2. 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.CHEM

3. WHAT DO YOU WANT TO DO? CLICK ON BUTTON OF YOUR CHOICE GO TO LECTUREGO TO INSTRUCTIONS SELF-ORG.CHEM

4. 1 THE ART OF DRAWING ORGANIC COMPOUNDS SELF-ORG.CHEM

5. 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 SELF-ORG.CHEM

6. C 7 H 12 N 2 O SEVERAL TYPES OF MOLECULAR RENDERINGS FOR EVERY COMPOUND Empirical formula Atomic composition Atom connexions Spatial distribution Partial Charge distribution …and others… SELF-ORG.CHEM Ball & stick 3 3 Molecular orbitals

7. CARBON SKELETONS: THE MOLECULAR CHASSIS Open-chain (aliphatic) Aromatic rings Cyclic compounds Saturated carbon Rings (alicyclic) CCCC ….. 4 O=C—C—N-- Drawing molecules = placing atoms and bonds correctly C A R B O N B A C K B O N E S 4 SELF-ORG.CHEM

8. Building our first molecule Iso-butanol C 4 H 10 O 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 CH 3 CH 2 CH CH, CH 2, 2xCH 3, OH OH SELF-ORG.CHEM Group composition 5

9. 3-D RENDERINGS Stick or wire model Ball & stick model Space-filling model showing Van der Waals volumes = H =C=C = O = N = Cl = S SELF-ORG.CHEM 6 Iso-butanol Color codes of elements Color codes of elements

10. 3-D SPECIAL CASES Electronic “envelope” Atoms Partial electronic charges SELF-ORG.CHEM 7

11. THE ABBREVIATED LINE RENDERING: A cleaner look Empirical formula C 24 H 48 O 3 … Classical condensed CH 3 CH 2 CH(CH 3 )CH(C 2 H 5 )C(CH 3 ) C …. gosh! LINE ABBREVIATED LINE STRUCTURE : Branched aliphatics HO O OH SELF-ORG.CHEM 8

12. THE MOLECULAR LINE RENDERING CH 3 CH 2 CH 2 CH 2 CH 3 = C C C C terminal methyls 5x2 + 2 = 12 H (saturated C) Line structure: Drawing aliphatic carbon backbones Condensed structure C H H H H 109º Saturated carbon SELF-ORG.CHEM 9 n-PENTANE: C 5 H 12 Methylenes

13. Drawing an aliphatic alcohol n-hexan-1-ol: C 6 H 14 O 6 5 4 3 2 1 1 2 3 4 5 6 Carbon numbering Alcohol unit or carbinol QUICK QUIZ Draw in line abbreviated form You have 30 sec 5 10 15 20 25 30 FLUNKED! Click mouse to start clock SELF-ORG.CHEM 10

14. DRAWING LINE STRUCTURES OF MORE COMPLEX ALIPHATICS AND OTHER COMPOUNDS 1234 Identify the molecular backbone forming the longest chain (magenta units above) Count carbons and determine length of main chain Assign 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 SELF-ORG.CHEM STEPS 41236758 C 12 H 24 O 11

15. branches Putting the four steps to work SELF-ORG.CHEM 12 41236758 1 2 3 4 RECOGNIZE BACKBONE COUNT & DRAW ADD SUBSTITUENTS DONE! 4 1 2 3 6 7 5 8 CH 3 O backbone

16. Line structures in non linear shapes CH 3 O All depict the SAME compound SELF-ORG.CHEM 13 Other ring-template renderings TEMPLATE

17. Templates for drawing natural products SELF-ORG.CHEM 14 GERANIOL Beta FARNESENE NEROLIDOL

18. Building more complex aliphatics N H NH 2 CH 3 OH COOH S Example 1 Example 2 SELF-ORG.CHEM 15

19. DRAWING MULTIPLE BONDS IN ALIPHATICS Four kinds of multiple bonds in aliphatics: 1234 ALKENES ALKYNES NITRILES C=C C≡C C≡N C=O KETONES aldehydescarboxylates esters 16 C=O (end) SELF-ORG.CHEM

20. DRAWING FUNCTIONALIZED ALIPHATIC ALKENES/ALKYNES SELF-ORG.CHEM 17 41236758 O CN O OCH 3 1 2 3 4 5 6 7 8 OCOOCH 3 CN ALSO DRAWN AS:

21. DRAWING AROMATICS Classic drawing of benzene Modern rendering of benzene Fused aromatic rings Substituents on rings More complex polycyclics Hetero- aromatics Nicotine SELF-ORG.CHEM 18

22. Bicyclics Functionalized polyclics Functionalized polyclics DRAWING ALICYCLICS SELF-ORG.CHEM 19 3-membered: cyclopropanes 4-membered: cyclobutanes 5-membered: cyclopentanes 6-membered: cyclohexanes 7-membered: cycloheptanes 8-membered: cyclooctanes

23. COMBINING ALIPHATIC, AROMATIC & ALICYCLIC CARBON BACKBONES SELF-ORG.CHEM 20 Draw backbone Add functional groups Cholesterol in your arteries & tissues 12

24. FLAT AND 3-D MOLECULES: THE MOLECULAR PLANE BENZENE Molecular plane Also planar: SELF-ORG.CHEM 21 PLANAR (2-D) MOLECULES: AROMATICS TILTING BENZENE…

25. is… Molecular plane Molecular plane ABOVE (the beta side) BELOW (the alpha side) CYCLOHEXANE IN 3D CONFORMATIONAL ANALYSIS 22 NON-PLANAR ALICYCLICS: A BRIEF VIEW SELF-ORG.CHEM 1,3-DIMETHYL CYCLOHEXANE TILTING CYCLOHEXANE…

26. Good rendering but… These groups need to be defined whether up or down the molecular plane For example… If not defined, use wiggled or straight lines NON-PLANAR ALICYCLICS: A BRIEF VIEW SELF-ORG.CHEM 23 FUSED CYCLES IN 3D up down

27. 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 SELF-ORG.CHEM 24 COMPUTER SOFTWARE

28. 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 SELF-ORG.CHEM

29. COCAINE CONTEMPORARY MOLECULAR RENDERINGS SELF-ORG.CHEM ANEX 1

30. Public domain pictures Dry coca leaves Erythroxiline C 17 H 21 NO 4 H2CH2C H2CH2C CH CH 2 CH 3 N COOCH 3 Benzoate Erythroxilon coca COCAINE condensed structure Richard Willstätter 1872-1942 A-2 SELF-ORG.CHEM

31. Renderings of the Cocaine molecule Empirical formula Line Abbreviated 3-D structure C 17 H 21 NO 4 Sir Derek Barton 1918-1998 Line-abbreviated bicyclic structure carboxymethyl benzoate methylamino A-3 SELF-ORG.CHEM

32. Practice + practice +… more practice… 3-D view… a bit confusing Splitting model in sections MORE ABOUT THE 3-D STRUCTURE SELF-ORG.CHEM A-4

33. Source: http://www.merl.com/people/perry/NPR_ADF_TR.pdf Ronald Perry and Sarah Frisken. Mitsubishi Electric Research Laboratories,http://www.merl.com/people/perry/NPR_ADF_TR.pdf photo-realistic molecular renderings ULTRAMODERN COMPUTATIONAL RENDERING OF COCAINE SELF-ORG.CHEM A-5

34. 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 QUIT BACK TO MENU SELF-ORG.CHEM

35. INSTRUCTIONS FOR THIS PRESENTATION These slides are highly dynamic with sophisticated effects especifically designed for effective teaching-learning. You control movements and other effects either by waiting them to show or by clicking with keypad keys or mouse buttons, as usual. The Script contains the exact accompanying comments for the speaker for each slide and its effects. NEXT © SELF-ORG.CHEM

36. HOW TO HANDLE THIS LECTURE So please review this presentation before class along with the script and become familiar with effects for maximum performance When all the visuals are shown on screen a hexagon on the upper right corner will appear around the slide Number. This will tell you that the next click of the mouse will drive you to the next slide (or use the buttons at the bottom right) Nº NEXT

37. HOW TO HANDLE THIS PRESENTATION Go to subject index of module Go to slide Nº 1 of current subject Go back to preceding slide Move on to next slide Go to the last slide of current chapter Quit current lecture At the bottom-right there is a set of action buttons to jump to distant slides, restart or quit: GO TO LECTURE SELF-ORG.CHEM