Posts Tagged ‘Magnetism’

One more WATOC 2017 Report.

Thursday, August 31st, 2017

Conferences can be intense, and this one is no exception. After five days, saturation is in danger of setting in. But before it does, I include two more (very) brief things I have learnt.

  1. Sason Shaik introduced a theme he first investigated years ago, but for which no experiment had been devised for verification. He revived his theme when a journalist contacted him last year to report exactly such an observation, which I now recount. A Diels-Alder adduct was captured between a flat layer of gold atoms and the tip of a scanning-tunneling microscope. With the molecule exactly oriented, a strong external electric field (OEEF) was applied, in both senses of polarisation. This is exactly the model studied by Sason, who had argued thus. A Diels-Alder reaction can be modelled using VB theory as the avoided crossing of a covalent ground state with ionic excited states at the transition state. Depending on the polarisation of an applied external electric field and the orientation of the molecule, one of these ionic states can stabilized or destabilised by about 8 kcal/mol, thus either stabilising or destabilising the transition state itself by mixing with the covalent state.

    And so it was that the oriented molecule caught between a gold layer and an STM probe could be persuaded to undergo a retro-Diels-Alder far more easily than it would thermally. The technique can even be tuned to selecting between endo and exo isomers. Sason held out the prospect that the toolbox of the synthetic chemist, which already includes Δ, hν and ? (ultrasound) as reagents, might be extended using OEEF. He called this a smart reagent since it can be tuned to the reaction required (as of course can light). At the moment this technique can only be applied to one molecule at a time, but it might be just a matter of designing a suitable apparatus!

  2. Pavel Hobza talked about non-covalent interactions, an occasional theme on this blog. Amongst many interesting observations was that the DNA helix is not stabilised as such by the hydrogen bonding between the base pairs but by the π-Ï€ stacking between them. One of these examples caught my eye, the known weak “hydrogen bonded” weak complex between benzene and chloroform in the gas phase. The C-H hydrogen points directly to the ring centroid and the C-H vibrational wavenumber is blue shifted by 12 cm-1. At the time this (experimental) observation caused consternation, since all known hydrogen bonds (both strong and weak) were routinely characterised by the magnitude of their red shift (up to ~100 cm-1). In fact, as Pavel showed, this interaction is less electrostatic in nature and more like dispersion attraction. Accurate calculations including dispersion also predict a blue shift for this system. A question from the audience suggested that as many π-facial “hydrogen bonds” in the crystal state tend to point not to the ring centroid but to the ring edge, what would happen if the chloroform H were to slide across the surface of the ring until it reached the edge; would the CH shift invert to become red, implying a change from dispersion interaction to whatever is implied by a hydrogen bond?

Apologies to all those who gave fascinating talks which are unrecorded here. I hope some tiny and selective flavour nevertheless emerges of WATOC 17.

The dipole moments of highly polar molecules: glycine zwitterion.

Saturday, December 24th, 2016

The previous posts produced discussion about the dipole moments of highly polar molecules. Here to produce some reference points for further discussion I look at the dipole moment of glycine, the classic zwitterion (an internal ion-pair).

Dielectric relaxation studies of glycinewater mixtures yield values that range from 15.7D[1] to 11.9D[2] although these have to be derived using various approximations and assumptions for up to 4 independent Debye processes. Before proceeding to calculations, I looked at the properties of ionized amino acids in the solid state, using the following search query for the Cambridge structure database (CSD). 

The distance measures hydrogen bonds to the carboxylate oxygens and the torsion their orientation. The O…H hydrogen bond distances vary between 1.7-1.85Ã…, which are short. The orientation of the hydrogen bond can be to the in-plane oxygen “σ-lone pair” (torsion 0 or 180°) and also an out-of-plane ~Ï€ form (torsion ~60-90°).

In aqueous solution, it is normally assumed that glycine sustains five such strong H-bonds (three to the H3N+ group and two[3] to the carboxylate anion), forming a polarised “salt bridge” across the ion-pair. Two model types were subjected to calculation using ωB97XD/Def2-TZVPP/SCRF=water. Aqueous glycine without any added explicit water molecules yields a dipole moment of 12.9D (DOI: 10.14469/hpc/2000), which is within the range noted above.‡

The solvated form is shown below, in one specific conformation of the three studied (ωB97XD/Def2-TZVPP/SCRF=water). The calculated O…H hydrogen bond lengths fall into the range revealed from crystal structures. The calculated dipole moments range from 12.6 (DOI: 10.14469/hpc/2007), 15.3 (DOI: 10.14469/hpc/2006) and 14.9D (DOI: 10.14469/hpc/2005), which is a modest increase over the model with no explicit water molecules. The actual dipole is of course a Boltzmann average over these and other as yet unexplored conformations, as well as other values for the number of water molecules.

Given the difficulties in interpreting the dipole moment of a complex Debye system such as hydrated glycine, the agreement between the limited range of solvated models and the measured values seems reasonable, and provides at least some measure of “calibration” for the polar molecules commented on previously.


‡Optimized with the solvent field on. If a vacuum model is used, the proton transfers from the N to the O.

References

  1. M.W. Aaron, and E.H. Grant, "Dielectric relaxation of glycine in water", Transactions of the Faraday Society, vol. 59, pp. 85, 1963. https://doi.org/10.1039/tf9635900085
  2. T. Sato, R. Buchner, Å. Fernandez, A. Chiba, and W. Kunz, "Dielectric relaxation spectroscopy of aqueous amino acid solutions: dynamics and interactions in aqueous glycine", Journal of Molecular Liquids, vol. 117, pp. 93-98, 2005. https://doi.org/10.1016/j.molliq.2004.08.001
  3. T. Shikata, "Dielectric Relaxation Behavior of Glycine Betaine in Aqueous Solution", The Journal of Physical Chemistry A, vol. 106, pp. 7664-7670, 2002. https://doi.org/10.1021/jp020957j