Posted by: SR | February 10, 2008

Carbon-Sulfur [n]Helicenes: The Beginning.

*This is the second post of the Helicene series*

An unexpected discovery…that would be wonderful… But sometimes one research project could lead to another unexpectedly…. This was how we started the carbon-sulfur helicene project. So, when carrying out research projects, in addition to keeping our eyes wide open, we keep our mind open too.

Here is the story. In the mid 90s, one of the two major research projects in our lab was the synthesis and study of chiral conjugated π-systems with high configurational stability. Our focus was on derivatives of tetraphenylene.

tetraph_1.gifhorse.gifActually, tetraphenylene is an achiral, saddle-shape molecule derived from four phenylenes that are ortho-annelated to form an eight-membered ring in the center of the molecule. And, oh, I should mention that we gave it nickname as “horse”. You see, the symmetry of the tetraphenylene molecule may be broken by substitution or ring annelation to provide chiral π-conjugated systems with extraordinary high barriers for racemization. So, for a while tetraphenylene was a workhorse in our group… Visit this site for more information.

Anyway, we can’t keep doing the same things for a long, long, time, it’s boring, right?

So, in 1999 we started to explore conjugated π-systems of thiophenes. At that time, α-oligothiophenes were already quite popular in organic materials research field.

annelation.gifWe first looked into various modes of annelation of thiophenes using simple computational models. In α-oligothiophenes, the thiophene rings are connected at α-positions, forming a linearly extended, conjugated π-system. Ring annelations of such oligothiophenes would lead to a planar, rigid structure of quasi-linear oligomers (thienoacenes). We noticed that there were only a few reports of β-oligothiophenes and tetrathienylenes, which are thiophene-analogues of tetraphenylenes, aha…, our horses. Those structures in our consideration were achiral β-tetrathiophenes and its annelated analogue, an approximately planar cyclic β-octathiophene or [8]circulene. Then we moved on to consider analogous “defective” structures of [8]circulene missing one sulfur (seven annelated thiophene rings), surprise! surprise!, we got to see a on a computer screen a beautiful structure of helical β-heptathiophene. The space-fill was breathtaking! We were even more elated when we realized that such structure could be extended to all-thiophene, or carbon-sulfur, [n]helicenes, which could be viewed as fragments of a (C2S)n helical polymer. Take a look…(click the picture to see 3D model)


It was exciting to come up with the unique conjugated π-systems of electroactive oligothiophenes helical structures. As we know, [n]helicenes possess some of the strongest intrinsic chiral properties. So, these electroactive carbon-sulfur [n]helicenes may provide both extraordinary chiral properties and optical transparency, which are desirable properties for organic optoelectronic materials and devices.

OK, that was great! We began to focus our attention on the carbon-sulfur [n]helicenes.

But could we synthesize such molecules?

The third post of the Helicene series, Carbon-Sulfur [n]Helicenes: Syntheses, Structures and Properties, will follow….


  • The longest oligothienoacenes, octathienoacene (eight fused thiphene rings), was reported by the research group at Nagoya U. in 2007. Chem Euro J., 2007, 13, 548. 10.1002/chem.200601064.
  • The carbon-sulfur [8]circulene was claimed by the research group at Moscow State U. in 2006. The title of the article was “Sulflower”: A New Form of Carbon Sulfide, and it was highlighted as the Angewandte Chemie journal cover. (Angewandte Chemie International Edition, 2006, 45, 7367; doi:10.1002/anie.200602190).We would love to congratulate the authors for their work but there was a concern. First, the reported red color was a surprise; the cross-conjugated π-systems, [8]circulene, should be colorless. Second x-ray powder diffraction was reported, not single crystal x-ray structure…. Interestingly, a few days after this article appeared, an e-mail, the subject “wilted sulflower?, arrived, so we were not alone!

My personal note (that is, come after me, not the RajcaLab):

  • Wanna publish in Angewandte? Hype up with some fancy figures and catch words, ah the Angewandte’s songbook…And hey, a doll was published there, which seemed to catch Excimer off guard!

Helicene was recently posted by Molecule of the Day as example of chirality. The post included the link to the Wikipedia page that badly needed updated information. So, when you get to Wikipedia, keep in this in mind…you may miss tons of important stuffs…

Since helicene is one of the two major research projects in our group, we will take on to fill in some information.

Actually, the first racemic [n]helicence, [6]pyrrolohelicene was reported in 1927, followed by the racemic [5]helicence in 1933.

helicene1.gif[n]Helicenes structures possess n angularly (ortho) annelated (fused) aromatic rings, in which the steric repulsion of terminal rings force distortion from planarity, leading to helical π-conjugated structures. These molecules possess some of the strongest intrinsic chiral properties. Syntheses of structures with such high degree of ring annelation, and with significant strain are challenging. So, it took a long period of 23 years later before the first successful synthesis of non-racemic [6]helicene was reported by Newman and Lednicer in 1953.

14helicene_1.gif15thiahelicene_1.gifDuring the 60s and 70s, photochemical syntheses were developed, such method provided numerous [n]helicenes, with [14]helicene as the longest structure consisting of benzene rings. Various [n]helicenes consist of alternating benzene and thiophene rings were also synthesized by the photochemical methods, with the [15]helicene as the longest structure. The photochemical syntheses provided helicenes in low/moderate yield and with limited functionalities.

Katz group at Columbia have developed very efficient non-photochemical, gram-scale syntheses of functionalized enantiopure [n]helicenes (n = 5, 6, 7).


Recently, two novel classes of helicenes were reported: [n]heliphenes by the Vollhard group at UC-Berkeley and carbon-sulfur [n]helicenes by our group.


More posts will follow…perhaps a series of posts on each class of helicene structures.

  • Visit this site to see more cool carbon-sulfur helicene structures.
  • Recent review articles to read…
    • Andrzej Rajca, Suchada Rajca, Maren Pink, Makoto Miyasaka “Annelated, Chiral π-Conjugated Systems: Tetraphenylenes and Helical -Oligothiophenes”, SynLett, 2007,1799 – 1822 (account, invited) [Abstract].
    • Tomás Torroba, María García-Valverde, “Rigid Annulated Carbon-Sulfur Structures”, Angew. Chem. Int. Ed., 2006, 45, 8092-8096. [Abstract]
    • Shawn K. Collins, Martin P. Vachon, “Unlocking the potential of thiaheterohelicenes: chemical synthesis as the key”, Org. Biomol. Chem, 2006, 4, 2518-2524. [Abstract]
    Posted by: SR | January 26, 2008

    One Month Old, I am Just a Baby Blogger

    Exactly one month ago today, I started this weblog. One month old, I am just a baby blogger, still learning and developing. Maybe it is too early to say how productive this weblog will be. But, like we usually do when carrying out a research project, it is good to take a look at how we are doing along the way. OK, let’s take a look at the stats so far.

    Blog Stats: Total Views: 231; Best Day Ever: 23 — Sunday, January 13, 2008
    Totals: Posts: 6; Comments: 12; Categories: 7
    Spam: Akismet has protected your site from 1 spam comments

    Glad that we have 231 hits, not a big number, not that we expect the big number anyway, just hope the visits were worthwhile for those who stopped by. Hey, we even had the visits by blogger gurus, Jean-Claude Bradley, Mitch, and Ψ*Ψ, and hey, thanks for taking time to leave the comments. As expected, the most visits were referred from our group homepage.

    I still hope to have other lab members to join the fun with this weblog. I have approached a couple guys but so far no one jumped in yet. Heck, I don’t even know if they read my posts! I think blog, if utilized properly, is one of the great platforms for developing important skills such as writing, presentation, communication, and more importantly, for developing ideas and presenting them. I admire those, especially undergrad and grad students, who choose to write blog posts rather than doing other things, like playing video games, watching TV, etc. For me, this blog is more or less a way to relieve boredom…from the good life in the Corn Nation… Learning and developing should be good medicine for that! At the same times, I thought documenting some activities in and around the lab would be a good idea, especially I hope to write about some interesting experiences and technical details of some experiments that usually are not included in papers. I think these are good materials for blog posts and they might be of interest and helpful to some. All in all, this blog is like one bullet for two birds!

    Over all evaluation–with a few hits and only 6 posts, plus my failure to convince anyone in the lab to join in–I would give myself a D grade. What grade would you give me?

    Posted by: SR | January 13, 2008

    A Long, Tough Road Toward an Organic Magnet

    Yes, preparation of practical organic magnet remains a very difficult, challenging problem. Many may believe it is impossible, some may have doubt, some may say–waste of time! It is not easy to go against the nature…those electrons are happy to be paired, coupled their spins in opposite direction (antiferromagnetic coupling), forming chemical bonds, so why bother… Like most of us, loneliness is hard, so most going with the mainstream. Look at the history, Mose Gomberg got scoffed at for his report on the triarylmethyl radical in 1990 and he had to fight for over the period of 15 years to defense the free radical concept. And we all know the impact of his discovery, but no, Gomberg is not on the list of Nobel Laureates in Chemistry1. One thing I wonder though, why Gomberg ended his paper with this interesting statement.


    (M. Gomberg, “An Instance of Trivalent Carbon: Triphenylmethyl’’, J. Am. Chem. Soc, 1900, 22, 757-771 doi:10.1021/ja02049a006)

    Beside that strange statement, Gomberg’s courage gives us motivation to forge forward, toward the ultimate goal of organic magnet. It has been a long and tough road but we have made good progress.

    At the current stage, we know more or less how to rational design structures with a large number of strongly interacting unpaired electrons that give rise to net ferromagnetic couplings (Magnetic Ordering in an Organic Polymer, Science, 2001, 294, 1503-1505, doi:10.1126/science.1065477). It took us 13 years to get this far, 101 years since Gomberg reported the first organic radical. Here is the timeline of the development2


    The triarylmethyl polyradicals are unstable; they have to be handled at below 170 K in absence of oxygen. The magnetic ordering temperature of the triarylmethyl-based polymer at 10K is too low for any application. To make a practical material, we must implement the structure design with organic radicals (spin units) that are stable at normal working condition (on air at room temperature), while maintaining strong ferromagnetic couplings to reach ordering temperature above room temperature. These are two critical benchmarks we are striving to obtain.

    stable_rad.gifThere are only a few known highly stable organic radicals. Currently, we are working on the nitroxides and aminyls, following the bottom-up approach to prepare and study high-spin polyradicals that are stable on air at room temperature. Once again, we will learn, step by step, laying a solid foundation. We hope to find a way to reach our ultimate goal of an organic magnet that we will stick on our refrigerator doors…. Along the way, we will take advantage of what we have learned to prepare various nitroxides and aminyls that process good solubilities in aqueous solutions and investigate them for magnetic resonance imaging (MRI and EPRI) applications. For more information, visit this site.

    1Interesting discussion about this subject: Lennart Eberson, “Gomberg and the Nobel Prize”, Advances in Physical Organic Chemistry, 2001, 36, 59-84.

    2Learn more about this development here and here (the site is old and should be updated soon) and from the following review articles: A. Rajca, “The Physical Organic Chemistry of Very High-Spin Polyradicals”, Adv. Phys. Org. Chem., 2005, 40, 153-199; N M Shishlov, “From the Gomberg radical to organic magnets“, Russ Chem Rev, 2006, 75, 863-884 doi:10.1070/RC2006v075n10ABEH003621.

    We just got a new stereo microscope, the Meiji EMZ-5TR zoom stero microscope, with PBH stand and polarization accessories. Such microscope system is useful for detecting and viewing birefringent materials.

    Meiji EMZWhy do we need to have the microscope? Very so often, we need to look at the crystals to make sure that they are of good quality before we send them to our wonderful collaborator, Dr Maren Pink at IUMSC. In the past, we were able to use the microscope at the Crystallography facility located in the basement of the same building, with a very convenient access. With the former facility director, we even had permission to have a key to the facility, so we can use the microscope any time, in particular after the facility operating hours! Lately, this has became a hassle. We no longer have the key and very often we were unable to get to the microscope because the door to the facility were locked, even during the regular working hours. When we asked for permission to have the key, the facility director asked the higher-up for the general policy. Finally, we were told that we could have the key with the condition that we would be “responsible for any facility problems on a given evening or weekend” Oh, c’mon!!! Slow moving and lack of competitiveness in the heartland may not be that uncommon, but the lack of trust? It would be better for us not to be involved in such deal. For under $1700 we could get the microscope with polarizing accessories, a reticle (eyepiece micrometer) and a spare light bulb from the Capital Microscope Service (CMS). We hope to get the camera accessories in the future so we take some pictures of the crystals send them to Dr. Pink for consultations before we send the crystals to her. Of course, we will show off those interesting picture here too.

    Anyway, when the microscope package arrived, it took no time for us to assemble all the components together, except for one thing, the reticle…where to place it? The documentation came with the package did not include information about the reticle at all. This may be trivial to a lot people… it should go to the eyepiece… but how? Thanks to the WWW, Google and those who put together many useful informations out there. We found the website, microbus, and the problem solved. There are lots of chemistry website and blogs with interesting and useful informations…we hope to make contribution to the community too.

    X-ray crystallography is one of the valuable research tools, among NMR, MS, EPR, and SQUID magnetometry, routinely employ in our group. Generally, we rely on NMR and MS for structure determinations of the most important reaction intermediates and products. For new compound, we would try to crystallize them for x-ray analysis to confirm the structures. The recent case of diaza[12]annulene (read the discussion about it here) reminds us once again the importance of x-ray structure determination. In our experience, x-ray crystallography has proven to be essential in the synthesis of novel chiral π conjugated systems (see SynLett Account, DOI:10.1055/s-2007-984538). In some cases, our synthetic problems were resolved by obtaining x-ray structures of the “unkown” reaction products obtained unexpectedly, which helped us to understand and to change the synthetic strategy. Publication of such case will be forthcoming.

    A Look Back at 2007:
    It has been a heck of a year! I term of accomplishment, it was a reasonably good year for us with 7 publications (JPCC, JOC Note, JACS Communication, JACS Article, Tetrahedron Symposium-in-Print, SynLett Account and a Book Chapter). We also have a JPC manuscript accepted. We were happy (or better to say that we were relieved!) that our NSF grant was renewed and THANKS for the continued support since 1989. This was very rewarding. At the other end, our NIH proposals on the development of high-spin radicals as contrast agents for biomedical imaging did not received high enough scores. The proposal went through 3 submissions as RO1 project and a modified version was resubmitted as R21. It was frustrating, as we learned that novel ideas, good records and etc. were not good enough. Ah ha, the Correspondence to Cells, American Idol and NIH Grant Review, by Michele Pagano was quite interesting to read.

    Other good news includes the following awards: the 2007-2008 UCARE awards to undergraduate students: Bridget Foley, Nick Lehmann and Joshua Lovell; the Chemistry Department Graduate Research Assistant Award to Kausik Das; Andrzej Rajca received the Certificate of Recognition for Contributions to Students from the University of Nebraska Teaching and Learning Center and University of Nebraska Parents Association, and was named Professor of the Month (September 2007) by the UNL Mortar Board (The Black Masque Chapter). Congratulations to all!

    There was a big change in the lab, with Gaëlle Spagnoll, Makoto Miyasaka and Kausik Das moved on to their new horizons and with a warm welcome new members, Ch. V. Rajasekar, Sulagna Brahma Roy, Sandip Kumar Roy, Shuzhang Xiao, Arnon Olankitwanit and Santanu Sarkar, who brought us a fresh perspective and a brand new attitude.

    A Look Ahead:
    Good news, we will have a great start in 2008 with the Featured Article in the first issue of JOC. In term of publications, we expect to have quite a few. An article was already accepted for publication in the JPC and we are working on the following manuscripts: an invited article to the Journal of Sulfur Chemistry (January submission), 2 articles on high-spin nitroxides (almost done) and 2 articles on carbon-sulfur helicences. This new year, we wish to have good news from the NIH; our RO1 (A new class of spin labels) and R21 (High-Spin Nitroxide Diradicals for Biomedical Imaging) will be reviewed in February.

    In term of research, we expect to make good progress. Shuzhang Xiao has been hard at work and doing really well. We are just a couple steps from obtaining a [15]helicene; we also have in our hands a new [7]helicene and its analogous partial circulene.

    There will be another big change in the lab, with Ch. V. Rajasekar to complete his postdoc at the end of January. Due to medical emergency, Sulagna Brahma Roy and Sandip Kumar Roy will return to India to take care of their family. We wish them the best. Once again, we look forward to welcome new members–postdoctorals and students–if you are interest in working with us, just email me (srajca1 at unl dot edu).

    Best Wishes for a Very Happy New Year 2008 to All.

    Posted by: SR | December 28, 2007

    JOC Featured Article

    It appears that JOC will introduce a new category–Featured Article–in 2008. We learned this by surprise, when we received the galley of our article, Synthesis, Structure, and Conformation of Aza[1n]metacyclophanes (JOC ASAP, DOI:10.1021/jo702151n), with the Featured Article header. It was a very pleasant surprise!!! We received only the usual notification that our article was accepted for publication. It was a long waiting for the galley and for the ASAP to appear online, perhaps due to the new category. We think the category will be introduced in the 2008 Editorial, so we are eager to learn more about it.

    In fact, the manuscript was submitted to JACS and was rejected (rejection letter1). We then submitted the same manuscript (no revision) together with the JACS rejection letter to JOC and it was accepted without further review. OK, great, our work is published in JOC and the JACS editor think that about 50% of the general chemical community would feel that this work would be suitable for publication in JACS, because 50% of the reviewers thought so! Whew! The editor was under “increasing pressure to make sure that all JACS manuscript are of broad interest, and completely scientifically acceptable “. Well, all four referees said that our manuscript was of high quality, but two did not think that it was novel or broad enough for JACS. Our supporting information was 65 pages thick.

    The question is does it really matter where this manuscript is published?

    Topic for another post: dissemination of research results: does it really matter where the work is published?

    1identity of the editor was removed, so no bad feeling….

    UPDATE: the TOC Alert for the January 4 issue of JOC has just arrived in my inbox and our manuscript is one of the 6 Featured Articles. Here is the Editorial.

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