Chapter 1
If You Do Not Know Any Chemistry, This Chapter Is For You

As a professor, I regularly teach college-level chemistry courses. These courses present various materials, which are important for students who wish to continue their careers in chemistry. Although most people reading this book will not need all the information covered in these courses, understanding a few key concepts will allow them to understand various ways in which chemistry shows up in everyday life. In fact, one of the driving forces of compiling these stories is to show that even a basic understanding of chemistry can help us comprehend how the world and society work. In particular, I would like to bring readers up to speed on a few key chemical concepts that are referred to in this book (Figure 1.1).

Figure 1.1 Look at what hides behind the door of understanding chemistry.

Representing Atoms and Molecules in Chemistry

The first concept concerns the representation of atoms and molecules. Often, the structure of molecules can provide insight into its properties or the ways in which it will affect a human being, if ingested. Certain structural features will imbue molecules with particular properties. In addition, molecules with similar structures will often have similar properties. A detailed understanding of chemistry is not required to make this connection, but only the ability to see similarities.

Chemists represent an individual element with a capital letter, such as "C" for carbon, "H" for hydrogen, and "Fe" for iron, as listed in a periodic table. This letter represents all of the protons and neutrons in the atom's nucleus plus any electrons not involved in bonding. During most chemical reactions, the nucleus of atoms remains unchanged, so this simple representation of elements is helpful to chemists. If an oxygen atom is involved in a chemical reaction, it will remain an oxygen atom. Its structure and bonding may change, but the nucleus will be the same. An important exception is radioactive decay, where a nucleus can be changed and one element can change into another. This will be discussed later.

In the case of some metals and gases, the atom is not bonded (connected) to any other atoms; hence, the bulk material can be represented with the elemental symbol. A block of iron is made up entirely of iron atoms that can be represented by symbol Fe. Similarly, a balloon filled with helium can represented with the symbol He.

Although individual elements are important, chemistry truly becomes interesting when atoms start bonding together to form more complex structures. Two major types of bonds are ionic and covalent. In an ionic bond, one atom gives up one or more electrons, giving it a positive charge, while another atom gains one or more electrons, giving it a negative charge. Electrostatic forces bring the positive and negative ions together. However, when ionic compounds are placed in an appropriate solvent, such as water, the compounds break apart into their ionic species. The classic ionic compound is common table salt sodium chloride (NaCl). In the crystals of table salt, the sodium and chlorine atoms are being held together by the attraction of a positive and negative charge. When placed in water, table salt tends to break apart into its ionic species, in this case Na+ and Cl- (Scheme 1.1).

Scheme 1.1 The formation of an ionic bond in NaCl.

Ionic compounds are generally made with ionic bonds. Ionic bonds are easily identified because they are made by combining a metal (elements on the left-hand side of the periodic table) with a nonmetal (elements found in the upper right-hand corner of the periodic table). Ionic bonds are typically not formally drawn; rather, the ions are drawn together in a molecular formula where the overall compound is neutral. For example, FeCl3 means a Fe3+ ion bonds to three Cl- ions using ionic bonds. This simple discussion will allow for a better understanding of many ionic compounds with which you may be familiar (Table 1.1).

Table 1.1 Some common ionic compounds

Covalent bonds differ from ionic bonds in that electrons are shared rather than stolen to form a bond between two atoms. This means that covalent bonds are not easily broken into ionic species and do not break apart when dissolved in water. The sharing of two electrons between two atoms to form a covalent bond is represented with a single line. The water molecule is made up of two H-O single covalent bonds. Similarly, if four electrons are shared between two atoms, the covalent bond is shown with a double line and is called a double bond. Six shared electrons are depicted by three lines and called a triple bond. Molecular oxygen is made up of a double bond between the two oxygen atoms, and molecular nitrogen is made up of a triple bond between the two nitrogen atoms. Single, double, and triple bonds all have different properties and reactivity that are dependent on the types of atoms involved in the covalent bond. Even now, this basic description of covalent bonds can help you understand the structure of multiple simple molecules (Figure 1.2).

Figure 1.2 The structure of some simple molecules.

What makes covalent bonds so interesting is their ability to combine to form large molecular structures. Inorganic compounds do not have this ability. Literally, thousands of atoms can be linked together by covalent bonds to create such complex molecules as polymers, proteins, and even deoxyribonucleic acid (DNA).

This book focuses mostly on organic molecules, which are typically constructed with covalent bonds. Organic molecules were originally called "organic" because it was believed that these types of compounds could only come from living, organic sources, such as plants or animals. Once it was shown that organic molecules could be made from inorganic materials, the definition was expanded. The current definition states that organic molecules contain the element carbon. Organic chemistry is the study of carbon-containing molecules. For the purposes of this book, we will be focusing on the conversion of one organic molecule into another using reactions. Using these reactions, organic chemists create many pharmaceuticals, many plastics, and a multitude of other molecules.

The versatility of covalent bonds creates virtually limitless possible combinations of organic molecules, which is why organic chemistry is such a broad field of study. In college, an entire year of study is devoted to organic chemistry to obtain a typical chemistry degree. At this point, millions of organic compounds are known, with new ones being generated every day. One of the more interesting aspects of organic chemistry is the ability to combine atoms in new ways to make new organic molecules, many of which have never been seen in nature.1

Because of the large numbers of variations, organic molecules are commonly represented by structures as well as their formal names. In addition, due to a large and complex nature of organic molecules, they are often drawn using a condensed form. Because organic molecules typically have a large number of hydrogens in their structures, it is particularly common to represent hydrogens in an abbreviated form. In a condensed structure, the bonds attached to the hydrogens are omitted and the number of H's is represented with a subscript. Examples of these abbreviations are represented below using some simple organic molecules (Figure 1.3).

Figure 1.3 The condensed structure of some simple organic molecules.

Another important way in which hydrogens are abbreviated involves the benzene ring. This ring is immensely important in organic chemistry, and its presence can be seen in many important organic molecules. To simplify the structure, the hydrogens at the points of the benzene ring are commonly omitted. Moreover, the carbon atoms in the benzene ring are represented simply by lines denoting the covalent bonds (Figure 1.4).

Figure 1.4 The condensed structure of the benzene ring.

Lastly, the structures of polymers are usually represented using a type of abbreviation. Small molecules called monomers are connected in large numbers during a polymerization reaction to create large molecules called polymers. This process is represented in the name "polymer," which means many monomers. Because polymers are made up of a repeating monomer subunit, they are represented by the subunit surrounded by brackets. The monomer subunit is repeated a variable number of times, which is represented by the subscript "n." The actual number of monomers subunits in a polymer is usually unknown, which is why it is represented by a variable (Figure 1.5).

Figure 1.5 How polymers are represented.

Neurotransmitters

In this book,...