Wednesday, March 27, 2013

Unsubmission with Endnote style

If you ever submit a manuscript to Molecular Physics, do not use the Endnote style as provided by Thomson-Reuters (!!!

Instead of placing references in brackets [1], the standard Endnote style does so in superscript2 (and without brackets). Moreover, it not only does so in the text, but also in the reference list.. :-(
(further minor issues: grouping together of references, author names as entered and not by initials)

Because of using this Style, and not checking if it was correct (my mistake!), today our manuscript [3] was "unsubmitted" so I could redo the references and re-submit. Normally, a journal would simply ask for a (technical) revision, but this was the first time a manuscript was "unsubmitted".. Curious.
PS. After doing the revision of the references, it was accepted within the hour. :-)

If you need a better version of the Endnote Style for Molecular Physics, I've put it on my website (note, use the Shift+Click to Save As..). Please note that I'm not claiming it's perfect yet; simply, it corrects the glitches mentioned above.
PS. Of course, this is probably not limited to Mol. Phys. only, but also other journal styles need to be checked before submission!!

[3] Ll. Armangué, M. Solà, M. Swart, "Nuclear magnetic resonance shieldings of water clusters: Is it possible to reach the complete basis set limit by extrapolation?", Mol. Phys. 2013, accepted for publication (Special Issue in honour of Prof. Trygve Helgaker)

Final data for reference 3:
Mol. Phys. 2013111, 1332-1344
DOI: 10.1080/00268976.2013.793832

Tuesday, March 19, 2013

Interviewed by high-school students: "I still feel that I’m only just starting, I’m still learning a lot”

As I already described in an earlier entry, in November I went to a secondary school in Vilablareix to give a talk about "I'm a Chemist.....", and was interviewed by three students. It was done in Catalan, which is available at the website of school. Here I have translated it into English:

Marcel Swart: " I still feel that I’m only just starting, I’m still learning a lot”

Professor Marcel Swart is a computational chemist originally from The Netherlands. Tuesday November 20 he came to our institute to talk to the bachelor students about chemistry, in celebration of the Science Week. We used this opportunity and interviewed him as well.

When did you become interested in Chemistry?
I think it was somewhere in the fourth year of secondary school. In The Netherlands primary school lasts six years, and afterwards the length of secondary school depends on the level. The lowest level is only four years, but me, in preparation for going to university, I had six years of secondary school. I did not like at all the professor we had in the third year, because she presented Chemistry in the most boring way possible. However, the professor we had from the fourth year onwards opened my eyes and made me interested in it.

Did you ever think in abandoning it at some point in time?
Sometimes I joke about (for example at my Chem Coach Carnival that when I was sick in 1993 (Pfeiffer’s disease) I doubted if wanted to continue with the Chemistry study. But this is just an anecdote, I don’t think I would have ever done it.

When did you come to Catalonia? Was it for some particular reason?
I came for the first time in 2000, and returned many times, first only for holidays, but in 2003 and 2005 I came for a month to the Univ. Girona (UdG) for a research project. I liked it here so much that I applied for a position at the Institució Catalana de Recerca i Estudis Avançats (ICREA), which was awarded in 2005. First it was a ICREA-Júnior position (for a maximum of five years), with which I started working in Girona in May 2006. In 2009 I applied for promotion to ICREA-Senior, a permanent position which fortunately was awarded as well.
To me Girona reminds me a lot of the city of Groningen, with a lively atmosphere of university life and a city center that is really beautiful. I also recognize the mentality of the people of Groningen, which is very similar to that of the people in Girona. The people are a bit closed, but at the same time open to new things, with a curiosity how things function in real life, and with an attitude to arrange things very efficiently.

Was it difficult to learn and understand the Catalan language?
Yes. Before coming here I already had level C of castellano (Spanish), and in the first two visits (of a month) I could notice directly when the people in the group at the UdG switched from castellano to català: I could not understand one syllable (written it was not so difficult though). I learned catalan through courses at the UdG, and the first year and a half I mixed things up completely: I started a sentence in catalan, after two words switched to castellano, and at the end it could have been catalan again. After two years I spoke Catalan correctly, but I had lost the ability to speak castellano. It took me two to three years more to be able to speak castellano again, and switch between the two (although it still costs me).

How would you define your professional career?
I still feel that I’m only just starting, that I’m still learning a lot. (Right now, for instance, I’m learning how to act as leader of a small group of scientists.) Therefore, I’m not quite sure how to define my professional career. I suppose that if I would have to summarize it in one sentence, I would have to say that I am a computational chemist who has worked in the field of (bio)chemistry and who has travelled all over the world (USA, Canada, México, Japan, Europa) with chemical curiosity.

We have read the biography on your website and we have noted that you have won several prizes during your professional career. Which ones? And which one are you most proud of?
That depends on what one considers prizes. In the USA there are also people who put at their curriculum things like having received a scholarship to go to a conference of for a short research visit. I don’t do that, and I only put the real prizes: the Young Scientist Excellence Award 2005 (by the ICCMSE 2005 conference); the position of ICREA-Júnior in 2005; having been selected as “Young Inorganic Chemist of the Next Generation” and contribute to a special edition of the Inorganica Chimica Acta journal (2007); the permanent position of ICREA Research Professor in 2009; and the MGMS Silver Jubilee Prize 2012. This last one is the one I value very highly and of which I am very proud: “Competition for the prize was very strong this year, but Dr Swart's submission was truly outstanding” (
I am also very very proud of the two young investigators that finished their PhD thesis with me and Miquel Solà, both of whom won the special prize of the Premi Extraordinari de Doctorat en Química of the UdG: Mireia Güell in 2009 and Sílvia Osuna in 2010.

Did you make any chemical discovery?
Several. For example, we discovered that the reactivity of fullerenes changes drastically when a metallic cluster is inside the fullerene cage, and moreover, this can not be predicted by just looking at the reactant. Furthermore, we also discovered that a vanadium metal atom can be bound within a supermolecular cage (super[6]phane), and when it does this leads to a really strong interaction with the cage.

Where do we find Chemistry: at the ground, in the human body, in food…?
Chemistry is everywhere! Our body contains different enzymes that catalyze different processes that we need to survive. For example, respiration, where oxygen is transformed in water and carbon dioxide; and vice versa: photosynthesis that transforms carbon dioxide in oxygen. These processes are chemical reactions without which we won’t be able to live. And also food, the taste of our meals, everything is Chemistry. At our tongue we have many different receptors that distinguish the molecules by their taste; for this distinction we use (bio)chemistry. And another thing is DNA. Its form is determined by the different chemical interactions (phosphate, sugar, bases; hydrogen bonds, π-π stacking). The viability of the transcription of DNA (>99.99%) is based on these interactions.

According to an abstract we read, within football there is Chemistry. How can that be?
A football is nothing more and nothing less than a molecule of C60 (buckminsterfullerene): both have the same shape, with pentagons separated by hexagons. Sixty carbon atoms is the minimum needed in order to be able to separate twelve pentagons totally; the C60 fullerene is very symmetric (it has icosahedral symmetry) and therefore the C60 fullerene has an almost round form (similarly to a football).
Because there is a void inside the fullerene cage, where one could place atoms or molecules. Again we can make the comparison with a football, since one has to inflate it with air in order to be able to use it.

We have read that you are an expert in computational and theoretical chemistry. What is that exactly?
In computational chemistry one deals with the description of chemical processes by calculations. We use molecular modeling of the molecules, of their reactions, their structures in 3D and the barriers that the molecules have to cross within a reaction. This information is almost impossible to obtain by experiments; there one can only obtain how large the barrier is, but not the 3D-structure that corresponds to it. In order to better explain it, I always make the comparison with a journey from Catalonia to France: one can pass through La Jonquera, through Andorra, through Portbou or over the Canigó. The fastest one from Girona is clearly by La Jonquera, but where exactly is the highest point of the journey? And more importantly, how long do you stay there? In a journey from Girona to Perpignan (one hour by car), you are only one second at the highest point; in experiments they only see the stable points (Girona, Perpignan), but not the highest point. Therefore, obtaining information about the 3D-structure at the highest point is almost impossible without theoretical chemistry.

During the day, how many times do you think about Chemistry?
As a scientific investigator, I do not have a fixed working schedule, we’re very bad at that. Therefore, normally we work much more than the 37.5 hours that we should be doing every week. It also means that I think a lot about Chemistry, both in working hours at the UdG as at home, when I reflect upon things to do (new projects), things done (papers, talks) and things to improve (current studies).

If you could choose again a career, would you choose another one?
No. Chemistry is the central science between Biology, Physics and Mathematics, and in my opinion the most important one. It is the science that gives the taste of food, that controls diseases (Alzheimer’s), that allows us to survive (respiration, photosynthesis), etc.

Did you think that the students at the INS Vilablareix were interested in the topic?
Yes, I clearly think so. I hope that I have been able to raise a little bit of interest for Chemistry, which should not be related always with toxicity, etc. We have to get rid of this chemophobia and assess it much more positively. In particular, I hope I have been able to help some student who was doubting whether to choose or discard studying Chemistry at the UdG, and hope I have been able to convince him or her that yes, he or she should do so.

Before retiring, in a future very far away, which goals would you have liked to been able to accomplish?
I hope that I can continue educating many students and see how they transform from insecure boys and girls into young investigators that know how to do a good job and know how to present themselves. That would make me very very proud.
And of course, like many scientists, I am ambitious. I want to publish in high impact journals (Angewandte Chemie, Nature Chemistry, Journal of the American Chemical Society, Science, Nature). But I also think that even more important than the journal where one publishes is the feeling of satisfaction of work well done. Knowing that you have done a tremendous job with a study, and that you have been able to transform it in a really interesting scientific paper, is much and much more important than the journal where it is published in. However, before I retire I want to have at least a paper in Nature (or, as alternative, in Science).

Arnau López, Marc Sendra, Olaia Brugada

Robin, Talent of the year?

Summer 2015 . My wife's brother came to visit us for holidays, together with their six kids and the grandparents, for the first time s...