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Life Sciences Chemistry Mind Map

A holistic view of the mechanisms encountered in the first year chemistry module
by

Paul McDermott

on 9 February 2015

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Transcript of Life Sciences Chemistry Mind Map

Life Sciences Chemistry A MIND MAP Nearly every subject has a shadow, or imitation. It would I suppose,
be quite possible to teach a deaf and dumb child to play the piano.
When it played a wrong note, it would see the frown of it’s teacher,
and try again. But it would obviously have no idea of what it was
doing, or why anyone should devote hours to such an extraordinary
exercise. It would have learnt an imitation of music. And it would have
learnt to fear the piano exactly as most students fear what is supposed
to be mathematics.
What is true of music is also true of other subjects. One can
learn imitation history – Kings and dates, but not the slightest idea of
the motives behind it all; imitation literature – stacks of notes of
Shakespeare’s phrases, and a complete destruction of the power to
enjoy Shakespeare…….

(W. W. Sawyer) Atoms, Orbitals and Bonds Periodicity and Orbitals lectures 1 and 2 (1) Remember the positions of the key elements in the periodic table
because this will help you understand their characteristics such as
atomic radius and electronegativity (2) Electrons are arranged in orbitals around the nucleus that have
specific shapes and energy levels. (3) the further away
from the nucleus
the electron/orbital,
the higher energy
it will be (4) the greater the
number of nodes
an orbital has,
the higher energy
it will be (5) The important orbitals for this course
are the spherical s orbitals
and the dumbell
shaped
p orbitals Key Points from the lecture: The p orbitals are present
in every shell (other than
the 1st shell) as a set of 3
"degenerate orbitals" which
all lie in mutually
perpendicular planes lecture 3 Ionic Bonding and sp3
hybridisation Hope fully it's not too hard to see how these two topics link together. We looked in the first lecture at the important types of orbitals we need to know about for this course. In the lecture 3 screencast we are looking at how these types of orbital can combine to give the types of bonds we see in the drug molecules. Lecture 4 sp2 and sp hybridisation as well as
a bit of conjugation! It's hopefully quite easy to see how
these two concepts are connected We looked in the first lecture at the important types of orbitals we need to know about for this course. In the lecture 4 screencast we are looking at how these types of orbital can combine to give double and triple bonds. We also see how pi electrons (which are in different orbitals to the electrons in sigma bonds) behave differently. The most notable example of this is the conjugation phenomenon that I introduced you to. I also talked in the lecture about "aromaticity" this is a very specific type of conjugation phenomenon that will be covered in more detail later in the course. However I will put the criterior for aromaticity in here should you want to familiarise yourself with this concept now. Polarity Polarity and Functional Groups Polarity of course links in with bonding and periodicity
because we need to understand the orbitals that are
making the polar/non-polar bonds as well as the
electronegatvity of the atoms within each bond
(periodicity). Test yourself Assess the polarity of the following molecules: Moderately polar polar (water soluble) non-polar
(crosses the blood brain
barrier) Functional Groups Part 1 Part 2 Test Yourself Highlight and name all of the functional groups
in these molecules (you'll get the answer the next time
you click on the arrow). Acids and Bases Acids Bases Which nitrogen in each of the structures below do you think is the most basic (answers will appear the next time you click on the arrow). We talked a lot about electronegativity in these lectures
if you are not sure what this is then refer back
to the periodicity content as well as the
first video in the functional
groups section remember: The lower the pKa the stronger
the acid (and hence the weaker the base) Key mechanisms: Reactions of Functional Groups Electrophiles and Nucleophiles Hopefully it is clear to you now that you
need to understand functional groups to
be fully able to assess the acid base
character of the groups within a drug
molecule! The link between these two subjects is pretty clear
-and acid/base reaction is essentially an
electrophile/nucleophile reaction The p orbitals are present
in every shell (other than
the 1st shell) as a set of 3
"degenerate orbitals" which
all lie in mutually
perpendicular planes Stereochemistry Configurations Diastereomers Conformational
Isomerism Conformations of
Cyclohexane Assign the configurations of the chiral centres in each
of the molecules below: Stereochemistry and conformations link nicely into bonding and
hybridisation. With stereochemistry and conformations we are
looking at the specific 3D shape of molecules which is of course
determined by the hybridisation state of the atoms and the types
of bonds present. Draw all of the possible isomers of isocitric acid
and describe the relationship between each compound
(enantiomer or diastereomer): Nucleophilic Substitution SN1 and SN2 This is a direct extension on from the
reactions of functional groups lectures.
Nucleophilic substitution reactions are
reactions of electrophiles with nucleophiles. The connection between the SN1 and SN2 concepts and stereochemistry is very strong! For both of the nucleophilic substitution mechanisms we have considered the
"stereochemical outcomes". The link between these two subjects is pretty clear
-if your not sure why refer to the SN2 lecture not where
I talk about the correlation between nucleophilicity
and basicity. Example Questions Acid Catalysed
Hydrolysis Hydrolysis Base Promoted
Hydrolysis Example Questions (1). Highlight the functional group in enalapril
that is the most susceptible to hydrolytic
degradation. Fully explain your answer (2). Provide a full curly arrow mechanism for the acid
catalysed hydrolysis of enalapril (3). Provide a full curly arrow mechanism for the base
promoted hydrolysis of enalapril Hydrolysis Reactions are
Nucleophilic Acyl
"Substitution Reactions" Ester Synthesis Ester and Amide synthesis Reactions are
Nucleophilic Acyl
"Substitution Reactions" Example Questions Ester and Amide
Synthesis Amide Synthesis Enolates, the Aldol Reaction and the Michael Reaction Example Questions The Michael Reaction The generation of an enolate anion requires an "acidic proton" within the molecule (1). List 4 ways to synthesise an ester (i) Reaction of a carboxylic acid
with an alcohol using acid as a
catalyst (ii) Reaction of an acyl chloride
with an alcohol. (iii) Reaction of an acid
anhydride with an alcohol. (iv) Transesterification
under basic or acidic
conditions. (2). Provide an example mechanism for each of the reactions you have suggested (i). (ii). (iii). (iv). After the tutorial! (2). Suggest a possible structure for compound A
and provide a full curly arrow mechanism
for the conversion of compound A into
Nicotinamide After the Tutorial Addition Reactions to Alkenes lecture 18 If you are unsure about the exact structure
of an alkene then you should revisit the section
hybridisation before looking at the lecture 18
content The between these concepts is appreciated when you
think about the stereo and regiochemical outcomes of
both of the electrophilic alkene addition mechanisms
that are covered in lecture 18.
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