Category Archives: Random thoughts
In a nutshell, computational chemistry models are about depicting, reproducing and predicting the electronic-based molecular reality. I had this conversation with my students last week and at some point I drew a parallel between them and art in terms of how such reality is approached.
Semi empirical methods
Prehistoric wall paintings depict a coarse aspect of reality without any detail but nevertheless we can draw some conclusions from the images. In the most sophisticated of these images, the cave paintings in Altamira, we can discern a bison, or could it be a bull? but definitely not a giraffe nor a whale, most in the same way Hückel´s method provides an ad hoc picture of π electron density without any regard of the σ portion of the electron density or the conformational possibilities (s-cis and s-trans 1,3-butadiene have the same Hückel description).
More sophisticated semi-empirical Hamiltonians like PM3 or PM6 have better parametrizations and hence yield better results. We are still replacing a lot of information for experimental or adjusted parameters but we still cannot truly adopt it as truthful. Take this pre-medieval painting of one of the first Kings of England, Aelred the Unready. It is, by today standards, a good children´s drawing and not a royal portrait, we now see more detail and can discern many more features yielding a better description of a human figure than those found in Altamira or Egypt.
HF is the simplest of ab initio methods, meaning that no experimental results or adjustable parameters are introduced. Even more so, from the HF equations for a multi-electron system that complies with Pauli’s exclusion principle the exchange operator arises as a new quantum feature of matter with no classical analogue. Still, there are some shortcomings. Correlation energy is disregarded and most results vary according to the basis set employed. Take the impressionist movement, specially in France: In Monet´s Lady with Umbrella we have a more complicated composition, we observe many more features and although we have a better description of color composition some details, like her face, remain obscure. The impressionists are characterized by their broad strokes, the thicker the strokes the harder it is to observe details similar to what happens in HF when we change from a small to a large basis set, respectively.
CI (Configurations Interaction)
Extension of HF to a multi-reference method yields better results. In CI we take the original guess wavefunction -as expressed through a Slater Determinant- and extend it with one or many more wavefunctions; thus a linear combination of Slater Determinants gives rise to a broader description of the ground state because other electronic configurations are involved to include more details like the ionic and covalent pictures (configurations). The more terms we include the more real the results feel. If we take classical figurative paintings we have a similar result; most of these paintings are constituted of many elements and the more realistically each element is captured the more real the whole composition looks even if some are just merely indicated.
CCSD(T) full-CI, CASPT2
In Edwards Much’s the scream, we might think we have lost some information again and went back to impressionism but we know this is actually an expressionist painting; we can now not only observe details of the figurative portion of the image but Munch has captured his subject´s fear in the form of distorsions on the subjective reality. In this way, CCSD(T), full-CI and CASPT2 methods provide a description of the ground as well as the excited states which -in experimental reality- are only accessed through a perturbation of the elecron density by electromagnetic radiation. Something resembling radiation has perturbated the subject in The Scream rendering him frightened and wondering how to return to his ground state or if such thing will be even possible.
Density Functional Methods
At least due to its widespread use, DFT has risen as the preferred method. One of the reasons behind its success is the reduced computing time when compared to previous ab initio methods. So DFT is pretty much like photography, in which reality is captured in full but only apparently after selecting a given lens, an exposition, a filter, shutter speed and the occasional Photoshop for correcting issues such as aliasing. In photography, as in DFT, all details concerning the procedure or method for capturing an uncanny reproduction of reality must be stated in every case for reproduction purposes.
Now, in the end it all comes down to Magritte’s Pipe. Ceci n’est pas une pipe -or, ‘this is not a pipe’- reminds us that painting as with modeling we don’t get reality but rather a depiction of it. In this famous painting we look at an image that in our heads resembles that of a pipe but we cannot grab it, fill it with tobacco and smoke it.
The image above is a digital file, which translated becomes a scaled reproduction of an image painted by Magritte in which we see the 2D projection of the image of an object that reminds us of a pipe. In fact, the real name of this work is The Treachery of Images, definitely quite an epistemology problem on perception and knowledge but before I get too metaphysical I should finish this post.
Can you find where cubism or surrealism should be placed? with MPn methods, perhaps?
It was your idea. You had it. Or did it have you? But suddenly, you see it wrapped around someone else’s words. You read and gasp in denying shock. This can’t be! You read again trying to find your mistake, it is clearly a mistake on your part; to find it, you search for differences, preferably major ones that reveal that the identity of this idea is different to yours. You hope to just be mistaking it for yours. The wording is different, of course, you would have emphasized it differently, the way it deserved to be emphasized. But nevertheless its a mistreated version of yours. No matter what, this was yours. Was. Heartbroken, you try to save some face, by treating it differently; by treating it better!; by tending to those bits this third party is neglecting; by dumping it and getting a new and better one. You were so close. All in vain, for the fact is that this idea is no longer just yours, it seduced someone else’s mind and got brought to life by swifter hands. Now forever they will remain bound together as two celestial bodies are bound by gravity in the marriage of scientific annals, under the complicit auspice of editors and reviewers. Yes. You were the last to know this went on. It once made you feel so special, proud of your sparkling originality and your long hard work, brilliant even, but now you feel idle and exposed while in the dark.
You wish that at least you were perceived as a fool, as a laughing stock or even as an intellectual cuckold! But you are left worse than that: You are left with nothing. Empty handed. A runner up at best or part of the despised ‘me-too‘ kind, but only if you manage to get something out there at which the public scrutiny can roll their eyes. Still, that would be indeed better than having nothing to show for after all those long hours of shared intimacy with this idea. Angrily, you decide to blame others: technicians for delaying experiments; your collaborators for delaying revisions; your students for delaying data, and even the head of the department, maybe just for being other than yourself. You read again. The idea, no longer yours alone, stares back at you; no amount of hatred can change that. And then you wonder if you could have possible been on the other side before? You hope you have, for that means you are ahead in the game, but like in any game, sometimes you loose. Could your mind have been the seducing one before? You hope it has, for if it hasn’t it means you are playing alone in a corner of no interest to anyone, and what fun is that? What fun is a game in which you cannot win?
You mend fences. You accept that for this time someone was lucky but soon luck will come back and you will seduce other ideas; your hands will bring them to life and you will successfully collect the recognition for it, no matter how little the victory. Affairs with new ideas will come. Luck will come back. And it will come back to find you busily working or will not come back at all.
Pauli’s Exclusion Principle is a paramount concept in Quantum Mechanics which has implications from statistical mechanics to quantum chemistry, consequently, there are many different statements to summarize it depending on the forum. I occasionally joke with my students about how we learnt it in kindergarten an how we state it now at the end of our computational chemistry course.
So, are you a toddler or high up there with W. Pauli predicting the existence of sub-atomic particles at CERN? Which statement of Pauli’s Exclusion Principle sounds more familiar to you?
LOL just feeling a little humorous this morning!
So the World Cup is once again on top of us. I’m not a Football (Soccer) enthusiast but I’ve got to admit that the expectation of such a large and widely covered event is pretty contagious. This year, however, I’m very excited about the inaugural kick-off ceremony because a paraplegic teen will be the one to set the ball in motion, thanks to the use of an exoskeleton developed by the illustrious Brazilian researcher, Dr. Miguel Nicolelis, this patient will not only walk again but also perform a feat of equilibrium: kicking a football. More impressive than the exoskeleton itself is the brain-computer-machine interface since the patient will control the entire process by himself. Miguel Nicolelis is widely known and highly regarded in the scientific community; I’m not sure if he is that famous outside academia, but if he isn’t, he should be. The natural question about Dr. Nicolelis is what is he? Is he a robotics engineer? a neurologist? a programmer? a physician? The answer could be no other than ‘all of the above‘.
And even more impressive than all that, if that’s even possible, is the fact that this huge achievement of technology is presented at one of the most viewed sporting events on the planet. Brazilian organizers could have selected many things to kick-off this event: From Adriana Lima to Pelé; from a Samba line to aboriginal Amazonian people, but instead they chose to go with a scientific and technological breakthrough achieved by one of their own. I wonder if this is a way to tell the world they are interested in investing in science and technology as a way to pave the way of their economical and social development. Brazil is currently regarded as a fast growing nation economically although the social disparity seems to be still quite large. The message I’m getting, at least in principle, is that Brazil is a modern nation with high regard for scientific development on which they will rely their future.
Kudos to the Brazilian organizers who thought of placing this large scientific breakthrough in a sporting event, proving that this world should become boundless and the way to do it is through science.
Another year is almost done and as I write my annual report I realize this year has had several milestones for me as a researcher, most of which got recorded in this blog.
I published three papers in peer reviewed journals, one of which actually made the cover of J. Inclusion Phenomena, the other two were published in J. Phys. Chem. C and Eur. J. Inorg. Chem.; two more papers are currently under the reviewing process, one of which is further down the line in a journal whose title I dare not speak for fear of jinxing it! A small article on computational chemistry basics, entitled “Chemistry without Flasks” for a magazine edited by the National Council for Research and Technology (CONACyT) was also published early this year; during the summer we had the visit of quite a few internship students who got gather some data despite my absence; my more regular students, Maru and Howard presented one poster each at the National Congress of Chemistry organized by the Mexican Chemical Society, and Howard also presented another poster at the Mexican Reunion of Theoretical Physical Chemistry; Maru wrote and defended her thesis in May, which makes her the first student ever to graduate from my research group; I participated once again as a juror of the Mexican Science and Engineering Fair; and last but not least I got a promotion at the National System of Researchers (SNI).
New immediate challenges lie ahead and I shall face them rationally and passionately.
These are small accomplishments for larger research groups, I know, but I’m truly happy to see how our combined efforts, along with the support of the National Autonomous University of Mexico and the Institute of Chemistry, are slowly paying off! One can only hope the growth curve is not linear but exponential.
Thanks to every reader who has interacted with me through this blog; thanks for your comments, ratings, sharing and ‘likes’. May you all have a happy holiday season, winter break or New Year party, whatever it is you get to do these days!
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?
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.
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.
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.
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‘?
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.
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.
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.
This morning at around 9 AM, I guess, this little blog of mine reached a significant milestone: It reached 100,000 visitors!
The blog started about 3.5 years ago when I was still living in Romania working at the lab of the late Prof. Dr. Ioan Silaghi-Dumitrescu. Back then I started the blog as a way to make my research visible to others and maybe in that way I could gain some notoriety which could help me in the near future to land a fine research position. None of that happened. I remember we were having some issues with some PCM calculations in the lab and after a lot of hard work and a lot of asking we gather some tips to work with implicit solvation models in Gaussian. Prof. Silaghi suggested we should write them down and put them on the wall of the lab so we had them available at all times; it was then when I suggested we could place them in my little blog so we had them available online. This happened in September 2009, three years ago, and little did I know, this post became quite popular, it is still one of the most visited ones in the blog. Later on we had a similar problem while trying to visualize Natural Bond Orbitals, there was too much information but it was all scattered, so we did it again, we gathered some of the info and made a new post which became also quite popular.
Little have I written about my own work, mostly because of fear of being scooped, I guess.
I’d like to thank every reader who has ever liked, commented, rated, favorited, shared, reblogged, blogrolled, recommended any of my posts and the nearly 200 people who have subscribed or followed this little blog, as I like to call it.
I was first introduced to Bradbury’s writing in 1989 during my first year in junior high school (here in Mexico that is the 7th grade; I was eleven years old then) by my literature teacher Ángel Molina-Aja at LOGOS School, a progressive institution in southern Mexico City; so now with the departure of the grand master of Science Fiction I can’t help but to think about Ángel and his possible motivations for making us read ‘The Martian Chronicles‘ of all possible books. It is pretty obvious now that his intention was to engage us in literature (prior to ‘Chronicles‘ we read ‘The Hobbit‘) and to make us read something that would in turn make us want to read more and so by reading we would open a world of possibilities to ourselves. His job as a literature teacher wasn’t just to make us learn about literature but to learn how to appreciate it for the values that leaves in our lives, whatever our own inclinations were. As I’ve written before, science fiction is a usual common denominator to us people working in science because we deal with imagining how to bring to life things and ideas that are currently nonexistent. Whether we create new materials with new applications or we come up with wacky mathematical theories that describe the intricacies of the universe, we all have to first set our imaginations free and believe everything is possible. In this way we are sometimes less pragmatical (albeit not necessarily more creative) than lawyers, business people and the like. Education should then be formative, not informative, in order to make an intellectually resourceful population in every area of the human and social development. Here in Mexico the average reading habit is less than 1 book a year per person! and with the upcoming presidential elections and the respective campaigns, it becomes obvious that a poorly read people is a very manipulable one. And the idea of an ignorant population kept in line by the ruling powers through alienating them from literature is the main theme of Bradbury’s other masterpiece ‘Fahrenheit 451‘, in which a fireman is a person who starts fires in order to destroy books (it is widely known by now thanks to this novel that 451 degrees Fahrenheit is the temperature at which common paper ignites itself). In ‘Fahrenheit 451‘ books are banned because they make people unhappy and unsettled by showing them a world of possibilities that they may or may not achieve, so it is safer to just satisfy people basic needs, which include 24 hours of personalized TV programming on every wall of their homes (sounds familiar?), and by doing so they wont question their leaders or their position in society. They just wont have dreams! That’s the bottom line. The many troubles of my country won’t be solved by people reading Bradbury, but if I was engaged into literature by ‘Chronicles‘, among other books from other authors, and by that engagement I was able to discover the world of science and decide I wanted to become one, then the ripple or domino effect triggered by reading, reached its goal; a goal set by my teachers, to whom I will be always most thankful.
I wish I could post a picture of my old copy of ‘Chronicles‘ but I guess it’s back at my parents place all worn out. I have to remember taking a picture of it next time I visit my folks. Here is a picture of my old copy of the Spanish translation to ‘Chronicles‘ all worn out thanks to me and my sister, I guess. Thanks to my dad and his ninja-dropbox-skills for getting this picture for me!
Bradbury’s work and specially ‘The Martian Chronicles‘ romanticized the idea of space exploration. What a huge coincidence, in a sort of a poetic way, that his departure occurred on the same day as the transit of Venus, a phenomenon that will not occur for another 105 years. I wrote earlier on my facebook page that he did not died, that he only went back to Venus. I was close to not posting it for it might be in bad taste, but then I thought that I don’t know what happens when we die and nobody else in the world does either, so this is as valid as any other hypothesis but only more romantically so.
Rest in peace Mr. Ray Bradbury and may this be a thankful testimony for all those hours of rational entertainment and enlightenment.