Valence and stereochemistry

An understanding of the three-dimensional structures of molecules has played an important part in the development of organic chemistry. The first experiments of importance to this area were reported in 1815 by the French physicist J. B. Biot, who discovered that certain organic compounds, such as turpentine, sugar, camphor, and tartaric acid, were optically active that is, solutions of these compounds rotated the plane of polarisation of plane-polarized light. Of course, the chemists of this period had no idea of what caused a compound to be optically active because atomic theory was just being developed and the concepts of valence and stereochemistry would not be discovered until far in the future. 

The beginnings of stereochemistry were hardly more auspicious. The tetrahedral distribution of the valences of carbon was a necessary assumption to explain isomerism. Though there was some logic to the correlation of a tetrahedron with the number four, no successful general correlation between valence and stereochemistry was forthcoming for over half a century. Chemistry became empirical. Success could be achieved without asking the question, Why Synthetic organic chemistry flourished, while theoretical chemistry waned. 

The carbonyls are in general volatile compounds with an extensive chemistry which presents many problems as regards valence and stereochemistry. Some are reactive and form a variety of derivatives, as shown in Chart 22.1 for the iron compounds, while others are relatively inert, as for example, Cr(CO)6 etc. and Re2(CO)iQ. This rhenium compound, although converted to the carbonyl halides by gaseous halogens, is stable to alkalis and to concentrated mineral acids. A few carbonyls may be prepared by the direct action of CO on the metal, either at atmospheric pressure (Ni(C0)4) or under pressure at elevated temperatures (Fe(CO)s, Co4(CO)i2)- Others are prepared from halides or, in the case of Os and Re, from the highest oxide. The polynuclear carbonyls are prepared photo-synthetically, by heating the simple carbonyls, or by other indirect methods. 

The rules for aromaticity in the previous section do need qualification in one respect. We have throughout this chapter assumed implicitly that it is possible to write at least one classical structure, i.e., a structure obeying the rules of valence and stereochemistry, for each molecule. Now this is not necessarily the case. Consider, for example, triangulene (28). However one struggles, one cannot write a structure in which all the carbon atoms are linked in pairs by double bonds. There are always two nonadjacent atoms left over. The reason for this can be seen at once if we star the molecule (29). There are two more starred atoms (total 12) than unstarred ones (total 10). Since each double bond in a classical structure must by definition link a starred atom to an unstarred one, it is clearly impossible to pair up the atoms into doubly bonded pairs unless the numbers of starred and unstarred atoms are the same. 

There is no question that, indirectly or directly, Kirrmann and Prevost were influenced by Lowry s theories for explanation of reaction mechanisms. Another important influence was Dupont, with whom they talked at length in the laboratory and who published a paper in 1927 in which he attempted to combine the electron octet theory of valence and Bohr s hydrogen electron model with classical concepts of stereochemistry. Dupont also adopted without reservation Lowry s application of ionic radicals in hydrocarbon chemistry. 66... 

With iron the trends already noted in the relative stabilities of oxidation states continue, except that there is now no compound or chemically important circumstance in which the oxidation state is equal to the total number of valence shell electrons, which in this case is eight. The highest oxidation state known is VI, and it is rare. The only oxidation states of importance in the ordinary aqueous and related chemistry of iron are II and III. The oxidation states and stereochemistries are given in Table 17-E-l. 

Isomer and Tautomer Search. A search types where bond order, hydrogen counts, certain atom valences, and bond or atom stereochemistry may be allowed to vary from those specified in the query. Such searching allows re-... 

The experiments by Werner and his associates on cobalt coordination compounds accomplished two things they increased the chemical knowledge in this extensive area (more than 700 compounds) and helped Werner develop his ideas on coordination theory and stereochemistry. It was only after he had received the Nobel Prize (191S) and after his death (1919) that his ideas of primary and secondary valence were confirmed. Unfortunately, Werner s span of active life was short (1893-1915). A listing is given of his co-workers who researched cobalt compounds. These resulted in 52 papers by Werner, 75 with co-authors, and at least 10 unpublished theses. Research to 1960 on cobalt coordination compounds has been summarized in Gmelins Handbuch der anorganischen Chemie (1963). 

To end up with a predictive pharmacophore model, it is necessary to start with reliable structural and biological data. First of all, it is important to have correct 3D structures of all compounds under study. Thus, atomic valences, bond orders, protonation state and stereochemistry have to be checked carefully. Also the consideration of different possible tautomers is necessary when the bioactive form is not exactly known. Another prerequisite is the existence of a similar binding mode of all ligands under study. Experimental data, from competition experiments or protein-ligand crystal structures, can clearly point out that the ligands interact with the same binding epitope in a similar way and not on distinct binding sites. 

Methyl and simple alkyl radicals are essentially planar with sp2 hybridization and the single electron in a p orbital, in contrast to the analogous silyl radicals which are pyramidal with approximately sp3 hybridization for all the valence orbitals three bonding and one singly occupied. The evidence is for this comes from ESR and stereochemistry studies. 

In conjunction with understanding why liquid water is essential to life, students also investigate the flexibility of carbon in bonding, appreciating that a half-filled valence shell allows a diversity of molecular structures. This also allows introduction of functional groups and stereochemistry. Again Spartan is used to build molecules and investigate the shapes of molecules. 

Bond orbitals and stereochemistry. The number and direction of the valence bonds in compounds depends on the particular electron orbitals which form the bonds. The principles may be seen by referring to 6-coordinated cobalt, planar 4-coordinated nickel, and, tetrahedral 4-coordinated... 

Ligand complexation of vanadium by iV-(L-l-carboxyethyl)-7V-hy-droxy-L-alanine in vivo by fruit bodies of Amanita muscaria produces the blue complex, amavadin (571) 69, 418). The structure and stereochemistry of this most unusual compound has been proved by total synthesis 418), and the valence state of the metal in amavadin has been studied by electron spin resonance spectroscopy 287). 

Magnetic measurements find intensive applications in the study of transitional metal 7r-complexes. Such data can give information that is useful for the elucidation of valency, bond type, and stereochemistry of such compounds. 

Cobalt exists in the +2 or +3 valence states for the majority of its compounds and complexes. A multitude of complexes of the cobalt(III) ion [22541-63-5] exist, but few stable simple salts are known (2). Werner s discovery and detailed studies of the cobalt(III) ammine complexes contributed gready to modem coordination chemistry and understanding of ligand exchange (3). Octahedral stereochemistries are the most common for the cobalt(II) ion [22541-53-3] as well as for cobalt(III). Cobalt(II) forms numerous simple compounds and complexes, most of which are octahedral or tetrahedral in nature cobalt(II) forms more tetrahedral complexes than other transition-metal ions. Because of the small stabiUty difference between octahedral and tetrahedral complexes of cobalt(II), both can be found in equiUbrium for a number of complexes. Typically, octahedral cobalt(II) salts and complexes are pink to brownish red most of the tetrahedral Co(II) species are blue (see Coordination compounds). 

No completely general and quantitative theory of the stereochemical activity of the lone-pair of electrons in complex halides of tervalent As, Sb and Bi has been developed but certain trends are discernible. The lone-pair becomes less decisive in modifying the stereochemistry (a) with increase in the coordination number of the central atom from 4 through 5 to 6, (b) with increase in the atomic weight of the central atom (As > Sb > Bi), and (c) with increa.se in the atomic weight of the halogen (F > Cl > Br > 1). The relative energies of the various valence-Ievel orbitals may also be an important factor the F(a) orbital of F lies well below both the s and the p valence... 

In his valence bond theory (VB), L. Pauling extended the idea of electron-pair donation by considering the orbitals of the metal which would be needed to accommodate them, and the stereochemical consequences of their hybridization (1931-3). He was thereby able to account for much that was known in the 1930s about the stereochemistry and kinetic behaviour of complexes, and demonstrated the diagnostic value of measuring their magnetic properties. Unfortunately the theory offers no satisfactory explanation of spectroscopic properties and so was... 

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