REPOSITORY > RESULTS

Abstract

X-rays are diffracted on electron clouds and thereby provide a mean to observe 3-dimensional structure of
molecules at atomic level. Using medium resolution diffraction data (2Å and lower) we have shown that
averaging of electron density maps generated from sets of randomly distributed atoms and can reduce noise
and model bias of the maps and thereby assist in their correct interpretation.
When the crystals are so well ordered that diffraction data at ultra-high resolution can be collected
(beyond 0.6Å), these data provide information not only about the core electrons surrounding the atomic
nucleus, but also contain information about the fine distribution of electron density. Such data thus provide
the insight into distribution of electron density clouds in covalent bonds as well as shifts of electron density.
To approach interpretation of experimental data to the theoretical quantum mechanical models, we have
developed a crystal structure refinement procedure based on mathematical model of quantum mechanics
and named it “wave function coefficients” (WFC). WFC electron density is calculated from one “quasimolecular
orbital” which is the sum of all atomic orbitals of the molecule. Our current model, analogously
with quantum mechanical models of the Hartee-Fock level, does not consider the effects of atomic
movements and distributions encompassed in crystallographic B-factor. The obtained WFC representation
of electron density was used to calculate the electrostatic potential around the molecules. To take into
account the solvation effects of the media by solving the Poisson Boltzmann equation point charge models
must be provided. Partial charges were determined by minimizing the least-squares difference between the
electrostatic potential and the potential from the point charges. In the case of protein model unexpectedly
large main-chain charge fluctuations were observed thus challenging the current understanding of
polarizability of amino acid residues in protein structures.