Organic Chemistry with a Biological Emphasis Volume I
Tim Soderberg, University of Minnesota, Morris
Pub Date: 2016
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The text covers the first semester of a traditional two-semester sequence of sophomore organic chemistry. It presents topics using functional group read more
The text covers the first semester of a traditional two-semester sequence of sophomore organic chemistry. It presents topics using functional group approach. The text contains the indexes for both Part I and Part II texts. The Part I text that is being reviewed here includes the topics that are commonly taught in the first semester such as bonding, structure, stereochemistry, spectroscopy (IR, UV-vis, NMR) and spectrometry (MS). The text has a chapter covering organic reactions mechanisms thermodynamics and kinetics. There is also a chapter on acid-bases that provides a nice summation of pKa values for various functional groups. The last chapter focuses on substitution reactions with an emphasis on mechanisms. A nice feature is the inclusion of several important biological reactions and mechanisms, as well as including biological functional groups, for example phosphates, in conjunction with the "regular" functional groups traditionally presented to students at this level.
The text is very accurate with the respect to the material and content. The inclusion of several examples, particularly the one at the beginning of each chapter, and the underlying theory and data/information/ behind them is done quite nicely. There are relatively few typos (I only found 5 in 450+ pages) and each paragraph/topic is presented in a direct, comprehensible way.
The material for sophomore organic chemistry is fairly constant for the past 50 years or so. That is, there are the same reactions, same nucleophiles, pKa values do not change, spectroscopic functional group absorbances are the same, etc. There should never be a dramatic or significant variation in the material. What Prof. Soderberg did is use a wide variety of biological, industrial, and historical significant examples to present these topics. I call these the "hooks" that bait students to stay interested. I think he is a fine fisherman and should catch several students who normally would not engage.
The presentation of the material is done is a very clear, well-organized manner. There is of course the nomenclature of organic chemistry, but it is not to overwhelming. One thing I particularly liked was the simplicity of structures being drawn in reactions and mechanisms. The author chose to use primarily 3 colors; black for parts of molecules that do not change and blue and red for those that do change in the course of a reaction. Even for potential electron distribution maps on molecules, the absence of gradient coloring is much easier for me to visualize the reactive and non-reactive parts of molecules. This also really helps in seeing different conformations and stereochemistry relationships. The text also does not present many cases of reactions where students are told "just accept this now and we will fill in the picture next semester". I like that he sticks to the material that students have already learned to illustrate new topics even though there are several other examples. The text gives a digestible amount of information to learn and this should not overwhelm students.
The author is consistent in his nomenclature and uses IUPAC throughout each chapter. Few common names are used other than to illustrate the amount of jargon we have in the field.
I like how the text is broken into sections within each chapter. Each section and subsection of the text is easily assignable and generally contains only one topic. It is very nicely indexed and complements the modular approach taken by the author.
It does not get into the minutiae for each topic but gives a nice overview and really emphasizes the basics. I like taking the numerous functional groups as one and putting them into different topics, especially spectroscopy & spectrometry and acidity. This in my mind makes nucleophilicity far easier to visualize and understand and clarifies the different mechanisms. I really like how the text presents stereochemistry using amino acids and biological molecules.
There were only 3 weblinks that I was unable to get to work. All the others were well-chosen and illustrated the topic nicely. The web links were graphically drawn nicely, ISO 9001 compliant where necessary, and operational.
This is a nicely written text. No major grammatical flaws and a pleasantly surprising small number of typos.
This text presents a wide variety of topics using both biological and non-biological examples. I really appreciate the author's humor for opening each chapter with a particular example. Who can say that about most organic texts?
An excellent text. It is an in-depth and pretty detailed. There are couple of annoyances where tables break across pages but that is more visual editing than pedagogical. It is accurate, well-presented and develops the tremendous amount of information in a clear and understandable way.
This text book is not meant to be similar to other traditional organic chemistry texts, as mentioned in the introduction, and it is different. read more
This text book is not meant to be similar to other traditional organic chemistry texts, as mentioned in the introduction, and it is different. With primary attention focused on biological chemistry, the coverage and the order of topics in this text don’t follow the “usual” way. In Volume I, the first two chapters serve as review of basic structure and bonding theories. The review is even more comprehensive than other organic text, with a lot useful information covered, like MO theory, non-covalent interactions (intermolecular forces) and physical properties. Followed by conformation and stereochemistry, which is the topic any organic book must include, the structure determination that include IR, UV, Mass and NMR are discussed in chapter 4 and 5. A rather unique chapter, which is “instruction to organic reactivity and catalysis”, is then included in this text book. Usually these topics are discussed as part of the reaction chapter in other text, but I like the idea of taking it out as a separate chapter. It provides enough attentions to reaction theories; also give a good chance to include enzyme function (some topics are illustrated by using enzyme catalysis examples in this book), which is very critical topic for bioorganic chemistry. Chapter 7 is about organic compounds as acids and bases, again as review and preparation to following topics, this chapter is complete and helpful. Only Nucleophilic substitution reactions are included up to Volume I, with more reactions coming in Volume II. Since only Volume I (chapters 1-9) is available for now, it is not very confident to talk about the comprehensive for the whole book. However from the Table of Contents for Volume II, I believe all appropriate subjects will be included for the purpose of illustrate bio-organic reactions in living system. Even comparing to other organic texts, not all necessary organic reactions are (will be) discussed in this book, for example the reactions with alkenes, alcohols, but it is understandable because of the special purpose for this book. No glossary in this text. No printed index for this book. The electronic index is available in .pdf version by using “find” or “search” function. But it usually take rather long time to search a term through the whole book with 409 pages. Not sure whether the solution manual available for the book? It will be great to have some answers included as part of the text for convenience to students’ studies.
Generally speaking the contents are accurate. However, not error/typo free completely, some errors/typos are spotted and are listed as follow:
Pg 20, 1.3B, “zig-zig” shape, should be “zig-zag” shape;
Pg 58, 2nd line, “while ?3* has three nodes…”, should be “while ?4* has three nodes…”;
Pg 75, in the paragraph below the two structures, the font of letter ? (delta) is not consistent to the font in the structure;
Pg 110: the introduction of the term “stereocenter” is not exact accurate, the more complete definition of stereocenter is: the atom at which an interchange of groups produces a stereoisomer.
Pg 112, last line, one “that” should be removed.
Pg 251, the equation of is incorrect, should be ?G? = ?H? - T ?S?
Pg 272, last paragraph, “covalent inhibitor” should have been mentioned in earlier sentence.
Pretty up-to-date as a text book. References are cited for examples from recent research papers. Necessary update with most recent progress should be easy.
Clear, easy to read. Terms are usually highlighted in bold, with enough explanation in the context.
Yes, good consistency maintained.
The text is well divided into small reading sections, with logical order. Because of the nature of organic chemistry topic, background knowledge is always necessary for some topics, it is not always realistic to reorganize or realign the subunits.
The topics are presented in clear and logical fashion. There are some issues, however, are concerned for the format of the book. No page number available in the Table of Contents. No numbers are assigned to the structures, pictures and diagram. So it is not that easy to refer to any of those in the text. The tables are all compiles at the end of the text, instead of inserting into the text.
No any problems spotted in .pdf version.
No any concerns.
No any concerns.
Overall, it is an interesting and useful book. With large amounts of examples from living systems (amino acids, peptide, protein, enzyme, sugar, etc), students have chances to learn, understand and apply organic concepts into biological reaction context. It provides good connections between organic chemistry and biochemistry. For same reasons, it is not a choice for traditional organic chemistry course.
I like very much that the author has placed spectroscopy early in the book. I have fund that students are much happier when they learn how the read more
I like very much that the author has placed spectroscopy early in the book. I have fund that students are much happier when they learn how the structures of the organic compounds are actually determined. It also makes it easier to set more challenging assignment questions early in the course. Having stereochemistry introduced early is also an asset for the reasons mentioned above in regards to setting more challenging assignment questions. I realize that the target audience for the textbook is not that of a traditional organic chemistry course. I think that if an instructor supplemented additional information on the two types of elimination reactions (E1 and E2) during the coverage of nucleophilic substitutions (Chapters 8 and 9), it could easily be used for all students taking an introductory organic chemistry course. Several of the topics could be presented in more detail; e., g. the author uses the term stereocenters (US spelling) without mentioning that students will likely come across the terms asymmetric centre, stereogenic centre, chirality centre in other textbooks and research papers. The same is true for enantiomeric excess (% ee) – the term optical purity (that is used in other textbooks) could also be mentioned. It would have been usual to discuss the assignment of R and S when labeled compounds are considered; i.e., the use of deuterium or carbon-13 to examine metabolic pathways. Some textbooks also use “degree of unsaturation” instead of “index of hydrogen deficiency”. It would also be good to have actual spectra presented in the problems for Chapter 5, rather than just the numbers. There are not sufficient problems at the end of Chapters 6, 8 and 9.
There are not too many typos, and the material is presented in a correct fashion. The author needs to be careful to clearly distinguish between ions and molecules. In the procedure for assigning R or S to the lactate ion at the bottom of page 116, he uses the term “lactate molecule” – also at the top of page 111, 113, 137 and others. The pain reliever ibuprofen is spelled incorrectly in Exercise 3.8 on page 117. There is also an error on page 123 in the structure of D-galactose – the author states that the compound has two sterocentres inverted relative to D-glucose. D-galactose differs from D-glucose by inversion of only one stereocentre (at C-4). He correctly shows (on the same page) the structure of D-mannose that has C-2 inverted relative to D-glucose. The author also introduces the prefixes alpha and beta (α and β) for the two cyclic forms of D-glucose, but does not explain what they refer to.
Any changes in terminology can easily be made to the textbook. The use of many biological examples will be attractive to life science students, but may need to be skipped or assigned as optional readings if the textbook is being used for a more “traditional” organic chemistry course.
The writing is clear and crisp. I get the feeling that author imagined that a student was sitting next to him as he explained the material from paragraph to the next.
The author needs to choose of way of representing ionic charges; i.e., 2+ or +2. Problem 2 on page 50 uses both. Other than this minor point, the author has done an excellent job in being consistent.
The text chapters/material could be easily modified/moved from one place to another.
The figures/tables/reaction mechanisms should be numbered/labeled to make it easier for the instructor to direct students to particular examples in the textbook. It would also aid the discussion points if a reference to a particular diagram on a particular page could be made. It would be useful to also have the page numbers included in the table of contents.
I had no difficulty accessing the textbook online, and the diagram/figures were clear and easy to read in the printed version of the textbook.
I have no concerns with the grammar, nor sentence structure used throughout the textbook, the writing is very clear and understandable.
Not really applicable with the material presented in this textbook.
I would suggest combining Volumes 1 and 2 into a single textbook; that way, individual instructors could pick and choose the order of topics that would best suit their organic chemistry course. The chapters do not have to be in the desired order, but having all the material in one volume would be better. It would also be desirable to ensure that any US spellings are changed for the Canadian market.
Volume I by itself does not cover all topics addressed by most first semester Introductory Organic Chemistry courses. For example the topic of read more
Volume I by itself does not cover all topics addressed by most first semester Introductory Organic Chemistry courses. For example the topic of nucleophilic substitution is covered in Vol I Chapters 8 and 9, while elimination is covered in Vol II Chapter 14. Typically these topics are both addressed in a first semester Introductory Organic Chemistry course. Volumes I and II would both need to be used/printed or instructors would have to rearrange chapters to suit their course objectives. Some topics lack the depth of coverage that is typically included in a traditional organic chemistry textbook. For example, the important concept of hyperconjugation (SN1 carbocation stability) is not mentioned. In chapters 4 and 5, the topics of IR and NMR theory and interpretation seem to be cut short. The end of chapter problems may need to be supplemented by the instructor, particularly for chapters 4 and 5 (Structure determination), which do not include any actual spectra except for question p5.14. Some of the Biological emphasis topics are typically not covered in detail in traditional organic chemistry textbooks. Some instructors may find this helpful if they want to include further Biological examples. Other instructors may find this distracting and exclude these topics and sections entirely. There is no index or glossary, however the author does suggest that in the electronic document or webpage the search function may be used. A table of contents is included.
The content appears to be fairly accurate, but many typos were observed. A list of errors and suggestions has been submitted with this review.
Nomenclature needs to be updated to current IUPAC recommendations. With respect to locant placement, Pentan-3-one is preferred to 3-pentanone. Also chirality centre is preferred to stereocenter. Otherwise the content is up-to-date, and should not become obsolete in the near future. Additions can be easily implemented.
The author has a friendly, and fairly accessible writing style. Jargon and technical terminology is defined appropriately. Sometimes idioms and colloquialisms are used, which may impede accessibility to English as a Second Language and international students.
Ionic species are inconsistently represented. For example: Mg +2 or Mg 2+. The ACS style guide recommends the latter. Otherwise, the text is internally consistent.
The text is broken down into chapters and chapter sections. It should be easily reorganized or realigned.
The order of topics will need to be adjusted to suit the learning objectives of typical Canadian Introductory Organic Chemistry courses, and to suit the individual instructor’s preferences in order. This will require using chapters from Volume II. Otherwise there is a logical and clear presentation of topics. Figure numbers and references that use figure numbers in the text would make the text much clearer and easier to follow for students. When referencing to other concepts within the textbook, include hyperlinks and page numbers.
There were no significant interface issues encountered with either the online, .pdf and professionally printed/bound copies of this text. Images and Tables were clear when printed.
Several typos were found, but the text was understandable. No major or recurring grammatical errors were found.
No cultural insensitivities or offenses were found.
As mentioned previously, the order and depth of topics will need to be adjusted to suit the learning objectives of typical Canadian Introductory Organic Chemistry courses, and to suit the individual instructor’s preferences in order. This may require using chapters from volume II or new content being written. Spelling should be changed from U.S. English to Canadian English. Additional worked examples, and end of chapter questions would also improve the text. A list of errors and suggestions has been included.
Table of Contents
Chapter 1: Introduction to organic structure and bonding, part I
- Section 1: Drawing organic structures
- Section 2: Functional groups and organic nomenclature
- Section 3: Structures of some important classes of biological molecules
Chapter 2: Introduction to organic structure and bonding, part II
- Section 1: Covalent bonding in organic molecules
- Section 2: Molecular orbital theory
- Section 3: Resonance
- Section 4: Non-covalent interactions
- Section 5: Physical properties of organic compounds
Chapter 3: Conformation and Stereochemistry
- Section 1: Conformations of open-chain organic molecules
- Section 2: Conformations of cyclic organic molecules
- Section 3: Chirality and stereoisomers
- Section 4: Labeling chiral centers
- Section 5: Optical activity
- Section 6: Compounds with multiple chiral centers
- Section 7: Meso compounds
- Section 8: Fischer and Haworth projections
- Section 9: Stereochemistry of alkenes
- Section 10: Stereochemistry in biology and medicine
- Section 11: Prochirality
Chapter 4: Structure determination part I - Infrared spectroscopy, UV-visible spectroscopy, and mass spectrometry
- Section 1: Mass Spectrometry
- Section 2: Introduction to molecular spectroscopy
- Section 3: Infrared spectroscopy
- Section 4: Ultraviolet and visible spectroscopy
Chapter 5: Structure determination part II - Nuclear magnetic resonance spectroscopy
- Section 1: The origin of the NMR signal
- Section 2: Chemical equivalence
- Section 3: The 1H-NMR experiment
- Section 4: The basis for differences in chemical shift
- Section 5: Spin-spin coupling
- Section 6: 13C-NMR spectroscopy
- Section 7: Solving unknown structures
- Section 8: Complex coupling in 1H-NMR spectra
- Section 9: Other applications of NMR
Chapter 6: Overview of organic reactivity
- Section 1: A first look at some organic reaction mechanisms
- Section 2: A quick review of thermodynamics and kinetics
- Section 3: Catalysis
- Section 4: Comparing biological reactions to laboratory reactions
Chapter 7: Acid-base reactions
- Section 1: Acid-base reactions
- Section 2: Comparing the acidity and basicity of organic functional groups– the acidity constant
- Section 3: Structural effects on acidity and basicity
- Section 4: Acid-base properties of phenols
- Section 5: Acid-base properties of nitrogen-containing functional groups
- Section 6: Carbon acids
- Section 7: Polyprotic acids
- Section 8: Effects of enzyme microenvironment on acidity and basicity
Chapter 8: Nucleophilic substitution reactions
- Section 1: Two mechanistic models for nucleophilic substitution
- Section 2: Nucleophiles
- Section 3: Electrophiles
- Section 4: Leaving groups
- Section 5: SN1 reactions with allylic electrophiles
- Section 6: SN1 or SN2? Predicting the mechanism
- Section 7: Biological nucleophilic substitution reactions
- Section 8: Nucleophilic substitution in the lab
About the Book
The traditional approach to teaching Organic Chemistry, taken by most of the textbooks that are currently available, is to focus primarily on the reactions of laboratory synthesis, with much less discussion - in the central chapters, at least - of biological molecules and reactions. This is despite the fact that, in many classrooms, a majority of students are majoring in Biology or Health Sciences rather than in Chemistry, and are presumably taking the course in order to learn about the chemistry that takes place in living things.
In an effort to address this disconnect, I have developed a textbook for a two-semester, sophomore-level course in Organic Chemistry in which biological chemistry takes center stage. For the most part, the text covers the core concepts of organic structure, structure determination, and reactivity in the standard order. What is different is the context: biological chemistry is fully integrated into the explanation of central principles, and as much as possible the in-chapter and end-of-chapter problems are taken from the biochemical literature. Many laboratory synthesis reactions are also covered, generally in parallel with their biochemical counterparts - but it is intentionally the biological chemistry that comes first.
About the Contributors
Tim Soderberg teaches Organic and Bioorganic Chemistry at UMM, as well as General Chemistry labs. He received a B.A. in English from Amherst College in 1987, and a California teaching credential from San Francisco State University in 1989. After teaching English as a Second Language in Tokyo, Japan for about five years, he returned to the United States and enrolled at Sonoma State University where he completed all of the undergraduate Chemistry, Calculus, and Physics courses necessary to enter a graduate Chemistry program. He came to UMM in the Fall of 2000 after receiving his Ph.D. in Biological Chemistry from the University of Utah under the direction of Professor C. Dale Poulter. His graduate research focused on the enzymology of two prenyltransferase enzymes: one that modifies tRNA, and one that is involved in the early biosynthesis of ether-linked membrane lipids in archaea. His research at UMM focused on characterization of enzymes in the pentose phosphate pathway in Archaea.