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Henry Rzepa's Blog

Henry Rzepa's Blog
Chemistry with a twist
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Chemical ITAcademic PublishingAutomatic ProcessingData ManagementDigital Object IdentifierQuímicaInglês
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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. The attributes of A[cite]10.1038/sdata.2016.18[/cite] include: (meta)data are retrievable by their identifier using a standardized communication protocol. the protocol is open, free and universally implementable.  the protocol allows for an authentication and authorization procedure.

Interesting ChemistryAnionic Metal SurfaceCambridgeChemical BondingChemistryQuímicaInglês
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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 ).

Chemical ITAcademic PublishingDataCiteDigital Object IdentifierDigital TechnologyQuímicaInglês
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In recent years, findable data has become ever more important (the F in FAIR). Here I test that F using the DataCite search service. Firstly an introduction to this service. This is a metadata database about datasets and other research objects.

Chemical ITAcademic PublishingAmerican Chemical SocietyAuthorBusiness IntelligenceQuímicaInglês
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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.

Reaction MechanismAnimationCarbenium IonCationsChemical ElementsQuímicaInglês
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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.

Chemical ITAmerican National Science FoundationBond LengthChemDrawChemicalQuímicaInglês
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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.

Curly ArrowsInteresting Chemistry/RTActivation EnergyActivation Free EnergyQuímicaInglês
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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.

Interesting ChemistryAaron SwartzAcademic PublishingAPIBusiness IntelligenceQuímicaInglês
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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. Firstly, a reminder that when an article is published, the publisher collects information about the article (the “metadata”) and registers this information with CrossRef in exchange for a DOI.

Interesting ChemistryBiblical ManuscriptsBook DesignBook Of KellsBooksQuímicaInglês
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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.  I thought it would be of interest to list how these colours were achieved. Black ink was made from oak-galls mixed with iron sulfate and acetic acid from wine or vinegar.