Chemistry Blog

Feb 05

The Wolfram|Alpha “Reagent Properties Widget”

Update: CAS Number added to output
Update 2: DESKTOP GADGETS are here! See awesome update below!
Update 3: Check out the companion widget which calculates out the rest of the values for your reagent table (g, mmol, mL)!

If you’re like me, you don’t remember chemicals’ physical properties off the top of your head. You’re ready to run a reaction, and it’s time to fill out your reagent table. This usually means pulling out your calculator or the Aldrich catalog. Sure you can look it up online, but you always wonder if someone had some fun with a Wikipedia page – would you second guess if someone changed one of the digits in a Wikipedia entry? Maybe you used that chemical a few pages back… or was it in the last notebook?

I’ve really grown to like Wolfram|Alpha. I like the interface and the way they present the data. So I created a small Wolfram|Alpha widgit specifically for filling in reagent tables. Type in the chemical name, and it returns the molecular formula and structure (just to verify you entered the right compound), and tells you the molecular mass, density, boiling point (if you need to distill that liquid first), and a few other physical properties – everything you need to fill in your reagent table. It also recognizes chemical formulas, like TiCl4, and shorthand notation, like EtOH.

So be sure you bookmark this page and use this widgit next time you’re ready to run a reaction and can’t quite remember the density of that liquid.


Update 2: A few people, both in the comments and by email, asked if I could make a desktop gadget for the reagent table widget. Ask and you shall receive! Read about their development here.

NOTE: they’re not perfect and have some annoying bugs. The PCSmall version opens the results in a new internet explorer window, but works fine otherwise. The PCLarge version remains on the desktop with a flyout for the results, more like a ‘real’ gadget… but for whatever reason, the X button doesn’t work and you can’t make the flyout go away, so it stays large with your results open. Also, you must hit the enter button, the Submit button is not clickable. The Mac version’s X button works fine, but has scroll bars for the resulting flyout, and you can’t click and drag the scroll bars to see results. You must click in the results flyout and use the arrow keys to navigate.

Bad news: they have annoying aesthetic problems. Good news: they work, and you have the reagent table widget on your desktop for your reagent table needs at any time.

Download the Mac version here
Download the PC(Large) version here
Download the PC(Small) version here

Installation instructions: download them and open them. The computer takes care of the rest!

Jan 28

Pipettes and bulbs: always surprises for the experimentalist

Still, be nice to your pipette bulbs!A pipette bulb is a good friend to a chemist; a 5-inch or a 9-inch glass pipette is only a good backscratcher without a ‘rabbit rubber’, as my undergraduate stockroom would label them. (Really, I’m not kidding.) There’s always a couple in my lab coat pocket.

Anyhow, I’ve always insisted that there is no need to force the bulb onto the pipette; pinching the pipette bulb at the very edge of the collar and gently placing the pipette snugly into the collar is all you need. In the picture to the right, you’ll see an example of that having been done to the left-hand pipette. I have also maintained that you’ll get significantly less suction power if you insist (as many students do) on forcing the pipette into the pipette bulb.* The pipette on the right has close to 1 cm of its end rammed into the bulb.

Yet, I am chagrined to note that there is not a significant difference in the amount of KMnO4 solution drawn into the pipettes. How disappointing — what will I find to disdain now?

A parting shot for a pet peeve: folks who roll the collar (if possible) down onto the pipette, as if, uh, um, er, uh, utilizing a prophylactic. That’s really unnecessary. Just sayin’.

*Obviously, if you were to place the entire end of the pipette into the bulb, then you would not be able to force enough air out to generate a vacuum.

Jan 27

Skillful writing of an awful research paper

Apparently, laboratory instructors and undergraduate mentors aren’t the only ones with the bane of reading insanely terrible research papers – the editor of the ACS journal Analytical Chemistry, Royce Murray, clearly has had his fill as well, according to his editorial in the current ASAPs.

His humor is very similar to that found in The Onion, and reminded me of How to Write a Scientific Paper on Improbable Research.

Brilliant. The only thing that has made me laugh out loud this hard lately was catching a part of the show ‘Ancient Aliens’ on the History Channel last night in which someone said that “one possible explanation of why the Mayans vanished was because they were aliens.”

In all seriousness, though, it is an understatement to say it’s quite obvious that scientific writing isn’t emphasized as well as it should be, it should be addressed at the undergraduate level as early as possible.

Jan 23

Yes, it’s been done: coffee flavour chemistry

When I was much younger, and my interest in chemistry was just beginning to influence my thoughts of post-secondary school and (a lifetime away) a career, there were hints of my destiny that came in the form of somewhat perverse interests.

One of these was my profound interest in the chemical constituents of coffee. A non-chemist simply sees a cup of coffee for what their nervous system and digestive see it: a black liquid that tastes bitter, inhibits your appetite, and gives you about a two hour energy boost. However, being the child of two coffee snobs who also happened to be career scientists, I had different notions.

What makes a good cup of coffee? People have their preferred brands, countries of origin, or even vintages, if you have that much money to throw away. There are even those who eat an obscenely expensive bean that has been digested and excreted by the Asian palm civet. But can you actually taste the difference? And more importantly, what makes up the difference in flavour?

Most coffees are simply described in terms of acidity, roast, and some vague notes about other flavours (vanilla, caramel, berries, chocolate). This, to me, was completely unsatisfactory. Little did I know that coffee flavour chemistry is a legitimate field of study, as is the study of flavours and scents in general.

In my slightly-more-recent searches on the topic, I stumbled across a book entitled Coffee Flavour Chemistry; a better match for my childhood fascination could not have been conceived. Though now somewhat out of date, the book represented a major achievement in the field in 2002 when it was written by Ivon Flament, and contains some very interesting information and a comprehensive review of the work done in identifying coffee’s chemical components. It identifies over one thousand compounds present in both green and roasted coffee beans, describing their aromas and their significance in the overall flavour of the coffee. Intuitively, the most important constituents of coffee flavour are the ones with the highest “signal-to-concentration” ratio, or how easily they can be detected at a certain concentration. Some of the most important constituents can be seen below, with their described flavours:

The majority of these compounds are of course formed via the well-known Strecker degradation and the Maillard reaction.  These, as well as other important aspects of the roasting of coffee beans, are discussed within the book.

Perhaps what I found most interesting are the techniques used to determine what are called “odour activity values”, which essentially amount to a quantification of how strong a compound’s odour is at a given concentration.

The methods used for finding these values are actually gas-chromatographic olfactometry, which is exactly what you think it is: they run a GC, and have someone sniffing the end of the column, who presses a button each time they smell a compound. I laughed at this when I read it, not because it’s unreliable (quite the contrary), but because imagining running a column with a panel of “sniffers” at the end instead of a mass spectrometer is quite an image indeed.

The original method (GC-olfactometry) was purely qualitative in terms of odours, but later methods known as CHARM (a proprietary technique involving dilution-to-threshold) and AEDA (aroma extract dilution analysis, a similar method) have overshadowed it in recent years. Yet another method, named with a classic, groan-inducing acronym is “GC-SNIF”, which stands for “gas chromatography-surface of nasal impact frequency”, in which panels of test subjects are used to determine how “smellable” a compound is at a single concentration, producing averaged and normalized curves for the detection of smells.

Apart from being a funny image, these methods of analysis (which are almost always used in conjunction with purely analytical methods) illustrate an interesting point about flavour chemistry. While GC or LC data, as well as mathematical methods such as canonical analysis or principal component analysis are useful for predicting simple properties, the use of human organoleptic testing is essential to actually understanding the results.

Another salient point that was mentioned was the perception of quality. In a 1986 paper, Liardon and Spadone discovered that while the degree of coffee roasting was correlated to a large number of compounds and their concentrations, the quality of the coffee did not appear to be correlated to any of them. One of the few quantitative differences that could be established based on quality was that between green C. arabica and C. robusta beans. Robusta tended to have higher concentrations of methanol, acetone, pyridine, methylpyrazine, and furfural, and also seemed to be unique in that they contained methyl formate, t-butyl alcohol, and furfuryl alcohol, not found in Arabica strains. Robusta beans are widely perceived to be inferior in flavour and aroma to arabica beans, which is why many coffee packages will declare themselves to contain “100% arabica beans” to avoid confusion and distinguish themselves.

So what does this tell us? After skimming through the book I came away with two lessons: the first is that while computers and statistical analyses become more and more powerful every day, it seems there is usually a place for subjective human-generated data.  Without olfactory analyses from panelists, much of the work on coffee and its constituents would have been completely useless. The second is that while this data is essential to understanding the importance of certain compounds in generating a specific flavour, it is almost worthless when trying to establish a causal link between specific compounds and the perceived quality of the coffee (edit: this is not strictly true for identifying fundamental flaws in the bean due to parasites, mould, or poor growing conditions, which can all be identified by screening for certain compounds). For the most part, as everyone has heard so many times in their life: there’s just no explaining some people’s tastes.

However, I think for most of us in grad school, the fact remains that the most important compound in coffee is one which contributes almost nothing to its odour profile:

Jan 21

Kudos to the Fagnou Group

I am continuously impressed by the publications that have appeared since Prof. Keith Fagnou’s shocking passing a little over a year ago. The chemical community still mourns; it is clear from these post-mortem publications that Fagnou’s – and his clearly dedicated and talented graduate students and post-docs – brilliance lives on. (Note – this is the same article that appears on Chemical Crystallinity.)

The chemistry that Fagnou has truly spearheaded, direct C-H functionalization, is a method of forming C-C, C-N, C-B, etc bonds without having to prepare one of the coupling partners, as in traditional transition-metal catalyzed cross-coupling reactions. Palladium, rhodium and ruthenium are commonly used catalysts in direct C-H functionalization reactions. Fagnou has published a great deal on arylation reactions of a wide variety of substrates and even a bit on direct benzylation reactions. Some fairly recent reviews are linked in a previous post at my own blog.

A recent publication in Journal of Organic Chemistry (doi: 10.1021/jo102081a), “Predictable and Site-Selective Functionalization of Poly(hetero)arene Compounds by Palladium Catalysis,” published by David Lapointe and coworkers, explores the development of two approaches to selectively functionalizing multi-ring systems – 1) using site-selective reaction conditions, and 2) a pathway with a particular order of reactivity according to a concerted metalation-deprotonation (CMD) mechanism. It is well-known in the field that a great many (hetero)arenes can be functionalized with (painfully) rigorous fine-tuning of the catalyst, ligand, additives, and other reaction conditions. Some substrates have been more difficult to functionalize than others, and selectivity of particular positions on these rings is always an issue – this publication tackles both issues.

To explore site-selective functionalization, the group used compounds with more than one available C-H bond for direct functionalization, and using multiple protocols specific for specific C-H bonds (Larossa’s conditions for C2 arylation of indoles, Gaunt’s Cu-catalyzed C3 arylation of indoles which is actually selective for meta to amido groups, and their own protocols for arylation of perfluorobenzenes and aromatic N-oxides) were able to successfully and selectively functionalize targeted C-H bonds in moderate yields. Here is an example with some decent yields, with reaction times ranging from 16 – 24 hours:

The alternative approach relies upon the CMD pathway as the operative mechanism, which favors electron-deficient substrates.  Several years ago, Echavarren published support of this mechanism by finding a preference for the most acidic C-H bond and requirement for a carbonate base, and Fagnou established the use of a pivalate additive, which was speculated to play a crucial role via CMD.   A recent mechanistic paper with aromatic N-oxides as the substrates strongly supports this mechanism.   The metal first inserts into the aryl-X bond, as expected, and in the key transition state, the pivalate coordinated to the metal deprotonates the C-H bond while the palladium forms a bond to the same C.  Reductive elimination (not shown) releases the arylated product.

In the current paper DFT calculations were found to agree quite well compared to competition reaction results of a series of heterocycles to elucidate the order of reactivity of the substrates.  Those presented in the paper are as follows, in order of reactivity – this is extremely convenient for the synthetic chemist who would like to utilize this chemistry.  And it’s just plain neat – the kind of thing that will hopefully end up in a textbook someday. (Note: the last two substrates are either switched in the text or switched in the image – they don’t agree in the paper and I haven’t looked at the supporting information closely.)

Reaction conditions: 0.5 eq. of each of two heteroarenes in the competition experiment, 0.125 eq. 4-bromotrifluorobenzene, Pd(OAc)2 5 mol%, PCy3.HBF4 (10 mol%), PivOH (30 mol%), K2CO3 (1.5 eq.), DMA (0.3M), 100ºC.

And finally, for an example of the method in action – note that the difference between using this method and the previously described is that here, there aren’t necessarily general optimized conditions available for each of the substrate classes here.  Examples of a few of these are peppered throughout the arylation literature but they aren’t like indoles, pyridines, N-oxides, perfluorobenzenes, imidazoles, and pyrazoles and don’t have their own special set of conditions (that I’m aware of at the moment).  Yields of included substrates range from 65-80%. Instead of optimizing conditions for each, the site of reactivity can be predicted with good specificity – here the indolizine C-H bond over the more electron-rich thiophene’s:

Instead of an aryl bromide, benzyl chloride can be used as the coupling partner as well, with published yields from 55-84%.

  • Lapointe, D., Markiewicz, T., Whipp, C. J., Toderian, A., Fagnou, K. (2011). Predictable and Site-Selective Functionalization of Poly(hetero)arene Compounds by Palladium Catalysis Journal of Organic Chemistry : 10.1021/jo102081a

Jan 19

Chemistry Dictionary for Word Processors – Version 3.0

**Get V3.0 here.**

Version 3.0 is here! User-Submissions! OO.o Extension!

Since releasing Version 2.0 of the Chemistry Dictionary in December 2008, we have had a user-submission form on this blog. If there were words missing from Version 2.0 of the Chemistry Dictionary, users could submit the suggested word and the words would be held in limbo until I got around to updating to Version 3.0.

Well, 2 years later, I finally got around to it. I emptied out the limbo file and went through each submission. Some were gibberish. Some were words that were legitimately misspelled, and thus of course not in the dictionary. Some appeared to be foreign or alternative spellings, and were also dismissed. The surviving words were added into the dictionary file to populate Version 3.0.

Also, I finally found a coherent walk-through on how to turn the dictionary file into a Dictionary Extension for Writer Versions 3.0 and higher. This was a big concern when 2.0 was launched. Version 2.0 had a workaround method of using the dictionary file in OO.o, but I couldn’t find a simple and easy way to make and submit a Dictionary Extension, so that project got shelved.

As I was sifting through the Limbo List, I found a forum with user-friendly instructions to make a Dictionary Extension. So, you open source users, you may now download the Chemistry Dictionary Extension from the main repository of Dictionary Extensions here. Even though it hasn’t officially been released until now, it’s already been downloaded almost 300 times according to the OO.o website (as of 1/19/11).

There is an install.txt file in the zip file which spells out how to install the dictionary for new users. It also includes update instructions for users wanting to upgrade from Version 2.0.

Also, a special note to Mac users. If you use iWork, you’ll have to install a separate version of the dictionary. See Update #1 below for information on using the chemistry dictionary with iWork. Unfortunately, the iWork files are still Version 2.0 and have not been updated to Version 3.0.
Update (1/29/11): the iWork file and installation instructions have been incorporated into the standard download. All word processors should be able to install the dictionary file from one download.

Enjoy Version 3.0!!!

(this post has been reformatted to preserve links to the dictionary file from other sources. We’ve also created a convenient, shortened url for the dictionary:

Read the original December, 2008, post and download the dictionary file here

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