Introduction to Organic and Biochemistry

Background information

Introduction
Chapter 1: Structure of organic compounds
Chapter 2: Properties of organic compounds
Errata

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Introduction

This page provides an introduction to Ch 1-2 of the Intro Organic/Biochem (X402) book, by Ouellette. We will not formally cover these two chapters, but you may well find them very useful.

Intro Organic/Biochem (X402) does assume some knowledge of introductory chemistry. Ch 1 (Structure of organic compounds) and Ch 2 (Properties of organic compounds) of Ouellette review some of this background.

To help guide you with these background chapters, here is my analysis of them. Of course, people's backgrounds vary widely, and people will vary in how they want to deal with these two introductory chapters. I encourage each of you to at least browse these two chapters, perhaps making your own personal outline. Then, study carefully those sections that are key background and that you feel need some study. Otherwise, refer to these sections as needed. I will point to them as they become relevant.

Some of you may want to do some review or advance preparation before the course starts, and this page should help you with priorities. Note that using other chemistry books for such review is also good. In fact, using a book with which you are already familiar can be a very good review.

Even with familiar topics, you may find an unfamiliar twist in these chapters. In presenting the background material, Ouellette tends to use more examples from organic chemistry than you probably encountered for the same topics in introductory chemistry. If you review these topics in advance, don't worry about the organic details, but emphasize the ideas.

For visitors... Even if the details, referring to a specific book, do not apply to you, the material below should give you an idea of how your general background in chemistry is relevant to starting organic chemistry. Most organic books start with, or somehow include, some review of these topics. Remember, going back and reviewing a chem book that you used in a previous course is often very good. You are familiar with the book, and reviewing that book can be one good way to get back to speed.

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Chapter 1: Structure of organic compounds


For Ch 1, the most important sections at the start are 4, 7, 10, 11. Sections 4 & 7 are background material; it is important that you review these as necessary and bring yourself up to speed. Sections 10-11 are important, but might reasonably be considered new material, which you can deal with as we go through Ch 3. Note that Sect 1.2, which is mostly "advanced", contains one important basic topic.

Here is a brief overview of Ch 1 by section:

1.1. Inorganic and organic compounds. Good introduction. Look it over.
1.2. Atomic structure. If you are serious about going on in organic chemistry, you do need to understand the orbital model of atoms. However, for this course, it is somewhat of an "advanced topic". That is, we will discuss orbitals from time to time, but it is not a critical topic. The last part of the section, on valence electrons, is important. You should know how to read the number of valence electrons for main group elements directly from the periodic table.
1.3. Atomic properties. Most important is electronegativity (EN). In particular, you should know the general trend of EN.
1.4. Types of bonding. Key background section. You need to know generally about ionic and covalent bonds. Understanding polar covalent bonds requires EN, from Sect 1.3. If you have trouble with this section, you might want to review a beginning chem book.
1.5. Formal charge. Minor; we rarely discuss formal charge in this introductory course.
1.6. Resonance. We will talk about resonance structures and resonance stabilization from time to time. You can read this section when it comes up. The first time will be in Ch 5.
1.7. Molecular shape. The other key background section.
1.8. Orbitals and molecular shapes. Discusses the hybrid orbitals that are ubiquitous in organic chemicals. See note above for Sect 1.2 about orbitals. We will discuss this along with Ch 3 (and later chapters). But again, if this is your weakest point it is not a serious problem.
1.9. Functional groups. Preview of several upcoming chapters. It is good to look at this, and to know it is there, but don't worry about this section for now. If a functional group comes up, you can glance at this section to help identify it. However, I will not hold you responsible for functional groups until we have formally covered them, in their own chapters.
1.10. Structural formulas. Discusses various ways to draw structural formulas for organic molecules. Important; we will discuss this along with Ch 3.
1.11. Isomers. Important; we will discuss this at several points, starting in Ch 3.
1.12. Nomenclature. A useful brief introduction to an issue that we will deal with as we go through the chapters.
Explorations with Models. Anything you do with this section of any chapter is good. Making models is very helpful in organic chemistry.

As you go through the Ch, study the examples and do the problems along the way. The answers to all the in-chapter problems are at the back of the book, as are the answers to the odd-numbered exercises (end of chapter). If you can do most of exercises 1-10 & 19-22 at the end of the chapter, that would indicate that you are reasonably well prepared for the course. Anything you do beyond that would be considered "getting ahead". I am happy to discuss any of these, or to look at your work, even before the course starts.


For Ch 2, the most important section at the start is Sect 1. Several other sections will be useful, but you can read them as needed during the course. It is common that students taking X402 need some review on acids and bases, oxidation and reduction, and chemical equilibrium. Any reading you do on these topics in advance is good, but don't feel that it is "necessary" to do so. Some of the material in this chapter is frankly more advanced than we need for X402, but may be useful for those going on in organic chemistry.

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Chapter 2: Properties of organic compounds

Here is a brief overview of Ch 2 by section:

2.1. Structure and physical properties. Intermolecular forces, such as dipole interactions, hydrogen bonds, London forces. Relevant to physical properties such as boiling point. This section builds on Sect 1.4. Very important background.
2.2. Chemical reactions. A brief introduction to the remaining parts of the chapter. Little substantive content per se, but worth browsing.
2.3. Acid-base reactions. Good introduction to acids and bases. Includes Bronsted-Lowry and Lewis descriptions. In this course, we will usually use the former. Be sure you understand about Bronsted-Lowry acid-bases. Review at the start, or as needed during the course. Those who are going on in organic chemistry should learn about Lewis acids-bases.
2.4. Oxidation-reduction reactions. Good introduction to redox reactions. You should know some of this from introductory chemistry. Review as needed, perhaps as it comes up. Note that in intro chemistry one generally learns about redox in terms of electron count; in organic chemistry it is usually more convenient to count H and O atoms, as Ouellette discusses here. I have a Practice quiz on this topic which will help you see how these two ways of counting redox are equivalent.
2.5. Classification of organic reactions. This is quite different from the classification of reaction types you probably encountered in introductory chemistry. Not important for us, but perhaps useful for perspective. It may be most useful as a review, once you have encountered several reaction types. For example, we meet addition reactions in Ch 4 and substitution reactions in Ch 5. At that point, you might want to read the appropriate parts of this section, to help you make a clear distinction between these two reaction types. Be careful to not worry about parts of this section that have not yet come up.
2.6. Chemical equilibrium. Includes Le Chatelier's principle, which we will use in discussing which direction a reaction will go. Review as needed. The quantitative parts are less important for us, except as noted for the next section.
2.7. Equilibria in acid-base reactions. Application of Section 2.6 to the reactions introduced in Sect 2.3. Includes the ionization of water, and Kw. We will not use this much, but Ka values are a useful way to describe acids, so some qualitative understanding is helpful.
2.8. Structure and acidity. A more advanced discussion of acidity than we need for this course. Those who are going on in organic chemistry may want to read this at some point, even after the course.
2.9. Reaction mechanisms. A more advanced discussion of reactions than we need for this course. Those who are going on in organic chemistry may want to read this at some point, even after the course.
2.10. Reaction rates. Good introduction to reaction rates. Includes ideas of effective collisions, activation energy, transition state, reaction coordinate diagrams (Fig 2.5), catalysts. You should know about these before starting this course, but this material is sometimes glossed over in introductory courses. This section may be good for study at the start, or refer to it as needed during the course.

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Errata

Ch 2. p 62 #1. Model shown is for the wrong compound. The correct compound is pentane, CH3CH2CH2CH2CH3. For a picture of the correct model, see p 95 #5.


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Last update: September 12, 2009