ICCOSS XX: What’s in a name

In one of the sessions on ‘crystal engineering’, Guy Orpen told us about his hesitation to use this term: is it really engineering? The problem is reproducibility. If an engineer sets out to make a bicycle, and ends up with a submarine, he won’t be happy. Now if a scientist sets out to make a bicycle and finds that he made a submarine, he’ll be delighted. Yes, yes, it’s not quite a bicycle, but hey it is a means of transportation, only in water, right? And now having discovered this one by serendipity, we’ll make better submarines! In fact, the role of serendipity has been widely acknowledged throughout the conference.

We saw further work on co-crystals, and it shouldn’t come as a surprise that they are becoming so widely investigated. As I mentioned yesterday, one of the problems of drug molecules is poor solubility; and not all drug molecules are ionizable. In fact, according to Ashwini Nangia, 80% of the compounds in the R&D pipeline pose a solubility problem. This can be improved by inserting the active pharmaceutical ingredient (API) into a lattice with a second component – the trick is not to change to the API’s desired properties in the process. And besides pharmaceutical applications, co-crystallizing two compounds represents a chemical challenge in itself. What makes two molecules crystallize into one lattice rather than form two separate homo-crystals? Are co-crystals really that different from salts? Well, yes. As Christer Aakeroy explained, a cation cannot exist without an anion, whereas a molecule is happy on its own. And so he has set up a ‘molecular dating agency’ in his lab, and looks at various combinations to determine some rules on what affinities make molecules pair up in a co-crystal.

Another intriguing point about the crystalline solid state is polymorphism – salts, solvates, co-crystals and various combinations of these exist, and to complicate things further they all exist in different polymorphs. The form a compound will adopt depends on a lot of factors, and is hard to calculate, predict, or even understand. For example, Ram Jetti (from Matrix Laboratories, Hyderabad) showed us that for one drug molecule, temazepam, with 3 polymorphs reported in the literature, he was able to find no less than 10 new crystalline forms.

Add to this the fact that solids are a lot less inert than it first seems – this much was made clear in the solid-state reactivity sessions – and that surfaces and defects also play crucial roles in solid state reactivity, as we heard from William Jones (“sorry to take away from the perfection of single crystals”)… “one needs to be fearless to go into this mess” as Dario Braga puts it.

But I’m running out of time again, and will tell you tomorrow about some other exciting points that came up.

Anne

Anne Pichon (Associate Editor, Nature Chemistry)

ICCOSS XX: A colourful start

Hello from Bangalore! I  have to say I’m pretty excited to be here, both because of the conference programme and the location. This is my first time in India, and  although, admittedly, I have only been here 2 days, it is easy to see why Bangalore is called the ‘Garden City’ – magnificent trees and luxuriant vegetation everywhere . This is even more true when it comes to our conference venue, the Indian Institute of Science, which has enormous charm. Our Convener, Guru Row, told us yesterday in the opening remarks that the Institute is now becoming a College, and will be welcoming undergraduate students in just three weeks – now, this is a place I wouldn’t mind going to university!

Yesterday went on with a tightly packed schedule (this is, after all, a conference on the organic solid state – ahem) and a great line up of speakers. We heard a lot about molecular structure of solids, and how to approach their structure-property relationship. Properties, and in turn applications, are increasingly becoming the focus of investigations, yet at the same time to look at properties it is crucial to look at structures in fine details.

This is no easy task. As J Moorthy puts it, “small and simple molecules – especially ones that participate in hydrogen bonding, typically have large and complex crystal structures”. He illustrated crystal packing interactions through a picture from Gulliver’s Travels: “weak yet powerful”.

Talking about properties, a pretty sought after one is the presence of cavities for further host-guest chemistry. Tony Coleman shared with us his definition of porosity – very similar to Len Barbour‘s – “things go in, things go out”, of non-porosity “nothing comes in, nothing comes out”, and of multi-porosity “things go in, things come out a different way”. We also heard a lot about co-crystals, and how they’re very useful in pharmaceuticals – for example crystallising a drug with another molecule can improve its stability and solubility – but are proving trickier than they seemed. In a nutshell, their properties are unpredictable.

In any case, we’re seeing a lot of pretty, and colourful, X-ray structures. This isn’t surprising in a conference on this topic – but did you know that X-ray crystallography came out first of CNN’s ‘top 10 modern discoveries’? We heard this from Mike Zaworotko.

Unfortunately I don’t have time to tell you more about the sessions – although I wouldn’t risk writing too many details about the session on charge densities, a great way to investigate a structure in its finest details but that involves a lot equations – I’m on my way to another day looking just as busy and interesting.

Anne

Anne Pichon (Associate Editor, Nature Chemistry)

Nature Chemistry Impact Factor

For those of you who care about such things, Nature Chemistry now has an Impact Factor (IF). It is 17.9 (or, if you really want us to quote it to three decimal places, it’s 17.927). We realise that the IF is far from a perfect metric; really, we do. And we also appreciate that there are a range of opinions out there amongst our audience on the matter — some of you love the IF, some of you hate it. For those of you who aren’t about to click away in a rage or aren’t sick of IFs, I’m going to drill a little more deeply into our number and what it might mean, if anything.

The 2010 IFs (the ones just released in 2011) are calculated for any given journal by looking at the number of citations it received in 2010 to the articles it published in 2008 and 2009. This total number of citations is then divided by the total number of ‘citable items’ published in 2008 and 2009, and the number you get is the IF. So, it really boils down to the average number of times papers published in 2008 and 2009 get cited in 2010 – if that has any meaning! If a journal has a 2010 IF of 7.5, it means that — on average — each paper from 2008 and 2009 was cited 7.5 times in 2010.

Averaging brings with it some problems. Each paper might have been cited 7.5 times on average, but in reality, some papers will have been cited lots more than that and others might not have been cited at all. One (or a few) very highly cited papers can have a huge effect on the IF of a journal (see the wonderful example of Acta Cryst. A from last year!).

Another bone of contention for some is the use of ‘citable items’. Not everything that a journal publishes counts as a ‘citable item’ — typically only research articles and reviews do. For example, in Nature Chemistry, ‘front-half’ material such as Editorials, Book Reviews, Commentaries and News & Views articles are not counted as citable items and so do not add to the denominator in the IF calculation. Any citations that they do receive, however, are counted in the numerator. Note that this is not a special exception made for Nature Chemistry or Nature journals in general, this type of citable-item categorization is made for all journals.

Also, the sources of the exact numbers used to calculate the IFs are not easy to find. Sure, you can get a total of citations from Web of Science for an individual item or for a given year’s worth of content in a journal, but that does not usually include all of the citations used in the IF calculation. See this post at The Scholarly Kitchen for more details on how impact factors are calculated. Bearing this in mind, however, let’s take a closer look at Nature Chemistry content from 2009.

Nature Chemistry published 82 citable items in 2009; that was 17 review-type articles (Reviews & Perspectives) and 65 primary research papers. Of course we also published many other pieces of content that are not counted as citable items (as described above). Based on our rough calculations, it appears that just under 10% of our total citations in 2010 to these 2009 pieces of content were to these non-counted items, just over 27% of the citations were to the review-type articles and just over 63% were to the research articles.

And if you’re interested, the top five 2009 papers based on 2010 citations are (subscription required to access all of the articles apart from the third on the list, which was in our first ever issue that is currently available for free):

REVIEW: Nanostructured functional materials prepared by atom transfer radical polymerization (77 citations in 2010)

New insights into the structure and reduction of graphite oxide (60)

REVIEW: Towards the computational design of solid catalysts (52)

Bimetallic Pd(III) complexes in palladium-catalysed carbon–heteroatom bond formation (51)

Amyloid-β protein oligomerization and the importance of tetramers and dodecamers in the aetiology of Alzheimer’s disease (37)

There don’t appear to be any obvious trends in terms of articles in one particular subject area (physical, organic, inorganic, bio, analytical) consistently receiving more citations than any other. And there seems to be no correlation between how much an article is cited and how many page views it has received. We do note that what could be considered to be more traditional ‘organic’ papers typically get more page views than other sub-disciplines, but this is not reflected by an increased citation rate.

A few quick numbers for you about the citations our 2009 content received in 2010: of the 82 citable items, the most cited paper received 77 citations and the least cited paper received 1 citation. The other 80 articles fell somewhere in the middle. The top 40 of these had a citation count of 11 or more and the lower 40 each had somewhere from 2 to 10 citations — hence the median number of cites was 10.5. The mean, on the other hand, is 14.5 if you’re interested. And now compare those numbers to the actual IF, which is 17.9.

So, what does this tell us? I’m not really sure. Other than perhaps IF calculations are a strange and mysterious thing.

Stuart

Stuart Cantrill (Chief Editor, Nature Chemistry)

Blogroll: MicKIE mouse

[As mentioned in this post, we’re posting the monthly blogroll column here on the Sceptical Chymist. This is July’s article]

“What would happen, hypothetically, if a baby mouse could grow up eating only deuterated food and water? Could you make an unusually heavy mouse?” asked Sharon Neufeldt in an entertaining post on her ‘I can has science?’ blog. Assuming that the elemental make-up of a mouse is pretty similar to that of a human, Neufeldt estimates it would be 10% heavier — but not “a fat mouse, just a more dense mouse.” Of course, those readers familiar with the kinetic isotope effect and cellular function will realize that the poor, if hypothetical, heavy mouse would not last long with all its hydrogen atoms swapped for deuterium. As Neufeldt discusses, “a carbon-deuterium bond can be 6.5 times slower to break than a carbon-hydrogen bond”, which could have pretty drastic consequences to your mouse “cells won’t be able to function properly and [the mouse] will start to die.”

But what about enriching the mouse with 13C? The smaller kinetic isotope effect might help the mouse’s health, but the weight gain wouldn’t be anywhere near as striking at a mere 1.5%. Neufeldt also points out another flaw in her plan: it would cost over $600 a day to feed her mouse on commercially available 13C-labelled glucose. At that price, she said she might as well treat the mouse to three meals a day at her favourite French restaurant.

One of the most positive and publicly visible uses of chemistry has to be in art conservation and restoration so it’s great to see that Chemical & Engineering News’ Sarah Everts has launched a new blog on this topic, called Artful Science. Posts have so far covered topics as different as the chemistry behind fading blue pigments, the isotope techniques used to discover whether the influx of South American silver really did cause the ‘Price Revolution’, and using DNA from ancient Maori cloaks to track feather trade routes.

Speaking Frankly: Encounters of the scientific kind

Frank Leibfarth is a graduate student trying to make his way through the academic maze. Find him contributing to the Sceptical Chymist or continue the conversation on Twitter @Frank_Leibfarth.


I am finishing the third year of graduate school and finally starting to feel like a real scientist. The feeling of inferiority that comes with being a young researcher is still hiding just under the façade I’ve fashioned to hide it, but I’m slowly learning that I cannot and should not know everything, that no one does, and that maybe that’s OK. So now I’m blogging, hoping that my musings on the philosophy of science, how we conduct it, communicate it, and interface it with society will entertain, enrage, or otherwise interest you. Either way, I hope the topics I bring up here will only be the start of vibrant discussions, which I encourage us to continue through the comment thread or other social-media outlets.

With that, I wanted to discuss the role of creativity in science and how our current education system helps/hinders it. Inspired by a recent conference I attended, where revolutionary ideas and those pursuing them shone brightly, I pose the question: Can you learn (or teach) creativity? I feel both humility and excitement to know that my generation will soon be expected to carry the torch of scientific innovation… but what will we create and how do we go about doing it? ‘Creative’ is a verb usually reserved for artists and musicians, but was Linus Pauling creative in the same way as Bob Dylan?

To push the frontiers of knowledge, one must first understand their boundaries. Graduate education seems adept at this: an immersive education style after which you surface with a lot of knowledge but not much direction in terms of applying it. There is a fundamental disconnect, however, with the consumption and creation of knowledge, and I contend that our education system provides no mechanism to teach us how to make that leap. The best advisors foster creativity in their students, but should we rely solely on their abilities (after all, there is also no mechanism to ‘teach’ one how to be an academic, but let’s save that for another post). Creating new products, ideas, and understanding is the pinnacle of scientific achievement, and one of the strongest reason governments have for funding academic research.

Like many things, I suppose there is no ‘correct’ answer. Personally, I am trying to make this transition, trying to emulate the creativity of my scientific elders, and it is not easy. At the same time, I do not think anyone can magically teach me to create. I’ve always found that if I keep banging my head against a wall, eventually the bricks will start to crack. Let’s hope for the best. In the mean time, does anyone have any suggestions on fostering this elusive creativity from their own experience?

Reactions – Shuli You

Shuli You is a Professor of Organic Chemistry in the State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, and works on methodology development, total synthesis, and medicinal chemistry.

1. What made you want to be a chemist?

I was good at chemistry in high school and then chose chemistry as major in university. Now I really enjoy being a chemist by developing new tools that allow the facile access to novel molecules with interests.

2. If you weren’t a chemist and could do any other job, what would it be – and why?

In reality, if I did not get the chance to study in the college, I would be a farmer now carrying on my parents’ job. However, if I can choose, I would like to be an editor for a scientific journal. In that way, I want to try my best to make sure that every submission is fairly treated.

3. What are you working on now, and where do you hope it will lead?

We are working on the new methodology development based on C–H bond direct functionalization and asymmetric dearomatization. I hope that eventually our methodologies can be used by every chemist to produce the molecules they are interested in.

4. Which historical figure would you most like to have dinner with – and why?

Fredrick G. Banting, who won the 1923 Nobel Prize for his discovery of insulin. I was so intrigued by the story on the discovery of insulin, and I have so many questions to ask.

5. When was the last time you did an experiment in the lab – and what was it?

This reminds that I have not done lab work for quite a while. Last time I did something on asymmetric Friedel-Crafts reaction was about one year ago. Now I really miss the very beginning of my independent career during when I had a lot of time to do experiments.

6. If exiled on a desert island, what one book and one music album would you take with you?

It is definitely not a book on chemistry. It is a hard choice, and I probably will take “The Da Vinci Code” by Dan Brown and then a music collection of late pop singer Teresa Teng.

7. Which chemist would you like to see interviewed on Reactions – and why?

Professor Lixin Dai from our department. Professor Dai is a noble man, great chemist, and a person with unique character.

Elemental memories

In order to keep our element writing competition to the forefront in everyone’s minds, I thought I’d re-heat an old post – my first post on The Sceptical Chymist, no less! In that post I look back into the depths of time, at my first ever science lesson in school. Magnesium featured heavily, which is why I’m re-heating the post. The element has already been covered in the In Your Element series ($/£), by organometallic chemist Paul Knochel.

I still vividly remember my first science lesson back when I was a 9 year old, over 20 years ago. The school buildings were quite new (10 or so years old at the time), so the little lab was pretty well kitted out. But what the teacher, Mr Challinor, really tried to instil in us during that first lesson was the fact that science wasn’t just about Bunsen burners or any of the other complicated apparatus we were all seeing for the first time. A scientist’s most important tools, he said, are your eyes, to observe what was happening.

One of the first experiments I remember him showing us was incredibly simple, but also incredibly powerful. He told us about how atoms make up everything around us, and then about how burning something was essentially just adding oxygen to it. He probably briefly mentioned the phlogiston theory – which, like Phil Ball, I don’t think is quite deserving of the laughing and pointing we give it nowadays. After all, I remember during that first lesson thinking that most things end up much smaller after you’ve burnt them – think about how much smaller ashes are than a pile of sticks, for example. So a phlogiston-type theory fits a lot of day-to-day experiences.

In order to prove that things really do get heavier once you’ve burnt them, he carefully weighed some magnesium foil in a crucible, then set fire to it. After the bright white flame died away, he re-weighed the crucible and guess what? The weight had indeed increased.

As well as teaching us about atoms and combustion, something else he did in that experiment also stands out – and it’s probably a more important lesson than correcting what people thought 300 years ago. He got one of the class to watch over his shoulder as he did the weighing (we couldn’t all fit around the balance). This was just to show that he wasn’t making it all up, that we shouldn’t believe him ‘just because he said so’, but to show what he said had happened actually did. That’s a pretty important first lesson in science for anyone, but especially for a 9 year old: don’t just take someone’s word for it, see for yourself.

Now, magnesium was an important part of the experiment, but not the point of the experiment itself. But would I have remembered it as well without that incandescent burning whiteness? I guess I’ll never know, but the whole experience also neatly fits with a recent blogpost at the Guardian, by a teacher and filmmaker who suggests that doing experiments or practicals for the sake of it isn’t the best use of class time. Before we all leap to the defence of our favourite childhood memories, it’s worth noting that the author tries to make it clear that he’s not suggesting ditching all experiments, just making better use of fewer. See what you think.

Neil

Neil Withers (Associate Editor, Nature Chemistry)

Reactions – Christopher O’Brien

Christopher O’Brien is in the School of Chemical Sciences at Dublin City University and works on the development of robust catalytic synthetic methodology and target oriented synthesis.

1. What made you want to be a chemist?

I always liked chemistry I was taken aback at an early age by the beauty of it. As to what made me do what I do and the way I do it, that stems from a conversation I had with my grandmother from my father’s side. I think it was at the start of my undergraduate degree at UMIST, or may be slightly earlier, that my granddad was diagnosed with early stage Alzheimer’s. I can’t remember whether my conversation with my grandmother was before or after my granddad forgot who I was. The doctors’ were beating around the bush giving the usual false hope. So I told my grandmother frankly what was going to happen and that she should say her goodbyes as sooner or later he would not know who she was. Alzheimer’s can progress rapidly and in the case of my granddad in the space of one year he had forgotten who I was. To illustrate this during my degree I took a year out to work in Europe for Philips. When I left he knew who I was when I returned he did not. Overtime he forgot most people. Interestingly, just before an Alzheimer’s suffer dies he or she can have one moment of clarity. Fortunately, it was during this time that Alice was able to say goodbye to Len.

So now I am driven to develop synthetic methodology so that medicinal chemists etc. have the tools they need. I hope in the future no-one has to have a conversation with their grandmother like I did or witness the slow disintegration of a loved one.

2. If you weren’t a chemist and could do any other job, what would it be – and why?

I would be a patent lawyer or a computer programmer. I remember in my early teens spending hours coding a program on an Acorn Electron. I still remember fixing a sprite that was not behaving. I also studied some patent law at university and it has come in very useful.

3. What are you working on now, and where do you hope it will lead?

Now I am working on selective catalytic processes that I hope to integrate into larger multi-catalytic self-assembling arrays. My group also tackles target oriented synthesis of compounds that target certain biological problems.

4. Which historical figure would you most like to have dinner with – and why?

Even though I think you should learn from history or you will repeat it I don’t believe in idolising people. So I have no interest in meeting any historical figures. Instead I would like to have dinner with my Granddads as I never had the chance to speak to them before they died or lost their memory due to Alzheimer’s disease.

5. When was the last time you did an experiment in the lab – and what was it?

The last experiment I did in the lab was a few weeks ago and it was the generation of a special base for the catalytic Wittig reaction. I try to remain in the lab as much as possible.

6. If exiled on a desert island, what one book and one music album would you take with you?

I’d take a copy of the SAS survival handbook. I don’t plan on staying on the desert island for long I have things to do. As for music may be the theme music to The Great Escape for motivational purposes.

7. Which chemist would you like to see interviewed on Reactions – and why?

I would like to see Ryan Gilmour at ETH Zurich interviewed as I think he is doing some interesting chemistry.

Element of the month: Cobalt close-up

As we announced in this post, we’ll be posting here some anecdotes or characteristics of the element featured each month in the ‘in your element’ section of the journal.

In our June issue, David Lindsay from the University of Reading and William Kerr from the University of Strathclyde write about cobalt — an element thought to be named after evil sprites (kobold in German) — check out the article to find out why! [subscription required]

But cobalt later went on to show its good side. It is an essential trace element in the human body, found in a group of co-enzymes called cobalamins. Vitamin B12, a cobalamin, features the only naturally occurring organometallic bond that cobalt engages in: a cobalt–carbon bond. B12 is pretty crucial for life as it plays a role in the formation of blood as well as the function of the brain and nervous sytem. Oh, and according to Wikipedia, it also treats cyanide poisoning — a use that is hopefully less in demand.

Find out a variety of catalytic characteristics of organocobalt complexes from Lindsay and Kerr’s essay — including a serendipitous discovery that has led to the well-known Pauson–Khand reaction. That being said, Pauson apparently refers to it as the Khand reaction, however. I wonder how Khand calls it?

Anne

Anne Pichon (Associate Editor, Nature Chemistry)

Reactions – Sota Sato

Sota Sato is from the Department of Applied Chemistry, School of Engineering in The University of Tokyo, and works on coordination chemistry based on organic synthesis to produce self-assembled huge, well-defined molecules and to reveal the magnetic properties of discrete molecules for application in NMR analysis.

1. What made you want to be a chemist?

Definitely, there were many teachers in my life who guided me to become a chemist. As an elementary school child, I was fascinated by butterflies for their diversity of color and wing patterns and for the mysterious change in figure from a grub to an imago. My uncle, Mitsuo Jinkubo, and father, Kazumune Sato, taught me about the fascinating living world and related concerns of the natural environment. In junior high school I found that important things hidden behind textbooks can be accessed through chemical experiments, and finally my high school teacher and my first co-author, Toyokazu Usui, taught me how to become a chemist with a letter article: in a sense, I became a chemist at that time.

2. If you weren’t a chemist and could do any other job, what would it be – and why?

I wanted to be involved in the professional area where overwhelming personal techniques play a central role. My grandfather, Saburo Sato, who is now 101 years old and an extremely dexterous artisan of scientific quartz glass, impressed me and I thought about becoming a craftsman. Unfortunately however, I found that I am not good with my fingers. Accordingly I was interested in a profession backstage in the theater, where massive scale lighting systems and sound equipment are operated in a tense atmosphere, because stage business is always in progress in front of an audience. I imagined that to operate these complex systems at will based on a wide and deep knowledge of them would bring me satisfaction, producing dream-like scenes.

3. What are you working on now, and where do you hope it will lead?

I am working on synthetic chemistry, to develop a methodology to synthesize the world’s largest molecule and to find a new application based on molecular design. Molecules with a new class of structures often lead to a practical usage; rather I hope the chemistry will entice the scientific playful spirit of both professional chemists and other interested people.

4. Which historical figure would you most like to have dinner with – and why?

Tenshin Okakura (1863-1913), who was a pioneer of aesthetics in the Japanese Meiji period. Against the established Japanese painting circle, he struggled to produce a new paradigm and also introduced Japanese arts and ways of thinking to foreign countries. I want to know how he thought in turbulent frontier and how he made the decision to cut open a novel field in art. I am very sad to hear about the loss of Rokkakudo in Kita-ibaraki City, the historical small architecture where Okakura spent much time for contemplation, which was lost in a huge earthquake and resulting tsunami in Mar. 2011. But it is also really encouraging to know that funding and intense effort are going towards rebuild it as part of restoration after the disaster.

5. When was the last time you did an experiment in the lab – and what was it?

After getting my current job as chemist several years ago, I have not had a chance to perform synthetic experiments by myself. I do fragmented but difficult pieces of experiments supporting my students. I am sure that the style is efficient, but I’m not sure that I am satisfied as much as I was as a doctoral course student…. My tiny synthetic chemistry in a flask in my hands still seems shining for me even though the final solution always gets brown with unknown trace amounts of chemicals.

6. If exiled on a desert island, what one book and one music album would you take with you?

Once I traveled alone to isolated islands in Japan and found that I did not need books or music. I enjoyed watching the unusual scenery day and night and listening to the natural music, such as the sound of the wind, waves, or animals. If I was in such a precious situation, which I have not been recently, I would not need artificial works, but I dare to pick my favorite piano music “Suite Bergamasque” by Claude Debussy in case of a completely boring island.

7. Which chemist would you like to see interviewed on Reactions – and why?

Prof. Dr. Jeffrey M. Stryker, an organometallic and organic chemist in the University of Alberta. I spent a couple of months as a visiting student in his laboratory during my doctoral course. He is a very strict, intelligent chemist, and I like his warm personality with an open mind.