Not just me, everyone! I'm going to try and avoid the melons:boobies analogy, but it will be hard difficult given the context. It works the same way as Viagra does, but is less targetted.

Citrulline is present in watermelons and is converted to arginine in the body. Arginine promotes nitric oxide, or laughing gas synthesis. Nitric oxide relaxes blood vessels which lets the blood flow through us - yes, everywhere.



So nitric oxide, eh? I recall being put under by laughing gas when I was getting cavities drilled. Neither the doctor nor the nurse complimented me on my way out, so it either didn't happen, or they were unimpressed. This must mean that erectile dysfunction happens because the arteries and whatnot become too tense and can't flow the blood through our system fast enough, or with enough vigor.

I found this on ScienceDirect, aka science by press release. Sometimes they mention in the article where the work is being published, in which case I would look it up and cite that instead. This isn't the case, so I just have to take in what they wrote.

Photo: Flickr

Godspeed.

[Comments: 0] [Tags: food, science]

A paper entitled 'Floating Tip Nanolithography' appeared in my RSS reader this morning. I make it a point to scoff when I see the nano- prefix being overused, but this got me questioning the whole field (assuming nanolithography is considered a field?), not just the world itself. There's too much nanostuff, but that's the point I'm making here. (And in the paper they do say: "NANO" revolution, sigh.) Why do nanolithography at all? Is this just some proof of concept idea?

The wiki entry tells me that it's used for creating microcircuitboards. Okay, that's useful enough, but from what I've seen from nanolithography papers, it's just people writing the names of their universities on a surface.



Here, a paper shows that by using a hot, floating AFM tip, they can get better resolution. They coat a gold surface with a polymer, then melt it off. Good, now you can write your name more clearly. With this method they were able to draw smaller images, with letters 100nm wide, while some of the older techniques (for example, physically scratching a surface with a sharp AFM tip) weren't able to clearly write.

Is there more to this field that I'm missing?

Milner, A.A., Zhang, K., Prior, Y. (2008). Floating Tip Nanolithography. Nano Letters DOI: 10.1021/nl801203c

[Comments: 0] [Tags: journals, science]

This is really getting out of hand. We are just putting the term 'nano' in front of anything. 'Hey! That TEM image looks kinda like an amphibian of some sort... Let's put the word nanotoad in our paper!' This is by no means a complete list, but here are just some of the terms which are being used. The references I include aren't necessarily the first to use the term; I don't feel like doing all that extra searching.

I'm starting out with some normal, acceptable ones before I get into the weird ones.

Nanoparticle (doi: 10.1038/nbt1100)
This was one of the first terms used, and is perfectly acceptable.

Nanocrystal (doi: 10.1002/anie.200705806)
Nothing special about this one, fairly boring term. Could be replaced with nanoparticle in some cases, but it's fine.

Nanosphere (doi: 10.1021/ja028650l)
Most nanoparticles are nanospheres, but I suppose this is a more descriptive term.



Nanotube (doi: 10.1021/nl0804295)
With a title like: "Synthesis of High Aspect-Ratio Carbon Nanotube “Flying Carpets” from Nanostructured Flake Substrates", I was really disappointed to not find the term "nano-flying carpet".

Nanorod (doi: 10.1021/ic8000416)
Nothing wrong with this one, it's descriptive and reasonable enough.

Nanowire (doi: 10.1126/science.1157131)
In this paper, they were so close to saying the phrase 'nanotree'; I appreciate them not, but not for the purpose of this article.

Nanoislands (doi: 10.1002/adma.200701383)
Nanoislands are usually just the source of nanorods, (or nanowires...) but do they really need a name?

Nanorice (doi: 10.1002/adma.200701782)
Another term which could be replaced with nanorod. From the image below, I see how that makes you think of rice, but it's still a nanorod!



Nano-whiskers (doi: 10.1063/1.1418446)
How many different ways do we need to say nanorod???

Nano-checkerboard (doi: 10.1021/cm800473m)
I admittedly didn't read this too carefully, but playing a game of nanocheckers or chess was never brought up. Sad.



Nanomedicine (doi: 10.1038/nnano.2008.114)
I imagine that this is about the science of healing Keebler elves. This is actually a picture of snap, crackle, and pop; are they the same thing as the Keelber elves?



Nano-horn (doi: 10.1016/S0009-2614(99)00642-9)
Nano-aggregate
Look at the picture below, would you call that a horn? I suppose there's a resemblance, but there really is no need for this term. And nano-aggregate? Why not just aggregate; the term aggregate doesn't necessarily apply only to the macroscale. Two unnecessary 'nanoterms' in one paper, sigh.



Nanomanipulation (doi: 10.1038/nnano.2008.114)
In this article, they use 'molecular cranes' to manipulate things on the nanoscale. The lack of pictures makes me sad.

Nanotweezers (doi: 10.1126/science.286.5447.2148)
A nice follow to nanomanipulation.



Nanolithography (doi: 10.1126/science.286.5439.523)
Nano-Plotter
C'mon! Firstly, I see no use for this, but secondly... nanolithography... ugh.



Nanochannels (doi: 10.1002/adma.200701490)
I suppose this one's okay, but it still doesn't sit right with me.

Nanodiamond (doi: 10.1038/nnano.2008.99)
'Will you marry me?' *opens ring box*
'Uhhh... is that an empty ring?'
'No, silly; it has a nanodiamond!'

Nano-HPLC (doi: 10.1021/ac000497v)
Great, now the 'nanoterms' have moved from materials chemistry to analytical, swell.

Honorable Mention (ref: Newsvine)
Unfortunately it's just called a microscopic noodle bowl, and not nanonoodles.



Maybe I'll write a follow up to this, there are certainly more terms I could pull up, but for now I'm too annoyed to go on.

Godspeed.

[Comments: 0] [Tags: ranting, science]

I do believe I have successfully synthesized the precursors to a) Slimer, b) Nickelodeon Gak, or c) Flubber.



Godspeed.

[Comments: 2] [Tags: science, lab pictures]

I was doing some stumbling, I came across the following image from the UN Environmental Programme. Click on the link and look at the whole thing, I have bits and pieces throughout the post, but without looking at it, you won't get as much out of this.



Oceans are huge; this is nothing new, but I never knew that they compose 97.5% of the water on earth. Think about it, the great lakes, the Nile, the Amazon, the polar ice caps, all completely dwarfed.



I had no idea how much groundwater there was. I mean, the earth's crust is enormous, and it all has water, but it's something that I had never thought of before. Same with glaciers, but I'm less surprised than I was about groundwater.



The only thing here that really surprised me was that last one, because I never really think about plants and animals being composed of water. Sure, in elementary school you learn that we're made up something like 2/3 water, but all of the animals on earth don't really take up that much space relative to everything else. I assume plants take up a lot more than animals; I wish they had broken that down as well. I would venture to guess that plants take up at least 95% of that category, any other guesses?

So if you do the calculations, freshwater lakes only compose 0.00674% of the water on Earth. Very interesting stuff. Again, it's pretty cool to look at the whole image as one piece, so here's the link again.

Godspeed.

[Comments: 0] [Tags: science]

I learned how to use the furnace for thermal decomposition today. I let it run for a while. Unfortunately, I didn't factor in the fact it's cooling from 950 degrees Celsius into my going home timeframe. It's been like an hour and a half now...

Godspeed.

[Comments: 0] [Tags: ranting, science, lab pictures]

All I know about viruses I learned for the seminar that I gave a month ago or so. I've never taken biochem or virology, so there's my disclaimer.



Vaccinia (MVA) is a poxvirus, the class of viruses which includes smallpox. They're not fun organisms; the damage they do on cells is shown in the image above. MVA is a complex virus; it's not icosahedron or helical, and there's an intracellular and extracellular version. As far as viruses go, that's pretty complicated, they're generally more simple than this, structure-wise. Additionally, the Helenius group at ETH Zurich has been researching how they act as a trojan horse to cells.

MVA enters a cell by floating up next it, and blebbing it. Blebbing? It's essentially forming an amoeba-like arm and poking and prodding at it. Then, the cell tries to eat the virus, and bam, it's in. Wait, why? If I hear someone knocking at the door, I go look in the peephole. If I see a Jason mask and a shotgun, my first instinct is to not open the door. However, if they're wearing a Papa John's hat and holding a pizza, I'm going to open the door whether or not I ordered it. Do they have a Jason mask and shotgun behind their back? Who cares, pizza!



That's how MVA does its thing. Embedded on MVA's surface is phosphatidylserine (PS). This is present when other cells undergo aptosis, so it signals to the cell that there is going to be cell remnants left for it to eat. Then when it feels the poking and prodding of the blebbing, it starts to eat, and kaboom. That's why I chose an eating analogy. How do we know this is happening? They put different inhibitors onto the virus which will stop this from taking place. You can see from the graph below and the image above, this is effective in stopping the virus from entering. The black bars on the graph are the virus binding to the cell, and the white bars are the cells being infected. ANX5 is one of the inhibitors they tested.



I'd comment more, but uhh, I've told you everything I understand. I should take biochem one day.

Mercer, J., Helenius, A. (2008). Vaccinia Virus Uses Macropinocytosis and Apoptotic Mimicry to Enter Host Cells. Science, 320(5875), 531-535. DOI: 10.1126/science.1155164

Godspeed.

[Comments: 0] [Tags: journals, science]

In April's Journal of Solid State Chemistry, Honggang Fu's group published a paper on iron oxide nanoworms being used for water treatment. They don't actually use the term nanoworms; they just say "iron oxide with wormlike morphology", but nanoworms sounds cooler, and I've heard the term used before. Morphology is a good word, but it just doesn't match up.



Anyway, the idea is that they were able to create iron oxide that looks like it does in the image above. Creepy looking. They took iron nitrate, mixed it in with a big block copolymer and refluxed it. They have an idea of how it worked, the scheme is below, but this definitely seems like the kind of thing you just stumble upon when you're trying for something else. It's nice when science works out like that sometimes.



When they dipped it in solutions of chromium, it adsorbed onto the surface due to ion-exchange, and the nanoworms work better than a film of iron oxide because of the higher surface area. They got a higher removing capacity when they did the reflux at lower temperatures. This is seemingly because the nanoworms aggregate and anneal with higher temperatures, which would like to bigger worms (nanonightcrawlers?) and less surface area.

Worms: good for your compost, bad for your computer, but now good for your water purification.

WAN, L., SHI, K., TIAN, X., FU, H. (2008). Facile synthesis of iron oxide with wormlike morphology and their application in water treatment. Journal of Solid State Chemistry, 181(4), 735-740. DOI: 10.1016/j.jssc.2008.01.019

Godspeed.

[Comments: 0] [Tags: journals, science]

In an Inorganic Chemistry publication back in March 2008, Yadong Li's group at Tsingua Univ. synthesized CdSe nanoparticles that were small enough to fluoresce blue. Because of quantum confinement, nanoparticles (specifically quantum dots) fluoresce at shorter wavelengths with smaller radii. To synthesize quantum dots with radii this small is difficult; they must be smaller than 2 nm.



The method they employed was to first create nanoparticles by a microemulsion route, then mildly oxidize the nanoparticles to reduce them into smaller particles. The pretty picture you see above shows the nanoparticles after microemulsion on the left, then after further oxidation on the right.This was an effective route and they were able to create sufficiently small nanoparticles. I actually did a lengthy paper and presentation on the dynamics of nanoparticle synthesis by microemulsion this semester, so I enjoyed coming across a paper that employed it. It's advantageous because you can limit the nanoparticle size effectively.



The diagram above is the basic scheme for microemulsion synthesis. Basically, each microemulsion contains a reactant of the synthesis, and when they are forced together (in a reactor) exchange occurs and the reactants combine. Because there is limited reactant in each droplet, the size of the nanoparticle is controllable, and the size of the droplet regulates the size as well. The image is from this paper.

Anyhow, I enjoy the idea of using the sun in synthesis, but it kind of sucks for research labs that don't get too much of it. I don't see any problems with the paper - I'm pretty impressed. Maybe someday I'll make nanoparticles by a non-single source precursor method and will employ a microemulsion technique.

Liu, L., Peng, Q., Li, Y. (2008). An Effective Oxidation Route to Blue Emission CdSe Quantum Dots. Inorganic Chemistry, 47(8), 3182-3187. DOI: 10.1021/ic702203c

Godspeed.

[Comments: 0] [Tags: journals, science]

Back in March, I found a communication in JACS about determining the concentration of quantum dot nanoparticles by measuring their fluorescence burst counts by the Johnson group at York College. The QD solution (which could be in aqueous or organic solvent) was passed through a laser to induce the excitement and the different wavelengths emitted were separated by dichroic mirrors. The scheme is shown below.



They refer to this as a simple and accurate process. They do get good results, so I will give them accurate, but simple? I suppose if you work in lab that does a lot of laser chemistry, this might be simple, but not for me. Regardless, I don't think the method has that much going for it. There are other ways in which you can determine nanoparticle concentration, and other information about your system simultaneously. The one cool thing that this method does have going for it is that if you have a mixture of quantum dots that fluoresce at different wavelengths, you can measure both of their concentrations simultaneously.

However, back in 2004, there was a review in Accounts of Chemical Research, on using a carbon nanotube system to quantify nanoparticle concentration, by the Crooks group at Texas A&M. I wouldn't describe this as a simple system either, however. It involves embedding a carbon nanotube in an epoxy matrix, and creating an electrochemical system where the nanoparticles move by electrophoresis. A schematic is shown below.



The nanoparticles pass through the carbon nanotube, which has an ionic current passing through it. Based on the frequency and pulse height of the change due to the nanoparticle, they were able to obtain the concentration and nanoparticle size respectively. This has many advantages over the previous system. Firstly, the nanoparticles don't have to be quantum dots, non-fluorescing nanoparticles can be measured as well. Additionally, the nanoparticle size is being measured. This method is known as a Coulter counter.

These systems both have their pluses, but as you can tell, I prefer the carbon nanotube based system.

Zhang, C., Johnson, L. (2008). Simple and Accurate Quantification of Quantum Dots via Single-Particle Counting. Journal of the American Chemical Society, 130(12), 3750-3751. DOI: 10.1021/ja711493q

Ito, T., Henriquez, R.R., Crooks, R.M. (2004). A Carbon Nanotube-Based Coulter Nanoparticle Counter. Accounts of Chemical Research, 37(12), 937-945. DOI: 10.1021/ar040108+

Godspeed.


[Comments: 0] [Tags: journals, science]

Lindinger's group at the Nestle Research Center in Switzerland published a study back in March 2008 in Analytical Chemistry about analyzing coffee with mass spec. I read about this on Engadget then promptly forgot about it. I even gave a presentation on it for my Analytical class, only later to see this in my RSS bookmarks.

Basically by using PTR-MS (proton transfer reaction mass spectrometry) they did an analysis of different coffees. They emphasized that this was a data-driven study, not a chemical analysis study, because they weren't necessarily analyzing the different compounds individually. Rather, what they were doing was taking the results of the mass spec, then combining them with the 'results' of a 10-member panel of coffee experts to create a model. So they just took the intensities of the different peaks (all the compounds that had 108 m/z, 110 m/z, etc.) and compared them to the 'intensities' of the panel ratings. A rough scheme is shown below.



The panelists rated the intensity of different qualities (coffee, bitter, cocoa, roasted, woody, cereal, butter toffee, acid, citrus, winey, and flowery) of the coffee. They ran a blind study, and the panel was able to produce reproducible results, so they apparently know what they're doing. I would imagine they look something like this:



Once the model was created, they did PTR-MS on another set of coffees, had the panel do their tests, then compare how well the model was able to predict it. You can see in the graph below that they were pretty successful. You can see that there are only 8 qualities below; they decided to scrap a few qualities, but didn't really explain why. The ones that they got rid of were: winey, flowery, cereal. You can assume that they took those out because they didn't fit with the model as well, and that's probably because those qualities are made up. Nobody drinks coffee and thinks, oh that was nice and flowery. But not winey enough. Nonsense.



I'd like to see them create a model that determines if coffee is good or bad. Sure, that's even more arbitrary, but it's more useful. Then we could take samples from a bunch of different coffee shops, and finally scientifically prove that Starbucks' coffee blows.



Lindinger, C., Labbe, D., Pollien, P., Rytz, A., Juillerat, M., Yeretzian, C., Blank, I. (2008). When Machine Tastes Coffee: Instrumental Approach To Predict the Sensory Profile of Espresso Coffee. Analytical Chemistry, 80(5), 1574-1581. DOI: 10.1021/ac702196z

Photo: Louisiana State Museum
Photo: Flickr

Godspeed.

[Comments: 2] [Tags: food, journals, science]

A paper was published in JACS (see below for reference) a couple months ago by the Matsui group at CUNY Hunter. The idea is that you can uniquely identify a virus by measuring its electrical properties.



We're not talking about a solution of viruses, this is measuring the electrochemistry of one individual virus particle, a virion. I'm not going to go into the details of the method, otherwise this post would be pages long, but the gist is that you put a virus onto a film of gold, locate the virus with AFM, then use the AFM tip and the gold film as electrodes and run AC current through it. You can get a unique signature by looking at the capacitance versus frequency. The results for five viruses: AV5, SV40, MVA, CPMV, and HSV1 are shown below.



You can see that each virus is distinguishable from one another by both the pattern of the line, as well as the magnitude of the capacitance; there's overlap in a couple of places, but you can still distinguish them from each other. The paper stated that the unique identification of these viruses is made possible through the difference in protein compositions, which have different dielectric constants.

They left out quite a few important aspects in this paper. I talked to a virologist to learn more about viruses, which showed me many things they omitted. It makes sense since their flaws lie mostly on the biology side, because they really only spent a couple sentences talking about viruses themselves.

Firstly, they make little to no mention of the viruses size. They state that they range from 30-300 nm and give their sizes, but don't discuss any possible contribution. If you look at the equation for a parallel plate capacitor, you see that the distance between the electrodes plays a role. We can't use that equation here, but the concept still remains.



Secondly, even less mention of the viruses shape is included. Four of the five viruses they studied are icosahedrally shaped, so they can be treated roughly as spheres, but one is more complex than that. That complex virus is MVA, and an image of it is shown above. Additionally, they don't mention that there is an entire helical class of viruses which could be studied. Based on their orientation on the film, would they give different results, since there would be a different distance between the electrodes? Would this cancel out since they're measuring more than one virus and averaging?

Lastly, not all viruses are stable outside of a host cell, so this can't measure all viruses, which is a pretty big limitation. There's a chance that they could measure an infected cell rather than a virus particle in order to identify the virus, but that seems unlikely given the large 'background noise' the cell would provide, and it would be hard to factor in all of the different stages of infection.

Overall, the paper is good - it's a pretty novel idea, but it definitely needs more work. I could go on a lot more about this, since I gave my 25 minute long Graduate Student Literature Seminar on this paper, but I won't.

MacCuspie, R., Nuraje, N., Lee, S., Runge, A., Matsui, H. (2008). Comparison of Electrical Properties of Viruses Studied by AC Capacitance Scanning Probe Microscopy. Journal of the American Chemical Society, 130(3), 887-891. DOI: 10.1021/ja075244z

Godspeed.

[Comments: 0] [Tags: journals, science]

The title is a bit misleading - it's really a mix of two different things, so if you were expecting to see pale, eerie, floating vaginas, you're fucked up this isn't the article for you.



I was going through my RSS reader, and the following article popped out at me: Kidney Extracted Through The Vagina, First Time In Europe, Second In World. If that isn't one of the strangest images you've thought of, you have a twisted imagination. The idea is that you can reduce the amount of recovery time required, and scarring by going through the babyhole. Normally, you end up making a 6 cm incision, however with this method, you only need two smaller, 1 cm incisions. Oh wait, "Furthermore, another non visible incision is done in the internal part of the vagina, where the kidney is extracted." How is this a good idea??? To be fair, they're doing this to a 66 year old woman, so she probably doesn't get quite as much use out of it, but c'mon.



This is the image I was about to use, but then I saw the first image, and it fit better with the title. Earlier, I made a post about Nine Inch Nails' new album, Ghosts I. At the time, I had only downloaded for free, Ghosts I. A few days later I paid the $5 and downloaded Ghosts II-IV. I really enjoyed it. One of the feeds in my RSS reader is Pitchfork Media. They review music, so it helps me keep up with what's new, and if an album gets above an 8.0, I'll usually... acquire it. I was shocked to see that they gave Ghosts I-IV a 5.0. I disagree strongly with this, however there was a line in there which is very true. "Reznor stands to make millions from Ghosts, something that certainly wouldn't have been true if he'd released this two-hour 4xCD instrumental work on a major label." Anyhow, that's it for now.

Photo 1: Flickr
Photo 2: Flickr

Godspeed.

[Comments: 2] [Tags: music, science]

I'm definitely not sold on global warming one way or the other. I don't think there's enough data to rule it out or prove it, but I do think research should continue. I'm not so sure I would sue Al Gore over it, though the idea is entertaining. I bring this up because I came across a 2006 paper from the Annual Review of Physical Chemistry, "Atmospheric Field Measurements of the Hydroxyl Radical Using Laser-Induced Fluorescence Spectroscopy". I found this in search of a paper to write about for my dynamics class, and I think I'll use it.



For the most part, I enjoyed the paper, which is surprising given the amount of analytical and physical chemistry within. To say the least, they are far from my favorite subjects (even though I'm taking both this semester...). It also led me to discover the MCM; the Master Chemical Mechanism, which I spent some time browsing and was pretty impressed with.

I have a few criticisms here, the first of which being they're trying to write a novel. Here's what I mean:
p. 193: "The most important of these intermediates is the hydroxyl radical (OH), which is generated mostly in the daytime as a result of ozone photolysis to form electronically excited oxygen atoms, O(¹D), which react rapidly with water vapor to form OH."
p. 210: "The main contributor to OH initiation in both summer and winter is the reaction between O₃ and alkenes." ... "The fraction of OH initiation from O₃ + alkenes is approximately double that from the O(¹D) + H₂O reaction in the summer, but 100 times greater in the winter.
p. 212: "The largest source of OH by far is the reaction of HO₂ + NO, and thus OH levels reflect the rate of carbonyl photolysis, which occurs at longer wavelengths and thus is still significant in winter."

They're trying to guide us through the path in which they discovered things (I think), but it doesn't seem appropriate in the way they are writing things. My other criticism is that they talk about global warming without mentioning it's a theory. I know some people think that it has progressed beyond being a theory, but they should really be more objective in the scientific literature.

Edit:
Following up Martin's comment, I feel like I should clarify some things. I went through and reread what I have written on this issue, and gave it some thought. Criticizing the article for not referring to global warming is a theory seems rather silly now that I think about it, even though evolution (since it's the example that was used) is a theory, it's not really necessary to refer to as such. As for my personal views on global warming - I stand by that I'm not sold 100% one way or the other, however it's not the fact of whether it's happening that I question, rather the degree to which it's happening. I'm just arguing that people often exaggerate how fast this is taking place.

Heard, D.E. (2006). ATMOSPHERIC FIELD MEASUREMENTS OF THE HYDROXYL RADICAL USING LASER-INDUCED FLUORESCENCE SPECTROSCOPY. Annual Review of Physical Chemistry, 57(1), 191-216. DOI: 10.1146/annurev.physchem.57.032905.104516
Btw, I dislike DOIs that are this long.

Photo: Flickr

Godspeed.

[Comments: 4] [Tags: journals, science]

In my continued search for a paper to do my graduate student literature seminar, I came across this interesting paper.

Published about three weeks ago the web in JACS, researchers at the National University of Singapore have found a way to easily detect mercury in water. The method they are developing is very efficient because it can be performed in the field, without instrumentation, using just the naked eye in about 5 minutes.



Gold nanoparticles (NPs) are functionalized with two different strands of DNA - half of the NPs are functionalized with one strand, the other half with the other. Another strip of DNA twice as long is also added in the mixture. It is designed in a way that this long strip of DNA would not match up with itself, nor will any section of it match up with the two shorter strips that are bound to NPs under normal conditions. However, the system is designed so that the longer strip will bind with the two shorter strips (essentially taping two NPs together) if thymine (the T in GCAT base pair matching) would bind with itself. Mercury has a feature which is rather unique to it, in that it coordinates thymine bases in DNA to one another so that there is a mercury-thymine-mercury connection. Since this is unique to mercury, this method will ignore other metals such as lead, copper, calcium, and many others. The result of this is that nanoparticles will exist as free floating single units in a media which is free of mercury, however, with mercury present the nanoparticles will begin to connect to one another, and form a network, referred to as an aggregate.

Aggregation will show up as a color change. The science behind the color change is that the nanoparticles show a strong UV-Vis (ultraviolet-visible) absorption at a certain wavelength, which varies based on the size of the nanoparticle. This wavelength will change when an aggregate forms, and since color is based on the wavelength of light, this can be observed since these wavelengths are in the range visible to the human eye. Additionally if this aggregate grows large enough (and forms a polymer), precipitation can be observed in the solution.

Unfortunately, the amount of mercury present must be on the micromolar scale, which is a thousand more times more concentrated than the nanomolar scale, which is where the border between the acceptable and unacceptable levels of mercury lies according to the EPA. The current solution to this is to simply boil water down on site, however this does add to the work and time required for detection. This was published in JACS as a communication, and in their conclusion they talk about their plans for future work which would allow detection on a smaller scale by improving upon this method.

Xue, X., Wang, F., Liu, X. (2008). One-Step, Room Temperature, Colorimetric Detection of Mercury (Hg2+) Using DNA/Nanoparticle Conjugates. Journal of the American Chemical Society, 130(11), 3244-3245. DOI: 10.1021/ja076716c

[Comments: 0] [Tags: journals, science]

I'm a bit late posting on this, since it was published on the web in JACS almost a month ago... but oh well. Jones talks about the two conventional approaches to CO₂ capture - absorption into amine solutions and adsorption into porous silica systems. Their approach is take these methods and efficiently combine them into a method which uses both of their strong points.



As you can see in the diagram above, (and if not, I'm explaining it) the amines are bound to the surface of the silica. The result is referred to as a "hyperbranched aminosilica material". This is abbreviated as SBA-HA, for a reason which is not that clear. I had to look into this for a while before I could figure it out, but the SBA stands for 'Santa Barbara Amorphous type material', since the mesoporous silica was discovered at UC Santa Barbara. They show SBA-HA to bind CO₂ more efficiently than previous materials, and best of all - reversibly.

Reversibly binding CO₂ is an effective means of CO₂ capture because the material can be flushed out (in this case with argon), and be used again. This would be applicable for use with flue gas, which essentially just means gas that comes out of a smokestack. Jones reported up to 12 cycles without a loss in capacity though for industrial uses this would need to be tested on a much longer timescale. The next logical question in terms of application would be to figure out what to do with the CO₂ once captured.

In searching for related materials, other than finding out I was far from the first person to write about this, I also discovered that a patent was filed for the writers of this paper. Among other things, this paper corrected my previously ignorant idea that absorb and adsorb were just different spellings of the same word... the former means pulling a substance into solution, whereas the latter means pulling a substance onto the surface of a material.

Very interesting stuff; I'll keep this topic in mind when choosing a paper to discuss for my "Graduate Student Literature Seminar".

DOI: 10.1021/ja077795v

Godspeed.

[Comments: 0] [Tags: science, journals]

Do you know what would really offend me? Let's say that I, a German civilian, were to meet someone named Dr. Baldwin. Then, during the course of conversation with him, I shockingly discovered he wasn't a real doctor, he had just received a PhD from some shoddy institution like Cornell or Stanford. They should make that illegal. Oh wait, it is!



According to an article in Chemical and Engineering News (C&EN), seven scientists working in Germany have broken this law. Which law? Well if you didn't receive your degree somewhere in the European Union, you're not allowed to call yourself a doctor without express written permission from the state. Apparently, the Max Planck Society, the research institute they are working for, is trying to have the law changed. Well, it's a good thing that I don't yet have a PhD, nor do I speak German.

Speaking of Max Planck, check out this article from Cracked.com.

Photo: Flickr

Godspeed.

[Comments: 1] [Tags: politics, science]

My students wrote these on the whiteboard for me on Thursday. They're amazing.

Godspeed.

[Comments: 5] [Tags: science]

Of course. Science goes ahead and creates tearless onions AFTER I stop working at Quizno's. All of those days, being the newest guy, having to cut the onions could have been less miserable. I would have to go stand in the walk-in refrigerator and let my eyes recover during those onion cutting sessions.

I'm all for scientific progress, but let's try and get these things worked out when they would still be useful for me!

Godspeed.

[Comments: 0] [Tags: science, food]

The above picture is what they call a "CAT Scan" of a section of the earth. Basically you send measure the speed and distance that seismic waves move through land. Combining a large amount of data yielded the above. The colored sections are places where the speed was measured to be faster than normal and the waves traveled farther than usual. Why would this be? Well on the outer edge of the circle, there is ocean. Waves move faster through and farther in water. So from this we can determine that there is water where there is color. Okay, great, except, do you notice anything weird? Well, there is water... underground.

The article which I read this from was entitled: "Massive New Ocean Discovered Deep Inside Earth's Interior". Wow, an underground ocean. This is from a science/tech site called the Daily Galaxy. I get their feed delivered to my RSS reader. It's generally good stuff, however this is unacceptable.

Why is this unacceptable? Let's go to their source; a press release from Washington University in St. Louis. The story here is entitled: "3-D seismic model of vast water reservoir revealed". If you read the Daily Galaxy article, you are lead to believe that they discovered an underwater ocean! However, this quote is found in the WashU press release: "If you combine the volume of this anomaly with the fact that the rock can hold up to about 0.1 percent of water, that works out to be about an Arctic Ocean's worth of water."

There is a major difference between "underground ocean" and "rock that holds some water". Please note, that I am not knocking the science here, just the way it was presented by the Daily Galaxy. They do include the quote: "The researchers estimate that up to 0.1 percent of the rock sinking down into the Earth's mantle in that part of the world is water, which works out to about an Arctic Ocean's worth of water." In my opinion, that's insufficient, it does not clearly state what is taking place here. How could this have been done better you may ask. Let's move on to National Geographic. Their article is entitled: "Huge Underground "Ocean" Found Beneath Asia", similar to that of the article from the Daily Galaxy. I appreciate that the word 'ocean' is in quotes, but the key difference here is the article itself. I quote from the fifth line:

"But nobody will be exploring this sea by submarine. The water is locked in moisture-containing rocks 400 to 800 miles (700 to 1,400 kilometers) beneath the surface.

It isn't an ocean. [The water] is a very low percentage [of the rock], probably less than 0.1 percent."

Science writing is important, it lets people who don't spend their lives working in science understand what's happening in the science world. However, we must realize that people doing "science writing" are essentially acting as translators. It is very important that the message is not skewed! Before I read the source, I was left with the impression that we discovered a new ocean!

[Comments: 0] [Tags: science, ranting]

I decided that I should probably start regularly reading science journals. Since I also should be updating Will and Beyond with content, why not combine the two? Every week I will read through 'Science' and will summarize any articles I find interesting. If I didn't find anything that caught my interest, or I feel like doing more, I will look in other journals as well.

This week I looked at Science, Vol. 317, No. 5844, 9/14/07. Nothing really caught my interest, so I looked in the Journal of the American Chemical Society, JACS, Vol. 129, No. 37, 9/19/07.

Here, two articles caught my eye.

Modular Total Chemical Synthesis of a Human Immunodeficiency Virus Type 1 Protease

Human Immunodeficiency Virus Type 1 is more commonly known as HIV-1, the more widespread and contagious form of HIV. HIV-1 protease (HIV-1 PR) is a component of HIV-1 which is present in propagation/reproduction of the virus within the body. The exact catalytic mechanism of this is currently unknown. Being able to synthesize this protease would help us further understand it, and come closer to knowing exactly how the virus reproduces itself.

HIV-1 PR is composed of 2 99-residue polypeptide chains. This means that each of the 2 chains has 99 amino acids bound together in a certain sequence. In order to fully synthesize the protease, 4 smaller chains, about 25 peptides long were made by SPPS, solid phase peptide synthesis. The 4 chains were to be bound together with native chemical ligation, where they are connected by amide-thiol bonds. The thiols are later removed by Ramel nickel desulfurization.

However, when this was attempted, precipitation issues were encountered; the products would aggregate (clump up) and come out of the solution as a solid. In order to prevent this, another tactic was attempted; strings of the amino acid Arginine were bound to the end of one of the 4 small peptide chains. Arginine has been found to keep polypeptides in solution, though the reason is still unknown at this point. 10 Arginine units were bound to one of the 4 chains, and then each of the other chains was able to be connected one by one. The new issue arose of how to remove the Arginine once the 99 peptide chain was constructed. They thought that once constructed, the protease would act as it does when in the body and attempt to begin reproduction. The first step of this is to cleave the end of the chain and bind to another unit. This was successful.

The final product was made in 12% yield, which is a relatively high yield compared to other methods of creating peptide chains. The reaction took about 4 days, and was characterized (identified/verified) by LCMS (Liquid Chromatography Mass Spectroscopy) and MALDI (Matrix Assisted Laser Desorption/Ionization). These methods both take the mass of the product, which can be compared against the theoretical mass. An x-ray structure of the product was obtained by X-ray Crystallography and the product was seen to be bonded together as hoped.

This is a good step in the process, and the novel way that this was made keeps it free from contamination from enzymes which are encountered with other synthetic methods.

DOI: 10.1021/ja072870n

Paclitaxel-Functionalized Gold Nanoparticles



Paclitaxel is a drug which is used in cancer chemotherapy. Traditional drug delivery methods are not effective for all drugs; one major issue is that the hydrophobic nature of some drugs prevent it from being dissolved in the bloodstream and administered normally. A method to circumvent this problem is to enclose the drug in a hydrophobic surrounding, known as a micelle. However, a problem with this method is that this results in a very large product and this can be caught in the reticuloendothelial system, the RES, which is a system to fight foreign substances in the body, and is composed of part of the bone marrow, thymus, and liver.

Another approach is to make a smaller delivery system to avoid capture in the RES. This is done through nanoparticle delivery. Molecules of the drug are embedded onto the surface of a small metal nanoparticle. Gold is a common choice because of the ability to put organic groups onto it through an alkane-thiol bond. Even with this method, there are still problems - it can only be measured qualitatively because it is hard to characterize because of issues with solubility. They found that by using a 2 nm gold core, these issues don't arise.

Paclitaxel was bound to a hexaethylglycol (HEG) chain. A phenol thiol (4-mercapo-phenol) was bound the surface of the gold particle and these two were linked together by combining the carboxyl terminated end of the HEG with the phenol to form an ester. The HEG was chosen as a linker because it increases the solubility in water, and also minimizes destruction of the drug by the RES (which is called opsonization).

This was performed successfully. It is a 9 step process, of which many steps show 90%+ yield. The final product was characterized by NMR and (nuclear magnetic resonance) IR (infrared) spectroscopy. SEC (size exclusion chromatography) showed a good yield of the product with no side reactions resulting in small products. It was shown through TGA (thermogravimetric analysis) that there are approximately 73 (+/- 4) molecules per particle, which results in about the nanoparticle being composed of 60% Pacitaxel, which is an extraordinarily high organic to metal ratio. The product was also seen through TEM (transmission electron microscopy). This novel approach will be able to be used for lots of applications in drug delivery.

DOI: 10.1021/ja075181k

Godspeed.

[Comments: 1] [Tags: science, journals]

Ever looked at the back of some bottle of body wash or shampoo and seen that long list of complicated looking ingredients, and wondered what it all does? There's so many things, what could each one of them possibly do?

Me too, but seeing as I'm a chemist, I figure why not investigate, and learn about some molecules. Plus, wouldn't it be impressive if someone looks at the back of something, and says, man I wonder what so and so does, and you quickly retort a scientific sounding response.

I took a bottle of Irish Spring Body Wash, and analyzed each of on the ingredients listed on the bottle. The order indicates the relative amounts, so there is more of the first listed component than the second, and so on. Enjoy!



Water
Water covers 71% of the surface of the earth. You're probably pretty familiar with it. Odds are you drink in it, and bath in it. What is it doing in my soap? Well, if you just had all of these chemicals concentrated, it would be pretty strong, and not very good for you. However diluted, these chemicals can do their wonders, which are described below.



Sodium Laureth Sulfate
Sodium laureth sulfate is a synthetic detergent. It is abbreviated as SLES. Its effect is to act as a foaming agent, and is an efficient cleaner. The alkyl end of the molecule (the zigzagging end on the right) is fat/oil soluble (soluble meaning that it can be dissolved in a certain substance), so it is able to bind to oils in our skin. The sulfate end on the right is composed of sulfur and oxygen, and is water soluble. Because the molecule has two ends soluble in different materials, it can act as an anchor to pull excess oil from our skin, and can still be washed away. The section of the molecule surrounded by paranthesis and marked with an n indicates that that section of the molecule will repeat n time, where n is a whole number. Often times with SLES, n is 2 or 3.

This compound can be classified as a detergent, and a surfactant. A surfactant is a molecule that reduces the surface tension of what it is emerged in.

There are rumors that this compound is carcinogenic (causes cancer), however these are just rumors; it is not true. It's biggest danger is being irritating to those with sensitive skin. It is very common in soaps and toothpastes, etc. For more on this being disproven as being carcinogenic, see below in the references.



Cocamidopropyl Betaine
Cocamidopropyl Betaine has similar properties to that of SLES. It is abbreviated as CAPB. You can see that it has a similar structure. The alkyl chain on the left is again fat/oil soluble, and the carboxylate (the carbon and two oxygens) group on the right is water soluble, and has the same effect as the sulfate in SLES.

The difference between these two molecules is that CAPB is a milder detergent, and it is a more viscous (thicker) compound. Why is it more viscous? Well, it's complicated, if you're feeling brave, feel free to delve into some fluid dynamics, it's not my sort of thing though. The short, simplified version is that bulkier molecules which have strong intermolecular forces (forces that pull the molecules together) are more likely to be a solid, or a viscous liquid. The nitrogen to the right of the oxygen in the line structure is a hydrogen bond donor, and the two double bonded oxygens act as hydrogen bond acceptors. Hydrogen bonding, is what makes water such an interesting molecule.

CAPB essentially dilutes SLES, and makes it less irritating, but not so much as to render it ineffective.



Sodium Chloride
Sodium chloride has a much more common name; salt. You encounter salt every day, and is the reason that salty foods are high in sodium; because salt is made of sodium. However what is it doing in my cleaning agent? Well, it has two major functions.

It "softens" water. You've probably heard of hard water. Hard water is laced with magnesium and calcium ions, which leave a residue, or scum in your bathtub, etc. The way sodium chloride softens water, is by "exchanging ions" with the magnesium and calcium ions. This reduces the negative effects of the magnesium and calcium ions, and helps prevent the residue from being left on you or your bathtub.

Salt is also an antiseptic, which helps prevent and clean bacteria from your skin.



Decyl Glucoside
This is another detergent/surfactant. It is one of the milder agents listed here, and also acts as one of the best foaming agents. As you can tell from the lack of (+)'s and (-)'s shown in its structure, it is non-ionic surfactant, which generally means it is more environmentally friendly, and it is also much less likely to be left as a residue.



Fragrance
Well, this is a vague term. Fragrance chemistry is a pretty specialized fields, and is pretty self-explanatory. It consists of engineering different compounds or mixtures of to produce a certain scent. So, "fragrance" could be a whole slew of things. I'm not going to go into it because it's useless since they don't tell us which fragrances they're using. If you're interested, google something along the lines of "fragrance used in soaps".

DMDM Hydantoin
Now this is interesting. This molecule is a preservative, which releases formaldehyde. Yeah, formaldehyde. Your first thought was probably of dead bodies, but formaldehyde is actually used in more things than you probably know about. For instance, it is even used in vaccinations, and to treat warts. All new to me. It is used in our product because formaldehyde is used to kill bacteria and fungi, and acts as preservative. These are also two reasons it's used to preserve dead bodies actually.

Formaldehyde is toxic to the body, becuase it is converted into formic acid. This has the effect of lowering the pH of our blood (making it more acidic), which is very bad. However, luckily our body is buffered, which means it resists changes in pH. I won't go into great detail here, but I will list just a few ways the body does this. our blood has carbon dioxide in it, which produces carbonic acid to neutralize any excess base we might have in us. Bicarbonate is in our blood as well which acts as a base to get rid of any acid in our blood. One of the main functions of the kidney is to excrete acid; our urine is much more acidic than our blood. In case you were wondering, our blood has a pH of about 7.4, which is just slightly more basic than water, which is often used as a standard, and has a pH of 7.

That was quite a tangent, but hopefully an interesting one.



Polyquaternium-7
Another interesting molecule. Polyquaternium-7 actually coats hairs on the body with a very thin film. The purpose is to make the hair less electrostatic and easier to comb, which will make it feel smoother. This is true for both the hair on your head, and body hair. If you're interested in seeing some cool microscopic pictures of hair before and after being coated with Polyquaternium-7, click on the "Morphological analysis of polymers on hair fibers by SEM and AFM" link in the references below.



Tetrasodium EDTA
Another component whose purpose is to soften water. Tetrasodium EDTA has four (which is why it's TETRA) sodium ions, which can be exchanged with magnesium and calcium ions from hard water. EDTA is very common in laboratory use for general ion exchange purposes.



Citric Acid
Get ready for it, Citric acid is used to... soften water! A recurring theme, but it is important. However, that is not the only purpose of citric acid. You're most used to hearing about citric acid from being in fruits. It makes foods taste sour (acidic). In terms of our product, citric acid also opens up the outer layer of hair, the cuticle, and allow the other detergents and such to have a deeper cleaning effects.



FD&C Green No. 3
FD&C stands for the US Food, Drug and Cosmetic Act. There are currently seven artificial food colorings permitted in the US. Natural food colorings such as caramel coloring, often found in cola are in a separate category. The name of FD&C Green No. 3 is Fast Green FCF. The reason food colorings are different colors (as well as why anything a different color) is due to the wavelength that light is absorbed at in a molecule. This varies based on structure and composition of a molecule. This coloring is used to give the product it's green color.



FD&C Yellow No. 5
See the above item for a brief explanation on food coloring and their name. The name of the FD&C Yellow No. 5 compound is Tartrazine. Its structure is shown below. This is the dye found in Mountain Dew and simliar sodas. There is an urban legend that ingesting this dye will shrink your testicles and/or penis. This is nonsense. Anyhow, this coloring helps reduce the intensity of the green in the product.



I hope you enjoyed this journey of chemistry, please leave any feedback in the commments below. If you enjoyed this and want more, just suggest a product.

References:
Wikipedia - Sodium Laureth Sulfate
Rumor: Sodium Lauryl Sulfate Causes Cancer
Wikipedia - Cocamidopropyl Betaine
Ingredients - Cocamidopropyl Betaine
Wikipedia - Viscosity
The Many Uses of Salt
Other Uses for Salt
Wikipedia - Decyl Glucoside
The Difference between anionic and nonionic surfactant, and its application to detergent
Ingredients - DMDM Hydantoin
Wikipedia - Formaldehyde
Morphological analysis of polymers on hair fibers by SEM and AFM
Wikipedia - Tetrasodium EDTA
Wikipedia - Citric Acid
Wikipedia - Fast Green FCF
Wikipedia - Tartrazine
Urban Legends Reference Pages: Mountain Dew Shrinks Testicles
Wikipedia - Water

[Comments: 22] [Tags: science]