Breaking the dogma: PCB-derived semiquinone free radicals do not form covalent adducts with DNA, GSH, and amino acids.

Covalent bond formations of free radical metabolites with biomolecules like DNA and proteins are thought to constitute a major mechanism of toxicity and carcinogenesis. Glutathione (GSH) is generally accepted as a radical scavenger protecting the cell. In the present study, we investigated a semiquinone radical (SQ(●-)) metabolite of the semivolatile 4-chlorobiphenyl, using electron paramagnetic resonance spectroscopy, and oxygen consumption. Proton nuclear magnetic resonance ((1)H NMR) and liquid chromatography-mass spectrometry (LC-MS) were also employed to elucidate the radical interaction with DNA, amino acids, and GSH. We found that DNA and oligonucleotides stabilized SQ(●-) by electron delocalization in the π-stacking system, resulting in persistent radical intercalated, rather than forming a covalent bond with SQ(●-). This finding was strongly supported by the semiempirical calculation of the semioccupied molecular orbital and the linear combination of the atomic orbitals, indicating 9.8 kcal mol(-1) energy gain. The insertion of SQ(●-) into the DNA strand may result in DNA strand breaks and interruption of DNA replication process or even activate radical mediated secondary reactions. The presence of amino acids resulted in a decrease of the electron paramagnetic resonance (EPR) signal of SQ(●-) and correlated with their isoelectric points. The pH shifts the equilibrium of the dianions of hydroquinone and influenced indirectly the formation of SQ(●-). Similar findings were observed with GSH and Cys. GSH and Cys functioned as indirect radical scavengers; their activities depend on their chemical equilibria with the corresponding quinones, and their further reaction via Michael addition. The generally accepted role of GSH as radical scavenger in biological systems should be reconsidered based upon these findings, questioning the generally accepted view of radical interaction of semiquinones with biologically active compounds, like DNA, amino acids, proteins, and radical scavengers like GSH.

A thermodynamic approach to alamethicin pore formation.

The structure and energetics of alamethicin Rf30 monomer to nonamer in cylindrical pores of 5 to 11Å radius are investigated using molecular dynamics simulations in an implicit membrane model that includes the free energy cost of acyl chain hydrophobic area exposure. Stable, low energy pores are obtained for certain combinations of radius and oligomeric number. The trimer and the tetramer formed 6Å pores that appear closed while the larger oligomers formed open pores at their optimal radius. The hexamer in an 8Å pore and the octamer in an 11Å pore give the lowest effective energy per monomer. However, all oligomers beyond the pentamer have comparable energies, consistent with the observation of multiple conductance levels. The results are consistent with the widely accepted "barrel-stave" model. The N terminal portion of the molecule exhibits smaller tilt with respect to the membrane normal than the C terminal portion, resulting in a pore shape that is a hybrid between a funnel and an hourglass. Transmembrane voltage has little effect on the structure of the oligomers but enhances or decreases their stability depending on its orientation. Antiparallel bundles are lower in energy than the commonly accepted parallel ones and could be present under certain experimental conditions. Dry aggregates (without an aqueous pore) have lower average effective energy than the corresponding aggregates in a pore, suggesting that alamethicin pores may be excited states that are stabilized in part by voltage and in part by the ion flow itself.

A thermodynamic approach to alamethicin pore formation.

The structure and energetics of alamethicin Rf30 monomer to nonamer in cylindrical pores of 5 to 11Å radius are investigated using molecular dynamics simulations in an implicit membrane model that includes the free energy cost of acyl chain hydrophobic area exposure. Stable, low energy pores are obtained for certain combinations of radius and oligomeric number. The trimer and the tetramer formed 6Å pores that appear closed while the larger oligomers formed open pores at their optimal radius. The hexamer in an 8Å pore and the octamer in an 11Å pore give the lowest effective energy per monomer. However, all oligomers beyond the pentamer have comparable energies, consistent with the observation of multiple conductance levels. The results are consistent with the widely accepted "barrel-stave" model. The N terminal portion of the molecule exhibits smaller tilt with respect to the membrane normal than the C terminal portion, resulting in a pore shape that is a hybrid between a funnel and an hourglass. Transmembrane voltage has little effect on the structure of the oligomers but enhances or decreases their stability depending on its orientation. Antiparallel bundles are lower in energy than the commonly accepted parallel ones and could be present under certain experimental conditions. Dry aggregates (without an aqueous pore) have lower average effective energy than the corresponding aggregates in a pore, suggesting that alamethicin pores may be excited states that are stabilized in part by voltage and in part by the ion flow itself.

Xenobiotic geometry and media pH determine cytotoxicity through solubility.

Polychlorinated biphenyls (PCBs), a class of 209 individual congeners, have become persistent and ubiquitous environmental contaminants. The health impacts of PCBs, such as cancer, cardiovascular disease, developmental toxicity, and neurotoxicity, have been widely reported, but for many of these, the mechanisms of toxicity are still poorly understood. Many mechanistic studies involve cultured cells where the biological activity is dependent upon the solubility of the xenobiotic. In the present study, we investigated the factors that determine solubility as measured by diffraction spectroscopy and have modeled, with semiempirical and ab initio molecular orbital methods, the dihedral angle and calculated the dipole moment of a series of monofluorinated analogues (F-PCBs 3) of 4-chlorobiphenyl (PCB 3) as model compounds in vacuum and in water. We found a strong positive correlation between the dihedral angle, the rotation energy, the cavitation energy, the solubility, and the cytotoxicity in three human cell lines. The dipole moment was of minor influence. We also determined the influence of pH changes in a medium containing 10% fetal bovine serum (FBS), changes that could be expected when cells in culture are removed from a CO 2 incubator even for a short time. We found that the solubility is strongly affected by the pH and that this effect is not reversed by subsequent pH readjustment. In a study examining cytotoxicity, we showed that the actual pH and the pH history of a medium containing FBS were of major influence. We suggest that pH-driven changes in the tertiary and quaternary structure of albumin are responsible. These observations have implications for studies of the biological activity of semisoluble compounds, like PCBs and related compounds.

Inelastic scattering dynamics of Ar from a perfluorinated self-assembled monolayer surface.

Dynamics of Ar atom collisions with a perfluorinated alkanethiol self-assembled monolayer (F-SAM) surface on gold were investigated by classical trajectory simulations and atomic beam scattering techniques. Both explicit-atom (EA) and united-atom (UA) models were used to represent the F-SAM surface; in the UA model, the CF3 and CF2 units are represented as single pseudoatoms. Additionally the nonbonded interactions in both models are different. The simulations show the three limiting mechanisms expected for collisions of rare gas atoms (or small molecules) with SAMs, that is, direct scattering, physisorption, and penetration. Surface penetration results in a translational energy distribution, P(Ef), that can be approximately fit to the Boltzmann for thermal desorption, suggesting that surface accommodation is attained to a large extent. Fluorination of the alkanethiol monolayer leads to less energy transfer in Ar collisions. This results from a denser and stiffer surface structure in comparison with that of the alkanethiol SAM, which introduces constraints for conformational changes which play a significant role in the energy-transfer process. The trajectory simulations predict P(Ef) distributions in quite good agreement with those observed in the experiments. The results obtained with the EA and UA models are in reasonably good agreement, although there are some differences.

Role of projectile and surface temperatures in the energy transfer dynamics of protonated peptide ion collisions with the diamond {111} surface.

The effects of temperature on energy transfer during collisions of protonated diglycine ions, Gly(2)-H(+), with a diamond {111} surface were investigated by chemical dynamics simulations. The simulations were performed for a collision energy of 70 eV and angle of 0 degrees with respect to the surface normal. In one set of simulations the initial surface temperature, T(surf), was varied from 300 to 2000 K, while the Gly(2)-H(+) vibrational and rotational temperatures were maintained at 300 K. For the second set of simulations the Gly(2)-H(+) vibrational temperature, T(vib), was varied from 300 to 2000 K, keeping both the Gly(2)-H(+) rotational and surface temperatures at 300 K. Increasing either the surface temperature or Gly(2)-H(+) vibrational temperature to values as high as 2000 K has, at most, only a negligible effect on the partitioning of the incident collision energy to the surface and to the vibrational and rotational modes of Gly(2)-H(+). To a good approximation, the initial surface and peptide ion energies are nearly adiabatic during the collisional energy transfer. This adiabaticity of the initial peptide ion energy agrees with experiments (J. Phys. Chem. A 2004, 108, 1). A more quantitative analysis of the effects of T(vib) and T(surf) shows there are small, but noticeable, effects on the energy transfer efficiencies. Namely, increasing the vibrational or surface temperature results in a near-linear decrease in the energy transfer to the degrees of freedom associated with this temperature.

Wavelet Transforms for Determining Time-Dependent Vibrational Frequencies.

Fourier transforms of autocorrelation functions are typically used to calculate spectra and transport properties, but they require oscillations periodic in time (a stationary time series). The time-scale relation revealed by a wavelet transform (WT), on the other hand, gives a relation between time and pseudo-frequency that is used here to calculate vibrational frequencies for HONO and to detect the molecule's trans-cis conformational change in ab initio molecular dynamics simulations. Thus, the WT shows potential for giving new insights into nonstationary time series frequently encountered in chemistry and physics.