Chemical databases: curation or integration by user-defined equivalence?

There is a wealth of valuable chemical information in publicly available databases for use by scientists undertaking drug discovery. However finite curation resource, limitations of chemical structure software and differences in individual database applications mean that exact chemical structure equivalence between databases is unlikely to ever be a reality. The ability to identify compound equivalence has been made significantly easier by the use of the International Chemical Identifier (InChI), a non-proprietary line-notation for describing a chemical structure. More importantly, advances in methods to identify compounds that are the same at various levels of similarity, such as those containing the same parent component or having the same connectivity, are now enabling related compounds to be linked between databases where the structure matches are not exact

A review of conventional and emerging technologies for hydrogels sterilization

Funding This work was financially supported by Fundaçao ˜ para a Ciˆencia e Tecnologia (FCT), Portugal, through the project STERILAEROGEL – Green method to prepare sterilised biopolymer-based aerogel (POCI01–0145-FEDER-032625) and Strategic Projects FCT-MEC PEst-C/EQB/ UI0102/2019, UIDB/00102/2020 and Programmatic Project UIDP/ 00102/2020 of the CIEPQPF, and UI/05704/2020 of the ciTechCare. C. S. A. Bento acknowledges for PhD grant UI/BD/151008/2021 and M. C. Gaspar acknowledges FCT for the financial support under Scientific Employment Stimulus – Individual and Institutional Calls (CEECIND/ 00527/2017 and CEECINST/00060/2021).Hydrogels are extensively used in the biomedical field, as drug delivery systems, wound dressings, contact lenses or as scaffolds for tissue engineering. Due to their polymeric nature and the presence of high amounts of water in their structure, hydrogels generally present high sensitivity to terminal sterilization. The establishment of an efficient sterilization protocol that does not compromise the functional properties of the hydrogels is one of the challenges faced by researchers when developing a hydrogel for a specific application. Yet, until very recently this aspect was largely ignored in the literature. The present paper reviews the state of literature concerning hydrogels sterilization, compiling the main findings. Conventional terminal sterilization methods (heat sterilization, radiation sterilization, and gas sterilization) as well as emerging sterilization techniques (ozone, supercritical carbon dioxide) are covered. Considerations about aseptic processing are also included. Additionally, and as a framework, hydrogels’ polymeric materials, types of networks, and main biomedical applications are summarily described.info:eu-repo/semantics/publishedVersio

An open source chemical structure curation pipeline using RDKit.

Funder: European Molecular Biology Laboratory; doi: http://dx.doi.org/10.13039/100013060BACKGROUND: The ChEMBL database is one of a number of public databases that contain bioactivity data on small molecule compounds curated from diverse sources. Incoming compounds are typically not standardised according to consistent rules. In order to maintain the quality of the final database and to easily compare and integrate data on the same compound from different sources it is necessary for the chemical structures in the database to be appropriately standardised. RESULTS: A chemical curation pipeline has been developed using the open source toolkit RDKit. It comprises three components: a Checker to test the validity of chemical structures and flag any serious errors; a Standardizer which formats compounds according to defined rules and conventions and a GetParent component that removes any salts and solvents from the compound to create its parent. This pipeline has been applied to the latest version of the ChEMBL database as well as uncurated datasets from other sources to test the robustness of the process and to identify common issues in database molecular structures. CONCLUSION: All the components of the structure pipeline have been made freely available for other researchers to use and adapt for their own use. The code is available in a GitHub repository and it can also be accessed via the ChEMBL Beaker webservices. It has been used successfully to standardise the nearly 2 million compounds in the ChEMBL database and the compound validity checker has been used to identify compounds with the most serious issues so that they can be prioritised for manual curation

Catálogo Taxonômico da Fauna do Brasil: setting the baseline knowledge on the animal diversity in Brazil

The limited temporal completeness and taxonomic accuracy of species lists, made available in a traditional manner in scientific publications, has always represented a problem. These lists are invariably limited to a few taxonomic groups and do not represent up-to-date knowledge of all species and classifications. In this context, the Brazilian megadiverse fauna is no exception, and the Catálogo Taxonômico da Fauna do Brasil (CTFB) (http://fauna.jbrj.gov.br/), made public in 2015, represents a database on biodiversity anchored on a list of valid and expertly recognized scientific names of animals in Brazil. The CTFB is updated in near real time by a team of more than 800 specialists. By January 1, 2024, the CTFB compiled 133,691 nominal species, with 125,138 that were considered valid. Most of the valid species were arthropods (82.3%, with more than 102,000 species) and chordates (7.69%, with over 11,000 species). These taxa were followed by a cluster composed of Mollusca (3,567 species), Platyhelminthes (2,292 species), Annelida (1,833 species), and Nematoda (1,447 species). All remaining groups had less than 1,000 species reported in Brazil, with Cnidaria (831 species), Porifera (628 species), Rotifera (606 species), and Bryozoa (520 species) representing those with more than 500 species. Analysis of the CTFB database can facilitate and direct efforts towards the discovery of new species in Brazil, but it is also fundamental in providing the best available list of valid nominal species to users, including those in science, health, conservation efforts, and any initiative involving animals. The importance of the CTFB is evidenced by the elevated number of citations in the scientific literature in diverse areas of biology, law, anthropology, education, forensic science, and veterinary science, among others

Ab Initio and DFT Benchmark Study for Nucleophilic Substitution at Carbon (SN2@C) and Silicon (SN2@Si

Abstract: To obtain a set of consistent benchmark potential energy surfaces (PES) for the two archetypal nucleophilic substitution reactions of the chloride anion at carbon in chloromethane (S N 2@C) and at silicon in chlorosilane (S N 2@Si), we have explored these PESes using a hierarchical series of ab initio methods [HF, MP2, MP4SDQ, CCSD, CCSD(T)] in combination with a hierarchical series of six Gaussian-type basis sets, up to g polarization. Relative energies of stationary points are converged to within 0.01 to 0.56 kcal/mol as a function of the basis-set size. Our best estimate, at CCSD(T)/aug-cc-pVQZ, for the relative energies of the [Cl Ϫ transition state and the stable [Cl-SiH 3 -Cl] Ϫ transition complex is Ϫ10.42, ϩ2.52, and Ϫ27.10 kcal/mol, respectively. Furthermore, we have investigated the performance for these reactions of four popular density functionals, namely, BP86, BLYP, B3LYP, and OLYP, in combination with a large doubly polarized Slater-type basis set of triplequality (TZ2P). Best overall agreement with our CCSD(T)/aug-cc-pVQZ benchmark is obtained with OLYP and B3LYP. However, OLYP performs better for the S N 2@C overall and central barriers, which it underestimates by 2.65 and 4.05 kcal/mol, respectively. The other DFT approaches underestimate these barriers by some 4.8 (B3LYP) to 9.0 kcal/mol (BLYP)