Posts Tagged ‘Chemistry’
Monday, October 31st, 2016
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?
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Tags:animation, Bicyclic molecule, chemical record, Chemistry, City: Cambridge, Cycloalkane, Cyclopropanes, Java, Molecular geometry, Organic chemistry, potential energy surface, Safari, Web browser, X-ray
Posted in crystal_structure_mining, reaction mechanism | 7 Comments »
Tuesday, October 4th, 2016
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).
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Tags:Analytical chemistry, chemical information, chemical insight, Cheminformatics, Chemistry, Chemometrics, Clyde Fare, Company: GitHub, computation chemical research projects, computational chemistry, computing, Cross-platform software, driver, GitHub, Jan Szopinski, machine learning, open sourcing software development, opensource healthchecker software, Peter Murray-Rust, public web sites, Python, quantum chemical calculation, quantum chemical codes, quantum chemical data, quantum chemical research, Quotation, Server & Database Software, simulation, Software, supervisor, sustainable software conference prize, Technology/Internet
Posted in Bradley-Mason Prize for Open Chemistry | No Comments »
Thursday, September 22nd, 2016
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. However this did not look at the potential stereoelectronics in this species, which I now address here.
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Tags:Amines, Artemisinin, Chemistry, Functional groups, Hexamethylene triperoxide diamine, Organic chemistry, Organic peroxides, Peroxide, perturbation energy interaction, Stereoelectronics
Posted in Interesting chemistry | 1 Comment »
Thursday, September 1st, 2016
Bromoallene is a pretty simple molecule, with two non-equivalent double bonds. How might it react with an electrophile, say dimethyldioxirane (DMDO) to form an epoxide?[cite]10.1039/C6CC06395K[/cite] Here I explore the difference between two different and very simple approaches to predicting its reactivity. 
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Tags:chemical bonding, chemical reaction, Chemistry, Delocalized electron, double bond, energy, energy difference, HOMO/LUMO, lowest energy, Molecular orbital, Natural bond orbital, Nature, Physics, Quantum chemistry, stable HOMO-1
Posted in reaction mechanism | No Comments »
Monday, August 8th, 2016
The previous post contained an exploration of the anomeric effect as it occurs at an atom centre X for which the effect is manifest in crystal structures. Here I quantify the effect, by selecting the test molecule MeO-X-OMe, where X is of two types:
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Tags:Anomer, Anomeric effect, Atomic orbital, Carbohydrate chemistry, Carbohydrates, Chemical bond, chemical bonding, Chemistry, Hydrogen bond, interaction energy, Lone pair, Physical organic chemistry, Quantum chemistry
Posted in Interesting chemistry | No Comments »
Saturday, August 6th, 2016
In the last few posts, I have explored the anomeric effect as it occurs at an atom centre X. Here I try to summarise the atoms for which the effect is manifest in crystal structures.
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Tags:Acetals, Alkane stereochemistry, Anomer, Anomeric effect, Atomic orbital, Carbohydrate chemistry, Carbohydrates, Chemical bond, Chemistry, interaction energy, Lone pair, Physical organic chemistry, Stereochemistry
Posted in crystal_structure_mining, Interesting chemistry | No Comments »
Monday, August 1st, 2016
In March, I posted from the ACS meeting in San Diego on the topic of Research data: Managing spectroscopy-NMR, and noted a talk by MestreLab Research on how a tool called Mpublish in the forthcoming release of their NMR analysis software Mestrenova could help. With that release now out, the opportunity arose to test the system.
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Tags:Acrobat, analysis software, chemical, Chemistry, City: San Diego, format type chemical/x-mnpub, media type, Mestrenova, non-commercial open software packages, Nuclear magnetic resonance, Nuclear magnetic resonance spectra database, Nuclear magnetic resonance spectroscopy, PDF, public key, Science, Scientific method, spectroscopy, Technology/Internet
Posted in Chemical IT | 3 Comments »
Friday, July 8th, 2016
The previous post looked at anomeric effects set up on centres such as B, Si or P, and involving two oxygen groups attached to these atoms. Here I vary the attached groups to include either one or two nitrogen atoms.[cite]10.14469/hpc/936[/cite]
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Tags:Anomer, Anomeric effect, Carbohydrate chemistry, Carbohydrate conformation, Carbohydrates, Chemistry, Nitrogen
Posted in crystal_structure_mining | No Comments »
Friday, June 12th, 2015
In the preceding post, I discussed the reaction between mCPBA (meta-chloroperbenzoic acid) and cyclohexanone, resulting in Baeyer-Villiger oxidation via a tetrahedral intermediate (TI). Dan Singleton, in whose group the original KIE (kinetic isotope measurements) were made, has kindly pointed out on this blog that his was a mixed-phase reaction, and that mechanistic comparison with homogenous solutions may not be justified. An intriguing aspect of the (solution) mechanism would be whether the TI forms quickly and/or reversibly and what the position of any equilibrium between it and the starting ketone is. This reminded me of work we did some years ago,[cite]10.1021/jo00389a050[/cite] and here I discuss that.
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Tags:Anomer, Anomeric effect, Carbohydrate chemistry, Carbohydrates, Chemistry, Dan Singleton, homogenous solutions, Ketone, Meta-Chloroperoxybenzoic acid, Organic chemistry, Tetrahedral carbonyl addition compound
Posted in reaction mechanism | 2 Comments »
Wednesday, June 10th, 2015
I have blogged before about the mechanism of this classical oxidation reaction. Here I further explore computed models, and whether they match the observed kinetic isotope effects (KIE) obtained using the natural-abundance method described in the previous post.
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Tags:ATM, Baeyer–Villiger oxidation, Chemistry, Dipole, energy, energy gradient, Kinetic isotope effect, Physical organic chemistry
Posted in reaction mechanism | 4 Comments »