This week marks the 10th anniversary of this little blog! It’s crazy to think a pet project that I took on during my last year as a postdoc is still going on after a decade of recording the work of our group in computational chemistry and it is also a happy coincidence that this year is the centennial anniversary of IUPAC and the sesquicentennial anniversary of the Periodic Table, for which 2019 has been designated as the International Year of the Periodic Table. I will release various posts celebrating this first decade of blogging and some regarding the IYPT2019 as soon as possible, also some major changes in layout and look are coming. It has been suggested to me that setting a patreon.com account could help me raise some funding for assisting underprivileged students but I’m not so sure yet.
By 2009 the chemistry blogosphere was already in full swing, so I got to it a bit late. (Is commenting ‘First!‘ still a thing?) At the time my job future seemed a bit uncertain, I had already spent two years as a postdoc in Romania and prior to that I worked for a private company in their research center here in Mexico so I started to ramble here so in upcoming job interviews I could point to a resource which gathered my thoughts and some achievements in a more informal fashion than a CV or a resume. (Plus, I like writing about things other than chemistry just for myself, maybe someday I’ll start a blog with some fiction writings I have here and there.) Quite frankly I didn’t think I could go back into academia so I was mainly looking for jobs in the R&D departments of various chemical companies, particularly in the field of coatings which was the one I already had some experience.
I never imagined this little blog would gain any attention, I think I had something like 2,000 views on the first year, now it’s up to 1,500 views a week! One of the first posts that gained popularity quite quickly dealt with the calculation of SCRF calculations and some parameters we were struggling to get right. Once I found the best parameters for running them, my boss, the late Prof. Dr. Ioan Silaghi-Dumitrescu at Babes-Bolyai University, asked me to email them to the group and post them physically in the lab so we wouldn’t loose them; I thought it would be a better idea to have them on the blog so we all could access them easily and at the same time share our findings with whomever had the same issues. Turned out that many people struggled with these parameters for SCRF calculations in Gaussian and from that moment on that became one of the underlying principles of the blog: “any problem we face in the lab is definitely faced by someone else, so lets share our solution”; the other principle of course was my blatant self promotion.
One of the most rewarding aspects of having kept this blog going on for so long is knowing that it is a modest resource that some people has found helpful. Attending conferences and having people telling me they like my posts and have found help in them is extremely gratifying. Also, academically it has allowed me to meet wonderful people with whom I’ve established very interesting collaborations in various countries like Iran, US, Slovakia, Czech Republic, Chile, Bulgaria and many more.
Very early I started getting direct questions to specific problems and to the best of my abilities I’ve tried to answer them although I not always have the time to do so and for that I apologize to all the readers who didn’t get an answer; up until now keeping this blog has been a spare-time endeavor which not always gets the priority it deserves withing my academic tasks.
Thank you for reading, commenting and sharing these posts during this past decade! I truly appreciate it and it has been very important to me; I sometimes feel the posts go into the void but every now and then I’m approached by readers who have found the blog helpful and that is very rewarding. Here’s to ten more years!
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!
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?
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!
The first day of the #RealTimeChem event has gone by and here I am blogging about it in order to participate in the ensuing #RealTimeChemCarnival which is the blogging section, so to speak, of the aforementioned event. So, without further ado, this was my #RealTimeChem day:
Disclaimer: I’m not much of a Twitter man myself so I apologize in advanced for any dumb or stupid usage of it. I’m also new to Instagram and Vine, which I only downloaded on account of this event. Sorry for not taking snippets from the Twitter feed but I’m on Windows7 starter here and I don’t have such tools; I’m also not going to download some tool right now, sorry for that but if you know a better way, please do share it! I will be posting all week long so it might come in handy.
Editing sup. info. new paper on electronic interactions in rotaxane-like molecules with bio applications. Hope #RealTimeChem brings me luck!
We are almost done with this paper on drug delivery systems based on the architecture of calix[n]arenes. We’ve found some pretty interesting results about which features suit better certain drugs both in gas and solution phases. Most of my day had to do with editing the supporting information. Below, the picture that acompanied the previous Tweet.
Later on, along came a student whom, to be perfectly honest, I completely forgot about -my bad- but he was there and he was willing so off we went to work. Of course, being his first time, we had to start from scratch from the very basics of Gaussian’s use (and implicitly, the basics of the command line use in Linux). I’m not sure he wants his name to be posted here so he will remain in anonimity until otherwise stated. The associated Tweet read as follows:
Training a new student in using Gaussian, Gaussview and Linux. Lot of work to be done but he looks eager to learn 🙂
Being so much into #RealTimeChem worked as a serious motivator; the more you published the more you wanted to keep going! So all day long I had my head filled with things that I wanted to do, but I made a strong case about twitting only those things that I actually did and nothing in the lines of ‘thinking of …’ or ‘wishing I could…’ that sort of thing. I usually take little notes on google calendars about my day’s work as a means to keep track of my productivity, or sometimes, sadly, my lack thereof. This time Twitter was a loud witness of my activities which, hopefully, may be considered productive.
I teach a class on electronic structure each Tuesday, so I started preparing my class for tomorrow as a kind of break from editing that supporting information; the Twit read:
All day editing sup. info. has rendered me cross-eyed! Time 4 a break. Will reply work (chem) related email 🙂
and so I did. I got to reply to a professor in the far away island of Mauritius! He just invited me to participate in a virtual conference on computational chemistry. What a shame! It’d been nice to fly half way accross the world and set foot in that land! If you don’t know where Mauritius is, find Madagascar in southern Africa and then take a right on the Indic Ocean. As per his request, here I promote his event with all of you and with #RealTimeChem:
Then more e-mail
@joaquinbarroso 3h #RealTimeChem just accepted invitation 2 virtual conf.; accepted new intern by mail; now reviewing 2 applications for conference stipends
I didn’t finish reviewing these kid’s work but I think they might get their plane tickets from the local council for science and technology.
As I wrote earlier, I’m not a Twitter man so I get easily overwelmed by all the information generated within. I wanted to go home but before I got to read some Tweets and I was astonished by the enormous ammount of messages in the lines of ‘submitted a grant, now when can I do the corresponding research?‘; ‘grading! what a torture!’ and some others that indicated people was doing administrative work when they really wanted to get their hands dirty in the lab. This was a surprise to me because I imagined that most Twitter users and therfore, #RealTimeChem participants would be young students who are the ones who actually are up to their necks in chemistry! of course I Tweeted about my little observation in two messages.
So interesting 2 notice
#RealTimeChem deals more with research administration than wth research! I thought it’d be the other way around!
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.