Using correlated parameters for improved ranking of protein-protein docking decoys

A successful protein–protein docking study culminates in identification of decoys at top ranks with near‐native quaternary structures. However, this task remains enigmatic because no generalized scoring functions exist that effectively infer decoys according to the similarity to near‐native quaternary structures. Difficulties arise because of the highly irregular nature of the protein surface and the significant variation of the nonbonding and solvation energies based on the chemical composition of the protein–protein interface. In this work, we describe a novel method combining an interface‐size filter, a regression model for geometric compatibility (based on two correlated surface and packing parameters), and normalized interaction energy (calculated from correlated nonbonded and solvation energies), to effectively rank decoys from a set of 10,000 decoys. Tests on 30 unbound binary protein–protein complexes show that in 16 cases we can identify at least one decoy in top three ranks having ≤10 Å backbone root mean square deviation from true binding geometry. Comparisons with other state‐of‐art methods confirm the improved ranking power of our method without the use of any experiment‐guided restraints, evolutionary information, statistical propensities, or modified interaction energy equations. Tests on 118 less‐difficult bound binary protein–protein complexes with ≤35% sequence redundancy at the interface showed that in 77% cases, at least 1 in 10,000 decoys were identified with ≤5Å backbone root mean square deviation from true geometry at first rank. The work will promote the use of new concepts where correlations among parameters provide more robust scoring models. It will facilitate studies involving molecular interactions, including modeling of large macromolecular assemblies and protein structure prediction. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.     

Synthesis of molluscicidal agent cyanolide a macrolactone from D-(-)-pantolactone

An efficient synthesis of potent molluscicidal agent cyanolide A, a glycosidic 16-membered macrolide, starting from D-(-)-pantolactone is reported. Highly stereoselective aldol, oxa-Michael addition, and Yamaguchi macrolactonization are the key steps in the present synthesis.     

A new non-destructive method for chemical analysis of particulate matter filters: the case of manganese air pollution in Vallecamonica (Italy)

Total Reflection X-ray Fluorescence (TXRF) is a well-established technique for chemical analysis, but it is mainly employed for quality control in the electronics semiconductor industry. The capability to analyze liquid and uniformly thin solid samples makes this technique suitable for other applications, and especially in the very critical field of environmental analysis. Comparison with standard methods like inductively coupled plasma (ICP) and atomic absorption spectroscopy (AAS) shows that TXRF is a practical, accurate, and reliable technique in occupational settings. Due to the greater sensitivity necessary in trace heavy metal detection, TXRF is also suitable for environmental chemical analysis. In this paper we show that based on appropriate standards, TXRF can be considered for non-destructive routine quantitative analysis of environmental matrices such as air filters. This work has been developed in the frame of the EU-FP6 PHIME (Public Health Impact of long-term, low-level Mixed element Exposure in susceptible population strata) Integrated Project (www.phime.org). The aim of this work was to investigate Mn air pollution in the area of Vallecamonica (Italy).     

Cu<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript>Ni<Subscript>1−<Emphasis Type="Italic">x</Emphasis></Subscript> alloy nanoparticles embedded SiO<Subscript>2</Subscript> films: synthesis and structure

Cu–Ni fcc alloy nanoparticles (NPs) of tunable atomic ratios were generated in SiO₂ films. The films were prepared using the Cu(NO₃)₂ and Ni(NO₃)₂ co-doped inorganic–organic hybrid silica sols by single dipping. Transparent, crack-free, glassy SiO₂ films of 310 ± 10 nm in thickness embedded with high mol percent of Cu–Ni alloy NPs were yielded after annealing at 750 °C in 10% H₂-90% Ar atmosphere. Nominal compositions of the films were 20 mol% (Cu–Ni)-80 mol% SiO₂. Optical spectral study of the heat-treated films showed disappearance of Cu plasmon bands due to Cu–Ni alloy formation. Grazing incidence X-ray diffraction (GIXRD) studies revealed the formation of Cu–Ni alloy (2:1, 1:1 and 1:2) NPs inside the SiO₂ film. GIXRD showed a systematic shifting of the diffraction peaks with respect to the fcc Cu–Ni alloy composition, maintaining the nominal ratios. Transmission electron microscopy (TEM) studies of the representative Cu_0.5Ni_0.5-doped film showed existence of homogeneously dispersed Cu–Ni alloy NPs of average size 6.35 nm inside the SiO₂ matrix. The energy dispersive X-ray scattering (EDX) analysis of the individual NPs using the nano-probe (scanning TEM mode) confirmed the presence of both the Cu and Ni with the desired atomic ratio.     

Simultaneous Hydrogen Generation and Exciplex Stimulated Emission in Photobasic Carbon Dots

Photocatalytic water splitting is a promising approach to generating sustainable hydrogen. However, the transport of photoelectrons to the catalyst sites, usually within ps-to-ns timescales, is much faster than proton delivery (∼μs), which limits the activity. Therefore, the acceleration of abstraction of protons from water molecules towards the catalytic sites to keep up with the electron transfer rate can significantly promote hydrogen production. The photobasic effect that is the increase in proton affinity upon excitation offers means to achieve this objective. Herein, we design photobasic carbon dots and identify that internal pyridinic N sites are intrinsically photobasic. This is supported by steady-state and ultrafast spectroscopic measurements that demonstrate proton abstraction within a few picoseconds of excitation. Furthermore, we show that in water, they form a unique four-level lasing scheme with optical gain and stimulated emission. The latter competes with photocatalysis, revealing a rather unique mechanism for efficiency loss, such that the stimulated emission can act as a toggle for photocatalytic activity. This provides additional means of controlling the photocatalytic process and helps the rational design of photocatalytic materials.