Chemistry 265005

I. Chapter I
A. Chemistry Bonding and Chemical Structure
1. Organic Chemistry
a. Old Definition: derived from living organisms, eg. Nicotine,
vitamin C, camine, morphine
b. It was an early belief that nothing would be able to be synthesized
in a laboratory that was organic
c. Change in beliefs—Wöhler, 1828
d. Formula that changed it all!

i. NH 4 OCN   H 2 N  CO  NH 2
heat

ii. Ammonium cyanate conversion to urea!

iii. It was thought to be unextractable
e. New Definition- Carbon
i. But not all carbon… over 10 million identified from
natural/synthetic means, 1000 new ones each day
2. Why Carbon?
a. Small
b. Intermediate EN—2.5
c. Strong bonds with CHON and some metallic complexes
3. Variety of Bonds!
a. Why Organic Chemistry?
b. Important
c. Insights into medicine/biology, language of interaction for biology
d. Foundation of chemical industry
i. Plastics
ii. Textiles
iii. Nutrition
e. Solving “grand challenges”
i. Pollution, “green chemistry”
ii. Sustainable energy sources (biofuels)
4. Schematic View of the Atom
a. Proton, neutron, electron
b. Nucleus diameter approximately 10-15, 10-14 protons are most of
the mass
c. An extranuclear space of approximately 1 A contains e-
d. ID—protons
e. Isotope—same element different number of neutrons
i. 12C, 14C, 13C: NMR
B. Chemical Properties determined by valence shells
1. Each shell contains 2n2 electrons
2. Subshells—orbitals; s, p, d, f
 a. S—1 per shell
b. P—three per shell
c. D—set of five per shell 3 and higher
3. Pauli exclusion principle: 2 electrons if they are antiparallel can occupy
an orbital
a. Pairing of electron spins
i. More energy to pair
ii. Separation between shell and subshell decreases with
energy
4. Pauli and Aufbau—lowest
energy level first
5. Hund’s Rule—equal, then
half filled
6. 4 bonds to something
with 4 valence… like
Carbon
C. Lewis Dot Structure
1. Gilbert N Lewis
2. Dot Structure
a.
a.
a.
a.
a.
a.
Symbol of an element representing nucleus and all of the inner shell
electrons
i. Dots are valence electrons
ii. In molecules valence are spread on orbitals
3. Walte Kossel: 1916, Octet Rule
a. Atom Gains electron to become an anion (-)
b. Looses to become a cation (+)
c. Shares—Neutral
D. Types of Bonding
1. Ionic Bonding—resulting from electrostatic attraction of anion and cation
2. Covalent Bonds—Shared electrons
3. Polar covalent—Partial Charge, localized on certain atoms
4. Electronegativity: Atom attraction for electrons
a. Increasing electronegativity change is more polar
E. Pauling EN scale
1. Increases left to right in row
2. Bottom to top
3. Fluorine is most EN element
4. Rules of Thumb
 a. Ionic if ∆EN>1.9
 
Na    F  Na  F
 
b.   
c. In forming NaF, single 3S electron is transferred to partially filled
balance shell of F
F. Simples covalent bond, H2
1. Ethylene example
II. Lewis Structures
A. Determine number of valence electrons
B. Determine arrangement of molecule
C. Connect by Single bonds
D. Arrange remaining so that atoms fills octet
E. NB as a single line
F. In Neutral Molecules
1. H has one bond
2. C has four bonds
3. N has three bonds and 1 lone pair
4. O—2 bonds – 2 lone pairs
5. Halogens, 1 bond, 3 lone pair
III. Formal Charge
A. Keeping track of electrons
B. Polar and nonpolar covalent
1. Sharing in different degree
2. Ex:
3. Polar Bonds may result in NP molecules
4. Dipole Moment (μ)
a. Polarity of covalent bonds
b. Product of change on either atom of polar bond is distance times
electrical charge
c. Μ=electrical charge x bond length (Debes)
d. Is a vector!!!
IV. Lewis structure--resonance
A. Delocalization of charge
B. Resonance arrow
C. Real structure is hybrid of contributing structures
1. Allows delocalization of charge, more stable than contribuants
2. Key Rules!
a. Valid Lewis structures
b. Only electrons can be delocalized
c. Preference 1: Valencce shells filled, octet
d. Preference 2: Maximum number of covalent bonds
e. Preference 3: Least separation of charge
 f. Preference 4: Negative charge on more electronegative atom
D. Atomic Connectivity: how connected
E. Molecular Geometry: Situated in space
F. Bond lengths: decrese with increasing Bond Order
1. Increasing atoms from higher periods within a column
G. Bond Angle:
1. Bond angles cannot be explained with simple s and p orbitals
2. VSEPR
3. Based on atoms surrounded by regions of electron density
4. Eg 4 regioins in Methane
5. 2 regions in C02 and in ethyne (180)
6. 3 regions, trigonal planar (120)
7. 4 regions, tetrahedral (109.5)
H. Dihedral Angle
1. Torsional Angle
a. Created by two intersecting planes
2. Geometry determined by:
a. Bond Length
b. Bond Angle
c. Dihedral Angle
I. Dipole Moment
1. Determine if a molecule is polar
2. Does it have polar bonds?
3. Molecular geometry
4. Dipole moment (μ): vector sum of individual bond dipole in molecule

O C O
5.
6. Dipole for that = 0 – why it exists as a gas
7. BF3 dipole =0
O
H
C

8. H Formaldehyde, dipole towards Oxygen

9. Has to do with strength of attraction between molecules
a. Melting point
b. Boiling Point
c. Solubility for solids/liquids
10. Classification depends on structure
a. Ion-Ion
b. Ion-dipole
c. Dipole-Dipole
d. H-Bond
e. VdW
 i. Induced transiently
ii. Dispersion force
11. Dipole-Dipole
a. Between polar molecules
b. Positive end of 1 molecule aligns with negative end of another
larger dipole cause higher melting point
12. H-Bond
R O H O

R
O
a. H O
b. Strong dipole-dipole attraction must have N-H, or O-H
c. Heavy directional and short range
i. 1.7—2 A
ii. OH more polar than NH
d. VdW attraction
i. All interactions
ii. Temporary dipole-dipole interaction
iii. Larger atoms more polarizable
iv. Branching lowers b.p, because of decreased surface
contact between molecules
e. Solubility
i. Like dissolves like
ii. Molecules
iii. Too much energy to break H bonds when interacting with
nonpolar solvent
V. Quantum Mechanics
A. Stoney: electron as a charged particle
B. JJ Thompson discovered
C. deBroglie—wave particle duality
D. Heisenburg—accuracy is limited
E. Electron is a 3d standing wave that vibrates in a fixed location
F. Wave function describes mathematically
1. φ, energy of electron in an atom
2. each wave function is associated with an orbital
G. Orbital
1. Allowed energy state for an electron, ψ2 probability function, e- density.
2. First electronic shell, 1s orbital, 2e, psi describes size, shape, orientation,
and energy
a. PHASES NOT CHARGE!!!
b. ψ2 is highest at nucleus
3. 2 s orbital, 1 node
 4.
5. 2 p orbital
a. Psi is positive in one lobe in another psi squared

b.
i. 3 degenerate orbitals
H. Wave Interactions
1. LCAO: MO’s bonding or antibonding on same atom hybrid orbitals
2. General Rules
a. Conservation of AO’s
b. #MO=#AO
c. Rule for MO
i. Combination of n atomic= n MO’s
ii. Mos increase energy arrangement
iii. AUFBAU—beginning LUMO
i. LUMO—lowest unoccupied MO
ii. HOMO—Highest occupied MO
iv. Stability of covalent bonds depend on amt of electrons in
bond length
3. Same Phase (sigma)

4. Opposite (sigma star)

5. With P orbitals
VI. Problem: Tetravalency of Carbon requires 4 unpaired electrons
A. Solution: Excited state
B. Orbital Hybridization of carbon
C. Hybrization lowers energy because electron pairs end up further apart
VII. Hybrid orbitals
A. 2 or more AO - hybrid orbitals
B. Hybridization is LCAO in one atom! Just prior to bonding
C. 3 types
1. Bond length, sp shorter than sp3 because electron distance from nucleus
2. Sp3
a. 4 vespr electron pairs
 b. Tetrahedral geometry
c. 109.5 bond angle
3. Hybridization of N
a. Trigonal pyramidal
VIII. CHAPTER 2
A. ALKANES
B. Classes of Compounds
1. Hydrocarbons
2. Oxo (sulfur)
3. Nitro (Phosphorous) cmpds
C. Functional Group: Atom/Atom within molecules
1. Physical chemical properties
D. Why Important?
1. Units in organic classes?
2. Characteristic chemical reactions (classes)
3. Basic for naming
E. Hydrocarbons
1. Alkane: Single bond, sp3 carbon
2. Cycloalkane: Carbon in a ring
3. Alkene: Double bond, sp2 carbon
4. Cycloalkene: double bond in ring
5. Alkyne: triple bond: sp carbon
6. Aromatic: generally contains benzene ring
7. Alcohols
a. OH hydroxyl group
b. Sp3
c. Alcohols are classified as primary (1) secondary (2), tertiary (3)

1 R C OH R'

H R2 C OH

R2
R3

1 R C OH

8. Amines:
a. Amino group, sp3, Nitrogen
NH2

i. methylamine
 9. Aldehyde and Ketone
a. Contain a carbonyl (C=O) group
O

R C H
Aldehyde

R2 R1
b. Ketone
F. Carboxylic Acid
1. Contain COOH group
G. Carboxylic Ester
1. Derivative of Carboxylic acid in which carboxyl is hydrogen replaced by
carbon group
H. Amide
1. Derivative of COOH which, OH group is replace by amine (NH 2)
2. Invoke resonance, to understand why planar not volatile, highly
crystalline
I. Structure of Alkanes
1. Containing, C, H, only single bonds arranged in open chain
2. Aliphatic: Alkane
3. Ratio: CnH2n+2
4. Same C/H ration for linear or branched
J. Isomerism—same molecular formula, but different arrangement of atoms
K. Constitutional isomer
1. Differ in bonding sequence
2. Same otherwise
IX. IUPAC Nomenclature
A. Prefix: Number of carbon in parent
B. Infix: Nature of C-C bond
C. Suffix: Class of compound
D. Infix:
1. –an- all single bonds
2. –en- at least 1 double bond
3. –yn—1 or more triple bond
E. Suffix
1. e hydrocarbon
2. ol alcohol
3. al aldehyde
4. amine amine
5. one ketone
6. oic acid, carboxylic acid
 F. Parent Name
1. Longest chain
2. Substituent: group bonded to parent chain
3. Alkyl group: substituent derived by removal of hydrogen from alkane
4. Symbol, R and suffix =yl
G. Rules
1. Longest continuous carbon chain:
a. Determines base name
b. If 2 possible, use with most substituent
2. Number carbons within longest chain
a. End closest to first attached group
b. Lowest number for substituents
H. Alkanes properties:
1. Solubility: hydrophobic
2. Density: less than 1.5 mL
3. BP: low for branch, increasing with C
4. MP increasing more C for number
a. Packing element
X. Branched Alkanes
A. Lower bp with increasing branching
B. Higher mp with increasing braching
C. Uses of Alkanes
1. C1-C2: gases (NG)
2. C3-C4 : liquefied petroleum gas (LPG)
3. C5-C8: gasoline
4. C9-C16: diesel, kerosene, jet fuel
5. C17-up: lubricating oil, heat oils
D. Origin: petroleum refining
E. Reactions:
1. Cracking and hydrocracking
2. Long chain alkene (cat) shorter chain
F. Halogenation
G. Combustion
1. Relative Stabilty
2. Cyclo more energy
H. Conformations
1. Molecular shape and dihedral angle
2. Conformation
a. Free rotation of C-C single bond
b. Conformer: a specific conformation
3. May differ in energy and will prefer certain conformers
a. Lowest E is most prevalent
4. Molecules rotate thought all conformations, by jagged motion
I. Diehedral Angle
 1. 2 planes
2. Eclipsed (0)
3. Staggered (60)
4. Eclipsing not good for energy
5. Ethane conformer
a. Staggered
b. Lowest energy
6. Newman projection
7. Torsionial Strain
a. Eclipsed interaction strain
b. Resistance about single bond caused by eclipsing interaction
c. Between ethane is approx 3.0 kcal/mol
d. C-H approx 1 kcal/mol
e. C-CH approx 1.3 kcal/mol
f. Anticonformation – 180 for butane
g. Gauche—60 butane
8. Steric strain:
a. NB interaction with VdW
b. Angle when aroms are forced closer than their atomic radii allow
9. Stable Conformation of 2,3 dimethyl butane
H CH3 CH3
CH3 H H3C H CH3 H

CH3 CH3 H3C H H CH3

CH3 CH3 CH3
-60 degree Gauche 60 degree Gauche 180 anti state gauche
3 CH3--CH 3CH3-CH 2CH3-CH
Lowest possible energy
10. Higher Alkanes
a. Anti is lowest in energy
i. Far apart as possible
b. Syn-pentane Interaction
i. Steric hindrance that two terminal Me groups experience
in one of the all staggered conformations of n-pentane
c. In Macromolecules, interferences occurs in every 5 carbon