CH 3. Nomenclature, Conformations & Stereochemistry

A. Functional Groups and Naming

1. Representations, classes and nomenclature

a. Structural recognition

• A functional group is a characteristic arrangement of atoms that often controls chemical behavior.

• A carbon skeleton can be saturated or contain π bonds; functional groups containing oxygen, nitrogen, sulfur or halogens are identified by their connectivity.

• A single molecule can contain several functional groups, and each must be considered when predicting its properties.

b. Carbon framework and heteroatoms

• Alkanes contain only C–C and C–H single bonds; alkenes contain C=C and alkynes contain C≡C.

• Alcohols contain C–OH and ethers contain C–O–C. The oxygen of a carbonyl group is doubly bonded to carbon.

• Halides contain C–X (X = F, Cl, Br or I); amines contain a nitrogen bonded to carbon and/or hydrogen.

c. Substitution at carbon

• A carbon attached to one other carbon is primary (1°); one attached to two carbons is secondary (2°); one attached to three carbons is tertiary (3°).

• A carbon attached to four carbon atoms is quaternary (4°).

• The classification refers to the particular carbon atom, not the total size of the molecule.

d. Saturated hydrocarbons

• An acyclic alkane has the molecular formula CₙH₂ₙ₊₂. Carbon normally has four bonds, and a simple alkane carbon is approximately tetrahedral (sp³).

• Cycloalkanes with one saturated ring have formula CₙH₂ₙ. The ring removes two hydrogens relative to the corresponding acyclic alkane.

e. Constitutional isomers

• Constitutional isomers have the same molecular formula but different atom connectivity.

• Pentane, 2-methylbutane, and 2,2-dimethylpropane all have the formula C₅H₁₂ but distinct carbon skeletons.

• A drawing flipped or rotated without changing bonds is not a different constitutional isomer.

f. Parent and locants

• Choose the longest continuous carbon chain for the parent name; where equal choices exist, apply substituent and locant rules.

• Number the chain to give the set of substituent positions the lowest possible locants, comparing at the first point of difference.

• Name branches as substituents and list different substituents alphabetically, ignoring multiplicative prefixes such as di- and tri-.

• Use parentheses and local numbering for complex substituents.

• Select a parent containing the principal functional group; its priority controls the suffix. Appropriate suffixes distinguish acids, esters, amides, aldehydes, ketones, alcohols, alkenes and alkynes.

g. Repeated substituents

• Use di-, tri- or tetra- for repeated identical groups and report each location.

• Separate numbers with commas and separate a number from a word with a hyphen.

• For example, CH₃–CH₂–CH(CH₃)–CH₂–CH₂–CH₃ is 3-methylhexane.

h. Condensed and skeletal notation

• Condensed formulas group bonded atoms in readable sequences; parentheses indicate a branch connected to the preceding atom.

• In bond-line structures, each unlabeled endpoint or vertex denotes a carbon and enough hydrogens are implied to satisfy normal valence.

• Heteroatoms and hydrogens attached to heteroatoms are normally shown explicitly.

i. Cyclic frameworks

• Cycloalkanes are saturated hydrocarbons with at least one ring.

• Small rings experience a combination of bond-angle and eclipsing strain; cyclopropane is highly strained.

• Cyclohexane can adopt a low-strain chair conformation rather than a flat hexagon.

j. Rings and related structures

• For a simple substituted cycloalkane, compare the ring and attached chain when selecting the parent. Number ring substituents to give the appropriate lowest locants.
• Constitutional isomers have the same molecular formula but different connections. Conformers retain the same connections and differ by rotation or ring motion.
• Bicyclo[a.b.c] names count the atoms in each bridge between bridgeheads, excluding the bridgeheads; add two to obtain the total skeletal atom count.

Relationship	What changes?
Constitutional isomers	Atom connectivity
Conformers	Torsion angles / ring shape
Configurational stereoisomers	Persistent spatial arrangement

k. Naming

• Select the appropriate parent containing the multiple bond and assign its locant. Use -ene, -yne, -diene or -en-yne as appropriate.
• A terminal CH₂= group has two identical hydrogen substituents on one carbon and cannot display E/Z isomerism.

B. Newman Projections

1. Rotation, torsional energy and sterics

a. Single-bond rotation

• Rotation about a C–C σ bond creates conformations without changing bond connectivity.

• Conformations interconvert readily at room temperature unless restricted by a ring or severe steric constraints.

• Newman projections depict the positions of groups while looking directly along a C–C bond.

b. Staggered and eclipsed

• A Newman projection looks down a bond. The front atom is a point and the back atom a circle. Rotation changes the dihedral angle.
• Staggered ethane has lower energy than eclipsed ethane because eclipsing increases torsional strain.

• In staggered conformations, front and rear bonds are offset; in eclipsed conformations they align. For ethane, torsional energy changes periodically with the dihedral angle.

c. Butane conformations

• Anti butane places the methyl groups 180° apart and is the lowest-energy staggered conformer. Gauche places them 60° apart and has a steric penalty.
• An energy maximum is an eclipsed geometry; a minimum is a staggered conformer. Conformational interconversion normally does not require breaking a sigma bond.

C. Cyclohexane Chair Conformations

1. Ring geometry and conformational stability

a. Axial and equatorial bonds

• A chair cyclohexane has six axial and six equatorial C–H bond directions.

• Axial positions alternate up and down around the ring, and equatorial positions point roughly outward.

• A chair flip exchanges axial and equatorial positions while keeping each substituent on its original up or down face.

• A chair flip changes ring conformation rather than connectivity and preserves configuration at a stereogenic center. For a monosubstituted cyclohexane, the substituent exchanges axial and equatorial positions.

Feature	Geometry	Interpretation
Axial	Approximately parallel to ring axis	Alternates up and down
Equatorial	Projects roughly outward	Often favorable for large substituents
Chair flip	Axial ↔ equatorial	Retains up/down configuration
Cis/trans	Relative ring face	Not altered by chair flip

• For E2 in a cyclohexane chair, the reacting β-H and leaving group may need a trans-diaxial arrangement; the elimination mechanism is developed in CH 4.

b. Sources of strain

• Angle strain arises when bond angles depart from their preferred values; torsional strain comes from eclipsing. Steric crowding can add another contribution.
• Cyclopropane has severe angle strain; cyclobutane puckers, cyclopentane adopts nonplanar conformations, and cyclohexane strongly favors a chair.

c. Relative configuration

• Cis substituents lie on the same ring face; trans substituents lie on opposite faces. These relationships do not change during a ring flip.
• For two substituents, first mark up/down, then assign axial/equatorial in the chosen chair.

• Up/down ring-face orientation differs from axial/equatorial placement in a particular chair. A ring flip changes the latter but does not change cis/trans configuration.

d. Stability and fused rings

• Axial substituents experience 1,3-diaxial interactions. Compare total axial penalties, rather than counting only one substituent.
• For 1,2- and 1,4-disubstitution, trans can be diequatorial; for 1,3-disubstitution, cis can be diequatorial. Fused rings may restrict the accessible conformations.

Positions	Diequatorial relationship
1,2	trans
1,3	cis
1,4	trans

• Bulky substituents often favor equatorial placement because an axial substituent experiences destabilizing 1,3-diaxial interactions.

D. R/S, E/Z, Enantiomers and Diastereomers

1. Configuration, symmetry and optical properties

a. Connectivity and stereoisomer relationships

• Constitutional isomers have the same molecular formula but different atom connectivity. Stereoisomers retain connectivity and differ in spatial arrangement.

• Enantiomers are nonsuperimposable mirror-image stereoisomers. Diastereomers are stereoisomers that are not mirror images; suitable cis/trans and E/Z pairs belong to this category. Different spatial arrangements can give different physical properties.

b. Chirality, tetrahedral centers and molecular symmetry

• A chiral molecule cannot be superimposed on its mirror image by rotation or translation; an achiral molecule can. Chirality is a property of the whole three-dimensional structure.

• A tetrahedral carbon with four different substituent groups is a common stereogenic center; one with two identical groups is not. A molecule with stereocenters can still be achiral through internal symmetry, and some chiral molecules have no tetrahedral carbon stereocenters.

Relationship	Mirror images?	Superimposable?
Enantiomers	Yes	No
Diastereomers	No	No
Identical structures	May be	Yes

c. Wedges and dashes

• A solid wedge represents a bond directed toward the viewer.
• A dashed bond represents a bond directed behind the page.
• Ordinary lines are drawn approximately in the plane of the page.
• Changing how a molecule is oriented on paper does not necessarily change its configuration.

d. First point of difference

• Higher atomic number at the directly attached atom gives higher priority. For isotopes of the same element, higher mass number gives higher priority.
• At a tie, compare the next layer as ordered lists of attached atoms, starting from highest atomic number, until a difference appears.

e. Multiple bonds

• Treat multiple bonds using duplicate-atom conventions for the priority comparison. This is a ranking device, not a statement that actual duplicate atoms exist.
• A longer chain does not automatically outrank a shorter one; the first difference in the atomic-number comparison determines the result.

f. Orient the lowest priority

• Point group 4 away. Trace 1 → 2 → 3: clockwise is R and counterclockwise is S.
• If group 4 points toward the viewer, reverse the apparent result. A rotation of the whole molecule does not change configuration.

g. Permutation and labels

• Swapping any two groups reverses a single tetrahedral center; two such swaps restore its original configuration.
• R/S does not predict the sign of optical rotation. An R compound can be either (+) or (−).

h. Reading a Fischer projection

• The intersection of a Fischer projection represents a tetrahedral center. Horizontal bonds project toward the viewer; vertical bonds project away.

• Rotating the complete Fischer projection by 180° in the page preserves configuration; a 90° rotation generally changes it. Apply CIP priorities to the actual substituents before assigning R or S.

i. Assigning configuration

• Apply ordinary CIP priorities. If priority 4 is on a horizontal bond, reverse the apparent clockwise/counterclockwise assignment.
• Do not equate a vertical chain direction with a universal R/S label; compare the actual substituents at each center.

j. Geometric Isomerism

• Rotation around a double bond requires disrupting π overlap; geometrical arrangements can therefore remain distinct.
• For simple appropriately substituted alkenes, cis refers to corresponding groups on the same side and trans to opposite sides.

k. Requirement for E/Z

• Each carbon of the double bond must have two different attached groups for E/Z stereoisomerism to exist.
• A terminal CH₂= group cannot display E/Z because one carbon has two identical hydrogen atoms.

l. E and Z

• Rank the two groups attached to each alkene carbon using CIP rules. Higher atomic number wins; at a tie, compare successive attached-atom lists.
• High-priority groups on the same side give Z; opposite sides give E. Cis/trans and E/Z describe different comparisons and should not be interchanged automatically.

• Assign priorities from substituent identity, not from arbitrary top/bottom positions in the drawing.

m. Stereoisomer counting and symmetry

• For n independent tetrahedral stereocenters, 2ⁿ is an upper limit on configurational stereoisomers. Symmetry, meso forms and equivalent configurations can reduce the count; count distinct structures rather than drawing duplicates.

• Inverting every center can produce an enantiomer, while inverting only some often gives a diastereomer. Molecular identity and symmetry must still be checked.

n. Meso symmetry and optical inactivity

• A meso compound contains stereogenic centers but is achiral because its overall structure has the required internal symmetry. The stereocenter count alone cannot establish molecular chirality; internal symmetry can reduce the number of distinct stereoisomers below 2ⁿ.

• A pure meso substance is optically inactive through molecular achirality. A racemate is optically inactive because the equal and opposite rotations of its enantiomers cancel. These are different explanations.

o. Specific rotation

• Specific rotation normalizes observed rotation to path length and concentration under specified wavelength, temperature, solvent and concentration conventions.
• Enantiomers rotate plane-polarized light equally and oppositely under identical conditions. Diastereomers have no such simple equal-and-opposite relationship.
• Under the common solution convention, [α] = αobserved/(l × c), with l in dm and c in g/mL; confirm the concentration convention used by a reference.

• The sign of rotation, (+) or (−), does not determine an R/S descriptor. Measured rotation depends on concentration, path length, temperature and wavelength.

p. Composition

• For a mixture containing only two enantiomers, ee = |% major − % minor|. A 70:30 mixture has 40% ee.
• Using rotation to estimate ee requires the pure-enantiomer reference and compatible measurement conditions. A zero rotation alone does not prove that a sample is achiral or pure.

• A racemate contains equal enantiomer amounts and has zero net rotation under usual conditions. An 80:20 enantiomer mixture has 60% ee.

q. Chiral recognition

• Enantiomers have identical properties in many achiral environments, apart from opposite optical rotation and interactions with polarized light.
• A chiral reagent, catalyst, receptor, or stationary phase may distinguish between two enantiomers.
• Biological interactions are frequently stereoselective because biomolecules are chiral.

r. Configuration versus optical rotation

• A reaction can retain or invert a configuration at a stereogenic center, depending on the mechanism.
• R/S descriptors may change when the substituent priorities change, even if the three-dimensional arrangement is retained.
• A racemic or enriched product distribution depends on reaction pathway and stereochemical environment.