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.

Aspherical‐Atom Modeling of Coordination Compounds by Single‐Crystal X‐ray Diffraction Allows the Correct Metal Atom To Be Identified

“…[42] 8 This requirement is less important than in a direct quantum chemical treatment, as projection onto the Hansen/Coppens multipole model ensures that the scattering-factor model is the same even with different basis sets. 9 The terminology "projection" onto the multipole model was introduced by Koritsµnszky et al [48] and, in this context, means the process of reproducing theoretical EDD through least-squares fit of multipole parameters. These are not the final page numbers!…”

Protonation of Ferrocene: A Low‐Temperature X‐ray Diffraction Study of [Cp2FeH](PF6) Reveals an Iron‐Bound Hydrido Ligand

“…After initial invariom refinement of the Cp system with elongated CÀHb onds, [21,22] aspherical atom refinement with tailor-made scattering factors from as ingle-point energy computation (M06/defTZVP), projected onto the Hansen/ Coppens multipole model, confirmed the presence of the hydrogen atom and gave reduced standard uncertainties and av alue of 1.49(4) for the Fe1 À H11 bond. Owing to the placement of the ferrocene moiety on at wofold rotation axis,t wo equivalent, equally occupied (50 %) H11 positions were determined.…”

New Polymorphs of the Phase-Change Material Sodium Acetate

“…The ADDSYMM routine of the program PLATON [14] also suggests the higher symmetry at 300 K when disorder is ignored, but figures of merit show that the structure is indeed orthorhombic. After initial IAM refinements with SHELXL [15], we have subsequently carried out invariom refinements [8] that used fixed pseudoatom scattering factors derived from density functional theory (DFT) computations on both new forms of sodium acetate with the XD2006 suite of programs [16]. Table 2 lists invariom scattering-factor names, the respective local-atomic site symmetry and the model compounds that provide the local chemical environment from which these scattering factors were computed.…”

“…We recently obtained two so far unknown tetragonal and orthorhombic crystal forms of sodium acetate. Accurate structure determinations of both new structures reported here rely on refinements with aspherical scattering factors of the invariom database [8]. These results are compared to conventional refinements using the independent atom model (IAM).…”