Posts Tagged ‘chemical bonding’
Thursday, March 23rd, 2017
It is not only the non-classical norbornyl cation that has proved controversial in the past. A colleague mentioned at lunch (thanks Paul!) that tri-coordinate group 14 cations such as R3Si+ have also had an interesting history.[1] Here I take a brief look at some of these systems.
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References
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J.B. Lambert, Y. Zhao, H. Wu, W.C. Tse, and B. Kuhlmann, "The Allyl Leaving Group Approach to Tricoordinate Silyl, Germyl, and Stannyl Cations", Journal of the American Chemical Society, vol. 121, pp. 5001-5008, 1999. http://dx.doi.org/10.1021/ja990389u
Tags:2-Norbornyl cation, Carbocations, chemical bonding, Chemistry, metal, Physical organic chemistry, Reactive intermediates, search query, tri-coordinate
Posted in crystal_structure_mining | 8 Comments »
Friday, March 10th, 2017
A few years back, I did a post about the Pirkle reagent[1] and the unusual π-facial hydrogen bonding structure[2] it exhibits. For the Pirkle reagent, this bonding manifests as a close contact between the acidic OH hydrogen and the edge of a phenyl ring; the hydrogen bond is off-centre from the middle of the aryl ring. Here I update the topic, with a new search of the CSD (Cambridge structure database), but this time looking at the positional preference of that bond and whether it is on or off-centre.
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References
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H.S. Rzepa, M.L. Webb, A.M.Z. Slawin, and D.J. Williams, "? Facial hydrogen bonding in the chiral resolving agent (S)-2,2,2-trifluoro-1-(9-anthryl)ethanol and its racemic modification", Journal of the Chemical Society, Chemical Communications, pp. 765, 1991. http://dx.doi.org/10.1039/c39910000765
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H.S. Rzepa, M.H. Smith, and M.L. Webb, "A crystallographic AM1 and PM3 SCF-MO investigation of strong OH ⋯π-alkene and alkyne hydrogen bonding interactions", J. Chem. Soc., Perkin Trans. 2, pp. 703-707, 1994. http://dx.doi.org/10.1039/P29940000703
Tags:Ammonia, Ammonium, aromaticity, Cations, Centroid, chemical bonding, Chemistry, Hydrogen bond, Phenyl group
Posted in crystal_structure_mining | No Comments »
Thursday, March 2nd, 2017
The thread thus far. The post about Na2He introduced the electride anionic counter-ion to Na+ as corresponding topologically to a rare feature known as a non-nuclear attractor. This prompted speculation about other systems with such a feature, and the focus shifted to a tetrahedral arrangement of four hydrogen atoms as a dication, sharing a total of two valence electrons. The story now continues here.
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Tags:chemical bonding, Chemistry, Electride, free energy, Interesting chemistry, Ion, Nature, Physical chemistry, Valence electron
Posted in Uncategorised | 1 Comment »
Saturday, December 31st, 2016
My holiday reading has been Derek Lowe’s excellent Chemistry Book setting out 250 milestones in chemistry, organised by year. An entry for 1920 entitled hydrogen bonding seemed worth exploring in more detail here.
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Tags:10.1021, aqueous solution, Chemical bond, chemical bonding, Chemistry, Derek Lowe, Historical, Hydrogen, Hydrogen bond, Intermolecular forces, Lowe's, Nature, Supramolecular chemistry
Posted in Uncategorised | 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.
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Tags:Chemical bond, chemical bonding, Chemical nomenclature, Chemistry, Conjugated system, double bond, energy, Interesting chemistry, Nature, Nonmetal, Organic chemistry, Physical organic chemistry, search query, Substituent
Posted in crystal_structure_mining | 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.
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Tags:Aviation, Bond order, Carbon–carbon bond, Chemical bond, chemical bonding, Interesting chemistry, naive search, search query, single bond
Posted in crystal_structure_mining | No Comments »
Sunday, 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.
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Tags:Carbenes, chemical bonding, energy barrier, free energy, Functional groups, General, Ligand, Mesoionic carbene, Organometallic chemistry, Persistent carbene, quantum mechanical solution, Reactive intermediates, Transition metal carbene complex, Valence, Valence electron
Posted in crystal_structure_mining | No Comments »
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?[1] Here I explore the difference between two different and very simple approaches to predicting its reactivity.
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References
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D. Christopher Braddock, A. Mahtey, H.S. Rzepa, and A.J.P. White, "Stable bromoallene oxides", Chemical Communications, vol. 52, pp. 11219-11222, 2016. http://dx.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 »
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, Interesting chemistry, Lone pair, Physical organic chemistry, Quantum chemistry
Posted in Uncategorised | No Comments »