Beruflich Dokumente
Kultur Dokumente
Weeks 1, 2, 3 & 4
Lecture 1
Chemistry: What is it good for?
To understand the properties of all matter
To understand the interactions of materials
To understand biological processes
To develop new drugs (antibiotics, anti-cancer agents...)
To develop new materials (plastics, ceramics...)
The first synthetic chemists (making new molecules)
1828; Wohler prepares urea
Ionic Compounds
Complete transfer of one or more electrons occurs, creating ions.
Covalent Compounds
Bonding electrons are shared between atoms
Overlap of electronic orbitals gives rise to bonding orbitals, or
covalent bonds
What
bonds?
are
covalent
Electronic
Configuration
Describes
the
orbitals
a given element
occupied
by
electrons for
Orbital Theory
The space around a nucleus in which an electron is most likely to be
residing is termed an orbital
What does an orbital look like?
The further from the nucleus, the
higher the energy of the orbital
The shape of an orbital varies with type
Electronic Configuration
Energy levels of orbitals...
Lecture 2
Formation of covalent bonds
A covalent bond is formed by the sharing between atoms of unpaired
electrons
Unpaired electrons are always in the outer (valence) shell highest
energy occupied orbitals
Two theories used to describe covalent bond formation;
o Valence bond theory
o Molecular orbital theory
Valence bond theory
Lewis structures
A simple way of representing covalent bonds is by Lewis structures;
o valence electrons are represented by dots
o a stable molecule exists when an inert gas configuration is
achieved for all atoms (stable octet rule)
methane
methanol
Carbon:
1s2 2s2
methane,
2p2
CH4
excited state
How
do
we
account
for
experiments that confirm that all
four bonds in methane are of the
same length and strength?
Hybridisation
hybridised to generate four equivalent
Tetrahedral geometry
Methane, CH4
Ethane, C2H6
Oxygen and nitrogen can also be sp3hybridised;
Representation of molecules
Lewis structure;
Line structure;
o C-C bonds
o C-H
o
o
Alkanes
drawn as lines
bonds omitted
non-C,H atoms drawn
only H s not bonded to C shown
e.g.
octane
Structural isomers
Alkanes with four or more carbons can exist as structural isomers
Structural isomers have the same molecular formula, but have different
bond connectivity
aspirin
and
acetozone
are
structural isomers with different
chemical properties
it is not possible to derive
molecular structures from their
trivial names systematic names
are required
Isomers of hexane
2methylpentane
3methylpentane
2,3dimethylbutane
Functional groups
Organic molecules may incorporate functional groups
Alcohol
Halide
Carboxylic acid
Amine
OH
F,Cl,Br,I
CO2H
NH2
CH3CH2OH
(ethanol)
CH3I
(iodomethane)
CH3CO2H (ethanoic acid)
CH3CH2NH2 (ethylamine)
Conformational isomers
There is free rotation about a -bondan infinite array of conformations
is possible through rotation
a conformer is one specific conformation of a molecule
different conformers are isomers - they differ by the arrangement of
atoms in space
Lecture 3
Conformers of butane
Conformation
of
longchain alkanes
The most stable conformer of long-chain alkanes is when all antistaggered conformations are adopted, leading to a characteristic zigzag or sawtooth structure.
Lipids
Phospholipids are principle components of cell membranes (lipid
bilayer)
Contain long alkane chains that stack together
Polar groups exposed to aqueous environment
Cycloalkanes
Cycloalkanes have a cyclic structure, and general formula CnH2n
Named by including cyclo prefix
10
Cyclopentane
Cyclohexane
Ring Flipping
Two chair conformations exist which interconvert by ring-flipping
Ring-flipping interchanges axial and equatorial substituents
11
Substituted cyclohexanes
Equatorial substituents result in more
conformation due to decreased steric interactions
Disubstitued cycloalkanes
Rings prevent free rotation around
single bonds
Isomers can exist when two or more
substituents are attached.
The isomers do not interconvert
(would require breaking of C-C
bonds).
These isomers are stereoisomers they differ by the arrangement of
atoms in space
Also
called
cis/trans
isomers,
diastereomers
Cycloalkanes
12
stable
Lecture 4
Stereochemistry
Tetrahedral carbons with 2 or 3 groups are
identical to their mirror
images
A tetrahedral carbon with 4 different groups is
NOT superimposable on its mirror image
These
non-superimposable
mirror images are therefore
different substances;i.e. they are isomers
Steoeoisomers
Molecules that are non-super
imposable mirror-image are a
subclass
of
stereoisomers
bond connectivity but differ in the
arrangement of atoms in space)
Specifically they are enantiomers
(same
Chirality (handedness)
Molecules that possess non-superimposable mirror images are said to
be chiral (from the Greek cheir ; hand )
How can we determine if a molecule is chiral?
o It must not contain a plane of symmetry
A tetrahedral carbon with 4 different groups has no plane of symmetry;
such a carbon atom represents an asymmetric centre or stereogenic
centre
Terminology
A molecule is chiral if it is not superimposable upon its mirror image
(which is true if it does not contain a plane of symmetry).
The two non-identical mirror image compounds are called enantiomers.
With a few important exceptions, enantiomers have identical physical
and chemical properties.
Molecules with one asymmetric/stereogenic centre (an sp3-hybridised
carbon with four different groups attached) are always chiral and exist
in enantiomeric forms.
An example: lactic acid
Lactic acid posesses one asymmetric centre and therefore two
stereoisomers (enantiomers) exist
Enantiomers
13
Absolute stereochemistry
The (+)- and (-)- description of enantiomers is an observable physical
property, but does not give information about the configuration of the
asymmetric centres
The Cahn-Ingold-Prelog rules allow the description of the specific
configuration of asymmetric centres; (R)- and (S)-descriptors
14
Rule 2:
o If two directly attached atoms are the same,
compare the second atoms in each group
Rule 3:
o Treat multiple bonds as the equivalent
number of single bonds
Rule 4:
o View the molecule so that you are looking down the bond from
carbon to group 4
anticlockwise
(S)-configuration
clockwise
(R)-configuration
4 pointing away
1-2-3 anticlockwise
(S)-configuration
(S)
lactic acid
4 pointing away
1-2-3 clockwise
(R)-configuration
(R)
glyceraldehy
de
15
Lecture 5
The Thumb Rule
Assigning (R)- and (S) If the lowest priority substituent is pointing out of the page:
Rotate the molecule so that it is pointing into the page, then apply
the rules as normal
Reverse the anticlockwise/clockwise rule
Use the thumb rule
More Terminology
An equal misture of enantiomers is termed a racemic mixture
It can be difficult to separate enantiomers from a racemic mixutre as
they have the same physical and chemical properties (m.p., b.p.,
solubility, reactivity)
Chiral Drugs
Sedative / anti-nausea
16
teratogen:
causes
birth
defects
(stunted growth of fetal
limbs)
Lecture 6
More than one asymmetric centre
Each asymmetric centre has two possible configurations (R or S)
A molecule with n asymmetric centres has (a maximum of) 2n
stereoisomers
17
Alkenes
Alkenes have the general formula CnH2n
Geometry
Contains C=C bond
Planar arrangement of atoms
Geometry of carbons is trional planar
C=C bond length 1.33 (c.f. 1.54
C=C bond strength 640 kJ.mol-1
for C-C)
(c.f. 360 for C-C)
Hybridisation
Alkene carbons are sp2-hybridised
Two p and one s orbitals are mixed to give
three sp2 hybrid orbitals
The sp2 orbitals have a trigonal planar
arrangement, with the remaining p orbital
perpendicular to the plane
Bonding
Head-to-head overlap of sp2 bybrid orbitals gives rise to a (sigma) bond
Sideways overlap of the p orbitals gives rise to a (pi) -bond
The -bond is weaker than the -bond due to less efficient orbital
overlap
Naming
Alkene names end in ene
18
Isomers
Stereoisomers are possible due to lack of rotation about C=C bond
Stereoisomers
diastereomers (non-mirror-image
stereoisomers)
cis-trans
isomers,
geometric
isomers
19
Lecture 7
E/Z-nomenclature of alkenes
Rules for assigning E/Z-stereochemistry of alkenes very similar to R/Sstereochemistry of stereogenic carbon atoms
20
Rule 2:
o If the high priority groups are one the same side (Z)o If the high priority groups are one the opposite side (E)-
Aromatic compounds
Historically, aromatic
distinctive odours
Benzene
Stability
Structure
21
Benzene is a regular hexagon; all C-C bonds are the same length
(139 pm; intermediate between a C-C single bond (154 pm) and a
C=C double bond (134 pm)).
Benzene: Reactivity
H2 / Pd(cat.)
rapid
reaction
at,
ambient temp., pressure
slow reaction at
temp., pressure
Br2
rapid
bromination
(addition reaction)
no reaction (substitution
occurs) if catalyst added
22
high
Lecture 8
Benzene: Structure
Proposed structures of benzene:
Benzene: Resonance
23
24
Heterocyclic aromatics
Nomenclature
25
26
1,3-disubstituted benzene
meta-substituted
(Greek; after)
1,4-disubstituted benzene
para- substituted
(Greek; beyond)
2-nitrophenol
ortho-nitrophenol
(o-nitrophenol)
3-bromobenzoic acid
meta-bromobenzoic acid
(m-bromo...)
1-iodo-4-nitrobenzene
p-iodonitrobenzene
(p-iodo...)
27
Lecture 9
Alkynes
Alkynes have the general formula CnH2n-2
Geometry
Contain CC double bond
Linear arrangement of atoms
Sp hybridisation
Bonding
Head-to-head overlap of sphybrid orbitals gives rise to a (sigma) bond
Sideways overlap of two sets of p orbitals gives rise to two
perpendicular -bonds
28
Naming
Alkyne names end in yne
Allenes
Functional groups
C-C and C-H bonds are strong and non-polar, and are therefore
relatively unreactive
The more reactive bond types/groupings are termed functional groups;
e.g. carbon-carbon multiple bonds
o alkenes (C=C)
o alkynes (CC)
o aromatic compounds
functional groups incorporating heteroatoms (non-C,H)
29
30
31
Lecture 10
1, 2, 3, 4 centres
Carbon can have up to four other carbons attached (referring to sp3carbons only)
o 1 C-C bond
1, 2, 3 functional groups
A functional group attached to a 1 centre is referred to as a 1
functional group (and so on) (most commonly for alcohols & alkyl
halides)
tertiary
(3)
alcohol
Secondary
(2)
alcohol
primary
(1)
alcohol
secondary
bromide
(2)
alkyl
tertiary (3)
alkyl
chloride
primary (1)
alcohol
32
The molecular ion can break down into fragment or daughter ions
The ions are separated according to their mass (m) and charge (z)
Mass spectrometer
33
34
UV Spectroscopy
UV Spectra
35
butadiene:
hexatriene:
octatetraene:
benzene:
max
nm
217
max
nm
258
max
nm
-carotene:
290
max = 206,
254 nm
36
max = 455 nm
Lecture 11
IR Spectroscopy
Characteristic IR absorptions
2800-3000
ignore!
(in
most
organic compounds)
Alcohols (O-H)
3400-3600
Amines (N-H)
3300-3500
similar to O-H
Carbonyl compounds
(C=O)
1670-1780
contained
in
many
functional groups e.g.
esters,
amides,
37
fingerprint region
<1500
ketones etc.
used only to match
identical compounds
IR Spectra
Structure of an unknown
38
These spin states are of slightly different energies. If they are irradiated
with the appropriate frequency, the nuclei of the low-energy state
absorb the energy and spin-flip to the high energy state.
Typically, superconducting magnets of 5-12 tesla (T) are used, requiring
radiowaves (200-500 MHz) for resonance
1H and 13C nuclei are most commonly used, as they allow for a map
of the carbon-hydrogen framework of a molecule to be determined
Only 1% of carbon nuclei are 13C, so carbon NMR spectroscopy is less
sensitive that hydrogen NMR (proton NMR) spectroscopy
NMR Spectroscopy
The radiofrequency required to bring a nucleus into resonance is
proportional to the strength of the magnetic field.
However, every nucleus is surrounded by electrons which set up tiny
local magnetic fields
Each type of nucleus resonates at a slightly different frequency (the
differences are in parts per million, ppm!), depending on the effective
field at each nucleus.
39
Beffective =
Bapplied Blocal
40
41
Lecture 12
13C NMR spectroscopy
Peak Integration
bromoethane
2 signals
ratio 2 : 3
2bromopropane
2 signals
ratio 1 : 6
42
43
IR spectrum: C=O, no OH
UV spectrum:
system
highly
conjugated
44
45