Liquid Carbon

Liquidcarbon @ Coronene.com

Wed, 07 Oct 2009 06:46:31 GMT

Hey everyone! Liquidcarbon is now officially a part of

Carbon-Based Curiosities!!!11one!

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Digging Chemdraw.

Fri, 26 Jun 2009 10:40:50 GMT

Folks, we're about to reach the highest Dan of Chemdraw, the mastery of which enables you to make molecules without even lifting your ass from the chair. Yeah, dream on.

Last time I was talking about some basics, and also hotkeys, which are absolutely crucial to productivity in any computer work. Quoting myself, "what ChemDraw really lacks is the hotkeys for switching between different drawing tools" — now I refute this statement. Find a file called CS Chemdraw HotKeys.txt under ChemDraw Items folder. On XP it's hiding somewhere in the Application Data dumpster, I hope you can find in on a Mac (yeah, I'm a PC, whatever). You can manually edit the hotkeys in there. Here's how I have it set up:

1 TOOL_MARQUEE
! TOOL_LASSO
2 TOOL_SOLIDBOND
@ TOOL_ACYCLICCHAIN
3 TOOL_TEXT
4 TOOL_ARROW
$ TOOL_CYCLOBUTANE
5 TOOL_CYCLOPENTANE
% TOOL_CYCLOPROPANE
6 TOOL_CYCLOHEXANE
^ TOOL_BENZENE

  It's a little funny that these settings sit in a separate .txt file, but this is what we get when we don't provide much needed feedback to the developers. I'm going to write them. Some of them (arrows, brackets) actually don't work.

  Finally, I present you... the "making" of the notorious aspidophytine. *exasperated gasp* However, let us not be overly cynical, for The Man actually gave us ChemDraw. I learned it from the preface to "The Logic of Chemical Synthesis". Moreover, in all his publications EJ actually abides by his original style used in the book, which quite different from what's commonly used. You can read about a recent synthesis of aspidophytine here at TotSyn.com. And, seriously, Angewandte, you waved the haplophytine flag like a year ago already, and it's still "almost published" in the VIP papers. Haplophytine is the bigger cousin of aspidophytine, which might have killed many more Japanese grad students. We just don't know about it, because they go straight to ~~heaven~~ North Korea.

  Note how my cursor doesn't even leave the screen to reach for different drawing tools. Note the use of Rotate and Join tools. This was the fifth try, I believe. This is at native speed, try beating my 71 seconds!

http://www.youtube.com/watch?v=bv6LJybdxII

Recorded with the outrageously awesome and free CamStudio. Drawn at 200% magnification. Drawing settings used:

Fixed Length: 0.525 cm
Bold Width: 0.07 cm
Line Width: 0.035 cm
Margin Width: 0.07 cm
Hash Spacing: 0.084 cm
Font: Calibri, size 9

Hail yeah!

Tue, 09 Jun 2009 02:58:45 GMT

Rejoice, my friends, for the ACS removed the stupid first page that annoys readers from all its publications. I like to think that it was a result of visiting the ACS Publications booth at the meeting in Salt Lake City. In the other news: Alfa Aesar is working on redesigning their labels to make them more informative.
I have to admit though that the meeting wasn't quite to my expectations.

Rise. And shine.

Fri, 08 May 2009 08:09:58 GMT

One of the reason why human is human is that he has his place in the world. But the desire to do chemistry is a manifest of his willingness to rise above it. If only he knew how many eyes is he exposing himself to, he'd never, ever do it. If only he saw a tiny fraction of those staring at him, he'd die of fear.

Actually, it is originally about hallucinogenic drugs.

Gallium heart beating.

Wed, 15 Apr 2009 14:59:43 GMT

Saturday Night Distillation.

Sun, 29 Mar 2009 10:03:04 GMT

  As one of those spoiled by flash chromatography (and solvent columns), I realized that I forgot when was the last time I distilled anything. After that insane month preceding the ACS meeting, I decided that my homecoming to the hood should commence from distilling furfurylamine, which I use quite a lot as a starting material. No matter what I do, this 250 mL bottle with orange liquid would never end, so I helped it. Not a desperate call for purification in this case, it usually works fine, giving 90+% yields, but it seemed like in a couple of cases the amides wouldn't crystallize because of this colored crap that dragged on from the amine — requiring a column to make it solid.

  I spent a good hour looking for the distillation equipment. I looked everywhere. The only possible apparatus good for about 150 mL was finally assembled, consisting exclusively of the parts occuring only once. It appears that nobody distills things on this scale in our lab. 1–2 L setups and Kugelrohr were much easier to find. I used house vacuum, since the subject boils a little bit too high at about 145 °C at 1 atm. It came out pale-yellow. I used a capillary to bleed in air and was lazy to set it up under nitrogen. But... I took NMR of my fractions. As far as I could tell, all of them contained satisfactorily pure furfurylamine. The brown residue was enriched in some crap, and most of the water came out in the first one. The latter was evidenced by a very broad peak (~0.15 ppm @ half-height) centered at 1.49, as opposed to moderately broad (~0.07) at 1.42 in the main fraction (all in chloroform, stored over calcined, powdered pot carb). And I'm definitely not the winner in "The most original and appropriate choice of an internal standard" nomination. For the absence of mesitylene, 2,4,6-collidine seemed like a good replacement. It is not. Yay long-range coupling.

  It seems like the main justification of these efforts is going to be the augmented aesthetic appeal of pale-yellow over bright-orange.

Murphy's #1 in industry.

Fri, 13 Mar 2009 03:40:38 GMT

  In particular, the unexpected appearance in early 1998 of a more thermodynamically stable form (Form II) of ritonavir (Norvir, Abbott Laboratories, protease inhibitor for the treatment of HIV), with different dissolution properties compared to those of the earlier commercial Form I. Form II is <50% as soluble as Form I, resulting in the observed poor dissolution behavior and eventual withdrawal of the capsule from the market. This incident had serious implications for the marketed product and the patients receiving the drug. The project was suspended until a modified procedure was found. Renitidin, sertraline, and frentizole are some important examples of pharmaceuticals that exhibit polymorphism.
  This is from this OPRD ASAP; they were dealing with a similar issue. They have ultimately performed some 3600 recrystallization before they found the right one.
  Reminds me how easy my life is and how badly I suck at recrystallizations.

想像と創造：1-ヒドロキシインドール化学と夢への挑戦

Fri, 06 Mar 2009 02:34:34 GMT

I have no idea what it means. But I believe I do know what kind of plants they want to fill the Gobi desert with. Carrots, yeah. For sure. This is probably the most mindblowing abstract I've ever read.

Keywords: enmein; evaluation of originality; 4-substituted indole; ergot alkaloid; 1-hydroxytryptophan; making desert full of plants.

Peace, folks. We're good Jedi. Right, Chancellor?

Thu, 26 Feb 2009 02:01:03 GMT

["Chemoselective Ligation and Modification Strategies for Peptides and Proteins", ACIE 2008 10030]

Does it work as an excuse for genetic engineers?

POO!

Thu, 29 Jan 2009 01:57:36 GMT

Kiss goodbye your palladium.

Fri, 23 Jan 2009 16:26:03 GMT

  It's ACIE puns, originally brought to you by Excimer. He talks business, ladies and g. Check this out:

  Is the scientific community about to kiss awake iron catalysis, a topic that has been dormant for decades?

  Credits are due to MIT for bringing in very likeable and smart women. There's not only Alice Ting. Meet Prof. Sarah O'Connor and check out her periwinkle chemistry! I suppose there's no need to tell who's on the right.

100% drinkable.

Mon, 08 Dec 2008 03:43:00 GMT

We need CHANGE!

Wed, 12 Nov 2008 03:32:49 GMT

  As you can see, the project pretty much stalled. I was hoping to make the 100th post special, but at times it seems like I'm overly obsessed with numbers. And with being special.

  Is it November already? Really? Believe it or not, grad school takes up a lot of time. Not that I'm not having any fun, I might actually be having too much, both inside and outside of the lab.

  For instance, someone came in today with a statement about another labmate who recently dyed her hair: "As I was lying naked in my bed this morning, I thought about your hair." Now, isn't it wonderful to work in the environment where you can say that and nothing happens? As it turned out, his thoughts were about using our dye on her hair. The dye happens to be a turn-on thiol-reactive compound, and hair is famous for it's high sulfur content. Of course, instead of dying the hair on her ~~I reached down my pants and pulled out some test subjects~~ we cut a small lock. Pretreated with DTT to break down disulfides it worked beautifully, giving off strong green(ish) light under 365 nm lamp. It appears to be quite stable, too. DIY Dye FTW, and you're all next!

Left—pretreated with DTT, right—uhm, make a guess.
The Eppendorfs look kinda... phallic.

And just for the fun of it, here's an assignment I had. Azadirachtin, baby.

Organocatalysis is DEAD.

Sun, 07 Sep 2008 06:12:45 GMT

  YOU are in HELL. Bow down to your new god. Bwa-ha-ha.
  Unfuckingbelievably cool stuff. Shiny, too.

  Merging Photoredox Catalysis with Organocatalysis: The Direct Asymmetric Alkylation of Aldehydes: aldehyde, α-bromocarbonyl compound, 20 mol. % Imidazolidinone™, 0.5 mol. % Ru(bipy)₃Cl₂, 15W household lamp. Boom.

The Quass.

Sun, 24 Aug 2008 10:45:37 GMT

Making quick updates without illustrative material is hard. Drawing chemical schemes takes long. Writing without illustrations takes talent. [Insert circle-closing statements here] Keeping a blog up and running takes quick updates. Thus, I can has a camera?
Meanwhile, go read what other people are writing about. Ψ*Ψ was deeply touched by chemophilic junk-sucking foot pads for chemophobes. Here's also something from someone she's citing:

If you can see it, touch it, taste it, smell it, or otherwise collect alittle of it in a jar, IT'S CHEMICAL! That includes water, snake venom, aspirin, farts, wood, steel, plutonium, blood, orange juice from concentrate, orange juice not from concentrate,[...] etc., etc. Pretty much anything but unicorns, hugs, and sunshine.

There is a pretty successful brand of kvass in Russia that... oh, wait: kvass (aka quass) is a beverage made of bread. Go read it if you've never heard of it. Anyway, although it is not intended to be preserved for prolonged periods of time, people can't make it themselves but want to drink it. So here comes mass production and bottling, resulting in something pretty far from the original, but still quite decent and tasting like nothing else. Now, some wise-ass came up with a name "Nikola", and launched a campaign with the advertising slogan "Kvass is not Cola, drink Nikola", expressing the opposition to Cola drinks. Ni is a form of negation in Russian, and Nikola (Никола) is a male name. The opposition is further underlined by the website name: transliteration rules, as vague as they are, prescribe to transliterate the letter к as k, not c. Both Russian к and Latin k, unlike Latin c, are always pronounced [k] (if pronounced, opening digraph kn does not count). But, see, they're not Cola.

Well, I was fine with that, and bought the stuff every now and then, even in a Russian store in the US for some ridiculous money. And what do I see when I come back? A new slogan. "YES for kvass, NO for chemistry." I don't even care that the word chemistry is in quotation marks. The message is clear.

(no, not all ads in Russia are that lousy)

Well, fuck you then. I will later write them to explain how they lost a customer and advise on the way to kill themselves.

The three-in-the-morning-way of communicating ideas looks somewhat... strange on re-reading. Or is it just as usual?..

Go ponies!

Fri, 01 Aug 2008 06:12:24 GMT

  I was looking for this article that had something to do with drowning ponies — for some obscure scientific purpose. I think it was Chembark who brought it up about a year ago, but I don't remember exactly, and his search is down. If anyone can direct my attention to that talk it would be cool. I couldn't google my way through either. I even went to ISI — apparently, ponies are featured in some 1400 studies. Such as this one.

  The effect of X-radiation upon the quality and fertility of stallion semen. "These findings indicate that the exposure of stallion spermatozoa to x-radiation up to doses of 10 μSv does not have deleterious effects upon spermatozoal motility, morphology, longevity or fertility. The exposure received during examination using an x-ray security screening system is likely to be lower than this dose."

  We all learned something today (and some of us even yesterday^z). We learned that we are safe, because terrorists won't be able to put bombs in ponies. At the same time, ponies can still happily reproduce. Also we^y learned a new sciencey word: theriogenology. What we did not learn, simply because we^y don't want to know that, is the way they obtained their samples.

   z: I mean myself.
   y: I mean myself again.

Sir Frederick Hopkins (1861–1947).

Sat, 26 Jul 2008 20:45:02 GMT

Note how close to modern is the design of the Soxhlet extractor. This guy sure used it a lot to get all them vitamins.

via tema

At the entrance to the tunnel.

Sat, 19 Jul 2008 21:38:11 GMT

  First week of graduate school was spent on settling down, drinking, retrieving a lost bag from Delta, drinking more, sleeping and learning to play Wii while drinking. The latter activity made me think I'm too old for the modern games. They're too damn complicated and require massive investments of time and effort to reach some proficiency. Otherwise it's not fun to lose all the time. Can anyone see parallels with science?

  As I'm approaching the 100^th post, I'd like to make some conslusions and/or resolutions. Well, to start with, I do not regret at all I started the blog. It used to take me hours to write several lines in the beginning. Even though there's still a lot to work on in this respect, lack of English can't be an excuse for not writing anymore. Now it's about being focused. During rare short periods of active blogging and lab work, I would often write something before heading to the bench. Hitting 'post' after a fifth revision gives feeling of some achievement and force to proceed.

  But to make the blogging really worth it, in other words, to reach the level of our giants, it at least needs to be more regular. I am thinking about teaming up with someone. Expect changes soon. Hopefully, to the best.

The true look of glycoproteins.

Sun, 29 Jun 2008 17:26:46 GMT

In search for the cover image of the issue 5148 of Science (1994), in which the expression of GFP in E. Coli and C. elegans was reported, I downloaded the front matter (36 MB). Along with the funny ads of the latest software for Windoze 3.11 and DOS, dorky pictures of scientists seeking more viable cell cultures while staring in the general direction of the sky at dawn through their Petri dishes, there was something absolutely mind-blowing.

Well, could I possibly resist?

The article mentioned above was cited over 2700 times by now. This is another illustration of the GFP impact, which now brought to us this forgotten piece of... of... ART.

I will be glad to see more examples of funny scientific ads. Anyone? :)

OMFFSM BODIPYs in water!

Fri, 06 Jun 2008 10:03:51 GMT

Here's what showed up in GoogleAds on my Clustrmaps page.

Reminds of Chicago with their perverted but amusing relationships with the Chicago river, such as reversing the flow (so much crap, it all goes in our lake, let's send it to Mississippi!) or dying the river on St. Patrick's day. It used to be fluorescein, now they wouldn't tell what the dye is. It is claimed to be safe for the fish. The process takes 5 minutes (hooray for strong absorption) and the color disappears by the end of day.

JACS Beta.

Tue, 27 May 2008 18:16:59 GMT

JACS^β

The world is changing.
Though I'd prefer video podcast to my goggles, while I'd be lying on the warm sand and sipping on mojito.

GFP nukes!

Mon, 19 May 2008 22:25:27 GMT

It's been a week since I got back home from the US, and it's been a lot of drinking, though it should have been a lot of reading and writing — I'm defending the diploma in June. As always happens during the period of intense reading and writing (and drinking), I've got a lot to talk about, but I feel uncomfortable doing so before I advance at least a little.
My research here has something to do with the green fluorescent protein and its chromophore. Thus, I can't help illustrating its impact. The chromophore is found in the ~~(epi)~~center.

Albert Hofmann: 1906–1943–2008.

Wed, 30 Apr 2008 21:15:56 GMT

Twists and turns...

Tue, 29 Apr 2008 23:46:47 GMT

I like to think that I understand organic chemistry on somewhat fundamental level, being able to talk, for not too long, about frontier molecular orbitals, conformational analysis and subtle structural features that influence peculiarities in chemistry of compounds in question. So now I've got the crystal structure of a compound which gives a ground to muse about all of the aforementioned stuff. And guess what? It brought more new questions than answers, having chosen to adopt an unexpected conformation that contradicts its reactivity observed in solution. Sometimes a hero in a role-playing game finds a relic plate armor — but he cannot put it on, for he lacks the skill 'plate armor'. It seems like calculations and advanced NMR experiments are required to properly understand what is going on with my chemistry... no time for that. The positive part is that we know most of what we need to for the first paper, but before it's out I'd like to say that I know the ways of our molecules...

Decent graphical abstract?

Sat, 19 Apr 2008 04:05:25 GMT

Reagent on the left; reagent+analyte on the right. Excitation with handheld UV lamp (365 nm).

See also

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