Concepts Of Structural Chemistry Research Articles

The Cambridge structural database (CSD): important resources for teaching concepts in structural chemistry and intermolecular interactions

Abstract The Cambridge Structural Database (CSD) is a repository of all published organic and metal-organic crystal structures of small molecules. These compounds have been crystallized under different conditions and have variable bond parameters and molecular landscapes. Entries in the database therefore serve as real models that can be used to illustrate structural properties such as bond angles, bond distances, torsion angles and other intra- and intermolecular interactions. This paper illustrates how the CSD programs ConQuest and Mercury can be used to search the database for 3D molecular structures to teach concepts such as molecular geometry, symmetry and group theory, organometallic chemistry and intermolecular interactions involving hydrogen bonding and Full Interaction Maps (FIMs) to explore molecular landscapes for halogen bond interactions. Results obtained from these studies are beneficial to understand and predict crystal properties as well as the structural properties of molecules and ions in crystal environments.

How big are atoms in crystals?

Atoms and bonds are central concepts in structural chemistry, but neither are concepts that arise naturally from the physics of condensed phases. It is ironic that the internuclear distances in crystals that are readily measured depend on the sizes of atoms, but since atoms in crystals can be defined in many different ways, all of them arbitrary and often incompatible, there is no natural way to express atomic size. I propose a simple coherent picture of Atoms-in-Crystals which combines properties selected from three different physically sound definitions of atoms and bonds. The charge density of the free atom that is used to construct the procrystal is represented by a sphere of constant charge density having the quantum theory of atoms in molecules (QTAIM) bonded radius. The sum of these radii is equal to the bond length that correlates with the bond flux (bond valence) in the flux theory of the bond. The use of this model is illustrated by answering the question: How big are atoms in crystals? The QTAIM bonded radii are shown to be simple functions of two properties, the number of quantum shells in the atomic core and the flux of the bond that links neighbouring atoms. Various radii can be defined. The univalent bonded radius measures the intrinsic size of the atom and is the same for all cations in a given row of the periodic table, but the observed bonded radius depends also on the bond flux that reflects the chemical environment.

Resonance assisted hydrogen bonds in open-chain and cyclic structures of malonaldehyde enol: A theoretical study

In 1989 Gilli, Bellucci, Ferretti and Bertolasi introduced the notion of Resonance Assisted Hydrogen Bonding (RAHB) one of the most fruitful concepts in structural chemistry. After reviewing our previous contributions to this topic, the present work analyzes theoretically this concept especially in non-cyclic structures. Geometries, electron densities and Laplacian at the bond critical points, cooperativity through many body interaction energies, deformation energies as well as NMR properties (chemical shifts and 2hJOO coupling constants) are used for the discussion.

Are resonance-assisted hydrogen bonds ‘resonance assisted’? A theoretical NMR study

The concept of resonance-assisted hydrogen bonds (RAHBs) is one of the most frequently used concepts in structural chemistry. Computed equation-of-motion coupled cluster singles and doubles (EOM–CCSD) O–O and N–N coupling constants through intramolecular X–H–X hydrogen bonds ( 2h J X–X) and MP2 1H chemical shifts of the X–H–X protons have been used to investigate RAHBs in model saturated and unsaturated systems. The computed results suggest that the NMR properties of these molecules do not receive significant contributions from resonance, but are a consequence of the σ-skeleton framework.