Structure and reactivity, PJW

Structure

Levels of structure

The
structure and geometry of molecules
, comprising:
- Chemical formulas
  - Empirical formulas
  - Molecular formulas
- Connectivity
  - Structural formulas
    - Lewis structures
    - Skeletal formulas
- Configuration
  - Absolute configuration (basically which enantiomer)
    - use
      stereocentre
      based on its absolute configuration
      - for asymmetric carbon, use R-S notation
      - for
        E-Z notation
- Conformation (3D shape that can change without breaking and making bonds, by rotation about bonds)

Connectivity is the domain of

regiochemistry, whereas configuration and conformation come under stereochemistry

Table of types of structure and isomerism

**The different levels of structure and the corresponding types of isomerism**
Level of structure	Type of isomerism	Definition of isomers
Chemical formula	Isomerism	Isomers have the same chemical formula but are otherwise different somehow.
Connectivity	Structural isomerism (constitutional isomerism)	Structural isomers have the same chemical formula but different connectivity. Structural isomerism is a subset of isomerism.
Spatial arrangement	Stereoisomerism	Stereoisomers have the same connectivity but a different spatial arrangement (a different 3D shape). Stereoisomerism is a subset of isomerism.
Chirality	Enantiomerism	Enantiomers have the same connectivity and spatial arrangement except they have opposite chirality, i.e. opposite absolute configuration. Enantiomers are non-superposable mirror images of each other Enantiomerism is a subset of stereoisomerism
Configuration	Diastereomerism	Diastereomers have the same connectivity but a different (but not opposite) configuration and are thus not mirror images of each other. Diastereomers are stereoisomers that are not enantiomers Diastereomerism is a subset of stereoisomerism
Configuration	Cis–trans isomerism	Cis–trans isomers have the same connectivity but a different spatial arrangement, are not mirror images of each other, and are not conformers of each other. Not being conformers means cis–trans isomers cannot be superposed by interconverted by rotations about formally single bonds alone. This usually requires the presence of a bond about which rotation is restricted, such as a double bond or a bond in a ring. Cis–trans isomerism is a subset of diastereomerism
Conformation	Conformational isomerism	Conformers have the same connectivity and configuration but a different spatial arrangement and can be interconverted by rotations about formally single bonds. They can be mirror images of each other, but this is not a requirement. Conformational isomerism is a subset of diastereomerism

Law of definite proportions
Asymmetry
Chirality (mathematics)
chiral symmetry
Chirality (chemistry)
Chiral ligand
Asymmetric synthesis, asymmetric induction

IUPAC Gold Book definitions

IUPAC
Gold Book

connectivity: "In a chemical context, the information content of a line formula, but omitting any indication of bond multiplicity."
constitution: "The description of the identity and connectivity (and corresponding bond multiplicities) of the atoms in a molecular entity (omitting any distinction arising from their spatial arrangement)."
superposability: "The ability to bring two particular stereochemical formulae (or models) into coincidence (or to be exactly superposable in space, and for the corresponding molecular entities or objects to become exact replicas of each other) by no more than translation and rigid rotation."
projection formula
absolute configuration
relative configuration
configuration (stereochemical): "...the arrangements of atoms of a molecular entity in space that distinguishes stereoisomers, the isomerism between which is not due to conformation differences."
conformer
rotamer
polytopal rearrangement

Relationship between structure, bonding, and electrons

Resonance between Lewis structures and the associated delocalisation of electrons
Orbital hybridisation
- part of valence bond theory, together with pair bonding and resonance
- Hybridization Theory, a YouTube preview of an educational DVD
Molecular orbital theory
- less useful than valence bond theory for day-to-day back-of-the-envelope organic chemistry but an exceptionally powerful tool for more a detailed, precise, accurate and fundamental understanding of chemical bonding
- for more detail, see:
  - Level 1 quantum mechanics
  - Level 2 quantum mechanics
  - Level 2 molecular orbital theory
  - Level 2 Hückel theory
  - Level 3 orbitals in organic chemistry
  - Level 3 molecular electronic structure
  - Level 3 molecular spectroscopy and structure

Orbitals and axial chirality

orthogonal pi bonds

Ketenes, R₂C=C=O, also have orthogonal pi bonds but no substituents on oxygen, so ketenes do not exhibit axial chirality

Reactivity

Chemical reactions involve the movement of electrons between chemicals (e.g. redox), usually resulting in the making and breaking of chemical bonds
Oxidation levels in organic compounds
The chemicals taking part in a reaction can best be categorised as acids, bases, nucleophiles, or electrophiles. There are several
Brønsted–Lowry acid-base theory
.

Acids vs. bases

Acids are proton donors. They do one thing: protonate.
Bases are proton acceptors. They also do one thing: deprotonate.

Electrophiles vs. nucleophiles

Electrophiles are electron acceptors (≈ Lewis acids), as are oxidizing agents

Nucleophiles are electron donors (≈ Lewis bases), as are reducing agents

Hard and soft

Electrophiles and nucleophiles can each be further classified as hard or soft, or more realistically, where they lie along the hard-soft spectrum
- For details, see later courses on
  dicarbonyl compounds, retrosynthetic analysis, orbitals in organic chemistry

**Summary of the chemical properties of hard and soft species**
Property	Hard	Soft
Oxidation state	high	low or zero
Polarizability	low	high
Electronegativity	high	low
HOMO of the Nu⁻	low-lying	high-lying
LUMO of the E⁺	high-lying	low-lying

Hard electrophiles react best with hard nucleophiles, as they have:
- small atomic or ionic radii
- high oxidation states
- low polarizabilities
- high electronegativities
- low-lying
  LUMOs
  (electrophiles)
- if the reacting electrophile and nucleophile are very hard, redox can happen (formally, complete transfer of electrons from nucleophile to electrophile instead of sharing)
Soft electrophiles react best with soft nucleophiles, as they have:
- large atomic or ionic radii
- low (or zero) oxidation states
- high polarizabilities
- low electronegativities
- high-lying HOMOs (nucleophiles) and low-lying LUMOs (electrophiles)
HSAB theory is also used in inorganic chemistry:
Level 2 transition metal chemistry (hard and soft metals and ligands
)

Substitution reactions

Nucleophilic substitution:
- S_N1 goes with racemization
- S_N2 goes with inversion
  - S_N2 animation
  - The true mechanism may be more complicated in some cases
- esterification, transesterification, ester hydrolysis