This presentation is protected by international copyright laws. The material here contained cannot be copied in any form unless expressively authorized

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

the individual purchaser. All rights reserved

© Miguel E. Alonso-Amelot 2011

SELF-ORG.CHEMSELF-ORG.CHEM

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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


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


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


Ball & stick

33

Molecular orbitals

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

(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


Group composition

CH3 CH CH2

CH3

OH

5

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


6

Iso-butanol

Color codes of elements

Color codes of elements

OH

3-D SPECIAL CASES

Electronic “envelope”

Electronic “envelope”

AtomsAtomsPartial

electronic charges

Partial electronic charges


7

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


8

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


9

n-PENTANE: C5H12n-PENTANE: C5H12

Methylenes

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


10

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


CH3CH2CH(CH3)CH(OCH3)CH2C(CH3)2CH2CH3CH3CH2CH(CH3)CH(OCH3)CH2C(CH3)2CH2CH3

STEPS

4 12367 58

C12H24O 11

branches

Putting the four steps to work


12

CH3CH2CH(CH3)CH(OCH3)CH2C(CH3)2CH2CH3

4 12367 58

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

Line structures in non linear shapes

CH3O

CH3O

OCH3

CH3O

OCH3

All depict the SAME compound


13

Other ring-template renderings

TEMPLATE

Templates for drawing natural products


14

OH

GERANIOL

Beta FARNESENE

OH

NEROLIDOL

OH

OH

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


15

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

16

TRANSCIS

CH3CH2CH2C N

C=O (end)


DRAWING FUNCTIONALIZED ALIPHATIC ALKENES/ALKYNES


17

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:

HCCH

CH

CHCH

HC

DRAWING AROMATICS

Classic drawingof benzene

Modern renderingof benzene

Fused aromatic rings

Substituentson rings

More complexpolycyclics

Hetero-aromatics

Nicotine


18

COOH

OH

O

O

N

N

N

N

N

H

BicyclicsBicyclics

O SH

Functionalizedpolyclics

Functionalizedpolyclics

DRAWING ALICYCLICSSELF-ORG.CHEMSELF-ORG.CHEM

19

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

COMBINING ALIPHATIC, AROMATIC & ALICYCLIC CARBON BACKBONES


20

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

FLAT AND 3-D MOLECULES: THE MOLECULAR PLANE

H

H

H H

H

H

BENZENEBENZENEMolecular plane

Also planar:


21

PLANAR (2-D) MOLECULES: AROMATICS

TILTING BENZENE…

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…

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

23

FUSED CYCLES IN 3D

up

updown

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


24COMPUTER SOFTWARE

HO

HO

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


COCAINE

CONTEMPORARY MOLECULAR RENDERINGS


ANEX 1

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

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

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

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

SELF-ORG.CHEMSELF-ORG.CHEMA-5

http://www.merl.com/people/perry/NPR_ADF_TR.pdf

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

END OF MODULE QUITBACK TO

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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