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1 Chemistry 3719 - Organic Chemistry I Professor : Dr. Peter Norris Office : 6014 Ward Beecher Telephone : (330) 941-1553 Email : [email protected] Websites : http://www.as.ysu.edu/~pnorris/public_html www.chemfinder.com Lecture needs : Carey Molecular models Adobe Acrobat Reader Web access YSU YSU Molecular Models – www.darlingmodels.com May be used on exams, will be used in lecture YSU YSU

Chemistry 3719 - Organic Chemistry Ipnorris.people.ysu.edu/Semesters/3719F2007/Chapter1web.pdf · 2007. 8. 24. · H : C : : : C : H HCC H C : : C H H HH CC H H H H Double bonds -alkenes

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  • 1

    Chemistry 3719 - Organic Chemistry I

    Professor : Dr. Peter NorrisOffice : 6014 Ward BeecherTelephone : (330) 941-1553Email : [email protected] :

    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 : [email protected]

    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.HPO4AcHN

    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 CH

    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.