Wednesday, December 26, 2007


I just recently learned that oak barrels (used in wine and beer making) can be "sanitized" by burning sulfur in them to produce gaseous sulfur dioxide. This doesn't actually sanitize the barrel, but it inhibits the growth of mold and bacteria.

This is especially useful if the barrel is being stored for any length of time. Keeping an atmosphere of SO2 inside the barrel keeps the peskys away.

Before wine or beer is added to the barrel, it is critical that the SO2 gas be fully removed or H2S can form. That would smell and probably taste awful.

I'm planning on experimenting with oak chips in some future batches of beer. Conditioning in oak barrels would be awesome, but not practical (at this point).

The picture is from the Ithaca Beer Brewers Blog.

Tuesday, December 25, 2007

Merry Christmas....

Merry Christmas my wonderful blog reader. And if you don't celebrate Christmas, than Merry Tuesday to you. And if you don't celebrate Tuesdays then you are a real bastard, bastard!

My spiced ale is in the bottle. It is not carbonated enough yet, but I do know the nutmeg is way tooooooo strong. We'll see how it is in a few weeks. A bit late, but hopefully good.

Regardless, enjoy this.

Thursday, December 20, 2007

Brewing Chemistry: Part 4- Iodide and starch

During the mashing of the grains, the amylase found in the barley is used to break down unfermentable starch into fermentable glucose. The goal is to break down as much of the starch as possible.

Starch comes in two different forms, amylose and amylopectin. They are both polymers of glucose. Amylose is a linear polymer, and amylopectin is a branched polymer. There is usually more amylopectin in a given sample starch, but it is the amylose that can be used to identify the mashing progress.
A common and simple test for the presence of starch is the iodine test. A solution of iodine (I2) and iodide (I-1 from something like potassium iodide, KI) is added to the sample. The iodine/iodide solution is reddish, but in the presence of amylose it turns dark blue (almost black).

First of all, iodine (I2) is not terribly soluble in water. The addition of iodide (I-1) makes it soluble by forming an I3-1 complex ion.

Amylose adopts a coiled or helix shape. When I3-1 is added it gets trapped in the coils of amylose. The iodine atoms trapped in the coils can be in the form of I3-1 or I5-1 or more iodine atoms (I'm not sure and I don't know if anyone is). The resulting interaction between the amylose and the iodide complex results in a shift of the light being absorbed by the iodide complex. This happens because there is transfer of charge to the starch molecule. This affects the energy spacing of the electrons in the iodine.

The result is a complex that does not absorb light in the blue region of the visible spectrum.

Monday, December 17, 2007

Momentary silence

Final exams are in full swing. My blog silence may continue for a bit. I plan on actually getting back to some chemistry of brewing when things slow down. Until then, you can enjoy one of my baby pictures.

Courtesy of

Wednesday, December 12, 2007

Things I hate

During this time of year, things get busy. The semester is ending in the typically frantic manner, and I have little time to do things not related to school. I'm not complaining. That's just the nature of my job.

It seems that during this time of year, I'm reminded of things I really hate. Here are a few examples:

I hate fantasy football. My team had a great week but got creamed in the first round of playoffs nonetheless.
I hate football pick 'em leagues. I really suck.
I hate grading papers. I assign papers because it very important that our students be able to write and practice makes perfect. But, I hate reading these. I don't know how the folks in the English department handle it. It drives me nuts.
I hate needing one simple item from Wal-mart (or any store) and having to deal with the horrid hoards of people. I'm a big (and the like) fan.

On a happy note, I plan on brewing tonight. During the partial mash and boil periods, I will read and grade papers. Sounds like fun....

On a totally random note, the movie Tron is awesome. I just watched it again (like I said, I'm very busy). For a 1982 movie, it is superb.

Friday, December 7, 2007

Chemdraw upgrade

Since updating to OS 10.5, I have not used the Chemdraw 9.1 program on my computer. Shortly after updating to Leopard, I downloaded a demo version of Chemdraw 11.0 just for the fun of it, and used that for 2 weeks. I didn't really intend on purchasing it since version 9 does everything I needed.

Well, the two week trial ended and I reverted back to Chemdraw 9.1. Everything was great until I tried to save my file. Apparently, while using OS 10.5, Chemdraw 9.1 can't save. I got the spinning wheel and then Chemdraw would quit. I tried everything. Uninstall, install, repeat.

Eventually, I had a choice. Go back to 10.4 or buy Chemdraw 11.0. Well, like they say, once you go 10.5 you never go back (or something like that). I asked my IT friend if they would foot the bill. They said yes. Apparently, the $270[1] for software is nothing in the grand scheme of IT. So, I now have Chemdraw 11.0.

Since I am a Mac guy and since Cambridge Software is slowly becoming more and more Mac-unfriendly, I purchased the Chemdraw Pro version of 11.0 since the Ultra version contains lots and lots of cool features that work only on a Windows machine.

For how I use it, I have not noticed any big changes or improvements. The interface looks nicer, but the functionality is essentially the same (at least for how I use it).

The one thing I really wish they would include is a shortcut button for the "distribute" function. I use this all of the time. When I have a number of structures, I like them distributed evenly. The "center" and align functions all have shortcut buttons, but not the distribute. Unless there is some way to set this up, I will always be annoyed by this shortfall.

I'm also annoyed by the fact that in all of my installing and uninstalling and upgrading, I forgot to save my stationary files (i.e. document settings). Which means, I'll need to recreate these someday. Oh well, that was my fault. I had different settings for exams, reports, and other things. I hate the ACS document settings for use on exams. The nice thing is, version 11 has Wiley settings which are very close to what I use for exams.

[1] The $270 is the upgrade price for Chemdraw Pro with the educator discount.

Tuesday, December 4, 2007

...starting at center...E.J. Corey....

Yesterday I got an email from the folks at Wiley Scientific. They wanted me to know that the current issue of Journal of Pharmaceutical Sciences was available free of charge. The complimentary online access is in honor of Professor William Higuchi. I first thought to myself, "who the hell is William Higuchi." After further thought I realized, if a publication such as this is going to make such a fuss over someone, that someone is probably very important in that field. Perhaps I am a bit naive when it comes to the big players in the world of pharmaceutics. Well, to be honest, I should drop the "perhaps" in that last sentence.

I found myself in the same situation I find my students in. Most of my students (at least early on) have never heard of E.J. Corey, Woodward, Sharpless, Trost, Grubbs, etc... I had never heard of Higuchi but upon reading the article in the JPS and on his website, I realized he is quite the deal in pharmaceutics.

I'm much more familiar with organic chemists. A few years ago, as a way of putting the players in this field in perspective for my students, I started using sports analogies. This worked for 80% of my students. The other 20% were annoyed that once again I had boiled something down to sports [1].

I'll stick with the NBA since most of the players are fairly recognizable.
E.J. Corey is the Larry Bird of Chemistry
Grubbs is the Kobe Bryant of Chemistry
Sharpless is the Magic Johnson of Chemistry
Hoffmann is the Scottie Pippen of Chemistry
Nicolaou is the Karl Malone of Chemistry

These are fairly big names and they correspond to big names in the NBA. Frankly, the names get swapped around all of the time, but the point is made that if Chemistry was a spectator sport, we would know all of these names.

So, who are your superstar chemists and what sports figure are they analogous to? Who is the Michael Jordan of Chemistry? Better yet, who is the Luke Walton, Stephan Marbury, Vlade Divacs etc... of Chemistry?

[1] For me, most of my analogies involve sports or kindergarteners, but the kindergartener thing is another post.

Saturday, December 1, 2007

Perspective is everything.

The family and I went out and cut down our Christmas tree recently. We went to a tree farm and spent a while picking out just the right tree. We eventually picked one out and killed it (i.e. cut it down). It was a bit big, but we didn't think too much of it until we got it home.

Once we got it to the front door, the massive size became evident. Until I had some perspective, I didn't realize how big it was. The fact that it seemed to weigh about 200 pounds should have been a clue. With a bit of shoving and pushing we got it inside and stood it up. Thankfully, we have a vaulted ceiling. So, there was room, barely. The thing is over 10 feet tall.

I've always wanted a really big tree, but this is ridiculous. I tried taking a picture, but it doesn't do it justice. I'll let you use your imagination.

Thursday, November 29, 2007

A real inconvenient truth

So, of all of the human activities to blame on global warming, the Canadian government is pointing the finger at its beer drinking citizens and their beer fridges.

Thanks a lot for screwing up the planet you Canadian beer drinkers!!!!


Wednesday, November 28, 2007

Perpetuated yeast

I racked my Spiced Winter Ale yesterday. It tasted pretty dang good. The gravity had only dropped to 1.022. So, my alcohol content may be a little lower than I was shooting (6% vs. 6.9%). Oh well, it was good. The spices were a bit strong but that should mellow in the secondary and then in the bottle.

I was pleased how it turned out because of the yeast I used. A month before I made this batch I stole some yeast (Wyeast 1056) from a yeast starter and capped it in a sanitized bottle. I stored this in my refrigerator for a month. When I was ready to use it again, I opened the bottle and made another starter from it. Fermentation took place and no weird flavors showed up. I'm pretty confident the yeast survived my manipulations and storage.

I plan on using this procedure regularly in the future to stretch my yeast a little further.

Friday, November 23, 2007

backup, backup, backup, backup......

A recent story written by Derek about 3.5 inch floppy disks and a dissertation brought back some memories for me. The fact that I am currently looking for an external hard drive to store my rapidly expanding digital information also stirred these memories. I am looking for a 500 GB drive which would be 2.5E5 times larger than the good old fashioned 3.5 inch floppy drive I stored my MS thesis on.

I was in grad school (for the first time) back in the mid-90s. I was doing work on organometallics (heavy on the organo, light on the metallics), specifically porphyrins. After a couple of years, I was offered a teaching position, and I opted for a MS and the pursuit of wealth in the world of academia.

The internet was still in its youth, but it was a rapidly growing toddler that was learning to run. Netscape was still good, and computers were becoming much more than glorified word processors.

I bought a Macintosh PowerBook 520c (the 'c' means "color"). I love that computer ("love" in the present tense. I still have this computer and use it occasionally). It was a workhorse when I wrote my thesis. I would often have 6-8 applications running at the same time, and the little thing only crashed once.

As I wrote my thesis, I realized my paranoia of losing my work was directly proportional to the thesis length. I became a compulsive saver. I would save everything I had on a 3.5 inch floppy drive. I started saving everything on just one disk. As my work got longer and longer, I started saving 2 copies. Then an event occurred that threw me deep into backup paranoia.

I was writing at home. I decided to have a beer while writing at my desk. It was a 22 oz microbrew and I had poured it into a tall glass (see where this is going?). I was typing away enjoy what I recall as bing a pale ale. I don't know what happened, but due to what was some sort of flailing arm movement I knocked the beer over.

Sudden panic. Beer every where. My bed was next to my desk and there was enough beer on my quilt so I threw that on the wood floor to sop up the beer that was cascading off of my desk. I quickly assessed the situation. Somehow, somehow, very little beer got on my computer. It had only splashed on the display and on a few keys. My stylewriter printer on the other hand got the worst of it. It would never recover. I cleaned up the mess, tried heroic efforts to resuscitate the printer, and apologized to my PowerBook for putting it in harms way.

That's also when I decided to increase the number of copies I backed up. It eventually became 10. I would literally spend about 30 minutes backing everything up each day. The floppy disks were dispersed everywhere to ensure the survival of at least one if a catastrophic beer spill of biblical proportions were to occur.

When I returned to grad school to finish my Ph.D., I followed a similar pattern, albeit with CDs. I was eventually burning 3-4 CDs daily.

Yes, I was paranoid.

Wednesday, November 21, 2007

Another pardon

As is the tradition, President Bush pardoned the White House Thanksgiving turkey today (actually, turkeys). This little tradition dates back to 1947. Every year since Truman was in the White House, the National Thanksgiving Turkey (yes, that is its official title) is presented to the president and he ceremoniously pardons it.

I'm sick of these bird being pardoned. It is time to send one of these to the White House dinner table. I'd love it if Bush said, "ah hell, let's cook this baby up. Dick, get yer gun!"

Bush still has one Thanksgiving left in office. I think he should be the first to not pardon the bird After all, he's had the balls to invade two countries in 5 years. It shouldn't be too hard for him to wack a bird. Besides, who is left that he could piss off.

Happy Thanksgiving everyone (even those not from the USA). Have a beer.

Monday, November 19, 2007

If I had a dollar....

...for every visitor I have had to this blog, I would have enough to buy the sweetest all-grain brewing system ever.

21100 and counting.

Thanks for visiting.

Friday, November 16, 2007

Tannins and icky beer

Tannins are astringent, bitter tasting compounds. Chemically, tannins refer to a broad class of polyphenols. They are often differentiated from other polyphenols in that, tannins precipitate proteins. Ann Hagerman at Miami of Ohio University has a great pdf online that explains tannins much better than I could.

They are not desired in beer. However, they are found in the hulls of the grains whence comes the goodness that eventually becomes beer. During the mashing process, the starches get enzymatically broken down to maltose. However, if the mashing or sparging water is too hot, detrimental amount of tannins can be leached from the grains. It is well known that for most things, the solubility in water increases as the temperature of the water increases. So, this makes sense.

However, the pH of the mash can also affect the solubility of tannins. If the pH is too high (the "normal" pH of a mash is around 5.2) the solubility of tannins increases. This has to do with the presence of the phenolic functional group.

Shown is catechin, a common (and fairly simple) tannin found in a brew kettle near you [edit: The structure shown is missing one OH group. I'll fix it later].

As any sophomore organic chemistry student will tell you, the OH groups bonded to the aromatic rings (the group that puts the "phenol" in "polyphenol") are willing to lose their protons to a base. The pKa of phenol is about 10. I don't know what it is for catechin, but I'm sure it is in that vicinity.

As a result, if the pH of the mash get too high, more and more of the tannins will lose the proton. The result is charged, ionic compound which has a higher water solubility than the neutral species. As a result, the result of this result results in more tannins dissolved in the water.

So, what affects the pH of the water in the first place? You'll just have to wait and find out.

Winter Ale

With winter approaching (that son-of-a-bitch), I decided it is time brew a beer that makes the long cold Minnesota nights a bit shorter. I once again went to my brewing cupboard and took an inventory. With the help of The Beer Recipator, I crafted a recipe for a spiced Winter ale.

I've very proud of this batch because I took a lot of care crafting it, but I also paid a lot of attention to some specifics. For example, I actually took the time to calculate my mashing (partial) efficiency which turned out to be about 75%. I hope the extra care pays off.

Here's the details copied from the Recipator summary. I didn't include in the summary the spices I included. For the last 15 minutes of the boil I added 3 cinnamon sticks, 0.5 tsp nutmeg, 0.25 tsp ground cloves. During the last minute of boil I added one split vanilla bean. It smelled great.


Brewer: - Email: -
Beer: spice Style: Robust Porter
Type: Partial mash Size: 5 gallons
51 HCU (~22 SRM)
Bitterness: 31 IBU
OG: 1.067 FG: 1.014
Alcohol: 6.9% v/v (5.4% w/w)
Grain: 1 lb. 11 oz. American 2-row
1 lb. Wheat malt
.5 lb. American crystal 120L
11 oz. British crystal 50-60L
4 oz. British chocolate
Mash: 75% efficiency
Boil: minutes SG 1.112 3 gallons
5 lb. Light dry malt extract
Hops: 1 oz. Cluster (5.7% AA, 60 min.)
.5 oz. Kent Goldings (6.9% AA, 60 min.)
.25 oz. Chinook (12.2% AA, 60 min.)
1 oz. Cascade (6.9% AA, 15 min.)

The yeast I used was Wyeast 1056, American Ale. I brewed with this yeast about a month ago. I saved a bit from the starter and placed it in a sanitized beer bottle and capped it. I stored it in my fridge for almost a month. I made another yeast starter and rejuvenated the yeast. Hopefully it is still healthy enough to make good beer. We will see.


OK, I've been using Leopard for a few days now. My first impressions are that it is awesome. I've run into no compatibility issues thus far. I like the look which clearly Apple has focused on as much as function.

One big noticeable improvement is the speed. I'm using a PowerBook G4 (1.5 GHz with 768 MB RAM). By most standards, that is getting old. Leopard has made my machine run a lot faster and smoother.

The only issue I have noticed (and I'm not sure to what extent Leopard is to blame) is in syncing. When syncing my computer to a server, it doubled some of my files. One had a "-local" suffix and the other had a "-network" suffix. I'm still trying to figure that one out.

I still wish Apple would do something about Appletalk, but maybe they can't just dump it. I don't know. It's just an annoyance.

Is it worth the cost? Well, for me it didn't cost a thing. My employer covered that. Would I, personally, shell out the $130 to update? Maybe. The change from 10.4 to 10.5 is not too drastic. If I was still running 10.3 on an iBook, I would do it in a minute.

Wednesday, November 14, 2007


During my first semester of grad school long ago, I took a Physical Organic class. It was a great class. The teacher was from Poland and spoke with a moderate accent, not thick enough to be indecipherable, but occasionally some words were totally different.

One day we were talking about diastereomers. Now, for the non-chemists out there, I'm not going to try to explain it. It would take more time that I want. For those of you who need refresher, Eliel defines diastereomers as: "Stereoisomers that are not related as mirror images. They usually differ in physical and chemical properties."

The correct (or at least most understood) pronunciation is: die'-ah-stair'-e-o-merz. OK, not the way Webster would have written it, but you get the point. Well, on day in class, my Polish prof pronounced it: dee-ah'-stur-oh'-murs (note the accent on the second syllable). Say it out loud. It sounds quite different than the "normal" way of saying it.

We were in class when this happened and it took a few minutes to figure out what he was saying. Yet, since we were familiar with diastereomers, we eventually figured it out.

However, this prof also taught Sophomore level Organic Chemistry. The students in that class had never heard of diastereomers before. As a result, the class of about 300 all learned to pronounce it as dee-ah'-stur-oh'-murs. It was hilarious to have a student come to the chemistry help center and ask for help on "dee-ah'-stur-oh'-murs" from the TA. I wonder how many of them still pronounce it wrong.

Monday, November 12, 2007

A preview

I hate to say it, but I've been busy lately. Too busy to blog (is that an appropriate use of the word 'blog'). Tonight I bottled my house ale (Metathesis Ale). I'm going to try to keep this one on hand at all times. I like it a lot.

While I haven't been blogging (seriously, can I use 'blogging' as a verb?), I've been running a lot of ideas through my mind that I want to write about. If you are interested, here are a few of the things you can expect to see on this blog before April:

1) Tannins and how they affect beer (Look out for the pKa).
2) Mac OS 10.5. I just got it loaded today (finally). I will give you my impressions.
3) ChemDraw 11 (a.k.a. Ultra (2008 version)) I'm trying a demo to see if I want to replace my 2005 version.
4) Harvesting yeast from a yeast starter and storing it for 2 weeks.
5) Brewing water chemistry
6) why I ALWAYS type 'chemistyr' instead of 'chemistry'
7) How people from Poland pronounce "diastereomers" funny (based on one experience).
8) The use of gelatin in a secondary to act as a clarifying agent.
9) The chemistry of paints and paint binders.

Now, I hopefully will get to these.

Monday, November 5, 2007

beer activities

I racked my Guinness clone to a secondary. It tastes great.

I cracked my first Carbon Black Oatmeal Stout. It is dark and pretty good. It's only been in the bottle for 6 days. That is WAY too early to open a bottle, but it is SO hard to wait. This should age quite nicely. Very rich and full bodied.

Friday, November 2, 2007

This tastes like burning

A couple of my students told me about this little "trick." Take a piece of Big Red gum and remove the wrapper. Lick the wrapper and place on your skin (shiny side out). The forehead works great, especially for the unsuspecting.
After a few minutes, the effect will be noticeable. A burning sensation is eventually accompanied by a bit of skin irritation. Try it. This is what my arm looked like after 5 minutes (the picture's not great, but you get the point):

Of course, there is chemistry at play here. The culprit is the same thing that gives Big Red (and other cinnamon-flavored gums) it's character... cinnamaldehyde.

I wonder if there is an MSDS for Big Red. If there was, I bet chewing it would not be acceptable.

Sunday, October 28, 2007

Brew weekend

I brewed my Guinness Stout clone on Saturday night and bottled my Carbon Black Oatmeal stout. I have two batches to bottle during the next few days.

Here's my Guinness Stout recipe. It's from Clone Beers by Tess and Mark Szamatulski. Normally, when I clone a beer, I simply try to get close. If I get something I like, I do little to try to get it to be a perfect match. Cloning Guinness, however, is a different story. I want it to be as close as I can get it. Therefore, I try to follow the recipe as closely as possible. Here is the partial mash recipe I used:

1.5 lb 2-row British pale malt
12 oz. roasted barley
4 oz. 55°L crystal malt
4 oz. flaked barley
3 oz acid malt
4 lb Mountmellick LME
1 oz Target hops
0.5 oz Kent Golding hops
WYeast 1084 Irish ale

My Carbon Black Oatmeal
Partial Mash:
3 lb 2 Row British Pale Malt
1 lb flaked oats
8 oz. Munich malt
4 oz Belgian Special B malt
8 oz. roasted barley
3 lb Dark DME
0.5 lb Light DME
1 oz Bullion hops (6 AAU) (60 minutes)
0.5 oz Willamette (4 AAU) (15 minutes)
WYeast 1098

This is a lot of stout, but it will all be ready for the cold of winter when a nice full bodied stout is just what the weather ordered.

Friday, October 26, 2007

Sounds like a challenge

We all have drinking stories, but try to top these.


it's been over a week since I last posted. I get really annoyed when I do that.

I'll fill that void with a beer update.

I bottled a Pale Ale that may have not have been the real thing. When I brewed it, I used some pale malt as part of a partial mash. The problem is, I didn't label the bag and in hindsight, I don't think it was pale malt at all. In fact, I have no idea what it was. The original gravity (this included 3 lbs DME) was about 1.036. That's kind of low. The final gravity was 1.010. It actually tasted OK when I bottled it. In a couple of weeks I'll know what I got. I do not mind low alcohol beers as long as they have some taste and flavor.

I also racked a oatmeal stout and another batch of my Metathesis pale ale to secondaries. Both are in my garage chilling at 55-50°F. I racked a Anchor Steam clone to a secondary and put that in my basement.

I started a yeast starter tonight to make a Guinness Clone. IMHO, Guinness is the greatest beer EVER. Nothing compares to Guinness. Even the "crap" that gets sold in the USA is better than anything. I've cloned it before. The goal is not to make a perfect match but to get something close that you enjoy. I've done well every time I've cloned it. I'm doing a partial mash Guinness clone tomorrow for the first time. I'm betting it will be good even if it isn't exactly like Guinness.

Wednesday, October 17, 2007

A great day in the history of me finding things I lost

I was digging through a pile of old poster board piece I used at an ACS conference back in 2002±1 and look what I found:

My long-lost autographed photo of E.J. Corey.

So far this week, I have found many things I have been missing for a while including my 5/16 and 1/4 inch socket, and a hex wrench. Now, I've found this picture. Awesome.

Saturday, October 13, 2007

So much for the English language

I know this has nothing to do with chemistry or beer, but sometimes I need to vent. I love sports. I love football a lot, but I hate football commentators a lot. Face it, they are idiots.

The play-by-play guys are usually OK, but the color commentators are simply the worst people on the face of the earth. OK, maybe it's not that bad, but you must admit, they tend to say some really stupid things. I say stupid things all of the time. I know how it can happen, but the difference is I try not to say them over and over.

I'm referring to the cursed sports cliché. The phrase #1 is overused and #2 doesn't make any sense in the first place.

There are many. Some come and go. Others persist like a bad rash. The one that inspired this gripe is one of the stupidest. I heard it thrice today and I didn't even spend much time watching football today.
The phrase: "he caught the ball at its highest point." Idiots. No he didn't catch it at its highest point. When the ball was at its highest point, it was probably 20 feet high. No one can jump that high except maybe my childhood hero, Javier.

A better and as effect phrase would be "he caught the ball at the apex of his jump." See, you get to use the word "apex." That is a really cool word. The guys in the booth with you will look in amazement and decide that for a washed-up, former NFL star, you just might be "OK"

And another thing.... the word "literally" is not to be used as a word of emphasis. It means what you are saying happened in fact. So, don't say "he was literally flying down the sideline" unless the running back had sprouted wings and was actually flying like a bird down the sideline.

I know, I know. "Literally" can be used in an informal way to add emphasis. I'm just saying that that usage should be reserved for special occasions.

Thursday, October 11, 2007

OMG!!!! Beware the evil water

The video is about 10 minutes long and ends abruptly, but anyone with a basic understanding of chemistry (or anything, really) will be amused by this crap-filled video selling something to the ignorant.

My favorites: white copper sulfate and "only plants use inorganic minerals." There are many more.

There are a lot of blogs that address this type of thing (see Respectful Insolence for one high quality example). It is essentially, scam artists sucking money from the scientifically ignorant. I don't want to be that type of blog, but I couldn't pass this one up.

Wednesday, October 10, 2007

GC, columns, and hydrocarbons

The Chemistry department at a major university in our area has a program through which they get rid of "stuff." When labs close or move, they have a ton of stuff they need to get rid of. Some of the stuff is junk, but there is always some very useful and valuable stuff. Fritted funnels, ground glass joints, TLC plates, cannulas etc...

My colleague recently made a trip and picked up 5 GC columns. The condition (and for some the type) of these columns was unknown. I've been installing them in our Varian GC and conditioning and testing them.

I was testing a column from J&W. DB624, 30m long, 0.32 mm bore, 1.8 micron film, apparently designed to analyze pesticides. I injected some hexanes (mixed isomers). The separation was awesome. See below:

I thought, wow, for $0 we really got an awesome column, and we did. The column is in perfect shape. Probably used 5 times. Who knows.
I continued to test it and decided since I got such good hydrocarbon separation, I would inject some ligroin. Ligroin is a poor mans replacement for hexanes. It is essentially defined as a hydrocarbon mix with a certain boiling range. For ligroin the range is 60-90°C. According to the Wikipedia article it consists of C7 to C11. It is less refined and thus less expensive.

I injected some into the GC and here is what I got:
Look familiar? From what I can tell based on this one analysis, the cheap ligroin one buys from Sigma-Aldrich is identical in composition to the more expensive hexanes.

Here's a side by side comparison (hexane is on top and ligroin on the bottom. It's not as dark because it was in red and got grayscaled by the printer):

I guess you learn something everyday.

Monday, October 8, 2007

Frescos and chemistry

Tomorrow in lab, my Chemistry of Art class will be making frescoes. The following is from one of the handouts they will be given describing frescoes. It's a bit long, but perhaps interesting.

Of all of the painting techniques available, the technique of fresco painting involves the greatest number of chemical reactions. The study of the science behind frescos gives us the opportunity to discuss these reactions and chemical equations.

The technique of fresco is one of the oldest and most durable forms of painting. Frescos have been created for thousands of years, and thanks to their robust nature many have survived the millennia. Not only have frescoes been painted for thousands of years, they are also geographically widespread. This is due to the fact that the materials used to make a fresco (lime, sand and colored clays) are widely available and easy to process.

The term fresco means “fresh” in Italian. The essential feature of a fresco is that pigment is applied to a wet (fresh) surface of lime plaster. Some of the earliest frescoes found in Greece date back to 200 B.C.. During the Italian Renaissance of the 15th and 16th centuries, the fresco painting technique was perfected. One of the best known examples of a fresco from this era is Michelangelo’s painting of the Sistine Chapel ceiling.

Fresco Anatomy: To understand the chemistry of a fresco, we first must understand what a fresco is. Frescos are most often painted on walls and ceilings. Typically a layer of plaster is applied directly to the wall to smooth the surface of the wall. This first layer is called the arricio layer. Once this layer has dried and hardened, a second layer of plaster is applied called the intonaco. It is in this layer that the pigments are applied. However, the pigments must be added before the intonacco layer dries. For this reason, the artist must work fast and without attempting to do too much. If this layer dries before the pigment is added, the artist is out of luck.

Fresco Chemistry: The chemistry of a fresco starts with the reaction used to make the materials needed for the fresco. The basic raw material for a fresco is limestone. Limestone is calcium carbonate (CaCO3) and is an abundant mineral found throughout the world. The first step is to convert the limestone into lime (or quicklime). Lime is calcium oxide (CaO) and is formed by heating calcium carbonate to over 800° C. Carbon dioxide is a by-product of the reaction. The chemical equation describing this reaction is shown in reaction 1.

The lime is a white solid that has a very high melting point. Long before the advent of electricity and on demand lighting, huge chunks of lime were heated until they glowed white. This light was used to illuminate theater stages, thus the origin of the term “limelight.” The carbon dioxide by-product is a gas and simple diffuses away.

The next step involves a process known as “slaking.” Water is added to the calcium oxide in order to “slake” it. The product of this reaction is calcium hydroxide (Ca(OH)2) also known a “slaked lime.” See reaction #2 above

Lime is allowed to slake for years. This “aging” process allows as much of the calcium oxide to react. Calcium oxide is not very soluble in water. As a result, it takes a long time for the water to interact fully with the calcium oxide. Traditionally, the lime was slaked in large pits and is often referred to as “pit lime.” The slaking process produces heat as a by-product. A reaction that produces heat is called an “exothermic.”

The calcium hydroxide that forms is only slightly soluble in water. This results in a white, milky suspension with water. This suspension is a very caustic substance as calcium hydroxide is a strong base. Care must be taken when dealing with this substance since prolonged exposure can result in serious damage to the skin.

It is at this point that the artist uses the material. Slaked lime (calcium hydroxide) is mixed with sand to form the actual plaster that is applied to the wall. Typically, course sand is used for the arricio layer of plaster and fine sand is used for the intonaco layer of sand.

Once the intonaco plaster has been applied the pigments are added. The pigments are usually a suspension in water. What that means is that the pigments do not dissolve in water. When the pigments are applied to the plaster, they get absorbed into the plaster and eventually become part of the intonaco rather than a coating on the surface. After the intonaco plaster has been applied, the artist must finish the painting before it dries. Usually an artist will only attempt to paint a section 3-5 square meters in area. In addition, since the calcium hydroxide is very basic (alkaline), the pigments must be stable in an alkaline environment.

The drying of the plaster is a physical change. In this process, the slaked lime does not change chemically. The water simply evaporates leaving the dry slaked lime on the wall. What makes a fresco so robust is the chemical reaction that occurs slowly after the water is gone. Carbon dioxide from the atmosphere reacts with the calcium hydroxide to form calcium carbonate as shown in reaction 3 shown above.

The formation of the calcium carbonate (identical in chemical composition to the original limestone) results in a very hard and stable surface that traps the pigments. This reaction is very slow and occurs over the course of decades and even centuries.

Wednesday, October 3, 2007

Fire!!!!! of a different type.

Dear blog reader,

You are going to have to read "between the lines" for this post. I don't want to get googled for the wrong reasons, if you know what I mean (or at least you soon will).

Anyways, in the first organic lab of the semester, I go through a fairly extensive safety lecture. Included in that I remind them to wash their hands after every lab. I usually add, quite seriously, that they should be sure to wash their hands BEFORE they use the bathroom. What you may not feel on your hands, WILL be felt by your more sensitive areas. It is usually met with snickers, but the advice is serious albeit a bit humorous.

I need to learn to take my own advice.

I wasn't working in lab- I was making jalapeño poppers at home. My recipe is below, but it involves slitting the peppers and scraping the seeds out. I did this to 10 peppers. Then, in the vernacular of my house, I went potty. I failed to wash my hands before going.

A few minutes later... well, let me just say I wasn't happy with myself. I'm wasn't rolling on the floor in pain, but I was very uncomfortable for several minutes. It reminded me of the old "Ben-Gay in the jockstrap" practical joke. But I wasn't laughing.

After about 30 minutes the pain subsided. I had finished preparing my jalapeño poppers and had started to consume them. Man, were they good. Here's the recipe:

4oz cream cheese
a small handful of shredded Montery Jack cheese
6 strips of chopped up and well cooked bacon
several dashes of hot sauce

The peppers are split and the seeds are removed. The peppers are filled with the filling, and then dipped in the following mixture:
1 egg
1 cup flour
enough milk to make the mixture like thin Elmer's glue

The excess is drained off and the peppers are rolled in bread crumbs (I prefer panko crumbs). They are deep fried for 2 minutes. Let cool and enjoy. Follow by a milk of magnesia chaser and loperamide HCl in the morning.

I hope you can learn from my experience. It's a bit embarrassing to tell, but it makes a good story.

Tuesday, October 2, 2007


Remember the good ol' days of Beavis and Butthead? They were, for good or bad (mostly bad), a cultural icon, albeit a short-lived one. The creators and MTV got into a lot of trouble for B&B's affinity for "fire" [I'm not sure how to type "fire" the way Bevis said it]. I remember people were up in arms because B&B were seemingly inspiring arson and the like.

Nonetheless, I couldn't help but think of them lately and their love for "fire."

Our Math and Science division is having a fall picnic this week, complete with bonfire.

I.... I, your humble crappy blog writer, have been asked to start the bonfire [OK, that's not really true, I simply usurped the privilege from my science colleagues].

I am going to ignite the fire using nothing other than chemistry!!! Now sure, lighting a match IS chemistry, but it is too traditional. I want to light the fire in a way that is dazzling.

At this moment, I am going to use my old standby reaction, thermite. I can do that with no problem. The beauty of it is that the fire would be started totally by the movement of electrons from one element to another. No covalent bonds would be broken [at least in the starting of the fire]. What a wonderful way of transferring energy to the wood and thus igniting it.

However, I'm open to suggestions.

Wednesday, September 26, 2007

Time is valuable

If you have read this blog before, you know I like to complain about how little time I have and how busy I am. Well, that's what all bloggers talk about at one time or another, but for me it is different.

I sat down tonight and listed all of the tasks I need to finish in the next few days. Here is a partial list of things I am trying to fit into my busy schedule in no particular order:

Read the last third of Harry Potter #1
Watch the last four episodes of The Office: Season three
Listen to Beethoven's 6th or 7th symphony while following along with the score
Rack my Metathesis Ale to the secondary
Prepare for my Friday lectures
Optimize conditions for the SPME analysis of peppermint candies for my instrumental analysis class
Buy and XBox and play Halo 'til my fingers bleed
Pull everything out of my garden
Mow my lawn
Finish the trim in my basement

As you can see, I really need to prioritize and get to work.

For tonight, I think I will drink some Boston Lager clone, fold clothes and watch the rest of The Office: Season three. While, ignoring the things I really should be doing.

Monday, September 24, 2007

Favorite reaction and a name for my beer

OK, the poll cleared nothing up. Since there was no clear cut favorite, I'm taking matters into my own hands.

I am going to name my pale ale after my favorite reaction I have never had a chance to run. I've always been a fan of metathesis reactions, particularly alkyne metathesis reactions. However, I have never had an occasion to run one.

I'm not sure why I like metathesis reactions so much, but the splicing of two distinct and potentially large molecules together to make a new molecule is really sexy.

I'm a big fan of Fürstner's work with alkyne metathesis. I had the pleasure of driving him to and from the airport once. Shown below is his recent sythesis of Latrunculin A (I stole this from his website).

The biggest use of alkyne metathesis is in ring closing, as seen above. This is usually followed by Lindlar reduction to the alkene. The controlled formation of a Z-alkene is an advantage alkyne metathesis has over alkene metathesis which can result in E/Z mixtures.

A major disadvantage is that E-alkenes are difficult to form. Birch reductions work great, but only in the absence of any useful functional group. When I was driving Fürstner to the airport in 2001, I asked him about this limitation. He just smiled a little smile and said, "we're working on it." That told me something was imminent. And it was. In 2002, Fürstner reported the following. Of course, at nearly the same time Trost reported a similar procedure. So it goes...

So, what does this have to do with beer?

Well, I am naming my beer: Metathesis Ale.

What's your favorite reaction you have never run?

Friday, September 21, 2007

Where's the chemistry?

I realize I've been lax in posting stuff related to chemistry. Sorry.

I plan to post something related to chemistry in the next post.

Until then read this C&EN article on coffee, my 0ther favorite brewed beverage.

Thursday, September 20, 2007

Fat Tire: The Return of the King

OK, maybe The Arrival of the King is better title. I am pleased to report.... Fat Tire is now available in my town. I am mere miles away from a local source.

If you have read this blog before, you are probably sick of hearing me talk about Fat Tire and how I love it. I have tried to clone it three times. First time... yuck!!! The second time was nicht so gut!!! The third time resulted in a much better beer. It was good, but was it like the real Fat Tire?

I had no way of finding out... until now. BEHOLD:
I bought that here in my own town and drank it, and it was good. It is a fine beer for many reasons, but I love the toasted barley finish it has. It is such a satisfying flavor in my opinion.

So, how does my Fat Tire clone compare? Well, not very well. My beer is still quite good, but man, it ain't not Fat Tire. As you can see the color is way off.
I'm on the right there. The only thing I had in my favor was the head. My beer retained a nice full head for a lot longer than the original. I'm not sure if that really matters, but hey, I've got something.

So, there you go. Now I can quite bitching about not having access to Fat Tire, and I will never try to clone it again.

Wednesday, September 19, 2007

Barry Bonds' ball

While I try to decide on a name, here's something to entertain you:

Monday, September 17, 2007

Beer names

I mentioned a long time ago that I want to name my beers. I still haven't come up with anything good. So, I thought I would try out the new poll feature of Blogger and let you, the reader decide.

I am brewing a pale ale tonight. It is one of my favorites. It is a loose clone of Mirror Pond Pale Ale (one of my all time favorites). It is loaded with cascade hops. Tonight I am experimenting with some amarillo hops as flavor hops. I'll know in a few weeks how it worked.

Anyways, I need help naming this beer. Check out the poll to the right and offer up your suggestions. Don't like the options? Give your own ideas in the comments.

FYI, here's the recipe:

2 lb Pale malt
1 lb crystal malt
90 minutes at 152°F
3 lbs pale dry malt extract
1 oz cascade hops for 45 minutes
0.5 oz amarillo hops for 15 minutes
0.25 oz cascade hops for 15 minutes

in a week I will dry hop with 1.75 oz of cascade hops.

Sunday, September 16, 2007

Too few hours

I'm sorry, 24 hours is not nearly enough to do all of the stuff I want and need to do.

Today, I spent about 10 hours installing trim in my basement. I watched only 5 minutes of football. For me, Sundays are typically spent getting annoyed by the Minnesota Vikings and keeping track of my fantasy football team. Not today. It was all spent putting fancy pieces of wood on the wall. That's OK, I needed to get the trim done. This one-year project is three years old.

The biggest thing I missed was brewing. I was going to brew a pale ale today, but that never happened. Hopefully, I will be able to brew tomorrow night. However, I also need to can what few tomatoes my garden produced. Maybe that will be a Tuesday project.

Thursday, September 13, 2007

Brew season opener

The temperature in Minnesota is dropping. That means the basement will soon be at proper fermentation temperature. All summer, even with air conditioning, the coldest the basement would get was about 72° to 74° F. That is a tad too high for fermenting beer.

But now, it's time to start brewing again. The 2 month layoff was made tolerable by a well stocked beer cellar. The temperature should soon be a very nice 66° to 68° F. When the temperature drops too low for the carboys to sit on the basement floor, I either set them on a shelf or bring them upstairs.

I'm also going to try to do some garage lagering. It's not a perfect approach. That would require a refrigerator.

I'll keep you posted on my brewing activities.

Wednesday, September 12, 2007


I have not had much time to post lately, which is the reason for this post.

First of all, I love my job. I love teaching. I think I'm moderately good at it. If my efforts are not beneficial at least they are not detrimental. Of course, I may be totally wrong. I know full well I am not the best teacher, but I work hard to be like the best teachers I have had and admire.

What annoys me the most is the non-faculty people (i.e. staff on 12 month contracts) I work with that take every chance they get to throw the old "must be nice to have summers off" crap around. I seriously believe that they think I (and my faculty colleagues) spend the entire summer sitting on the beach sipping margaritas, while they were toiling away navigating endless paperwork and waxing floors.

Now, I must also say right now that this is not a "woe is me" type post (i.e. rant). I am not saying I have it harder than anyone else. What I am saying is being a teacher is a hell of a lot of work. And frankly a lot of work that I really enjoy.[1]

First, I do get most of my summers "off." What that really means, is that I am not on a schedule. My time is usually much more flexible and less constrained by forces I can't control. That is one of the perks I love about this job. HOWEVER, that does not mean I have nothing to do!! From when the semester ends to when it begins again, I have labs to clean, machines to maintain, curriculum to device, usually a new course to plan, chemicals to dispose of etc... There is a lot of work that has to be done. Plus I run a science camp that takes a lot of time.[3] True I am not locked into the 8-5 schedule, but I am doing many things.

Second, teaching is a 12 month job crammed into 9 months. Seriously!!! With all of the things one has to do as a teacher at the college level[4] time is the most valuable commodity. Tonight, for the first time since the start of the semester, I am not working on school related things. A typical schedule involves me arriving at school by 8:30 am (after dropping off a child at preschool) and working until 5PM. I go home and once the children are in bed around 8PM, I start preparing for the next day. On weekends sometimes Saturday but almost always Sunday night, I am working on school things. And, it's not like all of these hours are making me excel at my job. They are necessary to give the students what they pay for and to accommodate the endless hours of committee work required to make a college work.

Sorry for the long rant. I'm not looking for your pity, but you must understand, teaching is a lot of work and it requires long hard hours and many sacrifices.

At least I am very well paid. For my labors, I pull in a 7 figure salary.[5]

[1] sorry, I'm getting a little crazy with the bold and italixs.[2]
[2] I really think "italics " should be spelled with an "x." It just looks cool.
[3] But I really enjoy it.
[4] I can say nothing about other levels since I have no experience.
[5] If you count the digits after the decimal point or convert my dollars to centidollars.

Tuesday, September 11, 2007

Thursday, September 6, 2007

Never fly Nepal Air

hmmmmmm, I wonder what the in flight meal is.

Another, among many, reasons why I try to avoid airlines from Nepal.

Friday, August 31, 2007

Michael Jackson

I just learned that Michael Jackson passed away on Wednesday. If you know anything about fine wine and beer, I don't have to tell you that this is not the Michael Jackson you are thinking of.

Michael Jackson is widely regarded as the #1 authority on beer, wine, scotch etc... but mostly beer.

He brought beer respect and in so doing, helped to create and define the craft brewing industry as we know it today.

He will be missed, but he left a lasting legacy.

Wednesday, August 29, 2007

And they're off....

Well, the semester is underway. All systems are go.

Today I taught my Chemistry of Art course, Organic Chemistry, and Instrumental Analysis. Plus, I did an organic lab today as well. It turned out to be a long day (I also mowed my lawn).

A few weeks ago, I was really nervous about the Instrumental Analysis course. Now, I'm starting to get really excited about it. I'm team teaching it with a colleague. I am going to focus on instrumental chromatography (GC and LC) and structural elucidation (NMR, IR, MS and UV-Vis). My colleague is going to cover what amounts to instruments used for advanced analytical analysis. In the end, I hope our students will have a general understanding of how instruments are used and what they can (and cannot) tell us.

I'm not going to get into the electronics of instruments. We will talk about signal-to-noise, but not about A/D converters and rectifiers or Zener-stabilized voltage regulators. I'd rather talk about J-couplings, COSY and McLafferty rearrangements.

Our first experiment will probably be the analysis of isooctane in gasoline using GC-FID. I'm going to have them change columns and everything. It should be fun.

Tuesday, August 28, 2007

E.J. and Roald will have to wait

One of my goals of the ACS was to get an autograph from E.J. Corey and Roald Hoffmann. I got neither. I was stricken with guilt when the time of their appearances coincided with a couple of talks I really wanted and needed to go to. I gave in to my guilt and went to the talks.

The registration fee for the ACS convention is a rather steep $385. Throw in a hotel for 4 nights for at least $800, travel at about $200 (from MN) and food etc... The final total can end up close to $2000. Granted, my employer picks up the tab, but for my small school, $2000 is a significant amount of money. I could use that $2000 in a lot of different ways (like research).

The bottom line is that, I couldn't squander the (expensive) opportunity to learn and advance myself as a teacher, just to get a few autographs. The autographs would be really cool, but in the end, they are just ink on paper. I chose knowledge in my head over that.

Sunday, August 26, 2007

Boston brewpub review #3

Finally, I get to the last one. The school year starts tomorrow. I will be very busy. Hopefully, posting will not decrease too much, but don't be worried if I am not as active until oh....May :)

The final brewpud I went to was Boston Beer Works. There are three locations in Boston. I went to the Fenway location. It is (depending on the time of day and year) in the shadows of Fenway Park.

I may have chosen the wrong location. Because at the Fenway location, the service SUCKED. Really, it was terrible. I sat at the bar and haven't been this ignored since my senior prom in high school. And it's not like the bartenders were busy. Besides, I was ordering (or trying to) beer. Beer is a very easy drink to make.

In the 2+ hours I was there, I was only able to enjoy 2 beers. Both were fine. One was an oatmeal stout, the other was an IPA (cask conditioned). To be honest, the IPA was very good. Sure wish I could have had another.....

The ONLY redeeming value of Boston Beer Works is that they only sell beer and wine. Not only that, they ONLY sell their own beer. No Miller Lite here. That I think is a very good thing. In smaller cities, brewpubs can't get away with that. They often need to sell Miller Lite to survive.

So, what can I say about Boston Beer Works? Not much. The service sucked. I am usually a very good tipper. For me, the default tip is 20%. I would have given a 0% tip, but that goes against my core principles (though it has happened on occasion). I think I gave a 5% tip. But even at 5% they could have made some money if they would have allowed me to spend more money at their restaurant.

I hope this was an anomaly. All I know is I will never go back.

Thursday, August 23, 2007

Boston brewpub review #2

Cambridge Brewing Company (CBC).

CBC is a fine brewing company. They brew beer that is excellent and make food that is very good. If ever in the Boston area, I suggest stopping by.

When I got to the brewpub, I was worried because there was a mass of people around the bar and nary one bar stool open. When I am out on my own I prefer to sit at the bar. It's just a personal preference. I did discover one seat open and grabbed it. I found the large group was apparently there to celebrate the graduation from MIT of an individual in some financial/economics area.

What intrigued me more about the CBC was that beer was served not just in pitchers but in towers! These 3 liter towers of happiness were hard to miss. While I was there the graduation group ordered at least 8 of these towers. I was impressed.

At first, I was really annoyed because the service was AWFULLLL. Seriously, it took almost an hour for me to order one beer and food. I will give the bartender a break since she was the only one behind the bar with a million people in the bar. As the evening unfolded, it became obvious she was not a total jerk, and in fact not a jerk in the least (just over worked).

First the food: I ordered the blackened pub steak. This was awesome. I wish I could have this everyday. It was excellent. I ordered medium rare but it came out medium, but that's the only criticism. The creme brulee I had for desert was tops. From my experience, the food at CBC is unsurpassed.

Now, the beer:
I first ordered one of their special brews. This was called something like "le amour de jour." I wrote the name of the beer in the copy of C&EN I was reading at the time[1], but I cannot find where I wrote it!!!! I must rely on my worthless memory. Anyways, it was Belgium styled beer that did not interest me at all. I didn't like it. I was not a typical brewpub style, but the brewers didn't pretend that it was. In the beer menu they indicated that it was something of an unusual beer. I agree. It was a quality product, but one I didn't really prefer.

I next tried the porter. This was excellent. This was a bit of a departure from the traditional porter. It didn't have the same bite, but I liked it.. a lot. A very good beer. The steak I ate was covered in a sauce made from a porter reduction. Very good.

I also tried the barelywine. I only had a sample of this 13% ABV drink, but it was very yummy.

The seasonal IPA they had was excellent as well. I could drink this all night.

In the end, the CBC proved to be an excellent provider of beer and food. The service was lousy at first, but improved as the demands on the bartender lessened.

If you are ever in Boston (especially the MIT or Harvard area) check this place out.

[1] Remember, I am a nerd and I read Chemical and Engineering News at bars when I am waiting for food.

Wednesday, August 22, 2007

Boston brewpub review #1

RockBottom Brewery

OK, it is not a home-grown brewpub unique to Boston. But, it was within walking distance of my hotel, I had just flown in, and I had about 2 hours of "airplane" sleep during the last 48 hours. I didn't want to put too much effort into it.

I plopped myself at the bar in front of a widescreen HDTV and watched the Yankees game that was on. If you want a fun time, watch a Yankees game at a bar in Boston. It was even better because Clemens was pitching. Boston fans do not like the Yankees and it shows.

Anyways, I ordered beer. With most brewpubs, the beer is almost always good. Rarely have I had a beer I would call bad. There are types of beer I prefer and some I don't.

The beer at Rock Bottom is pretty dang good.

They had a cask conditioned Irish Stout. Superb. Very delicious and served at the perfect stout temperature. They also had the Irish Stout on tap. Good, but too cold to really enjoy what a stout is all about.
I sampled the cask conditioned IPA also. Delicious. Cascade and centennial hops were evident.
The Munich Gold was a wonderful Saaz hop experience.

The food and service were both great. After 4 beers and in the state I was in, I headed back to my hotel room and was asleep by 9PM. No big night on the town for me.

What's wrong with the following?

I saw this on a poster in the Organic division. I'm not going to tell you what number or who it was by to protect the guilty.

What is wrong with this:

Any student in the first two weeks of sophomore level organic should be able to ID what is wrong. And this was on a poster displayed at the ACS convention!!!! The structure was simple too. It's not like she was trying to draw a very complex structure. Only when a complicated 3D structure is being drawn can things like this occur.

Little things like this annoy me. There's no excuse for putting this on your poster, even if you are cute. Sorry.

Tuesday, August 21, 2007

More ACS review

This is going to be short.

Today I went to a number of talks. I went to the Cope award lectures today and heard the fastest talk ever. Andre Charette said more English words in 40 minutes than I even know. I've never heard someone talk so fast during a lecture. I'm familiar enough with his work to know what he was talking about (mostly), but wow, did he cover a lot in a little amount of time.

I also caught the lectures by MacMillan, MacGillivray and Frechet. All were good, but the nature of these talks is that they essentially review many things they (i.e. their grad students) have done. It is hard to get any detail out of them. The really good stuff is to be found in the 20 minute sessions in the smaller rooms. I'm visiting those tomorrow.

Tonight I met up with Paul (Chembark) and one of his frequent commenters, Eugene. We had a few drinks and shared a few laughs and talked shop. It was nice to have met them.

I have yet to post my brewpub review. Time is surprisingly limited. I have been to three of them in Boston (Rockbottom [actually a macro-brewpub], Cambridge Brewing Company, and Boston Beer Works). I will try to get something out ASAP. Now it is time to sleep.

Monday, August 20, 2007

Boston ACS review

Hi, from Boston. The ACS convention is going great. I've learned a lot of things. For now I am going to stick with Chemistry. In a future post I will delve into the local microbrews (I've hit two so far).

So... Chemistry. This is what I did during the last two days.

On Sunday, I attended a number of lectures on the Chemistry of Art and Forensic Chemistry as they relate to Chemical Education. These were mostly great. Especially my talk :)

In the evening I attended the poster talks and drank as much free beer as I could handle in 2 hours. I drank a lot of Heinekin, but I also visited with a number of presenters.

This morning, I got out of bed to sit in some workshops about Spartan from Wavefunction. Then I sat in a few more lecture before heading back to the hotel for a nap that was interrupted by a weird nightmare (of afternoonmare). The 50 minute nap became 10 minutes.

Anyways, I went to a brewpub for supper (details to come) and then the ACS poster talk (SciMix). It was illuminating.

I met a few friends from Holland in the hotel bar tonight and had few drinks.

Now, I am ready for bed.

I will try to post more about the two brewpubs I have visited so far tomorrow. I hope to visit one more tomorrow.

Stay tuned. More to come.

Friday, August 17, 2007

Off to Boston soon

I'm off to Boston for the ACS soon. I present a paper on Sunday afternoon.

My only other goal of the trip is to get an autograph from E.J. Corey and Roald Hoffman on the same piece of paper (or something). I did get an E.J. autograph a few years ago when I was still in grad school, but I cannot find it in any of my things. I think a lab mate stole it.

I may try to do some updates about the conference while I'm there, but enough bloggers do things like that. What I might do is blog about beer and the ACS.

Which leads me to my question:

I will be staying in the downtown Boston area (area'r in the vernacular). Does anyone who reads this blog know of any good brewpubs in Boston. I've been to one near Harvard (don't remember the name), but I don't know of any others. The main stipulation is that it must be accessible using cheap public transportation from the Boston Commons vicinity.

Tuesday, August 14, 2007

perty picture

Thanks to the Kutti at Jungfreudlich I was able to make the following picture with the glowing humulone structure. I don't have time to figure stuff like this out on my own so having a screencast to guide me was awesome.

Check out Kutti's very useful instructions. Soon you too will be making your blog look cooler.

Hint: What I did find was that it looks better when the ChemDraw structure uses a line width of about 0.065 cm. The bottom right structure have a line width of 0.065 cm and the one on the left has a width of 0.090 cm.

Monday, August 13, 2007

Time to get crazy...

Wow, it's been a week since I posted something! Where did my week go? Things are starting to pick up steam on the academic side of life.

Fall faculty meetings are starting this week, next week I am in Boston for the ACS convention and when I get back, school starts. Needless to say, I have a lot of work to do in the next few weeks.

Summer... she is a sailin'.....

On the beer side, I spent my night bottling my honey wheat. I put another round of bottles in the dishwasher to be sanitized during the night. I plan on bottling my IPA tomorrow. That will empty my beer pipeline and fill up nearly every bottle I have. The beer cellar is full.

Tuesday, August 7, 2007

Instrumental Analysis: part 2

A number of comments on my previous post reminded me of one my most boring days as a student.

The gist of what some said was "don't be boring." In other words, a 3 hour lecture in front of a machine noone will use is not going to be the most useful.

Now, for the story: During my Junior year at my undergraduate institution I was enrolled in an Instrumental Analysis class. There were so many times that we were bored to tears.

The old professor was a work of art. Due to some physical injuries that never healed right, he walked like Igor from Frankenstein. He was a nice guy, but not the most dynamic.

One day, we were covering IR. We already had use IR extensively and were proficient at it. So he decided to take us back to the good old days.

Any chemist knows that IR had a glorious period in the history of Chemistry. There was a time when every effort was made to obtain exquisite IR for the main reason that the IR spectra and a melting point of a derivative were essentially the only characterization data available.

Now days, IR has been supplanted by "bigger and better" technology particularly NMR. It has been relegated to a "carbonyl identifier."

The old professor wanted to show us how it was done back in the day. So, he pulled out two salt plates. Looked at them in disgust and declared that they needed to be polished. He produced a wooden box about the size of a 1965 Minneapolis phonebook. He opened the box and with a gleam in his eye, presented his salt plate polishing equipment. I don't remember everything contained in his box, but I do remember two piece of felt of varying softness.

The prof went to town polishing the salt plates. Rubbing specifically in a "figure 8" pattern, he went from one piece of felt to another. I can see him frantically and in a most exuberant manner moving the salt plate as fast as he could as he rubbed in on the felt. This lasted nearly 15 minutes. Meanwhile, we just stood there and watched (i.e. acting like bored undergraduates).

After what seemed like an eternity of him polishing his plates, he was finished and he lifted the perfectly polished up for us to behold. The gleam was brighter than ever in his eyes. He was so proud to give us this old school lesson. He was perhaps reliving his own glory days. He held the plate up at eye level when the plate slipped from his physically deformed fingers, fell to the floor and shattered into a millions pieces.

I remember him uttering a very sad whimper. He said little and sent us home for the day.

We actually felt bad for him, and while the end result was pretty lame, we learned how important IR had been at one time. We gained an appreciation for what pre-NMR chemists had to do.

Sunday, August 5, 2007

Instrumental Analysis

Hey chemistry folk!

I am team teaching an instrumental analysis course this Fall. We hope to cover all of the major types of instrumentation and how they are used. I will also include a bit of structural elucidation.

Any opinions on texts available? Any suggestions?

If you were taking this course now (knowing what you know now) what would you most value?

Thanks for doing some of my work for me.

Saturday, August 4, 2007


While I grout and do other work around the house, I have 15 gallons of beer waiting to be bottled. I hate bottling. I dream of kegging my beer someday. I need to suck it up and just do it.

Friday, August 3, 2007


OK, I have to get the depressing post off the front page, so to speak.

I have spent several hours during the past few days, installing a ceramic shower in our basement. Tonight, I finished the grout. Adding grout (what is the verb for this? Grouting? maybe) is a pain in the butt.

It is also a pain in the hands since it is basic. I should know better. I'm a chemist, and I know exactly what a caustic substance will do to my skin (i.e. turn some of it into soap). However, I didn't wear gloves. After a couple days of this, my skin is dry and it feels funny.

My hands feel like when I'm using a base bath and the elbow length glove springs a small leak in one of the fingers and the glove fills up with base bath. That's always a lot of fun.

Wednesday, August 1, 2007


What a horrible day.

If you didn't hear, a major bridge collapsed without warning in Minneapolis, Minnesota tonight. There were nearly 50 cars on the bridge at the time. It could have been much worse. Thankfully, only one lane was open due to construction work. But yet, the results are terrible.

At the time that I write this, 7 are confirmed dead. Sadly, 20 are missing. The logical presumption is that the 20 will probably not be found alive. I hope I am wrong.

I have driven on this bridge countless times. I have family and friends that used this bridge today. Thankfully, most of the people I know that could have been on this bridge have been accounted for.

I realize this is nothing compared to some of the horrors that have happened in this country and in the world, but for me, this hits a little too close to home. I can't help but be affected.

If you are so inclined and want to help, the local Red Cross phone number is:
and the website is:

UPDATE: 9 are now confirmed as dead, 60 wounded and 20 still missing. WTF!!!!!

Another UPDATE: Apparently there have only been 4 killed so far. This is still terrible, but it is good news. Of course, the reckless use of the word 'confirmed' by the local press last night has me a bit annoyed.

Saturday, July 28, 2007

I'm no Cal Ripken or Ernie Tyler!

I am proud of the fact that I have not missed a day of school or work due to illness or injury since 5th grade (and that may have been questionable).

However, I am no Cal Ripken Jr.. Ripken is being inducted into the Baseball Hall of Fame for good reason. He played in 2,632 consecutive baseball games, and he was a great player.

However, Ripken is no Ernie Tyler. Ernie worked as an umpire attendant for the Baltimore Orioles for 3,769 consecutive games. Not bad. He is missing his first games ever to attend Ripkens induction into the Hall of Fame.

Tuesday, July 24, 2007

Rack 'em up

I had a busy beer weekend that was long overdue. I bottled my ESB and transfered the three other batches to secondaries.

That took a lot of busy work.

By bottling my ESB I had an empty carboy (remember my beer lineup). I borrowed a friends 5-gallon carboy which I used to hold my sanitizing solution so I could use it for all three carboys.

The process went something like this: I emptied the ESB carboy, cleaned it and added the sanitizing solution. After a bit of a soak, I transfered the sanitation solution to the borrowed carboy and racked the next beer to the freshly sanitized carboy. I repeated this process two more times.

I used Star-San as my sanitizing solution. According to the MSDS, Star-San is 50% phosphoric acid (H3PO4), 15% dodecylbenzene sulfonic acid (see below) and 10% isopropyl alcohol (the remainder is a secret, though the majority is probably water).

I presume the phosphoric acid and IPA kill anything living in my carboy and the dodecylbenzene sulfonic acid acts as a detergent.

Saturday, July 21, 2007


I just signed in and my site meter was at 11111. That was weird.

That converts to 31 in the decimal system, but telling you that would flag me as a nerd.

Thursday, July 19, 2007

Why I was able to become a chemist

Paul at one of the premiere chemistry blogs just wrote a post on why he became a chemist. This got me to thinking, "why did I become a chemist?" Well, that got me to thinking about not why I became a chemist, but why was I able to become a chemist.

Sure, having a brain helps. Having parents who encourage you to read instead of watch TV really helps[1]. Having parents who encourage you in general to study and learn really helps.

I always had a natural interest in science. I was amazed at how things worked, natural and man-made. By the third grade I was determined to become a neonatal surgeon. Obscure choice for an 8-year old? Yes, but true nonetheless. I would wear my pajamas backwards because they looked like scrubs. I never changed my mind until I was lured away in college by the mistress that is "Chemistry."

Yes, I was one of those pre-meds we in academia all really love to love[2]. I was slowly lured away by chemistry, but the final nail in that coffin was when I took Advanced Organic Chemistry during J-term. Brutal and hardcore, but I loved it.

But, how did I get to that point? Well, I was prepared very well. Here are a few of the most important individuals in my academic training that made it possible for me to become a chemist.

Mr. Willems in high school. I had him for Biology, Chemistry and Physics. He did a lot with a limited budget. He was very well organized and orderly. He didn't just teach us facts and trivia. So much of today's HS curriculum deals with learning about facts and trivia[3]. Mr. Willems taught us to think through problems using basic principles. This is a skill that has helped me greatly. Of course, there are some facts that must be memorized. One of the most valuable things he forced us to memorize in Chemistry was the names and formulas of the common polyatomic ions. This proved to be incredibly valuable later in my college career.

Mr. Bolda in high school. I had Mr. Bolda for most of my HS math. He was also my track coach. He was your prototypical nerd that many HS students tend not to embrace, but he was a very good teacher. One that, despite his mannerisms, any reasonable student would respect[4]. I did respect him. This was in the days before every HS in the world offered AP calculus. What Mr. Bolda did offer was a solid foundation in trigonometry and problem solving. I still use the problem solving skills he taught us in HS. I got to college with the skills need to breeze through most of a math minor.

Mrs. Kjeer in college. Staying with the math theme, I had Mrs. Kjeer for almost all of my college math (calculus I and II, differential equations, multivariable calc...). It was my very first day of college, 8AM class. We walked into our classroom and were met by this young and attractive calculus teacher who seemed to be hopped up on too much caffeine. This was NOT what we were expecting. When we got into the class, we learned quickly she knew what she was talking about and she wasn't hopped up on an alkaloid. She loved what she was doing. This coupled with uncompromising standards, an infectious excitement for calculus and the ability to back up what she said inspired us. I took as much math from her as I could. This helped me in ways I don't even realize.

Mrs. Weberg in college. Finally, I get to an actual chemistry professor. Mrs. Weberg inspired many students to become chemists, and provided the tools to do so. I had her for General and Organic. Mrs. Weberg was a great teacher. She knew what she was talking about and knew how to get students to learn. However, most importantly, she was like a mother to so many students. She was a very nurturing person and it wasn't always in the lovey dovey way. She was a mother after all, and she knew that every now and then, the best way to motivate a student is to kick them in the butt. She was stern when she had to be and compassionate when she had to be. We learned as much about life as we did about Chemistry. What she did was create a situation with clear standards and the motivation to reach those standards.

There are others to be sure, but these are four of the more important ones for me.

In retrospect, all of these individuals had some common traits. They loved what they did. They had high and uncompromising standards. They provided as much support as a student may need or request. They realized there is life outside of the classroom.

I try to model how I teach and interact with my students around what these individuals did. I usually fall far short of what they did, but I try.

They are why I was able to become a chemist.

[1] Don't get me wrong, I watched a lot of Transformers and He-Man back in the day...
[2] Some of the words in this sentence are inaccurate.
[3] Read your states expected education outcomes.
[4] Of course, not all HS students tend to be reasonable in this regard. Mr. Bolda eventually quite teaching. I do not know where he is now.