July 24, 2017

Organic Compounds

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Structures & Names of Organic Compounds
Chemistry Lab

Dr. Robert F. Szalapski
Modified May 2013

§ 1. Purpose

So far we have studied the naming of inorganic compounds. For example, we have studied ionic compounds such as \mathrm{NaCl} and covalently bonded molecules such as \mathrm{H}_{2}\mathrm{O}. Organic chemistry concerns the chemistry associated with living things, and it is largely based on carbon. In this lab we will explore organic molecules by building molecular models, drawing chemical structures and learning how to name organic molecules. Some organic molecules have traditional or common names, but systematic naming conventions have been established by IUPAC, the International Union of Pure and Applied Chemistry.

The figures in this document were created using the freeware version of ChemSketch.

§ 2. Background

The Reference Tables for Physical Setting/CHEMISTRY, 2011 Edition, contain three tables concerning organic compounds.

  1. Table P, Organic Prefixes

  2. Table Q, Homologous Series of Hydrocarbons

  3. Table R, Organic Functional Groups

You need to be very familiar with these tables. Organic compounds oftentimes contain chains of carbon atoms, and the length of the chain determines the prefix used. The chemistry of organic compounds depends upon the presence of certain functional groups.

The molecules that we will be discussing are mainly composed of carbon (\mathrm{C}), hydrogen (\mathrm{H}), oxygen (\mathrm{O}) and nitrogen (\mathrm{N}). The number of covalent bonds formed by each is summarized in Table 1.

Symbol Name Number of Covalent Bonds
\mathrm{C} carbon 4
\mathrm{H} hydrogen 1
\mathrm{O} oxygen 2
\mathrm{N} nitrogen 3
\mathrm{F} fluorine 1
\mathrm{Cl} chlorine 1

Table 1.  Number of covalent bonds by atom.

We will also be discussing the halogens, fluorine (\mathrm{F}), chlorine (\mathrm{Cl}), bromine (\mathrm{Br}) and iodine (\mathrm{I}); all make a single covalent bond, and fluorine and chlorine are shown explicitly in the table.

Molecules are categorized according to their functional groups. A functional group is a particular arrangement of atoms that lead to predictable properties or reactivity. The meaning of a functional group will be clarified in the sections that follow.

§ 3. Lab Activity

§ 3.1. Alkanes

An alkane is a straight carbon chain with all single carbon–carbon bonds. As shown in Table 1, each carbon atom needs four bonds. Carbons at the end of the chain are bonded to one other carbon, so they will be bonded to three hydrogens. Carbons elsewhere in the chain will be bonded to two other carbon atoms, so they will be bonded to two hydrogens. See Figure 1.

Figure 1.  Methane, ethane and propane are three alkanes. The “ane” ending is added to the prefix from Table P in the Reference Tables.

The naming of alkanes proceeds as follows. Consider the molecule labeled “propane”. It is a three-carbon chain with only single bonds between the carbon atoms, hence it is an alkane. (Single bonds are indicated by a single line between the two atoms.) In Table P we see that three carbon atoms correspond to the prefix “prop” to which we add the “ane” ending; prop+ane = propane, and so the molecule is named appropriately.

Notice the entry for alkanes in Table Q. Under the heading “General Formula” we see the expression \mathrm{C}_{n}\mathrm{H}_{{2n+2}}. For the molecules shown in Figure 1 we predict the chemical formulae as given in Table 2.

Name Number of Carbons \mathrm{C}_{n}\mathrm{H}_{{2n+2}}
methane 1 \mathrm{C}_{1}\mathrm{H}_{{2\cdot 1+2}}=\mathrm{C}\mathrm{H}_{{4}}
ethane 2 \mathrm{C}_{2}\mathrm{H}_{{2\cdot 2+2}}=\mathrm{C}_{2}\mathrm{H}_{{6}}
propane 3 \mathrm{C}_{3}\mathrm{H}_{{2\cdot 3+2}}=\mathrm{C}_{3}\mathrm{H}_{{8}}
pentane
octane

Table 2.  Application of the formula \mathrm{C}_{n}\mathrm{H}_{{2n+2}} for alkanes.

Count the hydrogen atoms on each molecule in Figure 1 and confirm that the general formula works.

§ Questions and Activities

For this part of the lab use the Reference Tables.

  1. Draw pentane and octane in the space provided in Figure 2 and Figure 3.

  2. Complete Table 2 for pentane and octane.

  3. Do your predictions for the formula of pentane and octane agree with your drawings?

  4. Build a molecular model of pentane. Have the instructor inspect your model and initial here.

 

 

Figure 2.  Draw pentane in the space above.

 

 

Figure 3.  Draw octane in the space above.

§ 3.2. Alkenes

Alkenes are similar to alkanes, but at least one pair of carbon atoms are double bonded. As a result there will be fewer bonds available for bonding to hydrogen. Because alkanes contain the greatest number of hydrogen atoms possible we say that they are saturated. Alkenes by contrast are unsaturated. You have probably heard about saturated and unsaturated fats and oils with regard to food. It refers to the absence or presence of double bonds between carbon atoms.

Examples of alkenes appear in Figure 4.

Figure 4.  Ethene and propene are examples of alkenes. The presence of two double bonds indicates a “diene” such as propadiene. Notice the double bonds between carbon atoms indicated by a double line.

Two carbon atoms, according to Table P, indicate the prefix “eth”, and the double bond implies the ending “ene”; eth+ene = ethene. For longer carbon chains there is an added complication in that the we need to indicate the position of the double bond. Prop-1-ene indicates that the double bound is connected to the first carbon. We always begin counting from the end closest to the double bond, so with a three-carbon chain the double bond is always connected to the first carbon. For propene it really isn’t necessary to include the position, but for longer molecules it is.

Notice the entry for alkenes in Table Q. Under the heading “General Formula” we see the expression \mathrm{C}_{n}\mathrm{H}_{{2n}}. For the molecules shown in Figure 4 we predict the chemical formulae as given in Table 3. (Notice that the formula does not apply to dienes.)

Name Number of Carbons \mathrm{C}_{n}\mathrm{H}_{{2n}}
ethene 2 \mathrm{C}_{2}\mathrm{H}_{{2\cdot 2}}=\mathrm{C}_{2}\mathrm{H}_{{4}}
propene 3 \mathrm{C}_{3}\mathrm{H}_{{2\cdot 3}}=\mathrm{C}_{3}\mathrm{H}_{{6}}
hex-1-ene
hex-2-ene
hex-3-ene

Table 3.  Application of the formula \mathrm{C}_{n}\mathrm{H}_{{2n}} for alkenes.

Count the hydrogen atoms on each molecule in Figure 4 and confirm that the general formula works.

§ Questions and Activities

For this part of the lab use the Reference Tables.

  1. Draw hex-1-ene, hex-2-ene and hex-3-ene in the space provided in Figure 5–Figure 7.

  2. Complete Table 3 for hex-1-ene, hex-2-ene and hex-3-ene.

  3. Do your predictions for the formula of hex-1-ene, hex-2-ene and hex-3-ene agree with your drawings?

  4. Build a molecular model of hex-3-ene. Have the instructor inspect your model and initial here.

  5. What allows us to say that hex-1-ene, hex-2-ene and hex-3-ene are isomers?

 

 

Figure 5.  Draw hex-1-ene in the space above.

 

 

Figure 6.  Draw hex-2-ene in the space above.

 

 

Figure 7.  Draw hex-3-ene in the space above.

§ 3.3. Alkynes

An alkyne is like an alkane with one carbon–carbon triple bond. The example ethyne appears in Figure 8.

Figure 8.  Ethyne is an example of an alkyne. Notice that the triple bond between carbon atoms is indicated by three parallel lines.

Two carbon atoms, according to Table P, indicate the prefix “eth”, and the triple bond implies the ending “yne”; eth+yne = ethyne. For longer carbon chains there is an added complication in that the we need to indicate the position of the triple bond.

Notice the entry for alkynes in Table Q. Under the heading “General Formula” we see the expression \mathrm{C}_{n}\mathrm{H}_{{2n-2}}. For the molecules shown in Figure 8 we predict the chemical formulae as given in Table 4. (Notice that the formula only applies to chains with a single triple bond.)

Name Number of Carbons \mathrm{C}_{n}\mathrm{H}_{{2n-2}}
ethyne 2 \mathrm{C}_{2}\mathrm{H}_{{2\cdot 2-2}}=\mathrm{C}_{2}\mathrm{H}_{{2}}

Table 4.  Application of the formula \mathrm{C}_{n}\mathrm{H}_{{2n-2}} for alkynes.

Count the hydrogen atoms on each molecule in Figure 8 and confirm that the general formula works.

§ Questions and Activities

For this part of the lab use the Reference Tables.

  1. Draw all isomers of butyne in Figure 9. Name them carefully properly indicating the position of the triple bond.

  2. Complete Table 4 for all isomers of butyne.

  3. Do your predictions for the formula for isomers of butyne agree with your drawing?

  4. Build a molecular model of one isomer of butyne. Have the instructor inspect your model and initial here.

  5. What is the correct name for the improperly named molecule but-3-yne?

Figure 9.  Draw all isomers of butyne in the space above.

§ 3.3.1. Alykl Groups

Sometimes one carbon chain is a part of a larger molecule. For naming purposes start with the name of the alkane, drop the ”e” and add a ”yl” ending. Refer to Figure 10.

Figure 10.  The methyl and ethyl groups are examples of alkyl groups.

Look at the molecule in Figure 11.

Figure 11.  Methyl propane is a propane with a methyl group connected to the second carbon atom.

We begin by identifying the longest carbon chain which is three carbon atoms long, so the base name is propane. What remains is a methyl group connected to the second carbon, so the proper IUPAC name is 2-methylpropane. Because there is only one choice for the position of the methyl group we can say methylpropane without ambiguity.

§ Questions and Activities

For this part of the lab use the Reference Tables.

  1. What would be the correct name for the improperly named molecule 1-methyl propane?

§ 3.4. Halide Functional Groups

Halides refer to the Group 17 elements fluorine (\mathrm{F}), chlorine (\mathrm{Cl}), bromine (\mathrm{Br}) and iodine (\mathrm{I}); from Table R in the Reference Tables we see that these four halides have the prefixes fluoro, chloro, bromo and iodo, respectively. Some examples of molecules including halides appear in Figure 12.

Figure 12.  Tetrachloromethane and 2chlorobutane are examples of halide-containing hydrocarbons.

Fluorinated and chlorinated hydrocarbons have many uses. Many are excellent solvents for use in the chemistry laboratory and the chemical industry. They can be very useful as cleaners. Some have been used as fire retardants, and others have been used in compressors for refrigeration or air conditioning. Unfortunately we have learned that they are very bad for the ozone layer, and many are carcinogenic. As a result usage of these types of chemicals has been significantly reduced.

§ Questions and Activities

For this part of the lab use the Reference Tables.

  1. In the space allowed in Figure 13 draw the structure for chloroethane.

  2. Is it ambiguous to specify chloroethane rather than 1chloroethane?

  3. Build a molecular model of chloroethane. Have the instructor inspect your model and initial here.

 

 

Figure 13.  Draw chloroethane here.

§ 3.5. Alcohol Functional Groups

You have probably heard about alcohols without understanding their chemical significance. The simplest alcohol is methanol which is also called wood alcohol because it can be obtained from wood. Methanol is very poisonous, and methanol ingestion causes blindness. Ethanol is the alcohol that is available in alcoholic beverages. You may have isopropyl alcohol in your medicine cabinet to use as a disinfectant. What all alcohols have in common is an \mathrm{OH} group bonded to a carbon atom. See Figure 14.

Figure 14.  The alcohol functional group is an \mathrm{OH} connected to a carbon atom in some larger molecule. R is used to indicate the rest of the molecule in a generic manner. Ethanol is an example of an alcohol.

Ethanol is named as follows. The prefix from Table P for a two-carbon chain is “eth” to which we add the proper ending; eth+anol = ethanol. There is an older naming scheme where the same alcohol is called ethyl alcohol. Similarly methanol is sometimes called methyl alcohol. In fact the proper IUPAC name for isopropyl alcohol is propan-2-ol, but without ambiguity it is sometimes written 2-propanol. The reason for placing the number right next to the -ol ending is because it is a better scheme for more complex molecules that may have multiple functional groups.

§ Questions and Activities

For this part of the lab use the Reference Tables.

  1. In the space allowed in Figure 15 draw the structure for propan-1-ol.

  2. In the space allowed in Figure 16 draw the structure for propan-2-ol.

  3. What is the correct name for the improperly named molecule propan-3-ol?

  4. How many isomers are there for propanol with a single \mathrm{OH} functional group?

  5. Make a molecular model of propan-2-ol. Have the instructor inspect your model and initial here.

 

 

Figure 15.  Draw propan-1-ol here.

 

 

Figure 16.  Draw propan-2-ol here.

§ 3.6. Ether Functional Groups

The basic structure of an ether is shown in Figure 17.

Figure 17.  An ether has an oxygen atom bonded to two different carbon atoms. \mathrm{R}_{1} and \mathrm{R}_{2} represent two different groups of atoms.

An example of an ether appears in Figure 18.
In this case the \mathrm{R}_{1} and \mathrm{R}_{2} groups of Figure 17 are replaced by the ethyl and methyl alkyl groups as discussed in Section 3.3.1.

Figure 18.  Ethyl methyl ether is an oxygen atom bonded to one ethyl and one methyl group.

§ Questions and Activities

For this part of the lab use the Reference Tables.

  1. Draw the structure for diethyl ether in Figure 19.

  2. Draw the structure for dimethyl ether in Figure 20. (Think about the meaning of the prefix “di-”.)

 

 

Figure 19.  Draw the structure of diethyl ether.

 

 

Figure 20.  Draw the structure of dimethyl ether.

§ 3.7. Aldehyde Functional Groups

An aldehyde has an oxygen atom doubly bonded to a carbon atom at the end of a carbon chain. See Figure 21.

Figure 21.  An aldehyde has an oxygen doubly bonded to a carbon chain.

A carbon atom doubly bonded to an oxygen atom is known as a carbonyl group, and its placement at the end of a chain makes it an aldehyde.
To name an aldehyde begin with the name of the alkane with a carbon chain of the same length, drop the“e” at the end of the name and add “al”. For example, butane-e+al = butanal.

Probably you have heard of formaldehyde which is used to preserve dead tissue. The proper IUPAC name is methanal. Note that one never needs to specify the position of the aldehyde group because it is always at the end.

§ Questions and Activities

For this part of the lab use the Reference Tables.

  1. Draw the structure of methanal (formaldehyde) in the space allowed for Figure 22.

  2. Construct a molecular model of methanal (formaldehyde). Have your instructor inspect it and initial here.

 

 

Figure 22.  Draw the structure of methanal (formaldehyde) here.

§ 3.8. Ketone Functional Groups

The ketone functional group is similar to the aldehyde functional group except the double bonded oxygen atom is bonded to a carbon atom that is not at the end of the chain. See Figure 23.

Figure 23.  Propanone is an example of a ketone.

Recall that a carbon atom doubly bonded to an oxygen atom is known as a carbonyl group; its placement away from the end of a chain makes it a ketone.
Aldehydes and ketones are classified separately because, despite many similarities, some of their chemical properties are quite different. To name a ketone start with the name of the related alkane, drop the “e” and add “one”. For example, propane-e+one = propanone.

§ Questions and Activities

For this part of the lab use the Reference Tables.

  1. Draw the structure for 2-butanone in the space allowed for Figure 24.

  2. What is the correct name for the improperly named molecule 1-butanone?

  3. What is the correct name for the improperly named molecule 3-butanone?

 

 

Figure 24.  Draw 2-butanone in the space provided.

§ 3.9. Carboxyl Functional Groups (Organic Acids)

The carboxyl group has a carbon atom double-bonded to an oxygen atom and also bonded to an alcohol group. Do not confuse the carboxyl group with the carbonyl group. See Figure 25.

Figure 25.  The carboxyl group and two examples, methanoic acid and propanoic acid.

The carboxyl group always occurs at the end of a carbon chain because, with four bonds per carbon atom, there are simply not enough bonds for it to bond to two other carbon atoms. To name an organic acid start with the name of an alkane, drop the “e” and add “oic acid”. For example, propane-e+oic acid = propanoic acid. While a carboxyl group may look like the combination of an aldehyde and an alcohol, it introduces all new chemical behaviors.

Methanoic acid is also known as formic acid. The name derives from the Latin word formica because this chemical was first obtained by distilling a certain type of ant with a stinging bite. Ethanoic acid is more commonly known as acetic acid; vinegar is a primarily acetic acid and water.

§ Questions and Activities

For this part of the lab use the Reference Tables.

  1. Draw ethanoic acid (acetic acid) in the space provided for Figure 26.

  2. Create a molecular model of ethanoic acid. Have your instructor inspect it and initial here.

 

 

Figure 26.  Draw ethanoic (acetic) acid in the space provided.

§ 3.10. Esters

Do not confuse esters described in this section with ethers described in Section 3.6. The ester functional group is shown in Figure 27.

Figure 27.  The ester functional group.

Perhaps an ester is most easily understood from how they are synthesized in the chemistry laboratory. See Figure 28.

Figure 28.  An ester is formed by dehydration synthesis with an organic acid and an alcohol.

An ester is formed by dehydration synthesis with an organic acid and an alcohol. An alcohol and an organic acid combine to form an ester and water. An example of an ester is shown in Figure 29.

Figure 29.  Propyl acetate (propyl ethanoate) is an ester. Note that not all carbons have been explicitly drawn. A carbon atom is implied where lines intersect and no atom has been specified.

Propyl acetate (propyl ethanoate) is formed from 1-propanol and acetic (ethanoic) acid. The OH group from the organic acid combines with a hydrogen from the alcohol to form a molecule of \mathrm{H}_{2}\mathrm{O}, and the carbon from the organic acid connects to the oxygen from the alcohol. The result is like an ester with a carbonyl group attached to the oxygen atom.

§ Questions and Activities

For this part of the lab use the Reference Tables.

  1. In the space provided for Figure 30 draw the structure of ethyl acetate.

  2. In the space provided for Figure 31 draw the structure of methyl propanoate.

  3. Figure 28 shows the dehydration synthesis of an ester. Circle the atoms of the reactants that will become part of the \mathrm{H}_{2}\mathrm{O} molecule.

  4. Create a molecular model of ethyl acetate. Have your instructor inspect it an initial here.

 

 

Figure 30.  Draw ethyl acetate (ethanoate) in the space provided.

 

 

Figure 31.  Draw methyl propanoate in the space provided.

§ 3.11. Amine Functional Groups

The amine functional group introduces nitrogen into organic chemistry. See Figure 32.

Figure 32.  The amine functional group.

If all three groups, \mathrm{R}_{1}, \mathrm{R}_{2} and \mathrm{R}_{3}, are replaced with hydrogen atoms this is just ammonia, \mathrm{NH}_{3}. Oftentimes the hydrogen atoms are replaced with alkly groups.

§ Questions and Activities

For this part of the lab use the Reference Tables.

  1. Draw methyl amine in the space provided in Figure 33.

  2. Draw trimethyl amine in the space provided in Figure 34. (Think about the meaning of the prefix “tri-”.)

  3. Create a molecular model of methyl amine. Have your instructor inspect your model and initial here.

 

 

Figure 33.  Draw methyl amine in the space provided.

 

 

Figure 34.  Draw trimethyl amine in the space provided.

§ 3.12. Amides

The amide functional group is shown in Figure 35.

Figure 35.  The amide functional group has a carbon atom double-bonded to an oxygen atom and single-bonded to a nitrogen atom.

The amide functional group has a carbon atom double-bonded to an oxygen atom and single-bonded to a nitrogen atom. An amide is created by a dehydration synthesis with an organic acid and an amine. Notice that the amide functional group looks like an ester with a nitrogen in place of an oxygen. (Compare Figure 35 with Figure 27.) The dehydration synthesis of an amide is shown in Figure 36.

Figure 36.  The dehydration synthesis of an amide.

A hydrogen atom previously bonded to the nitrogen in the amine combines with \mathrm{OH} from the carboxyl group to form a molecule of \mathrm{H}_{2}\mathrm{O}. The result is a carbonyl group attached to a nitrogen.

Examples of amides are shown in Figure 37.

Figure 37.  Two examples of amide molecules.

N-methyl acetamide is formed from the dehydration synthesis of acetic acid with methyl amine. N-methyl propanamide is formed from the dehydration synthesis of methyl amine with propanoic acid. Amides are named as follows. Take the name of the organic acid and replace the “oic” ending with the “amide” ending. Any groups that were attached to the amine are listed out front with the ”N-” prefix to specify that they are attached to the nitrogen. Note that we could also have alkyl groups with numeric prefixes if they were connected to the primary carbon chain from the organic acid.

§ Questions and Activities

For this part of the lab use the Reference Tables.

  1. In the space allowed for Figure 38 draw the structure of methanamide.

  2. In the space allowed for Figure 39 draw the structure of N-methyl propanamide.

  3. In Figure 36 circle the atoms from the organic acid and the amine that will become \mathrm{H}_{2}\mathrm{O}.

  4. Create a molecular model of N-methyl propanamide. Have your instructor inspect it and initial here.

 

 

Figure 38.  Draw the structure of methanamide.

 

 

Figure 39.  Draw the structure of N-methyl propanamide.

§ 4. Amino Acids

This is a bonus section. It connects with things that were learned in Living Environment.
Amino acids are the the building blocks of proteins. Proteins are chains of amino acids connected by amide bonds. See Figure 40.

Figure 40.  Dipeptide synthesis through the formation of a peptide (amide) bond by dehydration synthesis.

An amino acid is a carbon atom bonded to an amine, a carboxyl group and some third group that we sometimes indicate as \mathrm{R}. In Figure 40 two amino acids are distinguished by un-named groups \mathrm{R}_{1} and \mathrm{R}_{2}. Through dehydration synthesis an amide bond is formed. In the context of amino acids this bond is called a peptide bond, and two linked amino acids is called a dipeptide.

Again look at Figure 40. Notice how each amino acid has an amine group at one end and a carboxyl group at the other. Then observe that the dipeptide has the same feautures, an amine group at one end and a carboxyl group at the other end. It is therefore possible to connect amino acids at either end, and there is in no principle a limit to the length of the polypeptide chain that results. In Living Environment you learned how DNA sequences code for polypeptide sequences that make up the protein structures of organisms.

§ Questions and Activities

For this part of the lab use the Reference Tables.

  1. Circle the atoms in Figure 40 that will become an \mathrm{H}_{2}\mathrm{O} molecule.

  2. Extra Credit: Create a molecular model of a dipeptide. Use “metal atoms” to indicate the \mathrm{R} groups. Have your instructor inspect the model and initial here.

  3. Given time we will attach all of the dipeptides of the class to create a short polypeptide.

 

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