PCCP Blog

When investigating dyes, we almost always address the molecular system experimentally in a solution, and theoretically in the gas phase. Greisch and co-workers circumvent this problem by doing both in condensed phases as well as the gas phase. To me, it explained a phenomenon that I have come across several times: the >1800 cm^-1 shift between ab initio calculated transition energies and the observed spectra. A difference e.g. ZINDO methods is compensated for, and why these are the tinctorial chemist’s choice when predicting spectra from molecular structures. With this paper it is demonstrated that if you want to design gas phase dyes, DFT calculations can be used.

The focus of the paper is the triplet energy, triplet lifetime and triplet deactivation of rhodamine dyes, addressing their use in STED super-resolution microscopy and the triplet state mediated photodegradation. While that motivation is good, I am too excited about the gas phase fluorescence spectra and their use in benchmarking computational approaches. Emission spectra of isolated ionic dyes, can also answer some of the questions regarding counter ion effects, symmetry and solvation that has been around for half a century. I am eagerly awaiting the next installment promised at the end of this paper.

By Dr Thomas Just Sørensen

Read the full details of this PCCP paper today:

Intrinsic fluorescence properties of rhodamine cations in gas-phase: triplet lifetimes and dispersed fluorescence spectra
Jean-François Greisch, Michael E. Harding, Mattias Kordel, Wim Klopper, Manfred M. Kappes and Detlef Schooss
Phys. Chem. Chem. Phys., 2013, 15, 8162-8170
DOI: 10.1039/C3CP44362K

This article is part of a collection to coincide with the theme of Bunsentagung 2013: ‘Theory meets Spectroscopy’. You may be interested in the other articles in this collection too.

It’s no secret that I find rare gas chemistry very exciting, so when I came across this article by Jien-Lian Chen et al. I knew immediately that it would form the subject of my next blog post. The group, based in Taiwan, have performed calculations that predict a new series of rare gas molecules. Whilst this is, in itself, an exciting achievement, what really grabbed me was that they predict these molecules to be relatively stable – stable enough to be detected experimentally.

As far as I am aware, that is the holy grail of theoretical rare gas chemistry, as there is still very little experimental data on molecules of this kind. The group’s calculations were rigorous, comparing a variety of high-level computational methods and finding good agreement between them. They predicted the strength of the bonds to be significant, and examined the most likely unimolecular dissociation pathways and found sizable barriers to each of them for this class of molecule. All this adds up to a real possibility for generating some new, experimental rare gas data.

So what are these fantastic new molecules? They take the general form F–RG–BNR, where RG can be Argon, Krypton or Xenon, and R can be quite a variety of small groups. Interestingly, they found that the stability of the molecule was largely unaffected by the identity of the R group, indicating that it may be possible to study even more of them than were covered in this investigation.

All we need now is for somebody to work out how to synthesise these molecules in a spectroscopically useful environment, and perform the experiments to confirm the theoretical predictions. Experimental spectroscopists, consider the challenge issued!

By Victoria Wilton

Read the full details of this PCCP article:

Theoretical prediction of new noble-gas molecules FNgBNR (Ng = Ar, Kr, and Xe; R = H, CH₃, CCH, CHCH₂, F, and OH)
Jien-Lian Chen, Chang-Yu Yang, Hsiao-Jing Lin and Wei-Ping Hu
Phys. Chem. Chem. Phys., 2013, 15, 9701-9709
DOI: 10.1039/C3CP50447F

Elangannam Arunan and Devendra Mani of the Indian Institute of Science have investigated an interesting C···Y bond, a “carbon bond”, which occurs when one of the hydrogen atoms of methane is replaced by an electron withdrawing group.

Weak interactions are very important in molecules of life, such as water and DNA, in supramolecular chemistry and in crystal design and engineering. Traditionally, these interactions were classified as hydrogen bonding and van der Waals interactions, but in recent decades, other weak interactions, such as halogen bonds, chalcogen bonds and pnicogen bonds, have been investigated and classified. An interesting question is whether carbon atoms can also play a role in weak interactions, in addition to the more electronegative elements known to take part.

When one of the hydrogen atoms in methane is replaced with an electron withdrawing group, such as -OH or –F, the CH₃ tetrahedral face becomes a positive centre. Using NBO analysis and vibrational frequency data, Arunan and Mani showed that this positive centre could accept electron density from atoms like O in water, giving rise to a novel C···Y bond, which could be called a carbon bond.

Arunan says that given the abundance of alkyl groups in biological systems, such carbon bonding interactions could play a significant role in biology, which has yet to be recognised. “Hydrogen bonds are just sufficiently strong and can be broken and made under ambient conditions, helping life.  Carbon bonds are weak, and if they were not much of what we know about life could not be.”

For more details, read their article:

The X-C•••Y (X=O/F, Y=O/S/F/Cl/Br/N/P) ‘carbon bond’ and hydrophobic interactions
Devendra Mani and E Arunan
DOI: 10.1039/C3CP51658J