The generalized invariom database (GID)

Abstract

Invarioms are aspherical atomic scattering factors that enable structure refinement of more accurate and more precise geometries than refinements with the conventional independent atom model (IAM). The use of single-crystal X-ray diffraction data of a resolution better than sin / = 0.6 Å À1 (or d = 0.83 Å ) is recommended. The invariom scatteringfactor database contains transferable pseudoatom parameters of the Hansen-Coppens multipole model and associated local atomic coordinate systems. Parameters were derived from geometry optimizations of suitable model compounds, whose IUPAC names are also contained in the database. Correct scattering-factor assignment and orientation reproduces molecular electron density to a good approximation. Molecular properties can hence be derived directly from the electron-density model. Coverage of chemical environments in the invariom database has been extended from the original amino acids, proteins and nucleic acid structures to many other environments encountered in organic chemistry. With over 2750 entries it now covers a wide sample of general organic chemistry involving the elements H, C, N and O, and to a lesser extent F, Si, S, P and Cl. With respect to the earlier version of the database, the main modification concerns scattering-factor notation. Modifications improve ease of use and success rates of automatic geometry-based scatteringfactor assignment, especially in condensed hetero-aromatic ring systems, making the approach well suited to replace the IAM for structures of organic molecules.

Methodical aspects of experimental studies for the relationship of static and dynamic features of crystal structure: application of various atomic scattering factors to study the vibrational characteristics of molecular crystals

“…Prior to refinement, the X-H dis tances were normalized to the values from the database of "in varioms" 14 In the MUL model, the coordinates for all non hydrogen atoms, anisotropic ADP, and multipole parameters to the octa pole level (l = 3) (and for the chlorine atoms, to the hexade capole level (l = 4)) were refined for F hkl . Before refinement, the X-H distances were normalized to values obtained by the quan tum chemical calculations of the associates (see further).…”

Six questions on topology in theoretical chemistry

“…Consequently, we asked ourselves why we were actually pursuing these analyses if we don't learn new things about chemistry? The answer was that we were developing library methods based on transferability assumptions that can quickly and reliably reconstruct an electron density from building blocks in order to get better experimental geometries and derived properties, such as interaction energies, that cannot be guessed [81,82]. However, in my opinion performing topological analysis of compounds in usual bonding situations in the ground state is not more than collecting stamps, but the interesting applications involve method development and chemical problems.…”

Electrostatic potential of dynamic charge densities

“…Dynamic properties of multipole models. Dittrich et al (2005) have published high-resolution X-ray diffraction data of dl-serine as measured at temperatures of 20, 100 and 298 K. They reported MP models based on invariom refinements (Dittrich et al, 2013) against all three datasets. Their results demonstrated a consistent description of the aspherical atomic electron densities, independent of temperature.…”

“…These MP models involve isotropic displacement parameters for H atoms. H-atom distances C-H and N-H were fixed to values from the invariom database (Dittrich et al, 2013). Then for each temperature, anisotropic displacement parameters were computed for H atoms, employing the SHADE3 server (Madsen, 2006).…”