PubMed Health⌕ Search

Biomedical subjects

Pavel Jungwirth

Publications and source records attributed to Pavel Jungwirth.

At least 19 recordsLinked to original sources

Quantification and rationalization of the higher affinity of sodium over potassium to protein surfaces.

For a series of different proteins, including a structural protein, enzyme, inhibitor, protein marker, and a charge-transfer system, we have quantified the higher affinity of Na+ over K+ to the protein surface by means of molecular dynamics simulations and conductivity measurements. Both approaches show that sodium binds at least twice as strongly to the protein surface than potassium does with this effect being present in all proteins under study. Different parts of the protein exterior are responsible to a varying degree for the higher surface affinity of sodium, with the charged carboxylic groups of aspartate and glutamate playing the most important role. Therefore, local ion pairing is the key to the surface preference of sodium over potassium, which is further demonstrated and quantified by simulations of glutamate and aspartate in the form of isolated amino acids as well as short oligopeptides. As a matter of fact, the effect is already present at the level of preferential pairing of the smallest carboxylate anions, formate or acetate, with Na+ versus K+, as shown by molecular dynamics and ab initio quantum chemical calculations. By quantifying and rationalizing the higher preference of sodium over potassium to protein surfaces, the present study opens a way to molecular understanding of many ion-specific (Hofmeister) phenomena involving protein interactions in salt solutions.

Animals↗

Homogeneous freezing of water starts in the subsurface.

Molecular dynamics simulations of homogeneous ice nucleation in extended aqueous slabs show that freezing preferentially starts in the subsurface. The top surface layer remains disordered during the freezing process. The subsurface accommodates better than the bulk the increase of volume connected with freezing. It also experiences strong electric fields caused by oriented surface water molecules, which can enhance ice nucleation. Our computational results shed new light on the experimental controversy concerning the bulk vs surface origin of homogeneous ice nucleation in water droplets. This has important atmospheric implications for the microphysics of formation of high altitude clouds.

Journal Article↗

Adsorption of polycyclic aromatic hydrocarbons at the air-water interface: molecular dynamics simulations and experimental atmospheric observations.

Adsorption of benzene, naphthalene, anthracene, and phenanthrene at the aqueous surface is investigated by means of molecular dynamics simulations. Potentials of mean force, i.e., free energy profiles obtained when moving the studied molecules across an aqueous slab were evaluated. In all cases, deep surface free energy minima, corresponding to orders of magnitude of surface enhancement of the aromatic molecule, were located. This enhancement, which increases with the size of the solute, points to the importance of the aqueous surface for the chemistry of polycyclic aromatic hydrocarbons (PAHs). Supporting evidence in the atmospheric environment related to the heterogeneous chemistry of PAHs on water droplets and planar surfaces is summarized. There is good agreement between the hydration free energies computed from MD calculations and the experimentally determined values. Data pertaining to the importance of the air-water interface in the adsorption and transport of PAHs on micron sized water droplets are described. The relevant data on adsorption and reaction (ozonation and photochemical) at the air-water interface of planar surfaces and droplets are also summarized.

Adsorption↗

Propensity for the air/water interface and ion pairing in magnesium acetate vs magnesium nitrate solutions: molecular dynamics simulations and surface tension measurements.

Molecular dynamics simulations in slab geometry and surface tension measurements were performed for aqueous solutions of magnesium acetate and magnesium nitrate at various concentrations. The simulations reveal a strong affinity of acetate anions for the surface, while nitrate exhibits only a very weak surface propensity, and magnesium is per se strongly repelled from the air/water interface. CH3COO- also exhibits a much stronger tendency than NO3- for ion pairing with Mg2+ in the bulk and particularly in the interfacial layer. The different interfacial behavior of the two anions is reflected by the opposite concentration dependence (beyond 0.5 M) of surface tension of the corresponding magnesium salts. Measurements, supported by simulations, show that the surface tension of Mg(NO3)2(aq) increases with concentration as for other inorganic salts. However, in the case of Mg(OAc)2(aq) the surface tension isotherm exhibits a turnover around 0.5 M, after which it starts to decrease, indicating a positive net solute excess in the interfacial layer at higher concentrations.

Journal Article↗

First steps towards dissolution of NaSO4- by water.

NaSO(4)(-)(H(2)O)(n) (n = 0-4) clusters have been generated in the gas phase as model systems to simulate the first dissolution steps of sulfate salts in water; photoelectron spectroscopy and theoretical calculations indicate that the first three water molecules strongly interact with both Na(+) and SO(4)(2-), forming a three-water solvation ring to start to pry apart the Na(+)SO(4)(2-) contact ion pair.

Journal Article↗

Cluster model for the ionic product of water: accuracy and limitations of common density functional methods.

In the present study, the performance of six popular density functionals (B3LYP, PBE0, BLYP, BP86, PBE, and SVWN) for the description of the autoionization process in the water octamer was studied. As a benchmark, MP2 energies with complete basis sets limit extrapolation and CCSD(T) correction were used. At this level, the autoionized structure lies 28.5 kcal.mol(-1) above the neutral water octamer. Accounting for zero-point energy lowers this value by 3.0 kcal.mol(-1). The transition state of the proton transfer reaction, lying only 0.7 kcal.mol(-1) above the energy of the ionized system, was identified at the MP2/aug-cc-pVDZ level of theory. Different density functionals describe the reactant and product with varying accuracy, while they all fail to characterize the transition state. We find improved results with hybrid functionals compared to the gradient-corrected ones. In particular, B3LYP describes the reaction energetics within 2.5 kcal.mol(-1) of the benchmark value. Therefore, this functional is suggested to be preferably used both for Carr-Parinello molecular dynamics and for quantum mechanics/molecular mechanics (QM/MM) simulations of autoionization of water.

Journal Article↗

Simulated surface potentials at the vapor-water interface for the KCl aqueous electrolyte solution.

Classical molecular dynamics simulations with polarizable potential models were carried out to quantitatively determine the effects of KCl salt concentrations on the electrostatic surface potentials of the vapor-liquid interface of water. To the best of our knowledge, the present work is the first calculation of the aqueous electrolyte surface potentials. Results showed that increased salt concentration enhanced the electrostatic surface potentials, in agreement with the corresponding experimental measurements. Furthermore, the decomposition of the potential drop into contributions due to static charges and induced dipoles showed a very strong effect (an increase of approximately 1 V per 1M) due to the double layers formed by KCl. However, this was mostly negated by the negative contribution from induced dipoles, resulting in a relatively small overall increase ( approximately 0.05 V per 1M) with increased salt concentration.

Chemistry, Physical↗

Surface segregation of dissolved salt ions.

Surface segregation of iodide, but not of fluoride or cesium ions, is observed by a combination of metastable impact electron spectroscopy (MIES) and ultraviolet photoelectron spectroscopy (UPS(HeI)) of amorphous solid water exposed to CsI or CsF vapor. The same surface ionic behavior is also derived from molecular dynamics (MD) simulations of the corresponding aqueous salt solutions. The MIES results show the propensity of iodide, but not fluoride, for the surface of the amorphous solid water film, providing thus strong evidence for the suggested presence of heavier halides (iodide, bromide, and to a lesser extent chloride) at the topmost layer of aqueous surfaces. In contrast, no appreciable surface segregation of ions is observed in methanol, neither in the experiment nor in the simulation. Furthermore, the present results indicate that, as far as the thermodynamic aspects of solvation of alkali halides are concerned, amorphous solid water and methanol surfaces behave similarly as surfaces of the corresponding liquids.

Ions↗

Selected biologically relevant ions at the air/water interface: a comparative molecular dynamics study.

Interfacial behavior of selected biologically and technologically relevant ions is studied using molecular dynamics simulations employing polarizable potentials. Propensities of choline, tetraalkylammonium (TAA), and sodium cations, and sulfate and chloride anions for the air/water interface are analyzed by means of density profiles. Affinity of TAA ions for the interface increases with their increasing hydrophobicity. Tetramethylammonium favors bulk solvation, whereas cations with propyl and butyl chains behave as surfactants. The choice of counter-anions has only a weak effect on the behavior of these cations. For choline, sodium, chloride and sulfate, the behavior at the air/water interface was compared to the results of our recent study on the segregation of these ions at protein surfaces. No analogy between these two interfaces in terms of ion segregation is found.

Air↗

Determination of the electron affinity of the acetyloxyl radical (CH3COO) by low-temperature anion photoelectron spectroscopy and ab initio calculations.

The electronic structure and electron affinity of the acetyloxyl radical (CH3COO) were investigated by low-temperature anion photoelectron spectroscopy and ab initio calculations. Photoelectron spectra of the acetate anion (CH3COO-) were obtained at two photon energies (355 and 266 nm) and under three different temperatures (300, 70, and 20 K) with use of a new low-temperature ion-trap photoelectron spectroscopy apparatus. In contrast to a featureless spectrum at 300 K, a well-resolved vibrational progression corresponding to the OCO bending mode was observed at low temperatures in the 355 nm spectrum, yielding an accurate electron affinity for the acetyloxyl radical as 3.250 +/- 0.010 eV. This experimental result is supported by ab initio calculations, which also indicate three low-lying electronic states observed in the 266 nm spectrum. The calculations suggest a 19 degrees decrease of the OCO angle upon detaching an electron from acetate, consistent with the vibrational progression observed experimentally.

Journal Article↗

Specific ion effects at protein surfaces: a molecular dynamics study of bovine pancreatic trypsin inhibitor and horseradish peroxidase in selected salt solutions.

The distribution of sodium, choline, sulfate, and chloride ions around two proteins, horseradish peroxidase (HRP) and bovine pancreatic trypsin inhibitor (BPTI), is investigated by means of molecular dynamics simulations with the aim to elucidate ion adsorption at the protein surface. Although the two proteins under investigation are very different from each other, the ion distributions around them are remarkably similar. Sulfate is always strongly attached to the proteins, choline shows a significant, but unspecific, propensity for the protein surfaces, and sodium ions have a weak surface affinity, while chloride has virtually no preference for the protein surface. In mixtures of all four ion species in protein solutions, the resulting distributions are almost a superposition of the distributions of sodium sulfate and choline chloride, except that sodium partially replaces choline close to the proteins. The present simulations support a picture of ions interacting with individual ionic and polar amino acid groups rather than with an averaged protein surface. The results thus show how subtle the so-called Hofmeister and electroselectivity effects are in salt solution of proteins, making all simplified interaction models questionable.

Amino Acids↗

Electron binding energies of hydrated H3O+ and OH-: photoelectron spectroscopy of aqueous acid and base solutions combined with electronic structure calculations.

The electronic structure of hydrated H3O+ and OH- is probed in a water jet by photoelectron spectroscopy employing 100 eV photons. The first ionization potential for OH- at 9.2 eV and the second ionization potential for H3O+ at 20 eV are resolved, corresponding to the removal of an electron from the 2ppi highest occupied molecular orbital and from the 1e orbital, respectively. These assignments are supported by present computational results based on a combination of molecular dynamics and ab initio calculations.

Journal Article↗

Aqueous ionic and complementary zwitterionic soluble surfactants: molecular dynamics simulations and sum frequency generation spectroscopy of the surfaces.

An aqueous ionic surfactant, 1-dodecyl-4-(dimethylamino)pyridinium (DMP) bromide, and the corresponding zwitterion 2-[4-(dimethylamino)pyridinio]dodecanoate (DPN) were explored by means of molecular dynamics (MD) simulations and, for the ionic system, by infrared-visible sum frequency generation (IR-vis SFG). The molecular structure of the interfacial layer was investigated for the ionic and zwitterionic systems as a function of surfactant concentration, both in water and in salt (KF or KBr) solutions, by MD simulations in a slab geometry. The buildup of the surface monolayer and a sublayer was monitored, and density and orientational profiles of the surfactants were evaluated. The difference between the ionic and zwitterionic systems and the effect of the added salt were analyzed at the molecular level. The results of MD simulations were compared to those of nonlinear optical spectroscopy measurements. IR-vis SFG was employed to study the DMP ionic surfactant in water and upon addition of simple salts. The influence of added salts on the different molecular moieties at the interface was quantified in detail experimentally.

Ions↗

Valence- and dipole-bound anions of the thymine-water complex: ab initio characterization of the potential energy surfaces.

The potential energy surfaces of the neutral and anionic thymine-water complexes are investigated using high-level ab initio calculations. Both dipole-bound (DB) and valence-bound (VB) anionic forms are considered. Four minima and three first-order stationary points are located, and binding energies are computed. All minima, for both anions, are found to be vertically and adiabatically stable. The binding energies are much higher for valence-bound than for dipole-bound anions. Adiabatic electron affinities are in the 66-287 meV range for VB anions and the 4-60 meV range for DB anions, and vertical detachment energies are in the 698-977 meV and 10-70 meV range for VB and DB anions, respectively. For cases where literature data are available, the computed values are in good agreement with previous experimental and theoretical studies. It is observed that electron attachment modifies the shape of the potential energy surfaces of the systems, especially for the valence-bound anions. Moreover, for both anions the size of the energy barrier between the two lowest energy minima is strongly reduced, rendering the coexistence of different structures more probable.

Anions↗

Ultrasonic velocities, densities, viscosities, electrical conductivities, Raman spectra, and molecular dynamics simulations of aqueous solutions of Mg(OAc)2 and Mg(NO3)2: Hofmeister effects and ion pair formation.

The ultrasonic velocities, densities, viscosities, and electrical conductivities of aqueous solutions of magnesium nitrate and magnesium acetate have been measured from dilute to saturation concentrations at 0 < or = t/degrees C < or = 50. The temperature derivative of the isentropic compressibility, kappa(s), became zero at 2.28 and 2.90 mol kg(-1) for Mg(OAc)2 and Mg(NO3)2 solutions, respectively, at 25 degrees C. The total hydration numbers of the dissolved ions were estimated to be, respectively, 24.3 and 19.2 at these concentrations. Differences in kappa(s) for various M2+ salts, using the present and literature data, correlated with reported M2+-OH2 bond lengths and to a lesser extent with cationic charge densities (ionic radii). The influence of anions on kappa(s) appears to follow the Hofmeister series and also correlates approximately with the anionic charge density. Substantial differences between Mg(OAc)2(aq) and Mg(NO3)2(aq) occur with respect to their structural relaxation times (derived from compressibility and viscosity data) and their electrical conductivities. These differences were attributed to a much greater ion association in Mg(OAc)2 solutions. Raman spectra recorded at 28 degrees C confirmed the presence of various types of contact ion pairs including mono- and bidentate complexes in Mg(OAc)2(aq). In Mg(NO3)2(aq), only noncontact ion pairs appear to be formed even at high concentrations. The experimental results are supported by molecular dynamics simulations, which also reveal the much stronger tendency of OAc- compared to NO3- to associate with Mg2+ in aqueous solutions. The simulations also allow an evaluation of the ion-ion and ion-water radial distribution functions and cumulative sums and provide a molecular picture of ion hydration in Mg(OAc)2(aq) and Mg(NO3)2(aq) at varying concentrations.

Journal Article↗

Brine rejection from freezing salt solutions: a molecular dynamics study.

The atmospherically and technologically very important process of brine rejection from freezing salt solutions is investigated with atomic resolution using molecular dynamics simulations. The present calculations allow us to follow the motion of each water molecule and salt ion and to propose a microscopic mechanism of brine rejection, in which a fluctuation (reduction) of the ion density in the vicinity of the ice front is followed by the growth of a new ice layer. The presence of salt slows down the freezing process, which leads to the formation of an almost neat ice next to a disordered brine layer.

Biophysics↗

Nonresonant ionization of oxygen molecules by femtosecond pulses: plasma dynamics studied by time-resolved terahertz spectroscopy.

We show that optical pump-terahertz probe spectroscopy is a direct experimental tool for exploring laser-induced ionization and plasma formation in gases. Plasma was produced in gaseous oxygen by focused amplified femtosecond pulses. The ionization mechanisms at 400- and 800-nm excitation wavelengths differ significantly being primarily of a multiphoton character in the former case and a strong-field process in the latter case. The generation of the plasma in the focal volume of the laser and its expansion on subnanosecond time scale is directly monitored through its density-dependent susceptibility. A Drude model used to evaluate the plasma densities and electron-scattering rates successfully captures the observations for a wide range of pump intensities. In addition, rotational fingerprints of molecular and ionic species were also observed in the spectra.

Journal Article↗