Posts Tagged ‘Functional groups’
Saturday, August 25th, 2018
Symbiosis between computation and experiment is increasingly evident in pedagogic journals such as J. Chemical Education. Thus an example of original laboratory experiments[1],[2] that later became twinned with a computational counterpart.[3] So when I spotted this recent lab experiment[4] I felt another twinning approaching.
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References
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A. Burke, P. Dillon, K. Martin, and T.W. Hanks, "Catalytic Asymmetric Epoxidation Using a Fructose-Derived Catalyst", Journal of Chemical Education, vol. 77, pp. 271, 2000. http://dx.doi.org/10.1021/ed077p271
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J. Hanson, "Synthesis and Use of Jacobsen's Catalyst: Enantioselective Epoxidation in the Introductory Organic Laboratory", Journal of Chemical Education, vol. 78, pp. 1266, 2001. http://dx.doi.org/10.1021/ed078p1266
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K.K.(. Hii, H.S. Rzepa, and E.H. Smith, "Asymmetric Epoxidation: A Twinned Laboratory and Molecular Modeling Experiment for Upper-Level Organic Chemistry Students", Journal of Chemical Education, vol. 92, pp. 1385-1389, 2015. http://dx.doi.org/10.1021/ed500398e
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M. Meazza, A. Kowalczuk, S. Watkins, S. Holland, T.A. Logothetis, and R. Rios, "Organocatalytic Cyclopropanation of (E)-Dec-2-enal: Synthesis, Spectral Analysis and Mechanistic Understanding", Journal of Chemical Education, vol. 95, pp. 1832-1839, 2018. http://dx.doi.org/10.1021/acs.jchemed.7b00566
Tags:Ammonium, Benzyl group, Cations, chemical diagrams, Chemistry, condensation, final product, Functional groups, Iminium, Interesting chemistry, Methyl group, Name reactions, Organic chemistry, possible diastereomeric products, relative energy, Vector Graphics, web browsers
Posted in Uncategorised | 9 Comments »
Wednesday, August 8th, 2018
White City is a small area in west london created as an exhibition site in 1908, morphing over the years into an Olympic games venue, a greyhound track, the home nearby of the BBC (British Broadcasting Corporation) and most recently the new western campus for Imperial College London.♣ The first Imperial department to move into the MSRH (Molecular Sciences Research Hub) building is chemistry. As a personal celebration of this occasion, I here dedicate three transition states located during my first week of occupancy there, naming them the White City trio following earlier inspiration by a string trio and their own instruments.
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Tags:acetic acid, Acid, Amide, Amine, carboxylic acid, Chemistry, Company: BBC, Company: British Broadcasting Corporation, energy, Ester, exhibition site, free energy barrier, Functional groups, Hydrogen bond, Imperial College, Imperial College London, Interesting chemistry, Ionic product, Newspaper & Magazine Printing Services, Non-ionic product, Olympic games, Organic chemistry, White City Trio
Posted in Uncategorised | 6 Comments »
Tuesday, December 26th, 2017
Recollect the suggestion that diazomethane has hypervalent character[1]. When I looked into this, I came to the conclusion that it probably was mildly hypervalent, but on carbon and not nitrogen. Here I try some variations with substituents to see what light if any this casts.
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References
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M.C. Durrant, "A quantitative definition of hypervalency", Chemical Science, vol. 6, pp. 6614-6623, 2015. http://dx.doi.org/10.1039/C5SC02076J
Tags:chemical bonding, Chemistry, diazo, Diazo compounds, Diazomethane, diazomethane-like systems, Functional groups, Hypervalency, Hypervalent molecule, Molecular geometry, Organic chemistry, Recollects
Posted in Uncategorised | 8 Comments »
Wednesday, 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.
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References
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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. http://dx.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 »
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.
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References
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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. http://dx.doi.org/10.1021/jp0123841
Tags:Amines, Artemisinin, Chemistry, Functional groups, Hexamethylene triperoxide diamine, Interesting chemistry, Organic chemistry, Organic peroxides, Peroxide, perturbation energy interaction, Stereoelectronics
Posted in Uncategorised | 1 Comment »
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 »
Wednesday, June 22nd, 2016
I previously used data mining of crystal structures to explore the directing influence of substituents on aromatic and heteroaromatic rings. Here I explore, quite literally, a different angle to the hydrogen bonding interactions between a benzene ring and OH or NH groups.
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Tags:10.1021, 10.1107, 10.5517, aromaticity, benzene, Centroid, chemical bonding, Chemical IT, data mining, Functional groups, Hydrogen bond, Physical organic chemistry, Pyridine, Simple aromatic rings, Supramolecular chemistry
Posted in crystal_structure_mining | 3 Comments »