Sławomir Ostrowski

What does the HOMA index really measure

The HOMA index was generalized to the function of a property of chemical bonds such as, e.g., characteristics in BCPs. The new HOMA indices strongly correlate with the classical one for a variety of cyclic hydrocarbons unsaturated or not. Thus, the indices reflect a more general property then aromaticity: the savoricity.

Chirality Measures of α-Amino Acids

To measure molecular chirality, the molecule is treated as a finite set of points in the Euclidean R(3) space supplemented by k properties, p(1)((i)), p(2)((i)), ..., p(k)((i)) assigned to the ith atom, which constitute a point in the Property P(k) space. Chirality measures are described as the distance between a molecule and its mirror image minimized over all its arbitrary orientation-preserving isometries in the R(3) × P(k) Cartesian product space. Following this formalism, different chirality measures can be estimated by taking into consideration different sets of atomic properties. Here, for α-amino acid zwitterionic structures taken from the Cambridge Structural Database and for all 1684 neutral conformers of 19 biogenic α-amino acid molecules, except glycine and cystine, found at the B3LYP/6-31G** level, chirality measures have been calculated by a CHIMEA program written in this project. It is demonstrated that there is a significant correlation between the measures determined for the α-amino acid zwitterions in crystals and the neutral forms in the gas phase. Performance of the studied chirality measures with changes of the basis set and computation method was also checked. An exemplary quantitative structure–activity relationship (QSAR) application of the chirality measures was presented by an introductory model for the benchmark Cramer data set of steroidal ligands of the sex-hormone binding globulin.

On Stability, Chirality Measures, and Theoretical VCD Spectra of the Chiral C58X2 Fullerenes (X = N, B)

The stability of all 23 C(58)N(2) and C(58)B(2) heterofullerenes in the singlet and triplet states was determined at the B3LYP/6-31G** level. In equilibrium mixture the achiral (1,4) C(58)N(2) isomer would be populated in ca. 95.8%, the chiral (1,16) one in ca. 3.3%, and the achiral (1,4) C(58)B(2) in 100%, whereas all triplet state isomers are less stable. Fourteen out of 23 C(58)X(2) are chiral. Four different chirality measures were calculated by our own CHIMEA program: pure geometrical, labeled, mass, and charge. Intercorrelations between the measures for all chiral compounds indicate that the pure geometrical chirality measure is unstable and should not be used in QSAR predictions of the other molecular properties, while the labeled and mass-weighted ones are promising QSAR descriptors. For each chiral C(58)N(2) molecule, some very strong VCD bands, of intensity comparable with that in the IR spectra, can serve in identification and characterization of the isomers.

On the HOMA index of some acyclic and conducting systems

The geometrical aromaticity HOMA index can be useful for acyclic linear systems. It approaches a horizontal asymptote as the periodic linear system increases in size. For the unsaturated polymers such as polyenes or polythiophenes, the index seems to be a fair measure of the π-electron delocalization and thus to be a good simple tool for the design of conducting polymers.

On AunAt clusters as potential astatine carriers

To understand interactions between astatine atoms with gold clusters the AunAt and AunX clusters, n = 12 or 13, X = F, Cl, Br, and I, were calculated at the DFT level using basis sets with a quasi-relativistic pseudopotential and the D3 Grimme correction for the dispersion interactions. Among the studied clusters of various geometries, the interaction energy of At to the clusters is the smallest. Yet, consideration of the electron detachment from the X− anion and generation of a H2 molecule and OH− anion from water shows that the formation of the astatine gold clusters is favored.

Facilitation of the PED analysis of large molecules by using global coordinates.

Global coordinates have been found to be useful in the potential energy distribution (PED) analyses of the following large molecules: [13]-acene and [33]-helicene. The global coordinate is defined based on much distanced fragments of the analysed molecule, whereas so far, the coordinates used in the analysis were based on stretchings, bendings, or torsions of the adjacent atoms. It has been shown that the PED analyses performed using the global coordinate and the classical ones can lead to exactly the same PED contributions. The global coordinates may significantly improve the facility of the analysis of the vibrational spectra of large molecules.