Basic Organic Chemistry Notes

  • Organic chemistry is the study of carbon compounds, excluding carbon oxides, carbonates, carbides, and carbon disulfide.
  • This classification is based on convenience due to the large number of carbon compounds.
  • Organic chemistry is important for technology, drugs, dyes, rubber, food, and clothes.
  • It is fundamental to biology, medicine, and related courses.

Why Carbon Forms Many Compounds

  • Carbon atoms can bond with each other to form chains of thousands of atoms (catenation) and rings of various sizes.
  • Other atoms, like hydrogen, oxygen, halogens, nitrogen, sulfur, and phosphorus, attach to these chains and rings.
  • Each unique arrangement corresponds to a different compound with its own chemical and physical properties.

Characteristics of Organic Compounds

  1. Formed by covalent combination.
  2. Do not ionize or conduct electricity.
  3. Mostly insoluble in water but soluble in non-polar solvents.
  4. Generally have low melting and boiling points.
  5. Burn in excess air to produce CO2 and H2O, and in limited amounts, produce CO and H_2O.

Homologous Series

  • Compounds are studied in groups called homologous series to simplify organic chemistry.
  • A homologous series is a family of compounds with:
    • The same general molecular formula.
    • Similar chemical preparation methods.
    • Members differing by a -CH_2 (methylene) group or a molecular mass of 14.
    • Similar chemical properties, with reactivity varying along the series.
    • Physical properties changing gradually in the same direction; for example, melting/boiling points and density change with carbon atom number.

Functional Group

  • A functional group is an atom or group of atoms common to a family, determining its behavior.
  • Bonds like C-C in alkanes, C=C in alkenes, C≡C in alkynes can also be functional groups.
  • Other examples include hydroxyl -OH in alkanols, carboxy -COOH in alkanoic acids, amino -NH_2 in amines, carbonyl -CO in alkanals and alkanones, and cyano -CN in nitriles.

Bonding in Organic Compounds

The Carbon Atom
  • Carbon has a central role in organic chemistry.
  • Atomic number of carbon is 6.
  • Ground state electronic configuration: 1s^22s^22px^12py^1, indicating two unpaired electrons, suggesting divalency.
  • However, carbon is tetravalent, which is explained by:
    • Excitation: One 2s electron is promoted to the 2p orbital, resulting in the excited configuration 1s^22s^12px^12py^12p_z^1.
    • This new arrangement has four unpaired electrons, enabling the formation of four bonds.
Hybridization
  • If carbon formed four bonds with unpaired electrons in the excited state, the bonds wouldn't be equivalent.
    • One non-directed bond (2s spherical orbital).
    • Three directed bonds at right angles (three 2p orbitals).
  • However, methane's four C-H bonds are identical and symmetrically arranged at 109°28'.
  • Hybridization accounts for this: mixing two or more pure atomic orbitals from the same quantum level to create equivalent orbitals that can overlap maximally.
  • These new orbitals are known as hybrid orbitals.
  • Three important types of carbon hybridization give four valencies: sp^3, sp^2, and sp.
sp3 (Tetrahedral) Hybridization
  • Mixing one 2s and three 2p orbitals to form four equivalent sp^3 hybrid orbitals arranged tetrahedrally (pointing towards the corners of a regular tetrahedron) at 109°28' to each other.
  • Occurs when carbon forms four single bonds, as in methane (CH_4).
  • The four hybrid orbitals overlap with 1s orbitals of four hydrogen atoms to form four sigma \sigma bonds arranged tetrahedrally.
  • All H-C-H bond angles are 109°28'.
  • Combination of two carbon atoms in ethane results from the axial overlap of two sp^3 atomic orbitals, one from each carbon atom, forming a strong bond.
sp2 (Trigonal) Hybridization
  • Mixes one 2s and two 2p atomic orbitals to give three equivalent sp^2 hybrid orbitals, which are equilateral and directed at angles of 120° to each other.
  • The unhybridized 2p orbital is perpendicular to the plane of the three orbitals.
  • Ethene (C2H4) is an example where carbon atoms are in this hybridization state.
  • Two sp^2 orbitals from each carbon overlap with 1s orbitals of two hydrogen atoms to form C-H bonds, while the third sp^2 orbital of each carbon overlaps to form a C-C bond.
  • Unhybridized p-orbitals of the two carbon atoms overlap to form a pi \pi bond.
  • The additional \pi bond draws carbon atoms closer, resulting in a C=C distance of 0.134 nm, compared to the C-C distance in ethane (0.153 nm).
  • Distribution of electrons in the two lobes means that a negative charge region is available for attack by electrophiles (electron-seeking reagents).
  • The characteristic reactions of C=C are with electrophilic reagents.
sp (Diagonal) Hybridization
  • Hybridization of one 2s and one 2p orbitals forms two equivalent collinear sp hybrid orbitals directed at 180° to each other.
  • Two 2p orbitals (i.e., 2py and 2pz) remain unhybridized and are perpendicular to each other and to the plane of the sp orbitals.
  • Ethyne (C2H2) is an example where the carbon atoms are in sp hybridization.
  • One sp hybrid orbital of each carbon atom overlaps to form a sigma \sigma bond with one hydrogen atom.
  • The remaining sp hybrid orbitals overlap to form a C-C bond.
  • Two unhybridized P orbitals of each carbon atom overlap to form a \pi bond.
  • The ethyne molecule is effectively sheathed in negative charge and is very susceptible to electrophilic attack.
  • The carbon atoms are drawn closer, making the C≡C bond distance 0.121 nm, with the C-H bond length 0.110 nm.

Classification of Organic Compounds

  • Organic compounds are classified according to molecular structure into aliphatic, alicyclic, aromatic, heterocyclic, and polycyclic or polynuclear.
Aliphatic Compounds
  • Carbon atoms are joined in chains, which may be straight or branched.
  • Examples: CH3-CH2-CH2-CH3 (butane), CH3-CH2-CH(CH3)-CH3 (2-methylbutane).
    • Can be saturated (single bonds only) or unsaturated (double or triple bonds).
Alicyclic Compounds
  • Carbon atoms join to form a ring.
Aromatic Compounds
  • Special types of alicyclic compounds with rings based on benzene (C6H6) with alternating double bonds.

Isolation and Purification of Organic Compounds

  • Organic compounds are found with other compounds and need isolation and purification to be studied or utilized.
  • The purity of organic compounds can be monitored using physical properties such as boiling points for liquids and melting points for solids.
Solvent Extraction
  • A separation technique based on differences in solute solubilities in different solvents.
    • Involves partitioning of solute molecules between two immiscible phases.
  • Types of extraction: solid-liquid and liquid-liquid extractions.
Nernst's Law of Distribution
  • K_d = Solute species in Phase 1 / Solute species in Phase 2
  • Where K_d is the distribution constant or partition coefficient.
Distillation
  • Separation and purification of liquids based on differences in boiling points or volatilities.
Types of Distillation
  • Simple Distillation: Used for mixtures with few components and wide boiling point differences.
  • Fractional Distillation: Used for mixtures with many components or close boiling points; uses a fractionating column to improve separation.
  • Steam Distillation: Uses steam as a carrier for components of a mixture that are immiscible with cold water.
Recrystallization
  • Purifies contaminated solid compounds based on differences in the solubility of a substance in hot and cold solvents.
Zone Melting
  • Purifies solid organic compounds by melting and resolidifying them, causing pure substances to aggregate and solidify in one area while impurities collect at the other end.
Chromatography
  • Separates mixtures based on the distribution of components between a mobile phase and a stationary phase.

Elemental or Qualitative Analysis

  • Determines the elements present in a compound; typically includes tests for carbon, hydrogen, oxygen, nitrogen, sulfur, and halogens. There is no specific test for oxygen.

Tests

Test for Carbon and Hydrogen
  • Heat the compound with copper(II) oxide:
    • Carbon is oxidized to carbon dioxide (turns lime water milky).
    • Hydrogen forms water droplets (turns anhydrous copper(II) tetraoxosulphate(VI) blue).
Sodium Fusion (Lassaigne's) Test for N, S, and Halogens
  1. Heat a small piece of sodium with the substance in an ignition tube, then drop it into distilled water.
  2. Grind the contents and filter.
  3. The filtrate is tested for nitrogen, sulfur, and halogens- containing ions such as CN^-, S^{2-}, and X^- (halogen).
(a) Test for Nitrogen
  • Add iron(II) tetraoxosulphate(VI) to the filtrate, heat, then add dilute tetraoxosulphate(VI) acid to acidify. A Prussian blue precipitate or coloration indicates nitrogen.
(b) Test for Sulphur
  • (i)Add sodium nitroprusside to the filtrate; a purple coloration indicates sulphur.
    • (ii) Acidify filtrate with ethanoic acid and add lead ethanoate; a black precipitate PbS indicates sulphur.
(c) Test for Halogens
  • If nitrogen or sulphur are absent, acidify the filtrate of nitrogen or sulphur with dilute trioxonitrate(V) acid HNO3 and add silver trioxonitrate(V) AgNO3. A precipitate indicates the presence of a halogen:
    • White precipitate for Cl^-.
    • Cream-yellow precipitate for Br^-.
    • Yellow precipitate for I^-.
      -If nitrogen or sulphur are present add dilute HNO3 acid and boil to expel hydrogen cyanide and/or hydrogen sulphide, then add dilute HNO3 and AgNO_3

Quantitative Analysis

1. Estimation of Carbon and Hydrogen
  • Compound is heated at about 700°C in oxygen with copper(II) oxide.
  • Carbon becomes CO2, hydrogen becomes H2O.
  • Masses of CO2 and H2O are estimated by absorption in weighed tubes containing soda-lime and anhydrous magnesium(II) tetraoxochlorate(I), respectively.
2. Estimation of Nitrogen
(a) Duma's Method
  • Compound is heated in oxygen with copper(II) oxide.
  • Carbon becomes CO2, hydrogen becomes H2O, sulphur becomes SO_2.
  • Nitrogen and halogens evolve freely. Nitrogen volume measured and converted to STP, then mass is calculated.
(b) Kjeldahl's Method
  • Compound is heated with conc. tetraoxosulphate(VI) acid.
  • Nitrogen converts to ammonium tetraoxosulphate(VI).
  • Solution made alkaline with excess sodium hydroxide.
  • Released ammonia is titrated with standard acid, nitrogen mass calculated.
3. Estimation of Halogen (Carius Method)
  • Heat compound at approx. 200°C with fuming HNO3 and AgNO3 in sealed tube for 5 hours.
  • Halogen converts to AgX. AgX is washed, dried, and weighed. Mass of halide in compound calculated.
4. Estimation of Sulphur (also Carius Method)
  • Compound is heated with fuming HNO_3.
  • Sulphur converts to tetraoxosulphate(VI) acid.
  • Acid is washed out and converted to barium tetraoxosulphate(VI) by adding barium chloride.
  • Barium tetraoxosulphate(VI) is filtered off, washed, dried, and weighed. Amount of sulphur is calculated.
Empirical Formula
  • Demonstrates relative numbers of each atom kind in a molecule, is calculated beginning with percentage compotion of said compound
MO Formula
  • Describes actual atoms of each kind in this molecule obtained with empirical formula if the relative molecular mass
STRUCTURAL ISOMERISM

Electronic Effects in Organic Molecules

Electron Displacements
  • Atoms are joined by directed valency bonds with a shared pair of electrons (covalent).
  • If the share is between two identical atoms, the electron pair cloud is symmetrical about the midpoint between nuclei (non-polar).
  • When unlike atoms are joined, the electron pair cloud is asymmetrical (polar).
Inductive Effect
  • A permanent effect occurring in organic molecules with a greater electron affinity of electronegative atoms. The effect is shown using chlorobutane (CH3-CH2-CH2-CH2-Cl).
  • Chlorine attracts the electron pair to itself, acquiring a partial negative charge, and the carbon atom acquires a partial positive charge.
Electromeric Effect
  • This temporary effect involves the complete transfer of shared electrons.
Mesomeric Effect and Resonance
  • Occurring where a compound exiists in a state is a combination that can help in description of compound properties
Hyperconjugation
  • Is a permanent effect involving a sigma \sigma bond it is present when a c-h bond is conjugated to a \pi bond.
Tautomerism
  • This is the state of being dynamic while still readily reversable
    • This doesn't present itself in the solid state