Geometry assigning

Elements present in groups III through VII as well as some of the transition elements form pentacoordinated molecules although at present the group V elements make up the major fraction of such substances. The most prevalent geometry assigned to these molecules is the trigonal bipyramidal structure. 

To facilitate the comparison of a RS s cis/trans and concave/convex needs with those allowed by a template, CAMEO included in the ring data record a special geometry attributes table (GAT) that tells which template bonds can support a cis or a trans double bond, and which atoms jut out or in (or are junction atoms). (The CFS of every atom could be stored in the GAT or elsewhere, or calculated on the fly after retrieval of the template.) Figure 56 illustrates the geometries assigned. 

Virtual coupling in the H NMR spectrum can help geometry assignments for complexes involving phosphines such as PMes or PMe2Ph. If... 

To date all the symmetries adopted by transition metal ions in melts are very simply related to the octahedron and tetrahedron. The T and O centers discussed in detail in Section 4.4 have not had specific geometries assigned to them but they are probably distorted versions of and Oh, respectively. In the same way that the dodecahedral symmetry can arise from double of flattened tetrahedra (Section 4.3 and Ref. 196), so a T Oh transformation through a trigonal pyramid (Cgy) and a trigonal bipyramid ( >3 ) is easily visualized (Fig. 48). One might then expect O-center spectra to resemble those of Ni(II) in D h symmetry and indeed a considerable likeness is apparent between the spectrum of a known complex (Fig. 49D),(27d that of the proposed NiCla (Fig. 34), and the O-center spectra depicted in Fig. 33. Unfortunately, no trigonal pyramidal complexes of Ni(II) appear to be known. 

Z-matriccs arc commonly used as input to quantum mechanical ab initio and serai-empirical) calculations as they properly describe the spatial arrangement of the atoms of a molecule. Note that there is no explicit information on the connectivity present in the Z-matrix, as there is, c.g., in a connection table, but quantum mechanics derives the bonding and non-bonding intramolecular interactions from the molecular electronic wavefunction, starting from atomic wavefiinctions and a crude 3D structure. In contrast to that, most of the molecular mechanics packages require the initial molecular geometry as 3D Cartesian coordinates plus the connection table, as they have to assign appropriate force constants and potentials to each atom and each bond in order to relax and optimi-/e the molecular structure. Furthermore, Cartesian coordinates are preferable to internal coordinates if the spatial situations of ensembles of different molecules have to be compared. Of course, both representations are interconvertible. 

One way to describe the conformation of a molecule other than by Cartesian or intern coordinates is in terms of the distances between all pairs of atoms. There are N(N - )/ interatomic distances in a molecule, which are most conveniently represented using a N X N S5munetric matrix. In such a matrix, the elements (i, j) and (j, i) contain the distant between atoms i and and the diagonal elements are all zero. Distance geometry explort conformational space by randomly generating many distance matrices, which are the converted into conformations in Cartesian space. The crucial feature about distance geometi (and the reason why it works) is that it is not possible to arbitrarily assign values to ti... 

The assignment of bands has been carried out using ab initio calculations, unfortunately using the erroneous Ehrlich geometry (Section 4.04.1.3.1). There is a linear relationship between the calculated energy levels (eigenvalues) and the experimental ones IEexp = 0.37 + 0.75IE<,aic, (c.c.) = 0.994. 

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