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Henry Rzepa's Blog

Henry Rzepa's Blog
Chemistry with a twist
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Chemical ITCrystal_structure_miningComputingContextDataCiencias QuímicasInglés
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FAIR data is increasingly accepted as a description of what research data should aspire to; **F**indable, **A**ccessible, **I**nter-operable and R e-usable, with Context added by rich metadata (and also that it should be Open). But there are two sides to data, one of which is the raw data emerging from say an instrument or software simulations and the other in which some kind of model is applied to produce semi-

HistoricalHypervalency1-DecyneCH2Chemical BondingCiencias QuímicasInglés
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I started this story by looking at octet expansion and hypervalence in non-polar hypercoordinate species such as S(-CH 3 ) 6 , then moved on to S(=CH 2 ) 3 . Finally now its the turn of S(≡CH) 2 . As the triple bonds imply, this seems to represent twelve shared valence electrons surround the sulfur, six from S itself and three from each carbon.

HypervalencyChemical BondChemical BondingChemical PolarityChemistryCiencias QuímicasInglés
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Previously: “Non-polar” species such as SeMe6, SMe6, ClMe3, ClMe5 all revealed interesting properties for the Se-C, S-C or Cl-C “single” bonds. The latter two examples in particular hinted at internal structures for these single bonds, as manifested by two ELF basins for some of the bonds.

Chemical ITChemistComputingInformationInformation ScienceCiencias QuímicasInglés
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PIDapalooza is a new forum concerned with discussing all things persistent, hence PID. You might wonder what possible interest a chemist might have in such an apparently arcane subject, but think of it in terms of how to find the proverbial needle in a haystack in a time when needles might look all very similar.

Chemical ITHypervalencyChemical BondChemical BondingChemistryCiencias QuímicasInglés
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A few years back, I took a look at the valence-shell electron pair repulsion approach to the geometry of chlorine trifluoride, ClF 3 using so-called ELF basins to locate centroids for both the covalent F-Cl bond electrons and the chlorine lone-pair electrons.

HypervalencyChemical BondingCity: AachenHypervalent MoleculeMolecular GeometryCiencias QuímicasInglés
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One thread that runs through this blog is that of hypervalency. It was therefore nice to come across a recent review of the concept[cite]10.1039/c5sc02076j[/cite] which revisits the topic, and where a helpful summary is given of the evolving meanings over time of the term hypervalent.

Crystal_structure_miningBondBond Valence MethodChemical BondChemical BondingCiencias QuímicasInglés
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An N-B single bond is iso-electronic to a C-C single bond, as per below. So here is a simple question: what form does the distribution of the lengths of these two bonds take, as obtained from crystal structures?  The Conquest search query is very simple (no disorder, no errors). When applied to the Cambridge structure database (CSD) the following two distributions are obtained.

Chemical ITGeneralAcademic PublishingArticle Processing ChargeAuthorCiencias QuímicasInglés
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We have heard a lot about OA or Open Access (of journal articles) in the last five years, often in association with the APC (Article Processing Charge) model of funding such OA availability. Rather less discussed is how the model of the peer review of these articles might also evolve into an Open environment. Here I muse about two experiences I had recently.

PericyclicReaction MechanismAnimationBicyclic Ring ProductEnergy Derivative Gradient NormCiencias QuímicasInglés
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I noted in my WATOC conference report a presentation describing the use of calculated reaction barriers (and derived rate constants) as mechanistic reality checks. Computations, it was claimed, have now reached a level of accuracy whereby a barrier calculated as being 6 kcal/mol too high can start ringing mechanistic alarm bells.