Wednesday, December 1, 2010

Rochelle's salt

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.

Sunday, November 28, 2010


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.

Thursday, October 14, 2010

art in science

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!

Tuesday, October 12, 2010

shit like this amazes me

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.

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.

Monday, October 11, 2010

what? I don't get it

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.

Sunday, September 12, 2010


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

Saturday, September 4, 2010

ACS goodness

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.

Friday, September 3, 2010

konami code

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.

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

Thursday, August 26, 2010

JACS awesomeness

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"

Thursday, August 19, 2010

new position

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?

Sunday, August 15, 2010

that's ... cute

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

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.

Thursday, August 12, 2010


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.

Monday, August 2, 2010

public works

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.

Monday, July 12, 2010

periodic awesomeness, fuck yeah!

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.

Friday, July 2, 2010

now that's GLOBAL deprotection

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:


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.

Friday, May 21, 2010


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.

Sunday, May 16, 2010

that looks familiar

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.

Thursday, April 1, 2010

graphical abstract flub

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

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.

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.

Friday, March 26, 2010

nice legs

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!

Monday, March 15, 2010

nice drawing

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.

Sunday, March 14, 2010

Friday, February 26, 2010

The most useful thing Nicolaou has ever done

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.

Friday, February 12, 2010

Thursday, February 11, 2010

wild weather

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!

Saturday, February 6, 2010

snow, glorious snow

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

Friday, February 5, 2010

storm watch 2010!

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!

Friday, January 29, 2010


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.

Wednesday, January 13, 2010

that's the key 2

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.

Monday, January 11, 2010

that's the key

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.

Friday, January 8, 2010

what kind of horseshit is this?

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.


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