Aspherical-atom scattering factors from molecular wave functions. 1. Transferability and conformation dependence of atomic electron densities of peptides within the multipole formalism

Abstract

In this study, the feasibility of building a database of theoretical atomic deformation density parameters applicable to the construction of the densities of biomacromolecules and to the interpretation of their X-ray diffraction data is discussed. The procedure described involves generation of valence-only structure factors of tripeptides calculated from theoretical densities at the B3LYP level and the re®nement of multipole parameters against these simulated data. Our results so far indicate that the backbone pseudoatoms extracted in such a way are highly transferable and fairly invariant with respect to rotations around single bonds in the peptide framework. The ultimate goal is to use the aspherical-atom database for improved macromolecular re®nements that are based on high-resolution data and for prediction of electrostatic properties of larger molecules.

A Theoretical Databank of Transferable Aspherical Atoms and Its Application to Electrostatic Interaction Energy Calculations of Macromolecules

“…The aromatic trivalent nitrogen type, N311, differs from aromatic carbons by not having electron deficiency lobes above and below the plane (d 20 is not populated).…”

“…The atoms are close to neutral and vary from +0.11(6) (C363) to -0.15(4) (C360) electron units. In the first 10 atom types, representing atoms participating only in a single ring, the multipoles d 33+ , d 20 , and d 11+ are dominant. They describe respectively the deformation density along the three bonds, the π density above and below the ring, and the difference between the density in the exocyclic and cyclic bonds.…”

The success story of crystallographyThis Laue centennial article has also been published inZeitschrift für Kristallographie[Schwarzenbach (2012).Z. Kristallogr.227, 52–62].

“…This called for the establishment of data banks containing the parameters of the most important pseudo-atoms, defined with respect to well chosen local coordinate systems. The data banks available at present are ELMAM2 (Domagała & Jelsch, 2008) with pseudo-atoms derived from high-resolution diffraction data, UBDB (Koritsanszky et al, 2002) with pseudo-atoms obtained from single-point calculations, and Invariom (Dittrich et al, 2006) with pseudo-atoms derived from geometry-optimized calculations. These data banks can be used to obtain more precise atomic coordinates and displacement parameters by taking care of the asphericity shifts.…”

The success story of crystallography

“…This called for the establishment of data banks containing the parameters of the most important pseudo-atoms, defined with respect to well chosen local coordinate systems. The data banks available at present are ELMAM2 (Domagala & Jelsch, 2008) with pseudo-atoms derived from high-resolution diffraction data, UBDB (Koritsanszky et al, 2002) with pseudo-atoms obtained from single-point calculations, and Invariom (Dittrich et al, 2006) with pseudoatoms derived from geometry-optimized calculations. These data banks can be used to obtain more precise atomic coordinates and displacement parameters by taking care of the asphericity shifts.…”