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ORGANIC CHEMISTRY: STRUCTURE AND NOMENCLATURE

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Structure and Nomenclature

The structure and formula of functional groups consist of a fixed number of elements and a specific chemical bonding . This could be single ,double or triple bond. Some common names and categories of functional groups in organic chemistry are listed below;

Functional groups

These are atoms or group of atoms in a molecule or compound that determines the way the molecule reacts with other molecules or atoms. There are several functional groups and their formula. Examples include alkanes RCH-, Alkanols RH2C-OH, Aldehydes RHC=O, Ketones R2C=O, Carboxylic acids RCOOH, Amides RCONH2, Esters RCOOR and more such as nitro R-NO2, amines RCNH2 etc.

The R group is represents an aliphatic group or an alkyl group. Examples includes a  Methyl group -CH3 from parent name ; methane CH4. Therefore, methyl chloride has formula of CH3Cl. Similar examples are Ethyl groups CH3CH2– , Propyl groups CH3CH2CH2 -, Butyl groups CH3CH2CH2CH2 – and Pentyl groups  CH3CH2CH2CH2CH2–

Alkanes:

The name ‘ane‘ is used to name all alkanes. General formula is CnH2n+2 where n is the number of carbon atoms in the compound. This is also the formula for saturated hydrocarbons. Examples include; Methane CH4, Ethane C2CH6 , Propane C3H8, Butane C4H10, Pentane C5H12, Hexane C6H14, Heptane C7H16, Octane C8H18, Nonane C9H20 , Decane C10H22, Undecane C11H24, Dodecane C12H26

Basics for naming alkanes 1.

Basics for naming alkanes 2.

Naming complex alkanes

You can get more information about structure and nomenclature by watching this video of structural isomerism of butanes and hexane.: click here

Alkenes

These have formula of CnH2n : These are unsaturated hydrocarbons with at one carbon-carbon double bond. The name of these compounds end with suffix ‘ene’. Examples include; Ethene C2H4, Propene C3H6 , Butene C4H8 , Pentene C5H10, Hexene C6H12, Heptene C7H14 , Octene C8H16 , Nonene C9H18

Alkynes

The formula of alkynes is given as CnH2n-2 . They are unsaturated hydrocarbons with at least one carbon-carbon triple bond. The suffix ‘yne’ replaces the ending of the ‘ane’ of the parent alkane. Examples include Ethyne C2H2, Propyne C3H4 , Butyne C4H6 , Pentyne C5H8, Hexyne C6H10, Heptyne C7H12 , Octyne C8H14 , Nonyne C9H16

You can get extra information about alkanes, alkenes and alkynes and other functional groups by watching the video on structural isomerism.

More detailed information on functional groups will be discussed later.

FUNCTIONAL GROUPS AND CHEMICAL NOMENCLATURE:

Besides alkanes, alkenes and alkynes, the presence of heteroatoms will introduce the rest of the functional groups in organic chemistry. Common heteroatoms are oxygen, nitrogen, halogens, sulfur and phosphorus.

IUPAC rank the functional groups with respect to oxidation and several other factors such including;

  1. Oxidation (oxidation number of carbon atom in group or number of oxygens, least number of hydrogens in the functional group.
  2. Acidity, resonance stabilization of the group or conjugate base or carbanion or carbocation, ease of formation of carbanion from alpha carbon; ease of undergoing substitutions and elimination reactions (derivatization).
  3. Number of oxygen atoms (or least number of non-protic hydrogens); presence of electron withdrawing groups; hybridization (sp>sp2>sp3);
  4. Stability of group or carbanion or carbocation formed.

These above factors will rank the functional groups in order of importance in determining the suffix name = [last name] of an organic compound.

Carboxylic acids (-O=C-OH) > Sulfonic acids (CSO3H)> carboxylic acid anhydrides(-H2CO=C-O-C=OCH2-)> esters(-O=COCH3) > acyl halides(O=CCl)

Amides (O=CNH2>, nitriles(-C=N)> aldehydes (HC=O)> ketones(-CH2C=OCH3)

Alcohols(-C-OH) >Mercaptan (-C-SH)>amines(C-NH2) >alkynes(-C=C-)>alkenes(-CH=CH-)

Alkanes CH3-CH2CH3) >

> alkyl halides (-H2C-Cl)>ethers(-H2C-O-CH2-) >azides or azido alkanes -H2C-N3> nitro groups(-H2C-NO2) [ These will occur as prefixes since they are ranked lower than alkanes]

RANKING ORDER 

Ranking order of common functional groups that determines the last parent name of organic compounds: Highest determinant to least determinant.

Please watch all the videos on naming of alkanes [1, 2 and 3] and also structural isomerism to familiarize yourself on how to name organic compounds before you proceed to other functional groups.

Rules for naming:

  1. Start the with the name of the number of carbons as in alkanes but replace the ending “ane” with last name of the most important functional group in the compound. [e.g. Write the name of CH3COOH. The line structure is given below,
CH3COOH = Ethanoic acid (aka acetic acid). This name is derived from 2 carbon alkane = ethane and the COOH group carboxylic acid = ‘oic acid‘
  • CH3CH2OH naming is simple: [2 carbons =parent name is ethane, Functional group present =OH alcohol implies last name is alkanol = ol. Therefore, name of compound is Ethanol. CH3CH2SH name is also derived from 2 carbon parent ethane and functional group present as Sulfur = thiol or mercaptan therefore name is Ethyl mercaptan or Ethanethiol. CH3CH2-NO2 name is derived from 2 carbon parent name ethane, and functional group nitro NO2– is below alkane ranking so can only name it as a prefix “nitro”, therefore the name of the compound is nitroethane.
  • Numbering is similar to alkanes and every other functional group is given a number at the carbon where it begins.
  • Use dashes to separate numbers from names. [e.g. [ e.g BrCH2COOH = 2-Bromoethanoic acid, CH2=CHCOOH = 2-Propenoic acid], BrCH=CHCOOH is called 3-bromo-2-propenoic acid, BrCH=CH-C=C-COOH [this has 5 carbons in longest chain implies pentanoic acid], numbering and naming: Carbon#2 alkyne= yne , Carbon #4 alkene= ene ,number 5 has Bromine=bromo. Therefore, name will be 5-Bromopent-4-en-2-ynoic acid
  • Use comas to separate numbers that represent the same substituent attached multiple times to carbons in the compound. Examples of this is shown in the video for naming alkanes.
  • The carbon of highest ranked functional group in the compound should be included in counting the continuous carbon chain that determines the name of the compound. This applies even if it is not the longest chain. However, check to see if you can get the smallest number as possible for the main functional group and the other functional groups and substituents as well as the overall sum of the numbers used in the numbering. This is very important especially when the functional groups occur on the middle carbons. e.g., Write the name of the compound.
  • CH3C=OCH3 [3 carbons =parent name is propane; functional group present is ketone=alkanone implies last name is “one“. Therefore, name of compound is propanone, however functional group C=O is at number # 2, implies proper name is 2-propanone or Propan-2-one, CH3C=OCH2CH(CH3)CH2COOH This contains a carboxylic acid functional group COOH (most important) so naming should end oic acid. The longest chain containing the COOH group is 6 carbons= hexanoic acid. Carbon number 3 is bearing a methyl substituent (CH3) and carbon number 5 is having a ketone C=O functional group implies first name use for ketone =oxo. Therefore, the name will be 3-methyl-5-oxohexanoic acid. The other example is writing the name of CH3C=OCH2CH=CHC=CH. The line structure is drawn below;
This can be named as in two different ways and then use the rule of SMALLEST integer summation to determine the correct answer. ; First, start the count from left to right 7 carbons = heptane; highest ranked functional group present = ketone=heptanone parent name; Positions =carbon number 2 is ketone implies 2-heptanone; position 4 is alkene = 4-ene and position 6 is alkyne =6-yne. Therefore, name will be 4-hepten-6-yn-2-one. The sum of the number [4+6+2=12]. However, naming from right to left will be; parent name =6-heptanone; Carbons 1 is alkyne=1-yne, and carbon 3 is alkene= 3-ene. Therefore, name will be 3-hepten-1-yn-6-one. The sum of numbers [3+1+6=10]. The name with the smallest sum of numbers is correct which is 3-hepten-1-yn-6-one
  • The other example is finding the name of the compound shown below;
The name of this compound is tricky in that, the main functional group, alcohol OH is not in the longest continuous carbon chain = cyclohexane. Therefore, cyclohexyl group is named as a substituent and the longest continuous chain contains the OH group is 3 carbons= propanol. The OH is on carbon number 2= 2-propanol parent name. The cyclohexyl group is attached to carbon number 1 when counting from left to right. Therefore, the name of the compound is 1-cyclohexyl-2-propanol. Try naming by counting from right to left will give the wrong answer according to the smallest number summation rule. [SMALLEST NUMBER SUMMATION RULE].

OTHER RULES

  1. If the number is 1, you can ignore number one in most cases. e.g., 1-ethanol or Ethan-1-ol is usually called Ethanol.
  2. Functional group only takes the last name if it ranks the highest in the compound otherwise only their first names are used. e.g., Ketone is alkanone or last name is “one”. However, if it is not the highest ranked then the first name is “oxo“. Alcohol OH group last name is alkanol =”ol”, but first name is hydroxy if it is not the highest ranked functional group in the compound. e.g., HOCH2CH2CH=O; [3 Carbon = parent name is propane, there are 2 functional groups Aldehyde CH=O alkanal = “al” and also there is alcohol OH group. However, aldehyde is more oxidized than alcohol, so it ranks higher. so, the name of the compound will be 3-hydroxypropanal]. HSCH2CH2OH is called 2-mercaptoethanol because the –OH ranks higher than –SH
  3. Besides the highest ranked functional group, the rest of the names are written in alphabetical order, but numbering can be different. e.g., alkene =ene comes before alkyne =yne but alkyne takes the smallest number when only both are present except in a symmetrical compound when alkene takes the smallest number.
The compound has 7 carbons in longest continuous chain = heptane parent. There are both alkene and alkyne at carbon 1 and 6. Compound is not symmetrical, so alkyne takes smallest number 1 and also the last name = heptyne. There is methyl group on carbon 6. Therefore, name of 6-methyl-6-hepten-1-yne
The compound has 6 carbons in longest continuous chain = hexane parent. There are both alkene and alkyne at carbon 1 and 5. Compound is symmetrical, so alkene takes smallest number but the last name is still alkyne = hexyne. There is methyl group on carbon 6. Therefore, name of 1-hexen-5-yne
The compound is an ester containing. an alkene. The is a methyl group on the right side so the name starts with methyl. The other side has 4 continuous carbon chain = butane parent = butanoate for an ester. The carbon 2 on the left side has alkene or double bond =ene. There is a methyl group on carbon 3 at the left side.
Therefore, the name will be Methyl 3-methyl-2-butenoate.
Compound has a Methyl group on the right side =naming starts with methyl. The left side has 2 longest continuous carbon chain and one methoxy group substituent on carbon 2. Therefore, the name of the compound is Methyl 2-methoxyethanoate.
This is an ether=alkoxy alkane. The longest continuous carbon chain takes the parent name. This is 6 carbons at the right of the oxygen= hexane. The left side of the oxygen can be named as first name. You can choose the longest continuous carbon chain at the left to be 3 carbons= propane parent= propoxy with tert-butyl substituent on carbon 2 counting from the oxygen. This will give the name as Propoxy-(2-tert-butyl)hexane. The other name which is very IUPAC is to ignore the tert-butyl and count the longest continuous carbon on the left to be 4 carbons from the oxygen=butane=Butoxy with methyl substituents on carbon 2 and then two methyl groups on carbon 3. This will give the name as 1–(2,3,3-trimethylbutoxy)hexane. Both names are correct, but the latter is the IUPAC name.
This can be named in three different ways. First the longest continuous carbon chain is on the left side = 6 carbons= hexane. The count starts at the oxygen, so Bromine is on carbon 6=6-Bromo. Now the right side of the oxygen gives 3 different ways to name. First, you can take the whole right side as a tert-butyl group so the name will be 6-bromo-1-tert-Butoxyhexane. The other name which is more IUPAC is to count the longest continuous chain on the right side from the oxygen as 3 carbons = propane=propoxy attached at carbon 2 to the oxygen =2-propoxy There is a methyl substituent also on carbon 2= 2-methyl-2-propoxy. Therefore, the name will be 6-bromo-1-[2-propoxy(2-methyl)]hexane or 6-bromo-1-[2-methyl-2-propoxy]hexane. The other best IUPAC name is imagining the compound as a halo alkane with an alkoxy substituent at carbon number 6. Therefore, count the longest chain on the right as 3 carbons=propane=propoxy and the carbon 2 attached to the oxygen = 2-propoxy. The methyl group is also attached at carbon 2. which gives a 2-methyl-2-propoxy. Therefore, the name will be 1-bromo-6-[2-methyl-2-propoxy)]hexane. The last name is the most preferred by IUPAC name because halo alkanes are ranked higher above ethers so the bromine should take carbon number 1 instead of 6. Therefore, the IUPAC name again will be 1-bromo-6-[2-methyl-2-propoxy)]hexane.
Clue: The alkene double bond is higher in rank than the chlorine. Start counting from the right side so that alkene gets a smaller number. The stereochemistry is E at carbon 2 alkene and S at carbon 4 Chlorine. Therefore, the name is (E,4S)-4-chloropent-2-ene.
This is an ester. The acid part has C=O always takes the last name, and, in this case, it has 2 carbons = acetate or ethanoate. Now let’s name the alcohol side. It has 6 carbons in the longest continuous chain in the alcohol side and is attached to the oxygen at carbon3 =3-oxyl. There is an alkyne and an alkene. Let’s count from right to left to give alkyne smallest number carbon1. The alkene C=C will be at carbon 4. There is a methyl substituent at carbon 4. The stereochemistry at the oxygen on carbon 3 is S because the alkene in this case takes precedence over the alkyne because it is bonded to more carbons than the alkyne C-C bonds if you split them to check. The stereochemistry of the alkene is E at carbon 4 to 5. The IUPAC name will be [(E,3S)-4-methyl-4-hexen-1-yn-3-yl]ethanoate or [(E,3S)-4-methyl-4-hexen-1-yn-3-yl]acetate
Counting the carbon at the oxygen as carbon 1 gives the alkene C=C number 1. This is an alkene with alkoxy group oxygen bonded to carbon 1. Longest chain containing C=C is 4 = 1-butene. The longest chain on the right side of the oxygen is 4 carbons = butane and is bonded at carbon 2 to the oxygen = 2-butoxy. There are two methyl substituents on carbon 3 = dimethyl. The stereochemistry of the alkene is E and that at carbon 2 is R. Therefore, the IUPAC name will be [(E,2R)-3,3-dimethylbut-2-oxy]but-1-ene

OTHER EXAMPLES :

The highest ranked functional group present in the compound is C=O ketone= alkanone =one located on carbon 1(shortest route count from left to right). The benzene ring aka phenyl group is also attached to carbon 1.

1-phenyl-1-propanone or 1-phenylpropan-1-one or 1-phenylpropanone

The highest ranked functional group present in the compound is C=O ketone= alkanone =one located on carbon 2 (shortest route count from right to left). The benzene ring aka phenyl group is attached to carbon 1.

1-phenyl-2-propanone or 1-phenylpropan-2-one

The first compound is benzaldehyde and the second compound is called cyclohexanone.

Practice naming these compounds below

Video of structure and nomenclature of alkanes: click here

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