Electron Flow in Organic Chemistry E-Book

Paul H. Scudder

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 1096

Veröffentlichungsjahr: 2023

Beschreibung

Electron Flow in Organic Chemistry

Teaches students to solve problems in Organic Chemistry using methods of analysis that are valuable and portable to other fields

Electron Flow in Organic Chemistry provides a unique decision-based approach that develops a chemical intuition based on a crosschecked analysis process. Assuming only a general background in chemistry, this acclaimed textbook teaches students how to write reasonable reaction mechanisms and use analytical tools to solve both simple and complex problems in organic chemistry. As in previous editions, the author breaks down challenging organic mechanisms into a limited number of core elemental mechanistic processes, the electron flow pathways, to explain all organic reactions—using flow charts as decision maps, energy surfaces as problem space maps, and correlation matrices to display all possible interactions.

The third edition features entirely new chapters on crosschecking chemical reactions through good mechanistic thinking and solving spectral analysis problems using organic structure elucidation strategies. This edition also includes more biochemical reaction mechanism examples, additional exercises with answers, expanded discussion of how general chemistry concepts can show that structure determines reactivity, and new appendix covering transition metal organometallics. Emphasizing critical thinking rather than memorization to solve mechanistic problems, this popular textbook:

• Features new and expanded material throughout, including more flowcharts, correlation matrices, energy surfaces, and algorithms that illustrate key decision-making processes
• Provides examples from the field of biochemistry of relevance to students in chemistry, biology, and medicine
• Incorporates principles from computer science and artificial intelligence to teach decision-making processes
• Contains a general bibliography, quick-reference charts and tables, pathway summaries, a major decisions guide, and other helpful tools
• Offers material for instructors including a solutions manual, supplemental exercises with detailed answers for each chapter usable as an exam file, and additional online resources

Electron Flow in Organic Chemistry: A Decision-Based Guide to Organic Mechanisms, Third Edition, is the perfect primary textbook for advanced undergraduate or beginning graduate courses in organic reaction mechanisms, and an excellent supplement for graduate courses in physical organic chemistry, enzymatic reaction mechanisms, and biochemistry.

Leseprobe

ELECTRON FLOW IN ORGANIC CHEMISTRY

A DECISION-BASED GUIDE TO ORGANIC MECHANISMS

Third Edition

Paul H. ScudderNew College of FloridaSarasota, Florida, USA

Copyright © 2024 by John Wiley & Sons, Inc. All rights reserved.

Published by John Wiley & Sons, Inc., Hoboken, New Jersey.Published simultaneously in Canada.

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Preface

PREFACE TO THE STUDENT

Critical Thinking Approach

I want you to do well in organic chemistry. And even more, I would like you to understand why people become so interested in the field that they choose to make it their life's work. As a professor who taught Organic for 40 years, I recognized that probably less than 10% of the students in my Organic course were there of their own free will; almost all were taking Organic because it was required for something else. This makes for a tough audience. I wanted to engage my students and show them that Organic was not entirely dreary memorization of material out of a five‐pound textbook. Organic can, not only be interesting, but also be important and relevant to their life, and can develop essential critical thinking skills that carry over to other fields.

It was more important for me to teach scientific critical thinking to my class of prospective biologists, biochemists, physicians, and chemists than to simply teach one more example of any reaction. Every student in my class needed to learn how to reason through complex problems. Organic Chemistry is full of these, and so the puzzles that my students would solve, in learning the scientific method, would be organic reactions. I asked my students to give me reasonable hypotheses for how a reaction works. As a puzzle to solve, organic reactions can teach critical thinking skills, which then can be applied to many other fields. I certainly want my physician to be great at critical thinking, for that is the essence of an accurate diagnosis.

Secrets to Success

This section gives you some of the secrets to success that have come from research on why some people succeed and others do not. Many books have been written on this topic, and ideas that will help you do well in Organic are summarized here. A long time ago, professor Lewis Terman of Stanford University developed the original IQ test and followed up on the youth that had top scores on that test. He found almost no correlation with how they turned out later in life. If smarts do not correlate with success, then what does? Recent research has turned up two character traits that can predict success, and the good news is that they are both learned and are not inherent. The learned traits are “mindset” and “grit,” so let's look at each.

Mindset is the work of psychology professor Carol Dweck of Stanford University. She showed that people often had attitudes toward challenges that mostly fell into two categories. The “fixed mindset” group felt that their abilities were inherent, something they were born with, and not able to change. If they were “not good at math,” then they would find another topic that came easily. If they failed, they took it personally, because it seemed they were not smart enough to succeed in that area. They often felt that working hard on a topic would not make up for a lack of an inherent gift. Therefore, they gave up easily.

Those with a “growth mindset” believed that ability was not inherent, but built through effort and practice. They realized that they could get better at something by working at it. For example, nobody becomes good a playing a musical instrument without a lot of practice. A growth mindset response to doing poorly at something was to work harder, not to quit. They just had not finished learning the topic or skill. If you look back at something you can do well, you will find that you spent a lot of time working at it. With a growth mindset, you can achieve much more than someone with a fixed mindset. Instead of saying, “I can't do it” just say, “I can't do it yet” and keep at it.

The second trait, “grit,” is the work of psychology professor Angela Duckworth of the University of Pennsylvania. She defines grit as the perseverance and passion for long‐term goals. Someone with the growth mindset needs grit to keep working at what they have not learned “yet.” A good predictor of future success is the growth mindset, joined with the grit to not give up when things get difficult. Giving up is not a success strategy for anything.

The Challenge of Organic Chemistry

Organic Chemistry is a difficult topic; it is a cumulative year‐long course, and is unlike any science course you have had before. Many other courses could be broken into separate modules with individual exams, and then it was off to a new topic. Organic Chemistry is one very long interconnected story. It is much more like a foreign language, where what you learn on day one is still needed at the end of the year. However, we tend to remember things that are recent and those things that we use a lot. The year‐long nature of an Organic Chemistry course therefore requires much practice to retain the material for the length of the course. Cramming just does not work, but in the long run practice does.

This text uses 18 elemental mechanistic units, the electron flow pathways, to explain all organic reactions. These units are used over and over again and become the core of understanding how all the organic reactions work. The continual repetition of these basic units helps you retain the material and allows you to understand why these reactions occur. It is much easier to understand and retain information that makes conceptual sense.

An Expert Systems Approach to Organic Chemistry

Critical thinking requires us to ask, “Does this make sense?” If not, it's probably wrong. A believable scientific hypothesis has to be reasonable and pass cross‐checks. We need to “generate and select” alternatives, which is the essence of a good critical thinking process. The map of all alternatives can be represented as a tree, what AI calls the “problem space.” This text extracts the essence of the field: the conceptual tools, the general rules, the trends, the modes of analysis, and everything that one would use to construct an expert system. We need an efficient way to navigate this problem space from start to goal. For that, we need a small set of essential principles, or “control knowledge,” to guide our route selection decisions toward an acceptable answer.

This text makes use of analysis tools common to expert systems, but rare in organic chemistry texts (such as flow charts as decision maps, correlation matrices to show all possible interactions, and simplified energy surfaces used as problem space maps). Good intuition comes from your automatic use of control knowledge to guide your decisions. If you can internalize this expert‐system decision process, you will develop a chemical intuition and are well on your way to becoming an expert yourself. How to learn organic chemistry using this critical thinking approach is the essence of this book.

A Link to Biochemistry

For many students in a chemistry, biology, or premedical curriculum, the next course they will take after a year of Organic Chemistry is a year of Biochemistry, the organic chemistry of living cells. Since the cell is the world's best organic chemist, biochemistry has much to teach us about elegant reaction mechanisms. How does a cell manage to make all the compounds it needs from simple reactants, in water, at room temperature, and producing only the correct shape and not the useless mirror image? Organic Chemistry and Biochemistry are much more interesting when you think of them as an opportunity to learn the secrets of how life works. This text makes use of biochemical reaction mechanism examples to help you understand the magic and the elegance of the chemistry of living systems. It is just a taste of the things to come in a biochemistry course. You can see why physicians need to know organic and biochemistry, for if you can understand how a living system works, you might be able to repair it when things start to go wrong. I wish you success in this endeavor.

TO THE INSTRUCTOR

Unique Decision‐Based Approach Expanded

This third edition provides students with something that they cannot get anywhere else: a chemical intuition based on learning and internalizing a cross‐checked‐decision process. An important part of the scientific method is the ability to postulate a reasonable hypothesis. This text teaches students how to write reasonable reaction mechanisms, and assumes only a general chemistry background. This text provides tools for handling large amounts of information. It emphasizes the “why?” of organic chemistry in order to help make sense of all the material.

To be able to teach students to make good decisions, we need to teach “control knowledge,” which is the essence of a good intuition. These are checks of reasonability that include, among other things: stability trends, compatibility with the media pH, evaluation of energetics, and similarity to known processes. In addition to using flow charts to illustrate the problem analysis process, the third edition increases the use of energy surfaces as problem space maps to help with illustration of these concepts, while continuing the rigorous mechanistic approach to organic chemistry.

Originating with the first edition of this text was the concept of mechanisms being built from a limited number of elementary electron flow pathways, and that learning to assemble these pathways in a reasonable manner is all that is necessary to master mechanisms in organic chemistry. The impressive advantage that a decision‐based approach has over memorization is that it engages the student. The instructor can ask questions like, “Why did it do this and not that?” New reactions become puzzles to solve, not simply another item to memorize.

This text uses several concepts and tools new to most undergraduate organic texts (but common in advanced texts) to aid in understanding the most difficult sections of the typical organic course. Hard–soft acid–base theory is used to guide decisions and to explain and predict the dual reactivity of many species. This text uses energy surfaces as maps of the terrain so that students have a physical model to help with the more complex decisions. Energy surfaces serve as bigger building blocks for multistep mechanisms.

Changes From The Second Edition

Besides the usual clarifications and modifications necessary to bring the text up to date, the text has been expanded to reinforce a decision‐based approach. There are more flowcharts, correlation matrices, and algorithms that illustrate decision processes. Energy surfaces, normally the domain of graduate texts, serve as concept maps and allow students to visualize alternative routes.

All curly electron flow arrows are now in red to make those arrows stand out from the drawn structures. Color is also used to highlight and focus the reader's attention on parts of the molecule when deciding what parts have changed and to illustrate viable routes on the energy surfaces.

The text has been made more accessible to beginning students by adding more background discussion of how General Chemistry concepts can be used to show that structure determines reactivity. Proton transfer mechanisms and predictions of acid–base reactions are introduced early, in Chapter 3, setting up the discussion of organic reactions. To increase readability, all frontier molecular orbital theory reactivity explanations have been moved much later, to Chapter 13, “Qualitative Molecular Orbital Theory and Pericyclic Reactions.”

Chapter 10, “Choosing the Most Probable Path,” has been expanded with energy surfaces linked together like large building blocks to show the problem space terrain for each example and to show how the reactant structure and reaction conditions influence the route favored. This chapter develops a general approach to all organic reactions by showing how to focus on the most reactive centers and choose the best route. The ∆pKa cross‐check developed for Prof. Jorgensen's CAMEO expert system for predicting organic reaction products is often used in this text for deciding reasonable reaction energetics.

New Chapters

A new Chapter 11, “Cross‐checks and Decision Boundaries,” focuses on the “control knowledge” of good mechanistic thinking. What makes for a reasonable mechanistic hypothesis? This chapter collects all of the more important mechanistic cross‐checks introduced earlier in the text, and shows the critical thinking needed to avoid many of the common errors pulled from student exams and other sources. It presents what basic principles had been forgotten in the erroneous example and discusses more reasonable alternatives.

Chapter 14 also new, “Organic Structure Elucidation Strategies,” closes out the text by summarizing useful tactics to solve spectral problems. In my years teaching a problems‐based Structure Elucidation course, I found many books that were good collections of spectral problems, other texts that covered the instrumentation theory of how the spectra originated, but only a few books that detailed strategies on how to approach solving these problems.

A larger collection of important tools is gathered together in the appendix, including a new section, “A Bridge to Transition Metal Organometallics,” designed to cover the gap between organic mechanisms and transition metal organometallics by retaining a few electron‐pushing concepts to aid in the understanding of organometallic mechanisms.

Answers to Odd Numbered Problems Provided Within the Text

Since this text is often used independently of a classroom setting, having the answers to a group of problems is beneficial for testing the understanding of the material. Since this text is also used in courses, having assignable problems that do not have their answers in the back of the book is also desired for assigned homework. The answers to the odd numbered problems are in the back of the book. Each mechanistic answer comes with a detailed problem space map and discusses and evaluates alternate routes.

More Biochemical Examples

Biochemical examples give added relevance for the biology majors and premedical students who make up a significant portion of the undergraduate organic students. The elegance of biochemical processes in optimizing a low energy route can be appreciated and understood by looking at enzymatic mechanisms. These examples also provide a bridge if this text is to be used for review of organic before a biochemistry or enzymology course.

Online Aids

No matter what you hand out on the first day of class, your exams are your syllabus. Unfortunately, the students’ universal test of importance of any material is, “Is this going to be on the exam?” Therefore, if you do not alter the way you test on the material, you have not significantly changed your course. In addition to the answers to all the exercises, supplemental exercises with detailed answers for each chapter are included in the solutions manual for this text to aid in implementing a decision‐based approach to organic chemistry.

Applications

This textbook is designed to be flexible in its instructive role. It can be used in the major's undergraduate organic chemistry course as a short, highly mechanistic supplemental text. It can be used as the primary text in an advanced undergraduate or beginning graduate course in organic reaction mechanisms, or as a supplemental review text for graduate courses in physical organic chemistry, enzymatic reaction mechanisms, or biochemistry.

This text is the product of forty years of teaching organic chemistry at New College, the Honors College of the State of Florida. I am so grateful to have been given that opportunity.

Acknowledgments

I would like to thank all that have helped to bring this book to fruition, especially my father, Prof. Harvey I. Scudder, who helped me refine an algorithm‐based teaching approach, and my Ph.D. mentor, Prof. Barry M. Trost. I am indebted to my students, who helped me work through the many versions of this text, to my colleagues at New College, and to the reviewers of this manuscript. I will maintain an errata list and encourage anyone to send me errors not on the list. I gratefully acknowledge the encouragement of my parents, and my wife, son, and daughter, who inspired me to keep writing in the face of an ever‐growing project. Finally, I would like to thank all those at John Wiley & Sons who made the publication of this book possible.

This book is dedicated to my students, who have taught me to question everything.

1BONDING AND ELECTRON DISTRIBUTION

1.1 THE DECISION‐BASED APPROACH TO ORGANIC CHEMISTRY

Decision‐based AI Approach of this Text; Problem Spaces as Maps of Possible Alternatives; Types of Tree Searches; Generate and Select Search Strategy; Control Knowledge for Decisions; Overview of the Early Chapters; the Principle of Electron Flow from Electron Rich to Electron Poor; Nucleophiles (Lewis Bases) Seek Positive Charges and Electrophiles (Lewis Acids) Seek Negative Charges

1.2 IONIC AND COVALENT BONDING

Valence Electrons; Electronegativity; Ionic, Covalent, and Polar Covalent Bonds

1.3 LEWIS STRUCTURES AND RESONANCE FORMS

Drawing Lewis Structures to Keep Track of Electrons. Number of Valence Electrons; General Bonding Trends; Formal Charges; In Resonance Forms Only Electrons Move, Not Atoms; Deciding on Major and Minor Resonance Forms

1.4 CURVED‐ARROW NOTATION

Full‐Headed Curved Arrow Moves Two Electrons; Half‐Headed Curved Arrow Moves One Electron; Electron Source; Electron Sink; Charge Is Conserved; Direction of Electron Flow; Good Arrow Pushing Habits; Common Errors

1.5 NOMENCLATURE AND ABBREVIATIONS

Line Structure; First 10 Alkanes; Common Functional Groups; Abbreviations

1.6 THE SHAPES OF MOLECULES

Valence Shell Electron Pair Repulsion (VSEPR) Theory; Groups of Electron Pairs Adopt Positions Around a Central Atom of Least Electron Charge Repulsion

1.7 AN ORBITAL VIEW OF BONDING

Review of s and p Orbitals Used in Bonding; Using p Orbitals to Make the Sigma and Pi Bonds of Nitrogen; Hybridization of the Atomic Orbitals of Carbon, sp, sp2, sp3; CC Single Bonds and Free Rotation, Conformational Isomers; CC Double Bonds; High Barrier to Rotation: Cis and Trans; CC Triple Bonds; Cumulenes

1.8 MOLECULAR REPULSIONS, ATTRACTIONS, AND HYDROGEN BONDING

Steric Hindrance, Nonbonded Repulsion; van der Waals Radii; Common Groups Ordered by Size; Dipole Attractions; Hydrogen Bonding; Cation–Pi Interactions; Donor‐Acceptor Complexes

1.9 CONJUGATION, VINYLOGY, AROMATICITY

Overlapping p Orbitals Behave as One System, Have Greater Stability; Vinylogy Is the Extension of the Properties of a System by the Insertion of a Double Bond; Unbroken Loop of p Orbitals with 4n + 2 Pi Electrons Has Aromatic Stabilization

1.10 SUMMARY

Structure Determines Reactivity; Lewis Structures and Electron Flow Arrows Allow Us to Keep Track of Electrons and Explain Reactions

1.1 THE DECISION‐BASED APPROACH TO ORGANIC CHEMISTRY

The Preface mentioned that this decision‐based approach to organic chemistry is modeled after the scientific method. A good hypothesis is just a reasonable guess. You will learn how to recognize alternatives and how to judge which alternative is most reasonable. This is the essence of critical thinking, a crucial skill for scientists, physicians, and life in general. You will develop a good intuition, for intuition can be considered just an internalized decision process. We will use the artificial intelligence concepts of problem spaces and tree searches to help you develop this intuition for organic chemistry.

1.1.1 Introduction to Problem Spaces

If you were planning a road trip across the US, you would need a map of the highways. It would allow you to see all routes from your starting city to your goal city. You would then choose the best route for what you wanted to see and the time you had for the trip. This is exactly the process you want to go through for understanding organic chemistry. We need a map and the ability to choose the best route. Our maps of problems are called problem spaces and are often shown as trees, with a decision to be made at each branch point.

Figure 1.1A illustrates a generic problem space and some of the approaches to working from the start at the top of the tree at point S down to the expected answer. If that route is from S to A to D to I, some students may attempt to memorize “S goes to I” without understanding the process involved. In order to provide a greater understanding, instructors spend book and class time explaining the expected route to the answer. However, students may see the “lightning strike” to product as shown in Figure 1.1