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Summary Organic And Biosynthesis
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Summary: organic and biosynthesisLecture 1: Recap basic chemistry - Chapter 1, 2, 5, 6
18-10-2021
Chapter 1: Remembering general chemistry
Carbon shares electrons, the atoms on the left of carbon give
up electrons (Li, Be, B) and the electrons on the right accept
electrons (N, O, F). When an atom has 8 atoms in its outer
shell, it obeys the Octet rule. All atoms try to reach this rule.
Valence electrons are the electrons that are in the outer shell
of an atom. Boron has 3, carbon has 4, nitrogen has 5, oxygen
has 6 and halogens have 7. Halogens form 1 bond (3 lone
pairs), oxygen can form 2 bonds (2 lone pairs), nitrogen can form 3 bonds (1 lone pair), carbon can form 4
bonds. If carbon doesn’t form 4 bonds, it is reactive: carbocation, carbanion, radical. If nitrogen doesn’t
form 3 bonds: ammonium ion, amide ions. If oxygen doesn’t form two bonds: hydronium ion, hydroxide
ion.
In the periodic table, the electronegativity gets higher in the upper right corner (F highest). Electronegative
atoms pull on the electrons, leading to distribution of electron density in molecules. Nonpolar covalent
bonds are bonds between atoms with similar electronegativity. Polar covalent bonds are bonds between
atoms with different electronegativity. Lewis structures consider the charge distribution and lone pairs on
an atom. First the valence electrons are counted. Negative charge adds an electron, positive charge
removes one.
Atomic orbitals
Atomic orbitals are the regions of space around the nucleus where an electron is most likely to be found.
1s and 2s orbitals are spheres. P orbitals have lobes with opposite phases. If hybridization occurs, sp3 (or
sp2 or sp) orbitals are formed. These have a large and small lobe. Methane has four sp3 orbitals that each
bind to the s orbital of hydrogen, leading to bond angles of 109.5 degrees. S orbitals overlap to form sigma
bonds. When there are double bonds, there is sp2 hybridization. In this case there are 120-degree bonds. P
orbitals form the π-bond (the second bond). In case of a triple bond, there is sp-hybridization, leading to
one sigma bond and two π-bonds. Such bonds have 180-degree bond angles.
Chapter 2: Acids and bases
Brønsted acids donate protons, Brønsted bases bind
protons. Lewis acids accept a share in an electron pair,
Lewis base donates a share in an electron pair. In
chemistry, ‘acids’ are often proton-donating acids, and
‘Lewis acids’ are often non-proton donating acids.
Chapter 5: Alkenes
Nucleophilic substitution reaction
Electrophiles have a positive charge, a partial positive
charge, or an incomplete octet. Nucleophiles have a
negative charge, a lone pair, or a π. Nucleophiles react
with electrophiles. This occurs for example in a two-step
nucleophilic substitution reaction. The mechanism of a
reaction is the step-by-step description of the process by
,which reactants are converted into products, using curved arrows to indicate the electron flow. Curved
arrows always start at the nucleophile. The electrons that come from the bond that is broken need to go
somewhere, often this is to the best leaving group. Octet rule is very important.
Reaction diagrams
Reaction coordinate diagrams show the energy changes in each step of a reaction. The transition state
shows partially broken and partially formed bonds. The reactants and the products have a certain level of
free energy. The energy between the starting level and the
eventual product is the free energy change (∆G°). If ∆G° is
negative, the conversion gives rise to a stable product,
compared to the reactant. It has to do with thermodynamic stability. The activation energy (Ea or ∆G‡) has
to do with kinetic stability. It is the energy between a starting level and a transition state. If ∆G‡ is large,
the reactant is kinetically stable because it reacts slowly. Between the reactants and products, there are
intermediates. Looking at the activation energies of different transition states gives the rate limiting step
(highest activation energy). Catalysts help lowering the energy barrier (∆G‡), without changing the energy
of the starting point of endpoint. If occurring naturally, it is called an enzyme.
Chapter 6: The reactions of alkenes
Carbocations and electrophilic addition reactions
In the case of electrophilic addition reactions to double bonds of aromatic rings, carbocations are formed
as an intermediate state. Double bonds
attack the proton of a strong acid, creating
a carbocation (electrophile) and a
negatively charged compound
(nucleophile). After this, the nucleophile
can bind the carbocation. The first step is
the rate limiting step. Carbocations
become more stable (less reactive) if it has a lot of substitutions: tertiary carbocations are more stable than
primary carbocations.
Hyperconjugation
Alkyl groups can decrease the concentration of positive charge on a carbon through hyperconjugation. In
this case, the empty p orbital and the sigma
bonds overlap, leading to sharing of the positive charge. When a charge is removed or delocalized, an atom
gets more stable. That also count in this case: more hyperconjugation leads to more stability of the
carbocations.
Lecture 2: Delocalized electrons - Chapter 8 18-
10-2021
,Localized electrons belong to a single atom or are shared by two atoms
via bonds. Delocalized electrons are shared by three or more atoms (partial double bonds). This occurs for
example in benzene. The carbon-carbon atoms have bonds that are shorter than single bonds but longer
than double bonds. They are sp2 hybridized and have bond angles of 120 degrees. P orbitals overlap with
each other to make π bonds in both directions, leading to a cloud of π electrons both under and on top of
the ring. This is illustrated in resonance contributors (neither are ‘real’) or in the resonance hybrid (closer
to reality). Conjugating double bonds (double – single – double) also
have p orbitals that can overlap.
Rules for drawing resonance contributors
1. Only electrons move, atoms never move
2. Only π electrons and lone pair electrons move, sigma electrons never
move
3. The total number of electrons in the molecule never changes
4. Electrons always move to an sp2- or sp-hybridized atom, never to a
sp3 atom
Determination of sp-, sp2- or sp3-hybridized atoms: look at steric number; the number of atoms + lone
pairs bound to the atom of interest. If the steric number is 4: sp3. If the steric number is 3: sp2. If the steric
number is 2: sp.
Stability
If one of the resonance contributors is more stable than the other, it contributes more to the resonance
hybrid than the less stable contributor. Less stable contributors occur when:
There are separated charges in one of the contributors, but not in the other one
There is an incomplete octet
There is a positive charge on an electronegative atom (+ on oxygen)
There is a negative charge on an electropositive atom (- on carbon)
Delocalization energy
Delocalization energy (resonance energy) is the
extra stability a compound has as a result of having
delocalized electrons. The resonance hybrid is
more stable than its contributors. The greater the
number of relatively stable resonance contributor
(and the more equivalent their structures), the
greater the resonance energy. Carboxylate ions have greater delocalization energy than carboxylic acid.
Isolated and conjugated dienes (double bonds)
Conjugated dienes have overlap in p orbitals, leading
to partial π bond formation. In cumulative and isolates
dienes, there is no overlap of p orbitals.
Carbocation stability
Carbocations are often formed in transition states. The stability of a carbocation indicates the reactivity of
the compound. Carbocations get more stable by hyperconjugation, but also by resonance stabilization. This
can be achieved by allylic cations and benzylic cations.
Resonance and electronic effect on pKa
, Carboxylic acid is a stronger acid than alcohol because of inductive electron withdrawal and electron
delocalization. Inductive electron withdrawal and resonance stabilization lower the pKa. For knowing
relative pKa, you can look at the conjugate base of an acid. The more resonance the conjugate base has,
the stronger the acid is. When there are electron withdrawing substituents (withdrawal through sigma
bonds), the pKa decreases. When there are electron donating substituents, there is increase in pKa.
Aromatic rings
A compound is aromatic when it has an uninterrupted cloud of π
electrons (cyclic, planar, every ring atom must have p orbital). There must
be an odd number of pairs of π electrons, and it cannot be sp3 hybridized.
Lone pair electrons are π electrons if they can form a π bond in a
resonance contributor. Antiaromatic compounds have uninterrupted
clouds of π electrons, but an even number.
Electrophilic aromatic substitution reactions
Aromatic compounds such as benzene can undergo substitution
reactions. The intermediate state again forms a cation. However, it is not
the same as addition of an electrophile to an alkene, because
otherwise aromaticity would be lost, and
aromaticity is wanted because it is more stable.
Lecture 3: Reactions of carboxylic
acids and derivatives - Chapter
15 19-10-2021
What are carbonyl compounds and
carboxylic acids (derivatives)?
A carbonyl group is a C with a double bonded O. Overlap of p orbitals gives rise to the
π bond. If there is an R group or aromatic group attached to C, it is called an acyl
group. It can be a carboxylic acid (OH), ester (OR’), acyl chloride (Cl-) or amide (NH2)
(the latter 3 are called carboxylic acid derivatives). The leaving group can be
substituted by another group. This is not possible in ketones and aldehydes
(lecture 4), and therefore such groups have different reactivities. Not all leaving
groups are equally good. To the relative ability to leave, you look at the pKa of the
conjugate acid. The lower the pKa, so the stronger the acid, the weaker the base,
and the better the leaving group. HCL has very low pKa, so Cl- is a very good
leaving group. NH3 has a high pKa, making it a worse leaving group. In ketones and aldehydes, the leaving
groups are very strong bases, so they do not leave the carbonyl compound. Carbonyl compounds have 120
degrees bond angles (because of sp2-hybridization). Carboxylic acids and derivatives have two resonance
contributors, that stabilize the compound. The carbonyl carbon is delta positive (electrophile), whereas the
oxygen is delta negative.
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