Organic and biosynthese
FIEN ROZENDAAL
LECTURE 1
Aspirin was first used in Egypt. Pure aspirin was isolated from the bark of willow
trees. Aspirin (salicylic acid) was converted into acetyl salicylic acid, which provided
better properties. High dose aspirin high risk of stomach bleeding.
In these days chemistry is gaining importance due to the application of biomolecules
as innovative therapeutics.
There are different routes for the production of paracetamol. PCA can only arise with
the route that start with chlorobenzene. By all the other routes, PCA is not formed.
The other routes (phenol and nitrobenzene) and can also form little amounts of
chemicals that can cause risks. Thus there is no completely save route, but there are
many safety rules.
Mebendazol:
• a generic medicine
• highly effective, broad-spectrum antihelmintic agent
• A package with 6 tablets costs 3.5 Euros
• ‘oldfashioned medicine’ (old-fashioned and innovative therapeutics remain major
challenges)
used for worm infection in young children
Nonpolar covalent bond = bonded atoms are the same or have similar
electronegativities.
H--H F-- F C-- C C-- H
Polar covalent bond = bonded atoms have different electronegativities.
electronegativity = how
strong an atom pulls
electrons. Electrons are
pulled to the electron with
the highest negativity.
Were the pair has shifted
can be point out with an
arrow (dipole).
Lone pairs plays an
1
,Nitrogen has one lone pair. If nitrogen does not form three
bonds, it is charged.
Oxygen has two lone
pairs. If oxygen does not
form two bonds, it is
charged
A halogen has three lone pairs. If hydrogen or halogen does
not form one bond, it has a charge (or it is a radical).
Determine the total number of valance
electrons of NO3-.
(5 + 6 + 6 + 6 = 23). Because they are
negatively charged, add another electron = 24.
An atomic orbital is the region of
space around the nucleus where an
electron is most apt to be found.
We have 3 p orbitals. The
lobes of a p atomic orbital
have opposite phases
Four Orbitals are Mixed to
Form Four Hybrid Orbitals.
An sp3 orbital has a
large lobe and a small lobe
2
,Exam question:
The 4 C-H
bonds have the
same length. All
the bond angles
are the same
(109.5°)
Carbon bonds to 3 atoms, so it needs to hybridize 3 atomic
orbitals.
Between the two H
atomes (vertical) the angle is 116,6 degrees en between the carbon and H above of
below the angle is 121,7 degrees.
Carbon bonds to 2 atoms, so it needs to hybridize 2 atomic orbitals. Hybridization
give than 2 hybrid orbitals (sp). 2 orbitals are left unhybridized.
Lewis acid: a species that accepts a share in
an electron pair
Lewis base: a species that donates a share in
an electron pair
“acid” = a proton-donating acid / “Lewis acid” = a
non-proton-donating acid All bases are Lewis
bases because they have a pair of electrons
they can share.
Electrophile has a positive charge/ partial
positive charge or an incomplete octet.
A nucleophile has a negative charge, a lone pair, or a π bond
An electrophile reacts with an electrophile. You first organic reaction is a two step
reaction.
3
, Carbocation is highly unstable.
pi bond has broken o bond has formed
O bonds are stronger than pi bonds because they have more overlap
Single bonds between atoms are always sigma bonds. Double bonds are comprised
of one sigma and one pi bond. Triple bonds are comprised of one sigma bond and
two pi bonds
A reaction coordinate diagram shows the
energy changes that take place in each
step of a
reaction.
Kinetic Stability is indicated by ∆G‡
If ∆G‡ is large, the reactant is kinetically stable because it reacts slowly.
If ∆G‡ is small, the reactant is kinetically unstable because it reacts rapidly.
Thermodynamic Stability is indicated by ∆G°
If ∆G° is negative, the product is thermodynamically stable compared to the reactant.
If ∆G° is positive, the product is thermodynamically unstable compared to the
reactant.
State in starting material and final
product = transition state. Transition
states have partially formed bonds.
4
FIEN ROZENDAAL
LECTURE 1
Aspirin was first used in Egypt. Pure aspirin was isolated from the bark of willow
trees. Aspirin (salicylic acid) was converted into acetyl salicylic acid, which provided
better properties. High dose aspirin high risk of stomach bleeding.
In these days chemistry is gaining importance due to the application of biomolecules
as innovative therapeutics.
There are different routes for the production of paracetamol. PCA can only arise with
the route that start with chlorobenzene. By all the other routes, PCA is not formed.
The other routes (phenol and nitrobenzene) and can also form little amounts of
chemicals that can cause risks. Thus there is no completely save route, but there are
many safety rules.
Mebendazol:
• a generic medicine
• highly effective, broad-spectrum antihelmintic agent
• A package with 6 tablets costs 3.5 Euros
• ‘oldfashioned medicine’ (old-fashioned and innovative therapeutics remain major
challenges)
used for worm infection in young children
Nonpolar covalent bond = bonded atoms are the same or have similar
electronegativities.
H--H F-- F C-- C C-- H
Polar covalent bond = bonded atoms have different electronegativities.
electronegativity = how
strong an atom pulls
electrons. Electrons are
pulled to the electron with
the highest negativity.
Were the pair has shifted
can be point out with an
arrow (dipole).
Lone pairs plays an
1
,Nitrogen has one lone pair. If nitrogen does not form three
bonds, it is charged.
Oxygen has two lone
pairs. If oxygen does not
form two bonds, it is
charged
A halogen has three lone pairs. If hydrogen or halogen does
not form one bond, it has a charge (or it is a radical).
Determine the total number of valance
electrons of NO3-.
(5 + 6 + 6 + 6 = 23). Because they are
negatively charged, add another electron = 24.
An atomic orbital is the region of
space around the nucleus where an
electron is most apt to be found.
We have 3 p orbitals. The
lobes of a p atomic orbital
have opposite phases
Four Orbitals are Mixed to
Form Four Hybrid Orbitals.
An sp3 orbital has a
large lobe and a small lobe
2
,Exam question:
The 4 C-H
bonds have the
same length. All
the bond angles
are the same
(109.5°)
Carbon bonds to 3 atoms, so it needs to hybridize 3 atomic
orbitals.
Between the two H
atomes (vertical) the angle is 116,6 degrees en between the carbon and H above of
below the angle is 121,7 degrees.
Carbon bonds to 2 atoms, so it needs to hybridize 2 atomic orbitals. Hybridization
give than 2 hybrid orbitals (sp). 2 orbitals are left unhybridized.
Lewis acid: a species that accepts a share in
an electron pair
Lewis base: a species that donates a share in
an electron pair
“acid” = a proton-donating acid / “Lewis acid” = a
non-proton-donating acid All bases are Lewis
bases because they have a pair of electrons
they can share.
Electrophile has a positive charge/ partial
positive charge or an incomplete octet.
A nucleophile has a negative charge, a lone pair, or a π bond
An electrophile reacts with an electrophile. You first organic reaction is a two step
reaction.
3
, Carbocation is highly unstable.
pi bond has broken o bond has formed
O bonds are stronger than pi bonds because they have more overlap
Single bonds between atoms are always sigma bonds. Double bonds are comprised
of one sigma and one pi bond. Triple bonds are comprised of one sigma bond and
two pi bonds
A reaction coordinate diagram shows the
energy changes that take place in each
step of a
reaction.
Kinetic Stability is indicated by ∆G‡
If ∆G‡ is large, the reactant is kinetically stable because it reacts slowly.
If ∆G‡ is small, the reactant is kinetically unstable because it reacts rapidly.
Thermodynamic Stability is indicated by ∆G°
If ∆G° is negative, the product is thermodynamically stable compared to the reactant.
If ∆G° is positive, the product is thermodynamically unstable compared to the
reactant.
State in starting material and final
product = transition state. Transition
states have partially formed bonds.
4
