Structure of the aqueous electron: assessment of one-electron pseudopotential models in comparison to experimental data and time-dependent density functional theory

The prevailing structural paradigm for the aqueous electron is that of an s-like ground-state wave function that inhabits a quasi-spherical solvent cavity, a viewpoint that is supported by numerous atomistic simulations using various one-electron pseudopotential models. This conceptual picture has recently been challenged, however, on the basis of results obtained from a new electron-water pseudopotential model that predicts a more delocalized wave function and no well-defined solvent cavity. Here, we examine this new model in comparison to two alternative, cavity-forming pseudopotential models. We find that the cavity-forming models are far more consistent with the experimental data for the electron's radius of gyration, optical absorption spectrum, and vertical electron binding energy. Calculations of the absorption spectrum using time-dependent density functional theory are in quantitative or semiquantitative agreement with experiment when the solvent geometries are obtained from the cavity-forming pseudopotential models, but differ markedly from experiment when geometries that do not form a cavity are used.     

Effect of n-alkanes and peptides on the phase equilibria in phosphatidylcholine—water systems

Abstract

The phase equilibria in phosphatidylcholine (PC)-n-alkane-²H₂O systems have been studied to elucidate the driving forces for the transition between a lamellar liquid-crystalline (L _α) phase and a reversed hexagonal (H _II) phase. A tentative phase diagram for the system dioleoyl-PC (DOPC)-n-dodecane-²H₂O was determined. DOPC forms an L _α phase up to at least 90°C in excess water. However, an H _II phase was formed at room temperature at both low and high water concentrations in DOPC-n-dodecane-²H₂O mixtures. The phase equilibria were also studied in PC-n-dodecane-²H₂O systems containing PC with different degrees of acyl chain unsaturation. The water and dodecane concentrations required to induce the formation of an H _II (or isotropic) phase increase in the order dilinoleoyl-PC ～ DOPC < 1-palmitoyl-2-oleoyl-PC < dipalmitoyl-PC. The effect of n-alkanes with different chain lengths (C₈–C₂₀) on the phase equilibria in DOPC-n-alkane-²H₂O mixtures was studied. Although the number of alkane carbon atoms added per DOPC molecule was kept constant, the ability of the alkanes to promote the formation of an H _II phase was strongly chain length dependent; the ability decreased when going from octane to eicosane. Finally, some PC-peptide-²H₂O systems were investigated. Gramicidin (hydrophobic) had a similar influence on the phase equilibria as the alkanes. Melittin (amphiphilic) induced the formation of an isotropic phase, while insulin and duramycin (water soluble) had no, or a very limited, ability to induce a non-lamellar phase, respectively. Our results are discussed in the light of simple physical models dealing with the self-assembly of amphiphiles.     

The first branching point in porphyrin biosynthesis: a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase

In humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen-III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen-III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol(-1) at 298.15 K. The rate-limiting step was found to be the initial proton transfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various active site residues as well as several other functional groups.     

Investigations of the energy flow of X-ray wavefields in crystals

The energy flow of the X-ray wavefields in the Laue case of diffraction and its importance for X-ray topography and interferometry are discussed.     

Vibrational transitions in Rydberg matter clusters from stimulated Raman and Rabi‐flopping phase delay in the infrared

Recently, rotational spectra of giant Rydberg matter (RM) clusters were studied in the radio frequency range (Mol. Phys. 105 (2007) 933–939), giving high‐precision bond distances in the nanometer range. However, the theoretical and experimental problem of vibrational motion or, rather, coupled electronic‐vibrational motion in the RM clusters is still unsolved; but it is expected that broad phonon bands will exist. Spectroscopic signatures from space make it likely that RM is a common form of matter in the Universe, and phonon bands in this spectroscopic range have not been taken into account so far. Spectroscopic results are now reported on transitions in the range 0.01–20 cm⁻¹, using primarily infrared (IR) lasers to probe the RM in a tunable open cavity with a Fabry–Perot interferometer to aid in the identification of the shifts. Stimulated Raman scattering from electronic transitions and Rabi‐flopping from electronic states in the clusters are observed. The broad stimulated Raman peaks are assigned to one and two consecutive vibrational (electronic‐vibrational) transitions. Theoretical values predicted for vibrations (phonon maxima) and electronic processes are in reasonable agreement with the experimental results. Improved calculations are needed to verify the assignments of the vibrational phonon distributions. Copyright © 2008 John Wiley & Sons, Ltd.