Friday, February 22, 2013

On icebergs

Still we ponder the nature of hydrophobic hydration: is it more ‘ice-like’ in some sense? Apparently so, say Dor Ben-Amotz and colleagues at Purdue (J. G. Davis et al., Nature 491, 582; 2012 – paper here). They use Raman spectroscopy to monitor vibrational spectra of water hydrating linear alcohols ranging from methanol to heptanol, and see more tetrahedral ordering of water molecules, and fewer weak hydrogen bonds, at low temperatures. But for hydrophobic chains longer than about 1 nm this hydration structure gives way to one in which the water is more disordered and has weaker H-bonds at higher temperatures. This scale-dependent crossover is reminiscent of that proposed by Lum, Chandler & Weeks above about 1 nm (J. Phys. Chem. B 103, 4570; 1999).

The nature of the hydration shells of methanol, ethanol and propanol have been probed using THz spectroscopy by Vladimir Matvejev of the Free University of Brussels and colleagues (J. Phys. Chem. B 116, 14071; 2012 – paper here). They estimate that the shells comprise about 14, 23, 23 and 31 molecules for methanol, ethanol, 1- and 2-propanol, respectively, and the water molecules are retarded by a factor of around 1.4.

In a somewhat similar vein, L. Luca of the University of Perugia and colleagues use GHz-THz light scattering to probe the hydration of mono- and disaccharides (J. Phys. Chem. B 116, 14760; 2012 – paper here). They find that slowing of water collective reorientation (by relatively large factors of 5-6) occurs only over relatively short distances (3-4 Å or essentially the first hydration layer), regardless of the size of the sugar molecules. This retardation involves considerably more water molecules than those few instantaneously hydrogen-bonded to the sugar.

A more generic approach to small-molecule solvation is described by Alla Oleinikova and Ivan Brovchenko of the Dortmund University of Technology (J. Phys. Chem. B jp306781y – paper here). They use MC simulations to study water structure around spherical solute particles 3-10 Å in size that vary from strongly hydrophobic to strongly hydrophilic. In all cases there is a density depletion relative to the bulk due simply to the missing-neighbour effect. For strongly hydrophobic particles there is a drying transition at the surface. Similar effects are seen for other fluids, but the directional hydrogen bonding of water enhances them.

Water in useful places: there is likely to be water molecules forging a hydrogen-bonded assembly in the mammalian photoreceptor melanopsin in the retina, which triggers the biological clock, according to Sivakumar Sekharan and colleagues at Cornell (JACS 134, 19536; 2012 – paper here). Their first-principles calculations of the active site suggest that two water molecules bridge the Schiff base and residues on the peptide, accounting for the blue shift of the optical absorption relative to the closely related rhodopsin.

Cytochrome c might control water access to its heme centre to tune the reduction potential via hydration changes, according to quantum MD simulations of Isabella Daidone of the University of L’Aquila and colleagues (C. A. Bortolotti et al., JACS 134, 13670; 2012 – paper here). They find that a yeast cytochrome has two channels that it can open to admit water, altering the reduction potential and thus refining processes of electron transfer.

How water evaporates from the air-water interface has been studied in detail by Patrick Varilly and David Chandler at Berkeley (J. Phys. Chem. B jp310070y – paper here). They find that the escape trajectory of a water molecule can be described in terms of two parameters: the distance from the instantaneous interface and the velocity along the surface normal. The results seem to imply that evaporation has zero activation energy, as some but not all experiments have suggested.

Fresh variety in the structures of ice confined to nanopores is reported by Jaeil Bai and Xiao Cheng Zeng of the University of Nebraska (PNAS 109, 21240; 2012 – paper here). Their simulations indicate that a bilayer of ice-like water molecules in slit-like pores about 7-9Å apart can be transformed under pressure to an amorphous phase and then to a very-high-density amorphous phase at 250K and 3 GPa. For rapid compression to 6 GPa an entirely new VHD ordered phase is found in which the water molecules are linked into square nanotubes.

Andreas Barth and colleagues at Stockholm University propose that studying changes in the water absorption bands in infrared spectroscopy can offer a way of quickly and remotely monitoring for binding of a ligand to a target protein in drug development (S. Kumar et al., J. Phys. Chem. B 116, 13968; 2012 – paper here). Specifically, they look at the bands diagnostic of ‘bound’ water in the binding cavity, and see this decline as ligand binding expels the water. They have so far looked at rather high protein concentrations, but think that the approach should work at lower concentrations with brighter light sources.

Hydrophobic drugs can be rendered more water-soluble by adding certain solutes known as hydrotropes. Although this has been long known, the mechanism is not clear. Seishi Shimizu of the University of York and colleagues have studied the question using thermodynamic theory (the so-called fluctuation theory of solution) and measurements of thermodynamic quantities (J. J. Booth et al., J. Phys. Chem. B 116, 14915; 2012 – paper here).

Junrong Zheng at Rice University and coworkers report evidence for strong segregation of ions and water in strong electrolyte solutions of thiocyanate ions (J. Phys. Chem. B jp310153n – paper here). The clustering is enhanced by the addition of strongly hydrated ions such as fluoride, whereas iodide ions tend to associate with the SCN clusters. In any event, the aqueous systems are strongly inhomogeneous.

Finally for now – though lots more still to catch up on – I have a brief article on the Chemistry World site (here) on a recent paper by Thomas Kühne and Rustam Khaliullin at Mainz (Nat. Commun. 4, 1450; 2013 – paper here) that seems to shed light on the arguments over XAS studies of liquid water by Anders Nilsson and colleagues (Wernet et al., Science 304, 995; 2004). Views on whether there was a controversy here in the first place will doubtless vary, but it seems that this new work provides a useful perspective on what the XAS work was showing. Anders gave me some rather extensive remarks on his view of the matter, which I thought might be usefully reported here. Forgive me for presenting them here unmediated – they will hopefully at least clarify Anders’ current position on this. Everything that follows is from him:

I find this paper to represent a very important step forward. It is very close to our original suggestion in the Wernet et al. Science paper that many molecules will be in instantaneous configurations with one strong and one weak hydrogen bond, i.e. asymmetric configurations. XAS measures the electronic structure on a timescale of a few attoseconds which means that the molecules have no time to move so we are only detecting snapshots of space-averaged frozen configurations (also stated in the original Wernet et al. paper).

However, there is a difference. In real water we expect the asymmetry between the strong and weak bonds to be much larger than based on the structures from the current simulation. It is mentioned in the methods section but not directly in the main text. Here is the underlying experimental evidence that requires no spectroscopy interpretation.

I attach a recent study (JCP in press, Skinner et al.) where we together with Benmore’s group have undertaken a major effort to determine a more accurate O-O pair distribution function (PDF) of ambient water. This is based on 4 new x-ray diffraction data sets (only 3 are consistent at high Q), all with a much higher Q cut-off than any previous measurements where we have also taken serious care to remove any OH contributions. Figure 9a shows the O-O PDF with very small error bars with a first peak height of 2.57. If you comparethis with the O-O PDF presented in the supplementary material it is clear that the simulations have an overstructured main peak. For the PBE functional, used in the main text, the peak height is 3.3. The TPSS –D3-FF simulation shown in the supplementary information has a peak height of 3.1, still overstructured but less so than the PBE. The consequence in the asymmetry is clearly visible in terms of the weak bond energy distribution from fig. 3a and S3a where the latter has more contributions towards lower energies. If we have to further dramatically understructure the liquid down to a peak height of 2.57 in the O-O PDF we expect the asymmetry to become much larger. In my opinion their asymmetry is only a lower limit.

Most likely the underlying reason for the asymmetry is in the many-body cooperativity effects that only an electronic structure simulation can capture as demonstrated in the current paper, and which is not represented by classical force fields. It has been known that the cooperativity effect is strongest when you have one strong donor and one strong acceptor bond. Thereby for 2 hydrogen bonded structures the energy per hydrogen bond is higher than for 4 bonded or tetrahedral coordinated structures. We discussed this in a few sentences in the Wernet et al. paper with references that I have underlined with yellow in the attachment. I also attach a recent review by Lars, Congcong and myself on water (A. Nilsson et al., J. Mol. Liq. 176, 2; 2012) where we discuss the importance to further develop simulations and in particular the importance of many-body effects in an electronic structure description where it is also essential that the latter includes van der Waals interactions.

Another interesting aspect in their study is the dynamics indicating that the strong and weak bonds switch place on ultrafast time scales. This is also in line with our previous discussions. I underline in the Leetma et al. paper (J. Chem. Phys. 129, 084502; 2008) how we discussed ultrafast measurements where the strongly H-bonded OH group in one water molecule could switch places with the weak one. The difference was only that we assumed that the switching occurred via librations whereas in their simulations it is mostly via translational motions of other molecules.

We had a last sentence in our Wernet et al. paper of a more speculative nature that with mostly only one strong donor and one strong acceptor bond per molecule, one-dimensional structures should appear which could be chains or rings. I noticed that they have a sentence regarding molecular chains at each instant connecting the strong bonds. Very nice.

Another point not related to the current paper that could also be of interest for you is the recent paper by Overduin and Patey (J. Phys. Chem. B 116, 12014; 2012) that discusses our PNAS Huang et al. paper based on simulations coming to similar conclusions regarding inhomogeneities in the liquid but only using a different language in terms of concentration fluctuations of two different classes of structures.

I think Kühne and Khaliullin put the picture in terms of a symmetry breaking in order to be not too far away from the most accepted tetrahedral picture of water. But if you really look at what they claim, which is also aligned with us, is that most molecules will be in an asymmetric position at all instances when taking a snapshot. It is simply that an OH group that is either weak or strong switches on a rather fast timescale. This would mean that the symmetric position is never really seen. It is only when you average over a long time that it looks like it is mostly in the tetrahedral position. Like me make analog. Take a pendulum that swings back and forth. The speed at the end points are close to zero and at the middle position it is highest. It means that the pendulum spends most time at the end points and extremely little time at the middle position. If you take the average position it will be the middle position but it is hardly ever visited. You could in such a picture claim that the equilibrium position is in the middle if you average over a single period but the pendulum will spend very little time there. The question is how the surrounding will be affected by such a motion. If I understand correctly the paper it is the surrounding that indeed infer the asymmetry. They claim that it is the translational motion of the other molecules that provides the mechanism of the switching. This should mean in my opinion that it is the end points of the asymmetric motion that makes the interaction with the surrounding and not the time averaged position. If it would have been dominated by a more internal motion such as librations it could have had less effect on the surrounding.

In water my own belief is that it is somewhat more complicated. Let me come to my current picture of water at the end of these comments.

I think it is currently not possible to observe the asymmetry based on the current status of pump-probe IR spectroscopy. Please don't quote me on this but I believe that we are still missing some major understanding about IR spectroscopy. The vibrational life time as a local oscillator in H20 is too short. Nearly all experiments on ultrafast dynamics are based on isotope substitution with HDO impurities in either H2O and D2O and measurements of the time resolved development of the OH or OD frequency. It is then assumed that HDO has equal probabilities for all molecular positions in the liquid. This assumption has never been proven. Based on our understanding of water in terms of fluctuations of two local structures, tetrahedral (low density water) and asymmetric (high density water) the latter has more contributions to the free energy through stronger bond energy whereas the latter has more entropy. I attached a slide from one of my presentations so you can see what I mean (hit a return in slide show mode to see the motion). There you also see the switching of the two bonds. Since the asymmetric configuration will provide more entropy and the HDO is already asymmetric it is likely that HDO will reside more in asymmetric configurations. Furthermore, we can anticipate through quantum effects that also the OD and OH hydrogen bonds are different. I would assume that OD will more likely be situated with the strong bond and OH more in the weak bond. This was observed in a recent PRL by Misha Bonn's group (attached) where they showed based on sum frequency generation spectroscopy and simulations that there is a strong preference for OH to point to the vacuum and OD to the liquid side for HDO at the water-air interface. At this point I think caution needs to be exercised regarding pump probe IR since these measurements might only be probing some fraction of all possible molecular motions. We (Lars) are currently further investigating the HDO dynamics based on quantum simulations. There are also recent indications that the pump pulse disturbs the dynamics and these measurements might not always represent the equilibrium motions.

We are currently using the new x-ray laser at Stanford, the Linac Coherent Light Source (LCLS) to various problems related to water. The machine provides completely new opportunities. We are planning a future step to open up dynamics. In particular x-ray correlation spectroscopy with x-ray lasers could provide new answers. This is probably 2 years away. Since the x-ray laser is fully coherent there will be a speckle pattern due to diffraction also from a disordered material. The plan is to make probe-probe measurement to thereby study equilibrium dynamics. You split the x-ray beam into two pulses with a controllable delay and the change in the speckle pattern will give information about how molecules have moved between the two pulses. These will be most challenging experiments but hopefully can be done and would open for completely new avenue's to probe dynamics in liquids. Naturally one challenge will be to not allow the first pulse to disturb the system but water is quite forgiving for hard x-rays since it is a low Z liquid.

We have demonstrated in a number of papers that this asymmetry can't been seen in diffraction since the data is not completely perfect. The difficulty is to have a technique that is only sensitive to the hydrogen bonding asymmetry around individual molecules. You can have a total hydrogen bonding average through a linear combination of water molecules with nearly no hydrogen bonds and fully tetrahedral water that on average would be like an asymmetric species. It is the rehybridization of the molecular orbital structure leading to local OH orbitals instead of delocalized H2O orbitals that makes XAS sensitive. I attach a paper where we discuss this (Nilsson section 3.5). It has to do with O2p and O2s hybridization and XAS only provides intensity for the O2p part in the orbitals. It is quite involved. Maybe it is time for a simpler review so many can understand these effects.

Here is our current picture of water. At high temperatures (close to boiling and above) water behaves as a simple liquid where most interactions are isotropic (dominated by van der Waals interactions). This is a structure where many molecules are in very disordered shells and without having a well defined first and second shell (this structure you get from ab initio MD simulations with van der Waals functionals even at ambient temperature, see discussion in my previous mail in paper "fluctuations in ambient water"). This type of non directional orientations gives high flexibility for various motions and high entropy. As the liquid cools down the water molecules starts to stick to each other through directional hydrogen bonds. This will appear in two classes of configurations, tetrahedral and asymmetric. In the tetrahedral structures each molecules are in 4 hydrogen bonds, this provides the lowest enthalpic energy. Since cooperatively effects makes the bonds stronger if water is bonded to other waters that are also in tetrahedral structures, these start to clump together in small local regions. Since the molecules are stuck with four bonds the motion is very restricted (see the attached slide) and thereby low entropy.

The other alternative is to form asymmetric structures. Here the hydrogen bond energy per molecule is higher than in the tetrahedral structures but since it is fewer bonds the enthalpic energy is lower. With less directional hydrogen bonds you have more flexibility for motions and thereby higher entropy (see slides). In this structure there are also non isotropic molecular interactions causing interstitial molecules. These are therefore called by us and others, preferable in the supercooled community, as high density water. Another way of viewing such species is that we start not with hexagonal ice but with high density amorphous or very high density amorphous ices where we have a large collapse of the second shell. In these ices we have also a local tetrahedral bonding but with other angles towards the second shell (often call interstitials). Here we induce asymmetric distortions around these tetrahedral bonded molecules in the first shell but simultaneous keeping the interstitials ( see fluctuations in ambient water). We have also seen this in water at an interface recently published in the Nature journal Scientific Reports (see attached Kaya et al.). There are fluctuations between the tetrahedral structures and asymmetric or high density structures. As we cool the liquid down the molecules in the asymmetric structures converts more and more into the tetrahedral structures which grows in size since the enthalpic energy contributes more to the free energy with decreasing temperature. The timescales in the fluctuations between these two classes should also slow down (not yet determined). There is also a continuous change in the asymmetric structures with temperature. The switching time is expected to slow down and thereby also the amplitude in the motion with decreasing temperature. We will be approaching more and more a local tetrahedral arrangement. However, not as in hexagonal ice but more towards high density ices with still many interstitials. That the density is decreasing below 4C is simply due to that we are at the same time converting many molecules into tetrahedral structures which have a more similar structure as hexagonal ice but disordered more towards low density amorphous ice (low density water) with the second shell at the tetrahedral angle causing an open network with low density. In my opinion we have to consider both these two classes of fluctuations (between tetrahedral and asymmetric and within asymmetric) separate but most likely there should also be some coupling.

It is these fluctuations between tetrahedral and asymmetric structures plus the varying fluctuations in the asymmetric structures that depends on temperature, pressure and interactions with solutes, interfaces, biomolecules etc. We can imagine that for instance an interface disfavors tetrahedral structures (such as in Kaya et al.) creating a dominance of asymmetric high density structures but through the interaction with the interface the switching time and amplitude will be affected between the strong and weak bonds.