Welcome to the homepage of              Pavel Jungwirth


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Open Positions:
Motivated and molecular simulations inclined PhD. and Ms. students always welcome!

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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: +420 220 183 184

"One should not increase, beyond what is necessary, the number of entities required to explain anything." (Occam's razor)

"For every phenomenon, however complex, someone will eventually come up with a simple and elegant theory. This theory will be wrong." (Rothchild's rule)

"The "reductionism" of evolutionary science is purely tactical. We do what we can do in the face of an awsome amount of diversity and complexity." (Tactical reductionism by Richerson and Boyd)

Latest news:

PNAS has just published our discovery of a binding motif which holds together arginine-rich cationic peptides. We know from school that ions or charged groups carrying a charge of the same sign repel each other. In aqueous media, however, this electrostatic repulsion is significantly reduced and can be compensated by other molecular forces. Using molecular dynamics and X-ray scattering our international team encompassing Lund, Prague, Grenoble, and Zagreb, unraveled a new binding pattern, wherein the positively charged side chains of arginine amino acids bind to each other in the presence of negatively charged terminal groups or side chains of peptides or proteins. Subsequently, we have identified an analogous motif in more than two hundred biologically significant structures in the protein database. Our findings provide the key to the understanding of the self-association mechanism in oligo-arginines with implications for ther potential biological roles including a cell penetration ability.

In the role of a J. Phys. Chem. editor:

We have just published with my colleague-editor Arun Yethiraj a viewpoint on how we think a suitable manuscript for JPC on biomolecular or polymer simulation should look like. Maybe you'll find this useful or at least amusing...


We have published with our experimental and computational colleagues our best attempt to summarize what we know about the Hofmeister series today. In the last decade, we have been obsessed with ion-specific (Hofmeister) effects on proteins and this Feature Article may be viewed as a sort of therapy converting an unhealthy obsession into a molecular understanding.


Angewadte Chemie has selected the continuation of our "balcony experiments" with alkali metals in water for inside cover (below). As Phil says: "Explosions are sooo much last year science," so this year we followed the non-explosive (but vigorous) reaction of a sodium/potassium alloy drop gently placed on water. And with our colleagues from Braunschweig - Sigurd and Tillmann, we saw amazing chemistry happening. This includes blue solvated electrons visible with a naked eye despite their ephemeral lifetime, colorful evaporation of the alkali metals, a burning red drop, ... and, amazingly, the final "transmutation"of the metal drop into a transparent "marble" of molten hydroxide supported at the water surface via the Leidenfrost effect (same as that stabilizing water drops on a hot stove or that allowing you (not me!) to walk on hot ashes). Words cannot describe the beauty of this in full so go ahead and check our youtube video

The story has been also covered in the popular science literature, see:
Chemistry World
New Scientist


Chemistry World of the Royal Society of Chemistry selected our study of the mechanism of alkali metal explosions in water in their editorial Cutting edge chemistry in 2015 under a rather appropriately chosen title "Back to school":)

(Older) News:

The Journal of Physical Chemistry Letters has published a Viewpoint of mine entitled Biological water or rather water in biology? (JPCL 2015, 6, 2449). The key message, summarized in a somewhat lighter tone in my amateurish drawing below, is as follows: While water with dissolved ions and osmolytes is essential for establishing homeostasis, it is primarily the biomolecule itself which carries the biological function. It is perfectly justifiable to talk about water in biology and discuss the role of interfacial water around biomolecules with its distinct properties. However, I would argue that the often used term "biological water", with all its connotations toward a hypothetical state of cellular "vicinal water" carrying biological function, is bringing us dangerously close to the long obsolete concept of "vis vitalis" and should, therefore, be dropped.

(Older) News:

Nature Chemistry published on January 26, 2015 results of our "balcony experiments" on alkali metal explosions in water. This is NOT what we normally do, but we love the blasts (especially Phil does!) and we want to understand why the thing explodes. Because it should not - the steam and hydrogen gas produced at the interface between the alkali metal and water should effectively separate the two reactants quenching thus the reaction. So, why the hell DOES it explode? Using high speed cameras, molecular dynamics simulations, and back-of-the-envelope calculations we found out the the key piece missing in the puzzle is a Coulomb explosion of the metal prior to the steam and hydrogen blast. As electrons leave the metal for water (to react there creating hydrogen and hydroxide) the metal charges positively to the extent that it becomes unstable (so called Rayleigh instability, same as in electrospray) and shoots out metal spikes into water, ensuring thus efficient mixing of reactants and enabling the explosive behavior. There was also a minor explosion in the popular science literature following our blast, see e.g.:
Chemistry World

(Older) News:

The editors of the January 14, 2015 issue of JACS chose as the cover ilustration our picture showing in an artistic way ionization of aqueous DNA by synchrotron radiation and the corresponsing ionization energies of the individual aqueous DNA bases. In the words of the Editor: "Ionizing radiation can induce oxidative damage to DNA, including double-strand breaks, which can lead to mutations and possibly cancer. To theoretically predict the rate of certain indicators of this damage, researchers need several pieces of information, including the one-electron redox potential of the five nucleobases. However, it has been difficult to measure these properties electrochemically, and other recent approaches have not considered the bases in aqueous solution, their native habitat. Now Petr Slavicek, Bernd Winter, Pavel Jungwirth, Stephen E. Bradforth and colleagues have determined the one-electron redox potentials of nucleic acid bases in water with a combined experimental-computational approach.They use liquid-jet photoelectron spectroscopy to measure the vertical ionization energies of nucleobase components, including purine and pyrimidine nucleotides, nucleosides, pentose sugars, and inorganic phosphate, then use quantum chemistry calculations to estimate the reorganization energies to the change in nucleobase charge. By combining these two data sets, the authors have determined sufficiently accurate reduction potentials for nucleobases in their native environment; values that could help to clarify the rate of oxidative damage to DNA in sunlight and higher-energy sources of radiation."

Our closely tied group of versatile scientists in the new building of the Institute - Summer 2016

From the left: Tomas Martinek, Pauline Delcroix, Aniket Magarkar, Barbara Jagoda-Cwiklik, Stepan Timr, Elise Duboue-Dijon, Hector Martinez-Seara, PJ, Roman Pleskot, Josef Melcr, Vladimir Palivec, and Ondrej Tichacek.

Missing from the picture: Phil Mason, Katarina Baxova, Krystof Brezina, Jan Kadlec, and Tereza Perlacova.

Group of oak-huggers in front of the Institute - Fall 2015

Standing (from the left): Josef Melcr, Daniel Knopf (visiting), Roman Pleskot, Martina Roeselova, Jana Hladilkova, Katarina Baxova, Eva Pluharova, Daniel Bonhenry, Barbara Jagoda-Cwiklik, Lukasz Cwiklik, Alena Habartova, Frank Uhlig, and Miriam Kohagen.

Hanging (from the left): Phil Mason, Stepan Timr, PJ, Tomas Martinek, and Vladimir Palivec.

Arguably our best group photo ever - Spring 2013

More photos...

Photo: Lecture
Photo: Simulation
Photo: Experiment
Photo: Field Study
Photo: Conference Tour
Photo: Public Relations
Photo: Collaborating (Three Beauties)
Photo: Performing (Research)
Photo: Old Computer Facility
Photo: New Computer Facility
Photo: Becoming JPC Editor
Photo: Visiting at ENS Paris
Photo: Hanging Hofmeister
Photo: Working at Rush Uni Chicago
Photo: Becoming Finland Distinguished Professor
Photo: Group Tree Spring 2014
Photo: Group Tree Winter 2013
Photo: Group Tree Summer 2011
Photo: Moving to New Offices October 2016

The editors of the March 2014 issue of Electrophoresis (Special Issue on Fundamentals) picked for the cover our figure showing electrophoretic mobilities of neutral markers in aqueous salt solutions. In the related article we demonstrate using capillary electrophoresis and molecular dynamics simulations two things: i) that neutral markers can have non-zero electrophoretic mobilities thanks to specific interactions with salt ions from the solution and ii) quantitatively, these mobilities depend on the chemical composition of a particular marker. As a result, we show that there is no "perfect" neutral electrophoretic marker, since any marker can acquire a non-zero mobility due to interactions with dissolved ions. This mobility is typically small, but clearly measurable.

A cover on the January 30, 2014 issue of the Journal of Physical Chemistry B shows our most recent joint experimental and computational study aimed at elucidating the orientational distribution of a fluorescence dye in a model phospholipid membrane. Combination of ab initio and molecular dynamics calculations yeilded a distribution which is in a very good agreement with the result obtained from fluorescence detected linear dichroism. The ultimate goal is to develop our approaches into a technique capable of yielding detailed quantitative structural information on membrane proteins in living cells.

Science has covered our recent JPCL paper on the structure of the hydrated electron as a short article in the section Editor's Choice. This paper entitled Unraveling the Complex Nature of the Hydrated Electron presents ab initio molecular dynamics simulations of an electron in liquid water performed by my students Frank Uhlig and Ondrej Marsalek. As the picture below suggests we indeed got the hydrated electron under a (quantum mechanical) magnifying glass!

Chemical & Engineering News recently published an article about Hofmeister effects showing results from our JACS 2012, 134, 10039 paper with Paul Cremer's and Christian Hilty's groups at Texas A&M University.

Victoria Buch Memorial Issue: Below is the cover of the special JPCA issue in memory of late Victoria Buch (1954-2009) put together by her colleagues. Check this issue out and remember Victoria as a great scientist, warm friend, and passionate human rights activist!

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.

Pairing between like-charged side chains in polyarginine. 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 other groups 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.

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.

"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.

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" about 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 being aware of the fact that true pH, defined via hydronium activity, is the same at the surface as in the bulk.) 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. The picture below shows a snapshot from a MD simulation with surface bound hydronium and bulk hydroxide.

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.

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 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.