We have investigated reversible single-wall carbon nanotube (SWNT) oxidation by quantitative analysis of the oxide-induced absorption bleaching and luminescence quenching at low pH. These data, in combination with DFT structure calculations, suggest that the nanotube oxide is a 1,4-endoperoxide. At low pH, the endoperoxide protonates to create a hydroperoxide carbocation, introducing a hole in the SWNT valence band. Nanotube luminescence is extremely sensitive to quenching by hole-doping, while the absorption is relatively robust.

The difference between oxide and hydrogen passivation of small Si nanocrystals is explored by all-electron, hybrid functional DFT calculations with unrestricted geometry optimization. Oxide passivation lowers the band gap by about 2.4 eV for Si 35 cores and by about 1.5 eV for Si 66 cores. The oxide-passivated nanocrystals have optically forbidden, indirect-gap-type transitions whereas the hydrogen-passivated nanocrystals have optically allowed, direct-gap-type transitions. The HOMO and LUMO are delocalized in both species. This result explains the experimental observation that hydrogen-passivated Si nanocrystals luminesce in the blue whereas oxide-passivated Si nanocrystals luminesce in the yellowred.

All-electron static and time-dependent DFT electronic calculations, with complete geometrical optimization, are performed on tubular molecules up to C(210)H(20) that are finite sections of the (5,5) metallic single wall carbon nanotube with hydrogen termination at the open ends. We find pronounced C-C bond reconstruction at the tube ends; this initiates bond alternation that propagates into the tube centers. For the especially low band gap molecules C(120)H(20), C(150)H(20), and C(180)H(20), alternation increases, and a second nearly isoenergic structural isomer of different alternation is found. A small residual C-C bond alternation and band gap may be present in the infinite tube. The van Hove band gap forms quickly with length, while the metallic Fermi point (at the crossing of linear bands) forms very slowly with length. There are no end-localized states at energies near the Fermi energy. The HOMO-LUMO gap and the lowest singlet excited state, whose energies show a periodicity with length as previously calculated, are optically forbidden. However, each molecule shows an intense visible "charge transfer" transition, not present in the infinite tube, whose energy varies smoothly with length; this transition should be an identifying signature for these molecules. The static axial polarizability per unit length increases rapidly with N as the "charge transfer" transition moves into the infrared; this indicates increasing metallic character. However, the ionization potential, electron affinity, chemical hardness, and relative energetic stability all show the length periodicity seen in the HOMO-LUMO gap, in contrast to the optical "charge transfer" transition and the static axial polarizability. These periodicities, due to a one-dimensional quantum size effect as originally modeled by Coulson in 1938, nevertheless cancel in the calculated Fermi energy, which varies smoothly toward a predicted bulk work function near 3.9 eV. A detailed study of C(190)H(20) with up to eight extra electrons or holes shows the total energy is closely fit by a simple classical charging model, as is commonly applied to metallic clusters.

Virtual screening by molecular docking has become a widely used approach to lead discovery in the pharmaceutical industry when a high-resolution structure of the biological target of interest is available. The performance of three widely used docking programs (Glide, GOLD, and DOCK) for virtual database screening is studied when they are applied to the same protein target and ligand set. Comparisons of the docking programs and scoring functions using a large and diverse data set of pharmaceutically interesting targets and active compounds are carried out. We focus on the problem of docking and scoring flexible compounds which are sterically capable of docking into a rigid conformation of the receptor. The Glide XP methodology is shown to consistently yield enrichments superior to the two alternative methods, while GOLD outperforms DOCK on average. The study also shows that docking into multiple receptor structures can decrease the docking error in screening a diverse set of active compounds.

The existence of a large number of proteins for which both nuclear magnetic resonance (NMR) and X-ray crystallographic coordinates have been deposited into the Protein Data Bank (PDB) makes the statistical comparison of the corresponding crystal and NMR structural models over a large data set possible, and facilitates the study of the effect of the crystal environment and other factors on structure. We present an approach for detecting statistically significant structural differences between crystal and NMR structural models which is based on structural superposition and the analysis of the distributions of atomic positions relative to a mean structure. We apply this to a set of 148 protein structure pairs (crystal vs NMR), and analyze the results in terms of methodological and physical sources of structural difference. For every one of the 148 structure pairs, the backbone root-mean-square distance (RMSD) over core atoms of the crystal structure to the mean NMR structure is larger than the average RMSD of the members of the NMR ensemble to the mean, with 76% of the structure pairs having an RMSD of the crystal structure to the mean more than a factor of two larger than the average RMSD of the NMR ensemble. On average, the backbone RMSD over core atoms of crystal structure to the mean NMR is approximately 1 A. If non-core atoms are included, this increases to 1.4 A due to the presence of variability in loops and similar regions of the protein. The observed structural differences are only weakly correlated with the age and quality of the structural model and differences in conditions under which the models were determined. We examine steric clashes when a putative crystalline lattice is constructed using a representative NMR structure, and find that repulsive crystal packing plays a minor role in the observed differences between crystal and NMR structures. The observed structural differences likely have a combination of physical and methodological causes. Stabilizing attractive interactions arising from intermolecular crystal contacts which shift the equilibrium of the crystal structure relative to the NMR structure is a likely physical source which can account for some of the observed differences. Methodological sources of apparent structural difference include insufficient sampling or other issues which could give rise to errors in the estimates of the precision and/or accuracy.

Static and time-dependent density functional calculations, geometrically optimized and including all electrons, are described for silicon nanocrystals as large as Si(87)H(76), which contains 163 atoms. We explore and predict the effect that different sp(3) passivation schemes-F or H termination, thin oxide shell, or alkane termination-have on the HOMO and LUMO, on the optical spectra, and on electron transfer properties. Electronegativity comparisons are a useful guide in understanding the observed deviation from the simple quantum size effect model. Nanocrystals containing Al or P impurity atoms, either on the surface or in the interior, are explored to understand electrical doping in strongly quantum-confined nanocrystals. Surface dangling bonds are found to participate in internal charge transfer with P atom dopant electrons.

No abstract

The reactive blending composites of isotactic polypropylene (PP)/octavinyl polyhedral oligomeric silsesquioxane (POSS) were prepared in the presence of dicumyl peroxide. Comparison of the rheological behavior of physical and reactive blending composites was made by oscillatory rheological measurements. It was found that the viscosity of physical blending composites drops at lower POSS content (0.5-1 wt %) and thereafter increases with increasing POSS content; that of reactive blending composites increases with increasing POSS content and displays a solid-like rheological behavior at low frequency region when POSS content is higher than 1 wt %. The deviation of reactive blending composites from the scaling log G 0 -log G@ of linear polymer in Han plot, upturning at high viscosity in Cole-Cole plot, and from van Gurp-Palmen plot are related to the gelation behavior reactively. V V C 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 526-533, 2008