Wednesday, December 19, 2012

Spin states: a real problem (?)

From 18 to 21 September 2012 took place the CECAM/ESF Workshop on Spin states in biochemistry and inorganic chemistry at the Z-Cam center in Zaragoza (Spain). This meeting joined experimentalists and theoreticians working in the field, who gave wonderful presentations of their work, but also led to lively discussions of not only successes, but also drawbacks, challenges and state-of-the-art studies.

Participants of the workshop
On 18th December 2012 the workshop appeared in Nature Chemistry, within the News & Views section (written by Miquel Costas and Jeremy Harvey, thanks!!):

"Spin states: Discussion of an open problem", M. Costas, J.N. Harvey, Nature Chem. 2013, 5, 7-9

The workshop has now also been highlighted in RSEQ's Anales de Química (Noticias, p. 70). (Update3: Link address restored to new location)

More pictures of the workshop can be found in an earlier post.

The workshop is also mentioned in a Perspective in International Journal of Quantum Chemistry that I've been asked to write (and add a Cover for it):

M. Swart
"Spin states of (bio)inorganic systems: successes and pitfalls"
Int. J. Quant. Chem. Perspective 2013113, 2-7

Cover for Perspective in International Journal of Quantum Chemistry
Both the workshop and the Perspective are also featuring in an interview that ChemistryViews made with me:
"The Challenges of Accounting for Spin-States of Molecules"

The IJQC Perspective made it to the Editor's Choice for 2012

Wednesday, October 24, 2012

My Chem Coach Carnival

This week on Twitter there is the #ChemCoach carnival, as organized by @SeeArrOh in which my hand was forced by doing a retweet... (but forced in a nice way). So now I'm obliged to contribute to the carnival.. (day 1, day 2, day3..)

picture by M.P. Johansson
Your current job. I'm an ICREA Research Professor at the University of Girona. ICREA stands for Institució Catalana de Recerca i Estudis Avançats, i.e. the Catalan research institute, which does not have its own facilities but places the Research Professors within the Catalan universities. Basically it means that ICREA hires excellent investigators to do breathtaking research, performed within the universities (or other research centers). 
I'm a Chemist.... working in the Institute of Quantum Chemistry and Catalysis (IQCC), and work on different things: method development, DNA, transition-metal complexes, iron proteins, fullerenes, supramolecular cages.

What you do in a standard "work day." I'm a computational chemist, so basically I spend lot of time in front of the screen. But also there are administrative meetings, scientific meetings, etc. that I have to attend, so there is not much chance of getting RSI. And then as well, there are (undergrad/Master/PhD) students and postdocs to supervise, so I'm lucky if I can sit two to three hours uninterrupted in front of the screen. Fortunately, my group is not so big yet so I do still have time to do so.
But let me get me back to the question, what it is that I do in a standard "work day". Being a computational chemist, I spend lots of hours looking at numbers. I guess I inherited that from my father who was accountant at a local printing house. These numbers give for instance the Cartesian coordinates (x,y,z) of atoms within a particular molecule, or reaction barriers, or vibrational frequencies.
A Fe-complex that we recently studied
Apart from the numbers, I also play around a lot with visualizing the results. This is much more insightful, because as the saying goes, "one picture is worth a thousand words". Again, I guess I inherited this from my father who was very keen on graphics.

What kind of schooling / training / experience helped you get there? I went to the best university (Groningen) in The Netherlands for chemistry at that time. Right now, with the crisis and the budget cuts, I'm not sure if they still are in the same position, but at that time they were first-class in many chemistry disciplines (e.g. Feringa, Berendsen). According to THE it is still in the top100 universities in the world, so I guess they are still going strong. The theoretical chemistry group at that time was very good (Nieuwpoort, Broer, van Duijnen, Snijders), and I learned most of what I know now in that period. Apart from the education "in-house", I was also privileged to be able to go to the two Quantum Chemistry summer schools (Ry, Denmark; ESQC, Tjornarp, Sweden), an annual "summer" school (in December!) in Belgium (Han-sur-Lesse), and had travel funding with my PhD project that allowed me to visit 2-3 international conferences each year.
After my PhD I went for a postdoc in a completely new area (iron chemistry), and switched after two years to again another subject (DNA/RNA, SN2 reactions). I learned a lot of project management in my postdocs, because the first one was really tough (lousy equipment) and the second one an immediate success.
Chocolate cake

How does chemistry inform your work? Chemistry is all around us, inside us, going through us, so I can't actually separate Chemistry from myself or my work. It is what Harry Gray told last year at the ICBIC meeting in Vancouver: "the two most important reactions in the world are photosynthesis and respiration", which are both in the field of bioinorganic chemistry (I was there myself, and so was Nature Chemistry). But there is more to it than that because the people in Girona have a craving for chocolate (I know that there are many more people that like chocolate, but here they are addicted to it). Understanding why that is, and why people like chocolate is again simply Chemistry. We have taste receptors in our body that screen everything that we drink, eat, inhale, and one of them is called the Sweet Taste Receptor (hT1R2/hT1R3). These receptors are so-called G-Protein Coupled Receptors, which have become quite en vogue since a few weeks.

Finally, a unique, interesting, or funny anecdote about your career. During my study I became ill (Infectious mononucleosis, or in Dutch: Ziekte van Pfeiffer), so was ordered to bed for two-three months for complete and full rest. I was that tired that I did not want to do study anymore and was ready to quit*. At the final stages, my girlfriend (now wife) gave me the material for one course (Reaction Mechanisms, Carey/Sundberg), for which I might just be able to be in time for the exam. This material revived my spirits, I recuperated promptly and became Chemistry workaholic ever since.

*I doubt that I would have quit my study, but at least Carey and Sundberg helped my recuperation tremendously.

Thursday, September 20, 2012

CECAM/ESF Workshop on Spin states in biochemistry and inorganic chemistry

Here are more pictures by Mikael Johansson:

The conference picture is available at the CECAM website:

This week I'm organizing a CECAM/ESF workshop in Zaragoza at the Z-Cam node of CECAM, with many good talks, good discussions and nice people. Here are some pictures:

Friday, August 17, 2012

My longest project so far

Just today we were told that a paper of us has appeared online:
Chem. Eur. J. 2012, 18, 12372-12387
(UPDATE: it has been published with page numbers at 24-9-2012)

It is a collaboration with the groups of Prof. Wijmenga (Nijmegen, NL), Prof. Bickelhaupt (Amsterdam, NL), Sychrovsky (Prague, CZ) and Prof. Sponer (Brno, CZ), which started in 2006 when I was still in Amsterdam in the group of Matthias Bickelhaupt.

A few years before we had published a Communication in the Journal of the American Chemical Society:
J. Am. Chem. Soc. 2004, 126, 16718-16719
that dealt with the calculation of NMR chemical shifts of DNA base pairs. As a result, Sybren Wijmenga contacted us if we could do something for the calculation of NMR chemical shifts as a function of the glycosidic torsion angle. This angle determines how the DNA base rotates over the sugar moiety, as shown in the following figure:

Rotation of the DNA base over the sugar moiety
This rotation has a profound effect on the NMR chemical shifts, as shown in the paper, but exactly how was not clear from experiments. Moreover, there were NMR signals that were not clearly understood, and theory might help here. It took some time to get all correctly (in fact, approximately six years!!), but it was worth the wait. Have a look...

Sunday, August 12, 2012

Preparations for CECAM workshop on Spin states

In a few weeks time, I'll be organizing a CECAM workshop on "Spin states in biochemistry and inorganic chemistry", with an impressive line-up of speakers: Larry Que, Jeremy Harvey, Per Siegbahn, John Perdew, Kara Bren, Martin Kaupp, Ulf Ryde, Eckard Münck, Kristine Pierloot, Miquel Costas, Bob Scheidt, Markus Reiher, etc. etc. See:
(and note, it will be highlighted in Nature Chemistry)

I have prepared a Google Maps with the most important places for the workshop, and interesting things to visit in Zaragoza:

The hotel for the participants is the *****-star hotel Palafox in the city center:
The workshop will be held at the Z-Cam center (Calle Mariano Esquillor s/n, Edificio I+D, 50018 Zaragoza), and transportation will be arranged for the participants from the hotel to Z-Cam in the morning and evening.

There is a fast train connecting Barcelona and Zaragoza, for which it is best to reserve a place through the online system of Renfe (Spanish train company):
There is a train connecting Barcelona Airport with Sants station from which the fast train (AVE) leaves:
Airport - Sants train schedule (select Aeroport as Departure and Barcelona-Sants as Destination)

Right now we're working on the last preparations, and I was looking back for some pictures I took on a previous visit. Here they are:

Monday, August 6, 2012

This is what a scientist looks like

A few months ago, I saw on Twitter a fascinating page to show that scientists are not nerds, geeks, un-social people, but instead are normal people:

And of course, I decided to send a picture of myself to be added. It took a while (some months), but this weekend my entry was present:
(update: I sent the picture on March 17 and was thus posted on August 6)

The picture is from somewhere in France, and shows me enjoying some paintings.

A thing I found very surprising is the large amount of belly dancers on these pages; especially when I saw it for the first time, something like half of all entries were with belly dancers. Searching quickly, I found only one:
Belly Dancing Scientists

Monday, June 11, 2012

MGMS Silver Jubilee Prize 2012

Some days ago I received a very very nice e-mail message, starting with:

"I am pleased to inform you that the MGMS prize committee has decided to award the 2012 Silver Jubilee prize to you."

And today it has been announced officially at the MGMS (Molecular Graphics and Modelling Society) web-site:
(and on

I am very honored to have received this prize!!

a picture of the prize

Saturday, June 9, 2012

DFT Popularity Poll 2012

For the third time, we are holding an (annual) online popularity poll of density functionals.
The form for participation can be found at:

More info about the poll, the reasons for holding it, and the news-item for last year's poll can be found at

Enjoy, give your preferences, and come back in October when we will have the results of this year's poll!!!

Thursday, January 26, 2012

Results for the #DFT2011 popularity poll: and the winner is...

Last year we held the second edition of the annual popularity poll for density functionals, between June 1st and October 1st; this week we have published the news-item about the poll results, and constructed the PACO2011 functional from these.

For the second year in a row, the winner was PBE0, and not the widely used B3LYP (which came second). The news-item shows all the data, in a nice format.

And just a curiosity: the news-item has been downloaded more than 1000 times within the first two days.

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...