Introduction to organic and bioorganic molecules & …gjrowlan/intro/lecture1.pdfIntroduction to...
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1 Introduction to organic and bioorganic molecules & reactions dr. gareth j. rowlands: arundel 402: [email protected]
Transcript of Introduction to organic and bioorganic molecules & …gjrowlan/intro/lecture1.pdfIntroduction to...
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Introduction to organic andbioorganic molecules & reactions
dr. gareth j. rowlands: arundel 402: [email protected]
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Course outline• Drawing molecules
• Nomenclature
• Bonding and structure - from an organic perspective
• Infra-red spectroscopy
• Reaction mechanisms and the "curly arrow"
• Stereochemistry
• Substitution reactions
• Elimination reactions
• Organic chemistry and biology (time permitting)
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What is organic chemistry?
The chemistry of living systems? Azadiractin is an insect anti-feedant from the Indian neem tree. Never synthesised by man. Originally thought that a 'vital force' was required, then in 1828...
OH
O
O
O
AcOMeO2C H
OH
O OHCO2Me
OO O
O
azadiractin
N C OH
NHH
Hheat
H2N NH2
O
ammonium cyanate urea
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What is organic chemistry?
Organic chemistry now covers most of the periodic table and permeates every part of our lives.
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H2 13 14 15 16 17
Li B C N O F
Na Mg3 4 5 6 7 8 9 10 11 12
Al Si P S Cl
K Ti Cr Cu Zn Se Br
Pd Sn I
Os Hg
NH
N
NN
SN
N
O O
O
PrEtO
sildenafil(Pfizer's Viagra)
MeO2C
CN
CN
CO2Me
superglue(two repeat units)
OO
NH
NH2
OH
O
O
aspartame(NutraSweet)
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What is organic chemistry?
Organic chemistry is vital for the understanding of biology, from how the molecules of our bodies are formed to how they interact and react.
proline
NH OH
O
NH
HN
NH
HN
O
O
O
O
HO
N
NH
peptide
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Drawing molecules
Full (Kekulé) structures are cluttered. We are mainly interested in the functional groups so skeleton representation highlights these.
CCC
NC
H
CO
O HHH
HH
HHH
C
CC
C
CC C
CC
OH
N
OH
H
H
H
H
CC
CC
CO
H
O
NC
H H
H H H H
H H
HHH
H
HH
H
proline phenylalanine leucine
NH
O
OH
orNH
CO2H
CO2H
NH2
CO2H
NH2
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Drawing molecules II
Molecules are drawn as a 'zig-zag' to represent true shape. We must remember that molecules are 3D. The 3D shape has important biological ramifications.
CO2H
(R)-leucinenatural
H2N H
CO2H
NH2
CO2H
NH2(S)-leucineunnatural
or
OMe OMe
H
HH O
H
H HH
H
HH
H
Me
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Drawing molecules III
Change your drawings to suit the reaction you are describing. Remember that the drawings are just shorthand.
NH
NH
O
OO O
(S)-thalidomideNH
NH
O
OO O
(R)-thalidomide
CO2MeCO2Me
O
O
H H
NaH
O
O
H
O
O
H
NaH
≡ ≡
H
3D shape can have important consequences!
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Abbreviations
Hydrocarbon chains rarely of interest so are often abbreviated. This leads to the examiners favourite trick of giving the same reaction but with different substituents!
H3CH2CH2CH2C ≡ Butyl ≡ Bu
H
H
H
H H H H
H H≡
Remember that 'organic elements' are for terminal chains only.
OH
O≡ BuCO2H
Bu OH
O+ MeOH H
Bu OMe
O
Et OH
O+ PrOH H
Et OPr
O
H2N Bu OH
OXH2N OH
O
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Abbreviations II
'Wild cards' can stand for nearly anything (chemists are lazy)
CO2H
NH2≡ Ph
CO2H
NH2≡OH
O
PhCO2H
O
OH
O
O
≡ ArCO2HO2N NH2 ≡ Ar NH2
asparin
CO2H
NH2≡ RCO2H OH
O≡ ROH
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Summary of abbreviationsabbreviation name structure abbreviation name structure
Me methyl CH3 R substituent any
Et ethyl Ph phenyl
Pr propyl Ar aryl any aromatic
Bu butyl Bn benzyl
i-Pr iso-propyl Ac acetylO
i-Bu iso-butyl vinyl
s-Bu sec-butyl allyl
t-Bu tert-butyl X halide F, Cl, Br or I
