Quantum chemical “Aufbau” principles: how to estimate the shape of highly flexible (bio-)polymers? A recursively extendable “chemion picture” of Euler-Hückel-type

Abstract

Abstract An outline is given of how to split the n-dimensional space of torsion angles occurring in flexible (bio-)polymers (like alkanes, nucleic acids, or proteins, for instance) into n one-dimensional potential curves. Forthcoming applications will focus on the “protein folding problem,” beginning with polyglycine. Context In accordance with Euler’s topology rules, molecules are considered to be composed of “vertices” (atoms, ligands, bonding sites, functional groups, and bigger fragments). Following Hückel, each vertex is represented by only one basis function. Starting from the “monofocal” hydrids CH$$_4$$ 4 , NH$$_3$$ 3 , OH$$_2$$ 2 , FH, and SiH$$_4$$ 4 , PH$$_3$$ 3 , SH$$_2$$ 2 , ClH as anchor units, “chemionic” Hamiltonians (of individual “chemion ensembles” and proportional nuclear charges) are constructed recursively, together with an appropriate basis set for the first five (normal) alkanes and some related oligomers like primary alcohols, alkyl amines, and alkyl chlorides. Methods Standard methods (“Restricted Hartree-Fock RHF” and “Full Configuration Interaction FCI”) are used to solve the various stationary Schrödinger equations. Two software packages are indispensable: “SMILES” for integral evaluations over Slater-type orbitals (STO), and “Numerical Recipes” for matrix diagonalizations and inversions. While managing with only two-center repulsion integrals, “implicit multi-center integrations” lead us to the non-empirical fundament of Hoffmann’s “Extended-Hückel Theory.”