Chemistry Blog

Autocorrelation Fail

Sorry to interrupt the intense discussions!

I’ve been sitting in the same position and working on this lab report since 2PM (I just finished a couple minutes ago, at 11PM), it was fun for a while until I realized that I have six spreadsheets open and my poor antique computer refused to run Excel any longer. I had to give up either FireFox or iTunes, so I wrote the rest of my report in silence. I could’ve sworn that the last time I turned around to look out the window, it was still bright outside…

And you know what Noel likes to do when she’s in the middle of working on stuff… she blogs!

After a series of very serious topics, I figured I’d bright something humorous to the blog. Since there hasn’t been any most of those puppehs-that-look-like-giant-Asian-skunks around, I thought I’d share something from my personal stash. I’m not sure how many of our dear readers are familiar with The Fail Blog. Take a swing at it, it’s the latest graduate student time waster. Anyway, I present my latest failure…

That was not (supposed to be) noise!!!!!!! Ah chemistry… I’d still like to congratulate myself for finishing the report like a champ.

Noel

P.S. Dear pchem GSI’s, if you’re reading this, my data turned out perfectly. Please give me an A.

Addressing Marinov’s Element 122 Claim

Note 1: It is an unfortunate consequence of the internet age to be forced to address public misconceptions of research that is published by press-release rather than peer-review. Society & science are not served well from the absence of even cursory peer-review. It should be noted that some of the authors in the paper have a colorful past, but the critique below will be on evidence provided within the manuscript the authors have submitted.

In Marinov’s element 122 paper, Evidence for a long-lived superheavy nucleus.., a fantastical claim is made for the identification of element 122 with standard thorium samples. It should be strenuously noted that element identification (id est determination of the number of protons, atomic number (Z)) can not be definitively determined by mass spectrometry when the exact mass of the element is not known. Yes, there are many models that can extrapolate what the mass of an unknown isotope should be, but overly broad best guessing is not the way science in conducted.

The paper infers a mass accuracy for their mass spectrometer of 0.040 amu and this error will be used to determine the validity of their data. The first figure showing evidence of element 122 is shown below.

The figure shows their data from summing the thorium sample 5 times from their 1st run.

As the figure is lacking a significantly intense peak near 292.010 amu corresponding to ²³⁸U⁴⁰Ar¹⁴N⁺ that is seen in later runs, I would be forced to chalk those signals to inherent noise in the instrument, especially as no blank spectrum was provided as reference for this data series.

The figure shows their data from summing the thorium sample 60 times from their 2nd run. Top spectra is sample, bottom spectra is of the blank.

The peaks from ²³⁸U⁴⁰Ar¹⁴N⁺, mentioned earlier, can be clearly seen in this spectrum. The authors fail to scale the blank’s intensity (y-axis) to the same level as the sample which makes comparisons unnecessarily difficult. The blank’s intensity axis is larger than that of the samples, which is very unusual as one tends to have to zoom into a blank rather than zoom out to make a scientific point. I am also confused as to what the peaks labeled x1/5 mean (was data altered to scale these peaks down?), I do not know. As the x1/5 peaks in the blank are not seen in their thorium sample, one has to wonder why this is so. Has the detection limit already been reached?

The figure shows their data from summing the thorium sample 200 times from their 3rd run. Top spectra is sample, bottom spectra is of the blank.

This data set has the largest statistics as it is a sum of 200 spectra. The blank in this figure has obvious peaks near 292.230 and 292.280 amu. The blank peak at 292.230 is also seen in the sample spectrum, and is now a dominant peak in that spectrum. Any good data set should be at least 3 times the peak height of blank noise, when the signals are so close together, but this is not the case in this figure. Even if referencing the 2nd blank peak at 292.280, the signals attributed to element 122 are at best 2-2.5 times blank background peaks.

The claim that there was no molecular ion formation from hydrocarbon presence from their vacuum pump is also not realistic. From the sensitivities claimed in the paper the presence of pump oil should of been detected.

The authors give several theoretical hypotheses why element 122 should be stable, but these claims will not be evaluated as I see no convincing evidence of the identification of element 122.

Note 2: Link to paper: Evidence for a long-lived superheavy nucleus with atomic mass number A=292 and atomic number Z=~122 in natural Th
Note 3: First coverage of claim was from The Physics ArXiv Blog: First superheavy element found in nature

Mitch

Note 4: Mitch is a nuclear chemistry PhD student at UC Berkeley studying the chemistry and physics of elements above Lawrencium (Z>103) in the Heavy Element and Actinide Chemistry group.

Why does it matter? (Women in Undergraduate Chemistry)

Background: I wrote this post with intention to publish on my personal blog. When I was done, I found it pretty relevant to the atmosphere of the Chemistry Blog. Also, I thought it would be unfortunate to leave this topic unattended.

As the end of the semester approaches, I find that there is a direct correlation between the closeness to finals and the deterioration of my physical appearance. Although I consider myself lucky for being pretty decent looking, I unfortunately repay this gift by livin’ it up like a real chemist-in-training.

My GRE is in two days. I’ve been hiding out in my cave and studying all day. I need a shower. My hair is oily and tangly. My glasses are dirty and I haven’t changed out of these clothes since Friday. Last night, I was intrigued by this train wreck in my bathroom mirror when I realized something that I should have brought up long ago: it wasn’t very long after I started college when I realize looking a little sloppy actually gives me an edge in school.

My mother always nags at me for wearing the same darn thing everyday: hooded sweater, t-shirt, acid-burned jeans and flip flops (sneakers if attempting synthetic methods). I wasn’t like this in high school. I was put-together, moderately sociable, generally happy, and was presented with several prom date candidates as situation arose. Those days are long gone now. Now I look more like an emo little boy getting lost in a fancy college.

My first day in freshman chemistry lab wasn’t what I imagined it to be. It gave me some sad preview on breaking into this community as a female student: the condescending way my male classmates talked to me, the way they hogged all the work in a collaborative procedure because “you don’t know what you’re doing,” the way they bossed me around for the trivial chores… Even my (male) graduate instructors treats me differently.

Sometime I wondered if there was anything I could do, anyone I could talk to. But no. Instead, I put my long hair in a ponytail and put on my oversized t-shirt. Somehow when you look like one of the guys, everything is OK.

I wondered if any other girl in class felt the same way.

The situation did get a bit better as I move up the food chain. I started to know quite a few graduate students and departmental staff. I even began to mentor my own little group of 1st/2nd-year minions. But even now, walking into my final year as an undergraduate, I get odd stares if I run errands around the lab facility with a fitted shirt and my long hair flowing on a sunny afternoon.

Hello, am I the only girl in this whole freaken building?

The answer is obviously no. But the few female staff that manage to get by without getting funny looks all strangely managed to morph themselves into the stereotype of a successful female scientist: unrefined, quiet, and invisible.

Now don’t even get me started on the number of times I get hit on by my graduate instructors during class and the many “hey, my face is UP HERE” moments during academic discussions. Do you know that you are whistling at a girl who is too young for you to buy a drink for? It’s so not fair. I work as hard as you are, I do just as well in everything that you do, why can’t you show some respect?

So please, stop acting like a sleazy pig. Because of the things you say and do, I feel obligated to look frumpy and completely covered up. I feel self-conscious for looking and acting feminine. I feel embarrassed to participate in an academic discussion or show any signs of comparable intelligence. I even feel a little inadequate on performing tasks that I am perfectly capable of doing. It’s the type of workplace discrimination that nobody would ever acknowledge or address.

Also, one day, I would like my dignity back. I’m just a 20-year-old who’s trying to make something out of herself.

Molecular Strain: Make me, I dare you

Roald Hoffmann and Henning Hopf have a great new paper out in Angewandte titled Learning from Molecules in Distress. The paper is a romp through the field of “unhappy” hydrocarbon chemistry. It starts with a rationalization of the field of highly strained molecules, but quickly goes to the psychology of sadomasochism and vexing contemporary philosophical dilemmas as the Trolley problem and the Swampman.

On an aside, the Swampman thought experiment is thus,

“Suppose lightning strikes a dead tree in a swamp; I am standing nearby.My body is reduced to its elements, while entirely by coincidence (and out of different molecules) the tree is turned into my physical replica. My replica, The Swampman, moves exactly as I did; according to its nature it departs the swamp, encounters and seems to recognize my friends. It moves into my house and seems to write articles on radical interpretation. No one can tell the difference.“

As many of the elements in your brain get replaced within a month or so from the food you eat, this really shouldn’t be such a dire philosophical dilemma, than a common curiosity of everyday life. But I understand lightning is more theatrically appealing than a sandwich.

This is all within the context of explaining the glamorous life of the investigative synthetic experimentalist. Mission accomplished, if that was an intended goal. The paper also does discuss chemistry, and special attention was given to cyclic ozone 1, dicarbon dioxide 2, hexaazabenzene 3, and hexaprismane 4.

The masochistic chemist has 2 problems with the synthesis of these types of molecules. The first is near and dear to my heart, stability. Although, these molecules lie in a potential minimum and thus are thermodynamically “stable”, they can be quite reactive with itself or other molecules within the atmosphere or the medium it finds itself in. Plus, even thermodynamic stability have qualifiers, the size of the potential well may be so shallow to never see these peculiars at room temperature, which is likely the case for hexaazabenzene.

The second problem for molecules in distress is the inability of a clear synthetic strategy to the target; these molecules are unknown for a reason. Thus, the ever enterprising physical organic chemist needs to utilize chemistry outside a pure organic chemistry approach and may have to chase these molecules down within the complexation with metals, or in low temperature inert matrixes, or even perhaps atom by atom in an STM. In any case this paper is a fun read and should definitely be shared.

Mitch

Note 1: The Hoffmann & Hopf paper: Learning from Molecules in Distress
Note 2: Paper originally covered by CBC: kinky!
Note 3: RajaLab Weblog has covered some interesting sulfur helicene chemistry: Carbon-Sulfur [11]Helicenes: Syntheses, Structures and Properties
Note 4: Also covered by selenized: the value of making things

Irradiation to enhance food safety

Does anyone remember the E. Coli breakout back in 2006? I do. There has never been a quicker way to convince a 19-year-old to eat vegetables until you take lettuce out of their sandwiches for a couple of months.

According to the LA Times report[1], these greens are washed in potent chlorine bath, often up to three times, before they are bagged and shipped to the retailer. This standard procedure has a reported 90% effectiveness in killing the microorganisms that may cause harmful effects to the human body.

I don’t know about you, but I would rather not take that 10% chance to get sick. In the single breakout of E. Coli due to cross contamination with the cattle back in 2006, 200 people became ill and three lost their lives. That’s the 10% chance that nobody should have to take.

This past month at the ACS National Meeting in New Orleans, researchers from the USDA presented their findings and results of radiation treatment of fresh produces. Irradiation of high energy beams of photons or electrons, said the scientist, can disrupt the DNA of these pathogens. While the chlorine rinse offers a 90% effectiveness in killing bacterias on the surface of the leaves, it is not able to penetrate beneath the surface. Irradiation method has a reported >99.9% effectiveness in wiping out pathogens such as E. coli, salmonella and listeria, and the high energy beams allows penetrating power that works inside and outside the leaves.

Some members of the scientific community are calling irradiation one of the “few intervention steps that indeed can penetrate the leaf surface and kill microorganisms.”

Irradiation for enhancement of food safety is permitted for some hamburger meat, poultry and spices, but not for fruits and vegetables. However, there has not been any health problems associated with eating irradiated food. So why is FDA steering away from adopting an improved method that could potentially save lives?

Consumer experts and food safety researchers offer some of their speculations:

1. Irradiation may damage the apparence of the product, which may not be as appealing to the customers
2. Nobody would buy lettuce from a bag with a radiation sticker
3. The treatment could shorten shelf lives of the products
4. Technically, irradiated produces cannot be certified organic

Though reasonable, it is hard to believe that the above mentioned points would stop either FDA or independent research institutes from further investigating in a method that could possibly be so much more potent in eradicating pathogens than the existing practice. Perhaps these novel ideas would not suffer as much if we could deliver more transparent and correct ideas regarding the applications of radiation.

Using innovative ideas to improve the quality of our everyday lives, isn’t that what science is all about?

Noel

[1] USDA scientists say irradiation could be key to food safety

P.S. True to scientific spirit and for the benefit of the minorities out there, I will summarize and translate my discussion in lolcat. I can has radeashuns: on ur vegitablez, keelin ur baktiriaz.

Edit: Originally mentioned by Bethany Halford and Lisa Jarvis in Chemistry Newsbytes.

“Danishefsky 2-component reaction”

This JACS communication by Danishefsky’s group is inspired by the well-known Passerini 3-component (isonitrile + aldehyde + acid) and Ugi 4-component (isonitrile + aldehyde + amine + acid) reactions. They ask the question if isonitriles 1 react with carboxylic acids 2. At room temperature, they do not, but under microwave irradiation they furnish N-formyl amides 3 in good yields. The authors go on to propose the mechanism shown, which could probably be further supported by isotope labeling.

They wanted to apply this new kind of reaction to the synthesis of asparagine-linked glycopeptides. Therefore glycosylisonitrile 4 was reacted with aspartate 5. Instead of the expected product, ester 6 was formed. In the paper, the formation of a “β-GlcNAc donor” by participation of the NAc group is assumed. Its structure is not specified, but I suppose it could be something like 7.

To get around this problem, non-participating neighboring groups like OBn and N₃ were used (8). Now, reaction under the same conditions furnished the expected glycosyl amino acids 9. Even better, the reaction was anomerically specific; that is, β-isonitrile 8 gave exclusively the β-linked product 9, while α-isonitrile 10 yielded only 11.

The formyl group could also be converted into methyl or completely removed, which sets the stage for building up a peptide chain. What is really striking about this new type of reaction is its simplicity. To quote the paper: “[The results described herein]… might well have been discovered a century ago.” Why has nobody ever tried this before? Is it because of the bad smell of isonitriles?

Suicides in Chemistry

This past week we lost a 1st year chemistry graduate student to suicide at UC Berkeley. I attempted to do some googleing to see what kind of suicide rate chemistry students have, but there seems to be no recent numbers or studies on the matter. Which is understandable, because which institution or field would eagerly make this information available. I was personally unfamiliar with the student or his personal demons that lead him to choose his tragic path, but one always has to wonder how much influence his PI or group dynamics play a role in these decisions, whether it is fair to do so or not.

I usually advice entering graduate students that the 1st year is the hardest, but honestly I would say it only gets harder. As graduate years go by, you simply become accustomed to long hours and higher stress. My advice to any young undergraduates is to build a solid support network when you enter graduate school. You will need it…

Edit 1: Press of the suicide: Chemistry Student Found Dead In Apparent Suicide
Edit 2: Good articles on the old suicide in the Corey group

• NYT: Lethal Chemistry at Harvard
• C&EN: Examining the underpinnings of suicide
• C&EN: Smoothing the Passage

Mitch

Mitch on TV

Tune in to cheer on for our beloved blogger, Mitch, for his television debut this weekend. He will be featured on American Latino TV as an outstanding member of the cultural community. In this interview, he will be talking about how he chose the path as a nuclear chemist, and his aspiration to educate today’s youth on chemistry using the internet.

A complete listing of available channel can be found on this page:

http://aimtvgroup.com/altv/wheretowatch/

Social Networking ACS Presentations

Several people have requested the powerpoint presentations of Maz&Noel’s talk and my talk as well. So, for their convenience and yours if you weren’t able to attend, here are the talks we delivered in the chemical education symposium titled Using Social Networking Tools to Teach Chemistry:

• Development of chemical forums, blogs, wikis, RSS feeds, crowdsourcing, and social bookmarking websites for chemistry.
• Incorporating social networking tools to facilitate participation and discussion in nuclear chemistry.

The session was surprisingly well attended and even got a mention by Lisa Jarvis in the new C&EN blog here: Chemistry and the Interweb. I also got to meet the face behind the Noel O’Blog and a few others.

Mitch

From ACS New Orleans

Hey there, from New Orleans! ACS 2008 kicked off today with the early morning registration rush that is required for every ACS meeting. This one, however, was awesomely bad, as the organizers, displaying true ig-nobel prize worthy genius, nearly caused an uprising from the mob of chemists waiting for their ID-cards.

So here’s what happened. Around 8 in the morning, chemists of all sorts spilled into the registration hall at the convention center in the French quarter of New Orleans. To register for the conference, each person had to first enter their information into the onsite computers, pay a fee, and then go collect the printed out ID cards. The first part of this procedure went fine, and it took only minutes for myself, Mitch, and Noel to pay the registration fee and get in line for the ID card. However, the wait for picking up the admission badge is where everything went haywire.

Instead of intelligently placing the printers next to the ID card readers so that new registrees could grab their papers and assemble their own ID’s, the organizers decided to have 3 printing stations where the ACS hosts would carefully complete the complicated task of folding the papers in half, inserting them into a plastic holder, and lacing an ACS lanyard through the tag.

One particularly loud lady, the “supervisor” - we were told so by other employees who refused to accept responsibility of the brewing crisis- especially endeared herself to the crowd. After waiting 20 minutes or more to reach the front of said printing line, the self-proclaimed “lady in red” was…well, let me paint the picture for you.

Imagine yourself, after waiting for what has felt like hours of standing in a much too long line, checking your watch every few minutes because your chance to hear about element 108 and the plans to make 120 is literally ticking away. Finally you begin to reach the front of the line: you can hear names being called and briefly think about how nice it would be to get your tag. But wait…something is wrong. You hear people’s names called, followed by groans, moans and subdued protests. Thats not right…you think to yourself. Then you hear the words that make you hope…no pray, that this little “lady in red” does not call your name.

“John Blahblah!”

“Yeah, here!”

“Sir, Back of the line please!”

“WHAT?!?!?!?!”

“Sir, Back Of The Line.”

And there it is. The bottle-neck in the registration process that eventually led to this:

was caused by the assumption that chemists can’t make their own nametags. Yes, the above picture is Mitch becoming an honorary ACS crowd manager as he hands out the plastic ID card holders to near-unruly chemists. Although, I probably didn’t help the situation by loudly telling people not to budge if told to move to the back of the line. What can I say…I am just a rebel.

So Kudos to the ACS event organizers. The first few hours of the first day of the conference was a complete hash, a prime example of how NOT to manage a huge national conference’s registration. For all those unfortunate chemists who missed the morning talks, or decided to forgo the idiotic ID to actually attend those talks, or were just generally upset by the morning’s administrative malfunctions, I hope you comment on this post. Or just comment if you find it funny. Or if you want to make fun of me. Whatever.

-Maz