Storing the wisdom: chemical concepts and chemoinformatics

The purpose of the paper is to examine the nature of chemical concepts, and the ways in which they are applied in chemoinformatics systems. An account of concepts in philosophy and in the information sciences leads to an analysis of chemical concepts, and their representation. The way in which concepts are applied in systems for information retrieval and for structure–property correlation are reviewed, and some issues noted. Attention is focused on the basic concepts or substance, reaction and property, on the organising concepts of chemical structure, structural similarity, periodicity, and on more specific concepts, including two- and three-dimensional structural patterns, reaction types, and property concepts. It is concluded that chemical concepts, despite (or perhaps because of) their vague and mutable nature, have considerable and continuing value in chemoinformatics, and that an increased formal treatment of concepts may have value in the future

Storing the wisdom: chemical concepts and chemoinformatics

The purpose of the paper is to examine the nature of chemical concepts, and the ways in which they are applied in chemoinformatics systems. An account of concepts in philosophy and in the information sciences leads to an analysis of chemical concepts, and their representation. The way in which concepts are applied in systems for information retrieval and for structure–property correlation are reviewed, and some issues noted. Attention is focused on the basic concepts or substance, reaction and property, on the organising concepts of chemical structure, structural similarity, periodicity, and on more specific concepts, including two- and three-dimensional structural patterns, reaction types, and property concepts. It is concluded that chemical concepts, despite (or perhaps because of) their vague and mutable nature, have considerable and continuing value in chemoinformatics, and that an increased formal treatment of concepts may have value in the future

The computer storage, retrieval and searching of generic structures in chemical patents : the machine-readable representation of generic structures.

The nature of the generic chemical structures found in patents is described, with a discussion of the types of statement commonly found in them. The available representations for such structures are reviewed, with particular note being given to the suitability of the representation for searching files of such structures. Requirements for the unambiguous representation of generic structures in an "ideal" storage and retrieval system are discussed. The basic principles of the theory of formal languages are reviewed, with particular consideration being given to parsing methods for context-free languages. The Grammar and parsing of computer programming languages, as an example of artificial formal languages, is discussed. Applications of formal language theory to chemistry and information work are briefly reviewed. GENSAL, a formal language for the unambiguous description of generic structures from patents, is presented. It is designed to be intelligible to a chemist or patent agent, yet sufficiently ABSTRACT formaLised to be amenabLe to computer anaLysis. DetaiLed description is given of the facilities it provides for generic structure representation, and there is discussion of its Limitations and the principLes behind its design. A connection-tabLe-based internaL representation for generic structures, caLLed an ECTR <Extended Connection TabLe Representation) is presented. It is designed to represent generic structures unambiguousLy, and to be generated automatically from structures encoded in GENSAL. It is compared to other proposed representations, and its implementation using data types of the programming Language PascaL described. An interpreter program which generates an ECTR from structures encoded in a subset of the GENSAL Language is presented. The principles of its operation are described. Possible applications of GENSAL outside the area of patent documentation are discussed, and suggestions made for further work on the development of a generic structure storage and retrieval system based on GENSAL and ECTRs

QSAR Modeling: Where Have You Been? Where Are You Going To?

Quantitative Structure-Activity Relationship modeling is one of the major computational tools employed in medicinal chemistry. However, throughout its entire history it has drawn both praise and criticism concerning its reliability, limitations, successes, and failures. In this paper, we discuss: (i) the development and evolution of QSAR; (ii) the current trends, unsolved problems, and pressing challenges; and (iii) several novel and emerging applications of QSAR modeling. Throughout this discussion, we provide guidelines for QSAR development, validation, and application, which are summarized in best practices for building rigorously validated and externally predictive QSAR models. We hope that this Perspective will help communications between computational and experimental chemists towards collaborative development and use of QSAR models. We also believe that the guidelines presented here will help journal editors and reviewers apply more stringent scientific standards to manuscripts reporting new QSAR studies, as well as encourage the use of high quality, validated QSARs for regulatory decision making

Modificação superficial de nanocontentores de inibidores de corrosão para melhoria da compatibilidade com revestimentos protetores

The application of organic coatings is one of the most widely used preventive measures to protect metal alloys against corrosion. Typically, anti-corrosion coatings combine passive and active protection, the former being based upon barrier effect of the matrix against ingress of active species and the later due to the presence of corrosion inhibitors directly dispersed in the coating matrix. Nevertheless, the direct addition of corrosion inhibitors to coating formulations often leads to detrimental effects, thus impairing the overall coating performance. To circumvent this limitation, micro and nanocontainers as hosting structures for storage and controlled release of corrosion inhibitors, have been proposed. If this release is triggered by adverse conditions that result in corrosion initiation self-healing takes place, which can bring great benefit to high-performance applications. The work presented in this thesis aims at modifying the nanocontainers surface in order to enhance the role of inhibition and barrier properties of the coatings as well as improving their dispersibility and compatibility within the coating. This latter part of the study had not been in general addressed in the scientific literature and requires interaction with the coating producer in order to match the desired properties for a commercial formulation. Two nanocontainers to store the corrosion inhibitors were selected: layered double hydroxides (LDH) and silica nanocapsules (Si_NC). The surface modification of LDH loaded with 2-mercaptobenzothiazole (2-MBT) with poly(styrene sulfonate)/poly(allylamine hydrochloride) by the layer-by-layer self-assembly technique allowed the incorporation of a second corrosion inhibitor, cerium nitrate, but at the same time improve the coating barrier properties of the hybrid sol-gel coatings. Moreover, the release profile of 2-MBT was also changed with this surface modification. This lab-scale work was extended to an industrial collaboration with a steel producer. In this case, the modification of gluconate loaded LDH with alginate lead to improvement in coating barrier properties of a polyamide-based coating. In the case of Si_NC several functional groups were grafted onto these silica-based nanomaterials, allowing a thorough analysis of the effect the surface chemistry on the dispersibility and compatibility with coatings. Tests were carried out in systems with increasing complexity from solvents, to hybrid sol-gel formulations and water- and solvent-based coating formulations industrially available. The coating barrier properties were mainly assessed by electrochemical impedance spectroscopy, often complemented with other electrochemical methods. Spectroscopic and surface-characterization techniques, and in some cases standard tests carried out under an industrial environment were also used. The results prove the importance that the surface modification has on the nanocontainer dispersibility and in the nanocontainer/coating compatibility. These results obtained show that surface modification of these nanocontainers can tune the interaction with coating matrix, opening prospects for the industrialization of these controlled-release technologies in the area of protective coatings.A aplicação de revestimentos orgânicos é uma das medidas preventivas mais utilizadas na proteção contra corrosão em ligas metálicas. Tipicamente, revestimentos anti-corrosão combinam proteção passiva e ativa, sendo a primeira baseada no efeito barreira do revestimento contra o ingresso de espécies ativas e a segunda devido à presença de inibidores de corrosão dispersos diretamente na matriz do revestimento. Não obstante, a adição direta de inibidores de corrosão a formulações de revestimentos leva normalmente a ocorrência de efeitos negativos, assim prejudicando a desempenho global do revestimento. De forma a contornar esta limitação, micro e nanocontentores, estruturas hospedeiras para o armazenamento e libertação controlada de inibidores de corrosão, têm sido propostos. Se esta libertação for desencadeada por condições adversas que resultam na iniciação de corrosão o efeito de autorreparação tem lugar, o que pode trazer grandes benefícios em aplicações de elevada desempenho. O trabalho apresentado nesta tese tem como objetivo a modificação superficial de nanocontentores a fim de melhorar o papel da inibição e das propriedades barreira de revestimentos, assim como a melhoria da dispersibilidade e compatibilidade dentro do revestimento. Este último é geralmente um tópico que não é abordado na literatura científica e que ao mesmo tempo necessita de um certo nível de interação dos produtores de formulações para revestimentos de forma a corresponder às propriedades desejadas numa formulação comercial. Dois nanocontentores, com comprovada atividade como reservatórios de inibidores de corrosão, foram selecionados: hidróxidos duplos lamelares e nanocápsulas de sílica. A modificação superficial de hidróxidos duplos lamelares intercalados com 2-mercaptobenzotiazol com poliestireno sulfonato/hidrocloreto de polialilamina pela técnica de automontagem camada-a-camada permitiu a incorporação de um segundo inibidor de corrosão, nitrato de cério, ao mesmo tempo melhorando as propriedades barreira do revestimento de sol-gel hibrido. Além de que, o perfil de libertação do 2-mercaptobenzotiazol também foi alterado com a modificação da superfície. Este trabalho à escala laboratorial foi estendido para uma colaboração industrial com um produtor de aço. Neste caso, a modificação de hidróxidos duplos lamelares intercalados com gluconato com alginato levou a melhorias nas propriedades barreira de um revestimento de base poliamida. No caso de nanocápsulas de sílica diversos grupos funcionais foram ligados a estes nano-materiais a base de sílica, permitindo uma análise detalhada do efeito que a química de superfície tem na dispersibilidade e compatibilidade com revestimentos. Testes foram realizados em sistemas com uma complexidade crescente, desde solventes, ate formulações de sol-gel hibrido e revestimentos comerciais de base aquosa e solvente. As propriedades barreira dos revestimentos foram, na sua maioria, avaliadas por espetroscopia de impedância eletroquímica, frequentemente complementada com diferentes técnicas eletroquímicas, espectroscópicas e de caracterização de superfície, e em alguns casos com testes padrão realizados em ambiente industrial. Os resultados provaram a importância que a modificação da superfície tem na dispersão dos nano-contentores e na compatibilidade entre nano-contentores e revestimentos. Os resultados obtidos demostram que a modificação da superfície destes nanocontentores pode permitir ajustar a sua interação com a matriz do revestimento, abrindo perspetivas para a industrialização destas tecnologias de libertação controlada na área dos revestimentos de proteção.Programa Doutoral em Ciência e Engenharia de Materiai

Remote Sensing in Agriculture: State-of-the-Art

The Special Issue on “Remote Sensing in Agriculture: State-of-the-Art” gives an exhaustive overview of the ongoing remote sensing technology transfer into the agricultural sector. It consists of 10 high-quality papers focusing on a wide range of remote sensing models and techniques to forecast crop production and yield, to map agricultural landscape and to evaluate plant and soil biophysical features. Satellite, RPAS, and SAR data were involved. This preface describes shortly each contribution published in such Special Issue

Deterritorializing the Future

Understanding how pasts resource presents is a fundamental first step towards building alternative futures in the Anthropocene. This collection brings together scholars from a range of disciplines to explore concepts of care, vulnerability, time, extinction, loss and inheritance across more-than-human worlds, connecting contemporary developments in the posthumanities with the field of critical heritage studies. Drawing on contributions from archaeology, anthropology, critical heritage studies, gender studies, geography, histories of science, media studies, philosophy, and science and technology studies, the book aims to place concepts of heritage at the centre of discussions of the Anthropocene and its associated climate and extinction crises – not as a nostalgic longing for how things were, but as a means of expanding collective imaginations and thinking critically and speculatively about the future and its alternatives. Contributors: Christina Fredengren, Cecilia Åsberg, Anna Bohlin, Adrian Van Allen, Esther Breithoff, Rodney Harrison, Colin Sterling, Joanna Zylinska, Denis Byrne, J. Kelechi Ugwuanyi, Caitlin DeSilvey, Anatolijs Venovcevs, Anna Storm and Claire Colebrook

Deterritorializing the Future

Understanding how pasts resource presents is a fundamental first step towards building alternative futures in the Anthropocene. This collection brings together scholars from a range of disciplines to explore concepts of care, vulnerability, time, extinction, loss and inheritance across more-than-human worlds, connecting contemporary developments in the posthumanities with the field of critical heritage studies. Drawing on contributions from archaeology, anthropology, critical heritage studies, gender studies, geography, histories of science, media studies, philosophy, and science and technology studies, the book aims to place concepts of heritage at the centre of discussions of the Anthropocene and its associated climate and extinction crises – not as a nostalgic longing for how things were, but as a means of expanding collective imaginations and thinking critically and speculatively about the future and its alternatives. Contributors: Christina Fredengren, Cecilia Åsberg, Anna Bohlin, Adrian Van Allen, Esther Breithoff, Rodney Harrison, Colin Sterling, Joanna Zylinska, Denis Byrne, J. Kelechi Ugwuanyi, Caitlin DeSilvey, Anatolijs Venovcevs, Anna Storm and Claire Colebrook