Testing

1. chemistry
and living systems
123.101

2. an
introduction
to
chemistry
and...

3. ...how
it relates
to
living
things

4. the study guide contains
all the information you need

5. my lectures contain
explanation
and examples

6. but as I’m not here...
!
...the Prof will have to do

7. my notes are available from:
www.massey.ac.nz/~gjrowlan/teaching.html

8. Ready?

9. Unit One Part 1: introduction
pic: Aquarium
of the Pacific

10. Unit One Part 1: introduction
these are not random
pictures; the molecule is
a potential painkiller
called epibatidine which
is isolated from poison
dart frogs...
pic: Aquarium
of the Pacific

11. why do we need
organic chemistry?

12. ...because its fun??
why do we need
organic chemistry?

13. why do we need
organic chemistry?
...it keeps me in a job?
Or...

14. if we wan t t o
understand
living systems...

15. we need to
understand the
individual organs...

16. ...to understand
organs, we have to
understand cells...

17. ...and still we have to
get smaller and
smaller...

18. ...and to do this we must understand the
molecules that make up these systems
Me
N
Me Me
N Fe N
HO2C(H2C)2
N
HO2C(H2C)2 Me
haem

19. ...lets stop with
atoms & electrons!
And none of this
maths malarkey.
but we don't need
Image Credit: NIST/University of Colorado
to get carried away...

20. simple chemical
principles control
biology

21. Me Me Me
11
12
Me Me
Rhodopsin H
11-cis-retinal N
(aldehyde not imine) Opsin
photon
Me Me Me Me
isomers and the Me N
H
visual cascade all trans-retinal
starts VISUAL CASCADE
Opsin

22. $
chemistry
and medicine

23. penicillin G
antibacterial
H H
N S
Me
O N Me
O
CO2H
http://staff.science.uva.nl/~dcslob/lesbrieven/maarten/Bacterien.html

24. penicillin G
Chemistry explains
how penicillin blocks antibacterial
bacterial cell wall
synthesis. H H
N S
Me
O N Me
O
CO2H
http://staff.science.uva.nl/~dcslob/lesbrieven/maarten/Bacterien.html

25. F
OH OH O
H N O Ca2+
N
O Me
Me
2
Liptor
cholesterol treatment
US$ 12.9 billion

26. the language
of chemistry...

27. First we need to be
able to communicate
with each other...
the language
of chemistry...

28. There are three ways
of talking about
chemicals...
the language
of chemistry...

29. MACROSCOPIC
bulk
properties
MICROSCOPIC SYMBOLIC
atoms & chemical
molecules formulae

30. macroscopic
representation
physical
properities
©DC Comics

31. macroscopic
representation
physical
properities
obviously important
(if you happen to
get dunked in a vat
of the stuff)
©DC Comics

32. macroscopic
representation
physical
properities
but ignored in this
lecture...lets just
leave it for the lab...
©DC Comics

33. how do we represent
molecules?

34. microscopic
representation

35. how we represent the
actual molecules
themselves...
microscopic
representation

36. hexane
molecular orbital
representation

37. hexane
electrons spread over
entire molecule...true
but not very useful!
molecular orbital
representation

38. hexane
space filling
representation

39. hexane
shows us the atoms
and their relative
size...but bonds hard
to see
space filling
representation

40. hexane
ball and stick
representation

41. hexane
atoms, bonds, shape,
it has it all. Time
consuming to draw
so...
ball and stick
representation

42. symbolic
representation

43. symbolic
representation
quick and dirty ways
to represent
molecules

44. C3H7
empirical
formula

45. C3H7 just the ratio of
atoms...
empirical
formula

46. C3H7 ...too many
possibilities!
C6H14C24H56 12H28
C
C15H35C30H70
C27H63 3H7
C18H42 C C21H49
formula 33H77 9H21
C C
empirical

47. C6H14
molecular
formula

48. C6H14
exact number of
atoms...
molecular
formula

49. C6H14
...but not how they
H H H H
are connected
H H
H H
H C C H H C H H H
H C H H H
C C C H C C
H C C H C C H
H HH C H H C C C
H H H H H C H
H H H H H H H
H H
H H H H H H
H
C
C
C
C
C
C
H
molecular
H H H H H H
formula

50. CH3CH2CH2CH2CH2CH3
condensed
formula

51. CH3CH2CH2CH2CH2CH3
bonding sorted...
condensed
formula

52. CH3CH2CH2CH2CH2CH3
H H O Me
H C H H H Me N
N
H
C
C
C
C
H (CH3)2CHCH(CH3)CH3
O N N
H H H C H
H H ...but bulky...and Me
some structures
condensed would be confusing!
formula

53. H H H H H H
C C C H
H C C C
H H H H H H
structural
formula

54. H H H H H H
C C C H
H C C C
H H H H H H
now we’re talking;
atoms, bonding,
shape. It has it all.
But...
structural
formula

55. H H H H H H
C C C H
H C C C
H H H H H H
...can be messy and
time consuming...
H
C
H2C CH
OH
OH H2C
N
H H2C C CH2
H
C C N CH
HC C H C 2
N H
N C
C CH
OMe HC C CH3 structural
formula
C O
H

56. skeletal
(structural) formula

57. Quick, easy and
tells me
everything...but do
you understand
what it means?
skeletal
(structural) formula

58. other
representations
H
H
C H O O
H H C C CHO
H C C H H
H H H
OH Et H
CHO
Et H
H OH HO
Ph
CH3 H CH3
H CH3
Ph
Fischer Newman Sawhorse
projection projection projection

59. do not use this
representation!
H H H H H H
H C C C C C C H
H H H H H H

60. do not use this
representation!
H H H H H H
H C C C C C C H
H H H H H H

61. ...key to this course
is understanding /
interpreting these
symbols
©Lucasfilms

62. understanding
skeletal (structural)
formulae

63. 4
H
H C H
H
H H
C C
H H
H C C H
CARBON
O
H C H
C O
H H

64. 4
H
H C H
H
carbon always has H H
four bonds...
C C
H H
H C C H
CARBON
O
H C H
C O
H H

65. 1
H
H C H
H
HYDROGEN H
C C
H
H H
O
H C H
C O
H H
H H O
C C H
H C O
H N H
H

66. 1
H
H C H
H
HYDROGEN H
C C
H
H H
O
H C H
C O
H H
hydrogen always has
one bond... H H O
C C H
H C O
H N H
H

67. 2
H H
C O
H C H
H H
H H
H H
C C
H C C H
H O H
H H O
C C H
H C O
OXYGEN H N H
H

68. 3
H H O
NITROGEN H
C
C
C
O
H
H N H
H
H H
C N H
H C C
H H
H
H C C N
H

69. 2
C H
O H
N H
ELECTRONS

70. 2
we’ll explain why in a
C H
later lecture...
O H
N H
ELECTRONS

71. so how do we draw
skeletal formulae?

72. HO
HO
OH
O
O O
NH2 O
Cl
OH O O
HO Cl OH
O O O
H H H
O N N N
N N N
H H H
HN O O O
O
HO NH2
OH
HO OH
C CH
Vancomycin
can be
all and removed

73. HO
HO
OH
O
O O
O assume each corner
NH2 Cl
OH O O is a carbon...
HO Cl OH
O O O
H H H
O N N N
N N N
H H H
HN O O O
O
HO NH2
OH
HO OH
C CH
Vancomycin
can be
all and removed

74. HO
HO
OH
O
O O
NH2 O
Cl
OH O O
HO Cl OH
O O O
H H H
O N N N
N N N
H H H
HN O O O
O
NH2 ...and it will always
HO
have four bonds.
OH
HO OH
C CH
Vancomycin
can be
all and removed

75. example
one
H H H
C
C C
H C
H H

76. example
one
remove H
H H H
C C
C C C C
H C C
H H
–H

77. example
one
H H H
C C
C C C C
H C C
H H
–H –C
now remove C

78. example
two
H
H C H
C C
C C
H C H
H

79. example
two
H remove H
H C H C
C C C C
C C C C
H C H C
–H
H

80. example
two
H
H C H C
C C C C
C C C C
H C H C
–H –C
H
now remove C

81. example
three
H O
H
C H
H C
O
H N H
H

82. example
three
remove C–H
BUT
H O O leave all others!
H
C H C C H
H C
O C O
H N H N H
H H
only
remove
CH

83. example
three
O
H O O OH
H
C H C C H NH2
H C
O C O
H N H N H
CO2H
H H
NH2
only
remove
–C
CH now remove C

84. example
four
reverse
CO2H
HO
NH2

85. example
four
reverse add C to corners
CO2H C CO2H
HO HO C
+C
NH2 NH2

86. example
four
reverse
H H
CO2H C CO2H
HO HO C C CO2H
HO C
+C +H
NH2 NH2
H NH2
Add H to make all C
have four bonds

87. example
four remember C has
reverse four; O has two
bonds and H has
one
H H
CO2H C CO2H
HO HO C C CO2H
HO C
+C +H
NH2 NH2
H NH2
H H O H H O H H O
H
C C C C H C C H
HO C O HO C O HO C O
H NH2 H NH2 H NH2

88. CHO
NC CO2H
example
five
reverse

89. H
CHO H C
CHO
C C H H
C C C
NC CO2H NC C C CO2H
H H H
add C to corners
and H to make four
bonds
example
five
reverse

90. H
CHO H C
CHO
C C H H
C C C
NC CO2H NC C C CO2H
now get three bonds
H H H
to N; two bonds to
O and one to H
H O
H C C
C C H
H H
C C C O
example N
C C C C H
five H H H O
reverse

91. 4
what have
....we learnt?
or gan ic ch emist ry is
easy if we can count to...

92. 4
what have
....we learnt?
oh, and it’s really
important!
or gan ic ch emist ry is
easy if we can count to...

93. Acknowledgments
gareth
(Dr. GJ Rowlands)
would to
like
thank
Trevor Kitson
Massey University
& the 101 students
www.massey.ac.nz/~gjrowlan