Category Archives: Teaching
We celebrate the successful thesis defense of Gustavo “Gus” Mondragón who has now completed his Masters degree and is now on to getting a PhD in our group. Gustavo has worked on the search for multiexcitonic states and their involvement in the excitonic transference between photosynthetic pigments, specifically between bacteriochlorophyll-d molecules (BChl-d) from the bchQRU chlorosome whose whole structure is shown in the gallery below. To this end, Gustavo has studied and implemented the Restricted Active Space method with double spin flip (RAS-2SF) with the use of QChem5.0, a method that has required the use and understanding of states with high multiplicities. Additionally, Gustavo has investigated the influence of the environment within the chlorosome by performing ONIOM calculations for the spectroscopic properties of a BChl-d dimer, finding albeit qualitatively a batochromic effect, probably an expected result but nonetheless an impressive feat for the level of theory selected.
There’s still a lot of work to do in this line of research and although we’re eager to publish our results in this excitonic transference mechanism we want to be completely sure that we’re taking every possibility into consideration so we don’t incur into any inconsistencies.
Gustavo cultivates many research interests from excited states of these pigments to biochemical processes that require the use of various tools; I’m sure his permanence in our lab will bring lots of interesting results. Congratulations, Gus! Thank you for your hard work.
It is with great pride that I’d like to announce that for the first time we have a Masters Student graduated from this Comp.Chem. lab: María Eugenia “Maru” Sandoval-Salinas has finished her graduate studies and just last Friday defended her thesis admirably earning not only the degree of Masters of Science in Chemistry but doing so with the highest honors given by the National Autonomous University of Mexico.
Maru’s thesis is for many reasons a landmark in this lab not only because it is the first graduate thesis published from our lab but also the first document on our work about the study of Photosynthesis, a long sought after endeavor now closer to publication. It must also be said that Maru came to this lab when she was an undergraduate student five years ago when I just recently joined UNAM as a researcher fresh out of a postdoc stay. After getting her B.Sc. degree and publishing an article in JCTC (DOI: 10.1021/ct4004178) she now is about to publish more papers that I’m sure will be as highly ranked as the previous one. Thus, Maru was a pioneer in our lab giving it a vote of confidence when we had little to nothing to show for; thanks to her hard work and confidence, along with that of the students who have followed her, we managed to succeed as a consolidated research group in the field of computational chemistry.
More specifically, her thesis centered around finding a mechanism for the excitonic transference between pigments (bacteriochlorophyl-a, BChl-a) in the Fenna-Matthews-Olson (FMO) complex, a protein trimer with seven BChl-a molecules in each monomer, located between the antenna complex and the reaction center in green sulfur bacteria. Among the possible mechanisms explored were Förster’s theory, a modification to Marcus’ theory and finally we explored the possibility of Singlet Fission occurring between adjacent molecules with the help of Dr. David Casanova from the Basque Country University where Maru took a short research stay last autumn. Since nature doesn’t conform to any specific mechanism -specially in a complex arrangement such as the FMO- then it could be possible that a combination of the above might also occur but lets just wait for the papers to be published to discuss it. Calculations were performed through the TD-DFT and the C-DFT formalisms using G09 and Q-Chem; comparing experimental data in CH3OH (SMD implicit calculations with the SVWN5 functional) were undertaken previously for selection of the level of theory.
Now, after two original theses written and successfully defended, an article published in JCTC and more in process, at least five posters, a couple of oral presentations and countless hours at her desk, Maru will go pursuit a PhD abroad where I’m sure she will exceed anyone’s expectations with her work, drive, dedication and scientific curiosity. Thank you, Maru, for all your hard work and trust when this lab needed it the most, we wish you the best for you earn it. You will surely be missed.
A couple of weeks ago I was invited to give a talk to a small university in southern Mexico called ‘Universidad de la Cañada‘ in the state of Oaxaca, one of the most underprivileged states in our nation. This institution is a rather small one but the work they are doing over there with as little resources as they have is truly remarkable . UNCA offers degrees in pharmacy, pharmacology, food sciences, clinical chemistry and other topics that aim to supply the needed human resources for the various industries that are settled in the region. There is a true feeling of togetherness at UNCA since they have little pieces of equipment yet they are all fully shared among researchers regardless of who received the finance to acquire them. Last year, two of their students came for a two months stay, after which, Alberto and Eduardo got their names on a publication of our research group. It was nice to see them again and even nicer to learn they are about to finish their studies and that they will come back again to our lab in late July.
Every year at UNCA there is a Pharmacology Day on which the students show the results to their research projects during a poster session and listen to lectures by guest speakers from various universities around Mexico. Most of their projects were aimed to the isolation of natural products from local resources and their usage in several kinds of consumer products. UNCA is in a very small town, village I might say, surrounded by mountains and vegetation; the view was spectacular as you may see from the pictures below. Thank you very much to my good friend Dr. Carmen Hernández-Galindo for inviting me to participate and share our work with their students, I hope we may go back again and keep a fruitful exchange between our groups.
During this talk, I took the opportunity to talk about the aforementioned paper in the context of molecular recognition and their in silico design but I think I should have talked more about the computational strategies that are most employed in the pharmaceutical industry. Never mind. I hope I get the opportunity to right this wrong. Still it was nice to give Alberto and Eduardo the opportunity to brag a little about being published authors.
Kudos to Rola Aburto, Dr. Margarita Bernabé, Dr. Rocío Rosas, and all the academic staff at UNCA for their invaluable dedication to teaching science against all odds, I can testify, through the hard work of their students, hat their effort is paying off.
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?)
I’ve been neglecting this blog a lot lately! It would seem as little or nothing is going on in our lab but it’s quite the opposite, a lot of good stuff is going on and most of the excitement comes from the results obtained by a few more interns.
Alberto and Eduardo came just as the previous group of interns left. They’re both undergrad students in Pharmaceutical Sciences at Universidad de la Cañada in southern Mexico. My good friend, Dr. María del Carmen Hernández, referred them to me to do a stay during their summer vacations. They are taking where the previous interns (Paulina, Eliana, Javier and Daniel) left and have now obtained the interaction energies for five different host-guest aducts for 3-phenyl-1H-bezofuro[3,2-x]pyrazole, a tyrosine III kinase inhibitor, currently under research for the treatment of leukemia, better known to us as GTP. As before, our molecular carriers are a wide selection of functionalized-calix[n]arenes. These calculations turned out to be rather lengthy; they were all performed at the B97D/6-31+G(d,p) level of theory in order to account for dispersion forces in pi-pi interactions between the aromatic rings in both species.
The third recent addition to our lab is Monserrat Enriquez, who is a PhD student under the supervision of my good friend Dr. Eddie López-Honorato (if you haven’t checked his blog on nuclear energy and materials for nuclear reactions containment go now and follow it; encourage him to post more often!). Monserrat will be co-advised by me. Her project lies within the scope of molecular recognition, materials recovery and bioremediation; calculations and simulations will help the experimental team to point the synthesis of sequestrating agents in the right direction, or, at the very least, to have a better understanding of the forces and interactions lying beneath the formation of such complex structures.
Last but not least, Luis Enrique is back with a vengeance! He is determined to finish his study on other tyrosine kinase inhibitor drugs. Luis Enrique is an undergrad Chemistry student here in Toluca at the Autonomous Mexico State University, so he will come on his spare time and work from home every now and then; who knows! maybe he’ll end up with a dissertation by the time he finishes his undergrad studies!
But I’m to be left alone pretty soon, as Alberto and Eduardo will stay for a couple of weeks more and Luis Enrique will be here on his spare time. Monserrat will leave on Friday back to Saltillo in Northern Mexico to continue working on the experimental part of her research while working on her calculations from a distance.
Thanks to them for their invaluable help in the development of our research group, for their enthusiasm and hard work. You are now a part of this lab and its doors will always welcome you back!
For the last five weeks we had guests in our lab coming from different places of the country: Tepic (west), León (Center) and Mexico City (Right in the middle!). During those five weeks they worked in the field of computational chemistry helping our research efforts with a couple of drug carrying molecules. They learned about computational chemistry and drug design; about wavefunctions and density functionals; about population analysis and vibrational frequency analysis. Dead hours were a bit complicated to handle because the convergence of each calculation takes some time and, as opposed to a wet-chemistry lab, I couldn’t just ask them to purify starting materials or distillate solvents. A question to other theoretical/computational chemists: What could I have asked young undergrad students (with backgrounds ranging from engineering to pharmacy) to do during those dead hours? What did I do wrong? Anyway, they manage to spend a good time since they all got along quite well.
Now they are back to their hometowns getting ready for the congress, hosted by the same organization that awarded them the stipend to come and spend their summer with us (The Dolphin Program / Programa Delfín) as well as to going back to school in a few more weeks. I asked* them to write a guest post for the blog telling their experience, which is presented below. Thanks to you all for choosing our lab to get your internship this summer!
Javier Camacho (Mexico City)
Hi, I’m Javier from ESIQIE-IPN
The dolphin program has given me the opportunity to experience how is to be in a high-level scientific research. Login to CCIQS next to the imminent Dr. Joaquin Barroso Flores, left me a pleasant experience. The great contribution that gives this line of research has allowed me to meet new horizons, beyond the area of engineering, to which I belong.
The theoretical chemistry and computational chemistry together, are a great weapon to develop virtual optimizations that allow us to find drug transport agents, without making the vast amount of laboratory tests that are required. Explaining that this is one of the many applications that can be used.
To undertake this experience has left me very satisfied, be guiding a person who likes his work and want to show what he knows, it makes me very happy. After these long weeks of work and perseverance, with certainty affirm the interesting and productive it is to be part of the investigation in Mexico.
I thank the Dolphin Program, gives CCIQS the UAEM-UNAM and Dr. Joaquin for opening the doors to this great opportunity to start my story as a researcher.
Paulina Pintado (Tepic, Nayarit)
Hi my name’s Paulina and I came as part of Dolphin Research Program that gives the opportunity of participates in a real work of investigation with a professional at the topic. In this occasion I came to work with Ph.D. Joaquin Barroso in a small project of his line of research; namely theoretical drug carriers design. In this six weeks besides to learn more aspects about my career, in this case Theoretical Chemistry applied to pharmaceutical industry; I tested the experience of travel to another town just by myself, live with people from different parts of the country with distinct customs and visit few places of the town.
This summer will always be memorable ‘cause this internship is an important event for my professional experience and also for my personal development and I hope many others students have the courage to try get into the world of scientific research.
So just remains for me to thank to Ph.D. Joaquin Barroso for giving me the chance to do this internship in his lab I hope you continue having success in your work, I feel pretty glad to met him and my others research’s mates.
Daniel Carteño (Mexico City)
Ey my name’s Daniel and this summer of 2013 i had been the opportunity to do a research internship in Toluca under P.H.D. Joaquin Barroso, and during this period of time I´ve learnt a bit about His research work, not only this is an important experience for my educational history, but it also is for my personal life. Learnt about theoretical chemistry open my vision of this discipline, because when I thought about chemistry I´ve never imagine a computational laboratory, this the most important part, nowadays the researches have been removed due to they are so expensive and finally the conclusion is not expected, when you use a super computer like me and my work team used, it doesn’t matter if you have a mistake or do something wrong, only you have to write again the keywords and the only thing you spend is time. Even in Mexico theoretical chemistry is not famous in my opinion is a useful work tool. This research internship was highly satisfactory and hope do it again i´m glad
*Their contributions were completely voluntary and no editing of their original texts has been made.
This week has been a happy one since four new additions to our staff have been made, at least for the summer, that is. Paulina, Eliana, Javier and Daniel have come to our lab from various different towns across the nation to spend six weeks working hard in small projects related to our lines of research; namely theoretical drug carriers design. This time the drug under study is known as GTP or 3-phenyl(1H-benzofuro[3,2]pyrazole and calixarenes will once again act as the potential carriers.
They all came as part of the Dolphin Research Summer Program (link in Spanish only) in which college students spend a few weeks doing research in the lab of their choosing. This is the first time I participate as a tutor and I find it a great opportunity for young students to get familiar with certain aspects of science they wont learn inside school.
So far these past three days have been quite intense with them learning how to edit and submit a Gaussian calculation in a Linux environment. I’ve already taught them about geometry optimizations, frequency analysis, (natural) population analysis and Fukui reactivity indices calculation. There is much more to learn still, of course, but so far so good. I believe the major drawback so far has been their own eagerness since they’d like to have all the data imediately! Unfortunately they’ll have to wait for their initial calculations to converge. We started this week by doing some simple analysis of all the properties described above for the Cytosine-Guanine base pair at the B97D/6-31+G(d,p) level of theory. Luckily their calculation crashed promptly, and I find that lucky because that gave me the opportunity to teach them how to relaunch a failed calculation, which, unfortunatelly will happen more often than not.
So, welcome guys! Thanks for choosing this lab for doing your internships. I hope you find our research interesting and motivating, may this be the first step into a full time research career. Also, kudos to the Dolphin Staff for helping promote science in young Mexican students. Stay tuned for a guest post from all of them once they finish their time here.
Today is truly a landmark in our lab because on this day, María Eugenia “Maru” Sandoval-Salinas has defended her thesis and has thus obtained her B. Sc. in Chemistry. She is the first student under my supervision to achieve this goal, and I hope it won’t be long until we get some more, although now the bar has been set quite high. For the time being, Maru is pursuing a career in the pharmaceutical industry but has every intention of coming back to the lab for her Masters degree; she has a reserved spot here with us at CCIQS.
Maru’s thesis deals mainly, but not exclusively, with calculating the interaction energies of calix- and thia-calix[n]arenes with the tyrosine kinase inhibitor Imatinib, which is widely used in the treatment of Chronic Myeloid Leukemia (CML), in order to rationally design a drug delivery agent for this drug. Her work is (a huge) part of an article currently under revision that I only wish had been published before her defense. Still, we await for that paper to be published in the next few weeks.
Throughout her stay at our lab, Maru was a dedicated student willing to learn new skills every time. As she replied today to one of the questions: “it’s not so much how many calculations I got right, but how many I got wrong!“. I find deep meaning in this sentence, perhaps deep enough as to consider it an aphorism, because indeed the more we try the more we fail, and the more we fail the more we learn and the closer we get to success.
Congratulations, Maru! I personally thank you for all the hard work invested in your thesis, all the long hours in front of the computer and your disposition to learn and work during the last 1.5 years. I’m certain you’ll find success in any venture you undertake; and I’m certain of it because you never stop trying.
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.
Here is a link to an article I was invited to write by my good old friend, Dr. Eddie López-Honorato from CINVESTAV – Saltillo; Mexico, for the latest issue of the journal ‘Ciencia y Desarrollo’ (Science and Development) to which he was a guest editor. ‘Ciencia y Desarrollo’ is a popular science magazine edited by the National Council for Science and Technology (CONACyT) of which I’ve blogged before.
This magazine is intended for people interested in science with a general knowledge of it but not necessarily specialized in any field. With that in mind, I decided to write about the power of computational chemistry in predicting some phenomena while shedding light in certain aspects of chemistry that are not that readily available through experiments. The article is titled ‘Chemistry without flasks: Simulating chemical reactions‘. The link will take you to the magazine’s website which is in Spanish, as is the article itself, and only to the first page; so, below I translated the piece for anyone who could be interested in reading it (Hope I’m not infringing any copyright laws!). Don’t forget to also check out Dr. López-Honorato’s blog on nuclear energy research and the development of materials for nuclear waste containment! Encourage him to blog more often by liking and following his blog.
Chemistry without flasks?
Typically we think of a chemist as a scientist who, dressed in a white robe and protected with safety glasses and latex gloves, busily working within a laboratory, surrounded by measurement equipment, glassware and bottles with colored substances; pours one substance onto other substance, transforming them into new substances while noting that the chemical reaction occurs through color changes, heat release , perhaps gas, and occasionally even an explosion.
Thus chemistry, the study of the material processing involves active experimentation to accomplish chemical reactions subsequently confirmed, although indirectly, that the changes have been conducted in the microscopic world, moreover, in the molecular and atomic world. The chemist plans these changes based on the knowledge he has of the chemical properties of the substances of which he started and, like any other substance, are due to its molecular structure, i.e., the spatial arrangement of the atoms that form it.
Under this archetypal image just posed, then it’s at least funny to think that there is a branch of chemistry named Theoretical Chemistry.
What is theoretical chemistry?
Theoretical chemistry is a kind of bridge between chemistry and physics; using laws and equations that govern the subatomic world, to calculate the molecular structure of a substance, more specifically calculate the distribution of electrons surrounding the molecule forming a cloud, which interact with the electron cloud of another molecule to form a new substance. It is based on the knowledge of the electron density cloud or we can understand and predict the chemical properties of any substance. We can then define theoretical chemistry as the set of physical theories that describe the distribution and properties of the electron cloud belonging to a molecule, in this particular mathematical description we call electronic structure and this is the starting point for descriptions and chemical predictions.
What is it good for?
Through theoretical chemistry we can find answers to fundamental questions about the structure of matter. Consider a molecule of water, which has the chemical formula H2O. This formula implies that there are two hydrogen atoms attached to an oxygen atom But what spacial structure does a water molecule have? The simplest geometry it could take would be a linear structure, in which the angle formed by the three atoms is 180 °. However, the water molecule has an angle of 109 °, far from a linear structure. In Figure 2 we can see the result of the calculation of the electronic structure of H2O, it observed that the electron cloud that exists on the oxygen atom also has a place in space and thus push the hydrogen atoms bringing them together instead of allowing them to take a more comfortable conformation.
Figure 2. Oxygen remaining electrons (red cloud around the oxygen atom) that are not chemically push the hydrogen atoms towards each other.
The industrial area currently impacted by the application of theoretical chemistry is the pharmacist, as they generate a new drug involves significant investment in financial and human resources, so predicting the properties of a molecule with pharmacological activity before synthesizing is highly attractive. Therefore it has been generated within the theoretical chemistry field, otherwise known as branch Rational Drug Design.
Drugs acting on our organism when active molecules interact directly with the various proteins which are distributed in the tissue cells. If the structure of the protein is known and we attack is known also a drug which acts on it, then we can design similar drugs having greater efficacy in the treatment of diseases. But it is not only fit one molecule to another, but to calculate the energy of interaction, the energy of dissolution and the probability that this interaction can be observed experimentally (Figure 3). The calculation of the interaction energy between the drug and the protein tells how strongly attract each other, a weak attraction drug will result in a low efficiency, while a greater attraction involve a more effective drug.
How do you calculate a molecule?
All matter exists in the universe is made of atoms, which in turn are composed of a nucleus of protons and neutrons surrounded by a cloud of electrons. When two or more atoms combine to form a molecule combining do their electron clouds and how do these combinations are best described by the equations of quantum mechanics, the branch of physics that describes the behavior of the subatomic world. However, due to its complexity, the equations of quantum mechanics can only be accurately resolved in the simplest cases such as the hydrogen atom, which consists of a single electron orbiting a proton. We must therefore resort to a range of methods and approaches to tackle cases of chemical interest and even biological.
For years the only available computers could solve the approximate equations for small molecules, no later than thirty atoms, which which can be interesting, but not entirely useful. Today modern supercomputing equipment (which may amount to up to tens or even hundreds of powerful computers connected together to work cooperatively) allow us to make models with hundreds of atoms molecules such as proteins or DNA fragments.
While the software available to perform these calculations is developed continuously for the last thirty years has been the progress in the design of computer systems able to perform thousands of operations per second the cornerstone that has made the theoretical chemistry a predictive tool commonly used. Today the branch known as Molecular Dynamics, which studies the interactions between molecules over time, has benefited from the development of the latest game consoles, as their processors, known as graphics processing units (GPUs , for its acronym in English) are able to perform calculations in parallel: Many of the images seen in our video games are actually calculated, not animated, this means that the console must calculate how to answer each item on the screen According to each stimulus we introduce. Conversely, if the images were animated, the answers would be always the same and the game would become unrealistic. Each game event should be calculated almost immediately to maintain its fluidity and emotion, in such a way that these GPUs have to be able to perform several mathematical operations simultaneously.
Traditionally molecular dynamics is based on the equations of classical physics, which only see the time evolution of molecules like solid objects collide, hundreds of molecules floating in water or other solvent. With the advent of GPUs can include dynamic calculating the electronic structure so we can peek into biological processes such as DNA replication or the passage of nutrients through a channel protein embedded in the membrane of a cell.
Since the fundamental understanding of the distribution of electrons in a molecule, its structure and properties to rational drug design, new materials based on molecular modeling theoretical chemistry is a powerful tool which is constantly progressing. The development of computer systems increasingly powerful detail allows us to meet the electronic processes involved in a chemical reaction while we can predict the real-time progress of molecular transformations. All this brings us ever closer to the dream of modern alchemists: transform matter to obtain substances with properties designed to pleasure.
In the nineteenth century, the American philosopher Ralph Waldo Emerson, wrote: “Chemistry was born from the dream of the alchemists to turn cheap metals into gold. By failing to do so, they have accomplished much more important things. ” And yes. Today we delve into the innermost secrets of nature not only to understand how it works but also to modify its operation on our behalf.