1

Chemistry 3719 - Organic Chemistry I

Professor : Dr. Peter NorrisOffice : 6014 Ward BeecherTelephone : (330) 941-1553Email : pnorris@ysu.eduWebsites :

http://www.as.ysu.edu/~pnorris/public_html

www.chemfinder.com

Lecture needs:

• Carey

• Molecular models

• Adobe Acrobat Reader

• Web access

YSUYSU

Molecular Models – www.darlingmodels.com

May be used on exams, will be used in lectureYSUYSU

2

Lab needs:

• Pavia, Lampman, Krizand Engel

• Goggles

• Lab coat

• Bound notebook

YSUYSU

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

YSUYSU

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)

YSUYSU

3

Chemistry 3719 Personnel

Dr. Peter Norris3719 lecture

Dr. John Jackson3719 recitation

Calvin Austin3719 lab

Lucas Beagle3719 lab

Lemuel Carlisle3719 lab

Brian Dobosh3719 lab

Mike Evans3719 lab

Ashley Malich3719 lab

Kevin White3719 lab

YSUYSU

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 : pnorris@ysu.eduYSUYSU

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

YSUYSU

4

"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, 1035-1049.

>40 total, most with YSU undergrad or MS students as coauthors

"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.

"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.

"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.

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.

YSUYSU

YSUYSU

YSUYSU

5

YSUYSU

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)

YSUYSU

From Organic Chemistry to Biology, Medicine, Pharmacy, etc.From Organic Chemistry to Biology, Medicine, Pharmacy, etc.

YSUYSU

N-acetylneuraminic acid

Tamiflu - Giliad/Roche

Relenza - GSK

From Scientific American – www.sciam.com

CO2EtO

NH3.HPO4

AcHN

O CO2H

H2N NH

AcHN

OHOH

OH

O CO2H

AcHN

OHOH

OH

OH

6

VancomycinYSUYSU

Staphylococcus Staphylococcus aureusaureus –– Norris/FaganNorris/Fagan

Gram-positive, cluster-forming coccus, causes food poisoning, endocarditis, osteomyelitis, septiceamia, infections on implants

Organic Chemistry – Materials and Uses

Organic Chemistry

chemicalsynthesis

NewCompounds

NewMedicines

medicinal

chemistry

materials

chemistry

NewMaterials

Pharmacy,Medicine

Nanotech,Engineering

Biochemistryand

Chemical Biology

Proteomics,Genetics

~1800 – Organic Chemistry : the chemistry of natural products based on carbon

2006 – Organic Chemistry : “molecular engineering”

Chemistry 3719Chemistry 3719--37203720

H

CH

HH

7

Timeline1807 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

OHcatalytic H+

+OH

O

O

O

OH

OH

OH

OH

HO HO OH

OH

HO O

O

HHH+

transfer

OH

O

O

OH

H2O

OH

O

(- H2O)

(- H2O)

(- H+)

Teaching Philosophy: Organic Chemistry as a Language

H2N

O

NH2

UREA - 1828

Natural Products Chemistry

Ley, Veitch, Beckmann, Burke, Boyer and Maslen. ACIEE, August 2007

8

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 electronFigure 1.1

9

Boundary surfaces of a 1s and 2s orbitalFigure 1.2

Boundary surfaces of the 2p orbitalsFigure 1.3

Electronic Configurations of Atoms

10

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).

1

1.3 Covalent Bonding - Electrons Shared

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

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

2

Important Electronegativity Values

H

2.1

Li Be B C N O F

1.0 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

H . + H . H : H Hydrogen atoms Hydrogen molecule

C + 4 H C

H

H

H

H

Lewis dot representations of molecules

B.D.E

+104 kcal/mol

B.D.E

+104 kcal/mol

B.D.E. = bond dissociation energy

1.3 Lewis Dot Structures of Molecules

3

1.4 Double bonds and triple bonds

H C C HH : C : : : C : H

C : : CH H

H HC C

H

H

H

H

Double bonds - alkenes

Triple bonds - alkynes

1.5 Polar covalent bonds and electronegativity

H2 HF H2O

CH4 CH3ClBased on electronegativity

LiLiHHδδ−− δδ++

FF::........HH

δ+δ+ δ−δ−

1.6 Structural Formula - Shorthand in Organic Chemistry

CH3CH2CH2CH3

H H

HH H

H HH

HH

CH3CH2CH2CH2OH OH

H ClH

HH

HH H

HHH

H Cl

4

1.6 Constitutional Isomers

HCHH

O C HH

HH C C O H

H

H

H

H

Same molecular formula, completely different chemical and physical properties

1.7 Formal Charge

Formal charge = group number

- number of bonds

- number of unshared electrons

O NO

OH

OO

O

1.8 Resonance Structures - Electron Delocalization

OO

O OO

O

CH3C

O

O

CH3C

O

O

Table 1.6 – formal rules for resonance

5

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

6

Trigonal planar geometry of bonds to carbon in H2C=O

Linear geometry of carbon dioxide

1.10 Molecular dipole moments

Figure 1.7

• Curved arrows are used to track the flow of electrons in chemical reactions.

• Consider the reaction shown below which shows the dissociation of AB:

1.11 Curved Arrows – Extremely Important

A B A+ + B-

7

Many reactions involve both bond breaking and bond formation. More than one arrow may be required.

Curved Arrows to Describe a Reaction

H O + C

H

H

H

Br C

H

O

H

HH + Br-

1.12 Acids and Bases - Definitions

ArrheniusAn acid ionizes in water to give protons. A base ionizes in water to give hydroxide ions.

Brønsted-LowryAn acid is a proton donor. A base is a proton acceptor.

LewisAn acid is an electron pair acceptor. A base is an electron pair donor.

H AB .. B H A–..

+

1.13 A Brønsted-Lowry Acid-Base Reaction

A proton is transferred from the acid to the base.

+ +

base acid conjugate acid

conjugate base

8

hydroniumhydronium ion (Hion (H33OO++))

HH BrBrOO

HH

HH

.... ....

HH

HH

.... OO HH BrBr––.... ....

....

............

....++

Proton Transfer from HBr to Water

basebase acidacid conjugate conjugate conjugateconjugateacid acid basebase

++ ++

[H3O+][Br–]

[HBr]Ka =

H BrO

H

H

.. ..

H

H

.. O H Br–.. ..

..

......

.. ++ +

pKa = – log10 Ka

Equilibrium Constant for Proton Transfer

H O H + H Br H O H + BrH?

Acids and Bases: Arrow Pushing

H O H + H Br H O H + BrH

H O H + H Br H O H + BrH

[H3O+][Br–]

[HBr]Ka = ~ 106 for HBr, pKa = - 5.8

9

Need to know by next class:pKa = -log10Ka

STRONG ACID = LOW pKa WEAK ACID = HIGH pKa

HI, HCl, HNO3, H3PO4 pKa -10 to -5 Super strong acids

H3O+ pKa – 1.7

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

10

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 acid-base reactions by relying exclusively on pKa values.

CH

HH

H CH

HH

pKa ~60

Essentially not acidic

Corresponding base

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

ElectronegativityAcidity increases across periodic table as the atom attached to H gets more electronegative (HF>H2O>H2N>CH4).

least electronegative most electronegative

11

Inductive EffectsElectronegative groups/atoms remote from the acidic H can effect the pKa of the acid.

pKa = 16 pKa = 11.3

CH3CH2O H CF3CH2O H

• O – H bond in CF3CH2OH is more polarized

• CF3CH2O- is stabilized by EW fluorine atoms

Resonance Stabilization in AnionDelocalization of charge in anion (resonance) makes the anion more stable and thus the conjugate acid more acidic

e.g. (CH3CO2H > CH3CH2OH).

CH3C

O

O

CH3C

O

O

CH3C

OH

O

CH3 CH2 OH CH3 CH2 O

pKa ~16

pKa ~5

1.16 Acid-base reactions - equilibria

H Cl NaOH NaCl + H2O+

H3C

O

OHNaOH

H3C

O

ONaH2O+ +

H2OCH3ONaNaOHCH3OH + +

The equilibrium will lie to the side of the

weaker conjugate base

12

1.17 Lewis acids and Lewis bases

FF33BB ++ OOCHCH22CHCH33

CHCH22CHCH33

•••• ••••–– ++

FF33BB OOCHCH22CHCH33

CHCH22CHCH33

••••

Lewis acidLewis acid Lewis baseLewis 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.