Chapter 1
Structure and Properties

A general opinion of chemists adopted by textbooks is that in chemistry, structure1 is a central concept: the key to everything. Properties2 of a given substance depend on the number and nature of its constituting atoms and their mode of connection (connectedness). It is less obvious but quite important that looking at structural formula, a well-versed chemist should be able to deduce many properties of a substance. In order to exploit this possibility, in this chapter, we are going to define some basic principles associated with structure and properties. After having defined the concept of structure, we will proceed to discuss correlations of structure and properties, with special emphasis on the spatial features of structure and properties derived from changes thereof. First of all, we will discuss properties derived from the spatial structure of typical organic compounds; but for the sake of completeness, the stereochemical features of inorganic compounds will be dealt briefly as well.

1.1 The Covalent Bond and the Octet Rule

The covalent nature of the chemical bond, assuming a shared pair of electrons, was first proposed by G. N. Lewis in 1916 [1]. According to this concept, by sharing two electrons, two hydrogen atoms can establish a stable bond by forming a closed shell of electrons similar to that of the noble gas helium (Figure 1.1).

Figure 1.1 Formation of the covalent bond of the hydrogen molecule.

In the Lewis structures, electrons are symbolized by dots. The amount of energy required to dissociate a hydrogen molecule to two hydrogen atoms is called the bond dissociation (or bond) energy. In the case of H2, this is quite high: 435 kJ mol-1.

While with hydrogen molecule the number of electrons present in the valence forming shell is limited to two, in the Lewis model, molecules composed from elements of the second row (Li, Be, B, C, N. O, F, and Ne) in the valence shells contain eight (shared and unshared) electrons. Most organic compounds follow the octet rule: on formation of their compounds, electrons are taken up, and elements are shared or removed in a way that they should assume a stable structure involving eight valence electrons. When in compounds of carbon, nitrogen, oxygen, and fluorine, the octet rule is valid, their electron configuration is analogous to that of the noble gas neon. Lewis representation of some simple molecules is shown in Figure 1.2.

Figure 1.2 Covalent bonds in some simple molecules (Lewis representation).

Such structures showing the distribution of electrons (Lewis structures) are useful aids for understanding covalent bond formation, but it is simpler to use the s.c. Kekulé formulas.3 The latter are derived from Lewis formulas by replacing a shared pair of electrons with a line connecting the corresponding atomic symbols. Nonbonding electrons are shown by dots. Examples for structural formulas drawn according to this principle are shown in Table 1.1. As a further simplification of Kekulé formulas, nonbonding electrons are not shown since these can be readily calculated following the octet rule.

Table 1.1 Lewis and Kekulé formulas of some simple molecules

As illustrated in Table 1.1 by ethene, formaldehyde, acetylene, and hydrogen cyanide, atoms may share more than one pair of electrons forming in this way multiple bonds. Compounds of boron, such as BH3 or BF3, are exceptional in a way that the valence shell of boron is not filled up with electrons as would be required by the octet rule. Accordingly, these compounds have a high affinity to electrons and are very reactive.

Valence is the number of those valence electrons, which must be taken up or shed that the valence shell should attain the octet state (Table 1.2). In their covalent compounds, the number of bonds adjoined to an atom is equal to the valence of the given atom. Valences listed in Table 1.2 are typical of atoms common in organic compounds.

Table 1.2 Valence states of selected elements common in organic compounds

1.2 Representation of Chemical Structures

For the representation of simpler compounds, condensed Kekulé formulas are suitable; but this is a cumbersome way to represent more complex compounds. Thus, cyclic compounds are best represented by further simplified, s.c. linear formulas. Application of linear formulas is exemplified by formulas for cycloalkanes (Figure 1.3).

Figure 1.3 Representation of cycloalkanes by linear formulas.

Linear formulas are also convenient to depict open chain compounds (Figure 1.4).

Figure 1.4 Representation of open-chain compounds with linear formulas.

When drawing linear formulas, for simplicity, symbols of carbon atoms, the pairs of electrons, and hydrogen atoms attached to carbons are omitted. Accordingly, all end points, breaking points, and points of branching represent a carbon atom. Multiple bonds are shown by an appropriate number of parallel lines. Heavy atoms other than carbon are shown by their atomic symbols together with the hydrogen atoms attached.

Additional ways of representation are shown in Figure 1.5 by the example of methanol, pyridine, and the antidepressant escitalopram. Representations include the following:

• A: Name (trivial or systematic)
• B: Condensed formulas (generally suitable for printing in a single line)
• C: Kekulé formulas (showing all the atoms and bonds)
• D: Linear formulas (hydrogens omitted, breaking, branching, and end points represent carbon atoms; heavy atoms are shown with the hydrogen attached)
• E: Stereoformulas4 (depicting the spatial orientation of bonds)
• F: Ball and stick model (often used to depict X-ray structures or computed models)
• G: Space-filling model (approaches the electron distribution).

Figure 1.5 Various modes of representation for methanol, pyridine, and the antidepressant escitalopram.

Figure 1.5 well demonstrates that for smaller open-chain organic compounds (e.g., methanol), it is the condensed or Kekulé formula that is the most appropriate for the demonstration of the two-dimensional features of the structure. In case of smaller cyclic compounds (e.g., pyridine), the linear formulas are most often used. To depict more complex structures (e.g., escitalopram), condensed or Kekulé representations are practically useless, and therefore a combination of linear and stereo representation is recommended. The complete stereostructure of molecules can be best depicted by a simplified representation of 3D structures. In Figure 1.5, two possible modes of representation of molecular models that is, ball and stick and space-filling models are shown.5 As can be seen with more complex molecules, space-filling models refer to their overall shape, while the details of the structure are less apparent.

1.3 Description of Chemical Structure

Chapters of the rules of International Union of Pure and Applied Chemistry (IUPAC) for naming compounds [3] do not give a precise definition of what should be understood under "chemical structure." Therefore, we define in a general way as chemical structure as it is understood by crystallographers: chemical structure is an accurate description of the spatial arrangement of the constituting atoms (atomic nuclei) in space.

The exact spatial arrangement of atoms can be described, for instance, by their Cartesian coordinates.6 From a structural point of view, however, it is not the absolute position and orientation of the molecule that is decisive; therefore, it is often more useful to describe the relative position of atoms by s.c. internal coordinates7 (Figure 1.6). Internal coordinates for the description of molecules are the bond lengths (r), the bond angles (a), and the torsion angles (?).8

Figure 1.6 Characterization of molecules consisting of two, three, and four atoms with internal coordinates.

For the description of molecules containing two atoms (I), besides defining the type of atoms (A, B), it is sufficient to give the bond length as a single internal coordinate. In organic molecules, the value of bond lengths varies in a relatively narrow range (Table 1.3).

Table 1.3 Characteristic values of bond lengths commonly occurring in organic...