Chapter 25 Organic and Biological Chemistry

Chemistry, The Central Science, 11th edition Theodore L. Brown; H. Eugene LeMay, Jr.; and Bruce E. Bursten

John D. Bookstaver Organic and Biological St. Charles Community College Chemistry

• Organic chemistry is the chemistry of carbon compounds. • Carbon has the ability to form long chains. • Without this property, large biomolecules such as proteins, lipids, carbohydrates, and nucleic acids could not form.

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• There are three hybridization states and geometries found in organic compounds: – sp3 Tetrahedral – sp2 Trigonal planar – sp Linear

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• There are four basic types of hydrocarbons: – Alkanes – Alkenes – Alkynes – Aromatic hydrocarbons

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• Alkanes contain only single bonds. • They are also known as saturated hydrocarbons. – They are “saturated” with hydrogens.

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• Lewis structures of alkanes look like this. • They are also called structural formulas. • They are often not convenient, though…

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…so more often condensed formulas are used.

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• The only van der Waals force is the London dispersion force. Organic and • The boiling point increases with the length Biological of the chain. Chemistry © 2009, Prentice-Hall, Inc. Structure of Alkanes

• Carbons in alkanes are sp3 hybrids. • They have a tetrahedral geometry and 109.5° bond angles.

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• There are only σ- bonds in alkanes. • There is free rotation about the C—C bonds.

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Isomers have the same molecular formulas, but the atoms are bonded in a different order.

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• There are three parts to a compound name: – Base: This tells how many carbons are in the longest continuous chain.

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• There are three parts to a compound name: – Base: This tells how many carbons are in the longest continuous chain. – Suffix: This tells what type of compound it is.

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• There are three parts to a compound name: – Base: This tells how many carbons are in the longest continuous chain. – Suffix: This tells what type of compound it is. – Prefix: This tells what groups are attached to the chain.

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1. Find the longest chain in the molecule. 2. Number the chain from the end nearest the first substituent encountered. 3. List the substituents as a prefix along with the number(s) of the carbon(s) to which they are attached. Organic and Biological Chemistry

If there is more than one type of substituent in the molecule, list them alphabetically.

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• Carbon can also form ringed structures. • Five- and six-membered rings are most stable. – They can take on conformations in which their bond angles are very close to the tetrahedral angle. – Smaller rings are quite strained.

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• Alkanes are rather unreactive due to the presence of only C—C and C—H σ-bonds. • Therefore, they make great nonpolar solvents.

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• Alkenes contain at least one carbon–carbon double bond. • They are unsaturated. – That is, they have fewer than the maximum number of hydrogens. Organic and Biological Chemistry

• Unlike alkanes, alkenes cannot rotate freely about the double bond. – The side-to-side overlap in the π-bond makes this impossible without breaking the π-bond.

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This creates geometric isomers, which differ from each other in the spatial arrangement of groups about the double bond.

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Structure also affects the physical properties of alkenes.

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• The chain is numbered so the double bond gets the smallest possible number. • cis-Alkenes have the carbons in the chain on the same side of the molecule. • trans-Alkenes have the carbons in the chain on opposite sides of the molecule.

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• One reaction of alkenes is the addition reaction. – In it, two atoms (e.g., bromine) add across the double bond. – One π-bond and one σ-bond are replaced by two σ-bonds; therefore, ΔH is negative. Organic and Biological Chemistry

• It is a two-step mechanism: – The first step is the slow, rate-determining step. – The second step is fast.

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In the first step, the π-bond breaks and the new C—H bond and a cation form.

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In the second step, a new bond forms between the negative bromide ion and the positive carbon.

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• Alkynes contain at least one carbon–carbon triple bond. • The carbons in the triple bond are sp-hybridized and have a linear geometry. • They are also unsaturated. Organic and Biological Chemistry

4-methyl-2-pentyne

• The method for naming alkynes is analogous to the naming of alkenes. • However, the suffix is -yne rather than -ene.

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• Alkynes undergo many of the same reactions alkenes do. • As with alkenes, the impetus for reaction is the replacement of π-bonds with σ-bonds.

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• Aromatic hydrocarbons are cyclic hydrocarbons that have some particular features. • There is a p-orbital on each atom. – The molecule is planar. • There is an odd number of electron pairs in the - π Organic and system. Biological Chemistry

Many aromatic hydrocarbons are known by their common names.

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© 2009, Prentice-Hall, Inc. Reactions of Aromatic Compounds • In aromatic compounds, unlike in alkenes and alkynes, each pair of π-electrons does not sit between two atoms. • Rather, the electrons are delocalized; this stabilizes aromatic compounds. Organic and Biological Chemistry

• Due to this stabilization, aromatic compounds do not undergo addition reactions; they undergo substitution. • In substitution reactions, hydrogen is replaced

by a substituent. Organic and Biological Chemistry

• Two substituents on a benzene ring could have three possible relationships: – ortho-: On adjacent carbons. – meta-: With one carbon between them. Organic and – para-: On opposite sides of ring. Biological Chemistry

Halogenation

Friedel-Crafts Reaction Reactions of aromatic compounds often require a catalyst. Organic and Biological Chemistry

The term functional group is used to refer to parts of organic molecules where reactions tend to occur.

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• Alcohols contain one or more hydroxyl groups, —OH. • They are named from the parent hydrocarbon; the suffix is changed to -ol and a number designates the carbon to which the hydroxyl is

attached. Organic and Biological Chemistry

• Alcohols are much more acidic than hydrocarbons.

– pKa ~15 for most alcohols. – Aromatic alcohols

have pKa ~10.

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• Ethers tend to be quite unreactive. • Therefore, they are good polar solvents.

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• The carbonyl group is a carbon-oxygen double bond. • Carbonyl compounds include many classes of compounds.

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In ketones, there are two carbons bonded to the carbonyl carbon.

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• Acids have a hydroxyl group bonded to the carbonyl group. • They are tart tasting. • Carboxylic acids are weak acids.

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• Esters are the products of reactions between carboxylic acids and alcohols. • They are found in many fruits and perfumes. Organic and Biological Chemistry

Amides are formed by the reaction of carboxylic acids with amines.

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• Amines are organic bases. • They generally have strong, unpleasant odors.

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• Carbons with four different groups attached to them are handed, or chiral. • These are optical isomers or stereoisomers. • If one stereoisomer is “right-handed,” its enantiomer is “left-handed.”

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S-ibuprofen • Many pharmaceuticals are chiral. • Often only one enantiomer is clinically active.

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• Proteins are polymers of α-amino acids. • A condensation reaction between the amine end of one amino acid and the acid end of another produces a peptide bond. Organic and Biological Chemistry

• Hydrogen bonding in peptide chains causes coils and helices in the chain. • Kinking and folding of the coiled chain gives proteins a characteristic shape.

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• Most enzymes are proteins. • The shape of the active site complements the shape of the substrate on which the enzyme acts; hence, the “lock- and-key” model. Organic and Biological Chemistry

Simple sugars are polyhydroxy aldehydes or ketones.

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• In solution, they form cyclic structures. • These can form chains of sugars that form structural molecules such as starch and cellulose.

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Two of the building blocks of RNA and DNA are sugars (ribose or deoxyribose) and cyclic bases (adenine, guanine, cytosine, and thymine or uracil).

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These combine with a phosphate to form a nucleotide.

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Nucleotides combine to form the familiar double-helix form of the nucleic acids.

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