Tuesday, February 2, 2010

The post-Christmas glut

Well, it was always going to be this way: after several weeks away from the blog there’s now a big stack of papers to catch up on. The list here is incomplete, but more will follow.

One of the most interesting and important papers in this current stack is a MD study by Ronen Zangi of the notion of structure-making and structure-breaking in Hofmeister effects (J. Phys. Chem. B 114, 643; 2010 – paper here). In short, this study offers little succour for that concept, which has long overstayed its welcome. Ronen looks at the correlation between the propensity of various ions to alter the hydrophobic interaction (and thus to salt in/salt out) and changes in structural and dynamical properties they induce in the solvent. While there is a monotonic relationship between the reduction in hydrophobic interaction and the increase in ‘water structure’ as measured by the partial radial distribution factors, Ronen says that he could not identify ‘one property that can predict the change in the strength of the hydrophobic interacitons’. Nor could such properties predict the transition from salting-in to salting-out behaviour. Changes in dynamics, meanwhile, were induced by changes in the ion-water interaction, and not changes that the ions introduce to the ‘structural ordering’ of the water itself. As a result of all this, it seems that predicting whether a particular ion will induce salting-in or salting-out cannot be done on the basis of the properties of the salt solution alone, in the absence of the solute, and the whole notion of kosmotropes and chaotropes seems misleading. It would be nice to think that this paper will serve to banish those terms, but I suspect they will sadly take rather more dislodging than that.

Shekhar Garde and his colleagues have extended their earlier work on the conformations of polymers at surfaces (S. N. Jamadagni et al., Langmuir 25, 13092; 2009 – paper here). They have previously shown (J. Phys. Chem. B 113, 4093; 2009) that hydrophobic polymers adsorb preferentially at the interface between water and a hydrophobic surface (or air), and that the polymers here have significantly different structure and dynamics to those in the bulk. The present study looks in more detail at what is going on there, considering surfaces with a range of chemistries from hydrophilic to hydrophobic. The ‘test polymers’ are hydrophobic 35-mers, and the surfaces are SAMs with different terminal groups. The preferential adsorption at hydrophobic surfaces seems to be due to changes in water dynamics: the water has greater density fluctuations here and lower free energy of cavity formation, making it more able to solvate hydrophobes. The polymers have greater translational diffusion and conformational flexibility, typically flattening into pancake-like shapes.

I’ve been looking somewhat into the literature on nanobubbles, and it seems increasingly clear that it is very much in a state of flux and probably in need of some sort of snapshot review. How and when do nanobubbles form in the bulk and at surfaces? How long-lived are they, and how do they survive at all? There are many questions, and the answers so far are diverse. Detlef Lohse and his coworkers have a new contribution on the subject (B. M. Borkent et al., Langmuir 26, 260; 2009 – paper here). They try to clarify the shape of nanobubbles on hydrophobic surfaces (HOPG) using AFM, saying that they seem uniformly to have contact angles of about 119 degrees even for radii as small as 20 nm. It seems that some cantilevers can deposit material on the surfaces, making them rougher and altering the contact angle.

Robert Bryant and coworkers at the University of Virginia have used magnetic relaxation dispersion spectroscopy to characterize the dynamics of protons in a protein (BSA) backbone and its hydration water (G. Diakova et al., Biophys. J. 98, 138; 2010 – paper here). They find remarkably constant relaxation behaviour in the protein over a wide frequency range (0.01-300 MHz). Water dynamics contribute significantly to the relaxation on timescales of tens of ns, thanks to some rare, rather highly constrained, perhaps buried, hydration waters.

There’s a fascinating exploration of the various functional roles that protein hydration waters can have by Matteo Ceccarelli abd colleagues at the University of Cagliari in Italy (M. A. Scorciapino et al., JACS ja909822d – paper here). They have looked at myoglobin as a model system using MD, and observe three distinct ways in which waters modify the intrinsic dynamical behaviour of the protein. They can (1) block access to or escape of ligands from a binding site; (2) change internal dynamics by expanding the distances between residues in the manner of a ‘wedge’; (3) assist ligand transport, in effect by ‘washing it away’.

Another lovely example of water molecules playing an active role in an important biological process is provided by Göran Wallin and Johan Åqvist at Uppsala (PNAS pnas.0914192107 – paper here). They show that a water molecule trapped at the active site of peptide bond formation on the ribosome serves in a proton shuttle, while a second water molecule helps to stabilize the negative charge on the substrate.

Erik Sunde and Bertil Halle at Lund show how water proton magnetic relaxation dispersion measurements can provide information on slow protein dynamics by virtue of the exchange between buried and bulk water molecules (JACS 131, 18214 (2009) – paper here). In effect, the internal water molecules serve as a probe of protein motions with a relaxation timescale comparable to the exchange time (typically 0.1 ns to 10 microseconds).

An intriguing demonstration that the chemistry of hydrated ions can be critically dependent on the geometry of the surrounding water network is provided by Rachael Relph at Yale and colleagues using vibrational spectroscopy of clusters (R. A. Relph et al., Science 327, 308 (2010) – paper here). They find that the extent to which NO+ reacts with water to form HONO varies with different numbers and arrangements of hydration water molecules (1-4). It’s an intriguing demonstration of geometrical effects in hydration, though what it can say in general about hydration in bulk solution is less immediately clear to me. There’s a commentary by Katrin Siefermann and Bernd Abel in the same issue (paper here).

Finally, just for fun, I’ve indulged in a little speculation here about the possibility of quasicrystalline water. There is a lot more behind all this that I was not able to include, following discussions with John Finney and Alan Mackay in particular. The upshot is that Alan gives at least some cause to think it may be possible in theory to construct a plausible H-bonded network with a quasicrystalline geometry. Whether one could make it in practice is, of course, quite another matter.

1 comment:

直到遠遠 said...

We could learn a lot from crayons. Some are sharp, some are pretty and some are dull, Some have weird names , and all are different colors, but they all have to live in the same box.............................................