Mad Scientists

GRC notes

2012-01-22T16:45:00.000-05:00

Apparently I started this post a long time ago, and forgot about it. I finished it up some time over a year after I started it, but better late than never, right?

I had the distinct pleasure of going to a Gordon Research Conference this summer, and the only bad thing I have to say about it is that I wish I had started to go to them earlier. It was totally awesome.

That being said I went unprepared for some of the activities and issues, and wanted to document them here just on the off chance one of you hasn't been yet, but will go in the future. I went to the natural products meeting at the Tilton school, but I expect a lot of this will be true for other meetings, as well.

We stayed in dorms without locks on the doors. Odd, and reasonable under the circumstances, but if you have valuable shit or are neurotic, you might need to spring for a hotel nearby. I recommend the dorms, and you can request to share a room with a buddy if you want. I got paired up with a stranger and had no issues at all, he was a really nice guy.

The shower was communal, and down the hall (obviously) so you may want to bring some flip-flops to walk to and from the shower. We got little hotel soaps every day, but no shampoo. If you have preferred toiletries you should bring them, just in case.

Right as I walked in from the bus, there was a sign in area, right next to a "purchase drinks for the week area". Beers for the week were $30 and sodas $15. Since it's pretty easy to drink $30 in one night, I though it was quite a deal, and people were already heavily taking part in the libations. We had dinner, the talks started the first night, and the the heavy drinking began. After the bar closed at midnight the coolers of beer were brought out, and a short while later the grill was fired up, and brats were served to all comers. It was a lot of fun, everyone was really nice, and it was a great opportunity to chat with old friends and meet new people as well.

This brings up three important points together:
Drink in moderation, there is a whole week of all nighters to look forward to, don't overdo it if you want to go the distance.
If you don't drink it might be a drag to hang out with all the drunks, so be prepared.
If you don't eat meat it might be a drag to hang out with all the hungry drunks, so be prepared.

Most nights there were people out till well after 3 AM, and often a few stragglers made it to sunrise. The morning talks always seemed to come much too early.

If you don't pace yourself it can make for great entertainment for the rest of us when we get to hear you retching in the communal bathroom the next morning and then make fun of you later in the day.

There are periods during the day for rest relaxation between talks. I didn't know, and didn't bring any clothes for hiking/swimming/softball etc. If you can find out what the activities are ahead of time, plan to do them, they are a lot of fun, and are great opportunities to meet new people and hang out in an informal situation while not loaded.

If you don't know what the activities are, or what recreation there is nearby, it's not a big deal. Bring some clothes that are good for the outdoors, and ask someone the first night what there is to do the rest of the week. Often these meetings are attended by people many, many times, and they are very familiar with what there is to do.

Have fun, meet new people, have some drinks (or not, you pussy), and learn some chemistry!

wordy wordness

2011-12-17T19:40:00.000-05:00

I'm fond of language, and I like to think of myself as a decent writer. I may or may not be a decent writer in the grand scheme of things, but I feel that I'm above average with respect to the field I'm in and the people I've had the opportunity to work with.

To me language, and specifically the English language with all its various and sundry adjectives and adverbs, can really give straightforward concepts real color and texture in the way they are perceived.

That made him less believable.

His credibility was damaged.

The confidence in him was shattered.

"I could carve out of a banana a judge with more backbone than that." Roosevelt declared.

A proper wordsmith can take common terms and rearrange them into something special. There are people in all fields that exemplified this, for example in organic chemistry Professor Danishefsky writes beautiful and eloquent papers that not only describe beautiful science but are beautiful themselves.

Of course these few individuals are counterpointed by an army of hacks that get tired of using "yield" for yield and want to flower up their speech, but seem unable to structure a story that is both accurate and understandable. Sometimes journal articles read like a high-school student wrote a bad parody of Shakespearean scientific practices. The use of 50 cent words can be a beneficial addition to a well-written passage, but won't salvage a limp story. Embedding a few sparkly gems in a turd does a poor job of disguising the fact that it is a turd.

In the last few years some turns of phrase have taken on an odd sort of popularity in the science world, and I find it a little disconcerting. I have heard "inform" being bandied about lately, which is not a problem itself, but the usage tends to be somewhat galling.

Hopefully the data will inform you research.

Use what you find to inform your literature searching.

Inform my research? You mean all I have to do is tell my research something and it will do it? Wow, if only I knew that years and years ago!

What exactly is this inanimate object/concept going to do when I tell it these lovely factoids? Maybe I should inform my car next time I'm going to drive it, or maybe I need to inform my toilet that I'm going to violate it next time I eat a super greasy meal after 10 beers.

It may be a hangover (see what I did there!) from my graduate advisor jumping on anyone that anthropomorphized anything, but this seems to be a particularly obvious situation that makes little to no sense.

I guess there will always be people writing and presenting their work, and trying to emulate those that they look up to. I just wish they would proofread more often.

Side note: if you want to increase your douche-itude by using words like "exogenous" to describe additives to your flask, think about what the phrase actually means and implies before you publicize it. For example reagents that commonly come in their own bottle are always exogenous with respect to the reaction, and if you claim something is exogenous that implies that another is endogenous. If you can't think of an endogenous example, then you shouldn't be able to think of an exogenous one either.

back from the dead

2011-11-26T16:29:00.006-05:00

I moved earlier this year, and while looking through some stuff recently I stumbled onto an old treasure. When I was in graduate school a friend of mine modified a neat click type pen ad gimmick, and customized it for me. I used the pen happily for a few years after until it ran out of ink.

From then I think it kicked around in different desk drawers until I found it a few weeks ago. I was able to take an ink cartridge from a coworkers pen and fit it to the custom ride, and bring it back into daily use.

every time you click, a different message is displayed

yay USPS

2011-07-26T19:55:00.003-04:00

I'm pretty sure I snapped this pic a few years ago, but forgot to post it.

I'm one of untold millions that are pretty hooked on Netflix services who, love or hate them, have a pretty good business going; their stock went from ~$40 to a high of $300 in less than 2 years! Typically I have no problems with their services (ignoring for the moment their new pricing structure), with few problems spaced very far apart. There was one time where a disk didn't arrive, that was most likely a post office problem, and it took me a while to realize I hadn't gotten it. Netflix, of course, sent me a replacement after I clicked into the 'problem' area on their website, and everything was forgotten.

Some time later I got this in the mail:

One valuable scrap of paper.

Apparently my disk and containing materials were forcefully disconnected from each other, leaving only this poor, lonely address to fend for itself. In an attempt to assuage the damage caused to the psyche of the disenfranchised sheet, they bagged it comfortably up and sent it on it's happy way to the final destination, not unlike Paddle to the Sea.

The thing I find most humorous about this is that I can't think of a scenario where the people working with this scrap wouldn't know what it was, and the value to the customer that it no longer held. They need to perform their due diligence, and finish the job, whether it makes sense or not, but I wonder if the person prepping the lone survivor saw the humor in the obvious futility of the situation.

the old bait and switch

2011-05-04T22:44:00.007-04:00

I don't know a whole lot about fluorine chemistry, and I think it's safe to say that not many people do. It's like a magic element that can act like other elements, only harder to deal with.

Because of this when I see papers with interesting fluorine chemistry, especially the incorporation of a fluorine, I like to check them out. Last week this beauty popped up in the Org. Let. ASAPs, and I was enthused to read more and maybe learn something.

that's one wild step!

I was cheerfully greeted by the same image in the abstract for the paper itself.

So I was a little taken aback when I read on further and saw this.

That looks a lot like there are both more reagents AND steps in that transformation. I understand leaving out the solvent and temperature, but the other reagent and step? That seems a little gratuitous, especially since it is still a neat transformation.

I can't imagine they left it out on accident or forgot, but I would hate to think that it was an advertising ploy. Try this reaction, you'll LOVE IT! Just mix it all together and BAM, product! Oh and don't forget that other stuff we didn't mention on the outside of the container. Batteries not included.

nice addition

2011-04-07T20:46:00.003-04:00

In my current gig I get to read all sorts of articles on topics foreign to me, in journals I'd never heard of before. All in all pretty sweet, I must say.

Every now and then I stumble onto something kooky, and today I found one worth mentioning. This was at the end of an article, after the references.

Chemtech, 1990, 20, 1, 31-37

A nice, funny, way of delivering some solid advice.

great title

2011-03-18T09:53:00.002-04:00

This article fell into my inbox via ISI alert:

A density functional theory study of the ‘mythic’ Lindlar hydrogenation catalyst

Really caught my eye, although I didn't read it.

Rochelle's salt

2010-12-01T14:57:00.002-05:00

When using aluminum reagents such as LAH, DIBAL, or AlCl₃, it's common to have problems with emulsions in the workup. The simplest and most straightforward solutions to garner homogeneous solutions is to use aqueous mineral acids, but that's not always an option. If, like my last several projects, the substrates are alkaloids you can lose product to the aqueous layer, and acid labile groups can be chipped off. There are a number of ways around this, and one of the most popular and effective non-acid workups is aqueous Rochelle's salt.

Those of you that have used Rochelle's salt in work ups know that sometimes it works a treat, and other not too well. lately I noticed something in my experiments, and wanted to see if you guys have had similar experiences or knew of proper documentation.

When I would work up an AlCl₃ reaction, sometimes it clarified, and sometimes not. The Ph went up to almost neutral from the tartrate, but not strongly basic (Ph 8-10) like I would prefer for best recovery of my amine. After some poorer than expected yields I added saturated aqueous ammonia (ammonia water, NH₄OH) to the stirring workup mixtures. Typically the layers would split immediately, and my recoveries went way up.

It was both surprising and pleasantly welcome.

porchetta

2010-11-28T14:07:00.008-05:00

I've been too busy to post anything in a while, but some friends and I took some time off yesterday evening too cook and hang out.

Last week, I stumbled on to Gianni TV, and watched his cooking videos one of which has a great looking porchetta. Oddly I had been thinking for a while I wanted to make a braciole or pinwheel steaks, so this really motivated me to cook it. As it happened whole pork loins were also on sale for really cheap at a store near my house, so that was the clincher.

I roll cut the loin.

As it happened there was fresh sage and rosemary in my landlords garden, so in it went with garlic after a quick chop.

I spread it out evenly, and added fresh cracked pepper. I've made butterflied pork loin stuffed with sauteed onions and swiss before, and thought it was great, so I added it to this one as well.

After rolling and tying, it was rubbed with olive oil, covered with pepper and salt, put on a bed of the same herbs, and a bit of wine and water was added.

It was cooked in two stages. At 350 till it was done, rested till the internal temp was coming back down, and at 500 until nicely browned and crispy.

Resting after stage one, don't the silicone ties look like earthworms?

And that's when the camera battery died. It came out tasty, I added more wine and reduced the drippings to make a jus, and we had some turnips and carrots with it. Overall it was pretty bad ass.

art in science

2010-10-14T15:23:00.004-04:00

I saw this hanging in a friend's lab in my building; he said it came from one of the custodial staff a while back.

It's a pencil drawing, with the expected smudges from age, and it's really, really well done. I think it's wild that a custodian would have such impressive skills, want to draw a lab apparatus, and then donate the product!

shit like this amazes me

2010-10-12T20:04:00.005-04:00

I didn't look to see if there was an easier way to do this or not, but it would surprise me if there weren't. Look at the transformation from 5 (the first compound) to 13, near the end.

Org. Let. ASAP

They turned a compound with a 3-carbon chain with 2 oxygenated centers into a compound with 5 skeletal carbons and 4 oxygenated centers in 13 steps. 13 steps!! They even used a chiral auxiliary to re-set the only chiral center in the starting material, making the choice of using it questionable.

The longest linear sequence is 24 steps, not including the 12 step synthesis of the other half of the target. In the end making it the crude equivalent of 1 step per member of the macrolactam, ouch.

what? I don't get it

2010-10-11T13:57:00.004-04:00

I have a New Yorker daily cartoon desk calendar. It was a gift last xmas, and sometimes it's nice to start the day with a cute or funny cartoon. Unfortunately the New Yorker is a poor resource for this. I often wonder why people would read that particular rag, and after having the cartoons, I wonder even further. Some don't even make sense:

There were definitely some good ones in there, but by and large they were weak or poor. I would have expected the calendar to be a showcase, a sort of best of, but I certainly hope it isn't, now that I've seen the dismal quality of the humor. It's almost as bad as the typical syndicated newspaper cartoon, except these guys have more time to write and, presumably, should have done a better job.

One of the few saving graces was a blog article, retelling another blog article, on boing boing earlier this that saved a good quarter of the cartoons (more than half were beyond saving). Simply replace the caption with "Christ, what an asshole!", and magically the humor is repaired.

hipsters

2010-09-12T13:45:00.005-04:00

Hipsters are pretty easy targets for poking fun, but this vid I saw at boingboing is is just too well done to pass up.

ACS goodness

2010-09-04T21:30:00.000-04:00

Jim will like this one.

I was at the ACS this last week, and saw a few nice typos. First off I'll admit that my boss' presentation had one in it that I apparently missed when I proofread it, but small typos in talks are hardly an issue. As long as they don't interfere with the big picture or fuck up the talk they are gone so fast that most people will never notice them. I think the only reason I noticed the one in his talk was due to my familiarity with the talk.

I'm not going to cover all of them, I don't remember them and it would be even more boring than my usual posts, but I though I might cover some fun ones.

One rather nice girl was showing a pretty good chunk of work on a poster, and I was taking my time to try to read it all. I stumbled a bit when I got to this over an arrow:

I had to think for a second as to what it was, even though I knew exactly what it was for. I asked why she had written out the structure, and she replied to remove confusion for non-synthetic chemists and undergrads. I thought that was particularly odd, since i would think that it was significantly more confusing than putting the name of the reaction or listing the ingredients. I expect she was trying to clarify the reaction more than just writing "Swern", but there is more than one way to make the reagent she had, in fact. It seems obvious to me that if you are trying to clarify it, the reagent list is the way to go.

She wasn't too pleased when I pointed out she was missing the counter ion, and was even less pleased when I pointed out that in two other places on the poster she had written "Swern" over arrows.

Only a few posters later I saw a neat reaction, with a witches brew of reagents. It caught my eye for a few reasons: I have tried things like it before with little luck, and the prior poster girl and I had a nice conversation about it and her successes. This new poster had a deprotonation alpha to an alkene with a Schlosser's base like mixture (aka superbase, LICKOR, and others, KO-t-Bu/nBuLi). The thing that caught my eye was that this particular mix had no nBuLi. When I asked her, pointedly, if the reaction went without butyllithium, and she replied "Yes! ... NO!", and looked at her poster to see what was going on.

In that case I can't really blame her, it was most likely an honest mistake, and there were definitely a lot of thing going on on her poster, so one small detail would be easily lost in the mix. The thing about this one that surprised me was that the two hour poster session was within 15 minutes of being over, and no one had noticed it and mentioned it. It seems that any decent looking girl with a poster that has any reasonable amount of work can slide by just a tad easier than a dude in the same circumstance when she's surrounded by drunk nerds.

Earlier in the week I had a conversation with a friend, this ACS meeting being his first, about how the men hung around the girls at posters like vultures. He laughed when I called it a time honored tradition, he thought I was joking.

konami code

2010-09-03T19:30:00.004-04:00

JACS-beta has a new feature to try out, that is kinda weak to begin with, but better yet you need to use the Konami code to try it! They even give the code for you to try!

I've been sort of fond of the set up that the ACS journals have been using to show the titles and graphical abstracts of journals, and I suppose it's good that they are continually trying to improve it. However making it into a cascade of tiles that are smaller than in current use, that then blow up to boxes that are larger, seems like an odd solution. I may not like it, but that could be due to the fact that I like the status quo, in this case.

New features notwithstanding, what's the point of using the Konami code to roll out the beta? Using a "secret code" and publishing it widely? It's like a lame attempt to get geek cred with a crowd split between the so dated and lost they won't get the reference, and the crowd that is so tech savvy they will immediately dismiss it as a poor attempt at looking "cool". I doubt the narrow cross section between those two factions represents a significant enough demographic to warrant this particular stunt. It seems to me a second, mirrored, page, or a simple on/off button would have done the trick.

I haven't tested it, but it wouldn't surprise me if the wonderful new grid view takes a reasonable amount of front side resources, thus putting the kung-fu grip (in the bad way) on smaller institution's older computers.

Update:
This fellow is claiming to be the one who is behind the JACS beta Konami code.

JACS awesomeness

2010-08-26T13:51:00.003-04:00

JACS is so awesome. Can you count how many buzzwords are in this gem in ASAPs today?

I'm sure this is a very important contribution to something. Almost as important as my pending JACS paper.

"Graphene Decorated Nanopenis Catalyzed Asymmetric Green C-C Bond Forming Hydrogenation"

new position

2010-08-19T10:41:00.005-04:00

It's that time of year again when chemists looking for work prepare for the feeding frenzy of the fall ACS national meeting. While perusing the day's new postings I saw this:

Is this some new type of position I'm unaware of?

that's ... cute

2010-08-15T18:42:00.003-04:00

I stumbled onto this today, while trying to catch up on my ASAPs

Org. Lett. ASAP

The reactions depicted by the arrow on the right had me confused for a second, until I realized that the upper reaction is number 2, and the lower is number 1.

While I've never seen that before, or even considered it, I guess it makes sense since the arrow is going up. I mean why stick with the western convention of reading top to bottom if the arrow is heading up, right?

It makes sense. Sorta. Kinda. Almost.

update!

2010-08-12T16:40:00.003-04:00

The hanging wire seems to have gotten just a bit worse in the last few days.

There is another little orange card, that I didn't read, but the biggest question in my mind now is what is this even for? It can't be that important if it's been that badly damaged for this long and is still not being fixed. I'm fairly certain the only reason Pepco even came out was because concerned citizens called about the downed wire, not because someone's power was out.

public works

2010-08-02T21:43:00.003-04:00

I live in a pretty nice neighborhood, in a pretty nice town, in a county with high taxes. It's pretty expensive to live here, no downtown Manhattan or San Francisco, to be sure, but still pretty high. Last spring during the economic meltdown the house next door actually sold for significantly higher than the asking price, even.

In general I would say that it is well represented in the quality of public works. The roads suck now, but this last winter is the true culprit and areas of improvement are constantly popping up.

However at the end of my street is this oddity.

You can just make out the lovely yellow streamers.

This issue laden scenario showed up quite some time ago, perhaps a month or more ago, and has changed little since then. Bhy the time I noyiced it someone had already "protected us" by hanging the yellow prophylactics on it, conveniently making it more accessible to children who couldn't previously reach it.

At the time I first saw it, I assumed the tape had come from a concerned citizen. It was put on poorly, and in uneven lengths. The dangling the wire was out of the way, relatively speaking, over a roundabout that sees only moderate use. There were no workers to be seen, and no cones or safety equipment at all. None of this bothered me at the time, because who gives a shit, really? I figured it would be dealt with after some bitchy phone calls from some concerned parents.

Now several weeks, at least, later it's still there but has picked up a new feature.

That's awesome, passing the buck, then letting everyone know you did so they stop calling. I'm not sure what's funnier, the fact that they politely asked people to stop bugging them, or the fact that they have a printed label sticker for this very purpose.

periodic awesomeness, fuck yeah!

2010-07-12T13:54:00.003-04:00

I stumbled onto this beauty via Boing Boing today:

sold by Modern Toss, out of England (obviously)

I love the fact that it has a certain periodicity to it. The upper right 'element' "Tit" is about as light and unreactive as it gets, and the lower left has "You Stupid Fucking Arsehole Cunt" which is pretty fucking heavy. There is also a nice vertical trend, as well.

How they mismatched the example Cock and the actual Cock colors and values is beyond me, but the general product is excellent.

now that's GLOBAL deprotection

2010-07-02T18:35:00.005-04:00

I stay the hell away from sugar chemistry. In fact as a general rule I try to not even read papers about it. It's not that I don't like it, it's that it scares the shit out of me.

Sugar chemistry is an odd field where it seems that chemistry from other common areas doesn't work, and chemistry that works in sugar chemistry doesn't always translate to general organic reactions well. The reactions within the field, unfortunately, don't always work either.

When I happened on this today, I would have otherwise skipped it except for the compelling graphical abstract, that I have blown up here:

JOC ASAP

These guys took off 21 TBS protecting groups all at once. I gather from the text this may not be all that unusual, but it sure surprised me, especially when it is presented in visual form. The overall yield was ~28% which is an average of ~94% per protecting group. I have, unfortunately, had a lot of worse yields in taking a single protecting group off of a robust molecule in the past.

Sure puts a total synthesis "global deprotection" in a different light for me. Kudos to the sugar chemists, you insane fuckers.

googleness

2010-05-21T13:39:00.006-04:00

Google is a surprisingly useful and powerful tool. As an odd show of this, today's Google Doodle for the 30th anniversary of Pac Man, a playable Pan Man game:

After the game is done the Google search for "PAC-MAN 30th Anniversary" comes up, and more of the hits are related to the Google Doodle than Pac Man itself.

It often amazes me when the news bringer is making more news that what it is supposedly covering.

that looks familiar

2010-05-16T17:10:00.005-04:00

Check out my new and old motorcycle keys.

I went to go see The Business play on Thursday, and while I was at the show my motorcycle was stolen. Again.

Miraculously, it was also found and returned the next day, with the helmet still attached.

Apparently pushing a motorcycle out of a parking spot and a couple of blocks down the street in front of busy restaurants and bars, all the while bits and peices of the dangling helmet breaking off as you go doesn't alarm anyone.

Oddly the next day someone saw it and thought it shouldn't be there and called the cops, go figure.

After it had been towed to a lot by order of the police ($240, cash only, for almost 2 miles tow), I went and picked it up. The thieves hadn't had much time with it so all they had really done, aside from dropping it a few times, was break open the ignition lock. Luckily I was able to easily hotwire it, after having had some practice in the recent past.

I guess I need to invest in an alarm.

graphical abstract flub

2010-04-01T14:04:00.006-04:00

This isn't a terribly big mistake, but still, I wonder why people don't spend more time correcting their papers.

JACS ASAP multicomponent craziness

In this case it's actually in the graphical abstract, and the part that they used color to try to make it more easily understood makes it worse. The blue ethyl group on the diethylzinc becomes the blue methylene in the molecule. First, the ethyl to methylene is a bit of an exotic leap, and even a student should realize, after a moments thought, that's not a trivial transformation. Second, anyone who is familiar with Simmons-Smith chemistry would recognize that diethylzinc plus diiodomethane means zinc carbene, and the ethyl part is not used at all. All they had to do was make the CH₂ of the diiodomethane blue to be correct, and it somehow slipped past them. Too bad.

In unrelated news Alexakis and his crazy phosphoramadites have a nifty new-to-me reaction.

Org Let ASAP

1,4-Addition to aldehydes, and enantioselective no less. Is it general? For a highly specialized reaction, some might say yes, but in truth, no it's not. Is it amazing and life changing? If you aren't Alexakis or one of his researchers working on it then no, no it's not.

However it's still pretty neat, and I expect anyone who had done copper promoted 1,4-additions, and/or enantioselective additions will think it's pretty neat.

nice legs

2010-03-26T18:42:00.003-04:00

I took the red eye back from ACS last night/this morning and perhaps the best part of the whole deal was this little gem I witnessed while bleary eyed and taxiing towards my gate:

Seems like this wonderful product might also have accessory benefits like toughening up a too-tender box with up to 275 lbs. of resistance!

nice drawing

2010-03-15T15:13:00.006-04:00

Today as I was perusing the ASAPs, I came upon this one almost immediately:

The graphic looks like there's a lot going on, I like RCM, and they even have an exclamation point in the title! I had to read on!

Anyway, I was immediately greeted with this Scheme:

And the first line threw me a little. It took me a second to figure out what was wrong with it, and all I can say is that it's most likely a hang over from organic chemistry classes. When [3,3]-rearrangements are covered the professors always hammer home the point to look for potential [3,3]-situations whenever there are double bonds present, count to six from the bonds, etc, etc, and then test heavily over the material. In reality, except for groups that use rearrangement chemistry often, [3,3]-rearrangements are no more common than any other reaction, but the automatic counting and checking remain, like a Pavlovian response. I knew something was wrong with the first reaction, but I couldn't put my finger on it.

I actually had to get out pencil and paper and try to do the reaction as drawn, and I couldn't. First I was irked because it's a pet peeve of mine when people flip or rotate molecules to no real gain, like it appears they have done here with the R groups traveling from the left to the right, but that wasn't the biggest problem. I like to think I know some chemistry, but I couldn't get from starting material to product. I read some of the body text finding "The 1,4-diene-ester 9a was prepared by orthoester Claisen rearrangement of the corresponding 1,5-hexadien-3-ol (8a, Aldrich) with catalytic propionic acid or phenol in the case of 8b7 to afford 9b in reﬂuxing triethyl orthoacetate.", while that reinforced the [3,3] business, it provided no more insight as to why this was so hard to figure out, and it conspicuously only mentions one of the two starting materials. I could easily draw a different reaction that provided the product when R = H, but it wouldn't work when R = Me.

I finally went to the supplemental information, and found the starting materials' names: 1,5-hexadien-3-ol, as expected, and 6-methylhepta-1,5-dien-4-ol which I've drawn for you here:

Eagle eyed observers might notice a small difference in the locations of the alcohol groups with respect to the left hand side of the molecules, as drawn, trying to replicate the way 8a,b are drawn in Scheme 2. It's pretty bad that the editors don't catch shit like this, but how do you fuck this stuff up on your own molecules? I understand that they were doing the same reaction multiple times, and most likely wanted to draw both molecules in one to save space, but it seems like it should have been drawn out the long way at least once during all this. Then the later flipping nonsense would be fairly obvious.

happy pi day

2010-03-14T14:47:00.002-04:00

The most useful thing Nicolaou has ever done

2010-02-26T13:54:00.004-05:00

I typically think that Nicolaou has contributed very little to the endeavor of total synthesis (unless you count using the same series of 3 reactions over and over again to make 1 mg of huge molecules important). But he has finally done something useful (while still managing to just combine two separate and well established reactions). I could have used this when I was banging my head against a wall for 6 months-a year trying to do an oxidative cleavage.

memory

2010-02-12T19:24:00.001-05:00

wild weather

2010-02-11T15:26:00.005-05:00

Here's the snow while I was digging the other day:

Here's the street out front after the storm, and a Metro parking lot:

Then yesterday it snowed again and it was windy, so I don't know how much but it might have been a foot.

Then today it was sunny and the temperature was ~20 degrees warmer than yesterday. There were huge puddles and small rivers all over the place.

mmmmm ... I bet that's some tasty water

It's supposed to snow again early next week, I can't wait!

snow, glorious snow

2010-02-06T16:03:00.002-05:00

Well, we got some snow last night, and I'm pretty much stuck here now. Motorcycling in the snow may be fun but it's not very practical, and the Metro stops servicing to above-ground platforms at 8+ inches of snow (insert "that's what she said" joke here) so I have no way to get to work aside from walking 6 miles.

I decided to make myself somewhat useful, and dig out some pathways around the house. I love the snow and winter, so it was actually pretty nice to be outside in it for a few hours, but being a nerd I think the manual labor is going to royally kick my ass in the aftermath for the next few days.

as you can plainly see, it's uphill both ways

storm watch 2010!

2010-02-05T15:59:00.004-05:00

I'm in the middle of the terrifying snowstorm that's ROCKING the mid-atlantic! When I got up early to go to work today "just in case" the storm closed everything down before I could make my escape the train platform was BARREN! In fact no one got on the train I used to go to work! When I got to the lab every one of the brave souls I work with had braved the distinct possibility of snow that had been predicted! It was truly awe inspiring!

Several hours later, after virtually every school and government office had been closed, the snow began! Here is a harrowing look into the snowy, snowy eyes of potential doom outside the lab!

brrrrrrr ... just looking at it brings back harrowing memories!

Because I had gotten up so early "just in case", I left early because I was tired as fuck, and not a moment too soon! Look at this incredible accumulation in the foreground already! It's only 2:30 pm!

oh dear Lord! just look at the limited visibility!

I thank my lucky stars and the sweet Lord above I was able to make it home through this harrowing, harrowing event!

nerdiness

2010-01-29T10:12:00.002-05:00

It's a little cold today, ~25 degrees Fahrenheit, and on the Metro ride in I ended up walking behing someone who had apparently taken a bath in cologne. The first thing that popped into my head was "How is that even volatile under these conditions?", followed closely by "I'm really glad I won't be around that guy when he's in a warm building."

I think maybe I need to get out more and do some non-science things.

that's the key 2

2010-01-13T17:40:00.004-05:00

After the mild debacle the other morning, I wasn't too surprised to find yet another problem on the way home. Apparently the taillight doesn't come on when the run circuit is jumped, and nothing else. This little tidbit was conveyed to me by a nice motorist who took the time to tell me on my way home at night. I wish I had known that before dark, but at least there were no issues due to it.

I did a small bit of research, and found I just needed to jump four of the five wires in the starter. Conveniently two of those wires come from one being split after the ignition connector that I was jumping already, so I just needed to connect the two pairs at the junction connector. Instead of making two different wire jumpers, like the little piece of shit I was already using, I cut the Molex type connector off of the old broken ignition, soldered the ends together, and after some heat shrink I had my new key.

Which should last me until the weekend when I have time to actually work on the ignition switch. I even cut the tooth off of the connector so it doesn't lock in place, and I can remove it in only several minutes of dicking with it in the parking lot.

Pretty swank, huh?

If I'm not mistaken, I now have the key to a great number of motorcycles out there. Just proves to me how important it is to lock the bike down to something.

that's the key

2010-01-11T13:26:00.004-05:00

My motorcycle was stolen this last summer, and miraculously found and returned two months later. I was going to write about the repair process, but after I started I figured no one would give a shit but me. However, today something funny happened related to all of that, so I'm going to share.

The thieves apparently kept the bike and rode it themselves, as opposed to stripping and selling it. To bypass the ignition, they simply removed it and wired in a standard style wall mount light switch from a house; inelegant, but effective. Motorcycles are expensive to repair, and parts from the original equipment manufacturer (OEM) are often overpriced, and occasionally underquality, versus aftermarket parts. I did most of the repairs myself to save money, but I did have some parts ordered from Suzuki and put on by a good local shop. One of those parts was a new ignition.

The new ignition started to act up shortly after installing it and then it getting rained on a few times. I blew it off, since I had had the old ignition in the same configuration for several years with no problems. Now, after getting snowed on and not being used for most of a month it doesn't seem to work at all. Yesterday I thought I would be clever and put a switch on in a similar fashion to the thieves, but actually do a good job. I ran to Radio Shack, got some parts, and went home and cobbled something together. Preliminary tests were ok, and I left it for today's morning commute all based on this switch:

Now if it had worked fine, I would obviously not be writing this. It worked well for a while then died in a somewhat dramatic sputtering fashion while zipping along today. Luckily there was a bit of notice, so no big surprises came. I stopped (of course), and since it was ~30 degrees out, I wanted a quick fix to get on my way. A moment or two's poking and prodding confirmed that my switch installation job was probably shoddy, and I made the simplest shortcut I could with the parts at hand:

behold - my new key

Oddly, it occurs to me that this is probably about as secure as a real key, due to the ease with which one can roll off or hotwire a motorcycle anyway. Someone who recognized what was missing and what to do about it would not be slowed at all by the most complicated ignition system, however everyone else should be confused as shit by the current set up.

what kind of horseshit is this?

2010-01-08T16:51:00.009-05:00

I was reading my ASAPs today and happened upon K. N. Houk and N. K. Garg talking about indoles. I've had a couple of projects about them, and I'm always interested to see what people have to say about installing things at the 4-position. It's a difficult position to access, and a lot of drugs and natural products are functionalized there. The first table dealt with just that:

They didn't label which isomer was preferred in the yield column, so I assumed that it was left number to left product, and right number to right product. It also makes sense since the C-5 substitutions are almost always preferred over the C-4. My eyes drifted to the "C-5 preferred" in the far right column before I had read what the column actually was. I was confused, since C-5 is generally preferred, and it seemed like every other case showed C-5 preference. Momentarily excited I thought that maybe all the other cases were C-4 specific, and this was the lone C-5 in a very poorly labeled table! I saw the superscript b , looked to the bottom of the table to see what it denoted, and wonder of wonders it says "Attack at C-5 is favored (see the SI)." That amount of unneeded and uninformative redundancy is among the stupidest things I've seen lately.

Nowhere else does it give any real information about the reactions, or what the table really means, however ti does say to look at the "SI" elsewhere. Two superscript references to the same thing. How efficient, and vacuous.

I got the "SI", which I assumed was the supporting information, and found the following jewel:

What the fuck is that? Why would you even do that? How hard would it have been to put it in anyways? Why wouldn't you just put the number for the reference right in table as opposed to the completely uninformative "b"? The reference is already mentioned in the paper and wouldn't have even needed any additional text.

Weak.

edit: Forgot to put Garg's name in the initial link to spread the blame.

things I've learned recently

2009-12-10T16:25:00.000-05:00

I've had a run of less than optimal luck recently when it comes to health issues. Everything is fine now, but I think I've learned (or re-learned in some cases) some useful things.

Flu:
If you're feeling a bit under the weather and don't know if you should go to work or not, here's a clue, don't. You're just going to cough on your hand, use a doorknob, and get someone like me sick who will curse you for being such an asshole.

It's a good idea to have things on hand in the pantry for times of sickness. I forgot this cardinal rule and was totally out of Gatorade or any of its generic knockoffs, and was subsequently too sick to go out and get some. Rehydration is of the utmost importance when you're pissing out your ass every 15 minutes, and the human body is quite bad at absorbing pure water. By accessing the sodium channels in the GI tract, water is absorbed much more readily.

Canned chicken broth is like a magic fucking bullet, and has an extended shelf life. After a few days of not being able to hold anything down, including water, a warm cup of this poultry flavored brine is the most sublime dinner treat ever. And, of course, the salt helps to rehydrate.

Rabies:
Rabies is a deadly disease, everyone knows this, but by the time you show symptoms you're fucked. If you actually show symptoms of having rabies the chances of dying are greater than 99.99%. If you take the vaccine prior to that the chances of survival are very good.

The modern vaccine is no where near as bad as old vaccine with the multitude of injections in the abdomen, however it is much more expensive at ~$1500. These days only five shots are needed: immunoglobin, and four rabies vaccine shots over two weeks (days 1, 3, 7, and 14). All are intramuscular (IM), and the the immunoglobin, the "first shot" is 6 x 2 mL vials for someone ~195 lbs. As a reference a typical vaccine booster shot is in the neighborhood of 1 mL in the arm. This shot is actually 3 or 4 big-ass, deep tissue shots (e.g. thigh or buttocks).

If you get bitten by a dog take the time right then to find out if the dog has had its shots. Don't assume that just because it's a healthy looking poodle-like dog in one of the richest neighborhoods in the US that everything is fine, and he/she must be healthy.

There are several ways to test for rabies in humans, but no individual test is sufficient by itself. One of the tests involves spinal fluid. I'll let your imagination run wild with that one.

If for some reason you get bitten and are stupid enough not to get the necessary information right then, and need to go back and find the dog more than two weeks later do it regardless of how unlikely the possibility of success seems. The kindness of strangers can be truly surprising sometimes.

If a dog were to have rabies such that its saliva were infectious the life expectancy for the animal is less than five days. Quarantine guidlines for animals is ten days, just to be sure. Therefore just getting to see the furry bastard walking around two weeks later is sufficient to clear a bite victim of being used as a pin cushion.

nice simple method

2009-11-17T12:12:00.001-05:00

Saw this today in the JOC ASAPs.

I'm a fan of any new method, or method improvement that is simple, efficient, straightforward, and useful. While I haven't ever made a sulfonamide that wasn't a protecting group, they are handy for other things, and pop up in drugs as well. These guys got the reaction to work with one set of conditions on electron rich and poor aromatic thiols, a few aliphatic as well, and it appears to be selective and mild as well.

In fact the only things I can negatively comment on at all are that I would have liked to see more aliphatic examples, and acetonitrile is an expensive solvent. However, I bet that within the next year or so people will be buying cars in stupid numbers again, and acetonitrile will come back down in price.

Edit: I somehow gave the wrong journal title, but the right link. Thanks to Dr. Miller for pointing it out.

great idea

2009-11-11T13:58:00.003-05:00

Yesterday our lab and another had the privilege to go have lunch with Philip S. Portoghese and see him give a seminar later. During lunch we were talking about journals and the state of the business of journals, he's been the editor of J. Med. Chem. for 37 years, and ACS's new headache inducing paper journal format where they have two pages of material per page of paper came up. I mentioned that it felt like I was reading a girlie magazine whenever I turned it sideways to flip through the issue, and someone else in attendance remarked that we should have a centerfold with a reaction or compound of the month. What an awesome idea! People would be vying for the cover with pretty pictures, but others would be competing to get the centerfold with great science! Truly an idea who's time has come!

edit:
I said something stupid, and would like to clarify. You usually get the cover by publishing good work, but the cover itself is something pretty that is related to the work, and usually not the work itself.

The centerfold could be pure, unadulterated, awesome science.

Somebody Explain

2009-11-04T19:01:00.002-05:00

Am I missing something?

This is a really expensive and complicated way to do a sophomore organic reaction. Instead of making the silyl enol ether and treating it with stoichiometric CAN and 2,6-di-tBuPy (both expensive and used in large excess 2 eq and 4 eq respectively), why not just deprotonate with LDA and add an allyl halide?

Can anyone think of a reason to do this reaction (aside from somehow publishing it in Org Lett)?

ignorance is bliss

2009-10-30T13:48:00.001-04:00

Our secretary is a true sweetheart, but is also rather fond of drama, especially if it is totally unnecessary. A recent example includes someone attributing her name to a work order incorrectly. This would usually involve a simple "that wasn't me" phone call or email to rectify, but for her she planned out an involved strategy of who needs to be contacted and provisions for difficulty with backup plans. In reality the order actually has nothing to do with her at all, excepting the bookkeeping error, and she could simply ignore the problem and it would go away.

Typically when I talk to her, like after a morning greeting, I'm prepared for some sort of soliloquy on her crushing life events. I try to remain stoic throughout. She's a sweetie, so I don't want to shut her down, but I also don't want to add fuel to the fire. Typically I give her some noncommittal remarks, and, if I actually have any knowledge of the area, some help.

Today she was extra excited and proceeded to tell me a story about a man who had some rare condition and had kept a gorilla in his basement and fought with it for several years until it had actually killed him, even tearing off his arm at one point. I, politely, called bullshit, and recommended she check it on snopes.com. She continued like she hadn't heard anything so I nodded, repeated myself, she continued, I spelled snopes.com for her, and then left. A little while later she said she had found the article and tried to give it to me, so I chatted with her, but didn't take the article and left.

Eventually I had a minute and was curious so I actually looked it up using some nice generic, but defining terms, and it popped right up as hit number one. As it turns out it's an onion article, and her lack of understanding was so goddamned hilarious I couldn't decide whether to tell her or not. In the end I told her. There was no practical way to follow the progress of the story as she told it to other people, so the entertainment value was pretty much used up, and it was time for some modicum of damage control.

wow

2009-10-23T10:35:00.003-04:00

It's hard to say if this is completely and utterly awesome, or just another interesting blip on the radar that may someday make it into textbooks.

JACS ASAP, DOI: 10.1021/ja9061097

I had and organic prof. years ago who referred to fullerenes as full of shit arenes, due to all the press they had garnered with little real applications found. They still have produced relatively little, especially when compared to sibling compounds such as carbon nanotubes, but every now and then something really neat like this comes out.

Also I learned a new word today, that I wish I hadn't: Suicidality.

practicality

2009-10-19T17:00:00.000-04:00

This went to ASAP a little while ago. The method is interesting, and apparently successful, but the thing I liked most about it was one of the footnotes.

It's a bit unfortunate that a good method needs to be supported for not being catalytic, or any other little darling of the day, but it's nice to see it done once in a while.

It seems like most people who use buzzwords, especially in the title of the article, really do the buzzword in question a disservice, and it has little to do with the method besides poor advertising.

fun weekend

2009-09-18T19:56:00.000-04:00

Esther came to town for a visit this last weekend, and we got to do some fun stuff. In addition to the fun stuff we ran into some interesting and odd things too, two of which I thought I would share.

On Saturday we thought we would go to Old Town Alexandria and check out the Torpedo Factory. We'd never been and heard it was neat, if the chance arises to go there, I recommend it. that place was pretty damn cool.

On the way out of town to go there we knew it was going to be a long day, so we stopped off at the CVS to get some water bottles to take. And the expected customers for a Saturday morning were milling around the store. Only one thing stood out, and I wouldn't have noticed it at all if I hadn't happened to look over at just the right time. There was a little old lady browsing in an aisle who looked for all the world like any middle America grandmother except for one thing. She had no nose. Where her nose had once, presumably, been was a flat spot covered by a triangular band-aid. For just a moment I involuntarily thought of Vincent D'Onofrio's character Pooh-Bear from the Salton Sea, and subsequently of his pet/torture device badger Captain Stubing. Rather an odd juxtaposition for a nameless granny.

I couldn't find a pic of him without the bad prosthesis, sorry

The other encounter happened when we went to a movie one night. We saw District 9, and pretty early on I had to go to the bathroom, and I felt it would be best to get it out of the way before all the crazy action really started in earnest. It just so happened that there was a unisex singlr bathroom right outside our theater that was open. As I approached it, I could see through the slightly open door that someone had already vomited in there. I peeked my head in to see how bad it was, to determine if I could still use it, or would need to look for another. I was shocked to see that not only had someone basically turned their entire alimentary canal inside out, but they had placed the bulk of the detritus as far from the toilet and trash can as possible while still residing in the same room.

In addition to the grotesque landscape was a not unpleasant odor of blueberries or raspberries. So I was able to use the bathroom in relative comfort, even in that state. I went back after the movie to snap these pics and the odor had persisted.

sweet, sweet buzzwords

2009-09-16T10:35:00.005-04:00

I saw this beauty this morning while having my morning tea, and it just cements in my mind how badly people want to latch onto popular, and often useless, nomenclature. Perhaps the best example of worthless jargon that is used frequently is "chemoselective" which appears to have no proper definition, and adds nothing to the chemist's lexicon that wasn't already available, but a close second these days seems to be "organocatalytic".

David MacMillan appears to be a great chemist, and an ok guy, but the real fame in his chosen area seems to be based largely on sales tactics. His classic contributions to the area are merely improvements on existing methods. Is that bad? Of course not, but now everyone else wants in on the game.

I think it's a bit odd to call most of these things "organo" catalized reactions anyway, because the active centers typically are nitrogen. Anchimeric assistance is often provided by oxygen or other nitrogens, and the hydrocarbon organic portion is typically scaffolding, as in many inorganocatalized reactions.

In today's example the authors most likely wanted to add some pizazz to their paper with needless, and inappropriate, jargon. It's too bad, really, because the method is actually quite nice, and doesn't need the added tripe. While the title proudly claims the method is organocatalytic, the graphical abstract has a nice large fluorine cation, and no carbon to be seen.

The fact that it says salts in the title should be a giveaway, but it never hurts to look on a bit further. The first depiction of the catalyst is given in scheme 2, where we see it's N-ﬂuoropyridinium
triﬂate. That's like calling a reduction with tetrabutylammonium borohydride organostoichiometric.

Some very quick math shows that the hydrocarbon portion of the salt is only 31.2% of the mass of the compound, and that the inorganic active fluorine is just below that at 30.8%. To really beat this dead horse lets look at a heavily skewed example of a common inorganic catalyst, tetrakis(triphenylphosphine)palladium. This common catalyst and catalyst precursor has more than 10 times the hydrocarbon mass per mole and the portion of the catalyst that is hydrocarbon is over 80%, that's even better than the carbon rich MacMillan catalyst (5S)-(−)-2,2,3-trimethyl-5-benzyl-4-imidazolidinone monohydrochloride at 69% hydrocarbon.

Suffice to say I wish people's chemistry would stand on its own two feet but it seems everyone knows that massaging the system works better, and if someone else has laid the groundwork why not capitalize on it.

lab accidents

2009-09-06T17:24:00.005-04:00

I'm pretty lucky in that I have very few of them, and they tend to be minor. Oddly, however, the worst lab accidents have always been doing mundane things. The things that can really go awry are usually surrounded by a lot of care and multiple layers of safety and protection, so if things go wrong it's not too bad. Messy, but not damaging.

The few accidents I have had that involved personal injury typically come from things I really didn't expect, and therefore I wasn't watching like the paranoid neurotic I typically am. Quite a while ago I was doing a liquid liquid extraction and, since I wear glasses anyway, I wasn't wearing safety glasses. A lone drop flew off the drip tip of the funnel and arced perfectly over my glasses into my eye. I don't remember what was exactly in the funnel at the time, but it was probably the usual mix of aqueous mineral acid and product mixture in organic solvent. I do remember that it was so stunningly painful that it took specific effort on my part to maintain my grip on the funnel, and keep my hands and arms from involuntarily relaxing and dropping it.

My eye picked up a slight yellow tint for the rest of the day, and shortly thereafter I grew some small bumps on my lower eyelid in a cluster. I don't know if they came from that incident or not, but they were an almost daily reminder of it for about 10 years until they grew out and fell off earlier this year.

In grad school, on two separate occasions, I was putting the cap on an NMR tube, and the tube broke directly between the two sets of fingers holding the tube and cap respectively. Both times I accidentally pushed the shards into either hand. The first time it was about 2 am, and I wanted to get one last NMR in before I left. I was bleeding so bad from one of the cuts I couldn't really do anything but hold a paper towel on it, and there was no one left in the lab, or on my floor that I could find. I had to sit there like an idiot until it stopped bleeding sufficiently that I could tape it shut with label tape. We were, of course, out of band aids. When I got home much later, after cleaning up the mess I had made, I changed the tape out for a bandage. It was interesting/gross to see that I had cut a question mark shaped hole as the tube attempted to get a core sample, and it was a challenge to remove the tape off without the flap peeling up and separating from the fat and collagen layers. I now throw out severely chipped and cracked NMR tubes, and put the caps on very very carefully.

Earlier this week I was getting ready to go home for the night, and was shutting everything down at my hood and bench. I kneeled, turned off my pump, and raised the trap out of the dry ice/acetone filled dewar. The dewar tipped over and poured its contents down the front of my shin and into my shoe. I was happy to see it hadn't broken and sent glass flying while deafening me, while at the same time I was stomping and shaking my shoe to remove the acetone from around my ankle. Oddly, and thankfully, there was little damage. My sock did soak up quite a bit in the front and freeze, unfortunately. An immediate survey showed the damage was minor, I finished shutting down and split. When I got home, I figured I would photograph it for fun. I have a great series of a fluid filled, swollen, and highly colored ankle healing from hitting my shin a few years ago, you just never know when this stuff will come in handy.

I apologize for the shitty pictures. Apparently my recently replaced phone had a protective film covering the INSIDE of the lens cover that I was unaware of until today.

The night of the "incident"

the hair was already gone,
too many cheap ski boots took care of that in my youth

As you can't really see, the affected area is reddened and swollen pretty evenly. There is already a bit of ridging where the elastic of the sock was. It felt a lot like a reasonably bad sunburn.

Several days later:

Most of the swelling and redness are gone except in the most burned part. Doesn't hurt anymore except for when direct pressure is applied. Usually on accident, and is quite a surprise.

Today:

Look at how clear that is when you remove that little piece of fucking plastic! The color is somewhat unpleasant looking, but it feels fine, and is healing well.

Interestingly, a few days ago the same thing happened, and without any surprise or real thought my knee shot forward to catch the dewar and balance it until I had a hand free to right it. I think perhaps it's time to reevaluate my pump trap system.

2009-08-20T19:36:00.003-04:00

Back to lab today for the first time in almost a week, in many ways I love ACS meetings, in many ways my liver hates them.

A few weeks ago an acquaintance was in town for a night as he passed through, so Liam and I took him out to Adams Morgan for some drinks. While we were there he got flyered, and spent some time trying to pass it off on someone else for fun, while we made fun of him. Eventually I had a look at the flyer, which was covered in scantily clad chicks, so I kept it for later inspection. It's been sitting on my desk at home ever since, and periodically I pick it up and and check it out. This amazing little card never seems to disappoint and has revealed something new to me on almost every occasion.

hubba, hubba

Of course I grabbed it cause it's covered in scantily clad hot chicks, but the nature of the chicks is pretty intriguing, as well. All are black, all have pretty significant booty, and pretty much all are facing away from the camera or otherwise presenting their assets. "Birthday Sex Bash", "U Turn Me Out Sex Bash" ... wow! Now that's advertising!

Notice the completely naked girl in the forefront of the first side? That's not a pole wedged betwixt her cheeks, it's a sword.

A later assessment revealed some more details of interest, in nice small letters "No Athletic Wear" and "This is a Nigga Free Zone". Holy shit that's a bold statement.

Somehow, inexplicably, I missed what might be the best part. I was googling the names of the companies involved to see if there was any info about this place. Where was it? Is it a club, or a warehouse party-type set up? Were there police reports? I found an article describing this very flyer, which pointed out something very important I had missed. While on the front it says "Gentleman Only 25 years and Up", on the back it says "Ladies Night No Dudes Allowed 21 Years and Up". They are apparently trying to tap into a market of both chicks and dudes that want exactly the same thing in their smut! Absolutely amazing!

If that place was anywhere near here I think I would live there!

then profit!

2009-08-13T12:45:00.005-04:00

Today's Org. Lett. ASAPs had this gem.

Things like this piss me off a bit but mostly confuse me. At first blush everything seems fine, they even clarify that the mechanism is proposed. Step one is a straightforward sequence of additions which is (probably) inaccurately described as a Diels-Alder, but the second step is pretty interesting. It includes the addition of a nucleophile to a tertiary carbinol under basic conditions. I can think of a couple of reasonable mechanisms that lead to the drawn product, but they aren't immediately obvious. In fact the one I like best doesn't even use that particular intermediate. In any case it seems to me to be a significant intellectual leap to the final product, and the authors a) don't actually know what's going on, b) think that it's the direct displacement of the carbinol, or c) know what is going on, but can't be bothered to describe it, even though they wrote the scheme in the first place.

None of those options is particularly satisfying, and these types of half baked situations always remind me of the South Park episode with the underpants gnomes and their business plan.

CRC

2009-08-06T10:51:00.002-04:00

In today's JACS ASAP is a review of the 90th edition of the CRC Handbook. This thing has been around for so long that it never occurred to me that I didn't know what CRC stood for, until my octagenarian coworker asked to borrow my "rubber book". When he saw my confusion, he explained that the rubber book was a reference put out by the Chemical Rubber Company.

This huge tome may be the best know of all science reference books. I was actually really surprised to see a review of it. To me it seems that if you like reference information in book form, it's fairly obvious you need this book. I mean it's been out for 95 years, how could you not know about it?

As a side note, they seem pretty good about adding things to it, and seldomremoving old info. Sometimes the internet isn't the best place to find old information, but if it's chemistry and physics it's in the CRC handbook. They even take out errors from older versions. A collegue wanted to remove some water via an azeotrope that he found in the CRC. I thought it sounded like it wouldn't work (azeotropes tend to form between polar and nonpolar liquids, not polar and polar - good bit of minutiae to know), and after a little looking we found out it was a mistake that was removed from later versions.

big brass balls

2009-07-31T20:34:00.003-04:00

I read a neat paper today in JACS. These guys used a laser to induce crystallization in a gel as a super sweet way to control crystal nucleation. As an example of their laser-jock prowess they exhibited Figure 1:

Laser? I hardly knows her!

In an odd way I love it when people do things like this. It's like they're saying "Our shit is so awesome we can dick around and pull off things only dreamt of a few decades ago as an exercise in fun and games", but in a much less insulting way.

more errors

2009-07-30T19:37:00.003-04:00

Jim should like this one. In today's JACS ASAPs someone has a four component reaction, and published this graphical abstract on the website:

nice colors

I looked at it for a second not knowing what was wrong, but that something was up. Then I noticed that they have the same nitrile containing amide twice with different colors and slightly different drawing conventions. I assume that they used the colors for clarity of functional group positioning in the product, and that the difference in nitrile representation is simply a typo. However they may just be trying to make themselves look good, and indicate more strongly that the two components that are the same component are in fact two components. As everyone knows the greater the number of components in your multi-component reaction, the larger your chemistry phallus appears to be.

traveling

2009-07-22T18:11:00.004-04:00

I spent this last week helping my Hot Baby move to California. Aside form the usual bits of car trouble and bad weather, it went very well.

The first part was spent in Austin packing, preparing and saying goodbye to people. I miss Austin a lot, but seeing things like the Cathedral of Junk, which I was unaware of when I lived there, make me miss it even more. Here's a grainy video I took of one small part of the Cathedral.

not bad for a vid from a phone, really

The drive to the bay area was long and, mostly, uneventful with some beautiful views once we were out of west Texas. Once we made it to the East bay, the usual housing issues were resolved, and there was even some time for sightseeing. We even had a chance to go out with Hillary and Dave for dinner and drinks one night.

As it turns out, all the bad things you hear about Oakland are entirely true. just look at the size of the rats in out hotel bathroom!

the dark one is longer than the toilet bowl when layed out

Feynman Lectures

2009-07-15T15:15:00.003-04:00

I just found out about this really cool series of lectures at Cornell by Richard Feynman on physics. I have only watched the first lecture, but he does better than anyone I have ever seen at describing in a simple and interesting way the process of scientific discovery. Highly recommended.

There are seven lectures included on various topics. Click here to watch.

Allyl Amines - A Long Standing Problem

2009-07-14T12:40:00.004-04:00

According to a recent journal article I read, allyl amines are among the most useful of synthetic intermediates. I happen to agree. If only there were a convenient and cost-effective way to make these compounds. Let me think. OK. Amines are good nucleophiles. And allyl halides are great electrophiles. Maybe if I mixed those together, I could get my precious allyl amine.

No. You idiot. That is way too complicated. There is a MUCH easier way. Just mix this "simple" gold catalyst with your amine and an allene at 100 degrees for 12 hours. And BAM! you got an allyl amine.

But wait you ask. What about other allenes than the one in the abstract picture above. Don't worry, they tried those too.

Finally, an easy way to make N-allyl morpholine! Check out the awesome E/Z selectivity with unsymmetrical allenes! Allenes as starting materials, what a great idea! They are so easy to make, especially these low molecular weight ones!

The world was waiting for a solution to this long standing problem in organic chemistry. Thank you for this. Nobel! Nobel!

Tip of the hat to Dr. B. Mike O'Keefe for pointing out this gem.

highly Michael

2009-07-02T13:25:00.005-04:00

I'm having my lunch and reading and the very first article I see is this:

I'm sure many of you saw this before me, but damn. That's a pretty big fuck up, in my book.

Edit:

Moments later I saw that the very next paper has a botch in its graphical abstract.

The chemistry isn't earth shattering, but I was so confused by the graphical abstract, that I read it to see what the hell was going on. In a way their mistake got me to read a paper I would have otherwise blown by.

It's like Org. Lett. has taken the week off from editing for the holidays.

gram scale

2009-07-01T12:13:00.003-04:00

It took me a few months longer than I would have liked, but I finally got there. Here are two large (if I do say so myself) bottles of >99% ee enantiomers of my branching point compound. There should be more than 100 g of each, and there is a bit more coming through the resolution still. This is the culmination of seven steps and one resolution.

take that, Baran

It took a hell of a lot longer to get here than I had planned, but now I should be able to make dozens of targets and their enantiomers without ever having to repeat any of those steps again.

gross, but funny

2009-06-29T14:57:00.002-04:00

I've had an ingrown hair along my jawline for a long time now. I don't get ingrown hairs too often, and usually when I do it comes out with some fussing/scratching/picking. This little bastard had resisted all my weak attempts to free it, and just festered. It was also in a place that was difficult for me to see, so it was hard to see what could be done about it.

Early last week I had finally had enough and decided to actually take care of it, and to even try to do it the proper way to provide the best results. I scratched the dead skin off the top of it, then put a concerted effort into not touching it for several days except to clean it. I shaved carefully around that area, and let it rest a day. I waited until right after a hot shower, and then took a clean pin and gingerly poked at it. Immediately a small loop of hair popped out! I put the pin in the loop and popped the end out, and that little fucker was ~1/8" long. I left it, and figured I would leave it a day, shave then, and hopefully the issue would be resolved.

Two or three hours later it was still a bit sore, and similarly irritating. I went to the bathroom, and gave it a small pull, and a lot more hair came out! The whole thing came out and wasn't attached at the root anymore. In the end it was more like 1/2" than the originally exposed 1/8". It was such an odd feeling and sight that I snapped a pic.

frodus

2009-06-23T10:01:00.004-04:00

Seminal spazzcore band Frodus, who broke up before I had the pleasure of listening to them, have regrouped almost 10 years later and are playing once again! On Saturday they played the Black Cat, and I went, all bright eyed and bushy tailed, excited to see them.

I showed up early enough to see the end of the first, and all of the second acts. The first act immediately made me think of the "space rock" stage at fun fun fun fest lat year, and I was left wondering what they were doing playing this show. My buddy said it sounded like they had tried really hard to write one good song, and then played it over and over again. We grabbed some beers and sat in the back and waited for the next act.

The next act was much the same, stylistically. If you go to a punk show, and see the guitarist of any of the bands "rocking out" by gently rotating his body back and forth while he nods, also gently, something is wrong. They sounded like they had grown up listening to Don Cabellero, and really, really wanted to be that good, but it was too hard so they added some lyrics and hoped no one would notice.

At this point I was getting nervous. I didn't own any Frodus records, could I have heard the only good songs and the rest sounded like these other guys? Had I made a grave error in judgement? I was actually jumpy as they were tuning up and taking the stage.

They came out and started off like a bomb exploding and I could feel waves of relief come crashing down on me. The first 3 songs were like one long crescendo building to an insane sonic peak. I tried to get some pics, but there was just too much movement for the camera in my phone to capture it.

you wouldn't even know it was Frodus if it weren't for the base drum

It was almost like it was planned to have oddly misplaced music as the intro, it made the aural assault of the headline seem that much more significant.

Another thing they did, which I REALLY thought was great was to eschew the "encore". Encores are total bullshit, and I think I've only ever seen one real one. Even that one was pretty expected.

At the end of the set, Frodus stopped, the singer said it was time for a period of reflection, cause encores are stupid, and they brought out chairs and sat there for a minute in silence. They then got up, played more, thanked everyone, then the show was over.

If you have the chance to see Frodus, do it.

another great scheme

2009-06-19T13:47:00.006-04:00

Once again I'm at my desk trying to plow through ISI's weekly barrage of information, and I happened on this beauty:

Ann. N.Y. Acad. Sci. 2009, 1163, 330-339

Obviously not the worst one, but still has some nice features. Again we see the complete disposal of the typical left to right, top to bottom method of layout most people in the western world are familiar with. Who doesn't like to needlessly read charted information the goes up?

The first little loopy section has 3 different sizes of arrowheads, when one or two would have sufficed, and later in the scheme there are another two different styles of arrowheads used for no reason.

There is text above the arrows, below the arrows, and even some partially upside down text.

Perhaps the best part is that there are no structures for just over half the compounds. That always clarifies a scheme. I'm sure everyone reading the paper know what 1,2-dihydroreticulinium and salutaridine look like, but not tyrosine or morphine.

I suppose the strange part is that the structures are drawn pretty well, for an author that can't keep the font size and capitalization consistent.

edit:

I almost immediately found this one after posting:

Russ. Chem. Bull., Int.Ed. 2008, 57, 6, 1277-1284

All the lines around the piperidines are supposed to be hydrogens. I assume they used the cyclohexane drawing tool in ChemDraw and just left all the lines. For some reason they took them out in some of the other drawings that weren't in table form, and in at least one case used a drawing with all the extra lines, and actually put an H on the one they were specifically talking about without madifying ant of the rest. It's like some sort of odd selective vision on the author's part.

xmas trip

2009-06-14T15:40:00.007-04:00

I kept forgetting to post this, but better late than never.

This last holiday season my girlfriend and I went to visit my parents for a few days. My girlfriend and I live in different states, and see each other only once every two or three months. The though it's weird to have sex under my parents roof was a little disconcerting, but desperate times call for desperate measures.

On the flight there, my lady and I were discussing how we were going to pull this off with a minimum of fuss. We figured condoms were the way to go, so my mom wouldn't have to launder DNA impregnated sheets, and I grabbed a flight sickness bag so we could use it as our own personal trash bag for a later, surreptitious, disposal.

Everything went as planned, and I ended up packing the little goodie bag and bringing it back home with me. After I had landed and was commuting back, it occurred to me that I had inadvertently left a nice trap for the TSA. There wasn't a note in my bag indicating it had been searched, which actually surprised me a bit. In addition to packing the latex balloons of genetic material, I had a bunch of tools I had purchased on the trip as well.

Here is a series of me unpacking what I had flown back with.

bag full of dirty laundry

xmas socks and underwear from mom

there's some more interesting things

and the goods

In retrospect, I think it would have taken some actual effort to come up with a better trap for the TSA. Too bad they didn't fall for it.

resolution step 2

2009-06-13T18:34:00.003-04:00

I recrystallized the material from the resolution, and the ee went up to 98.9%. Perhaps I didn't use a sufficient volume of solvent or enough wash. In any case it will be easy to recrystallize again to get the ee up enough.

I took the mother liquor from the bulk resolution, which was heavily enriched in the diasteromer salt, and free based it. The opsque, dark brown, mixture was treated with D-tartaric acid, and crashed out to give the much more enriched salt. Interestingly, when the boiling solution of base was added to the boiling solution of acid, in similar concentration to the racemic case, the salt started to come out of solution even before I was done mixing the two. The already highly enriched enantiomer gave almost optically pure material (96.8% ee) that had only a hint of color. In a typical resolution of this compound from racemic I expect to get >75% ee, so this was a pleasant surprise.

I didn't add a pic of the mother liquor because it was on the rotovap when I took this, and I expect everyone is familiar with what a flask full of tar being stripped looks like.

I recrystallized the D-tartrate salt to get the ee up, and it took nearly twice the volume of solvent it would have if it were 75% ee, presumably due to the significantly higher optical purity.

resolution

2009-06-11T15:31:00.005-04:00

I was taking the products from the distillation and resolving them via their tartrate salts, and decided that was inefficient to do individually on a reaction by reaction basis. I saved up the products from all the remaining reactions I had, and started the resolution on a large scale today. On the left is all the product from the distillations of material in 7 volumes of solvent, and on the right is an equivalent of acid in about 7 volumes as well.

They are heated to boiling and then combined (adding the amine to the acid), and, when it works well, the salt starts to crystallize out immediately.

After cooling it is filtered and washed. One of the wonderful things about a good chiral resolution that is not often mentioned is that in addition to increasing diastereo purity, it increases chemical purity as well.

The product should be > 99.5% ee after one recrystallization, and I can take the dark mother liquor, free base the salt, and crystallize it with D-tartaric acid to get it with >99.5% ee.

art?

2009-06-11T09:04:00.004-04:00

I was distilling some material yesterday. At the end there was a small amount of tar left that was free flowing at the distillation temperature, and the last volatile material was coming over a drop at a time. I shut off the heat to the oil bath and left, and when I came back sometime later I was greeted with this.

At first it reminded me of Eddie VanHalen's guitar, Frankenstein:

But now I think it looks more like a Jackson Pollock knock-off.

nice set up

2009-06-08T11:53:00.006-04:00

I'm pushing a bunch of material through a known reaction that, before my boss and I improved it, sucked. It worked very well on small scale and the yield and quality of the product dropped off precipitously as it was scaled up. Now the reaction can be performed on most any scale and yields of purified product are typically 90% or above.

Now there is only one small problem, the solvent for the reaction is triglyme. I run the reaction quite concentrated, but I still have hundreds of milliliters of solvent to deal with that has 50-100 g of crude product in it. Extraction on this scale is doable, but vacuum distillation is not only easier and faster in this case, it leads to significantly more pure product.

Herein lies the issue, triglyme is a bitch to distill. It has a relatively high boiling point, typically 80-100 centigrade with the vacuum my pump generates, and is prone to bumping. By prone to bumping I mean that the shit bumps almost continuously when contaminated with a product mixture, and treated in the fashion I usually treat short path distillations.

The first time I ran this reaction at 50 g scale in 500 mL of triglyme, I distilled a significant portion of the solvent off starting with the 1 L flask the reaction took place in, rinsed into a 250 mL flask, and removed the remaining solvent, rinsed into a 100 mL flask and distilled the product. There was some bumping over of the product, but not too much, and the reaction-purification sequence took all day. All in all not too bad for a 50 g reaction, but I still needed to put a few hundred more grams through it in the coming days.

I remembered a set up my boss had mentioned to me in another context once that he used for distillation of a heat sensitive compound. Many people are aware of the falling film distillation apparatus, and they are available from places like Aldrich for the low low price of $800 for the lovely 24/40 model.

an easily broken paper weight that cost almost as much as an ounce of gold

When my boss needed to do some sensitive distillation a long time ago, he made up an exceedingly useful contraption to effect very similar conditions using common lab glassware. My target compounds are plenty stable to heat, but I thought the apparatus would be usefull to deal with the bumping issue. Here is my practice run with the apparatus.

sweetness!

It's a 3-neck 250 mL rbf fitted with a stopper, a pressure equalizing addition funnel, and a short path. Notice that the addition funnel has a glass stopcock, teflon stopcocks do not work well at all for vacuum applications. The oil bath is heated to ~150 centigrade and the mixture is added to the hot flask a little at a time. It distills rapidly, and there is never a significant amount at any one time so the bumping is inconsequential, additionally I spin the shit out of it (1,000-1,200 rpm) which helps quite a bit. This pic is a practice run, and contains the solvent from the 50 g reaction containing a trace of product, hence the slight color. I was able to distill off 500 mL water white solvent leaving the crude product in 30-40 minutes this way.

When I ran the reaction on 100 g scale I was able to distill off all the solvent, and then distill the product in less than half the time the first 50 g reaction distillation took.

Waste Disposal

2009-06-02T15:48:00.004-04:00

Let say that hypothetically you are a member of an organic research group at a well regarded department. What would you do with this form?

Yeah, I know it's complicated. Sure you are here to get a PhD in organic chemistry, but that doesn't mean that you can fill out one of these crazy hard waste disposal forms. Good thing that we keep these forms conveniently stored in a folder with easy to follow instructions.

Where can I find instructions to dispose of wastes of space?

Dreamweaver

2009-06-01T13:23:00.004-04:00

Brandon, Tim, and I climbed dreamweaver yesterday. Dreamweaver is my most ambitious route to date, a 1600 ft ribbon of snow, ice, and rock that leads to the summit of Mt Meeker at 13,911 ft. We left Ft Collins at 2:30 am, were on the trail by 4 am, were on the summit around noon, and back to the car at 3 pm. Why don't I feel like moving today?

I MET DALE!

2009-05-26T15:21:00.003-04:00

The best session beer in the front range is Dale's Pale Ale.

So imagine my surprise when I was at the new and improved Oskar Blues Brewery in Longmont. We were minding our own business when an "employee" showed up on a bike. My friend Terri visiting from Austin said "I think that is Dale". And I looked at him and doubted that he was indeed the Beer Baron. So just to prove her wrong I asked if he was indeed Dale. And he just said "Yeah". I had to get a picture.

Jason, I know you are jealous.

Magic Cyclooctane

2009-05-15T12:20:00.003-04:00

You've heard of the magic eight ball? Let me introduce you to the magic cyclooctane. Are you having trouble with your chemistry? Ask the magic cyclooctane and your question will be answered!

Just print it out and put it on another piece of paper. Put a thumbtack through the s-orbital in the middle and spin to get an answer.

Prebiotic RNA Chemistry

2009-05-14T10:16:00.004-04:00

An article scheduled to be published in Science today describes a route to the RNA nucleotides from simple precursors found on prebiotic earth. I read about it in the NY times (also here).

There are a few things that I thought were really cool about this. One, that there were actual organic structures published in a NY times article. As far as the science goes, this excerpt from the article was striking.

"The diagram above shows, in blue, the reaction that doesn't work and, in green, the new work-around.

"Working through all possible chemical combinations for 10 years, Dr. Sutherland's team discovered a different and quite unintuitive route. Their reaction system, shown in green, combines the carbon-nitrogen chemistry that leads to the bases with the carbon-oxygen chemistry that makes the sugars. They make a half-sugar/half-base (11), add another half-sugar (12) and then a half-base to make an intermediate (13) that easily becomes ribo-cytidine phosphate."

I guess what I thought was interesting was how scientists' nomenclature and classification of the chemical 'parts' of RNA, the sugar backbone, a base, and a phosphate group, stopped them from considering alternative retrosyntheses which don't involve these pieces and prevented thinking of alternate bond disconnections.

Finally, I thought total synthesis was bad. Imagine total synthesis where the only starting materials you have to work with are simple organic compounds known to exist 1 billion years ago on earth. Maybe that's why it took this guy 10 years to make something you can probably buy from aldrich.

hot twig action

2009-05-12T12:56:00.003-04:00

Now that I've beaten down my pile of journals I'm really going against my nature and keeping on top of them. This little beauty is from last year, but at least it hasn't been on my desk languishing for all that time.

People in general are into all sorts of weird shit, but as soon as the weirdness is something sexual it becomes taboo, and everyone wants to discuss it while denying any odd proclivities on their part. Perhaps not unexpectedly sexual deviation in the animal kingdom is rare, most likely due to a combination of lower occurrence and lack of documentation, but occasionally it shows up while some bio guy is there with a camera.

Science, 2008, 320, 591

The event went on for 45 min, which makes me wonder if it was at all like a bunch of guys sitting around watching a porn. 5-10 minutes of excitement, 10-15 minutes of discomfort upon realization that you are aroused when surrounded by nothing but people you can't/won't involve in any sexual activity, and then boredom until the event is over.

The stick business makes total sense though, who doesn't want some good lumber every now and then.

the wonders of palladium

2009-05-08T17:26:00.016-04:00

I've been making jewelry lately as a hobby. Right now I'm part way through a really nice ring for my girlfriend, and when I was designing the ring for her I figured I would make a simple band for myself too. I don't really like to wear jewelry, and certainly don't want something fussy or easily damaged, so simpler was better.

These days gold is hovering around $1,000/oz (using the bastard troy ounce and not the much more useful and common avoirdupois ounce) and platinum is somewhat higher. Kitco has a nice set of precious metal charts with both current and historic prices (www.kitco.com/charts/). Interestingly palladium is a jewelry metal that has some working properties that are similar to platinum, and this last year the palladium market took a shit, dropping to below $200/oz for a bit.

So when I ordered the metal for my lady, I got some Pd for me, to use when there was a lull in projects. As it happened the other night one popped up, and I had the bar of Pd with me at the time. I did a couple of simple operations to turn my little grey rod of 95.0% Pd into a flat bar to make into a ring shank.

I'm such a nerd I even make notes to myself as I'm working on recreational shit

I rolled it down a few more times, and then annealed it to ease the bending processes to come, and, wouldn't you know it, that little fucker blistered on me.

top view, one is on the left and one middle right

profile of other side of the bar

I'm a little pissed, since the thing is essentially ruined, but I've never worked with this metal before so I don't know if I fucked up or it was a bad ingot to begin with. Hopefully the company I got it from will help me out.

need tutors for electochemistery so importent

2009-05-02T11:51:00.002-04:00

Apparently there are some pretty sharp chemists in Wyoming. Here is an email I just got for MASTER level tutoring. From the subject line of the email I am under the impression that it was very "importent" that these students in "electrochemistery" get a tutor. I will let them make their case.

Dear
My name is Naha Al- habis and my friend name is Reeham we are MASTER student in chemical engineering we need a help to understand some problem in electrochemistry so which time do you have so we could come and ask you about it and we need an appointment as soon as possible bcoz we are from Laramie and we should hand in it in friday 8th of may and in monday and thursday we have an exam so plz give me a response as soon as possible.
Thank you

nerdiest thing ever a.k.a I'm really bored

2009-04-30T12:21:00.002-04:00

I have been spending my mornings taking care of Nora, and sometimes it can get boring. Luckily, I can steal internet from the neighbors. Since perusing porn is not an option, I opted for you tube. And I stumbled on a mash-up of Star Wars and organic chemistry. While the wisdom dispensed by Obi-Wan would not be of much use to graduate students and postdocs, I guess these tips could be useful for people taking sophomore organic.

I also found some inspiration in academia on you tube. I aspire to be as hip as this guy, even if he isn't really teaching his students anything.

reading. yay.

2009-04-26T19:19:00.003-04:00

I accidentally porked myself, and ran out of 2-propanol this week. When we ran low I sent in a request from stock, who happened to be out, and then put in a drop-ship order from Aldrich which hasn't arrived yet.

I'm in the middle of crystallizing and recrystallizing a couple hundred grams of compound, so I really don't want to start screwing around with something else. To utilize the time since I went dry on Friday until tomorrow I've been catching up on some sweet sweet reading. My massive pile of journals has really taken a hit this week.

Bet you didn't realize there was a speaker back there, did you?

In my little fantasy world, this pile will go away soon, and I will then stay on top of the reading in a more consistent manner. Unfortunately the pragmatist in me realizes it is much more likely that I will be so incredibly sick of reading this shit that I will let it pile right back up again.

Congratulations Colorado

2009-04-20T19:53:00.007-04:00

I would like to congratulate myself and my statemates here in Colorado for being so thin. Have a look at a map I stole from an article related to obesity drugs in a recent issue of C&E news.

And notice the only state that is blue (under 20% obesity) in the whole US in 2007. Forget obesity drugs, people need to get their fat asses outside.

awww ... that's so cute

2009-04-17T18:31:00.003-04:00

The dreamy P. S. Baran just published yet another JACS paper!

One of the things that I find amusing about this particular publication is that they very proudly proclaim "Gram-Scale, Enantiospecific Total Syntheses of Kapakahines B (1) and F (2)", and the whole scheme represents six steps. They even re-comment [gram-scale] under four of the six steps so you can be sure as to which are done on this huge, huge scale.

J. Am. Chem. Soc., ASAP

The other wonderus addition in this landmark effort is his new custom arrows! Those plain old arrows for schemes in ChemDraw must not have been up to his standards. I bet in the coming months those of you in academia will be deluged by student presentations using these jewels, and other similar knock offs. Another wonderful fluff addition (like the utterly useless chemoselective) courtesy of TSRI.

Well I'm off to work up my reaction. I had took 86 g of impure material laying around from prior runs of step 2. I figured I'd push it through in hopes of having > 1 g at step 7.

Pet Peeves

2009-04-16T10:40:00.002-04:00

Perhaps my biggest pet peeve is people ignoring traffic rules or more specifically people purposely violating traffic rules to be perceived as polite. An example of this that really gets my blood boiling is when someone is going straight or turning right but waves you through a left turn. Just go, then I can go. That's how it works.

Riding a bike makes this conundrum even worse. On my ride to work there are two 4-way stops, round trip = 4 4-way stops. In three cases I am going straight or turning left. I guess a lot of people don't understand the physics of how a bicycle works. It is much easier to resume the speed you were once traveling if you don't come to a complete stop. If another car arrives at the stop first, I start to slow down to give them time to continue through the intersection. But what typically happens is that they just SIT THERE and wait for me to come to a complete stop then wave me through. YOU ARE NOT HELPING ME ASSHOLE. Compounding this problem are the cyclists who ignore stop signs. HIT THEM.

That is all.

always use protection

2009-04-10T12:41:00.002-04:00

I was unpacking the day's Aldrich order, and I was amused and irritated by the onion like layers packing materials. These two 100 mL bottles of DCE were packages thusly: box, packing foam, mylar (sealed), box, packing foam, can, padding, pp or pe bag (sealed), bottle. That's 9 sweet layers of protection of various, and redundant, types. The packed product was about 8 cubic feet to contain just over 12 cubic inches of chemical or approximately 99.9% filler. I feel so safe now!

you know you're a chemist when ...

2009-04-03T13:13:00.001-04:00

I was walking to work from the Metro station and could hear a shitload of fire trucks and ambulances. All I could think was: "Please, please, please don't be my hood!".

I made a new natural product

2009-04-01T13:48:00.003-04:00

Nora Anne Miller

Nature Chemistry

2009-03-26T18:44:00.004-04:00

The Nature Publishing Group, which puts out such high quality journals as Nature and Nature Chemical Biology, has just published the first issue of their new journal: Nature Chemistry. The goal of this new journal is to be sort of like JACS without all of the shit. At least that's what I thought until I stumbled on this steaming pile.

P.S. Don't ask me what happens to the pyran double bond. They screwed it up.

incredible awesomeness

2009-03-26T11:24:00.002-04:00

In my experience it's pretty unusual to have a reaction that not only works well, it actually provides a more pure product than the starting material. I stumbled onto just one of those this week. I have several steps that have been worked out in the route I use and several others I've improved. This little beauty is one of the ones worked out for me, and it seems to be a doozy. I had never put material into the reaction that wasn't clean until last week. I had some residue from crystallizing the starting material that was mostly sm, but had several other spots. I submitted it to the reaction and came out with product that was almost as clean as the ones with clean sm!

To push the reaction a bit, and to try to maximized my amounts of material, I put a really dirty mixture of compounds in. Lane 1 is mother liquor from an 80 run of the prior rxn, lane 2 is similarly from a 40 g run, and has very little sm left in it, and lane 3 is them combined. Probably less than half starting material, but amounts to a wet weight of almost 100 g. I boiled it in acid overnight, and lane 4 shows the results of taking a drop and working it up. Not the most pristine thing, but pretty damned awesome nonetheless.

unadulterated sweetness

some people just can't count

2009-03-25T16:48:00.004-04:00

I have a huge sodium hydride reaction going today, almost 100g of 60% NaH, so I've been trapped in front of the hood babysitting all afternoon. It's really boring to stare at that reaction and make sure it doesn't vomit fort it's hateful contents, but is exceedingly preferable to the alternative.

While killing time in between additions I was catching up on some journals and saw this beauty:

Org. Lett., 2008, 10 (21), 4739-4742

I'm impressed by any significant amount of work that can be done in two steps, especially since they seem to add two distinct groups and deprotect in those two short steps. I flipped through the article to find the schemes with the method and its application and came to this:

Scheme 2 shows the appending of the steroid moiety and deprotection in 3 steps. I thought that was odd since they weren't doing as much as they supposedly would in the end, and had already exceeded the alloted steps. I read on and they show the application in scheme 3, and it took 4 steps to get it done. I flipped to the last page only to find out that was it. No more schemes, or discussion. The two step synthesis was completen in a paltry four steps. They were even kind enough to point out in the conclusion that they did indeed perform only two steps (highlighted in yellow), in direct conflict with the scheme. Apparently researchers in California can count vessels as steps. I wonder why they didn't go all the way and call it a domino or multi component reaction?

I also wonder how this made it past review.

yet more journals

2009-03-18T16:56:00.004-04:00

I posted about my pile of reading a while ago, and it has somehow gotten away from my pretty badly. I've tried to get on top of it, and even had gotten the pile to a somewhat diminished state versus its prior grandeur, but any ground I had advanced upon has been lost and then some.

Oddly none of them are that old. Some are several months old, but I don't think any are from before early fall (unlike my pile of C&EN in the shitter at home), and none have been on my desk for more than a month or two. It seems that I've gotten to the point where I can wade through a pile of dead trees this size every month or two now, but the people providing the pile have similarly advanced in their abilities.

I guess this is part of why I seem to have gotten so neurotic about keeping up with the ASAPs of the journals I actually care about. I'm afraid to get behind in yet another huge pile of reading.

fun with credit cards

2009-03-13T11:18:00.002-04:00

I got a new card recently mostly because of the 0% for the first year. A few days ago I got an email saying I could choose, or make, the image for the front of my card. My mind was awash with the possibilities of crude and insulting things I might use, but I figured it was too good to be true. I waded through the basic process until I got to the upload your own image part, which had "guidelines". As an aside it had choices of canned images to use and it automatically presented the most popular ones. It seems pretty stupid to me to want a "custom" image and pick one from a most popular list. Sort of like getting something labeled custom off the shelf at Target. The list of limitations cheerily described as guidelines removed all of my areas of interest rather rapidly, not unsurprisingly, but also has an interesting laundry list of shit that's seemingly unacceptable. No sex, violence, or copyrighted material, sure, but no Olympics? Two of my favorites are no competitive marks/names, and any photo that might result in non-acceptance or other problems at point of sale.

JACS Finally Redeemed Itself

2009-03-11T15:32:00.003-04:00

JACS sucks and I have commented on this before. This is how I usually read JACS: I scan through the abstract graphics and look for organic structures. If there are pretty nanotubes or clouds or lightning bolts or puzzle pieces, etc., then I skip it. That is until I stumble on an abstract graphic with a sperm cartoon.

So I read further. And these guys actually made this thing above so that they could release progesterone using light. You hit the compound with a laser and it releases progesterone. And you ask "Why is that useful and what is the deal with the sperm?" They used this technique to measure changes in the swimming pattern of human sperm in the presence of progesterone. That got me curious. Then this sentence at the end of the paper got me really curious.

"Supporting Information Available: Full experimental details, UV, 1H, and 13C NMR spectra, full characterization of all new compounds described herein, full experimental details of the
photochemical studies, sperm preparation, and biological measurements." Emphasis mine.

Yep. Sperm preparation. So I had to go to the supplemental info file. And here is how they "prepare" the sperm:

"Sperm Preparation: Human semen samples were obtained from healthy volunteers. Fresh ejaculates were allowed to liquefy at room temperature for 30–60 min. Sperm were purified by a “swim-up” procedure. About 2 ml liquefied semen was layered at the bottom of a 50 mL falcon tube, which contained ~ 4 mL of human tubal fluid (HTF). HTF comprised (in mM): 97.8 NaCl, 4.69 KCl, 0.2 MgSO4, 0.37 KH2PO4, 2.04 CaCl2, 0.33 sodium pyruvate, 21.4 sodium lactate, 2.78 glucose and 21 HEPES, adjusted to pH 7.3-7.4 with NaOH. Motile sperm were allowed to swim up in HTF at 37 oC for 60–90 min. “Swim-up” sperm were pooled and washed 3 times (900×g, 15 min, RT). Number of sperm was determined in a Neubauer cell counter. Washed sperm were resuspended in HTF containing 4 mM NaHCO3 and 3 mg mL-1 human serum albumin (HSA) (Irvine Scientific, USA) (HTF++) at a density of 2 × 107 mL-1 This sperm suspension was incubated for 2-3 h at 37 oC and then used for further experiments."

You think organic chemistry sucks. Imagine having to purify some "healthy volunteer's" sperm. And since when is a fresh ejaculate not "liquified" at room temp?

perhaps the best shirt ever made

2009-03-08T20:47:00.004-04:00

I went to Boston this weekend for Chi-Li's wedding, which was pretty awesome. Of course during the ceremony, after the usual boilerplate, when the preacher turned to Chi-Li and said "Chi-Li ..." he was immediately cut off by Chi-Li's "I do!". Everyone laughed, I wished I had been filming it instead of just taking snapshots, the preacher played it off well, with an "OK!", and then continued on with the more proper sequence of incantations. It was a very Chi-Li moment.

After the reception, which was also awesome, a bunch of us took off for the real reason people go to their friend's weddings, drinking with your buddies. Among the many people in attendance was Rich whom I hadn't seen since the fall ACS last year. He surprised me with a shirt he had bought at a concert quite a while ago. The shirt was so awesome, he had gotten one for himself and another for me, and waited all this time to surprise me with it. To say the least it's absolutely incredible. Words hardly do it justice.

Breaking Bad

2009-03-04T15:22:00.006-05:00

If you haven't seen Breaking Bad, you must put this on your netflix queue immediately. The first season just came out on DVD, and I watched all seven episodes in two days. The next season just started, and this is perhaps the only reason I would consider getting cable.

If you are not familiar with the show, it is about a mild mannered high school chemistry teacher/chemistry badass who finds out that he has terminal cancer and decides to cook meth to leave his family with a means to support themselves when he dies. He quickly generates a buzz, since his chemistry skills enable the manufacture of an extremely pure product. There are a number of sweet chemistry references in the show, and I won't mention them here because I don't want to spoil it for any of my three readers.

The show is based in "scientist 1's" hometown of Albuquerque, New Mexico, which provides for a stunning landscape in which to cook meth. Enjoy!

nitpicky bullshit

2009-03-02T08:53:00.007-05:00

I didn't make it all the way through my ISI alerts on Friday, so I'm trying to finish them up now and I actually found one that was worth keeping and had some good references. In general I only read chemistry journals, except when a good article is presented to me from a non-chem source like this. Most chemical journals follow similar formats of footnote/end note so I'm not too familiar with other styles, but I do realize they exist. On days like today, however, when I get exposed to other formats, I wonder why.

Here is, I can only assume, a successful and popular format I stumbled onto today from an Elsevier journal Toxicology. Early on it the paper I found some refs that looked like they might be worth fetching and saving:

Handily linked, but the link only takes you to the endnote. Wow, way to use technology to the utmost. Anyway, I went to the end of the article a little surprised there was no number, but knew that some people like to have no reference numbers. I can't guess as to why that would be a good thing, but I don't publish in those journals, so it's really not my problem or concern. I get to the end of the article, and the 4 references I want are in 4 different places on 2 pages:

Now THAT'S convenience! It appears that they are in alphabetical order, which makes sense, but they're still all over the place. I had to flip back and forth from the front to the back every time I looked up the new paper due to my weak memory and inability to remember the names for any length of time. Luckily only one guy was referenced more than once, and the papers were in two different years. I had wondered why the body references had no reference number, but did have a year. I still am not sure what would happen if you had to reference some sort of super stud who published in your field many, many times per year every year. I think the reader would be forced to just get every reference listed and see which was important. Obviously much better than having them individually numbered.

The actual end notes themselves are rather poorly constructed as well:

I went to look up J. Pharmacol. and after not finding it (actually saving me quite a bit of time) re-examined the ref to find that it was actually Br. J. Pharmacol. The incredibly clean lines of the formatting free text had slid right over my brain like a chamois leaving nary a residue. Once I had the journal correct, I glanced back to find the year and had to re-read the whole thing again to realize the year is buried with the authors, before the title. How nice. To make the footnotes somewhat discernible from each other so you can find them in the document's jumbled entrails, they moved the year away from it's surrounding info.

All of this to get the lovely benefits of "Singhal et al., 1999; Boronat et al., 2001; Hatsukari et al., 2003; Kapasi et al., 2004" vs "⁵".

Accepting Submissions for the Worst Named Reaction

2009-02-25T12:38:00.004-05:00

Usually, in my extensive experience, named reactions work pretty well. I mean they wouldn't be famous reactions if they worked like shit. Right?

That brings me to the Reimer-Tiemann reaction. This thing sucks. In my particular case, the reaction was a complete disaster. Here is a generic version of the reaction if you are not familiar with it (everyone out there except Jason).

In an effort to optimize this reaction, I consulted a recent review. Here are some of the accolades from the article.

"Even 105 years after its discovery, conditions for the Reimer-Tiemann reaction cannot said to have been optimized. This is not too surprising for a reaction in which a quantitative yield has never been reported, and in which useful yields of 3-10% are not unususal."

Nice. I guess I should have consulted this before embarking on a route invoving the "Reamed"-Tiemann reaction. Any other suggestions for the worst named reaction?

Talk About a Mad Scientist

2009-02-16T18:11:00.004-05:00

Carl Djerassi is pissed.

I don't think that you want to piss this guy off. For a chemist, he looks like he could kick some ass. He is pissed because Trost failed to reference the isolation of bryostatin in his recent Nature paper on its total synthesis. I'll let Carl speak for himself:

"who isolated the bryostatins? Who established their structures? Who initially pursued their anticancer activity? Without these achievements, the synthesis would simply constitute chemical acrobatics that never would have been accepted by Nature.

These decade-long efforts by G. R. Pettit's group at Arizona State University are concealed by reference to a generic review article authored by others. There are a couple of "et al." references that also mask Pettit's name. This demeaning treatment of the key work of earlier investigators in the field of natural products by chemists who then undertake the total synthesis of the molecule in question is unfortunately all too common—either because of sloppiness or as a discreet attempt to eliminate any reference to the initial discoverers.

Trost's treatment of Pettit is particularly egregious given the well-known fact in the chemical community that the spectacularly laborious decade-long efforts of one of the heroes of marine natural products chemistry—the person who personally collected the bryozoan, isolated the bryostatins, established their constitution, and pursued their anticancer activity against all odds—were terminated through a draconian closure of his laboratory by the new administrators of Arizona State University."

I love organic chemistry pissing contests. I think that Djerassi could definitely kick Trost's ass. And when was the last time Trost developed a drug that 100 million people use daily?

no love for Barry, sorry Mike

Maggots, Fly Eggs, and Rodent Hairs

2009-02-14T16:57:00.003-05:00

Sounds delicious!

YUM!

We can thank the FDA for our yearly intake of about 1-2 pounds of this delicacy per year. I was recently enlightened about the FDA guidelines relating to bug parts in various foods. Here are some real "limits" on shit that is allowed in your food.

"Tomato juice, for example, may average “10 or more fly eggs per 100 grams [the equivalent of a small juice glass] or five or more fly eggs and one or more maggots.” Tomato paste and other pizza sauces are allowed a denser infestation — 30 or more fly eggs per 100 grams or 15 or more fly eggs and one or more maggots per 100 grams.

Canned mushrooms may have “over 20 or more maggots of any size per 100 grams of drained mushrooms and proportionate liquid” or “five or more maggots two millimeters or longer per 100 grams of drained mushrooms and proportionate liquid” or an “average of 75 mites” before provoking action by the F.D.A.

The sauerkraut on your hot dog may average up to 50 thrips. And when washing down those tiny, slender, winged bugs with a sip of beer, you might consider that just 10 grams of hops could have as many as 2,500 plant lice. Yum.

Giving new meaning to the idea of spicing up one’s food, curry powder is allowed 100 or more bug bits per 25 grams; ground thyme up to 925 insect fragments per 10 grams; ground pepper up to 475 insect parts per 50 grams. One small shaker of cinnamon could have more than 20 rodent hairs before being considered defective.

Peanut butter — that culinary cause célèbre — may contain approximately 145 bug parts for an 18-ounce jar; or five or more rodent hairs for that same jar; or more than 125 milligrams of grit.

In case you’re curious: you’re probably ingesting one to two pounds of flies, maggots and mites each year without knowing it"

La Clair hexacyclinol, again

2009-02-13T13:08:00.003-05:00

A few years ago James La Clair published a synthesis of hexacyclinol, and it was immediately met with skepticism. Rychnovsky studied the NMR data for the natty-P and others and via comparison proposed a new structure, that was eventually made by Porco and proved to be both the compound in question, and have the Rychnovsky proposed structure.

La Clair commented in Nature: "La Clair now says that he and Porco may have made two different molecules that happen to have very similar NMR spectra."

As far as I know La Clair has not done any more in this area, to defend himself or otherwise, which is odd considering he claimed to have more than a gram of the material in question on hand.

Today in Org. Lett. a paper came out specifically examining this problem of the different compound-same NMR spectra issue.

Org. Lett. ASAP

Where 2 is the Rychnovsky proposed correct structure, and 1 is the original La Clair claimed structure.

This seems to me to be a lot like backhanding La Clair right in the face while calling him a bitch.

That and flogging a dead horse.

I shouldn't post this

2009-02-12T17:58:00.002-05:00

I have a feeling this post is a bad idea, but I have a few things a need to get off my chest. As a grad student, I had an idea of how science is done. People do work in the lab, write up their impeccable results, and then submit their work to a peer reviewed journal. Once in the journal's hands, the editor sends the paper to a number of the author's "peers" who evaluate the paper closely for scientific merit. Once these peers decide that the science described is accurate and important, they accept it. If not, the paper is rejected. As the three loyal Mad Scientists readers know, that idea is purely fiction.

Here is what really happens. Often, incompetent people do sloppy work and then submit it to third rate journals in a language that barely resembles English, and the paper is accepted and published with virtually no peer review. Why? Because these idiots work for a boss who has to publish to get funding and promotion, and third rate journals have to publish something.

Why do I care? Because I keep getting these horrible papers from my boss who is the one who is supposed to be peer reviewing them. He just cut-and-pastes my comments to the editor and as a result his workload is greatly diminished. But I have to read this crap and today I've had enough. While I guess this stuff is supposed to be confidential, since I was not formally told that, I have decided to post a slightly edited to protect the innocent version of my comments to the editor of this prestigious journal. Enjoy!

"While the science is sound, the language used to describe the work is difficult to understand and rife with grammatical errors. I count at least 15 examples in this brief manuscript where the authors have left out an essential article, such as a, an, or the.
For example:
- …XXXXXs operate through Zn-dependent mechanism.
- …there is urgent need for more useful drugs.

In many cases, singular forms of words are used where plurals are required.
- XXXXXs are well validated anticancer target.
- The choice of cap groups was based on the XXXXXs previously reported by us and other group.

In other cases, a complete sentence is almost impossible to understand.
- We also investigated the ability of this set of compounds to block the cancer cell growth as their potential utility in cellular level with the special attention towards pancreatic cancer.
- The results have impinged upon cancer drug discovery research, predicting the restriction of the use of isoxazole moiety near XXXXX catalytic region.

I cannot accept this manuscript for publication in its current form. The work should be rewritten with a critical eye focused on the myriad grammatical errors and cumbersome language. The peer review process is essential for the dissemination of important and timely scientific knowledge. I am proud to review the work of my colleagues, when I feel they have spent an ample amount of time on the finished product. However, when insufficient time is spent simply proofreading a manuscript, then my time is wasted reading an unfinished product. In order to conserve everyone’s limited time, I encourage the authors to proofread their work prior to submission in the future."

Blue Ice

2009-02-10T13:38:00.008-05:00

Why does some ice look blue?

and some ice looks white?

It turns out that it all has to do with the frequencies of light absorbed by water molecules. The vibrational modes that are absorbed by the O-H bonds in water fall in the red end of the visual spectrum. So water absorbs red light and blue is transmitted. But we only see it if the ice is sufficiently thick and the light is passing through the ice so as to absorb more red and transmit more blue.

For once, vibrational spectroscopy is useful.

more great proofreading errors

2009-02-04T00:07:00.003-05:00

I was flipping through that paper based laxative C&EN this morning on the train to work, and this caught my attention from the corner of my eye. I don't know if seeing errors readily means I'm becoming better at my job, or the asshole I always swore I would never be, but it seems to happen a lot.

look off to the right there

For people who don't know what the error actually is, it's a subtle, but very very important, mistake. When I got in, I showed it to a South Korean Professor that is here in the lab on sabbatical, and he said "Wow, they should get the Nobel prize!", then winced when he recognized the company as South Korean, and then quietly cursed under his breath. Once a prof, always a prof.

finally!

2009-02-02T14:03:00.002-05:00

For years now I've wished there was a good science spelling dictionary in MS Word, and have even had discussions about how MS has really dropped the ball be essentially having no science/engineering version available. I've used the add feature in Word to build my own, but it's tedious and every now and again the custom dictionary file ends up getting lost or erased when a major incident takes place or I swap/upgrade computers. For some reason I never remember to back that shit up.

Azmanam, an enterprising grad student, went to the effort to create his own decent list, he developed it and collaborated with Antony Williams of chemspider.com to further increase the volume to ~104,000 words!

If you want this little gem go to www.chemistry-blog.com/dictionary, read about it, and download it.

I tried the instructions included in the zip, and some of the tips on the site with no success. Being trapped with a relatively old Mac at work is not helpful some days. To work around the issue, and greatly simplify things, I opened the new file and the existing custom dictionary, copied the contents of the new file, pasted into the old dictionary, saved, and was done.

Chinese Martial Arts

2009-01-28T17:16:00.001-05:00

His royal highness, Dr. Hui Li, has directed me to some "exciting" new Chinese marital arts moves. I hope you enjoy!

Sunderhaus Sighting

2009-01-25T12:52:00.003-05:00

The Fort Collins community is abuzz due to the recent alleged sighting of the illustrious Jim Sunderhaus. Accounts differ, but a number of unrelated sources have confirmed that Jim was indeed in the area. We have it on good authority that Mr. Sunderhaus will be permanently relocated to the Fort Collins area in the next few months. The Williams group will never be the same.

a picture of Jim in his native habitat