Molecular Structure:
Introduction and Review
Lecture Supplement page 3
O
H3C
O
O
O
H3C
O
CH3
OH
CH3
N
H
O
CH3
OH
HO
O
H
H
O
O
O
CH3
O
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)
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
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
Molecular Representations
How do we draw molecules?
The Rules
•  is a covalent bond (electron pair shared by two atoms)
CH3NH2
H
H
C
H
H
N
NH2
H
: is a lone (nonbonded) electron pair
•
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
•
Formal charges must always be shown (unless FC = 0)
•
Three-dimensional geometry does not always have to be shown
H
H
H
•
bond projects outward towards viewer
bond recedes away from viewer
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
O
O
H3C
O
CH3
OH
CH3
N
H
O
CH3
OH
HO
O
H
H
O
O
O
CH3
O
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 and can be a fun toy!
•“How to use your model kit” tutorial is available on Prof. Hardinger’s course website
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
Molecular Representations
What do I have to know about nomenclature?
•Naming of simple molecules
•Drawing structure of simple molecules from name
•Examples:
Cl
2-chlorobutane 
CH3
 3-methylcyclohexanol
OH
The Electron Count Counts
Review Lewis structure tutorial at course web site
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
H
Pentavalent carbon very bad
H
•3rd row elements easily violate “octet rule”
O
O
P often has 10 electrons
O
P
O
O
S often has 12 electrons
O
S
O
O
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
The Electron Count Counts
Formal Charge Self-Test
•Verify the formal charges in the following molecule:
NH2
O
N
N
H2N
O
N
N
O
O
P
O
HO
O
OH
O
P
O
O
O
HO
OH
NAD
Coenzyme in biological oxidation reactions
N
The Electron Count Counts
Formal Charge Self-Test
•Verify the formal charges in the following molecule:
NH2
O
N
N
H2N
O
N
N
+1
O
O
P
O
HO
O
O
P
O
O
O
HO
OH
-1
N
OH
-1
NAD
Coenzyme in biological oxidation reactions
All other atoms in this molecule have formal charge of zero
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
Electrons in Bonds
Pauling EN values for elements important to Chemistry 14C
EN  with  distance from
fluorine
H = 2.1
EN decreases
C = 2.5
N = 3.0
O = 3.5
F = 4.0
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.
Polar Covalent Bonds
Uneven electron distribution leads to partial charges
d+ XY dEN (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
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
d+
H
N
N
dN
N
d+
H
dN
O
H
Adenine
Thymine
N
CH3
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
Identify the Functional Groups in Taxol
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.)
The relationship between Lewis Structures, Valence Shell
Electron Pair Repulsion Theory (VSEPR) and Hybridization
Molecular Formula
↓
Propose a good Lewis Structure (fulfill octet rule, minimize formal charges)
↓
Use VSEPR to “space out” groups as far away from each other as possible
(this final geometry is referred to in the chart below as the “electron
arrangement”)
↓
Choose the hybridization scheme that gives the desired geometry
• Discuss handout on hybridization
Atomic Positions and Molecular Geometry
Methane
H
109.5o
H
H
•Four electron clouds around central atom  tetrahedral shape
•Equal repulsion by all H  equal H-C-H angles (109.5o)
H
Water
H
104.5o
O
H
•Four electron clouds around central atom  tetrahedral shape
•Lone pair/lone pair repulsion > H/H repulsion  H-O-H angle < 109.5o
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
Bonds, Molecular Geometry, and Orbitals
What orbitals are used for organic molecules?
H (1s) + C (2s, 2px, 2py, 2pz)  C-H bonds
Example: Methane (CH4)
orthogonal
H-C-H bond angle 90o
+
H 1s + C 2px + C 2pz  wrong H-C-H bond angle!
Therefore this orbital combination incorrect
Verify with your model kit
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
•C sp3 + H 1s  C-H bond
H
sp3
H
C
H
109.5o
H
Molecular Conformations
Acyclic molecules:
H3C
CH3
H
H
H
H
Eclipsed
H3C
H
H
H
H
CH3
Staggered
CH3
Cyclic molecules:
CH3
H
H
Axial
Equatorial
Additional material available on course web site