Introduction to Organic Chemistry: Structures, Functional Groups, and Isomers

Posted on Nov 4, 2024 in Chemistry

Basic Organic Chemistry

Organic chemistry is the study of carbon compounds. Carbon atoms are unique in their ability to form very stable chains and rings. These structures can combine with other elements such as hydrogen, oxygen, nitrogen, sulfur, and phosphorus.

Understanding organic chemistry is essential to understanding the molecular basis of the chemistry of life: Biochemistry.

General

The main differences between organic and inorganic compounds are due to changes in the composition, the type of bonds, and molecular polarity.

Symbols and Structures

Atoms are typically linked by strong covalent bonds in which different atoms share electron pairs.

Because carbon has 4 electrons in its outer orbit, it can form bonds by sharing as in the case of methane: CH4.

Tetrahedron

The molecular shape is essential for understanding the phenomena that occur at the molecular level of life.

Merge Capabilities

The valences with which other elements found in organic compounds of living cells are:

  • Hydrogen = 1
  • Oxygen = 2
  • Nitrogen = 3
  • Sulfur = 2
  • Phosphorus = 5

An example is the different combinations of methanol, which combine 1 carbon, 1 oxygen, and 4 hydrogen atoms.

Some Structural Features of Organic Compounds

Organic molecules can be linear or branched chains. They can be open-chain or cyclic, saturated or unsaturated, and be carbocyclic or heterocyclic.

  • Simple bonds are saturated.
  • Double and triple bonds are unsaturated.
  • Many organic molecules contain rings of carbon atoms.

A carbon ring is a structure of three or more carbon atoms that form a closed cycle: cyclic compounds.

  • If the ring contains only carbon: carbocyclic
  • If the ring contains atoms other than carbon, such as O, N, or S: heterocyclic

The rings of cyclic compounds can be condensed into simple polygons.

(It is understood how the carbons are linked)

Condensed structural formulas reduce the volume with little sacrifice of information.

HH

| |

HCCH becomes

| |

HH

CH3-CH3 or

HC3-CH3

It is possible to understand even the most single bonds. CH3CHCH2CH2CH3

|

CH3

Sometimes parentheses are used to pack more structures.

Functional Groups

The study of organic chemistry is organized around functional groups.

Molecular fragments that include nonmetals other than C and H, or that have double or triple bonds, are the specific sites of the organic compounds most frequently attacked by other chemicals.

Each group defines a functional organic family.

Although there are over six million compounds, only a handful of functional groups exist, and each defines a family of these compounds.

The major functional groups found in living organisms are:

  1. Aliphatic alkyl groups
  2. Hydroxy groups
  3. Amino groups
  4. Carbonyl groups
  5. Carboxyl groups
  6. Hemiacetals
  7. Acetals

Saturated Hydrocarbons

Oil

Atoms consist of only two elements: carbon and hydrogen. The covalent bonds between carbon atoms can be single, double, or triple. The carbon skeletons may be chains or rings.

Classification of Hydrocarbons

  • Alkanes: Saturated hydrocarbons with only single bonds, can be open or closed chain.
  • Alkenes: Hydrocarbons with one or more carbon-carbon double bonds, either linear or cyclic skeletons.
  • Alkynes: Hydrocarbons with one or more triple bonds.

Hydrocarbons

(containing only carbon and hydrogen)

Alkanes and Cycloalkanes

Saturated hydrocarbons

Aliphatic compounds from any family are those without aromatic benzene rings.

All hydrocarbons, saturated or not, have common physical properties.

  • They are insoluble in water due to their low polarity.
  • Those with one to four carbons per molecule are usually gaseous at room temperature.
  • Those with 5 to 16 carbon atoms are liquid at room temperature.
  • Further to this, they are waxy solids.

Nomenclature

  1. Identify the continuous chain of carbon atoms longer than the structure that is the main chain for the nomenclature.
  2. Add a prefix -ane that specifies the number of carbon atoms in the main chain. The prefixes, to C-10, are:
    • Met- 1 C
    • Et- 2 C
    • Prop- 3 C
    • But- 4 C
    • Pent- 5 C
    • Hex- 6 C
    • Hept- 7 C
    • Oct- 8 C
    • Non- 9 C
    • Dec- 10 C
  3. In the case of cycloalkanes, the application looks like: Cyclopropane, cyclobutane, cyclohexane, etc.
  4. Numbers are assigned to each carbon of the main chain, starting from the ends to give the location of the first branch, the smaller of two numbers possible.
  5. Determine the correct name of each branch (or any other atom or group).
  6. Any branch consisting only of carbon and hydrogen single bonds has just called an alkyl group, and the names of all these groups end in -yl and can be considered as an alkane with one hydrogen less.
  7. Add as a prefix the name of the alkyl group or another substituent, the number of the location of it, before the final name. Separate the issue of the name with a hyphen.
  8. If two or more groups are attached to the main chain, each is appointed and located with a number. The IUPAC nomenclature always uses hyphens to separate the numbers from words and sorts the names of alkyl groups in alphabetical sequence in the final name.
  9. When two or more substituents are identical, use prefixes such as di- (for two), tri- (for three), tetra- (four), etc., and specify the location number of each group. The numbers are always separated by a comma.
  10. When there are identical groups on the same carbon, the number repeats it in the name.
  11. To name a cycloalkane, the prefix cyclo- is placed before the name of the open-chain alkane having the same number of carbon atoms in the ring.
  12. When necessary, the atoms are numbered ring with 1 in the position that has a substituent and follows the direction in which the following substituent is closer to carbon 1.

Chemical Properties of Alkanes

  • Combustion = CO2 + H2O
  • Halogenation = substitution reactions
Combustion of Alkanes

All hydrocarbons are capable of burning, and from certain mixtures of alkanes, energy is obtained.

CH3CH2CH3 + 5O2 3CO2 + 4H2O

It sheds 531 kcal/mol of propane.

Halogenation of Alkanes

Methane, ethane, and other alkanes react with the first three members of the family of halogens: fluoride, chloride, and bromide. They do not react appreciably with iodide. The general reaction can be expressed as follows:

RH + X2 R-X + HX

Where X = F, Cl, Br

Unsaturated Hydrocarbons

Nomenclature of Alkenes

  1. Use the ending -ene for all alkenes and cycloalkenes.
  2. As a prefix to this end, we count the number of carbon atoms in the longest sequence that includes the double bond. Then use the same code that would apply if the compound was saturated.
  3. In open-chain alkenes, the main chain is numbered from the end to provide the lowest number to the first carbon double bond to be achieved. This rule gives precedence to the numbering of the double bond on the location of the first substituent in the main chain.
  4. For cycloalkenes, you should always give position 1 to one of the double bond carbons. To decide which carbon gets this issue, we must number the carbon atoms in the ring 1 through the double bond in that direction comes first to a substituent.

Chemical Properties of Alkenes

Addition Reactions

The carbon-carbon double bond adds H2, Cl2, HX, H2SO4, and H2O and is attacked by strong oxidizing agents.

  • Hydrogen binds to a double bond and becomes saturated.
  • The net effect of hydrogenation occurs at the molecular level of life.
  • Chlorine and bromine are also added to the double bonds.
  • Hydrogen chloride, hydrogen bromide (HX type compounds, asymmetric), and sulfuric acid are easily added to the double bonds.
  • Water is added to the double bond to produce alcohols. This occurs in the presence of a catalyst (acid or a suitable enzyme).
  • The carbon-carbon double bond makes the molecule susceptible to attack by strong oxidizing agents.
  • Oxidation products may be ketones, carboxylic acids, carbon dioxide, or mixtures thereof. (Alkanes are inert to oxidizing agents).

Alkynes: Hydrocarbons with Unsaturated Triple Bonds

Nomenclature: ending -yne.

The locations of the alkyne substituent groups branched and substituted alkynes are also indicated by numbers.

Reactions of Alkynes

Because the triple bond has joints similar to the double bond, alkynes give the same type of addition reaction as alkenes.

The Benzene Ring and Aromatic Compounds

The benzene ring undergoes substitution reactions rather than addition, despite its high degree of unsaturation.

Nomenclature

The names of several monosubstituted benzenes are direct. The substituent is indicated by a prefix to the word benzene. For example, nitrobenzene, fluorobenzene, chlorobenzene.

1,3,5-tribromobenzene

Ortho, meta, and para are the terms for relations 1,2-, 1,3-, and 1,4-. For example: o-dichlorobenzene, m-dichlorobenzene, p-dichlorobenzene.

Hydroxy Groups

-OH, when bonded to a hydrocarbon chain, produces a compound called alcohol. They are named with the suffix -ol. Ethanol: CH3CH2OH. Carbohydrates have multiple -OH groups.

Amino Groups

-NH2. These compounds are amines. They come from the partial or total replacement of the hydrogens of ammonia, NH3. They are named with the suffix -amine (alkyl amines).

The group is hydrophilic and reactive, and hydrogen can be replaced by other groups.

Propylamine Cyclohexylamine

Carbonyl Group

-C=O. It is one of the most important reagents, both in cells and in organic chemistry in general. There are two main types of carbonyl compounds:

  • Aldehydes have the group -C=O
  • H
  • Ketones have a group instead of H, i.e., they will be in the middle of a hydrocarbon chain.

Carboxyl Group

-COOH or -C=OH

The term comes from the combination of carbo- for carbonyl and -xyl for hydroxyl.

The suffix -oic acid is used to name them.

Examples: methanoic acid HCOOH, ethanoic acid CH3COOH, propanoic acid CH3CH2COOH

Derivatives of Carboxylic Acids

RC-Cl acyl (or acid) chloride O

Acid anhydride RCOCR OO

RCOR ester O

RC N Nitrile

Priority Rules for Nomenclature

  1. Alkyl
  2. Triple bond
  3. Double bond
  4. Amine
  5. Alcohol
  6. Ketone
  7. Aldehyde
  8. Amide
  9. Halides
  10. Carboxylic acid

Hemiacetals

They are formed from the reaction of an aldehyde or ketone with an alcohol.

Acetals

They are formed from a hemiacetal with another molecule of alcohol.

These groups are particularly important in carbohydrate chemistry.

H OH OR

RC=O RC- RC-OR OR

H

Isomerism

Subdivision of Isomers

Isomers

(different compounds with the same molecular formula)

  • Constitutional isomers: isomers whose atoms have a different connectivity.
  • Stereoisomers: Isomers that have the same connectivity but differ in the arrangement of their atoms in space.
  • Enantiomers: Stereoisomers that are non-superimposable mirror images.
  • Diastereomers: stereoisomers that are not mirror images.
  • Epimers: They differ in the composition of a single chiral carbon.
  • Anomers: They differ in the configuration of the hemiacetal carbon.

Examples

Constitutional isomers

Examples

Stereoisomers

Examples

Diastereomers

Epimers