Chemistry Blog

Introductory Sections (for a Paper or Your Thesis)

Posted by : Phil | On : 18-11-2009 | Comments (0)

Long-term Experiments

Posted by : Phil | On : 23-10-2009 | Comments 2

I recently read this Nature article, where is described what is probably one of the longest experiments ever to be conducted. A population of E. coli was kept for 20 years (!) in a nutrient solution (low on glucose), and samples were taken and deep-frozen after 2000, 5000, 10000, 15000, 20000 and 40000 generations. The authors sequenced the genome of the sample bacteria to investigate the rate of mutations. Up to generation 20K, the number of mutations grew steadily to a total of 45. The adaptation to the environment, however, only increased strongly in the beginning. It was concluded that the most beneficial mutations were the first to occur. After generation 20K, a change in the mutT gene caused a rapid increase in the mutation rate to result in 653 mutation at generation 40K, but with a neutral signature, i.e. no further adaptation. What I find most fascinating about this extreme long-term experiment is the confidence of the researchers that it would be possible to analyze the genes at a later point; this was not at all self-evident in the late ’80s! In addition, some work had to be done each day, for twenty years. What if the power had failed for a week or so? Of course, this unique opportunity to watch evolution as it happens is very intriguing. An experiment that took even longer was awarded this year’s Ig Nobel Prize in medicine: Donald L. Unger of Thousand Oaks, CA, cracked the knuckles of his left hand, but not his right hand, every day for 50 years to see...

Vice President of Research resigns at ETH

Posted by : Phil | On : 21-09-2009 | Comments 2

Another case of scientific fraud has been uncovered, unfortunately at my home university, ETH Zurich. Quote from the official e-mail: “More than ten years ago, as has just been confirmed by an internal investigation, research data was falsified in a research group then headed by Peter Chen, who is now Vice President Research and Corporate Relations. It would be extremely difficult to find out exactly who manipulated the data.” As a consequence, Chen steps down as head of research of ETH at the end of the month. He will continue working as a professor. Apparently, somebody in his group had falsified spectra, which was proven by a repeating pattern in the background noise, as well as by the fact that the results could not be reproduced. The spectra were obtained by “zero-kinetic-energy photoelectron spectroscopy” of hydrocarbon radicals. At the time a doctoral student and a postdoc were involved in the project, however, the lab books and some raw data are missing. The two publication in question were withdrawn. Additionally, the student withdrew his doctoral thesis, but retracted the withdrawal later. As of now, it has not been possible to prove the guilt of a specific person, and all people involved deny falsifying the data. http://www.ethlife.ethz.ch/archive_articles/090921_Peter_Chen_Ruecktritt_MM/index_EN

Leaving the Lab

Posted by : Phil | On : 17-08-2009 | Comments 6

After 3+ years of manual labour (not counting undergrad studies) it is time to leave the hood and write up the thesis. I must say, it’s been a very good time, with good colleagues in the lab and also some reasonable results. I now have about two weeks left to finish the stuff that I’m currently working on. After all this time, it will feel strange to leave my workspace behind and move to a desk. I know my hood so well, the way all the labware is sorted, that I could probably set up a column blind-folded. Time to move on! From now on, I’ll be spending my days in front of the computer screen. In the beginning, I expect the paperwork to be a nice change, but I’m pretty sure that it will get boring really quickly. For my future career, I cannot imagine having a desk job, although I’m sure the point will come where I’ll have no choice. The writing time will give me a taste of that future. Looking back, somehow I feel that I have not accomplished very much during my PhD. It seems to me that I could have obtained the same results in much less time. Some of the problems I encountered now seem pretty trivial to me, so I ask myself why I spent so much time on them. I guess it’s always like that in retrospect… Anyway, I’ll add a picture of a kitten (taken from here).

Condensed Print Format

Posted by : Phil | On : 19-06-2009 | Comments 8

My boss has pointed out this piece of news covered by C&EN. Apparently, starting from July, all ACS journals will be printed in a “rotated and condensed” format, that is two pages on one printed page in landscape format. This is an effort to reduce printing and distribution costs. In my opinion, this change is just one further step towards purely electronic journals that are not printed at all. I think this will deeply affect the way we present our data and how we look at formatting. Preparing a manuscript in a way meant for printing is different from one which will never appear in print. Some may welcome this change because it saves paper, others will probably miss the possibility of flicking through a new issue of JACS. Although I rarely go to the library to pick up a printed journal, I admit to reading printouts very often (see this post). Update: Apparently, in 2010 the print versions will stop completely, with the exception of JACS, Acc. Chem. Res. and Chem. Rev. See also Nature News.

Talking to Guests

Posted by : Phil | On : 18-06-2009 | Comments (1)

Whenever a guest speaker is invited to my institute, it is the custom for a few members of our group to speak with him/her about their projects. Normally you have a time slot of about 15 minutes. It is always a good idea to check the guest’s home page first, in order to find out what topics he will be particularly interested in. For instance, somebody doing research in a biological field will not want to know all the details of my synthesis. On the other hand, a synthetic chemist will not be interested in the invasive mechanism of the bug I’m fighting. By now I have a small presentation of abot 20 slides, of which I will focus on the ones most interesting to the guest. I always like it best when the guests show some interest and ask questions. In those cases I stop giving a “talk” and enter into the discussion. Sometimes the questions are really hard to answer, but they are always very interesting because they look at my work from a new angle. If I get into a real discussion, the usual quarter of an hour seems like a very short time! It can be a pity to have to stop a good conversation because other people are waiting on the other side of the door, waiting to see the guest.

Printing

Posted by : Phil | On : 25-05-2009 | Comments 11

Most of the printing of our group (~30 people) is done on just one laser printer. I often find myself walking from the lab to the group library, where the printer is located, and back because of paper jams or printing orders that have misteriously vanished into the digital nirvana. This is making me crazy! Somehow I am unable to proofread a manuscript on my computer screen, so I always need a printout. Maybe I should try and get my own printer. This leads me to my question: Do you often print papers for reading, or do you always read the PDFs directly? I try to read most things directly, but the papers I cite the most, I also keep in printed form.

Puns

Posted by : Phil | On : 24-04-2009 | Comments 3

Angewandte is kind of famous (or infamous) for the puns in the graphical abstract subheadings. I came across this one: Kaim, Hosmane, Záliscaron, Maguire and Lipscomb, ACIE, Early View: To “B” or not to “B”, which is about average for an ACIE pun. Fair enough. Further down the page there was this one: Winchester, Whitby and Shaffer, ACIE, Early View: To Bi or not to Bi. Seriously, are we running out of puns?

Elemental analysis

Posted by : Phil | On : 19-04-2009 | Comments 19

What analytical data are necessary to characterize a new compound in organic synthesis? In the times before NMR, melting points, elemental analysis and IR used to be the available methods (and UV, if applicable). Nowadays, EA isn’t required by the journals anymore andv IR is probably going to disappear soon. Additionally, the significance of melting points is quickly decreasing because mostly people take the product as it comes off the column without recrystallizing it. Are we losing something there? A number of people argue that the ability to get crystalline compounds is essential to be a good chemist, so recrystallization should always be done if possible. As a reward, you get EA-pure solids that are also easy to handle and may give you the occasional X-ray crystal structure (if you want to grow crystals). On the other hand, an additional effort is required: you need substantial amounts of material, which is no problem in a short synthesis, but can be a problem if it takes twenty steps to get to the product. If I have tediously made 50 milligrams of a material, I don’t really want to give ten away to be burned. I wonder if elemental analysis is still a necessity today. In most cases you get all the information you need from NMR (identity and purity). What EA gives you is confirmation that your compound is pure as well as dry. Still, is it worth the trouble or just a waste of time? I suppose it all depends on the kind of research you’re doing. If you are “target-oriented”,...

Not simple analogues, but ligands for biological switches

Posted by : Phil | On : 03-03-2009 | Comments (0)

A while ago I blogged about a paper where a set of structures analogous to estrogen were made. Now a follow-up paper has appeared in Protein Engineering, Design and Selection. The aim was actually not to make simple analogues of estrogen, but to use the compounds to create specific receptor proteins. Starting from the human estrogen receptor α, the authors employed directed evolution: they changed the residues in proximity of the ligand by mutagenesis, screened the resulting mutants, and selected the best receptor mutants for the next round. After the third round of directed evolution, they came up with an optimized mutant that bound to CV3320 with an EC50 of 55 nM, while the affinity to 17β-estradiol was reduced by a factor of 10 (4 nM). While the authors admit that the selectivity over 17β-estradiol could still be improved, it still is a nice piece of work that demonstrates the power of directed evolution. This way, a protein receptor for a substrate that does not occur in nature can be made. Such a receptor can be used to make biological switches.

Hot news on an old story

Posted by : Phil | On : 13-02-2009 | Comments 4

Some stories never seem to end. The hexacyclinol story is one of them. Is it over now? I assume most readers will be familiar with the controversy about the two proposed structures of hexacyclinol, the original one (1) and a revised one (2), and about a total synthesis of 1 by James LaClair that was challenged by Rychnovsky and Porco on the basis of calculations and a synthesis of 2. The debate has been extensively covered in the blogosphere, e.g. in C&EN and by Derek Lowe. Proposed structures of hexacyclinol There is some new evidence now. An Italian group have simulated the 1H and 13C NMR spectra of both structures using DFT calculations (Org. Lett. ASAP). The calculated spectra seem to point to 2 as the correct structure. In addition, 1 cannot have the same spectra as 2 according to the calculations. The authors summarize: “The structure of hexacyclinol is confirmed to be 2. Furthermore, if 1 had been synthesized or was formed from an unforeseen reaction, its NMR spectra are sufficiently different from those of 2 as to guarantee their distinction.” This seems to exclude LaClair’s claim that structure 1, which is the target of his total synthesis, happens to have the same spectral data as 2. The authors of the paper are of course reluctant to draw the obvious conclusion. Update: This piece of news has been covered in Derek Lowe’s blog. There has been quite a discussion, with James LaClair participating in person! It has also appeared in The Chem Blog.

Polyethylene bags

Posted by : Phil | On : 06-02-2009 | Comments 18

Politicians in Switzerland have suggested to ban the polyethylene plastic bags used in supermarkets for environmental reasons. I am no expert, but I guess a thin plastic bag cannot be so bad as long as it’s properly disposed of. What really grabbed my attention was the statement of one politician, who said that the combustion of these bags releases dioxin. Of course he was talking about polychlorinated dibenzodioxins (PCDDs) such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), which was involved in the Seveso disaster and was a contaminant of Agent Orange that caused many of its severe health effects. Any chemist can see immediately that there is no way polyethylene will release PCDDs because it contains no chlorine. Such a statement immediately indicates how little research the politician has done. I think this is indicative of a way of thinking predominant among a large part of the population here. Let me put it in a formula: Chemistry = Evil. It really annoys me when I see how little knowledge there is to support this general damnation of all things related to a scientific branch. In addition, because chemistry is bad, some people not only refuse to learn about it, but they are even proud of their lack of knowledge! I’m sure you have heard sentences like “You know, I never understood chemistry at school”, meaning “chemistry is for nerds and you don’t really need it in daily life”. Consider the same statement about art or literature,...

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Introductory Sections (for a Paper or Your Thesis)

Long-term Experiments

Vice President of Research resigns at ETH

Leaving the Lab

Condensed Print Format

Talking to Guests

Printing

Puns

Elemental analysis

Not simple analogues, but ligands for biological switches

Hot news on an old story

Polyethylene bags

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