This page summarizes some of research projects where I took a part in the past. Some of them are finished now, in some of them I am not involved any longer. The paragraphs were copied from the Current projects section at the moment, when the respective project became obsolete, and they weren’t changed/edited. Therefore, from a grammatical point of view, they usually aren’t completely correct (use of wrong tense, …).
Homogeneous nucleation of water
(with P. Jungwirth)
Methods of molecular dynamics are used to study the homogeneous nucleation of water in the slab arrangement. This process play very important role in the atmosphere where supercooled water transforms into ice without heterogenous crystallization nucleus.
We are trying to answer the question whether this type of nucleation proceeds from the surface or from the bulk. Experiments indicate that both mechanisms are possible. Theoretical methods might therefore provide (not only) atmospheric scientists with highly relevant information and help in better understanding of the behavior of supercooled water.
Our study now extends towards the partitioning of salt at the ice/water interface (this topic is connected with one of our previous projects, discussed below). We would also like to see in the simulations how does the presence of amphiphilic contaminants (namely aliphatic alcohols) influence the homogeneous nucleation and freezing processes.
Theoretical study of zeolites
(with P. Nachtigall)
Zeolites play very important role in many technological processes and are widely used in catalysis.
Our current project concerns the distribution of sodium and calcium cations in zeolites with low Si/Al ratio - we currently study the LTA zeolite where the amounts of silicon and aluminium atoms are the same. Connection to experiment is established by predicting the vibration spectra of CO molecules adsorbed in the material.
Ion interactions with proteins - (not only) molecular ions
(with P. Jungwirth)
Preferential adsorption of different ions at the protein surfaces is studied by molecular dynamics simulations.
Recently we studied the adsorption characteristics of several ions (sodium, choline, chloride, sulfate) on the surface of Horseradish Peroxidase. Experiments show that a superactivity can be induced in this protein by sulfate anions. On the other hand, presence of the choline decreases the activity of the protein. This difference is partially caused by pH changes of the solution as the effect of the added salt. However, pH is not the only effect.
Simulations show that different ions have tendency to bind to different sites at the protein surface. This fact can serve as an explanation of the effect of ions on the protein activity.
Sulfate increases activity mainly by pH change and binds to the charged groups at the protein surface. Choline, on the other hand, has tendency to bind to hydrophobic residues. Solvent-exposed hydrophobic residues are usually found mainly in the active site. Therefore, choline will have higher probability to bind at/near the active site and decrease the activity of the enzyme.
Brine rejection from freezing salt solutions
(with P. Jungwirth)
In 2005, we mostly finished our extensive study of water freezing and brine rejection from freezing salt solutions. Our group was the first one in the world that was able to study this well known natural process using the methods of computational chemistry.
We employed the methods of molecular dynamics to observe the dynamics of the process that occurs during freezing of salt solutions. Salt badly soluble in ice is rejected to the surrounding environment. This process has large natural (water masses circulation in the ocean, possible role in thundercloud electrification) and technical (desalination) cosequences.
The figure (click to get bigger picture) shows snapshots from the MD simulations of the freezing of salt water (sodium - green, chloride - brown). Ions are rejected/repelled from the freezing water (ice lattice) into the remaining liquid phase.
On 31st July 2006, German scientific portal Wissenschaft.de mentioned our work on the brine rejection in this article (the pdf printout of the article can be found here in case the original page is no longer available).
Structure and dynamics of ions at the air/water interface
(with P. Jungwirth)
Results of the recent research (both experimental and theoretical) indicate that the ‘classic’ picture of the air/water interface devoid of ions (Onsager-Samaras theory of electrolytes and interfaces) is valid only for small and nonpolarizable species. Big, soft, polarizable ions show profound affinity towards the interface. Polarization interactions therefore play a crucial role in this process.
Study of the propensity of different ions for the air/water interfaces has long ‘tradition’ in the group of Prof. Jungwirth. We studied the aqueous interfaces of various electrolyte solutions using the molecular dynamics with polarizable potentials.
The project started with simple atomic inorganic ions (halides) and evolved into the study of simple molecular ions (nitrate, sulfate, azide, thiocyanate). In the last period we investigated solvation properties of simple symmetric tetraalkylammonium cations (C=1-4) and some cations with long hydrophobic tails.
The figure (click to get bigger picture) shows the side view of the distribution of ions throughout the water slab. Interfaces are located in the upper and lower parts of the picture. Following ions are involved: cations - tetrabutylammonium, sodium (green); anions - iodide (violet), bromide (orange).
