Chemistry 3719 - Organic Chemistry I
Professor :
Office :
Telephone :
Email :
Websites :
Dr. Peter Norris
6014 Ward Beecher
(330) 941-1553
[email protected]
http://www.as.ysu.edu/~pnorris/public_html
www.chemfinder.com
Lecture needs:
• Carey
• Molecular models
• Adobe Acrobat Reader
• Web access
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Molecular Models – www.darlingmodels.com
May be used on exams, will be used in lecture
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Lab needs:
• Pavia, Lampman, Kriz
and Engel
• Goggles
• Lab coat
• Bound notebook
YSU
Chemistry 3719 and 3720 (and labs)
Lectures
•
Structure and nomenclature of compounds and groups
•
Physical properties and analysis of materials
•
Reactivity and transformations with reagents
•
Importance of organic compounds in other subjects
Labs
•
Glassware and equipment used to prepare organics
•
Instrumentation used to analyze compounds
•
Keeping a good notebook of lab preparations
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Chemistry 3719R and 3720R (Recitation)
Objectives
•
Practice the problems sets, old exams
•
Practice the problems from the book
•
Ask ?? of a professional chemist (other than lecture Prof)
•
To encourage students to keep up with material (quizzes)
When: 12-12.50 or 1-1.50 on Mondays
(1 Semester hour, Separate grade to 3719/3719L)
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Chemistry 3719 Personnel
Dr. Peter Norris
3719 lecture
Lemuel Carlisle
3719 lab
Dr. John Jackson
3719 recitation
Brian Dobosh
3719 lab
Mike Evans
3719 lab
Calvin Austin
3719 lab
Lucas Beagle
3719 lab
Ashley Malich
3719 lab
Kevin White
3719 lab
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Some does and don'ts for 3719 and 3720
Does
• Prepare for lecture and lab; read ahead
• Ask questions at any time; lecture, recitation, office hours
• Use all of your resources; email, website, tutors
• If you struggled in General Chemistry, seek help soon
Don'ts
• Don’t get behind, blow off class, ignore the available help
• Don’t wait until October to say “dude, I thought I knew the stuff.”
• Don’t complain when you get 20/100 if you ignore the above
Get help : [email protected]
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Peter Norris B.Sc., Ph.D.
Born :
1965, Liverpool, England
B.Sc. Chemistry :
1986, Salford University, England
Ph.D. Organic Chemistry: 1992, The Ohio State University
Post-doctoral :
1993-96, American University, Wash’n DC
Assistant Professor :
1996-2000 YSU Chemistry
Associate Professor :
2000-2004 YSU Chemistry
Full Professor :
2004 – present YSU Chemistry
40 publications, graduated 23 Masters degree students since 1998
~ $1,000,000 in grant money since 1999
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Research and Publication
"Crystal and molecular structure of 6,7-dideoxy-1,2;3,4;9,10-tris-O-(1-methylethylidene)D-erythro-alpha-D-galacto-undecopyranosid-8-ulose," T. D. Weaver, M. Zeller, and P.
Norris, J. Chem. Cryst., 2006.
"N-Glycoside neoglycotrimers from 2,3,4,6-tetra-O-acetyl-beta-D-glucopyranosyl azide,"
D. P. Temelkoff, M. Zeller, and P. Norris, Carbohydrate Research 2006, 341, 1081-1090.
"Application of Bis(diphenylphosphino)ethane in Staudinger-type N-Glycosyl Amide
Synthesis," D. P. Temelkoff, C. R. Smith, D. A. Kibler, S. McKee, S. Duncan, M. Zeller,
M. Hunsen, and P. Norris, Carbohydrate Research, 2006, 341, 1645-1656.
"Crystal structure of 1-(2,3:5,6-di-O-isopropylidene-beta-D-mannofuranosyl)-1H[1,2,3]triazol-4,5-dicarboxylic acid diethyl ester," H. Seibel, P.L. Miner, P. Norris, and T.R.
Wagner, J. Chem. Cryst., 2006.
"Cu(I)-Catalyzed formation of D-mannofuranosyl 1,4-disubstituted 1,2,3-triazole
carbohybrids," P.L. Miner, T.R. Wagner, and P. Norris, Heterocycles 2005, 65, 10351049.
>40 total, most with YSU undergrad or MS students as coauthors
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What is Organic Chemistry?
The study of the compounds that contain carbon and
the reactions of those materials (millions known)
Why a whole year of Organic?
Carbon can bond in multiple ways to form a huge
number of different molecules, and these compounds
form the basis of many different disciplines, e.g.:
Biology (DNA, proteins, carbohydrates)
Medicine and Pharmacy (Aspirin, Taxol, AZT)
Chemical Engineering (oil, plastics, fine chemicals)
Forensics (Biological materials, chemical tests)
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From Organic Chemistry to Biology, Medicine, Pharmacy, etc.
OH OH
O
CO2H
OH
AcHN
OH
N-acetylneuraminic acid
O
CO2Et
AcHN
NH3.HPO4
Tamiflu - Giliad/Roche
OH OH
O
CO2H
OH
AcHN
H2N
NH
Relenza - GSK
From Scientific American – www.sciam.com
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Staphylococcus aureus – Norris/Fagan
Gram-positive, cluster-forming coccus, causes food poisoning,
endocarditis, osteomyelitis, septiceamia, infections on implants
Vancomycin
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Organic Chemistry – Materials and Uses
Organic
Chemistry
chemical
synthesis
materials
New
Materials
chemistry
New
Compounds
medicinal
chemistry
New
Medicines
Biochemistry
and
Chemical Biology
Nanotech,
Engineering
Proteomics,
Genetics
Pharmacy,
Medicine
Chemistry 37193719-3720
H
C
H
H
H
~1800 – Organic Chemistry : the chemistry of natural products based
on carbon
2006 – Organic Chemistry : “molecular engineering”
6
Timeline
1807
Berzelius introduces the term “Organic Chemistry” to describe
the study of compounds isolated from nature
1828
Wöhler makes urea, the first natural organic compound to be
synthesized in the laboratory
1890
Fischer studies the chemistry of proteins, carbohydrates and
the nucleic acids - Biochemistry
1950
Woodward and Eschenmoser complete the first total synthesis
of Vitamin B12. NMR begins to be useful.
1990
Kishi, Nicolau, Smith, Schreiber, etc. complete total syntheses
of compounds such as Brevetoxin B, Taxol, etc.
2000
Chemical Biology, Molecular Engineering
Teaching Philosophy: Organic Chemistry as a Language
O
O
catalytic H+
OH
+
O
OH
(- H2O)
(- H +)
H2O
O
H
O
O
H
OH
OH
O
OH
O
(- H 2O)
O
H
HO
OH
HO OH
H+
transfer
HO
O
H
H
O H
O
Natural Products Chemistry
O
H2N
NH2
UREA - 1828
Ley, Veitch, Beckmann, Burke, Boyer
and Maslen. ACIEE, August 2007
7
Carey Chapter 1 - Chemical Bonding
“Structure determines properties”
• Atomic and electronic structure of atoms
• Ionic and covalent bonding
• Electronegativity and polar covalent bonds
• Structures of organic compounds - representations
• Resonance within molecules
• Shapes of molecules
• Molecular orbitals and orbital hybridization
Periodic Table of the Elements
1.1 Atoms, electrons, and orbitals
Probability distribution for an electron
Figure 1.1
8
Boundary surfaces of a 1s and 2s orbital
Figure 1.2
Boundary surfaces of the 2p orbitals
Figure 1.3
Electronic Configurations of Atoms
9
Electronic Structure of Atoms
Atom
Atomic No.
Electronic Structure
H
1
1s1
He
2
1s2
Li
3
1s2 2s1
Be
4
1s2 2s2
B
5
1s2 2s2 2px1
C
6
1s2 2s2 2px1 2py1
N
7
1s2 2s2 2px1 2py1 2pz1
O
8
1s2 2s2 2px2 2py1 2pz1
1.1 General Concepts
• Orbitals higher in energy further they are from nucleus.
• Designated by principal quantum number (1, 2, 3, etc.).
• Degenerate orbitals (same energy) fill up singly before
they double up (Aufbau).
• Maximum of two electrons per orbital, each having
opposite spin (Pauli exclusion principle).
• Impossible to know both the speed and location of an
electron at the same time (Heisenberg uncertainty).
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1.2-1.3 Bonding
Atoms trying to attain the stable configuration of a
noble (inert) gas - often referred to as the octet rule
1.2 Ionic Bonding - Electrons Transferred
1.3 Covalent Bonding - Electrons Shared
type of bond that is formed is dictated by the
relative electronegativities of the elements involved
Electronegativity
the attraction of an atom for electrons
1.2 Ionic bonding
Electrons Transferred
Big differences in E.N. values
Metals reacting with non-metals
1
Important Electronegativity Values
H
2.1
Li
Be
1.0
B
C
N
O
F
2.0
2.5
3.0
3.5
4.0
Cl
3.0
Br
2.8
I
2.5
1.3 Covalent Bonding - Similar electronegativities
Lewis dot representations of molecules
H.
+
H.
Hydrogen atoms
H:H
B.D.E
Hydrogen molecule
+104 kcal/mol
H
C
H
+4H
B.D.E
C
H
H
+104 kcal/mol
B.D.E. = bond dissociation energy
1.3 Lewis Dot Structures of Molecules
2
1.4 Double bonds and triple bonds
Double bonds - alkenes
H H
C::C
H
H
H
H
C
C
H
H
Triple bonds - alkynes
H:C:::C:H
H C
C H
1.5 Polar covalent bonds and electronegativity
H2
HF
H2O
CH3Cl
CH4
Based on electronegativity
δ+
H
.. δ−
F:
..
δ−
H
Li
δ+
1.6 Structural Formula - Shorthand in Organic Chemistry
H HH H
H
H
CH3CH2CH2CH3
H
H
H H
CH3CH2CH2CH2OH
H Cl
H
H
H
H
H H
H
H
H
H
OH
Cl
3
1.6 Constitutional Isomers
H H
H C C O H
H H
H
H
H C O C H
H
H
Same molecular formula, completely different
chemical and physical properties
1.7 Formal Charge
O
H O N
O
Formal charge =
group number
- number of bonds
O
O
- number of
unshared
electrons
O
1.8 Resonance Structures - Electron Delocalization
O
O
O
O
O
CH3
C
O
O
O
O
CH3
C
O
Table 1.6 – formal rules for resonance
4
1.9 Shapes of Molecules
Shapes of molecules are predicted
using VSEPR theory
1.9 Shape of a molecule in terms of its atoms
Figure 1.9
Table 1.7 – VSEPR and molecular geometry
5
Trigonal planar geometry of bonds to carbon in H2C=O
Linear geometry of carbon dioxide
1.10 Molecular dipole moments
Figure 1.7
1.11 Curved Arrows – Extremely Important
•
Curved arrows are used to track the flow of
electrons in chemical reactions.
•
Consider the reaction shown below which shows
the dissociation of AB:
A
B
A+
+
-
B
6
Curved Arrows to Describe a Reaction
Many reactions involve both bond breaking
and bond formation. More than one arrow
may be required.
H
H
O
+
H
C
H
Br
H
O
H
C
H
+
Br
-
H
1.12 Acids and Bases - Definitions
Arrhenius
An acid ionizes in water to give protons. A base
ionizes in water to give hydroxide ions.
Brønsted-Lowry
An acid is a proton donor. A base is a proton
acceptor.
Lewis
An acid is an electron pair acceptor. A base is an
electron pair donor.
1.13 A Brønsted-Lowry Acid-Base Reaction
A proton is transferred from the acid to the base.
B .. + H
base
acid
A
+
B
H
+ .. A –
conjugate conjugate
acid
base
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Proton Transfer from HBr to Water
hydronium ion (H3O+)
H
.. O .. + H
H
+
.. O
..
.
Br
.. .
H +
.. –
.. Br ..
..
H
H
base
acid
conjugate
acid
conjugate
base
Equilibrium Constant for Proton Transfer
H
.. O .. + H
H
.. O+
..
.
Br
.. .
H
.. –
.
+ .. Br
.. .
H
H
[H3O+][Br–]
Ka =
[HBr]
pKa = – log10 Ka
Acids and Bases: Arrow Pushing
H O H
+
H Br
?
H O H
H
+
Br
H O H
+
H Br
H O H
H
+
Br
H O H
+
H Br
H O H
H
+
Br
Ka =
[H3O+][Br–]
~ 106 for HBr, pKa = - 5.8
[HBr]
8
Need to know by next class:
pKa = -log10Ka
STRONG ACID = LOW pKa
WEAK ACID = HIGH pKa
HI, HCl, HNO3, H3PO4
pKa -10 to -5
H3O+
pKa – 1.7
Super strong acids
RCO2H
pKa ~ 5
acids
PhOH
pKa ~ 10
get
H2O, ROH
pKa ~ 16
weaker
RCCH (alkynes)
pKa ~ 26
RNH2
pKa ~ 36
Extremely weak acid
RCH3
pKa ~ 60
Not acidic at all
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1.14 What happened to pKb?
• A separate “basicity constant” Kb is not necessary.
• Because of the conjugate relationships in the
Brønsted-Lowry approach, we can examine acidbase reactions by relying exclusively on pKa values.
H
H C H
H
H
H C
H
pKa ~60
Corresponding base
Essentially not acidic
Extremely strong
1.15 How Structure Affects Acid/Base Strength
Bond Strength
• Acidity of HX increases (HI>HBr>HCl>HF) down the periodic table as
H-X bond strength decreases and conjugate base (X:- anion) size
increases (basic strength of anion decreases).
strongest H—X bond
weakest H—X bond
Electronegativity
Acidity increases across periodic table as the atom attached to H gets
more electronegative (HF>H2O>H2N>CH4).
least electronegative
most electronegative
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Inductive Effects
Electronegative groups/atoms remote from the acidic H can effect the
pKa of the acid.
CH3CH2O H
CF3CH2O H
pKa = 16
pKa = 11.3
• O – H bond in CF3CH2OH is more polarized
• CF3CH2O- is stabilized by EW fluorine atoms
Resonance Stabilization in Anion
Delocalization of charge in anion (resonance) makes the anion more
stable and thus the conjugate acid more acidic
e.g. (CH3CO2H > CH3CH2OH).
CH3 CH2 OH
CH3 CH2 O
pKa ~16
CH3
O
O
C
C
CH3
OH
O
CH3
O
C
O
pKa ~5
1.16 Acid-base reactions - equilibria
H Cl + NaOH
NaCl
O
CH3OH
H2O
O
+
H3C
+
NaOH
OH
+
+
H3C
NaOH
ONa
CH3ONa
H 2O
+
H2O
The equilibrium will lie to the side of the
weaker conjugate base
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1.17 Lewis acids and Lewis bases
F3B
CH2CH3
+ •• O ••
CH2CH3
Lewis acid
–
F3B
CH2CH3
+
•
O•
CH2CH3
Lewis base
Product is a stable substance. It is a liquid with a
boiling point of 126°C. Of the two reactants, BF3 is a
gas and CH3CH2OCH2CH3 has a boiling point of 34°C.
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