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We analyzed the frequency with which intraligand contacts occurred in a set of 1300 protein-ligand complexes [ Plewczynski et al. J. Comput. Chem. 2011 , 32 , 742 - 755 .]. Our analysis showed that flexible ligands often form intraligand hydrophobic contacts, while intraligand hydrogen bonds are rare. The test set was also thoroughly investigated and classified. We suggest a universal method for enhancement of a scoring function based on a potential of mean force (PMF-based score) by adding a term accounting for intraligand interactions. The method was implemented via in-house developed program, utilizing an Algo_score scoring function [ Ramensky et al. Proteins: Struct., Funct., Genet. 2007 , 69 , 349 - 357 .] based on the Tarasov-Muryshev PMF [ Muryshev et al. J. Comput.-Aided Mol. Des. 2003 , 17 , 597 - 605 .]. The enhancement of the scoring function was shown to significantly improve the docking and scoring quality for flexible ligands in the test set of 1300 protein-ligand complexes [ Plewczynski et al. J. Comput. Chem. 2011 , 32 , 742 - 755 .]. We then investigated the correlation of the docking results with two parameters of intraligand interactions estimation. These parameters are the weight of intraligand interactions and the minimum number of bonds between the ligand atoms required to take their interaction into account.

Optical quality lithium salicylate (LiSal) single crystals have been grown from water and methanol solutions for thermal neutron detection studies. The results of structural studies showed that LiSal crystallizes from water as a stable modification different from the monohydrate LiSal·H2O reported previously. Growth from methanol results in the formation of unstable crystals of LiSal·MeOH that quickly degrade in air due to the loss of methanol. Initial radiation detection tests showed a good neutron/gamma separation in water-grown modification making LiSal in its single crystal form a potential material for thermal neutron detection.

Si nanocrystals 1−10 nm in size highly resistant to oxidation were prepared by thermal (680 °C) or gold-induced (450−600 °C) decomposition of tetramethylsilane and tetraethylsilane using trioctylamine as an initial solvent. Transmission electron microscopy analysis of samples obtained in the presence of gold showed that Si nanocrystals form via solid-phase epitaxial attachment of Si to the gold crystal lattice. The results of computational modeling performed using first principles density functional theory calculations show that the enhanced stability of nanocrystals to oxidation is due to the presence of N or N-containing groups on the surface of nanocrystals.

Ge nanoparticles with sizes from 1 to 15 nm were synthesized by thermal decomposition of the germane precursors trichlorogermane, tetraethylgermane, and tetrabutylgermane. Experiments were performed in the organic solvents trioctylamine, squalene, and octacosane, which have boiling points in the temperature range from 380 to 429 °C. The use of high-boiling-point solvents extended the temperature range of the reactions, thus enabling the experiments to be conducted with organogermane precursors which have high decomposition points above 400 °C. Characterization by X-ray diffraction and transmission electron microscopy showed that, depending on the reaction temperature, the final decomposition products consist of amorphous Ge nanoparticles, nanocrystals, or nanowires that grow only in the 〈110〉 direction.

First principles electronic structure simulations are used to study the atomistic detail of the interaction between organic surfactant molecules and the surfaces of CdSe semiconductor nanoparticles. These calculations provide insights into the relaxed atomic geometry of organics bound to semiconductor surfaces at the nanoscale as well as the electronic charge transfer between surface atoms and the organics. We calculate the binding energy of phosphine oxide, phosphonic and carboxylic acids, and amine ligands to a range of CdSe nanoparticle facets. The dominant binding interaction is between oxygen atoms in the ligands and cadmium atoms on the nanoparticle surfaces. The most strongly bound ligands are phosphonic acid molecules, which bind preferentially to the facets forming the sides of CdSe nanorods. The calculated relative binding strengths of ligands to different facets support the hypothesis that these binding energies control the relative growth rates of different facets, and therefore the resulting ...

We present a two-step synthesis route that yields nanometer-size crystalline germanium in the form of a black powder. It relies on high temperature decomposition of tetraethylgermane (TEG) in organic solvents. The presence of pure germanium with diamond structure is unambiguously attested by powder XRD measurements. Low-resolution TEM indicates that the particles are between ∼5 to 30 nm in size, depending on the synthesis conditions. The as-synthesized Ge powders can be stored in air for months and no oxidation occurs. The Ge powders are sparingly soluble in conventional solvents because Ge nanocrystals are likely embedded in a matrix composed mainly of CC, C−C, and C−H bonds. The presence of residual organic byproducts impedes probing of the optical properties of the dots. Also, we discuss drawbacks and open challenges in high-temperature solution synthesis of Ge nanocrystals that could also be faced in the synthesis of Si nanocrystals. Overall, our results call for a cautious interpretation of reported ...