July 04, 2008

Reactions - Stephen Davey

1. What made you want to be a chemist? The serious but predictable answer is a couple of really good science teachers, so thanks should go to the inspirational Andrew Munro and Jeremy Bushrod. The fun answer is John Nettles....

Radicals Shake Up Molecules

Until now, it was usually thought that colliding molecules get the shakes as the result of energy transfer solely from the smashing of the molecules, but some new research adds a second means by which colliding molecules become vibrationally excited--it is being called the "Tug o' War Mechanism". The new experiment, transforming the textbook story, waccording toformed in the lab of Richard Zare, chair of the Department of Chemistry at Stanford University. This work on energy transferring, or inelastic, collisions is featured in the July 3, 2008 issue of the journal Nature........

Physicists create millimeter-sized 'Bohr atom'

HOUSTON -- June 30, 2008 -- Nearly a century after Danish physicist Niels Bohr offered his planet-like model of the hydrogen atom, a Rice University-led team of physicists has created giant, millimeter-sized atoms that resemble it more closely than any other experimental realization yet achieved. The research is available online in Physical Review Letters.......

July 02, 2008

The Seven Deadly Sins of Science

Literature and editorials in popular journals on the subject of ethics have sparked tremendous debate about the ethical behavior of our peers and some have suggested implementation of ethics courses, computational techniques to root out fraud and even oaths to promote ethical behavior amongst newly minted scientists. While, at least in the case of the “Toronto Oath” vanity may be playing a larger part than practicality, it nevertheless establishes that high level debates are transforming into action on college campuses. Before people expand on this concept of an “oath” or other silly contrite devices which appear to be ineffective (at least for lawyers in any regard), it may be worthwhile to contemplate the issue in a far more philosophical context. Firstly, we must ask ourselves if loose ethics is a new phenomenon or if it is simply a constant which is just being promulgated by blogs (of which I would take some blame) and other traditional media in a flavor-of-the-week news cycle. While the tools may not exist to establish that fact, it may be worth considering that overzealousness on behalf of some bloggers and journal editors will only create problems and exasperate the lean patients of reviewers and readers alike. Thus, it is within this context that a division of ethical behavior by magnitude of import is devised, just as a division of moral transgressions was formed by the Catholic Church. Establishment of the Seven Deadly Sins in the Catholic tradition traces its roots to the 4th century where, at some point, it became necessary to distinguish sins which were trivial (venial) from those which were grave or mortal sins. The need for a distinction between being bad and being really, really bad seems odd given that in science, as well as (presumably) matters of the soul, we all strive to be perfect and any infraction is serious. Thus, just as it wasn’t the intent of Pope Gregory I to create two types of sin, one more permissible then the other, so it isn’t my intent to suggest that there exists a permissible type of fraud. There are cases, of course, where forgiveness may come easily and cases where forgiveness may not come at all. It also helps to put many people’s mind at ease that when they read documents most people will not have committed one of these more egregious transgressions and thus we, as readers, needn’t worry about questioning the truthfulness of the data but, rather, the competence of the scientist.

First, let me propose the Seven Deadly Sins of Science:

Plagiarism: The copying of other’s work and ideas as your own with the intent to deceive. Further defined as the intellectual theft of the ideas of others, even though they have not been published and publishing them as your own idea be they lifted from a conference, grant proposal or paper which you have been given to review. Additionally, the copying of one’s own work with the intent to provide the spurious impression of an extensive publication record is an egregious sin.

Fabrication: Inventing data which does not exist or suggesting procedures and experiments were preformed when they were not

Falsification: Altering, manipulating, distorting or skewing data. Disregarding data which conflicts with other data or not reporting data which might lead other’s to reasonably believe your conclusion is incorrect

Suppression: Not reporting or publishing data which may contradict your previous findings, assertions and assumptions.

Negligence: Failing in due diligence to ensure truthful and accurate reporting from subordinates or taking data and results from others known to have insufficient qualifications, suspicious motives or are known incompetent even though their results substantiate or further your claims.

Inhumanity: Performing experiments on living subjects which are not within the scope of sound science, do not have in place rigorous controls, have not been authorized by a veterinarian when necessary. More egregiously: from patients which have not given their express consent or from human subjects which cannot be reasonably expected to provide consent because they are subordinates, minors or mentally unfit. Most egregiously: publishing, acting upon, or providing easy access to those who would wish to use results for the sole purpose and intent to kill others.

Sabotage: Purposefully destroying others’ work, providing low grant application scores without merit, rejecting papers as a reviewer for trivial reasons, in an effort to slow or impede the work of others in your field.

In each of these cases, the intent is malicious or self promoting and ultimately results in the propagation of misinformation, harm to someone else’s career so that one’s own career may be advanced or deliberate cruelty, likely out of revenge. Violation of these boundaries are considered the most severe and violating them is almost certainly done willfully. Take a rather notorious case in point: Hwang Woo-Suk, who is guilty of multiple infractions: willful misrepresentation, fabrication, falsification and using ova from female subordinates are all cardinal sins and such gross levels of fraud are rare. Who could also forget Ms. Bengu Sezen, who’s obvious falsification and fabrication of data resulted in a stunning seven retractions by the group of Dalibor Sames, who himself has been accused of being complicit in his own willful negligence by failing to dutifully follow up when other researchers were piling on evidence that her results were not reproducible.

But it is with Dr. Sames I have drawn the line. As I have argued here before, I am neither convinced nor compelled to believe that Sames’ actions were indeed cardinal ethics violations but rather, a combination of his ego, youth and well played deception on the part of Bengu Sezen. Does that let him off too easily? And if so, what are the consequences of letting someone off easily? After all, punishing someone serves one of two basic functions: to correct and prevent behavior and/or to obtain a sense of revenge. If punishing someone only serves to make ourselves feel better (and thus has no higher purpose) then it’s merely revenge and a wasted effort. If anyone thought Sames were stupid enough to make the same mistake twice, maybe a serious consideration by granting agencies and the Office of Research Integrity would be in order. Then there is Leo Paquette who, by his own account inadvertently plagiarized material from two different sources on two different occasions. Such actions being unintentional yet repeated seems unlikely to an absurd degree, yet Dr. Paquette’s contributions to the field have been tremendous and, in light of that, even committing a cardinal ethical transgression such as blatant plagiarism can be forgiven though never really forgotten. Now, had Dr. Paquette fabricated the data (something that even very senior and respected scientists have been caught doing) then forgiveness may not have come at all. Thus, even within this series of seven transgressions, there are still shades of grayness.

[to be continued...]

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July 01, 2008

DD11: Stanford and Scripps

So, the conference is over, but the work of a Nature Chemistry editor isn't. As you might have heard on the podcast, we're combining our conference visits with trips to nearby chemistry departments. So the day after we'd wrapped up...

June 30, 2008

Pyrotechnics For The Planet

Chemists seek environmentally friendlier compounds and formulations for fireworks and flares.

Tethered Molecules Act As Light-driven Reversible Nanoswitches

Researchers at Penn State have developed a way to attach a photosensitive molecule to a surface that can be switched between two configurations in responses to varying wavelengths of light.

NChem Research Highlights: total synthesis, multimetallic complexes, and photoresponsive elastomers

It’s time for another batch of research highlights. First up, fresh back from his trip to Korea, Steve writes about a counterintuitive approach to creating stereocentres: by destroying them first! Second, the story of greedy metal complexes. Neil tackles the...

June 28, 2008

University of Notre Dame [ed. second one. This one is better though.]

Facilities and instrumentation:

We are rather instrument rich. There is only an infrequent line for the NMR and only if you choose not to be trained on both Bruker and Varian instruments. With 8 instruments ranging from 300 - 800 MHz, there’s no excuse to not have access to one or have a need for a higher field instrument. The only place (as far as I know) that has more and with any higher field is Wisconsin, and that’s a national lab. There are three X-ray diffractometers available for general use, which I believe is also a regional high, a kappa, a 3 circle and a powder. (There are something on the order of 7 diffractometers in the building, but most of them belong to specific groups.) The guy that runs the place, Bruce Noll, is something of a hard ass, but a generally excellent teacher. He was trained by the same guy at UK, who is also a reputed crystallographic master. Dunno much more than that. The mass spec facility is in the process of obtaining 3 new instruments after being awarded a rather huge NSF grant for the purchase of large instruments(?). The current new kid is a MALDI-TOF that has isotopic resolution all the way up to 4000 daltons and can give you low res up to 10,000 daltons. But I’m not a mass spec person, so I’ll only say that the two new instruments are supposed to be even better. Turn-around time is less than 24 hours in most cases, depending upon what you need done. The present workhorse is a 16 year old turd, so when it’s replaced, the place will obtain mini rockstar status next to UIUC. The department is also part of a new Imaging consortium funded with about 6 million bucks that will provide general access (in addition to the labs that already have them) confocal microscopy, animal imaging facilities, SEM, TEM, AFM, so on an so forth for pretty cheap user fees. We also have, as general access instrumentation, several Van de Graaff and a pretty tight linear accelerator in our DOE lab, which is next door. Indeed, I can’t think of a single instrument that isn’t available on this campus with the exception of a cyclotron, which is an hour away at Argonne.

The buildings these fine instruments are housed in are ugly, but their rather unattractive nature doesn’t appear to affect their function, so if “ugly” is the worst thing I can say about the place, it’s not doing too bad. In any regard, it’s something that paint could fix, should some administrator take notice that they do, indeed, work in a building where each floor is colored with a unique shade of vomit.

Faculty

The faculty are generally strong. Mobashery, Miller, Sevov, Castellino, Smith, Taylor and Wiest are all probably at the top of their game and produce some very interesting chemistry, even though I’m not overly qualified to comment on some of them. I suppose they’ve hired a new faculty member here every 3 years or so, thus it’s hard to say how many of them will turn out. I have no idea, honestly, how we rank in individual programs. I can clearly see that we are ranked abysmally in US News and World Report but the amount of peer reviewed grant money that we get is oddly in contrast to where we stand. It would leave me to assume that we are either unranked in the individual programs or ranked rather poorly. I have only this to say about the situation: I don’t really care. I don’t know what goes into the ranking, I don’t know how people arrive at their conclusions, but from all the available data, it appears as though ND is a very good department with no limitations and, as sad as it may be, these “rankings” serve only to worsen the quality of incoming students.

Location

South Bend is not the highlight of the midwest, but for $12 you can hop a train (that allows you to drink beer openly) to Chicago. Indianapolis is 2 hours south and the airport here is always good for getting you out. There is a bus that stops on campus that takes you directly to Chicago’s O’Hare, so transportation isn’t an issue. In the grand scheme of things, I’m in the lab 10 hours a day, so whatever awesome existence that exists outside (or doesn’t exist) I’d not know of it. I can eat pretty much whatever I want and there has been a recent profusion of high end Jazz clubs and the Fiddler’s Hearth is possibly one of the sweetest Irish Pubs I’ve ever been to. They serve Guinness for, like, $3 a pint because everything is cheap as hell out here. The little stipend they hand out is enough to live by yourself in a two bedroom apartment whilst eating out most nights because you’re too lazy to cook for yourself. A buck goes far in The Bend.

The whole “Catholic thing”

Here’s a section that’s probably not included in a lot of reviews, but it should be mentioned: The department is secular. This is because science is secular. This university understands that and respects that. The Catholic backdrop adds more kitsch to the place with its “touchdown jesus” and potentially trademarked phrase “Catholic Character” and the annual planting of the crosses for the unborn (and semiannual vandalism of said event by those rabble rousing libruls) then it adds any sense of Christian mores, but it does attract a lot of lectures on morality and ethics in science and, I think, if this place were smart, they would capitalize on that like Tuskegee did. Those lectures are actually very interesting and not available with such frequency and debate at most schools. So, Catholic kitsch and interesting lectures are the only observable outcome of Catholicism here. It’s a small price to pay. If you’re Catholic, of course, it’s gotta be like a Jesus themed Disneyland or something.

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June 27, 2008

Reactions - Aline Miller

1. What made you want to be a chemist? As a child I remember being given a chemistry set and spending many hours in the family greenhouse mixing different coloured liquids and causing things to heat and sometimes burn (much...

June 25, 2008

Amazing green moving light thingy. It's chemistry!

This is one of the best chemistry videos, nay one of the best videos, full stop, I’ve ever seen. The video accompanies a paper (abstract here, subscription needed for full paper) in Organic Letters about a photochromic molecule (one that...

June 24, 2008

Oooh, isn’t that cool.

In one of the more spectacular examples of recent photochromic research, Jiro Abe and Co., in a very recent Organic Letters ASAP (doi: 10.1021/ol801135g), have demonstrated the very rapid formation and disappearance of a “green shit colored chromophore” upon shining UV light into a tube filled with a hexaarylbiimidazole derivative (vide infra, bitch).

The reaction is rapid and, most interestingly, rapidly reversible, which means that the formation of the green colored product is short lived and the color disappears, most notably faster than the diffusion forces can dissipate the greenish cloud. While the technology isn’t quite new, I’d have to say this is actually published in the incorrect journal. This is potential JACS and/or Angew material, given the rate of reversal and the demonstrable theatrics. Org Lett is an interesting journal and I don’t wince at publishing there, but “greener” pastures should have been waiting for this little idea. For example, if you own a pair of transition lenses, perhaps “green shit color” isn’t quite the tint you’re going for, but you’d be happy to know that formation of that tinge would be instantaneous upon exposure to UV light and its disappearances just as instantaneous. That beats unwittingly walking into a stairwell without realizing it because your goddamn glasses are still tinted from being outside.

To be sure you are as amazed as me, here is a YouToube from a movie in the SI:

“Posted with permission from Org. Lett., ASAP Article, 10.1021/ol801135g, Web Release Date: June 19, 2008.
Copyright © 2008 American Chemical Society.”

Obviously pretty fucking wicked. The visual splendor may not be sufficient, but the paper goes to great lengths to explain and characterize this process and does so in excellent fashion.

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June 23, 2008

The University of Pittsburgh

Facilities:

The Chevron Science Center at Pitt is home to the largest division of the School of arts and Sciences. This is readily apparent, as Chevron is one of the most notably large buildings on the entire campus next to the cathedral of learning. When completed in the mid 70’s Chevron was noted as runner up to the most outstanding chemistry facility in the country. Since that time, the building has seen some of the inevitable effects of age set in, most notably in the undergraduate labs. As such, the university has attributed a large sum of money to the building for renovation. As of now, major construction is occurring in the brand new undergraduate labs, and a renovation of the entire building starting on the 14th floor down is underway. It is exciting to be in the department at this time, and I personally look forward to teaching in the new labs.

Directly behind the main building, rests a second building of the department, Eberly hall. Eberly is home to the chemistry library, a number of computational and physical groups, as well as the mass specs, HPLC/MS, IR’s, polarimeters, etc. In addition, many classrooms are located in this building. In terms of the classrooms, each are equipped with multimedia: speakers, projectors for computers, etc., which makes both learning and teaching an especially convenient and enjoyable experience. A research stockroom provides chemicals, equipment, and glassware. The university has a full time glass-blower, electronics shop, and machine shop available five days a week. It really is a self sustaining community, and at times wish they had a cafeteria and a lot of couches so I could just move in.

Instrumentation:

The building is home to every possible instrumentation which defines a world-class research institute. Included for every-day use is four 300MHz and a 500 MHz NMR’s. IR’s, polarimeters, MS, HPLC/MS, an XRD, and everything else you need for purification and structure elucidation/confirmation. Many groups have their own instrumentations, but these are available to any student with the proper level of training.

Faculty:

The organic division dominated the department. Home to many synthetic groups (The Wipf, Koide, Curran, Nelson, and Brummond groups to name a few). Especially exciting is the recent synthesis of FR901464 by the Koide group and their highly potent analogue, meayamycin. The Curran group has a number of exciting project that include fluorous and radical chemistry. The Wipf group is the largest, with professor Wipf himself teaching a notoriously difficult and stimulating advanced synthesis course. In terms of rankings, the last time an extended list was available from US News, the Organic division was ranked either 15th or 13th overall. This does make for a highly competitive environment, however, and typical work days in the synthetic groups are 12+ hours a day six days a week.

Pittsburgh:

Is a great town to live. Cheap cost of living, a great sports city, and plenty of fun things to do on a graduate student’s income. I am especially proud of this institution and happy of the choice I made to come here. This department is highly recommended, and especially enticing to consider because of some of the rising stars in the department, and new facilities.

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June 18, 2008

University of North Carolina - Chapel Hill

Facilities:

UNC is currently “building for the future”, which means there will be active construction projects going on here for the next decade or so while each scientific department gets a new home base. For instance, Chapman Labs (Phys Chem, Physics, ChemE) is a brand-new (2006) building where may of the Chem visiting speakers are hosted in the cozy new Eastman seminar room with wood paneling and touchscreen monitors / projectors. Caudill Labs is also new (2007) which is where bench chemists (org, inorg) and laser chemists (pchem, analytical) have most of their labs. It has huge floor-to-ceiling windows, lots of hoods (which sometimes depressurize the building!), and a decent set of desks with ethernet and power strips.

Instrumentation:

We have NMRs enough to support ourselves, the local small companies in RTP, and several small schools and high schools in the area. Bruker 300, Bruker 400 (2), and Bruker 500MHz compliment a Varian 600, which can all be reserved by anyone after mandatory training on changing probes, shimming, etc. Many organic groups have their own HPLC / SFC, GCs, chiral GCs, and IR / polarimeter, along with 1-2 gloveboxes for each inorganic group. We have a staffed MS facility that can do HRMS on demand and even 24-hr turnaround, if you feel like dropping a full grant on one spectrum. I’m not as familiar with the equipment for the analytical and PChem labs, but I know we have EPR, Ar lasers, cap. electrophoresis, and a few labs that take apart and upgrade MS and uPLC to actually design new instrumentation.

Rankings Comparison:

Last I checked, we were something like tied for 16th overall, which I think is pretty accurate. The analytical people know their stuff, and it’s a great department if you want to be an instrumental person at a big pharma or chemical concern (Dow, DuPont, etc). Inorganic has folks dabbling in alternative energy, metal-organic frameworks, alkane metathesis, and organometallic synthesis. Organic has both a strong TS presence as well as 2-3 methods / catalysis groups, and a strong (young) biochem / materials background. We have something like 150-200 grad students, if department size matters to you.

Faculty:

Near as I can tell, everyone gets along. I haven’t heard about any longstanding grudges or vicious barfights, and assistant profs mingle with Chaired professors at beer socials and seminars. Everyone maintains an “open-door” policy, which means if I have a question about materials or polymers, I can just go up to a prof’s office and tap on the door, and ask away. Many groups go out to lunch on Franklin St. weekly, sometimes with their boss in tow!

Summary:

It’s a good place to work, if you don’t mind the intense summer heat or occasional lines for NMRs. It’s fairly laid-back, but most people still end up with 2-3 good papers to graduate on.

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June 15, 2008

University of Groningen, The Netherlands

Department: Stratingh Institute for Chemistry

University: University of Groningen, The Netherlands

Before I start off, let me explain a few things. First of all, I’ve chosen to submit this anonymously. This is not because I deliberately want to say bad things about certain aspects of my department. I just want to be able to be fully honest and, as most of you probably know, people in highly placed positions can freak out when they read honest things (even if these things are facts). Secondly, Engrish is not my first language, so please bear with me despite any poor grammar that you might encounter. Finally, introducing myself, I’ve been working here as a graduate student in the field of organic chemistry for a few years, so I like to believe that I’ve had the time to get to know my department.

Faculty: The department consists of lots of people and lots of research areas. The biggest is Prof. Feringa’s group, which consists of roughly 60 (under)graduate students and postdocs, and which focuses on quite a few different areas (asymmetric catalysis, molecular switching, motors, organogels, and more). The group of Prof. Hummelen is somewhat smaller (can’t find a number right now) and focuses on organic materials and devices. Finally, the inorganic part of the department consists of roughly 15 people who focus on reactivity/catalysis and switchable coordination compounds. Professor Hessen left this group not too long ago, and I believe they are currently looking for a replacement. There is a lot of cooperation between the groups inside the department, as well as with groups outside the department (like, for example, a few physics groups which reside in the same building). The research itself is exciting and lots of different things are happening in the different groups, which is nice, as you get to learn about many different kinds of chemistry. And everyone seems to be able to get along which each other, at least, I haven’t heard of any serious problems between people. So, the mood is generally good.

Work: I heard that graduate students and postdocs in the US (and also in a lot of other countries) generally are expected to work 6 days a week, or at least five days + a few evenings. In our department, this is not expected; if you punch in at half past eight and punch out around six, your professor will be contend with you, provided of course that you are productive between those times. Some students, especially people who just came from abroad and who don’t really know what to do in their spare time as they don’t really know their way around the city, choose to also work in the evenings and/or weekend. And that’s OK of course, though some of the senior staff members here insist you take at least the whole weekend off. (A supervisor telling you to take the weekend off, how cool/odd is that?) Postdocs usually work a bit more than graduate students, especially if they play an important role in the group. Regarding the work itself, most of it of course is labwork. As a graduate student, you might have some teaching duties, depending on what kind of position you have (more on this later). There are quite a few meetings, to name a few: group meetings, subgroup meetings, research updates, organic synthesis problem/practice sessions (not compulsory, by the way). I sometimes get a bit fed up with attending all of them. Just let me work, OK?

Jobs: Recently, the university decided that in order to save money, they would offer less ‘normal’ graduate student positions and instead introduce a new position called the ‘bursaal’ (no idea how this translates to English). Basically, these bursaal positions have a lower salary in order to save the university money. However, as the income taxes in The Netherlands are regarded as ‘pretty high’ (I don’t exactly know how they compare to other countries), this would mean a bursaal would hardly make any money. What the university has therefore done, or what I at least understand of it, is that they have made a deal with the government so that bursaals don’t pay any income taxes. Therefore, normal gruadate students and bursaals have the same net salary. Sounds fair, right?

Well, it isn’t. Not paying any taxes because of some weird university-government deal means that some agencies see you as unemployed (the bursaal position technically doesn’t exist). I have a colleague who is from abroad and who can’t get health insurance because of this (whereas having health insurance is compulsory by law). Not paying taxes also means you don’t build up a pension. And if your four years of graduate research are up, you have to find a new job or leave, because you can’t get money from the state if you stay unemployed (as the bursaal position doesn’t exist, you never had a job in the first place, so you cannot be unemployed; after all, you can’t loose a job you don’t have). Being a bursaal, you also don’t have any teaching duties, otherwise you would have a real job and the university would have to pay you the salary of a normal graduate student. So, no teaching duties, which means you don’t get any experience in this field. Just to name a few drawbacks of this position.

Whether you’re offered a bursaal position or a ‘normal’ graduate student position depends on who you get to work for, and what you will be working on. Generally, professors prefer to hire graduate students as they need people who are allowed to teach, correct exams, supervise practical courses, etc. But they occasionally just have to hire a bursaal for an ‘unmanned’ research project.

Kyle wrote in his blogpost And then there were children: “You came to grad school to become a better chemist, not to give up on being a goddamn human being for 5 years.” Well, here’s what it boils down to: a bursaal position doesn’t stop you from being a human being, but it does make it way more complicated (to name one aspect: how are you supposed to support children with such a position?)

Facilities: The building we reside in is old and thus new buildings are being built. One of them is already finished, and consequently most of the facilities which are not closely tied to a single research group (such as the administration, most of the canteen, the library) have moved there. Which is a bit of a pain, having to put on your coat every time you want to look up something in the Encyclopedia of Reagents for Organic Synthesis. The guy that has all of the office equipment has also moved, so every time I’m out of sticky notes or someone steals my red stapler I have to walk to the other building. And for some strange reason this guy currently refuses to sell us credits for the photocopier, which means that if we’d like to Xerox anything, we have to pay out of our own wallets. Not very convenient, but transitions like this are never painless, so I won’t make a big deal out of it.

I always thought of a university as a school, even if there about as many graduate students/postdocs as undergraduate students (undergraduate students just follow courses for the first three years, then join one of the research groups for the final two years of their education). You might agree with me, until you see the prices of the food in our canteen. I’m not sure if they are very different from those in other universities, but the bottom line is that undergrads usually can’t afford to eat there every day, which I find ridiculous. The reason: the canteens of the University of Groningen aren’t owned by the university itself, and therefore want to make money. The food itself is not bad (though this is according to Dutch standards, and the Dutch are not exactly known for their fine ‘cuisine’), although it is lacking a bit in variety.

Computers are often quite irritating, by the way. We have a system called (translated): the university workplace. The operating system is installed locally on each computer, but your documents and settings are kept on a network drive. Initially, no applications are locally installed. Instead, they are kept on the network and are installed locally when you run them for the first time. Email goes through a web-based client, similar to Gmail or Hotmail, but you can set up Outlook Express or something similar to retrieve your mail for you if you like (IMAP, so it’s all kept on the server). In theory, this might sound like a good set-up, however, it is poorly implemented, because it is extremely slow. Logging in takes a few minutes, starting applications can take quite long, and the web-based mail client is so slow it’s irritating everyone. I’m not sure why this is the case; the network connections are certainly up to it, so I guess the servers are just too slow. Additionally, sometimes a server problem renders all computers inoperable for a few days, which is a real pain.

Equipment: We’ve got the lot. NMR machines range from 200 to 500 MHz, and there is also a 600 MHz which is usually used by the guys from the spectroscopy department, but I’m sure they can do a measurement for you if it is really necessary (never actually needed that many MHz’s). We can do IR, UV/vis, CD, mass, HPLC, GC(MS), AFM, STM, ellipsometry, you name it. Some of the machines, like the AFM, the STM and the ellipsometer, aren’t from our department, but this is where the good connections with other research groups/departments come in handy. Most machines are maintained really well. A few machines are old and might need to be convinced to do their job (we have a CD spectrometer and Optistat that often need to be kick-started), but once working, they produce reliable results. And from my personal experience, they are more reliable than some of the newer machines we have, which seem to break down more often (I’m looking at you, Büchi rotavaps).

The surrounding area: There is much I can say about Groningen, or the whole of The Netherlands for that matter, but I’m not that fond of tourism, so I’ll keep it concise. Groningen is located in the north of The Netherlands and is the biggest city there. By our standards, it’s pretty far from the much more densely populated west (Amsterdam, Rotterdam, The Hague), and consequently, the northern provinces of the Netherlands, and with it Groningen, are pretty isolated from the rest of The Netherlands and a completely different place altogether. There are a lot of schools in Groningen, which means a lot of students (roughly 45,000, against a total population of 185,000), which means that there is a lot of stuff that you can do in your spare time (as students have loads of it, which makes a nice business).

Summary: I really like it here in this department, and this city and I definitely can recommend you to come here as a graduate student, postdoc, or whatever. The research is good, the working environment is pleasant and the location is nice. But please, if you are looking for a position as a graduate student, be careful. Some don’t mind having a bursaal position, but some do, so if you’re offered a bursaal position think carefully about it.

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June 14, 2008

Weird Words of Science: isotope


The periodic table is the map of the chemical world. Columns collect atoms which share properties - all of the elements on the far right - He, Ne, Ar… - are all gases and all nearly chemically inert. The region at the bottom harbors elements more likely to be radioactive. Metals pool in the middle.

Each atom of an element has a characteristic number of protons - positively charged particles - in their nucleus. An atom with five protons is boron. One with 82? Lead.

Most atoms also have a number of uncharged particles - neutrons - in their nuclei as well. The sum of the number of protons and neutrons in a given nucleus is called its mass number. A boron atom with six neutrons has a mass number of 11: five protons and six neutrons. Take away a neutron and it’s still boron, but the mass number is now 10.

Atoms with different mass numbers but the same number of protons are termed isotopes. Most elements have several naturally occuring isotopes. The most abundant form of the element carbon has a mass number of 12. One percent of carbon atoms, however, have an extra neutron and a mass number of 13.

Scottish novelist and physician Margaret Todd coined the term for her distant relative Frederick Soddy at a dinner party in 1913. He had described his research to her and she responded that any good discovery need a Greek term to describe it. She suggested combining the Greek “iso” for same and “topos” for place - to emphasize that the mass number of an element doesn’t affect it’s place in the periodic table: argon-36 and argon-40 are both inert gases. Soddy went on to win the Nobel Prize in 1921 for his discovery - perhaps because his distant relation had coined him a such good term?

Progress, happy birthday and shoutouts

I’ve begun my 4th year in the lab and ended my 2nd year of blogging. Well… more like 4th year and 4th month, actually. I’m pretty pleased with my progress. I’ve published two papers and am getting ready to submit another and have yet 3 more to write (one being, apparently, a totally unfashionable book chapter. Which I still think is more awesome than a review article. Since, at the very least, I can sell the free copy of the book I get for over $100. Try doing that with a copy of ChemComm. So suck it.) The work at the bench is essentially done, though I continue to toil there on my “pet projects” that I really want to get off the ground. One project in particular may well tickle the balls off my boss if it works… but I’m not going to tell him until I’m done and it worked (It will… the laws of physics are always on my side.)

I do, however, want to just give a shout out to how much blogging has helped me. That not only includes the other bloggers out there like Mitch and Excimer and Psi*Psi and TotSyn (just to name but a few) but also the commenters. It has also made me a part of a much larger community than my own department could offer and I’ve relied on a lot of them for help. I have to say, I wouldn’t have progressed this far if it weren’t for this blog - which is quite the antithesis of what my boss was concerned with when he found out about it. Far from taking time away from research, it has given me fresh perspective on it and provided a constant stream of the “state of the state of the art” of the most important aspect of any field - the people that are in it.

Now is about the time I start looking for that next step, I suppose, in my academic training - focus on writing my papers and pushing the people who have papers I’m supposed to be on into writing theirs. As far as the blog goes, I have one more year on the contract with the server I’m on and then it’s lights out! Like Dylan Stiles and Paul Bracher before me, these blogs are transient things and here too, I shall pass. Below the fold you’ll find references to all the lit reviews I’ve done in the preceding 12 months. Don’t be alarmed, it’s just for my own archiving.

I’d like to give you, dear and gentle reader, the opportunity to complement or criticize the blog and make suggestions as to what you like or dislike.  I may or may not take them into consideration and, indeed, may well lash out at you, but at least I’ll read them all.

HE, Q., LUO, Y., CHEN, P. (2008). Elucidation of the mechanism of enzymatic browning inhibition by sodium chlorite. Food Chemistry, 110(4), 847-851. DOI: 10.1016/j.foodchem.2008.02.070

Jiang, L., Althoff, E.A., Clemente, F.R., Doyle, L., Rothlisberger, D., Zanghellini, A., Gallaher, J.L., Betker, J.L., Tanaka, F., Barbas, C.F., Hilvert, D., Houk, K.N., Stoddard, B.L., Baker, D. (2008). De Novo Computational Design of Retro-Aldol Enzymes. Science, 319(5868), 1387-1391. DOI: 10.1126/science.1152692

Ikeda, T., Stoddart, J.F. (2008). Electrochromic materials using mechanically interlocked molecules. Science and Technology of Advanced Materials, 9(1), 014104. DOI: 10.1088/1468-6996/9/1/014104

Berná, J., Goldup, S., Lee, A., Leigh, D., Symes, M., Teobaldi, G., Zerbetto, F. (2008). Cadiot–Chodkiewicz Active Template Synthesis of Rotaxanes and Switchable Molecular Shuttles with Weak Intercomponent Interactions. Angewandte Chemie International Edition, 47(23), 4392-4396. DOI: 10.1002/anie.200800891

Trost, B., Zhang, T. (2008). A Concise Synthesis of (−)-Oseltamivir. Angewandte Chemie International Edition, 47(20), 3759-3761. DOI: 10.1002/anie.200800282

Killops, K.L., Campos, L.M., Hawker, C.J. (2008). Robust, Efficient, and Orthogonal Synthesis of Dendrimers via Thiol-ene “Click” Chemistry. Journal of the American Chemical Society, 130(15), 5062-5064. DOI: 10.1021/ja8006325

Jux, N. (2008). The Porphyrin Twist: Hückel and Möbius Aromaticity. Angewandte Chemie International Edition, 47(14), 2543-2546. DOI: 10.1002/anie.200705568

Ternes, M., Lutz, C.P., Hirjibehedin, C.F., Giessibl, F.J., Heinrich, A.J. (2008). The Force Needed to Move an Atom on a Surface. Science, 319(5866), 1066-1069. DOI: 10.1126/science.1150288

Sasaki, T., Tour, J. (2008). Synthesis of a New Photoactive Nanovehicle: A Nanoworm. Organic Letters, 10(5), 897-900. DOI: 10.1021/ol703027h

MEHTA, G., ROY, S. (2008). Enantioselective total synthesis of the novel antiproliferative metabolite (+)-hexacyclinol. Tetrahedron Letters, 49(9), 1458-1460. DOI: 10.1016/j.tetlet.2008.01.014

Qin, L., Banholzer, M., Xu, X., Huang, L., Mirkin, C. (2007). Rational Design and Synthesis of Catalytically Driven Nanorotors. Journal of the American Chemical Society, 129(48), 14870-14871. DOI: 10.1021/ja0772391

Falk, K.G., Nelson, J.M. (1907). . Journal of the American Chemical Society, 29(12), 1739-1744. DOI: 10.1021/ja01966a007

TAKAHASHI, K., TANABE, K., OHNUKI, M., NARITA, M., ICHISAKA, T., TOMODA, K., YAMANAKA, S. (2007). Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors. Cell, 131(5), 861-872. DOI: 10.1016/j.cell.2007.11.019

Yu, J., Vodyanik, M.A., Smuga-Otto, K., Antosiewicz-Bourget, J., Frane, J.L., Tian, S., Nie, J., Jonsdottir, G.A., Ruotti, V., Stewart, R., Slukvin, I.I., Thomson, J.A. (2007). Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells. Science, 318(5858), 1917-1920. DOI: 10.1126/science.1151526

Han, J., Jose, J., Mei, E., Burgess, K. (2007). Chemiluminescent Energy-Transfer Cassettes Based on Fluorescein and Nile Red. Angewandte Chemie International Edition, 46(10), 1684-1687. DOI: 10.1002/anie.200603307

Baskin, J.M., Prescher, J.A., Laughlin, S.T., Agard, N.J., Chang, P.V., Miller, I.A., Lo, A., Codelli, J.A., Bertozzi, C.R. (2007). From the Cover: Copper-free click chemistry for dynamic in vivo imaging. Proceedings of the National Academy of Sciences, 104(43), 16793-16797. DOI: 10.1073/pnas.0707090104

Soo Choi, H., Liu, W., Misra, P., Tanaka, E., Zimmer, J.P., Itty Ipe, B., Bawendi, M.G., Frangioni, J.V. (2007). Renal clearance of quantum dots. Nature Biotechnology, 25(10), 1165-1170. DOI: 10.1038/nbt1340

Song, F., Garner, A., Koide, K. (2007). A Highly Sensitive Fluorescent Sensor for Palladium Based on the Allylic Oxidative Insertion Mechanism. Journal of the American Chemical Society, 129(41), 12354-12355. DOI: 10.1021/ja073910q

Yanagisawa, M., Tashiro, K., Yamasaki, M., Aida, T. (2007). Hosting Fullerenes by Dynamic Bond Formation with an Iridium Porphyrin Cyclic Dimer: A “Chemical Friction” for Rotary Guest Motions. Journal of the American Chemical Society, 129(39), 11912-11913. DOI: 10.1021/ja0747526

Soloshonok, V., Ueki, H., Yasumoto, M., Mekala, S., Hirschi, J., Singleton, D. (2007). Phenomenon of Optical Self-Purification of Chiral Non-Racemic Compounds. Journal of the American Chemical Society, 129(40), 12112-12113. DOI: 10.1021/ja065603a

Jiang, X., Vieweger, M., Bollinger, J., Dragnea, B., Lee, D. (2007). Reactivity-Based Fluoride Detection: Evolving Design Principles for Spring-Loaded Turn-On Fluorescent Probes. Organic Letters, 9(18), 3579-3582. DOI: 10.1021/ol7014187

Li, X., Fan, L., Liu, D., Sung, H., Williams, I., Yang, S., Tan, K., Lu, X. (2007). Synthesis of a Dy@C82 Derivative Bearing a Single Phosphorus Substituent via a Zwitterion Approach. Journal of the American Chemical Society, 129(35), 10636-10637. DOI: 10.1021/ja074321n

Koide, Y., Urano, Y., Kenmoku, S., Kojima, H., Nagano, T. (2007). Design and Synthesis of Fluorescent Probes for Selective Detection of Highly Reactive Oxygen Species in Mitochondria of Living Cells. Journal of the American Chemical Society, 129(34), 10324-10325. DOI: 10.1021/ja073220m

Long, J.H., Johnson, W.A. (1907). . Journal of the American Chemical Society, 29(8), 1214-1220. DOI: 10.1021/ja01962a012

Kavanaugh, C.J., Trumbo, P.R., Ellwood, K.C. (2007). The U.S. Food and Drug Administration’s Evidence-Based Review for Qualified Health Claims: Tomatoes, Lycopene, and Cancer. JNCI Journal of the National Cancer Institute, 99(14), 1074-1085. DOI: 10.1093/jnci/djm037

PARK, H., LEE, H., SHIN, M., LEE, K., LEE, H., KIM, Y., KIM, K., KIM, K. (2007). Effects of cosolvents on the decaffeination of green tea by supercritical carbon dioxide. Food Chemistry, 105(3), 1011-1017. DOI: 10.1016/j.foodchem.2007.04.064

Scheerer, J., Lawrence, J., Wang, G., Evans, D. (2007). Asymmetric Synthesis of Salvinorin A, A Potent κ Opioid Receptor Agonist. Journal of the American Chemical Society, 129(29), 8968-8969. DOI: 10.1021/ja073590a

Cao, H., Xiong, Y., Wang, T., Chen, B., Squier, T., Mayer, M. (2007). A Red Cy3-Based Biarsenical Fluorescent Probe Targeted to a Complementary Binding Peptide. Journal of the American Chemical Society, 129(28), 8672-8673. DOI: 10.1021/ja070003c

YANG, D., KONG, D., ZHANG, H. (2007). Multiple pharmacological effects of olive oil phenols. Food Chemistry, 104(3), 1269-1271. DOI: 10.1016/j.foodchem.2006.12.058

Zhang, J., Du, P., Schneider, J., Jarosz, P., Eisenberg, R. (2007). Photogeneration of Hydrogen from Water Using an Integrated System Based on TiO2 and Platinum(II) Diimine Dithiolate Sensitizers. Journal of the American Chemical Society, 129(25), 7726-7727. DOI: 10.1021/ja071789h

(22 less then last year.  Damn. )

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June 12, 2008

University of Maryland, College Park

University of Maryland, College Park.
Department of Chemistry and Biochemistry

Facilities: The chemistry department is made up of five main wings, and there are a few biochemistry professors in a buliding that is a five minute walk away. Most of the wings are old and were built a long time ago. Probably during the time that Neil Gordon and Marker were here. Wing one gets real hot in the summers and real cold in the winters, so it’s not a very pleasant place to be in and to be doing research, especially if you’re on the top floor. The first wing and the biochemical wing (wing five) also get called out for having an unusual number of cokcroaches who became mutated by asbestos and mercury that accumulated there over the last 80 years. Wing one also has a population of wild mice and at least one bat in the basement beside the NMR room. While this can seem as a negative, I believe it frees up instrumentation for the less squeamish after dark. There are bats flying outside anyways all the time. You only don’t see them if you’re blind (they operate at night so you might have a valid excuse). If you don’t like bats, don’t come to Maryland. That said, we have a new wing that was built recently that is quite large and is everything you expect from a modern research facility. It’s a pleasure to do research in those labs. The fumehoods are large and outlets are abundant, and the temperature is controlled throughout the year. The building houses the lasers of our photochemists and physical chemists along with organic research labs and undergraduate organic teaching labs. The library is just a short walk away. The building has a beautiful lunch area as well that lets in a lot of natural light. It’s the perfect place to be in during the current heat wave.

Equipment: The equipment is awesome. Everything is available. Minor complaints are the really old EPR and FAB machines that keep breaking down. Otherwise, the Maldi and HPLC-ESI-MS are online most of the time (unless someone contaminates them) and you can use them if you’ve been trained not to break them. It doesn’t seem to help, but at least they get repaired fast enough. Most of the professors are happy to share the equipment, so you have access to Solvent purification systems, GC/MS, HPLC lasers, etc… that is stashed away in individual labs. We do have an X-Ray center with a Powder X-ray crystallographer and a really good spectroscopist who can solve a structure even if it’s completely different from what you think it is in record time. We have five NMRs. One 400 for general use and one automatic. Also a 400 with a very sensitive probe and a 500 (special heteronuclear probe) and 600 as well. The biochemist in the separate building also have a 600 or two I believe. Getting NMR time is not a problem. The person in charge has been in this department for 30 years and the whole facilty runs like a well oiled machine. It’s true that the training for each subsequent instrument is draconian, but as a plus the instruments are hardly off-line and you can do any experiment and any nucleus you want. From what I’ve heard, we have one of the best NMR situations in the country and it mostly has to do with the person in charge. There is been some very interesting host-guest chemistry that has only been possible because the guy in charge keeps up with the latest techniques and gets the latest probes. A bit of a minus is the large number of contract jobs that we get from NIH and biochemistry companies that are right beside us, so you actually might find that all the NMRs are booked. Crazy!

Faculty: I’m not a member of the faculty, but commenting as an outsider, it seems like a bit of a mixed bag that you would find at any other similar top 50 place. There are people who don’t care about getting grants and/or research. There are ambitious people who want to win a Nobel and/or become famous. Old profs who are easy going and old profs who are still slave-drivers and new profs who want to get tenure. The faculty page lists a lot of people who aren’t actually in the department (affiliate professors), but we are a large department and every discipline of chemistry is represented. There are people who hate each other, but it hasn’t come to much of a boil. They hired a new chair from the outside five years ago because the department was going downhill and was divided. This cannot be in a flagship campus with a top ten physics program, so they just threw a lot of money at us and we got out new chair. The new chair is clearly insane. He always talks about how we’re going to be in the top 10 soon and how it’s important to raise our productivity and multi task. He also keeps firing the business office staff on a regular basis for what appears to be no reason at all. But he also is very effective at what he does and he clearly go the job done. That’s why he got re-elected for a second term. The faculty is less divided and he got rid of some dead wood and we actually rose pretty high in the rankings in the last four years, which is what he wanted. It’s likely we’ll be in the top 20 in the next four years if things keep going the same way. The chair is very good at pulling in money and hiring away established people from other departments. It’s not really hard to become a top twenty school considering we have the best department in the Washington D.C. area, which isn’t saying much. Still, because NIH and a large concentration of biotech is right there, it seems logical that we should be able to pull it off. Some of the recent assistant prof hires haven’t produced that many papers, and the bar for tenure appears to have gotten pretty big around here in line with the grandiose visions (a person with an okay publication record for five years ago didn’t get tenure recently). So you may have to choose carefully if you would like to work with a new professor when you come here. We seem to be hiring a new person every year.

The Surrounding Area: Well, it’s D.C. You can choose to live in a far away suburb with a car. That makes it possible to afford the rent on your meagre stipend, but the car price might push you into poverty with gas and repairs. Or, you can choose to live in one of the most expensive housing markets in the country inside the Capitol Beltway on your meagre stipend. If you do this, you are foolish for having a car, the metro system is quite good if you live close to a stop. The rent will be astronomical, but at least it will be easier to budget. The university it situated in a dead suburb that has a few crappy bars. I usually go out to the city on the weekends. The bar scene is fantastic and is something that only the locals in DC know about it. Most tourists come for the Smithsonian and to see the White House and what-not. I did all that, and I still go to the National Arboretum regularly, but it’s the amazing outdoor restaurants and bars that keep me going back to the city on the weekends to relax. I also enjoy walking around Georgetown when it’s not too hot out. It’s a nice part of the city and the university is beautiful (even if their chemistry department is worse than ours). While I used to live in the ghetto area for a bit, I don’t recommend it as some days I came home from the lab to find a murder scene outside of my house. And it wasn’t the triple deaths during a shoot-out one block outside my apartment that forced me to move to College Park, it was the high rental price in the ghetto. How do they expect non-drug dealers to afford that? I guess they were looking for these people called ‘young professionals’. I recommend renting in College Park since it’s still the cheapest suburb and it’s right beside the university, and then going out to Silver Spring or Adams Morgan via metro on the weekends. As a plus, you can say to all your friends that you have lived inside the Beltway. As a minus, you can say to all your friends that you have lived inside the Beltway. Ultimately, DC is one of the most fun metropolitan areas in the country. It’s huge and there is something for everyone here. We even have great theater and classical music (free at the Kennedy Center!).

Sumary: We have a great program that is being dragged by force, sometimes against it’s will, upward in the rankings. We have great equipment and a great location. The stipend is getting bigger but still has trouble matching the cost of living in DC. We’re all poor here. The faculty is not automatically well recognized except for a couple of people, yet. We also have an uncertain situation in terms of how easy or hard it is to get tenure. I find about half the students apathetic and most are not as ambitious as they would be in a top ten place. While this is good in creating an easy-going atmosphere, this makes life harder for profs who want to get tenure or who want to win a Nobel. The state is cutting funding, but our chair seems to find the money somewhere. I don’t know if we’ll be top 20 in four years like he wants (this is why I commented earlier that he might be insane), but it’s hard to argue that we’re probably in the top 30 or 35 now. I realize rankings are stupid, but this feeling of trying to improve no matter what has sort of permeated the department a little bit, and for a grad student, that means that if you’re willing to work hard, success and top publications will be yours for the taking.

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June 10, 2008

Angry (and bitter)

I remember in undergrad, the age of graduate students could be measured by the layers of bitterness, much in the same way (and as easily as) the age of layered rocks could be ascertained by the striation of color and texture in the Badlands. The bitterness wasn’t a veneer, like the haughty sense of supreme knowledge they had, it was something that came from the core. Nor was it just the arrogance and the self-righteousness they developed as a result of moving “up.” I wondered if that was the natural result of school and the dysfunctional relationships with advisers, awkward relationships with cohorts, or if it was trying, trying, trying so hard to appear so smart for so long in the face of daunting competition.

I mostly worked around TSers as an undergrad, that’s the limit of my experience, but I can’t imagine it’s a local phenomenon. I was made aware of the fact by my little old grandmother who, in her advanced years has come to dispense with niceties and preambles, told me that I had become so “angry and bitter.” The comment was precipitated by my disgust for my uncle’s misuse of antibiotics. I forcefully advocated that he should get very ill and end up in the hospital or go to prison for failing to complete not one but TWO regiments of antibiotics. She was probably reacting to the forcefulness of the way I put it, but it at least made me think. I’m about to start my 5th year and am about to start writing my thesis within a few months. I’m not a bitter 8th year with no publications. I think, when all is said and done, I’ll have what I would consider a “successful” graduate career with multiple ACS journal publications. Maybe I’m just horribly arrogant and it comes off as angry and bitter?! I’ve been accused of being cocky since I got here (it’s my nature) but never angry and never bitter.
When was the last time I had a vacation? December, probably. Maybe that’s what I need.

In the end, it seems as though the anger and bittnerness goes away, since the PhDs (at least in industry) were hardly ever bitter. Arrogant, but not angry and bitter - at least not at Eli Lilly. I’ve only worked with one post doc that I would consider “angry and bitter” but the last I checked he was working at Target as a cashier… with a PhD… the man had serious issues. So, it’s a transient thing that I’ve always chalked up to graduate school. I wish I knew what caused it and if I’m “coming down” with it. I need some serious introspection, I think.

By the by… I’ve gotten pretty much nothing for personal reviews of schools. Last time I had to stop the friggin flood of them and now I’ve gotten ONE. WTF happened? My stats clearly show NO decline in readership. Are you people just afraid to talk of the wonderful shit in your department or what?

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June 09, 2008

North Carolina State University - Chemical Engineering

For the Chem Engineers, user “ChemE” has sent me this. I’m rather ignorant about Chemical Engineering, though I do know they are more employable and paid more than chemists - at least according to this week’s C&E news.
As you read this, please consider emailing me a description of your department! I’m very keen on getting well written emails regarding the facilities at these very excellent schools (even though some of them have been written before, I would like something nice. No offense to the prior authors.) Rutgers, University of Notre Dame, Louisiana State, SUNY Buffalo, and Virginia Polytech. Please email me at kylefinchsigmate at gmail.com, I’m looking into a small pilot program with these schools and would love to get started. More on that later. Please enjoy this rather well written description of NCSU’s ChemE department:
Department: Chemical Engineering
University: North Carolina State University

Before the review, a few words about your reviewer so you can take note of my biases. I have completed my first year at NCSU’s chemical engineering graduate program. I came here immediately after college, which consisted of two years at Rose-Hulman Institute of Technology in Terre Haute, IN, and two final years at Northwestern University. I have enjoyed my time at NCSU so far, I got the adviser and project I wanted, and the Man has yet to screw me in some sort of fashion. Nonetheless, I’ll attempt to keep this review as objective as possible.

Facilities: First, the website sucks. I know it, the students know it, the faculty knows it, and it’s being worked on. Our department occupies the first two floors of a three-year-old, three-story building (MatSci on top) on NCSU’s Centennial Campus. The Campus will eventually contain the entire engineering college, along with a number industrial labs and headquarters. “Eventually” is still a few years away, however, and there’s construction occurring year round. Conveniently, a library sits about a five minute walk away which houses many of the technical volumes you might need. You can obtain books from the main campus library through this satellite library, as well (on a daily basis). Despite having a new building, it’s apparent our department has already started to outgrow the available space. My office is actually a converted lab, which is unfortunate because my lab needs space for a number of instruments. I’m not sure how the designers over looked this constraint. There’s a parking deck next to the building that costs ~$280 a year for a permit.

I should point out that the bio-related research occurs in two different buildings. One is a building that houses academic and industrial research labs, and the other is a brand new (< 1 year) building that houses the biotech program. I can’t speak on the quality of these facilities, but I haven’t heard any complaints. If you’re seriously interested, I could get an opinion from someone in the buildings.
Equipment: Speaking of instruments, I have yet to find anything unavailable. My own group has a GPC/SEC, IR, two ellipsometers, a number of contact angle measurers and eventually an instrument to measure birefringence in polymer solutions (my current research project). We let a number of other groups in and out of the department use these instruments. I know of one group with an AFM in the building, but there are AFMs and SEMs available in a shared instrument facility on campus (8 minutes walk, 3 minute drive with parking the aforementioned permit covers). One group here does significant amounts of electrospinning, and another group’s lab serves as a show space for rheometry instruments supplier, so they have a ridiculous amount of high end, brand new equipment. There’s a 64-CPU cluster (I think it’s 64) in the building if you’re into that sort of thing, and one of the faculty heads the Center for High Performance computing, which has even more computing power. I’m not sure what bio-related instrumentation exists in the previously mentioned “bio buildings,” but I can find out if you’re really interested. In short, instrumentation is not a problem at this large state university. If it’s not at the actual University, you can drive twenty five minutes west to UNC or Duke. If it’s not there, you just might have to invent it.
Faculty: First of all, it really appears they get along. I see significant collaboration within the department, and haven’t heard any gossip of people really hating each other. I can think of one adviser who had a student leave the group (happened before I got here), but that’s the worst I heard, and the older students let the first years know it happened. Certainly some advisers are more popular than others, but we have a large faculty, and I see good interdisciplinary work. At this point, I get the feeling my advisor actually wants me to succeed. Based on his interactions with senior students in the group, that will continue. I’ve also found a number of other professors easy to approach, interested in what I have to say/ask, and quite friendly.
If my equipment descriptions didn’t give it away, we have a strong polymer showing here that runs the gamut from physics to processing to modeling. The two theoretical faculty are extremely well known in their field, though retirement might be approaching soon for one of them (though he did take a new student this year). We have a colloids/nanoscience group run by a star in the field. Other areas of work include ionic liquids, nanofab (including a brand new faculty this Fall), and of course the bio-faculty (more info from a better source available on request). Speaking only for my own group, we collaborate with professors in chemistry, the college of textiles (they cover polymers) and paper science (think paper substrates).
The surrounding area: I spent two years in one of the worst places in America, and two years in Chicago, so I have a couple of extremes to cast Raleigh and North Carolina against. It’s a nice place to live–plenty of typical attractions/entertainment, surprisingly good local restaurants (NOT chains), and you make above capita as a grad student. It’s certainly not a big city, but is a nice place to live. Chapel Hill, which is a better college town in my opinion, is about a twenty five minute drive away. Don’t go to Durham, it sucks. Several beaches are two hours away, and the Outer Banks are three hours. I’ve been to a few, and they’re actually pretty nice. Good fishing, good eating, pleasant. I have yet to make it to the mountains (about two hours west), but there’s acceptable skiing in the winter. The winters were easy for an upper midwest native, and the summers should be easy for someone from the South. It’s a good balance.
Summary: I think NCSU has an outstanding program, and I think it will continue to improve. My only complaint is the lack of space in a new building–no foresight from the designers. I’m not sure what the NSF ranked us, but US News put us in a tie at 20. I’m not exactly sure what that means, but it apparently means at least the top 20 schools crank out high caliber research and researchers. Apparently just like chemistry, chemical engineering suffers from the “high profile” problem. When I applied to grad schools, I could only name schools in the top ten. An hour long meeting with a professor at Northwestern revealed that eleven to twenty also produce quality research, and it’s not where you go, it’s who you work with. With that in mind, NCSU has well connected, recognized advisers in several fields. You will make money well above the cost of living, and find the opportunities to succeed as a researcher if you’re willing to work hard.

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May 18, 2008

Writing in Santa Fe

In about 8 hours, I should be taking off for Santa Fe and the 2008 Santa Fe Science Writing Workshop. I'm bringing some of the work I've done on the blog, trying to shape a longer and coherent narrative. There are about 40 students coming - from a range of backgrounds. Scientists, journalists, students. My instructor will be Laura Helmuth - the science editor for the Smithsonian.

May 02, 2008

How to tell if you're really a chemist

You pronounce unionized as UN-ionized not union-ized.
When you hear the word mole, you don't think of an animal.
Milli is a prefix, not a girl's name.

This Sceptical Chemist blog post suggests a new test to tell if you're really a chemist. What do you see when you look at this illustration by Joon Mo Kang? If the first things you see are five bonds to carbon, and three bonds to a hydrogen, you're a chemist. If that's all you see - you are really a chemist.

A couple of chemists missed the point of the illustration so completely they wrote to the NY Times to let them know of their chemical illiteracy. Another blogger was also vexed by the nonsensical molecule.

I'll admit it -- I saw five bonds.

April 29, 2008

The Grecian Bends: Ladies' Corsets and Henry's Law

In an earlier post I suggested there was a connection between ladies' corsets and Henry's Law. A general statement of Henry's Law is that the solubility of a gas in a liquid depends on the pressure of the gas above the liquid. An everyday example is soda. A can of soda is pressurized by exposing it to carbon dioxide having equivalent of about 2.5 times atmospheric pressure at room temperature. When you quickly lower the pressure of carbon dioxide over the liquid, say by opening the can, the solubility decreases and the gas adjusts by rapidly coming out of solution. Fizzing results (and eventually the soda goes flat).

When a diver dives the pressure of the gases breathed increases, and the amount dissolved in the blood increases. Diving to just 50 feet increases the total pressure to roughly that of the carbonated soda! Rapidly ascending reduces the pressure, just like opening the can of soda, and the gas rapidly comes out of solution - the diver's blood can "fizz". Bubbles in the blood and body tissues are clearly not a great thing, and the physiological effects range from the relatively minor (bubbles in the skin layers) and joint pain, to potentially lethal embolisms in the brain and lungs.

This phenomenon was first observed by Robert Boyle in 1670 who noted the formation of bubbles in the eyes of a snake that had been placed in a high pressure environment, then rapidly decompressed. "I once observed a viper furiously tortured in our exhausted receiver… that had manifestly a conspicuous bubble moving to and fro in the waterish humour of one of its eyes." Before the effects was widely understood, many construction workers suffered from "caisson workers' disease" while working in pressurized environments (caissons) under rivers.

Dive tables - a schedule for ascending from a dive that reduces the chance of decompression sickness - were first created for use by British Navy divers in the early 20th century. How do whales and dolphins cope without dive tables? Half-mile deep, hour long dives are not uncommon - and a rapid ascent from depth could cause a massive case of the bends. They may not be immune - recently researchers have found evidence for chronic decompression injuries in sperm whales. The whale bone in the photo above shows evidence of dysbaric osteonecrosis (bone death caused by rapid decompression).

What does this all have to do with ladies' corsets? In the 1870s tight corsets and big bustles were all the rage. The posture forced upon women wearing these fashionable undergarments was called the Grecian Bend. As decompression injuries caused a similar posture, workers on the Brooklyn Bridge christened the syndrome "the Grecian bends", soon shortened to "the bends".


The photograph of the whale bone is by Tom Kleindinst, Woods Hole Oceanographic Institution and is used with permission.

The image of the Grecian Bends is from the Library of Congress

April 14, 2008

Neurodevelopmental Disorders in Children: Autism and ADHD

While the generally accepted causes of neurodevelopmental disorders like Autism and ADHD include genetic and environmental factors, a wide range of toxic chemicals in the environment have also been associated with these disorders.

April 08, 2008

Concentrated Chemistry: American Chemical Society National Meeting

The American Chemical Society national meeting is on in New Orleans this week. Somewhere on the order of 10,000 chemists will be here for at least some of the week - it's noticeable on the streets to be sure.

The Nature Chemistry group win the prize for most challenging travel. Read the teaser at the Sceptical Chymist - and place your bet on whether United Airlines will get them home again. A road trip to London isn't going to be the solution to return travel woes (unless that Bering Strait tunnel project gets off the drawing board much sooner than anticipated...).

The ACS has an oral history project going...and I'm signed up to be videotaped this afternoon.

My favorite t-shirt seen at the meeting: The name's Bond. Ionic bond. Taken, not shared.

March 26, 2008

Random Facts about Ludwig B.

Not that Ludwig B. - the other Ludwig B: Ludwig Boltzmann, an Austrian physicist.

Boltzmann's name is familiar to many science students through the eponymous constant: 1.381 x 10-23 Joules/mole-Kelvin, which appears in many equations. The constant (usually written as k) arises from the proportionality between the absolute entropy of a system (S) and the number of possible arrangements of that system (W). Boltzmann's expression of the entropy, S=k ln W, is inscribed on Boltzmann’s tombstone in Vienna, Austria. Boltzmann did not write it in this form, however, Planck did.

Boltzmann also has two other equations named for him, the first is a diffusion equation used in neutron transport theory and the second describes particles in a gravitational field. In 1904, Boltzmann gave lectures on mathematics at the World’s Fair in St. Louis. He was also a popular lecturer in philosophy at the University of Vienna. Boltzmann is considered the founder of statistical mechanics, and a strong proponent of the “atomistic” view that underscored the importance of understanding the behavior of atoms and molecules in order to understand the bulk.


Loosely, the entropy is a measure of the "randomness" in a system.

March 24, 2008

Allotropes and architects: buckminsterfullerene

Responding to an earlier post on inert gases, a commenter wondered if buckminsterfullerene might act as an inhalation anesthetic - given that, like xenon, it's a large, polarizable ball of electron density. It might, if you could get enough to inhale. At room temperature, the vapor pressure is 5 x 10-6 torr. Very roughly, that's about a billionth of atmospheric pressure. For comparison's sake, the pressure of xenon necessary to induce anesthesia is about 500 torr, or 65% of normal atmospheric pressure. If you want higher pressures, you need higher temperatures: buckminsterfullerene sublimes (goes directly from the solid to the gas phase, like dry ice) just above 1000F. Not great to breathe...

While likely impractical as an anesthetic, buckminsterfullerene has asthetic properties. It's a highly symmetric molecule - having iscosohedral symmetry. Kroto and Smalley discovered the new allotrope of carbon, C60, in vaporized graphite and named it for the architect (Buckminster Fuller) who made famous the geodesic domes it resembled. Two more familiar allotropes of carbon are graphite and diamond.

Allotropes are differing forms of the same element. The roots of the word are Greek - allos for different and tropos for "turn of mind". A different turn of mind? It's what Smalley needed to propose the now iconic structure, over a beer at his kitchen table.


Another allotrope of carbon is lonsdaleite - named for Kathleen Lonsdale, an Irish crystallographer who determined the structure of benzene and my brother-in-law's godmother.

March 06, 2008

Inert gases aren't always inert

Earlier this week I posted about the intoxicating effects of nitrogen gas at high pressures, which leads divers to substitute helium for nitrogen. An astute reader wondered in the comments why argon wasn't used, as it is substantially cheaper. It turns out that argon is even more potent intoxicant than nitrogen at high pressures! But aren't argon and helium inert gases?

The elements in the last column in the periodic table comprise what IUPAC (the International Union of Pure and Applied Chemists is to chemists what the IOC is to sports) calls Group 18, but what most of us learned in high school to call the noble or rare, gases. Helium, argon, neon, krypton, xenon and radon are indeed all gases under standard conditions, but the modifier misses the mark by a bit.

Rare? Take a deep breath, you've just inhaled about 100 mg of argon. Almost 1% of the atmosphere is argon; there is almost three times as much argon in the air as there is CO2. "Noble" generally means "unreactive" to a chemist. The noble metals, such as gold and platinum are resistant to oxidation - they don't rust - unlike the "base" metals such as iron and copper. Much like gold and platinum, under the right conditions these inert gases can be made to react. The first noble gas compound - xenon hexafluoroplatinate - was synthesized in 1962, but there were earlier clues that these gases might not be completely unreactive. The anesthetic effect of xenon had been observed in the 1930s, and reports of its use in clinical settings appeared in the late 1940s.

The mechanism by which nitrogen, argon and xenon behave as anesthetics isn't completely understood. The best theories at the moment suggest that the gases interact with ion channels - but whether they binding chemically or physically is not clear.

March 04, 2008

Breathing Deeply

The tunnels deep beneath New York that bring crystal clear water from the reservoirs upstate to the city are aging. Divers are busy assessing the infrastructure - and it's literally a high pressure job. In order to avoid time consuming daily decompressions, the divers are living in a high pressure environment for weeks at time, almost 20 times normal atmospheric pressure. As AP reports, the pressures require that the men breathe a helium-oxygen mixture. Unfortunately, the reason given in the article for breathing the squeaky voice inducing mix: "the nitrogen in regular air is too heavy at 600 feet and their lungs could not handle the pressure." is utter nonsense.

Nitrogen does not weigh more under pressure, and the total pressure of the gas in the divers lungs is high, regardless of the identity of the gas (oxygen gas weighs more than nitrogen does, in fact). The real reason has to do with Dalton's law of partial pressures, and the fact that at high pressures, neither oxygen nor nitrogen are benign substances.

Dalton's law says that the pressure of each gas in a mixture is a function of the percentage of that gas and the total pressure of all the gases. For example, at 30,000 ft, where the total pressure is 0.3 atm and the fraction of oxygen in the air is 21%, the partial pressure of oxygen is 0.063 (humans need a partial pressure of about 0.1 atm to oxygenate their blood).

At the depth of the NYC tunnels, the total pressure is just over 18 atm, so the partial pressure of oxygen would be 3.8 atm. Above a partial pressure of roughly 1.5 atm oxygen gas is seriously toxic. The partial pressure of nitrogen 600 feet below the surface is about 14 atm. Nitrogen narcosis, rapture of the deep, sets in at pressures above 4 atm. At these depths, nitrogen is essentially an anesthetic!

Introducing an inert gas into the breathing mix, such as helium, reduces the percentage of oxygen and nitrogen in the air, thus reducing their partial pressure and reducing the danger of oxygen toxicity and nitrogen narcosis. The need for the specialized breathing mix has nothing to do with the heaviness of the nitrogen and everything to do with the toxic effects of these gases at high partial pressures.


Eliminating nitrogen completely from the mix can also reduce the potential for developing the bends (bubbles of gas that form in the tissues when pressure is reduced) - but that has to do with Henry's Law and ladies corsets, and is another blog post!

March 02, 2008

Hydrazine: Hype or Hypergol?

Last week the US government announced that it believes it has successfully breached the fuel tank on a dead satellite, effectively destroying the toxic fuel stored on board: 1000 pounds of hydrazine. Hydrazine is a simple nitrogen compound, two NH2 groups joined by a NN single bond. How does such a simple compound power a rocket?

Hydrazine is a hypergolic propellant - one that ignites as soon as it comes into contact with an oxidant (something that will react with it to effectively strip away some electrons from the reactant and force the molecule to bond differently, the changes in the bonds between atoms are what release the energy). Hypergolic is apparently a term coined by the German rocket program from hyper (very) + ergon (Greek for work) + ol (from oleum, the Latin for oil). Hydrazine is that, a liquid (if not particularly oily one) that can be used to push satellites around in orbit - to do work.

Hydrazine is a solid in the satellite's tanks, and once thawed can be catalytically and rapidly decomposed. Almost any metal will do, though iridium is the usual choice. The reactions produce lots of very hot gases, which you can direct through a thruster:


3 N2H4 → 4 NH3 + N2
N2H4 → N2 + 2 H2
NH3 + N2H4 → 3 N2 + 8 H2

A little thermochemistry can quickly tell you just how much energy you might produce from 1000 pounds of hydrazine. The overall reaction is:

5 N2H4 → 5 N2 + 10 H2

which releases 50,000 Joules of energy per mole of hydrazine. A mole of hydrazine weighs about 32 grams, so you get enough energy to make a cold cup of coffee hot from just over an ounce of hydrazine (do NOT try this at home!). If all the hydrazine in that satellite went up at once, it would release about 8 billion Joules (enough to keep the average US citizen in energy for more than a week).


A photo of a standard satellite thruster.

February 23, 2008

Melting Points

Pain perdu - a delicious part of my New Orleans heritage and better known in most of the US as french toast - has a long history. The earliest extant recipe is in Latin and dates to the 4th or 5th century! Friday brought a snow day for my kids, and come evening, some experimental time for me in my favorite home lab.

After a day spent teaching and shoveling in the sleet, I made pain perdu aux pommes from Simon Hopkinson's Second Helpings of Roast Chicken. Think french toast, vanilla custard, apples and caramel sauce. The first step in making the caramel sauce is to melt sugar over high heat. As I stirred the dry sugar in my heaviest sauce pot, alert for the first sign of melting, I flashed back to my days in an organic chemistry research lab. Melting points were used both to identify products (though even then, spectroscopic methods such as NMR were the gold standard) and to verify purity. Taking an accurate melting point required patience - and being attentive to the appearance of that first glistening drop of liquid in the fine capillary tube. It looked almost as if the crystals were sweating.

How is the purity of a compound related to its melting point? An impure sample will tend to melt over a few degree range, pure samples will melt at a sharp temperature. Impurities in a solid will also depress its melting point, in the same way that applying salt to ice (another application of chemistry appropriate for a snow day) lowers the freezing point. This phenomena also offers a low tech way to confirm the identity of a compound. Make a mixture of the sample to be identified and a known sample of (presumably) the same stuff. If the melting point is sharp and the same as the pure compound, the unknown is certain to be what you think it is. This will work even if the melting points of the two compounds are fortuitously the same.


A nice film of a melting in a capillary tube can be found at Wellesley's organic chem lab site.

February 19, 2008

Repackaging Vitamins: Niacin


Vitamins are small molecules (where small is relative to proteins!) that a living organism cannot synthesize, but are nevertheless required. The word vitamin was coined by a Polish biochemist, Kazimierz Funk by sandwiching together "vital" and "amine". Not all vitamins turned out to be amines (molecules with an NH2 group in them), however the name stuck.

One such non-amine "vital amine" has the structure shown below. It's a carboxylic acid (the COOH group). Originally designated as vitamin PP, it is now better known as the third of the B vitamin complex or B3. PP stood for pellagra preventing factor. Pellagra is a nutritional deficiency, once common in Italy, that results in rough skin - pella is Italian for skin.

The original common chemical name for B3 was nicotinic acid. (The synthetic form can be made by oxidizing nicotine with nitric acid.) In the late 1930s, niacin (NIcotinic ACid vitamIN) was adopted as the preferred name, to avoid confusion with nicotine. (I'm unclear why this was undesirable; smoking was pervasive.)

Repackaging scientific terms to make them less frightening for the general public is not just a historical phenomenon. Much more recently the application of NMR (nuclear magnet resonance) to medical imaging saw its "nuclear" dropped (thus forestalling any potential association with nuclear radiation) to become MRI (magnetic resonance imaging). It should be made clear, that like nicotinic acid, which contains no nicotine, NMR does not require nuclear radiation.

February 11, 2008

Biofueling the future

Whatever their motivation - be it energy independence for the U.S. or an attempt at fighting climate change for Europe - world governments are now heavily subsidizing biofuels.

February 06, 2008

Ant-acids

I'm teaching general chemistry this semester. Acids and bases are currently on our agenda, in particular how to assess the strength of an acid based on its molecular structure. When dissolved in water, strong acids, such as hydrochloric acid (HCl) or sulfuric acid (H2SO4) always transfer their protons (H) to water. For example: HCl + H2O → Cl + H3O+. Weak acids result when only some acid molecules transfer their protons to water. Organic acids, containing only carbon, oxygen, hydrogen and nitrogen, are generally weak acids. The archetypical weak organic acid is acetic acid, better known as vinegar: CH3COOH. It's not the simplest organic acid, that would be formic acid: HCOOH.

Formic acid was first characterized in the late 17th century. Naturalists had observed that the vapors emitted by ant hills were acidic (using the equivalent of litmus paper), and in 1671 John Ray extracted the pure acid by distilling the crushed remains of red ants. Formica is Latin for ant, hence the name translates pretty literally as "ant acid". Formic acid is at least partially responsible for the sting in bee stings, ant bites and stinging nettles.

Even though chemists call formic acid weak, a 0.10 M solution has a pH of 2.4 (for comparison's sake, the same concentration of HCl has a pH of 1.0).


I remember find ants all over my Formica counter in my post-doc days. Does the ubiquitous counter-top material have any connection to ants? Apparently not. It was originally created as a substitute for mica insulators. For mica....

January 17, 2008

Weird Words of Science: calcium

The isolation of metallic calcium was reported by Humphrey Davy 200 years ago this year. The name comes from the Latin for lime: calx. Compounds of calcium are like duct tape – they hold lots of stuff together. Calcium carbonate keeps clams covered, calcium oxide (lime) is the mortar that held the Roman Colliseum together, and calcium sulfate (plaster of Paris) has been holding broken bones in place for more than a millennium. Calcium