On the origin of dynamic instability of molecular systems

The vibronic origin of dynamic instability of molecular systems considered earlier, is here given a more complete and rigorous treatment. It is shown that the nonvibronic contribution to the curvature of the adiabatic potential arising due to nuclear displacements under fixed electronic density distribution, is always positive, and hence the only reason for dynamic instability is the pseudo Jahn-Teller effect. For some examples of special interest (planar equilateral NH₃, planar square CH₄ and linear H ₃ ⁺ ) the molecular excited states, responsible for the instability of the ground state, are revealed by means of ab initio calculations.     

A Novel Electron-Conformational Approach to Molecular Modeling for QSAR by Identification of Pharmacophore and Anti-Pharmacophore Shielding

Abstract

A novel method of pharmacophore identification and activity prediction in structure-activity (structure-property) relationships is worked out as an essential extension and improvement of previous publications. In this method each conformation of the molecular systems in the training set of the SAR problem is presented by both electronic structure and geometry parameters arranged in a matrix form. Multiple comparisons of these matrices for the active and inactive compounds allows one to separate a smaller number of matrix elements that are common for all the active compounds and are not present in the same arrangement in the inactive ones. This submatrix of activity represents the pharmacophore (Pha).

By introducing the Anti-Pharmacophore Shielding (APS) defined as molecular groups and competing charges outside the Pha that hinder the proper docking of the Pha with the bioreceptor, the procedure of Pha identification is essentially reduced to the treatment of a smaller number of simplest in structure most active and inactive compounds. A simple empirical scheme is suggested to estimate the APS numerically, while the contributions of different conformations of the same compound are taken into account by means of Boltzmann distribution. This enables us to make approximate quantitative predictions of activities.

In application to rice blast activity we reached an approximately 100% (within experimental error) prediction probability of the activity qualitatively (yes, no), and with r ² = 70% quantitatively.     

Theoretical prediction of intrinsic self-trapping of electrons and holes in monoclinic HfO2

We predict, by means of ab initio calculations, stable electron and hole polaron states in perfect monoclinic HfO2. Hole polarons are localized on oxygen atoms in the two oxygen sublattices. An electron polaron is localized on hafnium atoms. Small barriers for polaron hopping suggest relatively high mobility of trapped charges. The one-electron energy levels in the gap, optical transition energies and ESR g-tensor components are calculated.     

Dependence of viscosity of organic nonassociated liquids on structural and conformational characteristics of the molecules

Semiempirical equations are obtained for the dependence of the viscosity of organic nonassociated liquids on the structural and conformational characteristics of the molecules. The equations are used to compute the viscosities of organic compounds of different structural classes. It is shown that they can be used to take into account the effect of isomerization of the carbon skeleton of the molecule on the viscosity and also the temperature dependence of the viscosity.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 25, No. 5, pp. 563–567, September–October, 1989.     

Electronic and topological investigation of growth-regulating activity in the series of abscisic acid analogs

The structure-reactivity relationship in the series of abscisic acid analogs was investigated by means of the electronic structure parameters. The fragments of the molecules responsible for the activity (inactivity) in the investigated series of chemical compounds were determined by means of the electronic topological approach. The developed forecasting system makes it possible to undertake a purposeful search for new potentially active compounds.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 25, No. 5, pp. 590–594, September–October, 1989.     

Electronic structure and coordination to DNA fragments for coordination compounds of Cu(II) with amino-acids of composition CuA′A″

The MWH method has been used in calculations on the electronic structures of compounds of copper(II) with -amino-acids CuGLY(L-Ser), Cu(L-Alan)(L-Ser), CuGly₂·H₂O, as well as for the free amino-acids: alanine, glycine, and serine. The proper energies and eigenvectors have been derived together with the charges on the atoms, which indicate the mode of coordination in these systems with DNA fragments involving the formation of sandwich complexes, and this provides a qualitative explanation of the differences in antitumor activity between these compounds.Translated, from Teoreticheskaya i'Éksperimental'naya; Khimiya, No. 3, pp. 351–356, May–June, 1985.