STUDYING THE INTERACTIONS OF MOLECULES

Recall that a molecule is composed of 2 or more atoms chemically joined together.

There are different types of bonds that can hold elements together.

Biological molecules are organic or carbon based where carbon is bonded to carbon or hydrogen and may also include atoms of nitrogen, oxygen, phosphorus, and sulfur

VALENCE ELECTRONS: Electrons in the outermost orbital that determine an atoms chemical behaviour.

Noble gases – have full outer orbitals/thus they do not gain, lose, or share electrons (i.e. don’t participate in chemical reactions.)

All other elements attempt to gain, lose, or share valence electrons to achieve stable electron configurations like noble gases.

HENCE chemical reactions occur and chemical bonds form.

CHEMICAL BONDING (Intramolecular Bonding = Forces that hold atoms together within a molecule.)

1. IONIC transfer e-

electrostatic attraction between metal cation and non-metal anion

Form ionic solids Ionic solids form crystals that can pull apart

in water. All ionic compounds are water soluble.

Recall – Ions = atoms with a charge.Cation(metals) = when atoms lose e- they become positive.Anion(non-metals) =when atoms gain e- they become negative.Ionic Bond = attraction between a cation and an anion

Example: Na Na1+ + 1 e- (oxidation= LEO loss of electrons)O + 2 e- O2- (reduction = GER gain of

electrons)

CHEMICAL BONDING

2. Covalent Bonding Share electrons Two non-metal nuclei attract e- at the

same time and thus they are shared. Form molecules

Electrons can be shared equally forming a non-polar covalent

bond or unequally forming a polar covalent bond.

ELECTRONEGATIVITY Electronegativity – the measure of the

tendency of an atom to attract electrons. See figure 7 on page 14 for table of

electro- negativities Describe the electronegativity of the

biological atoms (C, H, O, N, S, P) O, N, and Cl are atoms with high

electronegativities C, H, and P are examples of atoms with lower

electronegativities

Polar Covalent Bonds When 2 atoms with significantly different

electronegativities share electrons those electrons are more strongly attracted to the atom with the higher electronegativity and cause that atom to have a partial negative

charge.(δ- ) The atom with the lower electronegativity

becomes a partial positive charge (δ+)

Non-polar covalent bonds When bonds are formed between atoms

that have similar electronegativities the electrons are shared fairly equally between the atoms.

Examples: diatomic molecules or the bonds between carbon and hydrogen atoms.

ELECTRONEGATIVITY AND CHEMICAL BONDING

Electronegativity difference (∆En) rule:

NONPOLAR POLAR COVALENTIONIC

0 0.5 0.6 1.6 > 1.7e- shared e- shared e- equally unequally

transferred

Polarity or charge of biological molecules greatly affects their behaviors and functions within a cell.

INTERMOLECULAR BONDING Intermolecular bonding

“between” molecules (attractive forces that allow molecules to associate together)

weaker than intramolecular Determine the state of substances at given

temperature and pressures. Collectively called vanderWaals forces. VanderWaal has “3 children” collectively known

as: London’s Forces Hydrogen Bonding Dipole dipole interactions (hydrophobic interactions)

INTERMOLECULAR BONDING

The two intermolecular interactions that are important for biological systems are:

1. Hydrogen bonding – strong – partial positive (δ+) hydrogen atoms are attracted to the partially negative (δ-) N, O, or F of another atom. (H-F, O-H, N-H).

This is extremely important in biological systems as water molecules form hydrogen bonds with one another. All cells are aqueous environments. So hydrogen bonds between biological molecules and water are very important!

INTERMOLECULAR BONDING2. Dipole-dipole Forces (Hydrophobic

Interactions) weak – occurs between polar molecules (δ+ side of one molecule is attracted to the δ- side of another molecule. Remember opposites attract!!). Thus polar molecules have a tendency to mix and interact! (Like dissolves like)

Since water is polar, all polar molecules are considered “water loving” or hydrophilic.

Non-polar molecules don’t mix with water and are called “water hating” or hydrophobic.

The natural clumping together of non-polar molecules is known as the hydrophobic effect. This plays a central role in how cell membranes form or the 3-dimensional shapes of proteins.

MOLECULAR POLARITY

Molecular polarity depends on1. The polarity of individual bonds

(which depends in part upon functional groups for biological molecules)

and2. the shape of the molecule (this

depends upon the distribution of electron orbitals)

ELECTRON ORBITALS It is impossible to

know exactly where electrons are at any given time

Scientists can determine locations where electrons are most likely to be found

These spaces are called orbitals. (s,p,d,f) see fig.4 pg.11

Hybridization of orbitals When atoms form

covalent bonds the orbitals hybridize.

Hybridization of orbitals

Hybridization of orbitals

Hybridization pushes bonding and non-bonding electrons as far apart as possible

Each hybridized orbital will hold 2 e-

To simplify we will assume that biological molecules will only possess up to 4 electron pairs (4 sp3 hybrid orbitals)

Shape depends on the number of bonding and non-bonding pairs of electrons. (see table 5 on page 15)

See table 5 on page 15 If the molecule has a symmetrical shape

(linear, trigonal planar, or tetrahedral) then if all bonds are the same (can be polar or non-polar) the molecule will overall be non-polar

If the molecule has an asymmetrical shape (bent, or pyramidal) and the bonds are polar then the molecule will be polar. However if the bonds are non-polar then the molecule will be non-polar

REMEMBERThe polarity of molecules greatly affects their behavior and function within a cell.