Organic Chemistry Reactions: Size, Shape & Stereochemistry

Introduction

• Organic chemistry reactions consider the size and shape of atoms and molecules.
• Most atoms range in radii from 0.4 to 1.5 A° (1 A°=10-8 cm.).
• Chemical bond lengths usually range from 0.7 to 3.0 A°.
• Heavier atoms/molecules are larger than lighter ones (volumes of hydrogen, carbon, chlorine, and iodine atoms are about 1 : 10 : 20: 50).
• Shapes of molecules are determined by the number/type of electrons available for bond formation and the character of bonds produced.
• Carbon compounds' shape is vital to organic reactions, due to mainly covalent bonds that are directional.
• Chemical reactions involve redistribution of electrons; changes in distribution accompany chemical change.
• Understanding reaction mechanisms comes from knowing how and why electrons move and redistribute themselves.
• Knowing stereochemistry, movement, and redistribution of electrons during reactions enables predicting consequences when adding chemical compounds.

Types of Organic Reactions

• Most organic reactions convert functional groups via reagent attack.
• Organic compounds attacked by reagents become substrates or reactants.
• Simple inorganic or organic compounds used to create transformations become reagents.
• Organic reactions proceed as: Substrate + Attacking agent → [Intermediate(s)] → Product(s).
• Convenient to classify reactions into four types:
  • Substitution or displacement reactions
  • Addition reactions
  • Elimination reactions
  • Rearrangements
• Complex reactions may fall into more than one type, individual steps are placed in categories listed.
• Reactions producing larger molecules by coupling smaller ones can be termed 'condensation reactions' (first step is addition, followed by elimination).

Substitution Reactions

• This replaces an atom or group in a molecule with a different atom or group
• E.g., CH3OH + HBr → CH3Br + H2O
• Reaction type depends on carbon atom's linkage:
  • Saturated or unsaturated
  • Initiated by electrophile, nucleophile or free radical (each category has three types)
  • Reactions are unimolecular or bimolecular

Addition Reactions

• Here atoms/groups are added to a molecule. Example: CH2=CH2 + HBr → CH3.CH2Br
• Presence of unsaturation (usually multiple bonds between two atoms) is a condition
• Pi (π)-bonds drive reactions
• Two σ-bonds form for each π-bond, hybridization changes: sp to sp² and sp² to sp³
• Classified further based on attacking reagent and molecularity

Elimination Reactions

• These are the reverse of addition, involving loss of atoms/groups to form multiple linkages.
• Loss commonly occurs from adjacent carbons to yield an olefin
• Unlike reactions mentioned above, they are not categorized by the attacking reagent's nature, but by basis of reaction's molecularity

Rearrangement Reactions

• These involve functional group migration to another position in the molecule that contains a double bond, or reshuffling the sequence of atoms in forming the basic carbon skeleton of the molecule to form a product with new structure
• E.g., CH2-CH2-CH=CH2 to CH2-CH=CH-CH2-X X
• Types vary based on atom/group migrating (anions/carbanions, cations/carbonium ions, and free radicals)

Classification of Reagents

• Electron-attracting or repelling groups in molecules create electron-deficient or electron-rich sites.
• This will predict reagent type for rapid reaction to occur
• An electron-deficient center (like methyl chloride's carbon atom) is readily attacked by negatively charged ions (OH-, CN-, etc.) or electron-rich species (OH-, HN:, R3N, etc.)
• Electron-rich compounds (like phenoxide ion) are readily attacked by positively charged ions (like C6H5N2+) or electron-deficient species (like sulfur atom of SO3).
• Charge presence helps reagent attacks, but it isn't essential.
• Unsymmetrical charge distribution can be induced by mutual polarization.

Electrophilic Reagents (Electrophiles)

• Electron-seeking or -loving, attacking substrates with maximum electron density.
• They have electron-deficient atoms/centers
• Two types:
  • Positive electrophiles: carry a positive charge, including protons, cations and carbon radicals carrying a positive charge (carbonium ions i.e H+, Br+, Cl+, NO2+, NO+, NH+, H3O+, R3C+, Ar-N=N)
  • Neutral electrophiles: do not carry a positive charge and include BF3, AlCl3, ZnCl2, carbon radicals with six electrons in the outermost orbit (carbenes). They are short of a pair of electrons to attain stable configuration and act as electron-seeking reagents.
• Positive electrophiles attacks electron substrates to accept an electron pair for sharing and form neutral

Nucleophilic Reagents (Nucleophiles)

• Possess at least one lone pair of electrons (nucleo-nucleus; phile- to love)
• possess higher electron density, they attack the substrate at the point of minimum electron density
• Two types:
  • Negative nucleophiles: carry excess electron pair and are negatively charged including halide ions, alkoxy ions, hydroxyl ions, and the carbon radicals carrying a negative charge (carbanion, like X-, HO-, RO-, NH2-, CN-, R3C-)
  • Neutral nucleophiles: are rich in electrons (unshared electron pair), but are electrically neutral. examples are (H-O-H, ROH, R-S-H, R-O-R, NH3, R-NH2, respectively)
• Negative nucleophiles attack the positively charged substrate to form a neutral molecule

Mechanism of Organic Reactions

• Describes the discrete steps involved in the reactants changing into products.
• Organic reactions break and make the covalent bonds in steps.

Breaking of Covalent Bonds

• Bond-breaking can happen in two ways:
  • Homolytic fission:
  • Atoms involved have like electronegativity.
  • AB turns into A. and B. (two free radicals)
  • Heterolytic fission:
  • Atoms involved have different electronegativity.
  • AB turns into ions A: and B+ if B is more electronegative.
  • AB turns into A+ and :B if A is more electronegative
  • Homolytic fission needs much less energy than heterolytic fission.

Homolytic Fission (Homolysis)

• This results in two fragments or atoms. Each has one electron of the pair that formed the bond. Electrically neutral, they are free radicals, e.g., H3C: X gives H3C. and .X
• Free radicals are atoms/groups with single unpaired electron.
• The fission results in formation of free-radicals that involves such fissions are free-radical reactions with a free radical reaction mechanism.

Heterolytic Fission (Heterolysis)

• Here the pair of electrons forming the covalent bond goes to a single atom/group creating ions. In a H3C-X compound split:
  • The pair leaves the organic group, staying with X for a negative charge. Organic group becomes positive. Can form carbonium ion or carbocation
  • The pair stays with the organic group, substituent X becomes positive with the organic group being negatively charged known as carbanion.
• Covalent bonds may cleave in homolytic or heterolytic ways in organic reactions; particularly at high temperatures, bonds cleave simultaneously

Reaction Characteristics

• Ionic reactions:
  • Rare in the gas phase; mainly in polar solvent solutions
  • Polarity of the solvent influences it.
  • Unaffected by light/oxygen/peroxides, but acids/bases catalyze it
    • Reaction rate rises with temperature
  • Unaffected by free-radical inhibitors; e.g., hydroquinone
• Free-radical reactions:
  • Occur in gasses (vapors) or non-polar solvents
  • Started/sped up by light, high heat, oxygen, or peroxides
  • Inhibited or prevented by free-radical inhibitors

Cyclic or Molecular Mechanism

• Reactions occur by electron transfer in cyclic order in/between molecules where the transition state is a six-membered ring

Reaction Intermediates

• Three reaction intermediates form due to organic reaction fission.
  • free-radicals (from homolytic fission)
  • carbonium ions
  • carbanions (from heterolytic fission) react with the reagent to form the products
• Study general aspects of reaction intermediates

Free Radicals

• Species with unpaired electron are called free-radicals that are electrically neutral.
• Unpaired electron causes radicals to seek another electron hence are very reactive.
• In a carbon with free-radicals the geometry is either planar or has inverted pyramidal shapes.
• Allkyl free radicals are planar structures. In the carbon atom is the sp² mixed state.
• Stabilies are common:
  • Benzy > Allyl > Tertiary > Secondary > Primary> Methyl > Vinyl

Carbonium Ions or Carbocations

• Positively charged species that contain a carbon atom with six electrons in three bonds and no pair of electrons in its valency shells.
• Named according to carbonium ion nomenclature or cation; cation used more
• They are classified as primary, secondary or tertiary depending on the carbon atom bearing the positive charge.
• Tendency to complete the octet of carbon. By combining with:Available anionic species or electron rich molecules or by losing an atom or group.
• Primary carbonium ions tend to perform conversions to rearrange into more stable (secondary or tertiary) forms

Method's Carbonium Ions form

• Direct lonisation
• Protonation of unsaturated compounds
• Protonation
• Decomposition of diamonium salts