Outstanding PhD. students and postdocs wanted!
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Address for Correspondence:
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Flemingovo nam. 2, Prague 6, CZ-16610, Czech Republic
Phone: +420 220 410 314
FAX: +420 220 410 320
Come to the
Water & Aqueous Solutions
Gordon Research Conference
this summer!!!
(ad from February 5 issue of Science)
The best graphical representation of our research topics I could think of is a dripping faucet. We model with molecular resolution structure and chemical dynamics of finite pieces of matter (clusters, droplets, systems with extended surfaces, solvated biomolecules,...). As faucets do (well, not the one below), we have a warm button (red) - systems at ambient conditions, and a cold button (blue) - cryogenic systems close to 0 K. Below is a list of several of our hottest (and coolest) topics.
Hottest News: Reaction of a proton and an electron toward a hydrogen atom is the simplest chemical process I can think of. It becomes, however, much more intriguing if it is happening in water. With Ondrej Marsalek in Prague, Tomaso Frigato and Burkhard Schmidt in Berlin, Joost VandeVondele in Zurich, and Steve Bradforth at USC we were able to capture using ab initio dynamics the molecular mechanism of this process with gory molecular detail. In agreement with kinetic measurements we showed that the process is a proton transfer (and not electron transfer) reaction, which is fast but not diffusion limited. The former is true since proton has a lower effective mass in water (it is "lighter") than hydrated electron. The latter is due to solvation effects. Namely, the two charged particles (i.e., proton and electron) have to first shed off their solvent shells before they can form the neutral hydrogen atom. The cost of this is almost as large as the binding energy of an H atom. The below journal cover shows the rection path by which a proton moves in a water cluster to a hydrated electron to form a hydrogen atom.
Hot News: Pairing between like-charged side chains in polyarginine. With Jiri Vondrasek and Jan Heyda in Prague, Phil Mason at Cornell, and Kim Collins at UMBI we have shown that the guanidinium cations forming arginine side chains tend to pair in water despite the obnious Couloumb repulsion between them. This work builds on previous work of Mason, Brady, and others who showed that guanidinium forms contact ion pairs in aqueous salt solutions. The present combined MD simulations and ab initio PCM calculations also allow us to trace this effect to a favorable combination of electrostatic, dispersion, and cavitation effects for the disc-shaped, quasi-aromatic guanidinium ions with an inhomogeneous internal distribution of charge. Analysis using the Protein Data Bank shows that such an associative behavior of arginine occurs frequently within (as well as inbetween) proteins with potential implications for enzymatic activities and protein association patterns. The below journal covers graphically depict side chain pairing in polyarginine and lack thereof in a control simulation of polylysine.
Less Hot News: Unraveling ionization processes in water and of aqueous biomolecules connected with indirect and direct ionization damage. With our colleagues Steve Bardforth and Anna Krylov (USC), Bernd Winter (BESSY Berlin), Tomaso Frigato and Burkhard Schmidt (FU Berlin) and Petr Slavicek (Inst. of Chem. Technol. Prague) we are investigating ionization processes in water, as well as for aqueous DNA components and side chain models of amino acids. Within the former, we follow the fate of the cationic hole in water (leading to H3O+ and OH) and the photodetached electron (leading to solvated electron). Within the latter, we are establishing vertical ionization potentials of aqueous DNA bases, nucleosides, nucleotides, and titratable side-chain groups of amino acids. We are combining ab initio calculations, DFT-based ab initio molecular dynamics, and methods employing a non-equilibrium polarizable continuum model to relate to photoelectron spectroscopy measurements. The below journal covers graphically depict ionization in aqueous protonated imidazole and the proton-transfer dynamics of the cationic hole in a water dimer.
Less Hot News: "Filming" ice nucleation and freezing in pure & salty water by simulation & experiment. With our German and Israeli colleagues Sigurd Bauerecker and Victoria Buch we have developed a concept of computational and experimental filming of freezing. On the experimental side, high-speed VIS and IR imaging provides a structural and thermal information about the proceeding freezing front with milisecond resolution. On the computational side, molecular dynamics simulations provide an atomistic picture of the initial state of ice nucleation at the sub-microsecond timescale. Homogeneous ice nucleation in salty water has been successfully simulated for the first time! The below journal cover graphically depicts the new concept of "filming" ice nucleation and freezing.
Older News: Is the surface of neat water ion-free, neutral, basic, or acidic? In our recent study (Buch, Milet, Vacha, Jungwirth, Devlin, PNAS 2007, 104, 7342; see also articles in Chemistry World and C&E News) we show that the surface monolayer is actually acidic with pH below 4.8 and pOH around 8. (We operationally define surface pH or pOH as the negative logarithm of hydronium or hydroxide concentration in the top-most layer.) We base this conclusion on ab initio and classical MD simulations of the ionic product of water, spectroscopic experiments, as well as on previous computational and experimental studies showing surface propensity of hydronium ions. This result can be relevant for aqueous systems with large surface to bulk ratio, such as microscopic atmospheric aerosols. It can also influence acido-basic processes at surfaces of hydrated proteins. Note that an (undisclosed) reader of our paper commented on the originality of our results. His or her comments together with our reply and the final decision of PNAS concerning this issue can be found here . A scientifically more interesting thing is that measurements of zeta potentials of oil droplets and air bubbles in water, titration experiments on oil suspensions in water, and disjoining pressure measurement on thin water films indicate that negative charge, interpreted as hydroxide ions, accumulates at water surface. We currenly have little clue concerning the origin of the discrepancy between these results on one hand and computer simulations, spectroscopic and surface tension measurements on the other hand. Possibly, different techniques are sensitive to varying regions of the interfacial layer. After all, the whole interface should be electrically neutral, so if one type of ions accumulates at the surface, the other should be enhanced in the subsurface. But clearly more work has to be done on this... The picture below shows a snapshot from a MD simulation with surface bound hydronium and bulk hydroxide.
Even Older News : Our study on the higher affinity of sodium over potassium to protein surface has appeared in PNAS (2006, 103, 15440). The results, which are pictorially shown below (sodium: green balls, potassium: blue balls, protein: RNase A), may provide hints as to why we are burning about 30 % of our available energy (1 meal per day!) to pump sodium out of the cell.
Much Older News: The Science magazine has elected our simulations
of ions at the air/water interface among the Top 10
Breakthroughs of the Year 2004
A good part of our efforts is directed towards elucidating the behaviour of ions at the air/water interface by a pragmatic combination of molecular dynamics simulations and ab initio quantum chemistry calculations. This study, which puts in question the traditional model of an ion-free surface of aqueous electrolytes, has also direct atmospheric implications (e.g., for the chemistry of aqueous sea salt aerosols or for thundercloud electrification). With Barbara Finlayson-Pitts and Doug Tobias we have put together a special issue of Chemical Reviews dedicated to structure and chemistry at aqueous interfaces, which summarizes recent computational and experimental findings. The below cover shows the active role of ions at the solution/wapor interface.
We have recently succeeded to freeze a slab of water from scratch. It is trivial to do it in the fridge but try it on the computer! Below is a JPCB cover showing that homogeneous ice nucleation starts preferentially in the subsurface. This has important implication for the microphysics of cirrus and polar stratospheric clouds and, consequently, for the global radiative balance of the Earth.
We have also looked into the onset of dissolution of complex salts recently. The below cover of PCCP shows the step-by-step hydration of NaSO4- by water molecules, as investigated by photoelectron spectroscopy and quantum chemical methods. Our ab initio calculations provide a detailed picture of the build up of the hydration shell and transition from a contact ion pair to a solvent separated ion pair.
Karl Popper showed us that nothing can be proved in science (only falsified). OK, nevertheless, here we show results from our simulations indicating the presence of iodide (but not fluoride or sodium) at the surface of water (but not methanol), supported by Metastable Impact Electron Spectroscopy. There is of course a small catch - simulations were done in water, while the experiment in glassy amorphous solid water, however, both have very similar structural properties.
This JPCB cover summarizes our reasearch demonstrating the different structure of the surface of aqueous acids, bases, and salts: In strong monovalent inorganic acids (such as HCl, HBr, or HI) both cations (hydronium) and anions exhibit propensity for the interface. There is a net accumulation of ions n the interfacial layer and, consequently, these acids reduce surface tension of water. In inorganic salts (such as NaCl and other alkali halides) and bases (such as NaOH) the cations are repelled from the surface while the anions exhibit a varying surface propensity (often enhanced at the surface and depleted in the sub-surface), depending on their polarizability, size, and other properties. As a result, there is a net depletion of ions from the interfacial layer and, consequently, these salts and bases increase the surface tension.
Multiply charged ions behave differently since the "bulk driving" electrostatic force is much stronger than for monovalent ions and overwhelms the "surface driving" polarization interactions. A good example is the sulfate dianion, which is very strongly repelled from the air/water interface. This is demonstrated on a 2005 J. Phys. Chem. B cover showing the ion-free surface layers of aqueous sulfate salts, which is also manifested in the experimental VSFG spectra.
Below is the cover page of a 2004 Australian Journal of Chemistry issue showing our simulations of ionic surfactants: aqueous tetra-butyl ammonium fluoride with cations at the solution/vapor interface.
Below is the cover page of a 2002 J. Phys. Chem. B issue containing our Feature Article "Ions at the Air/Water Interface" which summarizes our results on the propensity of heavier halides (chloride, bromide, and iodide) for the air water interface.
