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This presentation is protected by international copyright laws. The material here contained cannot be copied in any form unless
expressively authorized in writing by its copyright owner and is intended for educational purposes only. License is extended only to
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© Miguel E. Alonso-Amelot 2011
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WHAT DO YOU WANT TO DO?
CLICK ON BUTTON OF YOUR CLICK ON BUTTON OF YOUR CHOICECHOICE
GO TO LECTUREGO TO INSTRUCTIONS
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HO
HOH
ONH
O NH
O
O
N
O
O
MeO
MeO
OH
HHO
OH
HO
OH
O
H2N
OH
O
O
O
OH
OH
HO OH
OH
HO
OHOH
OH
O
OHOH
OH
OH
O
OH
HO
OH
OHHO
OHOH
O
OHOH
HO
OO
OH
OH
OHHO
OHO
OH
OHHOHO
OH
OH
OH
H2N
O
OH
OH
O 1
THE ART OF DRAWING ORGANIC COMPOUNDS
SELF-ORG.CHEMSELF-ORG.CHEM
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IN THIS LECTURE:
Aliphatics: Explicit Hydrogens vs abbreviated line rendering:
Drawing aliphatic compounds and branching
Drawing aromatics, planar structures
Drawing alicyclics and the problem of non-planarity on paper
A sophisticated example: the cocaine molecule
Molecules and drawing types: from empirical to three dimensional
2
24+ slides, approx time: 60-90 min
CLICK HERE
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C7H12N2O
SEVERAL TYPES OF MOLECULAR RENDERINGS FOR EVERY COMPOUND
SEVERAL TYPES OF MOLECULAR RENDERINGS FOR EVERY COMPOUND
Empirical formula Atomic composition
Atom connexions
Spatial distribution
Partial Charge distribution
…and others…
NH
NH
OH
N
N
H
HHO
H
H
SELF-ORG.CHEMSELF-ORG.CHEM
Ball & stick
33
Molecular orbitals
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CARBON SKELETONS: THE MOLECULAR CHASSIS
CARBON SKELETONS: THE MOLECULAR CHASSIS
Open-chain (aliphatic)
Aromatic rings
Cyclic compounds
Saturated carbon Rings (alicyclic)
C C C C…..
4
O=C—C—N--
Drawing molecules = placing atoms and bonds correctly
CA
RB
ON
BA
CK
BO
NE
S
CH3CH2CH(CH3)CH2CH2CH3
4SELF-ORG.CHEMSELF-ORG.CHEM
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(CH3)2CHCH2OH
Building our first moleculeBuilding our first molecule
Iso-butanol
C4H10O Empirical formula: atomic composition
Condensed formula 1: minimum connectivity
Expanded formula 2: better look at connectivity
Line structures or abbreviated line rendering, most useful and used universally
CH3
CH2CH
CH, CH2, 2xCH3, OH
OH
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Group composition
CH3 CH CH2
CH3
OH
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3-D RENDERINGS
OH
Stick or wire model
Ball & stick model
Space-filling model showing Van der Waals
volumes= H
= C= O
= N
= Cl
= S
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Iso-butanol
Color codes of elements
Color codes of elements
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OH
3-D SPECIAL CASES
Electronic “envelope”
Electronic “envelope”
AtomsAtomsPartial
electronic charges
Partial electronic charges
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THE ABBREVIATED LINE RENDERING:
A cleaner look
Empirical formula C24H48O3…
Classical condensed CH3CH2CH(CH3)CH(C2H5)C(CH3) C…. gosh!
LINE ABBREVIATED LINE STRUCTURE:
Branched aliphatics
HO
O
OH
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THE MOLECULAR LINE RENDERING
CH3CH2CH2CH2CH3 =
C
CC
Cterminal methyls
5x2 + 2 = 12 H (saturated C)
Line structure:
Drawing aliphatic carbon backbones
Condensed structure
C
H
HH
H
109º
Saturated carbon
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n-PENTANE: C5H12n-PENTANE: C5H12
Methylenes
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Drawing an aliphatic alcohol
n-hexan-1-ol: C6H14On-hexan-1-ol: C6H14O
6 5 4 3 2 11
2
3
4
5
6
CH3CH2CH2CH2CH2CH2OH OH
Carbon numbering
Alcohol unit or carbinol
QUICK QUIZ
Draw in line abbreviated formDraw in line abbreviated form
You have 30 sec
5
10
15
20
25
30
FLUNKED!
Click mouse to start clock
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DRAWING LINE STRUCTURES OF MORE COMPLEX ALIPHATICS DRAWING LINE STRUCTURES OF MORE COMPLEX ALIPHATICS AND OTHER COMPOUNDSAND OTHER COMPOUNDS
1
2
3
4
Identify the molecular backbone forming the longest chain (magenta units above)
Count carbons and determine length of main chainAssign numbers to main chain carbons from right to left
Substituents branching off appear in parenthesis (yellow atoms above)
Draw the line connections (bonds) based on the purple C and ignore all atoms except heteroatoms
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CH3CH2CH(CH3)CH(OCH3)CH2C(CH3)2CH2CH3CH3CH2CH(CH3)CH(OCH3)CH2C(CH3)2CH2CH3
STEPS
4 12367 58
C12H24O 11
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branches
Putting the four steps to work
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CH3CH2CH(CH3)CH(OCH3)CH2C(CH3)2CH2CH3
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1
2
3
4
RECOGNIZE BACKBONE
COUNT & DRAW
ADD SUBSTITUENTS
DONE!
4
1
23
67 5
8
CH3O
backbone
CH3CH2CH(CH3)CH(OCH3)CH2C(CH3)2CH2CH3
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Line structures in non linear shapes
CH3O
CH3O
OCH3
CH3O
OCH3
All depict the SAME compound
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Other ring-template renderings
TEMPLATE
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Templates for drawing natural products
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OH
GERANIOL
Beta FARNESENE
OH
NEROLIDOL
OH
OH
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Building more complex aliphaticsBuilding more complex aliphatics
NH
NH2
CH3
OH
COOH
S
CH3CH2CH2C(CH3)(NH2)CH2CH2CH(C2H5)CH(NHCH3)CH3
Example 1
Example 2
CH3CH2CH2C(CH3)(NH2)CH2CH2CH(C2H5)CH(NHCH3)CH3
(CH3)3CCH2CH(OH)CH(COOH)SCH2CH(CH3)2(CH3)3CCH2CH(OH)CH(COOH)SCH2CH(CH3)2
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DRAWING MULTIPLE BONDS IN ALIPHATICS
Four kinds of multiple bonds in aliphatics:
1
2
3
4
ALKENES
ALKYNES
NITRILES
C=C
CH3CH2CCCH2CH3C≡C
C≡NC N
C=O CH3CH2CH2C(O)CH3
O
KETONES
aldehydes carboxylates esters
H
O OH
OO
O
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TRANSCIS
CH3CH2CH2C N
C=O (end)
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DRAWING FUNCTIONALIZED ALIPHATIC ALKENES/ALKYNES
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4 12367 58
O
CN O
OCH312
3
4
56
78
(CH3)2CHC(O)CHCHCH(CN)CH2C(O)OCH3(CH3)2CHC(O)CHCHCH(CN)CH2C(O)OCH3
O COOCH3
CNALSO DRAWN AS:
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HCCH
CH
CHCH
HC
DRAWING AROMATICS
Classic drawingof benzene
Modern renderingof benzene
Fused aromatic rings
Substituentson rings
More complexpolycyclics
Hetero-aromatics
Nicotine
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COOH
OH
O
O
N
N
N
N
N
H
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BicyclicsBicyclics
O SH
Functionalizedpolyclics
Functionalizedpolyclics
DRAWING ALICYCLICSSELF-ORG.CHEMSELF-ORG.CHEM
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3-membered: cyclopropanes3-membered: cyclopropanes
4-membered: cyclobutanes4-membered: cyclobutanes
5-membered: cyclopentanes5-membered: cyclopentanes
6-membered: cyclohexanes6-membered: cyclohexanes
7-membered: cycloheptanes7-membered: cycloheptanes
8-membered: cyclooctanes8-membered: cyclooctanes
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COMBINING ALIPHATIC, AROMATIC & ALICYCLIC CARBON BACKBONES
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O
CH3O
HN
O
O
S
HO
Draw backboneDraw backbone
Add functional groupsAdd functional groups
Cholesterol in your arteries & tissuesCholesterol in your arteries & tissues
1
2
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FLAT AND 3-D MOLECULES: THE MOLECULAR PLANE
H
H
H H
H
H
BENZENEBENZENEMolecular plane
Also planar:
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PLANAR (2-D) MOLECULES: AROMATICS
TILTING BENZENE…
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is….
Molecular planeMolecular plane
ABOVE (the beta side)
ABOVE (the beta side)
BELOW (the alpha side)
BELOW (the alpha side)
CYCLOHEXANE IN 3D
CONFORMATIONAL ANALYSIS
22NON-PLANAR ALICYCLICS: A BRIEF VIEWSELF-ORG.CHEMSELF-ORG.CHEM
1,3-DIMETHYL CYCLOHEXANE
TILTING CYCLOHEXANE…
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Good rendering but…
These groups need to be defined whether up or down the molecular plane
For example…
If not defined, usewiggled or straight lines
NON-PLANAR ALICYCLICS: A BRIEF VIEWSELF-ORG.CHEMSELF-ORG.CHEM
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FUSED CYCLES IN 3D
up
updown
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3.28 Å
2.49 Å
107º
A protein ribbon model
A protein-DNA complex model
Protein Images created by the Structural BioInformatics Group Imperial College, London
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24COMPUTER SOFTWARE
HO
HO
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END OF THIS LESSON
PLEASE MAKE YOUR SELECTION:
Back to menu
QUIT
Do you want to go over an advanced exercise in molecular rendering: the structure of cocaine?, click here Go
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COCAINE
CONTEMPORARY MOLECULAR RENDERINGS
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ANEX 1
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Public domain pictures
Dry coca leaves
Erythroxiline
C17H21NO4
H2C
H2C
CH
CHCH
CH
CH2
CH3N
COOCH3
Benzoate
Erythroxilon coca
COCAINE condensed structure
Richard Willstätter 1872-1942
A-2SELF-ORG.CHEMSELF-ORG.CHEM
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Renderings of the Cocaine molecule
Empirical formula
COOCH3
OBzCH3N
Line Abbreviated 3-D structure
C17H21NO4
N O
OCH3
O
O
CH3
Sir Derek Barton 1918-1998
Line-abbreviated bicyclic structure
carboxymethyl
benzoate
methylamino
A-3SELF-ORG.CHEMSELF-ORG.CHEM
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N O
OCH3
O
O
CH3
Practice + practice +…
more practice…
3-D view… a bit confusing
N O
OCH3
O
O
CH3
Splitting model in sections
MORE ABOUT THE 3-D STRUCTURESELF-ORG.CHEMSELF-ORG.CHEMA-4
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Source: http://www.merl.com/people/perry/NPR_ADF_TR.pdf Ronald Perry and Sarah Frisken. Mitsubishi Electric Research
Laboratories,
photo-realistic molecular renderings
COOCH3
OBzCH3N
ULTRAMODERN COMPUTATIONAL RENDERING OF COCAINE
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If this example seemed too difficult
for you do not worry now. I just
wanted to push you to your limits
through a demanding ride. In time
and lots of practice, this will appear
quite easy to you
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When all the visuals are shown on screen a hexagon on the upper right corner will appear around the slide Number.
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Nº
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