Znaczenie i przykłady zastosowania banków pseudoatomów asferycznych w krystalografii małych cząsteczek i ich potencjalne wykorzystanie w krystalografii makromolekuł
Journal Title: Wiadomości Chemiczne - Year 2014, Vol 68, Issue 5
Abstract
X-rays are diffracted by the electron density of crystals. Thus, the correct analysis of a single crystal X-ray diffraction pattern can provide information about the distribution of the electron density. How precise and accurate the information could be is largely determined by the resolution of the data collected. The majority of X-ray diffraction data is collected at and below the standard resolution, dmin= 0.84 Å. Before the development of pseudoatom databases, such resolution permitted to carry out X-ray refinement only with the use of simple model of electron density called the Independent Atom Model (IAM). In the IAM, individual atoms are represented by the spherically averaged electron density distributions obtained by theoretical methods for isolated atoms in the ground state. The IAM does not take into account changes in the density distribution of individual atoms caused by such phenomena as chemical bond formation, charge transfer, lone electron pairs, etc. Only the geometrical information of the crystal structure is obtained from the IAM refinement. A more physical model has been introduced in which an atom is represented as a finite spherical harmonic expansion of the electron density around each atomic center and is called a pseudoatom. Such definition allows the pseudoatom electron density to be individually adjusted (by changing values of pseudoatom parameters) to account for density departure from spherical and neutral model. However, to refine pseudoatom parameters with experimental data subatomic resolution is required. It has been shown that the values of pseudoatom parameters are almost identical for atoms in similar chemical environments, i.e. atoms having similar local topology of connecting chemical bonds. Therefore it was possible to build a databank of different types of pseudoatoms and to use the bank to generate the Transferable Aspherical Atom Model (TAAM) for any organic molecule, including proteins and nucleic acids. There are three different pseudoatom databanks being developed: ELMAM2, GID and UBDB. They differ by the source of pseudoatom parameters and by the way how atom types are defined. Replacement of the IAM model by the TAAM in the refinement procedure of standard diffraction data leads to more accurate geometrical information and provide access to quantitative estimation of the electron density distribution and properties derived from it (dipole moment, electrostatic potential, etc.) for molecules in a crystalline environment. The review summarizes the research on the verification and application of pseudoatom databases.
Authors and Affiliations
Paulina Maria Dominiak
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