Organic Chemistry: Functional Groups

• Organic chemistry is the study of the structure, properties, composition, reactions, and preparation of carbon-containing compounds, which may contain many other elements, including hydrogen, nitrogen, oxygen, halogens, phosphorus, silicon, and sulfur.

Functional Groups

• A functional group is a specific group of atoms within a molecule that is responsible for a characteristic chemical behavior of that molecule.
• Molecules can be classified based on their functional groups.
• Functional groups undergo the same types of chemical reactions regardless of the structure of the rest of the molecule.
• The following are common functional groups:
  • Alkanes contain only C-C and C-H single bonds, and are generally unreactive.
  • Alkenes have C=C double bonds and undergo addition reactions.
  • Alkynes have C≡C triple bonds and also undergo addition reactions.
  • Aromatic rings contain alternating single and double bonds in a cyclic structure, and undergo substitution reactions.
  • Alcohols contain a hydroxyl group (-OH) bonded to a saturated carbon atom.
  • Ethers contain an oxygen atom bonded to two alkyl or aryl groups (R-O-R').
  • Aldehydes contain a carbonyl group (C=O) with at least one hydrogen atom attached to the carbonyl carbon.
  • Ketones contain a carbonyl group (C=O) with two alkyl or aryl groups attached to the carbonyl carbon.
  • Carboxylic acids contain a carboxyl group (-COOH).
  • Esters contain a carbonyl group with an oxygen atom bonded to the carbonyl carbon and an alkyl or aryl group (R-COO-R').
  • Amines contain a nitrogen atom bonded to one, two, or three alkyl or aryl groups, and are classified as primary, secondary, or tertiary amines, respectively.
  • Amides contain a carbonyl group bonded to a nitrogen atom (R-CO-NR'R'').
  • Halides contain a halogen atom (F, Cl, Br, I) bonded to an alkyl or aryl group.
  • Thiols contain a sulfhydryl group (-SH) bonded to an alkyl or aryl group.
  • Sulfides contain a sulfur atom bonded to two alkyl or aryl groups (R-S-R').

Reaction Mechanisms

• A reaction mechanism is a step-by-step sequence of elementary reactions by which overall chemical change occurs.
• Reaction mechanisms describe in detail exactly what takes place at each stage of a chemical reaction.
• Types of reaction mechanisms include:
  • Addition reactions occur when two or more molecules combine to form a larger molecule.
  • Elimination reactions involve the removal of atoms or groups of atoms from a molecule to form a double or triple bond.
  • Substitution reactions involve the replacement of one atom or group of atoms with another atom or group of atoms.
  • Rearrangement reactions involve the reorganization of atoms and bonds within a molecule.
• Key components of reaction mechanisms:
  • Nucleophiles are electron-rich species that are attracted to electron-deficient centers (electrophiles).
  • Electrophiles are electron-deficient species that are attracted to electron-rich centers (nucleophiles).
  • Leaving groups are atoms or groups of atoms that depart from a molecule during a reaction, taking a pair of electrons with them.
  • Carbocations are positively charged carbon atoms that are highly reactive intermediates.
  • Carbanions are negatively charged carbon atoms that are also reactive intermediates.
  • Radicals are species with unpaired electrons.
• Arrow pushing notation is used to illustrate the movement of electrons in a reaction mechanism. Arrows show the flow of electrons from a nucleophile to an electrophile or from a bond to an atom.
• Reaction intermediates are transient species that are formed during a multi-step reaction.
• Transition states are the highest energy point along the reaction pathway and represent the point at which bonds are breaking and forming.
• Energy diagrams illustrate the energy changes that occur during a reaction; they show the relative energies of reactants, products, intermediates, and transition states.

Stereochemistry

• Stereochemistry is the study of the three-dimensional structure of molecules.
• Isomers are molecules with the same molecular formula but different structural arrangements.
• Structural isomers have different connectivity of atoms.
• Stereoisomers have the same connectivity of atoms but different spatial arrangements.
• Enantiomers are stereoisomers that are non-superimposable mirror images of each other.
• Chiral molecules are molecules that are non-superimposable on their mirror images.
• A chiral center is an atom, usually carbon, that is bonded to four different groups.
• Diastereomers are stereoisomers that are not enantiomers.
• Meso compounds are molecules with chiral centers that are superimposable on their mirror images due to an internal plane of symmetry.
• Racemic mixtures contain equal amounts of both enantiomers and are optically inactive.
• Optical activity is the ability of a chiral molecule to rotate the plane of plane-polarized light.
  • Dextrorotatory compounds rotate the plane of polarized light clockwise (+).
  • Levorotatory compounds rotate the plane of polarized light counterclockwise (-).
• The Cahn-Ingold-Prelog (CIP) priority rules are used to assign priorities to the groups attached to a chiral center.
• R and S configurations are used to designate the absolute configuration of a chiral center based on the CIP priority rules.
• Conformational isomers (conformers) are isomers that can be interconverted by rotation around single bonds.
• Newman projections are used to visualize the different conformations of a molecule.
• Common conformations include:
  • Eclipsed conformation where the bonds on adjacent atoms are aligned.
  • Staggered conformation where the bonds on adjacent atoms are as far apart as possible.
  • Gauche conformation where two large groups are adjacent to each other in a staggered conformation.
  • Anti conformation where two large groups are 180 degrees apart in a staggered conformation.
• Cyclic compounds can also exhibit stereoisomerism; for example, cis and trans isomers of substituted cycloalkanes exist.
• Chair conformations are the most stable conformations of cyclohexane.
• Ring flipping in cyclohexane can interconvert axial and equatorial substituents.