Vladimir V. Shcherbukhin

Rapid conversion of molecular graphs to three-dimensional representation using the MOLGEO program

The MOLGEO program has been developed for the efficient conversion of molecular graphs into possible 3D molecular models. It rapidly generates acceptable 3D Cartesian coordinates from (i) the molecular connectivity and (ii) a table of bond lengths and angles which is user modifiable. Stereochemistry designated in the input structure is preserved throughout the optimization. The program accepts input files and provides output files in various formats as desired, including MOPAC, AMPAC, SMD, MMX, and MDL MolFiles. Our new depth-first search method for the rapid construction of a 3D model is described and compared with Crippens embedding algorithm. Results of geometry calculation for various sets of structures are presented and discussed. Possible useful applications of the MOLGEO program for QSAR research are described.

1,2,3-benzodithiazolyl radicals formed by thermolysis and photolysis of 1,3,2,4-benzodithiadiazines

Mild thermolysis (at 110–150°C) of 1,3,2,4-benzodithiadiazine 1 and its carbocyclic substituted derivatives 2–15 in hydrocarbon solvents quantitatively yields stable 1,2,3-benzodithiazolyl π-radicals 1•–15•. Kinetics of this reaction can be described as a first-order process. Arrhenius parameters of the effective rate constant are Ea = 80 ± 8 kJ mol−1, k0 = 106.4 ± 1.1 s−1 for 1 in squalane. Room-temperature photolysis of 1 in hydrocarbon solvents also affords radical 1• in nearly quantitative yield. Quantum yield of photolysis is wavelength dependent and is equal to 0.08 ± 0.01 at 313 nm in benzene. Experimental hyperfine coupling (hfc) constants in the ESR spectra of 1•–15• agree fairly well with those calculated at the B3LYP/CC-pVDZ level of theory. Spin density distribution in 1•–15• is in striking contrast to that of isomeric 1,3,2-benzodithiazolyls but resembles the distribution in correspondingly substituted benzyl radicals. ESR linewidths of radicals 1•-15• display some features likely related to spin-rotational relaxation.

HeI photoelectron spectra and π-electronic structure of substituted 1,3,2,4-benzodithiadiazines, formally antiaromatic 12π-electron compounds☆

Abstract The HeI photoelectron spectra of various 5-R-, 6-R- and 7-R-substituted derivatives of 1,3,2,4-benzodithiadiazine (R=F, Cl, CH3, CF3, OCH3), a formally antiaromatic 12π-electron compound, have been measured and assigned in the IE1–IE4 area by Koopmans’ correlation with 6-31G* eigenvalues. Despite a considerable localization (∼70%) of the highest occupied π-MO on the sulfur–nitrogen fragment, IE1 depends upon both position and character of the carbocyclic substituent R.

INVESTIGATION OF CARBOCATIONIC REARRANGEMENTS BY THE ICAR PROGRAM

The ICAR program for the elucidation of carbocationic rearrangement mechanisms is described. Chemical transformations of the given structure are generated by an exhaustive combinatorial procedure and subsequently evaluated with the use of a knowledge base. Multistep mechanistic pathways are rationalized with regard to thermodynamic and kinetic parameters of the rearrangements. Application of the program is discussed.

The ICAR program: Computer-assisted investigation of carbocationic rearrangements

Abstract The problem of computer-assisted generation of carbocationic rearrangements is considered. The formalized approach to the description of carbocationic transformations is presented and the ICAR program (Investigation of CArbocationic Rearrangements) is briefly described. The ICAR program combines the pure combinatorial methods of the generation of carbocationic transformations with a flexible system of empirical selection criteria. Main principles of constructive enumeration of rearranged pathways and examples of selection criteria are discussed. The results of the solution of several carbocationic problems are also briefly mentioned. For instance, it is shown that the well-known “adamantane-land” is incomplete and should be supplemented with new possible precursors of adamantane. The working PC-version of the ICAR program with users manual is included on disk in this issue.

Molecular Rearrangements of (-)-α-Cedrene in Superacids

Abstract The (-)-α-cedrene was for the first time rearranged into isomeric compounds with the zizaane and patchoulane skeletons. The possible mechanisms of carbocationic rearrangements were studied by methods of molecular mechanics with the use of the ICAR software .

Rearrangements of ledene and aromadendrene in superacids

Abstract Acid-catalyzed rearrangements of ledene and aromadendrene were studied for the first time. In superacidic media, conversion into compounds with the natural cubebane skeleton was discovered. A marked difference between the compositions of the conversion products of one and the same olefin in superacids and in ordinary acidic media was observed.

Computer generation of chemical structures using the gem program

A new program for generating chemical structures starting from the given molecular formula is described. The generation includes two stages. The first step is exhaustive combinatorial enumeration of molecular graphs with the given gross formula by the GEM structural generator. At the second step, these molecular graphs in the form of connectivity matrices are converted to 3D models by the MOLGEO program. The possible applications of this software are discussed.