Using molecular quantum similarity measures as descriptors in quantitative structure-toxicity relationships

In this paper molecular quantum similarity measures (MQSM) are used to describe molecular toxicity and to construct Quantitative Structure-Toxicity Relationships (QSTR) models. This study continues the recently described relationships between MQSM and log P values, which permits to use the theoretical MQSM as an alternative to the empirical hydrophobic parameter in QSPR studies. In addition a new type of MQSM is presented in this work: it is based on the expectation value of electron-electron repulsion energy. The molecular properties studied here, as application examples are aquatic toxicity, toxicology on Bacteria and inhibition of a macromolecule employing four different molecular sets.     

The Eu luminescence as a measure for chemical bond differences in solids

The well-known use of the emission of the Eu³⁺ ion as a probe for its site symmetry can be extended in suitable cases to give information on differences between chemical bonds in the neighbourhood of the Eu³⁺ ion.     

Shannon information entropy of fractional occupation probability as an electron correlation measure in atoms and molecules

A new method to determine electron correlation energy is presented for atoms and molecules. This method is based on Shannon information entropy that is obtained by fractional occupation probabilities of natural atomic orbitals. It is indicated that the Shannon entropy increases as the number of electrons increases and thus can be considered as a possible measure for the electron correlation in atomic and molecular systems. For neutral atoms and singly charged positive ions we proposed an expression for correlation energy with explicit dependence on the Shannon entropy and atomic number. The obtained correlation energies have been used to compute the first ionization potentials of the ground state of the main group elements from hydrogen through krypton. The calculated ionization potentials are in reasonably good agreement with their corresponding experimental values.We also developed the additivity scheme to find a connection between Shannon entropy and molecular correlation energy. The estimated molecular correlation energies show an excellent agreement with those obtained by elaborate G3 method with R² = 0.990.     

Comparative study of GQ and QG indices as potentially favorable molecular descriptors

In chemical graph theory, several degree-based topological indices are introduced and put forward in the development of quantitative structure-property relationships (QSPR)/quantitative structure-activity relationships (QSAR) studies. However, only a few of them are considered employable in the prediction of physical and chemical properties and biological activities of molecular compounds. Here, we focus our attention on some foremost characteristics of newly defined Geometric–Quadratic $$ and Quadratic–Geometric $$ indices such as prediction power, degeneracy and structure sensitivity. Based on these attributes, we discuss their comparison with other well-established degree-based topological indices with the help of statistical analysis and computational techniques on the data sets of octane, nonane and decane isomers. Some of the graphical approaches, statistical outcomes and computational tests exhibit the dominating nature of the $$ and $$ indices over other topological indices.     

1D 13C-NMR data as molecular descriptors in spectra--structure relationship analysis of oligosaccharides

Spectra-structure relationships were investigated for estimating the anomeric configuration, residues and type of linkages of linear and branched trisaccharides using 13C-NMR chemical shifts. For this study, 119 pyranosyl trisaccharides were used that are trimers of the α or β anomers of D-glucose, D-galactose, D-mannose, L-fucose or L-rhamnose residues bonded through a or b glycosidic linkages of types 1→2, 1→3, 1→4, or 1→6, as well as methoxylated and/or N-acetylated amino trisaccharides. Machine learning experiments were performed for: (1) classification of the anomeric configuration of the first unit, second unit and reducing end; (2) classification of the type of first and second linkages; (3) classification of the three residues: reducing end, middle and first residue; and (4) classification of the chain type. Our previously model for predicting the structure of disaccharides was incorporated in this new model with an improvement of the predictive power. The best results were achieved using Random Forests with 204 di- and trisaccharides for the training set-it could correctly classify 83%, 90%, 88%, 85%, 85%, 75%, 79%, 68% and 94% of the test set (69 compounds) for the nine tasks, respectively, on the basis of unassigned chemical shifts.     

Shannon entropy as a predictor of avoided crossing in confined atoms

Avoided crossing is one of the unique spectroscopic features of a confined atomic system. Shannon information entropy of the ground state and some of the excited states of confined H atom as a predictor of avoided crossing is studied in this work. This is accomplished by varying the strength of the confinement and examining structure properties like ionization energy and Shannon information entropy. Along with the energy level repulsion at the avoided crossing, Shannon information entropy is also exchanged between the involved states. This work also addresses a question: In addition to that regarding localization, what other property of the system can be extracted from Shannon entropy? Insightful connection is discovered between Shannon entropy and the average value of confinement potential, Coulomb potential, and kinetic energy.     

Composition and variability of soil solutions as a measure of human impact on protected woodland areas

A study was made of the sandy and loamy soils of the woodland areas of the Wielkopolski National Park (Poland) affected by acid rain. The basic properties of the soils were determined, revealing their strong acidification, poor buffering power, and the possibility of aluminium release. An analysis was made of the content of soluble, exchangeable, organic, amorphous, and free forms of aluminium. The concentration of exchangeable aluminium exceeded that of the form dissolved in soil water several times to tens of times. In soil solutions Ca/Al ratios in some horizons show very low values that could induce a nutrient deficit. In the sandy profiles the ratio even drops below the critical level of 0.1. In the surface horizon the dominant cation at all the sites is the aluminium ion. An analysis of anions shows a dominance of sulphate and chloride ions. In autumn nitrites were recorded at all depth levels, while in spring only in the surface layers. The highest fluoride concentrations were found to occur in profiles situated the closest to the emission source of fluorine compounds. The markedly higher concentrations of ammonium than nitrate ions can lead to increased acidification and eutrophication of the soil.     

Quantum topological molecular descriptors in QSAR analysis of organophosphorus compounds

A Quantitative structure–activity relationship study is performed on a set of organophosphorus compounds to reveal structural and quantum‐chemical features influencing the toxic effect. The properties derived from the topological analysis of the electron density have been used to model the toxicity data. A multiple linear regression analysis in conjunction with genetic algorithm is used in the study, followed by subsequent validation of the results. Obtained QSAR models are beneficial for virtual screening of toxicity for new compounds of interest. Because toxicity of organophosphorus compounds is dependent on conformational properties, a conformational search has been performed before optimization of geometries. All quantum‐chemical calculations are carried out at DFT/B3LYP level of theory with 6‐311++G(d,p) basis set. Frequency calculations are performed after full geometry optimization. Ab initio wave functions were obtained for further analysis and evaluation of quantum topological properties of target molecules. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012