Grimme’s Dispersion DFT-D3 in Gaussian #CompChem
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.
There are also some overlays that can be used to invoke the use dispersion in various scenarios:
IOp(3/74=x) Exchange and Correlation Potentials
| -77
-76 -60 -59 |
DSD-PBEP86 (double hybrid, DFT-D3).
PW6B95-D3. B2PLYP-D3 (double hybrid, DFT-D3). B97-D (DFT-D3). |
IOp(3/76=x) Mixing of HF and DFT.
| -33 | PW6B95 and PW6B95-D3 coefficients. |
IOp(3/124=x) Empirical dispersion term.
| 30
40 50 |
Force dispersion type 3 (Grimme DFT-D3).
Force dispersion type 4 (Grimme DFT-D3(BJ)). Force dispersion type 5 (Grimme D3, PM7 version). |
The D3 correction method of Grimme defines the van der Waals energy like:
 |
where coefficients 
are adjusted depending on the geometry of atoms i and j. The damping D3 function for is:
 |
where the values of s are adjustable parameters fit for the exchange-correlation functionals used in each calculation.
Is #OpenAccess a first world problem?
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. The Open Access (OA) supporters rightfully wish that all publications were accessible to anyone interested without having a middleman such as a big publisher controlling access and making a profit along the way.
A while ago there was a rather noble initiative in Mexico to have all publicly funded research fully available to everybody; sounds reasonable but here is the catch: Our research would have to be published in a public online platform created, managed and operated by the state with public money. This means the Mexican tax payers would have to pay not only for research to be done but to be stored and curated also. On top of that, this platform would require to become somehow visible to other researchers in other countries in order for it not only to gather attention and recognition from the larger scientific community but also to get their proper scrutiny; and that might not a be task that the state is good at doing. Furthermore, once our research is made public through this platform we might have a copyright problem when submitting it to a mainstream traditional journal with a quantifiable IF and whether we like it or not – whether we believe in it or not – IF is a quick go-to measure with which researchers are qualified by current and future employers, in fact, permanence in certain institutions as well as organizations rely on the continuous publishing of peer reviewed indexed articles.
When I started doing research here at IQ-UNAM dollars were about eleven pesos each, they are now over twenty yet my budget is still pretty much the same and is always in pesos, not dollars, so a larger gap keeps building up. So to me, paying for an OA is becoming more and more expensive everyday and although there are very prestigious, legitimate, peer reviewed, indexed OA journals the publication fee is an important factor to consider. If I indeed have the money available I may better think twice about saving it by going to a traditional journal and use it for other purposes. And in the end, fair or not, does everybody really want to read about my calculations? I really doubt so. My personal take is to publish in a traditional journal* and then blog about it in a more relaxed way here, plus making it visible in several platforms such as Mendeley, Academia.edu or ResearchGate and share it with others whenever possible.
It would be fairly easy to assume from the title and previous line that I oppose Open Access publications but then again that would be a wrong assumption. The broader answer is that I am for OA but that I don’t think the current scientific landscape makes it a terrific idea. First, employers would have to stop fixating in IFs and prestigious titles and then there would have to be enough money for paying OA’s or making the decision between paying the fee or using the money for other things; and that right there is what makes it a First World problem to me.
Women in #CompChem and the rest of STEM
In the past I’ve avoided this topic for various reasons. First, because I strongly believe that focusing on labels perpetuates them, and as scientists, we should always rise above them, for is science and not scientists what’s important. I remember my former PhD advisor, Prof. Cogordan, saying that “Liberties are exercised, not demanded“. Take Rosa Parks, for instance, her refusal to move to the back of the bus was an exercise of her liberty, and one that moved to a profound change, alas not without turmoil. But should I really call it a label? since it applies to roughly half the potential brain power available in the planet it then becomes a relevant question. Are equality and political correctness mutually exclusive terms?
It could be argued that I talk from a privileged position being a male scientist but since I’m a Mexican, non-white, non-US-based, male scientist those privileges are only so many.
I first began drafting this post way back before November 2016, when the misogyny displayed by a presidential candidate was in everyone’s mind to such a large extent that even when it even seemed prone to cause his demise it didn’t. The women’s march in D.C. has proven the topic to be still quite relevant though, and next April 22nd, Earth Day, a scientists march will take place to protest against policies that put science -and therefore mankind- in jeopardy. Some particular issues associated with the march will be the communication gag orders against scientific federal agencies; the consequences of the travel-ban to scientists from black-listed countries and, of course, the threat of having a misogynistic environment on the status of women in STEM careers.
Fact: There is a clear selection bias since there is still a large number disparity between men and women in academia throughout the world and since the number of academic position is growing at a much lower rate than the number of scientists competing for such positions, the race has become tighter and usually women take the worst part of the deal. There is a leaking pipeline in which women don’t reach the end of the race. I imagine in some cases it may have to do with maternity as it is still conservatively perceived by most countries but issues like harassment and condescension are not to be ignored.
Fact: Scientific curiosity is innate to all human beings -which confirms the above mentioned bias- therefore talking about encouraging young women to pursuit a career in STEM is plain stupid; they don’t need to be encouraged they must stop being discouraged somewhere along the path. The playing field for both genders should be leveled or science risks loosing half the population in these dire times in which all the brain power available is much needed. Also, I fear the continuous talk about these disadvantages could be off-putting for future generations of women who might be interested in undertaking STEM careers. Leveling the field for female and male scientists should be done and not just demanded but details about the mechanisms to accomplish it are still unclear and vary from one institution to another. Here in Mexico, for instance, all public universities have collective contracts, therefore every scientist in a given level earns as much as another in the same level. In other countries salaries are personally negotiated and therefore each scientists earnings vary, which has led to women earning less on average. Now, the ease with which levels are climbed within an institution are also a matter for debate. Does this mean that earnings and positions are the main problems women face in academia? Could they be the best starting points? Is the rate of enrollment the root of the problem? If so, are us teachers and professors to blame?
Another reason why I avoided this topic was because it would seem so patronizing on my part to give a shout-out to women whose work in computational chemistry I so much admire when I myself could only aspire to one day have work of their quality. They definitely don’t need my praises because they have well earned all our admiration. Nonetheless, here is a link to a great directory of women working in computational chemistry in which some great names are found such as Anna Krylov, Gloria Tabacchi, Romelia Salomón, Patricia Hunt, and so many more great scientists from all over the world. Here in Mexico we count with names such as Margarita Bernal, Patrizia Calaminici, Annia Galano, Estela Mayoral and so many other. It is hard to make a comprehensive list, and as I said before I could only aspire to have work with the same quality as theirs. The importance of recognizing and promoting women to take a career in computational chemistry will in short be addressed by the FemEx-NL-2017 conference next June 22nd in the Netherlands; their motto is “Promoting female excellence in theoretical and computational chemistry”, certainly a worthy and noble endeavor for a problem far from solved.
Perhaps another good reason for writing this post lies in the image below. It is a true statement but we should analyze the causality for it and fix whatever it is we’re doing wrong because it is certainly not the plumbing:
Comp. Chem. problems: no line for women’s restroom but men’s is out the door. 😦 #drugalchemy pic.twitter.com/BFlxXvd7H6
— David Mobley (@davidlmobley) May 17, 2016
I have a daughter. I want her to be able to do whatever she wants when she grows up without deterrence from unfairness. I want a world for her without labels so she never has the option of playing ‘The Woman Card’. It wouldn’t be fair for anyone around her.
This wont be the last post on this topic. Please share your views in the comments and criticism section. They are all welcome.
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Annual state of the Research Group
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!
Finite Element(s) Chemistry
(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. From a chemist standpoint, the reason why I’m so disgusted with them is the waste of rare elements which go into the making of their components: From Neodymium to Indium, most of these metals come from conflict zones in which they are extracted in the most precarious conditions imaginable, but furthermore, they are so scarce the production of electronics is almost unsustainable. I wont post any links to these infuriating videos so as to not direct traffic to any of them, instead I will direct your attention to a wonderful book titled The Elements of Power: Gadgets, Guns, and the Struggle for a Sustainable Future in the Rare Metal Age by David S. Abraham. (Sheesh! Nobody uses short titles anymore? Can you imagine Nabokov writing Lolita: A little girl with a not so little mind and the professor who picked up on that? I digress.) It is hard not to read this long-titled book and feel a tad guilty; it is in fact a bit blackmailing but above all, realizing what a wasteful society (ugh! I hate that word) we are makes a strong wake up call to the future of sustainability. I would never claim that the solution is renouncing to technology but instead to find a sustainable technology within the framework of current technology. Easier said than done -of course- but stopping waste of such precious resources should be the first step in everyones mind, and don’t even get me started on balloons filled with He! In all fairness, one can also find a lot of scary articles on line from dubious to respectful on how smartphones and other rare-metals-containing gadgets are damaging the Earth.
Last year I enjoyed reading Andy Weir’s novel The Martian (later a major motion picture from Alien’s director Ridley Scott), in which an astronaut is stranded in Mars -left for dead by his crewmates, with nothing but the finite supplies of the station and his knowledge of chemistry, botany and engineering, all of which allows him to survive by extending, but above all reusing, those resources which included not only food but O2, H2O and even hydrazine, H2N2 originally intended for fuel but from where he now gets H2 for synthesizing a larger supply of water by reacting it with the O2 pulled out of the CO2-filled Martian atmosphere. I’m pretty sure Weir didn’t intend this novel to be a metaphor but it definitely works well as one of the limited resources available on Earth and the necessity of optimizing their use, collecting and disposal. Resources on Earth seem infinite, or they at least they did back when the industrial revolution started.
I guess the point is that sustainability goes hand in hand with using the least resources to get new ones as well as with avoiding their waste. I think one must agree that Chemistry, like no other science, has shaped our world for better and worse.
I haven’t rambled on sustainability in a while. Feels bad. Must be the winter.
Mexican Phys.Chem. Meeting XVth edition
For the fifth year in a row my research group has participated in this traditional meeting on theoretical and computational chemistry, now at the beautiful city of Merida in southeastern Mexico.
Several distinguished international guests included Profs. Jose Luis Mendoza (Florida State University), Adrián Roitberg (University of Florida), Vincent Ortiz (Auburn University) and Paul Ayers (McMaster U. Canada); Their contributions rounded up nicely those of household names like Drs. Alberto Vela, Gabriel Merino (CINVESTAV) (the latter was also the main organizer), Jesus Hernández-Trujillo (UNAM), Jose Luis Gazquez (UAM-I), Óscar Jimenez (Guanajuato), and so many others who were also present.
My students presented four posters summarized below:
1) Maru Sandoval and Gustavo Mondragón on Photosynthesis, particularly the search for exciton transference mechanisms in both natural and theoretical arrangements of photosynthetic pigments. Some very exciting results have been observed; their publication is really near.
2) Raúl Torres and Gustavo Mondragón presented their work on arsenic removing calixarenes, published earlier this year, and the extension of said work to As(III) acids. Graphene oxide is now considered in our simulations as per the experimental work of our colleagues, Prof. Reyes Sierra and Prof. Eddie Lopez-Honorato.
3) Marco Diaz, Guillermo Caballero, Gustavo Mondragón and Raúl Torres had this poster on the calculation of sigma holes as descriptors for predicting pka values in organic acids. Their +1600 calculations project has found the best levels of theory (and ruled out some like B3LYP, of course) with some nice correlations. Yet, much work is still to be done but we’re on the right track.
4) Durbis Castillo presented his work on molecular docking and dynamics of a large library of HIV-1 entry inhibitors for which he uses the suite MAESTRO as a continuation of another project of ours. His enormous library is now in the hundredths of thousands and although we’re facing some technical difficulties, Durbis is thriving in his search. This is our first serious attempt towards a more mature drug discovery project; a manuscript should be ready in the first part of next year.
This guys and the rest of the lab who weren’t present are the ones who make our research flourish and they’ve all earned a day or two at the beach!
Here’s to fifteen more years of RMFQT!
Tribology – New paper in JPC A
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. My good old friend Dr. Armando Gama has studied through Dissipative Particle Dynamics (DPD) coarse-grained simulations the friction coefficients of having two slightly different molecules: erukamide and behenamide, which only differ in the presence of a double bond between carbon atoms 12 and 13 (Fig1).
Fig 1
Double bonds in erukamide pile together through pi-pi stacking interactions (Fig2) which are absent in behenamide which is why these last ones are able to slide better between each other (Fig3). Interaction energies calculated for the inner chains at the same level of theory are 44.21 and 34.46 kcal/mol for erukamide and behenamide, respectively. As per the suggestion of a referee we extended the calculations to a 2D system by placing seven molecules on graphene, which once again was kept at the optimized geometry of its isolated state, at four bonds of separation in order to prevent steric crowding (Fig 4).
Fig 4
The paper is now available at JPC-A. Thanks to Dr. Gama for this great opportunity to work with his team, I know it wont be the last.
Back in Pécsi Tudomanyegyetem (Hungary)
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.
As part of an agreement between the science councils of both Mexico and Hungary, our research proposal on the development of macrocyclic-based therapeutic agents for capturing micotoxins and other molecules was selected for financing. As before, the theoretical section will be handled by us, namely to some extent by Marco Diaz as part of his BSc thesis, while the experimental part will be handled by the group from Prof. Kunsagi’s lab and Dr. Lemli Beáta‘s. I’m very excited about living for a month here in Pécs but also about having a close friend, to whom I owe so much, working with me in an experimental-theoretical project that will further advance both our researches and careers. It was in fact the work of Profs. Kunsagi here in Pécs and Silaghi in Cluj, Romania, which got me interested in the supramolecular chemistry of calixarenes.
Lets hope we can manage to keep this collaboration between our labs going on for many years to come. For the sake of humor here are some old and new photographs.
New paper in PCCP: CCl3 reduced to CH3 through σ-holes #CompChem
I found it surprising that the trichloromethyl group could be chemically reduced into a methyl group quite rapidly in the presence of thiophenol, but once again a failed reaction in the lab gave us the opportunity to learn some nuances about the chemical reactivity of organic compounds. Even more surprising was the fact that this reduction occured through a mechanism in which chlorine atoms behave as electrophiles and not as nucleophiles.
We proposed the mechanism shown in figure 1 to be consistent with the 1H-NMR kinetic experiment (Figure 2) which shows the presence of the intermediary sulfides and leads to the observed phenyl-disulfide as the only isolable byproduct. The proposed mechanism invokes the presence of σ-holes on chlorine atoms to justify the attack of thiophenolate towards the chlorine atom leaving a carbanion behind during the first step. The NMR spectra were recorded at 195K which implies that the energy barriers had to be very low; the first step has a ~3kcal/mol energy barrier at this temperature.
Figure 1 – Calculated mechanism BMK/6-31G(d,p) sigma holes are observed on Cl atoms
1H NMR of the chemical reduction of the trichloromethyl group. Sulfide 4 is the only observed byproduct
To calculate these energy barriers we employed the BMK functional as implemented in Gaussian09. This functional came highly recommended to this purpose and I gotta say it delivered! The optimized geometries of all transition states and intermediaries were then taken to an MP2 single point upon which the maximum electrostatic potential on each atom (Vmax) was calculated with MultiWFN. In figure 3 we can observe the position and Vmax value of σ-holes on chlorine atoms as suggested by the mapping of electrostatic potential on the electron density of various compounds.
We later ran the same MP2 calculations on other CCl3 groups and found that the binding to an electron withdrawing group is necessary for a σ-hole to be present. (This fact was already present in the literature, of course, but reproducing it served us to validate our methodology.)
Figure 3 – Sigma holes found on other CCl3 containing compounds
We are pleased to have this work published in PhysChemChemPhys. Thanks to Dr. Moisés Romero for letting us into his laboratory and to Guillermo Caballero for his hard work both in the lab and behind the computer; Guillermo is now bound to Cambridge to get his PhD, we wish him every success possible in his new job and hope to see him again in a few years, I’m sure he will make a good job at his new laboratory.
Quick note on WFN(X) files and MP2 calculations #G09 #CompChem
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! Luckily we realized this problem very quickly and were able to fix it. We tried to generate the wfn(x) file with the following keywords at the route section
#p guess=(read,only) density=current
but we kept retrieving the HF values, which we noticed by running the corresponding HF calculation and noticing that every value extracted from the WFN file was exactly the same.
So, if you want a WFN(X) file for post processing an MP2 (or any other post-HartreFock calculation for that matter) ask for it from the beginning of your calculation in the same job. I still don’t know how to work around this or but will be happy to report it whenever I do.
PS. A sincere apology to all subscribers for getting a notification to this post when it wasn’t still finished.
