The Science and Engineering of Cocktails

Kevin Liu blogs about both food, at Science Fare, and cocktails, at Craft Cocktails at Home. Taking a science and engineering approach to the construction of food and drinks, he has a new book of the same name. While I haven't had time to dig into it completely yet, what I've seen is rather interesting and compelling. Best of all, you can get the eBook from Amazon for free until Saturday afternoon. So if you fancy learning about everything from the physics of creaminess to the precise balance between sweetness, sourness, and bitterness, give it a look. I'll be sure to give it a more thorough review at a later date.

Book Review: Imbibe!

Last week I posted a review of David Wondrich's book on the history of punch. Imbibe! moves ahead a bit in history, covering the evolution of its successor, the cocktail, in America and the world. The focal point of the book is "Professor" Jerry Thomas, one of the first celebrity bartenders and writer of the first bartender's guide in history. Thomas traversed and tended bar in the furthest reaches of the growing American nation, but ultimately reached his greatest fame in New York City.

The book then moves into the history of cocktails. The second chapter is devoted to techniques for their preparation, ranging from the late Colonial period (using a hot poker plunged into a mug of something to make it hiss and steam) to just before Prohibition (when the classic martini glass came into vogue). There is also quite a lot of discussion about ingredients, many of which were lost or fell out of favor around the beginning of the 20th century. While a number were just starting to filter back into existence when the book was published in 2007, we have a much more expanded repertoire now, with high proof cognacs, Old Tom and Hollands (genever) gins, and real absinthe available in the States, if not always readily. The subsequent chapters are devoted to the evolution of drinks from their beginnings in punch and the many categories of drinks that used to be distinct but have since been subsumed under the heading of 'cocktail'. The book also includes some small chapters on recipes for 19th century bitters and investigates the origins of the martini.

Along with Wondrich's book on punch, Imbibe! is a fantastic read for those wanting to learn more about the history of drinking. The research is thorough and the writing is engaging. The drinks aren't half bad either.

Improved Whiskey Cocktail
2 oz whiskey
1 tsp simple or gum syrup
0.5 tsp maraschino liqueur
0.125 tsp absinthe or pastis
2 dashes Angostura bitters

Combine all ingredients, stir with ice for fifteen seconds, then strain into a rocks glass and squeeze a piece of lemon peel over the drink to express the oils.

The nose is full of rye grain, though mellowed into sweetness, which is supplemented by a bit of the maraschino's funk. The sip begins smoothly and sweetly, but quickly transitions into strong rye, Ango bitters, and herbaceous notes from the pastis.

Though a little bit fiddly to construct (unless you have dashers for all of the liqueurs), this is a very tasty drink and a worthwhile improvement over the basic Old Fashioned or Whiskey Cocktail.

Book Review: Punch - the Delights of the Flowing Bowl

Where did cocktails emerge from? To find out, David Wondrich takes us back to the proto-cocktail - punch.

Distilled spirits became available for public consumption near the end of the 14th century, having previously been restricted to the domain of alchemists, apothecaries, and monks. However, early distilled spirits were often of poor quality - distillation techniques had not been refined, which meant that significant quantities of volatile chemicals like methanol and acetone, as well as heavier fusil oils remained in the final products. These spirits were rather harsh to drink on their own - remaining primarily a method for getting drunk, fast, and producing an absolutely atrocious hangover the next morning. While there were often tinctures made by soaking herbs and spices in spirits, as the higher proof allowed for greater extraction than fermented wine or beer, these were primarily seen as medical products, not a tipple to enjoy of an evening.

However, a new use was found for spirits due the burgeoning international trade beginning to flow into Europe at the end of the 17th century. Most importantly, trade with with Asia was expanding - the Dutch East India Company (VOC) was in its heyday and the British East India Company was growing as well. This meant that exotic spices and fruits were becoming more common in Europe, especially in the hands of the upper classes. This set the stage for the creation of punch.

Wondrich takes the reader through the pre-history of punch, then goes on to describe how it evolved over the centuries, trickling down to be the drink of more common men as well as the upper classes. Read about how much punch George Washington budgeted for serving to constituents while running for the Virginia House of Burgesses or how the coffee house culture of Enlightenment London was turned on to punch, sparking drunken discussions (and brawls) between some of the most notable men of the day. Punch was ascendent for almost two centuries until it was overtaken in the 19th century by the American innovation of the cocktail - a small, personal, bracing punch that could be drunk quickly instead of sitting with ones compatriots around the flowing bowl.

Throughout the book, there are recipes in their original state, which are also translated into more comprehensible modern measurements. Punch-making details are provided, such as how to make a proper oleo-saccrum (extracting citrus oils into sugar). This is a fantastic read, making a rather esoteric subject entertaining and enthralling. I highly recommend this book, especially for those of a booze nerd-y disposition.

Bombay Presidency Punch (adapted from David Wondrich)
1 oz Batavia arrack
0.5 oz Smith & Cross Jamaican rum
0.5 oz cognac
0.5 oz lime juice
1 oz palm sugar syrup (1:1)
1-2 oz soda water

Build over ice. Stir to combine and dust a little nutmeg on top.

The sip begins with mild sweetness, which carries through in balance with the lime. The funky notes of arrack and rum are smoothed out a bit by the cognac, while the soda water provides a bit of snap. Over time, the nutmeg filters into the drink.

This is possibly the ur-punch, being composed of ingredients that would have been available to members of the British East India Company stationed at their fortress in Bombay. The original version was made exclusively with Batavia arrack along with nutmeg from the Dutch East Indies, as well as locally-souced limes and palm sugar. However, splitting the base spirit with strong Jamaican rum and mellow cognac gives it even more depth. The soda water isn't really in keeping with the original (soda water wasn't invented until the late 18th century), but I find it adds a nice something to the drink that you won't get with less fizzy water. This punch is quite a crowd-pleaser - I've served it to people ranging from members of my lab to my own family and friends, always with great results.

Book Review: Peat Smoke and Spirt

Islay is one of the most well-known regions of scotch whisky production. The products of the island are very much 'love it or hate it', so it evinces some strong emotions.

Andrew Jefford's book is a chronicle both of the island and the distilleries that have made it famous. He clearly has a love for the island and made numerous trips to learn about the place. Importantly, he doesn't appear to have any particular biases towards or against any of the distilleries, appreciating each equally for what they have to offer.

Each chapter is broken up into two parts - first, a section looking at a historical period or feature (weather, terrain, etc.) of the island, then an overview of one of the island's distilleries.

The historical sections are very in depth, ranging from geologic (the island is composed of two landmasses that came together via tectonic drift), to the Medieval (the island was the seat of power for a Gaelic-Norse empire encompassing much of the western maritime Scotland), to the modern (the turbulent history of the 19th century). Admittedly I found these sections to be a bit much at times, as Jefford is rather... exhaustive. However, some of it, especially the sections on the 19th century, are useful for understanding the context in which many of the distilleries were created, but I found myself skipping large chunks after a certain point.

The sections about Islay's distilleries are an absolutely treasure-trove. Each is chock-full of history as well as first-hand experiences at the distilleries. Jefford makes a point of visiting the water sources for each distillery, both to get a sense of how they contribute to the whisky directly and the role they played in the distilleries' histories. There is also a vast amount of detail about the production methods each distillery uses, from the source of their malted barley, what kind of washbacks they use, the length of fermentation, the size, shape, and degree of filling of their stills, the shape and type of condenser attached to each of the stills, how long each distillation run takes and where cuts are made, and the conditions in which their whisky ages. While direct questions to the various master distillers about what makes each spirit unique were often met with negatives (I began to wonder what it was that actually made each distillery's product unique as the list of possibilities was officially whittled down significantly), Jefford does a lot to speculate what might make an impact (still shape and run dynamics seem to come out ahead). If you're ever wanted to know about the details of whisky production, this will provide you all sorts of information.

The book is especially interesting as it presents a snapshot of the distilleries in transition. The book was published in 2004, not long after the revival of Ardbeg and Bruichladdich, two of the island's most celebrated brands. Ardbeg had been under its new Glenmorangie/LVMH ownership for about seven years - long enough to start releasing new whiskies from their old stocks (the 17 year old and Uigeadail), but still new enough that their first bottles of 10 year old made from entirely new stocks were still in the future. Bruichladdich had been saved only a few years before the book was published and was still struggling to find its footing, throwing out a wild assortment of cask finished whiskies made from old stocks. Looking ahead, Kilchoman's foundation was still several years off. All of this is useful for someone who wants to understand the state of the scotch whisky industry in the 21st century.

Overall I think this is a very good book to read if you'd like to learn more about the history of Islay and its whisky. It's thorough, well-researched, and evinces a clear love for the place and its whisky. Highly recommended.

The PDT Cocktail Book

I picked up a copy of the PDT Cocktail Book a few months back as a sort of late Christmas present. While I was initially pulled in by the excellent design, I've found it to be generally well written and to contain quite a lot of good drink recipes.

PDT (Please Don't Tell) is a faux-speakeasy bar in New York City. It is accessed by entering a phone booth at the back of Crif Dogs and dialing the appropriate number, which causes the door to open. I'm sufficiently plebeian to find the idea of a bar that semi-intentionally hides itself to be a little off-putting, but I will admit that they've put out a rather nice book for use at the less exclusive place I like to call home.

The book is written by Jim Meehan, one of the bartenders at PDT, and illustrated by Chris Gall. The book opens with a set of suggestions for setting up a bar, ranging from design to equipment and supplies. There's a fairly strong slant towards professionals rather than the home bar, but much of the information is still applicable. The recipes are laid out in a standard alphabetical fashion, interspersed with recipes for any specialized ingredients (infusions, syrups, etc.). There's also an index in the back that lists all of the drinks by base spirit. Near the end there are sections with suggestions for varieties of spirits, liqueurs and other ingredients, a section talking about how to build seasonal cocktail menus, and finally a list of other books that will be useful to an aspiring bartender.

Overall I think this book is a reasonably good value for money. It's not the first book I would suggest to someone looking to set up a home bar (The Joy of Mixology wins hands down), but for those with a handle on the basics, the selection of recipes is broad and doesn't too often require fussy home made ingredients. One of my main quibbles with publications like Imbibe is that a too-large percentage of their recipes require making infusions or syrups that may not have a significant amount of utility except in that one drink, which is fine for a bar, but less useful at home. The PDT Cocktail Book does ask for some of them, but the percentage of recipes requiring that is fairly low.

And just to give you a taste of the kinds of drinks contained in this book:

Harvest Sling (by John Deragon)
1.5 oz Laird's Bonded Apple Brandy
0.5 oz sweet vermouth
0.5 oz Bénédictine
0.5 oz Cherry Heering
0.5 oz lemon juice
0.5 oz ginger beer

Combine all ingredients, shake with ice and pour unstrained into a chilled rocks glass.

This is a deliciously complex drink, evolving in stages across the mouth. The initial sip is only slightly sweet, with the liqueurs gaining force towards mid-palate, along with a hint of fresh apple flavor. The herbal notes of the Bénédictine come in strongly, leading smoothly into the finish. The finish is a wonderful melange of the sweet vermouth's bitter wine notes coupled with dark, dry cherry from the Heering and the oaky apple of the applejack. With time and dilution the bitter notes of the vermouth become somewhat more subdued, giving way to the applejack. A certain nuttiness also appears, which, when combined with the wine flavors of the sweet vermouth, remind me a lot of a good oloroso sherry. Overall this is a taste roller coaster.

Collaboration using Open Notebook Science in Academia book chapter

I am very pleased to report that the book chapter that I co-wrote with Andrew Lang, Steve Koch and Cameron Neylon is now available online: Collaboration using Open Notebook Science in Academia. This is the 25th chapter of Collaborative Computational Technologies for Biomedical Research, edited by Sean Ekins, Maggie Hupcey, Antony Williams and Alpheus Bingham.

Our chapter provides some fairly detailed examples of how Open Notebook Science can be used to enhance collaboration between researchers from both similar or distant fields. It also suggests certain paths towards machine/human collaboration in science. Hopefully it will encourage researchers who have an interest in Open Science to experiment with some of the tools and strategies mentioned.

I am also grateful to Wiley for choosing our chapter as the free online sample for the book!

This book discusses the state-of-the-art collaborative and computing techniques for the pharmaceutical industry, the present and future implications and opportunities to advance healthcare research. The book tackles problems thoroughly, from both the human collaborative and the data and informatics side, and is very relevant to the day-to-day activities running a laboratory or a collaborative R&D project. It can be applied to help organizations make critical decisions about managing drug discovery and development partnership. The book follows a “man- methods-machine” format with sections on how to get people to collaborate, collaborative methods, and computational tools for collaboration. This book offers the reader a “getting started guide” or instruction on “how to collaborate” for new laboratories, new companies, and new partnerships, as well as a user manual for how to troubleshoot existing collaborations.

Book Review: The Joy of Mixology

© Gary Regan, 2003

As I've noted before, Gary Regan's The Joy of Mixology is one of the books that helped to send me down the path of cocktail nerdery. Though nominally aimed at aspiring bartenders, this is an excellent book for anyone who wants to understand the theory behind cocktail recipes.

The book opens with a condensed history of cocktails, going all the way back to the 18th century when cocktails emerged as a drink form in Colonial America. As Gary points out, the cocktail is one of the few culinary inventions that is entirely unique to America rather than being derived from imported ideas.

In my opinion, the most useful aspect of this book is the way that drinks are broken into families and presented in spreadsheet form to show how changing the base spirit or an ingredient can produce an entirely new drink. For instance, the Margarita and Daiquiri are all in the sours mold of spirit, sour and sweet, with different spirits (tequila vs. rum) and sweeteners (orange liqueur vs. simple syrup). Understanding those foundations allows one to easily swap one ingredient for another to create new drinks. This has led Regan to create new cocktails to fill "holes" in the cocktail canon where there is an obvious and easy swap that for whatever reason had previously not been made.

The Joy of Mixology would be the first book I would tell someone who wants to learn more about cocktails to buy. It contains all the basic recipes you'll need to keep yourself and others happy. There's plenty of technique and recommendations for equipment you'll need. And it will give you a huge leg up on how to making your own cocktail recipes. If it's not on your shelf yet, go out and buy it right now.

Book Review: Beachbum Berry Remixed

© Jeff Berry, 2010

Jeff "Beachbum" Berry is, without a question, one of the most important figures in the current tiki revival. I am far from the first to sing his praises. While a self-professed bum, he has spent countless hours scouring old cocktail books and interviewing the remaining tiki bartenders to pry the secrets of lost tiki drinks from them. Given the secrecy surrounding a lot of tiki drinks, that was no easy task. The founders of tiki, namely Don the Beachcomber and Trader Vic, used all sorts of tricks to prevent their bartenders walking off with the most important drink recipes when they were hired away by rivals. Some of the trickiest ingredients, like "Don's Spices" and "Don's Mix" were such closely held secrets that it took decades of investigative work and no small amount of luck to figure out what they were.

Beachbum Berry Remixed contains most of the recipes from two of his earlier works, Grog Log and Intoxica!, which have been updated and reworked as necessary. In addition, there are a number of new recipes, both from Berry himself and from the growing legion of tiki-phile bartenders across the globe. All said and done, there are several hundred recipes, most tested and honed over the last decade. To make things even more interesting, the recipes are interspersed with bits of tiki history, from the long running debate over the creation of the Mai-Tai to the complex trail of leads that the 'Bum followed to determine the true recipe for the Zombie.

This is definitely the best book to get if you want an introduction to tiki. You'll get some good background and enough recipes that it's pretty much guaranteed there'll be something in there for everyone. To reduce the confusion of all the obscure ingredients, there's a list in the back that explains what everything is.

Even for the more established cocktailian, this is a must-have book. Think tiki drinks are all sugar and no balance? Peek through the Bum's work and be amazed. People like Donn Beach and Trader Vic were absolute geniuses behind the bar, carefully utilizing obscure components to create nuanced and balanced drinks. Not a huge fan of rum? There are drinks in here with just about every base spirit imaginable.

My one quibble with this book is that it should have been shipped spiral bound, especially considering that several of his earlier books came that way. Trying to make a drink and keep the book open at the same time is a bit of a pain. Thankfully you can just drop by your local FedEx/Kinko's and get it rebound, but that does cost a few extra dollars.

So, go forth and get Beachbum Berry Remixed! If you can't find it locally, check out Trader Tiki, where it's $5 off with free shipping.

Reaction Attempts Book Edition 1 and UsefulChem Archive

I am pleased to report that Andrew Lang and I have published the first edition of the Reaction Attempts book. It currently contains most of the Ugi reactions from the UsefulChem project and is associated with an April 27, 2010 snapshot archive of the entire UsefulChem project, including NMR spectra, spreadsheets, images and the entire lab notebook from Wikispaces.


At 582 pages the printing cost from LuLu amounts to $26.28. Not meant to replace electronic searches, it should prove to be a handy reference book for the lab to quickly browse through what was attempted for a given reactant, what the outcome was and the researcher involved.

We are hoping to include reaction attempts from other groups in future editions. More details can be found in the preface, reproduced below:

Reaction Attempts First Edition

Data Source: the UsefulChem project

Introduction

Open Notebook Science (ONS) refers to the practice of making the full contents of a laboratory notebook and all associated raw data files available in near real time.[1] This represents an opportunity for everyone to benefit from work in progress in an open research group. However, in order to make use of the information, it must be easily discoverable. A simple strategy to increase discoverability is redundancy over multiple communication platforms.

In another project - the Open Notebook Science Solubility Challenge[2] - we published non-aqueous solubility data in the form of physical and downloadable (PDF) books.[3] Although it is possible to search the solubility database using web query interfaces, exploration of a Google Spreadsheet, an XML feed, etc.[4], having a physical copy in the laboratory has proved to be very convenient in several instances. A similar format for reactions will also be useful.

The UsefulChem Project

UsefulChem started in 2005 as an organic chemistry Open Notebook Science project with a main goal of discovering new anti-malarial agents that can be prepared by simple and cheap syntheses.[5] Most of the reactions on UsefuChem are Ugi reactions, which involve the mixing of an amine, aldehyde, carboxylic acid and isonitrile in a solvent at room temperature generally for a few hours to days.[6] The multicomponent design of the Ugi reaction and the simple reaction conditions make it ideal for exploring large virtual libraries and selecting compounds of interest to make.[7]

Isolation of the Ugi products can be immensely simpler, cheaper and readily scalable if they precipitate in pure form from the reaction mixture. To this end, much of the research in the UsefulChem project focuses on reaction conditions that lead to this outcome.[8] This is in fact the origin of the ONS Solubility Challenge discussed above.[9]

The Reaction Attempts Database

In order to look for patterns in the reaction conditions which led to Ugi product precipitation, the CombiUgiResults Google Spreadsheet was set up.[10] Reactions indexed there can be sorted by precipitation outcome, solvent, reactant, concentration, etc. and links to the laboratory notebook pages can be followed for full details. However, this sheet is designed specifically for Ugi reactions and contains columns specifically for the aldehyde, amine, carboxylic acid and isonitrile.

In order to enable the tracking of other types of reactions, the information in the CombiUgiResults sheet was reformatted into two other sheets: ReactionAttempts[11] (containing reagents and reactants) and RXIDsReactionAttempts[12] (containing reaction conditions and results, such as solvent, concentration of limiting reactant, appearance of a precipitate, yield, etc.). The two sheets are connected via the use of a common ReactionID. This format permits the representation of any type of reaction, with an unlimited number of reactants and products.[13]

By definition, any Open Notebook Science project in a work in progress. The listing of a reaction in this database only means that the researcher attempted or is in the process of attempting it. Whatever the situation, a link to the laboratory notebook page is provided, where the most recent information is available. The philosophy used here is that partial information is always better than no information at all. Thus a researcher investigating the prior use a particular reactant in a Ugi reaction might find the report that a precipitate was obtained in methanol helpful for designing their own reactions, even if the characterization of the precipitate is still pending. At the very least, knowing that a certain researcher has at least attempted a similar reaction is enough information for initiating a discussion, which may lead to valuable insights.

Reaction Attempts on Chemspider

Although SMILES[14] are provided in the spreadsheets, the primary key to identify compounds is the ChemSpider ID (CSID)[15]. This allows us to render molecule images in the book automatically. In the case of the ONS Solubility Challenge book[3], use of the CSID enables a convenient way to calculate various descriptors for displaying values in the book.

In addition, the compounds in the Reaction Attempts database are indexed on ChemSpider as two Data Sources: ReactantsAttemptedReactions and ProductsAttemptedReactions[13]. In this way a substructure search for either reactants or products will identify indexed molecules. Clicking on the Syntheses tab in the ChemSpider record for a selected molecule will then reveal a list of hyperlinks to the relevant laboratory notebook pages.

Organization of the Book

In keeping with the layout of the ONS Solubility Challenge Book, the reactants are listed in alphabetical order. Each entry displays the list of reactions where the reactant was used. This includes a scheme with all reactants and product as well as key metadata: the researcher, reaction type, solvent, limiting reactant concentration, observation of a precipitate, comments and a reference (links to the laboratory notebook page).

In this edition, only Ugi reactions are included. The reaction schemes are laid out in the following order: carboxylic acid, amine, aldehyde and isonitrile. This should allow for easy comparison between schemes within a given record. Reactions where the Ugi product was isolated and characterized are marked with a green check and the percent yield is noted. Since the Ugi products do not have simple common names, they are not included as separate entries. However, all reactions where the synthesis of a specific Ugi product was attempted can be found by looking up the entries for any of the four reactants.

Although this compilation is not exhaustive, it does cover the vast majority of reactions in the UsefulChem project to date. Future editions will include other reactions from UsefulChem and other sources.

Archive

This edition is linked to the UsefulChem data archive (ZIP)[16], (DVD)[17] and interactive hosted archive format[18], ReactionAttempts (XLS)[19] and RXIDsReactionAttempts(XLS)[20] taken on 2010-04-27.

References

1. Open Notebook Science Wikipedia Entry http://en.wikipedia.org/wiki/Open_Notebook_Science
2. Open Notebook Science Solubility Challenge Wiki http://onschallenge.wikispaces.com
3. Bradley, J.-C. First Edition of ONS Solubility Challenge Book UsefulChem Blog (2009)
http://usefulchem.blogspot.com/2009/12/first-edition-of-ons-solubility.html
4. Open Notebook Science Solubility Challenge List of Experiments page http://onschallenge.wikispaces.com/list+of+experiments
5. UsefulChem Wiki http://usefulchem.wikispaces.com
6. Ugi Reaction Wikipedia Entry http://en.wikipedia.org/wiki/Ugi_reaction
7. Dömling, A., & Ugi, I. (2000). Multicomponent Reactions with Isocyanides. Angewandte Chemie International English Edition, 39(18), 3168-3210. http://www3.interscience.wiley.com/journal/73500473/abstract.
8. UsefulChem List of Experiments http://usefulchem.wikispaces.com/All+Reactions
9. Bradley, J.-C. Open Notebook Science Challenge UsefulChem Blog (2008)
http://usefulchem.blogspot.com/2008/09/open-notebook-science-challenge.html
10. CombiUgiResults Google Spreadsheet http://spreadsheets.google.com/ccc?key=plwwufp30hfpUERhse9y5Kw
11. ReactionAttempts Google Spreadsheet
http://spreadsheets.google.com/ccc?key=0Ak1R8T6wt4YQdG9NejNLcDNUMkVBVURGM01TR0NxdXc
12. RXIDsReactionAttempts Google Spreadsheet
http://spreadsheets.google.com/ccc?key=0Ak1R8T6wt4YQdGVENVFMWjdzaGd2REJTTnA4RG5vblE
13. Bradley, J.-C. Reaction Attempts on ChemSpider UsefulChem Blog (2010)
http://usefulchem.blogspot.com/2010/03/reaction-attempts-on-chemspider.html
14. SMILES Wikipedia Entry http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
15. ChemSpider Web Site http://www.chemspider.com/
16. UC archive Drexel server (ZIP) http://showme.physics.drexel.edu/usefulchem/archives/usefulchem2010-04-27.zip
17. UC archive on lulu.com (DVD) http://www.lulu.com/product/dvd/usefulchem-archive/10791847
18. UC interactive hosted format http://showme.physics.drexel.edu/usefulchem/archives/usefulchem2010-04-27/All%20Reactions.html
19. Bradley, J.-C.; Lang, A.. Reaction Attempts Reactants and Products. UsefulChem. 2010-04-27.

URL:http://spreadsheets.google.com/pub?key=toMz3Kp3T2EAUDF3MSGCquw&output=xls. Accessed: 2010-04-27.

(Archived by WebCite® at http://www.webcitation.org/5pIsFEbT9)
20. Bradley, J.-C.; Lang, A.. Reaction Attempts RXIDs. UsefulChem. 2010-04-27.

URL:http://spreadsheets.google.com/pub?key=teD5QLZ7shgvDBSNp8DnonQ&output=xls. Accessed: 2010-04-27.

(Archived by WebCite® at http://www.webcitation.org/5pIs2eh62)

ONS Solubility Book: Edition 3 with Notebook Archive

Edition 3 (2010-02-11) of the ONS Solubility Challenge book is now available.

We've been trying for some time to find a way to conveniently take a snapshot of our Open Notebooks and all associated raw data files. This could serve as a way to back up all of our work as well as provide a means of finding out the state of knowledge for a project at a given moment in time. There is also a tremendous benefit to confidently using the best of free hosted Web2.0 services out there (e.g. GoogleDocs and Wikispaces) without being concerned with changes in policies or access down the road.

Our recent use of the ONS Challenge Solubility book to periodically create releases of summarized data has opened up a convenient opportunity. And yesterday the last piece of the puzzle fell into place. Through a combination of fairly quick manual and automated tasks, Andrew Lang and I are able to push out a full snapshot of all relevant files and lab notebook pages and associate it with an edition of the book.

As described below, the archive is accessible interactively on a server, as a zip download or as a CD from LuLu. Perhaps we can also find a home on library servers in the future.

More details are provided in the preface for Edition 3 (2010-02-11):

This is the first edition to include a full archive of the ONS Challenge notebook. A space export from Wikispaces provides an initial version of all the HTML pages in the notebook with local hyperlinks to copies of all images and files uploaded onto the wiki. All of the Google Spreadsheets are automatically downloaded as Excel spreadsheets and placed in the same "files" folder as the images. NMR spectra, stored as JCAMP-DX files, are placed in the "spectra" folder. All of the HTML pages are reformatted to provide local references to both Excel spreadsheets and the JCAMP-DX files.

The notebook archive is meant to represent a snapshot of the state of all source documents at the time of the publication of an edition of this book. When used from a server with web services running, clicking on links to the spectra will allow interaction via a browser interface, including zooming in or out and integration of the NMR spectrum. When accessed in stand-alone mode after downloading or directly from a CD, everything will work the same, except that JCAMP-DX files must be open from JSpecView running on the desktop. Excel files will retain any calculations in the cells of the original Google Spreadsheets but dynamic values generated from calling web services - such the script that automatically integrates NMR spectra - will be frozen as simple values. However the link to the web service used will be stored in the cell as a comment. Links to external websites are not crawled and embedded Google Spreadsheets or videos are not copied. These will work but will reflect live data on the web.

The February 11, 2010 version of the notebook archive is available on a hosted site, on a CD or by download.

ONS Solubility Book: Edition 2 - with Predicted Values

The Second Edition (2009-12-27) of the Open Notebook Science Solubility Challenge book is now available. The issues with some missing text have been resolved, in addition to providing clickable links for the references in the PDF version.

However, the main difference is the addition of a new section on solubility predictions. The book is now somewhat larger than the first edition, coming in at 129 pages but still very affordable at $8.16 (covers printing and shipping costs from LuLu).

This was added to the preface:

Predicted Solubilities

In this edition, a new section is added to provide predicted solubility values for selected solutes in a range of solvents. Specifically, solutes are included when measurements from at least 5 different solvents are available. A method using Abraham descriptors depends on the experimental solubility measurements from several solvents to make predictions, which is detailed in that section of the book. For this reason, this edition also includes some aqueous solubility measurements, which are generally available from the literature. The focus of this collection remains on non-aqueous solubility.

Consistent with how the experimental measurements are made available, the predicted solubility values are provided as a work in progress. The purpose in providing them is to suggest solvents of interest for various applications. The boiling point of each solvent is also listed in the table to allow a convenient selection. When available, experimental measurements are listed next to the predicted values. This information can be helpful to gauge the usefulness of the model to some extent but does not guarantee its reliability for the other solvents. As more measurements are collected the reliability of the predictions is likely to increase and this will be reflected in future editions of this book.

Andrew Lang has been busily learning about building models using Abraham descriptors. As luck would have it, Michael Abraham just published an extensive collection of his descriptors for many solvents in a recent publication:

Abraham M.H.; Smith R.E.; Luchtefeld R.; Boorem A.J.; Luo R.; Acree Jr. W.E. Prediction of solubility of drugs and other compounds in organic solvents. J. Pharm. Sci. Early View Sept. 22 (2009) http://dx.doi.org/10.1002/jps.21922

This is an important step for the ONS Challenge project by taking us closer to the eventual goal of providing chemists an open tool for anticipating the solubility behavior of their reactants and products in a particular solvent. Researchers might think of trying new solvents after perusing their measured or predicted solubilization potential for a given solute.

We don't know how good the predictions will turn out but we will certainly find out in the coming months and report as we go. Even though the Submeta awards have all been distributed we still welcome measurement contributions.