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Organic Nomenclature Notes

Naming Organic Compounds

  • Organic chemistry possesses a varied chemistry with its own set of naming rules.

  • The range of elements is small.

Organic Nomenclature

  • Organic chemistry started around 1828 when Wöhler synthesized urea.

  • 2AgOCN + 2NH4Cl \rightarrow (NH2)_2CO (unbalanced)

  • Early names were convenient with related origins (e.g., urea from urine).

  • Common names include α-pinene and citral.

  • Friedrich Wöhler is a key figure.

Pharmaceutical Naming

  • Many names are used (e.g., from Merck index).

  • Examples:

    • Panadol (trade name, little information about the molecule).

    • p-hydroxyacetanilide.

    • p-Acetamidophenol.

    • N-Acetyl-p-aminophenol.

    • p-Acetyaminophenol.

    • Nobedon, APAP, Tabalgin, Dymadon, Naprinol, Panets, Homoolan.

    • Febrilix, Abensanil, Anaflon, Amadil, Eneril, Tralgon, Hedex, Pacemo, Parmol.

    • Tylenol, Lyteca Apamide, Acetaminophen.

  • IUPAC: N-(4-hydroxyphenyl)ethanamide; Paracetemol.

  • Drug naming can be complex.

IUPAC Organic Naming

  • A system was needed to provide a unique, globally understood name for each organic compound.

  • Correspondence between structure and name is important.

  • Result: IUPAC naming rules.

  • Many rules exist: http//www.acdlabs.com/iupac/nomenclature

  • Need to learn basic principles to understand and use IUPAC naming.

General vs Systematic

  • Both IUPAC and common names can be used.

  • Common (alternative) names: methyl alcohol, formaldehyde, acetic acid (sometimes ambiguous).

  • Systematic (IUPAC) names: methanol, methanal, ethanoic acid (unambiguous).

Systematic Nomenclature

  • Organic compounds (beyond alkanes) are named according to their functional group(s).

  • Examples:

    • R-OH: hydroxyl group, alcohols.

    • R-CHO: carbonyl group, aldehydes.

    • R-CO-R: carbonyl group, ketones.

    • R-CO_2H: carboxyl group, carboxylic acids.

  • The functional group that places the compound in its class is the highest priority functional group (HPFG).

Basic Nomenclature

  • Naming system is based on the number of carbon atoms and functional group(s) present.

  • Counting: Needed to count reliably to 10 using the root naming system (parent).

Numbering in Organics

  • Identify the Functional Group (FG) first, as the suffix and numbering are based on it.

    1. For aldehydes, carboxylic acids & derivatives, the C=O is always C1.

    2. For all other cases, the HPFG gets the lowest possible number in the parent chain.

    3. Chain branches are then given the lowest numbering.

    4. A FG attaches to a ring at C1.

General IUPAC Naming

  • The name of any compound with a chain of carbon atoms consists of 3-4 parts:

    • A prefix: relates to the number, type, and position of substituents (alphabetical order).

    • A parent: shows the number of carbon atoms in the parent chain (contains the HPFG).

    • An infix: shows the nature/numbering of any functional group in the parent chain.

    • A suffix: shows the class of compound (main functional group).

  • Example: H3C-CH(OH)-CH(CH3)-CH2CH2CH_3 is 3-methylhexan-2-ol.

  • On-line resources available.

Parent / Prefix Naming

  • The parent root is generally from the names of the parent alkanes.

  • Examples:

    • 1 Carbon: Methane (CH_4)

    • 2 Carbons: Ethane (CH3CH3)

    • 3 Carbons: Propane (CH3CH2CH_3)

    • 4 Carbons: Butane (CH3(CH2)2CH3)

    • 5 Carbons: Pentane (CH3(CH2)3CH3)

    • 6 Carbons: Hexane (CH3(CH2)4CH3)

    • 7 Carbons: Heptane (CH3(CH2)5CH3)

    • 8 Carbons: Octane (CH3(CH2)6CH3)

    • 9 Carbons: Nonane (CH3(CH2)7CH3)

    • 10 Carbons: Decane (CH3(CH2)8CH3)

  • A C3 skeleton becomes propan…; as a substituent (R), it becomes propyl…

Parent Naming Examples

  1. If the functional group is hydroxyl, the suffix is -ol (alcohol).

    • Longest chain is C3, so parent/suffix is propan-1-ol.

  2. If the functional group is an arene.

    • The parent stem is benzene.

    • With a C3 substituent, it's 1-propylbenzene.

Suffix Naming

  • Use flash cards and/or software tools to learn classes & naming.

  • Identify the functional group.

  • Map to the class of compound.

  • Map to a suffix that goes with the class.

  • Add suffix to the parent, then move to prefixes.

  • Example: Functional group: amino; Class: amine; Suffix: -amine; Parent/Suffix: pentanamine; Name: pentan-1-amine.

Prefix Naming

  • Prefixes often deal with substituent branches off the parent.

  • Mostly alkyl branches (R = CH3, CH3CH2…); aryl branch (R = aromatic) is phenyl (C6H_5).

  • List multiple substituents in alphabetical order (ignoring multiplying prefixes).
    *Functional group: hydroxyl; Class: alcohol; Suffix: -ol; Prefix/Parent/Suffix: cyclohexylmethylpropanol; IUPAC Name: 3-cyclohexyl-2-methylpropan-1-ol.

Prefix Naming II

  • Substituents off the parent are in alphabetical order.

    • 1-ethyl-2-methylcyclopropane (N.B. the cyclised alkane gets the cyclo- prefix).

  • Groups off an amino or amido N are indicated with N in front of the substituent.

    • N,N-dimethylethanamide.
      *Functional group: amido; Class: amide; Suffix: -amide; Parent/Suffix: N,N-dimethylethanamide.

Applying the System

  • Some naming quirks:

    • Propane + Cl \rightarrow 1-chloropropane.

    • Propane + OH \rightarrow propan-1-ol.

    • Chain modification uses an infix number: prop-1-ene.

  • Sometimes one-word names, sometimes two (e.g., diethyl ether = 1-ethoxyethane).

Naming Examples

  • General nomenclature: worked examples

    • H3C-CH=CH2 propene (carbon-carbon double bond, 3 carbon atoms).

    • CH3CH2CH2CH2COH pentanoic acid (carbon-carbon single bonds, -COOH group, 5 carbon atoms).

    • prop-1-ene, pentanoic acid

Priority of Functional Groups

  • With multiple functional groups, a priority order is used.

  • The HPFG determines the class, hence the suffix.

  • The subordinate functional group uses a prefix (e.g., 3-hydroxypentanoic acid).

  • Infix names: -en-, -yn-.

Tamiflu

  • The same approach is used for complex molecules.

  • Oseltamivir (Tamiflu): ethyl (3R,4R,5S)-4-acetamido-5-amino-3-(pentan-3-yloxy)-cyclohex-1-ene-1-carboxylate.

  1. Prefix: number, type, position of substituents.

  2. Parent: number of carbons in the parent chain.

  3. Infix: nature/numbering of functional groups in the parent chain.

  4. Suffix: class of compound, functional group(s).

Alkane Nomenclature

  • Alkanes have no functional group.

  • They are hydrocarbons: C and H only.

  • Carbon atoms are joined by single bonds only.

  • Two parts to the name:

    • Prefix: number of carbon atoms in the longest chain.

    • Suffix: -ane.

  • Alkanes form an homologous series differing by CH2. General formula: CnH_{2n+2}

  • ALK-ane (e.g., C(1)H4 Meth-ane, C2H6 Eth-ane, C3H8 Prop-ane, C4H10 But-ane, C5H12 Pent-ane, C6H14 Hex-ane, C7H16 Hept-ane, C8H18 Oct-ane, C9H20 Non-ane, C10H22 Dec-ane).

Alkyl Nomenclature

  • Alkyl substituents - carbon chains as branches

    • CH_3: Methyl (Me, C1)

    • CH3CH2: Ethyl (Et, C2)

    • CH3CH2CH_2: Propyl (nPr, C3)

    • CH3CH2CH2CH2 : Butyl (nBu, C4)

  • n- (normal) often used for non-branched alkyls but this is not IUPAC nomenclature!

Iso, Sec, Tert Nomenclature

  • Carbon chains as ‘branched’ branches with specific naming

    • iso-Alkyl

    • sec-Alkyl

    • tert-Alkyl substituents

    • (CH3)2CH: isopropyl (iPr, C3)

    • (CH3)2CHCH_2: isobutyl (iBu, C4)

    • CH3CH2CH(CH_3) - sec-butyl (secondary) (sBu, C4)

    • (CH3)3C: tert-butyl (tertiary) (tBu, C4)

IUPAC Naming of Alkanes

  • IUPAC rules for naming alkanes:

    1. The name of an alkane with an unbranched chain of carbon atoms consists of a prefix representing the number of carbon atoms in the chain and ends in the suffix –ane. n- (normal) often used for non-branched alkanes but this is not preferred IUPAC nomenclature (PIN)!

      • 6 carbons: n-hexane \rightarrow hexane

IUPAC Naming of Alkanes

  1. For branched-chain alkanes, the longest chain of carbon atoms is the parent chain

    • Number the parent chain so the carbon atom bearing the substituent is given the lowest possible number

    • methylhexane

IUPAC Naming of Alkanes

  1. Give a substituent on the parent chain a name and number. The number shows the carbon atom of the parent chain to which the substituent is bonded. Use a hyphen to connect the number to the name

    • 3-methylhexane

IUPAC Naming of Alkanes

  1. If there are two or more identical substituents, number the parent chain from the end that gives the lower number to the substituent closest to the end of the chain. Prefixes (di-, tri-, tetra- etc.) indicate the number of times a substituent is used.

    • 2,4-dimethylhexane

  2. IUPAC: number the parent chain from the end that gives the lowest term at the first point of difference; eg. the locant set ‘2,3,5,8’ is lower than ‘3,4,6,8’ and ‘2,4,5,7’

IUPAC Naming of Alkanes

  1. If there are two or more different substituents, list them in alphabetical order, and number the chain from the end that gives the lower number to the substituent closest to the end of the chain.

    • 5-ethyl-3-methyloctane not 3-methy-5-ethyloctane {alphabetical error} not 4-ethyl-6-methyloctane {numbering error}

IUPAC Naming of Alkanes

  • The prefixes di, tri, tetra etc. (and the hyphenated prefixes sec- and tert-) are disregarded for the purposes of placing the substituents in alphabetical order

    • 4-ethyl-2,2-dimethylhexane Not (2,2-dimethyl4-ethyl-hexane {alphabetic} Not 3-ethyl-5,5-dimethylhexane {numeric})

IUPAC Naming of Alkanes

  • Isopropyl (i-Pr) and isobutyl (i-Bu) group are special cases. We prefix iso- in alphabetical order with other substituents. Cyclo is the same.

    • 4-isopropyl-2-methylheptane

Summary Naming of Alkanes

  1. Find longest chain

  2. Find substituents

  3. Number so substituents are numbered lowest

    • Each must have a number

    • Commas between numbers

    • Hyphen to indicate substituent

  4. List in alphabetical order

    • Don’t include di,tri

    • Include iso, cyclo..

    • A hyphen between substituents

  5. Put it all together

    • No space/hyphen to parent

    • 4-ethyl-2,2-dimethylhexane hexane 2(di) x methyl and 1 x ethyl 2,2-dimethyl and 4-ethyl 4-ethyl-2,2-dimethyl

Naming Organic Compounds

  • Organic chemistry possesses a varied chemistry with its own set of naming rules.

  • The range of elements is small.

Organic Nomenclature

  • Organic chemistry started around 1828 when Wöhler synthesized urea.

  • 2AgOCN + 2NH4Cl \rightarrow (NH2)_2CO (unbalanced)

  • Early names were convenient with related origins (e.g., urea from urine).

  • Common names include α-pinene and citral.

  • Friedrich Wöhler is a key figure.

Pharmaceutical Naming

  • Many names are used (e.g., from Merck index).

  • Examples:-

    • Panadol (trade name, little information about the molecule).

    • p-hydroxyacetanilide.

    • p-Acetamidophenol.

    • N-Acetyl-p-aminophenol.

    • p-Acetyaminophenol.

    • Nobedon, APAP, Tabalgin, Dymadon, Naprinol, Panets, Homoolan.

    • Febrilix, Abensanil, Anaflon, Amadil, Eneril, Tralgon, Hedex, Pacemo, Parmol.

    • Tylenol, Lyteca Apamide, Acetaminophen.

  • IUPAC: N-(4-hydroxyphenyl)ethanamide; Paracetemol.

  • Drug naming can be complex.

IUPAC Organic Naming

  • A system was needed to provide a unique, globally understood name for each organic compound.

  • Correspondence between structure and name is important.

  • Result: IUPAC naming rules.

  • Many rules exist: http//www.acdlabs.com/iupac/nomenclature

  • Need to learn basic principles to understand and use IUPAC naming.

General vs Systematic

  • Both IUPAC and common names can be used.

  • Common (alternative) names: methyl alcohol, formaldehyde, acetic acid (sometimes ambiguous).

  • Systematic (IUPAC) names: methanol, methanal, ethanoic acid (unambiguous).

Systematic Nomenclature

  • Organic compounds (beyond alkanes) are named according to their functional group(s).

  • Examples:-

    • R-OH: hydroxyl group, alcohols.

    • R-CHO: carbonyl group, aldehydes.

    • R-CO-R: carbonyl group, ketones.

    • R-CO_2H: carboxyl group, carboxylic acids.

  • The functional group that places the compound in its class is the highest priority functional group (HPFG).

Basic Nomenclature

  • Naming system is based on the number of carbon atoms and functional group(s) present.

  • Counting: Needed to count reliably to 10 using the root naming system (parent).

Numbering in Organics

  • Identify the Functional Group (FG) first, as the suffix and numbering are based on it.

  1. For aldehydes, carboxylic acids & derivatives, the C=O is always C1.

  2. For all other cases, the HPFG gets the lowest possible number in the parent chain.

  3. Chain branches are then given the lowest numbering.

  4. A FG attaches to a ring at C1.

General IUPAC Naming

  • The name of any compound with a chain of carbon atoms consists of 3-4 parts:-

    • A prefix: relates to the number, type, and position of substituents (alphabetical order).

    • A parent: shows the number of carbon atoms in the parent chain (contains the HPFG).

    • An infix: shows the nature/numbering of any functional group in the parent chain.

    • A suffix: shows the class of compound (main functional group).

  • Example: H3C-CH(OH)-CH(CH3)-CH2CH2CH_3 is 3-methylhexan-2-ol.

  • On-line resources available.

Parent / Prefix Naming

  • The parent root is generally from the names of the parent alkanes.

  • Examples:-

    • 1 Carbon: Methane (CH_4)

    • 2 Carbons: Ethane (CH3CH3)

    • 3 Carbons: Propane (CH3CH2CH_3)

    • 4 Carbons: Butane (CH3(CH2)2CH3)

    • 5 Carbons: Pentane (CH3(CH2)3CH3)

    • 6 Carbons: Hexane (CH3(CH2)4CH3)

    • 7 Carbons: Heptane (CH3(CH2)5CH3)

    • 8 Carbons: Octane (CH3(CH2)6CH3)

    • 9 Carbons: Nonane (CH3(CH2)7CH3)

    • 10 Carbons: Decane (CH3(CH2)8CH3)

  • A C3 skeleton becomes propan…; as a substituent (R), it becomes propyl…

Parent Naming Examples

  1. If the functional group is hydroxyl, the suffix is -ol (alcohol).-
    Longest chain is C3, so parent/suffix is propan-1-ol.

  2. If the functional group is an arene.-
    The parent stem is benzene.

    • With a C3 substituent, it's 1-propylbenzene.

Suffix Naming

  • Use flash cards and/or software tools to learn classes & naming.

  • Identify the functional group.

  • Map to the class of compound.

  • Map to a suffix that goes with the class.

  • Add suffix to the parent, then move to prefixes.

  • Example: Functional group: amino; Class: amine; Suffix: -amine; Parent/Suffix: pentanamine; Name: pentan-1-amine.

Prefix Naming

  • Prefixes often deal with substituent branches off the parent.

  • Mostly alkyl branches (R = CH3, CH3CH2…); aryl branch (R = aromatic) is phenyl (C6H_5).

  • List multiple substituents in alphabetical order (ignoring multiplying prefixes).
    *Functional group: hydroxyl; Class: alcohol; Suffix: -ol; Prefix/Parent/Suffix: cyclohexylmethylpropanol; IUPAC Name: 3-cyclohexyl-2-methylpropan-1-ol.

Prefix Naming II

  • Substituents off the parent are in alphabetical order.-
    1-ethyl-2-methylcyclopropane (N.B. the cyclised alkane gets the cyclo- prefix).

  • Groups off an amino or amido N are indicated with N in front of the substituent.-
    N,N-dimethylethanamide.
    *Functional group: amido; Class: amide; Suffix: -amide; Parent/Suffix: N,N-dimethylethanamide.

Applying the System

  • Some naming quirks:-

    • Propane + Cl \rightarrow 1-chloropropane.

    • Propane + OH \rightarrow propan-1-ol.

    • Chain modification uses an infix number: prop-1-ene.

  • Sometimes one-word names, sometimes two (e.g., diethyl ether = 1-ethoxyethane).

Naming Examples

  • General nomenclature: worked examples-

    • H3C-CH=CH2 propene (carbon-carbon double bond, 3 carbon atoms).

    • CH3CH2CH2CH2COH pentanoic acid (carbon-carbon single bonds, -COOH group, 5 carbon atoms).

    • prop-1-ene, pentanoic acid

Priority of Functional Groups

  • With multiple functional groups, a priority order is used.

  • The HPFG determines the class, hence the suffix.

  • The subordinate functional group uses a prefix (e.g., 3-hydroxypentanoic acid).

  • Infix names: -en-, -yn-.

Tamiflu

  • The same approach is used for complex molecules.

  • Oseltamivir (Tamiflu): ethyl (3R,4R,5S)-4-acetamido-5-amino-3-(pentan-3-yloxy)-cyclohex-1-ene-1-carboxylate.

  1. Prefix: number, type, position of substituents.

  2. Parent: number of carbons in the parent chain.

  3. Infix: nature/numbering of functional groups in the parent chain.

  4. Suffix: class of compound, functional group(s).

Alkane Nomenclature

  • Alkanes have no functional group.

  • They are hydrocarbons: C and H only.

  • Carbon atoms are joined by single bonds only.

  • Two parts to the name:-

    • Prefix: number of carbon atoms in the longest chain.

    • Suffix: -ane.

  • Alkanes form an homologous series differing by CH2. General formula: CnH_{2n+2}

  • ALK-ane (e.g., C(1)H4 Meth-ane, C2H6 Eth-ane, C3H8 Prop-ane, C4H10 But-ane, C5H12 Pent-ane, C6H14 Hex-ane, C7H16 Hept-ane, C8H18 Oct-ane, C9H20 Non-ane, C10H22 Dec-ane).

Alkyl Nomenclature

  • Alkyl substituents - carbon chains as branches-

    • CH_3: Methyl (Me, C1)

    • CH3CH2: Ethyl (Et, C2)

    • CH3CH2CH_2: Propyl (nPr, C3)

    • CH3CH2CH2CH2 : Butyl (nBu, C4)

  • n- (normal) often used for non-branched alkyls but this is not IUPAC nomenclature!

Iso, Sec, Tert Nomenclature

  • Carbon chains as ‘branched’ branches with specific naming-

    • iso-Alkyl

    • sec-Alkyl

    • tert-Alkyl substituents

    • (CH3)2CH: isopropyl (iPr, C3)

    • (CH3)2CHCH_2: isobutyl (iBu, C4)

    • CH3CH2CH(CH_3) - sec-butyl (secondary) (sBu, C4)

    • (CH3)3C: tert-butyl (tertiary) (tBu, C4)

IUPAC Naming of Alkanes

  • IUPAC rules for naming alkanes:

  1. The name of an alkane with an unbranched chain of carbon atoms consists of a prefix representing the number of carbon atoms in the chain and ends in the suffix –ane. n- (normal) often used for non-branched alkanes but this is not preferred IUPAC nomenclature (PIN)!-

    • 6 carbons: n-hexane \rightarrow hexane

IUPAC Naming of Alkanes

  1. For branched-chain alkanes, the longest chain of carbon atoms is the parent chain- Number the parent chain so the carbon atom bearing the substituent is given the lowest possible number

    • methylhexane

IUPAC Naming of Alkanes

  1. Give a substituent on the parent chain a name and number. The number shows the carbon atom of the parent chain to which the substituent is bonded. Use a hyphen to connect the number to the name-
    3-methylhexane

IUPAC Naming of Alkanes

  1. If there are two or more identical substituents, number the parent chain from the end that gives the lower number to the substituent closest to the end of the chain. Prefixes (di-, tri-, tetra- etc.) indicate the number of times a substituent is used.-
    2,4-dimethylhexane

  2. IUPAC: number the parent chain from the end that gives the lowest term at the first point of difference; eg. the locant set ‘2,3,5,8’ is lower than ‘3,4,6,8’ and ‘2,4,5,7’

IUPAC Naming of Alkanes

  1. If there are two or more different substituents, list them in alphabetical order, and number the chain from the end that gives the lower number to the substituent closest to the end of the chain.-
    5-ethyl-3-methyloctane not 3-methy-5-ethyloctane {alphabetical error} not 4-ethyl-6-methyloctane {numbering error}

IUPAC Naming of Alkanes

  • The prefixes di, tri, tetra etc. (and the hyphenated prefixes sec- and tert-) are disregarded for the purposes of placing the substituents in alphabetical order-
    4-ethyl-2,2-dimethylhexane Not (2,2-dimethyl4-ethyl-hexane {alphabetic} Not 3-ethyl-5,5-dimethylhexane {numeric})

IUPAC Naming of Alkanes

  • Isopropyl (i-Pr) and isobutyl (i-Bu) group are special cases. We prefix iso- in alphabetical order with other substituents. Cyclo is the same.-
    4-isopropyl-2-methylheptane

Summary Naming of Alkanes

  1. Find longest chain

  2. Find substituents

  3. Number so substituents are numbered lowest-

    • Each must have a number

    • Commas between numbers

    • Hyphen to indicate substituent

  4. List in alphabetical order-

    • Don’t include di,tri

    • Include iso, cyclo..

    • A hyphen between substituents

  5. Put it all together-

    • No space/hyphen to parent

    • 4-ethyl-2,2-dimethylhexane hexane 2(di) x methyl and 1 x ethyl 2,2-dimethyl and 4-ethyl 4-ethyl-2,2-dimethyl