The Use of Chemical Reactivity Assays in Toxicity Prediction

The use of so-called “in chemico” methodology - abiotic assays that measure chemical reactivity - is gaining ground as relevant and reliable means of toxicity prediction. In this report we explain the basis of the in chemico approach to toxicity prediction and we review the studies that have developed the concept and its practical application since the 1930s, with special attention being paid to studies aimed at the development of Quantitative Structure-Activity Relationship (QSAR) models and read-across approaches. The studies covered in this review are limited to non-enzymatic experiments and to nucleophiles up to 50 amino acids. The main applications identified are related to the assessment of skin sensitisation, aquatic toxicity and hepatotoxicity. Various experimental measures of nucleophile depletion or adduct formation have been proposed as chemical reactivity descriptors, but no single protocol has emerged as the most generally useful. It is concluded that in chemico approaches provide a promising means of toxicity prediction within their applicability domains and should be further developed and investigated as alternative methods to animal testing, especially when used in the context of integrated testing strategies based on the use of multiple non-animal methods.JRC.DG.I.6-Systems toxicolog

Dissecting the hindered rotation of ethane

The existence of a rotational barrier of ca. 3 kcal mol À1 around the CÀC single bond in ethane has been known The steric repulsion still remains the most popular explanation of the hindered rotation of ethane. This effect is often understood as the increase in energy that accompanies the antisymmetrization of a wave function originally formed by strictly localized descriptions of two methyl groups brought up to the final ethane geometry where they overlap. This so-called Pauli repulsion is considered to be more important for the eclipsed conformation, The hyperconjugation [21] The electron delocalization effect can easily be assessed in valence bond (VB) theory calculations Previous energy decomposition analyses relied, in one way or another, on the definition of two methyl fragments. However, in the last years there have been a growing interest in other kinds of energy partitioning schemes, The diatomic terms naturally reflect the attractive or repulsive interactions between the atoms in the molecule. The onecenter terms correspond to the effective energy of each atom in the molecule; its value relative to that of the corresponding free atom accounts for the promotion that occurs upon bond formation. In this sense, it is important to recall that the oneand two-center contributions are static parameters. [26] They measure to which extent the energy of a given atom or atomic pair contributes to the total molecular energy at that geometry and with the wave function used at that point. Thus, the diatomic values cannot be put into direct correspondence with the dissociation energies, as dissociation involves changes in both geometry and wave function. The main advantage of this methodology for the present case is that one can decompose all energetic interactions within the molecule on the basis of a single ab initio calculation, without recurring to an arbitrar

Ability of non-animal methods for skin sensitisation to detect pre- and pro-haptens: Report and recommendations of an EURL ECVAM expert meeting

Significant progress has been made in the development, validation and regulatory acceptance of in chemico and in vitro test methods for skin sensitisation. Although these methods have been shown to perform relatively well (about 80% accuracy in predicting Local Lymph Node Assay (LLNA) classifications) a concern was raised on the regulatory acceptability of negative results since it was questioned whether these methods are able to predict chemicals that need to be activated to act as sensitisers. In order to inform ongoing discussions at the regulatory level in the EU, EURL ECVAM held an expert meeting on 10-11 November 2015 to analyse the extent to which in chemical and in vitro methods are able to correctly identify chemicals that need to be activated either through abiotic activation (pre-haptens) and/or through biotic (enzyme-mediated) mechanisms (pro-haptens) to acquire skin sensitisation potential. The expert group analysed a list of 127 chemicals, with available LLNA and in vitro data, 22% of which were considered to be pre- and/or pro-haptens. The pre-haptens, constituting the vast majority of chemicals requiring activation, where mostly correctly identified by both the in chemico and in vitro assays whereas the pro-haptens which represent a small subset of sensitising chemicals, were generally identified correctly by one of the cell-based assays. As a result, the expert group recommended that negative in vitro data should be accepted unless there is a compelling scientific argument that a substance is likely to be an exclusively metabolically activated pro-hapten.JRC.I.5-Systems Toxicolog

Evaluation of the availability and applicability of computational approaches in the safety assessment of nanomaterials: Final report of the Nanocomput project

This is the final report of the Nanocomput project, the main aims of which were to review the current status of computational methods that are potentially useful for predicting the properties of engineered nanomaterials, and to assess their applicability in order to provide advice on the use of these approaches for the purposes of the REACH regulation. Since computational methods cover a broad range of models and tools, emphasis was placed on Quantitative Structure-Property Relationship (QSPR) and Quantitative Structure-Activity Relationship (QSAR) models, and their potential role in predicting NM properties. In addition, the status of a diverse array of compartment-based mathematical models was assessed. These models comprised toxicokinetic (TK), toxicodynamic (TD), in vitro and in vivo dosimetry, and environmental fate models. Finally, based on systematic reviews of the scientific literature, as well as the outputs of the EU-funded research projects, recommendations for further research and development were also made. The Nanocomput project was carried out by the European Commission’s Joint Research Centre (JRC) for the Directorate-General (DG) for Internal Market, Industry, Entrepreneurship and SMEs (DG GROW) under the terms of an Administrative Arrangement between JRC and DG GROW. The project lasted 39 months, from January 2014 to March 2017, and was supported by a steering group with representatives from DG GROW, DG Environment and the European Chemicals Agency (ECHA).JRC.F.3-Chemicals Safety and Alternative Method

SpheraCosmolife: a new tool for the risk assessment of cosmetic products.

A new, freely available software for cosmetic products has been designed that considers the regulatory framework for cosmetics. The software allows an overall toxicological evaluation of cosmetic ingredients without the need for additional testing and, depending on the product type, it applies defined exposure scenarios to derive risk for consumers. It takes regulatory thresholds into account and uses either experimental values, if available, or predictions. Based on the exper­imental or predicted no observed adverse effect level (NOAEL), the software can define a point of departure (POD), which is used to calculate the margin of safety (MoS) of the query chemicals. The software also provides other toxico­logical properties, such as mutagenicity, skin sensitization, and the threshold of toxicological concern (TTC) to provide an overall evaluation of the potential chemical hazard. Predictions are calculated using in silico models implemented within the VEGA software. The full list of ingredients of a cosmetic product can be processed at the same time, at the effective concentrations in the product as given by the user. SpheraCosmolife is designed as a support tool for safety assessors of cosmetic products and can be used to prioritize the cosmetic ingredients or formulations according to their potential risk to consumers. The major novelty of the tool is that it wraps a series of models (some of them new) into a single, user-friendly software system

EURL ECVAM Status Report on the Development, Validation and Regulatory Acceptance of Alternative Methods and Approaches (2016)

Replacement, Reduction and Refinement of animal testing is anchored in EU legislation. Alternative non-animal approaches facilitate a shift away from animal testing. Cell-based methods and computational technologies are integrated to translate molecular mechanistic understanding of toxicity into safety testing strategies.JRC.F.3-Chemicals Safety and Alternative Method

Basis set superposition error effects, excited-state potential energy surface and photodynamics of thymine

En aquesta tesi he estudiat l'efecte de l'error de superposició de base (BSSE) en la planaritat d'algunes molècules. He observat que l'ús d'alguns mètodes de càlcul amb determinades funcions de base descriuen mínims d'energia no planars per les bases nitrogenades de l'ADN. He demostrat que aquests problemes es poden arreglar utilitzant el mètode Counterpoise per corregir el BSSE en els càlculs. En aquesta tesi també he estudiat la fotofísica de la timina i els resultats mostren que existeixen dos camins de relaxació des de l'estat excitat que permeten la regeneració de l'estructura inicial de forma ultraràpida.The effect of the basis set superposition error (BSSE) on the planarity of some molecules has been studied in this thesis. I have observed that the use of some correlated methods with certain basis sets lead to non-planar minima structures of nucleobases. I have shown that the use of the Counterpoise method fixes these pitfalls in all cases. I have also studied the photophysics of thymine in this thesis and my results show that there exist two decay paths that can regenerate the initial structure of thymine in less than tenths of picoseconds upon photon absorption

Photophysics of the pi,pi* and n,pi* states of thymine: MS-CASPT2 minimum-energy paths and CASSCF on-the-fly dynamics

The photodynamics along the main decay paths of thymine after excitation to the lowest pi,pi* state have been studied with MS-CASPT2 calculations and semiclassical CASSCF dynamics calculations including a surface hopping algorithm. The static calculations show that there are two decay paths from the Franck-Condon structure that lead to a conical intersection with the ground state. The first path goes directly to the intersection, while the second one is indirect and involves a minimum of the pi,pi* state, a small barrier, and a crossing between the pi,pi* and n,pi* states. From the static calculations, both paths have similar slopes. The dynamics calculations along the indirect path show that, after the barrier, part of the trajectories are funneled to the intersection with the ground state, where they are efficiently quenched to the ground state. The remaining trajectories populate the n,pi* state. They are also quenched to the ground state in less than 1 ps, but the static calculations show that the decay rate of the n,pi* state is largely overestimated at the CASSCF level used for the dynamics, Overall, these results suggest that both direct and indirect paths contribute to the subpicosecond decay components found experimentally. The indirect path also provides a way for fast population of the n,pi* state, which will account for the experimental picosecond decay component

Intramolecular basis set superposition error effects on the planarity of benzene and other aromatic molecules: A solution to the problem

Recently, the surprising result that ab initio calculations on benzene and other planar arenes at correlated MP2, MP3, configuration interaction with singles and doubles (CISD), and coupled cluster with singles and doubles levels of theory using standard Pople’s basis sets yield nonplanar minima has been reported. The planar optimized structures turn out to be transition states presenting one or more large imaginary frequencies, whereas single-determinant-based methods lead to the expected planar minima and no imaginary frequencies. It has been suggested that such anomalous behavior can be originated by two-electron basis set incompleteness error. In this work, we show that the reported pitfalls can be interpreted in terms of intramolecular basis set superposition error (BSSE) effects, mostly between the C–H moieties constituting the arenes. We have carried out counterpoise-corrected optimizations and frequency calculations at the Hartree–Fock, B3LYP, MP2, and CISD levels of theory with several basis sets for a number of arenes. In all cases, correcting for intramolecular BSSE fixes the anomalous behavior of the correlated methods, whereas no significant differences are observed in the single-determinant case. Consequently, all systems studied are planar at all levels of theory. The effect of different intramolecular fragment definitions and the particular case of charged species, namely, cyclopentadienyl and indenyl anions, respectively, are also discusse