Online Textbooks: ChemWiki Part 1

I remember buying my first O-chem books back when I was attending DVC (Diablo Valley College), a not-so-little community college here in the Bay Area. At first I checked the bookstore and lost my lunch when I saw the price of the new books. The text was $215, the lab manual was another $70, and the solutions manual was $100. Unfortunately, a new edition had been released that year, so even though the professor said that we could use older editions, many of the problem sets wouldn’t match up, so we’d have to get the problems from our classmates. In the end, the cheapest and most convenient route was to go online and buy the international editions. Even after extending the method to all my other classes, I still paid almost $500 for books that semester. Now I attended DVC before California went belly-up, so my classes were still a great bargain at $18 a unit. Since I usually took ~19 units, my total tuition cost was around $350 a semester. The cost of the books were actually greater than my cost of tuition. The sad thing is, this wasn’t an unusual case. Luckily this wasn’t too much of a hardship for me; I had a job on campus and money saved up. However, I knew a lot of students for whom the beginning of the semester meant not eating lunch in order to save up gas money.

Now students have probably been complaining about textbooks since time immemorial. Aristotle probably complained that his scribe made spelling mistakes in his copy of The Republic. Most of the time our bellyaching is justified. Not only do textbooks cost a lot, but there is often a gross amount of errors in them. Everyone knows that the first time you find a caption or answer wrong, it makes the rest of the book suspect. Also, these errors give the publishers a reason to release a next edition…that never seems to fix even half of the errors. However, they do switch around problem numbers, add a few pages of new content, and possibly even rearrange chapters. So now the professors lesson and homework plan, that goes by chapter numbers, page numbers, and problem numbers, is moot. And the student is effectively forced to buy the new edition (price “adjusted for inflation”) or suffer some inconveniences. Most choose to simply buy the new edition since tracking down the old one can be difficult and you have to be quick. Also, sometimes bookstores won’t buy back the old edition so if you had it, and an edition switch occurred before you finished your course track, you are up the creek.

Some of these issues can be addressed with online textbooks. The idea of supplementing physical texts with online modules has been around and implemented by publishers for many years. However, I’ve yet to see a good entirely online chemistry textbook. The advantages of online texts are of many: accessible anywhere you get 3G or Wi-Fi and have your mobile device, interactive learning capabilities, easy distribution, instant update/revision, and low cost publishing (server fees). Of course this won’t necessarily result the publisher make more money, but at 4 billion (yea, you read that correctly, billion) dollars a year, the industry doesn’t really need much help.

The student, however, does. We need these online textbooks, not just to save our wallet, but also to help prevent being stuck with an expensive and lousy text for a year that does a poor job of explaining the material. That expensive O-Chem book I bought really was terrible and it forced my professor to do a lot of extra work in teaching us not to follow the book’s direction of simply memorizing 500 reactions, but to see the patterns and the underlying physical explanations. In the end, we learned from his powerpoints and I paid $215 for a glorified reference book.

Well, some people are pioneering an effort to create an “Open Access Textbook”. In a perfect example of “chem 2.0″, UC Davis Professor Delmar Larsen is the project director of the ChemWiki, a truly free online textbook written by everyone, for everyone. In an absolutely Herculean effort, the developers and Larsen (Mary Obrien, Ron Rusay, Brent Krueger, Michelle McCombs) are trying to create a free and complete, as in covering all branches, chemistry textbook using a community of students, faculty, and outside experts from around the world. Of course they aren’t there yet, and there is still a long way to go but hey, their text literally gets better everyday.

Now I know you probably have a lot of questions: what about correctness and plagiarism? Could such a thing ever be considered an Authority? What do the publishers say? Does anyone actually use the thing? Well, it just so happened that a couple of weeks ago, I was at Davis for the Borge fellowship visitation and I had a chance to talk with professor Larsen who agreed to answer some of these questions for me. In a couple of days, I’ll post the interview here. For now, I suggest you go and check out http://chemwiki.ucdavis.edu/ and browse not just through the core, but the wikitexts and community as well.

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Book Review: Strategic Applications of Named Reactions in Organic Synthesis

It’s not often that a book redefines a genre, but Kürti & Czakó’s Strategic Applications of Named Reactions in Organic Synthesis (2005, Elsevier Academic Press) changes the landscape of named reaction books.  Without sounding too melodramatic, Strategic Applications will be the benchmark against which all future named reaction books will be judged – and they will all fail to live up to this new standard.  If you are an organic chemist, this book needs to be on your must buy list by the end of the day (have I hyped the book enough?)

Unlike The Periodic Table, Strategic Applications will not be a book you sit and read cover to cover.  Rather, Strategic Applications is an essential desktop reference in planning a synthetic route.  The most noticeable feature of the book upon first glance is the incredible breadth of detail given to each named reaction.  Each named reaction is given two complete (large) pages.  No more, no less.  The commentary begins with an Importance section giving a brief historical context as well as a general substrate scope and limitations.  As an example, the Suzuki Cross-Coupling begins:

In 1979, A. Suzuki and N. Miyaura reported the stereoselective synthesis of arylated (E)-alkenes by the reaction of 1-alkenylboranes with aryl halides in the presence of a palladium catalyst.  The palladium-catalyzed cross-coupling reaction between organoboron compounds and organic halides or triflates provides a powerful and general method for the formation of carbon-carbon bonds known as the Suzuki cross-coupling.  There are several advantages to this method: 1) mild reaction conditions; 2) commercial availability of many boronic acids; 3) the inorganic by-products are easily removed from the reaction mixture, making the reaction suitable for industrial processes; 4) boronic acids are environmentally safer and much less toxic than organo stannanes (see Stille coupling); 5) starting materials tolerate a wide variety of functional groups, and they are unaffected by water; 6) the coupling is generally stereo- and regioselective; and 7) sp3-hybridized alkyl boranes can also be coupled by the B-alkyl Suzuki-Miyaura cross-coupling.  some disadvantages are: 1) generally aryl halides react sluggishly; 2) by-products such as self-coupling products are formed because of solvent-dissolved oxygen; 3) coupling products of phosphine-bound aryls are often formed; and 4) since the reaction does not proceed in the absence of a base, side reactions such as racemization of optically active compounds or aldol condensations occur.

These introductions are followed by a general reaction scheme (click for larger):

Next is a detailed walk through of the detailed reaction mechanism.  As can be seen in the figure below, the most elegant aspect of this book is the careful use of color.  The reagents get their own colors, and new bonds formed are always black.  This is especially useful in reactions undergoing rearrangement, like the Ugi reaction:

The second page of each entry is dedicated to demonstrations of the title reaction in synthetic applications.  Several total syntheses are described with the step utilizing the named reaction highlighted.  I like this aspect.  It shows real-world applications and helps exemplify functional groups that tolerate the reaction conditions.

Each entry is extensively referenced, and even this is handled elegantly.  The references are split into three (sometimes four) categories: Seminal Publications, Reviews, Modifications and Improvements, and sometimes Theoretical Studies.  Several appendices at the back help your searching immensely.  The first lists all the named reactions in the book in chronological order of their discovery.  The next three appendices really help as they organize the reactions by reaction category (degradation, elimination, heterocycle formation…), reaction by affected functional group (from an alcohol, from a nitrile…), and reaction by target functional group (synthesis of epoxides, synthesis of oximes…)

This book is useful in many situations.  The other day the name of the Cannizaro reaction escaped me.  I couldn’t remember what it was called.  So I used the appendix for reaction by target functional group and looked up synthesis of carboxylic acids, and there it was!  I was writing a research proposal, and needed information on the Darzens glycidic ester condensation.  Thanks to the organization of the book, I was immediately directed to 4 reviews on the subject.  In my research, I was (am) having trouble with a directed ortho metalation reaction.  Forty reaction references appeared at my fingertips directing me to more information on the subject.  It’s also fun to browse through reactions I’ve never ever heard of (like the Hunsdiecker or Minisci Reactions).

I cannot stress enough how detailed and thorough and indispensable Strategic Applications is to the synthetic organic chemist.  When your book has a foreword by E. J. Corey and an introduction by K. C. Nicolaou, you know you’ve run into a winner.  Without question, this is the best named reaction book around.

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Book Review: The Periodic Table: Its Story and Its Significance

Quick! Jot down the definition of an element.  OK, now imagine you don’t know what an atom is.  The proton hasn’t been discovered yet.  Isotope isn’t even a word.  Now what do you do?  These were the issues with which the early chemists were struggling as the handful of known elements was being classified and organized.  Eric Scerri has chronicled this history nicely in his book The Periodic Table: Its Story and Its Significance (2006, Oxford University Press).

I don’t consider myself a history buff, but I really enjoy reading historical accounts of the development of our esteemed field.  The story presented in The Periodic Table was fascinating and engaging throughout.  Scerri (UCLA, editor Foundations of Chemistry) couched the history of the periodic table in the larger history of the discovery of the elements themselves.  How did new elements fit in with the current understanding of the periodic table?  What happened when the task became more difficult with the discovery of the noble gases – a family which no one predicted and which threatened to destroy the periodic system entirely?

The book had one official theme, and one unofficial theme.  First, can chemistry be explained by quantum mechanics; that is, can chemistry be reduced to physics?  Until the 1920s, the answer was definitely no.  It wasn’t even possible to construct the necessary equations once more than one electron was considered.  Scerri elegantly walks through a brief history of the evolution quantum mechanics as the math was invented to recognize the electron as both a wave and a particle.  With the new quantum mechanics, the quantization of the angular momentum of the electron is deduced from first principles for the first time.

However, Scerri also points out how various aspects of chemistry still cannot be derived from first principles.  For example, the Aufbau principle is experimentally known, but not derived independently.  The same is true for exceptions to Hund’s rule.  Several transition metals accept a less than full s orbital in order to add an extra electron to the d orbital.  Ab initio and the density functional approach have advanced quantum mechanics significantly, yet when the various failings are considered, Scerri notes that answer to the reductionist question is both ‘yes’ and ‘no.’

The theme Scerri spent the most time discussing concerns the nature of an element.  Are elements simple substances or basic substances?  And as a subtheme, how (if at all) do elements survive when combined in compounds?  Scerri could have done a better job defining the terms, as I didn’t have a firm grasp on this issue until I was reviewing my notes for this review.  I was confused throughout the book in this matter.  I think I finally get it.

The example given in the book involves the halogens.  Physically, fluorine and chlorine are gases, but bromine is a liquid, and iodine a solid.  Yet, chemically, they all form white solids when combined with elemental sodium.  Furthermore, when combined, neither the physical properties of elemental sodium nor the physical properties of elemental chlorine are manifest.  So there is a disconnect between the observable properties of an element (elements as simple substances) and the abstract, or chemical, properties of an element (elements as basic substances).

Different chemists had passionately held convictions on the matter, and it was fun to watch Scerri illustrate the disagreements throughout time.  Lavoisier was in the simple substance camp, Dalton and Mendeleev sided with the basic substance chemists.  It was interesting to watch these philosophies compete with each other throughout the book.  Scerri argues for the classification of elements as purely basic substances; however, his argument failed to resonate with me because I couldn’t keep the terms straight.  At times it felt like Scerri was arguing against it and for it on the same page.  I understand his point and agree that abstract properties (valence electrons, for example) are better descriptors of elements than physical properties, but his argument fails to convince me to rearrange the periodic table to put, for instance, helium above beryllium because both have two valence electrons.

As might have been expected from the comments to the previous post, the issue of atomic triads appeared throughout the book.  It was fascinating to read about them as they were discovered.  They were integral to initial discovery of the periodicity of the elements.  Chemists noticed that for certain groups of three chemically similar elements, the atomic weight of the middle element was approximately the average of the outer two elements.

Yet the theory was fundamentally flawed.  The periodic table is no longer organized fundamentally by atomic weight, but by atomic number.  While it is true that organization by atomic number actually makes more triads work, it also shows triads as merely a necessary coincidence given what we know about orbitals and how they’re filled.  Elemental triads only show that the middle element is equidistant between the two outer most elements.  Because the shells fill in order 2,8,8,18,18,32,32, the elements in the every other row are necessarily triads.  That is, all elements 3-10, 19-36, and 72-86 (correction: 9-12, 31-38, 71-80) are necessarily the middle of a triad.  It was important and interesting to see how they influenced the ability of chemists to develop the periodic law, but I don’t feel they have much more meaning today than a statistical coincidence of some groups of elements within a family.

Overall, the book was a very interesting read.  It’s nice to step out of the trees for a while and see the forest.  Chemistry is a pretty amazing field, and we constantly strive to push the boundaries of the status quo.  The only real way to get ahead, though, is to know where you came from.  I recommend Eric Scerri’s The Periodic Table for everyone interested in some of the stories of the origin of our profession.

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