Spectral and orbital based analyses of interactions in some biomolecules

Interactions of biomolecules with the environment and other functional groups play a signifcant role in biochemical reactions and thus are important for understanding the functionalities and diversities of life. Due to time and length scale issues, experimental studies of fundamental properties of biomolecules and their interactions with the environment are restricted. Therefore computer simulation of biomolecules and their interactions with the environment have long been a major interest of scientifc communities. In the past decades, researchers have made accelerated progress in elucidating the electronic structures of large biomolecules and in simulating the bio-molecular processes. In this study an analytical and computational method is developed and applied to probe the spectral and orbital-based electronic structural information from both coordinate space and momentum space. Hence giving it the name dual space analysis (DSA). In coordinate space, properties such as the geometric parameters, molecular electrostatic potentials, charge density distributions and chemical reactivity indices in the form of Fukui functions are studied applying different ab initio and density functional (DFT) methods. Effects of inter- and intra-molecular interactions on these properties are analysed. The spectral responses due to the isomerization and attachments of different molecular moieties in core and valence space are further elucidated. It is observed that different models in combination with different basis sets produce optimal results for different properties. In momentum space, the momentum distributions represent the atomic orbitals. Theoretical momentum distributions are simulated by Fourier transformations of the position space orbital wavefunctions to momentum space. They are validated by comparing with the experimental measurements from the electron momentum spectroscopy (EMS). The validated methods are thus applied in analysis of a series of biomolecules including different tautomeric forms of DNA bases and potential drug candidates composed of DNA bases and various modifcations of sugar moieties. As a result, the orbital based signatures and characteristics of tautomers, conformers and derivatives of important biomolecules are revealed.