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Basic Concepts

1.1 Introduction to Reaction Mechanisms

Chemical reactions are the processes by which chemicals interact to form new chemicals with different compositions. A new compound formed as a result of a chemical reaction does not bear the properties of the starting compounds; it has its own unique properties. In order for a chemical reaction to begin, some conditions (temperature, pressure, catalyst, etc.) must exist. For some compounds, it is sufficient to bring them together to start a chemical reaction. For example, water and sodium (provided they do not come in contact with air) are normally stable. However, a very violent reaction happens when these two come together. Sodium metal reacts rapidly with water to form a colorless solution of sodium hydroxide (NaOH) and releases hydrogen gas.

There is a common point regarding all chemical reactions, namely, transfer of electrons from one reactant to another (electron exchange). Therefore, one of the starting compounds should be capable of denoting electrons, while the other should accept electrons. In order for electron exchange to take place, some reactions require catalysts. A catalyst is a substance that can be added to a reaction to increase the reaction rate without being consumed in the process. The function of catalysts is to facilitate electron transfer by activating bond electrons and to lower activation energies (Ea). As a result of electron transfer, some bonds are broken, some bonds rearrange, and new bonds are formed.

Benzene is an unreactive compound in the presence of halogens (Cl2, Br2, or I2) because they are not electrophilic enough to attack the benzene ring and disrupt its aromaticity. However, the halogens must be activated by Lewis acid catalysts such as FeBr3 or AlBr3. FeBr3 accepts electron pairs from bromine and makes it much more electrophilic. For a detailed mechanism, see Section 6.6.

Let us roughly analyze the processes that occur during the reaction of sodium with water. We see that the hydrogen atom, which is bonded to oxygen, breaks off from oxygen and forms hydrogen gas by binding to another hydrogen atom; on the other hand, the neutral sodium atom is oxidized by donating an electron and forming an ionic bond with the hydroxyl anion. This reaction appears to be very simple. However, complex processes are involved. We need to understand how products are formed as a result of a reaction. When a reactant turns into a product, we should look at which intermediates are involved during this reaction.

If we have a good understanding of what is going on at the intermediate stages, then we can guess what kind of products are formed as a result of the reaction. The step-by-step sequence of the intermediate stages of a reaction until the product is formed is called the reaction mechanism.

We have to understand what is happening at the intermediate levels. Otherwise, if we try to learn about a chemical reaction by writing reactants on one side of the equation and products on the other side, we will not be able to master organic chemistry. If the reaction mechanism is learned well, then one can see that organic chemistry is as enjoyable and systematic as mathematics. This is because, once the reaction mechanism is known, it is possible to predict what reaction will occur between two reactants and what products will be formed. Otherwise, if the reactions are learned without examining the mechanism (a type of learning based on memorizing), it becomes clear that organic chemistry cannot be understood. Then, organic chemistry becomes extremely boring.

Let us go back to the beginning. We emphasized that all chemical reactions occur as a result of electron exchange. To decide whether a compound is an electron donor or not, it is necessary to examine its electronic structure. In other words, it is necessary to examine the bonds between atoms and how the bonds are polarized.

The elements share electrons so that each atom attains a noble gas configuration. For example, two chlorine atoms can each attain a filled second shell by sharing their unpaired valence electrons. A bond formed by sharing electrons is called a covalent bond. Similarly, the hydrogen molecule, H2, can also form a covalent bond by sharing electrons. The atoms that share the bonding electrons in the H-H and Cl-Cl covalent bonds are identical. Such bonds are called nonpolar covalent bonds. In some compounds, the bonding electrons are shared equally between the atoms.

In contrast, the bonding electrons between two different atoms are more attracted to one atom than to another because of different electronegativities (the ability of an atom in a molecule to attract electrons toward itself). The symmetrical distribution of the electrons between the two atoms is disrupted. This condition is called bond polarization.

If electrons are attracted more strongly by A, the electron density increases around atom A and decreases around B. Therefore, this polarization makes A and B atoms more reactive. In such a case, groups with high electron density prefer to bind to atom B, while those with low electron density prefer to bind to atom A. In order to understand the reaction mechanism, electron polarization between bonds must be known very well. In this chapter, we first discuss about bonds, and in the next section, we focus on bond polarization. Here, I would like to draw the attention of the reader to two concepts. The first is the inductive effect and the second is the mesomeric effect. For a student who knows and understands these two concepts well, it will be easier and more enjoyable to travel along the paths of organic chemistry that seem to be winding.

One of the other important points in organic chemistry, after learning bonding theory, is to think of molecules in a three-dimensional environment and estimate their true structures. This is an extremely simple thing. However, in order to understand it, it is necessary to work with simple organic models.

1.2 Covalent Bonding and Hybridization

In organic chemistry, unlike in inorganic chemistry, we deal with covalent bonds. Bonds are formed by overlapping of orbitals and the placement of electrons in these orbitals. Let us first look at how a hydrogen molecule is formed. The covalent bond between two hydrogen atoms is formed when the 1s orbital of one hydrogen atom overlaps with the 1s orbital of a second hydrogen atom as shown below. Overlapping orbitals can be pure orbitals as well as hybrid orbitals.

We will begin the discussion with the simplest molecule in organic chemistry, methane (CH4), with only one carbon atom. It is well known that the carbon atom is located in the center of the methane molecule, and it has four covalent C-H bonds. All the four bonds have the same length, and all bond angles are also the same (109.5°). This structure, which forms a smooth tetrahedron, is called a tetrahedral structure.

In the perspective formula, the hydrogen atoms shown with solid lines and the carbon atom are located in the paper plane. The bond represented as a dashed wedge projects behind the plane of the paper. The bond represented as solid wedge projects out of the paper (toward the viewer). To understand this structure of the methane molecule, it is necessary to first examine the electronic configuration of the carbon atom. The electronic configuration of the carbon atom is as follows:

The atomic orbitals of the carbon atom are shown in Figure 1.1. The 2s orbital is drawn larger than the 1s orbital. Because the 2s orbital is in a location more remote from the core, it covers a larger area than the 1s orbital. The energy levels of these orbitals are different. The energy level of the 2s orbital is lower than that of the p orbitals. The energy levels of the 2p orbitals are equal to each other; in other words, they are degenerated.

Figure 1.1 Atomic orbitals of the carbon atom.

The carbon atom has only two unpaired electrons in its electronic configuration. This indicates that this atom can form only two covalent bonds, but with two covalent bonds, it would not complete its octet configuration. However, we know that the carbon atom forms four covalent bonds. Now, we need an explanation why carbon forms four covalent bonds. Without unpaired electrons, this configuration does not allow four bonds to be made. With a small amount of energy, one electron from the 2s orbital can be promoted into the empty 2pz orbital (Figure 1.2). This energy is readily compensated for by bond formation.

Figure 1.2 Electronic configuration of the carbon atom in the ground state and the excited state.

Now, this configuration of carbon can form four covalent bonds. If carbon uses an s and three p orbitals to form these four bonds, the bond formed with p orbitals will be different from the bond formed with an s orbital. On the other hand, we know from spectroscopic studies that methane has a tetrahedral structure and the four C-H bonds in methane are identical. We have to answer the question How can the carbon atom form four identical bonds by using three p orbitals and one s orbital? Carbon uses the hybrid orbitals. To be able to generate this geometry, the 2s orbital on carbon is mixed with all the three 2p orbitals to make four equivalent sp3 orbitals with tetrahedral symmetry (Figure 1.3).

Figure 1.3 Electronic configuration of the carbon atom in the ground state and the hybridized state.

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