Scientific log of a computational chemist - "Make like a molecule and React!"

2025 was declared by UNESCO as the International Year of Quantum Sciences, bringing a lot of celebrations, however much of the discourse is dominated by physicists and quantum technologists, some of which proclaim the dawn of the new “quantum revolution”. Yet, amid the excitement, I can’t help but notice that quantum chemistry remains underrepresented, despite […]

Universidad Nacional Autónoma de México

2025 was declared by UNESCO as the International Year of Quantum Sciences, bringing a lot of celebrations, however much of the discourse is dominated by physicists and quantum technologists, some of which proclaim the dawn of the new “quantum revolution”. Yet, amid the excitement, I can’t help but notice that quantum chemistry remains underrepresented, despite being the discipline that has arguably done the most to turn quantum mechanics into a

Is Quantum Chemistry aligned with the Copenhagen or the Many Worlds interpretation of Quantum Mechanics?

The Computational Chemistry List  (CCL) is a web based forum in which is possible to discuss basically every aspect regarding computational chemistry, from fundamental concepts to technical assistance, the latter being the most popular form of posting.

The Computational Chemistry List

QSA(P)R and Machine Learning methods rely on finding correlations between molecular properties of known values for a given set of molecules in order to predict the properties of another set of molecules closely related to the former.

Calculating chemical descriptors with Mordred

I’m very honored to have been invited to this edition of this long standing event, the Virtual Winter School of Computational Chemistry. In this talk I walk through the basics of what are excitons and how do they move or transfer across matter; and of course, a primer on how to calculate the energy transfer with Gaussian. This is a very basic introduction but I hope someone finds it useful.

Exciton Energy Transfer-Talk at the Virtual Winter School of Comp.Chem. 2022

The HOMO – LUMO orbitals are central to the Frontier Molecular Orbital (FMO) Theory devised by Kenichi Fukui back in the fifties. The central tenet of the FMO theory resides on the idea that most of chemical reactivity is dominated by the interaction between these orbitals in an electron donor-acceptor pair, in which the most readily available electrons of the former arise from the HOMO and will land at the LUMO in the latter.

The HOMO-LUMO Gap in Open Shell Calculations. Meaningful or meaningless?

To chem or not -quite- too chem, that is the ChemNobel question: Whether &#8217;tis Nobeler in the mind to suffer The curly arrows of organic fortune Or to take rays against a sea of crystals And by diffracting end them. Me (With sincere apologies to WS) Every year, in late September -like most chemists- I [&#8230;]

Every year, in late September -like most chemists- I try to guess who will become the next Nobel Laureate in Chemistry. Also, every year, in early October -like most chemists- I participate in the awkward and pointless discussion of whether the prize was actually awarded to

 chemistry

or not.

To Chem, or not “Too Chem”? That is the #ChemNobel Question

The compound shown below in figure 1 is listed by Aldrich as 4,5,6,7-tetrahydroindole, but is it really? To a hardcore organic chemist it is clear that this is not an indole but a pyrrole because

Chemistry Makes the Chemical

Each year the Mexican community who works in the realm of computational and theoretical chemistry gathers to share the most recent work done around our country. This year, I tried to live Tweet the event and although I failed miserably in doing so -as well as in convincing others to join me- I’m trying to put together the things that caught my attention. I also tried to Storify it but I cannot embed the result here in WordPress.

XIV Mexican Reunion on Theoretical Physical Chemistry

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.

First graduated student!

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.

Article in ‘Ciencia y Desarrollo’ (Science and Development)

I was first introduced to Bradbury’s writing in 1989 during my first year in junior high school (here in Mexico that is the 7th grade; I was eleven years old then) by my literature teacher Ángel Molina-Aja at LOGOS School, a progressive institution in southern Mexico City;

Ray Bradbury (1920-2012) and his influence on me…

Canonical Molecular Orbitals are–by construction–delocalized over the various atoms making up a molecule. In some contexts it is important to know how much of any given orbital is made up by a particular atom or group of atoms, and while you could calculate it by hand given the coefficients of each MO in terms of every AO (or basis set function) centered on each atom there is a straightforward way to do it in Gaussian.

Percentage of Molecular Orbital Composition – G09,G16

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!

The #LatinxChem Twitter Poster Contest

Unrecognized potential number 6 in GetPot A rather silly error in Gaussian, but one that seems to be common and to which I haven’t found any posted solutions, so here goes mine.

Unrecognized potential number 6 in GetPot  A rather silly error in Gaussian, but one that seems to be common and to which I haven’t found any posted solutions, so here goes mine.

Unrecognized potential number 6 in GetPot

One of the first things I remember learning about chemistry in middle school (back in the early nineteen nineties) was how to write the electronic configuration of atoms using a sort of arcane code of numbers and letters in a weird progression hard to be rationalized, if not for a diagonal scheme that showed the precise way to fill orbitals with electrons as you moved forward the other big diagram of chemistry, the Periodic Table.

The X-Mas ‘Chemistree’ that came from Mexico – Prof. Jaime Keller

I kept getting this pesky error, with no apparent solution found online. It happened when copy-pasting coordinates from files in different platforms. I edited the input file many many times in Linux but only when I got to look at it in a Windows Notepad was that I saw the following lines: 6 0.000000000 0.000000000 Â Â Â Â -0.030561000  Where the “Â” symbols had to be removed by deleting every apparently empty space between coordinates.

Undefined symbol, angle beta, card X

My mind blew the day I learned about the existence of imaginary numbers. My high school teacher nonchalantly just brought them up as something that was invented to give an answer to what the square root of a negative number was. I imagine most students file that information under ‘

 irrelevant things I will never use in real life.

‘ Complex numbers have many applications in many fields, mostly via Euler’s theorem.

The contradictory “complexity” of the wave function

The 20

 th

Mexican Meeting on Theoretical Physical Chemistry (RMFQT) just occurred last week and it was a special edition for various reasons: The fact this meeting has been organized for two decades speaks volumes about a thriving national scientific community; being the 20th anniversary, the comitee saw fit to hold it at the very same place where it first began, Cuernavaca, an idyllic warm town just an hour south of Mexico City.

XX RMFQT – An homage to Prof. Alberto Vela

Preparing publication quality images from your calculations is essential. To pre-visualize images to get the best orientations of your molecule, DTK2.0 includes two options: a new GUI called DensToolKitViewer and DTKQDMol.

Getting Images with DensToolKitViewer2.0 – AIM with DTK2.0

This time I try delivering a personal video post to close this #IYPT2019 celebrations. I hope you find it interesting.   I invite you all to always imitate molecules and react!

The International Year of the Periodic Table #IYPT2019 and the Tie that Binds

It was my distinct pleasure for me to participate in the organization of the latest edition of the Mexican Meeting on Theoretical Physical Chemistry, RMFQT which took place last week here in Toluca. With the help of the School of Chemistry from the Universidad Autónoma del Estado de México. This year the national committee created a Lifetime Achievement Award for Dr. Annik Vivier, Dr. Carlos Bunge, and Dr. José Luis Gázquez.

XVIII RMFQT

Elucidating the pairing of non-hydrogen bonded unnatural base pairs (UBPs) is still a controversial subject due to the lack of specificity in their mutual interactions. Experimentally, NMR is the method of choice but the DNA strand must be affixed on template of sorts such as a polymerase protein. Those discrepancies are well documented in a recent review which cites our previous computational work, both DFT and MD, on UBPs.

Non-canonical Base Pairs show Watson-Crick pairing in MD simulations

The video below is a sad recount of the scientific conditions in Mexico that have driven an enormous amount of brain power to other countries. Doing science is always a hard endeavour but in developing countries is also filled with so many hurdles that it makes you wonder if it is all worth the constant frustration.

Computational Chemistry from Latin America

The Weak Link Approach (WLA) is a successful strategy for allosterically controlling the formation of cavities¹ and the access to them² through the action of reversible hemilabile-bond formation around an organometallic center.

Redox Allosteric Control – New communication in JACS

The RMFQT meeting is a long standing tradition within the Mexican Comp.Chem. community; a tradition that is now transcending our borders as more and more foreign students and researchers take part of this party, for it is a festive occasion indeed. This was the first time the RMFQT was held at a private institute, The Monterrey Institute of Technology.  As in previous years, our lab contributed with a four posters and one talk by yours truly.

XVII Mexican Meeting on Theoretical Physical Chemistry

Calculation of interaction energies is one of those things people are more concerned with and is also something mostly done wrong. The so called ‘

 gold standard

‘ according to Pavel Hobza for calculating supramolecular interaction energies is the CCSD(T)/CBS level of theory, which is highly impractical for most cases beyond 50 or so light atoms.

Post Calculation Addition of Empirical Dispersion – Fixing interaction energies

We’ve expanded the scope of our research interests from quantum mechanical calculations to docking and MedChem for over a year now; it has been a very interesting ride and a very rich avenue of research to explore. Durbis Castillo has led -out of his own initiative- this project and today he presents us with a guest post on the nuances of his project.

Our first dabble in #MedChem through #CompChem

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.

Another Great Year at the Lab! 2017

A yearly tradition of this Comp.Chem. lab and many others throughout our nation is to attend the Mexican Meeting on Theoretical Physical Chemistry to share news, progress and also a few drinks and laughs. This year the RMFQT was held in Puebla and although unfortunately I was not able to attend this lab was proudly represented by its current members.

XVI Mexican Meeting on Phys.Chem.

As we were hanging out recently, the idea came to us at the lab to create memes in order to summarize our work. We should be writing articles but hey, we needed the break, and so we shared them with each other in our last group meeting along with a good laugh. Here are some of the funniest ones.

#MemeYourThesis #MemeYourResearch

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.

Negotiations gone wrong and other recent scandals

If you work in the field of photovoltaics or polyacene photochemistry, then you are probably aware of the Singlet Fission (SF) phenomenon. SF can be broadly described as the process where an excited singlet state decays to a couple of degenerate coupled triplet states (via a multiexcitonic state) with roughly half the energy of the original singlet state, which in principle could be centered in two neighboring molecules;

Photosynthesis and Singlet Fission – #WATOC2017 PO1-296

The concept of

 electronic orbital

has become such a useful and engraved tool in understanding chemical structure and reactivity that it has almost become one of those things whose original meaning has been lost and replaced for a utilitarian concept, one which is not bad in itself but that may lead to some wrong conclusions when certain fundamental facts are overlooked.

No, seriously, why can’t orbitals be observed?

Out of some +1000 twitter accounts I follow about a quarter are related computational chemistry. The following public list isn’t comprehensive and prone to errors and contains researchers, programmers, students, journals, products and companies who gravitate around the use of

 in silico

methods for the understanding and design of chemical and biochemical compounds.

Some Comp.Chem. Tweeps

Ever since I read the highly praised article by Floyd Romesberg in Nature back in 2013 I got really interested in

 synthetic biology

. In said article, an unnatural base pair (UBP) was not only inserted into a DNA double strand

 in vivo

but the organism was even able to reproduce the UBPs present in subsequent generations. Inserting new unnatural base pairs in DNA works a lot like editing a computer’s code.

Unnatural DNA and Synthetic Biology

I was just asked if it is possible to perform DFT-D3 calculations in Gaussian and my first answer was to use the following  keyword: EmpiricalDispersion=GD3  which is available in G16 and G09 only in revision D, apparently.

Grimme’s Dispersion DFT-D3 in Gaussian #CompChem

The goal of any scientist is to generate new knowledge and then it would be a fair assumption that most scientists are inclined to share that knowledge with as many people as possible in a noble effort to improve the world in which we live; in fact, that is the very -underlying- reason why we publish articles of all our research, so every bit of knowledge generated in our labs goes not only on record but is available for testing and questioning.

Is #OpenAccess a first world problem?

I’m so glad to be back in Pécs, Hungary, at the lab of my good old friend Prof. Dr. Sándor Kunsági. It has been seven years since I was last here and so many things have happened and yet it feels like yesterday I was walking through these halls.

Back in Pécsi Tudomanyegyetem (Hungary)

Last week we posted some insights on finding Transitions States in Gaussian 09 in order to evaluate a given reaction mechanism. A stepwise methodology is tried to achieve and this time we’ll wrap the post with two flow charts trying to synthesize the information given.

The “art” of finding Transition States Part 2

As part of an ongoing collaboration with the University of Arizona (UA) and the Center for Advanced Research and Studies (CINVESTAV – Saltillo), we are looking into the use of calix[

 n

]arenes for bio-remediation agents capable to extract Arsenic (V) and (III) species from water.

New Paper in JIPH – As(V)@calix[n]arenes

As far as population analysis methods goes, the Quantum Theory of Atoms in Molecules (QTAIM) a.k.a Atoms in Molecules (AIM) has become a popular option for defining atomic properties in molecular systems, however, its calculation is a bit tricky and maybe not as straightforward as Mulliken’s or NBO.

Atoms in Molecules (QTAIM) – Flash lesson

Last week at the congress of the Mexican Society of Chemistry I presented some of our results in the study of photosynthesis. Below I embeded the talk.

Singlet Fission in the Fenna-Matthews-Olson Complex – A Talk

Computing spectroscopic features of molecules is always an interesting challenge, specially when intermolecular contacts are into play. Take vibrational spectroscopy for instance, all the non-covalent interactions present in a solid will have an important effect on the the calculated frequencies and their intensities. However calculating the spectroscopical properties of a solid quickly becomes a daunting task.

Simulation of Raman Spectroscopy and crystal cell effects – Selenium Carboxylate Eur. J. Inorg. Chem.

Well, I only contributed with the theoretical section by doing electronic structure calculations, so it isn’t really a paper we can ascribe to this particular lab, however it is really nice to see my name in JACS along such a prominent researcher as Prof. Chad Mirkin from Northwestern University, in a work closely related to my area of research interest as macrocyclic recognition agents.

New paper in JACS

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.

Visit to ‘Universidad de la Cañada’ in Oaxaca, Mexico

I always get very happy to have a new paper out there! I find it exciting but most of all liberating since it makes you feel like your work is going somewhere but most of all that it is making its way ‘out there’; there is a strong feeling of validation, I guess.

New paper in Computational and Theoretical Chemistry

Once again as every year we celebrate our internal symposium here at CCIQS, and like every year, my students presented some of their progress with their research projects. This time, three students, from three different levels, present posters regarding some of the data they’ve obtained.

Internal Symposium at CCIQS – 2014 edition

Originally posted on <a href="https://eutactic.wordpress.com/2014/01/21/nice-energy-level-diagrams-with-rxnlvl/">eutactic</a>: I have written a bit of code lately which automates the process of constructing chemical reaction energy level diagrams rather well. It&#8217;s called rxnlvl. It&#8217;s written in Python, outputs to SVG (Scalable Vector Graphics) and is GPL3. I&#8217;m not a ninja programmer by any stretch of the imagination, however the program&#8230;

eutactic I have written a bit of code lately which automates the process of constructing chemical reaction energy level diagrams rather well. It’s called

 rxnlvl

. It’s written in Python, outputs to SVG (Scalable Vector Graphics) and is GPL3. I’m not a ninja programmer by any stretch of the imagination, however the program is basically functional, and in my estimation yields quite attractive results.

Nice Energy Level Diagrams with rxnlvl

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.

More interns!

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;

Summer internships are Over

Having a new paper out is always fun and this week we got the wonderful news from the

 
 Journal of Physical Chemistry C
 

that a paper I co authored with Prof. Alireza Badiei at the University of Tehran in Iran and his student, who actually got us all in touch, Dr. Pezhman Zarabadi-Poor, was accepted for publication.

New paper in J. Phys. Chem. C

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.

100,000 visitors!

I don’t know why I haven’t written about the Local Bond Order (LBO) before! And a few days ago when I thought about it my immediate reaction was to shy away from it since it would constitute a blatant self-promotion attempt; but hell! this is my blog! A place I’ve created for my blatant self-promotion! So without further ado, I hereby present to you one of my own original contributions to Theoretical Chemistry.

The Local Bond Order, LBO (Barroso et al. 2004)

I am frequently asked how to include an extra set of basis functions in a calculation or how to use an entirely external basis set. Sometimes this question also implies the explicit declaration of an external pseudopotential or Effective Core Potential (ECP).  New basis sets and ECPs are published continuously in specialized journals all the time. The same happens with functionals for DFT calculations.

The Gen keyword in Gaussian. Adding an external basis set.

A new look was needed in this site! and some more changes will be made in the next few days. A new page was added with the topics of the courses I’ve taught here at UAEMex, namely QSAR and Molecular Modeling. Another page was added for you all to leave questions which are hard to fit into other places of this blog.

Fresh new look!

The Future of Sustainable Chemistry As part of the ongoing events of the International Year of Chemistry, I was interviewed last month for a webinar titled &#8220;The Future of Sustainable Chemistry&#8221; which in turn is part of a broader series of webinars called &#8220;The Future We Create&#8220;. These events are sponsored mainly by the DOW [&#8230;]

The Future of Sustainable Chemistry
 

As part of the ongoing events of the International Year of Chemistry, I was interviewed last month for a webinar titled “

 The Future of Sustainable Chemistry

” which in turn is part of a broader series of webinars called “

 The Future We Create

“. These events are sponsored mainly by the DOW Chemical Co. and organized by the 4goodmedia organization as a way to

The Future We Create (Part II, The webinar)

Next week, on december 8th, the Joint Center for Research in Sustainable Chemistry (to which I am ascribed) will host a

 Symposium on Green and Sustainable Chemistry

in which German Alumni -almost exclusively from Mexico- will participate with talks on the impact and development of new techniques on green chemistry. We’ll be honored with the visit of Prof. Dr. Reinhard.

Green and Sustainable Chemistry Symposium here at CCIQS

Once again I’ve run into the same ‘ol discussion: why DFT is better than HF. Of course DFT  has some advantages over HF in many cases, the inclusion of electron correlation through a parametrized functional being only one of them. What bothers me are the somewhat bogus statements that DFT defenders use;

Density Functional Theory

This is the first post on this new blog of mine. Other blogs I’ve participated/created are displayed below; they both reflect what have been major interests in my life: movies and food.

A new beginning

There are basically two kinds of electron correlation: static and dynamic.

Restricted Active Space with Double Spin Flip (RAS-2SF) in Q-Chem 5.x

Way off topic post that I began writing around the last World Series in October 2009. ‘

 Why do you like it?

‘ is the most recurrent question I get from my European friends and most in Mexico. The easy and short answer is because my dad got me into it since he likes it too. But what makes me keep on liking it? In few words I like it because it is complex.

Baseball

Recently, the journal ACS Central Science asked me to write a viewpoint for their First Reactions section about a research article by Prof. Alán Aspuru-Guzik from Harvard University on the evolution of the Fenna-Matthews-Olson (FMO) complex.

The Evolution of Photosynthesis

The new DensToolKitViewer just got even better! So, if you want to update DTKViewer to make the most of the new features, in this tutorial we shall compile and install DensToolKitViewer. We provide the explicit steps to compile under Ubuntu and under MacOSX. We will assume that the git repo is cloned in /home/your_username/Downloads.

Installing and uninstallng DensToolKitViewer

In this tutorial, we shall prepare a figure using DensToolKitViewer 2.1.0 (or later) to select the viewing angle of the molecule, for whenever the default view isn’t the optimal viewpoint or to get various for comparison.

In this tutorial, we shall prepare a figure using DensToolKitViewer 2.1.0 (or later) to select the viewing angle of the molecule, for whenever the default view isn’t the optimal viewpoint or to get various for comparison. Installation and main controls were already covered in a previous post, as well as an update for ease of use. We use the file N-N-dimethyl-Propen-1-amine.wfx which is located in the wffiles repo directory.

Using DensToolKitViewer to get the best viewpoint

Calculating reaction constants, in the correct physical way, requires accurate thermodynamic calculations involving solvation/desolvation energies at high levels of theory, because free energy deviations lower than 1 kcal/mol lead to reaction constant values off by an order of magnitude.

pka values for Arsonic Acids – New paper in ACS Omega

This new version of UVeh-Vis contains modifications of the graphical properties of the output plot: Font type, font size, legend style and widow size corrections.

UVeh-Vis v1.1 is now available

So you optimized your molecule, you found all real frequencies, you’re done! right? Well, maybe not. When molecules are well-behaved you probably can either use a restricted or an unrestricted method to find the optimized wavefunction and derive as many properties as you want from it; this occurs for most organic molecules and to some extent to main group elements with little to no radical character.

Is your Wavefunction stable?

Undergraduate students in our lab shown in the picture above, Emanuel Contreras (

 right

) and Humberto Estrada (

 left

), just added a python-based code to our GitHub page, with which you can automatically plot UV-Vis spectra obtained from excited state calculations such as TD-DFT, CCSD, RAS, etc.

Plotting UV-Vis spectra from QChem 5.0 calculations (UVeh-Vis)

Cubane (C8H8) and homocubane (C9H10) are very strained molecules. Substitution of a carbon atom for a nitrogen one to reduce the tension in homocubane has been elusive until recently (Fahrenhorst-Jones et al. 2022). In contrast to cubane, substitution of C by N can occur at four different positions, so the obvious question is which one [&#8230;]

Cubane (C

 8

H

 8

) and homocubane (C

 9

H

 10

) are very strained molecules. Substitution of a carbon atom for a nitrogen one to reduce the tension in homocubane has been elusive until recently (Fahrenhorst-Jones et al. 2022). In contrast to cubane, substitution of C by N can occur at four different positions, so the obvious question is which one would be the most stable.

Azahomocubanes – A New Paper in RSC Advances

Molecules. Atoms glued by bonds; nuclei incarcerated by electrons; electrons forming an inhomogeneous gas contained not by outer walls but by an electrostatic potential in its interior ironically named

 ‘external potential’

. Molecules. The study object of chemists. The fundamental construct on which the chemical understanding of the universe relies.

What do we talk about when we talk about molecules?

Once again, as the year before, I woke to my phone resembling a slot machine from any Vegas casino. #LatinXChem became a Trending Topic on Twitter early from it’s start on september 20th 2021, this year the Twitter poster session was divided into eleven categories (Ana, Bio, Comp, Edu, Eng, Env, Inorg, Mat, Nano, Org, Phys) with Nano and Comp being the ones with the most participants.

#LatinXChem – 2021 edition

Electronic excitations are calculated vertically according to the Frank—Condon principle, this means that the geometry does not change upon the excitation and we merely calculate the energy required to reach the next electronic state.

Geometry Optimizations for Excited States

I found this error in the calculation of two interacting fragments, both with unpaired electrons. So, two radicals interact at a certain distance and the full system is deemed as a singlet, therefore the unpaired electron on each fragment have opposite spins.

Fixing the error: Bad data into FinFrg

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.

On Putting up with Rejections Letters

The war against COVID-19 has been waged in many fronts. The computational chemistry community has done their share during this pandemic to put forward a cure, a vaccine, or a better understanding of the molecular mechanisms behind the human infection by the SARS-CoV-2 virus.

Worldwide CompChem in the Fight against COVID-19

This is a guest post by our very own Gustavo “

 Gus

” Mondragón whose work centers around the study of excited states chemistry of photosynthetic pigments. When you’re calculating excited states (no matter the method you’re using, TD-DFT, CI-S(D), EOM-CCS(D)) the analysis of the orbital contributions to electronic transitions poses a challenge.

Orbital Contributions to Excited States

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.

NIST CCCBDB – Vibrational Scaling Factors &amp; ThermoChem Data

The canonical molecular orbital depiction of an electronic transition is often a messy business in terms of a ‘

 chemical

‘ interpretation of ‘

 which electrons

‘ go from ‘

 which occupied orbitals

‘ to ‘

 which virtual orbitals

‘.

 Natural Transition Orbitals

provide a more intuitive picture of the orbitals, whether mixed or not, involved in any

 hole-particle

excitation.

Natural Transition Orbitals (NTOs) Gaussian

We’re always happy at the lab when a student defends their dissertation thesis and now it was the turn of Raúl Márquez-Avilés to do so with flying colors.

A New Gradúate Student. Raúl Márquez

Funny enough I was unable to log into my Linux (Ubuntu) session and I realized this might be a more common problem that it seemed. So, if you keep getting redirected to the login screen after typing your correct password over and over (and over and over), there’s no need to panic.

Locked out of your Linux Session

This week marks the 10th anniversary of this little blog! It&#8217;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 [&#8230;]

This week marks the 10th anniversary of this little blog!

10 Years of Blogging!

Quick Post on preparing Gaussian input files from PDB files. If you’re modeling biological systems chances are that, more often than not, you start by retrieving a PDB file.

Using PDB files for Electronic Structure Calculations

I just came back from beautiful Cancun where I attended for the third time the IMRC conference invited by my good friend and awesome collaborator Dr. Eddie López-Honorato, who once again pulled off the organization of a wonderful symposium on materials with environmental applications.

XXVIII International Materials Research Congress

The format of a research paper hasn’t changed much throughout history, despite the enormous changes in platforms available for their consumption and the near extinction of the library issue. Convenient electronic files such as PDFs still resemble printed-and-bound-in-issues papers in their layout instead of exploiting the seemingly endless capabilities of the electronic format. For instance, why do we still need to have page numbers?

Papers for the 21st Century

Calculating the p

 K

a value for a Brønsted acid is very hard, like really hard. A full thermodynamic cycle (fig. 1) needs to be calculated along with the high-accuracy solvation free energy for each of the species under consideration, not to mention the use of expensive methods which will be reviewed here in another post in two weeks time.

Estimation of pKa Values through Local Electrostatic Potential Calculations

Two new papers on the development of chemosensors for different applications were recently published and we had the opportunity to participate in both with the calculation of electronic interactions.

Calculation of Intermolecular Interactions for Sensors with Biological Applications

Photosynthesis, the basis of life on Earth, is based on the capacity a living organism has of capturing solar energy and transform it into chemical energy through the synthesis of macromolecules like carbohydrates.

Mg²⁺ Needs a 5th Coordination in Chlorophylls – New paper in IJQC

There’s an error message when opening some Gaussian16 output files in GaussView5 for which the message displayed is the following: ConnectionGLOG::Parse_Gauss_Coord().  Failure reading oriented atomic coordinates.

Error for Gaussian16 .log files and GaussView5

One of the most popular posts in this blog has to do with calculating Fukui indexes, however, when dealing with a large number of molecules, our described methodology can become cumbersome since it requires to manually extract the population analysis from two or three different output files and then performing the arithmetic on them separately with a spreadsheet or something.

Python scripts for calculating Fukui Indexes

Mexico City took a hard earthquake just a couple of weeks after the southern part of the country had another and 32 years to the day after the big one back in 1985 (I was seven back then).  If you wanna help this is a great place to do so. The Topos (Moles) Brigade is an elite rescue team that is taking out people from the rubble not just during this disaster but anywhere in the world where they’re needed.

Mexico City Earthquake

I began my path in computational chemistry while I still was an undergraduate student, working on my thesis under professor Cea at unam, synthesizing main group complexes with sulfur containing ligands. Quite a mouthful, I know. Therefore my first calculations dealt with obtaining Bond indexed for bidentate ligands bonded to tin, antimony and even arsenic; yes! I worked with arsenic once!

Collaborations in Inorganic Chemistry

Last Friday Durbis Castillo-Pazos became officially a graduated chemist.

A New Graduate Student – Medicinal #CompChem on HIV-1

#CompChem – Can Orbitals Be Directly Observed?

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.

The Gossip Approach to Scientific Writing

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.

I’m putting a new blog out there

Tribology isn’t exactly an area with which us chemists are most familiar, yet chemistry has a great impact on this branch of physics of high industrial importance. Tribology is basically the science which studies the causes and consequences of friction between surfaces.  The plastic bag industry requires the use of chemical additives to reduce the electrostatic adherence between sheets of plastic.

Dr. Joaquin Barroso's Blog

Density Functional Theory

Molmod ’09 at Babes-Bolyai University

A new beginning