Archive for the ‘Interesting chemistry’ Category
Monday, December 12th, 2016
Chemical and engineering news (C&EN) is asking people to vote for their molecule of the year from six highlighted candidates. This reminded me of the history of internet-based “molecules of the moment“. It is thought that the concept originated in December 1995 here at Imperial and in January 1996 at Bristol University by Paul May and we were joined by Karl Harrison at Oxford shortly thereafter. Quite a few more such sites followed this concept, differentiated by their time intervals of weeks, months or years. The genre is well suited for internet display because of plugins or “helpers” such as Rasmol, Chime, Jmol and now JSmol which allow the three dimensions of molecular structures to be explored by the reader. Here I discuss a second candidate from the C&EN list; a ferrocene-based Ferris wheel[1],[2] (DOI for 3D model: 10.5517/CCDC.CSD.CC1JPKYQ) originating from research carried out at Imperial by Tim Albrecht, Nick Long and colleagues.
(more…)
References
- M.S. Inkpen, S. Scheerer, M. Linseis, A.J.P. White, R.F. Winter, T. Albrecht, and N.J. Long, "Oligomeric ferrocene rings", Nature Chemistry, vol. 8, pp. 825-830, 2016. https://doi.org/10.1038/nchem.2553
- Inkpen, Michael S.., Scheerer, Stefan., Linseis, Michael., White, Andrew J.P.., Winter, Rainer F.., Albrecht, Tim., and Long, Nicholas J.., "CCDC 1420914: Experimental Crystal Structure Determination", 2016. https://doi.org/10.5517/ccdc.csd.cc1jpkyq
Tags:American Chemical Society, Bristol University, Chemical & Engineering News, Chemistry, Engineering, internet display, Karl Harrison, metal centres, Nick Long, Paul May, Tim Albrecht
Posted in crystal_structure_mining, Interesting chemistry | 2 Comments »
Thursday, December 1st, 2016
Following on from a search for long C-C bonds, here is the same repeated for C=C double bonds.
(more…)
Tags:Chemical bond, chemical bonding, Chemical nomenclature, Chemistry, Conjugated system, double bond, energy, Nature, Nonmetal, Organic chemistry, Physical organic chemistry, search query, Substituent
Posted in crystal_structure_mining, Interesting chemistry | 2 Comments »
Wednesday, November 30th, 2016
In an earlier post, I searched for small C-C-C angles, finding one example that was also accompanied by an apparently exceptionally long C-C bond (2.18Å). But this arose from highly unusual bonding giving rise not to a single bond order but one closer to one half! How long can a “normal” (i.e single) C-C bond get, a question which has long fascinated chemists.
(more…)
Tags:Aviation, Bond order, Carbon–carbon bond, Chemical bond, chemical bonding, naive search, search query, single bond
Posted in crystal_structure_mining, Interesting 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[1] 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.
(more…)
References
- A. Wierzbicki, E.A. Salter, E.A. Cioffi, and E.D. Stevens, "Density Functional Theory and X-ray Investigations of P- and M-Hexamethylene Triperoxide Diamine and Its Dialdehyde Derivative", The Journal of Physical Chemistry A, vol. 105, pp. 8763-8768, 2001. https://doi.org/10.1021/jp0123841
Tags:Amines, Artemisinin, Chemistry, Functional groups, Hexamethylene triperoxide diamine, Organic chemistry, Organic peroxides, Peroxide, perturbation energy interaction, Stereoelectronics
Posted in Interesting chemistry | 1 Comment »
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:
(more…)
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.
(more…)
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 »
Sunday, April 24th, 2016
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.
(more…)
Tags:dielectric, energy, Equilibrium chemistry, Fluorides, free energy, free energy barrier, Hydrogen bond, Hydronium, Inorganic solvents, Lithium fluoride, low energy final geometry corresponds, Oxides, PH, Properties of water, Self-ionization of water, Water, Water model
Posted in Interesting chemistry | 10 Comments »
Friday, April 22nd, 2016
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.
(more…)
Tags:dielectric, energy, free energy, Heat transfer, Heavy water, Kilocalorie per mole, model is to calculate the free energy difference, Properties of water, the free energy, thermodynamics, Tritiated water
Posted in Interesting chemistry | 4 Comments »