Morphology determination of small particles by electron microscopy and electrical conduction measurements

In this paper, we show that it is possible to deduce the actual morphology of small particle condensed onto an insulator by combining the granularity analysis from electron micrographs and the electrical sheet conductance of the deposit on its substrate. Assuming the particles are truncated ellipsoids, we determine the excentricity and the contact angle with the substrate for Au on amorphous carbon and MgO substrates.     

Calculating the knowledge-based similarity of functional groups using crystallographic data

A knowledge-based method for calculating the similarity of functional groups is described and validated. The method is based on experimental information derived from small molecule crystal structures. These data are used in the form of scatterplots that show the likelihood of a non-bonded interaction being formed between functional group A (the `central group') and functional group B (the `contact group' or `probe'). The scatterplots are converted into three-dimensional maps that show the propensity of the probe at different positions around the central group. Here we describe how to calculate the similarity of a pair of central groups based on these maps. The similarity method is validated using bioisosteric functional group pairs identified in the Bioster database and Relibase. The Bioster database is a critical compilation of thousands of bioisosteric molecule pairs, including drugs, enzyme inhibitors and agrochemicals. Relibase is an object-oriented database containing structural data about protein-ligand interactions. The distributions of the similarities of the bioisosteric functional group pairs are compared with similarities for all the possible pairs in IsoStar, and are found to be significantly different. Enrichment factors are also calculated showing the similarity method is statistically significantly better than random in predicting bioisosteric functional group pairs.     

Size effects in the CO-oxidation over supported Pd particles

Low pressure CO oxidation was studied over small supported Pd particles by means of static secondary ion mass spectrometry (SSIMS). The SSIMS spectra of adsorbed layers on Pd particles with diameters below ～7nm contained, besides other species, Pd _n X⁺ ions (X=C, O, CO;n=1–3). In experiments with Pd films, Pd _n C⁺ species were much less abundant or even absent from the mass spectra. We conclude that CO decomposed in appreciable amounts only on Pd particles. No significant influence of the support material (mica, MgO,α-Al₂O₃) was seen and posthumous TEM analysis revealed well defined particle morphologies with largely (111) and (100) facets. At total pressures below 10^?4 Pa, the relative carbidic intensities Pd _n C⁺/Pd _n ⁺ , which were taken as proportional to the carbon surface concentrations, first increased with increasing temperatures and then decreased after they passed a maximum at T=400–440 K. The smaller the particle size, the more intense were the maxima. For T ?440 K, carbon was removed from the surface via reaction with oxygen. Strong hysteresis effects in the C_ad and CO_ad concentrations occurred during temperature variation measurements. The Pd _n C⁺/Pd _n ⁺ ratios displayed maxima during heating but not during cooling. While the Pd _n CO⁺/Pd _n ⁺ ratios were always high at 300 K and always low at T>550 K, they were more intense in the medium temperature range when subjecting the samples to heating. These hysteresis effects are discussed in terms of asymmetric adsorption and reaction behaviour of CO/O₂ mixtures, involving inhibition of CO₂ formation by adsorbed carbon and carbon monoxide.     

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.     

Experimental and Computational Study of the Thermal Decomposition of 3‐Methyl‐3‐buten‐1‐ol in m‐Xylene Solution

An experimental study of the thermal decomposition of a β‐hydroxy alkene, 3‐methyl‐3‐buten‐1‐ol, in m‐xylene solution, has been carried out at five different temperatures in the range of 513.15–563.15 K. The temperature dependence of the rate constants for the decomposition of this compound in the corresponding Arrhenius equation is given by ln k (s^?1) = (25.65 ± 1.52) ? (17,944 ± 814) (kJ·mol^?1)·T^?1. A computational study has been carried out at the M05–2X/6–31+G(d,p) level of theory to calculate the rate constants and the activation parameters by the classical transition state theory. There is a good agreement between the experimental and calculated rate constants and activation Gibbs energies. The bonding characteristics of reactant, transition state, and products have been investigated by the natural bond orbital analysis, which provides the natural atomic charges and the Wiberg bond indices. Based on the results obtained, the mechanism proposed is a one‐step process proceeding through a six‐membered cyclic transition state, being a concerted and slightly asynchronous process. The results have been compared with those obtained previously by us (Struct Chem 2013, 24, 1811–1816) for the thermal decomposition of 3‐buten‐1‐ol, in m‐xylene solution. We can conclude that in the compound studied in this work, 3‐methyl‐3‐buten‐1‐ol, the effect of substitution at position 3 by a weakly activating CH₃ group is the stabilization of the transition state formed in the reaction and therefore a small increase in the rate of thermal decomposition.     

Structural and Kinetic Aspects of Blood Plasma Protein Adsorption on the Surface of Hydrophobic Polymers

Abstract

Due to the wide use of polymers in medicine, researchers are required to solve a very important problem–to understand the interaction between materials of nonphysiological origin and the surrounding biological liquids, and tissues, particularly blood.