The generalized invariom database (GID)

• Published in: Acta crystallographica. Section B, Structural science Vol. 69; no. 2; pp. 91 - 104
• Main Authors: Dittrich, B, Huebschle, C B, Propper, K, Dietrich, F, Stolper, T, Holstein, J J
• Format: Journal Article
• Language: English
• Published: 01-04-2013
• Subjects: Amino acids; Atomic structure; Diffraction; Mathematical models; Molecular structure; Organic chemistry; Scattering
• ISSN: 0108-7681; 1600-5740
• DOI: 10.1107/S0108768113002280

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[thetas]/ lambda = 0.6Aa-1 (or d = 0.83Aa) is recommended. The invariom scattering-factor 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 scattering-factor assignment, especially in condensed hetero-aromatic ring systems, making the approach well suited to replace the IAM for structures of organic molecules.