Lecture 1 1

CM1121 AY 2007-08 DR LU YIXIN

LECTURE 1 62

Lewis Basesbull Lewis bases can accept protons as well as Lewis acids therefore

the definition encompasses that for Broslashnsted basesbull Most oxygen- and nitrogen-containing organic compounds are Lewis

bases because they have lone pairs of electronsbull Some compounds can act as both acids and bases depending on

the reaction

CM1121 AY 2007-08 DR LU YIXIN

LECTURE 1 63

Non-Covalent Interactions

bull Dipole-dipole forcesbull Dispersion forcesbull Hydrogen bonds

CM1121 AY 2007-08 DR LU YIXIN

LECTURE 1 64

Dipole-Dipole Interactions

bull Occur between polar molecules as a result of electrostatic interactions among dipoles

bull Forces can be attractive of repulsive depending on orientation of the molecules

CM1121 AY 2007-08 DR LU YIXIN

LECTURE 1 65

Dispersion forces

bull Occur between all neighboring molecules ndash due to temporary dipoles

bull Electron distribution within molecules that are constantly changing giving molecules temporary dipoles

CM1121 AY 2007-08 DR LU YIXIN

LECTURE 1 66

Hydrogen Bond Forcesbull Most important non-covalent interaction in biological

molecules

bull Forces are result of attractive interaction between a hydrogen bonded to an electronegative O N or F atom and an unshared electron pair on another O N or F atom

CM1121 AY 2007-08 DR LU YIXIN

LECTURE 1 67

Hydrogen bond is very important in biological systems

α-helices

β sheets

N

N

N

N

N HHN N

O

OH

O

O

O

3-End

5-End

OO

5-End

O3-End

A

T

N

N

N

N

N HHN N

O

OH

N

N

N

N N

N N

O

O

H

H

NH

H

H

O

O

O

3-End

5-End

OO

5-End

O3-End

O

O

O

3-End

5-EndO

O5-End

O3-End

A

T

G

C

CM1121 AY 2007-08 DR LU YIXIN

LECTURE 1 68

Lecture 1 Summary (I)bull Organic chemistry ndash chemistry of carbon compoundsbull In condensed structures C-C and C-H are impliedbull Skeletal structures show bonds and not C or H (C is shown as a junction of two

lines) ndash other atoms are shownbull Molecular models are useful for representing structures for studybull Atom positively charged nucleus surrounded by negatively charged electronsbull Electronic structure of an atom described by wave equation

ndash Electrons occupy orbitals around the nucleusndash Different orbitals have different energy levels and different shapes

bull s orbitals are spherical p orbitals are dumbbell-shapedbull Covalent bonds - electron pair is shared between atomsbull Valence bond theory - electron sharing occurs by overlap of two atomic orbitalsbull Molecular orbital (MO) theory - bonds result from combination of atomic orbitals to

give molecular orbitals which belong to the entire moleculebull Sigma (σ) bonds - Circular cross-section and are formed by head-on interactionbull Pi (π) bonds ndash ldquodumbbellrdquo shape from sideways interaction of p orbitalsbull Carbon uses hybrid orbitals to form bonds in organic molecules

ndash In single bonds with tetrahedral geometry carbon has four sp3 hybrid orbitals

CM1121 AY 2007-08 DR LU YIXIN

LECTURE 1 69

Lecture 1 Summary (II)ndash In double bonds with planar geometry carbon uses three equivalent sp2 hybrid

orbitals and one unhybridized p orbitalndash Carbon uses two equivalent sp hybrid orbitals to form a triple bond with linear

geometry with two unhybridized p orbitalsbull Atoms such as nitrogen and oxygen hybridize to form strong oriented bonds

ndash The nitrogen atom in ammonia and the oxygen atom in water are sp3-hybridized bull Organic molecules often have polar covalent bonds as a result of unsymmetrical

electron sharing caused by differences in the electronegativity of atomsbull The polarity of a molecule is measured by its dipole moment μbull (+) and (minus) indicate formal charges on atoms in molecules to keep track of

valence electrons around an atombull Some substances must be shown as a resonance hybrid of two or more resonance

forms that differ by the location of electronsbull A Broslashnsted(ndashLowry) acid donatea a protonbull A Broslashnsted(ndashLowry) base accepts a protonbull The strength Broslashnsted acid is related to the -1 times the logarithm of the acidity

constant pKa Weaker acids have higher pKarsquosbull A Lewis acid has an empty orbital that can accept an electron pairbull A Lewis base can donate an unshared electron pairbull Non-covelent interactions dipole-dipole dispersion forces and hydrogen bonds

CM1121 AY 2007-08 DR LU YIXIN

LECTURE 1 70

Foods amp Fruits of the Day

bull McMurry Chapter 1 amp 2bull Links Pauling is the only person ever to receive

two unshared Nobel Prizes - for Chemistry(1954) and for Peace (1962)

bull Paulingrsquos achievements in Chemistry dealt with many aspects in molecular structures he introduced the concept of hybrid orbitals In the field of biochemistry his name is associated with helical structures of proteins Pauling won the 1962 Nobel prize for his efforts in behalf of the Nuclear Test-Ban Treaty Read more