Category Archives: RealTimeChem
Summer Interns 2014
Just as last year, the “Dolphin Summer Internship Program” (Programa Delfín) has started and this time it coincided with #RealTimeChem week. Four students from various cities (and accents) around Mexico have come to our lab in Toluca in order to spend about 7 weeks of research in the field of molecular modeling and within our research of molecular recognition in biochemistry. Karen, Cynthia, Jesús and Marco have started their training today as they arrived to CCIQS so we went over the (very) basics of quantum chemistry, the (very) basics of Linux and the basics of Gaussian09. (I should really think about developing some web tutorials or something because this impromptu training is very exhausting!)
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- Left to right: Karen Díaz, Cynthia González, Marco Linares and Jesús Beltrán
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- Left to right: Karen Díaz, Cynthia González, Marco Linares and Jesús Beltrán
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- My overweight self – Interns in the background
Their academic backgrounds are mostly centered around pharmaceutics and biochemistry although their ages range from the second to the fourth year of college education. Computational chemistry is pretty unknown to all of them; I’ll do my best to change that, while at the same time I make them aware of its power as a research tool and as a research field in itself.
Here is to a very productive summer! I hope we manage to get enough data for a paper and, more importantly, that they all get a good experience out of their time here, make new friends and learn something new that enriches their skills in this increasingly competitive world.
Taking the Joy of Chemistry into a Children’s Home
On Friday May 30th, my good friend Dr. Josefina Aldeco, my wife and I, visited a children’s home in Querétaro (central Mexico) and brought them a few cool chemistry experiments for a short show. This event was promoted by a non-profit organization called “Anímate a estudiar” (Dare to study), namely by Mrs. Paulina Milanés who is always looking for ways to encourage kids from poor backgrounds to pursue their goals through study; among other things, they provide backpacks with school supplies to orphan kids like the girls we visited.
As a way to inspire them, we handed each girl a balloon drawn in the shape of a brain and asked them to inflate them daily by reading; by doing their homework; by asking questions all the time; by working hard in pursuit of a brighter future for which their brains are the most powerful muscles.
Many reactions took place that Friday; not only inside the flasks and beakers before our little audience but also in their faces and their engagement with us. Little by little these girls got out of their shells and became more excited, up to the point of performing their own chemical reaction themselves by polymerizing some glue with borax in hot water. This was for sure the first time they got in contact with chemistry but the true goal was to set up a spark in their minds that one day may turn into a life opportunity. We are aware that one small chemistry show can’t really have that effect, but if many more scientists reach out to these kids there is a bigger chance of creating a ripple effect that convince disenfranchised children that studying is the way to take the wheel of their own future.
Science is about development; its about spreading knowledge and the love for knowledge. Although we most times sit high on our ivory towers it is paramount to remember that there is also a social component to the scientific activity. Kids are eager to learn, but most school systems do their very best to limit their curiosity and ambition. We hope these girls find in studying a way to a better, happier and safer future. Mexico has a large economic disparity; climbing the social ladder is very hard and even more so for women which makes these girls a very vulnerable social group in the next generation.
It only takes one day. One day and some potassium iodide; some mentos on a diet-coke (sorry, Gina, for the squirt!); some cobalt chloride on paper; some balloons some glue and some borax in hot water. But above all it takes a big commitment.
I hope you readers, computational and experimental chemists alike, take some time out of your busy schedules and share your passion for science with kids, specially those with the lowest opportunities of getting in touch with real scientists. You can also contribute to this noble effort by making a small pay-pal donation to www.animateaestudiar.org or to any other similar organization in your local community.
It only takes one day.
P.S. Thanks to Josefina from Universidad Autónoma de Querétaro for providing material and reagents. Please go and check out her blogs (here and here) and encourage her to write more often! (Did I mention she published in Science a few years ago?)
#RealTimeChem – Day 2
This initiative has turned out to be a lot of fun for me! I think so far the thing that has captured my attention the most is to grasp the realization that science, chemistry in this case, is performed by humans in small, and sometimes not so confident, steps, a description far from the pristine one we daily read throughout the plethora of journals. A similar former initiative, which should have been brought back during this week, was the #OverlyHonestMethods one. It’d be a lot of fun to have both hastags together during an entire week. The other thing I knew, but that #RealTimeChem has helped me understand is the fact that a lot of resources for research are needed and getting said resources consumes a lot of our time as researchers: grant submissions; applications revisions; meetings; academic events and a long etcetera occupy our time and attention and this isn’t necessarily a good thing all the time.
So here it is; my second day reporting my #RealTimeChem
Joaquin Barroso @joaquinbarroso 7h
Supporting information for our paper feels endless now. I want to launch calculations & I still have a ton of emails to reply!
Supporting information for our most recent paper consists of more than 200 figures corresponding to a few conformations from several compounds; this has consumed a lot of my time but I’m finally done with it! Now, its only a matter of time for us to submit it -we are aiming high!- and hopefully this may happen during #RealTimeChem. That would be cool!
Joaquin Barroso @joaquinbarroso 7h
Reaching out during #RealTimeChem Any ECP/basis/functional recommended for La & Pr? http://bse.pnl.gov has 2 by Cao but no reference 
No reply, unfortunately. I need to run some calculations for a small collaboration and these compounds include either La or Pr; I need a, preferably relativistic or quasirelativistic) effective core potential (maybe I should write a post illustrating the difference between ECP’s and pseudopotentials) for these atoms that is also compatible with some relatively simple electron density functional. The Basis Set Exchange library has one by Cao but its not referenced so there is only so much I can do with it.
Joaquin Barroso @joaquinbarroso 7h
Watching all the wheels of chemistry turn (slowly) during #RealTimeChem makes you realize why each paper represents years of hard work
Between reading a Tweet about a grant submission and another one about having a paper published there is a lot of time and hard work involved, not to mention frustration, a little procrastination and a lot of fun over the course of a few years. During those years some chromatography columns are performed, some flasks are smashed and spectra are recorded. And this all happens very, very slowly as opposed as how we read it in journals where people seem to have had an original idea, gone to their labs, set up a few experiments, recorded the results and written the paper, and all before dinner!
The hindrances and intricacies of chemistry now have an outlet: blog-syn.blogspot.com In this site, the little details about synthesis are gathered in a sort of #OverlyHonestMethods way, only not as embarrassing; only practical. In a way, blog-syn is what this blog of mine was supposed to be for the lab of Dr. Silaghi-Dumitrescu back in Romania when I first conceived it. Little by little, the wheels of science turn but with every turn they move mankind forward.
Joaquin Barroso @joaquinbarroso 3h
An industrious student calculating electronic structure of host-guest systems #realtimechem pic.twitter.com/2QdF3vyBCa
Sadly, Maru is about to leave us for a short period of time now that she has completed her thesis and is about to get her B. Sc. in Chemistry; she threatens to come back for a Masters degree, though. She has played a crucial role in the lab’s success so I thought of taking a picture of her while working on her workstation. @RealTimeChem, the official Twitter account of the event, favorited this photo.
Joaquin Barroso @joaquinbarroso 1h
Valence bond theory class @comunidadUAEMex #RealTimeChem nice Slater determinants! 😉 pic.twitter.com/boOrB2IoCx
Tuesdays I teach a class titled ‘Molecular Design and Reactivity‘ (terrible name, I know) and today’s topic was the Valence-Bond method which, I’m sure you all know, is only of historical relevance although some nice conceptions arise from it, like the fact that a wavefunction can be approximated as a linear combination of smaller wavefunctions each corresponding to a specific electron configuration. I mostly use Donald McQuarrie‘s book on Quantum Chemistry, in case you are wondering.
This is a long three hours class starting at 5pm, and the research center is far from the chemistry school, so I usually don’t go back to the office afterwards. So here I am, at Starbucks in downtown Toluca, but chemistry for today is far from over! I still need to review some applications from students who are seeking funds from the local council for science to attend a seminar on polymers this summer in Barcelona. I was also requested by the Journal of Inclusion Phenomena and Macrocyclic Chemistry to serve as a reviewer for a submitted paper. Both activities have deadlines in May but I want to get them done now so I can brag include them in my #RealTimeChem productivity report.
A few hours later…
Joaquin Barroso @joaquinbarroso 3m
Just Finished reading two proposals, I’m going to accept them both! 2 kids going 2 intl polymer seminar #RealTimeChem
And so I did it! Two students from a private university in the state want to participate in a polymer seminar in Spain. I think they have impressive results; too bad I had to sign a disclosure agreement so I can’t write anything about their project. Good for them and good for COMECyT for sponsoring outstanding students in science and engineering!
These past two days I haven’t personally launched any calculations; I haven’t had time to read any journals nor to write any applications or papers, yet I’m certain that the wheels at our lab are slowly turning, hopefully forward.
RealTimeChem week 2013 #RealTimeChem
RealTimeChem, in its first week-long edition, is coming to your Twitter feed next Monday April 22nd 2013, and I for one intend to participate.
I look forward to this event in order to get in touch with other chemists, not only theoretical but experimental ones as well, around the world sharing a passion for chemistry and technology. I guess most of the participants will be experimental chemists who will amaze us with their videos and pictures of cool looking reactions; I hope we, here at our computational lab, are up to the challenge with our calculations.
Participating is really simple, just Tweet as little or as much as you want to share about your work or studies around chemistry under the #RealTimeChem hastag and follow @RealTimeChem. There is also a group and an event set up on Facebook, check those out too. As I write this, its Friday at 8:oo PM and I’m still in the office, which means I have a lot of work to do, therefore I don’t feel like writing about all the details of the event, specially when others have done so in a much more eloquently fashion: Check out these posts (as well as the entire content of their blogs, they’re very cool!) by Dr. Galactic and The Organic Solution for all the details about the event’s mechanics and, yes, even prizes to the best tweets.
So get on board and tweet all week long under the #RealTimeChem hashtag and share your work with the world the way no journal will ever do: in real time and with the uttermost embarrassing methodology honesty.
