Organic Chemistry I Lecture Notes & Study Guide

Comprehensive vocabulary flashcards covering organic chemistry fundamentals including molecular structure, hybridization, acid-base chemistry, stereochemistry, reaction mechanisms (SN1, SN2, E1, E2), alkene/alkyne reactions, and thermodynamics.

$\sigma$ ("Sigma") Molecular Orbital

A bonding molecular orbital formed by constructive end-on-end overlap of atomic orbitals, in which electron density is shared symmetrically between both nuclei, resulting in a stabilizing interaction.

$\sigma^*$ ("Sigma Star") Molecular Orbital

An antibonding molecular orbital formed by destructive end-on overlap of atomic orbitals, characterized by no electron density between the two nuclei and higher potential energy, resulting in a destabilizing interaction.

$\pi$ ("Pi") Bond

A chemical bond resulting from the side-on overlap of unhybridized p orbitals aligned in the same plane on adjacent atoms. Rotation around this bond is restricted because rotation disrupts orbital overlap.

$sp^3$ Hybridization

The mixing of one $s$ orbital and three $p$ orbitals to produce four equivalent hybrid orbitals arranged in a tetrahedral geometry ($109.5^\circ$ bond angles), each with $25\%$ s-character and $75\%$ p-character.

$sp^2$ Hybridization

The mixing of one $s$ orbital with two $p$ orbitals to produce three hybrid orbitals oriented in a trigonal planar geometry ($120^\circ$ apart) with $33\%$ s-character and $66\%$ p-character, leaving one unhybridized p orbital.

$sp$ Hybridization

The mixing of one $s$ orbital with one $p$ orbital to produce two hybrid orbitals oriented in a linear geometry ($180^\circ$ apart) with $50\%$ s-character, leaving two unhybridized p orbitals.

Rehybridization of Conjugated Lone Pairs

The phenomenon where an atom bearing a lone pair adjacent to an $sp^2$-hybridized atom with a $\pi$ bond rehybridizes to $sp^2$ (instead of $sp^3$) to place that lone pair into an unhybridized p orbital for optimal $\pi$-overlap.

Formal Charge

A bookkeeping convention for tracking charges in a molecule, calculated as $\text{Formal Charge} = V - [N + B]$, where $V$ is valence electrons, $N$ is non-bonded electrons, and $B$ is the number of bonds.

Curved Arrow

A visual accounting convention that illustrates the movement of a pair of electrons from an electron-rich source (the tail: a lone pair or bond) to an electron-poor destination (the head). The three legal moves are bond to lone pair, lone pair to bond, and bond to bond.

Dipole Moment

The vector sum of individual polar bond dipoles across a molecule; molecules with polar covalent bonds may have an overall dipole moment of $0\text{ D}$ if symmetric bond dipoles cancel out.

Hydrogen Bonding

A strong non-covalent intermolecular attraction occurring between a partially positive hydrogen atom bonded to a highly electronegative atom ($O$, $N$, or $F$) and a lone pair on a nearby electronegative atom.

London Dispersion Forces

Weak, temporary attractive intermolecular forces resulting from instantaneous dipole fluctuations present in all molecules; their magnitude increases with greater molecular surface area.

Functional Group Priority (IUPAC)

The hierarchy used to assign parent suffix priority in IUPAC nomenclature: Carboxylic acid > Ester > Amide > Aldehyde > Ketone > Alcohol > Amine.

Isopropyl Group

A three-carbon branched alkyl substituent with the systematic IUPAC name 1-methylethyl, attached to the parent chain at the secondary central carbon.

sec-Butyl Group

A four-carbon branched alkyl substituent with the systematic IUPAC name 1-methylpropyl, bonded to the parent chain via carbon-2 of the butyl chain.

Isobutyl Group

A four-carbon branched alkyl substituent with the systematic IUPAC name 2-methylpropyl, bonded to the parent chain via carbon-1.

tert-Butyl Group

A bulky four-carbon branched alkyl substituent with the systematic IUPAC name 1,1-dimethylethyl, bonded to the parent chain through a tertiary carbon atom.

Dihedral Angle

The angle formed by three consecutive bonds ($A-C-C-B$) when viewing directly along the central carbon-carbon single bond axis in a Newman projection.

Torsional Strain

The energetic destabilization (twisting strain) caused by electron-electron repulsion between aligned adjacent bonds, which can be relieved by rotation around a single bond (e.g., $3.0\text{ kcal/mol}$ in eclipsed ethane).

Gauche Interaction

A steric interaction between two non-hydrogen groups located on adjacent carbons having a dihedral angle of $60^\circ$, contributing an energy cost of approximately $0.9\text{ kcal/mol}$ for two methyl groups.

Anti Periplanar Conformation

A staggered conformation in which two groups on adjacent carbons have a dihedral angle of $180^\circ$, representing the lowest energy and most sterically favorable arrangement.

Chair Conformation

The lowest-energy conformation of cyclohexane that is completely free of angle strain (bond angles $\approx 109.5^\circ$) and torsional strain because all adjacent $C-H$ bonds are staggered.

Axial Position

Positions on a cyclohexane chair that point perpendicular to the mean ring plane (straight up or straight down), parallel to the vertical axis of the ring.

Equatorial Position

Positions on a cyclohexane chair that point outward around the ring equator, slanted slightly up or down; energetically favored for bulky substituents to avoid steric strain.

1,3-Diaxial Interaction

An unfavorable steric interaction (destabilizing gauche-type repulsion) occurring between an axial substituent and the axial hydrogens located two carbons away on the same face of a cyclohexane ring.

A-Value

A numerical measure (in $\text{kcal/mol}$) of the free energy preference ($\Delta G$) of a substituent to adopt an equatorial orientation rather than an axial orientation in a cyclohexane ring.

Boat Conformation

A high-energy conformation of cyclohexane that is $6.9\text{ kcal/mol}$ less stable than the chair conformation due to eclipsing strain along carbon bonds and steric crowding (flagpole repulsion) between inward-pointing hydrogens.

Half-Chair Conformation

The highest-energy conformation of cyclohexane on the chair-flip pathway, situated $10.7\text{ kcal/mol}$ above the chair conformation, corresponding to its activation barrier.

Resonance Hybrid

The true, weighted-average electronic representation of a molecule whose electron distribution cannot be accurately depicted by a single Lewis structure, characterized by delocalized electrons and enhanced stability.

$\pi$-Donor

A heteroatom substituent bearing a lone pair ($O$, $N$, $S$) directly attached to an alkene or conjugated system that increases electron density and nucleophilicity through resonance delocalization.

$\pi$-Acceptor

A polarized unsaturated group ($C=O$, $C\equiv N$) conjugated with a double bond that withdraws electron density via resonance, rendering the adjacent alkene carbon electrophilic (electron-poor).

Homolytic Cleavage

The symmetrical cleavage of a covalent bond where each atom leaves with one of the bonding electrons, producing neutral free radicals; initiated by heat ($\Delta$) or light ($h\nu$).

Radical Chain Initiation

The primary step in a radical chain reaction that creates a net increase in reactive free radicals from non-radical precursors, typically via homolytic cleavage of a weak covalent bond by heat or light.

Radical Chain Propagation

A step in a radical chain reaction where a radical reacts with a stable non-radical molecule to generate a new product and regenerate a radical, resulting in no net change in the total number of free radicals.

Radical Chain Termination

A reaction step where two free radicals collide and combine to form a stable covalent bond, resulting in a net decrease in the radical count and halting the chain process.

Anti-Markovnikov Addition

An electrophilic or radical addition reaction where the incoming group (such as bromide in radical $H-Br$ addition or hydroxyl in hydroboration) becomes bonded to the less substituted carbon of an alkene.

ARIO Rule

A qualitative mnemonic used to evaluate the relative stability of conjugate bases and thus assess acid strength: Atom (electronegativity and polarizability), Resonance (delocalization), Inductive effects (electron-withdrawing groups), and Orbital ($sp > sp^2 > sp^3$).

Enantiomers

Stereoisomers that are non-superimposable mirror images of one another; they share identical physical properties (such as boiling point and melting point) but rotate plane-polarized light in equal and opposite directions.

Diastereomers

Stereoisomers that are not mirror images of one another; they have different physical properties (such as melting points, boiling points, and solubilities) and include cis/trans isomers and compounds with multiple stereocenters where some, but not all, configurations differ.

Meso Compound

An achiral compound that contains multiple stereocenters but possesses an internal plane of symmetry (or inversion center), rendering it optically inactive.

$S_N2$ Mechanism

A concerted, bimolecular nucleophilic substitution reaction where nucleophilic attack at the carbon $\sigma^*$ antibonding orbital and leaving group departure occur simultaneously, resulting in second-order kinetics ($\text{Rate} = k[\text{R-LG}][\text{Nu}]$) and complete inversion of configuration.

$S_N1$ Mechanism

A stepwise, unimolecular nucleophilic substitution reaction where the leaving group departs in a slow, rate-determining step to generate a flat carbocation intermediate, followed by fast nucleophilic attack, yielding first-order kinetics ($\text{Rate} = k[\text{R-LG}]$) and racemization.

Walden Inversion

The complete inversion of stereochemical configuration at an $\text{sp}^3$ carbon center resulting from backside attack by a nucleophile during an $S_N2$ reaction.

$E2$ Mechanism

A concerted, bimolecular elimination reaction where a strong base removes a proton while the leaving group is expelled simultaneously to form a new $\pi$ bond, requiring an anti-periplanar geometry ($180^\circ$ dihedral angle) between the $C-H$ and $C-\text{LG}$ bonds.

$E1$ Mechanism

A stepwise elimination reaction wherein rate-determining departure of a leaving group yields a carbocation intermediate, which is subsequently deprotonated by a weak base in a fast step to yield an alkene.

Zaitsev's Rule

An empirical rule stating that in elimination reactions, the major product formed is the more highly substituted, thermodynamically more stable alkene.

Hofmann Product

The less-substituted alkene product that predominates in elimination reactions when sterically hindered, bulky bases (such as potassium tert-butoxide, $t\text{-BuOK}$) are employed.

Bredt's Rule

A geometric rule stating that a double bond cannot form at a bridgehead position of a small bridged bicyclic system because orbital overlap ($\pi$-bonding) is prevented by an orthogonal ($90^\circ$) orientation of the p orbitals.

Polar Protic Solvent

A solvent with a relatively high dielectric constant containing acidic hydrogens bonded to electronegative atoms ($O-H$ or $N-H$) capable of hydrogen bonding, which solvates and stabilizes anions and promotes $S_N1$/$E1$ pathways.

Polar Aprotic Solvent

A solvent with a high dielectric constant (such as DMSO, DMF, or acetone) that lacks $O-H$ or $N-H$ bonds, leaving anions unencumbered by hydrogen-bonding shells and significantly enhancing their nucleophilicity for $S_N2$ reactions.

Oxymercuration-Demercuration

A two-step electrophilic addition reaction involving a cyclic mercurinium ion intermediate that converts alkenes into Markovnikov alcohols (or ethers) without carbocation rearrangements, followed by demercuration with $\text{NaBH}_4$.

Hydroboration-Oxidation

A two-step concerted addition of $\text{BH}_3$ across an alkene followed by alkaline peroxide treatment ($\text{H}_2\text{O}_2/\text{NaOH}$) that yields syn-addition, anti-Markovnikov alcohols with retention of configuration.

Epoxide

A highly strained three-membered cyclic ether (oxirane) synthesized from alkenes using peroxyacids (e.g., $m\text{-CPBA}$) that undergoes facile nucleophilic ring-opening.

Lindlar Catalyst

A poisoned palladium catalyst ($\text{Pd/CaCO}_3$ modified with lead and quinoline) that selectively hydrogenates alkynes with $\text{H}_2$ to yield cis-alkenes without reducing them further to alkanes.

Dissolving Metal Reduction

A reduction reaction using sodium or lithium metal in liquid ammonia ($\text{Na/NH}_3$) that selectively converts internal alkynes into trans-alkenes via radical anion intermediates.

Williamson Ether Synthesis

An $S_N2$ reaction between a deprotonated alcohol (alkoxide ion) and an unhindered primary alkyl halide or sulfonate to form an ether.

Hammond's Postulate

A principle stating that the structure of a transition state resembles the species (reactants or products) to which it is closer in free energy; thus, in an endothermic step, the transition state resembles the products, while in an exothermic step, it resembles the reactants.

Reaction Intermediate

A transient chemical species possessing fully formed bonds and sitting at a local potential energy minimum ("valley") on a reaction coordinate diagram, distinguishing it from a transition state.

Activation Energy ($E_a$)

The minimum kinetic energy difference between the starting reactants and the transition state required for a chemical reaction to occur, related to rate by the Arrhenius equation $k = A e^{-E_a/RT}$.