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

Obtaining hydrogen from water is one of those topics that attracts lots of attention from many fronts in chemistry; on paper, it can be clean, elegant, and deceptively simple. In practice, however, water is stubborn and breaking it apart requires catalysts, large energy inputs, or clever chemistry that juggles thermodynamics and kinetics.

Universidad Nacional Autónoma de México

Can Frustrated Lewis Pairs Really Split Water? A New Paper in Inorg. Chem.

Today, on the last day of 2015, we have received great news that our latest paper regarding thr study of calixarenes as drug delivery agents has been published in the Journal of computational chemistry (10.1002/jcc.24281)   This work represents the continuation of our previous paper published last year in JCTC regarding the use of delivery agents for drugs used in the treatment of chronic myeloid leukemia;

New paper in JCC – drug delivery agents

Earlier this week we had at our annual symposium at the institute of chemistry where we had distinguished international visitors such as Prof. Theodor Agapie, Prof. Lanny Liebeskind (associate editor of

 Organometallics

), Prof. Marc Petit and Prof.

Symposium at IQ-UNAM 2015

It is with great pleasure that I announce the graduation of another member of our research group: Luis Enrique “Kike” Aguilar defended his BSc thesis yesterday and is now counting the days left for the Autumn when he’ll move to the Netherlands for a masters in computational chemistry.

A new chemist is graduated

Prof. Mario Molina was awarded the Nobel Prize in Chemistry in 1995, the same year I started my chemistry education at the chemistry school from the National Autonomous University of Mexico, UNAM, the same school from where he got his undergraduate diploma. To be a chemistry student in the late nineties in Mexico had Prof.

Mario Molina, Nobel Laureate. Rest In Peace

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?

This is the second post on a series which will try to address common technical questions in computational chemistry that recursively appear on the CCL.  The Natural Bond Orbitals analysis is a powerful tool in population analysis calculations which is more robust than the traditional Mulliken approach, if for no better reason because its almost insensitive to the change of basis set while Mulliken’s P.A. is highly sensitive to basis set effects.

Natural Bond Orbitals (NBO) visualization

I’ve decided what will my topic be this edition of Molmod!

MolMod ’09

Science permeates into the collective mind of a society not only through school but also through the form of popular media such as the TV or in the case of this post comic books. For a long time now, the group of

Chemistry and comic books

#CompChem – Can Orbitals Be Directly Observed?

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

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

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

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

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

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!

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!

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

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

Although classifications and rankings do not define the range or scope of work a person/group can do, they are usually popular to look at, unfortunately these views are sometimes misleading in the decision making process, e.g. funding. How expensive is in average our science compared to that of say organic chemists?

Are theoretical/computational chemists real chemists?

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!

10 Years of Blogging!

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

(Ah! Mathematicians, did you see what I did there?)

There are a number of appalling videos on line in which iPhones are destroyed by various means.

Finite Element(s) Chemistry

A few weeks back we wrote about using WFN(X) files with MultiWFN in order to find σ-holes in halogen atoms by calculating the maximum potential on a given surface. We later found out that using a chk file to generate a wfn(x) file using the guess=(read,only) keyword didn’t retrieve the MP2 wavefunction but rather the HF wavefunction!

Quick note on WFN(X) files and MP2 calculations #G09 #CompChem

With pleasure I announce that last week our very own Gustavo “Gus” Mondragón became the fifth undergraduate student from my lab to defend his BSc thesis and it has to be said that he did it admirably so.  Gus has been working with us for about a year now and during this time he not only worked on his thesis calculating excited states for bacteriochlorophyl pigments but also helped us finishing some series of calculations on

A New Graduate Student

Sometimes you just need to optimize some fragment or moiety of your molecule for a number of reasons -whether because of its size, your current interest, or to skew the progress of a previous optimization- or maybe you want just some kind of atoms to have their positions optimized.

Partial Optimizations with Gaussian09

Having a long calculation terminated just because it ran out of time in the queue is very frustrating;

Restarting Calculations from rwf Files – Gaussian

As we approach to the end of another year, and with that the time where my office becomes covered with post-it notes so as to find my way back into work after the holidays, we celebrate another paper published!

New paper in JPC-A

RealTimeChem

, in its first week-long edition, is coming to your Twitter feed next Monday April 22nd 2013, and I for one intend to participate.

RealTimeChem week 2013 #RealTimeChem

So many things have happened since I last updated this blog but I will come to write on them when appropriate. Right now I’d like to share an invitation by Prof. Ponnadurai Ramasami from the University of Mauritius to the upcoming

 Virtual Conference on Computational Chemistry

from the 1st to the 31st of August.

Virtual Conference in Computational Chemistry VCCC-2014 (1st call)

A couple of weeks ago I posted a solution for a common error regarding .fchk files that will display the error below when opened with GaussView5.0. As I expected, this error has to do with the use of diffuse functions in the basis set and is related to a change of format between Gaussian versions.

Some .fchk files wont open in GaussView5.0 (Update)

Although the popularization of science is an important task, I’ve always believed it’s not always addressed properly and way too many attempts have been made to emulate Carl Sagan’s COSMOS TV show.

On the popularization of science

September’s issue of Scientific American is all about food; food and food science, that is. In it, there are a couple of articles on Genetically Modified Organisms (GMO’s) and there is also this blog post in their website being in favor of GMO’s, and I for one, stand by them.

My take on GMO’s

As part of the research project I’m working on here at the Babes-Bolyai University in Romania, I must now pay a visit to prof. Sandor Kunsagi-Mate in Pecs, Hungary. I’ve met prof. Kunsagi in several occasions before and I’m looking forward to working with him in his research team, although unfortunately he will have to leave next week to the far east to check on some of his multiple collaborations around the world.

Moving out

It’s been a long time since I last posted something and so many things have happened in our research group! I should catch up with them in short but times have just been quite hectic. I’m glad to publicly thank Prof. Frank Weinhold’s gesture to include this blog in the bibliography section of the new NBO6.0 website under the NBO-Related Websites tab.

Natural Bond Orbitals (NBO) Visualization with Chemcraft

In science one thing is true and universal: We need funding. Here in Mexico the main source of funding comes from the National Council for Science and Technology (Consejo Nacional de Ciencia y Tecnología, CONACyT) which is an institution that depends directly from the federal government. Over the years different policies have prevailed and right now we are not looking into a good future.

On my view about CONACyT’s funding scheme

Once again an awful title. This post follows my previous one on graphs and chemistry, and it addresses an old idea which I have shared in the past with many patient people willing to listen to my ramblings.

Wheel? I think knot!

One of the most successful posts this blog has ever published was on certain nuances of the solvation calculations on PCM in G03. However there are some differences in the SCRF modules between G09 and G03 and I here present some of them as well as some tips to work with the new version. The

 SCFVAC

keyword used to calculate the Gibbs Solvation Energy change is

 no

longer available.

Polarizable Continuum Model (PCM) in G09 (Part II)

After months of waiting I am now oficially hired as an associate researcher at the Chemistry Institute from the National Autonomous University of Mexico! Actually I will form part of the new Joint Center for Research in Sustainable Chemistry located outside the city of Toluca in Mexico. This new job comes as a great career opportunity in which long term perspectives are high.

Starting a new job! CCIQS-UNAM

The Institute of Chemistry of the National Autonomous University of Mexico becomes 70 years old this month, and to kickoff the year round celebrations our institution has organized a series of lectures with the notable presence of Nobel Laureate, and former student of this institute, prof. Dr. Mario Molina whose presence has become ubiquitous within the Mexican scientific community events given his status.

Instituto de Química de la UNAM. 70th Anniversary

Last week I had a presentation at the Chemistry Institute in which I talked about the research I’ve been doing during the last year. Here I insert a link to my

 
 prezi
 

presentation in which I make an outline of the project’s scope and goals, so not many results available yet.

Calixarenes design – Prezi

This post will become updated continuously in order to include as much of these useful tips as I find along the way, so if you are interested please subscribe so you don’t have to visit often. Some are old or even a bit obsolete in terms of software versions but I still include them so they can all be gathered in one place;

Some software trickery…

I usually read the whole info on the Statistics page that WordPress  provides to this blog in order to know how many visitors drop by during  the week; what other sites are sending me some traffic, if any, or what  searches are readers performing which leads them to my blog. Last week I  found this post title as one of the Google searches that ultimately  made someone find my blog.

How much do theoretical chemists make?

It seems a bit weird that there isn’t much information on this topic on the internet. Recently I’ve had to calculate some of these indices to explain an anomalous behaviour in lactones formation and out of curiosity I ran a small search on the net about how to calculate them.

How to calculate Fukui indices

I just recently found out this very blog of mine was found and ranked by the Chemical blogspace as number

 96

(out of about 250, before you ask). I still don’t know how do they do the math but it seems it has to do with the number of clicks a blog gets over a certain period of time and relating that somehow to the number of new posts over that same period.

The Chemical blogspace (Cb) has ranked this blog!

A new paper is coming out! These are always good news for someone whose productivity is evaluated by the number of his/her publications, and in my case the pleasure is double.

Inorganic Chemistry paper

The energy of your calculated transition state (TS) is lower than that of the reagents. That’s gotta be an error right? Well, maybe not.

Submerged Reaction Energy Barriers

I was recently invited to participate in a series called

 The Future We Create

. This event is the third installment in an ongoing conversation (sponsored by Dow Chemical) to explore how chemistry can collaborate with other sectors and concerned citizens to solve humanity’s most important challenges. The title of this installment is The Future of Sustainable Chemistry which will be aired next Tuesday! An official invitation follows.

The Future of Sustainable Chemistry; The Future We Create (Part I, invitation)

Statistical Mechanics is the bridge between microscopic calculations and thermodynamics of a particle ensemble. By means of calculating a partition function divided in electronic, rotational, translational and vibrational functions, one can calculate all thermodynamic functions required to fully characterize a chemical reaction.

Useful Thermochemistry from Gaussian Calculations

Today’s science is published mostly in English, which means that non-English speakers must first tackle the language barrier before sharing their scientific ideas and results with the community; this blog is a proof that non-native-English speakers such as myself cannot outreach a large audience in another language.

DFT Textbook in Spanish by Dr. José Cerón-Carrasco

We’ve covered some common errors when dealing with formatted checkpoint files (*.fchk) generated from Gaussian, specially when analyzed with the associated GaussView program. (see here and here for previous posts on the matter.)  Prof.

fchk file errors (Gaussian) Missing or bad Data: RBond

I had the honor to be invited by Dr. Michael Rauch from Schrödinger Inc. to work one of their online courses for learning how to use Materials Science (MS) Maestro. From their various options, I chose the Surface Chemistry course because it was an opportunity to brush on my knowledge about calculations on extended phases, which aren’t precisely my bread and butter.

My Week with MS Maestro – Schrödinger Inc.

Most organic chemistry deals with closed shell calculations, but every once in a while you want to calculate carbenes, free radicals or radical transition states coming from a homolytic bond break, which means your structure is now open shell. Closed shell systems are characterized by having doubly occupied molecular orbitals, that is to say the calculation is ‘restricted’: Two electrons with opposite spin occupy the same orbital.

Dealing with Spin Contamination

Literature in synthetic chemistry is full of reactions that do occur but very little or no attention is payed to those that do not proceed. The question here is what can we learn from reactions that are not taking place even when our chemical intuition tells us they’re feasible? Is there valuable knowledge that can be acquired by studying the ‘anti-driving force’ that inhibits a reaction?

New paper in Tetrahedron #CompChem “Why U don’t React?”

It is with great pleasure that I’d like to announce the thesis defense of

 Guillermo “
 
 Memo
 
 ” Caballero

and

 Howard Diaz

who in past days became the second and third students, respectively, to get their B.Sc. degrees with theses completed at our lab.

Two more students graduated!

This post was inspired by this other one, featured in WordPress’ Freshly Pressed section, on how should non-scientist read a scientific paper.

How to read (and perhaps even write) a scientific paper

Theoretical evaluation of a reaction mechanism is all about finding the right transition states (TS) but there are no guarantees within the available methods to actually find the one we need. Chemical intuition in the proposal of a mechanism is paramount. Let’s remember that a TS is a critical point on a Potential Energy Surface (PES) that is a minimum in every dimension but one.

Transition State Search (QST2 &amp; QST3) and IRC with Gaussian09

For over a decade these meetings have gathered theoretical chemists every year to share and comment their current work and to also give students the opportunity to interact with experienced researchers, some of which in turn were even students of Prof. Robert Parr, Prof. Richard Bader or Prof. Per Olov Löwdin. This year the Mexican Meeting on Theoretical Physical Chemistry took place last weekend in Toluca, where CCIQS is located.

XIth Mexican Reunion on Theoretical Physical Chemistry

A new paper has been published and that is always good news.

Paper published in Canadian Journal of Chemistry

If a mind is a terrible thing to waste, then wasting a collective mind is an even more terrible thing. During the past weekend the library at the institute of chemistry suffered a flood caused by a broken pipe just above it, which incidentally happens to be the lab were I used to work as an undergrad student. When it comes to scientific journals, our institute still relies a lot on paper issues for the oldest numbers;

Institute of Chemistry Library flood – UNAM

ChatGPT is a powerful language model developed by OpenAI that has the ability to generate human-like text. This model is trained on a vast amount of data and can be fine-tuned to perform a wide range of tasks, including computational chemistry. In this blog post, we will discuss the benefits and possibilities of using ChatGPT in computational chemistry.

ChatGPT in Computational Chemistry

As

I recently pointed out in an interview for a webinar titled

 The Future We Create

, (sponsored by the Dow Chemical Co.) I believe we must clearly differentiate the concepts of

 Green Chemistry

and

 Sustainable chemistry

or we take the risk of confusing

 purpose

and

 procedure

; instead, having them both clearly defined we can use their definitions as a working frame in order to solve the

Green Chemistry and sustainable development

It’s always hard to write about a computational method in a blog post since it could span for pages on end, so that’s why this post as the ones about NBO and PCM will only treat briefly the underlying physics (at a handwave level) and interpretation about the most popular choices within multiconfigurational methods which form part of the family of post Hartree-Fock methods*. If you are only interested in one of the many MC methods scroll down

Multiconfigurational methods (CI, CC, CASSCF, CASPT2)

Around early October the scientific community -or at least part of it- starts getting excited about what could be considered the most prestigious award a scientist could ever achieve: The Nobel Prize. The three categories that interest me the most are: Chemistry, Physics and Literature.

It’s that time of the year again… The Nobel Prizes

Another common question on CCL…  The use of Internal Redundant coordinates (through the Opt=ModRedundant option) must not be overlooked! This option performes a geometry optimization at each step while maintaining the scanned variable constant, which is referred to as a Relaxed Potential Energy Surface (PES) Scan. Using internal coordinates becomes compulsory and a well-defined Z-Matrix is preferable.

Rigid and Relaxed Potential Energy Surface Scans (PES Scan) in Gaussian 03 and Gaussian 09

My boss just told me a few days ago he may not be able to make it to a workshop in Bucharest, which is actually more of a bilateral conference between Romania and South Korea. So it seems I’m due up for making a presentation for this meeting on next Wednesday (that is the day after tomorrow!). The down side? I’m not available tomorrow (Sep.

Emergency talk. Calixarenes as guest molecules

This is my first post on a series I have in mind regarding frequent questions on the CCL regarding the use of some computational chemistry software, mostly Gaussian. Readers are still encouraged to contact the Gaussian Help Desk for further (and more accurate) help.

Polarizable Continuum Model (PCM) in G03

To calculate what the bonding properties of a molecule are in a particular excited state we can run any population analysis following the root of interest. This straightforward procedure takes two consecutive calculations since you don’t necessarily know before hand which excited state is the one of interest.

Population Analysis in the Excited State with Gaussian

Last week we had the visit of prof. H. F. Schaefer III here at Babes-Bolyai, that awarded him an

 honoris causa

doctorate for his contributions to computational chemistry, which I must say have been groundbreaking and paradigmatic. Nevertheless his visit is not without controversy.

Schaefer, Hawking and God

The word ‘

 umpolung

‘ is not used often enough in my opinion, and that’s a shame since this phenomenon refers to one of the most classic tropes or

 deus ex machina

used in sci-fi movies—prominently in the Dr. Who lore*—and that is ‘

 
 reversing the polarity
 

‘. Now, reversing the polarity only means that for any given dipole the positively charged part now acquires a negative charge, while the originally

Water splitting by proton to hydride umpolung—New paper in Chem.Sci.

I’m very excited and honored to participate in this year’s Virtual Winter School on #CompChem. This event started back in 2015 and this year the list of participants includes Nobel Laureate and legend Roald Hoffmann. The topics will range from drug design to quantum chemistry on quantum computers. Additionally, two workshops will be given for ADF and Gaussian.

Virtual Winter School on Computational Chemistry 2022

The admission process for graduate studies at the National Autonomous University of Mexico (UNAM) is about to begin and I have wide open spaces in my lab for people interested in getting a PhD in the field of applied computational chemistry.

I Want You!

The compound spiro-dibenzocycloheptatriene (figure 1) made headlines a year ago by claiming that the ipso carbon atoms across the molecule were bound together by a single electron σ bond.

The compound spiro-dibenzocycloheptatriene (figure 1) made headlines a year ago by claiming that the ipso carbon atoms across the molecule were bound together by a single electron σ bond. This is truly a seductive idea: that somewhere out there, in the shadows of open-shell aromatics, carbon atoms might form a

 single-electron σ-bond

— a unicorn of bonding, indeed.

One electron C-C bond or Weak Interaction? New paper in PCCP

The strength of a chemical bond can be defined as the change in enthalpy when a bond is homolytically broken into two radicals. Bond dissociation energy is thus the measure of the strength of a bond and, while it is temperature dependent, it can be calculated by DFT or ab initio methods.

Bond Dissociation Energy with Gaussian16

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 […]

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?

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

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

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

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

My biggest pet peeve regarding the perception of experimental chemists about theoretical chemistry relates to the physical interpretation of orbitals. Every now and then there’s a serious claim about having atomic/molecular orbitals experimentally observed (read:

 Can Orbitals Be Directly Observed?

What do we talk about when we talk about Empty Orbitals?

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?

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 Mexican Meeting on Theoretical Physical Chemistry is a national staple of our local scientific discipline. The nineteenth edition had to be a virtual conference due to sanitary restrictions still enforced in Mexico. Nevertheless, this was a successful meeting in which we tried new things, such as a live broadcast via our new official YouTube channel and a Twitter poster session covered under the hashtag #RMFQTXIX.

XIX RMFQT – National Meeting on TheoPhysChem

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

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

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

Molecular Orbitals (MOs) are linear combinations of Atomic Orbitals (AOs), which in turn are linear combinations of other functions called ‘basis functions’. A basis, or more accurately a basis set, is a collection of functions which obey a set of rules (such as being orthogonal to each other and possibly being normalized) with which all AOs are constructed, and although these are centered on each atomic nucleus, the canonical way in which they

Basis Set Superposition Error (BSSE). A short intro

I have written about extracting information from excited state calculations but an important consideration when analyzing the results is the proper use of the keyword

 density

. This keyword let’s Gaussian know which density is to be used in calculating some results. An important property to be calculated when dealing with excited states is the change in dipole moment between the ground state and any given state.

Density Keyword in Excited State Calculations with Gaussian

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

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

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

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

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.

Dr. Joaquin Barroso's Blog

On the popularization of science

Swine flu outbreak

MolMod ’09

Density Functional Theory

Molmod ’09 at Babes-Bolyai University

A new beginning