chemistry living and systems: 123.101 lecture 1
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Chemistrya n d l i v i n g s y s t e m s
Gareth Rowlands123.101
chemistryanintroductionto
and...
...howitrelatestoliving
things
the study guide contains all the information you need
my lectures contain explanationand examples
but as I’m not here...
...the Prof will have to do!
my notes are available from:www.massey.ac.nz/~gjrowlan/teaching.html
my notes are available from:http://www.slideshare.net/gjr2323
Slideshare is an awesome resource for learning about presentations
©Noukka Signe@Flickr
read each chapter in advance
I will give different examples. Do not expect me to read it to you...
Ready?
pic: Aquarium of the Pacific
Unit One Part 1: introduction
pic: Aquarium of the Pacific
Unit One Part 1: introductionthese are not random
pictures; the molecule is a potential painkiller
called epibatidine which is isolated from poison
dart frogs...
why do we need organic chemistry?
why do we need organic chemistry?
...because its fun??
why do we need organic chemistry?
...it keeps me in a job?Or...
i f we want to understand living systems...
w e n e e d t o understand the individual organs...
...to understand organs, we have to understand cells...
...and still we have to get smaller and
smaller...
N
NN
N
Me
Me
MeHO2C(H2C)2
Me
HO2C(H2C)2
Fe
...and to do this we must understand the molecules that make up these systems
haem
but we don't need to get carried away...
Image Credit: NIST/University of Colorado
...lets stop with atoms & electrons!And none of this maths malarkey.
simple chemical principles control
biology
isomers and the v isua l cascade
Me Me
Me Me
Me
NOpsin
HRhodopsin11-cis-retinal
(aldehyde not imine)
Me Me
Me
Me
NOpsin
H
Me
all trans-retinalstarts VISUAL CASCADE
photon
1112
$chemistry and medicine
penicillin Gantibacterial
HN
O N
S
O
H
CO2H
MeMe
http://staff.science.uva.nl/~dcslob/lesbrieven/maarten/Bacterien.html
penicillin Gantibacterial
HN
O N
S
O
H
CO2H
MeMe
http://staff.science.uva.nl/~dcslob/lesbrieven/maarten/Bacterien.html
Chemistry explains how penicillin blocks
bacterial cell wall synthesis.
N OHN
O
F
OH OH O
MeMe
Ca2+
2
Liptorcholesterol treatmentUS$ 12.9 billion
the language of chemistry...
the language of chemistry...
First we need to be able to communicate
with each other...
the language of chemistry...
There are three ways of talking about
chemicals...
SYMBOLICchemical formulae
MICROSCOPICatoms &
molecules
MACROSCOPICbulk
properties
©DC Comics
macroscopicrepresentation
physical properities
©DC Comics
macroscopicrepresentation
physical properitiesobviously important
(if you happen to get dunked in a vat
of the stuff)
©DC Comics
macroscopicrepresentation
physical properities
but ignored in this lecture...lets just
leave it for the lab...
how do we represent molecules?
microscopic representation
microscopic representation
how we represent the actual molecules
themselves...
molecular orbital representation
hexane
molecular orbital representation
hexane
electrons spread over entire molecule...true but not very useful!
hexane
space filling representation
hexane
space filling representation
shows us the atoms and their relative
size...but bonds hard to see
hexane
ball and stick representation
hexane
ball and stick representation
atoms, bonds, shape, it has it all. Time
consuming to draw so...
symbolic representation
symbolic representation
quick and dirty ways to represent molecules
C3H7empirical formula
C3H7empirical formula
just the ratio of atoms...
C3H7empirical formulaempirical formula
C3H7C6H14
C9H21
C12H28C15H35C18H42 C21H49
C24H56C27H63 C30H70
C33H77
...too many possibilities!
molecular formula
C6H14
molecular formula
C6H14exact number of atoms...
molecular formula
C6H14molecular formula
HC
CC
CC
CH
H H
H H
H H
H H
H H
H H
HC
CC
CC
H
H H
C H
H H
H H
H H
HHH
HC
CC
CC
H
H H
H H H H
H HCH H
H
HH
CC
CC
HH H
C H
H C
H HH
HH
HH H
...but not how they are connected
condensedformula
CH3CH2CH2CH2CH2CH3
condensedformula
CH3CH2CH2CH2CH2CH3bonding sorted...
condensedformula
CH3CH2CH2CH2CH2CH3
condensedformula
HC
CC
CH
H H
C H
H C
H HH
HH
HH H
(CH3)2CHCH(CH3)CH3N
N
Me
MeO
O
N
NMe
...but bulky...and some structures
would be confusing!
structural formula
HC
CC
CC
CH
H H
H H
H H
H H
H H
H H
structural formula
HC
CC
CC
CH
H H
H H
H H
H H
H H
H H
now we’re talking; atoms, bonding,
shape. It has it all. But...
structural formula
HC
CC
CC
CH
H H
H H
H H
H H
H H
H H
structural formula
N
OMe
N
OH
HCN
CCC
HC
HCCH
CCH
O
CH C
HN CH2
CH2H2C CH
H2CCH
HC
H2COH
CH3
...can be messy and time consuming...
skeletal (structural) formula
skeletal (structural) formula
Quick, easy and tells me
everything...but do you understand what it means?
other representations
CC
C
CC
H
O
HH
H HH
H
HH
H
H
OCHO
CHOH
CH3
OHEt
Ph
H
CH3
OH
H
HO
CH3HPh
Et H
Fischer projection
Newman projection
Sawhorse projection
do not use this representation!
H C C C C C C HH
H
H
H
H
H
H
HH
HH
H
do not use this representation!
H C C C C C C HH
H
H
H
H
H
H
HH
HH
H
©Lucasfilms
...key to this course is understanding / interpreting these
symbols
understanding skeletal (structural) formulae
4CARBON
HC
HHH
C CH
H H
H
CCO
H
H H
OH
H C C H
4CARBON
HC
HHH
C CH
H H
H
CCO
H
H H
OH
H C C H
carbon always has four bonds...
©ultraBobban@Flickr
why? a good question & one we
will partially answer later
1HYDROGEN
HC
HHH
C CH
H H
H
CCO
H
H H
OH
CCC
H NO
OH
HH
H
H H
1HYDROGEN
HC
HHH
C CH
H H
H
CCO
H
H H
OH
hydrogen always has one bond...
CCC
H NO
OH
HH
H
H H
2OXYGEN
HC
CO
H H
H HH
CCCOC
HH
HH
HH
HH
CCC
H NO
OH
HH
H
H H
3NITROGEN
CC
NC
H
H HH
HH
C CH
HH N
CCC
H NO
OH
HH
H
H H
so how do we draw skeletal formulae?
allC CHcan be removedand
NH
HN
HN
NH
HN
NH
HN
OO
O
O
O
HO OHOH
O O
O
NH2
OHHO
O
Cl
Cl
O
HOHO
OH
OO
NH2OH
O
Vancomycin
O
HO
allC CHcan be removedand
NH
HN
HN
NH
HN
NH
HN
OO
O
O
O
HO OHOH
O O
O
NH2
OHHO
O
Cl
Cl
O
HOHO
OH
OO
NH2OH
O
Vancomycin
O
HO
assume each corner is a carbon...
allC CHcan be removedand
NH
HN
HN
NH
HN
NH
HN
OO
O
O
O
HO OHOH
O O
O
NH2
OHHO
O
Cl
Cl
O
HOHO
OH
OO
NH2OH
O
Vancomycin
O
HO...and it will always have four bonds.
example one
HC
CC
CHH H
H H
example one
HC
CC
CHH H
H H
CC
CC
– H
remove H
example one
HC
CC
CHH H
H H
CC
CC
– H – Cnow remove C
example two
CC
CCC
CHH
H
HH
H
example two
CC
CCC
CHH
H
HH
H
CC
CCC
C
– H
remove H
example two
CC
CCC
CHH
H
HH
H
CC
CCC
C
– H – Cnow remove C
example three
CC
O
OH
H
HH
H NH
H
example three
only removeCH
CC
CO
O
N
H
HH
CC
O
OH
H
HH
H NH
H
remove C–HBUT
leave all others!
example three
only removeCH
CC
CO
O
N
H
HH
CC
O
OH
H
HH
H NH
H
This is key. Wecan only remove C–H bonds. We must leave
all others...
example three
– Conly
removeCH
CO2H
NH2
OH
O
NH2CC
CO
O
N
H
HH
CC
O
OH
H
HH
H NH
H
now remove C
examplefourreverse
HOCO2H
NH2
very important
examplefourreverse
HOCO2H
NH2
HOC
CCO2H
NH2C+
add C to corners
examplefourreverse
HOCO2H
NH2
HOC
CCO2H
NH2HO
CC
CO2HH H
H NH2C+ H+ Add H to make all C have four bonds
examplefourreverse
HOCO2H
NH2
HOC
CCO2H
NH2HO
CC
CO2HH H
H NH2C+ H+
HOC
CC
H H
H NH2O
OH
HOC
CC
H H
H NH2O
OH
HOC
CC
H H
H NH2O
OH
remember C has four; O has two
bonds and H has one
2OXYGEN
examplefourreverse
HOC
CC
H H
H NH2O
OH
neither of the O has two bonds
2OXYGEN
examplefourreverse
HOC
CC
H H
H NH2O
OH
O still does not have two bonds. This
structure is wrong
4CARBON
examplefourreverse
HOC
CC
H H
H NH2O
OH
C still does not have four bonds. This
structure is wrong
Functional Groupspages 16-29
©"lapolab"@Flickrlearn them
CO2H
CHO
NC
examplefivereverse
CO2H
CHO
NCC
CC
CO2H
CC
CC
C
CHO
NC
HH
H H H
HH
examplefivereverse
add C to corners and H to make four
bonds
CO2H
CHO
NCC
CC
CO2H
CC
CC
C
CHO
NC
HH
H H H
HH
CC
CC
CC
CC
C
C
C
HH
H H H
HH
O
H
NO
OHexample
fivereverse
now get three bonds to N; two bonds to O and one to H
examplesix
OHCC
CC
CCO2H
O
HO H H OH
H OHC
CC
CC
C
O
HO H H OH
H OHO
HO
OH
OHCC
CC
CCO2H
O
OHOH
OHOHC
CO2H
O
OHOH
OH
C+ H+
what have....we learnt?4organic chemistry is
easy if we can count to...
what have....we learnt?4organic chemistry is
easy if we can count to...
oh, and it’s really important!
before next lecture...
readUnit 1 Part 2 ©Noukka Signe@Flickr
(Dr. GJ Rowlands)
Acknowledgmentsgareth
wouldlike tothankTrevor Kitson
Massey University& the 101 students
www.massey.ac.nz/~gjrowlan
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