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Organic Chemistry Notes for Semester
Bradley University
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Organic Chemistry Organic chemistry: The study of the compounds of carbon. o Generally these contain C, H, O, or N and sometimes S, P, or a halogen. (fluorine, chlorine, bromine, or iodine). Why is organic chemistry a separate discipline within chemistry? Historical: Scientists at one time believed that a “vital force” present in living organisms was necessary to produce an organic compound. o The experiment of Wöhler in 1828 was the first in a series of experiments that led to the demise of the vital force theory. Number of organic compounds Chemists have discovered or made over 10 million organic compounds and an estimated 100,000 new ones are discovered or made each year. o By comparison, chemists have discovered or made an estimated 1 million inorganic compounds. Thus, approximately 85% of all known compounds are organic. The link to biochemistry Carbohydrates, lipids, proteins, enzymes, nucleic acids, hormones, vitamins, and almost all other chemicals in living systems are organic compounds. A comparison of organic and inorganic compounds (Table 10)
Obtaining Organic Compounds Isolation from Nature o to extract, isolate, and purify them from biological sources. Examples: penicillin, vitamin E, insulin, and anticancer drug paclitaxel.
Synthesis in the Laboratory
o Synthetic methods have become so sophisticated that there are few natural organic compounds that chemists cannot synthesize in the laboratory. o Compounds made in the laboratory are identical in both chemical and physical properties to those found in nature
VSEPR Theory Structural formula: Shows the atoms present in a molecule and the bonds that connect them. VSEPR model: The most common bond angles are 109°, 120°, and 180°.
Organic Structure- Number of Bonds In organic molecules, every carbon has four bonds. Complete the neutral organic molecule by filling in the missing hydrogen atoms and lone pairs Complete the neutral organic molecule by filling in the missing hydrogen atoms and lone pairs
Functional Groups: An atom or group of atoms within a molecule that shows a characteristic set of predictable physical and chemical properties. Functional groups are important because o They undergo the same types of chemical reactions no matter in what organic molecule they are found. o To a large measure, they determine the chemical and physical properties of a molecule. o They are the units by which we divide organic compounds into families. o They provide the basis on which we derive names for organic compounds. Alcohols: Contains an —OH (hydroxyl) group bonded to a tetrahedral carbon atom. Alcohols are classified as primary (1°), secondary (2°), or tertiary (3°). Amine: A compound containing an amino group (-NH 2 , RNH 2 , R 2 NH, R 3 N). Amino groups are classified as primary (1°), secondary (2°), or tertiary (3°). Aldehydes and Ketones: Each contains a C=O (carbonyl) group.
Aldehyde: Contains a carbonyl group bonded to a hydrogen; in formaldehyde, the simplest aldehyde, the carbonyl group is bonded to two hydrogens. Ketone: Contains a carbonyl group bonded to two carbon atoms.
Carboxylic acid: A compound containing a –COOH (carboxyl: carbonyl + hydroxyl) group. In a condensed structural formula, a carboxyl group may also be written –CO 2 H.
Carboxylic ester: A derivative of a carboxylic acid in which the H of the carboxyl group is replaced by a carbon group.
Amide: A derivative of a carboxylic acid in which the —OH of the carboxyl group is replaced by an amino group.
Functional Groups Summary Table
Chapter 11: Alkanes Alkanes: Hydrocarbons that contain only carbon-carbon single bonds. The first two alkanes are methane and ethane. Line-angle formula A line represents a carbon–carbon bond. A vertex and a line terminus represent a carbon atom. Hydrogen atoms connected to C are not shown in line- angle formulas.
The First Ten Alkanes with Unbranched Chains
Constitutional Isomers: Compounds that have the same molecular formula but different structural formulas (a different connectivity of their atoms ). For the molecular formulas CH 4 , C 2 H 6 , and C 3 H 8 , only one structural formula is possible. There are no constitutional isomers for these molecular formulas. For the molecular formula C 4 H 10 , two constitutional isomers are possible.
IUPAC Names- straight chain The IUPAC name of an alkane with an unbranched chain of carbon atoms consists of two parts: 1) A prefix shows the number of carbon atoms in the chain. 2) The suffix -ane: shows that the compound is a saturated hydrocarbon. Prefixes Used in the IUPAC Name each alkane
IUPAC Names - branched chains The name of an alkane with a branched chain of carbon atom consists of: o a parent name : the longest chain of carbon atoms. o substituent names: the groups bonded to the parent chain. Alkyl Groups: A substituent group derived from an alkane by removal of a hydrogen atom o Commonly represented by the symbol R–. o Named by dropping the -ane from the name of the parent alkane and adding the suffix -yl.
IUPAC Names - Alkane 1. The name for an alkane with an unbranched chain of carbon atoms consists of a prefix showing the number of carbon atoms and the ending -ane. 2. For branched-chain alkanes, the longest chain of carbon atoms is the parent chain and its name is the root name. 3. Give each substituent on the parent chain a name and a number. Use a hyphen to connect the number to the name. 4. If there is one substituent, number the parent chain from the end that gives the substituent the lower number. 5. If the same substituent occurs more than once: Number the parent chain from the end that gives the lower number to the substituent encountered first. Indicate the number of times the substituent occurs by a prefix di-, tri-, tetra-, penta-, hexa-, and so on. Use a comma to separate position numbers. 6. If there are two or more different substituents: o List them in alphabetical order. o Number the chain from the end that gives the lower number to the substituent encountered first. o If there are different substituents at equivalent positions on opposite ends of the parent chain, give the substituent of lower alphabetical order the lower number. 7. Do not include the prefixes di-, tri-, tetra-, and so on or the hyphenated prefixes sec- and tert- in alphabetizing; Alphabetize the names of substituents first, and then insert these prefixes. In the following example, the alphabetizing parts are ethyl and methyl , not ethyl and dimethyl.
Sources of Alkanes Natural gas: 90 to 95 percent methane. 5 to 10 percent ethane, and A mixture of other relatively low-boiling alkanes, chiefly propane, butane, and 2-methylpropane (isobutane). Petroleum: A thick, viscous liquid mixture of thousands of compounds, most of them hydrocarbons formed from the decomposition of marine plants and animals.
Cycloalkanes Cyclic hydrocarbon: A hydrocarbon that contains carbon atoms joined to form a ring.
Cycloalkane: A cyclic hydrocarbon in which all carbons of the ring are saturated (have only carbon-carbon single bonds). Five-membered (cyclopentane) and six- membered (cyclohexane) rings are especially abundant in nature. Nomenclature - To name a cycloalkane, prefix the name of the corresponding open-chain alkane with cyclo- , and name each substituent on the ring. - If there is only one substituent on the ring, there is no need to give it a location number.
o Reaction rate depends on the activation energy. Many alkene addition reactions require a catalyst. Addition of H 2 —Reduction Virtually all alkenes add H 2 in the presence of a transition metal catalyst, commonly Pd, Pt, or Ni. Polymerization: polymer: Greek: poly, many, and meros, part; any long- chain molecule synthesized by bonding together many single parts, called monomers. monomer: Greek: mono, single and meros, part. o Show the structure of a polymer by placing parentheses around the repeating monomer unit. o Place a subscript, n , outside the parentheses to indicate that this unit repeats n times. The structure of a polymer chain can be reproduced by repeating the enclosed structure in both directions.
Drawing the polymer from an alkene monomer 1. Draw a series of monomers in a line 2. Connect the carbon 2 of the double bond to carbon 1 of the next monomer. Remove the double bond. 3. Repeat
Polyethylene Low-density polyethylene (LDPE): A highly branched polymer; polymer chains do not pack well and London dispersion forces between them are weak. Softens and melts above 115°C. Approximately 65% of all LDPE is used for the production of films for packaging and for trash bags. High-density polyethylene (HDPE): Only minimal chain branching; chains pack well and London dispersion forces between them are strong. Has higher melting point than LDPE and is stronger Can be blow molded to squeezable jugs and bottles.
Aromatic Compounds Aromatic compound: A hydrocarbon that contains one or more benzene-like rings. Ring with alternating double and single bonds. Arene: A term used to describe aromatic compounds. - Ar–: A symbol for an aromatic group derived by removing an H from an arene.
Chapter 13: Alcohols, Ethers, and Thiols Alcohol nomenclature
- Name parent alkane
- Treat the –OH as a substituent with the highest priority possible
- Change ending of alkane to –ol to designate the alcohol Nomenclature (2 of 4)
Classification of alcohols Alcohols are classified as primary (1°), secondary (2°), or tertiary (3°), depending on the number of carbon groups bonded to the carbon bearing the –OH group.
Nomenclature- more than one -OH In the IUPAC system, a compound containing two hydroxyl groups is named as a diol, one containing three hydroxyl groups as a triol, and so forth. IUPAC names for diols, triols, and so on retain the final " - e " in the name of the parent alkane. We commonly refer to compounds containing two hydroxyl groups on adjacent carbons as glycols.
Physical Properties Dehydration: Elimination of a molecule of water from adjacent carbon atoms gives an alkene. o Dehydration is most often brought about by heating an alcohol with either 85% H 3 PO 4 or concentrated H 2 SO 4. Rates of dehydration reactions 1°alcohols are the most difficult to dehydrate and require temperatures as high as 180°C. 2°alcohols undergo acid-catalyzed dehydration at somewhat lower temperatures. 3°alcohols generally undergo acid-catalyzed dehydration at temperatures only slightly above room temperature. 3° alcohols >2° alcohols > 1° alcohols When isomeric alkenes are obtained, the alkene having the greater number of alkyl groups on the double bond generally predominates. (The more “substituted” double bond)
Dehydration-Hydration Acid-catalyzed hydration of alkenes to give alcohols (Chapter 12) and acid-catalyzed dehydration of alcohols to give alkenes are competing reactions. o The following acid-catalyzed equilibrium exists. In accordance with Le Chatelier's principle, large amounts of water favor alcohol formation, whereas removal of water from the equilibrium mixture favors alkene formation.
Oxidation Oxidation of a 1° alcohol gives an aldehyde or a carboxylic acid, depending on the experimental conditions. Oxidation of a 1° alcohol to a carboxylic acid is commonly carried out using potassium dichromate, K 2 Cr 2 O 7 , in aqueous sulfuric acid. Oxidation of a 2° alcohol gives a ketone. Tertiary alcohols are resistant to oxidation. In the presence of an acid catalyst they are prone to dehydration.
Ethers* NEW FUNCTIONAL GROUP** The functional group of an ether is an oxygen atom bonded to two carbon atoms. - The simplest ether is dimethyl ether. - The most common ether is diethyl ether. (“ether” is almost always diethyl ether) - Nomenclature Although ethers can be named according to the IUPAC system, chemists almost invariably use common names for low-molecular- weight ethers.
- Common names are derived by listing the alkyl groups bonded to oxygen in alphabetical order and adding the word “ether.” Cyclic ether: An ether in which one of the atoms in a ring is oxygen.
- Cyclic ethers are also known by their common names.
- Ethylene oxide is an important building block for the organic chemical industry. It is also used as a fumigant in foodstuffs and textiles, and in hospitals to sterilize surgical instruments.
- Tetrahydrofuran is a useful laboratory and industrial solvent.
Physical Properties Figure 13 Ethers are polar molecules in which oxygen bears a partial negative charge and each carbon bonded to it bears a partial positive charge. However, only weak forces of attraction exist between ether molecules in the pure liquid. - Consequently, boiling points of ethers are close to those of hydrocarbons of similar molecular weight. - Ethers have lower boiling points than alcohols of the same molecular formula. (no H-bonding)
Thiols (NEW FUNCTIONAL GROUP) Thiol: A compound containing an -SH (sulfhydryl group). - The most outstanding property of low-molecular- weight thiols is their stench. - They are responsible for smells such as those from rotten eggs and sewage. - The scent of skunks is due primarily to these two thiols.
Nomenclature - Thiols IUPAC names are derived in the same manner as are the names of alcohols. - To show that the compound is a thiol, the final -e of the parent alkane is retained and the suffix -thiol added. Common names for simple thiols are derived by naming the alkyl group bonded to –SH and adding the word “ mercaptan .” - Name each of the following alcohols and thiols - Name each of the following alcohols and thiols - Physical Properties Because of the small difference in electronegativity between sulfur and hydrogen (2 – 2 = 0), an S–H bond is nonpolar covalent. - Thiols show little association by hydrogen bonding. - Thiols have lower boiling points and are less soluble in water and other polar solvents than alcohols of similar molecular weight.
Oxidation of Thiols The most common reaction of thiols in biological systems is their oxidation to disulfides, the functional group of which is a disulfide (– S–S–) bond. - Thiols are readily oxidized to disulfides by O 2. - They are so susceptible to oxidation that they must be protected from contact with air during storage. - Disulfides, in turn, are easily reduced to thiols by several reducing agents including H 2 in the presence of a transition metal catalyst.
- Importance of Disulfide Bonds in Protein folding
- One of the functions of the amino acid cysteine is to stabilize the folding structure of a protein.
Chirality Chirality -is a property of asymmetry important in several branches of science. The word chirality is derived from the Greek χειρ ( kheir ), "hand," a familiar chiral object.
Chiral molecules and mirror images The mirror image of a chiral molecule is “non- superimposable” with itself The mirror image of a chiral molecule is “non- superimposable” with itself
Enantiomers Enantiomers: Nonsuperposable mirror images. As an example of a molecule that exists as a pair of enantiomers, consider 2-butanol. Now try to fit one molecule on top of the other so that all groups and bonds match exactly. The original and mirror image are nonsuperposable. o They are different molecules. Nonsuperposable mirror images are enantiomers. Recognizing chiral molecules The most common cause of enantiomerism in organic molecules is the presence of a carbon with four different groups bonded to it. o A carbon with four different groups bonded to it is called a stereocenter.
Enantiomers Summary Objects that are nonsuperposable on their mirror images are chiral (they show handedness). The most common cause of chirality among organic molecules is the presence of a carbon with four different groups bonded to it. We call a carbon with four different groups bonded to it a stereocenter. Objects that are superposable on their mirror images are achiral (without chirality). Nonsuperposable mirror images are called enantiomers. Enantiomers always come in pairs. Because enantiomers are different compounds, each must have a different name. Diastereomers : Stereoisomers that are not mirror images.
Stereoisomers of cholesterol The 2 n rule applies equally well to molecules with three or more stereocenters. Here is cholesterol.
Optical Activity Ordinary light: Light waves oscillating in all planes perpendicular to its direction of propagation. Plane-polarized light: Light waves oscillating only in parallel planes. Polarimetry Polarimeter: An instrument for measuring the ability of a compound to rotate the plane of plane-polarized light. Optically active: Showing that a compound is capable rotating the plane of plane-polarized light. Optical Activity Dextrorotatory: Clockwise rotation of the plane of plane- polarized light. Indicated by (+). Levorotatory: Counterclockwise rotation of the plane of plane-polarized light. Indicated by (–). Specific rotation: The observed rotation of an optically active substance at a concentration of 1 g/mL in a sample tube 10 cm long. Chirality of Biomolecules
Except for inorganic salts and a few low-molecular-weight organic substances, the molecules in living systems, both plant and animal, are chiral. Although these molecules can exist as a number of stereoisomers, almost invariably only one stereoisomer is found in nature. Instances do occur in which more than one stereoisomer is found, but these rarely exist together in the same biological system.
Enzymes How an enzyme distinguishes between a molecule and its enantiomer. Enzymes (protein biocatalysts) all have many stereocenters. o An example is chymotrypsin, an enzyme in the intestines of animals that catalyzes the digestion of proteins. o Chymotrypsin has 251 stereocenters. The maximum number of stereoisomers possible is 2 251! Only one of these stereoisomers is produced and used by any given organism. Because enzymes are chiral substances, most either produce or react with only substances that match their stereochemical requirements.
Thalidomide Because interactions between molecules in living systems take place in a chiral environment, a molecule and its enantiomer or one of its diastereomers elicit different physiological responses. One of the more infamous examples of this is thalidomide, a medication used to treat extreme morning sickness in pregnant women in Europe in the 1960s. One isomer was extremely effective, the other led to terrible birth defects
Amines Chapter 15 Structure and Classification Amines are classified as 1°, 2°, or 3° depending on the number of carbon groups bonded to nitrogen.
Aliphatic and Aromatic amines
Aliphatic amine : All carbons bonded to nitrogen are derived from alkyl groups. Aromatic amine : One or more of the groups bonded to nitrogen are aryl groups. Heterocyclic amine : An amine in which the nitrogen atom is part of a ring. Heterocyclic aliphatic amine: A heterocyclic amine in which the ring is saturated (has no C=C bonds). Heterocyclic aromatic amine: The amine nitrogen is part of an aromatic ring. Nomenclature IUPAC names - We derive IUPAC names for aliphatic amines just as we did for alcohols. - Drop the final -e of the parent alkane and replace it by -amine. - Use a number to locate the amino group on the parent chain. - IUPAC nomenclature retains the common name aniline for C 6 H 5 NH 2 , the simplest aromatic amine. - Name simple derivatives of aniline by using numbers to locate substituents or, alternatively, use the prefixes ortho ( o ), meta ( m ), and para ( p ).
Physical Properties Like ammonia, low-molecular-weight amines have very sharp, penetrating odors. - Trimethylamine, for example, is the pungent principle in the smell of rotting fish. - An N–H---N hydrogen bond is weaker than an O–H---O hydrogen bond, because the difference in electronegativity between N and H (3 – 2 = 0) is less than that between O and H (3 – 2. = 1). - We see the effect of hydrogen bonding between molecules of comparable molecular weight by comparing the boiling points of ethane, methanamine, and methanol. - All classes of amines form hydrogen bonds with water and are more soluble in water than are hydrocarbons of comparable molecular weight. - Most low-molecular-weight amines are completely soluble in water. - Higher-molecular-weight amines are only moderately soluble in water or are insoluble. Basicity of Amines Like ammonia, amines are weak bases, and aqueous solutions of amines are basic. - The acid–base reaction between an amine and water involves transfer of a proton from water to the amine. - Aliphatic amines all have about the same base strength, and are slightly stronger bases than NH 3. - Aromatic and heterocyclic aromatic amines are considerably weaker bases than aliphatic amines. - Note that while aliphatic amines are weak bases by comparison with inorganic bases such as NaOH, they are strong bases among organic compounds.
Reactions of Amines The most important chemical property of amines is their basicity. - Amines, whether soluble or insoluble in water, react quantitatively with strong acids to form
water-soluble salts.
- Acid-base reaction
Aldehydes and Ketones Chapter 16 Aldehyde and Ketone functional groups The functional group of an aldehyde is a carbonyl group bonded to a hydrogen atom. - In methanal (formaldehyde), the simplest aldehyde, the carbonyl group is bonded to two hydrogens.
In a hydride ion, hydrogen has two valence electrons and bears a negative charge.
In a reduction by sodium borohydride, hydride ion adds to the partially positive carbonyl carbon which leaves a negative charge on the carbonyl oxygen.
Reaction of this intermediate with aqueous acid gives the alcohol.
Reduction by NaBH 4 does not affect a carbon-carbon double bond or an aromatic ring.
In biological systems, the agent for the reduction of aldehydes and ketones is the reduced form of nicotinamide adenine dinucleotide, abbreviated NADH (Section 26) - This reducing agent, like NaBH 4 , delivers a hydride ion to the carbonyl carbon of the aldehyde or ketone. - Reduction of pyruvate, the end product of glycolysis, by NADH gives lactate.
Addition of Alcohols Addition of a molecule of alcohol to the carbonyl group of an aldehyde or ketone forms a hemiacetal (a half-acetal). - The functional group of a hemiacetal is a carbon bonded to one –OH group and one -–OR group. - In forming a hemiacetal, –H of the alcohol adds to the carbonyl oxygen and –OR adds to the carbonyl carbon. - Hemiacetals are generally unstable and are only minor components of an equilibrium mixture except in one very important type of molecule. - When a hydroxyl group is part of the same molecule that contains the carbonyl group and a five- or six-membered ring can form, the compound exists almost entirely in a cyclic
hemiacetal form.
A hemiacetal can react further with an alcohol to form an acetal plus water. - This reaction is acid-catalyzed. - The functional group of an acetal is a carbon bonded to two –OR groups. - All steps in hemiacetal and acetal formation are reversible.
- As with any other equilibrium, we can drive it in either direction by using Le Chatelier's principle.
- To drive it to the right, we either use a large excess of alcohol or remove water from the equilibrium mixture
- To drive it to the left, we use a large excess of
water.
Mechanism of Acetal Formation Step 1: Add a proton. Adding a proton to the carbonyl oxygen makes the carbonyl carbon stronger electrophile and more susceptible to attack by a nucleophile.
Step 2: Reaction of an electrophile and a nucleophile to form a new covalent bond. This step adds the first –OR group required for acetal formation. The intermediate formed is an oxonium ion.
Step 3: Proton transfer to another oxygen. The proton transferred is in red.
Step 4: Break a bond to form stable molecules or ions. In this case the stable molecule is H 2 O and the stable ion is a 3°carbocation.
Step 5: Reaction of an electrophile and a nucleophile to form a new covalent bond. This step adds the second –OR group of the acetal to what was the original carbonyl carbon.
Step 6: Take a proton away. Transfer of a proton to solvent gives the acetal and regenerates the H+ catalyst.
Keto-Enol Tautomerism A carbon atom adjacent to a carbonyl group is called an a-carbon , and a hydrogen atom bonded to it is called an a-hydrogen. An aldehyde or ketone that has a hydrogen on an a-carbon is in equilibrium with a constitutional isomer called an enol. - The name “enol” is derived from the IUPAC designation of it as both an alkene (- en -) and an alcohol (- ol ). - In a keto-enol equilibrium, the keto form generally redominates.
Hemiacetal and Acetal Hemiacetals are generally unstable and react with a second molecule of the alcohol to form a stable acetal and water. - Hemiacetal and Acetal Formation Aldehydes are often more reactive than ketones because the carbonyl carbon is more positive. - Hemiacetal and Acetal Formation Aldehydes are often more reactive than ketones because the carbonyl carbon is more positive.
The presence of two alkyl groups in ketones makes it more difficult for an alcohol to form a bond with the carbon in the carbonyl group.
Cyclic Hemiacetals - A cyclic hemiacetal forms when the carbonyl group and the -OH group are in the same molecule. - The compound exists almost entirely in a cyclic hemiacetal form. - Five- and six-atom cyclic hemiacetals and acetals are more stable than their open-chain isomers. - Formation of Cyclic Acetals A hemiacetal can react further with an alcohol to form an acetal plus
water.
- This reaction is acid-catalyzed.
- The functional group of an acetal is a carbon bonded to two –OR groups.
Formation of Cyclic Acetals: Glucose - Glucose forms a six-carbon cyclic hemiacetal when the hydroxyl group on carbon 5 bonds with the carbonyl group on carbon 1. - The hemiacetal of glucose is so stable that almost all the glucose exists as the cyclic hemiacetal in aqueous solution. - This reaction explains how sugar molecules can link together and form disaccharides and polysaccharides. - Glucose + Glucose = Maltose Maltose is a disaccharide consisting of two glucose molecules. - Locate the hemiacetal and acetal in the maltose molecule - Glucose + Glucose = Maltose - an acetal bond (shown in red) links two glucose molecules. - One carbon atom in glucose retains the cyclic hemiacetal bond (shown in green).
Addition of Alcohols All steps in hemiacetal and acetal formation are reversible. As with any other equilibrium, we can drive it in either direction by using Le Chatelier's principle.
Summary Reactions of Aldehydes and Ketones - Oxidation primary alcohol aldehyde carboxylic acid secondary alcohol ketone tertiary alcohol no reaction
- Reduction aldehyde alcohol ketone alcohol
Organic Chemistry Notes for Semester
University: Bradley University
