Monthly Archives: July 2009

Are theoretical/computational chemists real chemists?


Although classifications and rankings do not define the range or scope of work a person/group can do, they are usually popular to look at, unfortunately these views are sometimes misleading in the decision making process, e.g. funding. How expensive is in average our science compared to that of say organic chemists? It indeed depends on the computer facilities at hand and how much are they used, as well as the kind of synthesis performed by this hypothetical org. chem.

The line between theoretical and computational is becoming diffuse, and the branches are increasing (chemoinformatics, chemometrics, bioinformatics and so on.) But since they are somewhat intangible, the results of our calculations seem to often fall into the black box category and hence dismissed or taken with reserves.

There is no doubt that a lot of companies are making a lot of money by selling all kinds of software related to chemistry, from electronic structure calculations to molecular sorting and recognition as well as data analysis. It cannot be denied the enormous amount of scientific effort put in develop such products. Also, pharmaceutical companies make a full use of computational methods as a way to find new drugs in shorter times.

Not too long ago, in the Computational Chemistry List, there was a discussion about whether or not computational chemists were ‘arm chair scientists’ and I’ve been meaning to post on the subject since then. Are we arm chair scientist? maybe so. Is that a bad thing? Of course not! My father is a retired mathematician and I know for a fact that he seldom left his desk, let alone his office. The idea of being an ‘arm chair scientist’ was just obvious for him and there was no need to ever question it. A friend of mine from Mexico told me that there are very few experimental physicists there because for years it was cheaper to make theoretical physics than experimental. I think nowadays students are encouraged to undertake experimental physics in order to balance the ratio.

From my point of view computational chemists can be divided into the following three major categories:

1) Those who develop new theories regarding the electronic structure of molecules as well as new models for modeling its behavior and properties.

2) Those who develop new codes for solving long standing problems. Within this branch we can find also those who develop new basis sets, density functionals, pseudopotentials, semi-empirical methods, force fields, etc.

3) Those (such as myself) who use the products of the previous two branches and apply them into solving problems of chemical interest.

We certainly don’t tackle chemistry the same way our experimentalist colleagues but then again they don’t tackle chemistry the way they used to a hundred years ago. I remember that prof. Raymundo Cea-Olivares at UNAM used to say that chemistry has become ephemeral, since synthesis lasts a day and then the job turns into physics when acquiring and analyzing spectra in order to assess the compound’s identity.

One thing I’ve noticed is that apparently it has become trendy for every research group to develop its own code and those are not good news for people with good knowledge of theoretical chemistry as well as good chemical insight but with poor programming skills.

Just pouring my opinions on the subject…

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Inorganic Chemistry paper


A new paper is coming out! These are always good news for someone whose productivity is evaluated by the number of his/her publications, and in my case the pleasure is double. It turns out that despite the fact a scientist is continuously working, there isn’t always the possibility of having results put “out there”. Back in Mexico we have the “National Researchers System” in which the National Council for Science and Technology encourages us to keep on working by providing economical stimuli and evaluating our productivity by, yes, the number of papers published each year. For three years I worked for a private research center in which fundamental science was tackled as far as it was economically possible and cost effective. Practically all of the work carried out there was confidential since the company it belonged to is leader in its market, not only in Mexico but in Latin America and southern USA!  At this facility some papers were published from time to time (most of them came from research in molecular modeling) but not without struggle against the administrators. We can thank for most of the struggle (and the papers!) to Dr. Armando Gama-Goicochea, a great physicist as well as a great friend of mine.

Anyway, the bottom line here is that I’m excited about having a new paper coming out again, even if I’m nowhere close to being first author. This three year paper fastening seems to be over and let us hope it’s only the first of various now that I’m holding a postdoc position here in Romania.

In this paper we tackled the bonding properties of some Aluminum complexes with three chalcogeno triazoles. The electrostatic potential mapped onto a density surface of one of those compounds is currently shown in the header of this blog, btw. We concluded that the bonding in such compounds is mainly covalent as opposed to the more conventional electrostatic notion prevailing for such hard atoms. In order to get this information we resorted to Natural Bonding Analysis calculations with the RHF method and somewhat large basis sets in order to get a full description of the electronic density.

I very much like these systems in which several bonding possibilities occur. The fact that nature is chosing one out of many has always a reason which can be assessed by our models and may serve us to learn how to modify it’s behaviour.

Coordination Diversity of Aluminum Centers Molded by Triazole Based Chalcogen Ligands

Inorg. Chem., 2009, 48 (13), pp 5874–5883

Jocelyn Alcántara-García, Vojtech Jancik, Joaquín Barroso, Sandra Hidalgo-Bonilla, Raymundo Cea-Olivares, Rubén A. Toscano and Mónica Moya-Cabrera

Moving out


As part of the research project I’m working on here at the Babes-Bolyai University in Romania, I must now pay a visit to prof. Sandor Kunsagi-Mate in Pecs, Hungary. I’ve met prof. Kunsagi in several occasions before and I’m looking forward to working with him in his research team, although unfortunately he will have to leave next week to the far east to check on some of his multiple collaborations around the world. I’m also looking forward to use their computer facilities which I think are physically located in Budapest. Living near Budapest is something I’m also very much excited about since it’s one of my favorite cities in the world.
I haven’t read much about the University I’m going to, other than it’s the oldest university in Hungary dating back from the days in which King Matei Corvin ruled the Hungarian Empire. King Mathias was born in Cluj-Napoca, by the way. That’s a good 600 years now!
It’s always exciting to start anew in a completely different environment with a new research team. This time my chances of learning a bit of the language are pretty slim. In fact I’ve heard a lot of Hungarian here in Cluj and I haven’t learned too much, other than some isolated words.
Despite all the problems we face on a daily basis here at UBB I will miss Romania while I’m gone; it could be for a month or two. Romania has crawled under my skin, so even if I -often- complain about their ways and customs, it is now a part of me and I think I’m starting to feel homesick.
Pecs will be a nice adventure, I’m sure.

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