Elemental analysis

What analytical data are necessary to characterize a new compound in organic synthesis? In the times before NMR, melting points, elemental analysis and IR used to be the available methods (and UV, if applicable). Nowadays, EA isn’t required by the journals anymore andv IR is probably going to disappear soon. Additionally, the significance of melting points is quickly decreasing because mostly people take the product as it comes off the column without recrystallizing it. Are we losing something there?

A number of people argue that the ability to get crystalline compounds is essential to be a good chemist, so recrystallization should always be done if possible. As a reward, you get EA-pure solids that are also easy to handle and may give you the occasional X-ray crystal structure (if you want to grow crystals). On the other hand, an additional effort is required: you need substantial amounts of material, which is no problem in a short synthesis, but can be a problem if it takes twenty steps to get to the product. If I have tediously made 50 milligrams of a material, I don’t really want to give ten away to be burned.

I wonder if elemental analysis is still a necessity today. In most cases you get all the information you need from NMR (identity and purity). What EA gives you is confirmation that your compound is pure as well as dry. Still, is it worth the trouble or just a waste of time? I suppose it all depends on the kind of research you’re doing. If you are “target-oriented”, as medicinal chemists like me are, I do not think it is worth it, as long as the final compounds being tested are pure. I suppose this is being sloppy, but I want to get a series of compounds in a reasonable amount of time. It might be a bit different in a total synthesis project, where the focus is on the pathway rather than the target compound per se.

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Is convenience costing chemists? Part 1

Times are tough and few if any are untouched by the recent economic woes. While profits have fallen, research costs for a variety of fields have remained the same if not increased, especially in the chemical industry. Academia too is feeling the crunch and many universities are making policy changes to minimize expense. At most universities, chemistry is usually the department hardest hit by budgetary strangulation for the simple reason that doing chemistry often comes at a hefty price (I.e. reagents, apparatus, instrumentation maintenance and standards, heating/cooling expenses due to fume hood usage). Many chemistry departments burn through consumables, most of which are not exactly cheap. Unfortunately, even in the present age of microscale labs and experiments, there is still a significant amount of waste both in industry and in academia with respect to energy and research material. Thankfully, there are many simple solutions that involve a little extra time but pay dividends.

Progressive steps are being made. An example: at a nearby university, the chemistry department is implementing an energy saving program, modeled on an existing program at Harvard. It is being done because heating and cooling the chemical building is expensive, and energy costs have risen. According to the Harvard program’s estimates, leaving a typical fume hood (whatever that may be) wide open 24/7 all year long uses three times the energy of an average home! Now reflect upon how many fume hoods are in your laboratory.

For my part, I hope it doesn’t stop at simply closing the sash–there are numerous other things that scientists ought to be doing. Still, it’s a start. For those of you thinking “well, we itemize our budget to account for energy, consumables, and other ancillary costs. We have the money,” you might analyze it from a perspective of using only what you must. Considering that Harvard’s 30 some billion dollar endowment is the largest of any university and they somehow find the moral responsibility to simply close the fume hood sash when not in use, is it not something all chemists ought to do? Surely they can afford a few hundred thousand dollars per year for the convenience of forgetting to close their hood.

Pinching pennies is important now, historically, and probably more so in the future. Scientists pay for convenience. Many research in an atmosphere of high throughput, intensive research with demanding deadlines. For most chemists, it’s a simple matter of putting in a purchase order for the reagent you need and paying through the nose on hazmat, fuel, and packaging surcharges to have it overnighted for your trial synthesis. Easy? Yes. Cheap? No.

So, what to do?

In the next installment, I’ll discuss a few commonsense ways to save money, possibly a few natural resources, and most importantly, time.

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Cold Fusion Has Its Press Conference

Jeremy and I scored press passes to the recent Cold Fusion Press Conference at the ACS 2009 Spring Meeting. Unfortunately for them I’m a nuclear chemistry PhD student. Jeremy did a quick wrap-up of the press conference,^[CB] but I thought it would be useful to have a critical chemist perspective of their recent announcement. The press conference did nothing to address the violation of the most elementary of chemistry and physics that I painstakingly explained in this old post titled “The difference between cold fusion and cold fusion“, but I’ll move on to address their statements.

As this was a press conference and not a scientific talk there wasn’t any data that I can point to as evidence for a cold fusion claim. However, we can tear some sanity from their own words. I asked why they haven’t observed any gamma rays from their cold fusion experiments. Pamela Mosier-Boss was quick to reply that they indeed did measure gamma rays, but they “came in bursts… and are averaged away [over the duration of the experiment]“. Dissect that statement and reflect on it as a scientist. Think to yourself: “Hmmm… clusters of peaks coming all of a sudden but randomly”, “Hmmm… as they run the experiment they see these peaks average out?”, “What does this mean?”. You don’t have to be a spectroscopy expert to figure this one out. The answer is simple, they measured background. Background is a random process, it will come in bursts, they may even cluster to make a peak for a short time, but when you run it over the course of the whole experiment it is “averaged out”; that my friend is background you measured.

At an other point of the conference Mahadeva Srinivasan claims to be able to measure tritium, neutrons, and other ionizing radiation not by actually measuring them, but indirectly from looking at his electrodes and observing craters and holes and trying to ascribe the radiation that caused it. Sounds sort of reasonable unless you’ve ever done any electrodeposition, which is what the process he described would yield if running current through a wire. Here is a picture of an electrodeposited layer of europium oxide my fellow colleagues made in the lab.

You can see craters and valleys in the image. I hope their electrodes didn’t look anything as awful as this, but you can see for yourself that electrodeposition can create ugly surfaces. Which was a major reason for the Thin Film community’s move away from electrodeposition and embrace of Sol-Gel techniques, because it causes less cratering and produces homogeneous and uniform films.

So should I believe the claims of a scientist who does not understand the difference between background and peaks? Should I believe a scientist who doesn’t understand the basic consequences of his own technique? You don’t even have to be a nuclear chemist to call bull-shit on this one.

I want to end this on a positive note, because I’ve spent a lot of time hammering these cold fusion people over the years. Honestly, if they are measuring more energy out of their systems than the energy they are putting in, then this is fantastic news. If they see excess heat, then they need to chase this line of inquiry down. But nuclear fusion is not the right path. I truly want to believe these people are capable of measuring the amount of energy in their system versus the energy out correctly. But the electrochemistry they are performing is non-reversible and that makes energy accounting, in their dynamic system, a very difficult mess. The simple act of having gas bubbles float from your electrodes will deposit more energy into your solution, due to friction, then you would expect. And frankly, after listening to these people talk for 45 minutes I don’t believe they are capable of correctly accounting for energy in a dynamic system.

Mitch

P.S. Make up your own mind, a link to the press conference is here, Cold Fusion Press Conference. I ask my question around the 28 minute mark. Aaron Rowe from wired science blog is now my favorite science journalist, his question is asked at 34:50 minute mark.

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The Name(ing) Game

Cheryl Hogue’s recent piece entitled “Naming What’s in Cleaning Products” caught my attention earlier this past weekend (C&EN, February 23, 2009).  Cheryl does a great job covering the interface of chemistry and the environment—hitting the high points while remaining concise—and the brief article in question is no exception.  However, the issue at hand was rather concerning.

In a nutshell, activists from an Oakland-based firm called EarthJustice recently filed a lawsuit in New York State demanding that several manufacturers/distributors disclose ingredients on the label of their household chemical products (detergents, cleaning agents, etc.).  Companies named in the lawsuit include Church & Dwight, Colgate-Palmolive, Procter & Gamble and Reckitt Benckiser.  The suit accuses manufacturers of failing to comply with a New York law that was enacted over 30 years ago.  The legislation at issue was passed in 1976 and makes two specific requirements.  First, the law essentially bans the presence of phosphates and nitrilotriacetic acid in household chemicals sold within New York State.  Second, the law requires household chemical manufacturers to stamp a list of ingredients onto the labels of their products.  From what I understand, this act was implemented to protect the overall environment of New York State (from urban areas to surrounding watersheds).  Ultimately, EarthJustice claims that forcing companies to comply with the law purportedly will increase public awareness, which, in turn, will help the environment

The lead attorney for EarthJustice, Keri Powell, made this argument to C&EN:

“People deserve to know whether the products they use to wash their dishes, launder their clothes, and clean their homes could be harmful.” 

I’m skeptical of this argument/lawsuit for a couple of reasons.  First, if this law has been dormant for the past 30 years, why is EarthJustice now pushing the issue?  Was New York State asleep at the wheel?  Isn’t this something that should’ve been handled by the EPA?  I realize environmental awareness is a hot topic and a popular vehicle for political action.  While the act of suing over labels to protect the environment is (in my mind) illogical, I am troubled over whether the issue is truly legitimate or a way for an unbiased organization to grind a political act (yes, I’m being cynical and possibly paranoid). 

Second, and more concerning, Ms. Powell (and her colleagues at EarthJustice) assumes that proper labeling will, in fact, increase public knowledge.  Her assumption is entirely conditional (certainly not sufficient) on whether or not a reasonable consumer would understand what they read.  Example: my mother is obsessed with the product Goof Off and has two cans of it on hand at any given time.  However, if Goof Off was labeled with its ingredients, she couldn’t tell you the first thing about xylene (the main chemical in Goof Off).  It took her strapping, young (and most definitely handsome) son to explain the potential risks of using such a product.

Don’t get me wrong.  My diverse background in hard science has taught me two very important lessons: learn as much as you possibly can and label everything.  Consumer chemical awareness requires the same conditions, and simply forcing a company to slap a label on something doesn’t solve the problem.  In my mind, the issue of chemical awareness is similar to the “ban dihyrogen monoxide” prank conducted a few years back.  Without education (i.e. learning what the chemicals names actually mean), this proposed labeling crusade is largely irrelevant. 

Furthermore, chemical information is readily available (assuming you or your public library has access to the internet).  While there are a few exceptions, every chemical product (including those used at home) must have an MSDS, which can be found online.  Every MSDS identifies the chief ingredients in said product.  Granted, MSDS’s were created for the purposes of right-to-know information in industrial/commercial settings.  But, in my opinion, if John Q. Consumer can read a label, he can certainly read an MSDS.

I salute EarthJustice for all the work they’ve done to protect America’s environment.  Their commitment to public interest is genuine and deserves applause.  However, I think they are barking up the wrong tree with this lawsuit—dragging a whole bunch of companies through expensive court process to get something to happen that’s relevance is moot (at best).  My solution?  Shift the focus.  For example, serve the public’s interest by teaching them how to access/read/interpret chemical information.  Or educate the public on how phosphates are detrimental to the environment.  Lobby politicians to entirely ban certain household chemicals in the state (beyond the ppm limits currently set). 

Let’s assume EarthJustice wins the lawsuit.  What happens next?  Maybe it’s me, but I don’t see an end game in sight.  

P.S. In addition to C&ENews, this story has been picked up by Scientific American, the New York Times and the Los Angeles Times.

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I’m dumb, but it’s okay!

So like most grad students, I’ve been feeling extremely retarded lately. Experiments are giving me weird (and quite repeatable results) that throw a wrench into my understanding of what I’m doing, I’m ending up with different products from the same synthesis, and I’m getting all types of twinning (tropochemical, pseudo-merohedral, etc, etc) in an allegedly ’single’ crystal. In other words, I feel dumb.

However, after commiserating with my fellow grad students, and eventually with the parental units, I was lead to an interesting article published way back in the day in the Journal of Cell Science.

The importance of stupidity in scientific research

It definitely made me feel better, and I’d like to add some things that my dad (who was once a grad student and is now a chemistry prof as well) told me.

If you dont feel stupid every now and then…
1) …you’re not picking the ‘right’ research question
2) …you’re not working hard enough to get results that stump you
3) …you really dont understand enough about your project
4) …you’re way too arrogant and belong in business school instead (no, he really didnt say that)

But, he did add the caveats that you did need to feel smart and accomplished every now and then or else you just dont know what you’re doing (it goes along with #3)

so to everyone out there who feels dumb on occasion from their research, remember, it’s okay! Just keep on truckin!

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So you’re thinking about graduate school…

First off, I’d like to congratulate noel and everyone else who has gotten into graduate schools thus far. Considering the economy, applications are up and it’s even more competitive than ever. However, I have had some friends get rejected and start to freak out, which is of course, natural, and I asked, why do you want to go to graduate school?

I got the response: I want to be a professor. Okay, I said, of what? Um..a research professor, she said. Okay…why?

The pause really didnt come to me as a surprise. Yes, the economy is bad right now. However, graduate school should not be looked at as a way of escaping the real world. Grad school is hard, you will feel stupid, you will be frustrated and there will be multiple times you want to quit.

But, but..Boyie, I <3 chemistry. Bull. Crap. Maybe 1% of the people in graduate school love chemistry. People have multiple reasons for doing it, and most dont involve loving chemistry, but the thing is, most people who eventually succeed have /STRONG/ motivations to do it.

But, but…Boyie, I’m smart, isnt graduate school the next logical step? Again, I have seen LOTS of smart people drop out. Why? Various reasons such as “I just didnt think it was right for me”, “I felt stupid”, “I dont want to spend 5 years working on the same problem”, and “I just dont like research.” All those answers are things that could have been avoided. I am fortunate enough to attend a prestigious program and I know people would kill for the slots that have just opened up as a result of people dropping out. So really, think about why you want to go to graduate school.

When I was applying, my father and my undergraduate research advisors asked me the following questions as a reflection of sorts to see if I had the strength of will to make it. So, I present to you, the questions I was asked.

1) Why chemistry?
2) Why graduate school?
3) What do you see yourself doing in 5, 10, 15 years?
4) Is a PhD really required for that?
5) Again, why graduate school?
6) What do you like about research?
7) Name five influential people in your chosen field.
What did they do?
9) What do you want to contribute to science?
10) What do you want to contribute to chemistry?
11) Are you okay with feeling stupid?
12) Are you okay with slamming your head against a wall?
13) Finally, why graduate school in chemistry?

Yes, there were 13 questions, three repeat, but looking back on it it’s a very important question. So, for those of you about to enter, I highly recommend doing this exercise. Be honest with yourself for the answers, and g’luck!

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Do Big Dollars Affect the Little Guys?

D-Lowe certainly beat me to the punch this morning, but in my defense, I was working on a time-sensitive reaction in the lab when I heard the news. 

In the midst of economic turmoil, an interesting deal has been proposed—one that hits home to a lot of R&D chemists.  Both Bloomberg and the WSJ are reporting that Pfizer is in talks with Wyeth to merge the two companies for an estimated $60 B.  The rumor, among several media outlets, is that Pfizer’s backup plan is to buy Bristol-Myers Squibb or Amgen should the Wyeth deal sour. 

Recently, both companies have had their fair share of time in the media spotlight (apart from the proposed merger).  As reported by Chemistry World last December, Wyeth announced it would revamp its R&D business model by minimizing the number of major areas of therapeutic research while retaining the same research budget (c. $3 B).  Wyeth plans to focus on the following 6 areas: oncology, central nervous system, vaccines, musculoskeletal, metabolism and inflammation.  I can tell you (from my experiences in pharma) that it’s a better strategy put 20 researchers on different aspects of one project (a concerted effort) versus working in 20 different directions.

Meanwhile, in DC, the USPTO recently agreed to allow Pfizer to “repair” its invalid patent for Lipitor thus gaining US exclusivity until 2011 (more details here).  By the amount of revenue generated in sales ($13 B in 2007 alone), Lipitor is considered the best-selling drug in the world.  For whatever it’s worth, the controversy was sparked by the challenge and subsequent rejection of one of Pfizer’s prized patents in 2004.  Essentially, exclusivity keeps the cash cow alive for another couple of years while other therapies are pushed through the FDA.  You can find a more detailed description here.

While the deal may be good for Wall Street, I fear that it may do more harm than good, especially in the world of chemical employment.  As someone who’s currently hunting the job market (and watching several of my peers do the same), I see shrinking job opportunities in pharma.  Often, as two large companies merge, it’s usually followed by a period of hiring freezes (there become a lot of replicated jobs) then the new mega company begins to tighten the belt by cutting spending and laying off thousands of employees.  

I hope we can all make it through these shaky and uncertain times.

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Chemical Edutainment and Undergrad Labs

So it’s me, the writer of solidasarock, and well I’ve joined the chemistry forums blog team. Studying for qualifiers have been awful, so writing has been almost nonexistent, but with finishing off TAing and watching the first years teach lab and hearing their complains that were oh so similar to mine last year, I thought I’d tackle something that’s really prevalent in some chemistry departments, particularly, my department. And that would of course me chemical edutainment.

<insert 2 cents>

I had the privilege of teaching freshmen, juniors, seniors and graduate students in my TA load, and seeing how things were run here versus my undergrad alma mater is disappointing. Back in my alma mater, experiments were ‘boring’. We didnt go into the latest nanotechnology, but we did go over very valuable experimental techniques. Twenty-thirty titrations in the first semester lab alone was enough to drive one insane, and the qualitative analysis freshman lab of having to figure out what ions were in a mixture was difficult for us fishies. Then of course, there was our ‘reward’ lab where we synthesized YBCO and then did a iodometric titration to determine the oxygen content, and then lots of other random labs that, while ‘boring’ to the students, showed important concepts that helped us conceptualize concepts.

Let’s compare that to my new department. Freshmen here do not do multiple titrations till they die. They dont even determine the concentration of their titrant in a standardization. Here, they do one titration, and do it using a pH meter. We didnt use a pH meter in undergrad until junior year for our titrations since we had to get a feel for the end point before hand. From there, they move onto ‘ubersexy’ labs, such as the synthesis of CdSe nanoparticles, Au nanoparticles. Did they at least characterize these NPs? They did one UV-vis, didnt really get told what was the significance and then were told to move on. Then later they had experiments that had very little chemistry in it at all.

I remember asking why these labs were taught, and I was repeatedly told about the ‘educational value’ of them. They were short writeups with barely any real analysis for the students. I chagrined and did my duty as a TA and taught them the best I could, inserting concepts, that while tangentially related, would actually be covered on their exams. Needless to say, my students complained at the extra work I had ‘assigned’. So writing down a few questions and having them answer it as part of their lab report was making me into a tyrannical despot. My evaluations were crappy, and I had learned my lesson.

I then spoke with one of the lab coordinators who told me about the consumerism of undergrad. We, as the TAs, are the product, and of course, the customer is always right. Of course! They pay $ money to attend this fine institution, but if they arent getting actual quality and instead get frou frou labs that teach them little but keep them entertained where is the value?

Now this sounds like a rant. Where is your proof? Like I said, I also got to teach juniors and seniors later on in the year, and I, to my dismay would find my proof there. Here are a bunch of chemistry juniors and seniors. I was explaining the quantitative analysis lab, and asked if they had done serial dilutions before. Nope. No one had done it. Unless they were a lackey in a biochem lab and had to do serial dilutions all day for their grad/postdoc mentors. Come on, at the junior/senior level, serial dilutions should be a snap. I explained the concept, showed them how to do it, and in the end, I was still asked by juniors and seniors to whether they could get micropippeters to dilute 1000x in a 100 ml volumetric flask.

I was dumbfounded. I was aghast. I wanted to rant and rave, but I kept it in. I taught them what they needed to know and went over the concept again. I had asked if they had covered it in organic lab (since I didnt get to teach that), and they said no. I knew the freshman curriculum, and I know it wasnt covered there. There were these chemistry majors, almost ready to graduate, not knowing very basic experimental skills.

So I was on fire and wanted to teach hardcore again. I went into other concepts that tangentially related, were still useful, and that they could use the information. A lot of them were happy at the knowledge, some werent. Then fast forward to another lab. These were the same juniors and seniors. I had assigned all the questions in the lab, but some were deemed too difficult. They saw no point in those questions. Needless to say, they went to my lab coordinator and complained to their hearts content.

I had a serious talking to again. Once again, they were right, as the questions were too hard. Of course, I didnt say at this point that the lab coordinator had written the lab completely and we both deemed prior that the questions were of the right difficulty and should be good for juniors and seniors. Since I was no longer entertaining them, since I actually went from ‘nice guy TA’ to ‘no, you need to answer these questions’ I was evil. I was a bad TA.

I was distraught. I really felt like I didnt want to be a professor anymore if things were going to be like this. Then I got to teach grad students, who all went to undergrad elsewhere. Thank GOD for grad students. And now I want to be a professor again. Why? To change this system of edutainment in chemistry.

Chemistry should be fun, but to a certain extent. If you want kids to actually learn, you need to teach them important concepts, not just show them the latest and greatest sexy experiments that have little experimental value. Basic skills, especially critical thinking need to be taught. Students should be challenged in labs, cause if they’re easy, what’s the point?

</insert 2 cents>

That’s my two cents. What’s yours?

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Can chemical compounds be pluralized?

I wanted to extract a paragraph from an earlier post and open it up for further discussion.  When I was creating the chemistry dictionary file, one of the last things I did was apply the dictionary file to ASAPs of popular ACS journals.  Here’s what I wrote:

One of the biggest things I noticed during this vetting was the use of plurals in scientific writing.  Cyclopentenone is an actual compound and is in the dictionary.  If your research requires you to make a family of cyclopentenones, then the plural was probably not in the dictionary (it is now, though).  Although, that raises an interesting question: can you pluralize compounds like that?  Or is it more correct to say that a library of cyclopentenone derivatives was made?  Same thing with families of natural products.  Are they members of the brevetoxins?  Or are they more correctly members of the brevetoxin family of natural products?  I’m not sure I know the answer to that one.  One thing I do know is that I did not include plurals of elements.  Your ¹³C NMR doesn’t tell you that you have 2 carbonyl carbons.  It tells you that you have 2 carbonyl carbon atoms.

The ACS style guide (at least the 2nd edition) doesn’t comment explicitly on the use of plurals with chemical compounds.  What say you?

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Is Synthetic Organic Chemistry Dead?

Synthetic organic chemistry has come a long way in the course of the last century. At the beginning it was not much more than pure guesswork, mixing different things, heating and taking a guess what heteroaromatic might have formed. Nowadays, we have arrived at a point where it is possible to make almost any conceivable chemical structure by a rational approach, using the large toolbox of synthetic methods available today. Have we thus reached our goal? Is there nothing left to do in synthesis except improving the existing methodology?

Of course not. What we still need is a more profound understanding what is happening on the molecular level. Quite often we find ourselves faced with a synthetic problem where only one specific set of reaction conditions will work. Why this one? Nobody knows, and nobody can predict, so we have to try all possible conditions.

I would argue that the huge improvement in our understanding of reaction mechanisms and the complexity of chemical structures of today is largely related to the availability of more powerful analytical methods. A hundred years ago, melting points and elementary analysis were about the only ones, later on IR spectroscopy became available. But we all know that modern organic synthesis would be unthinkable without the help of NMR spectroscopy. Maybe a new method is just around the corner, waiting to be introduced. To gain more knowledge about mechanisms, we would need the ability to “look at” individual molecules, rather than ensembles of molecules as is the case today. A new method that could do this would definitely have a huge impact on organic synthesis.

While we observe billions of molecules at the same time with our analytics, in our mind we are still stuck with the single molecule that we draw on paper. In this way, we neglect all the interactions between molecules that can be very important for the outcome of a reaction. Take organolithium compounds as a simple example. We usually write “n-BuLi” as if it were an isolated species, although it is well-known that these compounds form clusters up to hexamers in solution, depending on the solvent and the concentration. From a theoretical point of view, it will be very important to devise models that take the interactions between molecules, molecule clusters and the solvent (more) into account.

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