Preface

In this course, we attempt to bring the basics of organic chemistry to the student needing to understand the nomenclature, chemical properties, and reactivity of carbonbased molecules. While there are far too many organic molecules in nature to discuss in any organic chemistry course, there are specific ways to clearly identify these molecules as well as certain trends in how these various molecules behave in chemical reactions. By the end of the course, you will understand how to identify and name organic molecules, their physical properties, and how they chemically interact with one another in a variety of types of chemical reactions.

Chapter one in the course begins the study of organic chemistry by introducing how organic molecules are put together. There really isn’t any difference between the way the atoms in organic molecules are put together and the way other chemical molecules are put together but it is worth reviewing, even if you have studied chemistry in the past. This chapter will focus on orbital theory and the particulars of organic molecular bonding as well as the shorthand involved in writing out organic molecular structures. Finally, the chapter talks about resonance chemistry as it applies to organic molecules.

Chapter two in the course covers the basics of nomenclature in identifying organic molecules. Because there are innumerable organic molecules and because they are based on just a few different types of atoms, there needs to be a way to identify what each molecule looks like by name alone. This leads to a discussion of the IUPAC nomenclature and coverage of the different functional groups in organic chemistry. You will need to understand how to name the different molecules you see in organic molecules, which is covered in this chapter. In addition, there will be a discussion of stereochemistry as it applies to organic molecules.

The topic of Chapter three in the course is organic solvent chemistry. For students who have participated in regular chemistry experiments, the solvent has typically been water. In organic chemistry, the solvent may or may not be water because many aspects of organic chemistry involve nonpolar substances that do not dissolve in water. Solvents

may or may not participate in chemical reactions themselves but are important to the chemistry of different molecules. Issues regarding solvation and solutions in organic chemistry are also covered in this chapter.

Chapter four begins a series of chapters on the different organic compounds and their properties. You will have learned about alkane, alkene, and alkyne nomenclature in previous chapters so the focus of this chapter is to learn more about these compounds and how they interact with one another and with other organic compounds. These substances can have a variety of different configurations, which need to be discussed as part of this chapter.

The focus of Chapter five in the course is the chemistry of aldehydes, ketones, and carboxylic acids. This is the first time the chemistry of oxygen comes into play in this course. Aldehydes and ketones are discussed together because they have very similar chemistry and reaction types. Carboxylic acids are also oxygen-related because they have a COOH side chain as their defining characteristic. They also have great reactivity and are seen in nature as fatty acids and other biochemically-important molecules. In all cases, you will come to understand their nomenclature, their physical properties, and some of the most important chemical reactions associated with these molecules.

Chapter six introduces the structure and chemistry of aromatic compounds. All aromatic compounds consist of a cyclic compound that carries resonance. The most common aromatic compound is benzene, which is very stable and has chemistry unique to the molecule. In this chapter, the nomenclature and chemistry of aromatic compounds will be covered as well as the different reactions that are seen in organic chemistry with these types of molecules.

The topic of Chapter seven in the course is the chemistry of alcohols and alkyl halides. Alcohols are organic compounds that have a hydroxyl group as its major functional group, often represented with the general formula of ROH, where R can be any number of organic chemistry alkyl groups. The hydroxyl group is highly reactive so that there are any number of reactions that can occur at this functional group. The chapter also covers the chemistry of alkyl halides, which are alkyl groups that have one or more

halogen side chains attached to it. The halogen is also highly reactive, with many possible chemical reactions associated with it.

Chapter eight in the course focuses on the organic chemistry associated with ethers, epoxides, and esters. Ethers and epoxides are related to one another in that certain types of cyclic ethers are referred to as epoxides. In both types of molecules, the general formula is ROR’, involving a variety of R side chains. These are molecules commonly seen in perfumes, industrial compounds, waxes, oils, and dyes. Esters are also commonly used in industry, being a part of the making of many products—the most common of which are the polyesters.

The topic of Chapter nine is the structure and chemistry of enols and enolates. Enols are also referred to as alkene alcohols, which are alkenes that have an alcohol group added to one of the carbon atoms. These are first alkenes but, chemically-speaking, they should be considered important for their electron-donating capacity. Enols can be mixed with alkali substances to make enolates, which are the conjugate bases of enols. Both of these types of molecules are best known for the many different types of reactions they participate in, which are covered in this chapter.

Chapter ten in the course changes nomenclature and reactions in organic chemistry to include molecules that contain sulfur. Sulfur compounds are somewhat similar to oxygen-containing molecules in that they belong to the same group but sulfur is a great deal larger than oxygen, leading to slightly different chemical reactivity unique to these molecules. The nature and chemistry of thiols and sulfides is discussed as part of this chapter.

Chapter eleven places a focus on the different nitrogen-containing molecules in organic chemistry. These types of molecules are not only important in basic organic chemistry; they are also important in numerous biochemical processes. The main type of molecule discussed will be the amine compounds, which are considered organic derivatives of ammonia. Like ammonia itself, amine compounds will have a certain degree of basicity, which leads to nucleophilicity of the nitrogen compounds in organic compounds.

Chapter twelve in the course begins to make sense of what you will learn in prior chapters on simpler molecules and applies it to more complex biochemical molecular structures. Sugars and carbohydrates are basically organic molecules that come from the phrase “carbon hydrates”. They contain only carbon, oxygen, and hydrogen atoms and have a specific generic formula, based on whether they are simple sugars, disaccharides, or more complex polysaccharides. The main focus of this chapter is to use organic molecular principles that will make sense after you know the basic reaction types involved.

The focus of Chapter thirteen in the course is to bring on more of the biochemistry involving organic chemistry principles by talking about the organic chemistry of amino acids, oligopeptides, and proteins. These are molecules that have nitrogenous compounds as the basis of their chemistry and that, like carbohydrates, exist as monomer units and polymers or polypeptides. These will also have reactions at their functional units, which involve a variety of different side chains and parts of the parent chain.

Chapter fourteen in the course studies the organic chemistry associated with lipids. The term “lipid” is a broadly reaching term that applies to a wide variety of molecules that are called lipids because of their biochemical nature and their lack of solubility in water. They can range from fatty acids to triglycerides to more complex molecules that are complicated to synthesize and even to understand how they are synthesized in body systems and in organic chemistry models. Lipids have poor solubility in water but are much more soluble in chloroform, benzene, ether, and acetone, which are either nonpolar or weakly polar.

The focus of Chapter fifteen and the final chapter of the course is the organic chemistry and biochemistry of nucleic acids, which are deoxyribonucleic acids and ribonucleic acids, commonly called DNA and RNA. These are molecules that contain ribose or deoxyribose sugars, phosphate groups, and nucleic acid bases, which are seen in paired form with DNA and sometimes with RNA. The transcription of nucleic acids and the translation to proteins is covered as part of the chapter as these are not generally made synthetically in an organic chemistry laboratory.