Posts Tagged ‘scientist’

Pidapalooza!

Thursday, November 10th, 2016

This is sent from the Pidapalooza event in Reykjavik, Iceland, and is a short collection of notable things I learnt or which attracted my attention.

Firstly, what IS PIDapalooza[1]? Well, it’s all about persistent identifiers, but don’t let that put you off! Another way of putting it is that it’s a way of finding things scientific on the Web. Not just publications, but conferences, social media, teaching, research datasets, infrastructure, grants, organizations, instruments, scientific objects and samples and no doubt much more. These (will) live in an inter-connected eco-system, and so the idea goes, will become an integral part of how a scientist accumulates and disseminates information nowadays. Yes, the conference itself has its own PID: 10.5438/11.0001  and the individual talks will also appear as both a collection and with their own  PID in the near future.

  1. The first example comes from WikiData, a collection of carefully curated data, from which can be dynamically assembled say a periodic table of the elements. All the data here is included from other objects, and everything is referenced by its PID. Since it’s all assembled from data, if say the name of element 118 is assigned, then it will automatically be absorbed into this presentation.
  2. This next example proved highly contentious, but is included here anyway. It is templated PIDs, as in http://doi.org/10.5446/12780#t=00:20.00:27 which allows navigation to a particular part of an object referenced by the PID. In this case a time code for a movie, but it might be say an active site in a protein, or a key atom or group in a molecular complex for example.  This might never happen (for reasons only the computer scientists currently understand!) but it does show one way in which the humble DOI might evolve.
  3. http://typeregistry.org exists for registering data types. It has almost no chemistry at the moment, but perhaps it should have! 
  4. There was a great deal about  ORCIDs, and the ways in which uses of this particular  PID are evolving.  For example, the next big effort is to use the ORCID system for organisations.  You will find my ORCID at the top of this post.
  5. PIDs are also being mooted for instruments. The idea is that instrumental capabilities, settings, calibration etc are often an integral part of the data acquisition for a project. So if data is generated using such a device, why not quote its  PID in any derived article so that others can more easily replicate a particular experiment in their own laboratory.
  6. A quote by one of the speakers was attributed to Bill Gates around 1997 “We need  banking. We don’t need banks anymore” (think how this might apply to 2016. Was he correct?).  This was followed by straw men such as: “We need publications. We don’t need publishers anymore”. Or “We need archiving. We don’t need libraries anymore”. Just like Gates’ own quote, the reality is of course far more complex.
  7. And PID fatigue;  I hope you are not getting too much of that at the moment.

There are lots more I have learnt which I need to fix/enhance/address in our own experiments in the use of PIDs in chemistry, so I have better get on with it now!

References

  1. ORCID., DataCite., Crossref., and California Digital Library., "PIDapalooza 2016", 2016. https://doi.org/10.5438/11.0001

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LEARN Workshop: Embedding Research Data as part of the research cycle

Monday, February 1st, 2016

I attended the first (of a proposed five) workshops organised by LEARN (an EU-funded project that aims to ...Raise awareness in research data management (RDM) issues & research policy) on Friday. Here I give some quick bullet points relating to things that caught my attention and or interest. The program (and Twitter feed) can be found at https://learnrdm.wordpress.com where other's comments can also be seen. 

  • Henry Oldenburg, founder member and first secretary of the Royal Society, was the first Open Scientist.
  • About 100 people attended the workshop. Of these ~3-5 identified themselves as researchers creating data, and the rest comprised research data managers, administrators, librarians, publishers (but see below) etc. Many were new to their posts.
  • Not publishing scientific data should become recognised as scientific malpractice.
  • Central libraries should pro-actively disperse their knowledge to data scientists in departments.
  • If a scientist is concerned that openly publishing their data might give advantage to their competitors, they are urged to counteract this by "being cleverer than the others". 
  • The three great bastions of open science are (a) Open Data, (b) Open access articles and (c) doing science openly. Examples of this third category include open notebook science (ONS), a form notably pioneered by Jean-Claude Bradley. One attribute of ONS was noted as no insider knowledge.
  • Learned societies should endow medals for Open Science.
  • (Some) publishers are reinventing themselves as Research Facilitators.

The plenaries are all well worth dipping into (certainly the video and in some cases all the slides are scheduled to appear).

If you are a researcher (undergraduate students, PGs, PDRAs, early career researchers and academics) you should immediately track down your local evangelist/expert in RDM and ask what the local infrastructures are (or will be shortly built). 

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Ionizing yet more ultra-strong acids with water molecules.

Friday, March 20th, 2015

This might be seen as cranking a handle by producing yet more examples of acids ionised by a small number of water molecules. I justify it (probably only to myself) as an exercise in how a scientist might approach a problem, and how it linearly develops with time, not necessarily in the directions first envisaged. A conventional scientific narrative published in a conventional journal tells the story often with the benefit of hindsight, but rarely how the project actually unfolded chronologically.‡ So by devoting 7 posts to this, you can judge for yourself how my thoughts might have developed (and I am prepared to acknowledge this may only serve to show my ignorance).

To pick up the story where it ended in the 6th post, I set off to hunt for a strong acid that might require precisely two water molecules to ionise it. So here are some more candidates:

Acid Acid…H length, Å OH length in 2H2O Data-DOI
bis-triflylamine NH=1.056 1.622 [1]
bis-triflylamine OH=1.575 1.007 [2]
Perchloric acid 1.024 1.540 [3]
Perchloric acid 1.514 (3H2O) 1.026 (3H2O) [4]
Perbromic acid 1.030 1.518 [5]
Fluorosulfonic acid 1.028 1.504 [6]
Fluoroselenic acid 1.025 1.522 [7]

Of these, perchloric acid is thought to be stronger than eg HBr, and indeed whereas the latter requires four water molecules for ionization, the former seems to require only three (I include this in the table above to show what happens to the bond lengths upon ionisation). But two is not quite enough, although it does appear to be on the edge. Nor does perbromic acid achieve this, or fluorosulfonic or fluoroselenic acids.

This search also illustrates another proclivity of humans, to set themselves targets, and on occasion fairly pointless targets. But one never knows whether even an apparently pointless target at the outset might not result in the discovery of something much more unexpected (even climbing Mt Everest might have brought some benefits to humanity, although I cannot name one here). I think a fair few discoveries have gone down that route. But, sadly, the hunt for acids ionized by precisely two water molecules in the gas-phase has not (yet?) borne such fruits.

‡We recently tried to write an article in such a chronological fashion. We had a hypothesis, initially thought we might be able to prove it, did more experiments and ultimately proved the hypothesis wrong (in solution!). The referees did not take to this perhaps slightly too honest account of our efforts. Since the hypothesis was wrong, why did we need to publish the story? Well, it did get published in the end, and you can make your own mind up.[8]

References

  1. H.S. Rzepa, "C 2 H 5 F 6 N 1 O 6 S 2", 2015. https://doi.org/10.14469/ch/191136
  2. H.S. Rzepa, "C 2 H 5 F 6 N 1 O 6 S 2", 2015. https://doi.org/10.14469/ch/191137
  3. H.S. Rzepa, "H 5 Cl 1 O 6", 2015. https://doi.org/10.14469/ch/191139
  4. H.S. Rzepa, "H 7 Cl 1 O 7", 2015. https://doi.org/10.14469/ch/191138
  5. H.S. Rzepa, "H 5 Br 1 O 6", 2015. https://doi.org/10.14469/ch/191140
  6. H.S. Rzepa, "H 5 F 1 O 5 S 1", 2015. https://doi.org/10.14469/ch/191143
  7. H.S. Rzepa, "H 5 F 1 O 5 Se 1", 2015. https://doi.org/10.14469/ch/191141
  8. P. Bultinck, F.L. Cherblanc, M.J. Fuchter, W.A. Herrebout, Y. Lo, H.S. Rzepa, G. Siligardi, and M. Weimar, "Chiroptical Studies on Brevianamide B: Vibrational and Electronic Circular Dichroism Confronted", The Journal of Organic Chemistry, vol. 80, pp. 3359-3367, 2015. https://doi.org/10.1021/jo5022647

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The Amsterdam Manifesto and crystal structures.

Tuesday, March 18th, 2014

I have mentioned the Amsterdam manifesto before on these pages. It is worth repeating the eight simple principles:

  1. Data should be considered citable products of research.
  2. Such data should be held in persistent public repositories.
  3. If a publication is based on data not included with the article, those data should be cited in the publication.
  4. A data citation in a publication should resemble a bibliographic citation and be located in the publication’s reference list.
  5. Such a data citation should include a unique persistent identifier (a DataCite DOI recommended, or other persistent identifiers already in use within the community).
  6. The identifier should resolve to a page that either provides direct access to the data or information concerning its accessibility. Ideally, that landing page should be machine-actionable to promote interoperability of the data.
  7. If the data are available in different versions, the identifier should provide a method to access the previous or related versions.
  8. Data citation should facilitate attribution of credit to all contributors

I just gave a talk at the ACS meeting in Dallas which touched upon the need to emancipate data according to these principles. My talk, in case you are interested, focused particularly upon item 6 above.[1]

Just after my talk I heard that crystallographic data was about to be emancipated (my phrase) and so I was interested to find out what this might mean, and how many of the above principles were being adhered to. Indeed, it is an interesting test to apply to any chemistry data that you might find out there. Thus 10.5517/cc10ftfp[2] is the DOI of a recently published crystal data structure. This adheres to points 1-3 and 5 above, and probably also 8. As I have already noted, 6 is the interesting one! So let’s go to the landing page and see what we find.

doi-x1

 

Firstly, note that you do not need any sort of access code to get to this page, it is open to all. But it is after all just a landing page, not actual data. Next, click on the Download button, and you get asked to identify yourself by providing a name, email address and affiliation as mandatory fields, as well as agreeing to conditions of use. I reproduce these conditions here:

“Individual CIF data sets are provided freely by the CCDC on the understanding that they are used for bona fide research purposes only. They may contain copyright material of the CCDC or of third parties, and may not be copied or further disseminated in any form, whether machine-readable or not, except for the purpose of generating routine backup copies on your local computer system“.

As with most such conditions, it is what one cannot do that is most interesting.

  1. Teach, as for example incorporating the data into lecture notes
  2. Make a copy, e.g. to place into this blog (is this for research purposes?)
  3. Do bona fide research purposes in fact allow a copy to be made, or does the second sentence over-ride the first in this regard, since it lists exclusions and research copying is not an exclusion.
  4. Judging from the landing page, it is pretty much impossible for any machine action to take place (item 6 in the Amsterdam manifesto). Even though the data is machine actionable, the landing page pretty much prevents this from happening. 

What did cause my eyebrows to shoot up was that I have to reveal my full identity and affiliation (which appears not to be actually checked) in order to get the data. Think about this. Do journals ask for this information when you download an article from them? (OK, they probably know your affiliation). Which scientist is reading which article (or viewing which data) could be construed as sensitive information after all. So why in order to acquire crystal data do you have to provide personal information? Surely, looking at data should be a private process if one wants it to be?

doi-x2

The release of crystal data in this manner, with a decent partial adherence to the Amsterdam Manifesto is an excellent start; this data after all is well curated and of high value. But I must call upon CCDC to rethink that landing page, the conditions of use and the mandatory gathering of personal information. Not quite there yet!

References

  1. "Digital data repositories in chemistry and their integration with journals and electronic laboratory notebooks", 2014. http://doi.org/10042/a3uza
  2. Sowa, Michał., Ślepokura, Katarzyna., and Matczak-Jon, Ewa., "CCDC 936802: Experimental Crystal Structure Determination", 2014. https://doi.org/10.5517/cc10ftfp

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The "shocking" Xe-Au bond.

Saturday, January 21st, 2012

Chemistry rarely makes it to the cover of popular science magazines. Thus when this week, the New Scientist ran the headline “Forbidden chemistry. Reactions they said could never happen“, I was naturally intrigued. The examples included Woodward and Hoffmann’s “symmetry-forbidden” reactions, which have been the subject of several posts here already. But in the section on nobel gas chemistry, the same Hoffmann is reported as having been shocked to hear of a compound of xenon and gold, both of which in their time were thought of as solidly inert, and therefore even more unlikely to form a union.


Science magazines are often fearful of showing molecular structures on their pages (much like mathematical equations) and so the “shocking” compound is not illustrated in the article; you can see the essential feature above (the counterion is the otherwise unremarkable Sb2F11–). Here, I include the 3D crystallographic coordinates (published in 10.1126/science.290.5489.117) which you can explore by clicking on the above graphic or view below as a rotatable 3D model.

Since the year 2000, when the above was reported, there have been very few additional examples, and so it remains a rare phenomenon. I thought it might be amusing to also give an example of the reverse phenomenon, a reaction that chemists said should happen, but which they had great difficulty in inducing, namely the formation of perbromate salts. The reaction was eventually induced by resorting to nuclear physics, and the radioactive transmutation of Se83 to Br83. Once chemists had been persuaded it really could be made, lots of more conventional ways of preparing perbromates were discovered.

Finally, I ponder how long it might take for magazines such as New Scientist to include interactive diagrams such as the below on the pages of the (increasingly) electronically delivered editions? Or indeed, when mainstream chemistry journals might start incorporating “HTML5” into their own production processes.

 

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The “shocking” Xe-Au bond.

Saturday, January 21st, 2012

Chemistry rarely makes it to the cover of popular science magazines. Thus when this week, the New Scientist ran the headline “Forbidden chemistry. Reactions they said could never happen“, I was naturally intrigued. The examples included Woodward and Hoffmann’s “symmetry-forbidden” reactions, which have been the subject of several posts here already. But in the section on nobel gas chemistry, the same Hoffmann is reported as having been shocked to hear of a compound of xenon and gold, both of which in their time were thought of as solidly inert, and therefore even more unlikely to form a union.


Science magazines are often fearful of showing molecular structures on their pages (much like mathematical equations) and so the “shocking” compound is not illustrated in the article; you can see the essential feature above (the counterion is the otherwise unremarkable Sb2F11–). Here, I include the 3D crystallographic coordinates (published in 10.1126/science.290.5489.117) which you can explore by clicking on the above graphic or view below as a rotatable 3D model.

Since the year 2000, when the above was reported, there have been very few additional examples, and so it remains a rare phenomenon. I thought it might be amusing to also give an example of the reverse phenomenon, a reaction that chemists said should happen, but which they had great difficulty in inducing, namely the formation of perbromate salts. The reaction was eventually induced by resorting to nuclear physics, and the radioactive transmutation of Se83 to Br83. Once chemists had been persuaded it really could be made, lots of more conventional ways of preparing perbromates were discovered.

Finally, I ponder how long it might take for magazines such as New Scientist to include interactive diagrams such as the below on the pages of the (increasingly) electronically delivered editions? Or indeed, when mainstream chemistry journals might start incorporating “HTML5” into their own production processes.

 

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Henry Armstrong: almost an electronic theory of chemistry!

Monday, November 7th, 2011

Henry Armstrong studied at the Royal College of Chemistry from 1865-7 and spent his subsequent career as an organic chemist at the Central College of the Imperial college of Science and technology until he retired in 1912. He spent the rest of his long life railing against the state of modern chemistry, saving much of his vitriol against (inter alia) the absurdity of ions, electronic theory in chemistry, quantum mechanics and nuclear bombardment in physics. He snarled at Robinson’s and Ingold’s new invention (ca 1926-1930) of electronic arrow pushing with the put down “bent arrows never hit their marks“.1  He was dismissed as an “old fogy, stuck in a time warp about 1894.”1 So why on earth would I want to write about him? Read on…

He did worthy (nowadays this could mean dull) chemistry on e.g. naphthalenes, but I want to focus on two articles from the period 1887-1890 (10.1039/CT8875100258  and 10.1039/PL8900600095). Let me set the scene by reminding of an earlier post showing the structure of a bis(stilbyl)ketone, dated 1921. The two aromatic groups (yes, they really are such) are drawn in the manner we would nowadays draw cyclohexane. This practice in fact continued in texts and articles for perhaps 30 more years! Not much sign of electronic accounting there then! And by a professor at Imperial College no less, where Armstrong had been.

Aromatic molecule, circa 1921

So when would you date the diagrams below? So called Clar2 representations, originating from the 1950s? The one on the bottom below cites Clar and dates from 2010, DOI: 10.3390/sym2031653, but the one above it comes from Armstrong’s 1890 article!

Two representations of pyrene, 2010 and 1890.

Clar representations are used to count electrons (as coming in six packs). But there is little doubt that Armstrong’s use of a “C” (or inner circle, which is exactly what it is) means six as well. The evidence I present below, taken from his 1887 article.

Armstrongs six pack

  1. He counts the six carbons as having a total of 24 what he calls affinities (definition: An attraction or force between particles that causes them to combine), or four per carbon. Let us make life easy and equate affinity=electron (remember, the electron itself was not yet discovered or named!). He disposes of 12 affinities/electrons to form what we now call six carbon-carbon σ bonds, and a further six for the  six C-H bonds.
  2. He is left with exactly six affinities/electrons, which he presupposes to act upon each other, in the manner of resultants (the old term for vectors). In fact, he replaces these six vectors by a circle (the inner circle) in his second article of 1890.
  3. He invents delocalization in all but name when he states that any one atom has an influence on other atoms not contiguous to it in the ring (he really did have o/m/p directing influence in mind here).
  4. He compares the introduction of a substituent (R, which comes from the old name Radicle) perturbing the distribution of the affinity to how electric charges perturb each other. So, the affinity behaves as if it might have electrical (from which the name electron came of course) properties? And it might be described by a vector?
  5. Remember, this is a scientist who in later life did not believe in electronic theories of chemistry? Really? Well, again in 1890:

Is this an affinity (=electronic) theory of chemistry?

  1. Here, he is refining his vector representation of affinities, saying that these vectors in effect define a circle, an inner circle no less. One that can be disrupted  (Robinson some 30 years later wrote of how the cycle of six electrons are able to form a group that resists disruption) when an additive compound is formed (his examples are all electrophiles, what we now call electrophilic addition) such that the remaining carbons become merely unsaturated. There seems little doubt he is describing what we now call a Wheland Intermediate.
  2. Is this really a man who did not believe in electronic theories of chemistry? What about that concluding paragraph then? The laws of substitution require a knowledge of the inner structure of (what we now call the aromatic) hydrocarbons?
  3. And that such speculations may suggest fresh lines of experimental inquiry? This all sounds very much like the modern use of quantum mechanics and its electronic eigenvectors to describe the probability distribution of electrons (remember, Armstrong did not approve of this either) to probe the inner structure of molecules and to suggest new experiments.

We have a real mystery. Armstrong got so very close to a modern theory of chemistry. Was he asleep when Stoney named the electron around 1891 and Thomson discovered it in 1897? If only he had followed his own advice! Ah well, just as well he was ignored in the 20th century when he preached against it all.

  1. W. H. Brock, “The case of the Poisonous Socks”, chapter 20, RSC Publishing, 2011, 978-1-84973-324-3
  2. Clar, E. The Aromatic Sextet; Wiley: New York, NY, USA, 1972.

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Mindless chemistry or creative science?

Saturday, September 3rd, 2011

The (hopefully tongue-in-cheek) title Mindless chemistry was given to an article reporting[1] an automated stochastic search procedure for locating all possible minima with a given composition using high-level quantum mechanical calculations. “Many new structures, often with nonintuitive geometries, were found”. Well, another approach is to follow unexpected hunches. One such was described in the previous post, and here I follow it to one logical conclusion.

One structure leads to another

The train of thought started with the recent speculation upon a zwitterionic intermediate in the photolysis of a dimethyl-pyrone. Closure of this is likely to require a very low barrier, and this leads to a bicyclic species, which could be written as a carbene. One then asks if carbon dioxide itself could be so represented? If so, could that carbene be stabilised with a metal, as below? A reality check, as noted in the earlier post, is that a similar complex with iron tetracarbonyl is known, and appears to be stable.

Sequestration of carbon dioxide?

Enter quantum mechanics, which will tell us exactly how stable. Firstly, the spin state of the complex has to be determined, and it turns out the singlet (low spin) is lower than either the triplet (medium spin) or quintet (high spin) states. It took around five minutes (ωB97XD/6-311G(d) ) to establish that the free energy of the reaction between carbon dioxide and iron tetra carbonyl is endothermic in free energy by ~100 kcal/mol. So no sequestration of CO2 by iron carbonyl then!

Iron tetra carbonyl-carbon dioxide complex. Click for 3D

As a scientist, I always find it fascinating how one can jump from one topic to a completely different one in just a few steps. But one always needs reality checks in doing so! Perhaps automated mindless searches (bounded by quantum mechanical reality checks) will perhaps one day come up with something really important. All us humans have to do is recognise this when it happens.

References

  1. P.P. Bera, K.W. Sattelmeyer, M. Saunders, H.F. Schaefer, and P.V.R. Schleyer, "Mindless Chemistry", The Journal of Physical Chemistry A, vol. 110, pp. 4287-4290, 2006. https://doi.org/10.1021/jp057107z

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A short history of molecular modelling: 1860-1890.

Saturday, February 5th, 2011

In 1953, the model of the DNA molecule led to what has become regarded as the most famous scientific diagram of the 20th century. It had all started 93 years earlier in 1860, at a time when the tetravalency of carbon was only just established (by William Odling) and the concept of atoms as real entities was to remain controversial for another 45 years (for example Faraday, perhaps the most famous scientist alive in 1860 did not believe atoms were real). So the idea of constructing a molecular model from atoms as the basis for understanding chemical behaviour was perhaps bolder than we might think. It is shown below, part of a set built for August Wilhelm von Hofmann as part of the lectures he delivered at the Royal College of Chemistry in London (now Imperial College).

The original August Wilhelm von Hofmann molecular model

This grand-daddy of all molecular models does have some interesting features. The most obvious is that the carbon atom at the centre is square planar (tetrahedral carbon was still 14 years in the future). What HAS survived to the present day is the colour scheme used (black=carbon, white=hydrogen, and not shown here, red=oxygen, blue=nitrogen, green=chlorine).  But another noteworthy aspect is the relative size of the white hydrogen, which is larger than the black carbon. This deficiency was however very soon rectified in 1861 by Josef Loschmidt, who published  a famous pamphlet in which he set out his ideas for the structures of more than  270 molecules (many of which by the way were cyclic, and this some four years before Kekule’s dream!). An example (#239) is shown below, which gets the relative sizes of the atoms more or less correct (OK, chlorine is shown with rather an odd shape). To get an idea of how good Loschmidt’s model actually was, click on the diagram to load a modern model, and compare the two! Even more impressive, these diagrams pre-date van der Waals work on the finite sizes of atoms, first presented in 1873.

Loschmidt’s molecular models. Click for 3D

To conclude, I cannot resist showing one more model. Hermann Sachse believed cyclohexane could not be planar. To try to convince people, in 1890 he included a  “flat-packed” model in the pages of a journal article,  evidently believing that people would cut it out, and assemble it into a 3D shape.

Flat-packed molecular model of cyclohexane

You might have noticed a theme in the present blog of presenting 3D models for many of the molecules I discuss (include the Loschmidt one above). For the historians amongst you, I note our 1995 article in which we updated[1] Sachse’s origami with an article featuring how to incorporate interactive models into journals (still sadly only too rare). Perhaps a history of the molecular model, and how it has been presented over 150 years might be an interesting one to trace!

References

  1. O. Casher, G.K. Chandramohan, M.J. Hargreaves, C. Leach, P. Murray-Rust, H.S. Rzepa, R. Sayle, and B.J. Whitaker, "Hyperactive molecules and the World-Wide-Web information system", Journal of the Chemical Society, Perkin Transactions 2, pp. 7, 1995. https://doi.org/10.1039/p29950000007

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