Intro to Organic Chemistry Nomenclature.pdf

Introduction to Organic Chemistry Nomenclature All organic compounds are made up of at least carbon and hydrogen. Carbon is a special element because it can make 4 bonds and hybridize its atomic orbitals.

Table 1: Organic Prefixes (based on number of carbon atoms in the molecule) # of Carbon atoms

Prefix

1

Meth-

2

Eth-

3

Prop-

4

But-

5

Pent-

6

Hex-

7

Hept-

8

Oct-

9

Non-

10

Dec-

Line Notation (Example= -ane)

3-D Structure

∙

With the exception of methane, the line structure shows linear arrangement of the organic molecule, with: - 𝐶𝐻3 at the start & end of the chain (head and tail) and, - 𝐶𝐻2 in the middle of the chain (body). Similarly, the 3-D structure shows the carbon atoms (black) and hydrogen atoms (white) arranged in the same way. 1

Wedge – Dash Notation Representing a molecule in 3-D is often done using the wedge and dash symbols, e.g. methane:

Line = in the plane of the paper Dash = behind the paper Wedge = in front of the paper

Table 2: Hydrocarbons (only carbon and hydrogen are present) Homologous Series

Bond Type

Hybridization

Formula

Suffix

Example Ethane

Alkanes

𝑠𝑝3 Single

𝐶−𝐶

𝐶𝑛 𝐻2𝑛+2

-ane

𝜎 Cyclobutane Cycloalkanes

2 H’s removed from ends of an alkane and C’s are joined

Varies

𝐶𝑛 𝐻2𝑛

Cyclo____-ane

Ethene Alkenes

𝑠𝑝

2

Double 𝐶 = 𝐶

𝐶𝑛 𝐻2𝑛

-ene

𝜎+𝜋

Alkynes

Ethyne

𝑠𝑝 Triple

𝐶≡𝐶

𝐶𝑛 𝐻2𝑛−2

-yne

𝜎+𝜋+𝜋

Alkanes are of great importance to the different classification systems and the naming of organic compounds because they consist of a carbon chain that forms the main structural unit of all organic substances. When an alkane carbon chain is modified in any way, even by the mere introduction of an 𝑠𝑝2 carbon or a heteroatom (atoms other than carbon and hydrogen), it is said to be functionalized. In other words, a functional group has been introduced and a new class of organic substances has been created. A functional group is a specific arrangement of certain atoms in an organic molecule that becomes the center of reactivity. That is, it is the portion of the structure that 2 controls the reactivity of the entire molecule and much of its physical properties. (Source: www.utdallas.edu/~scortes/ochem/OChem1_Lecture/Class_Materials/07_org_nomenclature1.pdf)

Table 3: Haloalkanes aka Alkyl Halides (at least 1 C – X bond, where X is a halogen) Series

Formula

Example

Alkyl Fluorides

𝐶−𝐹

Fluoromethane

Alkyl Chlorides

𝐶 − 𝐶𝑙

1-Chlorobutane

Alkyl Bromides

𝐶 − 𝐵𝑟

Bromomethane

Alkyl Iodides

𝐶−𝐼

Iodoethane

Shape

Halogens (F, Cl, Br, I) are usually not named in the suffix of a compound. They get named as substituents (fluoro, chloro, bromo, iodo). Table 4: Nitrogen Functional Groups Series

Structure

Nitrogen Hybridization

Suffix

Example Propanamide

Amides

𝑠𝑝3

-amide

Phenylamine Amines

𝑠𝑝3

-amine

Acetonitrile Nitriles

𝑠𝑝

-nitrile

3

Table 5: Oxygen Functional Groups Series

Structure

Oxygen Hybridization

Suffix

Example Acetyl chloride

Acyl Halides

𝑠𝑝2

-oyl halide

Ethanol Alcohols

𝑠𝑝3

-ol

Formaldehyde Aldehydes

𝑠𝑝2

-al

Acetic anhydride Anhydrides

𝑠𝑝2 and 𝑠𝑝3

anhydride

Acetic acid Carboxyls

𝑠𝑝2 and 𝑠𝑝3

-oic acid

Ethyl acetate Esters

𝑠𝑝2 and 𝑠𝑝3

-oate

Ethoxyethane (diethyl ether) Ethers

𝑠𝑝3

-ether

Propanone (acetone) Ketones

𝑠𝑝2

-one 4

Table 6: Alkyl Groups (branched alkanes and free radicals) Alkyl Groups 1 Carbon

2 Carbons

3 Carbons

4 Carbons

5 Carbons

Methyl

Ethyl

Propyl

Butyl

Pentyl

⧘−𝐶𝐻3

⧘−𝐶𝐻2 𝐶𝐻3

⧘−𝐶𝐻2 𝐶𝐻2 𝐶𝐻3

⧘−𝐶𝐻2 𝐶𝐻2 𝐶𝐻2 𝐶𝐻3

⧘−𝐶𝐻2 𝐶𝐻2 𝐶𝐻2 𝐶𝐻2 𝐶𝐻3

isopropyl (1-methylethyl)

sec-butyl (1-methylpropyl)

isopentyl (3-methylbutyl)

isobutyl (2-methylpropyl)

neopentyl (2, 2-dimethylpropyl)

tert-butyl (1, 1-dimethylethyl)

tert-pentyl (1, 1-dimethylpropyl)

The names of alkyl groups are the same as those of analogous alkanes, except that their names end in – yl, instead of –ane. Alky groups never exist by themselves. Rather, they are usually attached to another chain, which is why they are sometimes called substituents. Also, the IUPAC names are in parenthesis, while the common names are not.

The iso structural unit consists of two methyl groups attached to a common carbon. When this unit is present in an alkane or alky group, the common name starts with the prefix iso.

5

Geometrical Isomerism (Cis / Trans) Cis / trans isomerism is a form of stereoisomerism describing the orientation of functional groups within a molecule. In general, such isomers contain double bonds, which cannot rotate, but they can also arise from ring structures, wherein you have restricted rotation somewhere in a molecule. cis = "on the same side" trans = "across"

For example consider 1,2-dichloroethene (pictured above). If you were to use a molecular stereochemistry set to model these two molecules, they wouldn’t be the same; in fact they aren't the same. This is due to the restricted rotation of the 𝐶 = 𝐶 bond. If you have to take a model to pieces to convert it into another one, then you've got isomers. If you only need to twist it, they are not isomers. You can use this method to test for isomers. It’s worth looking at the symmetry of the molecules to determine whether either isomer is polar.

***Note: In the model, the reason that you can't rotate a 𝐶 = 𝐶 bond is that there are two links joining the carbons together. In reality, the reason is that you would have to break the pi bond. Pi bonds are formed by the sideways overlap between p orbitals. If you tried to rotate the carbon-carbon bond, the p orbitals won't line up any more and so the pi bond is disrupted. This costs energy and only happens if the compound is heated strongly. (source: http://www.chemguide.co.uk/basicorg/isomerism/geometric.html) General criteria for cis / trans isomers:  Restricted rotation (often carbon double bonds)  Two different groups on the left-hand carbon and two different groups on the right-hand one Physical properties of cis / trans isomerism: In general, you will notice that  

the cis isomer has the higher boiling point (polar, pack poorly as a solid) the trans isomer has the higher melting point (nonpolar, pack better as a solid)

6

Alkane Nomenclature (common name vs IUPAC name) Since alkanes are the most fundamental types of organic compounds, their structural features (a basic carbon chain, or skeleton) provide the basis for the nomenclature of all organic compounds. In the earliest nomenclature systems, substances were named based on their smell, or their natural source, etc., thus, given a common name. In modern chemistry, the International Union of Pure and Applied Chemistry (IUPAC) sets the rules for nomenclature of organic compounds. Every known organic substance has an IUPAC name. Since we are only focusing on introductory organic chemistry, i.e. simple molecules, there are a few rules to keep in mind for nomenclature. In general, there are five parts to naming:  functional groups (e.g. amines, alcohols…)  unsaturation (not mentioned in this guide),  parent chain (# of C’s – hexa-, hepta-, oct-…)  substituents (e.g. alkyl groups…) and,  cis / trans isomerism (for double bonds). IUPAC Rules 1. Identify the length of the longest, continuous carbon chain (count # of C’s) and select the appropriate prefix (meth-, eth-, prop-, but-, pent-, hex-, etc.). End with appropriate suffix (-ane, -ene, -yne, -yl, -ol, etc.). 2. Identify any branches, called substituents. The names of alkyl groups are the same as those of analogous alkanes, except that their names end in -yl, instead of –ane (see Table 6). Alkyl groups are usually the first part of the name and the carbon chain is the last part (e.g. Dimethylhexane). 3. Specify the exact position of any substituent(s) by numbering the main chain from the end closest to the substituent (could be from left to right, or from right to left!). 4. IF there are multiple substituents of the same kind, first specify each of their positions with a number, then use the prefixes di-, tri-, tetra-, etc. to indicate how many are present. Number the carbons of the parent chain from the end that gives the substituents the lowest numbers. If two or more side chains are in equivalent positions, assign the lowest number to the one which will come first in the name. 5. If there are multiple, different substituents present, name them in alphabetical order (e.g. butyl before propyl). Prefixes such as di-, tri-, tetra-, etc. are ignored when alphabetizing EXCEPT for iso. 6. If there are several options for choosing the longest continuous carbon chain, choose the one that yields:  the longest continuous carbon chain with the greatest number of simpler substituents, and  the name that has the lowest set of numbers indicating the substituent positions. In summary, the name of the compound is written out with the substituents in alphabetical order followed by the base name (derived from the number of carbons in the parent chain). Commas are used between numbers and dashes are used between letters and numbers. There are no spaces in the name.

(Source: www.utdallas.edu/~scortes/ochem/OChem1_Lecture/Class_Materials/07_org_nomenclature1.pdf)

7