CHAPTER 2:
Water
• Water Is the Medium for Life
o Life evolved in water due to the protection it provides from UV light.
o Organisms typically contain 70–90% water.
o Chemical reactions occur in aqueous milieu.
o Water is a critical determinant of the structure and function of proteins, nucleic acids, and
membranes.
• Structure of the Water Molecule
o The octet rule dictates that there are four electron pairs around an oxygen atom in water.
o These electrons are in four sp3 orbitals.
o Two of these pairs covalently link two hydrogen atoms to a central oxygen atom.
o The two remaining pairs remain nonbonding (lone pairs).
o Water geometry is a distorted tetrahedron.
o The electronegativity of the oxygen atom induces a net dipole moment.
o Because of the dipole moment, water can serve as both a hydrogen bond donor and acceptor.
o Hydrofluoric acid is a solution of hydrogen fluoride (HF) in water. Solutions of HF are colourless,
acidic and highly corrosive.
o It is used to make most fluorine-containing compounds; examples include the commonly used
pharmaceutical antidepressant medication fluoxetine (Prozac) and the material PTFE (Teflon).
Elemental fluorine is produced from it. It is commonly used to etch glass and silicon wafers.
• Hydrogen Bonds
o Hydrogen bonds are strong dipole-dipole or charge-dipole interactions that arise between a
covalently bound hydrogen and lone pair of electrons.
o They typically involve two electronegative atoms (frequently nitrogen and oxygen).
o Hydrogen bonds are strongest when the bonded molecules allow for linear bonding patterns.
o Ideally, the three atoms involved are in a line.
,o Hydrogen Bonding in Water
▪ Water can serve as both:
− an H donor
− an H acceptor
▪ Up to four H-bonds per water molecule gives water its:
− anomalously high boiling point
− anomalously high melting point
− unusually large surface tension
▪ Hydrogen bonding in water is cooperative.
▪ Hydrogen bonds between neighbouring molecules are weak (20 kJ/mol) relative to the H–O
covalent bonds (420 kJ/mol).
,o Importance of Hydrogen Bonds
▪ Source of unique properties of water
▪ Structure and function of proteins
▪ Structure and function of DNA
▪ Structure and function of polysaccharides
▪ Binding of substrates to enzymes
▪ Binding of hormones to receptors
▪ Matching of mRNA and tRNA
o Biological Relevance of Hydrogen Bonds
• Ice: Water in a Solid State
o Water has many different crystal forms; the hexagonal ice is the most common.
o Hexagonal ice forms an organized lattice and thus has a low entropy.
o Hexagonal ice contains maximal hydrogen bonds/ water molecules, forcing the water molecules
into equidistant arrangement. Thus:
▪ ice has lower density than liquid water
▪ ice floats
, • Water as a Solvent
o Water is a good solvent for charged and polar substances:
▪ amino acids and peptides
▪ small alcohols
▪ carbohydrates
o Water is a poor solvent for nonpolar substances:
▪ nonpolar gases
▪ aromatic moieties
▪ aliphatic chains
• Physics of Noncovalent Interactions
o Noncovalent interactions do not involve sharing a pair of
electrons. Based on their physical origin, one can
distinguish between:
o Ionic (Coulombic) interactions
▪ electrostatic interactions between permanently charged
species, or between the ion and a permanent dipole
o Dipole interactions
▪ electrostatic interactions between uncharged but polar
molecules
o van der Waals interactions
▪ weak interactions between all atoms, regardless of
polarity
▪ attractive (dispersion) and repulsive (steric) component
o Hydrophobic Effect
▪ complex phenomenon associated with the ordering of
water molecules around nonpolar substances
Water
• Water Is the Medium for Life
o Life evolved in water due to the protection it provides from UV light.
o Organisms typically contain 70–90% water.
o Chemical reactions occur in aqueous milieu.
o Water is a critical determinant of the structure and function of proteins, nucleic acids, and
membranes.
• Structure of the Water Molecule
o The octet rule dictates that there are four electron pairs around an oxygen atom in water.
o These electrons are in four sp3 orbitals.
o Two of these pairs covalently link two hydrogen atoms to a central oxygen atom.
o The two remaining pairs remain nonbonding (lone pairs).
o Water geometry is a distorted tetrahedron.
o The electronegativity of the oxygen atom induces a net dipole moment.
o Because of the dipole moment, water can serve as both a hydrogen bond donor and acceptor.
o Hydrofluoric acid is a solution of hydrogen fluoride (HF) in water. Solutions of HF are colourless,
acidic and highly corrosive.
o It is used to make most fluorine-containing compounds; examples include the commonly used
pharmaceutical antidepressant medication fluoxetine (Prozac) and the material PTFE (Teflon).
Elemental fluorine is produced from it. It is commonly used to etch glass and silicon wafers.
• Hydrogen Bonds
o Hydrogen bonds are strong dipole-dipole or charge-dipole interactions that arise between a
covalently bound hydrogen and lone pair of electrons.
o They typically involve two electronegative atoms (frequently nitrogen and oxygen).
o Hydrogen bonds are strongest when the bonded molecules allow for linear bonding patterns.
o Ideally, the three atoms involved are in a line.
,o Hydrogen Bonding in Water
▪ Water can serve as both:
− an H donor
− an H acceptor
▪ Up to four H-bonds per water molecule gives water its:
− anomalously high boiling point
− anomalously high melting point
− unusually large surface tension
▪ Hydrogen bonding in water is cooperative.
▪ Hydrogen bonds between neighbouring molecules are weak (20 kJ/mol) relative to the H–O
covalent bonds (420 kJ/mol).
,o Importance of Hydrogen Bonds
▪ Source of unique properties of water
▪ Structure and function of proteins
▪ Structure and function of DNA
▪ Structure and function of polysaccharides
▪ Binding of substrates to enzymes
▪ Binding of hormones to receptors
▪ Matching of mRNA and tRNA
o Biological Relevance of Hydrogen Bonds
• Ice: Water in a Solid State
o Water has many different crystal forms; the hexagonal ice is the most common.
o Hexagonal ice forms an organized lattice and thus has a low entropy.
o Hexagonal ice contains maximal hydrogen bonds/ water molecules, forcing the water molecules
into equidistant arrangement. Thus:
▪ ice has lower density than liquid water
▪ ice floats
, • Water as a Solvent
o Water is a good solvent for charged and polar substances:
▪ amino acids and peptides
▪ small alcohols
▪ carbohydrates
o Water is a poor solvent for nonpolar substances:
▪ nonpolar gases
▪ aromatic moieties
▪ aliphatic chains
• Physics of Noncovalent Interactions
o Noncovalent interactions do not involve sharing a pair of
electrons. Based on their physical origin, one can
distinguish between:
o Ionic (Coulombic) interactions
▪ electrostatic interactions between permanently charged
species, or between the ion and a permanent dipole
o Dipole interactions
▪ electrostatic interactions between uncharged but polar
molecules
o van der Waals interactions
▪ weak interactions between all atoms, regardless of
polarity
▪ attractive (dispersion) and repulsive (steric) component
o Hydrophobic Effect
▪ complex phenomenon associated with the ordering of
water molecules around nonpolar substances
