Augmented 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?
At 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 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:
- 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. http://dx.doi.org/10.2138/am-2015-5417
Hypervalency 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 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.
- H. Kudo, "Observation of hypervalent CLi6 by Knudsen-effusion mass spectrometry", Nature, vol. 355, pp. 432-434, 1992. http://dx.doi.org/10.1038/355432a0
The 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. Here I explore such isomerism for the elements Ge, Sn and Pb.
- J.A. Labinger, "Bond-stretch isomerism: a case study of a quiet controversy", Comptes Rendus Chimie, vol. 5, pp. 235-244, 2002. http://dx.doi.org/10.1016/S1631-0748(02)01380-2
The geometry of cyclo-octatetraenes differs fundamentally from the lower homologue benzene in exhibiting slow (nuclear) valence bond isomerism rather than rapid (electronic) bond-equalising resonance. In 1992 Anderson and Kirsch exploited this property to describe a simple molecular balance for estimating how two alkyl substituents on the ring might interact via the (currently very topical) mechanism of dispersion (induced-dipole-induced-dipole) attractions. These electron correlation effects are exceptionally difficult to model using formal quantum mechanics and are nowadays normally replaced by more empirical functions such as Grimme's D3BJ correction. Here I explore aspects of how the small molecule below might be used to investigate the accuracy of such estimates of dispersion energies.
- J.E. Anderson, and P.A. Kirsch, "Structural equilibria determined by attractive steric interactions. 1,6-Dialkylcyclooctatetraenes and their bond-shift and ring inversion investigated by dynamic NMR spectroscopy and molecular mechanics calculations", J. Chem. Soc., Perkin Trans. 2, pp. 1951, 1992. http://dx.doi.org/10.1039/P29920001951
- S. Grimme, S. Ehrlich, and L. Goerigk, "Effect of the damping function in dispersion corrected density functional theory", J. Comput. Chem., vol. 32, pp. 1456-1465, 2011. http://dx.doi.org/10.1002/jcc.21759