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Carbon Tet

Musings of an organic chemist

Updated: 2017-11-08T08:17:31.165-05:00


CS Support Forum - Safari Problem


Alan Gorman commented in my last post that the support staff at CambridgeSoft can find no problems accessing their support forums from Safari. I, on the other hand, have a completely different experience. I have made a video demonstrating the problems with their forums. This was recorded using Safari 5.0.1 on Mac OS 10.5.8 Leopard. I have tried on four different macs and the same problem occurs on all of them using Leopard or Snow Leopard.

One issue that you will see at the beginning is a problem with the first link on their support site. I can get that far if I am not logged in but accessing it as a guest. However, once I enter my login information the support forum web page simply will not load in Safari. Thinking this was a cookie problem I checked my settings. Even at the least secure setting to always accept cookies the error results.

I should note that the same server problem with the first link occurs in Firefox 3.5.11 as well. When I log in I get a similar error that says the page is not redirecting properly. "Firefox has detected that the server is redirecting the request for this address in a way that will never complete."

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ACS Blogging - Cambridgesoft


As I was wandering through the expo this morning trying to dry off after a soaking walk from my hotel, I stopped by the Cambridgesoft booth to chat about their Mac products excuses for software. It was very clear after inquiring about their development that they have no interest in trying to improve the Mac software. All I got was excuse after excuse about how we are only 5% of their clients and we really aren't worth investing in. Cambridgesoft is clearly a follower and not a leader when it comes to software development. They will only invest in their products if they are absolutely guaranteed to make a lot of money. What a pity. If they had this attitude when the company first started, they would not exist today. They still keep blaming all of the problems on Apple and Microsoft. Not that those companies don't share responsibility for the bugs. I guess it's time to give ChemDoodle a good trial. If i can get over the learning curve, it looks like the best solution for chemistry drawing on a Mac anytime soon.

Update: After lunch I returned to the expo and happened to bump into some of the McGraw Hill folks at the CambridgeSoft booth. They were showing their upcoming educational tools combining Connect with a ChemDraw plugin and Blackboard interface. This product looks very promising. Anyway, I got pulled back into some lengthy conversations. I do want to set the record straight. My rant above is all about CambridgeSoft's Mac support. Their windows products are actually quite good and improving all the time. Although I stand behind my statement that this company is a follower and not an innovator, I understand the economics of business. It is our job to let the company know that the market demand is out there. So, if all you pharmaceutical companies would just switch over to Macs and ask CambridgeSoft to start delivering their software to you, I would really appreciate it. And CambridgeSoft, I want to say please don't underestimate the growing Mac market. Frankly if you would just focus on making ChemDraw work well we would be ecstatic. And if you could make a simple Chem drawing app for the iPad that would be the icing on the cake!

ACS Liveblogging Sunday Morning


10:50 am Arrived a little late this morning. I know it is only Sunday morning, but the Boston convention center seems quite dead. It took me 20 minutes just to find the one coffee cart that was open. I will be looking for the Keith Fagnou memorial symposium soon. I missed Hartwig, Sanford and Yu. Jacobson is the last speaker. I'll try to catch some of his talk.

11:15 am Jacobson is talking up reaction calorimetry for kinetic analysis. Not really new but I suppose organic chemists haven't utilized this great technique.

11:26 am Some nice new insight into the Co-salen catalyzed epoxide hydrolysis being presented. It seems using a tosylate counter ion on the cobalt is very different from Cl or OAc. The rate doesn't seem to slow down but expoxide opening is very reversible due to the good leaving group ability of tosylate. This leads to racemization and poor kinetic resolution.

11:40 am Jacobson appears to be flustered today. He's stumbling over words and seems unsure of his slides. Never the less he still has great science to share. It appears that chirality on both the activated epoxide electrophile and the Co-OH nucleophile are important for kinetic resolution. Enantioselectivity is not dependent on the chiral backbone as the ligand complex forms the same stepped configuration of the arylation groups of the salen regardless of the backbone. It is only necessary that backbone allows them to have the same sense of chirality.

11:50 am Ooh. Cyclic oligomers of the salen ligand with local C2 symmetry. Very efficient HKR at only 0.001 mol% loading. Salens connected with ether linkages. Rate is much improved over the monomeric catalyst.

Boston or Bust


I am heading to Boston today for a few days at the ACS meeting. If I see anything worth reporting, I'll share it here. That being said, I usually find myself at ACS meetings not attending as many talks as I would like but instead networking with friends and acquaintances. I am looking forward to some good dining experiences!

Carbon Tetrachloride


(image) Who could not feel sorry for this much maligned molecule. Simple in its structure but so complex in its properties. It is a nonpolar solvent that is still the best for bromination chemistry. Sure it has its environmental issues and has largely been replaced but it will never go away completely. More about the history of carbon tet in a minute. Let's talk about this blog for a moment. Many people think I named this blog after tetrachloromethane. I suppose that was one aspect of the name that appealed to me but it really was much more than that. There is more to Carbon Tet than the halomethane. I thought the name could also connote 'Tetrahedral Carbon' which would play right into the topics of asymmetric synthesis and catalysis. And, besides, I just like saying 'Carbon Tet! Carbon Tet!'.

But this is a chemistry blog, so let's talk a bit more about the molecule. Carbon tet was first prepared way back in 1839. The French chemist Henri Victor Regnault reacted chloroform with chlorine producing carbon tet and HCl. Now it is made from methane but before the 1950s it was prepared by chlorination of carbon disulfide.

As a halocarbon it is not flammable. In the early part of the 20th century carbon tetrachloride was used to extinguish fires. It was placed into brass bottles with a pump which was used to spray carbon tet onto a fire. If you tour some of the mansions of Newport, RI you may find some of the historic homes had vessels of carbon tet mounted near the ceiling. In the case of a fire the contents would spill out into the room to help douse the fire. It was also used as a dry cleaning solvent as it is particularly good at dissolving nonpolar grease.

Since the 1980s production of carbon tetrachloride has dropped precipitously due to its role in the destruction of the ozone layer. Industry has all but abandoned its use though it is still used in small quantities for research purposes. Once a cheap solvent, carbon tet now costs more than gold. If you have any, hang on to it! It could be your hedge against inflation.

The Demise of the Chemistry Blog


Blogs come and blogs go. I know that. Mine has been defunct for almost two years. But so have many other chemistry blogs that I used to have in my blog list. Some have stopped blogging, some have joined forces with other blogs and some have just disappeared completely. I went through my blog list and pulled out all of the defunct blogs. I don't want Carbon Tet to be included in this list! I wonder if any of these blogs will wake back up? Regardless, CT is alive. Stay Tuned!

Defunct Chemistry Blogs

A Synthetic Environment
Atom Pushers Anonymous

Criminal Chemists


PZ Meyers, from the infamous Pharyngula blog, posted the other day about law enforcement taking things too far. It seems a college student from Canada was arrested on accusations of terrorism and bomb making. His crime? He was interested in chemistry. You see he set up a home chemistry lab to explore this wonderful world of science. I can see how this might cause some angst among the law enforcement professionals. But what is shocking is that even after they determined the lab was not a meth lab and not making bombs, they still detained the student for days. Watch out chemists, you're all criminals.

NIH to cut


A new NIH policy was announced yesterday and will be applicable to all proposals submitted on or after January 25, 2009. The policy cuts down on the number of times one can resubmit a grant proposal. Currently if a proposal is not funded an amended application can be resubmitted two more times. This policy will restrict all new application and all competing renewal applications to only a single resubmission.

They claim this will result in funding "high quality" applications earlier with fewer resubmissions. I don't know that this is the case. I worry about less proposals being funded.

"This policy applies to all applications, including applications submitted under the NIH Small Business Innovation Research (SBIR) and Small Business Technology Transfer (STTR) programs, Career Development Awards, Individual Fellowships, Institutional Training Grants, Resource Grants, Program Projects, and Centers. Currently no amendments are permitted for applications received in response to a Request for Applications (RFA) unless it is specified in the Funding Opportunity Announcement, in which case only one amendment will be permitted."

For the Science Geeks


(image) A friend sent me a link to this offering from Wine Woot of four wines labeled just for us science geeks. These Washington wines must be showing up in beakers everywhere! I know cesium, rhenium and and methyl, but what the heck is Ch?

Zerhouni Steps Down


I just received this email today from the NIH. The Bush appointed director of the National Institutes of Health is stepping down in October.
Dear Friends and Colleagues in the extramural community,

Today, I informed my NIH colleagues, including staff, scientists, administrators, contractors, and trainees that at the end of October, I will be leaving my position as NIH Director to explore new opportunities and to devote much of my attention to writing.

I have said repeatedly that NIH is one of the true “wonders of the world.” For over six years, I have had the unparalleled privilege of leading one of the great institutions in history. Whenever an individual participates in a clinical trial or prevention effort, visits the doctor, stays in the hospital, has a medical test, or undergoes a procedure or treatment, they are benefiting from the extraordinary contribution you make to NIH’s single, great mission: improving the public’s health.

NIH has also been in the spotlight during a revolution in the biomedical sciences, one that continues to have broad and profound implications for academic institutions, industry, nonprofits, professional and scientific organizations, the health care profession, Government, and most important, for the health of the world. I am extremely fortunate to have led NIH during these unique times, which have brought with them complex challenges and amazing opportunities.

Your work will continue to transform the future of the agency and to play a key role in that revolution. Every day, people benefit from new treatments and potential cures for disabling and fatal conditions that result from your commitment and tireless dedication, even in the presence of complex problems and unprecedented challenges.

As recipients of NIH funding, you are among the world’s best, brightest, and most innovative scientists in a most competitive and challenging era for all of us. It is because of you and your contributions to science and health that NIH is known as the “crown jewel” agency of the federal government and you have every right to claim a stake in the agency’s success.
I also want to take this occasion to express my deep personal appreciation to the countless grantees who selflessly serve the NIH as volunteers on study sections, advisory councils and the many other activities the agency often calls upon you to join.

I know that my sentiments are shared by my colleagues at the NIH, and our gratitude runs deep. We are grateful for your support and the contributions you make every day.

Please feel free to distribute this message to your colleagues.


Elias A. Zerhouni, M.D.
I'm not quite sure how I feel about this. I don't know that he did a fantastic job. He had some controversial moments. And I think he was largely behind the fiasco known as ($2 billion spent on and you can't buy a computer today that you can submit a grant with - no Mac OS, no Windows Vista).

Who wants to be an atom smasher?


It must be tough for your science to rely on a multibillion dollar machine the only works for a few days a year. Hard to make progress with such little instrument time.

Bad news for the world's largest atom smasher.

GENEVA, Switzerland (AP) -- The European nuclear research organization says repairs and the onset of winter will delay the startup of the world's largest particle collider until spring.

Chemical Boundary around the earth


They call it a "Chemical Equator. A 30-mile wide boundary separating the northern hemisphere's carbon monoxide pollution from the cleaner air in the southern hemisphere.

Here's more of the story.

It's Party Time


So, do you think this will encourage more kids to learn chemistry? I don't know but it is pretty cute.

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Nature's Cowboys


(image) Although I have never done research in the area, I have long been fascinated by molecular architecture that people create. Rotaxanes and catenanes have been targets for synthesis for many years. I often pondered whether this type of molecular assembly was purly synthetic or if there were natural analogs. All these years and I have never seen one from nature. Although, I should say, I have never searched for them. But I was quite astonished today when perusing the JACS ASAP articles to see this paper on the characterization of a lasso peptide. Finally confirmation that nature is indeed wiser than all of us and has probably already made anything that we can come up with. It's an interesting compound and makes me wonder why nature needs the lasso. Are there biological ranches with peptidic cowboys riding around? Does she use this to rope bacterial calves? I think I'll have to learn more.

Isolation and Structural Characterization of Capistruin, a Lasso Peptide Predicted from the Genome Sequence of Burkholderia thailandensis E264

Thomas A. Knappe, Uwe Linne, Séverine Zirah, Sylvie Rebuffat, Xiulan Xie, and Mohamed A. Marahiel

DOI: 10.1021/ja802966g

Better Living Through Chemistry


(image) Greetings Blog Readers. I know there's at least two of you out there. Thanks for sticking with me. I've been away from civilization for 10 days. Yes, finally, a long-deserved vacation. I was in the wilderness. No cell phone signals. No internet. No pressing deadlines. Well, I have those more than ever now that I'm back, but for a while I could forget about them. It was absolutely wonderful. I realized when I was out there among the bears that every part of our lives is made possible because of chemistry. Sure, I can talk about how I couldn't get to such beautiful places without refined gasoline and automobiles, at least I couldn't get there quickly nor easily. I could talk about how I really needed my synthetic fabric tent to protect me from the elements. I could talk about how the old Coleman stove performed beautifully to provide me with bacon, eggs and the essential nutrient, coffee every morning using Coleman fuel. But I won't talk about those things. They are the obvious ways in which chemistry aids us in daily living. No, I want to talk about how chemistry makes our world absolutely fascinatingly beautiful. From billion year old granite cliffs to multicolored bacteria that live in scalding hot sulfur infused water. None of this would be possible without chemistry. And it is the sheer beauty of nature's chemistry that soothes the soul and makes me realize why I am really here on this planet. To make lives better. We can do that through chemistry.

(image) Ok, I really am rambling. I had forgotten what a great vacation can do for one's perspective. Time to get back to the grindstone. Look for some organic chemistry soon!

Of Wine and Chemistry


I was away at a conference last week. One of those great small conferences where you can spend a lot of time interacting with people outside of the talks. It was great. I'm convinced the best science is discussed over beer and wine. I titled this blog post Wine and Chemistry because I like wine. It's not that I don't like beer. I do. I just can't drink very much of it before I feel bloated and uncomfortable. Thus I much prefer a nice red wine to drink while pondering the deeper aspects of asymmetric catalysis. I am not alone in this. Some friends of mine who were also at the conference are wine lovers and we had a nice little private wine tasting one evening. It was a wonderful experience as I got to taste a wine that was over 40 years old. The cork you see above is from that special bottle of Rioja. Although it was delicate and it broke when we pulled it from the bottle, it was in surprisingly good shape. The wine, on the other hand, was about 20 years past its prime. Not spoiled but it definitely was flat. It tasted like compost. That brings me to a little bit of chemistry. The wine was definitely oxidized but was not vinegar. It was stored well and the closure held up against the ravages of time. It was almost sherry like. Of course the one thing that distinguishes an oxidized wine like sherry is the presence of acetaldehyde. This had quite a bit of it. The tannins were completely gone. I wonder if there was any resveratrol left? Definitely not a wine I would pop and pour at a picnic but it was truly an experience to taste history.

Largazole and Histones


I have a certain affection for things that affect epigenetic regulation. Hence my interest in a class of enzymes called histone deacetylases (HDACs). These are zinc-dependent hydrolases that cleave the acetate group off of the lysine residues on the N-terminal tails of H3 histones. The bottom line is that deacetylation of these proteins that DNA wraps around turns off gene expression. In some cancers, tumor supressor genes are turned off and application of HDAC inhibitors turns them back on causing the cancer cell to die its normal death. That is a simplistic description. It is actually much more complicated than that. A simple animation of this is provided on the Methylgene web site.In January, the Luesch group from Florida reported (J. Am. Chem. Soc., 130 (6), 1806 -1807, 2008. 10.1021/ja7110064) the isolation and characterization of an antiproliferative natural product called largazole. They subsequently synthesized it and discovered it was an inhibitor for HDACs (J. Am. Chem. Soc., 130 (26), 8455–8459, 2008. 10.1021/ja8013727). The synthesis is pretty efficient encompassing 8 steps with an overall yield of 19%. That's not too bad. Andy Phillips, in Colorado, has just published another 8 step synthesis and have confirmed the Leusch findings (Org. Lett., ASAP Article, 10.1021/ol8013478 ). In addition they have done some NMR conformational studies to show the solution structure of this interesting molecule.What I find very interesting about this story is that the compound looks so very similar to cyclic peptide HDAC inhibitors developed in Japan (FK228, link to PDF). The sulfur gets buried into the active site pocket to bind the catalytic zinc while the cyclic structure binds to the surface of the enzyme. Both are necessary for the nanomolar level of inhibition of Class I HDACs that are observed for these compounds. Knowing the structure of FK228, I would have immediately made the connection between largazole's antiproliferative effects and HDAC inhibition. The original isolation paper does not speculate on that which makes me wonder if the Leusch group only made this connection later. I presume so.The way this story has unfolded reminds me that I need to search more broadly when I am looking for HDAC inhibitor structures. Just searching on the keyword 'hdac inhibitor' is not enough and probably misses some compounds that people haven't yet connected to HDACs.[...]

Atomic Noodles


Ok, I hear the voices from my last post and have decided to commit to trying to keep this blog going. My goal is to make sure I publish a post at least every week, if not more often. I've realized it doesn't have to be a chore and that I don't have to always have some latest greatest chemistry from the just uploaded ASAP's. I can do some fun stuff. I can even borrow from other stuff on the web. Why not? People do that all the time on their blogs.

Ok, then. How about a little bit of video? I know it's not directly chemistry, but it does fascinate me. From "The Ring of Truth: Atoms," here is Chef Kin Jin Mark pulling noodles.

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To be or not to be


Oh, I know I've been ignoring this blog. I wondered if anyone even read it. It has dropped down on my list of priorities. But now I read over at Homebrew and Chemistry that my blog is being chopped from at least one person's reading list. I suppose I should have seen it coming. The question is, will this inspire me to reinvigorate Carbon Tet or should I let it die in quiet peace? Perhaps if people leave a comment or two it might help me make up my mind.

Drink your pharmaceuticals


An interesting report on the state of our drinking water appeared today on CNN. We've often heard of municipal drinking water being polluted with things like lead, MTBA, pesticides, etc. But this report talks about finding lots of different pharmaceuticals in our drinking water - everything from sex hormones to antibiotics to, yep, antidepressants. Actually in some places more than 50 different drugs were detected. While the amounts are very tiny (ppb or ppt) very little is known about the effects of even small amounts of drugs over a long period of time like decades. I think Dr. David Carpenter says it best:
"We know we are being exposed to other people's drugs through our drinking water, and that can't be good," says Dr. David Carpenter, who directs the Institute for Health and the Environment of the State University of New York at Albany.



Depression seems to be the illness of the 21st century and for more than 15 years Selective Serotonin Reuptake Inhibitors have been the pill of choice. Yes, the number of prescriptions of these antidepressants (effexor, prozac, seroxat, etc) has increased exponentially. So much so that these drugs being excreted by humans is negatively affecting wildlife. With all the billions of dollars being spent on these drugs has anyone ever asked the question, Do they help? Well, psychologists at the University of Hull have reviewed the results of about 50 clinical trials. Their conclusions? SSRI antidepressants do not really seem to provide a benefit to most people as compared to placebos. Sure, there's a little evidence that they help to some extent the most severely depressed, but the large majority of the millions of prescriptions really are doing nothing but causing gender confusion among the fish and frogs.

The Air Has Landed


(image) The good, the bad and the ugly. Well, there's absolutely nothing ugly about the macbook air. It's absolutely gorgeous. Thin thin thin. It is much sturdier and lighter than I expected. It feels weightless. HUGE plusses for design and portability. The keyboard feels great. The screen looks fantastic. You can see some comparisons with my 15" macbook pro. It's definitely smaller by a long shot. I love the lighted keyboard. It seems to function even better than my MBP. 

(image) As for performance, it's not the quickest horse out of the gate but it certainly wasn't as pokey as I expected based on the reviews out there. For most major tasks - keynote, pages, word, web browsing - it performs just fine. It even compared with my 2.0 GHz MBP in iphoto - granted with far fewer photos in the library. I don't need anything more intensive really, so this is good.

(image) Did I mention it was thin? I can hardly tell it's in my bag when I carry it around. That's exactly what I need for traveling. For this reason it is fantastic for me.

(image) One thing I noticed was that the charger works either way it is plugged in. I know some people have complained that the cord bends too much when plugged in if the plug is behind you. No worries. You can just attach the connector the other way around and no more 180 cord bending. The one negative thing that I would say is a real fault is the slow slow battery charging. I just noticed that it is only 35% charged after an hour plugged in when it was down to 15%. Apple, without a replaceable battery, you need to do better than this! Hopefully this can be resolved with a software update soon.

Overall I give this one Three Thumbs Up!

Something in the air


And it will be in my hands some time today! Just in time for me to take it on the plane tomorrow. Yes, the new Macbook Air is a perfect travel partner. I'll give you my review of it soon.

A new precatalyst for Heck Reactions


(image) It's a beauty, isn't it? I mean, look at that monster! And it packs 4 palladium atoms per catalyst too. It just appeared in Organometallics (DOI: 10.1021/om7005613). They actually coupled together iodobenzene and styrene. The cool thing about this is that they could tune the reactivity of the catalyst by changing the metal complexed in the middle of the porphyrin. With M=MnCl it took almost 400 minutes for the reaction to complete, but with M=Mg it only took about 200 minutes. Ok, seriously. I don't mean to pick on Bart M. J. M. Suijkerbuijk, Sara D. Herreras Martínez, Gerard van Koten, and Robertus J. M. Klein Gebbink, but I really don't understand what the purpose of this research is. I guess you can get some understanding about the electronic nature of pincer ligands, but no one in their right mind would ever use something like this for a Heck reaction. It is pretty though. It even weighs 10 times more than your substrate. I guess that makes for easy weighing. Let's say you use 10 mol% of the catalyst. You can just use the same mass as iodobenzene and you're good to go.

Busy as a bee


That is me and why I have not posted lately. I still plan to. Don't give up on me. I'm still finding a few minutes here and there to read an article or two. If only the days were 72 hours long. *sigh*

Anyway, there's lots of buzz about Apple's new Macbook Air. Lots of negative comments going around on the mac forums. I don't understand this. Sure, this computer is not for everyone. Sure, this computer could not replace a primary computer. But let's be honest. This is a computer for travelers. This computer is ideal for me. I can't wait to get my hands on one. In the last five years I can't think of a single time I have used my optical drive while on a trip. Rarely have I ever had to use an ethernet cable while on the road and in the last two years I have never needed an ethernet cable. Who's going to travel with bulky firewire peripherals in their carry on bag? All these arguments against the macbook air are ludicrous. Obviously made by people who don't go on frequent short trips. So I ordered one as soon as they were announced.

 I know this is a chemistry blog. So let's talk about chemistry. This is the first laptop with a mercury free LCD display. And the glass contains no arsenic.