April 18th, 2019
In a previous post, I looked at the Findability of FAIR data in common chemistry journals. Here I move on to the next letter, the A = Accessible.
Read the rest of this entry »
Tags: Academic publishing, automatic processing, Data management, Digital Object Identifier, EIDR, FAIR data, Findability, Identifiers, Information, Information architecture, Information science, Knowledge, Knowledge representation, metadata, mining, Open Archives Initiative, RDF, Records management, representative, standardized communication protocol, Technical communication, Technology/Internet, Web design, Written communication, XML
Posted in Chemical IT | No Comments »
April 18th, 2019
The topic of this post originates from a recent article which is attracting much attention.[cite]10.1038/s41586-019-1059-9[/cite] The technique uses confined light to both increase the spatial resolution by around three orders of magnitude and also to amplify the signal from individual molecules to the point it can be recorded. To me, Figure 3 in this article summarises it nicely (caption: visualization of vibrational normal modes). Here I intend to show selected modes as animated and rotatable 3D models with the help of their calculation using density functional theory (a mode of presentation that the confinement of Figure 3 to the pages of a conventional journal article does not enable).
Read the rest of this entry »
Tags: anionic metal surface, Cambridge, chemical bonding, Chemistry, dihedral, energy, flat metal surface, metal, Natural sciences, Neutral Quartet, Physical sciences, Raman scattering, Raman spectroscopy, Resonance, spectroscopy, steric repulsion energy
Posted in Interesting chemistry | No Comments »
April 12th, 2019
In recent years, findable data has become ever more important (the F in FAIR). Here I test that F using the DataCite search service.
Read the rest of this entry »
Tags: Academic publishing, DataCite, Digital Object Identifier, Digital technology, Elsevier, Findability, Identifiers, Information, Information architecture, Information science, Knowledge, Knowledge representation, search service, Web design
Posted in Chemical IT | 1 Comment »
April 8th, 2019
The conventional procedures for reporting analysis or new results in science is to compose an “article”, augment that perhaps with “supporting information” or “SI”, submit to a journal which undertakes peer review, with revision as necessary for acceptance and finally publication. If errors in the original are later identified, a separate corrigendum can be submitted to the same journal, although this is relatively rare. Any new information which appears post-publication is then considered for a new article, and the cycle continues. Here I consider the possibilities for variations in this sequence of events.
Read the rest of this entry »
Tags: Academic publishing, American Chemical Society, author, Business intelligence, Company: DataCite, CrossRef, data, Data management, DataCite, editor, EIDR, Information, Information science, JSON, Knowledge representation, Metadata repository, Records management, Technology/Internet, The Metadata Company
Posted in Chemical IT | No Comments »
April 4th, 2019
Previously, I explored the Graham reaction to form a diazirine. The second phase of the reaction involved an Sn2′ displacement of N-Cl forming C-Cl. Here I ask how facile the simpler displacement of C-Cl by another chlorine might be and whether the mechanism is Sn2 or the alternative Sn1.
The reason for posing this question is that as an Sn1 reaction, simply ionizing off the chlorine to form a diazacyclopropenium cation might be a very easy process. Why? Because the resulting cation is analogous to the cyclopropenium cation, famously proposed by Breslow as the first example of a 4n+2 aromatic ring for which the value of n is zero and not 1 as for benzene.[cite]10.1021/ja01576a067[/cite] Another example of a famous “Sn1” reaction is the solvolysis of t-butyl chloride to form the very stable tertiary carbocation and chloride anion (except in fact that it is not an Sn1 reaction but an Sn2 one!)
Read the rest of this entry »
Tags: animation, Carbenium ion, Cations, Chemical elements, chemical reaction, Chemistry, Chlorine, computational chemistry, Cyclopropenium ion, Diazirine, energy, energy profile, free energy, Halogens, Natural sciences, Nucleophilic aromatic substitution, Oxidizing agents, Physical sciences, potential energy surface, SN1 reaction, Substitution reactions
Posted in reaction mechanism | No Comments »
April 1st, 2019
Members of the chemical FAIR data community have just met in Orlando (with help from the NSF, the American National Science Foundation) to discuss how such data is progressing in chemistry. There are a lot of themes converging at the moment. Thus this article[cite]10.1039/c7np00064b[/cite] extolls the virtues of having raw NMR data available in natural product research, to which we added that such raw data should also be made FAIR (Findable, Accessible, Interoperable and Reusable) by virtue of adding rich metadata and then properly registering it so that it can be searched. These themes are combined in another article which made a recent appearance.[cite]10.1021/acsomega.8b03005[/cite]
Read the rest of this entry »
Tags: American National Science Foundation, Bond length, ChemDraw, chemical, Chemistry, City: Orlando, Company: NSF, Force field, Intermolecular forces, Molecular geometry, National Science Foundation, natural product, Natural sciences, Orlando, Physical organic chemistry, Physical sciences, Quantum chemistry, Science and technology in the United States, Stereochemistry, steric energy, steric energy test, Strain, suitable free tool, unstable natural product, X-ray
Posted in Chemical IT | No Comments »
March 24th, 2019
There is a predilection amongst chemists for collecting records; one common theme is the length of particular bonds, either the shortest or the longest. A particularly baffling type of bond is that between the very electronegative F atom and an acid hydrogen atom such as that in OH. Thus short C-N…HO hydrogen bonds are extremely common, as are C-O…HO.‡ But F atoms in C-F bonds are largely thought to be inert to hydrogen bonding, as indicated by the use of fluorine in many pharmaceuticals as inert isosteres.[cite]10.1039/B610213C[/cite] Here I do an up-to-date search of the CSD crystal structure database, which is now on the verge of accumulating 1 million entries, to see if any strong C-F…HO hydrogen bonding may have been recently discovered.
Read the rest of this entry »
Tags: Chemical bond, chemical bonding, Chemical elements, Chemistry, Fluorine, Hydrogen, Hydrogen bond, Intermolecular forces, Natural sciences, perturbation energy, pharmaceuticals, Physical sciences, Refrigerants, search parameters, search query, Supramolecular chemistry
Posted in crystal_structure_mining | No Comments »
February 18th, 2019
Students learning organic chemistry are often asked in examinations and tutorials to devise the mechanisms (as represented by curly arrows) for the core corpus of important reactions, with the purpose of learning skills that allow them to go on to improvise mechanisms for new reactions. A common question asked by students is how should such mechanisms be presented in an exam in order to gain full credit? Alternatively, is there a single correct mechanism for any given reaction? To which the lecturer or tutor will often respond that any reasonable mechanism will receive such credit. The implication is that a mechanism is “reasonable” if it “follows the rules”. The rules are rarely declared fully, but seem to be part of the absorbed but often mysterious skill acquired in learning the subject. These rules also include those governing how the curly arrows should be drawn.† Here I explore this topic using the Graham reaction.[cite]10.1021/ja00947a040[/cite]‡
Read the rest of this entry »
Tags: /RT, activation energy, activation free energy, animation, arrow pushing, arrow-head, cellular telephone, Chemical kinetics, chemical reaction, Chemistry, computed energy, Ed Smith, energy, energy maximum, energy minima, energy plot, energy profile, energy surface, free energy, lecturer, mechanism, Natural sciences, Organic chemistry, overall reaction energy, Physical sciences, Reaction rate constant, Resonance, Transition state, Transition state theory, tutor, Tutorial
Posted in Curly arrows, Interesting chemistry | No Comments »
February 16th, 2019
The title of this post comes from the site www.crossref.org/members/prep/ Here you can explore how your favourite publisher of scientific articles exposes metadata for their journal.
Read the rest of this entry »
Tags: Aaron Swartz, Academic publishing, API, Business intelligence, CrossRef, data, Data management, Elsevier, favourite publisher, Identifiers, Information, Information science, Knowledge, Knowledge representation, metadata, mining, ORCiD, PDF, Pre-exposure prophylaxis, Publishing, Publishing Requirements for Industry Standard Metadata, Records management, Research Object, Scholarly communication, Scientific literature, search engine, social media, Technical communication, Technology/Internet, text mining, Written communication, XML
Posted in Interesting chemistry | 1 Comment »
January 22nd, 2019
The Book of Kells is a spectacularly illuminated gospel manuscript dating from around 800AD and held in Trinity College library in Dublin. Some idea of the colours achieved can be seen below.
Read the rest of this entry »
Tags: Biblical manuscripts, Book design, Book of Kells, Books, City: Dublin, County Meath, Dublin, Hospitality/Recreation, Illuminated manuscript, Kells, Manuscripts, Trinity College, Trinity College Dublin, Trinity College Library, Trinity College Library Dublin, Western art, Woad plant
Posted in Interesting chemistry | No Comments »