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A Chemist's Laboratory Notebook

Updated: 2016-02-04T14:56:20.109-05:00


Free Radicals


(Translation: Free radicals are everywhere...)
This is my daily weather website. For the past month or so, the advertisement at the top of page has been for Zellschutz (translation: cell protection) pills. According to the manufacturer's website, they contain a protective mixture of vitamins C and E, coenzyme Q10, selenium, and natural extracts from pomegranate, grapefruit, and green tea. Can antioxidants prolong your life and offer "cellular protection"? I think the verdict is still out on that.

But I do think it's funny that they've made the free radicals look like scary little bugs...They kind of look like bacteria (maybe), but certainly not free radicals...

Condensed Print


Starting this month, the printed version of ACS journals will appear in a new condensed-print format. Apparently the print-based journals are no longer in high demand (print subscriptions down 50% in just 2 years is quite a loss), so to save costs, they will be printing 4 columns of text on just one page. From the image on the website, it looks like the articles will be printed in “landscape” format, with the page turned 90 degrees and shrunken in size.

I don’t know about everyone else, but I am a big fan of real paper issues of journals. It is nice to just sit down with the newest issue of any journal and flip through the pages, stopping if something catches my eye. Sometimes I end up reading some really interesting (and off-topic) research that way. You can’t just flip through the electronic version like that. Sure, if I’m looking for a particular compound or searching for a synthesis, I prefer the electronic version. Yes, I agree that there are MANY benefits to the electronic version of any journal. But, those rare times when I have a bit of free time and the geek in me actually wants to read about chemistry, I’d rather sit down at my desk and flip through the paper version. If I need to squint and get out my magnifying glass just to read the articles, I won’t be able to enjoy that time any more.

They try to make this sound better by saying that the new format is environmentally friendly. (Factoid: an annual subscription to all ACS journals weighs more than ½ ton!) I do like the idea of saving the environment (don’t get me started), but I don’t really know that a condensed-format journal is the way to go. If they really wanted to promote long-term sustainability, they would eliminate the print version of the journal completely.

Maybe I’m a little old fashioned, but I’m sad that paper is going out of style.

(After a quick search, I also found this article on the Chemistry Blog about condensed print).

Happy Birthday...kind of...


Well, it's not exactly my birthday, but it is my 1-year Ph.D. birthday, and that is certainly worth writing about! It is really difficult to believe that one year ago around this time I was out celebrating the new title and enjoying every second of it. Other than my wedding day, the day of my final defense was one of the most memorable of my life.

So what has changed in the last year? Other than my new job in a new country, not much. Well, I guess there is a new addition to the family...

(image) ...but you can see he fits right in.

Hopefully now that I've settled into my new job, I will have a little more time to write here once again.



This is your desk:


This is your desk in grad school:


This is your desk in grad school 2 weeks before your final defense:


Periodic Table of Fruits and Nuts and Periodic Table of Vegetables


Does it make me a big dork because I want the Periodic Table of Vegetables for my new kitchen? The Periodic Table of Fruits and Nuts is pretty nice too...

Plants and your health...


(image) It's getting to be the time of year when I like to start putting all of my plants outside on the balcony. Usually I also like to plant a couple of windowboxes full of petunias. Add a couple of tomato plants, and I am set for the summer. This year though, with my final defense set for July 1 (GASP!), I don't have time for any of this "enjoying the sun" nonsense. Instead I'm limited to reading here about plants that are good for your heath.

Who ever thought that my spider plant could be cancel out the effects of the formaldehyde potentially found in my clothes?

Or that a gerbera daisy could protect me from the benzene in inks?

Not sure about the accuracy of these statements (I'd love to know their sources), but it is cool to think that my overabundance of plants (more than 20 in 600 sq. feet) is good for something other than just improving my mood.

Legal problems of Ph.D's in Germany


As some of you may know already, my husband is German, so what I read last night in C&EN (don't you think it is ridiculous that I often don't get C&EN until Friday?) really shocked me. Apparently some internationally-trained (non-EU) scientists in Germany are facing charges for using the title "Dr." on their websites and business cards. Before I started reading, I was sure that it must be something to do with the fact that the "Dr." title might be confused with a medical doctor in a foreign country. But as I read further, I realized this wasn't the case. According to Spiegel, this law stems from 1939--and in simplified terms states that foreign degrees are suspicious, and need to be verified. In those times, such a law might have made sense, but now it just seems outdated. Luckily, the German government has already started to fix things up; at a conference in Berlin last week (see point 5) it was decided that an American Ph.D's can use the "Dr." prefix in Germany as long as their degree was granted from an institution recognized by the Carnegie Foundation for the Advancement of Teaching.

Happy Pi Day!


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This video is kind of freaky, but it fits the pi day theme nicely. Enjoy!

New Bacteria isolated....from hairspray


Earlier today when I read the news online, I came across this article. Basically, researchers in Japan have discovered a new type of bacteria. And it lives in hairspray. Of course, I had to look up the original article, and I just want to know why researchers decided to search for "hairspray bacteria" in the first place. Of course I've heard of various cosmetic products becoming contaminated with bacteria, and I know that many bacterial species are thermophiles, acidophiles, or even both, but I just didn't think that hairspray would be such a great environment. The newest ingredient in your hairspray bottle is from the genus Microbacterium and researchers have proposed the name Microbacterium hatanonis (in honor of the scientist Kazunori Hatano, a Microbacterium expert). For those interested, the rod-shaped Microbacterium hatanonis is aerobic and Gram-positive.

On a side note, when I first read the article and saw the words "parsimony analysis," I had to laugh, because my brain could only think of the Parselmouths (the characters in the Harry Potter books that can speak the language of snakes). In reality, parsimony refers to the idea that "less is more," or that the simplest explanation for something is generally the best. In this paper, maximum parsimony analysis was carried out to create phylogenetic trees demonstrating the relationship between the new hairspray bacteria and other strains of Microbacterium.

Answers Research Journal?


First, I want to say I went to the Answers Research Journal website with a totally open mind. While I am not overly religious, I don't necessarily believe that science is at odds with religion. As an undergraduate I took a excellent class (I forget the name, it was something along the lines of "Great Issues in Science") and was first introduced to the writings of Paul Davies, Richard Dawkins, and Stephen Jay Gould. My favorite two "textbooks" from the class were "The Mind of God: The Scientific Basis for a Rational World," and "Origins: Cosmos, Earth and Mankind." If you are at all interested in science and/or religion and how the two subjects can come to terms with each other, I highly recommend these books as a place to start.Anyways, when my husband sent me a link to ARJ last week, I was intrigued. It seems as if the journal is an offshoot of the website According to their website, "ARJ is a professional, peer-reviewed technical journal for the publication of interdisciplinary scientific and other relevant research from the perspective of the recent Creation and the global Flood within a biblical framework." At first I had high hopes (I mean, it is "peer-reviewed and everything, that must count for something, right?) and was really hoping for some cool science or interesting theories on how (Christian) religion and science can really go hand in hand. Andrew Snelling, the editor, certainly has the scientific credentials (a Ph.D. in geology from the University of Sydney) necessary for making informed scientific decisions.So what did I find? Well, I only looked at the current issue, but I wasn't very impressed. Of the five articles, two were written by scientists from "Answers in Genesis" and one was written by a guy whose only credentials are his (home?) address. Two are also written in the first person (which in my opinion just doesn't work for scientific publications), and sound like sermons rather than peer-reviewed scientific research. I do have to admit, the article on Louis Pasteur is pretty interesting, and while I would classify this article on granite formation as opinion rather than research, it was entertaining (I hesitate to say informative) as well. Although I had high hopes and an open mind, I was really left a little disappointed at the end of it all.[...]

Face Research


(image) This is not chemistry related, but I thought it was too cool to pass up. The Face Research Laboratory is run by Lisa DeBruine and Ben Jones, two experimental psychologists currently working at the University of Aberdeen in Scotland. I think the face average is the coolest part of the website, but you can participate in one of their many studies here.

Nature Chemistry


Today over at the Sceptical Chymist, Stuart Cantrill revealed a preview of the Nature Chemistry website. The journal is set to open in April 2009. I must say I'm quite pleased with the color choice--the beautiful blue/violet color reminds me of the natural product analogs that one of my labmates is busy synthesizing.

Cheddar anyone?


(image) Why in the world would someone want to calculate the heat capacity of cheese? While I do enjoy a nice creamy Brie, fresh mozzarella (especially with tomatoes and fresh basil), and maybe once in a great while a strong stinky cheese (reminiscent of Limburger) that I tasted on the Azores, calculating the heat capacity of each individual cheese seems to be taking it a little far, doesn't it?

Apparently not. In order to design the perfect cooling systems for the food industry, it is important to know the heat capacity of the food you are dealing with. For cheese it seems like moisture content is key in heat capacity calculations. Formulas to calculate heat capacity for cheese tend to be more accurate for those cheeses with higher water content (soft cheeses). Who would have known?

Traditional Chinese Medicines as Modern Drugs?


Earlier today I read an article entitled "How many traditional Chinese medicine components have been recognized by modern western medicine?..." in ChemMedChem. Actually, the title is what attracted me to this article. I've always been interested in alternative and/or natural medicine (maybe that comes with being a vegetarian?*), and really try to avoid taking unnecessary medicines (other than the occasional necessities like ibuprofen and when I was really sick this summer, I ended up taking hydrocodone and paracetamol--a.k.a. vicodin--followed by trimethobenzamide, both of which I resisted initially). In my kitchen I also have a tea for just about any ailment--lemon balm (melissenblaetter in German) tea will cure just about anything. While I've never actually tried any traditional Chinese medicines, a comparison of the components found in these traditionally used herbs and minerals seemed like it might be an interesting read. Traditional Chinese medicine has been around for more than 4000 years and currently there are over 10,000 chemical components that have been extracted from almost 5,000 traditionally used Chinese herbs/minteals/animals found in the database of traditional Chinese medicines. Compared to Western medicine, this is pretty amazing. Synthetic drugs have only been around for about 100 years, and in one comprehensive medicinal chemistry database you can find about 8000 different molecules that have been approved for use as approved drugs. About 50% of these approved drugs are actually derived from natural products, so a logical conclusion is that there might be some striking similarities between the chemical components of traditional Chinese medicines and modern Western drugs. According to the Zhang group, there are 327 compounds found in both the traditional Chinese and Western drug databases, and approximately 900 chemicals that are structurally similar (>85% similarity) between the two. Not surprisingly, more than a hundred of the traditionally used Chinese remedies display the same pharmacological effects as their corresponding Western drug. The pharmacological effects of many of the natural herbs were recorded in ancient Chinese texts dating back to the Eastern Han dynasty (~25 AD to 220 AD). For instance, among the 12 chemical components of the herb Coptidis rhizoma (used to treat gastric conditions in traditional Chinese remedies) are berberine, columbamine, coptisine, jatrorrhizine and palmatine. Today calystigine/palmatine is known as an antibiotic, and a structurally similar compound called berberine is believed to be an inhibitor of Helicobacter pylori. The article also stresses the potential that traditional Chinese medicines could have in drug discovery efforts, in particular in finding multicomponent therapeutics that combine two or more active ingredients into one single dose to hit several targets at once. The herbs used in traditional Chinese medicine can easily have over 50 chemical components. Although each single component might not be active, in combination they might be able to potentiate the effects of other chemical components, or they might work in combination to produce unexpected results. Additionally, traditional Chinese medicines are often prescribed in combinations. Would it be possible to combine the well established formulae of traditional Chinese medicines with Western medicine to produce combinations of drugs with lower risks of adverse drug-drug interactions? Now that we know traditional Chinese medicine has somewhat of a scientific basis, hopefully more work will be completed in this area. Acupuncture has already gained acceptance in many Western societies, so maybe this is the wave of th[...]

Sciencedebate 2008


I haven't checked out the entire website yet, but this seems like a good idea. While there are certainly other important issues, why not encourage a presidential debate on science and technology? Several thousand scientifically minded individuals and organizations have already signed, including the American Association for the Advancement of Science (AAAS), Sigma Xi, Roald Hoffmann (Nobel Laureate), Robert Grubbs (Nobel Laureate), Richard Schrock (Nobel Laureate), Peter Agre (Nobel Laureate), Phillip Campbell (editor of Nature), and Rudy Baum (editor of Chemical and Engineering News).

(thanks to Mirth)



My husband works in what I consider to be the materials side of chemistry (he is currently the only chemist in a group of physicists), so even though I am an organic chemist at heart, I really enjoy reading about new developments in nanotechnology. Yesterday I came across a paper entitled "Conductive One-Handed Nanocoils by Coassembly of Hexabenzocoronenes..." and I actually thought it was pretty interesting. Coiled nanofibers have been made previously, but little is known about their conducting properties. This is mostly due to the fact that coiled assemblies of aromatic molecules are not overwhelmingly stable. If one could create coiled, single-handed, electroconductive nanostructures that were also stable, it would be possible to create tiny little electromagnets. Cool, huh? Hexabenzocoronene (HBC) with alkyl and triethylene glycol substituents can self assemble into nanotubes; appending norbornene groups at the end of the triethylene glycol chains leads to the formation of both right- and left-handed helical nanocoils upon self assembly (1). While these nanocoils can be stabilized by subsequent ring-opening methathesis polymerization (ROMP) of the norbornene groups, they are actually only the kinetic product of self assembly. Without the ROMP stabilization, they are eventually converted into the more thermodynamically stable nanotubes. This all seems fascinating enough, but members of the Aida lab were able to take things a step further using what they call the "sergeant and soldier effect" to control the formation of left- or right-handed nanocoils. Doping the original HBC/norbornene construct (1) with as little as 20% of HBC with a shortened linker containing a chiral handle (either R or S) produced single-handed coils (S enantiomer --> left-handed coils, R-enantiomer --> right-handed coils). After doping with I2, the coils are also conductive. It only takes a few sergeants to control an army! [...]

Periodic Table of Sentiments


(image) While elements like 18Is (I'm sorry) and 49Ty (Thank you) are certainly made up, I think that any chemist would get a chuckle out of receiving one of these lovely periodic table of sentiments cards from Pink Loves Brown...

Chemistry on TV...


(image) Today when I looked in the newspaper, I just happened to see an advertisement for this new show on AMC. I was so happy that both bromine and barium were pictured with the correct atomic number. Yay for the proper use of chemistry in the media!! Since I don't have cable, I won't be watching tonight, but from some of the pictures online, it seems that at least some chemistry might actually appear in the first episode. Bunsen burners, Erlenmeyer flasks, electron configurations, all that good stuff. Unfortunately safety doesn't seem to be a high priority. In the first picture, the high school chemistry teacher on "Breaking Bad" is shown in front of a flaming Bunsen burner without goggles. But I forgive them this time, as I did enjoy this quote from the show's blog: "Electrons change their energy levels. Molecules change their bonds. Elements combine and change into compounds. But that's all of life, right? It's the constant, it's the cycle." Yes, chemistry is life.

PCR, when you need to find out who the daddy is...


A biologist in my lab sent this out yesterday. It's from the Biorad website and only gets better the longer you listen. Enjoy.

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My husband made a nice little visual aid to go along with the post from yesterday...


How much are you worth?


(image) Some recent information to absorb (all rounded to the nearest thousand):

An average graduate student in the chemical sciences earns per year before taxes: $22,000 (wow, do i really get paid that much? it doesn't feel like it.)

Tuition paid per year on behalf of the graduate student: $12,000

Facilities and overhead paid per year on behalf of the graduate student: $13,000

Misc. expenses paid on behalf of the graduate student ("fringe"): $1,000

Being told that an average Ph.D. (assuming a full five year service) costs more than a quarter of a million dollars: PRICELESS

10 commandments for keeping a lab notebook


Another list, just in time for the new year! My boss recently reminded us what it takes to keep a proper lab notebook, and I wanted to share it with you.Here is the list:1) Reference for the reaction (from the literature or from one of your or another lab member's lab notebook, for instance Amanda's Notebook VI, page 228)2) Structure of reactants and expected products 3) Table with mgs/mmols/equivalents/densities/origins of reagents. That last one is really important. If you used a mysterious, old reagent that has been sitting on the shelf for 20+ years and got great results, when you buy a brand new bottle and don't get similar results, you have a reason. The impurities in reagent that is 99% from Sigma might not be exactly the same as a 95% reagent from a different supplier. Also, write down where you found the reagent. I don't know about your lab, but mine has about 10 different fridges/freezers, and sometimes it is difficult to remember exactly where you put something. 4) Reaction procedure--we all already do this, right? 5) How did you monitor the reaction? Draw your TLC or attach your HPLC trace. 6) Workup procedure--sometimes I get a little lazy here. 7) Purification procedure. Include the size of column, amount of silica used, etc. 8) Results. mgs of product obtained, % yield, and physical state of material -- bright orange powdery solid, 239 mg, 98% yield 9) Characterization of products. Include reference to your NMR (if you keep electronic copies, write down the filename!) and explain. For instance, 13C NMR (Amanda_VI_228b_pure), for spot at 0.6 Rf (1:1 EtOAc:Hexanes) consistent with expected product X.10) Don't forget to write down the date!And as a general rule, try to write down things within 24 hours of completing them. You tend to forget things if you wait too long. Anyone have anything to add to this list? While I generally know what to put in my chemistry lab notebook, I must say that I don't necessarily include all of these things every single time. Maybe that will be one of my resolutions for 2008. On a similar note, I also tend to do quite a bit of biology. Do any biologists out there have any suggestions for what to include in a biology lab notebook? [...]

10 Simple Rules for Graduate Students


One of the professors here recently sent around an article with advice for graduate students. As I'm already in my 5th year here, many of the 10 simple rules aren't so relevant for me any more, but I wanted to pass them along anyways. A short summary--1. Let passion drive you.You had better be excited about the project to which you are going to dedicate the next 5+ years of your life. If you don't like reading and thinking about it now, it probably won't grow on you. And those crazy experiments that come to you in the middle of the night? Go into lab the next day and try them out, because you never know what might work. 2. Select the right mentor, project and laboratory.Mentor: It's this simple: pick a mentor that you can get along with in a professional atmosphere. Young or old, male or female, it doesn't really matter as long as you respect him/her and can understand his/her expectations of you.Project: It is very painful to fail again and again for months at a time. Sure, it builds character, but that doesn't make it any easier. Make sure to talk with group members and find out the inside scoop as to what projects seem to have a lot of potential at the moment. Lab: Work with people you like or at least those you can stand to be around for 10+ hours a day, 6+ days a week. If you can't talk with your lab members at least in a work related fashion, you really are going to be struggling when it comes time to ask for help.3. Be an independent thinker.It is okay to disagree with your PI on a scientific hypothesis, as it will only make both of you stronger. Just make sure you have all the data to back yourself up.4. Balance is a necessary part of life. Go to the gym, plan movie nights on the weekends, make group dinners. Some of the best friends that I have made during graduate school are the ones that I met biking 30 miles one or two times each week. Although the field of chemistry is relatively large, the people you meet and work with now will be your peers/reviewers/interviewers in the future. It is good to have friends in the field.5. Think ahead to your career.Take advantage of everything your school has to offer. Take extra classes if you want. Try to have as many different experiences as possible so that you know what you would like to do when it comes time to look for a job. 6. Remain focused on your hypothesis, but don't let it take over your life. Set up experiments to prove your hypothesis, but set up just as many to disprove it. Don't forget the big picture. Sometimes proving that a theory is wrong is just as important as showing that it is right.7. Fix problems now. If you are struggling with some aspect of research or graduate school, talk to someone before it gets to be a big issue.8. Publish! Attend meetings!Other scientists may reveal tidbits of information at small meetings that they might not otherwise discuss in the literature. Often times these little things are the key to your success.9. Be confident (but not arrogant), be thick skinned.At some point your committee, group or class will question you until you feel like crying. More than likely this will happen multiple times. This is normal and hopefully will help you build confidence. Over prepare for everything.10. Pick your thesis committee wisely. Stay in contact with them throughout your time in graduate school.These will be the people writing your recommendation letters. Make sure they know when you make significant progress. Email the[...]

3-D Sugar Printer


(image) Well, the people at Evil Mad Scientist Lab-
oratories have come up with something pretty sweet--a 3-D sugar printer. I have always thought that three dimensional printers are very cool and I even remember the first time that I even learned that they exist--on my tour of the Beckman Institute at University of Illinois.

The basic concept of the 3-D sugar printer follows standard solid freeform fabrication techniques. Simple two dimensional layers are stacked on top of each other to form a more complex 3-D form. So how do the Evil Mad Scientists do this with sugar? First, a layer of low melting "granular printing media" (sugar) is placed on a flat surface. By applying a technique called selective hot air sintering and melting, a burst of hot air is applied to the sugar in preselected locations. As the sugar melts, it fuses together with other sugar grains and eventually a two dimensional image appears. Next, the flat surface is lowered slightly and a second layer of sugar is sprinkled on top. Again hot air from a heat gun is applied to the surface in preselected locations. This time the new two dimensional image that is formed is also attached to any overlapping fused spots in the underneath layer. Repeating this process over and over again eventually yields a three dimensional object made completely out of sugar!

The inventors claim that their production process is very similar to selective laser sintering (SLS), but at a fraction of the cost. SLS is commonly utilized in manufacturing and uses a very expensive high power CO2 laser (thousands of dollars), whereas the Evil Mad Scientists' technology only needs hot air from a $10 heating element.

If you are really interested, you can visit the CandyFab project, which has all the information you need to build one of these machines at home for yourself. Now I'm hungry--anyone up for some caramelized almonds?



On one of the bulletin boards outside of our labs someone recently posted a brochure about the Atomium, and it really caught my attention. This interesting-looking building was erected for the International Exhibition of Brussels in 1958 (the World Fair in Brussels). Based on the structure of solid iron (which by the way is body centered cubic) magnified 165 billion times, the Atomium was designed to "embody the audacity of an epoch that seeks to confront the destiny of man with scientific discovery." Though I don't believe the individual spheres of the building are 165 billion times bigger than a real life iron atom (an iron atom is approximately 2.5 Angstroms in diameter x 165,000,000,000 = 135 feet, and the actual building spheres are only about half that size), the distances between the atoms are supposedly magnified to that size.Visitors are only allowed in 5 of the 9 spheres--the base (Henri Storck sphere), where you will find an exhibit dedicated to the 1950's, the top restaurant sphere, the central (Waterkeyn) snack bar sphere, the sphere named after the Belgian artist Marcel Broodthaers, and the children's only sphere. At 115 feet long, the escalators found inside the tubes of the Atomium are some of the the longest in Europe.Why make a body centered cubic building modeled after the structure of iron?? It was a tribute to the steel companies that helped to sponsor the construction by providing raw materials.After seeing these pictures, I really want to visit. Thanks to Mirth (and her family) for the lovely photographs.Stairs connecting the spheres:A view to the outsideArtwork inside of the Atomium[...]