Organic Chemistry: Bonding

• 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
• Organic compounds are ubiquitous
• Organic chemistry overlaps with many other areas including medicinal chemistry, biochemistry, polymer chemistry, and materials science

Bonding

• Carbon has four valence electrons and readily forms four covalent bonds
• Carbon can form single, double, and triple bonds with itself and other elements
• The hybridization of carbon atoms determines the geometry of the molecule
• sp3 hybridized carbons have a tetrahedral geometry with bond angles of 109.5°
• sp2 hybridized carbons have a trigonal planar geometry with bond angles of 120°
• sp hybridized carbons have a linear geometry with bond angles of 180°
• Sigma (σ) bonds are formed by end-on overlap of atomic orbitals
• Pi (π) bonds are formed by sideways overlap of atomic orbitals
• Single bonds are sigma bonds
• Double bonds consist of one sigma bond and one pi bond
• Triple bonds consist of one sigma bond and two pi bonds

Functional Groups

• Functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules
• Alkanes contain only single bonds between carbon and hydrogen atoms and are relatively unreactive
• Alkenes contain at least one carbon-carbon double bond and are more reactive than alkanes
• Alkynes contain at least one carbon-carbon triple bond and are even more reactive than alkenes
• Alcohols contain a hydroxyl (-OH) group and can participate in hydrogen bonding
• Ethers contain an oxygen atom bonded to two alkyl or aryl groups
• 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) and are acidic
• Esters contain a carbonyl group bonded to an alkoxy group (-OR)
• Amines contain a nitrogen atom bonded to one, two, or three alkyl or aryl groups
• Amides contain a carbonyl group bonded to a nitrogen atom

Isomerism

• Isomers are molecules that have the same molecular formula but different structural formulas
• Structural isomers have different connectivity of atoms
• Stereoisomers have the same connectivity but different spatial arrangements of atoms
• Enantiomers are stereoisomers that are non-superimposable mirror images
• Diastereomers are stereoisomers that are not mirror images
• Conformational isomers are isomers that can be interconverted by rotation around single bonds
• Geometric isomers (cis-trans isomers) occur when there is restricted rotation around a bond, such as in alkenes or cyclic compounds

Reactions

• Addition reactions involve the addition of atoms or groups of atoms to a molecule, typically at a multiple bond
• Elimination reactions involve the removal of atoms or groups of atoms from a molecule, forming a multiple bond
• Substitution reactions involve the replacement of one atom or group of atoms with another
• Rearrangement reactions involve the reorganization of atoms and bonds within a molecule
• Oxidation reactions involve the loss of electrons or an increase in oxidation state
• Reduction reactions involve the gain of electrons or a decrease in oxidation state
• Acid-base reactions involve the transfer of protons (H+) from an acid to a base

Reaction Mechanisms

• Reaction mechanisms describe the step-by-step sequence of elementary reactions that make up an overall reaction
• Mechanisms show the movement of electrons during a reaction using curved arrows
• Curved arrows indicate the flow of electrons from a nucleophile (electron-rich species) to an electrophile (electron-deficient species)
• Carbocations are positively charged carbon atoms and are electrophilic
• Carbanions are negatively charged carbon atoms and are nucleophilic
• Radicals are species with unpaired electrons and are highly reactive
• SN1 reactions are unimolecular nucleophilic substitution reactions that proceed through a carbocation intermediate
• SN2 reactions are bimolecular nucleophilic substitution reactions that occur in a single step
• E1 reactions are unimolecular elimination reactions that proceed through a carbocation intermediate
• E2 reactions are bimolecular elimination reactions that occur in a single step

Spectroscopy

• Spectroscopy is the study of the interaction of electromagnetic radiation with matter
• Nuclear Magnetic Resonance (NMR) spectroscopy provides information about the structure and bonding of molecules by analyzing the interaction of atomic nuclei with a magnetic field
• Chemical shift in NMR indicates the electronic environment of a nucleus
• Splitting patterns in NMR provide information about the number of neighboring hydrogen atoms
• Infrared (IR) spectroscopy provides information about the functional groups present in a molecule by analyzing the absorption of infrared radiation
• Characteristic IR absorption bands can be used to identify specific functional groups
• Mass spectrometry (MS) determines the mass-to-charge ratio of ions, providing information about the molecular weight and structure of a compound
• Fragmentation patterns in MS can be used to deduce the structure of a molecule

Acids and Bases in Organic Chemistry

• Bronsted-Lowry acids are proton donors, and Bronsted-Lowry bases are proton acceptors
• Lewis acids are electron pair acceptors, and Lewis bases are electron pair donors
• The strength of an acid is measured by its pKa value
• Lower pKa values indicate stronger acids
• Factors that affect acidity include electronegativity, inductive effects, resonance, and hybridization
• Strong acids readily donate protons, while weak acids do not

Stereochemistry

• Chirality refers to the property of a molecule that is non-superimposable on its mirror image
• A chiral center is a carbon atom bonded to four different groups
• Enantiomers are pairs of chiral molecules that are mirror images of each other
• Diastereomers are stereoisomers that are not mirror images
• Optical activity refers to the ability of chiral molecules to rotate plane-polarized light
• A racemic mixture contains equal amounts of both enantiomers and is not optically active
• The Cahn-Ingold-Prelog (CIP) priority rules are used to assign absolute configurations (R or S) to chiral centers
• Meso compounds contain chiral centers but are achiral due to an internal plane of symmetry

Aromaticity

• Aromatic compounds are cyclic, planar, and conjugated systems with a specific number of pi electrons
• Huckel's rule states that aromatic compounds must have (4n + 2) pi electrons, where n is an integer
• Benzene is a classic example of an aromatic compound
• Aromatic compounds are very stable due to delocalization of electrons
• Electrophilic aromatic substitution is a common reaction of aromatic compounds
• Substituents on an aromatic ring can be activating or deactivating, and ortho/para-directing or meta-directing

Alkyl Halides

• Alkyl halides are organic compounds containing a halogen atom bonded to an alkyl group
• Alkyl halides can undergo nucleophilic substitution (SN1 or SN2) and elimination (E1 or E2) reactions
• The reactivity of alkyl halides depends on the structure of the alkyl group and the nature of the leaving group
• Primary alkyl halides favor SN2 reactions, while tertiary alkyl halides favor SN1 reactions
• Strong bases favor elimination reactions (E2)

Alcohols, Ethers and Epoxides

• Alcohols contain a hydroxyl (-OH) group
• Ethers contain an oxygen atom bonded to two alkyl or aryl groups
• Epoxides are cyclic ethers with a three-membered ring
• Alcohols can undergo dehydration to form alkenes or ethers
• Alcohols can be oxidized to aldehydes, ketones, or carboxylic acids
• Ethers are relatively unreactive but can be cleaved under acidic conditions
• Epoxides are highly reactive due to ring strain and can undergo ring-opening reactions with nucleophiles or acids

Aldehydes and Ketones

• 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
• Aldehydes and ketones can undergo nucleophilic addition reactions at the carbonyl carbon
• Common reactions include the formation of hemiacetals, acetals, hydrates, and imines
• Aldehydes are more reactive than ketones due to less steric hindrance and electronic effects

Carboxylic Acids

• Carboxylic acids contain a carboxyl group (-COOH)
• Carboxylic acids are acidic and can donate a proton
• Carboxylic acids can form esters by reacting with alcohols
• Carboxylic acids can be reduced to aldehydes or alcohols
• Derivatives of carboxylic acids include esters, amides, acyl halides, and anhydrides

Amines and Amides

• Amines contain a nitrogen atom bonded to one, two, or three alkyl or aryl groups
• Amines are basic and can accept a proton
• Amides contain a carbonyl group bonded to a nitrogen atom
• Amides are less basic than amines due to resonance stabilization
• Amines can react with aldehydes and ketones to form imines
• Amides can be hydrolyzed to carboxylic acids and amines

Polymers

• Polymers are large molecules composed of repeating structural units called monomers
• Addition polymers are formed by the direct addition of monomers to each other
• Condensation polymers are formed by the elimination of a small molecule, such as water, between monomers
• Common examples of polymers include polyethylene, polypropylene, polystyrene, and nylon
• Polymers have a wide range of applications in plastics, fibers, and coatings