Chapter 1: Nomenclature

Imagine you are in Tokyo and you need to mail a letter to someone in Buenos Aires. You do not speak Japanese or Spanish, but it does not matter - the postal system uses a universal addressing format that any postal worker on earth can decode. City, street, number. That is exactly what the IUPAC naming system does for organic chemistry. It gives every molecule a unique, unambiguous name that any chemist in any country can read and instantly draw the correct structure.

Before IUPAC naming existed, chemists used “common names” - names that described where a compound came from or how it smelled. Formic acid was named after ants (formica in Latin). Acetic acid came from vinegar (acetum). Butyric acid got its name from rancid butter (butyrum). These names are colorful, but they tell you absolutely nothing about the molecule’s structure. If someone tells you a compound is called “cadaverine,” you know it smells terrible, but you have no idea how many carbons it has or what functional groups are present.

IUPAC naming solves this problem. Every piece of the name encodes structural information. Once you learn the code, you can read any IUPAC name and build the molecule in your mind.

The Three Parts of Every IUPAC Name

Every IUPAC name is built from three components, and they map perfectly to a street address:

1. The parent chain (the “city”) - This is the longest continuous carbon chain in the molecule. It determines the root of the name. A four-carbon chain gives the root “but-.” A six-carbon chain gives “hex-.” The parent chain tells you the size of the backbone.

2. The suffix (the “street”) - This tells you the highest-priority functional group. An alkane gets “-ane.” An alcohol gets “-ol.” A carboxylic acid gets “-oic acid.” The suffix is the most important part because it tells you the molecule’s primary chemical identity.

3. The prefixes and locants (the “house numbers”) - These tell you what else is attached to the parent chain and exactly where. “2-methyl” means a methyl group (-CH3) is attached at carbon 2. “3-bromo” means a bromine atom sits at carbon 3. Locant numbers pin every substituent to a specific position.

The IUPAC Naming Algorithm

Here is the step-by-step process for naming any organic molecule. You will learn each step in detail in the sections that follow, but having the full roadmap now will help you see how the pieces fit together.

Step 1: Identify the longest continuous carbon chain. This becomes the parent chain and determines the root name (meth-, eth-, prop-, but-, pent-, hex-, etc.).

Step 2: Identify the highest-priority functional group. This determines the suffix (-ane, -ol, -al, -one, -oic acid, etc.).

Step 3: Number the chain. Start numbering from the end that gives the principal functional group the lowest possible locant.

Step 4: Name and number each substituent. Identify all branches and additional functional groups that are not the principal group. Assign each one a locant number.

Step 5: Assemble the name. List substituents alphabetically as prefixes, followed by the parent chain root and suffix. Separate numbers from letters with hyphens. Separate numbers from numbers with commas.

Putting It Together - A Quick Example

Consider a five-carbon chain with a methyl group at carbon 3 and no functional groups beyond single bonds.

• Step 1: Longest chain = 5 carbons = “pent-”
• Step 2: Only single bonds = suffix “-ane”
• Step 3: The chain has a methyl at position 3 either way you number it (it is in the middle), so numbering does not change anything here
• Step 4: One methyl substituent at carbon 3 = “3-methyl”
• Step 5: Assemble = “3-methylpentane”

That name tells any chemist: draw a five-carbon chain, attach a -CH3 at carbon 3, and fill everything else with hydrogens. Done.

Common Naming Pitfalls on the MCAT

Pitfall 1: Picking the wrong parent chain. Students often pick the chain drawn horizontally in a structural formula, but the longest chain may bend or zigzag through the drawing. Always trace every possible path to find the longest continuous chain.

Pitfall 2: Numbering from the wrong end. The principal functional group must receive the lowest possible locant. If you have an alcohol at carbon 2 or carbon 4, you number so it ends up at 2, not 4.

Pitfall 3: Forgetting alphabetical order for substituents. When multiple substituents are present, they are listed alphabetically in the name. Ethyl comes before methyl. Bromo comes before chloro. The multiplying prefixes (di-, tri-, tetra-) are NOT considered when alphabetizing. “Dimethyl” is alphabetized under “m,” not “d.”

Pitfall 4: Confusing hyphens and commas. Hyphens separate numbers from letters (2-methyl). Commas separate numbers from numbers (2,3-dimethyl). Getting this wrong does not change the molecule, but it can make answer choices look unfamiliar.

Formatting Conventions

A few formatting rules keep IUPAC names consistent:

Why This Matters Beyond Naming

Nomenclature is not a standalone topic on the MCAT. It is the gateway to every other organic chemistry concept. When a passage describes “the reaction of 2-bromo-3-methylpentane with sodium hydroxide,” you need to instantly see the structure to predict whether the reaction follows an SN1, SN2, E1, or E2 pathway. That prediction depends on the substrate’s structure - which you can only determine if you can decode the name.

Similarly, when a passage mentions “cyclohex-2-en-1-one,” you need to recognize that this is a cyclohexane ring with a double bond at C2 and a ketone at C1 - a conjugated enone - and that this structure is an excellent Michael acceptor. The name is not trivia. It is the key that unlocks reactivity.

Finding the parent chain is the first and most important step in naming any organic molecule. Get this wrong and every other part of the name falls apart - wrong root, wrong numbering, wrong substituents. The good news is that once you understand the principle, it becomes almost automatic.

Choosing the Main Highway

Think of a road map. When you give someone driving directions, you choose the main highway as your primary route - even if it curves, bends, or makes an L-turn. Side streets branch off the highway, but the highway is the backbone of the trip. The parent chain works the same way.

Rule 1: Find the Longest Continuous Chain of Carbon Atoms

The parent chain is the longest unbroken sequence of carbon atoms in the molecule. “Unbroken” means you can trace from one carbon to the next through single, double, or triple bonds without lifting your pencil.

This sounds simple, but structural drawings can be deceptive. Consider this structure:

    CH₃
    |
CH₃-CH-CH₂-CH₃

A quick glance might suggest the horizontal chain (CH3-CH-CH2-CH3) is four carbons long. But trace the longest path: start at the leftmost CH3, go through the CH, then up to the CH3 branch - that is only three carbons. Start at the leftmost CH3, go through the CH, then right to CH2, then right to CH3 - that is four carbons. So the parent chain is butane (4 carbons), with a methyl substituent at carbon 2.

Rule 2: When Two Chains Tie in Length, Pick the One with More Substituents

If two or more chains have the same number of carbons, choose the one that gives the molecule the greatest number of substituents. More substituents means smaller, simpler branches, which makes the name clearer.

For example, if a molecule has two possible six-carbon parent chains, one giving two methyl substituents and the other giving one ethyl substituent, choose the chain with two methyls.

Rule 3: The Parent Chain Must Include the Principal Functional Group

When the molecule contains a functional group that determines the suffix (like -OH for alcohols or -COOH for carboxylic acids), the parent chain must include the carbon bearing that functional group. Sometimes this means the parent chain is not the absolute longest chain in the molecule - it is the longest chain that passes through the principal functional group.

For example, if a molecule has a seven-carbon continuous chain that does not include a -COOH group, but a six-carbon chain does include it, the parent chain is the six-carbon chain. The carboxylic acid carbon must be in the parent chain because it determines the suffix.

The Carbon Chain Prefixes

Once you know the length of the parent chain, you need to know the prefix that matches. These prefixes are the foundation of all organic nomenclature, and you must know them cold.

The first four (meth, eth, prop, but) come from historical names - methanol from wood (Greek methy = wine + hyle = wood), ethanol from ether, propionic acid from the first fatty acid (Greek protos + pion = first fat), and butyric acid from butter. From five onward, the prefixes are simply Greek and Latin number words: pent (5), hex (6), hept (7), oct (8), non (9), dec (10).

Practice: Tracing the Parent Chain

Let’s work through a more complex example. Consider this structure:

        CH₃
        |
CH₃-CH₂-C-CH₂-CH₃
        |
        CH₂
        |
        CH₂
        |
        CH₃

At first glance, you might pick the horizontal chain: CH3-CH2-C-CH2-CH3, which is five carbons. But look again. If you start at the top CH3, go down to the central C, then continue down through CH2-CH2-CH3, that path is also five carbons (counting the central C and the chain going down: C + CH2 + CH2 + CH3 = 4 carbons from the central carbon, plus the top CH3 = 5 total).

Now try: start at CH3-CH2 on the left, go through the central C, then down through CH2-CH2-CH3. That path is: CH3 + CH2 + C + CH2 + CH2 + CH3 = six carbons. That is the longest chain. The parent is hexane.

The top CH3 and the right-side CH2-CH3 become substituents: a methyl at one position and an ethyl at another. Always trace every route before committing.

Numbering the Parent Chain

Once you have identified the parent chain, number it so the principal functional group (the one that determines the suffix) gets the lowest possible locant. If there is no functional group other than single bonds (a plain alkane), number so the substituents get the lowest set of locants.

“Lowest set of locants” means you compare the two possible numbering schemes position by position. For instance, if one direction gives substituents at 2, 3, and 5, and the other gives 2, 4, and 5, choose the first option because at the first point of difference (position 2 vs. position 2 is a tie, then 3 vs. 4), 3 is lower than 4.

Special Case: Chains with Double or Triple Bonds

When the molecule contains a double bond (alkene) or triple bond (alkyne), the parent chain must include the multiple bond, and the chain is numbered so the double or triple bond gets the lowest possible locant. We will cover this in detail in Section 1.4, but the key point here is that the parent chain must pass through the multiple bond even if a longer all-single-bond chain exists.

Alkanes are the plain vanilla of organic chemistry - just carbon and hydrogen, no double bonds, no functional groups, no drama. That is exactly why they are the best place to learn the full IUPAC naming process. Every rule you internalize here transfers directly to alkenes, alkynes, alcohols, ketones, and every compound the MCAT can throw at you. Master alkane naming, and half the nomenclature battle is already won.

The goal of this section is simple: given a structure, you should be able to write its IUPAC name in under thirty seconds. Given a name, you should be able to draw the structure in the same time. We build that speed with a five-step recipe that never changes.

The Five-Step Recipe

Every alkane name is built the same way. Follow these steps in order, every time:

1. Find the longest continuous carbon chain - this becomes the parent chain (covered in Section 1.2).
2. Number the chain from the end nearest the first substituent - to give the lowest set of locants.
3. Identify and name every substituent - each branch gets its own prefix (methyl, ethyl, propyl, etc.).
4. Alphabetize the substituents - ignore multiplier prefixes (di, tri) when alphabetizing.
5. Assemble: locant-substituent-locant-substituent-parent chain.

Let us walk through each step with a real example.

Step 1: The Parent Chain Sets the Suffix

Count the carbons in the longest continuous chain. The count gives you the root name, and the suffix -ane confirms it is an alkane (single bonds only).

Step 2: Number to Give Lowest Locants

Always number the chain so the substituents get the lowest possible set of numbers. If both directions give the same first locant, compare the second locant, then the third, and so on. This is called the first point of difference rule.

Example: a six-carbon chain with methyl groups on carbons 2 and 4 (numbered from the left) would be numbered 3 and 5 from the right. The set {2, 4} beats {3, 5} at the first point of difference, so we number from the left.

If the numbering is a tie at every locant, alphabetical order of the substituents breaks the tie - the substituent that comes first alphabetically gets the lower number.

Step 3: Name the Substituents

Every branch off the parent chain is a substituent. Name each substituent by counting its carbons and changing the alkane ending from -ane to -yl.

• -CH₃ = methyl (from methane)
• -CH₂CH₃ = ethyl (from ethane)
• -CH₂CH₂CH₃ = propyl (from propane)
• -CH(CH₃)₂ = isopropyl (common) or propan-2-yl (IUPAC)
• -C(CH₃)₃ = tert-butyl (common) or 2-methylpropan-2-yl (IUPAC)

For this chapter, we will use the common names (isopropyl, sec-butyl, tert-butyl) since those are the names the MCAT uses in passages. Full systematic names for branched substituents appear in Section 1.10.

Step 4: Alphabetize, Ignoring Multipliers

When a molecule has multiple types of substituents, they must appear in the name in alphabetical order by substituent name. Importantly, the multiplier prefixes (di-, tri-, tetra-) do NOT count for alphabetization.

• “3-ethyl-2,2-dimethylpentane” - ethyl (e) comes before methyl (m), even though “dimethyl” starts with d.
• “4-ethyl-3-isopropyloctane” - ethyl (e) comes before isopropyl (i).

Hyphenated prefixes like sec- and tert- are also ignored when alphabetizing, but iso- and neo- are part of the name and DO count for alphabetization order.

Step 5: Assemble the Name

Put it all together in the format:

locant-substituent-locant-substituent-parent chain

A complete worked example for the molecule with structure:

    CH₃    CH₃
    |      |
CH₃-CH-CH₂-CH-CH₂-CH₃

Following the recipe:

1. Longest chain = 6 carbons → hexane.
2. Number from the left so methyl groups land on C2 and C4 (set {2,4} not {3,5}).
3. Substituents = two methyl groups → dimethyl.
4. Only one substituent type, no alphabetization needed.
5. Assemble: 2,4-dimethylhexane.

Notice the punctuation: numbers are separated from each other by commas, and from letters by hyphens.

Handling Multiple Identical Substituents

When the same substituent appears more than once, use the multiplier prefixes: di- (2), tri- (3), tetra- (4), penta- (5), and so on. Each position still needs its own locant number.

• Two methyl groups = “dimethyl” with two locants: “2,3-dimethyl…”
• Three chloro groups = “trichloro” with three locants: “1,2,3-trichloro…”

When Substituents Have Substituents (Complex Branches)

If a substituent itself has branches, name the whole branch in parentheses and number its own carbons starting from the point of attachment to the main chain.

Example: a 4-carbon branch with a methyl group on its second carbon is named (2-methylpropyl) - also known by its common name isobutyl. In context, the name might look like “4-(2-methylpropyl)octane.”

This rule keeps long, complex names unambiguous. Section 1.10 drills deeper into these complex substituent names, but most MCAT questions stop at the common-name level (isopropyl, isobutyl, sec-butyl, tert-butyl, neopentyl).

Common Naming Traps

1. Not finding the longest chain. A 2D structure can hide the longest chain because of how it is drawn. Always count every possible path.
2. Wrong numbering direction. Students often number from the end closest to the “drawn left side” out of habit. The rule is lowest locants, regardless of visual orientation.
3. Forgetting to alphabetize. Even if it looks weird (like “ethyl” appearing before “methyl”), alphabetical order is the law.
4. Miscounting multiplier prefixes. “Trimethyl” needs three locants, not one. Missing a locant is a common error.
5. Ignoring the parent chain tie-breaker. When two chains are the same length, pick the one with more substituents. If they tie on substituents too, use lowest locants.

Worked Examples

Example 1: A 7-carbon chain with a methyl on C3 and an ethyl on C5.

Alphabetize: ethyl (e) before methyl (m). But check numbering first. Numbered from one end: ethyl-5, methyl-3 (set {3,5}). From the other end: ethyl-3, methyl-5 (set {3,5}). Tie. Go to alphabetical tie-breaker: ethyl should get the lower number, so ethyl at 3 wins. The name is 3-ethyl-5-methylheptane.

Example 2: A 6-carbon chain with two methyls on C2 and one methyl on C4.

Substituents: three methyls at positions 2, 2, and 4 → “2,2,4-trimethyl”. Name: 2,2,4-trimethylhexane (famously the high-octane component of gasoline).

Example 3: A 5-carbon chain with a bromo on C1 and a chloro on C3.

Alphabetize: bromo (b) before chloro (c). Numbering: bromo at 1, chloro at 3 (set {1,3}) or bromo at 5, chloro at 3 (set {3,5}). Set {1,3} wins. Name: 1-bromo-3-chloropentane.

What the MCAT Actually Asks

You will rarely be asked to name a compound from scratch in an AAMC exam. What you will see is a passage that references compounds by name and expects you to:

1. Recognize the structural implications of the name (chain length, branches, functional group).
2. Predict reactivity based on the structure implied by the name.
3. Compare two similarly named compounds to identify isomerism or polarity differences.

Practice going from name to structure (reverse nomenclature) as much as structure to name. The MCAT rewards the latter skill more than the former.

Alkanes have only single bonds, which makes them saturated - every carbon holds the maximum possible number of hydrogens. But many organic molecules contain double bonds (alkenes) or triple bonds (alkynes), and these “unsaturated” compounds need a way to indicate where the multiple bond is and what kind it is. That is where the suffixes “-ene” and “-yne” come in.

The Dating Analogy

Naming Alkenes

Alkenes contain at least one carbon-carbon double bond (C=C). Naming follows the same IUPAC rules as alkanes, with two modifications:

Modification 1: Replace the “-ane” suffix with “-ene.” Ethane becomes ethene. Propane becomes propene. Hexane becomes hexene.

Modification 2: The double bond gets a locant number. Number the parent chain so the double bond gets the lowest possible position. The locant indicates the first carbon of the double bond.

Example: A five-carbon chain with a double bond between carbons 1 and 2 is pent-1-ene (or 1-pentene in older notation). A double bond between carbons 2 and 3 is pent-2-ene.

General Formula for Alkenes

Acyclic alkenes with one double bond follow the formula CnH2n. Compare this to CnH2n+2 for alkanes - you lose two hydrogens for every double bond you add. This makes sense because forming a double bond requires each carbon to give up one hydrogen.

Naming Alkynes

Alkynes contain at least one carbon-carbon triple bond (C≡C). The suffix is “-yne,” and the locant rules are identical to alkenes.

Example: A four-carbon chain with a triple bond between carbons 1 and 2 is but-1-yne. Between carbons 2 and 3 is but-2-yne.

Acyclic alkynes with one triple bond follow the formula CnH2n-2. You lose four hydrogens compared to the corresponding alkane because a triple bond consists of one sigma bond and two pi bonds, replacing four C-H bonds.

Parent Chain Must Include the Multiple Bond

When a molecule has a double or triple bond, the parent chain must pass through that bond, even if a longer all-single-bond chain exists elsewhere. The multiple bond is more important than maximum chain length for determining the parent chain.

After ensuring the parent chain includes the multiple bond, number the chain so the double or triple bond gets the lowest locant.

Cis/Trans Designation for Alkenes

Because double bonds cannot rotate freely (the pi bond locks the geometry), groups attached to the double-bond carbons can be on the same side or opposite sides. This creates geometric isomers:

• Cis = same side. Both substituents of interest are on the same side of the double bond.
• Trans = opposite sides. The substituents are on opposite sides.

The cis/trans system works well when each double-bond carbon has one hydrogen and one non-hydrogen group. It becomes ambiguous when both carbons have two non-hydrogen substituents, which is why chemists developed the E/Z system.

E/Z Designation (Replaces Cis/Trans)

The E/Z system uses the Cahn-Ingold-Prelog (CIP) priority rules to assign priorities to the two groups on each carbon of the double bond. The higher-priority group on each carbon is identified, and then:

• Z (zusammen, German for “together”): The two higher-priority groups are on the same side of the double bond.
• E (entgegen, German for “opposite”): The two higher-priority groups are on opposite sides.

CIP Priority Rules (Brief Overview)

The Cahn-Ingold-Prelog priority system ranks substituents by atomic number:

1. Higher atomic number = higher priority. Br (35) > Cl (17) > O (8) > N (7) > C (6) > H (1).
2. If the atoms directly attached are the same, move outward and compare the next set of atoms along each branch until you find a difference.
3. Double and triple bonds are treated as if each bond were two or three single bonds to duplicate atoms. A C=O double bond treats the carbon as if it were bonded to two separate oxygen atoms.

You will study these rules in much greater depth in the Isomers chapter. For now, the key point is that E/Z assignments always use CIP priorities, not just “which group is bigger.”

Degree of Unsaturation (Index of Hydrogen Deficiency)

The degree of unsaturation (also called the index of hydrogen deficiency, IHD) tells you how many double bonds, triple bonds, or rings a molecule has compared to a fully saturated acyclic molecule with the same formula.

Example: C6H6 (benzene). DoU = (2(6) + 2 - 6) / 2 = (12 + 2 - 6) / 2 = $\frac{8}{2}$ = 4. Benzene has three double bonds and one ring = 4 DoU. Checks out.

Example: C3H6. DoU = (2(3) + 2 - 6) / 2 = (6 + 2 - 6) / 2 = $\frac{2}{2}$ = 1. This molecule has one degree of unsaturation - it could be propene (one double bond) or cyclopropane (one ring).

Naming Molecules with Multiple Double or Triple Bonds

When more than one double bond is present, use the multiplying prefix before “-ene”:

• Two double bonds: “-diene” (example: buta-1,3-diene)
• Three double bonds: “-triene” (example: hexa-1,3,5-triene)

For multiple triple bonds, use “-diyne,” “-triyne,” etc.

Each multiple bond gets its own locant. Commas separate multiple locants: buta-1,3-diene tells you there are double bonds starting at carbon 1 and carbon 3.

Terminal vs. Internal Alkynes

An important distinction for alkynes:

• Terminal alkyne: The triple bond is at the end of the chain (C1). The terminal carbon bears a hydrogen (R-C≡C-H). This hydrogen is slightly acidic (pKa ~ 25) because the sp-hybridized carbon holds the electrons tightly.
• Internal alkyne: The triple bond is in the interior of the chain (e.g., between C2 and C3). Both carbons of the triple bond are bonded to other carbons (R-C≡C-R’).

This distinction matters for reactivity. Terminal alkynes can be deprotonated by strong bases (like NaNH2) to form acetylide anions, which are excellent nucleophiles. Internal alkynes cannot.

Organic molecules do not always grow in straight lines. Carbon chains can loop back on themselves and form rings, creating cyclic compounds. Rings are everywhere in biology - cholesterol has four fused rings, glucose cyclizes into a six-membered ring, and the amino acid proline contains a five-membered ring. Knowing how to name these structures is essential for decoding MCAT passages.

The “Cyclo-” Prefix

Naming a cyclic compound is straightforward: take the name of the straight-chain alkane with the same number of carbons and add the prefix “cyclo-.”

• Three-carbon ring = cyclopropane
• Four-carbon ring = cyclobutane
• Five-carbon ring = cyclopentane
• Six-carbon ring = cyclohexane

That is it. The ring itself is the parent, and you simply count the carbons in the ring to get the root name.

General Formula for Cycloalkanes

Cycloalkanes have the formula CnH2n - the same as acyclic alkenes. This makes sense because forming a ring requires losing two hydrogens (the two end carbons bond to each other instead of to a hydrogen each). A ring counts as one degree of unsaturation, just like a double bond.

This means if you calculate the degree of unsaturation for a molecular formula and get DoU = 1, the compound could be either a cycloalkane or an alkene. The formula alone cannot distinguish them - you need structural information.

Naming Substituted Cycloalkanes

When a cycloalkane has substituents, follow these rules:

Rule 1: Decide whether the ring or the chain is the parent. If the ring has more carbons than any attached chain, the ring is the parent. If a chain has more carbons than the ring, the chain is the parent and the ring becomes a substituent (named as a “cycloalkyl” group).

Example: A cyclopentane ring (5 carbons) with a methyl group attached: the ring is the parent. Name: methylcyclopentane.

Example: A cyclopropane ring (3 carbons) attached to an octane chain (8 carbons): the chain is the parent. The ring is a “cyclopropyl” substituent. Name: cyclopropyloctane (with a locant for the attachment point).

Rule 2: When the ring is the parent with one substituent, no locant is needed. Methylcyclohexane has a methyl group on the ring. Since there is only one substituent, it does not matter where you start numbering - every position is equivalent. No number is needed.

Rule 3: When the ring has two or more substituents, number the ring. Assign locant 1 to the substituent that comes first alphabetically, then number in the direction that gives the other substituents the lowest locants.

Examples of Substituted Cycloalkanes

One substituent:

• Ethylcyclopentane (an ethyl group on a five-membered ring)
• No number needed

Two substituents:

• 1-ethyl-3-methylcyclohexane: ethyl at position 1 (alphabetically first), methyl at position 3. You number so the set of locants is as low as possible.

Three substituents:

• 1,2,4-trimethylcyclohexane: three methyl groups on a six-membered ring at positions 1, 2, and 4.

Naming Cycloalkenes

Cycloalkenes are rings that contain a double bond. The naming rules are:

Step 1: Name the ring with the “cyclo-” prefix and use the “-ene” suffix instead of “-ane.”

Step 2: The double bond always includes carbons 1 and 2. You do not need to specify “1-” for the double bond in simple cycloalkenes because it is implied.

Step 3: Number the ring starting at the double bond, going in the direction that gives substituents the lowest locants.

Example: Cyclohexene - a six-membered ring with one double bond. No locant for the double bond is needed.

Example: 3-methylcyclohexene - a six-membered ring with a double bond (at C1-C2, implied) and a methyl group at C3.

Cycloalkene General Formula

Cycloalkenes with one double bond follow the formula CnH2n-2. They have two degrees of unsaturation: one for the ring and one for the double bond.

Polycyclic Systems (Brief Mention)

Some molecules contain two or more rings that share carbons. These are polycyclic systems. The most common ones you will encounter on the MCAT are:

• Bicyclic: Two rings sharing one or two carbons (e.g., bicyclo[2.2.1]heptane, also called norbornane)
• Spiro: Two rings sharing exactly one carbon (e.g., spiro[4.5]decane)
• Fused: Two rings sharing two adjacent carbons and one bond (e.g., decalin)

You do not need to master the detailed naming of polycyclic systems for the MCAT. But you do need to recognize that fused ring systems like steroids (four fused rings) and decalin are polycyclic. When a passage gives you a polycyclic structure, focus on identifying the functional groups and stereochemistry rather than trying to generate the full IUPAC name.

Ring Strain

Ring size affects stability, and this sometimes appears in MCAT passages:

Three-membered rings (cyclopropane, epoxides) are highly strained because the internal bond angles are forced to 60° instead of the ideal 109.5° for sp3 carbons. This strain makes them reactive - which is why epoxides are excellent electrophiles in organic reactions.

Benzene is arguably the most important ring in organic chemistry. Its six-carbon aromatic ring appears in amino acids (phenylalanine, tyrosine, tryptophan), neurotransmitters (dopamine, serotonin), drugs (aspirin, ibuprofen), and countless biological molecules. If you can name benzene derivatives, you can decode a huge fraction of the organic molecules that show up on the MCAT.

Benzene as Parent

The simplest aromatic compound is benzene itself: C6H6, a six-membered ring with alternating double bonds (or more accurately, a ring of six sp2-hybridized carbons with fully delocalized pi electrons). Its degree of unsaturation is 4 (three double bonds + one ring).

When benzene is the parent, substituents are simply named as prefixes:

• Chlorobenzene (Cl on benzene)
• Nitrobenzene (NO2 on benzene)
• Bromobenzene (Br on benzene)

For a single substituent, no locant is needed - all positions on an unsubstituted benzene ring are equivalent.

The Ortho/Meta/Para System

When benzene has two substituents, you need to describe their relative positions. The ortho/meta/para (o/m/p) system does this elegantly using relative positions rather than numbers.

The three positions correspond to specific numbering:

Examples with Ortho/Meta/Para

• ortho-dichlorobenzene (o-dichlorobenzene): two Cl atoms on adjacent carbons (1,2 positions)
• meta-dinitrobenzene (m-dinitrobenzene): two NO2 groups separated by one carbon (1,3 positions)
• para-bromochlorobenzene (p-bromochlorobenzene): Br and Cl on opposite sides (1,4 positions)

When the two substituents are different, name them alphabetically. For p-bromochlorobenzene, “bromo” comes before “chloro.”

Common Named Benzene Derivatives

Several substituted benzenes have common names that are so widely used that IUPAC has accepted them as parent names. You must know these:

Phenyl vs. Benzyl

These two terms confuse students constantly. They describe different things:

Phenyl (C6H5-, abbreviated Ph): The benzene ring itself as a substituent, with the attachment point directly on the ring. When benzene is not the parent, it becomes a “phenyl” substituent. Example: 2-phenylpentane has a benzene ring attached at carbon 2 of a pentane chain.

Benzyl (C6H5CH2-): A benzene ring plus one CH2 group. The attachment point is the CH2 carbon, not the ring. Example: benzyl alcohol is C6H5-CH2-OH. The OH is on the carbon adjacent to the ring, not on the ring itself.

The key difference: phenyl attaches through the ring carbon. Benzyl attaches through a CH2 that is one carbon removed from the ring.

Naming Polysubstituted Benzene Rings

When benzene has three or more substituents, you must use numbered locants (ortho/meta/para only works for two substituents):

Step 1: If the compound has a common parent name (toluene, phenol, aniline, benzoic acid), use it. The named group is at carbon 1.

Step 2: Number the ring to give the lowest set of locants to all substituents.

Step 3: List substituents alphabetically with their locants.

Example: 2,4,6-trinitrotoluene (TNT). Toluene means the methyl group is at C1. Three nitro groups are at positions 2, 4, and 6.

Example: 3,5-dibromo-4-methylphenol. Phenol means OH is at C1. A methyl is at C4. Two bromine atoms are at C3 and C5.

When Is Benzene the Parent vs. a Substituent?

Benzene is the parent when:

• The ring has a higher-priority functional group than any attached chain
• The attached chains are short (six or fewer carbons)
• A common parent name applies (phenol, toluene, aniline, etc.)

Benzene is a substituent (phenyl group) when:

• The attached chain is longer than six carbons
• The chain contains the principal functional group (not the ring)

Example: C6H5-CH2-CH2-CH2-CH2-CH2-CH2-COOH. The chain has seven carbons including the COOH carbon. The chain is the parent (heptanoic acid), and the ring is a phenyl substituent: 7-phenylheptanoic acid.

The Arene Nomenclature Shorthand

In general organic chemistry, “Ar-” is used as a generic abbreviation for any aromatic (aryl) group, just as “R-” represents any alkyl group. When you see “ArOH” in a reaction mechanism, it means “an aromatic ring with an OH group.” This shorthand appears frequently in MCAT passages describing general reaction patterns.

If the carbon skeleton is the backbone of an organic molecule, functional groups are the personality. Two molecules can have the exact same number of carbons but behave in completely different ways because of their functional groups. Ethanol (CH3CH2OH) is the alcohol in your drink. Ethanal (CH3CHO) is a toxic aldehyde your liver must break down. Same two-carbon backbone, different functional group, completely different chemistry.

Functional groups are where reactions happen. The carbon-carbon single bonds in the backbone are relatively inert. But functional groups contain electronegative atoms, multiple bonds, or lone pairs that create regions of electron density that attract reactants. Every reaction mechanism you will study in organic chemistry starts with a functional group doing something.

The Six Functional Groups You Must Know Cold

The MCAT expects you to instantly recognize these functional groups, know their properties, and understand how they affect reactivity. This is not optional - if you cannot identify a functional group at a glance, you will struggle with every chapter that follows.

1. Hydroxyl Group (-OH)

The hydroxyl group is an oxygen atom bonded to a hydrogen atom, attached to a carbon. Molecules with -OH groups are called alcohols (when attached to an sp3 carbon) or phenols (when attached to an aromatic ring).

Key properties:

• Polar and capable of hydrogen bonding (both as donor and acceptor)
• Increases water solubility dramatically
• Can act as a weak acid (alcohols: pKa ~ 16, phenols: pKa ~ 10)
• Can be oxidized to a carbonyl (aldehyde, ketone, or carboxylic acid)

How to spot it in a name: The suffix “-ol” (ethanol, propan-2-ol) or the prefix “hydroxy-” when it is not the principal group (3-hydroxypentanoic acid).

2. Carbonyl Group (C=O)

The carbonyl group is a carbon double-bonded to an oxygen. It is the defining feature of several important compound classes:

• Aldehyde: Carbonyl at the end of a chain (R-CHO). Suffix: “-al”
• Ketone: Carbonyl in the interior of a chain (R-CO-R’). Suffix: “-one”
• Carboxylic acid: Carbonyl bonded to an -OH (R-COOH). Suffix: “-oic acid”
• Ester: Carbonyl bonded to an -OR (R-COO-R’). Suffix: “-oate”
• Amide: Carbonyl bonded to an -NH2 or NR2 (R-CONH2). Suffix: “-amide”

The carbonyl carbon is electrophilic (electron-poor) because oxygen pulls electron density away through the double bond. This makes carbonyl compounds susceptible to nucleophilic addition and nucleophilic acyl substitution - two of the most important reaction types on the MCAT.

3. Carboxyl Group (-COOH)

The carboxyl group is a carbonyl bonded directly to a hydroxyl group. It defines carboxylic acids - the highest-priority functional group in IUPAC naming.

Key properties:

• Acidic (pKa ~ 2-5 for most carboxylic acids)
• The conjugate base (carboxylate, -COO-) is stabilized by resonance - the negative charge is delocalized over both oxygens
• At physiological pH (7.4), carboxylic acids are almost entirely deprotonated (exist as -COO-)
• Forms derivatives: esters, amides, anhydrides, acid halides

How to spot it in a name: The suffix “-oic acid” (ethanoic acid, butanoic acid) or the prefix “carboxy-” when it is not the principal group.

4. Amino Group (-NH2)

The amino group is a nitrogen atom bonded to hydrogen atoms (and/or carbon atoms). It defines amines.

Key properties:

• Basic (accepts protons). The lone pair on nitrogen is available for bonding.
• At physiological pH, most amines are protonated (-NH3+)
• Nucleophilic - the lone pair can attack electrophilic carbons
• Can form hydrogen bonds

Classification by substitution:

• Primary amine (1°): R-NH2 (one carbon attached to N)
• Secondary amine (2°): R2NH (two carbons attached to N)
• Tertiary amine (3°): R3N (three carbons attached to N)
• Quaternary ammonium (4°): R4N+ (four carbons, permanent positive charge)

How to spot it in a name: The suffix “-amine” (ethanamine, propan-1-amine) or the prefix “amino-” (2-aminoethanol).

5. Phosphate Group (-OPO₃²⁻)

The phosphate group is a phosphorus atom bonded to four oxygen atoms. It is critical in biochemistry:

• ATP: Three linked phosphate groups store and release energy
• DNA/RNA: The sugar-phosphate backbone uses phosphodiester bonds
• Phospholipids: Phosphate head groups make membranes amphipathic
• Protein regulation: Phosphorylation (adding -PO4) activates or deactivates enzymes

Key properties:

• Strongly acidic (first pKa ~ 2, second pKa ~ 7)
• At physiological pH, phosphate groups carry a negative charge
• Can form phosphoester and phosphoanhydride bonds

The phosphate group is more of a biochemistry topic than an organic chemistry one, but the MCAT tests it across both subjects. Recognizing the phosphate group in a complex molecule (like a nucleotide or phospholipid) is essential.

6. Sulfhydryl Group (-SH)

The sulfhydryl (or thiol) group is sulfur bonded to hydrogen. It defines thiols.

Key properties:

• Weaker hydrogen bonding than -OH (sulfur is larger and less electronegative)
• More acidic than alcohols (pKa ~ 8-10 vs. ~ 16 for alcohols)
• Can form disulfide bonds (-S-S-) through oxidation
• Cysteine’s -SH group forms disulfide bridges that stabilize protein tertiary structure

How to spot it in a name: The suffix “-thiol” (ethanethiol) or the prefix “mercapto-” or “sulfanyl-.”

Summary Table: Key Functional Groups

Recognizing Functional Groups in Complex Molecules

On the MCAT, you will not see simple molecules like ethanol in isolation. You will see complex structures with multiple functional groups embedded in a passage about a biological process or drug mechanism. The skill is rapid pattern recognition - scanning a structure and identifying every functional group present.

Practice this by looking at amino acid structures, nucleotides, and drug molecules. For each one, circle every functional group you can find. If you can identify the functional groups, you can predict the molecule’s behavior: where it will be protonated or deprotonated, where it can hydrogen bond, where nucleophilic attack will occur, and where oxidation or reduction is possible.

Now that you know the major functional groups, it is time to learn how they change the IUPAC name. Each functional group has a specific suffix (when it is the highest-priority group) and a specific prefix (when a higher-priority group takes the suffix instead). This section covers the first five of the most important compound classes: alcohols, ethers, aldehydes, ketones, and carboxylic acids.

Naming Alcohols (-OH)

Alcohols contain a hydroxyl group (-OH) attached to an sp3-hybridized carbon.

IUPAC suffix: “-ol”
IUPAC prefix (when not the principal group): “hydroxy-”

Steps:

1. Find the longest chain that includes the carbon bearing the -OH group
2. Change the “-e” at the end of the parent alkane to “-ol”
3. Number the chain so the -OH gets the lowest possible locant
4. Name and number any substituents as usual

Examples:

• Methanol: CH3OH. One carbon + -ol = methanol
• Ethanol: CH3CH2OH. Two carbons + -ol = ethanol
• Propan-2-ol: CH3CH(OH)CH3. Three carbons, -OH at carbon 2 = propan-2-ol (older format: 2-propanol)
• Butan-1-ol: CH3CH2CH2CH2OH. Four carbons, -OH at carbon 1 = butan-1-ol

Classification of alcohols:
Alcohols are classified by the carbon bearing the -OH:

• Primary (1°): -OH is on a carbon bonded to one other carbon (e.g., butan-1-ol)
• Secondary (2°): -OH is on a carbon bonded to two other carbons (e.g., propan-2-ol)
• Tertiary (3°): -OH is on a carbon bonded to three other carbons (e.g., 2-methylpropan-2-ol)

This classification directly affects reactivity. Primary alcohols can be oxidized to aldehydes and then to carboxylic acids. Secondary alcohols are oxidized to ketones. Tertiary alcohols resist oxidation. This pattern is heavily tested on the MCAT.

Naming Ethers (R-O-R’)

Ethers have an oxygen atom bonded to two carbon groups. They are relatively unreactive, which makes them excellent solvents.

Ethers are named in two ways:

Common naming (more common on the MCAT): Name the two alkyl groups on either side of the oxygen, alphabetically, followed by “ether.”

• Diethyl ether: CH3CH2-O-CH2CH3 (two ethyl groups)
• Methyl tert-butyl ether (MTBE): CH3-O-C(CH3)3

IUPAC naming: The smaller alkyl group + oxygen is treated as an “alkoxy” substituent on the longer chain.

• Methoxyethane: CH3-O-CH2CH3 (methoxy group on ethane)
• 2-methoxypropane: CH3-O-CH(CH3)2

The “alkoxy” names are formed by replacing “-yl” with “-oxy”: methyl becomes methoxy, ethyl becomes ethoxy, propyl becomes propoxy.

Naming Aldehydes (-CHO)

Aldehydes have a carbonyl group (C=O) at the terminal position of a chain. The carbonyl carbon is always carbon 1.

IUPAC suffix: “-al”
IUPAC prefix (when not the principal group): “oxo-” or “formyl-”

Steps:

1. Find the longest chain that includes the carbonyl carbon
2. Replace “-e” with “-al”
3. The carbonyl carbon is automatically carbon 1 (no locant needed for the -CHO group itself)
4. Name and number substituents

Examples:

• Methanal: HCHO. One carbon + -al = methanal (common name: formaldehyde)
• Ethanal: CH3CHO. Two carbons + -al = ethanal (common name: acetaldehyde)
• Propanal: CH3CH2CHO. Three carbons + -al = propanal
• 3-methylbutanal: (CH3)2CHCH2CHO. Four carbons + -al with methyl at C3 = 3-methylbutanal

Since the aldehyde carbon is always at the end of the chain (carbon 1), you never need to specify its position - the “-al” suffix already tells you it is terminal.

Naming Ketones (C=O, internal)

Ketones have a carbonyl group in the interior of the chain, bonded to two carbon groups.

IUPAC suffix: “-one”
IUPAC prefix (when not the principal group): “oxo-”

Steps:

1. Find the longest chain that includes the carbonyl carbon
2. Replace “-e” with “-one”
3. Number the chain so the carbonyl gets the lowest possible locant
4. Name and number substituents

Examples:

• Propan-2-one: CH3COCH3. Three carbons, carbonyl at C2 = propan-2-one (common name: acetone)
• Butan-2-one: CH3COCH2CH3. Four carbons, carbonyl at C2 = butan-2-one (common name: methyl ethyl ketone)
• Pentan-3-one: CH3CH2COCH2CH3. Five carbons, carbonyl at C3 = pentan-3-one

Naming Carboxylic Acids (-COOH)

Carboxylic acids have both a carbonyl (C=O) and a hydroxyl (-OH) on the same carbon, at the end of the chain. They are the highest-priority functional group in IUPAC naming.

IUPAC suffix: “-oic acid”
IUPAC prefix (when not the principal group): “carboxy-”

Steps:

1. Find the longest chain that includes the carboxyl carbon
2. Replace “-e” with “-oic acid”
3. The carboxyl carbon is automatically carbon 1
4. Name and number substituents

Examples:

• Methanoic acid: HCOOH. One carbon + -oic acid = methanoic acid (common name: formic acid)
• Ethanoic acid: CH3COOH. Two carbons + -oic acid = ethanoic acid (common name: acetic acid)
• Propanoic acid: CH3CH2COOH. Three carbons + -oic acid = propanoic acid
• 2-methylpropanoic acid: (CH3)2CHCOOH. Three carbons + -oic acid with methyl at C2 = 2-methylpropanoic acid

Like aldehydes, the carboxyl carbon is always at the terminal position, so no locant is needed for the -COOH group.

Dicarboxylic Acids

When a molecule has a -COOH group on both ends, it is a dicarboxylic acid. The suffix becomes “-dioic acid.”

Several of these common names appear in the Krebs cycle: succinic acid (succinate) and oxalic acid (oxalate) are Krebs cycle intermediates. The MCAT will use these common names in biochemistry passages.

Summary: Suffixes for This Section

This section covers the remaining major compound classes you need for the MCAT: amines, amides, esters, and acid halides. These four groups are especially important because amides and esters form the backbone of proteins (peptide bonds are amide linkages) and lipids (triglycerides are triesters), while amines and acid halides appear throughout biochemical and synthetic pathways.

Naming Amines (-NH2, -NHR, -NR2)

Amines contain a nitrogen atom bonded to one, two, or three carbon groups (plus enough hydrogens to complete nitrogen’s three bonds).

IUPAC suffix: “-amine”
IUPAC prefix (when not the principal group): “amino-”

Steps:

1. Find the longest chain that includes the carbon bonded to nitrogen
2. Replace “-e” with “-amine”
3. Number the chain so the nitrogen-bearing carbon gets the lowest locant

Examples:

• Methanamine: CH3NH2. One carbon + -amine = methanamine (common name: methylamine)
• Ethanamine: CH3CH2NH2 (common name: ethylamine)
• Propan-2-amine: CH3CH(NH2)CH3 (common name: isopropylamine)

Secondary and Tertiary Amines

When nitrogen has two or three carbon groups, the additional groups are named with the prefix “N-” (capital N, to distinguish them from carbon-chain locants):

• N-methylethanamine: CH3NHCH2CH3. The parent chain is ethane with an -amine. The second group on nitrogen is a methyl, designated “N-methyl.”
• N,N-dimethylmethanamine: (CH3)3N. The parent is methanamine. Two additional methyl groups on nitrogen: “N,N-dimethyl.” (Common name: trimethylamine.)

Common Naming for Amines

In the common naming system, name all alkyl groups attached to nitrogen in alphabetical order, then add “-amine”:

• Diethylamine = (CH3CH2)2NH
• Triethylamine = (CH3CH2)3N
• Ethylmethylamine = CH3CH2NHCH3

Naming Amides (-CONH2)

Amides have a carbonyl group bonded directly to a nitrogen. They are carboxylic acid derivatives - formed when the -OH of a carboxylic acid is replaced by -NH2 (or -NHR or -NR2).

IUPAC suffix: “-amide”
IUPAC prefix (when not the principal group): “carbamoyl-”

Steps:

1. Name the parent carboxylic acid
2. Drop “-oic acid” (or “-ic acid” for common names) and add “-amide”

Examples:

• Methanamide: HCONH2. From methanoic acid, drop “-oic acid,” add “-amide” = methanamide (common name: formamide)
• Ethanamide: CH3CONH2. From ethanoic acid = ethanamide (common name: acetamide)
• Propanamide: CH3CH2CONH2

For N-substituted amides, use the “N-” prefix just as with amines:

• N-methylethanamide: CH3CONHCH3
• N,N-dimethylmethanamide: HCON(CH3)2 (common name: DMF, dimethylformamide - a very common solvent)

Naming Esters (-COOR)

Esters have a carbonyl bonded to an oxygen that is itself bonded to a carbon group. They are formed from a carboxylic acid and an alcohol.

IUPAC suffix: “-oate” (as part of a two-word name)

Steps:

1. Name the alkyl group attached to the oxygen (the “alcohol” part)
2. Name the parent carboxylic acid, dropping “-ic acid” and adding “-ate”
3. Write as two words: [alkyl group] [parent acid-ate]

Examples:

• Methyl ethanoate: CH3COOCH3. The oxygen-attached group is methyl. The acid parent is ethanoic acid, so the ester is methyl ethanoate (common name: methyl acetate).
• Ethyl methanoate: HCOOCH2CH3. The oxygen-attached group is ethyl. The acid parent is methanoic acid = ethyl methanoate (common name: ethyl formate).
• Ethyl propanoate: CH3CH2COOCH2CH3.

Esters in Biology

Esters are everywhere in biochemistry:

• Triglycerides (fats and oils): Three fatty acid chains ester-linked to glycerol
• Phospholipids: Fatty acids ester-linked to glycerol with a phosphate head group
• Aspirin: An ester of salicylic acid and acetic acid
• DNA backbone: Phosphodiester bonds link nucleotides

When an MCAT passage mentions “ester hydrolysis” or “saponification,” it is describing the breaking of the ester bond with water (hydrolysis) or base (saponification), regenerating the acid and alcohol components.

Naming Acid Halides (-COX)

Acid halides (also called acyl halides) have a carbonyl bonded to a halogen atom. They are the most reactive carboxylic acid derivatives.

IUPAC naming: Replace “-ic acid” of the parent carboxylic acid with “-yl halide.”

Examples:

• Ethanoyl chloride: CH3COCl. From ethanoic acid, replace “-ic acid” with “-yl chloride” = ethanoyl chloride (common name: acetyl chloride)
• Propanoyl bromide: CH3CH2COBr
• Methanoyl chloride: HCOCl (common name: formyl chloride) - although this compound is unstable

Carboxylic Acid Derivatives - The Big Picture

All four compound classes in this section (amides, esters, acid halides, and anhydrides) are derived from carboxylic acids by replacing the -OH group with something else:

This pattern - same core carbonyl, different group attached - is the foundation of nucleophilic acyl substitution reactions, one of the most heavily tested reaction types on the MCAT.

When a molecule has only one functional group, naming is straightforward - that group gets the suffix, and you are done. But most biologically relevant molecules have multiple functional groups. An amino acid has both a carboxylic acid and an amine. A sugar has multiple hydroxyl groups and an aldehyde or ketone. A fatty acid has a carboxylic acid, maybe some double bonds, and possibly a hydroxyl. How do you decide which group “wins” the suffix?

The answer is the IUPAC priority hierarchy - a VIP list that ranks every functional group from most important to least important. The highest-priority group gets the suffix. Every other group becomes a prefix.

The VIP List at a Party

The Priority Table (Highest to Lowest)

This table lists functional groups from highest to lowest IUPAC priority. The group highest on this list that is present in the molecule gets the suffix. Everything below it becomes a prefix.

How Priority Affects Naming - A Worked Example

Consider a molecule with four carbons, an -OH at carbon 3, and a -COOH at carbon 1.

Step 1: Identify all functional groups: carboxylic acid (-COOH) and alcohol (-OH).

Step 2: Determine which has higher priority. Carboxylic acid (priority 1) beats alcohol (priority 6). Carboxylic acid gets the suffix.

Step 3: The suffix is “-oic acid.” The parent chain is four carbons = butanoic acid.

Step 4: The alcohol group becomes a prefix: “hydroxy-” at carbon 3.

Final name: 3-hydroxybutanoic acid.

Notice that the -OH group does not get the “-ol” suffix. It becomes “hydroxy-” because a higher-priority group (carboxylic acid) has already claimed the suffix.

Numbering Rules in Detail

Once you know which group gets the suffix, numbering follows a clear hierarchy of tie-breaking rules:

Rule 1: Give the principal (suffix-determining) functional group the lowest possible locant. This is the most important rule. If the carboxylic acid can be at C1 or C5, it goes to C1.

Rule 2: Give multiple bonds (C=C or C≡C) the next lowest locant. If the suffix group is already placed, give the double or triple bond the lowest possible number.

Rule 3: Give substituent prefixes the lowest set of locants. Compare the locant sets position by position. At the first point of difference, the lower number wins.

Rule 4: If there is still a tie, give the lower locant to the substituent that comes first alphabetically.

Examples of Priority-Based Naming

Example 1: 5-aminopentan-2-ol

• Both -OH and -NH2 are present
• Alcohol (-ol) has higher priority than amine (-amine) in the IUPAC system
• The suffix is “-ol” (alcohol at C2)
• The amine becomes the prefix “amino-” at C5

Wait - actually, let’s check: is alcohol higher priority than amine? Looking at the table: alcohol is priority 6, amine is priority 7. Yes, alcohol outranks amine. So the suffix is “-ol.”

Example 2: 4-oxopentanoic acid

• Both a carboxylic acid and a ketone are present
• Carboxylic acid has highest priority, so suffix = “-oic acid”
• The ketone becomes the prefix “oxo-” at C4
• Parent chain is five carbons = pentanoic acid
• Full name: 4-oxopentanoic acid

Example 3: 3-hydroxyhexanal

• Both an aldehyde and an alcohol are present
• Aldehyde has higher priority than alcohol, so suffix = “-al”
• The alcohol becomes the prefix “hydroxy-” at C3
• Parent chain is six carbons = hexanal
• Full name: 3-hydroxyhexanal

The “Lowest Set of Locants” Rule

This rule is often tested on the MCAT because it requires careful comparison. When two numbering schemes give different locant sets, compare them number by number from left to right:

Numbering A: Substituents at 2, 3, 6
Numbering B: Substituents at 2, 4, 5

Compare: 2 vs. 2 (tie) → 3 vs. 4 → Numbering A wins because 3 < 4.

The comparison stops as soon as you find a difference. You do not add up the locants (that is a common misconception). You compare position by position.

Groups That Are Always Prefixes

Some groups never get a suffix because they are never the “principal” group. They always appear as prefixes:

The IUPAC system can name any organic compound unambiguously. So why do chemists still use common names like “acetone” instead of “propan-2-one”? Because common names are shorter, older, and deeply embedded in chemistry culture. Acetone has been called acetone since the 1830s. No one in a lab says “please pass the propan-2-one.” And the MCAT knows this - passages use common names constantly, especially for well-known compounds.

Your job is to know both naming systems and translate between them instantly. When a passage says “formaldehyde,” you need to see HCHO in your mind. When it says “ethanoic acid,” you need to recognize it as acetic acid (vinegar). This section gives you the definitive list of common names the MCAT expects you to know.

Why Two Systems Exist

Common names predate IUPAC naming by centuries. They came from sources (formic acid from ants), properties (glycerol from the Greek for “sweet”), or discoverers. These names carry no structural information - “acetone” tells you nothing about the three carbons or the carbonyl. But they are so widely used in biology, medicine, and industry that IUPAC officially accepts many of them as alternative names.

The Must-Know Common Names

Here is the definitive table of common names that appear on the MCAT. If you know all of these, you will never be caught off guard by a passage.

Carboxylic Acids and Derivatives

Aldehydes and Ketones

Aromatic Compounds

Alcohols and Ethers

Amines and Amides

Patterns to Notice

Several patterns make common names easier to remember:

The “form-” root comes from formic acid (methanoic acid). Compounds with one carbon in the acyl group use “form-”: formaldehyde (methanal), formamide (methanamide), formate (methanoate).

The “acet-” root comes from acetic acid (ethanoic acid). Compounds with two carbons in the acyl group use “acet-”: acetaldehyde (ethanal), acetone (propan-2-one), acetamide (ethanamide), acetyl chloride (ethanoyl chloride).

What the MCAT Actually Tests

The MCAT uses common names in two main ways:

1. In passage context: A passage might describe “the conversion of acetaldehyde to acetate” and expect you to recognize these as a two-carbon aldehyde being oxidized to a two-carbon carboxylate. If you do not know the common names, you cannot follow the passage.

2. In answer choices: A question might ask you to identify a product and list both common and IUPAC names among the answer choices. “Acetic acid” and “ethanoic acid” are the same compound - do not pick both or neither.

The MCAT rarely asks you to convert between naming systems directly (“What is the IUPAC name for acetone?”). Instead, it uses common names within passages and expects you to understand the structure and reactivity without breaking stride.

Amino Acid Common Names

Every amino acid has a common name (glycine, alanine, valine, etc.) that you must memorize for the MCAT. These are covered in the Biochemistry book, but the naming connection is important: amino acid names are purely common names - they bear no relationship to IUPAC nomenclature. “Glycine” does not tell you about its two-carbon backbone or its amino and carboxyl groups. You simply have to memorize each structure with its name and three-letter/one-letter abbreviations.

Quick Reference: Translating Names

When you encounter an unfamiliar common name on the MCAT, use these clues to decode it:

Every section up to this point has taught you one piece of the naming puzzle. Now it is time to assemble the full picture. Real MCAT molecules - amino acids, drugs, metabolic intermediates - are not simple one-functional-group compounds. They have two, three, or even four functional groups coexisting on the same carbon skeleton. Naming these polyfunctional compounds requires you to combine every rule you have learned into a systematic, step-by-step process.

The Complete Naming Algorithm

Here is the full process, from start to finish, for naming any organic molecule:

Step 1: Identify every functional group in the molecule. Scan the entire structure and list every functional group you see: -OH, -COOH, -NH2, -CHO, C=O, C=C, halogens, ethers, etc.

Step 2: Determine the principal functional group. Use the priority table from Section 1.10. The highest-priority group in the molecule gets the suffix. Everything else becomes a prefix.

Step 3: Identify the parent chain. Find the longest carbon chain that includes the principal functional group. This chain determines the root name.

Step 4: Number the parent chain. Start numbering from the end that gives the principal functional group the lowest locant. If there is a tie, give the lower locant to the double/triple bond. If there is still a tie, use the lowest set of locants for substituents.

Step 5: Name and number every substituent. Convert each non-principal functional group into its prefix form. Assign a locant to each.

Step 6: Assemble the name. List all prefixes alphabetically, followed by the parent chain root and suffix. Separate numbers from letters with hyphens. Separate numbers from numbers with commas.

Worked Example 1: An Amino Acid

Let’s name 2-aminopropanoic acid (the amino acid alanine).

Structure: CH3-CH(NH2)-COOH

Step 1: Functional groups present: carboxylic acid (-COOH) and amine (-NH2).

Step 2: Carboxylic acid (priority 1) beats amine (priority 7). Suffix = “-oic acid.”

Step 3: Longest chain through the -COOH: three carbons = propan-.

Step 4: Number from the -COOH end. The carboxyl carbon is C1 (always terminal for -oic acid).

Step 5: The amine at C2 becomes the prefix “2-amino.”

Step 6: Assemble: 2-aminopropanoic acid.

This is exactly how all amino acids are named systematically. The common name is alanine, but the IUPAC name tells you the structure: three carbons (prop-), a carboxylic acid (-oic acid) at C1, and an amine (amino-) at C2.

Worked Example 2: A Keto Acid

Let’s name 3-oxobutanoic acid (acetoacetic acid, a ketone body).

Structure: CH3-CO-CH2-COOH

Step 1: Functional groups: carboxylic acid (-COOH) and ketone (C=O in the chain interior).

Step 2: Carboxylic acid beats ketone. Suffix = “-oic acid.”

Step 3: Longest chain through the -COOH: four carbons = butan-.

Step 4: Carboxyl carbon = C1.

Step 5: The internal ketone at C3 becomes the prefix “3-oxo.”

Step 6: Assemble: 3-oxobutanoic acid.

Worked Example 3: Unsaturation Plus a Functional Group

Let’s name (E)-4-hydroxyhex-2-enoic acid.

Structure: A six-carbon chain with a carboxylic acid at C1, a trans double bond between C2 and C3, and a hydroxyl at C4.

Step 1: Functional groups: carboxylic acid, double bond, alcohol.

Step 2: Carboxylic acid is the highest priority. Suffix = “-oic acid.”

Step 3: Longest chain through -COOH and the double bond: six carbons = hex-.

Step 4: -COOH at C1. Double bond at C2 (hex-2-en-). -OH at C4.

Step 5: The alcohol becomes “4-hydroxy.” The double bond is indicated as “-2-en-” in the parent name. The E/Z designation (E)- goes at the beginning.

Step 6: Assemble: (E)-4-hydroxyhex-2-enoic acid.

Worked Example 4: A Halogenated Compound

Let’s name 5-bromo-3-methylpentan-2-one.

Structure: A five-carbon chain with a ketone at C2, a methyl branch at C3, and a bromine at C5.

Step 1: Functional groups: ketone, halide (Br), alkyl substituent (methyl).

Step 2: Ketone is the highest-priority suffix-eligible group. Suffix = “-one.”

Step 3: Five carbons = pentan-.

Step 4: Ketone at C2 = pentan-2-one.

Step 5: Methyl at C3 = “3-methyl.” Bromine at C5 = “5-bromo.”

Step 6: Alphabetical order: bromo before methyl. Assemble: 5-bromo-3-methylpentan-2-one.

Naming Compounds with Multiple Identical Functional Groups

When a molecule has two or more of the same functional group (e.g., two -OH groups), use multiplying prefixes:

• Two hydroxyl groups: “-diol” (e.g., propane-1,2-diol)
• Three hydroxyl groups: “-triol” (e.g., propane-1,2,3-triol = glycerol)
• Two carboxylic acids: “-dioic acid” (e.g., butanedioic acid = succinic acid)
• Two double bonds: “-diene” (e.g., buta-1,3-diene)
• Two amino groups: “diamino-” (e.g., 1,6-diaminohexane)

The Reverse Skill: Name to Structure

As we discussed in Section 1.1, the MCAT tests “reverse nomenclature” - reading a name and building the structure. Let’s practice this with a complex example.

Name: (Z)-2-amino-4-methylhex-4-enoic acid

Decode:

1. “-oic acid” = carboxylic acid at C1
2. “hex-” = six-carbon parent chain
3. “4-en-” = double bond starting at C4
4. “(Z)-” = higher-priority groups on same side of the double bond
5. “2-amino” = -NH2 at C2
6. “4-methyl” = -CH3 branch at C4

Build the structure:

• Draw six carbons in a chain
• Place -COOH at C1
• Place -NH2 at C2
• Place C=C between C4 and C5
• Place -CH3 at C4 (same carbon where the double bond starts)
• Arrange groups around the double bond so higher-priority groups are on the same side (Z)

This compound looks like an unusual amino acid - and indeed, many non-standard amino acids have exactly this kind of structure. The ability to build a structure from a name is the core skill the MCAT is testing.

Common MCAT Traps in Polyfunctional Naming

Trap 1: Confusing “oxo-” with “-one.” If the suffix is already taken (e.g., by -oic acid), a ketone becomes the prefix “oxo-,” not the suffix “-one.” Students who see an MCAT answer choice listing “3-oxopentanoic acid” sometimes don’t recognize that “oxo” means there is a ketone at C3.

Trap 2: Forgetting that double bonds change the parent chain ending. The parent chain is “hexan-” (no double bond) vs. “hex-2-en-” (double bond at C2). That “an” to “en” change is easy to miss in a long name.

Trap 3: Thinking all amino acids use the -amine suffix. In amino acids, the amine is never the principal group because the carboxylic acid always outranks it. The amine appears as the prefix “amino-.” The compound is named as an acid, not an amine.

Trap 4: Misordering prefixes. Prefixes must be in alphabetical order, ignoring di-, tri-, tetra-. “amino-” comes before “bromo-” which comes before “methyl-.” Scrambled prefix order is a common wrong-answer distractor.

Final Practice: Decode This Name

Name: methyl (E)-4-aminopent-2-enoate

Decode:

1. “-oate” at the end = ester
2. “methyl” at the beginning = the alkyl group on the oxygen side of the ester (from methanol)
3. “pent-” = five-carbon acyl chain
4. “2-en-” = double bond at C2
5. “(E)-” = higher-priority groups on opposite sides
6. “4-amino” = -NH2 at C4

This is a methyl ester of a five-carbon unsaturated amino acid. The structure: CH3-OOC-CH=CH-CH(NH2)-CH3 with (E) geometry at the double bond.