1. Molecular Representations
Organic Chemistry
Second Edition
David Klein
Chapter 2
Molecular Representations

2. Representing Molecules
There are many ways to represent molecules
Drawing Lewis structures are most time consuming

3. Representing Molecules
There are 3 constitutional isomers of propanol
Constitutional Isomers: compounds with same molecular formula but different connectivity between atoms. 

4. Representing Molecules

5. Representing Molecules
There are 3 constitutional isomers of propanol

6. Representing Molecules
Much time to draw Lewis structure of large molecules
Antibiotic Amoxicillin (below).
Lewis structure is cluttered, and time consuming to draw

7. Bond-line Structures
The Bond-line structure is easier to read and to draw

8. Bond-line Structures Looks odd because C atoms are not labeled
Clearer way for (bio)chemists to communicate

9. Bond-line Structures
Lines between atoms are covalent bonds (Like Lewis str)
Atoms and bonds are drawn along a zigzag that represent the geometry of the bond angles
Here, the C are sp3 hybridized: bond angle is 109.5

10. Bond-line Structures Lines between atoms are covalent bonds
Carbon atoms are not labeled.
Carbon (C) is imagined at each endpoint, vertex, and valley 2 4 6 1 3 5

11. Bond-line Structures The H of C-H bonds are NOT drawn
We know the number of H atoms on a C because we know the valence of C is 4
C1 is attached to 1 carbon; 3 H that are “hidden”
C2 is attached to 2 carbons; 2 H that are “hidden”
C3 is attached to 2 carbons; 2 H that are “hidden” 2 4 6 1 3 5

12. Bond-line Structures
Interpret the number and location of H atoms in a molecule
H atoms are not shown, but there are enough to complete the octet (4 bonds) to carbon

13. Bond-line Structures
How many number C- and H-atoms in each structure below

14. Bond-line Structures
Double bonds and triple bonds are drawn to show their sp2 and sp3 geometries, respectively
spx
spx
spx
spx

15. Bond-line Structures What is atom geometry of a sp2 center? sp center?
spx
spx
spx
spx

16. Bond-line Structures
Correct linear geometry

17. Bond-line Structures
Practice bond-line structures: This is how I will draw molecules from now on.
Number of C
Number of H

18. Bond-line Structures
Be able to convert Lewis structure or condensed structure to bond-line structure
Represent the bond angles with zigzags
Follow VSEPR and spread out the electron pairs on a central atom
Why is this “bad”?

19. Bond-line Structures Single bonds can rotate around axes
REPEAT: Single bonds can rotate

20. Bond-line Structures Single bonds can rotate around axes
REPEAT: Single bonds can rotate
Redraw the top structure after
a bond rotation

21. Bond-line Structures
Heteroatoms (atoms other than C and H) ARE LABELED with all hydrogen atoms.
Lone pairs e– are optional UNLESS instructed to show them
NEVER draw a carbon with more than 4 bonds!!

22. Bond-line Structures
Practice: Draw bond-line representations for the following Lewis structures

23. Bond-line Structures
Draw a bond-line structures for the molecule: CH2CH(CH2)4CH3
CH2CH(CH2)4CH3 Subscript 4 means 4 CH2 units in a row
CH2CH(CH2)4CH3 These Cs are connected
CH2CH(CH2)4CH3
This C is connected to 1 C and 2 H (that’s 3 bonds); What is the 4th bond?

24. Indentifying Functional Groups
Draw bond-line structures for the chemical reaction
This C is connected to 2 CH3 groups, 1 H, and another C.
If difficult to visualize, then draw Lewis structure

25. Indentifying Functional Groups
Draw bond-line structures for the chemical reaction
This C is connected to 2 CH3 groups and another C.
What is the 4th bond type?

26. Indentifying Functional Groups
Certain atoms bonded in specific arrangements, undergo specific chemical reactions
These atom arrangements are called functional groups
Functional groups are the reaction centers!

27. Indentifying Functional Groups
More functional groups are listed in table
alcOHol
KEYtone
something on
“Ether” side of O
KEYtone with ‘de Hydrogen’
Re: meTHIONine
“Thion” = sulfur
Thion+alcohol = thiol
“Carbon/oxy” + OH acid
Writing the mnemonic as an answer
on an exam results in NO credit

28. Indentifying Functional Groups

29. Bond-line Structures with Formal Charge
Identify formal charges (fc) in bond-line representations
fc’s hints where reactive centers are
Label all formal charges (lone pair e– are shown)

30. Bond-line Structures with Formal Charge
Neutral carbon atoms in a molecule have 4 covalent bonds
Sometimes carbon will have a +1 charge. How many bonds will carbon have?
Why are these CARBOCATIONS unstable?

31. Bond-line Structures with Formal Charge
Sometimes carbon will have a -1 charge.
What makes CARBANIONS unstable?
If carbon carries a charge in a molecule, the charge MUST be shown on the bond-line structure

32. Bond-line Structures and Lone Pair Electrons
Optionally lone pairs are omitted from bond-line strs.
lone pair e– can be determined,
if neutral OR
(+) or (-) form. chrg. is added

33. Bond-line Structures and Lone Pair Electrons
Optionally lone pairs are omitted from bond-line strs.
lone pair e– can be determined,
if neutral OR
(+) or (-) form. chrg. is added
If the formal charge is indicated, you can determine how many lone pairs e– are present

34. Bond-line Structures and Lone Pair Electrons
To calculate the number of lone pair e– for an atom
Note the formal charge
Compare the number of valence electrons that should be associated with the atom to the number of valence electrons that are actually associated with an atom (including 1 e– from each covalent bond)
Add appropriate number of e– to obtain the formal charge

35. Bond-line Structures and Lone Pair Electrons
However:
You can’t determine the formal charge on an atom unless you know how many e– there are on the atom
You must ALWAYS draw formal charges on a bond-line structure to eliminate confusion

36. Bond-line Structures and Lone Pair Electrons
How many lone pairs are on the oxygen atom below?

37. Bond-line Structures and Lone Pair Electrons
Neutral O should have 6 valence e– (group 6: periodic table)
It has a -1 charge (above), so it has one additional e– (6+1=7) assigned
1 e– is from O–C covalent bond
HOW many lone pairs does O have above?

38. 3D Bond-line Structures
We will use dashed and solid wedges to show groups that point back into the paper or out of the paper to represent a 3D molecule on a 2D piece of paper

39. Resonance Remember from General Chemistry, what is resonance?
Does the allyl carbocation have resonance contributors?

40. Resonance
Drawing lines between atoms inadequately represents covalent bonds in molecules with resonance
Determine hybridization of the carbons in the allyl carbocation
Calculate the steric number for each carbon
(# of σ bonds + # lone pairs)
When the steric number is 3, each C is sp2 hybridized

41. Resonance
If all of the carbons have unhybridized p orbitals, they can overlap
All three overlapping p orbitals allow the electrons to move throughout the overlapping area simultaneously
That’s RESONANCE!!

42. Resonance
The π e–exist on both sides of the molecule, so two resonance contributors represent the structure
Brackets indicate that both resonance contributors exist simultaneously

43. Resonance
Because neither of the contributors exists, the average (or hybrid) is much more appropriate
vs.
δ δ+
two contributors resonance hybrid
Analogy: a nectarine is a hybrid formed by mixing a peach and a plum. A nectarine is NOT sometimes a peach and sometimes a plum.
It is always a “hybrid” i.e., a nectarine.

44. Resonance Resonance makes a molecule MORE stable
Delocalization of electrons
Electrons can span a greater distance
electrons have more freedom to minimize repulsions
Electrons spend time close to multiple nuclei all at once maximizing attractions
Delocalization of charge
The charge is spread out over more than one atom. The resulting partial charges are more stable than a full +1 charge.
δ δ+
resonance hybrid

45. Curved Arrows in Resonance
We have used curved arrows to show electron movement
Curved arrows generally show electron movement for pairs of electrons
The arrow starts where the electrons are currently located
The arrow ends where the electrons will end up after the electron movement

46. Curved Arrows in Resonance
Rules for using curved arrows to show RESONANCE
bond electrons and lone pair e– can be mobile. Never break a single bond when drawing RESONANCE structures
Resonance occurs for electrons existing in overlapping p orbitals and adjacent lone pair e–
while electrons in single bonds (σ bonds) are NOT involved in RESONANCE.

47. Curved Arrows in Resonance
Rules for using curved arrows to show RESONANCE
Never exceed an octet for 2nd row elements (B, C, N, O, F)
I.e., never move electrons toward and sp3 atom
How about this arrow?

48. Curved Arrows in Resonance
Rules for using curved arrows to show RESONANCE
2nd row elements (B, C, N, O, F) will rarely but sometimes have LESS than an octet
i.e. if 2 atoms are sp2 and attached via a pi-bond, the electrons in π bond can move toward either atom and leave a formal charge behind
However, the π e- will typically favor the more electronegative atom
What will the resonance hybrid look like for this structure?

49. Formal Charge in Resonance
When using curved arrows to show RESONANCE, often structures will carry a formal charge that must be shown
Draw the resonance contributor indicated by the arrows below
Are any of the rules violated?
Show any formal charges on the contributors

50. Formal Charge in Resonance
In the resonance, the arrows tell us how to move the electrons to create the other contributor
NOTE: Lone pairs can be moved toward sp2 atom
Draw arrows showing the resonance in the reverse direction
You can also think of the arrows as showing the direction that charge will flow

51. Patterns in Resonance
There are 5 main bonding patterns in which resonance occurs. Recognize these patterns to predict when resonance will occur
Allylic lone pairs
Allylic positive charge
Lone pair of electrons adjacent to a positive charge (sp2 atom)
π bond between two atoms with different electronegativities
Conjugated π bonds in a ring
There are examples in the next few slides

52. Patterns in Resonance Vinyl atom: directly bonded to C=C double bond
Allyl atom: one atom away from a C=C double bond “atom–single bond=double bond” (ALLYLIC WORDS)
Label the vinylic chlorides and the allylic chlorides

53. Patterns in Resonance Identifying allylic lone pairs
Circle all of the allylic lone pairs
Draw arrows on each structure to show resonance

54. Patterns in Resonance Identifying allylic lone pairs
For each, show the resulting resonance contributor and all formal charges
Practice with conceptual check point 5

55. Patterns in Resonance Dealing with allylic positive charge
Only one curved arrow is needed
If there are multiple double bonds (conjugated), then multiple contributors are possible. Show the resonance contributors and curved arrows below
Draw a resonance hybrid
Practice with conceptual checkpoint 6

56. Patterns in Resonance A lone pair adjacent to a positive charge
Only one arrow is needed
Explain how the formal charges are affected by the electron movement in the following examples

57. Patterns in Resonance A lone pair adjacent to a positive charge
Consider the resonance in the NITRO group
ALLYLIC WORDS: “atom–single bond=double bond”
Draw all possible resonance contributors

58. Patterns in Resonance
A π bond between atoms of different electronegativity
The π electrons will be more attracted to the more electronegative atom
Why are formal charges are created by the electron movement?

59. Patterns in Resonance Conjugated pi bonds in a ring
Each atom in the ring MUST have an unhybridized p orbital that can overlap with its neighbors
Electrons can be shown to move clockwise or counterclockwise
What type of motion do the electrons actually have?
Practice with conceptual checkpoint 1

60. Patterns in Resonance
Summary figure

61. Patterns in Resonance
Show all of the resonance contributors for the following molecule
Notice that carbons with 4 bonds (sp3) isolate areas of resonance from one another

62. 1 Stability of Contributors
How do we assess the stability of resonance contributors?
Formal charge generally DECREASES stability, especially a +1 charge on an electronegative atom or -1 on a low electronegativity atom
COMPLETE OCTETS INCREASE stability
Draw the three resonance contributors for acetic acid
Assess the stability of each contributor, and draw a resonance hybrid

63. 1 Stability of Contributors
Draw a reasonable resonance contributor for the following molecule

64. 1 Stability of Contributors
The octet rule is usually a bigger factor than formal charge when assessing stability
For each structure, assess the stability of each contributor, and draw a resonance hybrid

65. 2 Delocalized vs. Localized
Generally, lone pairs adjacent to a C=C double bond are capable of resonance, but not in this case.
The electron movement above does not violate any of our rules, so why can’t the Nitrogen’s lone pairs be delocalized? - see next slide

66. 2 Delocalized vs. Localized
Recall that delocalized electrons must exist in an unhybridized p orbital overlapping with p orbitals on neighboring atoms
The Nitrogen’s lone pair is positioned perpendicular to the plane where the other pi electrons reside
Practice with SkillBuilder

67. Additional Practice Problems
How many carbon and hydrogen atoms are in the following molecule?

68. Additional Practice Problems
Draw the bond-line structures from the following formulas:
C(CH3)3CN
Cl2CH(CH2)5CO2H
CH3CHBrCH(NH2)C(CH3)3

69. Additional Practice Problems
Fill in any necessary formal charge on the molecule below

70. Additional Practice Problems
Fill in any necessary lone pairs in the structure below

71. Additional Practice Problems
Show the curve arrows that leads to the resonance contributor where the topmost O loses its charge and the carbocation also loses its charge