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Henry Rzepa's Blog

Henry Rzepa's Blog
Chemistry with a twist
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Chemical ITAcademic PublishingChemical IdentifiersChemical Names and Chemical TermsChemical Tagger PageCiencias QuímicasInglés
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I occasionally post about "RDM" (research data management), an activity that has recently become a formalised essential part of the research processes. I say recently formalised, since researchers have of course kept research notebooks recording their activities and their data since the dawn of science, but not always in an open and transparent manner.

Chemical ITCrystal_structure_miningBasesBürgi–Dunitz AngleCarbonylCiencias QuímicasInglés
Publicado

I have previously commented on the Bürgi–Dunitz angle, this being the preferred approach trajectory of a nucleophile towards the electrophilic carbon of a carbonyl group. Some special types of nucleophile such as hydrazines (R 2 N-NR 2 ) are supposed to have enhanced reactivity[cite]10.1016/S0040-4020(01)93101-1[/cite] due to what might be described as buttressing of adjacent lone pairs.

Interesting ChemistryDielectricEnergyEquilibrium ChemistryFluoridesCiencias QuímicasInglés
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The autoionization of water involves two molecules transfering a proton to give hydronium hydroxide, a process for which the free energy of reaction is well known. Here I ask what might happen with the next element along in the periodic table, F. I have been unable to find much about the autoionization of HF in the literature;

Interesting ChemistryDielectricEnergyFree EnergyHeat TransferCiencias QuímicasInglés
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Earlier, I constructed a possible model of hydronium hydroxide, or H3O+.OH– One way of assessing the quality of the model is to calculate the free energy difference between it and two normal water molecules and compare the result to the measured difference. Here I apply a further test of the model using isotopes.

Chemical IT10.17616Academic PublishingDataCiteEnergy Profile DiagramsCiencias QuímicasInglés
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I want to describe a recent attempt by a group of collaborators to share the research data associated with their just published article.[cite]10.1021/jacs.5b13070[/cite] I am here introducing things in a hierarchical form (i.e. not necessarily the serial order in which actions were taken). The data repository selected for the data sharing is described by (m3data) doi: 10.17616/R3K64N[cite]10.17616/R3K64N[/cite] A collaborative

Chemical ITAcademic PublishingAutomated Software AnalysisBASEChemical ContextCiencias QuímicasInglés
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Scientists are familiar with the term data, at least in a scientific or chemical context, but appreciating metadata (meaning "after", or "beyond") is slightly more subtle, in the sense of using it to mean data about data. The challenge lies in clarifying where the boundary between data and its metadata lies and in specifying and controlling the vocabulary used for these metadata descriptions.

GeneralInteresting ChemistryAmmoniaAqueous SolutionsBasesCiencias QuímicasInglés
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In the previous post I described how hydronium hydroxide or H3O+…HO–, an intermolecular tautomer of water, has recently been observed captured inside an organic cage[cite]10.1002/chem.201406383[/cite] and how the free-standing species in water can be captured computationally with the help of solvating water bridges.

Chemical ITAcademic PublishingEmbargoOpen AccessPublishingCiencias QuímicasInglés
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Publishing embargoes seem a relatively new phenomenon, probably starting in areas of science when the data produced for a scientific article was considered more valuable than the narrative of that article. However, the concept of the embargo seems to be spreading to cover other aspects of publishing, and I came across one recently which appears to take such embargoes into new and uncharted territory.