In the 19th century, organic chemistry was defined as the chemistry of carbon compounds. For most of human history, however, both simple chemicals and complex mixtures of chemicals have been used without an understanding of the science behind them. Indeed, plants have been “milked,” cut, boiled, and eaten for thousands of years as folk medicine remedies. Many naturally occurring materials contain important organic compounds that are well known in human history. People in ancient Assyria, Sumer, and Egypt chewed willow bark as an antipyretic treatment. In ancient India, Java, and Guatemala certain plants provided a deep blue substance used to color clothing. In recent times, the main constituent was identified as indigo. In the 18th century, Lavoisier made an important contribution to understanding the structure of organic molecules by burning natural materials in air.

A study of acid and base chemistry is fundamental to organic chemistry. Weak acids are defined as solutes that partially ionize in a reaction with water molecules. The curved arrow formalism and the concept of electron donation from an electron rich atom to an electron poor atom can be applied to many reactions other than acid-base reactions. The identification of electron-rich and electron-poor components of molecules and an understanding of the electron flow can be used to predict products in a variety of reactions. Strong acids ionize in water to a greater extent when compared to a weak acid. The relative strength of two bases can be measured by changing the focus to their reaction with a common acid. Electronegativity plays an important role in acid-base reactions.

The nature of the bond between two carbon atoms or between carbon and another atom is a fundamental concept in organic chemistry. Atoms are discreet entities that differ from one another by the number of protons, neutrons, and electrons that make up each atom. Protons and neutrons are found in the nucleus, of course, and electrons are found outside of the nucleus in discreet energy levels. Valence is the number of bonds an atom can form with other atoms when molecules are formed and remain neutral. In molecules that contain carbon the orbitals associated with carbon are different from the orbitals associated with atomic carbon. The molecular orbitals of two atoms used to form a covalent bond are different from the atomic orbitals of the individual atoms. Bond breaking is an endothermic process because it requires energy.

Carbon forms covalent single, double, and triple bonds to a variety of atoms. Carbon can bond with itself, which leads to an almost limitless number of organic molecules. This chapter discusses the structural features and nomenclature of a class of organic molecules with only carbon and hydrogen. The linear chain of an alkane can have other attached carbon atoms. Generating carbon chains of different lengths will lead to many different compounds. The nomenclature system used is based on the number of carbon atoms in the longest continuous chain. An alkyl substituent can be attached to any of the different carbon atoms of the longest linear chain except the terminal carbons because that would simply give a longer continuous chain. Methane has an interesting relationship with biology.

Discreet units of atoms with special physical and/or chemical properties are known as functional groups. More than one double bond or triple bond can be incorporated into organic molecules. Many naturally occurring compounds in nature have double or triple bonds. Terpenes are cyclic and acyclic compounds with the formula that are usually found in plants. Hemiterpenes consist of one isoprene unit. Isoprene itself is the only hemiterpene, but oxygen-containing derivatives are hemiterpenoids. Functional groups are collections of atoms that impart unique physical and chemical characteristics to a molecule. The amine-bearing carbon is the locant and must be part of the longest hydrocarbon chain. The nomenclature systems for an aldehyde and a ketone are slightly different.

The acid-base reaction is one of the most common reaction types in all of organic chemistry. Most of the reactions encountered in organic chemistry involve acid-base chemistry in one form or another. This chapter discusses acid-base reactions and reactivity of organic molecules. Bond polarization of the hydroxyl group does not completely explain the acidity of a carboxylic acid such as formic acid. When formic acid reacts with sodium amide, removal of the proton gives the resonance-stabilized formate anion as the conjugate base, with two resonance contributors. Since carboxylic acids are the most common organic acids, they will be used to examine structural variations that contribute to variations in acid strength. Differences in basicity between primary, secondary and tertiary amines can be attributed to inductive effects.

A chemical reaction is a process that converts the molecular or ionic structure of one substance to another substance. Chemical reactions usually yield one or more products, with a structure and properties different from the reactants. Reactions may go to completion or proceed in the forward or reverse direction until they reach equilibrium. An important reactive intermediate in many organic reactions is a positively charged carbon atom, a carbocation. A carbanion is a high energy intermediate, unstable, and very reactive. Since a carbanion has an excess of electrons, it will readily react with an electron-deficient carbon atom, so it is classified as a nucleophile. Energy can be transferred by collision with another atom or molecule. The energy released by such collisions is utilized in bond breaking and bond-making.

As molecules absorb energy from their surroundings, their incipient kinetic energy increases. One of the ways that molecules dissipate energy is by molecular vibrations that include the stretching and the bending of covalent bonds. The C—C single bonds found in an organic molecule can rotate. Propane is symmetrical with a central CH2 unit with a methyl group on either end. The “ethane model” used for propane and butane can be extended to other alkanes. Halogens have the same valence as hydrogen. The increase in steric hindrance is apparent and it influences the rotamer populations in organic compounds bearing halogen atoms. In planar cyclic alkanes there is another form of strain because all the C—H bond eclipse, which leads to a steric interaction and an increase in the strain energy.

This chapter focuses on a class of isomers that differ only in the spatial arrangement of attached atoms and groups about an atom. Enantiomers are different molecules, and each requires a unique name. A set of standardized rules of nomenclature have been developed that distinguish two enantiomers based on the relative position of atoms or groups. A chiral compound that is not enantiopure is a mixture of both enantiomers. Electromagnetic radiation travels as a transverse wave that consists of electric and magnetic fields that oscillate perpendicular to one another. A transverse wave oscillates perpendicular to the direction of the wave's advance. Stereogenic carbons are found in cyclic molecules but monosubstituted cycloalkanes are not chiral.

Hydrofluoric acid can react with alkenes, but much slower than the reaction of HCl, HBr or HI Indeed, hydrogen iodide reacts rapidly with alkenes, as will HBr and HCl. Although strong acids such as HCl or HBr react with alkenes, weak acids such as water and alcohols do not react directly with alkenes. Carbocations, however, are highly reactive intermediates, and once generated they easily react with weak nucleophiles such as water or alcohols. If an alkene reacts with an acid catalyst in an aqueous medium the product is an alcohol, but in an alcohol medium the product is an ether. The reaction of cyclohexene and methanol in the presence of an acid catalyst initially gives the expected carbocation. Elemental fluorine was thought to be too reactive and too dangerous for reaction with alkenes.

A nucleophile was defined as a species that donates two electrons to carbon to form a new covalent σ-bond. Using a Lewis base analogy, a nucleophile is a two-electron donor, but the product is not an “ate” complex. Nucleophiles react with a variety of molecules that have electrophilic carbon atoms in a reaction where one atom or group replaces another. When iodide and bromomethane collide, the energy transferred must be equal to the energy of activation in order to initiate a SN2 reaction. The polar and protic water can be contrasted with an aprotic solvent. The SN2 reaction is one of the more important transformations in organic chemistry since one functional group can be transformed into a different functional group. Halide ions are important nucleophiles to interconvert the halogen of alkyl halides.

Alkoxides are important nucleophiles, and the SN2 reaction of an alkoxide with an alkyl halide is the basis of the Williamson ether synthesis. As an electron donor, sodium ethoxide is most attracted to the electrophilic carbon that bears bromine. The ethoxide anion does indeed collide with that carbon. The activation barrier for a SN2 reaction with a tertiary halide is too high due to steric hindrance in the transition state. Cyclic halides with a secondary or tertiary center undergo E2 reactions when treated with base. There is greater conformational flexibility in cyclohexane derivatives and both cis- and trans-derivatives react. Once the carbocation intermediate is formed, both the nucleophilic hydroxide ion and water can collide with the positive carbon of the carbocation.

If a molecule is subjected to enough energy to break bonds, the molecule fragments into smaller pieces. These fragments provide structural information. Exposure to infrared light causes the bonds in a molecule to vibrate, but not break. Spectroscopy techniques analyze how radiation of a particular energy is altered by interaction with a molecule. The mass of the molecular ion is used to give the molecular weight of a sample. When irradiated with infrared light a molecule absorbs energy that will induce molecular vibrations, but this energy is not sufficient to break bonds. A hydrogen nucleus is a charged particle possessed of a property called “spin.” The NMR spectrum for an organic molecule is obtained by first dissolving the sample in a suitable solvent.

The organic molecules contain carbon, hydrogen, halogen, nitrogen, oxygen, or sulfur atoms. Many other elements form bonds to carbon, including mercury and copper. Compounds such as this are important examples of a class of compounds known as organometallics. Water, alcohols, terminal alkynes, and even amines react with a Grignard reagent to form the corresponding conjugate base and an alkane as the conjugate acid. The reaction that forms an organolithium reagent proceeds by a slightly different mechanism when compared to the formation of a Grignard reagent. Grignard reagents typically give poor yields in a coupling reaction with simple alkyl halides, as do organolithium reagents. Organolithium reagents are more reactive and stronger bases relative to a comparable Grignard reagent.

There is a class of reactions known as oxidation or reduction reactions that involve the gain or loss of two electrons. This chapter introduces a few oxidation reactions and the typical transformations associated with them. An oxidation is formally defined as a reaction accompanied by the loss of electrons from an atom or a group. In an oxidation reaction there are structural changes in the product relative to the starting material. These changes usually include either loss of hydrogen atoms or the replacement of a hydrogen atom bonded to carbon with a more electronegative atom, usually a heteroatom. Jones oxidation is a powerful oxidizing medium for the conversion of alcohols to ketones. The reaction of cyclohexene with osmium tetroxide gives a five-membered ring product, an osmate ester.

This chapter discusses two major chemical reactions of aldehydes and ketones. Reaction of nucleophiles with an aldehyde or ketone gives an alkoxide via acyl addition. Subsequent hydrolytic workup gives an alcohol. The carbonyl of aldehydes and ketones reacts as a Brønsted-Lowry base with a suitable acid to generate an oxocarbenium ion intermediate. An acyl addition reaction with an unsymmetrical ketone will create a stereogenic center. Acyl addition reactions of Grignard reagents with aldehydes or ketones give an alkoxide product, but there is no reactive intermediate. An important method to improve the reaction exploits the acid-base chemistry of aldehydes and ketones. The cyanide ion was shown to be a moderate nucleophile in acyl addition reactions.

The oxidation of one molecule is accompanied by the reduction of another. If an oxidation involves the loss of two electrons, a reduction involves the gain of two electrons. The structural changes in the reduction product are often measured by whether hydrogen is gained or if a heteroatom such as oxygen is lost. This chapter reviews important organic reactions that are classified as reductions. Just as an oxidation is a reaction in which two electrons are lost, a reduction is defined as a reaction in which two electrons are gained. Structural changes used to monitor a reduction are the gain of hydrogen atoms or loss of an oxygen atom or another heteroatom. Lithium aluminum hydride is a more powerful reducing agent than sodium borohydride, so it easily reduces ketones and aldehydes.

Carboxylic acid derivatives also contain a carbonyl unit, but they have a leaving group attached to the acyl carbon that facilitates acyl substitution reactions. Carboxylic acids contain a carbonyl that is connected to an OH unit in a COOH unit called the carboxyl group. The IUPAC nomenclature for carboxylic acids identifies the longest continuous chain for the acid that contains the CO2H unit. The nomenclature of each acid derivative is based on the carboxylic acid precursor, the “parent” acid. Esters are a combination of a carboxylic acid and an alcohol. Sulfonic acids form acid halides, anhydrides, esters, and amides. A detergent is a surfactant is usually an alkylbenzene sulfonate but more soluble in hard water than a soap.

Benzene and derivatives are aromatic hydrocarbons with one ring or several rings fused together. The aromatic character of benzene and derivatives have special stability, which imparts a unique chemical profile. The delocalized bonding in benzene is not properly described by a structure that shows localized single and double bonds. Two structures are needed to properly represent benzene, with a double-headed arrow to show they are resonance contributors. In benzene derivatives one or more hydrogen atoms have been replaced with alkyl groups, heteroatom substituents, or functional groups. Dimethylbenzene is an arene with two substituents on the ring and has the common name xylene.

Carbonyl derivatives with a proton on an a-carbon react with a suitable base to generate a carbon nucleophile called an enolate anion. Enolate anions react as a nucleophile in acyl addition, acyl substitution and alkylation reactions. A powerful base such as an organolithium is required to remove the proton from nitrogen. An acid-base reaction is an equilibrium. The nature of the base plays a major role in the position of the equilibrium after deprotonation of an aldehyde or ketone. An aldol condensation with different ketones can lead to very interesting aldol products. The ability to control the equilibrium of an aldol condensation reaction was accomplished when non-nucleophilic bases were developed.

When a starting material has two or more functional groups, one may influence how another functional group in the molecule reacts if the groups are close enough. This chapter discusses difunctional molecules and their chemical reactions. It discusses the fundamental principles of photochemistry. Photochemistry refers to reactions brought about by the absorption of light. Both UV and visible light can excite molecules to higher electronic states. Different functional groups absorb light according to their individual structure. Benzophenone is a common triplet sensitizer. The use of a sensitizer will influence the choice of the irradiation wavelength. Tuning of the wavelength plays a key role in the outcome of a photochemical path. The instrument used to measure the effect of UV light on a molecule is called an ultraviolet spectrophotometer.

This chapter will discuss the reaction of 1,3-dienes with alkenes to give cyclohexene derivatives in a pericyclic reaction known as a cycloaddition. Conjugated dienes react with alkenes to give cyclohexene products. If methoxyethene is heated with buta-1,3-diene, even higher temperatures and pressures are required. The stereochemistry of the alkene is retained in the cyclohexene product. When there is one substituent on the diene and one substituent on the alkene there is the possibility of diastereomers in the cyclohexene product. Another important aspect of the Diels-Alder reaction can be examined in the reaction of the monosubstituted diene 1-methoxybuta-1,3-diene and the monosubstituted alkene acrylonitrile.

Heterocycles or heterocyclic aromatic compounds are a class of aromatic compounds in which heteroatoms replace one or more of the ring carbons. This chapter focuses on nitrogen, oxygen, and sulfur heterocycles. It also discusses reduced heterocycles, which are cyclic molecules that contain nitrogen, oxygen, or sulfur. Alkaloids are a class of nitrogenous organic compounds of plant origin that have pronounced physiological actions on humans. Imidazole and pyrazole are important units in many pharmaceutical preparations and also in naturally occurring compounds. Pyrazine, pyrimidine, and pyridazine derivatives are common components of pharmaceutically important compounds. Cyanuric chloride is the main precursor to the herbicide atrazine, a widely used to prevent pre-emergence broadleaf weeds.

Some molecules contain both an amine and a carboxyl group, the amino acids. Polyamino acids are linked by amide bonds. Amide bonds are known as peptide bonds in peptides and enzymes. The nitrogen atom of an amine may have one, two, or three carbon groups attached to give primary amines, secondary amines, and tertiary amines, respectively. Carboxylic acids are readily converted to an amide by reaction of the corresponding acid chloride or ester with ammonia or an amine. Phthalimide is an imide derived from phthalic acid. Both an amine and a carboxylic acid are mono-functional compounds. The amine unnit reacts with the carboxylic acid under neutral conditions to give a zwitterion product, 2-ammoniopropanoate. Both the amine and the carboxyl of an amino acid undergo chemical reactions that are expected for each group.

Carbohydrates are multifunctional compounds that contain several hydroxyl units as well as a ketone, aldehyde, or a carboxyl unit. Carbohydrates are important in mammalian biology, as well as in the biology of plants and insects. Glycosides are molecules in which a sugar is bound to another substructure via a glycosidic bond. Nucleosides are the structural subunit of nucleic acids such as DNA and RNA. Nucleosides have a ribose unit and a pyrimidine or a purine nucleobase. Glycoses are chiral aldehyde-alcohol or chiral ketone-alcohol carbohydrates that are usually monosaccharides. Pentose and hexose derivatives form cyclic hemiacaetals. An amino sugar is a molecule in which a hydroxyl group has been replaced with an amine group.