Purdue University

CHM 26100: Organic Chemistry for

Chemical Engineers I

Electronic Textbook: On-line Resources for

the Study of Organic Chemistry

Compiled by

Prof. P. G. Wenthold

2014 Edition
Introduction – Why an On-Line Text?

I just have to say it: textbook prices are way out of hand.

One of the hidden costs to students that are generally underappreciated is the cost of

textbooks. Students and administrators will have serious discussions about the addition of a $40

a year fee for whatever topic (athletic, health, lab, etc) but the difference between a single used

textbook vs a new one is going to be 2 or 3 times that amount! Therefore, finding ways to cut

costs in textbooks is an important strategy to controlling costs for students.

Unfortunately, from University perspective, it’s not something that gets addressed very

easily. Textbooks are provided to the students via the book stores, and they are supplied by

textbook companies, whose objectives are to make money. Consequently, they will work to find

ways to keep revenues as high as possible, such as regularly provide updated editions so to limit

the market for used textbooks. Let’s be clear – I do not blame them. This is their business, and

they need to do what they can. However, they are doing it at the expense of students.

Over the years that I have taught the courses “Organic Chemistry for Chemical

Engineers” I have become increasingly frustrated with the textbook companies. I had chosen the

text I did because it was the best that covered the materials that I wanted to teach, and did the

best job of providing the correct perspective. However, even in that regard, it has never been

perfect, and I had to re-organize the material slightly. More importantly, as soon as I’d have

something set up to use based on the textbook, they would come out with a new edition, which

means I’d have to re-assess all my materials and assignments to see if they were consistent with

the new text. Add in the fact that the price was getting way out of hand ($280 for a year’s

worth of materials) and I got fed up.

Given that, I started thinking about what is the actual use of a textbook? It’s not in terms

of content, that is for sure. Everything you find in an introductory organic textbook is absolutely
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available elsewhere, for free. This has always been the case, of course, as the information is in

the library, but now we have the internet, which makes it conveniently available to all. The

challenge with having so much information on the internet is in finding the information that is

useful, and making sure it is of sufficient quality. However, if you can do that, there is a wealth

of great information available that comes in different formats. For almost every topic covered in

organic chemistry class, you can find web sites that talk about them, in various levels of detail.

You can find lecture presentations that cover these topics, you can find handouts and tutorials

that provide practice problems and give information on how to solve them. There are interactive

websites with structures and games, and of course there are videos. Videos range from

professors who have recorded their lectures to instructional videos put out by organizations like

Khan Academy or by organic chemistry instructors and tutors. Because organic chemistry is a

ubiquitous subject, being taught by pretty much institution of higher learning in the world, and

the material being taught in introductory courses is highly consistent throughout, there are

countless educational resources available on the internet.

So then, is it possible to take a course in Organic chemistry without a textbook? There

are certainly advantages to the textbook, that is undeniable. For example, the textbook has all

the information centralized in one location. Therefore, you can pull it off the shelf and,

regardless of the topic, look it up in the table of contents or in the index. Second, the textbook

uses a consistent style, and is going to be thorough in coverage without a lot of redundancy.

Third, and perhaps most importantly, an important component of the textbook is that the authors

provide practice problems to allow students to test their knowledge and understanding.

Moreover, it is also possible to purchase “solutions manuals” to use for assistance in solving

problems, to see if they are being done correctly.

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 In contrast, although all of the same information is available on the internet, it is

generally scattered all over. You can find it through web searches, which is somewhat like

looking in an index, but you cannot be assured of quality when you use this approach, and you

have be sufficiently knowledgeable to distinguish good information from bad. However, that is

where this “On-Line Text” comes in. The goal of this “book” is to provide an organized

collection of websites that cover the material taught in CHM 26100 and CHM 26200. By

organizing the links, it will hopefully allow students to use the wealth of information on the web

instead of using a textbook, or, at least an expensive new textbook.

In addition to being free, there are other advantages of using the resources on the internet

instead of a textbook. For example, the different types of media available will be useful to a

wider range of students. Those who learn best by reading textbooks can find detailed textbook-

like pages. However, others may benefit more from seeing lecture notes in presentation format,

whereas others may learn best from the videos, either by full lectures or by the shorter tutorials.

Finally, additional tutorials are available to help students learn how to solve problems and

interactive websites provide practice in doing so. In this book, I have tried to include different

types of resources for each topic to appeal to all types of learners. I encourage you to try out all

different types of media to determine what works best for you.

There are some limits to this type of approach. While it is helpful to provide a lot of

resources to allow students to find those that work best, it also results in a lot of redundancy.

Therefore, many of the links will say the same things, and provide the same information. In

these situations, students will need to recognize the extent of their learning, and figure out what

they can skip. There is no expectation that everyone will want or need to use all the links.

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 A second issue is the lack of a good index of course material. Of course, any topic can be

explored through additional web searching, but it’s not easy to determine whether something

specific is part of the course material. In this respect, a detailed table of contents provides the

best roadmap of what is included in this course.

Finally, one major drawback of an On-Line Text such as this is the lack of good, coherent

sets of practice problems. Although there are absolutely practice problems covering most topics

available on the internet, their quality is highly variable. On one end, you may find superficial

multiple choice questions, such as those in MCAT review pages, which do not require much in

terms of understanding or problem solving. On the other extreme, you can find great exam

questions that other instructors have used. However, you may or may not have access to

answers, and, even if you do, it may just be answers without any providing assistance with

solutions. At the current time, we are working to develop practice problems of our own to

include with each chapter, and, hopefully a solutions guide. For the time being, those problems

are provided separately on Blackboard.

On-Line Resources Included in this Text

Among the challenges in creating a resource such as this is in finding the appropriate on-

line resources to include. To this end, a major resource of the links that are included in this text

has been students who have taken the courses. As an extra credit activity, they have been finding

links to the topics covered in the courses. The links have been screened, at least superficially, to

assess content and quality. A major challenge in using the internet is that web pages come and

go, and links that worked at one time will die. The screening of links in this text is an ongoing

process, as is the process of adding new content.

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 Although the links provided come from a large variety of sources, we have discovered

that there are a few that are very commonly encountered, and provide good resources for of the

topics, although there are certainly aspects that will be missing. The common resources include:

1) The ChemWiki at UC Davis

2) Bill Reusch’s E-Text at Michigan State:
3) Carey’s 4th Edition Organic Text On-Line Resource
4) James Ashenhurst’s Blog
MasterOrganicChemistry.com
This is a blog, and not specifically content pages, but he covers a lot of the common
problems that are faced by organic students. More importantly, his approach to organic
chemistry instruction is very similar to what I use in the course. He does not cover
everything that we do in the course, but what he does cover, he does very well.
5) Khan Academy
Khan Academy provides short (10 – 15 minute) videos on a full range of educational
topics, including organic chemistry. They are good in content, and do cover most of what
we do in the course.
6) Leah 4 Sci
This is a resource provided by Leah Fisch, who is an organic tutor. I find her
presentation style to be clear and easy to listen to. She has a lot of videos available on
youtube, in addition to her own content pages. I prefer her videos.
7) Cliffs Notes
Note a very detailed resource, but covers important stuff. That’s the whole point of Cliffs
Notes.

There are a few other sites that we encounter regularly, although I haven’t found them to be as

comprehensive as those listed above. However, those that are useful are included.

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Organization of the Text

Because it is merely a collection of links, it is easy to organize the text in multiple ways.

The main text is going to be organized by chapters, as with any text, with sub-topics within each

chapter. Links for each chapter or sub-topic will be organized by type, such as web pages, slide

presentations or videos. Each chapter will contain a section with tutorials and with practice

problems. The material covered in the links may be broad, covering the complete chapter’s

worth, or may be very narrow, covering a very specific topic.

Links to the common sources described above will be included and clearly indicated.

However, each will also have its own section in the text, showing the applicable links for each

chapter and sub-topic, along with a those topics that are NOT covered. A detailed Table of

Contents is shown on the next page.

How to Use this Resource

This On-Line Text is meant to be used in conjunction with class. It is not meant to be an

independent resource, and certainly does not replace going to class. It is unlike a typical

textbook in that respect. However, it should serve as a very helpful resource to supplement your

course learning. The goal is to be a source of additional, possibly more detailed information

about the things we are addressing in the course, and to provide a variety of perspectives. The

hope would be that you could consult the topics ahead of time, by considering them in light of

the outlined notes that are provided with the course materials, just as you would with a regular

textbook. However, the links that are provided should also be a great source of information for

studying after lectures, as well. In fact, many of the links were submitted by students, like you,

who looked up a topic that had been mentioned in lecture and were seeking more information.

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That is what you can do with this – use it to get extra information on those topics you still might

have questions about after lecture. Shoot, in respect, you can do additional searches for topics

that aren’t covered adequately herein. Send the link, and it can be included in future editions!

The information is out there! And unlike a lot of information on the internet, most of it is

pretty reliable. Most of it is consistent with what you will find in textbooks. Granted, some of it

is of better quality than others, and some is covered more in depth, but you won’t find a lot that

is “wrong.”

The links provided here come in many flavors, from different sources. A lot of it is

highly redundant – the links have not really been screened to remove redundancy, not even

within the core resources. That’s ok. If you find a source that covers information that you

already know, skip it and move on. The important part is that you already know it. For other

topics, you may find that seeing it multiple times is beneficial.

Can you learn organic chemistry from the internet alone? Probably not. Then again, you

probably can’t learn it just from coming to class and listening to an instructor. Learning organic

chemistry takes a multi-faceted approach. This On-Line Text is just part of it. Good Luck!

The Dynamic Nature of an On-Line Text

One thing that will always be true with a resource that relies upon internet links is that it

will always need to be updated, to include new links and to cull those that are bad or (more

likely) dead. Fortunately, the content is easily updated. We always appreciate information about

dead links that you find within this document or any new ones that you think should be included.

In particular, look for the topics where the links lacking, where you think additional information

would be helpful. Send them along, and we can add them in.

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Table of Contents

Chapter 1. Introduction and Review

1. The Origins of Organic Chemistry
2. Principles of Atomic Structure
3. Bond Formation: The Octet Rule
4. Lewis Structures
4.1 Multiple Bonding
5. Electronegativity and Bond Polarity
5.1 Formal Charges
5.2 Ionic Structures
6. Resonance
6.1 Curved arrow notation
7. Structural Formulas
7.1 Molecular Formulas and Empirical Formulas
8. Acids and Bases
8.1 Arrhenius Acids and Bases
8.2 Brønsted-Lowry Acids and Basis
8.3 Lewis Acids and Bases
8.4 Acid/Base Equilibria

Chapter 2. Structure and Properties of Organic Molecules

1. Wave Properties of Electrons in Orbitals
1.1 Molecular Orbitals
1.2 Pi Bonding
2. Molecular Shapes and Hybridization
2.1 VSEPR
2.2 Drawing Three-Dimensional Molecules
2.3 General Rules of Hybridization and Geometry
3. Bond Rotation
3.1 Newman Projections
4. Isomerism
5. Polarity of Bonds and Molecules
6. Intermolecular Forces
6.1 Polarity Effects on Solubilities
7. Hydrocarbons
8. Functional Groups

Chapter 3. Structure of Alkanes

1. Classification of Hydrocarbons (Review)
2. Nomenclature of Alkanes
3. Physical Properties of Alkanes
4. Structure and Conformations of Alkanes
4.1 Newman Projections
4.2 Staggered and eclipsed conformations of ethane

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 4.3 Potential energy diagram
4.4 Origins of Torsional strain
5. Conformations of Butane
5.1 Anti vs Gauche
5.2 Types of strain
6. Combustion Reactions of Alkanes
7. Cycloalkanes
9.1 Bicyclic Molecules
9.2 Stabilities of Cycloalkanes; Ring Strain
8. Cyclohexane Conformations
8.1 Conformations of Monosubstituted Cyclohexanes
8.2 Cis-trans Isomerism in Cycloalkanes
8.3 Conformations of Disubstituted Cyclohexanes

Chapter 4. Stereochemistry
1. Chirality
1.1 Stereoisomers and Chiral Centers
2. Enantiomers
2.1 (R) and (S) Nomenclature of Asymmetric Carbon Atoms
3. Diastereomers
3.1 Different types of isomers
3.2 Meso Compounds
4. Physical Properties of Stereoisomers
4.1 Optical Activity
5. Racemic Mixtures
5.1 Enantiomeric Excess and Optical Purity
5.2 Resolution of Enantiomers
6. Chirality of Biological molecules

Chapter 5. The Study Of Chemical Reactions

1. Description of Chemical Reactions
1.1 Mechanism
1.2 Thermodynamics vs Kinetics
2. Equilibrium Constants and Free Energy
2.1 Enthalpy and Entropy
2.2 LeChatelier’s Principle
3. Free Radicals
3.1 Enthalpy Changes in Chlorination
4. Chlorination of Methane
5. The Free-Radical Chain Reaction
6. Kinetics and the Rate Equation
6.1 Activation Energy and the Temperature Dependence of Rates
7. Potential Energy Diagrams for Chemical Reactions
7.1 Rate of Multistep Reactions
8. Selectivity in Halogenation
8.1 Bond-Dissociation Enthalpies

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 8.2 The Hammond Postulate
9. Carbon Reactive Intermediates

Chapter 6. Alkyl Halides: Nucleophilic Substitution and Elimination

1. Nomenclature of Alky Halides
1.1 IUPAC
1.2 Common Names
2. Polarity of Alkyl halides
3. Substitution of alkylhalides
3.1 Nucleophiles and Electrophiles
3.2 Polarity and Reactivity
3.3 Substitution vs Elimination
4. Second-Order Nucleophilic Substitution: The SN2 Reaction
4.1 Mechanism, Stereochemistry and Potential Energy Diagram
5. Factors Affecting SN2 Reactions
5.1 Protic vs Aprotic Solvents
6. SN1 Reaction
6.1 Kinetics, stereochemistry and potential energy diagram
7. Factors Affecting SN1 Reactions
8. Properties and Structures of Carbocations
9. Comparison of SN2 and SN1
10. E1 Elimination
10.1 Zaitsev’s Rule
11. E2 Elimination
12. Comparing E1 and E2
13. Summary: Determining SN2, SN1, E2 or E1

Chapter 7. Structure and Synthesis of Alkenes

1. The Orbital Description of the Alkene double Bond

2. Elements of Unsaturation
3. Nomenclature of Alkenes
3.1 Nomenclature of Cis-Trans Isomers
4. Stability of Alkenes
5. Physical Properties of Alkenes
6. Alkene Synthesis
6.1 Elimination of Alkyl Halides
6.2 Alkene Synthesis by Dehydration of Alcohols

Chapter 8. Reactions of Alkenes

1. General Reactivity of the Carbon-Carbon Double Bond

2. Addition of HX to Alkenes

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 2.1. Markovnikov’s Rule
2.2. Free radical addition
3. Hydration of Alkenes
3.1. Oxy-Mercuration
3.2. Hydroboration
4. Halogenation of Alkenes
4.1. Halohydrins
5. Concerted Addition to Alkenes
5.1. Hydrogenation
5.2. Epoxidation
5.3. Diols
6. Oxidation to Carbonyls
7. Polymerization
8. Olefin Metathesis

Chapter 9. Structure and Reactivity of Alkynes

1. Nomenclature of Alkynes
2. Acidity of Alkynes; Formation of Acetylide Ions
2.1 Nucleophilic reactivity of acetylide anions
3. Synthesis of Alkynes by elimination Reactions
4. Electrophilic Addition Reactions of Alkynes
4.1 Acid-catalyzed addition
4.2 Other electrophiles
5. Oxidation and Reduction of Alkynes
5.1 Hydrogenation
5.2 Hydroboration
5.3 Permanganate and ozonolysis

Chapter 10. Structure, Synthesis and Reactions of Alcohols

1. Structure and Classification of Alcohols

2. Nomenclature of Alcohols and Phenols
3. Physical Properties of Alcohols
4. Acidity of Alcohols and phenols
4.1 Alkoxide ions
5. Synthesis of Alcohols
6. Oxidation
6.1 Oxidation states
6.2 Strong oxidizers
6.3 Mild oxidation
7. Alcohols as Nucleophiles and Electrophiles
7.1 Alcohols and alkoxides as Nucleophiles
7.2 Electrophilicity of alcohols

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 7.3 Reduction of Alcohols
8. Reactions of Alcohols with Hydrohalic Acids
8.1 Dehydration of alcohols
9. Reactions of Alcohols with Thionyl Chloride

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