Water is a Polar Molecule
- O-H bond distance is 0.958 A (1A = 10^-10 m) and the angle formed by the 3 atoms
is 104.5 degrees
- Oxygen contains 4 sp3 orbitals, which 2 are occupied by hydrogen and pairs of
electrons occupy the other 2
- Water molecules form hydrogen bonds: water is
polar in which the oxygen atom with its unshared
electrons carries a partial negative charge of -0.66e
and the hydrogen atom carries a partial positive
charge of 0.33e (e is the charge of the electron).
Neighboring water molecules orient themselves so that
the O-H bond of one water molecule (+’ve end) points
towards the electron pair of another water molecule (-
‘ve end). This intermolecular association is called a
hydrogen bond. H-bonds are characterized by an H - -
- A distance that is at least 0.5A shorter than the
calculated van der Waals distance (distance of closest
approach between two nonbonded atoms). For ex. H-
bonds = 1.8A, VDW = 2.6A). The energy of individual H-
bond is small (around 20KJ/mol). - Ice is a Crystal of Hydrogen-Bonded Water
Molecules: Each water molecule is tetrahedrally is
surrounded by 4 nearest neighbors to which it is H-
bonded. This causes water to have an open
structure that expands from freezing (ice is less
dense than water at 0 degrees). Ice has a larger
volume than water but the mass stays the same
when it’s in liquid form or solid. When water
freezes the volume increases thus its density
decrease and vice versa. The melting of ice
represents the collapse of the tetrahedral
orientation of H-bonded water molecules.
The structure of Liquid Water is
- Liquid water reorients itself many times.
The H-bonds are distorted, so the networks
of linked molecules are irregular and varied.
These networks continually break up and
re-form. Liquid water consists of a rapidly
fluctuating, 3D network of H-bonded
water molecules. The number of H-bonds
depends on temperature, where liquid
water at 0 degrees has approximately 85%
as many H-bonds as water in ice. Water
doesn’t not exist as individual molecules but
as oligomers – trimers, tetramers and etc.
The oligomers are highly transient or
dynamic as the H-bonds break and form on
the timescale of 10^-11 seconds. This is a
very high entropy situation.
-Effects of oligomeric nature on
properties of water: It behaves like it has a
higher molecular weight (high melting
points and boiling points). It is more viscous
than liquids than lack H-bonds.
The effects of water on the conformation of macromolecules
- Macromolecules are synthesized in a linear form, but biological function requires
that they assume the proper conformation. The folding structure must be stable
must be the most energetically favorable. The number of possible conformations for
a polypeptide or nucleic acid is virtually limitless. Many biochemists study structure
and the “folding” process- these occur largely in aqueous medium. Folding is
complicated, but must be driven energetically favourable nature of the folded structure-usually this is taken as the lowest energy conformation and depends on
non-covalent forces and effects, many involving water. Solubility and molecular
interactions/recognition will also depend on these factors. What are these forces or
effects, and what is water’s role?
Bond Energies and Electrostatic Interactions
-Covalent bonds are quite stable. The non-covalent interactions fall into a couple of
-Ionic interactions are between molecules that have opposite charges. Ionic
interactions can be quantified by Coulomb’s Law: the force (F) between any two
charged particles will be:
q1and q2are the charges on the particles
r is the distance between the particles
e (epsilon) is the “dielectric constant” of the medium; it is related to its polarity but
is, in fact, defined by Coulomb’s law.
Note: effect of dielectric constant, e - - a high dielectric constant reduces the
strength of the interaction - The medium can reduce the strength between charged particles. Vacuum has no
medium gives a dielectric constant of 1. Water has a very high dielectric constant.
This means that an interaction between these two charged groups on the surface of
a protein where it is totally aqueous It’s going to be less energetic.
Ion Solvation by H2O
- Why is water so effective at reducing the force
between ions? Polar water molecules orient
around ions to make favourable charged-dipole
interactions. Water basically shields’ the charge
interaction between other charged molecules.
These hydration sh