Category Archives: Internet
The Computational Chemistry Comparison and Benchmark DataBase (CCCBDB) from the National Institute of Standards and Technology (NIST) collects experimental and calculated thermochemistry—related values for 1968 common molecules, constituting a vast source of benchmarks for various kinds of calculations.
In particular, scaling factors for vibrational frequencies are very useful when calculating vibrational spectra. These scaling factors are arranged by levels of theory ranging from HF to MP2, DFT, and multireference methods. These scaling factors are obtained by least squares regression between experimental and calculated frequencies for a set of molecules at a given level of theory.
Aside from vibrational spectroscopy, a large number of structural and energetic properties can be found and estimated for small molecules. A quick formation enthalpy can be calculated from experimental data and then compared to the reported theoretical values at a large number of levels of theory. Moments of inertia, enthalpies, entropies, charges, frontier orbital gaps, and even some odd values or even calculations gone awry are pointed out for you to know if you’re dealing with a particularly problematic system. The CCCB Database includes tutorials and input/output files for performing these kinds of calculations around thermochemistry, making it also a valuable learning resource.
Every computational chemist should be aware of this site, particularly when collaborating with experimentalists or when carrying calculations trying to replicate experimental data. The vastness of the site calls for a long dive to explore their possibilities and capabilities for more accurate calculations.
Calculation of interaction energies is one of those things people are more concerned with and is also something mostly done wrong. The so called ‘gold standard‘ according to Pavel Hobza for calculating supramolecular interaction energies is the CCSD(T)/CBS level of theory, which is highly impractical for most cases beyond 50 or so light atoms. Basis set extrapolation methods and inclusion of electronic correlation with MP2 methods yield excellent results but they are not nonetheless almost as time consuming as CC. DFT methods in general are terrible and still are the most widely used tools for electronic structure calculations due to their competitive computing times and the wide availability of schemes for including terms which help describe various kinds of interactions. The most important ingredients needed to get a decent to good interaction energies values calculated with DFT methods are correlation and dispersion. The first part can be recreated by a good correlation functional and the use of empirical dispersion takes care of the latter shortcoming, dramatically improving the results for interaction energies even for lousy functionals such as the infamous B3LYP. The results still wont be of benchmark quality but still the deviations from the gold standard will be shortened significantly, thus becoming more quantitatively reliable.
There is an online tool for calculating and adding the empirical dispersion from Grimme’s group to a calculation which originally lacked it. In the link below you can upload your calculation, select the basis set and functionals employed originally in it, the desired damping model and you get in return the corrected energy through a geometrical-Counterpoise correction and Grimme’s empirical dispersion function, D3, of which I have previously written here.
The gCP-D3 Webservice is located at: http://wwwtc.thch.uni-bonn.de/
The platform is entirely straightforward to use and it works with xyz, turbomole, orca and gaussian output files. The concept is very simple, a both gCP and D3 contributions are computed in the selected basis set and added to the uncorrected DFT (or HF) energy (eq. 1)
If you’re trying to calculate interaction energies, remember to perform these corrections for every component in your supramolecular assembly (eq. 2)
Here’s a screen capture of the outcome after uploading a G09 log file for the simplest of options B3LYP/6-31G(d), a decomposed energy is shown at the left while a 3D interactive Jmol rendering of your molecule is shown at the right. Also, various links to the literature explaining the details of these calculations are available in the top menu.
I’m currently writing a book chapter on methods for calculating ineraction energies so expect many more posts like this. A special mention to Dr. Jacinto Sandoval, who is working with us as a postdoc researcher, for bringing this platform to my attention, I was apparently living under a rock.
Out of some +1000 twitter accounts I follow about a quarter are related computational chemistry. The following public list isn’t comprehensive and prone to errors and contains researchers, programmers, students, journals, products and companies who gravitate around the use of in silico methods for the understanding and design of chemical and biochemical compounds.
As if I didn’t have enough things to do I’m launching a new blog inspired by the #365papers hashtag on Twitter and the naturalproductman.wordpress.com blog. In it I’ll hopefully list, write a femto-review of all the papers I read. This new effort is even more daunting than the actual reading of the huge digital pile of papers I have in my Mendeley To-Be-Read folder, the fattest of them all. The papers therein wont be a comprehensive review of Comp.Chem. must-read papers but rather papers relevant to our lab’s research or curiosity.
Maybe I’ll include some papers brought to my attention by the group and they could do the review. The whole endeavor might flop in a few weeks but I want to give it a shot; we’ll see how it mutates and if it survives or not. So far I haven’t managed to review all papers read but maybe this post will prompt to do so if only to save some face. The domain of the new blog is compchemdigest.wordpress.com but I think it should have included the word MY at the beginning so as to convey the idea that it is only my own biased reading list. Anyway, if you’re interested share it and subscribe, those post will not be publicized.
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!)
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.
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?)
So many things have happened since I last updated this blog but I will come to write on them when appropriate. Right now I’d like to share an invitation by Prof. Ponnadurai Ramasami from the University of Mauritius to the upcoming Virtual Conference on Computational Chemistry from the 1st to the 31st of August. Deadlines can be consulted here and the most important is the abstract submission on June 30th. This conference is part of the official celebrations of the International Year of Crystallography so talks involving experimental determination of electron densities will be well suited.
I participated in the latest edition and I must say it was a very enriching opportunity to learn from so many other researchers from across the world without leaving my desk. I already know what my talk will be about, now that we are so close to finish and submit a paper on the absence of reactivity for an anti-aromatic set of molecules. (I think I’ll call it “The reactivity of molecules that never existed [but that maybe should have.].) All talks are sent either as pdf, powerpoint presentations, youtube videos, etc. and Q&A are done over e-mail.
So this is a calling to other computational chemists out there who want to participate in this virtual conference. Kudos to Prof. Ponnadurai Ramasami and lets hope we can crystallize his visit to Mexico during 2014 the International Year of Crystallography (pun intended) and here’s to me going sometime to Mauritius!
About a month ago my wife and I got invited by our good friend Dr. Ruperto Fernandez (his PhD is in transport logistics and engineering) to his final presentation for a course in managerial skills he’d taken for over six months, and while I wasn’t all that thrilled about waking up at 8 AM on a Saturday, I went to cheer my good friend and show him my sleepy support. His presentation dealt with negotiations and the required skills to master them, and while he agreed that there is a huge amount of talent involved in being a good negotiator, he also pointed out that some basic knowledge of the procedure can go a long way in helping us with little to no talent in achieving the best possible outcome. Basically, a negotiation involves the agreement between a person with something which another person wants; meeting both parties expectations at the fullest extent possible is the ideal endpoint for an iterative give-and-take between them. Or so it goes.
Recently a scandal that involved the biology freelance blogger DNLee, who blogs for Scientific American with the column The Urban Scientist, took place: DNLee was asked by Biology-Online.org to write for them. Then the negotiation started; she had something the editors wanted: her texts. She agreed to do it and presented her fee (second part of the negotiation process: “I got what you want and here is what I ask in return for it“), instead of having an offer made (third part of the negotiation process: “ok, that is what you want but this is what I can give you“) the blogger got a nasty message, which I believe maybe was intended to elicit a response to better accommodate the editor’s demands but that was nothing more than a plain nasty insult: The editor asked if she was the urban scientist or the urban whore (end of negotiation; nobody got anything. Furthermore, feelings were hurt, reputations questioned and the door for future negotiations between both parties was shut completely). If the editor was unable to pay any fee at all then the editor should have tried to convince the blogger of participating for free; I would have offered her a bigger space than a regular blogger, or maybe even invited her to participate as an editor. I’m not sure they have some sort of business model but something could have been arranged. Had this negotiation not met at any point in the middle then a polite thank you could have left the door open for a future time. DNLee has a reputation that allows her to charge for her writings, had it been me, I’d probably had done it for free but because I need more exposure than her who is already famous. Internet support came promptly and hard as can be seen here and here, not that it wasn’t called for, of course!
But the issue, sadly, didn’t end there, DNLee wrote about this in her blog at SciAm, but the post was later on deleted by the editors. Dr. Mariette DiChristina tweeted that the post wasn’t related to science so it didn’t fit in the site. Pressure in blogs and other social networks prompted SciAm to place the article back on the site. Click here to go to the post.
Calling someone a whore is simply unacceptable.
During his presentation, my friend Dr. Ruperto Fernandez, talked about a negotiation he had with a potential employer. According to his account of the process, it ended quite swiftly when he was offered a much lower salary than the one he currently earns. He said the offer had some good points that could have made him accept even 5 to 10% less income respect to his current salary, but much less than that would not help him cover the bills and that was a total deal-breaker. But the talk didn’t end there, some other joint projects were laid for them to work on together and the door is still open for the future when they may be able to match my friend’s expectations as biology-online should have done with DNLee.
It has been a rough couple of weeks for the Scientific American community; first this and now the leaving of a great science writer, Bora Zivcovic whose misconduct has forced his exit out of the popular magazine. So now the aftermath for both issues remains to be seen. Sexism, though, could be found to be a common denominator in both cases: one was a victim of it, the other one is guilty of inflicting it through various instances of sexual harassment. Should this mean that biology-online, Bora Zivcovic and the affiliated-to-the-two-previous parties, the Scientific American Magazine, are to be deemed as unworthy? I hardly think so. None of us is close to sanctity and we all make mistakes, some of them willingly and other unwillingly but we are accountable for each and every one of them nonetheless; but at the same time we should also be able to separate both sides of each story and keep the best of each side while keeping a close eye (and even a loud mouth) about the wrong in each side.
I wish nothing but the best to every person involved in any of these recent events. Why is it so hard for people to just ‘play nice‘? I’ve heard many times this world would be a better place if we cared more for each other, but sometimes it seems that its actually the opposite; that this world would be be better if we didn’t care so much: if we didn’t care about the color of our skin; our gender; our nationality or ethnicity; our sexual orientation; our social status. This brings me back yet again to that presentation by Dr. Fernandez, where he was asked to describe the way he was perceived by others at his workplace and he said he didn’t quite enjoy social interactions so he is perceived as serious and aloof but was always willing to join a new project, so when reached out for one of these he’s all smiles and work. Shouldn’t we all back off a little bit from each other from time to time?
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
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!
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.
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.
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.
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…
Just Finished reading two proposals, I’m going to accept them both! 2 kids going 2 intl polymer seminar
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.
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.
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.
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:
Training a new student in using Gaussian, Gaussview and Linux. Lot of work to be done but he looks eager to learn 🙂
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:
All day editing sup. info. has rendered me cross-eyed! Time 4 a break. Will reply work (chem) related email 🙂
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:
Then more e-mail
@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.
So interesting 2 notice
#RealTimeChem deals more with research administration than wth research! I thought it’d be the other way around!