Monthly Archives: April 2013
#RealTimeChem – Happy birthday DNA!
What a happy coincidence -if indeed it was- that #RealTimeChem week happened to coincide with the sixtieth anniversary of the three seminal papers published in Nature on this day back in 1953, one of which was co-authored by J. Watson and F. Crick; of course I mean the publication for the first time of the structure of deoxyribose nucleic acid, or DNA, as we now call it.
You can get the original Nature papers from 1953 here at: http://www.nature.com/nature/dna50/archive.html (costs may apply)
Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid 737
J. D. WATSON & F. H. C. CRICK
doi:10.1038/171737a0
Molecular Structure of Nucleic Acids: Molecular Structure of Deoxypentose Nucleic Acids 738
M. H. F. WILKINS, A. R. STOKES & H. R. WILSON
doi:10.1038/171738a0
Molecular Configuration in Sodium Thymonucleate 740
ROSALIND E. FRANKLIN & R. G. GOSLING
doi:10.1038/171740a0
Nature’s podcast released two episodes (called ‘pastcast’) to celebrate DNA’s structure’s birthday, one of them is an interview with Dr. Raymond Gosling who in 1953 worked under Dr. Rosalind Franklin at King’s College London in diffractometry of biological molecules. If you haven’t listened to them you can get them here at nature.com/nature/podcasts. Of course, the history around the discovery of DNA’s structure is not without controversy and it has been long argued that the work of Franklin and Gossling didn’t get all deserved credit from Watson and Crick. In their paper W&C acknowledge the contribution of the general nature of DNA from the unpublished results by Franklin’s laboratory but that is as far as they went, they didn’t even mention photo 51 which Crick saw at Wilkins laboratory, who in turn got it from Gossling at Franklin’s suggestion. Still, no one can deny that the helical structure with which we are now familiar is their work, and more importantly the discovery of the specific pairing, which according to Gossling was a stroke of genious that probably couldn’t have happened in his own group, but without Franklin’s diffraction and Gossling’s crystallization there was little they could do. Details about the process used to crystallize DNA can be heard in the aforementioned podcast, along with an inspiring tale of hard work by Dr. Gossling. Go now and listen to it, its truly inspiring.
For me it was not the story of a helix, that I was familiar with; it was the story of the specific pairing of two hélices
– Dr. Raymond Gosling
The iconic Photo 51 by Dr. Rosalind Franklin and Raymond Gosling (Source: Wikipedia)
Above, the iconic Photo 51 taken by Franklin and Gossling (have you ever noticed how most scientists refer to Franklin just as Rosalind but no one refers to Watson as James? Gender bias has a role in this tale too) To a trained crystallographer, the helical symmetry is evident from the diffraction pattern but going from Photo 51 to the representation below was the subject of hard work too.
Modern DNA representation (Source: Wikipedia)
There are million of pages written during the last 60 years about DNA’s structure and its role in the chemistry of life; the nature of the pairing and the selectivity of base pairs through hydrogen bond interactions, an interaction found ubiquitously in nature; water itself is a liquid due to the intermolecular hydrogen-bonds, which reminds us about the delicate balance of forces in biochemistry making life a delicate matter. But I digress. Millions of pages have been written and I’m no position of adding a meaningful sentence to them; however, it is a fascinating tale that has shaped the course of mankind, just think of the Human Genome Project and all the possibilities both positive and negative! DNA and its discovery tale will continue to amaze us and inspire us, just like in 2011 it inspired the Genetech company to set a Guiness World Record with the largest human DNA helix.
Genetech SF, Cal. USA (Source worldrecordacademy.com)
Happy birthday, DNA!
#RealTimeChem – Day 3
Welcome of the third installment of #RealTimeChem, the diary. As I did yesterday and the day before, I will summarize my day in chemistry throughout the Tweets sent over this event.
Sup. Info finished. Figs & tables will b ready today; on it. Off to a (video)conference by Dr. Marcos Hernandez @iquimicaunam #RealTimeChem
— Joaquin Barroso (@joaquinbarroso) April 24, 2013
(Haha, I found the button to include the feed!)
I finally finished editing that supporting information I’ve been Twitting about all week, now I’m back at the manuscript re-editing a bit. This is a problem I have that I’m sure is shared by most of you: I just can’t let go. If I’m writing a manuscript I’ll read it and change it over and over; if I’m working on a presentation, I will edit and reorder the slides almost ad infinitum if it were not for deadlines. Professor Cea-Olivares, of whom I’ve written before in this blog, used to say that projects are never finished but merely abandoned. In all fairness we are still not on the ‘not letting go’ phase, there are still some sections of the manuscript that need our attention; and when I say we, I mean me and my collaborator Dr. Rodrigo Galindo who is currently working at the University of Utah (BTW go check out his blog and persuade him to pick it up again!)
But in the middle of the day there was a conference at Instituto de Química, in Mexico City, that I wanted to listen to. Dr. Marcos Hernández is a good colleague of mine who deals with asymmetric organocatalysis. I like his work a lot and I hold him in high esteem so I asked for a video transmission of his talk to be sent over to CCIQS at Toluca. In the following two Twits you can get a glimpse of our video conferencing facilities.
Me. At the videoconference hall #CCIQS waiting for @iquimicaunam #RealTimeChem twitter.com/joaquinbarroso…
— Joaquin Barroso (@joaquinbarroso) April 24, 2013
— Joaquin Barroso (@joaquinbarroso) April 24, 2013
And we are good to go! Live from Mexico City, is Dr Marcos Hernandez conf @iquimicaunam during #realtimechem twitter.com/joaquinbarroso…
— Joaquin Barroso (@joaquinbarroso) April 24, 2013
Not all is work during RealTimeChem week, although perhaps it should be. Still, safety first! that’s our motto! (follow the link in message)
stock pic: important 2 remember: protect eyes & hands when u’re naked in a lab! twitter.yfrog.com/nymcyzp 4 those too excited by #RealTimeChem
— Joaquin Barroso (@joaquinbarroso) April 24, 2013
Today I took some time to have a few interactions with other participants of #RealTimeChem and got to follow very interesting people. Definitely, after this week I will become a more active Twitter user (ouch!). But the research must go on, and today Maru started working on rendering the electrostatic potential surfaces for a rather large set of calix- and thiacalix[n]arenes for our line of research on molecular recognition agents.
#RealTimeChem Electrstatic potential surface of a calix4arene 1 down 119 to go 😉 twitter.com/joaquinbarroso…
— Joaquin Barroso (@joaquinbarroso) April 24, 2013
#RealTimeChem same as before; top view; transparent surface. Which so u like better? Compchem yields nice pics too! twitter.com/joaquinbarroso…
— Joaquin Barroso (@joaquinbarroso) April 24, 2013
#RealTimeChem Another EPS (diff scale as in previous pic) twitter.com/joaquinbarroso…
— Joaquin Barroso (@joaquinbarroso) April 25, 2013
This is pretty much it for today; I’m very tired and I still need to work in other things so I’m off for now but stay tuned for more tomorrow when this blog will celebrate the 60th anniversary of the publication of DNA’s structure in Nature.
Cheerio!
#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 2013 – Day 1
The first day of the #RealTimeChem event has gone by and here I am blogging about it in order to participate in the ensuing #RealTimeChemCarnival which is the blogging section, so to speak, of the aforementioned event. So, without further ado, this was my #RealTimeChem day:
Disclaimer: I’m not much of a Twitter man myself so I apologize in advanced for any dumb or stupid usage of it. I’m also new to Instagram and Vine, which I only downloaded on account of this event. Sorry for not taking snippets from the Twitter feed but I’m on Windows7 starter here and I don’t have such tools; I’m also not going to download some tool right now, sorry for that but if you know a better way, please do share it! I will be posting all week long so it might come in handy.
Joaquín Barroso
Editing sup. info. new paper on electronic interactions in rotaxane-like molecules with bio applications. Hope #RealTimeChem brings me luck!
We are almost done with this paper on drug delivery systems based on the architecture of calix[n]arenes. We’ve found some pretty interesting results about which features suit better certain drugs both in gas and solution phases. Most of my day had to do with editing the supporting information. Below, the picture that acompanied the previous Tweet.
Today’s supporting info. +150 figures inserted into a Word file – I see rotaxanes!
Later on, along came a student whom, to be perfectly honest, I completely forgot about -my bad- but he was there and he was willing so off we went to work. Of course, being his first time, we had to start from scratch from the very basics of Gaussian’s use (and implicitly, the basics of the command line use in Linux). I’m not sure he wants his name to be posted here so he will remain in anonimity until otherwise stated. The associated Tweet read as follows:
Joaquin Barroso @joaquinbarroso 9h
1st Gaussian job 4 this new student #realtimechem http://instagram.com/p/Ya5oJbgQxk/
The new anonymous intern launching his very first Gaussian calculation – aww
and then,
Joaquin Barroso @joaquinbarroso 8h
Training a new student in using Gaussian, Gaussview and Linux. Lot of work to be done but he looks eager to learn 🙂 #RealTimeChem
Being so much into #RealTimeChem worked as a serious motivator; the more you published the more you wanted to keep going! So all day long I had my head filled with things that I wanted to do, but I made a strong case about twitting only those things that I actually did and nothing in the lines of ‘thinking of …’ or ‘wishing I could…’ that sort of thing. I usually take little notes on google calendars about my day’s work as a means to keep track of my productivity, or sometimes, sadly, my lack thereof. This time Twitter was a loud witness of my activities which, hopefully, may be considered productive.
I teach a class on electronic structure each Tuesday, so I started preparing my class for tomorrow as a kind of break from editing that supporting information; the Twit read:
Joaquin Barroso @joaquinbarroso 7h
Must not forget to prepare class 4 tomorrow. #realtimechem a new productivity tool! pic.twitter.com/7JFYuJ0FEJ
The book is “Quantum Chemistry” by Donald McQuarrie
Joaquin Barroso @joaquinbarroso 4h
All day editing sup. info. has rendered me cross-eyed! Time 4 a break. Will reply work (chem) related email 🙂 #RealTimeChem
and so I did. I got to reply to a professor in the far away island of Mauritius! He just invited me to participate in a virtual conference on computational chemistry. What a shame! It’d been nice to fly half way accross the world and set foot in that land! If you don’t know where Mauritius is, find Madagascar in southern Africa and then take a right on the Indic Ocean. As per his request, here I promote his event with all of you and with #RealTimeChem:
Joaquin Barroso @joaquinbarroso 3h
http://bit.ly/ZLre9V Virtual conference on comp. chem. in Mauritius. Please try the link. #RealTimeChem
Then more e-mail
Joaquin Barroso @joaquinbarroso 3h
#RealTimeChem just accepted invitation 2 virtual conf.; accepted new intern by mail; now reviewing 2 applications for conference stipends
I didn’t finish reviewing these kid’s work but I think they might get their plane tickets from the local council for science and technology.
As I wrote earlier, I’m not a Twitter man so I get easily overwelmed by all the information generated within. I wanted to go home but before I got to read some Tweets and I was astonished by the enormous ammount of messages in the lines of ‘submitted a grant, now when can I do the corresponding research?‘; ‘grading! what a torture!’ and some others that indicated people was doing administrative work when they really wanted to get their hands dirty in the lab. This was a surprise to me because I imagined that most Twitter users and therfore, #RealTimeChem participants would be young students who are the ones who actually are up to their necks in chemistry! of course I Tweeted about my little observation in two messages.
Joaquin Barroso @joaquinbarroso 2h
So interesting 2 notice #RealTimeChem deals more with research administration than wth research! I thought it’d be the other way around!
Joaquin Barroso @joaquinbarroso 2h
@RealTimeChem Is it measureable how much #RealTimeChem is chem. research & how much is adminstration/paperwork/grading? Might b interesting!
New paper in J. Phys. Chem. C
Having a new paper out is always fun and this week we got the wonderful news from the Journal of Physical Chemistry C that a paper I co authored with Prof. Alireza Badiei at the University of Tehran in Iran and his student, who actually got us all in touch, Dr. Pezhman Zarabadi-Poor, was accepted for publication.
The paper is titled “Selective Optical Sensing of Hg(II) in Aqueous Media by H-Acid/SBA-15: A Combined Experimental and Theoretical Study“; in it we explored the fluorescence quenching mechanism for a Hg(II) complex which forms the basis of a novel selective mercury detector. Geometry optimizations were carried out at the PBE0/6-31++G** PCM level of theory (along with the aug-cc-pVDZ-PP basis set and corresponding ECP for Hg), also the electronic spectrum of both the free acid and the Hg(II) complex was calculated.
(Frontier orbitals were depicted using Chemcraft)
Higher laying orbitals for Hg(II) complex
We can observe that HOMO and LUMO+1 are mainly located on the naphtalene ring allowing for the S0 -> S1 transition and back, which accounts for the molecular fluorescence. Other internal conversion processes were also assessed and discussed in the paper which accounts for the quenching effect. In short, we have obtained a full quantum description of the mechanism by which coordination of the free acid to Hg(II) alters the ligand’s electronic structure converting its emisive lowest-lying excited state to a dark state, i.e., quenching! Pretty cool stuff!
Once again thanks to both Dr. Zarabadi-Poor and Prof. Badiei for thinking about me for collaborating with them in this joint endeavor which hopefully wont be our last. A PDF copy of the article is available by direct request through this post.
Thanks for reading, sharing, rating and commenting.
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.
Dr. Joaquin Barroso's Blog 