Previously, I looked at models of how ammonia could be protonated by water to form ammonium hydroxide. The energetic outcome of my model matched the known equilbrium in water as favouring the unprotonated form (pKb ~4.75). I add here two amines for which R=Me3Si and R=CN. The idea is that the first will assist nitrogen protonation by stabilising the positive centre and the second will act in the opposite sense; an exploration if you like of how one might go about computationally designing a non-steric superbasic amine that becomes predominantly protonated when exposed to water (pKb <1)† and is thus more basic than hydroxide anion in this medium.
Posts Tagged ‘metal’
Ways to encourage water to protonate an amine: superbasing.
Friday, April 8th, 2016Tags:Acid, Acid dissociation constant, Amide, Amine, Ammonia, Ammonium, Bases, City: Cambridge, energy, from non-protic solution, Functional groups, General, Hydrogen bond, Hydroxide, Interesting chemistry, Lone pair, metal, Nitrile, relative free energy, search query
Posted in Uncategorised | 2 Comments »
Celebrating Paul Schleyer: searching for hidden treasures in the structures of metallocene complexes.
Saturday, April 2nd, 2016A celebration of the life and work of the great chemist Paul von R. Schleyer was held this week in Erlangen, Germany. There were many fantastic talks given by some great chemists describing fascinating chemistry. Here I highlight the presentation given by Andy Streitwieser on the topic of organolithium chemistry, also a great interest of Schleyer's over the years. I single this talk out since I hope it illustrates why people still get together in person to talk about science.
Tags:Centroid, chemical effect, chemical insights, chemical interpretation, Chemical IT, City: Erlangen, Country: Germany, Degree of a continuous mapping, Ferrocene, Hydrogen bond, individual search definition, Interesting chemistry, metal, overall search collection, Streitwieser, terminal H-positions, Torsion, X-ray
Posted in crystal_structure_mining | 6 Comments »
Discovery based research experiences: gauche effects in group 16 elements.
Wednesday, March 2nd, 2016The upcoming ACS national meeting in San Diego has a CHED (chemical education division) session entitled Implementing Discovery-Based Research Experiences in Undergraduate Chemistry Courses. I had previously explored what I called extreme gauche effects in the molecule F-S-S-F. Here I take this a bit further to see what else can be discovered about molecules containing bonds between group 16 elements (QA= O, S, Se, Te).
Tags:City: San Diego, Interesting chemistry, metal, non-metal, Singular spectrum analysis, Time series analysis
Posted in crystal_structure_mining | No Comments »
Deviations from tetrahedral four-coordinate carbon: a statistical exploration.
Sunday, September 6th, 2015An article entitled "Four Decades of the Chemistry of Planar Hypercoordinate Compounds"[1] was recently reviewed by Steve Bacharach on his blog, where you can also see comments. Given the recent crystallographic themes here, I thought I might try a search of the CSD (Cambridge structure database) to see whether anything interesting might emerge for tetracoordinate carbon.
References
- L. Yang, E. Ganz, Z. Chen, Z. Wang, and P.V.R. Schleyer, "Four Decades of the Chemistry of Planar Hypercoordinate Compounds", Angewandte Chemie International Edition, vol. 54, pp. 9468-9501, 2015. http://dx.doi.org/10.1002/anie.201410407
Tags:Angle, Cambridge, chemical bonding, Chemical IT, Cycloalkane, Cyclopropane, HTML, HTML element, Ligand, metal, search definition, search results, search software, Steve Bacharach
Posted in crystal_structure_mining | No Comments »
Mechanism of the Lithal (LAH) reduction of cinnamaldehyde.
Wednesday, April 1st, 2015The reduction of cinnamaldehyde by lithium aluminium hydride (LAH) was reported in a classic series of experiments[1],[2],[3] dating from 1947-8. The reaction was first introduced into the organic chemistry laboratories here at Imperial College decades ago, vanished for a short period, and has recently been reintroduced again.‡ The experiment is really simple in concept; add LAH to cinnamaldehyde and you get just reduction of the carbonyl group; invert the order of addition and you additionally get reduction of the double bond. Here I investigate the mechanism of these reductions using computation (ωB97XD/6-311+G(d,p)/SCRF=diethyl ether).
References
- R.F. Nystrom, and W.G. Brown, "Reduction of Organic Compounds by Lithium Aluminum Hydride. I. Aldehydes, Ketones, Esters, Acid Chlorides and Acid Anhydrides", Journal of the American Chemical Society, vol. 69, pp. 1197-1199, 1947. http://dx.doi.org/10.1021/ja01197a060
- R.F. Nystrom, and W.G. Brown, "Reduction of Organic Compounds by Lithium Aluminum Hydride. II. Carboxylic Acids", Journal of the American Chemical Society, vol. 69, pp. 2548-2549, 1947. http://dx.doi.org/10.1021/ja01202a082
- F.A. Hochstein, and W.G. Brown, "Addition of Lithium Aluminum Hydride to Double Bonds", Journal of the American Chemical Society, vol. 70, pp. 3484-3486, 1948. http://dx.doi.org/10.1021/ja01190a082
Tags:Al-H-Li bridge, dihydrocinnamyl alcohol reduction product, free energy, Imperial College, independent researcher, low energy escape route, lower energy alternative, metal, pence
Posted in reaction mechanism | 5 Comments »
Caesium trifluoride: could it be made?
Saturday, November 23rd, 2013Mercury (IV) tetrafluoride attracted much interest when it was reported in 2007[1] as the first instance of the metal being induced to act as a proper transition element (utilising d-electrons for bonding) rather than a post-transition main group metal (utilising just s-electrons) for which the HgF2 dihalide would be more normal (“Is mercury now a transition element?”[2]). Perhaps this is the modern equivalent of transmutation! Well, now we have new speculation about how to induce the same sort of behaviour for caesium; might it form CsF3 (at high pressures) rather than the CsF we would be more familiar with.[3] Here I report some further calculations inspired by this report.
References
- X. Wang, L. Andrews, S. Riedel, and M. Kaupp, "Mercury Is a Transition Metal: The First Experimental Evidence for HgF4", Angewandte Chemie International Edition, vol. 46, pp. 8371-8375, 2007. http://dx.doi.org/10.1002/anie.200703710
- M. Miao, "Caesium in high oxidation states and as a p-block element", Nature Chemistry, vol. 5, pp. 846-852, 2013. http://dx.doi.org/10.1038/nchem.1754
Tags:animation, energy, free energy barrier, free energy change, Hypervalency, Interesting chemistry, metal, pence, post-transition main group metal, potential energy surface
Posted in Uncategorised | 13 Comments »
The butterfly effect in chemistry: Bimodal M~S bonds?
Sunday, July 14th, 2013I noted previously that some 8-ring cyclic compounds could exist in either a planar-aromatic or a non-planar-non-aromatic mode, the mode being determined by apparently quite small changes in a ring substituent. Hunting for other examples of such chemistry on the edge, I did a search of the Cambridge crystal database for metal sulfides.
Tags:Cambridge, chemical reasons, Interesting chemistry, metal, metal sulfides, neutral systems, transition metal series
Posted in Uncategorised | No Comments »
Is dicarbon (C2) a molecule of chemical interest?
Wednesday, July 3rd, 2013C2 (dicarbon) is certainly interesting from a theoretical point of view. Whether or not it can be described as having a quadruple bond has induced much passionate discussion[1],[2],[3],[4]. Its occurrence in space and in flames is also well-known. But does it have what might be called a conventional chemistry? Other highly reactive species (cyclobutadiene is a well-known example) can often be tamed by trapping as a ligand coordinated to a metal and so one might speculate upon how C2 responds to the proximity of a metal. As is noted here[2], dicarbon as a ligand has been known a long time as part of what is referred to as carbide chemistry. In this regard it is thought of as the di-anion, C22- (and isoelectronic therefore with dinitrogen). Thus calcium carbide, but in fact the degree to which the dicarbon can absorb electrons is thought to be wide (as judged by the resulting C-C bond length, see[2]). Here I take a look at just one metal carbide[5] that caught my eye (there are hundreds of others, many no doubt equally interesting!).
References
- S. Shaik, D. Danovich, W. Wu, P. Su, H.S. Rzepa, and P.C. Hiberty, "Quadruple bonding in C2 and analogous eight-valence electron species", Nature Chemistry, vol. 4, pp. 195-200, 2012. http://dx.doi.org/10.1038/nchem.1263
- S. Shaik, H.S. Rzepa, and R. Hoffmann, "One Molecule, Two Atoms, Three Views, Four Bonds?", Angewandte Chemie International Edition, vol. 52, pp. 3020-3033, 2013. http://dx.doi.org/10.1002/anie.201208206
- G. Frenking, and M. Hermann, "Critical Comments on “One Molecule, Two Atoms, Three Views, Four Bonds?”", Angewandte Chemie International Edition, vol. 52, pp. 5922-5925, 2013. http://dx.doi.org/10.1002/anie.201301485
- D. Danovich, S. Shaik, H.S. Rzepa, and R. Hoffmann, "A Response to the Critical Comments on “One Molecule, Two Atoms, Three Views, Four Bonds?”", Angewandte Chemie International Edition, vol. 52, pp. 5926-5928, 2013. http://dx.doi.org/10.1002/anie.201302350
- E. Dashjav, Y. Prots, G. Kreiner, W. Schnelle, F.R. Wagner, and R. Kniep, "Chemical bonding analysis and properties of La7Os4C9—A new structure type containing C- and C2-units as Os-coordinating ligands", Journal of Solid State Chemistry, vol. 181, pp. 3121-3130, 2008. http://dx.doi.org/10.1016/j.jssc.2008.08.005
Tags:Interesting chemistry, metal, metal coordinating, Os-C
Posted in Uncategorised | 6 Comments »
Au and Pt π-complexes of cyclobutadiene.
Wednesday, May 15th, 2013In the preceding post, I introduced Dewar’s π-complex theory for alkene-metal compounds, outlining the molecular orbital analysis he presented, in which the filled π-MO of the alkene donates into a Ag+ empty metal orbital and back-donation occurs from a filled metal orbital into the alkene π* MO. Here I play a little “what if” game with this scenario to see what one can learn from doing so.
Tags:African Union, alkene-metal compounds, empty metal orbital, energy, filled metal orbital, free energy, Historical, Hypervalency, Interesting chemistry, lower energy form, metal
Posted in Uncategorised | 1 Comment »
The π-complex theory of metal-alkene compounds.
Monday, May 13th, 2013Tags:alkene-metal interaction, alkene-metal π-complex, cation Ag, Dewar, Dewar's Ag, Historical, Interesting chemistry, metal, metal d-orbitals, naked metal cations, ZTE C79 Cellular Phone
Posted in Uncategorised | 1 Comment »