Category Archives: Blogging
2017 was a complicated year for various reasons here in Mexico (and some personal health issues) but nonetheless I’m very proud of the performance of everyone at the lab whose hard work and great skills keep pushing our research forward.
Four new members joined the team and have presented their work at the national meeting for CompChem for the first time. Also, for the first time, one of my students, Gustavo Mondragón, gave a talk at this meeting with great success about his research on the Fenna Matthews Olson complex of photosynthetic bacteria.
The opportunity to attend WATOC at Munich presented me the great chance to meet wonderful people from around the world and was even kindly and undeservingly invited to write the prologue for an introductory DFT book by Prof. Pedro Cerón from Spain. I hope to Jeep up with the collaborations abroad such as the one with the Mirkin group at Nortgwestern and the one with my dear friend Kunsagi-Mate Sándor at Pecsi Tudomanyegyetem (Hungary), among many others; I’m thankful for their trust in our capabilities.
Two members got their BSc degrees, Marco an Durbis, the latter also single handedly paved the way for us to develop a new research line on the in silico drug developing front; his relentless work has also been praised by the QSAR team at the Institute of Chemistry with which he has collaborated by performing toxicity calculations for the agrochemical industry as well as by designing educational courses aimed to the dissemination of our work and QSAR in general among regulatory offices and potential clients. We’re sad to see him go next fall but at the same time we’re glad to know his scientific skills will further develop.
I cannot thank the team enough: Alejandra Barrera, Gustavo Mondragón, Durbis Castillo, Fernando Uribe, Juan Guzman, Alberto Olmedo, Eduardo Cruz, Ricardo Loaiza and Marco Garcia; may 2018 be a great year for all of you.
And to all the readers thank you for your kind words, I’m glad this little space which is about to become nine years old is regarded as useful; to all of you I wish a great 2018!
Communication of scientific findings is an essential skill for any scientist, yet it’s one of those things some students are reluctant to do partially because of the infamous blank page scare. Once they are confronted to writing their thesis or papers they make some common mistakes like for instance not thinking who their audience is or not adhering to the main points. One of the the highest form of communication, believe it or not, is gossip, because gossip goes straight to the point, is juicy (i.e. interesting) and seldom needs contextualization i.e. you deliver it just to the right audience (that’s why gossiping about friends to your relatives is almost never fun) and you do it at the right time (that’s the difference between gossips and anecdotes). Therefore, I tell my students to write as if they were gossiping; treat your research in a good narrative way, because a poor narrative can make your results be overlooked.
I’ve read too many theses in which conclusions are about how well the methods work, and unless your thesis has to do with developing a new method, that is a terrible mistake. Methods work well, that is why they are established methods.
Take the following example for a piece of gossip: Say you are in a committed monogamous relationship and you have the feeling your significant other is cheating on you. This is your hypothesis. This hypothesis is supported by their strange behavior, that would be the evidence supporting your hypothesis; but be careful because there could also be anecdotal evidence which isn’t significant to your own as in the spouse of a friend had this behavior when cheating ergo mine is cheating too. The use of anecdotal evidence to support a hypothesis should be avoided like the plague. Then, you need an experimental setup to prove, or even better disprove, your hypothesis. To that end you could hack into your better half’s email, have them followed either by yourself or a third party, confronting their friends, snooping their phone, just basically about anything that might give you some information. This is the core of your research: your data. But data is meaningless without a conclusion, some people think data should speak for itself and let each reader come up with their own conclusions so they don’t get biased by your own vision and while there is some truth to that, your data makes sense in a context that you helped develop so providing your own conclusions is needed or we aren’t scientists but stamp collectors.
This is when most students make a terrible mistake because here is where gossip skills come in handy: When asked by friends (peers) what was it that you found out, most students will try to convince them that they knew the best algorithms for hacking a phone or that they were super conspicuous when following their partners or even how important was the new method for installing a third party app on their phones to have a text message sent every time their phone when outside a certain area, and yeah, by the way, I found them in bed together. Ultimately their question is left unanswered and the true conclusion lies buried in a lengthy boring description of the work performed; remember, you performed all that work to reach an ultimate goal not just for the sake of performing it.
Writers say that every sentence in a book should either move the story forward or show character; in the same way, every section of your scientific written piece should help make the point of your research, keep the why and the what distinct from the how, and don’t be afraid about treating your research as the best piece of gossip you’ve had in years because if you are a science student it is.
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.
Like everybody else, we are doing a brief recount of the achievements of this lab during 2016 if for no better reason because it helps me map my annual report.
We published seven articles:
- A Mixed DFT-MD Methodology for the In Silico Development of Drug Releasing Macrocycles. Calix and Thia-Calix[n]Arenes as Carriers for Bosutinib and Sorafenib Journal of Computational Chemistry 2016, 37, 10, 940–946
- In silico design of calixarene-based arsenic acid removal agents J Incl Phenom Macrocycl Chem (2016) 85:169–174
- Aromatization of pyridinylidenes into pyridines is inhibited by exocyclic delocalization. A theoretical mechanistic assessment Tetrahedron 72 (2016) 4194-4200
- Reactivity of electrophilic chlorine atoms due to σ-holes: a mechanistic assessment of the chemical reduction of a trichloromethyl group by sulfur nucleophiles Phys. Chem. Chem. Phys., 2016, 18, 27300-27307
- Ab Initio Modeling Of Friction Reducing Agents Shows Quantum Mechanical Interactions Can Have Macroscopic Manifestation J. Phys. Chem. A, 2016, 120 (46), pp 9244–9248
- Crystal Structure and DFT Studies of 4-Methyl-N-(1-phenylethyl)-N´-(1-phenylethylidene)benzenesulfonohydrazide. Evidence of a carbene insertion in the formation of acetophenone azine fromacetophenone p-toluensulfonyl hydrazone. Canadian Journal of Chemistry 2016 (doi: 10.1139/cjc-2016-0183)
- Synthesis and Crystal Structures of Stable 4-Aryl-2-(trichloromethyl)-1,3-diaza-1,3-butadienes Synthesis 2016, 48, 2205–2212
Two students got their degrees:
- María Eugenia “Maru” Sandoval got her Masters Degree with a thesis on mechanisms for the excitonic transference in photosynthetic pigments.
- Gustavo “Gus” Mondragón got his Bachelor of Sciences Degree also with a thesis on mechanisms for the excitonic transference in photosynthetic pigments.
And even a patent was filed! (more on that next year when appropriate.)
We participated in the annual Mexican Meeting on Theoretical Physical Chemistry with four posters and the internal symposium both at CCIQS and the Institute of Chemistry.
2016 was a great year for us and we hope to have an even better 2017 but just as before it will only be possible thanks to the hard work and dedication of all the members of this lab, -some of which have now left us to pursuit higher ends like Maru Sandoval who leaves for Spain and Guillermo Caballero who is already at Cambridge- and also to my colleagues who keep inviting us to collaborate in exciting projects. We have new members in the lab and also new research interests but the one common denominator throughout the years in the lab is fun; having fun in doing chemistry always.
Thank you to everyone who has ever read this blog and to those who have dropped a line here and there; I know I’ve neglected this space during this year, I want to fix it in 2017. May next year be awesome for everyone; lets make it so!
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 post was inspired by this other one, featured in WordPress’ Freshly Pressed section, on how should non-scientist read a scientific paper. While the approach presented therein is both valid and valuable, I’d like to address the way I think a scientist should read a paper, given the fact that we need to read a lot of them at all times. Each scientist has their own reading style, not to mention their own writing style, and while my CV could indicate I don’t know how to do neither one, here I present to you my scientific-paper-reading style which I consider to be the most suitable for me.
I’d like to start by emphasizing that I dive into scientific literature in a bona fide fashion. That is not to say I’m totally naive or even gullible, but even when science is all about questioning and casting doubt onto all sorts of claims, we can’t re-develop every bit of science we need. At a certain point we must start
*gasp* believing trusting other scientists’ claims. Reading in what I call bona fide is not mutually exclusive with critical reading. This sort of scientific trust is earned, to a degree, mostly by two indicators: Author’s preceding reputation at the time of publication of any given paper as well as the journal’s. Both indicators aren’t without controversy and flaw.
The way I read a paper is the following: I start with the Abstract, then follow with the Conclusions, then the Results section, sometimes I read the details of the methodology and seldom read the Introduction. Let me explain.
I read the abstract first because I read in bona fide as I hope the authors wrote the paper in bona fide. If properly written, the abstract should include all the relevant information as to what was done, why, and how but also point to the knowledge derived from it all: Their conclusions! and that is why I follow with that section. I’m interested in knowing what the authors learned and ultimately want me to learn about their study. Once again I’m reading in bona fide, so I hope they weren’t tempering their results to fit their preconceptions, that all experiments were thoroughly self-judged, validated, correlated, referenced and controlled. Recently, my sister Janet, who is a physicist working on her PhD in neuroscience, told me about some friends of hers who never (shall I say, never have I ever?) read the conclusions as to not becoming biased by the authors. To me it seems like too much work having to scrutinize every piece of data again in order to come up with my own conclusions when authors, collaborators, people on the hallway down the lab (optional), referees and editors (vide infra) have already (hopefully) done it (properly). Still I put on my scientist badge and question everything I critically read in the results section trying thus to understand how did the authors reached their conclusions and asking myself if I could come up with something entirely different. No? OK, how about something slightly different? Still no? Well, do I agree with the authors on their findings and their observed results? And so on. I like thinking that my critical reading process resembles the Self Consistent Field method which iteratively reaches the best wavefunction for a set of certain given conditions, but it never reaches the exact one.
The methodology section is a bit tricky, specially when it comes to computational chemistry. Back when I was a grad student, working in an inorganic chemistry lab, I’d only read the methodology if I had any plans of reproducing the experiment, other than that I didn’t care too much if reagents were purchased from Aldrich or Fluka or if the spectrophotometer was a Perkin Elmer one, I just expected authors to have purified their reagents prior to usage and calibrated all spectrophotometers. Now in computational chemistry I read about the methods employed, which functional and what basis set were used and why were they selected are my most frequent questions, but the level of theory is usually stated in the abstract. I also take a look at what methods were used to calculate which properties; these questions are important when we have to validate our trust in the results in front of us.
Finally, I seldom read the introduction because, if the paper is relevant to my own research, I don’t need to read why is important or interesting, I’m already sold on that premise! that is why I’m reading the paper in the first place! If both me and the author act in bona fide, we both already know what the state of the art is, so lets move on because I have a ton of other papers to read. Hence, I read the introduction only when I’m trying to immerse myself in a new field or when reading something that seems interesting but which has little to do with my area of expertise. There is another reason why I almost never read introductions and that is that, even when I try to work in bona fide, there are a lot of people out there who don’t. Twice have I received the reviews from a mysterious referee who believes it would serve the work a great deal to cite two, maybe three, other papers which he or she lists for your convenience, only to find out that they all belong to the same author in each case and that they are not quite entirely related to the manuscript.
In the title of this post I also try to address the writing of a scientific paper, although I’m not an authority on it, I think today’s key phrase is bona fide. So to young and not so young scientists out there I’d ask you to write in bona fide, please. Be concise. Be convincing. Be thorough and be critical. This is science we are doing, not stamp collecting. It shouldn’t be about getting all sorts of things out there, it is about expanding the knowledge of the human race one paper at a time. But we are humans; therefore we are flawed. More and more cases of scientific misconduct are found throughout the literature and nowadays, with the speed of blogging and tweeting, we can point at too many of them. The role of bloggers in pointing this frauds, of which I’ve written before here, is the subject of recent controversy and possibly the topic of a future post. We are all being scrutinized in our work but that shouldn’t be an excuse to make up data, tinker or temper with it, to push our own personal agendas or to gain prestige in an otherwise wild academic environment.
I for one may never publish in Science or Nature; I may never be selected for any important prize, but even the promise of achieving any of those is not worth the guilt trip of lying to an entire academic society. I try then, to always remember that science is not about getting the best answers, but about posing the right questions.
What is your own style for reading papers? Any criticism to my style? How different is the style of a grad student from that of a researcher?
As usual thanks for reading, rating and commenting!
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.
Welcome of the third installment of #RealTimeChem, the diary. As I did yesterday and the day before, I will summarize my day in chemistry throughout the Tweets sent over this event.
— Joaquin Barroso (@joaquinbarroso) April 24, 2013
(Haha, I found the button to include the feed!)
I finally finished editing that supporting information I’ve been Twitting about all week, now I’m back at the manuscript re-editing a bit. This is a problem I have that I’m sure is shared by most of you: I just can’t let go. If I’m writing a manuscript I’ll read it and change it over and over; if I’m working on a presentation, I will edit and reorder the slides almost ad infinitum if it were not for deadlines. Professor Cea-Olivares, of whom I’ve written before in this blog, used to say that projects are never finished but merely abandoned. In all fairness we are still not on the ‘not letting go’ phase, there are still some sections of the manuscript that need our attention; and when I say we, I mean me and my collaborator Dr. Rodrigo Galindo who is currently working at the University of Utah (BTW go check out his blog and persuade him to pick it up again!)
But in the middle of the day there was a conference at Instituto de Química, in Mexico City, that I wanted to listen to. Dr. Marcos Hernández is a good colleague of mine who deals with asymmetric organocatalysis. I like his work a lot and I hold him in high esteem so I asked for a video transmission of his talk to be sent over to CCIQS at Toluca. In the following two Twits you can get a glimpse of our video conferencing facilities.
— Joaquin Barroso (@joaquinbarroso) April 24, 2013
— Joaquin Barroso (@joaquinbarroso) April 24, 2013
— Joaquin Barroso (@joaquinbarroso) April 24, 2013
Not all is work during RealTimeChem week, although perhaps it should be. Still, safety first! that’s our motto! (follow the link in message)
— Joaquin Barroso (@joaquinbarroso) April 24, 2013
Today I took some time to have a few interactions with other participants of #RealTimeChem and got to follow very interesting people. Definitely, after this week I will become a more active Twitter user (ouch!). But the research must go on, and today Maru started working on rendering the electrostatic potential surfaces for a rather large set of calix- and thiacalix[n]arenes for our line of research on molecular recognition agents.
— Joaquin Barroso (@joaquinbarroso) April 24, 2013
— Joaquin Barroso (@joaquinbarroso) April 24, 2013
— Joaquin Barroso (@joaquinbarroso) April 25, 2013
This is pretty much it for today; I’m very tired and I still need to work in other things so I’m off for now but stay tuned for more tomorrow when this blog will celebrate the 60th anniversary of the publication of DNA’s structure in Nature.
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.