Search

The IUPAC International Chemical Identifier (InChI) is a structure-based chemical identifier that encodes various aspects of a chemical structure into a hierarchically layered line notation. Because InChI is non-proprietary, open-source, and freely available to everyone, it is adopted in popular chemical information resources and software programs. This paper describes the InChI Open Education Resource (OER) (https://www.inchi-trust.org/oer/), designed to provide educators and other interested parties with resources, training material, and information related to InChI. Currently, the OER contains over 100 materials collected from various sources and provides users with search, filtering, and sorting functionalities to locate specific records. New relevant materials can be suggested by anyone, allowing the scientific community to share and find InChI-related resources. This paper will show how to use the InChI OER tag taxonomy to filter content and demonstrate two resources within the InChI OER; the ChemNames2LCSS Google Sheet and the InChILayersExplorer, an Excel spreadsheet that breaks an InChI into its layers. While the InChI OER is of value to a broader chemistry community, this paper seeks to reach out to chemical educators and provide them with an understanding of InChI and its role in the practice of science., (© 2023 the author(s), published by De Gruyter, Berlin/Boston.)

The International Union of Pure and Applied Chemistry (IUPAC) has a long tradition of supporting the compilation of chemical data and their evaluation through direct projects, nomenclature and terminology work, and partnerships with international scientific bodies, government agencies and other organizations. The IUPAC Interdivisional Subcommittee on Critical Evaluation of Data (ISCED) has been established to provide guidance on issues related to the evaluation of chemical data. In this first report we define the general principles of the evaluation of scientific data and describe best practices and approaches to data evaluation in chemistry.

We present a sequence-to-sequence machine learning model for predicting the IUPAC name of a chemical from its standard International Chemical Identifier (InChI). The model uses two stacks of transformers in an encoder-decoder architecture, a setup similar to the neural networks used in state-of-the-art machine translation. Unlike neural machine translation, which usually tokenizes input and output into words or sub-words, our model processes the InChI and predicts the IUPAC name character by character. The model was trained on a dataset of 10 million InChI/IUPAC name pairs freely downloaded from the National Library of Medicine's online PubChem service. Training took seven days on a Tesla K80 GPU, and the model achieved a test set accuracy of 91%. The model performed particularly well on organics, with the exception of macrocycles, and was comparable to commercial IUPAC name generation software. The predictions were less accurate for inorganic and organometallic compounds. This can be explained by inherent limitations of standard InChI for representing inorganics, as well as low coverage in the training data., (© 2021. The Author(s).)

Choosing the right mentors and role models has a profound impact in both our lives and professional careers; however, most often, not enough time or thought is given to this important decision. Because of that, we may miss some great opportunities and limit the potential benefits. In this invited contribution, I share my personal experience on nurturing the relationship with mentors and on choosing role models with my same values and a strong sense of service., (© 2021 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

Background: An inverted repeat is a DNA sequence followed downstream by its reverse complement, potentially with a gap in the centre. Inverted repeats are found in both prokaryotic and eukaryotic genomes and they have been linked with countless possible functions. Many international consortia provide a comprehensive description of common genetic variation making alternative sequence representations, such as IUPAC encoding, necessary for leveraging the full potential of such broad variation datasets., Results: We present IUPACPAL, an exact tool for efficient identification of inverted repeats in IUPAC-encoded DNA sequences allowing also for potential mismatches and gaps in the inverted repeats., Conclusion: Within the parameters that were tested, our experimental results show that IUPACPAL compares favourably to a similar application packaged with EMBOSS. We show that IUPACPAL identifies many previously unidentified inverted repeats when compared with EMBOSS, and that this is also performed with orders of magnitude improved speed.

How many candles?! The year 2019 has been named as the International Year of the Periodic Table in accordance with Mendeleev's work from 1869. In line with other celebratory events and articles to be found this year in Chemistry-A European Journal, here, Eric R. Scerri provides an historical account of the development of the periodic table and some of the debates and considerations surrounding this fundamental elementary ensemble., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

A new solid-state nuclear magnetic resonance (NMR) thermometry sample is proposed. The 207 Pb NMR chemical shift of a lead halide perovskite, methylammonium lead chloride (MAPbCl 3 ) is very sensitive to temperature, 0.905±0.010ppmK -1 . The response to temperature is linear over a wide temperature range, from its tetragonal to cubic phase transition at 178K to >410K, making it an ideal standard for temperature calibrations in this range. Because the 207 Pb NMR lineshape for MAPbCl 3 appears symmetric, the sample is ideal for calibration of variable temperature NMR data acquired for spinning or non-spinning samples. A frequency-ratio method is proposed for referencing 207 Pb chemical shifts, based on the 1 H and 13 C frequencies of the methylammonium cation, which are used asan internal standard. Finally, this new NMR thermometer has been used to measure the degree of frictional heating asa function of spinning frequency for a series of MAS rotors ranging in outer diameter from 1.3 to 7.0mm. As expected, the largest diameter rotors are more susceptible to frictional heating, but lower diameter rotors are subjected to higher frictional heating temperatures as they are typically spun at much higher spinning frequencies., (Copyright © 2017 Elsevier Inc. All rights reserved.)

In 2015, an International Union of Pure and Applied Chemistry (IUPAC) Task Group was formed to develop nomenclature recommendations for homodetic cyclic peptides produced from ribosomal precursors. Delegates of the 2015 International Conference on Circular Proteins (ICCP) were presented with the strengths and weaknesses of four published approaches to homodetic cyclic peptide nomenclature, and a summary of the ensuing discussion is presented here. This interim report presents a potentially novel suggestion-the use of Cahn-Ingold-Prelog rules to specify amino acid priority in homodetic peptides for consistent numbering. Indeed, this might be the first extension of the Cahn-Ingold-Prelog rules in five decades. The authors invite interested parties to contact the corresponding author with suggestions for the improvement of the proposed nomenclature; these ideas will be discussed and considered for inclusion in the final report., (© 2016 Wiley Periodicals, Inc.)

It is always a challenge to determine the total cellulase activity efficiently without reducing accuracy. The most common total cellulase activity assay is the filter paper assay (FPA) established by the International Union of Pure and Applied Chemistry (IUPAC). A new procedure to measure the FPA with microplate-based assay was studied in this work, which followed the main idea of IUPAC to dilute cellulase preparation to get fixed glucose release. FPAs of six cellulase preparations were determined with the microplate-based assay. It is shown that FPAs of cellulase Youtell, RCconc, R-10, Lerkam, Yishui and Sinopharm were 67.9, 46.0, 46.1, 27.4, 7.6 and 8.0 IU/ml respectively. There was no significant difference at the 95% confidence level between the FPA determined with IUPAC and the microplate-based assay. It could be concluded that the FPA could be determined by the microplate-based assay with the same accuracy and much more efficiency compared with that by IUPAC.

As we approach the 2014 San Francisco IUPAC Pesticide Chemistry Congress, we reflect on the 51 years of such congresses every 4 years since 1963. Meanwhile, our journal, Pesticide Science/Pest Management Science, has in parallel continually published relevant science for nearly as long (44 years from 1970)., (© 2014 Society of Chemical Industry.)

Phytoglycogen is a highly branched soluble α-glucan found in plants, particularly those with decreased activity of isoamylase-type starch debranching enzyme, such as sugary-1 (su-1) maize. An improved technique has been designed to extract and isolate phytoglycogen from the grain and leaves of su-1 maize with minimal degradation for structural characterisation. The structures of extracted phytoglycogen samples were analysed using size-exclusion chromatography (SEC, also termed GPC) and transmission electron microscopy (TEM) and compared with the structure of pig liver glycogen. The SEC weight molecular size distributions indicate that the extraction procedure with protease is most effective in obtaining pure phytoglycogen from grain, whereas that without protease at cold temperature followed by purification using a sucrose gradient is more effective for leaf material. The extracted and purified phytoglycogen samples from both grain and leaf contain wide distributions of molecular sizes (analysed by SEC and TEM), with the smallest being "individual" β particles, which collectively form larger α particles; the latter are dominant in the phytoglycogen samples examined here. The results show that phytoglycogen is similar to liver glycogen in both the range of molecular size distribution and in the presence of α particles., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Liquid chromatography-mass spectrometry (LC-MS) is considered today as a mainstay tool for the structure characterization of minor components like impurities (IMPs) and degradation products (DPs) in drug substances and products. A multi-step systematic strategy for the purpose involves high resolution mass and multi-stage mass studies on both the drug and IMPs/DPs, followed by comparison of their fragmentation profiles. Its successful application requires consideration of many practical aspects at each step. The same are critically discussed in this review., (Copyright © 2013 Elsevier B.V. All rights reserved.)

This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tools for working with these ontology files are also discussed. The article also examines the "mapping files" used to ensure correct controlled vocabulary terms that are placed within PSI standards and the fulfillment of the MIAPE (Minimum Information about a Proteomics Experiment) requirements. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Neutral Methacrylate Copolymer is a fully polymerised copolymer used in the pharmaceutical industry to permit pH-independent delayed release of active ingredients from oral dosage forms. This function has potential use with food supplements and this article describes available information on the safety of the substance. Oral administration of radiolabelled copolymer to rats resulted in the detection of chemically unchanged copolymer in the faeces, with negligible absorption. Safety studies revealed no adverse toxicity following repeated administration at doses of up to 2000 mg/kg bw/d in a sub-chronic study in rats or 250 mg/kg bw/d in a sub-chronic study in dogs. No reproductive toxicity occurred at up to 2000 mg/kg bw/d in rats or rabbits. The substance shows no evidence of genotoxicity, has low acute toxicity and no irritation or sensitisation potential. An ADI value of 20 mg/kg bw was concluded from two alternative approaches. Daily exposure from use in dietary supplements is estimated as up to 10.0 mg/kg bw in adults and 13.3 mg/kg bw in children. There would therefore appear to be no safety concerns under the intended conditions of use. The information provided is intended to support an evaluation that the substance may be "generally recognized as safe" (GRAS)., (Copyright © 2013 Elsevier Inc. All rights reserved.)

The screening and careful selection of excipients is a critical step in paediatric formulation development as certain excipients acceptable in adult formulations, may not be appropriate for paediatric use. While there is extensive toxicity data that could help in better understanding and highlighting the gaps in toxicity studies, the data are often scattered around the information sources and saddled with incompatible data types and formats. This paper is the second in a series that presents the update on the Safety and Toxicity of Excipients for Paediatrics ("STEP") database being developed by Eu-US PFIs, and describes the architecture data fields and functions of the database. The STEP database is a user designed resource that compiles the safety and toxicity data of excipients that is scattered over various sources and presents it in one freely accessible source. Currently, in the pilot database data from over 2000 references/10 excipients presenting preclinical, clinical, regulatory information and toxicological reviews, with references and source links. The STEP database allows searching "FOR" excipients and "BY" excipients. This dual nature of the STEP database, in which toxicity and safety information can be searched in both directions, makes it unique from existing sources. If the pilot is successful, the aim is to increase the number of excipients in the existing database so that a database large enough to be of practical research use will be available. It is anticipated that this source will prove to be a useful platform for data management and data exchange of excipient safety information., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Statistical principles described in ISO 5725-1 (1994) are a robust basis for evaluating cigarette smoke data from collaborative studies under the ISO 3308 machine smoking and for specifying the criteria for the removal of outlier data and determination of mean yields and their variability. However, the standard only provides recommendations on outlier removal that should be taken into account by experts who undertake data interpretation. The potential for over-interpretation of data from small numbers of laboratories is highlighted and recommendations made to deal with this possibility. Key variables to the statistical analysis, the number of cigarettes per replicate and replicates performed in each laboratory, the number of participating laboratories and the use of linear and rotary smoking machines in smoke collection, are identified and their relevance to obtaining robust data are considered. The statistical methods routinely used for data analysis from the ISO regime, are re-assessed for their suitability to analyse data obtained under the Canadian intense (CI) regime, where yield differences between linear and rotary smoking machines are found. This machine effect can lead to more outliers being detected and difficulties in outlier detection which may affect the provision of robust estimates of mean yields, repeatability and reproducibility., (Copyright © 2013 Elsevier Inc. All rights reserved.)