RESUMO
We report the ab initio prediction of a negative Barkas coefficient in lithium fluoride (LiF) insulator at low velocity (v<0.25 a.u., E_{kin}â¼2 keV). The electronic stopping power of protons in LiF has been extensively studied both experimentally and theoretically because of a controversial threshold effect. While our time-dependent density-functional theory simulations confirm the presence of a velocity threshold below which the proton stopping power vanishes, our calculations demonstrate that the antiprotons do not experience such a threshold. The combination of those two contrasting behaviors gives rise to an unprecedented negative Barkas effect: the stopping power of antiprotons is larger than that of protons. We identify that the slow antiproton at close encounter destabilizes a p orbital of the F^{-} anion pointing toward the antiproton. This particular orbital becomes highly polarizable and hence contributes much to the stopping power.
RESUMO
The GW approximation to the electronic self-energy is now a well-recognized approach to obtain the electron quasiparticle energies of molecules and, in particular, their ionization potential and electron affinity. Though much faster than the corresponding wavefunction methods, the GW energies are still affected by slow convergence with respect to the basis completeness. This limitation hinders a wider application of the GW approach. Here, we show that we can reach the complete basis set limit for the cumbersome GW calculations solely based on fast preliminary calculations with an unconverged basis set. We introduce a linear model that correlates the molecular orbital characteristics and the basis convergence error for a large database of approximately 600 states in 104 organic molecules that contain H, C, O, N, F, P, S, and Cl. The model employs molecular-orbital-based non-linear descriptors that encode efficiently the chemical space offering outstanding transferability. Using a low number of descriptors (17) the performance of this extrapolation procedure is superior to that of the earlier more physically motivated approaches. The predictive power of the method is finally demonstrated for a selection of large acceptor molecules.
RESUMO
Fluorescence represents one of the most powerful tools for the detection and structural characterization of the pathogenic protein aggregates, amyloid fibrils. The traditional approaches to the identification and quantification of amyloid fibrils are based on monitoring the fluorescence changes of the benzothiazole dye thioflavin T (ThT) and absorbance changes of the azo dye Congo red (CR). In routine screening it is usually sufficient to perform only the ThT and CR assays, but both of them, when used separately, could give false results. Moreover, fibrillization kinetics can be measured only by ThT fluorescence, while the characteristic absorption spectra and birefringence of CR represent more rigid criteria for the presence of amyloid fibrils. Therefore, it seemed reasonable to use both these dyes simultaneously, combining the advantages of each technique. To this end, we undertook a detailed analysis of the fluorescence spectral behavior of these unique amyloid tracers upon their binding to amyloid fibrils from lysozyme, insulin and an N-terminal fragment of apolipoprotein A-I with Iowa mutation. The fluorescence measurements revealed several criteria for distinguishing between fibrillar and monomeric protein states: (i) a common drastic increase in ThT fluorescence intensity; (ii) a sharp decrease in ThT fluorescence upon addition of CR; (iii) an appearance of the maximum at 535-540 nm in the CR excitation spectra; (iv) increase in CR fluorescence intensity at 610 nm. Based on these findings we designed a novel combined ThT-CR fluorescence assay for amyloid identification. Such an approach not only strengthens the reliability of the ThT assay, but also provides new opportunities for structural characterization of amyloid fibrils.