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Organic Chemistry with a Biological Emphasis - Volumes I & II by Timothy Soderberg, University of Minnesota, Morris is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, except where otherwise noted.
Organic Chemistry with a Biological Emphasis - Volumes I & II
Description: This textbook is designed 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.
Posted: May 30, 2013 | Updated: July 7, 2022
Author: Timothy Soderberg, University of Minnesota, Morris
Subject Areas
Biological/Physical Sciences, Chemistry
Original source
chemwiki.ucdavis.edu
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Reviews (4)
Avg:
Institution:Vancouver Island UniversityTitle/Position: Instructor
Q: The text covers all areas and ideas of the subject appropriately and provides an effective index and/or glossary
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.
Comprehensiveness Rating: 2 out of 5
Q: Content is accurate, error-free and unbiased
The content appears to be fairly accurate, but many typos were observed. A list of errors and suggestions has been submitted with this review.
Content Accuracy Rating: 4 out of 5
Q: Content is up-to-date, but not in a way that will quickly make the text obsolete within a short period of time. The text is written and/or arranged in such a way that necessary updates will be relatively easy and straightforward to implement
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.
Relevance Rating: 4 out of 5
Q: The text is written in lucid, accessible prose, and provides adequate context for any jargon/technical terminology used
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.
Clarity Rating: 5 out of 5
Q: The text is internally consistent in terms of terminology and framework
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.
Consistency Rating: 5 out of 5
Q: The text is easily and readily divisible into smaller reading sections that can be assigned at different points within the course (i.e., enormous blocks of text without subheadings should be avoided). The text should not be overly self-referential, and should be easily reorganized and realigned with various subunits of a course without presenting much disruption to the reader.
The text is broken down into chapters and chapter sections. It should be easily reorganized or realigned.
Modularity Rating: 5 out of 5
Q: The topics in the text are presented in a logical, clear fashion
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.
Organization Rating: 3 out of 5
Q: The text is free of significant interface issues, including navigation problems, distortion of images/charts, and any other display features that may distract or confuse the reader
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.
Interface Rating: 5 out of 5
Q: The text contains no grammatical errors
Several typos were found, but the text was understandable. No major or recurring grammatical errors were found.
Grammar Rating: 5 out of 5
Q: The text is not culturally insensitive or offensive in any way. It should make use of examples that are inclusive of a variety of races, ethnicities, and backgrounds
No cultural insensitivities or offenses were found.
Cultural Relevance Rating: 5 out of 5
Q: Are there any other comments you would like to make about this book, for example, its appropriateness in a Canadian context or specific updates you think need to be made?
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.
Institution:Kwantlen Polytechnic UniversityTitle/Position: instructor
Q: The text covers all areas and ideas of the subject appropriately and provides an effective index and/or glossary
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.
Comprehensiveness Rating: 4 out of 5
Q: Content is accurate, error-free and unbiased
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.
Content Accuracy Rating: 4 out of 5
Q: Content is up-to-date, but not in a way that will quickly make the text obsolete within a short period of time. The text is written and/or arranged in such a way that necessary updates will be relatively easy and straightforward to implement
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.
Relevance Rating: 4 out of 5
Q: The text is written in lucid, accessible prose, and provides adequate context for any jargon/technical terminology used
Clear, easy to read. Terms are usually highlighted in bold, with enough explanation in the context.
Clarity Rating: 4 out of 5
Q: The text is internally consistent in terms of terminology and framework
Yes, good consistency maintained.
Consistency Rating: 4 out of 5
Q: The text is easily and readily divisible into smaller reading sections that can be assigned at different points within the course (i.e., enormous blocks of text without subheadings should be avoided). The text should not be overly self-referential, and should be easily reorganized and realigned with various subunits of a course without presenting much disruption to the reader.
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.
Modularity Rating: 4 out of 5
Q: The topics in the text are presented in a logical, clear fashion
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.
Organization Rating: 3 out of 5
Q: The text is free of significant interface issues, including navigation problems, distortion of images/charts, and any other display features that may distract or confuse the reader
No any problems spotted in .pdf version.
Interface Rating: 4 out of 5
Q: The text contains no grammatical errors
No any concerns.
Grammar Rating: 4 out of 5
Q: The text is not culturally insensitive or offensive in any way. It should make use of examples that are inclusive of a variety of races, ethnicities, and backgrounds
No any concerns.
Cultural Relevance Rating: 4 out of 5
Q: Are there any other comments you would like to make about this book, for example, its appropriateness in a Canadian context or specific updates you think need to be made?
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.
Institution:Quest University CanadaTitle/Position: Professor
Q: The text covers all areas and ideas of the subject appropriately and provides an effective index and/or glossary
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.
Comprehensiveness Rating: 3 out of 5
Q: Content is accurate, error-free and unbiased
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.
Content Accuracy Rating: 4 out of 5
Q: Content is up-to-date, but not in a way that will quickly make the text obsolete within a short period of time. The text is written and/or arranged in such a way that necessary updates will be relatively easy and straightforward to implement
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.
Relevance Rating: 4 out of 5
Q: The text is written in lucid, accessible prose, and provides adequate context for any jargon/technical terminology used
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.
Clarity Rating: 5 out of 5
Q: The text is internally consistent in terms of terminology and framework
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.
Consistency Rating: 5 out of 5
Q: The text is easily and readily divisible into smaller reading sections that can be assigned at different points within the course (i.e., enormous blocks of text without subheadings should be avoided). The text should not be overly self-referential, and should be easily reorganized and realigned with various subunits of a course without presenting much disruption to the reader.
The text chapters/material could be easily modified/moved from one place to another.
Modularity Rating: 5 out of 5
Q: The topics in the text are presented in a logical, clear fashion
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.
Organization Rating: 3 out of 5
Q: The text is free of significant interface issues, including navigation problems, distortion of images/charts, and any other display features that may distract or confuse the reader
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.
Interface Rating: 5 out of 5
Q: The text contains no grammatical errors
I have no concerns with the grammar, nor sentence structure used throughout the textbook, the writing is very clear and understandable.
Grammar Rating: 5 out of 5
Q: The text is not culturally insensitive or offensive in any way. It should make use of examples that are inclusive of a variety of races, ethnicities, and backgrounds
Not really applicable with the material presented in this textbook.
Cultural Relevance Rating: 4 out of 5
Q: Are there any other comments you would like to make about this book, for example, its appropriateness in a Canadian context or specific updates you think need to be made?
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.
Institution:University of Northern British ColumbiaTitle/Position: International Student Services Representative
Q: The text covers all areas and ideas of the subject appropriately and provides an effective index and/or glossary
First of all, no index and glossary but the noticeable point was that Table of contents, and Tables was not having page numbers mentioned in it, This way its difficult to locate the topics and chapters, whenever you are referring this to someone.
It was great to have organic Nomenclature, functional group classification and how to write/draw organic structures in the first chapters. I was expecting to have Structure of biological molecules at the end of Chapter 2 as it covers important topics such as MO theory, resonance, covalent bonding and hybridization that must be included to define biological molecules mentioned above.
The name of the book didn't have alignment with the text of the book. From Chapter 1-8, its more organic chemistry's basic topics, not biological theory or reactions. So, for bio-chemistry perspective, this book won't be able to get good reference to recommend to someone. However, to get basic organic chemistry knowledge, this textbook can be good reference for First and second year students. Moreover, the layout of Table of Contents is not in an appropriate way.
I liked the idea of including Conformation and Stereochemistry as chapter 3 which was followed by Structure determination (Ch. 4) to evaluate the structure based on parameters learnt from Ch. 3 and spectroscopic techniques. In terms of characterization of organic/biological molecules, this textbook holds enough basic information.
I would have been helpful if all Nucleophilic reactions such as Nucleophilic substitution (SN1, SN2), Nucleophilic acyl substitution (Ch 11), Nucleophilic Carbonyl addition (Ch 10) included in Volume I. Then, Volume II can cover Electrophilic, oxidation/reduction and Radical reactions.
I found the greatest point is to have exercises at the end of each subtopic in each chapter. And the highlighted point here is that this book do provides the solution guide for the exercise questions. Its good to include in First and second year chemistry beginner level course and top familiarize students/ learners with the possible questions that they can have based on the general organic/biochemistry.
Moreover, the diagrams/structures are labelled and color coded properly, made them easy to understand and hence easy to refer to different heteroatoms like oxygen, nitrogen, molecules like Carbon dioxide etc.
However, the down point in chapter 5 is to have questions without spectra included, If the questions have spectra in it, it would have been very easy to understand the chemical shift, splitting patter, coupling constant etc. for chemical compounds.
Comprehensiveness Rating: 3 out of 5
Q: Content is accurate, error-free and unbiased
Overall the content was accurate. However following list of typos that I was able to find out in the textbook:
Pg 18: the definition of constitutional isomers can have its subgroups like chain isomerism, functional isomerism etc. to differentiate Glucose and Fructose structure. Similarly for Exercise 1.11.
Pg 20: The mentioned line have "in in" twice at the end. "In chapter 2, we will study the nature of the bonding on alkenes and alkynes, and learn that that the bonding in alkenes is trigonal planar in in alkynes is linear. "
Found out the definition and use of compound, molecule and ion is mixed up in this textbook. It could have been more clear that where to use compound, ion or molecule.
Pg 32, structure of FAD: I liked the idea of representing bulky groups as R substituent and providing audience with the information that R group will be used a future reference in FAD in upcoming chapters.
Bold highlighted names of the important terms: such as Bond length, bond dissociation energy, bond strength, cylindrical symmetry etc.
No titles to the diagrams.
Had included clear explanation in the supplementary material as well.
The Nomenclature terminology for sugars is not well explained as there is no infotrmation on how to define and distinguish alpha, beta, gamma and delta carbons?
Content Accuracy Rating: 4 out of 5
Q: Content is up-to-date, but not in a way that will quickly make the text obsolete within a short period of time. The text is written and/or arranged in such a way that necessary updates will be relatively easy and straightforward to implement
Up to date content, can be a good reference for near future, but new Nomenclature rules and more recent papers as a reference can be included easily later on.
Relevance Rating: 4 out of 5
Q: The text is written in lucid, accessible prose, and provides adequate context for any jargon/technical terminology used
Simple, easy to read and understand. Good text book for beginners of First and second year chemistry/bio-chemistry programs specially for international students studying in Canadian universities.
To follow the textbook is easy to clear basic concepts with given examples and exercises within the book.
Clarity Rating: 4 out of 5
Q: The text is internally consistent in terms of terminology and framework
Overall, it was consistent but ionic species representation is different everywhere in the textbook, as for Magnesium, it is written as Mg +2 and somewhere it is written as Mg 2+.
These types of simple/minor mistakes are possible in textbooks but can be eliminated easily.
Consistency Rating: 4 out of 5
Q: The text is easily and readily divisible into smaller reading sections that can be assigned at different points within the course (i.e., enormous blocks of text without subheadings should be avoided). The text should not be overly self-referential, and should be easily reorganized and realigned with various subunits of a course without presenting much disruption to the reader.
The table of content/text is very well organized based on the topics included in the textbook. Each topic is having main section dividing to sub sections that are numbered properly. Again easy to follow along.
Modularity Rating: 4 out of 5
Q: The topics in the text are presented in a logical, clear fashion
Overall the topics are presented in clear and simple fashion but below are few issues:
Figures/reactions/reaction mechanisms in the text are not numbered, difficult to locate or to give reference to.
The tables are also without numbers, no clue which table refer to what without reading the full paragraph corresponds to the table.
Moreover, in exercises and in main text, no spectroscopic diagrams to layout the spectra for better understanding of the characterization and evaluation of the structures of chemical compounds.
Already mentioned the Table of Contents Page numbers.
Organization Rating: 3 out of 5
Q: The text is free of significant interface issues, including navigation problems, distortion of images/charts, and any other display features that may distract or confuse the reader
I had not come across with any issues while accessing the text book, diagrams, reactions, reaction mechanisms and text is clearly printed and readable.
Interface Rating: 4 out of 5
Q: The text contains no grammatical errors
I haven't have any concerns with grammar or spelling issues except very Few typos but overall good job.
Grammar Rating: 4 out of 5
Q: The text is not culturally insensitive or offensive in any way. It should make use of examples that are inclusive of a variety of races, ethnicities, and backgrounds
I have not noticed any sensitive wording related to culture, gender, ethnicity, national origin, age, disability, sexual orientation, education and religion.
Cultural Relevance Rating: 4 out of 5
Q: Are there any other comments you would like to make about this book, for example, its appropriateness in a Canadian context or specific updates you think need to be made?
I would recommend this book combining both volumes (I and II) included for University/college level chemistry for first- and second-year chemistry/ bio-chemistry courses. It is written in simple language that is easy to understand for the beginners.
Moreover, if someone looking for general knowledge of Chemistry and biochemistry, this book is the good source.
However, as per the layout/presentation issues, it is not recommended at higher professional instituters.
Other suggestions had been included.
