Does combining molecules with augmented reality have a future?

March 28th, 2016
No Gravatar

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?

Read the rest of this entry »

How many water molecules does it take to form ammonium hydroxide from ammonia and water?

March 20th, 2016
No Gravatar

This 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.

Read the rest of this entry »

Research data: Managing spectroscopy-NMR.

March 16th, 2016
No Gravatar

At 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.

Read the rest of this entry »

Global initiatives in research data management and discovery: searching metadata.

March 7th, 2016
No Gravatar

The upcoming ACS national meeting in San Diego has a CINF (chemical information division) session entitled "Global initiatives in research data management and discovery". I have highlighted here just one slide from my contribution to this session, which addresses the discovery aspect of the session.

Read the rest of this entry »

Discovery based research experiences: gauche effects in group 16 elements.

March 2nd, 2016
No Gravatar

The 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). 

Read the rest of this entry »

Earth’s missing chemistry.

February 24th, 2016
No Gravatar

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[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:

Read the rest of this entry »

References

  1. 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

Real hypervalency in a small molecule.

February 21st, 2016
No Gravatar

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[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.

Read the rest of this entry »

References

  1. 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

Bond stretch isomerism. Did this idea first surface 100 years ago?

February 9th, 2016
No Gravatar

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.[1] Here I explore such isomerism for the elements Ge, Sn and Pb.

Read the rest of this entry »

References

  1. 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

A molecular balance for dispersion energy?

February 7th, 2016
No Gravatar

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[1] 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.[2] Here I explore aspects of how the small molecule below might be used to investigate the accuracy of such estimates of dispersion energies.

Read the rest of this entry »

References

  1. 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
  2. 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

LEARN Workshop: Embedding Research Data as part of the research cycle

February 1st, 2016
No Gravatar

I attended the first (of a proposed five) workshops organised by LEARN (an EU-funded project that aims to ...Raise awareness in research data management (RDM) issues & research policy) on Friday. Here I give some quick bullet points relating to things that caught my attention and or interest. The program (and Twitter feed) can be found at https://learnrdm.wordpress.com where other's comments can also be seen. 

Read the rest of this entry »