartments. Half-life data are commonly used as persistence indicators, but the availability of such data is limited to only a few organic compounds, thus QSAR (Quantitative Structure-Activity Relationships) models were used to predict such data...

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Research paper thumbnail of Current Status of Methods for Defining the Applicability Domain of (Quantitative) Structure-Activity Relationships

Alternatives to Laboratory Animals, 2005

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Research paper thumbnail of Prioritization of Chemicals Based on Chemoinformatic Analysis

Handbook of Computational Chemistry, 2017

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Research paper thumbnail of Aquatic ecotoxicity of personal care products: QSAR models and ranking for prioritization and safer alternatives’ design

Green Chemistry, 2016

New externally validated QSAR models for aquatic toxicity of PCPs are proposed and applicable in ... more New externally validated QSAR models for aquatic toxicity of PCPs are proposed and applicable in QSARINS for thea priorichemical design of environmentally safer PCPs.

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Research paper thumbnail of Referees for Volume 14

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Research paper thumbnail of Modeling ready biodegradability of fragrance materials

Environmental Toxicology and Chemistry, 2015

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Research paper thumbnail of Chemometrics in QSAR

Comprehensive Chemometrics, 2009

Todeschini, R., Consonni, V., & Gramatica, P. (2009). Chemometrics in QSAR. In S. Brown, R. T... more Todeschini, R., Consonni, V., & Gramatica, P. (2009). Chemometrics in QSAR. In S. Brown, R. Tauler, & R. Walczak (a cura di), Comprehensive Chemometrics (pp. 129-172). Oxford : Elsevier. ... There are no files associated with this item. ... Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

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Research paper thumbnail of On the Use of Local and Global QSPRs for the Prediction of Physico-chemical Properties of Polybrominated Diphenyl Ethers

Molecular Informatics, 2011

Polybrominated diphenyl ethers (PBDEs) are persistent chemicals that have been among the most mar... more Polybrominated diphenyl ethers (PBDEs) are persistent chemicals that have been among the most marketed flame retardants used all over the world in the last decades. PBDEs have been detected in all environmental compartments, as well as in humans and wildlife, where they are able to accumulate and exert their toxic effects. At present only a limited amount of experimental data is available to characterize the physico-chemical and toxicological behavior of PBDEs and similar brominated flame retardants. QSA(P)R approaches are very useful tools to predict missing data starting from the chemical structure of compounds. In this study several local QSPR models, developed specifically for the prediction of logKoa, logKow and melting point of PBDEs, were compared with predictions by global QSPR models, such as KoaWIN, KowWIN and MPBPWIN from the EPI Suite package, and AlogP and MlogP from DRAGON software, which were trained on heterogeneous and large datasets. The analysis addressed in the paper supported the identification of points of strength and weaknesses of both local models, and global models. The results are relevant to support decisions made by general QSAR users and regulators, when they have to select and apply one of the analyzed models to predict properties for PBDEs.

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Research paper thumbnail of QSAR Modeling is not “Push a Button and Find a Correlation”: A Case Study of Toxicity of (Benzo-)triazoles on Algae

Molecular Informatics, 2012

A case study of toxicity of (benzo)triazoles ((B)TAZs) to the algae Pseudokirchneriella subcapita... more A case study of toxicity of (benzo)triazoles ((B)TAZs) to the algae Pseudokirchneriella subcapitata is used to discuss some problems and solutions in QSAR modeling, particularly in the environmental context. The relevance of data curation (not only of experimental data, but also of chemical structures and input formats for the calculation of molecular descriptors), the crucial points of QSAR model validation and the potential application for new chemicals (internal robustness, exclusion of chance correlation, external predictivity, applicability domain) are described, while developing MLR-OLS models based on molecular descriptors, calculated by various QSAR software tools (commercial DRAGON, free PaDEL-Descriptor and QSPR-THESAURUS). Additionally, the utility of consensus models is highlighted. This work summarizes a methodology for a rigorous statistical approach to obtain reliable QSAR predictions, also for a large number of (B)TAZs in the ECHA preregistration list of REACH (even if starting from limited experimental data availability), and has evidenced some ambiguities and discrepancies related to SMILES notations from different databases; furthermore it highlighted some general problems related to QSAR model generation and was useful in the implementation of the PaDEL-Descriptor software.

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Research paper thumbnail of CADASTER QSPR Models for Predictions of Melting and Boiling Points of Perfluorinated Chemicals

Molecular Informatics, 2011

Quantitative structure property relationship (QSPR) studies on per- and polyfluorinated chemicals... more Quantitative structure property relationship (QSPR) studies on per- and polyfluorinated chemicals (PFCs) on melting point (MP) and boiling point (BP) are presented. The training and prediction chemicals used for developing and validating the models were selected from Syracuse PhysProp database and literatures. The available experimental data sets were split in two different ways: a) random selection on response value, and b) structural similarity verified by self-organizing-map (SOM), in order to propose reliable predictive models, developed only on the training sets and externally verified on the prediction sets. Individual linear and non-linear approaches based models developed by different CADASTER partners on 0D-2D Dragon descriptors, E-state descriptors and fragment based descriptors as well as consensus model and their predictions are presented. In addition, the predictive performance of the developed models was verified on a blind external validation set (EV-set) prepared using PERFORCE database on 15 MP and 25 BP data respectively. This database contains only long chain perfluoro-alkylated chemicals, particularly monitored by regulatory agencies like US-EPA and EU-REACH. QSPR models with internal and external validation on two different external prediction/validation sets and study of applicability-domain highlighting the robustness and high accuracy of the models are discussed. Finally, MPs for additional 303 PFCs and BPs for 271 PFCs were predicted for which experimental measurements are unknown.

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Research paper thumbnail of Development, Validation and Inspection of the Applicability Domain of QSPR Models for Physicochemical Properties of Polybrominated Diphenyl Ethers

QSAR & Combinatorial Science, 2009

ABSTRACT Polybrominated diphenyl ethers (PBDEs) are a group of brominated flame retardants (BFRs)... more ABSTRACT Polybrominated diphenyl ethers (PBDEs) are a group of brominated flame retardants (BFRs), which were widely used in a variety of consumer products. Because of evidences of toxicity effects on different organisms and humans, as well as the ubiquitary profile of these compounds, PBDEs are considered an emerging group of toxic and persistent organic pollutants. However, due to the small amount of experimental data available, still little is known about the properties of most of these chemicals. In this study several physicochemical properties, experimentally available for few PBDE congeners and hexabromobenzene (HBB), were investigated through a modelling approach based on quantitative structure–property relationships (QSPR). The OLS regression models, based on theoretical molecular descriptors, are calculated for Henry's law constant, melting point, subcooled liquid vapor pressure, water solubility, octanol-air partition coefficient, and octanol-water partition coefficient. These models can be useful to predict the big amount of missing data and to plan safer alternatives to dangerous BFRs. The innovative aspect of the proposed models, compared to those already published in the literature, is their development according to the OECD principles for regulatory acceptability of QSARs. This includes the validation for predictivity (both by internal and external statistical validation) and the inspection of the applicability domain.

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Research paper thumbnail of QSAR Modeling: Where Have You Been? Where Are You Going To?

Journal of Medicinal Chemistry, 2014

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Research paper thumbnail of Daphnia and fish toxicity of (benzo)triazoles: Validated QSAR models, and interspecies quantitative activity–activity modelling

Journal of Hazardous Materials, 2013

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Research paper thumbnail of FINAL GOAL of CADASTER to exemplify the integration of information, models and strategies for carrying out hazard and risk assessments for four classes of emerging pollutants: • Perfluorinated Compounds • Triazoles / benzotriazoles Prioritization of emerging pollutants on the basis of chemical st...

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Research paper thumbnail of ChemInform Abstract: SYNTHESIS OF ESTRAGOLE, A GENERAL ROUTE TO ALLYLPHENOLS FROM PROPENYLPHENOLS

Chemischer Informationsdienst, 1974

Bookmarks Related papers MentionsView impact

Research paper thumbnail of QSARINS ‐Chem standalone version: A new platform‐independent software to profile chemicals for physico‐chemical properties, fate, and toxicity

Journal of Computational Chemistry, 2021

Bookmarks Related papers MentionsView impact

Research paper thumbnail of QSARINS model 2 for log Koc

Research paper thumbnail of QSARINS model for hydroxyl-mediated tropospheric degradation using online descriptors

Research paper thumbnail of Physico-Chemical Property prediction of emerging pollutants:PFCs and (B)TAZs for environmental distribution

Bookmarks Related papers MentionsView impact

Research paper thumbnail of QSARINS model 1 for log Koc

2.1.Date of QMRF: 30/01/2015 2.2.QMRF author(s) and contact details: [1]Paola Gramatica Insubria ... more 2.1.Date of QMRF: 30/01/2015 2.2.QMRF author(s) and contact details: [1]Paola Gramatica Insubria University, Department of Theoretical and Applied Sciences (DiSTA), via J.H. Dunant 3, 21100 Varese (Italy) +390332421573 paola.gramatica@uninsubria.it http://www.qsar.it/ [2]Stefano Cassani Insubria University, Department of Theoretical and Applied Sciences (DiSTA), via J.H. Dunant 3, 21100 Varese (Italy) +390332421439 stefano.cassani@uninsubria.it http://www.qsar.it/ 2.3.Date of QMRF update(s): 2.4.QMRF update(s): 2.5.Model developer(s) and contact details: [1]Stefano Cassani Insubria University, Department of Theoretical and Applied Sciences (DiSTA), via J.H. Dunant 3, 21100 Varese (Italy) +390332421439 stefano.cassani@uninsubria.it http://www.qsar.it/ [2]Paola Gramatica Insubria University, Department of Theoretical and Applied Sciences (DiSTA), via J.H. Dunant 3, 21100 Varese (Italy) +390332421573 paola.gramatica@uninsubria.it http://www.qsar.it/ 2.6.Date of model development and/or...

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Research paper thumbnail of Modelling Of POP Environmental Persistence And Long Range Transport By QSAR And Chemometric Approaches

The Long Range Transport (LRT) potential of chemicals is due to the combination of their persiste... more The Long Range Transport (LRT) potential of chemicals is due to the combination of their persistence in the environment and their inherent tendency towards mobility, and is an undesirable property of POPs (Persistent Organic Pollutants). Finding the best combination of chemical properties to minimize LRT is a multicriteria problem that can be approached by MultiCriteria Decision-Making (MCDM) techniques. Utility functions have been applied to two proposed indexes, the “global persistence index” and the “mobility index”, allowing a ranking of the studied chemicals according to their LRT potential. The “global persistence index” was obtained by linear combination, by Principal Component Analysis of the half-life data in various environmental compartments. Half-life data are commonly used as persistence indicators, but the availability of such data is limited to only a few organic compounds, thus QSAR (Quantitative Structure-Activity Relationships) models were used to predict such data...

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Research paper thumbnail of Current Status of Methods for Defining the Applicability Domain of (Quantitative) Structure-Activity Relationships

Alternatives to Laboratory Animals, 2005

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Research paper thumbnail of Prioritization of Chemicals Based on Chemoinformatic Analysis

Handbook of Computational Chemistry, 2017

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Research paper thumbnail of Aquatic ecotoxicity of personal care products: QSAR models and ranking for prioritization and safer alternatives’ design

Green Chemistry, 2016

New externally validated QSAR models for aquatic toxicity of PCPs are proposed and applicable in ... more New externally validated QSAR models for aquatic toxicity of PCPs are proposed and applicable in QSARINS for thea priorichemical design of environmentally safer PCPs.

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Research paper thumbnail of Referees for Volume 14

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Research paper thumbnail of Modeling ready biodegradability of fragrance materials

Environmental Toxicology and Chemistry, 2015

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Research paper thumbnail of Chemometrics in QSAR

Comprehensive Chemometrics, 2009

Todeschini, R., Consonni, V., & Gramatica, P. (2009). Chemometrics in QSAR. In S. Brown, R. T... more Todeschini, R., Consonni, V., & Gramatica, P. (2009). Chemometrics in QSAR. In S. Brown, R. Tauler, & R. Walczak (a cura di), Comprehensive Chemometrics (pp. 129-172). Oxford : Elsevier. ... There are no files associated with this item. ... Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

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Research paper thumbnail of On the Use of Local and Global QSPRs for the Prediction of Physico-chemical Properties of Polybrominated Diphenyl Ethers

Molecular Informatics, 2011

Polybrominated diphenyl ethers (PBDEs) are persistent chemicals that have been among the most mar... more Polybrominated diphenyl ethers (PBDEs) are persistent chemicals that have been among the most marketed flame retardants used all over the world in the last decades. PBDEs have been detected in all environmental compartments, as well as in humans and wildlife, where they are able to accumulate and exert their toxic effects. At present only a limited amount of experimental data is available to characterize the physico-chemical and toxicological behavior of PBDEs and similar brominated flame retardants. QSA(P)R approaches are very useful tools to predict missing data starting from the chemical structure of compounds. In this study several local QSPR models, developed specifically for the prediction of logKoa, logKow and melting point of PBDEs, were compared with predictions by global QSPR models, such as KoaWIN, KowWIN and MPBPWIN from the EPI Suite package, and AlogP and MlogP from DRAGON software, which were trained on heterogeneous and large datasets. The analysis addressed in the paper supported the identification of points of strength and weaknesses of both local models, and global models. The results are relevant to support decisions made by general QSAR users and regulators, when they have to select and apply one of the analyzed models to predict properties for PBDEs.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of QSAR Modeling is not “Push a Button and Find a Correlation”: A Case Study of Toxicity of (Benzo-)triazoles on Algae

Molecular Informatics, 2012

A case study of toxicity of (benzo)triazoles ((B)TAZs) to the algae Pseudokirchneriella subcapita... more A case study of toxicity of (benzo)triazoles ((B)TAZs) to the algae Pseudokirchneriella subcapitata is used to discuss some problems and solutions in QSAR modeling, particularly in the environmental context. The relevance of data curation (not only of experimental data, but also of chemical structures and input formats for the calculation of molecular descriptors), the crucial points of QSAR model validation and the potential application for new chemicals (internal robustness, exclusion of chance correlation, external predictivity, applicability domain) are described, while developing MLR-OLS models based on molecular descriptors, calculated by various QSAR software tools (commercial DRAGON, free PaDEL-Descriptor and QSPR-THESAURUS). Additionally, the utility of consensus models is highlighted. This work summarizes a methodology for a rigorous statistical approach to obtain reliable QSAR predictions, also for a large number of (B)TAZs in the ECHA preregistration list of REACH (even if starting from limited experimental data availability), and has evidenced some ambiguities and discrepancies related to SMILES notations from different databases; furthermore it highlighted some general problems related to QSAR model generation and was useful in the implementation of the PaDEL-Descriptor software.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of CADASTER QSPR Models for Predictions of Melting and Boiling Points of Perfluorinated Chemicals

Molecular Informatics, 2011

Quantitative structure property relationship (QSPR) studies on per- and polyfluorinated chemicals... more Quantitative structure property relationship (QSPR) studies on per- and polyfluorinated chemicals (PFCs) on melting point (MP) and boiling point (BP) are presented. The training and prediction chemicals used for developing and validating the models were selected from Syracuse PhysProp database and literatures. The available experimental data sets were split in two different ways: a) random selection on response value, and b) structural similarity verified by self-organizing-map (SOM), in order to propose reliable predictive models, developed only on the training sets and externally verified on the prediction sets. Individual linear and non-linear approaches based models developed by different CADASTER partners on 0D-2D Dragon descriptors, E-state descriptors and fragment based descriptors as well as consensus model and their predictions are presented. In addition, the predictive performance of the developed models was verified on a blind external validation set (EV-set) prepared using PERFORCE database on 15 MP and 25 BP data respectively. This database contains only long chain perfluoro-alkylated chemicals, particularly monitored by regulatory agencies like US-EPA and EU-REACH. QSPR models with internal and external validation on two different external prediction/validation sets and study of applicability-domain highlighting the robustness and high accuracy of the models are discussed. Finally, MPs for additional 303 PFCs and BPs for 271 PFCs were predicted for which experimental measurements are unknown.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Development, Validation and Inspection of the Applicability Domain of QSPR Models for Physicochemical Properties of Polybrominated Diphenyl Ethers

QSAR & Combinatorial Science, 2009

ABSTRACT Polybrominated diphenyl ethers (PBDEs) are a group of brominated flame retardants (BFRs)... more ABSTRACT Polybrominated diphenyl ethers (PBDEs) are a group of brominated flame retardants (BFRs), which were widely used in a variety of consumer products. Because of evidences of toxicity effects on different organisms and humans, as well as the ubiquitary profile of these compounds, PBDEs are considered an emerging group of toxic and persistent organic pollutants. However, due to the small amount of experimental data available, still little is known about the properties of most of these chemicals. In this study several physicochemical properties, experimentally available for few PBDE congeners and hexabromobenzene (HBB), were investigated through a modelling approach based on quantitative structure–property relationships (QSPR). The OLS regression models, based on theoretical molecular descriptors, are calculated for Henry's law constant, melting point, subcooled liquid vapor pressure, water solubility, octanol-air partition coefficient, and octanol-water partition coefficient. These models can be useful to predict the big amount of missing data and to plan safer alternatives to dangerous BFRs. The innovative aspect of the proposed models, compared to those already published in the literature, is their development according to the OECD principles for regulatory acceptability of QSARs. This includes the validation for predictivity (both by internal and external statistical validation) and the inspection of the applicability domain.

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Research paper thumbnail of QSAR Modeling: Where Have You Been? Where Are You Going To?

Journal of Medicinal Chemistry, 2014

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Research paper thumbnail of Daphnia and fish toxicity of (benzo)triazoles: Validated QSAR models, and interspecies quantitative activity–activity modelling

Journal of Hazardous Materials, 2013

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Research paper thumbnail of Classification of environmental pollutants for global mobility potential

The environmental behaviour of global organic contaminants is known to be controlled by the physi... more The environmental behaviour of global organic contaminants is known to be controlled by the physico-chemical properties of the compounds themselves. The principal component analysis of some physico-chemical properties, particularly relevant in determining mobility potential (vapour pressure, Henry's law constant, water solubility, K(OW), K(OA) and melting point) allows a multivariate approach to a ranking of organic pollutants according to their intrinsic tendency towards mobility, and the definition of four a priori mobility classes for screening purposes. Quantitative structure-property relationships (QSPRs) were used to predict missing values for octanol/air partition coefficients. Finally, a classification method employing theoretical molecular descriptors was used to assign studied chemicals to four mobility classes. The proposed approach assesses, directly and simply, a pollutant's inherent tendency towards mobility using only knowledge of the pollutant's molecular structure; the approach is particularly useful for a preliminary screening and the prioritisation of organic pollutants of emerging environmental concern.

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Research paper thumbnail of Screening of pesticides for environmental partitioning tendency

The partitioning tendency of chemicals, in this study pesticides in particular, into different en... more The partitioning tendency of chemicals, in this study pesticides in particular, into different environmental compartments depends mainly on the concurrent relevance of the physico-chemical properties of the chemical itself. To rank the pesticides according to their distribution tendencies in the different environmental compartments we propose a multivariate approach: the combination, by principal component analysis, of those physico-chemical properties like organic carbon partition coefficient (Koc), n-octanol/water partition coefficient (Kow), water solubility (Sw), vapour pressure and Henry's law constant (H) that are more relevant to the determination of environmental partitioning. The resultant macrovariables, the PC1 and PC2 scores here named leaching index (LIN) and volatality index (VIN), are proposed as preliminary environmental partitioning indexes in different media. These two indexes are modeled by theoretical molecular descriptors with satisfactory predictive power. Such an approach allows a rapid pre-determination and screening of the environmental distribution of pesticides starting only from the molecular structure of the pesticide, without any a priori knowledge of the physico-chemical properties.

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