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Toga Party (No, not that kind) at UNAM 


Last Monday the School of Chemistry at the National Autonomous University of Mexico celebrated 50 years of their modern graduate studies program; as part of the celebrations a formal investiture ceremony for those of us who got our PhD’s after 1990 was organized.

It was a great opportunity to reconect with old friends and teachers, I even got to meet my old high school chemistry teacher, Dr. Salvador Sánchez who in no little way helped me decide to follow chemistry as a career choice, and Dr. Raymundo Cea who was my first thesis director in the first years of this century. The University Rector, Dr. José Narro, gave a speech on the challenges of chemistry in the upcoming years, and Dr. Helgi Jung-Cook spoke about the challenges a PhD student faces and how much rewarding is to finish. Much is yet to be done for the advancement of science in the world and even more in Latin America, but even so UNAM is doing a great effort of keeping a strong base of scientists available for all branches of social development by continuosly supplying the much needed human resources with the highest standards.

In all it was an emotional and inspiring ceremony but above all a fun way to look back to those days in grad school when little happened outside our labs. Thanks to my parents, my sister and my lovely wife and unborn daughter for joining us all in this celebration of Mexican chemistry. (all photo credits: My Dad.)

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CONACyT funding was approved!


A couple of months ago, maybe a little bit more, I got the news that the project I submitted to the National Council for Science and Technology (CONACyT) was approved! Now we only have to wait for the money to actually show up and that might take a while – a long while! Nevertheless this is always very good news and we are very excited about it because this means more money for research, specifically on the electronic molecular pathways of photosynthesis.

When I submitted the project I wrote a little post about the funding scheme which seemed, if not unfair, at least flawed, and I still believe in what I wrote. To be honest I thought it wouldn’t be funded but it turns out it was but I still think the reviewing process could be better.

There is a lot of research to do – too little time to do it.

Institute of Chemistry Library flood – UNAM


If a mind is a terrible thing to waste, then wasting a collective mind is an even more terrible thing. During the past weekend the library at the institute of chemistry suffered a flood caused by a broken pipe just above it, which incidentally happens to be the lab were I used to work as an undergrad student. When it comes to scientific journals, our institute still relies a lot on paper issues for the oldest numbers; we can order them online but it’s just easier to Xerox it at the library if you really need to read that old reference.

This morning the librarians were appalled when noticed not only the huge puddle on the floor but all the books and scientific journals that were dripping water from the shelves. The broken pipe has been fixed and the water on the floor has been mopped. It is now the books the ones that suffer the aftermath of this accident. Not only saving the information was important; wet paper is a great culture media for fungi which in turn could pose a health threat to all users. The administrative staff immediately got to work in recruiting academics and students to help the drying process: “Heal a book!“, they informally called it. Everyone grabbed an item and with the help of industrial blow dryers – the kind we use in chemistry labs to dry wet glassware – and an extraordinary amount of paper towels, each person got to dry the journals page by page.

I got an item that corresponded to the British journal New Scientist, which consisted of about fifteen issues from the year 1980. When I noticed the title in my hand I wanted to switch it. Should we save first those journals with the highest impact factor? or should we work on those that are most relevant to our own research? Should we throw away Chemical Abstracts now that the whole database is online? After all, New Scientist is a magazine which summarizes research that has already been peer reviewed and published; it is journalistic work, not peer reviewed science. But I was afraid to look pedantic so I got to work on drying it.

Kudos to the library staff on organizing in promptu “Heal a book!”

Students as well as the academic and administrative staff drying journals

Each person had their own technique. Some journals had their binding covers still in good shape so they were placed open standing on the floor in front of fans. Some placed paper towels carefully between pages and after a while they would remove them and then use the blow dryer. I thought that if I heated the edges of the paper and thus dried them, capillarity would drive the moisture in the innermost part of each page outwards. Didn’t quite work, at least not in a pragmatic time scale, so I went back to page by page.

I’m glad I did so. That way I was able to find some real pieces of history which could make any scientist nostalgic. For example: I took these photos with my iPod, and if you are by any chance reading this piece on an iPhone, you must find the following  picture about Swedish research endearing.

An ancient iPad or an edgy ‘Etch-a-Sketch‘?

Yes, online doodling games were already a thought back in 1980!

Are you subscribed to this blog? That means you got a notification by e-mail. So what? No big deal! Well, back in 1980 Britain was getting excited over a new form of comunication called the ‘Electronic Mail’ (available only at a couple of post offices). Besides, you wouldn’t have been able to get that message nor read this post on an HP Matrix Machine (you can’t even find a decent link in google about it nowadays!)

But scientists are not all about working, we like games too! So how about purchasing a ‘Hungarian Magic Cube‘ or a ‘Chess Computer‘?

An 80’s sensation!

E-chess

We also love a juicy piece of gossip. For instance, did you know that John Maddox was a controversial editor for Nature back in the 70’s who, as a student, went into chemistry because if he’d gone into physics he could’ve been drafted by the army in WWII to work on radars? Well me neither. But it seems that we should have known who he was, and now we do.

Sir John Maddox

There were many pieces of science news that nearly kept me in the library all night, if not for the fact that I had to drive 50 miles from Mexico City to my place in Toluca, but the one that captured my attention more than any other was the news of a European dream envisioned more than three decades ago; a dream from a group of scientists about looking for answers, like any other group of scientists, answers that are fundamental for the understanding of our universe and the understanding of matter, back when some of the biggest questions hadn’t even been fully posed, this group of visionaries agreed on taking the necessary steps to build an enormous subatomic-particle Supercollider for the European Center for Nuclear Research, better known as CERN.

The announcement of grand things to come

Back in 1980 I was already alive but I was only two years old. I could barely talk and had no idea what the word ‘future‘ meant, let alone what I’d become when it reached me. Now, even if I’m not a particle physicist I get excited about the news regarding the finding of the Higgs Boson and even if I’m not an astronomer I also get excited about pictures from the Curiosity Rover on Mars. I am a scientist. One out of hundreds of thousands or perhaps even millions, and this is part of my collective memory, the memory of the work of those who paved the road for us, those giants upon whose shoulders we struggle day by day to stand with dignity and against all odds. But here is the thing: those giants are actually made of dwarfs, millions of them; millions of us. Thousands and thousands of papers written, reviewed and published; papers that collectively gather the scientific experience summed up in rigorous experiments both successful and failed.

Preserving the information in those wet journals is important despite the fact you can get them all online. I hope one day a bored chemistry grad student goes to the library and browses old issues of New Scientist and other journals just for fun; they’ll go for a trip down a collective Memory Lane which will remind them that if they can dream it in the present, they can make it come true in the future.

The Local Bond Order, LBO (Barroso et al. 2004)


I don’t know why I haven’t written about the Local Bond Order (LBO) before! And a few days ago when I thought about it my immediate reaction was to shy away from it since it would constitute a blatant self-promotion attempt; but hell! this is my blog! A place I’ve created for my blatant self-promotion! So without further ado, I hereby present to you one of my own original contributions to Theoretical Chemistry.

During the course of my graduate years I grew interested in weakly bonded inorganic systems, namely those with secondary interactions in bidentate ligands such as xanthates, dithiocarboxylates, dithiocarbamates and so on. Description of the resulting geometries around the central metallic atom involved the invocation of secondary interactions defined purely by geometrical parameters (Alcock, 1972) in which these were defined as present if the interatomic distance was longer than the sum of their covalent radii and yet smaller than the sum of their van der Waals radii. This definition is subject to a lot of constrictions such as the accuracy of the measurement, which in turn is related to the quality of the monocrystal used in the X-ray difraction experiment; the used definition of covalent radii (Pauling, Bondi, etc.); and most importantly, it doesn’t shed light on the roles of crystal packing, intermolecular contacts, and the energetics of the interaction.

This is why in 2004 we developed a simple yet useful definition of bond order which could account for a single molecule in vacuo the strength and relevance of the secondary interaction, relative to the well defined covalent bonds.

Barroso-Flores, J. et al. Journal of Organometallic Chemistry 689 (2004) 2096–2102
http://dx.doi.org/10.1016/j.jorganchem.2004.03.035,

Let a Molecular Orbital be defined as a wavefunction ψi which in turn may be constructed by a linear combination of Atomic Orbitals (or atom centered basis set functions) φj

We define ζLBO in the following way, where we explicitly take into account a doubly occupied orbital (hence the multiplication by 2) and therefore we are assuming a closed shell configuration in the Restricted formalism.

The summation is carried over all the orbitals which belong to atom A1 and those of atom A2.
Simplifying we yield,

where Sjk is the overlap integral for the φj and φk functions.

By summing over all i MOs we have accomplished with this definition to project all the MO’s onto the space of those functions centered on atoms A1 and A2. This definition is purely quantum mechanical in nature and is independent from any geometric requirement of such interacting atoms (i.e. interatomic distance) thus can be used as a complement to the internuclear distance argument to assess the interaction between them. This definition also results very simple and easy to calculate for all you need are the coefficients to the LCAO expansion and the respective overlap integrals.

Unfortunately, the Local Bond Order hasn’t found much echo, partly due to the fact that it is hidden in a missapropriate journal. I hope someone finds it interesting and useful; if so, don’t forget to cite it appropriately 😉

Paper published in Canadian Journal of Chemistry


A new paper has been published and that is always good news. The paper entitled “Synthesis of new γ-lactones from preactivated monosubstituted pyrazines and TMS–ketene acetals” coauthored by Azucena Garduño-Alva, M. Carmen Ortega-Alfaro, José G. López-Cortés, Isabel Chávez, Joaquin Barroso-Flores, Rubén A. Toscano, Henri Rudler and Cecilio Álvarez-Toledano was a fruitful collaboration between several researchers from within the UNAM Institute of Chemistry and from other labs.

Therein, the lactone formation from pyrazines is analyzed, with some resulting orientations not quite in accordance with the common orientation patterns yield by electrondonor and electronwithrdawing groups. In order to assess the electronic structure of the intermediates and its influence on the resulting orientations, I performed a Fukui analysis based on the Natural Population formalism.

I will come back to this post and expand on the information once I get some more free time, thanks for your understanding. As usual the link to the paper can be located below and it is also available as a pdf file upon request to this author.
Thanks for reading!

Azucena Garduño-Alva, M. Carmen Ortega-Alfaro, José G. López-Cortés, Isabel Chávez, Joaquin Barroso-Flores, Rubén A. Toscano, Henri Rudler, Cecilio Álvarez-Toledano

Canadian Journal of Chemistry, 2012, 90(5): 469-482, 10.1139/v2012-016

www.CCIQS; The (not-quite) official website


The Joint Center for Sustainable Chemistry Research (Centro Conjunto de Investigación en Química Sustentable) was born in 2008 as a project between the Institute of Chemistry from the National Autonomous University of Mexico and the Chemistry School from the Mexico State Autonomous University aimed to the development of research in green and sustainable chemistry as well as that of human resources trained in the same areas.

I have found through the statistics page in this blog that CCIQS is a somewhat popular search term but unfortunately there is still no website available due to some technical dificulties. Therefore I here upload the link to our proto-website (only Spanish for the time being, sorry)

I hope this helps people find some info about what we do and how to get in touch with us. Opportunities for scholarships are available both for graduate and undergraduate students. If you are interested in working with us, please get in touch with the researcher of your choice and ask for any available positions; we look forward to having more students to interact with!

Supramolecular Chemistry to celebrate a Supra-collaboration


For over twenty years, there has been an ongoing scientific collaboration between the Institute of Chemistry  of the National Autonomous University of Mexico and the Faculty of Chemistry and Chemical Engineering of the Babes-Bolyai University located in the city of Cluj-Napoca, Romania. It all began back in the early nineteen nineties when Professor Lara, then director of Instituto de Química, extended an invitation to Professor Ionel Haiduc, who at the time served as Vice President of the Romanian Academy, to spend a few months in Mexico for a research stay. Later on prof. Dr. Ioan Silaghi-Dumitrescu and his wife paid a couple of visits to our institution also during the nineties; their last visit together occurred in 2002 when prof. Ioan Silaghi-Dumitrescu was asked to teach a small course on molecular modelling. It was during this visit that I came to know about the Babes-Bolyai University and more importantly, it was when I met both Prof. Ioan Silaghi and his wife Prof. Luminita Silaghi, an acquaintance that shaped many aspects of my life in the years to come. Other Romanian guests came to work at IQUNAM, such as Dr. Ion Grosu, who worked as a postdoc with Prof. Roberto Martínez in the Organic Synthesis department. Prof. Cristian Silvestru also collaborated with the group of Dr. Raymundo Cea-Olivares in the field of Main Group Metal Chemistry. Prof. Raymundo Cea-Olivares has been to Cluj-Napoca a couple of times visiting the lab of the late Prof. Silaghi. I went for a research stay during my Ph. D. in 2005 and then went back to occupy a postdoctoral position in late 2008 which lasted until 2010; I also participated in the MolMod seminar in 2007 while working at a private research center, then thinking I wouldn’t go back to academia. Dr. Liviu Bolundut, a then Ph. D. student of Prof. Haiduc’s, came to work with Dr. Monica Moya also in the field of Main Group Metal Chemistry. The interaction between our two institutions has a sound history.

As part of the celebrations of this year, the International Year of Chemistry, I issued an invitation to Prof. Ionel Haiduc and Prof. Luminita Silaghi-Dumitrescu, to give a couple of lectures at IQUNAM about their current research. Fortunately, they accepted and found the time in their tight schedules to come. We were also fortunate enough to get the official approval by the corresponding committee at UNESCO of making these conferences part of the official celebrations of IYC 2011 (In fact, they were the ones who came up with the name of the event which is the name of this post as well.) The scope of this visit also included to encourage our scientific community to keep the collaborations alive with UBB. We had these conferences twice, first at CCIQS here in Toluca and also at the original facilities of IQUNAM on the main University campus in Mexico City. Both events were successful in attracting a large number of researchers but more remarkably a large number of young students who have read about their work and are aware of their reputation on their respective fields; the following picture of our guests with young students of UAEMex, serves as proof.

But I get ahead of myself, for in fact we did more than just having lectures and showing them our new facilities. During the course of their stay,which lasted a bit more than a week, Professor Cea-Olivares and I took them around to do some tourism. During their first weekend I took them to the Folkloric Ballet at the Fine Arts Palace and to the Anthropology Museum, both in Mexico City. We also went together to the Aztec ruins of the city center and the larger archaeological site of Teotihuacan, where Mrs. Iovanca Haiduc even got to climb the Sun’s Pyramid, a challenge to which I decided to pass this time. Prof. Cea-Olivares took them outside Mexico City into Cuernavaca and Taxco, the latter being an old silver mining town famous for its jewelry stores filled with Ag merchandise. We all had a great time traveling around, chatting and in general enjoying each others company.

Haiduc Silaghi Barroso

At the Anthropology Museum with the Aztec Calendar

Haiduc Silaghi Barroso-Flores

At Teotihuacan

But now back to science. Prof. Haiduc’s lecture was titled “News in Supramolecular Chemistry”, in it he talked about the basics of supramolecular chemistry as the branch of chemistry that deals with the non-covalently bonded chemical species; the chemistry of secondary interactions as defined by Allcock in 1972. A survey of the existing x-ray structures database was performed by Prof. Haiduc along with his colleague Prof. Julio Zukerman-Schpector in Brasil, in order to find some previously overlooked patterns in intermolecular arrays containing Te (II) or Te (IV) along with aromatic groups, revealed that the Te – Ar interactions through the Π electrons cloud are found more often than previously believed. The most remarkable feature of this array is the fact that the electron density in the formation of such interactions stems from the Te atom (through the stereochemically active lone pair) and into the LUMO of the aromatic moiety in the second molecule. This represents a fascinating coordination mode for Te organometallic compounds!

Prof. Luminita Silaghi-Dumitrescu talked about her research on heterotopic As ligands, some of which exhibit remarkable new coordination patterns stabilizing dinuclear complexes with late transition metals. I felt nostalgic reading the names of old friends and colleagues who collaborated in the work described.

Prof. Haiduc (who is currently President of the Romanian Academy) shared many anecdotes about his times as a PhD student at the Lomonosov Institute  back in the Soviet Union under the supervision of Prof. Andrianov. From these anecdotes it is possible to extract the feeling of doing science during the Cold War period since he had to be weary of espionage, which by the way went both ways! He talked about secret research facilities and scooped papers. One could easily think that basic chemistry research would be far from the interest of high political powers who could find aeronautical research more interesting! A developed country is able to acknowledge the value of science in preserving a strategic position in the world. His old advisor, Prof. Andrianov, was considered a hero by the Soviet Party among other things for his work on Silicon based polymers which were used as lubricants in heavy machinery and vehicles during War War II. German tanks used regular carbon based oil which in the Russian winter became extremely viscous, practically became gels! while Silicon based oil could almost preserve its original viscosity at very cold temperatures.

In summary it was a great opportunity to learn from great chemists whose scientific reputations could easily overwhelm any scientist worth his salt! But it was above all things a great opportunity to meet once again dear friends from a dear country I once got to call home.

2011 – International Year of Chemistry

“Chemistry – Our life, our future”

Instituto de Química de la UNAM. 70th Anniversary


The Institute of Chemistry of the National Autonomous University of Mexico becomes 70 years old this month, and to kickoff the year round celebrations our institution has organized a series of lectures with the notable presence of Nobel Laureate, and former student of this institute, prof. Dr. Mario Molina whose presence has become ubiquitous within the Mexican scientific community events given his status. His presence is also relevant under the scope of the new branch of Instituto de Química, which is the Joint Center for Research in Sustainable Chemistry from which I write these lines. I have many fond memories of the time I spent there as a grad student; I specially miss the beautiful area on campus on which it’s located next to the buildings of other science institutes.

The lectures to be given are the following, click on them to download a small abstract from each:

Prof. Christer B. Aakeröy (Kansas State University)
“Supramolecular chemistry of co-crystals: From molecular dating to improved pharmaceuticals”

Prof. Wilhelm Boland (Max Planck Institute for Chemical Ecology)
“Sequestration of plant-derived glycosides by leaf beetles: a model system for evolution and adaptation of chemical defenses”

Prof. Rathnam Chaguturu (University of Kansas)
“Strategies for Uncorking the Drug Discovery Bottleneck: A Latin American Perspective”
References

Prof. A. M. Echavarren Pablos (Institut Català d’Investigació Química)
“New Gold-Catalyzed Reactions of Enynes and Beyond”

Prof. Bern Kohler (Montana State University)
“Four billion years of fun in the sun: How ultrafast events protect DNA from deadly UV rays”

Hopefully this time I will get to do a follow up (I still owe a follow up on last December’s symposium on Green Chemistry here at CCIQS)

And now gather ’round for some history!

The Institute of Chemistry (Instituto de Química) was founded on April 5th 1941 with the mission of organizing the -then small- existent chemistry community in Mexico. Since three years before that, former President Lázaro Cárdenas expropriated oil wells and refineries from foreign companies, there was a strong need for more specialized human resources in the different areas of chemistry who could develop our incipient  petrochemical industry. Thus, one of the first tasks of Instituto de Química was to develop a method which could provide all tetraethyllead (IV), an organomettallic compound which was used as an antiknock additive in gasolines, way before it was banned for being highly toxic.

Tetraethyllead - now toxic, this was an important component in gasoline as well as in other fuels

One of the major historical contributions of Instituto de Química was the work of Dr. Luis Miramontes (1925 – 2005), who worked in the development of the synthesis of progestin, a synthetic hormone which was used in the first oral contraceptive*; an amazing achievement for a 26 year old doctor! Along with Dr. Miramontes, Dr. George (now named Jorge, although née György in Hungarian) Rosenkranz, from the pharmaceutical company Syntex and Dr. Carl Djerassi, who is called the father of the pill, this enormous scientific but specially social groundbreaking achievement was accomplished. It has long being argued that a Nobel Prize should have been awarded to this international trio of chemists, but nevertheless worldwide recognition is due.

Dr. Luis Miramontes ca. 1951

*Miramontes L; Rosenkranz G; Djerassi C. 1951 Journal Of The American Chemical Society 73 (7): 3540-3541 Steroids .22. The Synthesis Of 19-Nor-Progesterone

Many are the achievements of Instituto de Química on many different branches of science; from synthetic organic chemistry to natural products research. The institute has hold six Professors Emeritus so far and continues to be one of the leading chemistry research facilities not only in Mexico and Latin America but in the world. Keeping track of our history helps us maintain our identity as scientists as well as to preserve our cultural heritage, all which in turn allows us to find paths into the future so we may keep on doing the inspirational science our country, and the world, needs. Many are also the issues on which we have to work in order to keep it competitive and to bring it back to the cutting edge of science. The research staff of the institute is highly committed to achieve so in the next few years by developing both relevant scientific knowledge and human resources who can make further contributions to the advancement of chemistry, and science in general, whithin our country.

This year is a year of chemical celebrations: From the International Year of Chemistry (IYC 2011) to the 7oth anniversary of Instituto de Química, as well as the 95th anniversary of the Chemistry School also at the National Autonomous University of Mexico. So ¡Feliz Cumpleaños, Instituto de Química!

Thanks for reading, rating and commenting!

Main entrance of the institute and current staff (well, most of it anyway)

2011, International Year of Chemistry

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