Chemdraw help

1. Medicinal chemistry
practical revision
chemdraw

2. "‫الرحمي‬ ‫الرمحن‬ ‫هللا‬ ‫سم‬‫ب‬"
‫تعني‬‫س‬‫ن‬ ‫به‬ ‫و‬......
‫تولك‬‫ن‬ ‫يه‬‫عل‬ ‫و‬..

3. Very important ……..
These are just tips and tricks for the exam
( as a revision )
……
You should study all what your
teaching assistant
demonstrated in your section….
I hope it helps 
......Menna abdelshaheed

4. Before starting
Must check on
View > show ….
• General toolbar
• Main toolbar
• Style toolbar
• Chemical warnings

5. File , save as
Get your different documents from
window in General toolbar
Save each step you do !

6. Select !!!
And select which ?
Before doing any function you should first select the structure , or
atom , or bond or
Whatever …. How would the software knows which of them to
work on ??!

7. To add an atom or bond , you must see the blue circle
otherwise the added may be drawn separate from structure …..!
To add a ring , if both rings share a bond
Very important !!!

8. Or to add a bond

9. TO ADD TEXT, JUST GO WITH MOUTH TO THE ATOM, CLICK ENTER THE TEXT
BOX APPEARS IMMEDIATELY

10. X
Fatal mistake !!!!
NH2 is actually separated from the structure

11. CL , wrong , This is not chlorine
Cl , right
…….Common mistake !

12. Clean up structure , to modify appearance of structure
Select structure , go to structure in toolbar , clean up structure
After clean up
After clean upRings are of different size !
Clean them up simply ….

13. Select structure
( blue box ), right click , add frame, as simple as that 
Choose the same type of frame in paper !!

14. When selected , color it immediately if needed

15. Copy structure and paste it
By continuous pressing of key ( CONTROL ) with continuous
pressing on left click ( mouse ), move it until new structure goes to
the right place

16. Draw equation :
Draw structures and arrow
Then align them immediately by selecting all of them , right click ,
Align , T/B centers
and after alignment !!! ( why after ? To avoid overlap )
you can now number structures , put each number in brackets if needed
and you can write gases , enzymes , whatever , on the arrow if present
you can highlight certain functional groups
….etc.,.

17. Before alignment !! Messy !!

18. Selected altogether by marquee

19. When selected , now right click on any structure ,
Align , T/B centers

20. Now , it looks great after alignment

21. Number the structures and add any required features

22. If he asked to highlight a hydrophilic functional group, now you can
do it

23. Structure
• Convert structure to name
Convert name to structure
…… Take care :
• There are No spaces
• Exactly the same as written in
paper
• Paste name below structure
• Right click on name , auto
update

24. Align equation
Draw equation > select all > right click > align > T/B centers
Then write names
Select all > right click > add frame > choose the type

25. Rotate structure
Select structure , right click , rotate , 2 things to choose :
• Angle
• Clockwise (CW) or Counterclockwise (CCW)

26. Must activate A first to add symbol , view , show
character map

27. Formula (written as CH2) from style toolbar
X 

28. Select structure , view ,
show chemical
Properties , select only
needed , paste

29. Shapes !!!
Scale and adjust , send to back (when
alone ) before going to the functional
group
to avoid conflict when selecting it
then move it there , you will find it back
to functional group

30. Size / scale

31. Highlight hydrophilic groups
X

Why highlighting a bond and part of
benzene !!!?
This is wrong

32. Green ,, round ,, rectangle ,, shaded around the
hydrophilic functional group

33. Move the arrow on them to
know name of each type
Charges , lone pair , H dot ,
radical , etc…

34. Object , show stereochemistry
( assign stereochemistry ),
Find e.g. (R) or (S) for example appears on structure

35. after stereochemistry , you may need to
clean up the structure
until no red warnings !
…

36. ENTER, TO ADD TEXT , E.G. ENTER, THEN TYPE NH2
ADJUST BONDS BY GOING TO SELECT ( MARQUEE )
THEN DESELECT THEN GO TO BOND OR ATOM AND ADJUST

37. Ascending order when they are arranged from
the smallest to the largest number
Descending ??

38. Atom number
Select structure , right click , atom , show atom number

39. Mass percent = Elemental analysis
View , analysis window
each atom is followed by its percentage in compound
e.g.

40. Magnify , General toolbar

41. 1H-NMR , 13C-NMR
Select structure , from structure ,
Predict H-NMR
Predict C-NMR
Will appear in a new window, save it

42. logP , Partition Coefficient
As LogP value increases, lipophilicity increases ,
hydrophilicity decreases
N.B.
lipophilicity = hydrophobicity ( passes membranes
easily, e.g. May pass BBB ( blood brain barrier )
Hydrophilicity = lipophobicity ( water soluble )

43. Hydrophilic and hydrophobic groups
Reference : Prof.Dr. Mohamed Abdelghafar
Chemical basis

44. Exact mass , from view , analysis window
Molecular weight , from view , analysis window

45. To compare between structures according to logP , Pka , boiling point
, elemental analysis ( mass percent ) ,….etc.
You can get the window from view ( show chemical properties,
analysis ,etc……. )
Then just select each structure, you will notice that values change for
each structure , paste the needed value for each one

46. Importance of chemical warnings
Totally wrong structure , atoms are not in right
place
Separate from structure
The right structure

47. File, Page setup, size of page , e.g. A3

48. CONTROL , MOUSE (LEFT) DRAG AND CLICK TO COPY PASTE
CONNECT FROM OUTSIDE TO INSIDE
ATTACHMENT POINT MUST BE FROM AN ATOM ALREADY
MAKE WAVY THEN ATTACH IT TO A BOND THEN TYPE
SELECT ALL AND MOVE OR DECREASE SCALE , DON’T HAVE TO MAKE
GROUP AT ALL !

49. Thank you