Archive for the ‘General’ Category

What’s in a name? Carbenes: a reality check.

Sunday, September 11th, 2016
No Gravatar

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.

(more…)

Journal innovations – the next step is augmented reality?

Wednesday, August 17th, 2016
No Gravatar

In the previous post, I noted that a chemistry publisher is about to repeat an earlier experiment in serving pre-prints of journal articles. It would be fair to suggest that following the first great period of journal innovation, the boom in rapid publication “camera-ready” articles in the 1960s, the next period of rapid innovation started around 1994 driven by the uptake of the World-Wide-Web. The CLIC project[1] aimed to embed additional data-based components into the online presentation of the journal Chem Communications, taking the form of pop-up interactive 3D molecular models and spectra. The Internet Journal of Chemistry was designed from scratch to take advantage of this new medium.[2] Here I take a look at one recent experiment in innovation which incorporates “augmented reality”.[3]

(more…)

References

  1. D. James, B.J. Whitaker, C. Hildyard, H.S. Rzepa, O. Casher, J.M. Goodman, D. Riddick, and P. Murray‐Rust, "The case for content integrity in electronic chemistry journals: The CLIC project", New Review of Information Networking, vol. 1, pp. 61-69, 1995. http://dx.doi.org/10.1080/13614579509516846
  2. S.M. Bachrach, and S.R. Heller, " The Internet Journal of Chemistry: A Case Study of an Electronic Chemistry Journal ", Serials Review, vol. 26, pp. 3-14, 2000. http://dx.doi.org/10.1080/00987913.2000.10764578
  3. S. Ley, B. Musio, F. Mariani, E. Śliwiński, M. Kabeshov, and H. Odajima, "Combination of Enabling Technologies to Improve and Describe the Stereoselectivity of Wolff–Staudinger Cascade Reaction", Synthesis, 2016. http://dx.doi.org/10.1055/s-0035-1562579

Oxane oxide: a tautomer of hydrogen peroxide.

Friday, April 15th, 2016
No Gravatar

If H3N+-O is viable compared with its tautomer H2N-OH when carrying water bridges, then why not try H2O+-O vs HO-OH?

(more…)

Azane oxide, a tautomer of hydroxylamine.

Friday, April 15th, 2016
No Gravatar

In the previous post I described how hydronium hydroxide or H3O+…HO, an intermolecular tautomer of water, has recently been observed captured inside an organic cage[1] and how the free-standing species in water can be captured computationally with the help of solvating water bridges. Here I explore azane oxide or H3N+-O, a tautomer of the better known hydroxylamine (H2N-OH).

(more…)

References

  1. M. Stapf, W. Seichter, and M. Mazik, "Unique Hydrogen-Bonded Complex of Hydronium and Hydroxide Ions", Chemistry - A European Journal, vol. 21, pp. 6350-6354, 2015. http://dx.doi.org/10.1002/chem.201406383

Hydronium hydroxide: the why of pH 7.

Thursday, April 14th, 2016
No Gravatar

Ammonium hydroxide (NH4+…OH) can be characterised quantum mechanically when stabilised by water bridges connecting the ion-pairs. It is a small step from there to hydronium hydroxide, or H3O+…OH. The measured concentrations [H3O+] ≡ [OH] give rise of course to the well-known pH 7 of pure water, and converting this ionization constant to a free energy indicates that the solvated ion-pair must be some ~19.1 kcal/mol higher in free energy than water itself. So can a quantum calculation reproduce pH7 for water?

(more…)

Ways to encourage water to protonate an amine: superbasing.

Friday, April 8th, 2016
No Gravatar

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.

(more…)

Does combining molecules with augmented reality have a future?

Monday, 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?

(more…)

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

Sunday, 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.

(more…)

A molecular balance for dispersion energy?

Sunday, 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.

(more…)

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

Quintuple bonds: resurfaced.

Sunday, January 31st, 2016
No Gravatar

Six years ago, I posted on the nature of a then recently reported[1] Cr-Cr quintuple bond. The topic resurfaced as part of the discussion on a more recent post on NSF3, and a sub-topic on the nature of the higher order bonding in C2. The comment made a connection between that discussion and the Cr-Cr bond alluded to above. I responded briefly to that comment, but because I want to include 3D rotatable surfaces, I expand the discussion here and not in the comment.

(more…)

References

  1. C. Hsu, J.K. Yu, C. Yen, G. Lee, Y. Wang, and Y. Tsai, "Quintuply-Bonded Dichromium(I) Complexes Featuring Metal-Metal Bond Lengths of 1.74 Å", Angewandte Chemie International Edition, vol. 47, pp. 9933-9936, 2008. http://dx.doi.org/10.1002/anie.200803859