AQUEOUS CHEMISTRY

Introduction
• Water is the medium of life
• Living organisms can be found in virtually every portion of the earth
that contains liquid water
• In the polar ice caps, prokaryotes and small eukaryotes survive in the
spaces between ice crystals
• Virtually wherever water is found, living organisms can be found there
as well (even several kilometer below the earth’s surface)
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• As a fundamental requirement for life, it is important to understand
the properties of water
• Molecular structure of biomolecules is in part governed by how their
component groups interact with water
• Water plays a role in how these molecules assemble to form larger
structures or undergo chemical transformation
• In fact, water itself—or its H+ and OH- constituents—participates
directly in many biochemical processes
Water molecules form Hydrogen bond
• The human body is about 60% by weight water, most of it in the
extracellular fluid (the fluid surrounding cells) and inside cells:
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• In an individual H2O molecule, the central oxygen atom forms
covalent bonds with two hydrogen atoms, leaving two unshared pairs
of electrons
• The molecule therefore has approximately tetrahedral geometry, with
the oxygen atom at the center of the tetrahedron, the hydrogen
atoms at two of the four corners, and electrons at the other two
corners
Continued
• As a result of this electronic arrangement, the water molecule is polar
• It has an uneven distribution of charge.
• The oxygen atom bears a partial negative charge and each hydrogen
atom bears a partial positive charge
• This polarity is the key to many of
water’s unique physical properties
Continued.
• Neighboring water molecules orient themselves so that each partially
positive hydrogen is aligned with a partially negative oxygen
• This interaction is known as Hydrogen bonding
• Each water molecule can potentially participate
in four hydrogen bonds (2 H atoms, 2 pairs of
unshared electrons) (in ice)
Continued.
• Theoretical calculations and spectroscopic data suggest that water
molecules participate in only two strong hydrogen bonds, one as a
donor and one as an acceptor, generating transient hydrogen-bonded
clusters such as the six-membered ring shown here
Effects of Hydrogen bonding
• Water is highly cohesive because of H-bonds
• High surface tension (allowing certain insects to walk on its surface)
• The cohesiveness of water molecules also explains why water remains
a liquid, whereas molecules of similar size, such as CH4 and H2S, are
gases at room temperature (25C)
• Water is less dense than other liquids because hydrogen bonding
demands that individual molecules not just approach each other but
interact with a certain orientation (ice floats, other solids denser)
Continued.
• What if there were no hydrogen bonds in water?
• Water would freeze at –100°C and boil at –91°C, making most of the
water on Earth steam, and life unlikely
• The many hydrogen bonds that link water molecules together help
water absorb heat without a great change in temperature
• Converting 1 g of the coldest liquid water to ice requires the loss of
80 calories of heat energy
• Converting 1 g of the hottest water to a gas requires an input of 540
calories of energy
Hydrogen bonds are a type of electrostatic
force
• Basic molecular constitution is defined by covalent bond
• Non-covalent bonds (H-bonds) govern the final 3-D shapes of
molecules and how they interact with each other
• 460 kJ/mol of energy is required to break a covalent (O-H) bond.
• But a hydrogen bond in water has a strength of only about 20 kJ/mol
• Other non-covalent interactions within biomolecules include ionic
bonds etc.
Hydrogen bonds
• Doesn’t only involve O and H, also occur between N and H, S and H
• N—H, O—H, and S—H as hydrogen donors
• Electronegative N, O, or S atoms as
hydrogen acceptors
• Complementarity of bases in DNA and
RNA is determined by their ability to form
hydrogen bonds with each other
Other electrostatic interactions
• Occur between particles that are polar but not actually charged

• van der Waals interactions (9 kj/mole)

• London dispersion forces (0.3 kj/mole)
Water is a Solvent
• Due to its polarity, water facilitates chemical reactions, both outside
and within living systems
• As a solvent, it dissolves a great number of substances, especially
those that are also polar
• Water molecules are able to form hydrogen bonds and participate in
other electrostatic interactions with a wide variety of compounds
• Water has a relatively high dielectric constant (a measure of a
solvent’s ability to diminish the electrostatic attractions between
dissolved ions)
The hydrophobic effect
• Hydrophilic: readily soluble (water loving), e.g. glucose
• Hydrophobic: relatively insoluble, lack polar groups (water fearing)

• When a nonpolar substance such as vegetable oil (which consists of

hydrocarbon like molecules) is added to water it does not dissolve but
forms a separate phase
Continued.
• In order for water and oil to mix, free energy must be added to the
system
• When a large number of nonpolar molecules are introduced into a
sample of water, they do not disperse and become individually
hydrated, each surrounded by a layer of water molecules
• Instead, the nonpolar molecules tend to clump together, removing
themselves from contact with water molecules
• The exclusion of nonpolar substances from an aqueous solution is
known as the hydrophobic effect
Continued.
• The hydrophobic effect governs the structures and functions of many
biological molecules.
• For example, the polypeptide chain of a protein folds into a globular
mass so that its hydrophobic groups are in the interior, away from the
solvent, and its polar groups are on the exterior, where they can
interact with water.
• Similarly, the structure of the lipid membrane that surrounds all cells
is maintained by the hydrophobic effect acting on the lipids.
Ampiphilic molecules
• Experience both hydrophilic and hydrophobic interaction
• E.g. palmitate
• H-C tail is nonpolar, and
the carboxylated head is
strongly polar
• Polar groups of amphiphiles orient themselves toward the solvent
molecules and are therefore hydrated, while the nonpolar groups tend
to aggregate due to the hydrophobic effect
• As a result, the amphiphiles may form a spherical micelle, a particle
with a solvated surface and a hydrophobic core
Continued.
• Amphiphilic molecules may form a sheet
rather than a spherical micelles, depending
on the relative size of hydrophilic
and hydrophobic portions
• E.g. amphiphilic lipids of biological
membrane make a two-layer
sheets called bilayers