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MOLECULAR STRUCTURE
INTRODUCTION AND REVIEW

H3C O
H3C O
O O OH
CH3
CH3
N O
CH3
H OH
HO H H
O O O O

CH3

Taxol: An anticancer drug

Basic Questions

Organic chemistry: What is it?

•The study of molecules containing carbon

Why all this fuss about carbon?

•Millions of molecules known from small set of elements (northeast corner of periodic table)
•Carbon is unique in its ability to form stable rings and chains

CH3

Example: Cholesterol CH3

HO

•Carbon compounds basis for life (as we know it)

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Basic Questions

Why should I study organic chemistry?

•Broadly applicable to other fields: Biochemistry, pharmaceuticals, biology, etc.

•Skills learned useful elsewhere: Information organization, critical/analytical thinking, etc.

How often should I study organic chemistry?

•Monday, Tuesday, Wednesday, Thursday, Friday, Saturday, Sunday…

Basic Questions

In Chemistry 14C we expand our knowledge of organic molecular structure by

exploring…

•Selected topics in structural theory: Resonance, conjugation, aromaticity,

stereochemistry, etc.

•Laboratory determination of structure: Spectroscopy

•Structure controls properties: Physical, chemical, biological

•Reaction chemistry (substance  substance) covered in Chemistry 14D

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Basic Questions
What is molecular structure?

Ocrevus

• A humanized anti-CD20
monoclonal antibody.

• It targets CD20 marker on B

lymphocytes (immune system
cells that damages nerve cells
in people with Multiple
Sclerosis) and hence is an
immunosuppressive drug.

C6494H9978N1718O2014S46
Molar Mass: 148 kg/mol

Basic Questions

What is molecular structure?

•Molecular structure = electron distribution (in bonds, in molecule) and positions of
atoms in space.

H-O-H bond angle 104.5o

•Example: Water
d+ H H
O
d- O-H bond length 0.96 Å

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Molecular Representations
How do we draw molecules?
The Rules
• Carbons do not always have to be drawn
CH3NH2
• Hydrogens can be omitted only if carbon not written as C
H H • All other atoms must always be shown
H C N
•  is a covalent bond (electron pair shared by two atoms)
H H

• : is a lone (nonbonded) electron pair

H
• Lone pairs do not always have to be shown
H
NH2
H • Formal charges must always be shown (unless FC = 0)

• Three-dimensional geometry does not always have to be shown

bond projects outward towards viewer

bond recedes away from viewer
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Molecular Representations

Applying the rules: Taxol, an anticancer drug

•Carbons do not always have to be drawn
•Hydrogens can be omitted only if carbon not written as C
•All other atoms must always be shown
•Lone pairs do not always have to be shown O

H3C O
H3 C O
O O OH
CH3
CH3
N O
CH3
H OH
HO H H
O O O O

CH3

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Molecular Representations
Your molecular model kit

Molecular model kit Benzene a-D-Glucopyranose

•Models useful to visualize, manipulate structures in three dimensions

•Compare molecular models of molecules in this review versus their “paper” structures

•Bring models to discussion sections

•Models can be used on exams

•Models are a good habit

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Molecular Representations

Do I have to memorize these structures?

•More often you see it, more important it is

•More important it is, greater chance you might need to know its structure
Common: Methane, glucose Uncommon: Taxol

•Pure memorization (the “m word”) rarely needed

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Molecular Representations

What do I have to know about nomenclature?

•Naming of simple molecules
CH3

 3-methylcyclohexanol

OH

•Drawing structure of simple molecules from name

Cl

2-chlorobutane 

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The Electron Count Counts

Review Lewis structure tutorial at course web site
http://www.chem.ucla.edu/~harding/

Valence shell electron count

•H full shell = two electrons (same as He)
•2nd row elements (CNOF): Eight electrons and four bonds maximum
The "octet rule"

H
H H
C Pentavalent carbon very bad
H H

•3rd row elements easily violate “octet rule”

O O

P often has 10 electrons O P O S often has 12 electrons O S O

O O

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The Electron Count Counts

Formal Charge
Definition: The charge on an atom in a Lewis structure if the bonding was perfectly covalent
and the atom has exactly a half-share of the bonding electrons. (The difference between the
number of electrons “owned” by a covalently bonded atom versus the same atom without any
bonds, i.e., a free atom of the same element.)

Significance
•Indicates electron excess or deficiency
•Desire to gain or lose electrons
•Electrostatic interaction between regions of charge

Determination of formal charge

•Review tutorial at course web site

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The Electron Count Counts

Formal Charge Self-Test

•Verify the formal charges in the following molecule:

O NH2

N
H2N N

O O
N N
N O
O O P O P O

O O

HO OH
HO OH

NAD
Coenzyme in biological oxidation reactions

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Electrons in Bonds

•Electron distribution can be…

…even (covalent bond)
…uneven (polar covalent bond or ionic bond)

Electronegativity (EN): Power of an atom to attract electrons to itself

High EN = strong electron attraction
Low EN = weak electron attraction

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Electrons in Bonds
Pauling electronegativity (EN) values for elements important to Chemistry 14C

EN  with  distance from fluorine

H = 2.1

C = 2.5 N = 3.0 O = 3.5 F = 4.0

EN decreases

P = 2.2 S = 2.5 Cl = 3.0

Br = 2.8

I = 2.5
EN decreases
EN decreases
Must I memorize electronegativity values?
•Not necessary…just do lots of problems. Learn them by frequent use.

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Polar Covalent Bonds

Uneven electron distribution leads to partial charges

d+ XY d-
EN (X) < EN (Y)

Result: Bond dipole or polar covalent bond

Magnitude of bond dipole influenced by...

•  EN difference  bond dipole
•  bond length  bond dipole
•Example: CH DEN = 0.4 but has low polarity due to short bond length

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Polar Covalent Bonds

Uneven electron distribution leads to partial charges

Consequences of bond polarity

•Electrostatic interaction with other ions or molecules

Influences chemical, physical, and biological properties

Example: Polar H-N bond  hydrogen bonding  DNA base pairing
O

N N
d+ d-
N H N
N

d- d+
N N H O CH3

Adenine Thymine

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Scientists generated the clearest

and most detailed image yet of Zika
virus. The virus’s structure, with the
green dots representing the glycan
loop, which might determine the
symptoms caused by Zika.

By visualizing the virus in such

detail, the researchers may find
pockets on its surface where the
drug molecules could attach.

Such features may help scientists

understand how vaccines and
antiviral drugs could interact with
Zika.

Sevvana et al. (2018). Refinement and

analysis of the mature Zika virus cryo-
EM structure at 3.1 Å resolution.
Structure.
https://doi.org/10.1016/j.str.2018.05.006

June 26, 2018 New York Times

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Covid-19

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Covid-19

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Covid-19 Controlling the spread

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Functional Groups

Functional group (FG): A characteristically

bonded group of atoms that determines
molecular properties regardless of what
molecule contains it.

FG Table: Thinkbook Appendix A

Why study FG?

Similar functional groups  similar properties

Expected skills:
•Identify FG within molecules
•Draw molecules with particular FG

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Atomic Positions and Molecular Geometry

Atoms = balls of electrons
...have mutual repulsion
...move as far apart as possible

e- cloud repulsion
bond angle

• repulsion causes  bond angle

•Larger electron cloud = stronger repulsion
•Approx. electron cloud size: H, F < lone pair, Cl, Br, I < group of atoms (CH3, OH, etc.)

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Atomic Positions and Molecular Geometry

Methane
H
CH4
109.5o •Four electron clouds around central atom  tetrahedral shape
H
H
•Equal repulsion by all H  equal H-C-H angles (109.5o)
H

Water H₂O
H
104.5o •Four electron clouds around central atom  tetrahedral shape
O
H •Lone pair/lone pair repulsion > H/H repulsion  H-O-H angle < 109.5o

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Bonds, Molecular Geometry, and Orbitals

Covalent bonds formed by overlap of orbitals

•Orbital: Mathematical equation that describes a volume of space in which there is

a certain probability of finding an electron of a certain energy.
•Orbitals can be drawn, but have no physical reality.
•Bond example: Two H 1s orbitals (spheres) overlap to form H-H bond:

Hydrogen atoms Hydrogen molecule

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Bonds, Molecular Geometry, and Orbitals

What orbitals are used for organic molecules? Example: Methane (CH4)
H (1s) + C (2s, 2px, 2py, 2pz)  C-H bonds

orthogonal
aka perpendicular
H-C-H bond angle 90o

+ H

H 1s + C 2px + C 2pz  wrong H-C-H bond angle!

Therefore this orbital combination incorrect

Verify with your model kit

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Bonds, Molecular Geometry, and Orbitals

Solution (Linus Pauling, 1931)

•Use mathematical combinations of s, px, py, and pz orbitals to form correct

number of bonds with correct geometry
•Combinations = hybrid orbitals

Hybridization scheme for atom with four electron groups

•Electron group = bond or lone pair
•CH4 geometry = tetrahedral; need four bonds and four hybrid orbitals
•Orbital conservation: Four hybrid orbitals come from four atomic orbitals
•s + px + py + pz  sp3 + sp3 + sp3 + sp3 methane
sp3 H
•C sp3 + H 1s  C-H bond 109.5o
aka CH4 is sp3
H C
H
hybridized
H

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Molecular Conformations
H3C CH3 H3C H
Acyclic molecules: H

H H H
H H H CH3

Eclipsed Staggered

CH3
Cyclic molecules:
H CH3

Axial Equatorial

Additional material available on course web site

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Break

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RESONANCE

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What Is Resonance?

Example
•Carbon monoxide C O versus C O

Which accurately represents the molecular structure?

•Open octet on carbon vs. formal charges ---- both decrease stability

How to analyze structure?

•Double bond (longer) versus triple bond (shorter)

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What Is Resonance?
The Lewis structure of CO

Laboratory analysis
•Double bond or triple bond?
H2C=O O=C=O carbon monoxide
CO length 1.21Å CO length 1.20Å CO length 1.13Å
shorter than C=O

•Dipole moment measurement favors double bond over triple bond.

Conclusion
•The Lewis structure that accurately represents CO is...

C O C O

Empirical observation: Actual structure is somewhere in between double and triple bond.

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What Is Resonance?
The Lewis structure of CO

Perhaps an equilibrium between two structures that differ in electron distribution?

C O C O

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Curved Arrows
C O C O

A curved arrow...
•Indicates electron redistribution
•Starts at electron source; points to electron destination:
Electron source Electron destination

•When arrow starts at bond, bond is broken:

H H

H C Cl H C Cl

H H

•When arrow points to atom or space between atoms, bond is formed:

H H

H C Cl H C Cl

H H

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What Is Resonance?
The Lewis structure of CO

Perhaps CO is equilibrium between two structures that differ in electron distribution?

C O
?X C O

•Equilibrium ruled out by empirical evidence.

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What Is Resonance?
The Lewis structure of CO
the average and most stable form

Empirical CO structure is intermediate between the Lewis structures:

C O C O
Adequate structure
Inadequate Inadequate

What is this “between” structure?

•Each inadequate structure has some, but not all, actual features of CO
•CO cannot be adequately represented by a single Lewis structure
•Therefore “blend” or “average” inadequate structures  composite structure

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What Is Resonance?
A definition

Resonance
•A molecule cannot be adequately represented by just one Lewis structure
•Two or more Lewis structures must be used

Resonance contributors C O and C O

How do we indicate a molecule has resonance?

NO =lib arrows
C O X C O C O C O

Equilibrium Resonance
Not accurate for CO Accurate depiction of CO

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Why Is Resonance Important?

• Common occurrence with Chem 14C atoms: C, N, O, F, Cl, Br, I, S, P

• Resonance delocalization increases stability: Electrons (charge) spread over
larger volume  stability
• Resonance influences molecular structure: Causes planarity

Resonance importance example: An acid-base reaction

O O

H O S O H + HO H O S O + H2O

O O

No resonance Has resonance

Less stable More stable

Keq > 1
H2SO4 stronger acid than H2O

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Drawing Resonance Contributors

Key: Recognize the four common electron pair shift patterns

H3C C CH2 H3C C CH2

O O

H3C C NH2 H3C C NH2

O O

H H

C C
H2C CH2 H2C CH2

What is electron pair shift pattern? Hint: Consider curved arrows

Lone pair and pi bond switch

Note: Not necessary to draw for both sides of

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Drawing Resonance Contributors

H H

C C
H2C CH2 H2C CH2

CH2 CH2

Boron has 5 e⁻
H H

C C
H2C BH2 H2C BH2

Open valence shell

What is electron pair shift pattern? Pi bond and open valence shell switch

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Drawing Resonance Contributors

}
(CH3)2N C(CH3)2 (CH3)2N C(CH3)2
Pi bond change
Common
(CH3)2C O (CH3)2C O

Br Br Sigma bond change

(CH3)2C C(CH3)2 (CH3)2C C(CH3)2 Rarely important

What is electron pair shift pattern? Lone pair and open valence shell switch with bond

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Drawing Resonance Contributors

What is electron pair shift pattern? Pi bonds switch

Common for benzene rings

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Which Resonance Contributor Represents Reality?

Once upon a study break...

X
Fantasy creatures Real creature
Neither fully represents reality A unicorn-dragon hybrid?

The carbon monoxide case:

C O
X C O Neither contributor fully represents CO

Resonance hybrid: A weighted average or blend of resonance contributors; the

most accurate representation of the electronic structure of a molecule.

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Drawing the Resonance Hybrid

Example: Draw the resonance hybrid for acetate ion, CH3CO2-.

O O O

1. Draw contributors
H3C O H3 C O H3C O

O
2. Draw the features that are the same for all contributors
• Sigma and pi bonds, lone pairs, and formal charges H3C O

3. Add features that are not the same for all contributors O d-
•Partial (shared) pi bonds shown as ----
•Partial (shared) charges shown as d+ or d- H3C d+ O d-

Resonance hybrid

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Do All Contributors Have Equal Importance?

Is a rhinoceros more unicorn or more dragon?

 contributor “stability” =  resemblance to reality =  contribution to hybrid

Therefore we need contributor preference (“stability”) rules:
- number and/or magnitude of rules violations
=  importance of individual contributor
=  contribution to resonance hybrid

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Resonance Contributor Preference Rules

Rule #1: The most important contributor has the least number of avoidable open
valence shells.

Example: H2C OH H2C OH

All valence shells filled Open valence shell on carbon

More important contributor Less important contributor

In some cases it may not be possible for all atoms to have full valence shells.

Rule #1 is more influential than all the other preference rules.

Rules #2-6 have no particular order of preference.

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Resonance Contributor Preference Rules

Rule #2: The most significant contributor has the maximum number of covalent
bonds.
H H

Example: C O C O

H H

Four covalent bonds Three covalent bonds

More important contributor Less important contributor

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Resonance Contributor Preference Rules

Rule #3: The most significant contributor has the least number of avoidable formal
charges.
H H

Example: C O C O

H H

No formal charges Two formal charges

More important contributor Less important contributor

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Resonance Contributor Preference Rules

Rule #4: If a contributor has unavoidable formal charge(s), the most important contributors
have these charges on the atom(s) that can best accommodate them.
•Negative formal charges best on atoms of high electronegativity O- better than C-
•Positive formal charges best on atoms of low electronegativity C+ better than O+
•Minimize formal charge magnitude +1 better than +2

O
O

Example:
CH3 CH2
CH3 CH2

Carbon EN = 2.5 Oxygen EN = 3.5

Less important contributor More important contributor

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Resonance Contributor Preference Rules

Rule #5: Resonance interaction (i.e., pi bond) is strongest between atoms in the
same row of the periodic table.
•Usually CNOF
•Usually outweighs electronegativity considerations (rule #4)

F C Cl F C Cl
Example:
H H

F, C both 2nd row C 2nd row; Cl 3rd row

More important contributor Less important contributor
Even though EN F > EN Cl

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Resonance Contributor Preference Rules

Rule #6: Other factors (such as aromaticity) that we will encounter later.

Violations to the resonance contributor preference rules exist, but are uncommon.

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End of lecture today

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