Organic Chemistry with a Biological Emphasis Volume I
Tim Soderberg, University of Minnesota, Morris
Copyright Year: 2016
Publisher: University of Minnesota Morris
Conditions of Use
Fantastic Textbook! The approach, teaching Ochem with biological examples, is the best that I have found for pre-medical and biological science students. It has most of a normal Ochem I course material; I find that I need to supplement a little... read more
Fantastic Textbook! The approach, teaching Ochem with biological examples, is the best that I have found for pre-medical and biological science students. It has most of a normal Ochem I course material; I find that I need to supplement a little bit with nomenclature, molecular orbital theory and spectroscopy. The order of the material is organized and intuitive. The problem sets are very good.
Very good. There are a few small typos, for the most part the textbook is accurate and well done.
The content of this textbook is relevant and applicable for students in the biological and pre-medical sciences. The textbook is not likely to be obsolete for a very long time
The textbook is well written, simple, well organized. The searchable PDF is great for students, and the text on Libretexts is easy to use.
Volume I can be rearranged a bit (spectrocopy can come anytime). However, the majority of the material builds upon previous concepts in this textbook, so rearranging may be challenging.
Fantastic organization. I really like this type of approach to Ochem
Usability is fine, an index and glossary would be nice. There are a few touches that would make the text excellent.
Only a few typos. Very nice overall
No better or worse than other Ochem textbooks that I have seen. I like the vignettes at the beginning of chapters, it is conceivable that those could be used to highlight discoveries of POC and address social justice issues.
Overall, this is a fantastic book!
This is an excellent book covering the fundamental concepts covered in a sophomore level organic chemistry course for majors. There are many interesting biological examples used that would be particularly useful for students majoring in biological... read more
This is an excellent book covering the fundamental concepts covered in a sophomore level organic chemistry course for majors. There are many interesting biological examples used that would be particularly useful for students majoring in biological sciences or interested in pursuing medicine. The textbook does not contain an index or glossary. However, given that the PDF files are available for download, it is fairly easy to search the documents.
Content is accurate, error-free and unbiased. There are plenty of examples provided. Solutions to the textbook problems are also provided in a supplemental PDF.
Many of the concepts listed as ‘fundamental’ chemical concepts that have not changed for a long time. Updates should be easy to make when necessary. The author’s contact information is readily available and it is noted on the website that this is a “dynamic textbook, meaning that it will be continuously undergoing revision”.
The writing style is typical of organic chemistry textbooks written for the sophomore level. Graphics and examples help illustrate the important concepts to students. Technical terminology appropriate for the subject matter is introduced and explained appropriately.
The textbook introduces some reactions early on as examples, then revisits them in great detail in later chapters. This early exposure is beneficial to students as they learn to generalize foundational concepts to many different types of reactions – both laboratory and biochemical, in nature.
While the text is divisible into smaller reading sections, it would be challenging to use it out of sequence for a first year organic chemistry student. Concepts that are introduced early on are built upon in later chapters. An instructor wishing to go out of order should pay careful attention to the assigned section to ensure students have adequate knowledge to be able to appropriately benefit from the assigned section.
There are several ways that organic chemistry topics in a first year course can be organized. This text takes the approach of introducing spectroscopy earlier than most texts and acid-base reactions later than most texts. It also introduces several reactions early on when discussing organic reactivity, then presents them in more detail in later chapters.
The PDF files are easy to navigate -- images are clear and many are colorful.
The text reads well with no grammatical errors.
This text focuses on the science of organic molecules and does not present any culturally insensitive or offensive material.
The text covers all subject but it would be helpful to add solutions for some problems so that students can gain a better understanding of the concepts to make sure they are on the right track. read more
The text covers all subject but it would be helpful to add solutions for some problems so that students can gain a better understanding of the concepts to make sure they are on the right track.
Concise explanation of the concepts.
Although somewhat lengthly, I enjoyed reading the scenarios in the beginning of each chapter. The text engages the audience and makes the theory of organic chemistry more relatable on a macroscopic level.
The text is accessible to a students who are learning the basics of organic chemistry.
The text is consistent.
The text is subdivided into sections that can be easily followed by the reader.
The topics in the text do not follow a traditional organic chemistry textbook which makes it more interesting for the reader.
There were no interface issues that I encountered.
No grammatical errors.
Tables in the back are useful synthesis of what was introduced in the text.
The textbook is a very thorough discussion of the organic chemistry of biological processes. read more
The textbook is a very thorough discussion of the organic chemistry of biological processes.
No major scientific errors noted.
The world of enzymatic reactions is rapidly evolving, but barring paradigm shifts in our understanding of their mechanisms the numerous examples in this textbook should stay relevant for a long time.
No issues with clarity.
No issues with terminology
Most sections contained one or two self-referential, but that is necessary and arguably helpful in an organic chemistry textbook.
It would be helpful if the book were laid out in a manner more consistent with a typical organic chemistry textbook. However, many later sections which would be encountered earlier (e.g. E1/E2 eliminations) could readily be assigned much earlier).
I wish it were a little easier to quickly navigate between different chapters using a TOC pane.
No grammatical errors.
This book does not have any culturally insensitive material.
Overall this is a great book for those looking to teach organic chemistry from a biological perspective. The first edition appears to lay a strong foundation for the second semester. The book is light on example problems and graphics (particularly for 3-dimensional concepts). If students can find additional practice problems, this would be a great resource.
Since the book is a PDF, control F (find) replaces the need for an index and at the end of each chapter there is a glossary of terms/key concepts/learning objectives of that chapter. In Volume I, there is a mixture of Organic I & II concepts... read more
Since the book is a PDF, control F (find) replaces the need for an index and at the end of each chapter there is a glossary of terms/key concepts/learning objectives of that chapter. In Volume I, there is a mixture of Organic I & II concepts covered, so it doesn't make a straight swap possible from our current text. As indicated by the title, it is full of context-rich biological examples that would be of interest to our health science, biology, biochemistry, and biomedical science majors. The topics covered are done with good detail and supporting links to Khan academy tutorial videos, JMol interactive models, and links to external sources like the SDBS Spectral database. There are plenty of practice questions incorporated with links to their key.
The content is great and includes excellent illustrations and examples of the topics.
This is a wonderful new approach to teaching organic chemistry. Rather than teaching it in the same order and way as it has been taught for decades, this new approach integrates topics with more biologically relevant functional groups. The order has been thoughtfully considered to make the connections on related topics as intuitive as possible for students. A new classic built ground up for health majors!
It is written in a good straightforward conversational tone with plenty of illustrations/examples.
Chapters are setup consistently from chapter to chapter. Logical framework. Terminology is introduced early and builds throughout.
As far as assigning readings to students, the sections are thorough and long. Since the book integrates topics classically found in different chapters seamlessly, it would be difficult to reorganize in a classical sequence order if that was intended. When used in the order given, the text integrates topics nicely.
The organization of the book is very well thought out. Chapters are consistently organized.
The chapter outline/table of contents could be quick linked to that page of the PDF and the chapter sub-headings enlarged/bolded to stand out a bit better for those scrolling to find a topic since the page numbers are not listed in the table of contents. Topic enhancers like interactive model links, video tutorials, and other links to external websites with supporting information (books, SDBS, etc) provide an enrichment of the content and additional ways to entice students to engage with the material. Access to external websites through internet availability is needed to fully enjoy the additional linked materials.
The text contains no grammatical errors.
With references to art forgeries, literature, and international examples from Scotland, Paris, Texas, and more there is a pretty diverse group of examples of Caucasian background.
Top of page 319 "one of one of" repeat in "working at the edge of Mushroom Spring in Yellowstone National Park, one of one of the many geothermal hot springs for which the park is so famous."
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... 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.
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... 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.
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... read more
<p> 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.</p>
<p> Generally speaking the contents are accurate. However, not error/typo free completely, some errors/typos are spotted and are listed as follow:</p> <p> Pg 20, 1.3B, “zig-zig” shape, should be “zig-zag” shape;</p> <p> Pg 58, 2nd line, “while ?3* has three nodes…”, should be “while ?4* has three nodes…”;</p> <p> Pg 75, in the paragraph below the two structures, the font of letter ? (delta) is not consistent to the font in the structure;</p> <p> 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.</p> <p> Pg 112, last line, one “that” should be removed.</p> <p> Pg 251, the equation of is incorrect, should be ?G? = ?H? - T ?S?</p> <p> Pg 272, last paragraph, “covalent inhibitor” should have been mentioned in earlier sentence.</p>
<p> 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.</p>
<p> Clear, easy to read. Terms are usually highlighted in bold, with enough explanation in the context.</p>
<p> Yes, good consistency maintained.</p>
<p> 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.</p>
<p> 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.</p>
<p> No any problems spotted in .pdf version.</p>
<p> No any concerns.</p>
<p> No any concerns.</p>
<p> 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.</p>
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 resonancespectroscopy
- 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 acidityconstant
- 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.