Glossary

45 core terms for nomenclature, stereochemistry, mechanisms, and spectroscopy, each with definition, use, example, and common misconception.

Principal characteristic groupNomenclature

The highest-priority characteristic group in a structure; it determines the suffix and strongly affects parent selection.

Details: When several groups are present, nonprincipal groups are usually expressed as prefixes. Priority is a nomenclature rule, not a general reactivity ranking.
Example: With a carboxylic acid and an alcohol, the acid supplies “-oic acid” and the OH group is named hydroxy-.
Common misconception: It does not mean “the most reactive group.”
Related terms: suffix, prefix, parent, functional-group priority

principal functional group 主基

Parent structureNomenclature

The structure chosen as the basis of the systematic name, using rules involving the principal group, skeletal size, rings, and unsaturation.

Details: The longest visible carbon chain is not always the parent. Inclusion of the principal group and multiple bonds can take priority.
Example: A chain containing –COOH may be selected even when another apparently longer route exists.
Common misconception: “Always choose the longest chain” is incomplete.
Related terms: principal group, numbering, parent hydride

parent chain parent hydride 主鎖

SuffixNomenclature

The ending attached to the parent name to express the principal group or features such as unsaturation.

Details: The principal group is normally represented once as a suffix; elision and locant placement follow specific rules.
Example: The -ol in propan-2-ol is the alcohol suffix.
Common misconception: A functional-group word cannot simply be appended arbitrarily.
Related terms: principal group, prefix, parent name

suffix characteristic group

PrefixNomenclature

A part placed before the parent name to describe substituents or characteristic groups that are not principal.

Details: Prefixes are combined with locants and ordered according to nomenclature alphabetization rules.
Example: bromo- and hydroxy- in 3-bromo-2-hydroxybutanoic acid.
Common misconception: Multiplicative prefixes such as di- are often ignored for alphabetization.
Related terms: substituent, locant, alphabetization

prefix substitutive prefix

LocantNomenclature

A number or letter identifying the position of a substituent, characteristic group, multiple bond, or stereogenic element.

Details: Commas separate numbers; hyphens separate numbers from words. Numbering direction follows formal comparison rules.
Example: 2 and 3 in 2,3-dimethylbutane are locants for methyl groups.
Common misconception: Do not choose a direction merely because one isolated number looks smaller.
Related terms: numbering, first point of difference, punctuation

locant number position

First point of differenceNomenclature

The rule of comparing two ordered locant sequences from left to right and choosing the one with the lower value at the first difference.

Details: Compare ordered locant lists lexicographically, not by their sums, after determining which feature receives priority.
Example: Between 2,3,5 and 2,4,4, choose 2,3,5 because 3 is lower than 4 at the first difference.
Common misconception: It is not a “lowest sum of locants” rule.
Related terms: locant, numbering, priority

lowest set locants first difference

SubstituentNomenclature

An atom or group attached in place of a hydrogen or another replaceable unit on the parent structure.

Details: Substituents include alkyl groups, halogens, and complex branched groups; complex substituents may require their own numbering.
Example: ethyl, bromo, and propan-2-yl can all function as substituent names.
Common misconception: A visually branching portion is not automatically the substituent; select the parent first.
Related terms: parent, prefix, complex substituent

substituent branch side chain

Multiplicative prefixNomenclature

A prefix indicating that an identical substituent or structural unit occurs more than once.

Details: Simple substituents commonly use di-, tri-, and tetra-; complex substituents may use bis-, tris-, and related forms.
Example: 2,2-dimethylpropane; 1,2-bis(hydroxymethyl)benzene.
Common misconception: Multiplicative prefixes are not always counted in alphabetization.
Related terms: prefix, alphabetization, parentheses

di tri tetra bis tris

AlphabetizationNomenclature

The ordering rule used when several prefixes appear before a parent name.

Details: Names are generally compared by the substantive prefix, ignoring locants and simple multiplicative prefixes.
Example: ethyl is cited before methyl.
Common misconception: Prefixes are not ordered by their numerical locants.
Related terms: prefix, multiplicative prefix, substituent

alphabetical order prefixes

CIP priority rulesStereochemistry

The Cahn–Ingold–Prelog rules used to rank ligands at stereogenic centers and double bonds.

Details: Compare atomic numbers of directly attached atoms, moving outward layer by layer when tied. Isotopes and multiple bonds have special conventions.
Example: Br ranks above Cl, O, N, C, and H by atomic number.
Common misconception: Priority is not assigned by whole-group molecular mass or visual size.
Related terms: R/S, E/Z, stereogenic center

Cahn Ingold Prelog priority

R/S configurationStereochemistry

Stereodescriptors that specify absolute configuration at a tetrahedral stereogenic center or related element.

Details: View the 1→2→3 sequence with priority 4 directed away; clockwise is R and counterclockwise is S. Reverse the result if group 4 points toward the viewer.
Example: With lowest-priority H away, a clockwise 1→2→3 sequence is R.
Common misconception: Do not judge the page-plane rotation without checking the direction of group 4.
Related terms: CIP rules, stereogenic center, enantiomer

stereodescriptor absolute configuration

E/Z configurationStereochemistry

Descriptors for alkene geometry based on the relative positions of the higher-priority substituent at each end of a double bond.

Details: Z means the two higher-priority groups are on the same side; E means opposite sides.
Example: If the higher-priority groups are drawn on the same side, the alkene is Z.
Common misconception: Do not replace CIP ranking with a simple “same groups” test.
Related terms: CIP rules, geometric isomerism

alkene stereochemistry entgegen zusammen

Stereogenic centerStereochemistry

An atom or other stereogenic element for which interchanging two ligands produces a stereoisomer.

Details: A tetrahedral carbon with four different ligands is common, but stereogenic elements are not limited to carbon.
Example: The carbon in CHBrClF is stereogenic.
Common misconception: A molecule with stereogenic centers is not necessarily chiral; meso forms exist.
Related terms: R/S, chirality, meso compound

chiral center asymmetric carbon

EnantiomersStereochemistry

A pair of stereoisomers that are nonsuperimposable mirror images.

Details: They share many properties in achiral environments but differ in optical rotation and interactions with chiral environments.
Example: For a molecule with one stereogenic center, its R and S forms are usually enantiomers.
Common misconception: R/S does not predict the sign of optical rotation.
Related terms: diastereomer, chirality, racemate

optical isomer mirror image

DiastereomersStereochemistry

Stereoisomers that are not mirror images of one another.

Details: They include molecules differing at some but not all stereogenic elements and E/Z isomers; their properties generally differ.
Example: (2R,3R) and (2R,3S) forms are diastereomers.
Common misconception: Not all stereoisomers are enantiomers.
Related terms: enantiomer, E/Z, meso compound

diastereoisomer stereoisomer

Meso compoundStereochemistry

A molecule containing stereogenic centers but achiral overall because of internal symmetry.

Details: Its mirror image is superimposable and the pure compound is optically inactive.
Example: meso-2,3-dibromobutane has R,S centers and an internal plane of symmetry.
Common misconception: Do not infer molecular chirality solely from the number of stereogenic centers.
Related terms: stereogenic center, chirality, diastereomer

meso internal symmetry

Lone pairElectrons & mechanisms

A pair of valence electrons represented as localized on one atom rather than shared in a covalent bond.

Details: Lone pairs commonly serve as the source of electron flow in nucleophilic attack, proton transfer, and resonance.
Example: A lone pair on hydroxide can attack a carbonyl carbon.
Common misconception: “Nonbonding” does not mean chemically inactive.
Related terms: nucleophile, curved arrow, resonance

孤立電子対 nonbonding electron pair

Formal chargeElectrons & mechanisms

A bookkeeping charge obtained by assigning half of every bonding pair to each bonded atom.

Details: Formal charge equals valence electrons minus nonbonding electrons minus total bond order; it is distinct from partial charge.
Example: A nitrogen with four ordinary single bonds usually has formal charge +1.
Common misconception: It is not the measured electron-density distribution.
Related terms: partial charge, valence, resonance

charge valence electron bookkeeping

Curved arrowElectrons & mechanisms

A notation used in mechanisms to represent movement of an electron pair or, with a fishhook, a single electron.

Details: A full arrow starts at an electron pair (bond or lone pair) and ends where that pair is placed. A fishhook represents one electron.
Example: An arrow from a C–Br bond to Br denotes heterolytic bond cleavage.
Common misconception: It does not directly show the path traveled by an atom.
Related terms: lone pair, nucleophile, bond cleavage

electron pushing arrow mechanism

NucleophileElectrons & mechanisms

A species that donates an electron pair to form a new covalent bond.

Details: Nucleophiles may be anionic or neutral; nucleophilicity depends on solvent, steric hindrance, and polarizability.
Example: CN⁻ can attack the carbon bearing a leaving group in a haloalkane.
Common misconception: Nucleophilicity and basicity are related but not identical.
Related terms: electrophile, base, SN2

nucleophile electron pair donor

ElectrophileElectrons & mechanisms

An electron-poor species or site that accepts an electron pair to form a new covalent bond.

Details: Electrophiles need not be cations; polarized neutral bonds can create electrophilic atoms.
Example: The carbonyl carbon of an aldehyde is an electrophilic center.
Common misconception: An electrophile is not necessarily positively charged.
Related terms: nucleophile, Lewis acid, polarization

electrophile electron pair acceptor

Leaving groupElectrons & mechanisms

An atom or group that departs from a substrate with the bonding electron pair.

Details: A good leaving group forms a relatively stable species after departure; strong bases are usually poor leaving groups.
Example: I⁻, Br⁻, and tosylate are common good leaving groups.
Common misconception: Leaving-group ability is not determined by bond strength alone.
Related terms: conjugate acid, SN1, SN2, E2

leaving group nucleofuge

ResonanceElectrons & mechanisms

A way to represent one species by contributors differing only in electron placement, not atomic connectivity.

Details: The actual structure is a resonance hybrid, not a molecule rapidly switching between separate contributors.
Example: In a carboxylate, negative charge is delocalized over two oxygen atoms.
Common misconception: Resonance contributors are not distinct species in equilibrium.
Related terms: delocalization, formal charge, conjugation

resonance contributor delocalization

Inductive effectElectrons & mechanisms

The transmission of electron-withdrawing or electron-donating effects through sigma bonds.

Details: It decreases rapidly with distance and can influence acidity and intermediate stability.
Example: A nearby chlorine substituent can increase carboxylic-acid acidity.
Common misconception: It is distinct from resonance transmission through conjugation.
Related terms: resonance effect, electronegativity, acidity

induction sigma bond electron withdrawal

CarbocationElectrons & mechanisms

A reactive intermediate with a positive charge centered primarily on carbon.

Details: Typical three-coordinate carbocations are planar and can be stabilized by hyperconjugation or resonance; rearrangements may occur.
Example: Simple tertiary alkyl carbocations are generally more stable than primary ones.
Common misconception: The simple substitution-order rule can be overridden by resonance and other effects.
Related terms: SN1, E1, rearrangement, hyperconjugation

carbenium ion cation intermediate

Transition stateElectrons & mechanisms

The non-isolable configuration at an energy maximum along a reaction coordinate.

Details: It has partial bonds and is written with double brackets and ‡; it is not an intermediate.
Example: The SN2 transition state has partial bonds to both nucleophile and leaving group.
Common misconception: A transition state is not merely a short-lived intermediate.
Related terms: activation energy, intermediate, reaction coordinate

activated complex energy maximum

Reaction intermediateElectrons & mechanisms

A species formed in one elementary step and consumed in another, corresponding to a local energy minimum.

Details: It does not appear in the net equation and may sometimes be observed or trapped.
Example: A carbocation formed during an SN1 reaction is an intermediate.
Common misconception: Distinguish an intermediate from a catalyst, which is regenerated.
Related terms: transition state, elementary step, catalyst

intermediate local minimum

SN1 reactionReaction classes

A nucleophilic substitution whose rate-determining ionization step is unimolecular in substrate.

Details: Typical SN1 chemistry is favored by substrates forming stable carbocations and polar protic media; rearrangement and stereochemical erosion can occur.
Example: Solvolysis of a tertiary haloalkane.
Common misconception: It does not necessarily give perfectly racemic product.
Related terms: carbocation, leaving group, SN2

unimolecular nucleophilic substitution

SN2 reactionReaction classes

A concerted substitution whose rate depends on both substrate and nucleophile.

Details: Backside attack causes inversion; low steric hindrance, strong nucleophiles, and polar aprotic solvents often favor the pathway.
Example: Attack of OH⁻ on methyl bromide.
Common misconception: A strong base does not guarantee SN2; E2 competition matters.
Related terms: nucleophile, leaving group, inversion

bimolecular nucleophilic substitution backside attack

E1 reactionReaction classes

An elimination involving unimolecular ionization to a carbocation before deprotonation.

Details: It competes with SN1, often gives the more substituted alkene, and may undergo rearrangement.
Example: Acid-catalyzed dehydration of a tertiary alcohol.
Common misconception: It is not a single concerted step.
Related terms: SN1, carbocation, Zaitsev rule

unimolecular elimination

E2 reactionReaction classes

A concerted elimination in which base removes a beta hydrogen as the double bond forms and the leaving group departs.

Details: An anti-periplanar C–H/C–leaving-group arrangement is commonly required; rate depends on substrate and base.
Example: Cyclohexane E2 reactions commonly require a trans-diaxial arrangement.
Common misconception: Not every beta hydrogen is geometrically available.
Related terms: base, anti-periplanar, SN2

bimolecular elimination anti periplanar

Carbonyl groupFunctional groups

A functional group containing a carbon–oxygen double bond.

Details: The bond is strongly polarized, making carbon electrophilic and oxygen electron-rich; reactivity varies with surrounding groups.
Example: Nucleophilic addition occurs at the carbonyl carbon of a ketone.
Common misconception: All carbonyl compounds do not have identical reactivity.
Related terms: electrophile, IR, nucleophilic addition

C=O aldehyde ketone acid ester

AlcoholFunctional groups

A class of compounds containing a hydroxy group bonded to carbon.

Details: OH is normally a poor leaving group but can be activated; hydrogen bonding affects boiling point and solubility.
Example: propan-2-ol is a secondary alcohol.
Common misconception: Phenols and carboxylic acids are not classified simply as ordinary alcohols.
Related terms: hydroxy group, oxidation, leaving group

OH hydroxy hydroxyl

IR spectroscopySpectroscopy

A method that measures absorption of infrared radiation by molecular vibrations, mainly to identify bonds and functional groups.

Details: The x-axis is usually wavenumber in cm⁻¹, often decreasing left to right; intensity and band shape also matter.
Example: Many carbonyl compounds show a strong absorption near 1700 cm⁻¹.
Common misconception: Do not identify a complete structure from one approximate table match.
Related terms: wavenumber, functional-group region, fingerprint region

infrared spectrum wavenumber

Chemical shiftSpectroscopy

The resonance position of an NMR signal expressed in ppm relative to a reference.

Details: It depends on shielding, anisotropy, electronegative atoms, and pi systems; ppm values are broadly field-independent.
Example: Aldehyde protons commonly appear near 9–10 ppm.
Common misconception: Do not assign a signal from chemical shift alone.
Related terms: shielding, downfield, NMR

delta ppm NMR shift

IntegrationSpectroscopy

The area of a ¹H NMR signal, used to estimate the relative number of protons in that environment.

Details: Integration gives relative, not inherently absolute, proton counts and may be unreliable for exchangeable or overlapping signals.
Example: A 3:2 integral ratio can suggest CH₃ and CH₂ groups.
Common misconception: Peak height is not the same as integrated area.
Related terms: 1H NMR, exchangeable proton, overlap

NMR integral area proton count

MultiplicitySpectroscopy

The splitting pattern of an NMR resonance caused by spin–spin coupling.

Details: The n+1 rule applies to simple first-order cases; nonequivalent coupling sets and strong coupling produce more complex patterns.
Example: In CH₃CH₂–, CH₃ is often a triplet and CH₂ a quartet.
Common misconception: The n+1 rule is not universal.
Related terms: coupling constant, equivalent protons, first-order spectrum

splitting singlet doublet triplet quartet

Coupling constantSpectroscopy

The line separation in Hz within a multiplet, measuring the magnitude of spin–spin coupling.

Details: Coupled signals share the same J; J values can report connectivity and geometry.
Example: Trans-vinylic coupling is often larger than cis-vinylic coupling.
Common misconception: Compare coupling constants in Hz, not ppm.
Related terms: multiplicity, Karplus relationship, NMR

J Hz spin spin coupling

Shielding and deshieldingSpectroscopy

The reduction or enhancement of effective magnetic field at a nucleus by its electronic environment.

Details: Greater shielding generally shifts a signal upfield to lower ppm; deshielding moves it downfield.
Example: Protons near oxygen are commonly deshielded.
Common misconception: Chemical shift is not controlled by local electron density alone.
Related terms: chemical shift, upfield, downfield

upfield downfield electron density

Mass spectrometrySpectroscopy

An analytical method that measures ion mass-to-charge ratios to obtain molecular-mass, composition, and fragmentation information.

Details: Ionization method strongly affects molecular-ion visibility and fragmentation.
Example: EI can produce a molecular radical cation M⁺• and fragment ions.
Common misconception: The highest-m/z peak is not automatically the molecular ion.
Related terms: molecular ion, base peak, fragmentation

MS mass to charge m/z

Molecular ionSpectroscopy

A peak corresponding to an ionized molecule that has not undergone major fragmentation.

Details: EI often gives M⁺•, while soft ionization commonly gives species such as [M+H]⁺ or [M−H]⁻.
Example: A compound of nominal mass 100 may show an EI molecular ion at m/z 100.
Common misconception: Do not confuse the m/z of [M+H]⁺ with neutral molecular mass.
Related terms: mass spectrometry, isotope peak, pseudomolecular ion

M plus molecular radical cation parent ion

Base peakSpectroscopy

The most intense peak in a mass spectrum, assigned 100% relative intensity.

Details: It reflects the most intense detected ion, which need not be the molecular ion.
Example: Alkylbenzenes often show a strong tropylium ion at m/z 91.
Common misconception: “Base” does not mean highest mass.
Related terms: molecular ion, fragmentation, relative intensity

base peak relative intensity 100

Isotope patternSpectroscopy

The cluster of peaks produced by naturally occurring isotopes and their abundances.

Details: One chlorine often gives an M:M+2 ratio near 3:1, while one bromine gives near 1:1.
Example: A brominated compound may show nearly equal M and M+2 peaks.
Common misconception: Do not automatically interpret isotope peaks as impurities.
Related terms: M+1, M+2, molecular ion

M+1 M+2 chlorine bromine

FragmentationSpectroscopy

The formation of smaller ions from a molecular ion or precursor through bond cleavage or rearrangement.

Details: Fragment stability and neutral losses provide structural clues; patterns depend strongly on ionization and collision conditions.
Example: Alpha cleavage is common for carbonyl compounds.
Common misconception: Not every mass difference has a unique structural assignment.
Related terms: mass spectrometry, molecular ion, neutral loss

fragment ion cleavage rearrangement

Degree of unsaturationSpectroscopy

A value calculated from molecular formula corresponding to the total number of rings and pi bonds.

Details: A common formula is C − (H+X)/2 + N/2 + 1; O and S are usually omitted and halogens count like H.
Example: Benzene C₆H₆ has DBE 4: one ring plus three double bonds.
Common misconception: DBE does not specify how rings and multiple bonds are distributed.
Related terms: molecular formula, mass spectrometry, structure elucidation

DBE IHD double bond equivalent