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Recent papers

See also Molecular studies for detailed information on activities of our research group

Most papers are in the PDF format. Figures are sometimes in different formats: TIFF, GIF, PostScript, and in the PCL language for HP LaserJet compatible printers. The PCL (HP) files are good for direct sending to a printer. This can be done from DOS (or DOS box in Window$, OS/2, ...) using command (assuming the printer on LPT1)
   copy /b figure.hp lpt1
or using PKUNZIP directly from a ZIP archive
   pkunzip -pb1 paperhp.zip
In Unix, direct printing depends on local settings. Sometimes the simplest command
   lpr -Pprinter figure.hp
works fine, sometimes there is a special "text" version of the printer driver (while the "normal" driver is for PostScript), sometimes there is an option to the lpr command disabling PostScript processing.

Jiri Genzer, Jiri Kolafa
Molecular dynamics of potential models with polarizability: comparison of methods
J. Mol. Liq., in press

Three methods for molecular dynamics of models with induced dipoles are optimized for accuracy and performance and compared: the predicted iteration method, the always stable predictor-corrector method, and the extended Lagrangian method (Car-Parrinello approach). The comparison criteria include thermodynamic quantities (energy, pressure, averaged induced dipoles), control quantities (total energy conservation, energy equipartition, errors in induced dipoles), and computer time. We recommend the always stable predictor-corrector method as a compromise between accuracy, speed, and simulation consistency.

Text (PDF)

Martin Lisal, Jiri Kolafa, Ivo Nezbeda
An examination of the five-site potential (TIP5P) for water
J. Chem. Phys. 117, 8892-8897 (2002)

Parametrization of the TIP5P model of water [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112, 8910 (2000)] has been examined by several computer simulation methods accounting properly for long-range forces. The structural and thermodynamic properties at a pressure of 1 atm over the temperature range (-25°C,+75°C) and the vapor-liquid coexistence have been determined. It is shown that the simple spherical cutoff method used in the original simulations to find optimized parameters of this 5-site model is inaccurate and that its results differ from those obtained by both the Ewald summation and reaction field methods. Consequently, the pivot property to which the parameters were adjusted, the location of the density maximum at 1 atm, does not agree with experimental values. The equilibrium properties then show only a fair agreement with experimental data and are uniformly inferior to those of TIP4P water over the entire coexistence range.

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Jiri Kolafa, Stanislav Labik, Anatol Malijevsky
The bridge function of hard spheres by direct inversion of computer simulation data
Molec. Phys. 100, 2629-2640 (2002)

The bridge function of the hard sphere fluid has been calculated from our new highly accurate Monte Carlo and molecular dynamics simulation data on the radial distribution function using the (inverted) Ornstein-Zernike equation. Both the systematic errors (finite size, grid size, tail) and statistical errors are analyzed in detail and ways to suppress them are proposed. Uncertainties in the resulting values of B(r) are about 0.001. In contrast with previous findings the bridge function is both positive and negative.

The MD simulation program

Jiri Kolafa, Ivo Nezbeda
Effect of short- and long-range forces on the properties of fluids.
III. Dipolar and quadrupolar fluids
Mol. Phys. 99, 11751-1764 (2001)

Using realistic pair potential models for acetone and carbon dioxide, both the spatial and orientational structure of these two typical multipolar (i.e. dipolar and quadrupolar, respectively) fluids is investigated in detail by computing the complete set of the site-site correlation functions, multipole-multipole correlation functions, and selected 2D correlation functions. The effect of the range of interactions on both the structural and thermodynamic properties of these fluids is studied by decomposing the potential into short- and long-range parts in the same manner as for water [Kolafa, J. and Nezbeda, I, 2000, Molec. Phys., 98, 1505; Nezbeda, I., and Lisal, M, 2001, Molec. Phys., 99, 291]. It is found that the spatial arrangement of the molecules is only marginally affected by the long-range forces. The effect of electrostatic interactions is significant at short separations and cannot be neglected but nevertheless the overall structure of the short-range and full systems is similar as well as their dielectric constants. These findings are also reflected in the dependence of the thermodynamic properties on the potential range with the short-range models providing a very good approximation to those of the full system.

Text (PDF)

Yi-Chia Lee, Jiri Kolafa, Larry A. Curtiss, Mark A. Ratner, and Duward F. Shriver
Molten Salt Electrolytes. I. Experimental and Theoretical Studies of LiI/AlCl₃
J. Chem. Phys. 114, 9998-10009 (2001)

Molten LiI/AlCl₃ with different molar ratios of LiI to AlCl₃ were prepared and characterized by Raman spectroscopy, thermal analysis, and impedance measurements. The LiI/AlCl₃ adducts melt at 70-80^oC and the Raman spectrum indicates that a variety of haloaluminates exist in the system. The 1:1 adduct has the highest ionic conductivity, 2e-6 S/cm at 25^oC, and the conductivity increases dramatically as the temperature is increased. Molecular dynamics simulations suggest that several haloaluminates are present in the adducts. Ab initio calculations were carried out on the species that were predicted by MD simulations and these results were compared with Raman spectra, and good agreement was obtained. Several ns long MD simulations allowed us to study the conductivity and relaxation processes in the 1:1 and 1:2 melts at higher temperatures.
Supplementary material

[1] Z. Akdeniz, G. Pastore, M. P. Tosi, Phys. Chem. Liq. 32, 191 (1996); Z. Akdeniz, G. Pastore, M. P. Tosi, Nuovo Cimento 20, 595 (1998).
[2] P. W. Schultz, G. E. Leroi, J. F. Harrison, Molec. Phys. 88, 217 (1996); S. T. Howard, Molec. Phys. 85, 395 (1995).
[3] T. Veszpremi, T. Pasinszki, M. Feher, J. Am. Chem. Soc. 116, 6303 (1994).
[4] http://www.icpf.cas.cz/jiri/macsimus.
[5] J. Kolafa, Molec. Simul. 18, 193 (1996).

Jiri Kolafa, Ivo Nezbeda
Effect of short- and long-range forces on the structure of water.
II. Orientational ordering and the dielectric constant
Mol. Phys. 98, 1505-1520 (2000)

Effect of short- and long-range interactions on the structure of water, both spatial and orientational, has been studied in detail by computing the full pair correlation function, site-site correlation functions, two-dimensional site-site correlation functions in the r_OO, r_OH and r_OO, r_HH planes, dipole-dipole correlation function, radial Kirkwood g-factor, and the dielectric constant. Two model potentials, the TIP4P and ST2 models, and their short-range versions have been considered at ambient, elevated, and supercritical conditions. The Ewald summation under different conditions has been used to investigate also their effect on results. An analysis of the results shows that although all site-site correlation functions for the short- and long-range systems are similar, the orientational ordering in systems of different range may be considerably different, this evidence being provided mainly by the dipole-dipole correlation function and the radial Kirkwood factor. The orientational ordering is only short-range in long-range systems, whereas in short-range systems the hydrogen bonding gives rise to a damped long-range regular pattern of alignment. Nonetheless, the resulting dielectric constants for the short- and long-range systems coincide within the combined error bars. All findings are more pronounced at low temperatures but they are otherwise only marginally temperature and density dependent.

Text (PDF) * Figures * Supplementary material

Jiri Kolafa, John W. Perram and Robert P. Bywater
Essential motions and energetic contributions of individual residues in a peptide bound to an SH3 domain.
Biophys. J. 79, 646-655 (2000)

      We have studied protein-ligand interactions by molecular dynamics simulations using software designed to exploit parallel computing architectures. We analysed the trajectories to extract the essential motions and estimated the individual contributions of fragments of the ligand to overall binding enthalpy.
      Two forms of the bound ligand are compared, one with the termini blocked by covalent derivatisation, and one in the underivatised, zwitterionic form. The ends of the peptide tend to bind more loosely in the capped form.
      We can observe significant motions in the bound ligand and distinguish between motions of the peptide backbone and of the side chains. This could be useful in designing ligands, which fit optimally to the binding protein.
       We show that it is possible to determine the different contributions of each residue in a peptide to the enthalpy of binding. Proline stands out as being the major contributor to binding enthalpy, in keeping with the known propensity for this family of proteins to bind proline-rich peptides.

Fulltext not available * Stereo figure of essential motions

Ivo Nezbeda and Jiri Kolafa
Effect of short- and long-range forces on the structure of water: Temperature and density dependence
Mol. Phys. 97, 1105-1116 (1999)

The individual effects of short-range and long-range forces on the structure of water, a prerequisite for developing a perturbation theory, are assessed using a decomposition of realistic water-water potential models into trial potentials. Computer simulations for one typical liquid density and a number of temperatures ranging from the freezing temperature up to supercritical ones, and for several densities on a supercritical isotherm were performed. The trial potentials were constructed from the ST2 and TIP4P potentials and it is shown that for both potentials the results are practically identical. It is shown that (i) regardless of the thermodynamic conditions and potential models used, the structure of water and the mutual orientational arrangement of water molecules, given by a set of site-site correlation functions, are determined nearly exclusively only by the short range forces, and (ii) for high density states the effect of the short range electrostatic part of the intermolecular potential on the spatial arrangement of the water molecules rapidly decreases with increasing temperature but does not become negligible.

Text (PDF) * fig 1 * fig 2 * fig 3 * fig 4 * fig 5 * fig 6 * fig 7 * fig 8 * fig 9 * fig 10 * fig 11 * fig 12 * fig 13
Figures (HP LaserJet 600dpi)

Jiri Kolafa
Azeotropic phenomena in the global phase diagram of the Redlich-Kwong equation of state
Phys. Chem. Chem. Phys. 1, 5665 (1999)

The global phase diagram of a binary mixture described by the Redlich-Kwong equation of state has been calculated for the molecule volume ratio b₁₁/b₂₂=13/7 and the linear mixing rule for molecular volumes. Boundary states separating regions with different topology of azeotropic lines ("horn" region with double azeotropy and "dish" region with an azeotropic line connecting two critical azeotropic points) are found and discussed in connection with other already known non-azeotropic phenomena.

Text (PDF) * Figures (TIFF 600dpi) * Figures (HP LaserJet 300dpi)

Jiri Kolafa, Ivo Nezbeda, Jan Pavlicek, and William R. Smith
Global Phase Diagrams of Model and Real Binary Fluid Mixtures.
II. Non-Lorentz-Berthelot Mixture of Attractive Hard Spheres
Phys. Chem. Chem. Phys. 1, 4233 (1999)

The global phase diagram of a binary mixture of attractive hard spheres described by the Boublik-Mansoori-Carnahan-Starling-Leland equation of state with a van der Waals mean field attractive term is investigated in its dependence on the ratio of the hard-sphere diameters and the strength of the attraction. Two values of the energetic combining rule parameter k₁₂, determining the deviation from the geometric mean rule, are considered. In addition to phenomena reported recently for k₁₂, the shield region of quadruple points is investigated for k₁₂=0.8, along with its associated azeotropic phenomena. For k₁₂=1.15, the mixture exhibits a rich set of low-temperature azeotropic phenomena: cusps on the p--T projections of azeotropic lines, exchange of branches of azeotropic lines, zero-temperature limited azeotropy, and double critical azeotropic points. Some of these azeotropic phenomena are described here for the first time.
(Presented at the 77. Bunsen-Kolloquium: 1st Workshop on Global Phase Diagram in Walberberg near Cologne, Germany, March 1999)

Text (PDF) * Figures (HP LaserJet 600dpi) * Figures (TIFF 600 DPI)

Yi Mao, J. Woenckhaus, J. Kolafa, M.A. Ratner, and M.F. Jarrold
Thermal Unfolding of Unsolvated Cytochrome c:
Experiment and Molecular Dynamics Simulations
J. Am. Chem. Soc. 121, 2712-2721 (1999)

The thermal unfolding of unsolvated cytochrome c has been examined in the gas phase using ion-mobility measurements. Measurements were performed for the +5, +6, and +7 protonated charge states from around room temperature up to 573 K. The (M+5H)⁵⁺ charge state remains folded at 573 K while (M+5H)⁶⁺ and (M+5H)⁷⁺ go through a series of unfolding transitions as the temperature is raised. Molecular dynamics simulations were performed using the CHARMM force field. The simulations are in qualitative agreement with the experimental results: the +7 charge states unfold as the temperature is raised and the +5 charge states remain compact. Addition of two protons to the +5 charge state flattens the energy landscape so that the folded and unfolded conformations have similar energies. Entropy presumably drives the unfolding of the +7 charge state as the temperature is raised.

For full text, visit this page (paper # 149).

Jiri Kolafa, Ivo Nezbeda, Jan Pavlicek, and William R. Smith
Global phase diagrams of model and real binary fluid mixtures: Lorentz-Berthelot mixture of attractive hard spheres
Fluid Phase Equil, 146, 103-121 (1998)

The phase behavior and global phase diagram of binary mixtures of attractive hard spheres described by a hard-sphere mixture equation of state with a mean field term and the Lorentz-Berthelot combining rule are examined in detail in dependence on the ratio of (i) the hard-sphere diameters and (ii) the strength of the mean field attraction. It is shown that in addition to the usual phenomena the studied mixture exhibits also the closed liquid-liquid immiscibility loop (Type VI and VII behavior) and a variety of new azeotropic phenomena. Topology of phase diagrams is discussed in detail with emphasis on the boundary states and is compared with that based on the one-fluid van der Waals equation approach.

Text (PDF) * Figures (HP LaserJet 300dpi)

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