Nucleoside and Nucleotide Nomenclature

Current nomenclature in the area of nucleosides, nucleotides, and nucleic acids comprises a mixture of (1) common names that have gained official recognition, (2) guidelines that have been derived and officially recommended by the International Union of Pure and Applied Chemistry (IUPAC)/International Union of Biochemistry and Molecular Biology (IUBMB), and (3) evolving usage that is derived by individual scientists and laboratories and subjected to peer review through publication. A working group was commissioned in 1998 by IUBMB to review guidelines for nucleotide (including oligonucleotide) nomenclature. As those guidelines are developed and made available, they will be referenced in future updates of this appendix. The main purpose of this appendix is to provide pertinent references that will direct the reader to the relevant guidelines or evolving nomenclature as described in the literature. When additional suggestions or guidance are appropriate, those comments are included as well.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143595/1/cpnca01d.pd

A ‘Periodic Table’ of mass spectrometry instrumentation and acronyms

The number of acronyms in mass spectrometry (MS) and hyphenated techniques are growing rapidly. The ever-widening range of users of MS technology has led to variations in terminology and how it has been applied. The International Union of Pure and Applied Chemistry (IUPAC) has undertaken a review of MS nomenclature resulting in an extensive publication, describing over 500 terms, and is the defining resource for mass spectrometrists. However, for less experienced users of MS, this IUPAC document may require greater explanation as it is not intended to explain the basis of these terms. Given this, the Analytical Methods Committee (AMC) of the Royal Society of Chemistry highlighted an alternative text was required to help understand these terms, how and why they are used in combination, that may be accessible to non-MS experts. This manuscript describes the structure of typical MS instrumentation (sample introduction, ionisation source, mass analyser, detector, data acquisition/processing) and hyphenated technologies whereby each section is discussed and summarised in context and presented as a recognisable tabulated format

Characterization of surface and porous properties of synthetic hybrid lamellar silica

Synthetic lamellar silica and hybrid lamellar silicas have been prepared by liquid crystal templating, template extraction and silanization. The samples have been characterized by thermogravimetric analysis (TGA), carbon analysis, spectroscopy, X-ray diffraction (XRD) and nitrogen adsorption. The XRD analyses have shown that the lamellar periodic stacking is preserved for all samples. The quantity and type of organic molecules at the silica surface have been evaluated by carbon analysis, TGA and spectroscopy. The covalent grafting of the solvent used for extraction of the initial surfactant has been highlighted by these analyses. The nitrogen adsorption analyses have revealed three categories of pores and two types of samples. The initial lamellar silica exhibits a very low specific surface area and plate-like type of pores. The second type of samples is made up of the hybrid samples and the initial substrate from whom the surfactant has been extracted. These samples show a significantly higher specific surface area with interlamellar spaces corresponding to narrow-slit like mesopores around 4 nm. The nitrogen adsorption data analysis has highlighted the presence of micropores within the silica sheets. The difference of the specific surface is due to pore blocking by the surfactant impeding the access to nitrogen into interlamellar spaces and by the silanes covering the pores once the surface modified. The presence of micro and mesopores combined to a high BET specific surface of 612 m²/g makes these lamellar silicas interesting materials for catalysis applications.Peer reviewe

Graphenes as Metal-Free Catalysts with Engineered Active Sites

[EN] This Perspective article highlights how recent discoveries on the activity of defective graphene to promote different organic reactions as metal-free catalysts has led to propose certain substructures present on these defective graphenes as active sites. The sustainability of using as catalysts graphenes obtained from biomass and the possibility to generate active sites by introducing defects on the sheet are the two main characteristics triggering research in this area. Emphasis is made in the need to gain understanding on the nature of the active sites and how this understanding requires the combination of conventional kinetic experiments as well as advanced characterization tools. The relationship between catalysis by graphene and that by organocatalysis has also been remarked.Financial support by the Spanish Ministry of Economy and Competitiveness (Severo Ochoa, Grapas, and CTQ2015-69153-CO2-1) and Generalitat Valenciana (Prometo 2013-014) is gratefully acknowledged. A.P. also thanks the Spanish Ministry of Economy and Competitiveness for a Ramon y Cajal research associate contract.Primo Arnau, AM.; Parvulescu, V.; García Gómez, H. (2017). Graphenes as Metal-Free Catalysts with Engineered Active Sites. The Journal of Physical Chemistry Letters. 8(1):264-278. https://doi.org/10.1021/acs.jpclett.6b01996S2642788

Evaluated kinetic and photochemical data for atmospheric chemistry: Volume II – gas phase reactions of organic species

This article, the second in the series, presents kinetic and photochemical data evaluated by the IUPAC Subcommittee on Gas Kinetic Data Evaluation for Atmospheric Chemistry. It covers the gas phase and photochemical reactions of Organic species, which were last published in 1999, and were updated on the IUPAC website in late 2002, and subsequently during the preparation of this article. The article consists of a summary table of the recommended rate coefficients, containing the recommended kinetic parameters for the evaluated reactions, and eight appendices containing the data sheets, which provide information upon which the recommendations are made

The derivation of the formyl-group oxygen of chlorophyll b in higher plants from molecular oxygen.

The mechanism of formation of the formyl group of chlorophyll b has long been obscure but, in this paper, the origin of the 7-formyl-group oxygen of chlorophyll b in higher plants was determined by greening etiolated maize leaves, excised from dark-grown plants, by illumination under white light in the presence of either H218O or 18O2 and examining the newly synthesized chlorophylls by mass spectroscopy. To minimize the possible loss of 18O label from the 7-formyl substituent by reversible formation of chlorophyll b-71-gem-diol (hydrate) with unlabelled water in the cell, the formyl group was reduced to a hydroxymethyl group during extraction with methanol containing NaBH4: chlorophyll a remained unchanged during this rapid reductive extraction process. Mass spectra of chlorophyll a and [7-hydroxymethyl]-chlorophyll b extracted from leaves greened in the presence of either H218O or 18O2 revealed that 18O was incorporated only from molecular oxygen but into both chlorophylls: the mass spectra were consistent with molecular oxygen providing an oxygen atom not only for incorporation into the 7-formyl group of chlorophyll b but also for the well-documented incorporation into the 131-oxo group of both chlorophylls a and b [see Walker, C. J., Mansfield, K. E., Smith, K. M. & Castelfranco, P. A. (1989) Biochem. J. 257, 599–602]. The incorporation of isotope led to as much as 77% enrichment of the 131-oxo group of chlorophyll a: assuming identical incorporation into the 131 oxygen of chlorophyll b, then enrichment of the 7-formyl oxygen was as much as 93%. Isotope dilution by re-incorporation of photosynthetically produced oxygen from unlabelled water was negligible as shown by a greening experiment in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea. The high enrichment using 18O2, and the absence of labelling by H218O, unequivocally demonstrates that molecular oxygen is the sole precursor of the 7-formyl oxygen of chlorophyll b in higher plants and strongly suggests a single pathway for the formation of the chlorophyll b formyl group involving the participation of an oxygenase-type enzyme

The effect of ultrasound pretreatment on some selected physicochemical properties of black cumin (Nigella Sativa)

Background In the present study, the effects of ultrasound pretreatment parameters including irradiation time and power on the quantity of the extracted phenolic compounds quantity as well as on some selected physicochemical properties of the extracted oils including oil extraction efficiency, acidity and peroxide values, color, and refractive index of the extracted oil of black cumin seeds with the use of cold press have been studied. Methods For each parameter, three different levels (30, 60, and 90 W) for the ultrasound power and (30, 45, and 60 min) and for the ultrasound irradiation time were studied. Each experiment was performed in three replications. Results The achieved results revealed that, with enhancements in the applied ultrasound power, the oil extraction efficiency, acidity value, total phenolic content, peroxide value, and color parameters increased significantly (P 0.05). Conclusions In summary, it could be mentioned that the application of ultrasound pretreatment in the oil extraction might improve the oil extraction efficiency, the extracted oil’s quality, and the extracted phenolic compounds content.info:eu-repo/semantics/publishedVersio