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Henry Rzepa's Blog

Henry Rzepa's Blog
Chemistry with a twist
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Crystal_structure_miningChemical ShiftsChloroformDeuterated ChloroformDeuterated MethanolChemical Sciences
Published

Chloroform, often in the deuterated form CDCl 3 , is a very common solvent for NMR and other types of spectroscopy. Quantum mechanics is increasingly used to calculate such spectra to aid assignment and the solvent is here normally simulated as a continuum rather than by explicit inclusion of one or more chloroform molecules. But what are the features of the hydrogen bonds that form from chloroform to other acceptors?

Chemical ITActive SiteBill GatesCity: ReykjavikCountry: IcelandChemical Sciences
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This is sent from the Pidapalooza event in Reykjavik, Iceland, and is a short collection of notable things I learnt or which attracted my attention. Firstly, what IS PIDapalooza [cite]10.5438/11.0001[/cite]? Well, it’s all about persistent identifiers, but don’t let that put you off! Another way of putting it is that it’s a way of finding things scientific on the Web.

Crystal_structure_miningInteresting ChemistryAngleMetalSubtended AngleChemical Sciences
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I am now inverting the previous question by asking what is the largest angle subtended at a chain of three connected 4-coordinate carbon atoms ? Let’s see if further interesting chemistry can be unearthed. Specifying only angles > 130°, the following distribution is obtained.

Crystal_structure_miningReaction MechanismAnimationBicyclic MoleculeChemical RecordChemical Sciences
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Is asking a question such as “what is the smallest angle subtended at a chain of three connected 4-coordinate carbon atoms” just seeking another chemical record, or could it unearth interesting chemistry?

Chemical ITCrystal_structure_miningChemical Sciences
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After sixty years of searching, the first non-templated double helical carbon-free inorganic molecular structure has been reported.[cite]10.1002/adma.201603135[/cite] That is so neat that I thought to load the 3D coordinates here for you to interact with and then to explore the prospect of using these coordinates to add some value with e.g. some chiroptical calculations.

Bradley-Mason Prize For Open ChemistryAnalytical ChemistryChemical InformationChemical InsightCheminformaticsChemical Sciences
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Peter Murray-Rust and I are delighted to announce that the 2016 award of the Bradley-Mason prize for open chemistry goes to Jan Szopinski (UG) and Clyde Fare (PG). Jan’s open chemistry derives from a final year project looking at why atom charges derived from quantum chemical calculation of the electronic density represent chemical information well, but the electrostatic potential (ESP) generated from these charges is very

Reaction MechanismAddition ProductFree-energy PathwayFunctional GroupsImineChemical Sciences
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The story so far. Imines react with a peracid to form either a nitrone (σ-nucleophile) or an oxaziridine (π-nucleophile).[cite]10.1016/S0040-4039(00)98582-4[/cite] The balance between the two is on an experimental knife-edge, being strongly influenced by substituents on the imine.

Interesting ChemistryAminesArtemisininChemistryFunctional GroupsChemical Sciences
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Compounds with O-O bonds often have weird properties. For example, artemisinin, which has some fascinating stereoelectronics. Here is another such, recently in the news and known as HMTD (hexamethylene triperoxide diamine). The crystal structure was reported some time ago[cite]10.1021/jp0123841[/cite] and the article included an inspection of the computed wavefunction.

Crystal_structure_miningReaction MechanismChemical Sciences
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Nucleophiles are species that seek to react with an electron deficient centre by donating a lone or a π-bond pair of electrons. The ambident variety has two or more such possible sources in the same molecule, an example of which might be hydroxylamine or H 2 NOH.