The Use of Computational Methods in the Grouping and Assessment of Chemicals - Preliminary Investigations

This document presents a perspective of how computational approaches could potentially be used in the grouping and assessment of chemicals, and especially in the application of read-across and the development of chemical categories. The perspective is based on experience gained by the authors during 2006 and 2007, when the Joint Research Centre's European Chemicals Bureau was directly involved in the drafting of technical guidance on the applicability of computational methods under REACH. Some of the experience gained and ideas developed resulted from a number of research-based case studies conducted in-house during 2006 and the first half of 2007. The case studies were performed to explore the possible applications of computational methods in the assessment of chemicals and to contribute to the development of technical guidance. Not all of the methods explored and ideas developed are explicitly included in the final guidance documentation for REACH. Many of the methods are novel, and are still being refined and assessed by the scientific community. At present, many of the methods have not been tried and tested in the regulatory context. The authors therefore hope that the perspective and case studies compiled in this document, whilst not intended to serve as guidance, will nevertheless provide an input to further research efforts aimed at developing computational methods, and at exploring their potential applicability in regulatory assessment of chemicals.JRC.I.3-Toxicology and chemical substance

Organic Chemistry with a Biological Emphasis Volume I

The traditional approach to teaching Organic Chemistry, taken by most of the textbooks that are currently available, is to focus primarily on the reactions of laboratory synthesis, with much less discussion - in the central chapters, at least - of biological molecules and reactions. This is despite the fact that, in many classrooms, a majority of students are majoring in Biology or Health Sciences rather than in Chemistry, and are presumably taking the course in order to learn about the chemistry that takes place in living things. In an effort to address this disconnect, I have developed a textbook for a two-semester, sophomore-level course in Organic Chemistry in which biological chemistry takes center stage. For the most part, the text covers the core concepts of organic structure, structure determination, and reactivity in the standard order. What is different is the context: biological chemistry is fully integrated into the explanation of central principles, and as much as possible the in-chapter and end-of-chapter problems are taken from the biochemical literature. Many laboratory synthesis reactions are also covered, generally in parallel with their biochemical counterparts - but it is intentionally the biological chemistry that comes first

Functionalisation of colloidal transition metal sulphides nanocrystals: A fascinating and challenging playground for the chemist

Metal sulphides, and in particular transition metal sulphide colloids, are a broad, versatile and exciting class of inorganic compounds which deserve growing interest and attention ascribable to the functional properties that many of them display. With respect to their oxide homologues, however, they are characterised by noticeably different chemical, structural and hence functional features. Their potential applications span several fields, and in many of the foreseen applications (e.g., in bioimaging and related fields), the achievement of stable colloidal suspensions of metal sulphides is highly desirable or either an unavoidable requirement to be met. To this aim, robust functionalisation strategies should be devised, which however are, with respect to metal or metal oxides colloids, much more challenging. This has to be ascribed, inter alia, also to the still limited knowledge of the sulphides surface chemistry, particularly when comparing it to the better established, though multifaceted, oxide surface chemistry. A ground-breaking endeavour in this field is hence the detailed understanding of the nature of the complex surface chemistry of transition metal sulphides, which ideally requires an integrated experimental and modelling approach. In this review, an overview of the state-of-the-art on the existing examples of functionalisation of transition metal sulphides is provided, also by focusing on selected case studies, exemplifying the manifold nature of this class of binary inorganic compounds

The Kinetics of Industrial Ammonia Combustion

This thesis uses experiments and modelling to determine the kinetics of industrial ammonia combustion over platinum gauzes. The study is motivated by the existing poor understanding of the kinetics under industrial conditions. A comprehensive literature review of ammonia combustion is given, which includes a historical study of the industrial process, the current understanding of the industrial reaction kinetics, and an overview of the surface reaction mechanism. For this study, to further investigate industrial combustion, a burner was built whose design parameters were based on individual plant data found in the literature. Two models of the system are presented, one for the kinetics, and another for the temperatures in the catalyst bed. The key finding from the kinetic model is how individual process parameters determine the selectivity of the combustion products. The temperature model shows that for combustion in air, the catalyst surface temperature is not constant throughout the gauze pack, as it is currently thought to be

Molecular Similarity and Xenobiotic Metabolism

MetaPrint2D, a new software tool implementing a data-mining approach for predicting sites of xenobiotic metabolism has been developed. The algorithm is based on a statistical analysis of the occurrences of atom centred circular fingerprints in both substrates and metabolites. This approach has undergone extensive evaluation and been shown to be of comparable accuracy to current best-in-class tools, but is able to make much faster predictions, for the first time enabling chemists to explore the effects of structural modifications on a compound’s metabolism in a highly responsive and interactive manner.MetaPrint2D is able to assign a confidence score to the predictions it generates, based on the availability of relevant data and the degree to which a compound is modelled by the algorithm.In the course of the evaluation of MetaPrint2D a novel metric for assessing the performance of site of metabolism predictions has been introduced. This overcomes the bias introduced by molecule size and the number of sites of metabolism inherent to the most commonly reported metrics used to evaluate site of metabolism predictions.This data mining approach to site of metabolism prediction has been augmented by a set of reaction type definitions to produce MetaPrint2D-React, enabling prediction of the types of transformations a compound is likely to undergo and the metabolites that are formed. This approach has been evaluated against both historical data and metabolic schemes reported in a number of recently published studies. Results suggest that the ability of this method to predict metabolic transformations is highly dependent on the relevance of the training set data to the query compounds.MetaPrint2D has been released as an open source software library, and both MetaPrint2D and MetaPrint2D-React are available for chemists to use through the Unilever Centre for Molecular Science Informatics website.----Boehringer-Ingelhie

Hallmarks of mechanochemistry: From nanoparticles to technology

The aim of this review article on recent developments of mechanochemistry (nowadays established as a part of chemistry) is to provide a comprehensive overview of advances achieved in the field of atomistic processes, phase transformations, simple and multicomponent nanosystems and peculiarities of mechanochemical reactions. Industrial aspects with successful penetration into fields like materials engineering, heterogeneous catalysis and extractive metallurgy are also reviewed. The hallmarks of mechanochemistry include influencing reactivity of solids by the presence of solid-state defects, interphases and relaxation phenomena, enabling processes to take place under non-equilibrium conditions, creating a well-crystallized core of nanoparticles with disordered near-surface shell regions and performing simple dry time-convenient one-step syntheses. Underlying these hallmarks are technological consequences like preparing new nanomaterials with the desired properties or producing these materials in a reproducible way with high yield and under simple and easy operating conditions. The last but not least hallmark is enabling work under environmentally friendly and essentially waste-free conditions (822 references).Slovak Grant Agency VEGA 2/0009/11, 2/0043/11Slovak Agency for Science and Development APVV VV-0189-10, VV-0528-11Russian Foundation for Basic Research 10-03-00942a, 12-03-00651aMinistry of Science and Higher education in Poland CUT/c-1/DS/KWC/2008-2012, PB1T09B02330, NN209145136, NN20914893

Globally Optimal Catalysts: Computerbasierte Optimierung von abstrakten katalytischen Einbettungen für beliebige chemische Reaktionen

In the context of inverse design of molecules with desired optimal properties, the long-term goal of this Thesis is to develop a general framework which tackles the design of molecular systems for an optimal catalytic effect onto arbitrary chemical reactions. For any given reaction, an arrangement of an additional molecular framework around this reaction center is sought such that the energetic reaction barrier is lowered as much as possible. As necessary abstraction layer, the so-called globally optimal catalyst (GOCAT) model is introduced, and, furthermore, evolutionary algorithms (EAs) are harnessed as implemented in our global optimization suite for chemical problems, ogolem, which was highly extended to allow for these catalysis optimizations. Starting with a maximally reductionistic approach for studying the non-bonding interactions, electrostatic GOCATs are introduced that consist of arbitrary numbers, distributions and strengths of partial point charges around reacting molecules, mostly surrounding these on a common exposed surface. In the end, two reactions are studied in detail within the general topic of electrostatic catalysis. Some of the initially present model approximations are already sufficiently lifted, still-existing ones are critically assessed and further future extensions to the framework are discussed. Moreover, many method development matters are addressed: They range from optimal shared-memory parallelization, exemplified for global parameter optimization of the reactive force field, ReaxFF, via diversity control parameters for the EAs, applied to a cluster structure optimization problem, to EA operator benchmarks and optimizations of abstract electrostatics.Im Kontext von inversem Design von Molekülen mit optimalen Eigenschaften versucht die vorliegende Arbeit als Langzeitziel eine passende Plattform zu entwickeln, welche das generelle Design molekularer Systeme für einen optimalen Katalyseeffekt auf beliebige chemische Reaktionen projektiert. Für eine gegeben Reaktion soll eine hinzukommende chemische Umgebung komponiert werden, welche die Reaktionsenergiebarriere so weit wie möglich vermindert. Als notwendige Abstraktionsschicht wird das sogenannte Modell des globally optimal catalyst (GOCAT) eingeführt und außerdem kommen Evolutionäre Algorithmen (EAs) zur Anwendung, wie sie bereits in unserem Programmpaket zur Lösung allgemeiner globaler Optimierungsprobleme der Chemie, ogolem, bereitgestellt werden, welches jedoch deutlich für diese Katalyseoptimierungen ergänzt wurde. Angefangen in einem maximal-reduktionistischen Ansatz werden elektrostatische GOCATs erarbeitet, die aus einer beliebigen Anzahl, Verteilung und Stärke von Partialladungen bestehen und rund um die reagierenden Moleküle drapiert werden, meist auf einer gemeinsamen exponierten Oberfläche. Insgesamt werden zwei Reaktionen detailliert untersucht im generellen Kontext von elektrostatischer Katalyse. Einige eingangs vorhandene Modellannahmen werden bereits systematisch verbessert, noch vorhandene kritisch beleuchtet und künftige Erweiterungen auseinandergesetzt. Weiterhin werden unterschiedliche Methodenentwicklungsaspekte angesprochen: Diese reichen von verbesserter Parallelisierung in Mehrprozessorarchitekturen, beispielhaft gezeigt anhand einer globalen Parameteroptimierung des reaktiven Kraftfeldes ReaxFF, über Diversitätskontrollparameter des EAs, illustriert mittels eines Clusterstrukturoptimierungsproblems, bis hin zu EA-Operator-Testevaluationen und allgemeinen abstrakten Elektrostatikoptimierungen

Adsorption Dynamics and Bonding Analysis of Organic Molecules on Silicon(001) Surfaces

In this thesis, the adsorption of ethylene, tetrahydrofuran (THF), cyclooctyne and 5-Ethoxymethyl-5-methylcyclooctyne (EMC) on Si(001) surfaces is studied using computational methods. While ethylene and THF act as model systems that allow to understand how unsaturated carbon-carbon bonds and ether groups interact with these surfaces, cyclooctyne and EMC are potential candidates for the formation of organic/semiconductor interfaces and therefore more application-oriented. The thesis is focusing on two aspects of adsorption: Bonding analysis and adsorption dynamics. In bonding analysis, periodic Energy Decomposition Analysis (pEDA), which allows to understand the formation of chemical bonds betwen molecule and surface, was applied. The reaction dynamics was simulated using two approaches: Statistical thermodynamics, which can be applied if thermodynamic equilibrium is achieved, and explicitly calculating the evolution of the system over time using ab initio molecular dynamics (AIMD). For ethylene, the results show that a dative bond between the carbon-carbon double bond and an empty orbital at a surface atom forms in the weakly bound intermediate state. In contrast to physisorbed intermediates on metal surfaces, this state is not mobile. Additionally, the influence of surface pre-coverage by atoms and molecules on the reactivity of ethylene is investigated in a second study. The study of THF reveals that the adsorption mirrors the acid-catalyzed cleavage of ethers in solution and that the mechanism is equivalent to a concerted nucleophilic substitution. For cyclooctyne, it is explained why the formation of two molecule-surface bonds stabilizes the system far more than the formation of four such bonds. Ring strain and enhanced dispersion interactions due to the size of the molecule lead to additional stabilization in comparison to linear alkynes like acetylene. In contrast to alkenes, cyclooctyne can adsorb either directly into the final state or via a short lived transient state. However, the lifetime of this transient state is so low that isolation at usual experimental conditions is not possible. The conclusive study of EMC shows that the molecule bonds selectively via the strained triple bond and therefore confirms its suitability as a building block for organic/semiconductor interfaces. The ether group does not affect the reactivity and adsorption dynamics of the triple bond and cyclooctyne results can be transferred to this part of the molecule. The reactivity of the ether group is influenced by the sterically demanding residue, however, adsorption of this group is highly unlikely. Overall, the studies in this thesis show that the application of chemical concepts and methods can bring in valuable contributions to the field of surface science. The pEDA in particular allows to describe the bonding between molecule and surface both qualitatively and quantitatively, and therefore enables an understanding of the relative energies between different adsorption structures. Furthermore, the investigation of the dynamics allows to predict how the system evolves on different time scales and which structures form preferably. The approaches presented in this thesis can most likely be transferred to other systems as well (e.g. adsorption on metal surfaces) and allow to deliver new insight into different fields of research in surface science and material science