Molecular conformation and electronic structure of compounds related to amides & thioamides - a study by ab initio & semiemperical molecular orbital methods

Abstract

The molecular conformation of amide derivatives is of paramount importance in understanding the factors which govern the conformations of peptides and proteins. A study of the barriers to internal rotation aids in understanding the forces giving rise to restricted rotation. The application of ab initio and semi-empirical methods (by the EHT, CEDO/2, INDO, MINDO/3) as well as by the PCILO procedures to understand the molecular conformation and electronic structure of a series of closely related amide and thionamide derivatives is made. The compounds considered belong to hydrazine carboxamides, thiocarbamate esters, biuret and diacetamide systems and selenoamides and selenoureas and their thio analogues. Another interesting feature of these compounds is the influence of the hydrazine lone pair. The effect of N-protonation is also investigated. This has relevance in the discussion of many biological problems. The description of bonding in terms of atomic charge densities and bond orders on appropriate population analysis are given. The variation in the electronic structure consequent to N-protonation, molecular conformation and substituents are discussed. The electrostatic potential calculations have also been made and the results correlated with N-protonation and electronic structure. Fourier analyses of the potential energy to various components involving the dipolar, back bonding and steric contributions have been accomplished. The results are useful in understanding the factors determining the barrier to internal rotation. The effect of replacement of sulfur by selenium in thioamides and selenoamides on electronic structure and molecular conformation is investigated.