Organic Chemistry IUPAC Nomenclature Demystified With A Simple Puzzle Piece Approach

IUPAC Nomenclature Demystified with a Simple Puzzle-Piece Approach, by Leah Fisch

Note from James: This is a guest post by Leah Fisch of Leah4Sci.com , an online resource for learning organic chemistry, MCAT preparation, and other science topics . This is an epic, comprehensive post on  organic chemistry IUPAC nomenclature. You might want to bookmark this page for future reference, and be sure to visit Leah’s Youtube Channel for more videos on nomenclature as well as other organic chemistry topics. Leah also tutors MCAT and organic chemistry. Her tutoring page is here. 

Table of Contents

1. Why Nomenclature Is So Important For Organic Chemistry Students
2. The Puzzle Piece Approach To Naming Organic Compounds
3. A Word About Line (Skeletal)  Structure Before We Begin Naming
4. Highlighter Trick For Identifying The Parent Chain
5. Parent Chain Length = The Molecule’s First Name
6. Ane, Ene, Yne = The Molecule’s Last Name
7. Numbering The Pi Bonds
8. Substituents Arise When The Highlighter Trick Fails On The Branches
9. If It Sticks Out, It’s A Substituent
10. How To Indicate Multiple Substituents
11. Alphabetize Multiple Substituent Types
12. Separating Numbers and Letters
13. Substituents WITH Substituents – What Happens?
14. ‘R’ Is The Rest of The Molecule
15. Functional  Groups As The Molecule’s Last Name
16. Putting Together  The Pieces: A Practice Example

1. Why nomenclature is so important for organic chemistry students

As an organic chemistry student, organic chemistry IUPAC nomenclature will be one of the first topics you encounter. But just because it comes first, doesn’t mean that you can simply tackle it and move on. Learning how to name organic compounds is the foundation upon which your entire organic chemistry knowledge will be based.

Much of organic chemistry is about reactions, mechanisms and products. But you will be asked about nomenclature every step of the way.

• Name the product of this reaction
• React  ‘molecule name’ with ‘other molecule name’
• Draw a complex multiple-functional-group product

Knowing how important your naming skills are to this course, you need to come up with a simple yet logical approach to naming even the most complex organic compound while taking into account all the different molecular prefixes, chain types, substituents, functional groups and more.

2. The Puzzle Piece Approach to Naming Organic Compounds

If I told you that I met a woman with a 4-part name and asked YOU to put the parts in order, I bet you’d get it on the first attempt.

Try it

• Jane
• Jr
• Doe
• Miss

Does your attempt look like this: Miss Jane Doe Jr ?

How did you get it right on the first shot?

I’m guessing it’s because you have an inherent understanding of the human naming system.

We all have a first and last name.

Some people have a prefix such as Miss, Doctor or Sir.

And some people have a suffix such as Jr, Sr, or III

Miss Jane Doe Jr breaks down as follows:

• Prefix = Miss
• First Name = Jane
• Last Name = Doe
• Suffix = Jr

Organic Compounds Follow a Similar Naming Pattern

• Prefix = substituent
• First Name = carbon chain number
• Last Name = type of chain
• Suffix = highest priority functional group

And so your simple approach is as follows: When you come across a complex molecule with multiple components to name, identify each one individually. Put its name on a list then view the list items as a puzzle that must be put together in a logical sequence.

3. A Word About Line (Skeletal) Structure Before We Begin Naming

When learning and practicing nomenclature you will find yourself drawing molecules over and over again. While Lewis structure may appear easier to read at first, you may put your sanity at risk having to draw out hundreds of C, H, and O atoms.

Instead, I recommend that you get used to drawing in line structure – also called skeletal structure or bond-line notation. This method is both faster to draw and easier to read. This entire tutorial will be illustrated in line structure. If you are not yet familiar with this method then I urge you to study the short video below.

4. The Highlighter Trick for Identifying the Parent Chain

Let’s refer back to Miss Jane Doe Jr. While she has four parts to her name, you can easily get away with just referring to her as Jane Doe. This is her ‘core’ name or her ‘parent name’.

The core skeleton of an organic compound is called its parent chain. This refers to the simple skeleton or backbone of the molecule, upon which all the functional groups and substituents are attached.

This is the first component to name and identify.

The parent chain is the longest continuing carbon chain in a molecule (there are some exceptions). Sometimes the parent chain will be written in a simple manner and sometimes the chain will wind and twist.

But as long as the carbons are connected, one to the next, to the next, this is considered the parent chain.

The highlighter trick is a trick to help you determine if a chain is continuous or not.

Place your highlighter at the very start of the molecule. Without lifting the highlighter, trace over every connected carbon. If you have to lift the highlighter to reach another carbon, then it’s not part of the parent chain.

5. Parent Chain Length – The Molecule’s First Name

Count the number of carbon atoms after identifying and highlighting your parent chain. I recommending actually numbering your molecule. This is a good habit to develop NOW as it will provide a reference point later on when you have to name multiple substituents and functional groups.

You will assign a first name to your molecule based on the number of carbons present in the parent chain as follows:

1. meth
2. eth
3. prop
4. but
5. pent
6. hex
7. hept
8. oct
9. non
10. dec
    You will definitely be required to memorize 1-10 above. Some professors may require you to memorize first names for carbons 11-20 as follows:
11. undec
12. dodec
13. tridec
14. tetradec
15. pentadec
16. hexadec
17. heptadec
18. octadec
19. nonadec
20. icosa

6. Ane, Ene, or Yne – The Molecule’s Last Name

Now that you have a first name, you need a last name too. The last name comes from the saturation of the parent chain, specifically the presence and location of double and triple bonds.

These molecules fall into 3 categories:

1. Alkane
2. Alkene
3. Alkyne

An alkane is a saturated molecule which does not contain any double (pi) bonds.

An alkane has a last name of ‘ane‘

An Alkene is partially unsaturated and contains a least one double or pi bonds.

An alkene has a last name of ‘ene‘

An Alkyne is the most unsaturated and contains a triple bond. This is 2 pi or double bonds between the same 2 carbon atoms.

An alkyne has the last name of ‘yne‘

(This method applies to the standard orgo 1 / orgo 2 curriculum containing mostly hydrocarbons and alkyl halides)

7. Numbering the Pi Ponds

When numbering a molecule with just  Pi  bonds, your goal is 2-fold:

1. Number the chain so that you have a total lowest set of numbers.
2. Designate the pi bond number as the lower of the 2 numbers to hit the pi bond.

Let’s apply these rules by naming the 3 compounds pictured below:

Molecule A:

This molecule does not contain any pi bonds. We can number from the right or left for a total of 5 carbons.

• 5 carbons in the parent chain for a first name of pent
• fully saturated (no pi) for a last name of ane

Molecule A is named pentane.

Molecule B:

Molecule B contains a single pi bond in the middle of the chain. We have the option of numbering from the right or the left given that the pi bond will be between carbon 3 or 4 from both directions. I’ve designated this in red and blue to help you see this clearly

In both scenarios the pi bond occurs between C3 and C4. The pi bond is numbered as ‘3-ene’ given that carbon 3 is the lower of the two numbers containing the double bond.

• Six carbons in the parent chain for a first name of hex
• Pi bond on carbon 3 for a last name of 3-ene

There are two ways to put this name together. Most professors will accept both. Ask your professor which method is preferred to ensure that you don’t lose any quiz/exam points.

Molecule B = hex-3-ene or 3-hexene

Notice that for the second version I pulled the number 3 to the front of the molecule. I like this method since it sounds nicer and flows better.

Molecule C:

Molecule C is a terminal alkyne meaning it has a triple bond at the very start of the molecule. Since the alkyne does not have any substituents, the end of the chain with the alkyne becomes number 1.

• Four carbons in the parent chain for a first name of but
  (Counting alkyne carbons can be tricky, I’ve added red dots to help you identify the 4 carbons)
• Alkyne on the first carbon for a last name of 1-yne

Putting the name together Molecule C = but-1-yne or 1-butyne

8. Substituents Arise When the Highlighter Trick Fails on the Branches

If only nomenclature ended as above with just a first and last name. But alas, simple doesn’t really exist in organic chemistry. So let’s build on this foundation and add puzzle piece components to our so far logical approach.

After highlighting your parent chain, you may find yourself staring at a carbon or two that is not yet colored. If you have to lift your highlighter to color these atoms, then they are not part of your parent chain.

9. If it Sticks Out – It’s a Substituent

These atoms or groups of atoms are considered your substituents, and represent the prefix ‘Miss‘ for Miss Jane Doe. The most common simple substituents include halogens and short carbon chains.

To Name a Halogen Substituent

To name a halogen substituent such as F, Cl, Br, I – drop the ending of the halogen name, and replace with ‘ide’.

Thus halogen substituents are named as follows:

• F = fluoride
• Cl = chloride
• Br = bromide
• I = iodide

Full name: 2-bromo pentane

Naming Simple Alkyl Substituents

Simple carbon branches are named similar to carbon parent chains.

• Count the carbon atoms and apply the same designation used above
• Use the ending ‘yl’ to imply that this is a substituent

For example, a 2-carbon substituent is named as follows:

2 carbons = eth

substituent ending = yl

Substituent name = ethyl

Full name: 3-ethyl pentane

10. Indicating Multiple Substituents

When more than one of the same substituent occurs, you have to use a new prefix to designate how many are present as follows:

1. no prefix needed, self understood
2. di
3. tri
4. tetra
5. penta

(You will likely encounter a max of five identical substituents in organic chemistry)

11. Alphabetize Multiple Substituent Types

Panic usually sets in when multiple types of substituents occur on the same molecule.

Don’t panic!

And certainly don’t try to name the entire compound in one shot.

Instead, write out your puzzle pieces one at a time. In my Organic Chemistry IUPAC Naming videos  you will notice that I mark off every component as I address it, by highlighting chains or circling substituents.

Let’s apply this approach to a simple multi-substituted compound pictured here. Then follow the puzzle piece approach as follows:

1. Highlight the parent chain
2. Number from the left for a total lowest set of numbers
3. Make a list on the side of the molecule with all your puzzle piece components (see image below)
   • eight carbons in parent chain for a first name of oct
   • double bond on second carbon for a last name of 2-ene
   • 2 single-carbon substituents on C2 and C4 for 2,4-dimethyl
   • 2-carbon substituent on carbon 5 for a prefix of 5-ethyl

Note on 2,4-dimethyl

Notice that there are two indications of the fact that there are two methyl groups present:

‘di’ indicates that there are 2 groups.

2,4 indicates the carbon atom where each methyl group occurs.

Now that we have a simple list of substituents – let’s put it all together. We have no functional group (last name) and so we follow the pattern of

prefix – first name – last name

But we have a problem.  There are two sets (not one)  of substituents present.

When faced with more than one type of substituent, order them alphabetically.

While it appears that dimethyl should precede ethyl, (d before e)  it’s actually the other way around.

The ‘di’ in dimethyl is an adjective and is not counted for alphabetical order.

Instead we look at the ‘m’ in methyl and ‘e’ in ethyl. Since ‘e’ comes before ‘m’ ethyl comes before dimethyl.

This also applies ‘tri’, ‘tetra’, etc.

The prefix ‘iso’ is an exception to this rule and will count as ‘i’ when considering alphabetical order.

Remember that with pi bonds you have the option of pulling the pi-bond number before the parent or first name.

This gives us two correct answers:

• 5-ethyl-2,4-dimethyloct-2-ene

• 5-ethyl-2,4-dimethyl-2-octene

I personally think the second version flows better but be sure to find out which version YOUR professor prefers.

12. Separating Numbers And Letters

Two more quick rules on the above:

1. Use commas between two numbers.
2. Use dashes between a number and letter regardless of which comes first.

13. But What Happens When a Substituent Has Its Own Substituent?

Now that you’re comfortable naming substituents, how do you name a molecule that has a substituent ON ITS SUBSTITUENT?

In other words, how do you name a branched branch?

The bad news: this process is tedious.

The good news: There is an acceptable shortcut.

You are more likely to be tested on the acceptable shortcut and so I won’t go into the tedious method here. However you can catch the complete explanation and correlation on my branched chain substituent video below:

Who Doesn’t Love a Shortcut?

There are 4 very common branched substituents that you will see again and again in your organic chemistry course. Since these branches are isomers of straight-chain substituents, they will be named as an isomer of the substituent they represent.

14. ‘R’ is the Rest of the Molecule

When you see ‘R’ anywhere on your molecule, recognize that this represents the Rest of the molecule. However, to keep things simple, and given that we are not looking at that portion of the molecule, just cut it all out and draw ‘R’ in it’s place. For the purpose of branched substituents, ‘R’ will represent the invisible parent chain.

Methyl and ethyl substituents are short substituents and can have no branched isomers.

A propyl substituent has a single isomer as pictured.

Propyl is a 3-carbon substituent. When connected in sequence (in a line) we simply call it propyl, however, when connected to the parent chain by the second instead of the first carbon, it gets the name ‘isopropyl’.

Iso is a group that you will see again later so recognize that an ‘iso-tail‘ is like a mermaid’s tail or fork in the road.

A butyl substituent has four carbons in a row. With more carbons we get more isomer opportunities, in fact, butyl has a total of four isomers as follows:

• Butyl has all four carbons in a row, attached to the parent by the first carbon.
• Secbutyl or 1-methylpropyl all four carbons still in a row, but secbutyl is attached to the parent by the ‘second’ or secondary carbon
• Isobutyl or 2-methylpropyl has a forked or ‘iso-tail’ on a 3-carbon substituent chain.
• Tertbutyl or 1,1-dimethylethyl is unique in that it has 2 methyl branches coming off the first carbon in a 2-carbon chain.

15. Functional Groups As The Molecule’s Last Name

And finally we have our last name. Functional groups come in many forms, from the alcohol OH groups to the carboxyl CO2H. When faced with a single functional group it becomes the last name of the molecule. When faced with more than one functional group you simply choose the group with the highest priority as the last night.

Visit This Table Of Functional Group Priorities for a quick review on functional group priority and appropriate last names.

16. Putting It All Together: A Practice Example

But let’s try a quick example. Here we have a 5-carbon chain with a CH3  functional group and CHO at the end.

We break this down as follows:

• 5 carbons in the parent chain for a first name of pent
• Only single bonds for a last name of ‘ane’
• Functional group on the right so we start numbering at the CHO
• CH₃ on carbon-4 for a prefix of ‘4-methyl’
• Aldehyde on the first carbon for a last name of ‘al’

Note that terminal functional groups such as carboxylic acid, aldehydes and more are implied to be on the first carbon and thus requires no numerical designation.

In putting the name together we follow the format of prefix -first name – last name – suffix

One final adjustment. Since ‘al’ starts with a vowel and ‘ane’ ends in a vowel, we drop the ‘e’ in ‘ane’ allowing the name to flow better for a final name of 4-methylpentanal

For even more organic chemistry IUPAC nomenclature tutorials, visit my website Leah4sci.com/naming for my complete 21 organic chemistry nomenclature video series taking you through the basics all the way to individual functional groups.

Thank you to Leah for writing this epic post about Organic Chemistry IUPAC Nomenclature! You can also follow Leah on Twitter at @Leah4Sci