Tagged: literature

CoverTime: may the cubane be with you

Another beautiful cover (frontispiece) from Angewandte Chemie….. And another proof (if you really need more) that chemists are huge nerds….

anie201681161-toc-0001-mThis time is a beautiful homage to the last Star Wars movie…… No, not talking about Jar Jar… and not even about a new fluorescent detectors for Midi-chlorians. Force sensors? Not even close…
But let’s go with some order:
I don’t know if you paid attention to it, but there are 25 authors on this paper… 26…. This should already give you the complexity of the research done in there…. 26….
7 Students
9 Doctors
10 Professors
Simply impressive, but in such huge work I would like they use the style of Natures where at the end of the paper there is also the “Author contributions”.

EDIT: Thanks to the power of internet, the firs author of the paper pointed out that the “author contribution” was under my eyes all the time in the supplementary information… So here we go (and again, pretty impressive):

Author Contributions: C.M.W., G.P.S. and J.T. conceived the project. C.M.W., B.A.C., H.X. and S.D.H. chose the cubane targets. B.A.C., H.X. and S.D.H. undertook the synthetic preparation of all cubane analogues and obtained the respective characterisation data. C.M.W. and B.A.C. wrote the paper with assistance from all authors. C.E.J.C. and H.M.C. designed the leteprinim study and analysed results. S.G. and M.T.S undertook the Phase I and II leteprinim metabolism study and analysed the results. A.K. and M.T.S. designed the benzocaine study and analysed results. B.C., A.R., D.W., and S.K.N. designed the SAHA mouse study and analysed results. C.-E.M. and G.H.W. designed the diflubenzuron study and analysed results. J.S. and J.D.V. designed the t-butylbenzene metabolism study and analysed results. G.M.B., C.J.P., and P.G.P. designed the SAHA cell line study and analysed results. S.W.L. performed the LogP analysis. P.V.B. performed the X-ray crystallographic structure determination for compounds 4 and 12. C.P. and J.Mc. designed the scabies study and analysed results.

 

Anyway, cubanes. I have always loved the cubane synthesis, mainly because the cubane molecule is so nicely perfect. There are also some beautiful pieces on the cubane by Roald Hoffman “in praise of synthesis” and in his book “on the Philosophy, Art, and Science of Chemistry”. Such beautiful, yet complex to synthesize, molecules….

And that’s naturally not the first time, most probably not the last one, that Star Wars enters the world of chemistry….

The classical example is “A supramolecular Star Wars Tie Fighter Ship” where Star Wars is even in the title. And this figure in the paper is just pure bliss:

star wars chemistry

Fun with chemical structures as well here.

Tie Fighter

And what about you, poor trekkies???? Worry not, almost any smartphone based analysis is called tricorder nowadays…..

 

Other CoverTime: the power of the metal, Robots, 80s vs 90s.

CoverTime: Robots

How nerd are you? Can you identify the robot in this cover (without googling)?

tripod

 

Did you get it?

This is a cover from a review in ACIE from the group of Ley about machine assisted organic synthesis. I’m a big fan of Ley and all the automatic things and remote control they have in the lab, but we are here for one and only one reason: The cover!

So, which kind of robot they used for the cover?
I’m pretty sure it’s a badass tripod from the war of the worlds.

warofworldsaliens

Now, let’s forget for one moment that the size of the tripod is huuuuuuge, and I guess is not going to fit in the lab, but my main question is: Why picking up an “hostile” robot?
Frankly speaking, the tripod is not such friendly robot one would have around…. True, it has quite a lot of flexible arms that are handy, but still….

And then I was wondering, which robot I would like to have in the lab? And here the topic gets complicated…..

A random decepticon, although they are not friendly, I just love the metallic voice “DECEPTICON” from time to time.

c-3PO is kind of useless, but it’s nice for the fun and the good atmosphere of the lab.

R2-D2 it will be like that non-english speaking labmate that is impossible to understand, but he fixes the HPLC like no one else.

Ash/Bishop, shall I trust him? Is he going to scoop all my research and send it to someone else?

Data, amazing guy, he knows every-fucking-thing. Maybe little bit arrogant and I-know-it-all-guy, but well, he has his reasons.

Number 5, maybe it’s a good choice. Still I don’t like how he moves.

Robocop, booooooring.

Chappie, undergrads for few minutes, PhD in one day and then he will be the best chemist ever.

Terminator, “I’ll be back”, yes but when? Why did you leave all this mess in the lab? Where are you going? No, you cannot just add Sarah Connor as author in the paper.

HAL 9000, come on, please distill some DCM, is not that dangerous.

 

And then I stopped thinking about that, the choice is way too difficult to be solved in one day. And you, which robot would you like to have in the lab?

 

Previous CoverTime: The power of the Metal, 80s vs 90s.

Videogames and science #2 “Dying Light”

Second post from the series “Videogames and Science”. First one here.

After finishing Far Cry 4 and The Walking Dead Season 2 (no science in both of them) I’m on Dying Light, an amazing free roaming zombie video game from the same people that did Dead Island (another zombie game that I loved). As most of the zombie games you need to do some quest while brutally slaughtering zombies here and there. Without saying that the game is pretty amazing and extremely fun to play let’s see how “science” is depicted in this videogame:

In one of the main quest you will go in a school looking for some “anti zombie drugs”. Here the science class:

IMG_6996

 

Like in “The Last of Us” science is primarily identified as microscopes…. Microscopes, microscopes everywhere… Then we have an Erlenmeyer flask and a huge Bunsen burner. And yes, I’m using a two hands ass-kicking head-removal axe.

IMG_7009Some other stuff: What looks like a separator funnel and a thermostat.

IMG_6999Very important safety flyers all over the room and….

IMG_7003

…. some safety guidelines.

IMG_7016 2

A classic periodic table…. Wait a minute…. Do you notice something weird? Yes, indeed, the colors! What happened to the colors? Which kind of weird periodic table is it? After a little research I discover that this is a wikipedia-made “periodic table by value“. Some programmer at Techland probably remembered that there were colors in the periodic table but didn’t know where….. Wikipedia keeps track of the change of everything, and the exact periodic table that is in the game is the version of July 2012.

IMG_7013Oh, look at that, some properly drawn chemical structures…. Even the reactions are correct…. And in fact they (probably) came from masterorganicchemisry.org. Interestingly, the masterorganichemistry.org article was also written in July 2012. The game was released in 2015…..

IMG_7015

Another (almost) well drawn chemical structure (there is a H missing on that nitrogen). But what’s that? Caffeine? Theobromine? I would have expected a caffeine molecule, but it is not. That molecule is a theophylline…. Now, someone badly drawn the caffeine molecule or was drawn on purpose? No one knows……

IMG_7018

 

The Pi, down to I don’t know which decimal…..

IMG_7022And last but not the least…. The Sierpinski triangle…. Almost in perfect time with the amazing Nature Chemistry paper on molecular Sierpinski assembly.

 

For now that’s all, I think I’ll need another 20/30h for finishing the game, so, see you with the next game (probably Bloodborne or The Witcher III) if there will be some science inside.

 

CoverTime: The power of Metal

nanoscale

One of the most “metal” cover I’ve ever seen is coming from a Chinese group: Gong’s publication on ZnO “nanopencil” featured the cover of Nanoscale. Let’s forget for one moment about the nano-whatever word and focus on the beauty of the cover: Two metal missiles flying under a heavy storm.

Two songs come up in my mind watching this cover:

 

and I can only imagine the group working on this, singing along this song in the lab after getting the cover published:

“Brothers of metal
We are fighting with power and steel
Fighting for metal that’s all that’s real
Brothers of metal will always be there
Standing together with hands in the air”

 

 

some journals 2

Please, please, please, when you are little bit depressed read this paper : http://innovativejournal.in/index.php/jpro/article/view/678 , it’s a laughing-tears-paper (LTP). 

It should have dealt with the conversion of -OH to -NH2 in one pot, or at least the abstract state that. 

Oxide

Now, after the first three lines…. Where the hell the nitrogen come from??? React alcohol, sodium oxide, TsCl and zinc and you will magically get some nitrogen. Amazing.

 

Oxide2

Ahhhhhh sodium azide, not sodium oxide. Ok, ok, at least now it makes a little bit more sense. Let’s go check the experimental section then:

Oxide3

And here the apotheosis of hilarity… First of all we are back on using sodium oxide but now the zinc disappeared.

Then we are not using 65-70C but we raised a little bit the temperature to 650C.

Then we need to quench few mmol with the fair amount of 5 LITERS of water.
Ok, now we have 5 L of water in the flask, we should deal with it.
What shall we do? Extract it with 25mL of ether!!!
5L of water….. and 25mL of ether….. ok….ok….
Now filter the ether off… well, we cannot really filter it off, are two liquids…. 
Right, right, then filtur it off. Ok, now makes way more sense, thank you. 
Now dry it over unhydrus sodium sulfate, pay attention that it must be unhydrus!!!
No, no please, stop, please stop, I’m dying. Please stop.

And then the last nail in the coffin…….

Purify it with a silica get!!!!

Applause, applause, applause. 

 

And thanks to one of my colleague that sent me this paper, fun for everyone from 6+.

The 5 stages of grieving a rejection

Snoopy paper1

I’m naturally talking about papers/grants/prizes/applications/orders rejection. 

Open you email and search for “regret” and “pleased” and you will unequivocally see that “regret to inform you” >>> ”pleased to inform you”. 

It’s monday morning, you are in a good mood, coming back in the lab for setting some experiment planned during the weekend. You pick up a cup of bad coffee and go to your desk, start the computer and start reading the work emails:

Object:  Decision on Manuscript ID XX-SHT-04-2014-012345

When you open there are only two words you are screening in the first 5 seconds: “REGRET” or “PLEASED”. Then, depending by the one found, the scream could be of joy or of intense pain. How could you deal with the n-times rejection?

Caro Wallis We regret to inform you

First of all let’s check what happens in your brain:

1- Denial and isolation.
Come on, it was a great paper, nice idea, months and months of work, unequivocal data. It’s impossible it was rejected, I need to read this mail again. And again. And again. Nope, still rejected. Maybe if I print this email I’ll manage to read it better. Printed and no, it is still rejected. Maybe it’s just because it was printed in black and white. Let’s try to print it in color. No, still rejected. 
It’s impossible, they should have sent this email by mistake, it’s not for me, it’s not for my amazing paper. 

2- Anger
Seriously? They reject this paper? How the hell can they do that? The referees must hate me, I know who they are. But why the editor didn’t say anything about this? He must be blind. I will never ever ever and ever submit another paper to this journal. Now let’s go smashing some 10mL cylinders in the lab, bleaching some dyes and shooting laser with MALDI.  

3- Bargaining
Maybe I should write to the editor. It’s an interesting paper, all the data is correct. He must see it. Maybe he will see that the referees are wrong. Maybe, maybe, maybe.… I may add new spectra, new data, new conclusion, maybe a horse head (it usually works). I can change the title, the authors list and even the corresponding author. But please accept this paper, I’ll referee 50 new papers….. I will even put the name of the editor in the acknowledgment and the name of the journal in my presentation slides. I can tattoo the journal logo on my forearm. I’ll only publish with your amazing journal for the rest of my life, and even my kids will only publish there and their kids as well. 

4- Depression
Why I am even doing all of this? Why I am doing research, and teaching, and writing grants, and papers than then will be rejected without any reason? I could have been in a company, earning 5 times what I’m earning now and for sure I would not working in the weekend. I could have been a barista on a beach somewhere in a warm place, and not here freezing in a cold lab. Ok, I quit. Let’s go to tell it to the rest of the people in the lab. Fu*k it, I’m done with this. They accept so many crappy paper and they cannot even realize how good was my paper. I’m soooo done with it. 
So long rest of the people in the department. See you in hell losers!!!!

5- Acceptance
Nothing to do, the editor agreed with the referees. Ok, I know it, it’s part of the game. It’s the part of the game that I don’t like, but I like to play the rest. What can I do? Now let’s do the worst part of all of this:
Changing the citation format for the new journal……  

How to deal with it? I like the Bernard Black way.

Google Safety Glasses

A couple of literature from “anonymous” sources….

The first scientific paper using google glasses (or at least chemistry related paper) is out. And what’s better than sponsoring it with this kind of amazing TOC????

Nn 2014 00614k 0012

Few questions arise from this picture. Are the google glasses safe for the lab? I know quite some safety sheriffs that will be not so happy to see people working around just with the google glass. Then, why on earth the labcoat is striped???? 
The paper is here, enjoy.

Second paper of the day…. Apparently T-BAG is a well known term in the surface chemistry world…… if you don’t know the other meaning, DO NOT walk around the department asking explanation to random people…. DO NOT!!!

NewImage

NewImage

paper here.

 

Protruding Nanoballs Vs Recessional Nanosuckers

Nanosuckers

Using “Protruding Nanoballs” and “Recessional Nanosuckers” in the same title is not something easily achievable. Luckily someone managed to do it: http://pubs.acs.org/doi/abs/10.1021/nl4048042 

In the paper some more amazing NanoThings:

“shrunken nanoball architectures”

“…produced a great amount of suction when applied to other surfaces, similar to the effect of suckers on an octopus’ tentacles”

“The overall structure changed from a nanosphere to a “nanosnowman”-like structure with a smaller ball affixed atop the larger one.”

“The nanocup structure had a relatively small opening mouth on top of a spherical cavity”

“No matter the length of immersion in acetonitrile or the size of the nanoballs, those nanoballs displayed homogeneity in size and the same period of sequence; that is, smaller nanoballs had larger spaces between them.”

“…the nanosucker design presented in this article is the only octopus- inspired design”

 

P.S. The research described in the paper is extremely interesting, and achieving such strong adhesion with dry film is quite impressive. Check the videos in the supplementary information for the stress test (and a brutal vertical video).

in-FXXXKing credible!!!!

Another day, another paper…. 

Finally papers are getting closer to the real lab life, and sooner or later I’ll be free to publish all the cursing I’m generally doing in the lab.

Fucking

The paper is “Conventional transmission electron microscopy” http://www.molbiolcell.org/content/25/3/319.abstract

If you read the paper (it can be quite interesting if you like the TEM) you will find also some other pearls like:

“In any event, embedding and curing in any resin should yield a hard “block” with the sample in it: congratulations, you’ve created a fossil.”

My top something papers of 2013

Web  Library  image

What are the top ten papers that you read this year? @JessTheChemist on her blog started this nice topic, followed by @KarlDcollins here and now I guess it’s my turn.

Before going on, maybe it’s nice also to check the top 100 papers according to altmetrics of 2013 (so, the most discussed on the web).

I changed field in July so most of the time I was reading the last 20 years of relevant literature that I was missing. Moreover I like to read quite a lot of different papers, If you think I’m mono thematic then probably you will be disappointed by this list.

and let’s go (as always not in any particular order):

1- Ultrastable silver nanoparticles. Pretty impressive paper on silver nanoparticles (or maybe better, clusters). Amazing monodispersity, fixed number of silver atoms and capping molecules. The TOC with 140g of dried silver nanoparticles is a joy for the eyes. Maybe I have some remarks on the word “Ultrastable”. How can something be more stable that stable? Are they better than superstable nanoparticles? What’s next? Fworld-Stable nanoparticles? Maybe it’s only my english…  Bad point is that so far we didn’t managed to repeat the synthesis, but who is working on the field know how difficult is sometime repeating the formation of nanoparticles….

2- Tactile perception limit. If you think that your finger can detect only surfaces with millimeter patterns, well, think it again. This paper shows that your finger can detect the differences in surfaces with micron size features. Please avoid any sexual jokes about fingers and micron-sized things. 

3- Devices and 3D printers. Using your cellphone as microscope for single nanoparticle detection, single molecules counting or albumine test in urine. How cool is that? I would say as cool as printing and modifying new materials or your own microfluidic reactors. This review on nano materials for breath test is also a nice reading.

4- Is it difficult to grow long carbon nanotubes? Fei Wei doesn’t think so as his team managed to grow half meter carbon nanotubes. And what about controlling the movement and the assembly of nano-objects? Edo Waks and coworkers proved that it is doable using flow control.

5- Passing information from DNA to another set of molecules without even using an enzyme? Doable.

6- And more or less on the same topic, how to synthesize a specific sequence of aminoacids without using an enzyme? Using the “robosome” of course. 

7- Editorials, perspectives, comments and so on: The “All you can tweet” editorial on Nature Chemistry is pure gold. Can natural products and material chemists talk to each other, I mean without weapons? A very nice discussion on the topic in a JACS perspective. Otto Wolfbeis in an Angewandte editorial asks where are all the sensors, labels and probes that we are synthesizing in the lab everyday. Why they are not on the market? That’s a very good question. George Whitesides also thinks about market in his “Cool, or simple and cheap? Why not both?” and I share his point of view on that. Little bit more controverse is his “Is the focus on “molecules” obsolete? but also in this case some (most) of his points are reasonable. 

8- Random stuff. Electronic Visualization in Chemistry: From Alchemy to Art, very cool paper on the evolution of graphics in chemistry. If you are into the data mining business you may want to read how to predict future events mining the web.

9- Last but not the least a PNAS paper titled “Penis size interacts with body shape and height to influence male attractiveness”. Right from the paper this cit: ”Before clothing, the nonretractable human penis would have been conspicuous to potential mates. This observation has generated suggestions that human penis size partly evolved because of female choice.” That’s science! 

 

So what are your favorite papers of 2013? discuss it on twitter using #chemclub2013