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Title: 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.
8
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
10
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
11
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!

14
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

15
Molecular Representations
What do I have to know about nomenclature?
  • Naming of simple molecules
  • Drawing structure of simple molecules from name

16
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
17
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-)

18
The Electron Count Counts
  • Octet Rule
  • 2nd row elements (CNOF) eight electrons and four
    bonds maximum

Pentavalent carbon very bad
19
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

21
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

23
Electrons in BondsPauling EN values for elements
important to Chemistry 14C

EN ? with ? distance from fluorine
24
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.

25
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

26
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
27
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
28
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
29
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
30
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
31
Functional Groups
  • Functional group characteristically-bonded
    group of atoms that determines molecular
    properties regardless of what molecule contains
    it.
  • Similar functional groups similar properties.

32
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.
33
Atomic Positions and Molecular Geometry
  • Atoms balls of electrons

have mutual repulsion move as far apart as
possible
e- cloud repulsion
34
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

37
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
38
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
39
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
40
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
41
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
42
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
45
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
48
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
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