Structures and Reactions of Organic Compounds

Overview: What Makes Organic Molecules Special?

Organic chemistry focuses on carbon-containing compounds. In this chapter, the emphasis is on how these compounds are built (structure) and how they change (reactions). Later chapters will examine particular classes of organic substances in detail (e.g. hydrocarbons, functional groups, natural products); here we look at general ideas that apply broadly to organic molecules.

Several key features distinguish organic structures and reactions:

• Carbon can form four covalent bonds and build long chains and rings.
• Small changes in structure can drastically change properties and reactivity.
• Reactions usually occur at specific, well-defined sites in the molecule.
• Electron movement (rather than whole atoms “jumping”) is the central theme of reaction mechanisms.

This chapter introduces the structural features and common reaction patterns that underlie all later organic chemistry topics.

Structural Features of Organic Molecules

The Carbon Skeleton

The “backbone” of an organic molecule is a network of carbon atoms linked by covalent bonds.

• Types of connectivity:
• Chains: straight (unbranched) or branched.
• Rings: carbocyclic (only carbon) or heterocyclic (contain other atoms like O, N, S).
• Bond types:
• Single ($\sigma$) bonds: allow free rotation, giving flexibility.
• Double and triple bonds (one $\sigma$ plus one or two $\pi$ bonds): more rigid, define planar or linear portions of the molecule and act as important reactive sites.

The carbon skeleton largely determines:

• Overall shape (linear, bent, branched, cyclic, planar, 3D).
• How close different parts of the molecule can get to each other (important for intramolecular reactions and biological recognition).
• Which functional groups can be attached and how they interact.

Saturation and Unsaturation

Two fundamental structural categories:

• Saturated compounds: only single C–C and C–H bonds (no multiple bonds). Example: alkanes (covered in detail in “Aliphatic Hydrocarbons”).
• Unsaturated compounds: contain C=C or C≡C bonds or aromatic rings.
• Double and triple bonds introduce regions of higher electron density.
• Unsaturation usually makes molecules more reactive (e.g. addition reactions to C=C).

Saturation vs. unsaturation strongly influences:

• Reactivity (unsaturated centers are common reaction sites).
• Geometry (planarity at double bonds, linearity around triple bonds).
• Physical properties (e.g. melting points in fats, discussed under “Fats”).

Functional Groups as Structural Motifs

Functional groups are specific groupings of atoms within molecules that have characteristic bonding and reactivity. Their detailed chemistry is covered in “Functional Groups” and the following chapters on particular classes (alcohols, amines, etc.), but here we note their structural role:

• They define reactive centers where most transformations occur.
• They introduce polarity and sites for hydrogen bonding.
• They often determine solubility and intermolecular interactions.

Common functional-group-bearing fragments:

• Heteroatoms like O, N, halogens attached to carbon.
• Carbon–heteroatom double bonds (C=O, C=N).
• Charged fragments in solution (e.g. $–\text{COO}^-$, $–\text{NH}_3^+$).

The same carbon skeleton can behave very differently depending on which functional groups are present and where they are located.

Electronic Distribution in Organic Structures

Bond Polarity

Even in neutral molecules, electrons are usually not evenly shared:

• Polar covalent bonds form when atoms of different electronegativity (e.g. C–O, C–N, C–Cl) share electrons unequally.
• The more electronegative atom carries a partial negative charge ($\delta^-$), and the less electronegative atom carries a partial positive charge ($\delta^+$).

Consequences:

• Partially positive carbons (e.g. next to O, halogens, or in carbonyls) tend to accept electron density in reactions.
• Partially negative sites (e.g. heteroatoms with lone pairs) tend to donate electron density or bind to positively polarized centers.

Formal Charges and Resonance

In organic structures, we often assign:

• Formal charges (e.g. $+\text{N}\text{H}_4^+$, $–\text{COO}^-$) to keep track of electron count and likely reactive behavior.
• Resonance structures for systems where electrons are delocalized (e.g. carboxylate ions, aromatic rings, conjugated systems).

Key points:

• Resonance structures are not “flipping” forms; the actual molecule is a hybrid.
• Delocalization usually stabilizes molecules or ions.
• Resonance often spreads charge over several atoms, reducing local reactivity but creating extended reactive regions (e.g. conjugated $\pi$ systems).

Understanding resonance is crucial for:

• Predicting where reactions happen (e.g. in aromatic substitution).
• Explaining acidity/basicity trends (e.g. stabilization of conjugate bases).

Shape and Stereochemistry

The 3D arrangement of atoms affects how molecules interact and how they react.

• Tetrahedral centers (sp³ carbon) can lead to stereoisomers if four different substituents are attached (chiral centers; discussed under “The Concept of Isomerism”).
• Barriers to rotation (e.g. about C=C bonds or due to bulky groups) create distinct conformations or geometric isomers.

Structurally:

• Stereochemistry often determines whether a reaction can occur (e.g. whether a nucleophile can approach a carbon).
• Many reactions create or destroy stereocenters; the outcome (which stereoisomer forms) is a central topic in organic reaction studies.

Where Reactions Occur in Organic Molecules

Organic reactions are rarely random; they typically occur at specific reactive sites determined by structure and electron distribution.

Typical Reactive Sites

1. Heteroatoms with lone pairs (O, N, S, halogens)
• Often act as nucleophilic centers (electron-rich) or bases.
• Typical roles: binding to positively charged or electron-poor centers, forming new bonds to carbon or protons.
2. Electrophilic carbon atoms
   These are carbons that are electron-poor or partially positive:
• Carbon attached to electronegative atoms (e.g. in C–Cl, C–O).
• Carbon in polar double bonds such as C=O and C=N.
• Certain carbocation intermediates (positively charged carbons).
3. $\pi$-Bonded carbons (C=C, C≡C, aromatic rings)
• Electron-rich $\pi$ bonds can act as nucleophiles in some reactions.
• Double bonds can be attacked by electrophiles, leading to addition.
• Aromatic rings react by substitution rather than simple addition, preserving aromaticity.
4. Acidic hydrogens
• Hydrogens bound to O, N, or certain carbons (e.g. next to carbonyl groups) can be removed (deprotonated).
• Deprotonation generates carbanions or other nucleophilic species that participate in carbon–carbon bond-forming reactions.
5. Leaving groups
• Atoms or groups that can depart with an electron pair (e.g. halides like Cl⁻, sulfonate esters).
• Their presence at carbon centers enables substitution and elimination processes.

The Role of Electron Flow

Most organic reactions can be described by movement of electron pairs from donors to acceptors:

• Nucleophiles: electron-pair donors, attracted to positive or electron-poor sites.
• Electrophiles: electron-pair acceptors, attracted to negative or electron-rich sites.

In structural terms, reactions typically involve:

• A nucleophile attacking an electrophilic carbon.
• A leaving group departing.
• A proton being transferred.
• A $\pi$ bond forming or breaking.

Visualizing electron flow (even without explicit mechanisms) helps:

• Predict plausibility of a proposed reaction.
• Understand why certain reactions do not occur.

Classes of Organic Reactions (Structural Perspective)

Detailed mechanisms and terminology are covered under “Reaction Types in Organic Chemistry” and “Reagents, Substrates, and Reactions.” Here we focus on how structure changes during major reaction classes.

Substitution

In substitution reactions, one atom or group is replaced by another. Overall connectivity of the carbon skeleton is usually retained.

Structural pattern:

• A carbon bears a substituent X (often a leaving group).
• Another species Nu (a nucleophile or reagent) takes the place of X.

General scheme:
$$
\text{R–X} + \text{Nu} \rightarrow \text{R–Nu} + \text{X}^-
$$

From a structural standpoint:

• Substitution alters the functional group attached to the carbon.
• It can introduce new functional groups (e.g. convert an alkyl halide to an alcohol or an amine).
• Stereocenters might be created or inverted, depending on the pathway and geometry.

Addition

Addition reactions add atoms or groups across a multiple bond, typically converting unsaturated structures into more saturated ones.

General scheme for a double bond:
$$
\text{R–CH=CH–R'} + \text{A–B} \rightarrow \text{R–CH(A)–CH(B)–R'}
$$

Structural effects:

• A $\pi$ bond is replaced by two new $\sigma$ bonds.
• The molecule gains atoms/groups but usually maintains or only modestly changes the carbon skeleton.
• Addition to unsymmetrical double bonds can give regioisomers (different positions of A and B) and possibly different stereoisomers.

In carbonyl addition (C=O), one group typically adds to carbon and another (often H) to oxygen, changing the oxidation state and functional group.

Elimination

Elimination is the reverse of addition: atoms or groups are removed, forming a multiple bond.

General scheme:
$$
\text{R–CH}_2\text{–CH}_2\text{–X} \rightarrow \text{R–CH=CH}_2 + \text{HX}
$$

Structural effects:

• A saturated segment becomes unsaturated.
• Two neighboring substituents (often H and a leaving group) are lost.
• Product structure often has fewer atoms but possibly more isomerism (e.g. multiple possible double-bond positions or geometries).

Rearrangement

In rearrangement reactions, the connectivity of atoms within the molecule changes without necessarily adding or removing atoms.

Structural features:

• Bonds between carbons and/or heteroatoms are reorganized.
• Functional groups may “move” to different positions on the skeleton.
• New carbon skeletons or ring systems can be formed.

Rearrangements are important for:

• Transforming simple precursors into more complex frameworks.
• Explaining unexpected isomer distributions in products.

Oxidation and Reduction (Organic Sense)

“Oxidation” and “reduction” of organic molecules are often recognized by changes in bonding to heteroatoms vs. hydrogen:

• Oxidation (in organic terms) generally means:
• Increase in C–O, C–N, or C–X bonds.
• Decrease in C–H bonds.
• Example structural changes: alcohol $\rightarrow$ carbonyl $\rightarrow$ carboxylic acid.
• Reduction generally means:
• Decrease in C–O, C–N, or C–X bonds.
• Increase in C–H bonds.
• Example structural changes: carbonyl $\rightarrow$ alcohol $\rightarrow$ alkane.

These processes change the oxidation level of carbon atoms and thereby the type of functional group present.

Structure–Reactivity Relationships

A central theme in organic chemistry is how structure governs how and how fast molecules react.

Influence of Functional Groups and Substituents

Different functional groups have distinct reactivity patterns:

• Carbonyl groups (C=O) are typically attacked at carbon by nucleophiles.
• $–\text{OH}$ and $–\text{NH}_2$ groups can act as both nucleophiles and bases.
• Halogens attached to carbon can serve as leaving groups, enabling substitutions and eliminations.

Substituents attached near a reactive center can affect:

• Electronic environment:
• Electron-donating substituents (e.g. alkyl groups) can stabilize positive charge or increase electron density.
• Electron-withdrawing substituents (e.g. –NO₂, –CN, carbonyls) can stabilize negative charge or make certain carbons more electrophilic.
• Steric environment:
• Bulky groups can hinder approach of reagents and favor some pathways over others.

These influences are often described by electronic effects (inductive, resonance) and steric effects, detailed in “Electronic Effects in Organic Compounds.”

Conjugation and Aromaticity

Conjugation (alternating single and multiple bonds with overlapping p orbitals) and aromaticity dramatically shape reactivity:

• Conjugated systems have delocalized $\pi$ electrons, lowering energy and allowing reactions that distribute charge across the system.
• In aromatic rings, maintaining aromatic stabilization is so important that typical reactions avoid breaking aromaticity; substitution is favored over addition.

Structurally, conjugation and aromaticity:

• Modify bond lengths (partial double-bond character).
• Change where positive or negative charge can be delocalized.
• Control where electrophiles or nucleophiles can attack.

Stability of Intermediates

Many reactions proceed via short-lived intermediates whose stability is highly structure-dependent:

• Carbocations (positively charged carbons): more stable if more substituted (tertiary > secondary > primary) and if charge is delocalized (e.g. allylic, benzylic).
• Carbanions (negatively charged carbons): more stable when adjacent to electron-withdrawing groups or conjugated systems.
• Radicals: stability trends often parallel carbocations, and conjugation/aromaticity can also stabilize them.

Knowing which intermediates are preferred helps predict:

• Which bonds will break or form.
• Which products will dominate (major vs. minor product).
• How sensitive a reaction is to substitution pattern.

Reaction Conditions and Their Effect on Structure and Outcome

Even with the same starting structure, different conditions can lead to different products.

Solvent Effects

Solvents influence organic reactions by:

• Stabilizing (or destabilizing) charged intermediates and transition states.
• Affecting solubility and thus which reactants can interact.
• Participating in reactions (e.g. substitution where solvent acts as nucleophile).

Polar vs. nonpolar, protic vs. aprotic solvents have different preferences for specific reaction types, which in turn influence structural outcomes.

Temperature and Energy Considerations

Temperature affects:

• Reaction rate: higher temperatures usually increase rates by helping overcome activation barriers.
• Product distribution: in some cases, low temperatures favor “kinetic” products (formed via the fastest pathway), whereas higher temperatures allow formation of more stable “thermodynamic” products.

Structurally, this can determine:

• Which isomer predominates (e.g. less substituted vs. more substituted double bonds).
• Whether rearrangements have time to occur.

Catalysts and Reagents as Structure-Directing Tools

Specific catalysts and reagents are chosen to:

• Activate certain functional groups (e.g. acids activate carbonyls for nucleophilic addition).
• Direct reactions to particular positions or functional groups.
• Control stereochemistry (e.g. chiral catalysts favor formation of one enantiomer).

From a structural viewpoint, reagents can be thought of as tools that:

• Make some parts of the molecule more reactive.
• Protect other parts (temporary modification) to prevent reaction.
• Steer transformations through particular intermediates or mechanisms.

Connecting Structure and Reactions in Practice

When analyzing or planning organic reactions, a structural viewpoint typically proceeds in steps:

1. Identify functional groups and reactive sites (polar bonds, $\pi$ systems, acidic H, leaving groups).
2. Assess electronic features (polarity, resonance, substituent effects) and steric hindrance.
3. Classify the reaction type (substitution, addition, elimination, rearrangement, oxidation, reduction).
4. Consider likely intermediates and their stability given the structure.
5. Predict possible products, including isomers, and assess which are more stable or more likely.

Subsequent chapters on specific families of organic compounds (hydrocarbons, functionalized molecules, natural products) will apply these general structural and reactivity principles to concrete examples, showing how small changes in structure can lead to large differences in chemical behavior.