Monthly Archives: July 2020

NIST CCCBDB – Vibrational Scaling Factors & ThermoChem Data

The Computational Chemistry Comparison and Benchmark DataBase (CCCBDB) from the National Institute of Standards and Technology (NIST) collects experimental and calculated thermochemistry—related values for 1968 common molecules, constituting a vast source of benchmarks for various kinds of calculations.

In particular, scaling factors for vibrational frequencies are very useful when calculating vibrational spectra. These scaling factors are arranged by levels of theory ranging from HF to MP2, DFT, and multireference methods. These scaling factors are obtained by least squares regression between experimental and calculated frequencies for a set of molecules at a given level of theory.

Aside from vibrational spectroscopy, a large number of structural and energetic properties can be found and estimated for small molecules. A quick formation enthalpy can be calculated from experimental data and then compared to the reported theoretical values at a large number of levels of theory. Moments of inertia, enthalpies, entropies, charges, frontier orbital gaps, and even some odd values or even calculations gone awry are pointed out for you to know if you’re dealing with a particularly problematic system. The CCCB Database includes tutorials and input/output files for performing these kinds of calculations around thermochemistry, making it also a valuable learning resource.

Every computational chemist should be aware of this site, particularly when collaborating with experimentalists or when carrying calculations trying to replicate experimental data. The vastness of the site calls for a long dive to explore their possibilities and capabilities for more accurate calculations.

On Putting up with Rejections Letters

Having a paper rejected is one of the certainties of academic life. While there are some strategies to decrease the probability of facing a rejection, today I want to focus on my tips to deal with them—particularly for the benefit of younger scientists.

There are two broad kinds of rejections: Desk Rejections and Rejections from reviewers. In any case, the best advice is never to take action after receiving the dreaded rejection letter. Take a day or two, then react accordingly with a cooler head. Remember, this isn’t about you it’s hard not to make it personal but trust me it isn’t.

The first kind, desk rejections, are provided directly from the chief or associated editors of the journal to which you submitted your work. They tend to be quick and rather uninformative except for maybe the incompatibility—to put it nicely—of your work with the scope of the journal. These are also sometimes the hardest to face since they make you feel your work is simply not good enough to be published; but they’re also the quickest and in the publish-or-perish scheme of things, time is key. After getting a desk rejection, if no other input is given, just try again; one tip—though not infallible—to chose a proper journal is to look at which journals are you citing in your own work and chose one with the highest frequency. Sometimes, editors might offer a transfer to another journal from the same publishing house; my advice is always say yes to transfers: the submission is made for you by the editorial staff, it sort of becomes recommended between the involved editors, and expedites the start-again process. Of course, a transfer does not mean you’re manuscript will get accepted but whenever offered there is a good chance the first editor thinks your work should be kept inside their editorial instead of risking you going to another publishing house. Appealing to a desk rejection is highly discouraged since it practically never works. Sure, you may think the editor will kick himself in the rear once you get the Nobel prize but telling them so, particularly in a colorful language, will not make them change their minds.

Rejections after peer review are trickier. If your manuscript went up to peer review, it means the editors in charge of it thought your work is publishable but of course it needs to be looked at by experts to make sure it was done in the right way with all or most things covered (you know what they say, two heads are better than one, try three!). Now, this kind of rejection takes longer, usually two or three weeks—sometimes even longer—but all things being fair, polite, and objective, they are also the most informative. Reviewers will try to find holes in your logic, flaws in your research, and when they find them they will not hold back their thoughts; you’re in for the hard truth. So of course this kind of rejection is also hard to take, makes you feel again like your work is not worthy, that you’re not worthy as a scientist. But the big advantage here is you now have a blueprint of things to fix in your manuscript: a set of experiments are missing? run them, key literature wasn’t cited? read it and cite it appropriately. Take peer review objectively but never dismiss it by trying to just go and submit it again to a different journal as is, for chances are you’ll get some of the same reviewers, and even if you don’t, it’s unethical to dismiss the advice of peers, they are your peers in the end, not your bosses but your peers, don’t loose sight of it. Also, it’s very frustrating for reviewers to find that authors managed to get published without paying the slightest attention to their suggestions. Appealing a peer review rejection is hard but doable and then you have to put on a scale what is it that you value the most: your paper in its original condition being published in that specific journal or fixing it and start again. An appeal upon a flat rejection is hardly ever won but it may well establish a conversation with other scientists (the referees) about their point of view on your work, just don’t think you’ve made instant buddies who will now coach you through academic life.

The peer review system is far from perfect, but if done properly it is still the best thing we’ve got. Some other alternatives are being tested nowadays to reduce biases like open reviews signed and published by reviewers themselves; double and even triple blind peer review (in the latter not even the editor knows the identities of authors or reviewers) but until proven useful we have to largely cope and adapt to single blind peer review (just play nice, people). In some instances the dreaded third reviewer appears, and even a fourth and a fifth. Since there are no written laws and I’m not aware of any journal specifying the number of referees to be involved in the handling of a manuscript there may be varied opinions among reviewers, so different as from ranging from accept to reject. This may be due to the editor thinking one or more of the reviewers didn’t do their job properly (in either direction) and then brings another one to sort of break the tie or outweigh the opinion of a clearly biased reviewer. If you think there are bias, consult with the editor if a new set of reviewers may be included to complete the process, more often than not they will say no but if you raise a good point they might feel compelled to do so.

Science is a process that starts at the library and ends at the library

Dr. Jesús Gracia-Mora, School of Chemistry UNAM ca. the nineteen nineties

These are truths we must learn from a young age. Any science project does not end at the lab but at the library, therefore I let my students—even the undergrads—do the submission process of their manuscripts along with me, and involve them in the peer review process (sometimes and to some limited extent even when I’m the reviewer) just so they now that getting a rejection letter is part of the process and should never be equated with the relative quality or self-worth of a scientist since that is hardly what the publication process looks at.

So, in a nutshell, if you got a rejection letter, get back on the proverbial saddle and try again. And again. And once again.

The #LatinxChem Twitter Poster Contest

For the past few weeks, some chemists of the worldwide Latinx community have been cooking an online project devoted to showcase the important contributions to chemistry made by workers, students, and researchers from Latinamerican origin.

The result is the #LatinXChem Twitter Poster Contest which will take place 7th September during a 24 hour span and the corresponding Twitter account @latinxchem (go follow it now! I’ll wait right here.)

All chemists from Latinx origin are called to participate by registering their posters in our website before August 25th. Upon registration, each poster should be classified into one of the eleven categories available and use the corresponding hashtag during the event (e.g. #LatinxchemTheo for the readers of this blog), in which prominent Latinx chemist will serve as reviewers and cast their votes for the best one in each category. Some prizes will be available, thanks to our kind sponsors (RSC, Chemical Science, ACS, Carbomex, The Brazilian Chemical Society, and more to come), but just for those registered works; if anyone wishes to present a poster without being registered at the website they can do so but eligibility for prizes remain for those who complete the register. Official languages for the poster are Spanish, Portuguese, and English.

Each category is organized by young prominent Latinx chemists; for the particular case of Computational Chemistry –the recurring theme of this blog– Prof. Fernanda Duarte (@fjduarteg) from Chile now working at Oxford University in the UK and yours truly (@joaquinbarroso) will be in charge of the #LatinXChemTheo section. Please check the website to learn about the other sections and the wonderful people working hard in the organizing committee (see below for the full list of the organizers and their Twitter handles).

The main goal of the event is to celebrate and showcase the espectacular research, education, and innovation brought to chemistry by a large and vibrant community dispersed throughout the globe of Latinx identification. We want to celebrate diversity by showcasing our contributions in the context of a global science interconnected with people from other groups.

So please visit our website, help us spread the word and get those posters ready, we’re eager to read, comment, Tweet and Retweet your work and show the world the drive and passion of Latinxs for chemistry, knowledge, and the betterment of the world through science.

Go follow us all and of course @LatinXchem too!

¡Gracias! Obrigado! Thank you!

Gabriel Merino Cinvestav Mérida, México @theochemmerida
Miguel A. Méndez-Rojas UDLAP, México @nanoprofe
Joaquín Barroso UNAM, México @joaquinbarroso
Javier Vela Iowa State University, USA @vela_group
Diego Solís-Ibarra UNAM, México @piketin
Braulio Rodríguez-Molina UNAM, México @MolinaGroup
Paula X. García-Reynaldos Science Communicator, México @paux_gr
Liliana Quintanar Cinvestav Zacatenco, México @lilquintanar
María Gallardo-Williams North Carolina State University, USA @Teachforaliving
Fernanda Duarte University of Oxford, UK @fjduarteg
Yadira Vega Tec de Monterrey, México @yivega
Gabriel Gomes University of Toronto, Canadá @gpassosgomes
Luciana Oliveira UNICAMP, Brasil @LuBruGonzaga
Cesar A. Urbina-Blanco Ghent University, Belgium @cesapo
Ariane Nunes HITS, Germany @anunesalves
Walter Waldman Brazil, @waldmanlab

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