October 13th, 2016
Chemists are as fond of records as any, although I doubt you will find many chemical ones in the Guinness world records list. Polytriangulanes chase how many cyclopropyl 3-rings can be joined via a vertex. Steve Bachrach on his blog reports some recent work by Peter Schreiner and colleagues[1] and the record for catenation of such rings appears to be 15. This led me to think about some other common atoms and groups. Here I have searched for crystal structures only; there may be examples of course for which no such data has been reported.
Read the rest of this entry »
References
- W.D. Allen, H. Quanz, and P.R. Schreiner, "Polytriangulane", Journal of Chemical Theory and Computation, vol. 12, pp. 4707-4716, 2016. https://doi.org/10.1021/acs.jctc.6b00669
Posted in crystal_structure_mining | 3 Comments »
October 4th, 2016
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 »
September 28th, 2016
The story so far. Imines react with a peracid to form either a nitrone (σ-nucleophile) or an oxaziridine (π-nucleophile).[1] The balance between the two is on an experimental knife-edge, being strongly influenced by substituents on the imine. Modelling these reactions using the “normal” mechanism for peracid oxidation did not reproduce this knife-edge, with ΔΔG (π-σ) 16.2 kcal/mol being rather too far from a fine balance.
Read the rest of this entry »
References
- D.R. Boyd, P.B. Coulter, N.D. Sharma, W. Jennings, and V.E. Wilson, "Normal, abnormal and pseudo-abnormal reaction pathways for the imine-peroxyacid reaction", Tetrahedron Letters, vol. 26, pp. 1673-1676, 1985. https://doi.org/10.1016/s0040-4039(00)98582-4
Tags: addition product, free-energy pathway, Functional groups, Imine, Nitrone, Nucleophile, Organic chemistry, Oxaziridine
Posted in reaction mechanism | No Comments »
September 22nd, 2016
Warning: Trying to access array offset on value of type null in
/var/www/html/rzepa/blog/wp-content/plugins/kcite-1.7.97/kcite.php on line
1013
Tags: Amines, Artemisinin, Chemistry, Functional groups, Hexamethylene triperoxide diamine, Organic chemistry, Organic peroxides, Peroxide, perturbation energy interaction, Stereoelectronics
Posted in Interesting chemistry | 1 Comment »
September 21st, 2016
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 H2NOH. I previously discussed how for this example, the energetics allow the nitrogen lone pair (Lp) to win out over the O Lp. Here, I play a similar game, but this time setting an NLp up against a π-pair.
Read the rest of this entry »
Posted in crystal_structure_mining, reaction mechanism | No Comments »
September 19th, 2016
I previously explored stabilized “carbenes” with the formal structures (R2N)2C:, concluding that perhaps the alternative ionic representation R2N+=C–NR2 might reflect their structures better. Here I take a broader look at the “carbene” landscape before asking the question “what about nitrenes?”
Read the rest of this entry »
Posted in crystal_structure_mining | 1 Comment »
September 11th, 2016
To quote from Wikipedia: in chemistry, a carbene is a molecule containing a neutral carbon atom with a valence of two and two unshared valence electrons. The most ubiquitous type of carbene of recent times is the one shown below as 1, often referred to as a resonance stabilised or persistent carbene. This type is of interest because of its ability to act as a ligand to an astonishingly wide variety of metals, with many of the resulting complexes being important catalysts. The Wiki page on persistent carbenes shows them throughout in form 1 below, thus reinforcing the belief that they have a valence of two and by implication six (2×2 shared + 2 unshared) electrons in the valence shell of carbon. Here I consider whether this name is really appropriate.
Read the rest of this entry »
Tags: Carbenes, chemical bonding, energy barrier, free energy, Functional groups, Ligand, Mesoionic carbene, Organometallic chemistry, Persistent carbene, quantum mechanical solution, Reactive intermediates, Transition metal carbene complex, Valence, Valence electron
Posted in crystal_structure_mining, General | No Comments »
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?[1] Here I explore the difference between two different and very simple approaches to predicting its reactivity. 
Read the rest of this entry »
References
- D. Christopher Braddock, A. Mahtey, H.S. Rzepa, and A.J.P. White, "Stable bromoallene oxides", Chemical Communications, vol. 52, pp. 11219-11222, 2016. https://doi.org/10.1039/c6cc06395k
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 »
August 17th, 2016
In the previous post, I noted that a chemistry publisher is about to repeat an earlier experiment in serving pre-prints of journal articles. It would be fair to suggest that following the first great period of journal innovation, the boom in rapid publication “camera-ready” articles in the 1960s, the next period of rapid innovation started around 1994 driven by the uptake of the World-Wide-Web. The CLIC project[1] aimed to embed additional data-based components into the online presentation of the journal Chem Communications, taking the form of pop-up interactive 3D molecular models and spectra. The Internet Journal of Chemistry was designed from scratch to take advantage of this new medium.[2] Here I take a look at one recent experiment in innovation which incorporates “augmented reality”.[3]
Read the rest of this entry »
References
- D. James, B.J. Whitaker, C. Hildyard, H.S. Rzepa, O. Casher, J.M. Goodman, D. Riddick, and P. Murray‐Rust, "The case for content integrity in electronic chemistry journals: The CLIC project", New Review of Information Networking, vol. 1, pp. 61-69, 1995. https://doi.org/10.1080/13614579509516846
- S.M. Bachrach, and S.R. Heller, "The<i>Internet Journal of Chemistry:</i>A Case Study of an Electronic Chemistry Journal", Serials Review, vol. 26, pp. 3-14, 2000. https://doi.org/10.1080/00987913.2000.10764578
- S. Ley, B. Musio, F. Mariani, E. Śliwiński, M. Kabeshov, and H. Odajima, "Combination of Enabling Technologies to Improve and Describe the Stereoselectivity of Wolff–Staudinger Cascade Reaction", Synthesis, vol. 48, pp. 3515-3526, 2016. https://doi.org/10.1055/s-0035-1562579
Tags: Academia, Academic publishing, Boom, Design, Design Services, Innovation, Internet Journal, online presentation, Preprint, Publishing, reaction energy profile, technology helps, Web browser, web-based molecular viewer
Posted in General | 1 Comment »