Conjugated σ bonds

The chemical bond is a fascinating construct, the pillar of modern chemistry I might add; the typical view of bars between atoms a chemist has of a σ chemical bond becomes challenged when we face this bowl compounds reported by Soichiro Kyushin in JACS where, for the first time, Si-bowl compounds were shown to exhibit σ bonds conjugated by means of DFT and TD-DFT calculations at the B3LYP/6-31G(2d,p) level of theory.

This goes to show the fascinating world yet to be discovered about chemical bonds and their conceptions.

DOI: 10.1021/jacs.7b00250

Nanohoop coordination compounds

Jeff M. Van Raden, Shayan Louie, Lev N. Zakharov and Ramesh Jasti reported in JACS the synthesis of Ru coordinated ‘nanohoops’, nanohoop being the name given to a cyclo-p-phenylene ring. This kind of nomenclature is proving to become more popular probably since it evokes an ordinary physical image, however this rings are neither hoops nor nano in the sense of nanotechnology. Be that as it may, the use of this N-doped rings were used to coordinate to Ru. TD-DFT calculations at the B3LYP/6-31G(d,p)-LANL2DZ(Ru) were employed to calculate the MLCT transitions (oscillator strengths were kind of low, 0.041, 0.187 and 0.110 for H-L, H(-3)-L and H(-5)-L, respectively) all in the UV section of the spectra.

The reason I got interested in this paper was because I think we could apply this scheme to calix[n]arenes to form less symmetrical patterns which could lead to interesting systems with non-linear optical properties.

DOI: 10.1021/jacs.7b00359

Structural features of Graphene Quantum Dots

Prof. Angela Violi et al. report in RSC Advances a thorough set of molecular dynamics simulations of small graphene sheets which aggregate to form Graphene Quantum Dots (GQDs). Substitution on the edges and size have an effect on the curvature and this in turn affects the aggregation (sounds like a confounding variable is called for). I only wish their simulation times were larger (only 20 ns); also I think a detailed electronic structure calculation on the most populated structures would have been cool and I’m up for it if the authors are too 🙂

I wonder if the authors will do some calculations on that new ferromagnetic Nitrogen-doped graphene recently reported in JACS because the resulting N-GQDs could result to be very cool!

Paolo Elvati, Elizabeth Baumeister and Angela Violi* : RSC Adv., 2017, 7, 17704 DOI: 10.1039/c7ra01029j


The current relevance of the hybridization model

Is C in CH4 tetrahedral because it’s sp3 hybridized or is it sp3 hybridized because it’s tetrahedral?

All models are wrong but some are useful.

-George Box

From my ResearchGate feed I came across this wonderful piece by Alabugin et al. from 2014 titled “Orbital hybridization: a key electronic factor in control of structure and reactivity” in the Journal of Physical Organic Chemistry

Therein the concept and utility of the hybridization model is analyzed in -what to me seems as- a somewhat ad-hoc manner without much thought to the causality of the model and the actual phenomena. For instance, the authors write about the promotion of electrons into an excited state only to have that energy expenditure compensated by the formation of bonds, a process which is not observed but rather is used only as illustration. As much as I like the NBO formalism, the authors claim that NBO is a particularly good model to quantify hybridization and its effects but once again the chain of caussality seems backwards to me since NBO is formulated on the basis of Löwdin’s Natural Hybrid Orbitals, so naturally (pun intended) NBO will be ad-hoc suited to study hybridization.

I could argue and write a lot about this topic (and I’ve had) and probably I will but if the post or posts became very lengthy I might as well just submit them for publication.


calix[4]arene as GP120 inhibitor – HIV1

Lun Tsou and co-workers reported back in 2013 the use of a calix[4]arene as an inhibitor of GP120, the entry protein on the surface of HIV-1 that makes one of the first contacts with cells to be infected.

Low citotoxicity and high effectiveness were observed and that is great news because we keep working on calixarenes as drug delivery agents, in this particular case the active portion (isophtallic acid) was covalently linked to the upper rim.

Bioorg Med Chem Lett. 2012 May 1; 22(9): 3358–3361. doi:10.1016/j.bmcl.2012.02.079.