Znaczenie i przykłady zastosowania banków pseudoatomów asferycznych w krystalografii małych cząsteczek i ich potencjalne wykorzystanie w krystalografii makromolekuł
Znaczenie i przykłady zastosowania banków pseudoatomów asferycznych w krystalografii małych cząsteczek i ich potencjalne wykorzystanie w krystalografii makromolekuł The importance and examples of application of aspherical pseudoatom databanks in small-molecule crystallography and their potential use in makromolecular crystallography
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.
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