Organic Chemistry 1 Study Guide

Lewis structures and formal charge

• Formal charge = valence electrons − nonbonding electrons − bonds. Formal charges add up to the overall charge.
• C, N, O and F never exceed an octet. In skeletal structures each carbon carries implied H up to 4 bonds; lone pairs are often omitted.

Bonding patterns and formal charge

Atom	+1	0	−1
C	3 bonds, no lone pair (carbocation)	4 bonds	3 bonds + 1 lone pair (carbanion)
N	4 bonds	3 bonds + 1 lone pair	2 bonds + 2 lone pairs
O	3 bonds + 1 lone pair	2 bonds + 2 lone pairs	1 bond + 3 lone pairs
Cl, Br, I	2 bonds + 2 lone pairs	1 bond + 3 lone pairs	4 lone pairs (halide)

Hybridization and geometry

Steric number = σ bonds + lone pairs. Single bond = 1 σ; double = 1 σ + 1 π; triple = 1 σ + 2 π.

Steric number, hybridization and shape

Steric no.	Hybrid, geometry	Examples
4	sp³, tetrahedral, 109.5°	CH₄; NH₃ pyramidal (≈107°); H₂O bent (≈104.5°)
3	sp², trigonal planar, 120°	C=C, C=O, carbocation C⁺
2	sp, linear, 180°	C≡C, C≡N, the C of CO₂

A lone pair next to a π bond is usually delocalized in a p orbital, so that atom is sp² (e.g. the N of an amide).

Resonance

• Move only π electrons and lone pairs. Never move atoms, break a σ bond, exceed an octet on C/N/O, or change the overall charge.
• Patterns: lone pair next to a π bond; + charge next to a π bond (allylic cation; allylic = on the sp³ carbon next to a C=C, benzylic = next to a benzene ring); lone pair next to a + charge; polar π bond (C=O ↔ C⁺–O⁻); alternating π bonds in a ring.
• Contributors are joined by ↔ (not ⇌); the real molecule is the hybrid. Equivalent contributors give extra stability (both C–O bonds of a carboxylate are the same length).

Example: in CH₃–O–CH₂⁺ ↔ CH₃–O⁺=CH₂, the second form is major: every atom has an octet (rule 1), even with + on O.

Intermolecular forces (strongest first)

1. Ion–dipole: ion + polar molecule (Na⁺ in water).
2. Hydrogen bonding: H on N, O or F (donor) to a lone pair on N, O or F (acceptor).
3. Dipole–dipole: permanent dipoles (acetone, CH₃Cl).
4. London dispersion: all molecules; grows with surface area and polarizability.

Ethanol (H-bond donor, bp ≈78 °C) vs dimethyl ether (same formula, bp ≈−24 °C). Longer chains raise bp; branching lowers it. Like dissolves like: water solubility of alcohols falls as the carbon chain grows.

1°, 2°, 3° (primary, secondary, tertiary): a carbon bonded to one, two or three other carbons. An alkyl halide or alcohol takes the degree of the carbon bearing –X or –OH; for amines the degree counts the carbons on N instead.

• Brønsted acid donates H⁺, base accepts H⁺. Lewis acid accepts an electron pair, base donates one.
• Lower pKa = stronger acid = weaker conjugate base. Each pKa unit is a factor of 10 in Ka.

Approximate pKa values (sources differ by about ±1)

Acid → conjugate base	pKa ≈
HI → I⁻	−10
HBr → Br⁻	−9
HCl → Cl⁻	−7
H₂SO₄ → HSO₄⁻	−3 (some tables −9)
ROH₂⁺ → ROH (protonated alcohol)	−2
H₃O⁺ → H₂O	−1.7
RCOOH → RCOO⁻ (acetic acid)	4.8
NH₄⁺ → NH₃	9.2
PhOH → PhO⁻ (phenol)	10
R₃NH⁺ → R₃N (alkylammonium)	10–11
H₂O → HO⁻	15.7
ROH → RO⁻ (ethanol; t-BuOH)	16; 18
Ketone α-C–H → enolate	19–20
RC≡CH → RC≡C⁻ (acetylide)	25
H₂ → H⁻ (NaH); (i-Pr)₂NH → LDA; NH₃ → NH₂⁻	35; 36; 38
Alkene C–H; alkane C–H	44; 50

ARIO: what stabilizes the conjugate base

More stable A⁻ = stronger acid. Usual order of importance (when factors disagree, trust measured pKa values):

1. Atom. Across a row, electronegativity: CH₄ < NH₃ < H₂O < HF. Down a group, size wins over electronegativity: HF < HCl < HBr < HI (the large, polarizable I⁻ spreads the charge); likewise thiols RSH (≈10) are more acidic than alcohols.
2. Resonance. Delocalized charge: acetic acid (≈4.8) vs ethanol (≈16).
3. Induction. Nearby electron-withdrawing groups, fading with distance: ClCH₂COOH (≈2.9) vs CH₃COOH (≈4.8).
4. Orbital. More s-character holds the lone pair closer: sp C–H (≈25) > sp² (≈44) > sp³ (≈50) in acidity.

Equilibrium direction

The equilibrium favors the side with the weaker acid (higher pKa), which is also the weaker-base side. log K ≈ pKa(acid formed) − pKa(acid consumed).

Example: HC≡CH + NH₂⁻ ⇌ HC≡C⁻ + NH₃. Acid consumed HC≡CH (≈25), acid formed NH₃ (≈38): log K ≈ 38 − 25 = 13, so it lies right. With HO⁻ the acid formed is H₂O (≈15.7): log K ≈ −9, so NaOH can’t deprotonate an alkyne.

Curved arrows for proton transfer

Two arrows: (1) base lone pair → H; (2) H–A bond → A. For CH₃COOH + HO⁻ → CH₃COO⁻ + H₂O: HO⁻ lone pair → acidic H, and O–H bond → carboxylate O. Never start an arrow at H⁺ (it has no electrons).

Functional group priority for naming (highest first)

Group	Suffix	Prefix
Carboxylic acid RCOOH	-oic acid	carboxy-
Ester RCOOR′	alkyl -oate	—
Amide RCONH₂	-amide	—
Nitrile RC≡N	-nitrile	cyano-
Aldehyde RCHO	-al	oxo-, formyl-
Ketone RCOR′	-one	oxo-
Alcohol ROH	-ol	hydroxy-
Amine RNH₂	-amine	amino-
Alkene, alkyne	-ene, -yne	(in parent name)
Halide, ether, nitro	—	halo- (chloro- …), alkoxy-, nitro-

Naming steps

1. The highest-priority group gives the suffix.
2. Parent chain: the longest chain containing that group. Most Ochem 1 textbooks also make it include the C=C/C≡C; the 2013 IUPAC rules prefer chain length, so follow your course.
3. Number for lowest locants, in order: (a) the suffix group; (b) C=C/C≡C (on an ene/yne tie, the double bond gets the lower number); (c) all substituents at the first point of difference; (d) alphabetical order.
4. Alphabetize substituents, ignoring di-, tri-, sec- and tert-, but not iso (isopropyl files under “i”).
5. Assemble: stereodescriptors (in locant order, in parentheses) + substituents + parent + suffix: (2E,4R)-4-chloropent-2-ene; (R)-butan-2-ol, older style (R)-2-butanol.

Rings: the carbon bearing the suffix group is C1 (3-methylcyclohexan-1-ol); in a cycloalkene the C=C carbons are C1 and C2. Roots C1–C10: meth, eth, prop, but, pent, hex, hept, oct, non, dec.

Newman projections

• Looking down one C–C bond: front carbon = where three bonds meet, back carbon = circle. Staggered (60°) is lower in energy than eclipsed (0°).
• Torsional strain comes from eclipsed bonds; steric strain from crowded groups (gauche, eclipsed).
• Ethane: eclipsed lies ≈12 kJ/mol (≈2.9 kcal/mol) above staggered, ≈4 kJ/mol per H/H eclipsing.

Butane about C2–C3 (approximate energy above anti)

Conformation (CH₃/CH₃ dihedral)	Energy ≈
Anti, staggered (180°)	0, lowest
Gauche, staggered (60°)	3.8 kJ/mol (0.9 kcal/mol)
Eclipsed, CH₃ over H (120°)	16 kJ/mol (3.8 kcal/mol)
Totally eclipsed, CH₃ over CH₃ (0°)	19 kJ/mol (4.5 kcal/mol), highest

Ring strain: cyclopropane > cyclobutane > cyclopentane > cyclohexane (≈0 in the chair).

Cyclohexane chairs

• Each carbon has one axial bond (parallel to the ring axis, alternating up/down) and one equatorial bond (pointing outward).
• Ring flip: axial ↔ equatorial for every group, but up stays up (a wedged group stays on the top face).
• Groups prefer equatorial to avoid 1,3-diaxial interactions (methylcyclohexane ≈95% equatorial at 25 °C). The best chair puts the largest groups equatorial; A-values are roughly additive, and t-Bu effectively locks the ring.

Approximate A-values (cost of axial vs equatorial)

Group	kJ/mol ≈	kcal/mol ≈
–Cl, –Br	2	0.4–0.5
–OH (solvent-dependent)	2.5–4	0.6–0.9
–CH₃	7.1	1.7
–CH(CH₃)₂	9.2	2.2
–C(CH₃)₃	≈20	≈4.9

cis/trans on rings

cis = same face (both wedges or both dashes); trans = opposite faces. A ring flip never converts cis into trans: they are diastereomers.

Disubstituted cyclohexanes: chair options (a = axial, e = equatorial)

Pattern	cis	trans	More stable
1,2-	a,e ↔ e,a	e,e ↔ a,a	trans
1,3-	e,e ↔ a,a	a,e ↔ e,a	cis
1,4-	a,e ↔ e,a	e,e ↔ a,a	trans

CIP priority rules

1. Higher atomic number of the attached atom wins: I > Br > Cl > S > F > O > N > C > H. Isotopes: higher mass wins (D > H).
2. Tie: list the three atoms on each tied atom (highest first) and compare pair by pair; the first point of difference decides. Move outward one sphere at a time.
3. Multiple bonds count as duplicated atoms: C=O counts as C bonded to (O, O); C≡C as C bonded to (C, C, C).

Example: –CH₂OH (O, H, H) outranks –C(CH₃)₃ (C, C, C): O beats C at the first comparison.

Assigning R/S

1. Rank groups 1–4 and point group 4 away from you (dash).
2. Trace 1 → 2 → 3: clockwise = R, counterclockwise = S.

• Group 4 on a wedge: read the direction, then reverse it.
• Swap trick: any one swap of two groups inverts the configuration. Swap group 4 onto the dash, assign, then reverse. Two swaps return the original.
• R/S does not predict the sign of rotation (+/−).

E/Z for alkenes

• Rank the two groups on each alkene carbon. Higher-priority groups on the same side = Z; opposite sides = E.
• cis/trans can disagree with Z/E: 2-bromobut-2-ene with its two CH₃ groups trans is Z, because Br outranks CH₃.
• A C=C in a ring of fewer than eight atoms must be cis.

Isomer relationships

• Different connectivity → constitutional isomers. Same connectivity, different 3-D arrangement → stereoisomers: mirror images → enantiomers; not mirror images → diastereomers (includes cis/trans, E/Z).
• Comparing descriptors: all centers inverted → enantiomers (unless meso: then the same compound); some inverted → diastereomers; none → same compound.
• Chiral = not superimposable on its mirror image. An internal mirror plane makes a molecule achiral.
• Meso = has stereocenters but is achiral (internal mirror plane): (2R,3S)-butane-2,3-diol, cis-1,2-dimethylcyclopentane.
• 2ⁿ rule: n stereocenters (count stereogenic C=C too) give at most 2ⁿ stereoisomers, fewer with meso forms. Tartaric acid: 2 centers, 3 stereoisomers (enantiomer pair + meso).

Optical activity

• Enantiomers: same mp, bp and solubility; equal but opposite rotation of plane-polarized light. Diastereomers differ in all physical properties.
• [α] = α ⁄ (c · l), c in g/mL, l in dm. Racemic (50:50) mixtures and meso compounds: [α] = 0.
• ee = % major − % minor = observed [α] ⁄ [α] of pure enantiomer × 100%. 75% R + 25% S = 50% ee.

Fischer projections

• Each cross point is a stereocenter. Horizontal bonds point toward you (wedges), vertical bonds away (dashes); the carbon chain runs vertically.
• A 180° rotation in the plane keeps the molecule; a 90° rotation gives the enantiomer. One swap of two groups inverts that stereocenter only (enantiomer for a single center, diastereomer if other centers are present); two swaps restore it.
• R/S: group 4 vertical → read 1 → 2 → 3 directly; group 4 horizontal → read, then reverse.
• A horizontal mirror line through the middle reveals a meso compound.

• Arrows move electrons. Tail on a lone pair or bond; head on an atom (new lone pair) or between atoms (new bond). Full head = 2 electrons; fishhook (half head) = 1 electron.
• Electrons flow from Nu/base (lone pair, π bond) to electrophile/acid (C⁺, δ+ C bearing a LG, C=O carbon, acidic H).
• A new bond to an atom that already has an octet means another bond to it must break. Never start at H⁺ or a + charge. Each step keeps the total charge.

The four electron-flow patterns

Pattern	Arrows	Example
Nucleophilic attack	1: Nu → electrophilic atom	Br⁻ + (CH₃)₃C⁺ → (CH₃)₃CBr
Loss of LG	1: C–LG bond → LG	(CH₃)₃C–OH₂⁺ → (CH₃)₃C⁺ + H₂O
Proton transfer	2: base → H; H–A bond → A	ROH + H₃O⁺ → ROH₂⁺ + H₂O
Rearrangement	1: C–H or C–C bond next to C⁺ → C⁺	1,2-hydride or 1,2-methyl shift

Concerted steps combine patterns: SN2 = attack + loss of LG (2 arrows); E2 = proton transfer + loss of LG (3 arrows).

Carbocation stability and 1,2-shifts

• 3° > 2° > 1° > methyl (alkyl donation: hyperconjugation, induction). Resonance (allylic, benzylic, or next to an O or N lone pair) adds strong stabilization. Vinyl and aryl cations are too unstable to form here, so no SN1/E1 at sp² carbons.
• A 1,2-hydride or 1,2-alkyl shift occurs when it gives a more stable cation (2° → 3°, or → resonance-stabilized). A strained ring next to C⁺ can expand by a 1,2-alkyl shift (4- → 5-, 5- → 6-membered) when that relieves strain or gives a more stable cation.
• Expect shifts wherever a free C⁺ forms: SN1, E1, HX addition, acid-catalyzed hydration, 2°/3° ROH + HX. None in SN2, E2, oxymercuration, hydroboration or X₂ addition.

Example: 3-methylbutan-2-ol + HBr: protonate OH, lose H₂O (2° C⁺), 1,2-hydride shift (3° C⁺), add Br⁻. Major product: 2-bromo-2-methylbutane.

Energy diagrams

• Transition state (‡) = energy maximum with partial bonds, never isolable; intermediate = a valley between steps (C⁺, radical). SN2/E2 show one hump; SN1/E1 show two or more (a small extra hump when a neutral Nu like H₂O must lose H⁺), and the first (C⁺ formation) has the highest barrier: it is the rate-determining step, so only [RX] appears in the rate law.
• Rate depends on the barrier ΔG‡, not on ΔG; a catalyst lowers ΔG‡ only. ΔG = ΔH − TΔS; ΔG < 0 means products are favored (K > 1). Elimination makes more molecules (ΔS > 0), so heat (larger TΔS) favors E over S.
• Hammond postulate: a transition state resembles the species closest to it in energy, so endothermic steps have late, product-like transition states. That is why carbocation stability controls SN1/E1 rates.

Radicals form by homolysis and are drawn with fishhook arrows. Stability: allylic/benzylic > 3° > 2° > 1° > methyl.

Halogenation mechanism (CH₄ + Cl₂, hν)

1. Initiation (makes radicals): Cl₂ → 2 Cl• (light or heat).
2. Propagation (chain; radical count unchanged): Cl• + CH₄ → HCl + •CH₃; then •CH₃ + Cl₂ → CH₃Cl + Cl•.
3. Termination (uses up radicals): any two combine, e.g. Cl• + •CH₃ → CH₃Cl; 2 •CH₃ → ethane.

Selectivity: Cl₂ vs Br₂

• Chlorination: exothermic H-abstraction (≈thermoneutral for CH₄), early transition state, poorly selective: ≈1 : 4 : 5 per H (1° : 2° : 3°, 25 °C). Propane → ≈45% 1-chloro + ≈55% 2-chloropropane.
• Bromination: endothermic H-abstraction, so the transition state is late and radical-like (Hammond postulate, section 6) and the full 3° > 2° > 1° radical stability difference shows up in the rates: highly selective, ≈1 : 80 : 1600. Propane → ≈97% 2-bromopropane. Use Br₂, hν to target the most substituted C–H.
• F₂ is too violent, I₂ too unreactive. A new stereocenter formed at a planar radical carbon comes out racemic.

Allylic bromination with NBS

NBS, hν (or ROOR), CCl₄ swaps an allylic H for Br. NBS keeps [Br₂] low, so Br₂ doesn’t add to the C=C. The allylic radical is delocalized, so Br can end up at either end: cyclohexene → 3-bromocyclohexene; but-1-ene → 3-bromobut-1-ene + 1-bromobut-2-ene (E/Z).

Turning –OH into a leaving group or a halide

Reagent → product	Mechanism, stereochemistry (substrates)
HBr, HCl (+ ZnCl₂), HI → R–X	3°/2°: SN1 (racemization, shifts possible); 1°: SN2
PBr₃ → R–Br	SN2: inversion, no shifts (1°, 2°)
SOCl₂, pyridine → R–Cl	SN2: inversion, no shifts (1°, 2°)
TsCl (or MsCl), pyridine → R–OTs	C–O bond untouched: retention; a later SN2 on R–OTs inverts (1°, 2°)

• Dehydration: conc. H₂SO₄ or H₃PO₄, Δ → alkene. Ease 3° > 2° > 1°; 2°/3° by E1 (Zaitsev, shifts possible). For control: TsCl, pyridine; then t-BuOK (E2).
• Alkoxides: ROH + NaH (or Na) → RO⁻ Na⁺ + H₂ (irreversible).

Alcohol oxidation

Alcohol	PCC, CH₂Cl₂ (also DMP, Swern)	Chromic acid or Jones (Na₂Cr₂O₇ or CrO₃, H₂SO₄, H₂O)
1°	aldehyde	carboxylic acid
2°	ketone	ketone
3°	no reaction	no reaction

Making alcohols from C=O and epoxides (the last Ochem 1 chapter in many courses)

Reagents	Result
NaBH₄, CH₃OH	aldehyde → 1° alcohol; ketone → 2° alcohol (esters and acids untouched)
1) LiAlH₄, dry ether; 2) H₃O⁺	same, and also reduces esters and carboxylic acids to 1° alcohols
1) RMgBr or RLi; 2) H₃O⁺	new C–C bond: formaldehyde → 1°; other aldehydes → 2°; ketone → 3°; ester (2 R add) → 3° alcohol
1) RMgBr + epoxide; 2) H₃O⁺	R attacks the less substituted C (SN2-like); ethylene oxide adds a –CH₂CH₂OH unit

Grignard reagents (RBr + Mg, dry ether) and RLi are strong bases: no O–H, N–H or COOH in the substrate or solvent (they would protonate R⁻ to R–H). RMgBr + CO₂, then H₃O⁺ → RCOOH.

Ethers

• Williamson: RO⁻ + R′X → ROR′ by SN2, so R′X must be methyl or 1°; put the bulky part on the alkoxide. (CH₃)₃CO⁻ K⁺ + CH₃I → t-BuOCH₃ works; CH₃O⁻ + (CH₃)₃CBr gives E2 (2-methylpropene).
• Cleavage: excess HBr or HI, Δ → two R–X (SN2 at methyl/1°, SN1 at 3°); an aryl alkyl ether gives phenol + RX.

Epoxides

• Made by alkene + mCPBA (syn, stereospecific), or halohydrin + NaOH (intramolecular SN2; O⁻ and X must be anti).
• Base or strong Nu (HO⁻, RO⁻, RS⁻, CN⁻, N₃⁻, acetylide; then a proton source): SN2 at the less substituted carbon.
• Acid (H₃O⁺, ROH/H⁺, HX): protonate O, then Nu attacks the more substituted carbon (more δ+, SN1-like transition state). Clear-cut when that carbon is 3°.
• Both modes attack from the back side (inversion there): anti opening, so cyclic epoxides give trans-1,2-products.

Example: 2,2-dimethyloxirane + CH₃O⁻/CH₃OH → 1-methoxy-2-methylpropan-2-ol. With CH₃OH, cat. H₂SO₄ → 2-methoxy-2-methylpropan-1-ol.

Degrees of unsaturation = (2C + 2 + N − H − X) ⁄ 2 (ignore O, S). Each ring or π bond = 1; C≡C = 2; benzene ring = 4. C₆H₁₂ → (12 + 2 − 12)/2 = 1: one ring or one C=C.

• ¹H NMR signals = sets of chemically distinct H (use symmetry). Integration = relative number of H.
• n + 1 rule: n equivalent neighboring H split a signal into n + 1 peaks (Pascal’s triangle). Equivalent H don’t split each other; O–H usually doesn’t (fast exchange).
• Ethyl = triplet (3H) + quartet (2H); isopropyl = doublet (6H) + septet (1H); tert-butyl = singlet (9H). J ≈ 7 Hz in alkyl chains; vinyl trans (≈12–18 Hz) > cis (≈6–12 Hz).
• ¹³C (one line per distinct C; heights not quantitative): sp³ C 0–50; C–O 50–90; C≡C 65–90; C=C and aromatic 100–160; C≡N 115–125; C=O 160–220.
• Mass spec: M⁺ = molecular mass (an odd M⁺ means an odd number of N). An M+2 peak about equal to M⁺ → one Br; about ⅓ of M⁺ → one Cl. Common losses: 15 (CH₃), 29 (C₂H₅), 18 (H₂O from alcohols).

Key IR absorptions (approximate)

Bond	cm⁻¹ ≈	Appearance
O–H alcohol	3200–3600	strong, broad
O–H acid	2500–3300	very broad
N–H	3300–3500	1° amine 2 peaks, 2° one
C–H: sp; sp²; sp³	≈3300; 3000–3100; 2850–3000	sp strong, sharp; sp² just above 3000, sp³ just below
Aldehyde C–H	≈2720, 2820	two weak peaks
C≡N; C≡C	≈2250; 2100–2260	C≡C weak or absent if symmetric
C=O	1650–1750	strong (ketone ≈1715, ester ≈1740)
C=C	1600–1680	medium to weak
C–O	1000–1300	strong

¹H NMR chemical shifts (approximate)

Proton type	δ ≈ (ppm)
Alkyl C–H (CH₃ < CH₂ < CH)	0.9–1.8
Allylic, benzylic, α to C=O	1.7–2.6
Alkyne ≡C–H	2–3
H–C–O, H–C–X	3–4.5
Vinyl =C–H	4.5–6.5
Aromatic Ar–H	6.5–8.5
Aldehyde –CHO	9–10
Carboxylic acid –COOH	10–13, broad
O–H, N–H	1–5, variable