Organic Chemistry
Table of Contents
1. Nucleophile
Chemical species that forms bonds by donating an electron pair.
Electron-rich or high electron density availability
- Negatively charged
- Polar molecule with partial negative charge (\(\delta-\))
- Neutral atom with lone pairs
All molecules and ions with a free pair of electrons or at least one pi bond.
2. Electrophile
They forms bonds by accepting an electron pair.
Electorn-deficient:
- Positively charged
- Polar molecule with partial positive charge (\(\delta+\))
- Neutral atom with empty orbital
3. Substituent
One or a group of atoms that replaces other group of atoms, and become a moiety in the resultatnt molecule.
Suffix is used for organic compounds that replaces:
- one hydrogen with single bond: -yl
- two hydrogens with double bond: -ylidene (sometimes, -ylidine)
- three hydrogens with triple bond: -ylidyne
3.1. Allyl Group
\[ \chemfig{[:30]=-[:-30]-R} \]
A site ajacent to the unsaturated carbon atom is called the allylic position or allylic site. The group attached to this site is sometimes described as allylic.
4. Substitution Reaction
4.1. SN1 Reaction
- Unimolecular Nucleophilic Substitution
The rate determining step is unimolecular.
Reaction involves carbocation intermediate.
Three step mechanism:
- R-X → R⁺ + X⁻ (Ionization)
- R⁺ + Nu → RNu⁺ (Nucleophilic attack)
- RNu⁺ + H₂O → RNu + H₃O⁺ (Deprotonation)
4.2. SN2 Reaction
- Bimolecular Nucleophiilic Substitution
The rate determining step is bimolecular.
One step mechanism:
- R-X + Nu⁻ → RNu + X⁻
5. Elimination Reaction
5.1. E1 Reaction
- Unimolecular Elimination
Two step process:
- R-X → R⁺ + X⁻ (Ionization)
- R⁺ + H₂O → R + H₃O⁺ (Deprotonation)
5.2. E2 Reaction
- Bimolecular Elimination
One step mechanism in which:
- C-H and C-X breaks
- C=C forms
5.3. Ei Mechanism
- Internal/Intramolecular Elimination
5.4. E1cB Reaction
- Unimolecular Elimination under conjugate Base
6. Transition State
Notated with superscript double dagger (‡).
6.1. Hammond Postulate
The transition state looks closer to reactants or products whichever closer in energy.
For example, The transition state of hydrogen abstraction (R–H—Cl) by chlorine looks similar to the reactants (RH + Cl∙), and one by bromine (R—H–Br) looks close to the products (R∙ + HBr).
7. Allylic Strain
- 1,3-allylic strain, A-strain
One conformer is favored over the other due to the interaction between two allylic substituents.
8. Isomerism
8.1. Constitutional Isomer
Atoms connected differently
8.2. Stereoisomer
Atoms oriented differently
8.2.1. Enantiomer
The mirror image
The mirror can be placed behind or aside.
Identical mechanical properties, opposite optical properties.
8.2.2. Chirality Center
Carbon atom connected to four different groups.
8.2.3. Cahn-Ingold-Prelog System
- Prioritize all four groups ajacent to chiral center based on the atomic number with highest first.
- R if 1-2-3 is clockwise seen behind the fourth priority group, S if 1-2-3 is counterclockwise.
If tie occurs look further into the chain, and compare the atomic-number-ordered lists of atoms from top to bottom.
If multiple chiral centers are present, the configuration is preceded by a locant. e.g. (2R, 3S)-3-Methyl-2-pentanol.
8.2.4. Specific Rotation
A compound is said to be optically active if it rotates the plane-polarized light.
\[ [\alpha] := \frac{\alpha}{c\ell} \] where \( \alpha \) is the observed rotation, \( c \) is the concentration, and \( \ell \) is the pathlength.
Specific rotation is dependent on temperature and wavelength.
The compound is called dextrorotatory if the light rotates positively (+), or levorotatory if the light rotates negatively (-).
The optical activity is dependent of temperature, and not one-to-one to the R/S system.
8.2.5. Racemic Misture
A solution containing both enantiomers is called a racemic mixture. It is optically inactive.
If one enantiomer is more than the other, the percent point difference is called the /enantiomeric excess (ee).
8.2.6. Diastereomer
Stereoisomers that are not enantiomers.
Diastereomers can have different mechanical properties.
Enantiomer relation forms equivalence class within the set of stereoisomers of a molecule. Each equivalence class represent a single diastereomer.
\( n \) chirality centers at most create \( 2^n \) stereoisomers of which \( 2^{n-1} \) diastereomers exists.
- cis- on the same side (of double bond, or ring).
- trans- on the other side (of double bond, or ring).
8.2.7. Conformer
Stereoisomer with different bond angle.
Conformers are considered to be the same species.
9. Synthesis
9.1. Tributyl Photsphate
- TBP
Nucleophilic attack of phosphoric acid onto butanol.
phosphoryl chloride POCl₃ (or phosphorus oxychloride) is used industrially in lieu of phosphoric acid.