1. S N 1 REACTIONS Dhruv Joshi IIT Bombay This animation shall help the user understand the mechanism of S N 1 (substitution Nucleophilic unimolecuar) reactions from a 3-dimensional perspective

2. Master Layout 5 3 2 4 1 THE USER CHOOSES ONE FROM THESE FOUR OPTIONS WHICH TAKES HIM TO FOUR DIFFERENT ANIMATION SCENARIOS THIS IS THE WORSPACE

3. Definitions of the components: 5 3 2 4 1 1.substrate: this is a molecule which is being attacked by the “nucleophile”, which usually has a leaving group attached to it 2.nucleophile: this is usually a negatively charged compound 3.Leaving group: this is a compound that can exist by itself in solution, and can easily get substituted by another molecule, the nucleophile

4. Analogy / Scenario / Action 1 5 3 2 4 The stepwise process has been described below: 1. The leaving group leaves from the molecule, leaving behind a positive charge on the carbon atom it was attached to

5. Stepwise description of process The goal of the IDD is to provide instructions to an animator who is not a expert. You have to describe what steps the animator should take to make your concept come alive as a moving visualization. Use one slide per step. This will ensure clarity of the explanation. Add a image of the step in the box, and the details in the table below the box. You can use any images for reference, but mention about it's copyright status The animator will have to re-draw / re-create the drawings Add more slides as per the requirement of the animation 1 5 3 2 4

6. Option 1: Methyl Chloride STEP 1 1 5 3 2 4 ActionDescriptionAudio Narration Workspace animationIn the workspace (black background) the figure shown to the left appears. The object to the left consists of 3 white spheres attached to a blue sphere via three rods, and a fourth Purple sphere attached to the blue sphere via another rod. 3D rotation possibleThe entire setup can be rotated by the user in 3 dimensions, for better viewing of the entire process.

7. VARIOUS VIEWS OF THIS MOLECULE IN 3 DIMENSIONS BACK VIEW ( THE BROWN SPHERE IS HIDDEN FROM VIEW)‏ SIDE VIEW (ALL ANGLES ARE 109° IN 3-DIMENSIONS)‏

8. VARIOUS VIEWS OF THIS MOLECULE IN 3 DIMENSIONS FRONT VIEW ( THE BLUE SPHERE IS HIDDEN FROM VIEW)‏ ANOTHER SIDE VIEW, (IT HAS BEEN ROTATED ABOUT THE AXIS JOINING THE BLUE SPHERE AND THE BROWN SPHERE) (ALL ANGLES ARE 109° IN 3- DIMENSIONS)‏

9. Option 1: Methyl Chloride STEP 2 1 5 3 2 4 ActionDescriptionAudio Narration Brown sphere breakawayThe brown sphere breaks away from the main structure, by moving towards the left slowly. While the sphere is moving, the rod connecting it to the blue sphere also gets longer and thinner, and finally disappears. (it goes from the shape given in step 1 to the shape given in this slide)‏ The leaving group leaves the molecule, leaving a carbocation behind. 3D rotation by user choice The entire setup can be rotated by the user in 3 dimensions, for better viewing of the entire process. Change in orientation of main structure The angles between the white spheres and blue sphere slowly go from 109° to 120°, while the brown sphere is leaving. The structure so left is an sp 2 carbocation.

10. Option 1: Methyl Chloride STEP 3 1 5 3 2 4 ActionDescriptionAudio Narration narrationHowever, since primary carbocations are not so stable, this structure cannot exist very well in solution. So the likelihood of formation of this structure is very less. 3D rotation possibleThe entire setup can be rotated by the user in 3 dimensions, for better viewing of the entire process. Brown sphere,movementThe brown sphere moves back to its original position, and along with it the rod also appears and the angles between all the rods become 109° Hence Methyl Chloride, or in general, methyl substrates, will not tend to undergo S N 1 reactions.

11. Option 2: Ethyl Chloride STEP 1 1 5 3 2 4 ActionDescriptionAudio Narration Workspace animationIn the workspace (black background) the figure shown to the left appears. The object to the left consists of spheres of different colours and rods attaching them to each other. All angles are 109° 3D rotation possibleThe entire setup can be rotated by the user in 3 dimensions, for better viewing of the entire process.

12. VARIOUS VIEWS OF THIS MOLECULE IN 3 DIMENSIONS BACK VIEW ( THE BROWN SPHERE AND ONE BROWN ONE ARE HIDDEN FROM VIEW)‏ SIDE VIEW (ALL ANGLES ARE 109° IN 3-DIMENSIONS)‏

13. VARIOUS VIEWS OF THIS MOLECULE IN 3 DIMENSIONS FRONT VIEW ( THE BLUE SPHERE IS HIDDEN FROM VIEW BEHIND THE BROWN SPHERE AND THE BLUE SPHERE AT THE BOTTOM IS HIDING ONE WHITE SPHERE)‏ ANOTHER SIDE VIEW

14. Option 2: Ethyl Chloride STEP 2 1 5 3 2 4 ActionDescriptionAudio Narration Brown sphere breakawayThe brown sphere moves to the left, the rod joining it becomes longer and thinner, and finally disappears out the left side of the animation stage. It goes from the state given in slide 1 to the one given in FIG2, and finally to the state given in FIG3 The leaving group leaves the molecule, leaving a carbocation behind. 3D rotation possibleThe entire setup can be rotated by the user in 3 dimensions, for better viewing of the entire process. Change in orientation of main structure Please see the next slide for more information about this. The structure so left is an sp 2 carbocation, which is primary, hence not very stable, but more stable than the methyl carbocation FIG2 FIG3

15. An explanation of the geometry of the structure 1 5 3 2 4 C1 C2 As the brown sphere leaves, the two white spheres attached to C1 change their angle with sphere C1, and becomes 120°. Similarly the angle between C2 and C1 becomes 120°. Below is the view given from the side: (The angles made by the white spheres with carbon C2 do NOT CHANGE)‏

16. Option 2: Ethyl Chloride STEP 3 1 5 3 2 4 ActionDescriptionAudio Narration Appearance of nucleophile The yellow sphere appears from the right, and moves in the direction shown by the white arrow towards C1. A nulceophile approaches the carbocation, in solution 3D rotation possibleThe entire setup can be rotated by the user in 3 dimensions, for better viewing of the entire process. FIG2 FIG3

17. Option 2: Ethyl Chloride STEP 4 1 5 3 2 4 ActionDescriptionAudio Narration Formation of productThe yellow sphere keeps moving towards C1 and the rod joining them appears, finally settling to the structure shown on the left. The angles also become 109° as they were before. The nucleophile forms a bond with the carbocation and the product gets made. Please note that the nucleophile could have approached from either side of the carbocation and so two products are possible. However, since these products are equivalent (since C-1 has two hydrogens attached and is achiral) so we observe only one product. 3D rotation possibleThe entire setup can be rotated by the user in 3 dimensions, for better viewing of the entire process. FIG2 FIG3

18. Option 3: isoPropyl Chloride STEP 1 1 5 3 2 4 ActionDescriptionAudio Narration Workspace animationIn the workspace (black background) the figure shown to the left appears. The object to the left consists of spheres of different colours and rods attaching them to each other. All angles are 109° 3D rotation possibleThe entire setup can be rotated by the user in 3 dimensions, for better viewing of the entire process.

19. VARIOUS VIEWS OF THIS MOLECULE IN 3 DIMENSIONS BACK VIEW ( THE BROWN SPHERE IS HIDDEN FROM VIEW, ALONGWITH TWO BLUE SPHERES WHICH ARE BEHIND THE TWO WHITE SPHERES WHICH ARE IN ATTACHED TO THE BLUE SPHERE IN THE CENTRE)‏ SIDE VIEW (ALL ANGLES ARE 109° IN 3-DIMENSIONS)‏ The spheres which are joined by arrows are the SAME SPHERE, IN A DIFFERENT VIEW

20. VARIOUS VIEWS OF THIS MOLECULE IN 3 DIMENSIONS FRONT VIEW ( THE BLUE SPHERE IN THE MIDDLE IS HIDDEN FROM VIEW ALONG WITH TWO WHITE SPHERES BEHIND THE BLUE SPHERES TO THE TOP AND BOTTOM LEFT)‏ ANOTHER SIDE VIEW,

21. Option 3: isopropyl Chloride STEP 2 1 5 3 2 4 ActionDescriptionAudio Narration Brown sphere breakawayThe brown sphere moves to the left, the rod joining it becomes longer and thinner, and finally disappears out the left side of the animation stage. It goes from the state given in slide 1 to the one given in FIG2, and finally to the state given in FIG3 The leaving group leaves the molecule, leaving a carbocation behind. 3D rotation possibleThe entire setup can be rotated by the user in 3 dimensions, for better viewing of the entire process. Change in orientation of main structure Please see the next slide for more information about this. The structure so left is an sp 2 carbocation, which is secondary, and so quite stable. It exists in a polar solution by itself and is susceptible to attack by a nucleophile. FIG2 FIG3

22. An explanation of the geometry of the structure 1 5 3 2 4 As the brown sphere leaves, the two blue spheres (C1 and C3) attached to C2 change their angle with C2 to 120°. Similarly the angle between the white sphere attached to C2 also becomes 120°. Below is the view given from the side: (The angles made by the white spheres which are attached to C1 AND C3 DO NOT CHANGE)‏ C1 C2 C3

23. Option 3: isopropyl Chloride STEP 3 1 5 3 2 4 ActionDescriptionAudio Narration Appearance of nucleophile Two yellow spheres appear from the left and right side and start moving towards the main structure in the direction shown by the arrows Since the intermediete structure is planar, the nucleophiles can approach from any direction to the carbocation 3D rotation possibleThe entire setup can be rotated by the user in 3 dimensions, for better viewing of the entire process. FIG2 FIG3

24. Option 3: isopropyl Chloride STEP 4 1 5 3 2 4 ActionDescriptionAudio Narration Formation of productThe yellow sphere from the left attacks the main structure and forms the product as shown. The angles all revert back to 109° as they were in the start. The nucleophile forms a bond with the carbocation and the product gets made. Please note that the nucleophile could have approached from either side of the carbocation and so two products could have been formed and both would be enantiomers. However, in this case that is not so, since the compound is achiral. 3D rotation possibleThe entire setup can be rotated by the user in 3 dimensions, for better viewing of the entire process. FIG2 FIG3

25. Option 4: tertiary-Butyl Chloride STEP 1 1 5 3 2 4 ActionDescriptionAudio Narration Workspace animationIn the workspace (black background) the figure shown to the left appears. The object to the left consists of spheres of different colours and rods attaching them to each other. All angles are 109° 3D rotation possibleThe entire setup can be rotated by the user in 3 dimensions, for better viewing of the entire process.

26. VARIOUS VIEWS OF THIS MOLECULE IN 3 DIMENSIONS BACK VIEW (SEVERAL SPHERES ARE HIDDEN FROM VIEW)‏ SIDE VIEW (ALL ANGLES ARE 109° IN 3-DIMENSIONS)‏ The spheres which are joined by arrows are the SAME SPHERE, IN A DIFFERENT VIEW

27. VARIOUS VIEWS OF THIS MOLECULE IN 3 DIMENSIONS FRONT VIEW ( THE BLUE SPHERE IN THE MIDDLE IS HIDDEN FROM VIEW ALONG WITH TWO WHITE SPHERES BEHIND THE BLUE SPHERES TO THE TOP AND BOTTOM LEFT)‏ ANOTHER SIDE VIEW,

28. Option 4: tertiary-butyl Chloride STEP 2 1 5 3 2 4 ActionDescriptionAudio Narration Brown sphere breakawayThe brown sphere moves to the left, the rod joining it becomes longer and thinner, and finally disappears out the left side of the animation stage. It goes from the state given in slide 1 to the one given in FIG2, and finally to the state given in FIG3 The leaving group leaves the molecule, leaving a carbocation behind. 3D rotation possibleThe entire setup can be rotated by the user in 3 dimensions, for better viewing of the entire process. Change in orientation of main structure Please see the next slide for more information about this. The structure so left is an sp 2 carbocation, which is tertiary, and so is extremely stable. It exists in a polar solution by itself and is susceptible to attack by a nucleophile. FIG2 FIG3

29. An explanation of the geometry of the structure - ANIMATOR 1 5 3 2 4 As the brown sphere leaves, the three blue spheres attached to C1 change their angle with sphere C1, and becomes 120°. Below is the view given from the side: (The angles made by the white spheres with C2,3,4 do NOT CHANGE. They are still 109°)‏ C2 C1 C3 C4

30. Option 4: tertiary Butyl Chloride STEP 3 1 5 3 2 4 FIG2 FIG3 ActionDescriptionAudio Narration Appearance of nucleophile Two yellow spheres appear from the left and right side and start moving towards the main structure in the direction shown by the arrows Since the intermediete structure is planar, the nucleophiles can approach from any direction to the carbocation 3D rotation possibleThe entire setup can be rotated by the user in 3 dimensions, for better viewing of the entire process.

31. Option 4: tertiary Butyl Chloride STEP 4 1 5 3 2 4 ActionDescriptionAudio Narration Formation of productThe yellow sphere from the right attacks the main structure and forms the product as shown. The angles all revert back to 109° as they were in the start. The nucleophile forms a bond with the carbocation and the product gets made. Please note that the nucleophile could have approached from either side of the carbocation and so two products could have been formed and both would be enantiomers. However, in this case that is not so, since the compound is achiral. 3D rotation possibleThe entire setup can be rotated by the user in 3 dimensions, for better viewing of the entire process. FIG2 FIG3

32. Links for further reading Reference websites: en.wikipedia.org/wiki/SN1_reaction Books: Research papers: