Molecular Structure: Introduction and Review

1
Molecular Structure Introduction and Review

• Lecture supplement Thinkbook page 4

2
Goal Review some relevant concepts from
Chemistry 14A and 14B
Important ideas that you probably already know
3
Basic Questions
Organic chemistry What is it?

• The study of molecules containing carbon
• Why all this fuss about carbon?
• Carbon is unique in its ability to form stable
  chains and rings ---gt millions of molecules known
  from a small set of elements (CHON)

4
Basic Questions
Organic chemistry What is it?

• The study of molecules containing carbon
• Why all this fuss about carbon?
• Carbon is unique in its ability to form stable
  chains and rings ---gt millions of molecules known
  from a small set of elements (CHON)

Cholesterol

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

5
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

6
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

7
Basic Questions
So thenwhat is molecular structure?
Molecular structure electron distribution (in
bonds, in molecule) and positions of atoms in
space.
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Molecular RepresentationsHow do we draw
molecules?

• The Rules
• ? is a covalent bond (electron pair shared by two
  atoms)
• 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
• Three-dimensional geometry does not always have
  to be shown

9
Molecular RepresentationsHow do we draw
molecules?

• The Rules
• ? is a covalent bond (electron pair shared by two
  atoms)
• 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
• Three-dimensional geometry does not always have
  to be shown

indicates bond is projecting towards viewer
indicates bond is receding away from viewer
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Molecular Representations

• Applying the rules Methane
• ? is a covalent bond
• Carbons do not always have to be drawn
• Formal charges must always be shown
• Three-dimensional geometry does not always have
  to be shown

Methane Major component of natural gas
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Molecular Representations

• Applying the rules Methane
• ? is a covalent bond
• Carbons do not always have to be drawn
• Formal charges must always be shown
• Three-dimensional geometry does not always have
  to be shown
• Bond is projecting towards viewer
• Bond is receding away from viewer

Methane Major component of natural gas
12
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

13
Molecular RepresentationsYour Molecular Model Kit

• 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!

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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
• Drawing structure of simple molecules from name

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Molecular Representations
What do I have to know about nomenclature?

• Naming of simple molecules
• Drawing structure of simple molecules from name
• Examples

2-chlorobutane gt
gt 3-methylcyclohexanol
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The Electron Count CountsReview Lewis structure
tutorial at course web site

• Valence shell electron count
• H full shell 2 (same as He)
• 2nd row elements CNOF full shell 8 (same as Ne)
• 3rd row elements easily violate octet rule
• P often has 10 e- (example PO43-) S often has
  12 e- (example SO42-)

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The Electron Count Counts

• Octet Rule
• 2nd row elements (CNOF) eight electrons and four
  bonds maximum

Pentavalent carbon very bad
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The Electron Count Counts

• Octet Rule
• 2nd row elements (CNOF) eight electrons and four
  bonds maximum

Pentavalent carbon very bad
20
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 (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

NAD Coenzyme in biological oxidation reactions
22
Electrons in Bonds

• Electron distribution can be
• even (covalent bond)
• uneven (polar covalent bond)
• Electronegativity (EN) power of an atom to
  attract e- to itself.
• High EN strong electron attraction
• Low EN weak electron attraction

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Electrons in BondsPauling EN values for elements
important to Chemistry 14C

EN ? with ? distance from fluorine
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Electrons in BondsPauling EN values for elements
important to Chemistry 14C

Must I memorize electronegativity values?

• Not necessaryjust do lots of problems. Learn
  them by frequent use.

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Polar Covalent BondsUneven electron distribution
leads to partial charges
X?Y
d
d-
EN (X) lt 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 BondsUneven electron distribution
leads to partial charges
Consequences of bond polarity

• Electrostatic interaction with other ions or
  molecules

Influences chemical, physical, and
biological properties
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Polar Covalent BondsUneven 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
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Polar Covalent BondsUneven 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
---gt hydrogen bonding
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Polar Covalent BondsUneven 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 ---gt hydrogen bonding ---gt DNA base pairing
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Polar Covalent BondsUneven 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 ---gt hydrogen bonding ---gt DNA base pairing
Adenine Thymine
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Functional Groups

• Functional group characteristically-bonded
  group of atoms that determines molecular
  properties regardless of what molecule contains
  it.

• Similar functional groups similar properties.

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Functional Groups

• Table Thinkbook page 12

You should be able to identify all of these
functional groups within molecules, as well as
draw molecules that contain them.
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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
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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
35
Atomic Positions and Molecular Geometry

• Atoms balls of electrons

have mutual repulsion move as far apart as
possible
e- cloud repulsion
36
Atomic Positions and Molecular Geometry

• Atoms balls of electrons

have mutual repulsion move as far apart as
possible
e- cloud repulsion
bond angle

• ?Repulsion ? bond angle

• Larger electron cloud stronger repulsion
• Approximate electron cloud size H, F lt lone
  pair, Cl, Br, I lt group of atoms

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Atomic Positions and Molecular Geometry

• Four e- clouds around central atom ? tetrahedral
• Equal repulsion by all H ? equal H-C-H angles
  (109.5o)

Methane
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Atomic Positions and Molecular Geometry

• Four e- clouds around central atom ? tetrahedral
• Equal repulsion by all H ? equal H-C-H angles
  (109.5o)

Methane

• Four e- clouds around central atom ? tetrahedral
• Lone pair/lone pair repulsion gt H/H repulsion ?
  H-O-H angle lt 109.5o

Water
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Atomic Positions and Molecular Geometry

• Four e- clouds around central atom ? tetrahedral
• Equal repulsion by all H ? equal H-C-H angles
  (109.5o)

Methane

• Four e- clouds around central atom ? tetrahedral
• Lone pair/lone pair repulsion gt H/H repulsion ?
  H-O-H angle lt 109.5o

Water
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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.

• Example Pair of H 1s orbitals (spheres) overlap
  to form H?H bond

Hydrogen atoms
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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.

• Example Pair of H 1s orbitals (spheres) overlap
  to form H?H bond

Hydrogen molecule
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Bonds, Molecular Geometry, and Orbitals
What orbitals are used for organic
molecules? Example Methane H
(1s) C (2s, 2px, 2py, 2pz) ? C?H bonds
px, py, pz orbitals orthogonal
py perpendicular to screen not shown
43
Bonds, Molecular Geometry, and Orbitals
What orbitals are used for organic
molecules? Example Methane H
(1s) C (2s, 2px, 2py, 2pz) ? C?H bonds
px, py, pz orbitals orthogonal
44
Bonds, Molecular Geometry, and Orbitals
What orbitals are used for organic
molecules? Example Methane H
(1s) C (2s, 2px, 2py, 2pz) ? C?H bonds
px, py, pz orbitals orthogonal
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Bonds, Molecular Geometry, and Orbitals
What orbitals are used for organic
molecules? Example Methane H
(1s) C (2s, 2px, 2py, 2pz) ? C?H bonds
px, py, pz orbitals orthogonal
H 1s C 2px C 2py ? wrong H?C?H bond angle!
46
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 for electron
  groups (lone pairs count!)
• Geometry tetrahedral need four bonds and four
  hybrid orbitals
• Orbital conservation 4 hybrid orbitals come from
  4 atomic orbitals
• s

47
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 for electron
  groups (lone pairs count!)
• Geometry tetrahedral need four bonds and four
  hybrid orbitals
• Orbital conservation 4 hybrid orbitals come from
  4 atomic orbitals
• s

px
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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 for electron
  groups (lone pairs count!)
• Geometry tetrahedral need four bonds and four
  hybrid orbitals
• Orbital conservation 4 hybrid orbitals come from
  4 atomic orbitals
• s px py

49
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 for electron
  groups (lone pairs count!)
• Geometry tetrahedral need four bonds and four
  hybrid orbitals
• Orbital conservation 4 hybrid orbitals come from
  4 atomic orbitals
• s px py pz

50
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 for electron
  groups (lone pairs count!)
• Geometry tetrahedral need four bonds and four
  hybrid orbitals
• Orbital conservation 4 hybrid orbitals come from
  4 atomic orbitals
• s px py pz sp3

51
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 for electron
  groups (lone pairs count!)
• Geometry tetrahedral need four bonds and four
  hybrid orbitals
• Orbital conservation 4 hybrid orbitals come from
  4 atomic orbitals
• s px py pz sp3 sp3

52
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 for electron
  groups (lone pairs count!)
• Geometry tetrahedral need four bonds and four
  hybrid orbitals
• Orbital conservation 4 hybrid orbitals come from
  4 atomic orbitals
• s px py pz sp3 sp3 sp3

53
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 for electron
  groups (lone pairs count!)
• Geometry tetrahedral need four bonds and four
  hybrid orbitals
• Orbital conservation 4 hybrid orbitals come from
  4 atomic orbitals
• s px py pz sp3 sp3 sp3 sp3

• C sp3 H 1s C-H bond