1 Structure and Bonding in Organic Molecules


Important Concepts


1-2            Coulomb Forces

Unlike charges attract

Like charges repel

Charges represented as + and – with circles, e.g.

Attraction/repulsion varies with 1/r2

Attraction > repulsion until valence shell is filled

Atoms share electrons until valence shell is filled

In molecules, shared electrons represented as dots between atoms

1-3            Ionic and Covalent Bonds

Electronegativity is a measure of electron attraction

Electronegativity increases to the right in the periodic table

Polarized bonds between unlike atoms

Ionic bonds between atoms on opposite sides of table

Form molecules by adding atoms with lower valence to higher valence atoms

VSEPR (Valence Shell Electron Pair Repulsion) can be used to predict the shape of molecules based on maximal seperation of electron pairs

1-4     Lewis Structures

Lewis structures represent molecules with pairs of electrons shown as dots drawn between atoms


1-5            Resonance Forms

Resonance is a formalism that is used when a single Lewis structure does not properly account for structure and properties of a molecule.

Resonance structures differ from each other only in the position of electrons.

Curved arrows are used to indicate the motion of electrons that would be necessary to covert one resonance structure into another.

Sometimes, resonance structures are considered to be equivalent and thus each contributes equally to a combination called a hybrid. More often, each resonance structure has unique features. Those factors used to evaluate which structure(s) will be a greater contributor to the hybrid are:

Number of bonds (the more bonds the better);

Completion of valance shells (the more filled valence shells, the better);

Charges---separation of charge is bad as is accumulation of like charges (e.g. two negative charges) on the same atom.

1-6            Atomic Orbitals

Electrons in atoms and molecules are quantized and have specific energies

Atomic orbitals are mathematical descriptions of electron density about an atom

The atomic orbitals (in order of increasing energy) are:

           1s; 2s; 2px 2py 2pz; 3s; 3px 3py 3pz; five 3d

           The 1s orbital has no nodes

           The 2s orbital has an internal spherical node

           The 2p orbitals have nodal planes (orthogonal to each other)

1-7            Molecular Orbitals

Molecular Orbitals are formed by the combination of atomic orbitals

In the simplest case, two atomic orbitals combine to form two molecular orbitals, one bonding and one antibonding orbital.

1-8            Hybrid Orbitals

Hybrid orbitals are formed by combining 2nd level atomic orbitals

s + 3p -> 4 sp3

s + 2p -> 3 sp2 + p

s + p -> 2 sp + 2p

sp3 tetrahedral

sp2 trigonal planar

1-9            Structures and Formulas of Organic Molecules

Bond-line formula notations is the most straightforward way of representing the connectivity in a molecule. Lines represent bonds between atoms and

the end of every line and all the junctions of lines are implied to be carbon atoms unless another element is represented. All atoms are assumed to have

valence shells filled by hydrogens which are not shown.