The Central Atom

In each of the examples given so far each element has achieved a noble gas configuration as a result of electron sharing. There are. however, many examples of stable covalent compounds in which noble gas configurations are not achieved, or are exceeded. In the compounds of aluminium, phosphorus and sulphur, shown below, the central atoms have 6. 10 and 12 electrons respectively involved in bondinc... 

The concept of oxidation states is best applied only to germanium, tin and lead, for the chemistry of carbon and silicon is almost wholly defined in terms of covalency with the carbon and silicon atoms sharing all their four outer quantum level electrons. These are often tetrahedrally arranged around the central atom. There are compounds of carbon in which the valency appears to be less than... 

An important reason for low coordination of iodide ions is that high coordination implies a high oxidation state of the central atom, which often (but not always) means high oxidising power— and this means oxidation of the easily oxidised iodide ligands. Thus the nonexistence of, for example, phosphorus(V) pentaiodide is to be explained by the oxidation of the iodide ligands and reduction of phosphorus to the -(-3 state, giving only PI3, not PI5. 

In empirical formulas of inorganic compounds, electropositive elements are listed first [3]. The stoichiometry of the element symbols is indicated at the lower right-hand side by index numbers. If necessary, the charges of ions are placed at the top right-hand side next to the element symbol (e.g., S "). In ions of complexes, the central atom is specified before the ligands are listed in alphabetical order, the complex ion is set in square brackets (e.g., Na2[Sn(OH)+]). 

Besides structure and substructure searches, Gmclin provides a special search strategy for coordiuation compouuds which is found in no other database the ligand search system, This superior search method gives access to coordination compounds from a completely different point of view it is possible to retrieve all coordination compounds with the same ligand environment, independently of the central atom or the empirical formula of the compound. 

To ensure that the arrangement of four atoms in a trigonal planar environment (e.g., a sp -hybridized carbon atom) remains essentially planar, a quadratic term like V(0) = (fe/2) is used to achieve the desired geometry. By calculating the angle 9 between a bond from the central atom and the plane defined by the central... 

However, one of the most successfiil approaches to systematically encoding substructures for NMR spectrum prediction was introduced quite some time ago by Bremser [9]. He used the so-called HOSE (Hierarchical Organization of Spherical Environments) code to describe structures. As mentioned above, the chemical shift value of a carbon atom is basically influenced by the chemical environment of the atom. The HOSE code describes the environment of an atom in several virtual spheres - see Figure 10.2-1. It uses spherical layers (or levels) around the atom to define the chemical environment. The first layer is defined by all the atoms that are one bond away from the central atom, the second layer includes the atoms within the two-bond distance, and so on. This idea can be described as an atom center fragment (ACF) concept, which has been addressed by several other authors in different approaches [19-21]. 

An sp sp- single bond where each of the central atoms is in Group VIA (for example, hydrogen peroxide) has a two fold barrier with optirn iitn torsional an glc of 90 degrees, as described by V2=-2,0 kcal/tnol. 

Various other ways to incorporate the out-of-plane bending contribution are possible. For e3plane bend involves a cakulation of the angle between a bond from the central atom and the plane defined by I he central atom and the other two atoms (Figure 4.10). A value of 0° corresponds to all four atoms being coplanar. A third approach is to calculate the height of the central atom above a plane defined by the other three atoms (Figure 4.10). With these two definitions the deviation of the out-of-plane coordinate (be it an angle or a distance) can be modelled Lt ing a harmonic potential of the form... 

Summing over the squares of the coefficients of the lower two orbitals (the upper orbital is unoccupied), we get electron densities of 1.502 at the terminal carbon atoms and 0.997 at the central atom. The charge densities on this iteration are... 

Trigonal pyramidal molecules are chiral if the central atom bears three different groups If one is to resolve substances of this type however the pyramidal inversion that mterconverts enantiomers must be slow at room temperature Pyramidal inversion at nitrogen is so fast that attempts to resolve chiral amines fail because of their rapid racemization... 

Like MM2, MM-t includes coupling between bond stretching and angle bending. If the angle is defined to include atoms i, j, and k, where k is the central atom, then MM-t couples stretching of the ik and jk bonds with the angle ... 

Other Polyatomic Anions. Names for other polyatomic anions consist of the root name of the central atom with the ending -ate and followed by the valence of the central atom expressed by its oxidation number. Atoms and groups attached to the central atom are treated as ligands in a complex. 

Exceptions to the use of the root name of the central atom are antimonate, bismuthate, carbonate, cobaltate, nickelate (or niccolate), nitrate, phosphate, tungstate (or wolframate), and zincate. 

Naming a Coordination Compound. To name a coordination compound, the names of the ligands are attached directly in front of the name of the central atom. The ligands are listed in alphabetical order regardless of the number of each and with the name of a ligand treated as a unit. Thus diammine is listed under a and dimethylamine under d. The oxidation number of the central atom is stated last by either the oxidation number or charge number. 

The basic stmcture of a naphthalocyanine dye can be seen in Figure 6 (12). By varying the central atom Y, the organic (polymeric) group at the central atom, and the substituents and X, an adjustment to the desired property profile, especially improved solubihty, can be achieved. Naphthalocyanines with sihcon as central atom evoke special interest, eg, the biaxiahy substituted silicon—naphthalocyanine (13) wherein the central Si bears... 

The chemical properties of phthalocyanines depend mosdy on the nature of the central atom. Phthalocyanines are stable to atmospheric oxygen up to approximately 100°C. Mild oxidation may lead to the formation of oxidation iatermediates that can be reduced to the original products (29). In aqueous solutions of strong oxidants, the phthalocyanine ring is completely destroyed and oxidized to phthalimide. Oxidation ia the presence of ceric sulfate can be used to determine the amount of copper phthalocyanine quantitatively (30). 

Structures of heteropolytungstate and isopolytungstate compounds have been determined by x-ray diffraction. The anion stmctures are represented by polyhedra that share corners and edges with one another. Each W is at the center of an octahedron, and an O atom is located in each vertex of the octahedron. The central atom is similarly located at the center of an XO tetrahedron or XO octahedron. Each such polyhedron containing the central atom is generally surrounded by octahedra, which share corners, edges, or both with it and with one another. Thus, the correct total number of... 

Chelates are often named merely as a complex, eg, cadmium complex with acetylacetone. A common practice ia the Hterature is to give the symbol of the central atom and an abbreviation for the ligand with or without an iadication of ionic charges, oxidation states, stmcture, or counterions, as ia the foUowiag Pb-EDTA, Cacit , Cu(en)2, Co(II)-(phen), [Cu(dipy)2]S04, [Ru(dipy)2(en)], and Na[Co(acac)2]. Ligand abbreviations are given ia Table 1. 

Fig. 10. Pharmacophores for angiotension-converting enzyme. Distances in nm. (a) The stmcture of a semirigid inhibitor and distances between essential atoms from which one pharmacophore was derived (79). (b) In another pharmacophore, atom 1 is a potential zinc ligand (sulfhydryl or carboxylate oxygen), atom 2 is a neutral hydrogen bond acceptor, atom 3 is an anion (deprotonated sulfur or charged oxygen), atom 4 indicates the direction of a hydrogen bond to atom two, and atom 5 is the central atom of a carboxylate, sulfate, or phosphate of which atom 3 is an oxygen, or atom 5 is an unsaturated carbon when atom 3 is a deprotonated sulfur. The angle 1- -2- -3- -4 is —135 to —180° or 135 to 180°, and 1- -2- -3- -5 is —90 to 90°.

Heteroeyeles structurally based on the phenalene ring system form an interesting elass, frequently possessing distinetive eolours. With nitrogen as the central atom we have the unstable 9b-azaphenalene (24), whieh has only fairly reeently been prepared and is still comparatively little studied (76JCS(Pl)34l). The cyclazine nomenclature is commonly applied to this and related compounds thus, (24) is (3.3.3)cyclazine. With further aza substitution, in positions alternant to the central atom, their stability increases the heptaazaphenalene (25) is (thermally) a very inert compound, derivatives of which, e.g. the triamine, have been known since the early days of organic chemistry (see Chapter 2.20). 

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