The shortest route to strychnine

Editor’s note: following on from their previous groundbreaking publication on this blog – in which they provided a comprehensive overview of chemical-free consumer products – Drs Goldberg and Chemjobber submitted another manuscript to Nature Chemistry. Despite being summarily rejected by the editor, many (many) months later – and in the wake of some poetic exchanges on Twitter – the manuscript (and cover letter) are now both posted here on the blog with the permission of the authors. In the spirit of the Christmas papers published by the BMJ, consider this (tongue-in-cheek?) comment on synthetic chemistry by Alex and CJ a holiday-season gift to our readers!

––––––––––––––––––––

An expeditious and parsimonious approach to strychnine
Alexander F. G. Goldberg and C.J. Chemjobber

Throughout and following its structural elucidation1-5 strychnine has captured the imagination of synthetic chemists. Beginning with Woodward’s landmark total synthesis, reported in 1954 (ref. 6), this storied molecule has enabled chemists to showcase the state-of-the-art7,8. Advances in the field of organic synthesis over the following decades have culminated in a synthesis as short as six linear steps from commercial materials9. Indeed, each subsequent publication on this strychnine has been a reflection of the leading concepts of the time.

In this vein, we sought in our approach to limit the use of harmful reagents — and harmless reagents — and maximize step economy, atom economy10, redox economy11, word economy12, time economy13, graduate student economy14 and economy15.

Our efforts were initiated and concluded by obtaining commercially available strychnine as a light yellow powder from Sigma-Aldrich. Gratifyingly, all spectral data matched those reported in the literature, and the purity was found, fortuitously, to be as indicated by the vendor.

In summary, we are delighted to have obtained multi-gram quantities of strychnine in the shortest synthetic sequence to date from commercial materials. Future work will likely not be directed toward similar approaches to brucine, cinchonine, and erythropoietin.

Author contributions

A.F.G.G. and C.J.C. contributed equally to the experimental work.

Acknowledgements

We thank Sigma-Aldrich in advance for their sense of humour; A.F.G.G thanks Christine Hansplant for her patience in waiting for this acknowledgement for her contribution to our previous publication.

Affiliations

Stan’s Exchange Secondhand Store, Edmonton, AB.

Competing Financial Interests

A.F.G.G. is handily in the pockets of Big Strychnine.

References

1. Leuchs, H. Über Strychnon und Pseudo-strychnon als Nebenprodukte der Darstellung des Pseudo-strychnins und über weitere Versuche in dessen Reihe. (Teilweise mit Fritz Räck.) (über Strychnos-Alkaloide, 110. Mitteil.) Chem. Ber. 73, 731–739 (1940). [LINK]

2. Briggs, L. H., Openshaw, H. T. & Robinson, R. Strychnine and brucine. Part XLII. Constitution of the neo-series of bases and their oxidation products. J. Chem. Soc. 903 (1946). [LINK]

3. Robinson, R. The constitution of strychnine. Experientia 2, 28–29 (1946). [LINK]

4. Woodward, R. B., Brehm, W. J. & Nelson, A. L. The structure of strychnine J. Am. Chem. Soc. 69, 2250 (1947). [LINK]

5. Woodward, R. B. & Brehm, W. J. The Structure of Strychnine. Formulation of the Neo Bases J. Am. Chem. Soc. 70, 2107–2115 (1948). [LINK]

6. Woodward, R. B., Cava, M. P., Ollis, W. D., Hunger, A., Daeniker, H. U. & Schenker, K. The Total Synthesis of Strychnine. J. Am. Chem. Soc. 76, 4749–4751 (1954). [LINK]

7. Bonjoch, J. & Solé, D. Synthesis of Strychnine. Chem. Rev. 100, 3455–3482 (2000). [LINK]

8. Cannon, J. S. & Overman, L. E. Is There No End to the Total Syntheses of Strychnine? Lessons Learned in Strategy and Tactics in Total Synthesis. Angew. Chem. Int. Ed. 51, 4288–4311 (2012). [LINK]

9. Martin, D. B. C. & Vanderwal, C. D. A synthesis of strychnine by a longest linear sequence of six steps. Chem. Sci. 2, 649–651 (2011). [LINK]

10. Trost, B. M. Atom Economy—A Challenge for Organic Synthesis: Homogeneous Catalysis Leads the Way. Angew. Chem. Int. Ed. 34, 259–281 (1995). [LINK]

11. Burns, N.Z., Baran, P. S. & Hoffmann, R. W. Redox Economy in Organic Synthesis. Angew. Chem. Int. Ed. 48, 2854–2867 (2009). [LINK]

12. Goldberg, A. F. G. & Chemjobber, C. J. A comprehensive overview of chemical-free consumer products. The Sceptical Chymist. [LINK]

13. Hayashi, Y. & Ogasawara, S. Time Economical Synthesis of (–)-Oseltamivir. Org. Lett. 18, 3426–3429 (2016). [LINK]

14. (a) Wang, P., Dong, S., Brailsford, J. A., Iyer, K., Townsend, S. D., Zhang, Q., Hendrickson, R. C., Shieh, J., Moore, M. A. S., Danishefsky, S. J. At Last: Erythropoietin as a Single Glycoform. Angew. Chem. Int. Ed. 51, 11576–11584 (2012) and references therein. [LINK] (b) Nicolaou, K. C., Heretsch, P., Nakamura, T., Rudo, A., Murata, M. Konoki, K. Synthesis and Biological Evaluation of QRSTUVWXYZA’ Domains of Maitotoxin. J. Am. Chem. Soc. 136, 16444–16451 (2014) and references therein. [LINK] (c) Aad, G. et al. (ATLAS Collaboration, CMS Collaboration) Phys. Rev. Lett. 114, 191803 (2015). [LINK]

15. Newhouse, T., Baran, P. S. & Hoffmann, R. W. The economies of synthesis. Chem. Soc. Rev. 38, 3010–3021 (2009). [LINK]

––––––––––––––––––––

Cover letter

Dear Stu,

Please find attached our latest manuscript for your consideration for publication in Tetrahedron Letters or whatever it’s called, entitled “An Expeditious and Parsimonious Approach to Strychnine.” This scalable approach features a broadly-applicable method for accessing complex bioactive natural products, and adheres closely to the principles of green chemistry. For instance, our approach to strychnine was solvent-free and atom-economical, and all raw materials were obtained from renewable sources, which were fully incorporated into the final product. We trust that you will find that traditional green chemistry metrics such as atom economy, effective mass yield and E-factor are second to none.

Furthermore, the future of funding for basic research remains uncertain and subject to the whims of oft closed minded and myopic politicians. Pressing, therefore, is the need for cost-effective methods for obtaining important natural products, especially for the purposes of the biological studies which we all say we’re going to get around to.

Indeed, our zero-step synthesis of strychnine from commercially-available materials is a superb model for efficiency in synthetic chemistry. We are confident that the application of this method to other commercially available natural products will accelerate discovery in our own field, as well as in the fields of chemical biology and analytical chemistry; as the 200th anniversary of strychnine’s isolation approaches, we consider this timely and unparalleled manuscript suitable for the broad scientific audience of your publication.

Thank you in advance for your consideration,
Alexander Goldberg & CJ Chemjobber

Under a fermium sky

Posted on behalf of Brett Thornton and Shawn Burdette. This blog post is an epilogue to the In Your Element (IYE) article on fermium.

– – – – – – – – – – – – – – – –

When exactly was fermium first created by humans? The date for fermium’s initial production is given in some sources as October 1952, while others claim November — both dates are given for the Ivy Mike nuclear weapons test, the first time humans created elements 99 and 100. The discrepancy apparently is because Enewetak Atoll, the site of the test, lies on the other side of the International Date Line from the United States. The Ivy Mike nuclear weapons test there occurred on 1 November 1952 local time, but 31 October 1952 in the U.S. mainland.

The Ivy Mike weapons test was the first thermonuclear device — or ‘hydrogen’ bomb — and this explosion injected large amounts of radioactive debris high into the atmosphere. In the stratosphere, this debris spread over the entire globe as fallout, which was no different than any other above-ground nuclear weapons test. (Concerns about fallout was a major impetus for the the Partial Test Ban Treaty in 1963, which banned all above-ground or above-water nuclear tests). Arkansas was one of the many places the fallout landed and, in 1952, someone there was watching the sky.

After the Ivy Mike test, initial studies had revealed that the fallout contained 244Pu, a previously unknown plutonium isotope with a relatively large number of neutrons compared to 238U, its likely source. Glenn Seaborg at the University of California Radiation Laboratory (UCRL) received a somewhat cryptic telegram informing him that the existence of 244Pu was classified, even if it was produced by unclassified means. The UCRL group had not produced 244Pu yet, but they knew it was possible now. Seaborg and his UCRL group were well-known as leaders in transuranium element research, having already helped with the discoveries of plutonium, americium, curium, berkelium, and californium. If anyone stumbled across or created 244Pu besides the people analyzing nuclear weapon test fallout, the ‘top men’ at UCRL would be the first suspects on the list.

The knowledge that 244Pu existed, even if classified, was enough to get the UCRL group thinking. This probably meant that six neutrons had been almost instantaneously fused into the nucleus of 238U, much faster than was possible in a high-neutron flux reactor. This prompted UCRL researcher Albert Ghiorso to request samples of the Ivy Mike debris. Ghiorso wondered exactly how many neutrons might have been added. Was 244Pu the heaviest isotope in the debris or were much heavier isotopes also present? (ref. 1). Seaborg was skeptical that so many neutrons could be added to a uranium nucleus, but supported the work. This eventually led to the UCRL group finding elements 99 (ref. 2) and 100 in that fallout debris, as we describe in the fermium IYE essay.

Back in Arkansas, Paul (née Kazuo) Kuroda was interested in nuclear fallout. Kuroda was a Japanese radiochemist who had studied natural radioactive soruces in Japan. He emigrated to the United States in 1949, and worked as a postdoctoral researcher at the University of Minnesota in analytical chemistry until 1952 when he received a faculty appointment at the University of Arkansas. At Arkansas, he returned to his previous interest in radioactivity by studying the local hot springs3. Soon after starting his independent career, Kuroda came across a quote from Edward Teller, one of the principal developers of the hydrogen bomb, stating that the ”radioactive and non-radioactive elements” (the fallout) left behind by a nuclear explosion could be studied to ”learn much about the bomb”.

The Teller quotes are found in Harold Urey’s 1952 book The Planets: Their Origin and Development. Teller was paralleling the isotopic signature in bomb fallout with the isotopic signature left by the creation of the solar system and Earth. Kuroda was puzzled that Urey’s book contained no follow-up on these ideas. Kuroda later wrote ”I therefore decided to initiate my own research project on radioactive fallout from nuclear weapons tests.” (ref. 4). In 1952, Kuroda only knew about the American atomic weapons tests in the Nevada desert, and assumed that any fallout in Arkansas came from these tests. Kuroda realized that the radioactive debris from large nuclear explosions would disperse over the entire planet after being injected into the stratosphere.

In the summer of 1953, Kuroda and his co-worker Paul Damon noticed high concentrations of fission products in the Arkansas rain. They published their results quickly5. Their publication ”On the artificial radioactivity of rainfall”, did not go unnoticed. In the autumn of 1953, they were ordered to stop studying fallout, because ”the study of radioactive fallout by non-authorized scientists was strictly forbidden by the U.S. government as a classified military secret” (ref. 4). Damon and Kuroda apparently were mostly silent about the order to stop, but in 1954, they published a report titled ”On the natural radioactivity of rainfall”, which included the pithy statement about artificial radioactivity in rainfall: ”Presumably, considerable work is underway, but has not yet been published.” (ref. 6).

The concentrations of Es and Fm in the fallout reaching Arkansas in 1953 must have been vanishingly small, so Damon and Kuroda would almost certainly not have been able to detect the new elements. They also lacked the huge hint the UCRL group received about the 244Pu produced in the Ivy Mike test, which was the key insight that inspired Ghiorso’s search for elements 99 and 100 (ref. 1). On the other hand, Kuroda and Damon might have noticed 244Pu on their own. We like to envision Kuroda and Damon as characters in a movie asking government agents ”exactly who is investigating the fallout?” Then, like at the end of 1981 film Raiders of the Lost Ark, when Indiana Jones is assured that ”top men” are studying the Ark of the Covenant, Kuroda was being told that ”top men” were looking into it. Unlike Raiders though, the ”top men” were actually looking at the fallout samples7, instead of packing them in a crate and then hiding the crate in a warehouse.

Why would studying radioactive fallout be classified? Likely because, as Ghiorso and Seaborg discovered, the existence of 244Pu was classified. 244Pu is the longest-lived isotope of plutonium, and is not useful for building a nuclear weapon, but as the quote from Teller plainly said, knowledge of the fallout could reveal ”much about the bomb”. In this case, the existance of a neutron-rich isotope like 244Pu found from the fallout analysis might reveal something about the large neutron flux of the weapon. So 244Pu’s existence suggested a high neutron flux — which was key to Ghiorso’s search for elements 99 and 100. In 1953, this was definitely information best kept secret. Of course, the American government could only stop American scientists from studying fallout in rain. Papers began appearing in other countries, especially once knowledge of the hydrogen bomb tests became widely known, and the long range at which fallout could be transported was realized8,9.

Befitting its numerologically significant position on the periodic table, fermium represents the heaviest element which has been forged in a nuclear reactor. The “fermium wall” prevents production of elements heavier than fermium by neutron absorption due to the short half-life (i.e., spontaneous fission) of 258Fm. To go beyond element 100, nuclear scientists had to turn to the same atom-at-a-time techniques — and the same heavy ion beams which were used to produce the first unclassified ”discovery” of fermium (see the IYE article).

In the 1950s though, you didn’t need an nuclear reactor or a convenient hydrogen bomb to find fermium — it fell from the sky.

Brett F. Thornton is in the Department of Geological Sciences (IGV) and Bolin Centre for Climate Research, Stockholm University, 106 91 Stockholm, Sweden. Shawn C. Burdette is in the Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609-2280, USA. e-mail: brett.thornton@geo.su.se; scburdette@WPI.EDU

References

1. Ghiorso, A. Chem. Eng. News 81, 174–175 (2003). [LINK]

2. Redfern, J. Nat. Chem. 8, 1168-1168 (2016). [LINK]

3. Kuroda, P. K., Damon, P. E. & Hyde, H. Am. J. Sci. 252, 76-86 (1954). [LINK]

4. Kuroda, P. K. J. Radioanal. Nucl. Chem. 203, 591-599 (1996). [LINK]

5. Damon, P. & Kuroda, P. Nucleonics 11, 59 (1953).

6. Damon, P. & Kuroda, P. Eos, Transactions American Geophysical Union 35, 208-216 (1954). [LINK]

7. Ghiorso, A. et al. Phys. Rev. 99, 1048-1049 (1955). [LINK]

8. Miyake, Y. Papers in Meteorology and Geophysics 5, 173-177 (1954). [LINK]

9. Miyake, Y. Papers in Meteorology and Geophysics 6, 26-37 (1955). [LINK]

Nature Chemistry’s Altmetric top 10 for 2016

Altmetric recently posted its usual top-100 list and, as usual, there was very little chemistry to be found on it (maybe the reasons behind that should be the subject of a long soul-searching post or editorial, but that’s for another day year). After I had a little moan on Twitter, @nunobimbo asked if we’d post Nature Chemistry‘s top 10 as we did back in 2013. So, here goes… (note: I only considered Articles that appeared in 2016 print issues and these numbers are correct as of Dec 14th, 2016).

––––––––––––––––––––

1. Fast and selective ring-opening polymerizations by alkoxides and thioureas
Xiangyi Zhang, Gavin O. Jones, James L. Hedrick & Robert M. Waymouth

nchem.2574-TOC
(Altmetric score for this list = 694)
(Page views as of the date of this list = 7,746)

––––––––––––––––––––

2. Imaging single-molecule reaction intermediates stabilized by surface dissipation and entropy
Alexander Riss, Alejandro Pérez Paz, Sebastian Wickenburg, Hsin-Zon Tsai, Dimas G. De Oteyza, Aaron J. Bradley, Miguel M. Ugeda, Patrick Gorman, Han Sae Jung, Michael F. Crommie, Angel Rubio & Felix R. Fischer

nchem-TOC-Fischer
(Altmetric score for this list = 447)
(Page views as of the date of this list = 7,553)

––––––––––––––––––––

3. Molecular rectifier composed of DNA with high rectification ratio enabled by intercalation
Cunlan Guo, Kun Wang, Elinor Zerah-Harush, Joseph Hamill, Bin Wang, Yonatan Dubi & Bingqian Xu

nchem.2480-TOC
(Altmetric score for this list = 343)
(Page views as of the date of this list = 4,136)

––––––––––––––––––––

4. Self-assembling biomolecular catalysts for hydrogen production
Paul C. Jordan, Dustin P. Patterson, Kendall N. Saboda, Ethan J. Edwards, Heini M. Miettinen, Gautam Basu, Megan C. Thielges & Trevor Douglas

Douglas_nchem.2416
(Altmetric score for this list = 331)
(Page views as of the date of this list = 8,092)

––––––––––––––––––––

5. A highly stretchable autonomous self-healing elastomer
Cheng-Hui Li, Chao Wang, Christoph Keplinger, Jing-Lin Zuo, Lihua Jin, Yang Sun, Peng Zheng, Yi Cao, Franziska Lissel, Christian Linder, Xiao-Zeng You & Zhenan Bao

nchem-TOC-Bao
(Altmetric score for this list = 285)
(Page views as of the date of this list = 27,427)

––––––––––––––––––––

6. The structural and chemical origin of the oxygen redox activity in layered and cation-disordered Li-excess cathode materials
Dong-Hwa Seo, Jinhyuk Lee, Alexander Urban, Rahul Malik, ShinYoung Kang & Gerbrand Ceder

nchem.2524-TOC
(Altmetric score for this list = 167)
(Page views as of the date of this list = 5,108)

––––––––––––––––––––

7. Neutral zero-valent s-block complexes with strong multiple bonding
Merle Arrowsmith, Holger Braunschweig, Mehmet Ali Celik, Theresa Dellermann, Rian D. Dewhurst, William C. Ewing, Kai Hammond, Thomas Kramer, Ivo Krummenacher, Jan Mies, Krzysztof Radacki & Julia K. Schuster

nchem.2542-TOC
(Altmetric score for this list = 157)
(Page views as of the date of this list = 3,610)

––––––––––––––––––––

8. A supramolecular ruthenium macrocycle with high catalytic activity for water oxidation that mechanistically mimics photosystem II
Marcus Schulze, Valentin Kunz, Peter D. Frischmann & Frank Würthner

nchem.2503-TOC
(Altmetric score for this list = 156)
(Page views as of the date of this list = 6,202)

––––––––––––––––––––

9. Force-induced tautomerization in a single molecule
Janina N. Ladenthin, Thomas Frederiksen, Mats Persson, John C. Sharp, Sylwester Gawinkowski, Jacek Waluk & Takashi Kumagai

nchem.2552-TOC
(Altmetric score for this list = 145)
(Page views as of the date of this list = 4,035)

––––––––––––––––––––

10. Diindeno-fusion of an anthracene as a design strategy for stable organic biradicals
Gabriel E. Rudebusch, José L. Zafra, Kjell Jorner, Kotaro Fukuda, Jonathan L. Marshall, Iratxe Arrechea-Marcos, Guzmán L. Espejo, Rocío Ponce Ortiz, Carlos J. Gómez-García, Lev N. Zakharov, Masayoshi Nakano, Henrik Ottosson, Juan Casado & Michael M. Haley

nchem.2518-TOC
(Altmetric score for this list = 144)
(Page views as of the date of this list = 5,248)

––––––––––––––––––––

(Note: it seems as though the page views on the metrics pages only go up to Dec 2… we’ll maybe have someone look into that…)

Another four bricks in the wall (part III)

Editor’s note: this post written by Brett Thornton and Shawn Burdette is a follow-up piece to the blog post ‘New kids on the p-block‘, the Commentary article ‘Another four bricks in the wall‘ published in the April 2016 issue of Nature Chemistry, and the blog post ‘Another four bricks in the wall (part II)‘.

———————-

Following IUPAC’s announcement of the assignment of discovery priority to elements 113, 115, 117, and 118 on 30 December 2015, the anxious wait began for the announcement of the actual proposed names. The discovery of elements has become increasingly rare, and the simultaneous confirmation and naming of four, though widely expected since the original reports had been around for some time, is almost certainly a once-in-a-lifetime event. IUPAC’s actions are simply the acknowledgement of the discovery honour, which is then followed by the naming of the element.

While waiting to learn what names the research groups in Japan (RIKEN), Russia (JINR), and the United States (ORNL & LLNL) would propose, we surveyed the landscape for what those names might be. As with past discovery announcements, speculation on element names is always rampant. Suggestions came from scientists, media members and the public at large. Proposals referencing figures from pop-culture especially were reported widely. Assuming that the names might be announced quickly, we put together our best predictions for the Sceptical Chymist blog on 26 January 2016 with a panel that also included Philip Ball, Kat Day, and Eric Scerri. We followed this up with a more in-depth Commentary discussing the possible names, published in the April 2016 issue of Nature Chemistry. How sagacious were our 26 January predictions? The first blog post included the names of all four of the elements, albeit on a longer list of 46 possibilities.

‘Moscovium’ was our top prediction, with 4 of our 5 experts guessing this would be the chosen for element 115. Kat was the outlier as she advocated for the longshots based on cultural or mythological sources. Picking moscovium hardly indicates that any of our panelists were blessed with the gift of clairvoyance. The name had been pushed by the Russian JINR group in the past, and they had been very public about their intentions to propose this name. Interestingly however, there seems to have been some information lost in translation when explaining the chosen name to the public. Several news outlets have reported that moscovium was named for the city of Moscow; however, the IUPAC report clearly states that the name is meant to recognize the Moscow region (PDF link here). For those unfamiliar with Russian geography, Moscow is the name of both a city and an oblast (province) that contains the city of Moscow, and the city of Dubna where the JINR is located. Dubna is approximately 130 km (81 miles) north of Moscow on the the northern edge of the Moscow oblast. Conflating the city and oblast of Moscow is the equivalent of saying New York City is the same thing as the entire state of New York.

For element 115, there were also strong indications that the name would refer to Japan in some way. Since RIKEN documents had mentioned the name ‘japonium’, we assigned it the highest odds followed by ‘nipponium’, ‘nihonium’ and ‘rikenium’. Once again 4 out of 5 panelists chose either a traditional pronunciation or the exonym for the nation of Japan. Only Brett correctly picked nihonium, although Eric and Shawn deserve partial credit for chosing ‘nipponium’ since even the Japanese people can’t come to a consensus on how to pronounce the name. Philip’s rationale that ‘japonium’ might better advertise the scientific contribution to the world, may have been trumped by the researchers’ desire to connect with the Japanese people with nihonium. Current and future generations of Japanese students can now look to the periodic table and see a clear emblem of their homeland’s scientific contributions. Although the IUPAC document does not state so explicitly, ‘nipponium’ seems to have been disallowed because of the invalidated discovery of element 43/nipponium (technetium), which appeared on some periodic tables in the early 20th century. The discoverers did note that nihonium also pays homage to Masataka Ogawa, who authored the element 43/nipponium report. Following recent studies, some investigators have postulated that Ogawa actually might have isolated, but misidentified element 75/rhenium before its recognized discovery. Regardless, Ogawa is obviously a revered figure in Japanese science as one of the founding fathers of chemistry in their country.

Without many clues about the possible choices for elements 117 and 118, our list of predictions then got a bit distracted. Wishful thinking may have clouded our judgement somewhat as we proposed many names based on historical chemists, Greek- and Latin-derived names, and even a bit of Slavic and Japanese mythology. As we alluded to in the Commentary, recent naming trends have generally not borrowed heavily from history, mythology, or Greek and Latin. Astatine and technetium, named in 1947, were the last Greek-derived names. Mythology-derived names ended with plutonium.

‘Quercine’ for 117 was Brett’s brainchild, a clever idea that evoked Oak Ridge, Tennessee in a subtle way, while honouring the Latin/Greek source tradition for halogen names. A fusion of both the traditional practices and modern naming trends. We ranked ‘quercine’ somewhat higher than ‘tennessine’/’tennessium’, which Shawn suggested, but at unfavourable odds. In the interim period between the publication of the first blog post and the Commentary, we gravitated toward ‘tennessine’ as a more reasonable guess — it was one of the illustrated elements, along with ‘quercine’, in the commentary. Thankfully, no one (to our knowledge) used our odds to accept wagers. If they had, the unfortunate bookmakers would have been taken to the cleaners by the 750/1 longshot tennessine, which is now the name of element 117.

Historical scientists have fared well in transactinide element naming: Ernest Rutherford, Neils Bohr, Lise Meitner, Glenn Seaborg, Georgy Flerov, and the somewhat unusual choice of Copernicus, who lived centuries before the periodic table was devised, all have been honoured with spots on the periodic table. So we thought there was a chance that one of the obvious historical scientists who had a role in forming the periodic table might earn a spot this time. Our favourites included ghiorsium/ghiorsonine (Albert Ghiorso, co-discoverer of an incredible 12 elements), moselium/moseleyon (for Henry Moseley), or berzelium (for Jacob Berzelius, who with his students discovered or co-discovered 10 elements). From there, we searched for other scientists whose work is associated closely with new element research. Even without any hints from the researchers, we reasoned that Yuri Oganessian, a scientist at JINR, was the most likely scientist to be honored with an element name. The announcement of ‘oganesson’, with the traditional noble gas ‘–on’ suffix, validated that prediction. Notably, the 83-year old Oganessian is only the second living scientist, along with Glenn Seaborg, to have an element named for them.

In the end, we predicted them all, and usually for the right element. As individuals, Philip and Brett each got two right; Philip picked ‘japonium’ instead of nihonium, and ‘ghiorsonine’ instead of tennessine. Brett chose ‘quercine’ rather than tennessine, and ‘moseleyon’ rather than oganesson. Eric had moscovium, and a near-miss with ‘nipponium’ instead of nihonium. Kat, rolled the dice on longshots, ‘octarine’ certainly had a euphonius halogen sound. Shawn? A near-perfect 3.5/4. He predicted moscovium, tennessine, and oganesson. The only miss, ‘nipponium’, the aformentioned variation of nihonium.

What’s next? Well, we look forward to the next time elements are added to the periodic table, but we’re back to the grind of ‘–ium’ suffixed elements for a long, long time now. What names seem left out at this point? As far as scientist-honouring element names go, the continued omission of Ghiroso, Moseley, and Berzelius is striking.

It’s interesting to note that with moscovium, there are now three ‘nationalistic triplets of nation-state/region-city’ on the periodic table, for Russia, the United States, and Germany—all productive element-discovering nations:

nationstateregion

Alternatively, one could include americium/californium/livermorium as a US triplet or germanium/rhenium/darmstadium for Germany. To which we humbly remind the Japanese RIKEN teams, don’t forget about Saitama prefecture and the city of Wako as you return to your particle accelerators! ORNL is also tantalizingly close to a triplet with americium/tennessine, so the obvious city choice from the blog list would be ‘oakridgium’, but they are welcome to steal ‘quercine’ and replace the halogen suffix to name ‘quercium’.

Finally, the choice of Mc as the symbol for moscovium is intriguing, as usually the symbol takes the first unused letter following the initial letter. Mo is already molybdenum, and we speculated that IUPAC would avoid Ms because of the mesyl group, but that didn’t stop the use of Ts for tennessine, despite confusion with tosyl group. So why Mc for moscovium? One possibility is the name of Moscow in cyrillic letters in Russian: Москва.

Another four bricks in the wall (part II)

Editor’s note: this post written by Shawn Burdette and Brett Thornton is a companion piece to the Commentary article ‘Another four bricks in the wall‘ published in the April 2016 issue of Nature Chemistry.

———————-

If discovering and naming new elements was not complex enough, the discoverers must also propose a two-letter symbol. For reasons that are presumably related to adherence to tradition and historical precedent, IUPAC guidelines require two-letter symbols for new elements, with the first letter capitalized and the second lowercase. Although that sounds simple, in reality, finding a suitable symbol for a new element can be nearly as tricky as selecting a name.

Most of the figures for the commentary on the 4 new elements required making educated guesses about what element symbols would correspond with the hypothetical names. Element symbols, like element names, follow an arcane set of rules. Symbols that have been used in the past, but abandoned, may not be reused. Since there are only 114 named elements, some using single-letter symbols, and 26 × 26 = 676 possible two-letter combinations, there initially appears to be lots of available symbols to choose from. Upon further inspection though, problems start to arise.

Part of this symbol problem arises from most element names coming from Indo-European languages, and principally Germanic and Latin languages, which share many common phonemes. Put another way, there are limited numbers of ways to put together letters in English that make sense, and some letters appear far more frequently in element symbols than others – see the chart below:

Letter occurrence frequency in the first 114 assigned element symbols, as of March 2016.

Letter occurrence frequency in the first 114 assigned element symbols as of March 2016.

 
As more and more elements are added to the table, choosing ‘valid’ symbols becomes more difficult. In the case of copernicium, researchers originally proposed the symbol ‘Cp’. As was pointed out in a letter to Nature, Cp previously had been used to denote ‘cassiopium’, a competing name for lutetium in the early 1900s that had appeared on periodic tables. IUPAC ultimately changed the symbol to ‘Cn’ to prevent confusion. Astute readers will recognize that Cp is also used to abbreviate cyclopentadienyl anion, however, none of the IUPAC documents list this as a potential issue. Others have pointed out that Cn was the symbol for ‘coronium’, a widely discussed element in the late 1800s and early 1900s. Coronium, which turned out to be highly ionized iron in the solar spectrum, was never placed on the periodic table. Perhaps the restriction on reusing a symbol need not apply if the element was never assigned a spot.

The illustration for ‘japonium’, our guess for element 113, uses the symbol ‘Ja’. Using the first 2 letters of the proposed name was as an easy derivation because no other element symbol contains the letter ‘J’. If we had guessed ‘nipponium’ however, there would be a dilemma. The single letter ‘N’ is taken by nitrogen. Ni is nickel, Np is neptunium, No is nobelium, so the first combination that is unclaimed is ‘Nn’. There are no double-letter element symbols, so while this might look odd, there are no IUPAC restrictions that would prevent this combination. Alternatively, it would be a clever maneuver to integrate the more familiar exonym ‘Japan’ with the Japanese name for their country and propose Ja as the symbol for nipponium. There is certainly precedence for unmatched chemical symbols. Na and Ag for sodium and silver, from the Latin names natrium and argentum, for instance. However, using symbols from another language has not been applied to newly discovered elements since the early 1800s, unless one counts the long fight over W for tungsten.

In the illustration for ‘moscovium’, a similar problem arises. Mo is molybdenum, so ‘Ms’ would be next in line. Unfortunately, Ms is a common organic chemistry abbreviation for the mesyl functional group (methylsulfonyl), though it’s unclear if this would be an obstacle to the symbol. In the event that organic abbreviations are deemed problematic, ‘Mc’ would be the next choice. Mv was widely used as a symbol for mendelevium before Md was adopted as the official symbol (ref. 1), and therefore would be unlikely.

Likewise, Te is taken by tellurium, so ‘tennessine’ could be ‘Tn’. Until the mid-20th century though, IUPAC defined Tn as the symbol for the 220Rn isotope, a use that persists in current literature. ‘Ts’, the other possible symbol, is the abbreviation in organic chemistry for tosyl groups (p-toluenesulfonyl). This poses a quandary if tennessine is the chosen name for element 117; all the obvious symbols derived from letters in the name might be off limits. If single-letter symbols were resurrected, ‘T’ might work, except tritium uses that letter as a chemical symbol.

There are 14 single-letter symbols (H, B, C, N, O, F, P, S, K, V, Y, I, W, and U). That might suggest that 12 are still available for new elements, but some have already been taken. D and T, as mentioned above, are deuterium and tritium respectively. G was ‘glucinium’, a competing name for beryllium. ‘A’ was an early symbol for argon before it was changed to Ar (ref. 1). When einsteinium was named in the 1950s, the original symbol proposed was ‘E’, but this was changed by IUPAC to Es (ref. 1). ‘M’ is often any generic metal in chemical equations. ‘X’ is any halogen. ‘R’ is an organic functional group. ‘J’ is commonly used for iodine in German-speaking countries. By process of elimination with a 26 letter alphabet, that leaves only L, Q, and Z as unclaimed single-letters.

Ultimately, we guessed Tn for tennessine to agree with the postal code and familiar abbreviation of the state. IUPAC however might prefer Ts because the abbreviation for tosyl is less well-defined by IUPAC than Tn was for thoron.

In the illustration for ‘octarine’, the symbol ‘Oc’ was an easy selection since the only other ‘O’ elements are O (oxygen) and Os (osmium). Although the illustration of scientists doesn’t include symbols, we can still speculate about what might be chosen for these hypothetical element names. ‘Ghiorsium’ could easily claim ‘Gh’ as only germanium (Ge) and gallium (Ga) use the letter ‘G’. For moseleyon, or any element named for Henry Mosley, ‘Ml’ or ‘My’ have to be selected since Mo already belongs to molybdenum, Ms has the complications already discussed for moscovium, and Me is the common abbreviation for methyl. William Ramsay’s namesake ramsayon, would likely use ‘Rm’, ‘Rs’, or ‘Ry’ after passing over the already claimed Ra, which is used by radon. As with japonium, Jo and Jl are theoretically open for ‘joline’ since there are no ‘J’ elements; however, joliotium was suggested for element 102 (now nobelium) with the proposed symbol Jo in the late 1950s, and Jl for element 105 (now dubnium) by IUPAC in 1994. Would a ban on reusing symbols lead to Ji, Jn or Je being preferred?

While symbol speculation might not have the allure of guessing the actual name of an element, the ultimate choice is no less important. The chemical symbol is the ‘face of the franchise’ for each element; though element names may vary between languages, the symbols are universal. The initial encounter with an element for chemistry students is as likely to be the symbol as the name. So perhaps it’s not surprising, that at times, the choice of chemical symbol has been as controversial as the name itself. Well, almost as controversial.

References

1. IUPAC: Commission de Nomenclature de Chimie Inorganique, in ‘Comptes Rendus de la Dix-Neuvième Conférence, Paris’, 1957, p. 93.

The 5th Molecular Sensors and Molecular Logic Gates Meeting

Editor’s note: this is a guest post on behalf of Prof. Tony James.

————————–

We are very excited about the upcoming 5th Molecular Sensors and Molecular Logic Gates (MSMLG) meeting in Bath from July 24th to 28th 2016. The MSMLG Award Lecture will be delivered by inspirational scientist and good friend Eric V. Anslyn. With great ‘Sense and Sensibility’ Eric was the unanimous choice of the Molecular Sensor and Logic Community for the 2016 MSMLG award.

We are delighted that the meeting includes a special conceptual lecture by Sir J. Fraser Stoddart (Sponsored by Chem from Cell Press) a founder of logic in chemistry and inspiration to many of the researchers at the meeting. We will then be treated to an Irish adventure by AP de Silva (Nature Chemistry Lecture) who will shed light and amuse us with his many important research stories based on his Sri Lankan origins a touch of serendipity and driven by friendship.

The meeting will be a true ’round table’ of exciting and delightful research by an unparalleled line-up of scientists from the molecular sensing and logic community. Held at the University of Bath during its 50th Anniversary in the delightful World Heritage City off Bath. For those wishing to attend the meeting registration will remain open till the 18th July 2016. For more information contact Tony James and Dan Pantos (www.msmlg2016.uk, msmlg2016@bath.ac.uk)

New kids on the p-block

Editor’s note: this is a guest blog post from Philip Ball, Shawn Burdette, Kat Day, Eric Scerri and Brett Thornton about those four new elements and what they might/should/could be called. We’d like you to get involved too, so please do comment!

—————————

On December 30, 2015, IUPAC (the International Union of Pure and Applied Chemistry) announced the confirmation of the experiments that produced elements 113, 115, 117, and 118, which completes the 7th row of the periodic table. The corresponding technical reports on the confirmations are available ahead of print online (here and here). The announcement created a great deal of excitement not only in the scientific community but also in the public, and touched off a wave of speculation about what the new elements will be named. IUPAC guidelines authorize the original discoverers to suggest an element name, and revisions to the rules propose several modifications including what form the suffixes of elements in group 17 and 18 should take. After the names have been submitted, IUPAC will sanction the names after a period for public comment. The IUPAC guidelines permit an element to be “named after a mythological concept, a mineral, a place or country, a property or a scientist”.

Except for a press release from the Joint Institute for Nuclear Research (JINR) on element 115 (available here) and Riken on element 113 (see page 16 of this pdf document), the research groups have been silent on what names might be submitted for IUPAC approval. Proposals for names have come in from a variety of quarters including several internet petitions on change.org. With all the suggestions and speculation, we thought it would be fun to try and guess what the researchers actually will propose to IUPAC. So we assembled a panel of experts that included freelance science writer Philip Ball, Worcester Polytechnic Institute professor of chemistry and biochemistry Shawn Burdette, chemistry blogger Kat Day, UCLA lecturer and author of several books on the periodic table Eric Scerri, and Stockholm University atmospheric chemistry researcher Brett Thornton. The panel brainstormed a list of ideas consistent with the IUPAC guidelines, as well as historical trends in element nomenclature. The panel also examined the names being put forward elsewhere. The list is compiled below (click on the table for bigger version) and includes odds on the likelihood that each name will be proposed to IUPAC (e.g., 1/2 odds corresponds to a 67% probability and 2/1 odds implies a 33%).

table1full

Based on the proposed names, each member of the panel has made a pick for each of the new elements. If we were actually gambling, picking a longshot name, while less probable would provide a bigger payout if correct. This would be how things work in a typical sports book; however, these picks are being made just for fun (click on the table for bigger version).

table_picks

The process of how the names were selected, the significance of the names, how the odds were determined, and why each panelist made their picks, will be the subject of a Commentary in an upcoming issue of Nature Chemistry. Since we don’t know the timetable on which names will be proposed, we wanted to initiate the project with this post on the Sceptical Chymist. This also gives you the opportunity to make picks of what name the researchers will submit to IUPAC. Did the panel miss a name that the researchers at RIKEN, the JINR, Lawrence Livermore National Laboratory (LLNL) or Oak Ridge National Laboratory (ORNL) might be considering? It has also been suggested that the discovery groups might want to consult with the research teams involved in the experiments that replicated their discoveries. Will they be consulted, and are there other names those researchers might advocate? The discovery team who created copernicium listened to public suggestions, will these research teams? Should they? Give us your picks as well as any suggestions for possibilities we omitted below. Remember IUPAC guidelines require elements to have names derived from mythology, minerals, places, properties or scientists. Make sure to identify yourself so we can credit you in the Commentary if we discuss your ideas.

Nature Chemistry’s 2014 impact factor citation distribution

As pointed out yesterday in a blog post by Stephen Curry (and indeed in at least one previous blog post), some journals publish their citation distributions (this has also been blogged about by Steve Royle too – and probably by many others that I’m not aware of, I’m sure). I’ve been interested in doing this for Nature Chemistry for a while now, but have never quite found the time – but after a brief exchange on Twitter this afternoon, I figured I should run the numbers… (what better way to spend a Friday evening?!).

So, according to Journal Citation Reports (JCR) from Thomson Reuters, the 2014 impact factor (announced in 2015) for Nature Chemistry was 25.325. How do they arrive at this number? Well, they count up how many times articles published in the journal in 2012 and 2013 were cited in 2014 and then divide that total by the number of ‘citable items’ (more on that later) that the journal published in 2012 and 2013. So, according to JCR, 2012/2013 content in Nature Chemistry was cited 6,458 times in 2014 and we published a grand total of 255 citable items in 2012/2013. Divide 6,458 by 255 and you get 25.325. Simple, eh?

Well, no. If you do a Web of Science (All Databases) search for Nature Chemistry for 2012-2013, you find that we actually published 451 items in those 2 years. There were 239 research papers (we call them ‘Articles’), 16 review-type articles (long ones we call ‘Reviews’ and shorter ones we call ‘Perspectives’), as well as Editorials, Commentaries, Research Highlights, News & Views articles and other ‘front-half’ material – all adding up to a total of 451 articles. It is only the Articles, Reviews and Perspectives (255 items) that count as citable items, however. What does this mean? It means that although the bottom half of the impact factor equation described above only includes these article types, citations to any of the journal content (including News & Views, Editorials, Commentaries, etc.) get counted in the top-half of the equation.

If you look at those 451 items in Web of Science, in 2014 they received a total of 6,402 citations (that’s already 56 fewer than the 6,458 used in the JCR impact factor calculation – so those extra 56 must be being pulled in from some other database by JCR). Of those 6,402 citations that are in Web of Science, Articles received 4,852 citations, Reviews/Perspectives received 1,206 citations and all the other front-half articles garnered a total of 344 citations, so the distribution of citations between different content types breaks down like this:

citation_breakdown

Now, just looking at the Articles and Reviews/Perspectives, we have a total of 255 items with 6,058 citations (we’re ignoring those 344 citations to other stuff) in 2014. That gives you an average of 23.8 citations (6,058 divided by 255) per Article/Review/Perspective. Of course, that is an average, and this is where citation distributions come in. If you list the articles in order from most cited to least cited and then plot article number versus citations, you get something that looks like this:

citable_items_decay

The most cited article is a Review (that was published in 2013) with 354 citations in 2014. Article number 2 on the list is a 2013 Perspective with 171 citations in 2014… and then we head to the end of the list where the 253rd, 254th and 255th articles all received 0 citations in 2014. That’s one way of plotting the data, but perhaps not the most useful. Another way to do it is shown below, whereby articles are put in bins defined by the number of citations received in 2014.

citable_items_distrubution

So that the graph is still meaningful, I lumped all of the 100+ citation papers into one bin at the end (a breakdown of what is included in there is shown on the graph). The official 2014 impact factor (25.3) is highlighted, along with the mean number of citations these article types actually received (23.8 – i.e., not inflated by the 344 citations included in the impact factor calculation that were actually cites to other content) as well as the median value too, which is 16. Only 29% of Articles/Reviews/Perspectives (that’s 73 of the 255) received more citations (26 or more) in 2014 than the calculated impact factor of the journal (25.3). The vast majority of articles received fewer citations (no more than 25) than the impact factor.

It’s well known that review-type articles are typically cited more than research papers (in chemistry at least and probably in other subjects too, I imagine) and so I repeated the analysis with just the research papers (the Articles) and left out the Reviews and Perspectives. The article number vs citations plot now looks like this:

articles_decay

The shape looks quite similar to the graph further up this post, but note that the scale on the y-axis is quite different. The highest-cited research paper was cited 151 times in 2014, with the 2nd, 3rd, 4th and 5th-placed Articles receiving 114, 113, 105 and 84 citations, respectively. If we plot the citation distribution, we get the following:

articles_distribution

After removing the Reviews and Perspectives from the equation, the mean number of citations received by just the research papers is now 20.3 rather than 23.8 (a drop of 3.5) and the median has dropped from 16 to 15. Only 61 of the 239 Articles (that’s 26%) received more citations (26 or more) in 2014 than the calculated impact factor of the journal; roughly three-quarters of all research papers received fewer. If you consider 20.3 to be the pure Article ‘impact factor’, this is still a very skewed metric, however. Of the 239 Articles, 86 of them (36%) received 21 or more citations in 2014 and the rest were cited 20 times or fewer.

When the 2015 impact factors get released in 2016, we’ll run the numbers again and compare the data to what’s above to see if anything has changed all that much.

Avoiding redundant tautologies in scientific writing

This is a guest post from Reuben Hudson at Colby College in response to one of Michelle Francl‘s recent Thesis columns.

—————

Chemists communicate with a lexicon rife with double endendres [ref. 1]. Some of our words take on new meanings after appropriation from general vocabulary and certainly our words cross into the public sphere with a similar alteration of the intended meaning, often resulting in humorous or nonsensical interpretations. Despite our urge for vigorous [ref. 2], concise [refs 3,4], and clearly understandable prose [ref. 5], Michelle Francl [ref. 1] suggests that we not avoid all ambiguous language ‘for it gives chemists a rich set of images to draw on, and as such, we shouldn’t discourage it, for we can’t look for what our language doesn’t let us imagine.’ I agree whole-heartedly with her encouragement to use, when appropriate, single phrases with multiple meanings, and take this opportunity to point out the equally common, seemingly opposite practice in the chemical literature of incorporating multiple, redundant inferences of the same meaning in a single phrase.

Redundancies are a part of quality science. Elegant reproduction can build a compelling argument. Reiteration of a thesis strengthens rhetoric. Unintentionally repeating again the same point, however, is a sign of ineptitude and detracts from effective communication.

Tautologies (redundancies for lack of style) can arise as a result of an incomplete understanding. Such is often the case with bilingual acronyms, where the acronym itself is retained, but the meaning clearly lost in translation, a laughable and excusable miscue. Consider ‘le protocol IP’ from French computer science (internet protocol protocol). Without the crutch of an improper translation, other redundant acronyms become more laughable and less excusable. Biologists first introduced the term, ‘HIV virus’ (human immunodeficiency virus virus), while physicists brought us LASER light (light amplification by stimulated emission of radiation light). Chemists are perhaps the worst when it comes to tautological acronyms. Any student of organic chemistry will remember one of the cornerstone reactions: the SN2 substitution (guess what ‘S’ represents). The CDC coupling reaction (cross dehydrogenative coupling coupling), a new innovation rolled out by green chemists, is a halogen-free means of carbon–carbon bond formation.

To this point, the discussion has ostensibly focused only on redundant acronyms. The careful reader will have also noticed the equally egregious use of tautological phrases within this very post, several of which see frequent use in scientific publications. An innovation is, by definition, something new. It is therefore tautological to say, ‘new innovation.’ An introduction is the first time something is presented. Thus, ‘first introduced’ is redundant for lack of style. Repeat means to say again, so it is superfluous to say, ‘repeat again.’ The title of this post is also tautological.

References

1. Francl, M. Nature Chem. 7, 533–534 (2015). [LINK]
2. Patience, P. A., Patience, G. S., Boffito, D. C. Can. J. Chem. Eng. 93, 2095–2097 (2015). [LINK]
3. Hudson, R. J. Chem. Educ. 90, 1580 (2013). [LINK]
4. Carr, J. M. J. Chem. Educ. 90, 751−754 (2013). [LINK]
5. Stewart, A. F. et al. J. Chem. Educ. doi:10.1021/acs.jchemed.5b00373 (2015). [LINK]

Materials Girl: Growing up

[Posted on behalf of Materials Girl]

The Materials Girl column was ‘born’ in August 2007 while I was 19 and halfway through undergrad. Back then, it was puzzling that other guest writers never seemed to have time to post. Undergrad was as busy as life got, and it didn’t take THAT long to write, right? Ah, youthful innocence – and whining! Considering my earlier posts, it’s a wonder that Stu and Neil patiently let me gripe instead of slapping me upside the head and pointing out that being an undergrad is relatively easy (#firstworldproblems). Then again, perhaps that clueless-but-learning perspective is part of the reason why they not only chose an undergrad blogger, but also let her keep writing on the Sceptical Chymist through grad school and beyond. For that, I am incredibly grateful – and rather abashed.

This year marks a decade since I graduated high school (and took Stu’s infamous o-chem class)! Clichés aside, the years have flown by and memories have begun blurring, despite the acute instances where time crawled and stress tended to reach extreme peaks. Scrolling through the Materials Girl log shows increasingly long gaps between posts – I’ve become one of those busy, beyond-undergrads whose occupations previously were such a mystery…

Being done with school is sometimes a strange reward. There was comfort in the structure of knowing exactly what path to follow, give or take nebulous major tasks in grad school such as ‘do novel research’ and ‘write a dissertation’. Nowadays, I must admit to feeling a bit of sadistic glee when seeing others undergo the same struggles. Whether it’s spotting undergrads studying the night away in coffee shops, hearing new grad students panic over prelims and qualifying exams, or seeing candidates slave away to prepare a final defense, I can smile and say that they’re all doable tasks (if not painful memories). If I survived, so can they.

Now that I’ve made time/procrastinated sufficiently to draft a new post, it’s back to writing papers and looking for open positions to follow my postdoc. Fingers crossed!