chapter 10, structure and bonding in alkanesadhunter.people.ysu.edu/teaching/chem506/notes10.doc ·...

Chemistry 506 Dr. Hunter’s Class Chapter 10. .

Chemistry 506: Allied Health Chemistry 2

Chapter 10, Structure and Bonding in Alkanes

Basics of Structure and Bonding

Introduction to General, Organic & Biochemistry, 5th Edition by Bettelheim and March: Chapter 10, Pages 309-352

Outline Notes by Dr. Allen D. Hunter, YSU Department of Chemistry, 2000.

Outline

10A SECTION(S) 10.1 WHAT IS AN ORGANIC CHEMICAL?.......................................3

10B SECTION(S) 10.2 SOURCES OF ORGANIC CARBONS...........................................5

10C SECTION(S) 10.3/4 STRUCTURES AND BONDING..................................................6

10D SECTION(S) 10.5/6 HYDROCARBONS AND ALKANES........................................17

10E SECTION(S) IUPAC NOMENCLATURE...................................................................21

10F SECTION(S) CYCLOALKANES..................................................................................24

10G SECTION(S) 10.7 SKIP..................................................................................................24

10H SECTION(S) 10.8 PHYSICAL PROPERTIES............................................................25

10I SECTION(S) 10.11 CHEMICAL PROPERTIES........................................................26

10J SECTION(S) 10.12 FUNCTIONAL GROUPS.............................................................27

10K SECTION(S) 18.2 AMINO ACIDS HAVING ALKYL SIDE CHAINS....................30

2000, Dr. Allen D. Hunter, Department of Chemistry, Youngstown State University

1


10A Section(s) 10.1 What is an Organic Chemical ?

Definition

Compounds of Carbon

Mostly Covalent Bonding

Related to Molecules of Life

Where do they come from?

Numbers

Total (> 10,000,000)

Fully isolated, characterized, and reported

New (> 500,000 / year)

Accelerating rate of discovery

Linear Synthetic Strategies vs. Combinatorial

Synthetic Strategies

Characterization Methods

Automation and Productivity


2


What is so Special about Carbon?

Bond Orders (single bonds, double bonds, and triple

bonds)

Strong Stable bonds to almost all atom types

Long chains

This is a unique combination


3


10B Section(s) 10.2 Sources of Organic Carbons

Nature and Organic Chemicals

Isolation from natural sources

natural products

Synthesis and Organic Chemicals

man made organic products

lab scale synthesis vs. factory scale synthesis

Production Choices from Dual sources

Cost Considerations and environmental considerations

Semi-Synthetic Organic Compounds


4


10C Section(s) 10.3/4 Structures and Bonding

How Do We Know Structures?

Analytical Data

Spectroscopic Methods

Sporting Methods

Specific absorption of light

NMR = Nuclear Magnetic Resonance (cf. MRI,

Magnetic Resonance Imaging)

Infra-Red (IR)

Ultra Violet-Visible (UV-Vis)


5


X-Ray Crystallography/Diffraction

Non-Sporting Method

Single Crystals

Hardware

Data Collection

Data Analysis

General Features of Structures

Complex 3D Shapes

109.5, 120, and 180 Bond Angles

1.2 – 1.55 Bond Distances (C-H 1

Structural Correlations with Properties


6


Molecular Formulae

Elements present

Number of atoms of each type

Molecular Weight

Not unique to molecules

e.g. C11H14O


7


Structural Formulae

Connectivity

3D Structures (unique)

Related to Properties

Mp, Bp, taste, toxicity, strength, etc.

Examples a few pages on


8


Rationalization by Lewis, VSEPR, and VBT Theories

Lewis Theory Review (section 3.6)

Lone pairs and bonds

Valence electrons

Rigorous Method

Count number of valence electrons

Place total number of valence electrons around each

atom to give it a complete octet


9


Quick and dirty Lewis method (for common "organic"

elements)

Bond Lengths

Bond Angles

H one bond and no lone pairs

F, Cl, Br, and I one bond and three lone pairs

O, S, Se, and Te two bonds and two lone pairs

N, P, As, and Sb three bonds and one lone pair

C, Si, Sn, and Ge four bonds and no lone pairs


10


VSEPR, Valence Shell Electron Pair Repulsion Theory,

Review

Molecular shapes bond angles

Four groups Tetrahedral, td

Three groups Trigonal planar

Two groups Linear

Number of "things"

4 things -> 109.5

3 things -> 120

2 things -> 180


11


Valence Bond Theory, VBT, Review

Hybridization

109.5 -> sp3

120 -> sp2

180 -> sp


12


Examples of Problem Types

Predict Lewis Structures

Predict hybridizations

Predict bond angles

Predict bond lengths

Worked Example(s) [For each of the following molecules, draw the

correct Lewis structure and predict the hybridizations, bond lengths and bond angles

around the * atoms.]


13


Structural Isomers

Definition

Same atoms but attached differently

Types

Positions of Atoms

Strait Chain vs. Branched Chain

Multiple Bonds vs. Rings

Examples [For following molecular formulae, draw all of the structural

isomers (up to a maximum of 5). Be sure that you show all atoms and bonds for

each.]

C2H6O


14


C4H10

C3H6


15


10D Section(s) 10.5/6 Hydrocarbons and Alkanes

Definitions

Hydrocarbon

(CnHm)

sources

Alkane

(CnH2n+2, e.g., C2H6, C5H12, C100H202)

only single bonds

Alkene

At least one double bond

Alkyne

At least one triple bond

Aromatic/Arene

"benzene like"

"alternating" single and double bonds around a ring


16


Examples of Alkanes

Methane (sources, cost), CH4

Ethane, C2H6

Propane, C3H8

Butane, C4H10

Know C1-C10 Alkane Names (Table 10.4) (Pent, Hex,

Hept, Oct, Non, Dec)

Molecular Weight -> Mp and Bp


17


Structures of Alkanes

Bond angles ( 109.5)

Bond distances ( 1.54 (C-C) and 1.0

Ring Strain (C3 and C4 rings)

Types of Carbons in Alkanes

1, Primary Carbon, CH3

2, Secondary Carbon, CH2

3, Tertiary Carbon, CH

4, Quaternary Carbon, C

Examples


18


Rotation Around Bonds in Alkanes

-Bonds, Sigma-Bonds

Free Rotation or Restricted Rotation?

Steric Effects, Rings

Alkane Structural Isomers

e.g. C5


19


10E Section(s) IUPAC Nomenclature

Steps

Find longest continuous chain (Alkane)

Number carbons in chain from end that give side chains

lowest number

Identify side chains

Name

Attachment Position(s)

Number of groups (di, tri, tetra, penta, hexa, hepta, octa,

nona, deca)

Assemble name (punctuation)

,

-


20


Side Chain Names

Alkyl (Table 10.4 for prefixes)

Methyl, CH3

Ethyl (C2H5)

CH2CH3

Propyl (C3H7)

n-propyl

iso-propyl

Butyl (C4H9)

n-butyl

iso-butyl

sec-butyl

tert-butyl


21


Pentyl, etc.

n-alkyl

Iso-alkyl

Halogens

Fluoro

Chloro

Bromo

Iodo

Examples


22


10F Section(s) Cycloalkanes

cyclo prefix

cyclobutane, cyclohexane, etc.

number from functional groups

Ring strain (C3 & C4)

Examples

10G Section(s) 10.7 Skip


23


10H Section(s) 10.8 Physical Properties

Physical State

Mp and Bp

Depends on MW

Van der Waals Forces

Intermolecular Bonding vs. Intramolecular Bonding

Non-Polar compounds

Definition of Polar vs. Non-Polar

Solubility

Non-polar organic solvents vs. water

Density

Cf. water


24


10I Section(s) 10.11 Chemical Properties

UNREACTIVE

Combustion (balance reactions)

__ CH4 C

__ C3H6 C

__ C6H6 C


25


10J Section(s) 10.12 Functional Groups

Framework vs. Functional Group

Identifying Functional Groups

Table 10.7, p342

Alkene

Alkyne

Aromatic

Alkyl Halide

Alcohol


26


Ether

Thiol (mercaptan)

Amine

Aldehyde

Ketone


27


Carboxylic Acid

Ester

Amide

Problems 10.1 – 10.51 (except 10.36 b, c, f, and 10.37)


28


10K Section(s) 18.2 Amino Acids having Alkyl Side Chains

Amino Acids (Building Blocks of Proteins)

Generic AA = H2N-CHR-CO2H

6 Nonpolar Alkyl Side Chains

Glycine, R = H

Alanine, R = CH3, methyl

Valine, R = CH(CH3)2, isopropyl

Leucine, R = CH2CH(CH3)2, isobutyl

Isoleucine, R = CH(CH3)(CH2CH3), sec-butyl

Proline, HN{CH2CH2CH2-ring}CH-CO2H


29


Index of Topics and Vocabulary

1

109.5...................................................................................6109.5...........................................................................11, 12120......................................................................................6120..............................................................................11, 12180..........................................................................6, 11, 121 ......................................................................................18

2

2 ......................................................................................18

3

3 ......................................................................................18

4

4 ......................................................................................18

A

Alanine...............................................................................29Alcohol..............................................................................26Aldehyde............................................................................27Alkane................................................................................16Alkane Names....................................................................17Alkane Structural Isomers.................................................19Alkanes..............................................................................17Alkene..........................................................................16, 26Alkyl..................................................................................21Alkyl Halide.......................................................................26Alkyne..........................................................................16, 26Amide................................................................................28Amine................................................................................27Amino Acids......................................................................29Amino Acids having Alkyl Side Chains............................29Analytical Data....................................................................5Arene..................................................................................16Aromatic......................................................................16, 26Attachment Position(s)......................................................20Automation..........................................................................2

B

balance reactions................................................................25benzene..............................................................................16bond angles..................................................................11, 13Bond angles.......................................................................18Bond Angles..................................................................6, 10Bond distances...................................................................18Bond Distances....................................................................6bond lengths.......................................................................13Bond Lengths.....................................................................10

Bond Orders.........................................................................3bonds....................................................................................9Bp ............................................................................8, 17, 24Branched Chain.................................................................14Bromo................................................................................22Butane................................................................................17Butyl..................................................................................21

C

C2H6...................................................................................17C3H8...................................................................................17C4H10..................................................................................17Carboxylic Acid.................................................................28CH4.....................................................................................17Characterization Methods....................................................2characterized........................................................................2Chemical Properties...........................................................25Chloro................................................................................22CnHm...................................................................................16Combinatorial Synthetic Strategies.....................................2Combustion........................................................................25complete octet......................................................................9Compounds of Carbon.........................................................2Covalent Bonding................................................................2cyclo prefix........................................................................23Cycloalkanes......................................................................23cyclobutane........................................................................23cyclohexane.......................................................................23

D

Dec.....................................................................................17deca....................................................................................20Density...............................................................................24di 20double bond.......................................................................16double bonds........................................................................3

E

Ester...................................................................................28Ethane................................................................................17Ether...................................................................................27Ethyl...................................................................................21

F

factory scale synthesis.........................................................4Fluoro.................................................................................22Framework.........................................................................26Free Rotation.....................................................................19Functional Groups.............................................................26


30


G

Generic AA........................................................................29Glycine...............................................................................29

H

Halogens............................................................................22Hept....................................................................................17hepta...................................................................................20Hex.....................................................................................17hexa....................................................................................20hybridization......................................................................13Hybridization.....................................................................12Hydrocarbon......................................................................16Hydrocarbons and Alkanes................................................16

I

Infra-Red..............................................................................5Intermolecular Bonding.....................................................24Intramolecular Bonding.....................................................24Iodo....................................................................................22IR 5Iso-alkyl.............................................................................22iso-butyl.............................................................................21Isoleucine...........................................................................29iso-propyl...........................................................................21IUPAC Nomenclature........................................................20

K

Ketone................................................................................27

L

lab scale synthesis................................................................4Leucine..............................................................................29Lewis Structures................................................................13Lewis Theory.......................................................................9Linear.................................................................................11Linear Synthetic Strategies..................................................2lone pairs............................................................................10Lone pairs............................................................................9Long chains..........................................................................3longest continuous chain....................................................20

M

Magnetic Resonance Imaging..............................................5man made organic products.................................................4mercaptan...........................................................................27Methane.............................................................................17Methyl................................................................................21Molecular Formulae.............................................................7Molecular Weight..........................................................7, 17Molecules of Life.................................................................2Mp............................................................................8, 17, 24MRI......................................................................................5Multiple Bonds..................................................................14MW....................................................................................24

N

n-alkyl................................................................................22natural products...................................................................4n-butyl................................................................................21NMR....................................................................................5Non....................................................................................17nona....................................................................................20Non-Polar...........................................................................24Nonpolar Alkyl Side Chains..............................................29Non-Polar compounds.......................................................24n-propyl..............................................................................21Nuclear Magnetic Resonance..............................................5Number carbons in chain...................................................20Number of "things.............................................................11Number of groups..............................................................20

O

Oct......................................................................................17octa.....................................................................................20octet......................................................................................9

P

Pent....................................................................................17penta...................................................................................20Pentyl.................................................................................22Physical Properties.............................................................24Polar...................................................................................24Primary Carbon..................................................................18Problems............................................................................28Production Choices..............................................................4Productivity..........................................................................2Proline................................................................................29Propane..............................................................................17Properties.............................................................................8Propyl.................................................................................21Proteins..............................................................................29punctuation........................................................................20

Q

Quaternary Carbon.............................................................18Quick and dirty Lewis method..........................................10

R

rate of discovery..................................................................2Restricted Rotation............................................................19Ring strain..........................................................................23Ring Strain.........................................................................18Rings............................................................................14, 19Rotation Around Bonds in Alkanes...................................19

S

sec-butyl.............................................................................21Secondary Carbon..............................................................18Semi-Synthetic Organic Compounds..................................4side chains..........................................................................20Sigma-Bonds......................................................................19single bond.........................................................................16


31


single bonds.........................................................................3Single Crystals.....................................................................6Skip....................................................................................23Solubility............................................................................24Sources of Organic Carbons................................................4sp ......................................................................................12sp2 ......................................................................................12sp3 ......................................................................................12Special about Carbon...........................................................3Spectroscopic Methods........................................................5Sporting Methods.................................................................5Stable bonds.........................................................................3Steric Effects......................................................................19Strait Chain........................................................................14strength................................................................................8Structural Correlations with Properties...............................6Structural Formulae.............................................................8Structural Isomers..............................................................14Structures and Bonding........................................................5Structures of Alkanes.........................................................18Synthesis..............................................................................4

T

taste......................................................................................8td ......................................................................................11tert-butyl............................................................................21Tertiary Carbon..................................................................18tetra....................................................................................20Tetrahedral.........................................................................11things..................................................................................11Thiol...................................................................................27toxicity.................................................................................8tri ......................................................................................20Trigonal planar...................................................................11triple bond..........................................................................16triple bonds..........................................................................3

U

Ultra Violet-Visible.............................................................5UNREACTIVE..................................................................25UV-Vis.................................................................................5

V

Valence Bond Theory........................................................12valence electrons..................................................................9Valence electrons.................................................................9Valence Shell Electron Pair Repulsion Theory.................11Valine.................................................................................29Van der Waals Forces........................................................24VBT...................................................................................12VSEPR...............................................................................11

W

What is an Organic Chemical..............................................2

X

X-Ray Crystallography/Diffraction.....................................6

-Bonds.............................................................................19


32



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