Enhancing the effectiveness of virtual screening by fusing nearest neighbor lists: a comparison of similarity coefficients

This paper evaluates the effectiveness of various similarity coefficients for 2D similarity searching when multiple bioactive target structures are available. Similarity searches using several different activity classes within the MDL Drug Data Report and the Dictionary of Natural Products databases are performed using BCI 2D fingerprints. Using data fusion techniques to combine the resulting nearest neighbor lists we obtain group recall results which, in many cases, are a considerable improvement on standard average recall values obtained for individual structures. It is shown that the degree of improvement can be related to the structural diversity of the activity class that is searched for, the best results being found for the most diverse groups. The group recall of active compounds using subsets of the class is also investigated: for highly self-similar activity classes, the group recall improvement saturates well before the full activity class size is reached. A rough correlation is found between the relative improvement using the group recall and the square of the number of unique compounds available in all of the merged lists. The Tanimoto coefficient is found unambiguously to be the best coefficient to use for the recovery of active compounds using multiple targets. Furthermore, when using the Tanimoto coefficient, the "MAX" fusion rule is found to be more effective than the "SUM" rule for the combination of similarity searches from multiple targets. The use of group recall can lead to improved enrichment in database searches and virtual screening.     

The effect of clay on the morphology of multiphase latex particles

The effect of montmorrilonite clay (MMT) platelets on the morphology of polystyrene/poly(methyl methacrylate) (PMMA) composite latex particles prepared via PMMA-seeded (semi-) batch emulsion polymerization of styrene was studied. It was found that the particle morphology obtained greatly depended on the ability of the clay platelets to diffuse through the polymer particle. Indeed, when the reactions were strictly under kinetic control, i.e., where the clay platelets were unable to diffuse during polymerization, anisotropic core-shell-like morphologies with split core were observed. A better mobility of the clay platelets could more or less restrict the diffusion of the second-stage polymers within the host polymer, leading to original kinetically controlled morphologies. In the case of a full migration of the clay platelets to the particle surface, the penetration of the second-stage polymer species in the seed latex was found to be more limited, enhancing the formation of secondary particles.     

Square Planar (SP-4) and Octahedral (OC-6) Complexes of Platinum(II) and -(IV) with Predetermined Chirality at the Metal Center

cis-Bis-homoleptic platinum(II) complexes, with predetermined helical chirality at the metal center, can be obtained by using strongly sterically interacting ligands. With this aim, two new ligands, (8R,10R)-2-(2'-thienyl)-4,5-pinenopyridine, th4,5ppy (2), and (8R,10R)-2-(2'-thienyl)-5,6-pinenopyridine, th5,6ppy (4), were synthesized and coordinated to platinum. The structures of the resulting complexes, Pt(th4,5ppy)(2) (5) and Pt(th5,6ppy)(2) (6), were determined by X-ray diffraction, and it was found that they both crystallize with a Delta-cis configuration. Thermal oxidative additions (TOA) of alkyl halides were performed with both complexes leading, in the case of 5, to a mixture of isomers and, in the case of 6, to isomerically pure products. The predetermination of chirality at the metal center is therefore preserved in the octahedral (OC-6) platinum(IV) complexes. Crystals of Pt(th4,5ppy)(2) (5) are orthorhombic, of space group P2(1)2(1)2(1), with a = 12.973(1) ?, b = 13.619(2) ?, c = 17.665(2) ?, alpha = beta = gamma = 90 degrees, and Z = 4. Final R = 0.0268 and R(w) = 0.0424 for 3101 observed reflections. Crystals of Pt(th5,6ppy)(2) (6) are hexagonal, of space group P6(1), with a = 11.5465(4) ?, b = 11.5465(4) ?, c = 35.356(3) ?, alpha = beta = 90 degrees, gamma = 120 degrees, and Z = 6. Final R = 0.0424 and R(w) = 0.0845 for 2660 observed reflections. Neither molecule possesses a crystallographic C(2) symmetry.     

Interatomic Coulombic decay in mixed NeKr clusters

We report the occurrence of interatomic Coulombic decay (ICD) in mixed NeKr clusters. A well-defined feature ranging from 9 to 12 eV in kinetic energy is observed in coincidence with the Ne 2s photoelectrons. It derives from an ICD process, in which an initial Ne 2s vacancy is filled by a Ne 2p electron and an electron is emitted from a 4p level on a neighboring Kr atom. We have studied the dependence of the effect on photon energy, cluster composition, and cluster size. Interestingly, the ICD electron energy increases slightly and grows a shoulder on going from 2% to 5% Kr in the coexpansion process, which we interpret in terms of surface versus bulk effects.     

Ion Interactions with the Carbon Nanotube Surface in Aqueous Solutions: Understanding the Molecular Mechanisms

We study the molecular mechanisms of alkali halide ion interactions with the single‐wall carbon nanotube surface in water by means of fully atomistic molecular dynamics simulations. We focus on the basic physical‐chemical principles of ion–nanotube interactions in aqueous solutions and discuss them in light of recent experimental findings on selective ion effects on carbon nanotubes.     

Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.

Thermodynamic data are often used to calibrate or test amomic-level (AL) force fields for molecular dynamics (MD) simulations. In contrast, the majority of coarse-grained (CG) force fields do not rely extensively on thermodynamic quantities. Recently, a CG force field for lipids, hydrocarbons, ions, and water, in which approximately four non-hydrogen atoms are mapped onto one interaction site, has been proposed and applied to study various aspects of lipid systems. To date, no extensive investigation of its capability to describe salvation thermodynamics has been undertaken. In the present study, a detailed picture of vaporization, solvation, and phase-partitioning thermodynamics for liquid hydrocarbons and water was obtained at CG and AL resolutions, in order to compare the two types or models and evaluate their ability to describe thermodynamic properties in the temperature range between 263 and 343 K. Both CG and AL models capture the experimental dependence of the thermodynamic properties on the temperature, albeit a systematically weaker dependence is found for the CG model. Moreover, deviations are found for solvation thermodynamics and for the corresponding enthalpy-entropy compensation for the CG model. Particularly water/oil repulsion seems to be overestimated. However, the results suggest that the thermodynamic properties considered should be reproducible by a CG model provided it is reparametrized on the basis of these liquid-phase properties.