Introduction to Organic Chemistry

• Organic chemistry is the study of carbon compounds.

Organic vs. Inorganic Compounds

• Inorganic compounds derive from mineral sources.
• Organic compounds derive from vegetable or animal sources.
• Living organisms consist of organic chemicals.
• Proteins make up your hair, skin, and muscles.
• DNA that controls your genetic heritage.
• Foods that provide nourishment.
• Medicines that provide healing.

Carbon's Bonding Properties

• With over 50 million known chemical compounds, carbon is essential
• Carbon is in group 4A, so it shares 4 valence electrons forming strong covalent bonds.
• Carbon atoms bond to each other in long chains and rings.
• Carbon alone can form diverse compounds, from methane to DNA with over 100 million carbons.
• Modern chemistry designs and synthesizes new organic compounds.
• New organic compounds include medicines, dyes, and polymers.

Atomic Orbitals

• Orbitals define the volume of space around an atomic nucleus where an electron is most likely found.
• Four types of orbitals (s, p, d, and f) each have unique shapes.
• Organic chemistry focusses on s and p orbitals.
• s orbitals are spherical with the nucleus at the center.
• p orbitals are dumbbell-shaped with orientations along perpendicular axes (px, py, pz).
• Of the d orbitals, 4 have a cloverleaf shape and the fifth is dumbbell-shaped with a doughnut around the middle.
• The 1st shell has 1s orbital and a capacity of 2 electrons
• The 2nd shell has 2s and 2p orbitals and a capacity of 8 electrons
• The 3rd shell has 3s, 3p, and 3d orbitals and a capacity of 18 electrons

Electron Configuration

• Electrons fill orbitals starting with the lowest energy levels

Ground-State Electron Configurations of Some Elements

• Ground-state electron configuration is the lowest energy arrangement of electrons in an atom

Covalent Bonding

• Methane (CH4) is an example of covalent bonding (the main constituent of natural gas).
• Covalent bonds form by sharing electrons not gaining or losing.

Molecules

• Molecules are the neutral collection of covalently bonded atoms.

Lewis Structures (Electron-Dot structures)

• Lewis structures show valence shell electrons as dots.
• Hydrogen needs two dots (electrons) for a stable configuration.
• Main-group atoms need eight dots (an octet) for stability.

Kekule Structures (Line-Bond Structures)

• A line between atoms represents a two-electron covalent bond.

Covalent Bond Quantity

• The number of covalent bonds depends on valence electrons needed for a noble-gas configuration.
  • Hydrogen needs one more valence electron, so it forms one bond.
• Carbon needs four more valence electrons, so it forms four bonds.
• Nitrogen needs three more valence electrons, so it forms three bonds.
• Oxygen needs two more valence electrons, so it forms two bonds.
• Halogens need one more valence electron, so they form one bond.

Lone-Pair (Nonbonding) Electrons

• Valence electrons, are not bonding, and exist as lone pairs.
• In ammonia(NH3), the nitrogen atom shares six valence electrons in three covalent bonds. Nitrogen has two remaining valence electrons in a nonbonding lone pair.

Estimating Bond Count

• Phosphorus is in group 5A, so it needs three bonds to make its octet and form PH3 with three hydrogen atoms

sp3 Hybrid Orbitals and the Structure of Methane

• Linus Pauling explained mathematically how one s orbital and three p orbitals can combine (hybridize). They then form four equivalent atomic orbitals with tetrahedral orientation.
• Orbitals with tetrahedral orientations are sp3 hybrid orbitals
• Superscript 3 in sp3 indicates the number of component atomic orbitals. It does NOT indicate the number of electrons occupying it

Alkanes

• Ethane (C2H6) is the simplest molecule containing a carbon-carbon single bond.

Alkenes

• Ethylene has a carbon-carbon doulbe bond .

Alkynes

• Acetylene has a carbon-carbon triple bond .

Hybridization

• H-C-C bond angles of 180° and is a linear molecule.
• C-H bonds length is 106 pm with strength 558 kJ/mol.
• C-C bond length is 120 pm and its strength is about 965 kJ/mol.
• Acetylene has the shortest and strongest carbon-carbon bond.

Hybridization of Nitrogen, Oxygen, Phosphorus, and Sulfur

• Ammonia (NH3) and water (H2O) structures are affected by unshared pairs of electrons.
• Phosphorus and sulfur are third-row versions of nitrogen and oxygen, and bonds are described by hybrid orbitals.
• Phosphorus/sulfur positions allow them to expand their octets and form more covalent bonds
• The O-P-O in phosphorus compounds is 110-112°, implying sp3 hybridization in the phosphorus orbitals.

Sulfur Molecules

• Thiols contain a sulfur atom bonded to one hydrogen and one carbon.
• Sulfides contain a sulfur atom bonded to two carbons.
• Methanethiol (CH3SH) is a thiol
• Dimethyl sulfide [(CH3)2S] is a sulfide
• Both molecules exhibit approximate sp3 hybridization around sulfur. This can be attributed to tetrahedral angle deviation.

Drawing Chemical Structure

• A line between atoms represent two electrons in a covalent bond.
• Shorthand notations simplify structure writing

Condensed Structures

• Carbons and hydrogens single bonds are implied not explicitly shown.
• CH3 indicates a carbon with three bonded hydrogens.
• CH2 indicates a carbon with two bonded hydrogens.
• Ex: 2-methylbutane can be written as follows: CH3CH2CHCH3, or CH3CH2CH(CH3)2

Skeletal Structures

• Skeletal structures simplify drawings.
• Carbon atoms located at line intersections and ends can be implied but are usually not shown.
• Hydrogen atoms bonded to carbon are implied but are not shown.
• Valence of 4 is assumed for carbon.
• All atoms that are not Carbon or Hydrogen are indicated.

IUPAC Nomenclature: Ordering

• Although groupings such as -CH3, -OH, and -NH2 are usually written with the C, O, or N atom first and the H atom second, the order of writing is sometimes inverted to H3C-, HO-, and H2N-. This is if needed to make the bonding connections in a molecule clearer.

Drawing Organic Molecules

• Organic molecules are usually drawn using either condensed structures or skeletal structures
• Carbon-carbon and carbon-hydrogen bonds aren’t shown in condensed structures.
• Only the bonds and not the atoms are shown in skeletal structures.

Interpreting Drawings

• An end of a line represents a carbon atom with 3 hydrogens, CH3.
• A two-way intersection is a carbon atom with 2 hydrogens, CH2.
• A three-way intersection is a carbon atom with 1 hydrogen, CH.
• A four-way intersection is a carbon atom with no attached hydrogens.

Bond Dissociation Energy

• Dissociation energy is the amount of energy consumed or liberated when a bond breaks or forms.
• The standard of measurement is kcal / mol

Reactions

• Reactions can be classified as Homolysis and Heterolysis

Homolysis

• results from the division of bonds resulting in fragments where each retains one electron

Heterolysis

• results from the division of bonds with both electrons going to one fragment

Types of Bonds

• A bond with the electrons shared equally between the two atoms is called a nonpolar covalent bond. The bond in H2 and the C¬C bond in ethane are nonpolar covalent bonds.
• In most bonds between two different elements, the bonding electrons are attracted more strongly to one of the two nuclei. An unequally shared pair of bonding electrons is called a polar covalent bond.

Measuring Polarity

• Bond polarity is measured via dipole moment. (μ) which is the amount of partial charge x by bond length (d).
• The symbol +δ means "a small amount of positive charge, conversely -δ means a small amount of negative charge.

Dipole

• Often symbolized by ->, where the arrow points from positive to negative.

Electronegativity

• Covalent bonds tend to be polar if atoms differ in electronegativity.
• Electronegativity tends to be the most potent the higher you go up and to the far right of the periodic table

Polarity Effects

• Bond polarities influence physical/chemical properties and influence the magnitude of melting/boiling point and solubility.
• Kind of reaction that can take place at that bond, and influence reactivity even at nearby bonds

Inductive Effects

• Inductive effect defines the ability of an atom to polarize a bond.
• It is the shifting of electrons in a σ bond in response to electronegativity.
• Metals (lithium/magnesium) inductively donate electrons.
• Reactive nonmetals (oxygen/nitrogen) inductively withdraw electrons.
• Inductive effects heavily influence chemical reactivity for chemical observation analyses.

Intermolecular Forces

• There are two types: 1) dipole-dipole interactions and 2) van der Wauls forces.

Dipole-Dipole Interactions

• Noncovalent electrostatic interaction between dipolar molecules; attraction between positive end of one polar molecule and negative end of another. In hydrogen chloride(HCl), positive hydrogen is attracted to negative chlorine.

Hydrogen Bonding

• Strong dipole-dipole attraction when hydrogen bonds to an electronegative atom. This is where the electronegative atom and an electron Ione pair are bonded
  • Ex: H H H-F-H-F H-O-н-о HH

Inter/Intra molecular bonds

• When the hydrogen bond is present between two atoms of two different molecules, then it is known intermolecular hydrogen bond. Ex: H H H--N:---H--N

• When the hydrogen bond is present between two atoms of the same molecule, then it is known as intra-molecular hydrogen bond. Ex: Hyılmajen huuul H N=0

Van der Waals Forces

• Are intermolecular forces responsible for holding molecules together in liquid/solid states.
• In symmetrical methane molecules, there is no net dipole moment, however, electron movement leads to temporary dipoles.

Energy of Activation (Eact)

• Activation energy = The minimum amount of energy that must be available through collision for a reaction to occur.

Types of Organic Reactions

• Organic chemistry hinges on three main reaction types: Substitution, Elimination and Addition

Substition Reactions

• A substitution reaction results in replaced atoms / atom groups. The most common results from Z (hydrogen or a electronegative heteroatom) that is more electronegative than carbon being replaced by Y.