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.
Does combining molecules with augmented reality have a future?
March 28th, 2016Augmented reality, a superset if you like of virtual reality (VR), has really been hitting the headlines recently. Like 3D TV, its been a long time coming! Since ~1994 or earlier, there have been explorations of how molecular models can be transferred from actual reality to virtual reality using conventional computers (as opposed to highly specialised ones). It was around then that a combination of software (Rasmol) and hardware (Silicon Graphics, and then soon after standard personal computers with standard graphics cards) became capable of such manipulations. VRML (virtual reality modelling language) also proved something of a false start‡ So have things changed?
How many water molecules does it take to form ammonium hydroxide from ammonia and water?
March 20th, 2016This is a corollary to the previous post‡ exploring how many molecules are needed to ionise HCl. Here I am asking how many water molecules are required to form the ionic ammonium hydroxide from ammonia and water.
Research data: Managing spectroscopy-NMR.
March 16th, 2016At the ACS conference, I have attended many talks these last four days, but one made some “connections” which intrigued me. I tell its story (or a part of it) here.
Earth’s missing chemistry.
February 24th, 2016At the precise moment I write this, there is information about 108,230,950 organic and inorganic chemical substances from the World's disclosed chemistry. So it was with a sense of curiosity that I came across this article in the American Mineralogist[1] entitled "Earth’s “missing” minerals" (the first in a series of articles apparently planned on the topic of the missing ones). The abstract is particularly interesting and whilst I encourage you to go read the article itself, I will quote some eye-catching observations from just this abstract:
References
- R.M. Hazen, G. Hystad, R.T. Downs, J.J. Golden, A.J. Pires, and E.S. Grew, "Earth’s “missing” minerals", American Mineralogist, vol. 100, pp. 2344-2347, 2015. https://doi.org/10.2138/am-2015-5417
Real hypervalency in a small molecule.
February 21st, 2016Hypervalency is defined as a molecule that contains one or more main group elements formally bearing more than eight electrons in their valence shell. One example of a molecule so characterised was CLi6[1] where the description "“carbon can expand its octet of electrons to form this relatively stable molecule“ was used. Yet, in this latter case, the octet expansion is in fact an illusion, as indeed are many examples that are cited. The octet shell remains resolutely un-expanded. Here I will explore the tiny molecule CH3F2- where two extra electrons have been added to fluoromethane.
References
- H. Kudo, "Observation of hypervalent CLi6 by Knudsen-effusion mass spectrometry", Nature, vol. 355, pp. 432-434, 1992. https://doi.org/10.1038/355432a0
Bond stretch isomerism. Did this idea first surface 100 years ago?
February 9th, 2016The phenomenon of bond stretch isomerism, two isomers of a compound differing predominantly in just one bond length, is one of those chemical concepts that wax and occasionally wane.[1] Here I explore such isomerism for the elements Ge, Sn and Pb.
References
- J.A. Labinger, "Bond-stretch isomerism: a case study of a quiet controversy", Comptes Rendus. Chimie, vol. 5, pp. 235-244, 2002. https://doi.org/10.1016/s1631-0748(02)01380-2