Blog Archives

Density Keyword in Excited State Calculations with Gaussian


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. The Transition Dipole Moment is an important quantity that allows us to predict whether any given electronic transition will be allowed or not. A change in the dipole moment (i.e. non-zero) of a molecule during an electronic transition helps us characterize said transition.

Say you perform a TD-DFT calculation without the density keyword, the default will provide results on the lowest excited state from all the requested states, which may or may not be the state of interest to the transition of interest; you may be interested in the dipole moment of all your excited states.

Three separate calculations would be required to calculate the change of dipole moment upon an electronic transition:

1) A regular DFT for the ground state as a reference
2) TD-DFT, to calculate the electronic transitions; request as many states as you need/want, analyze it and from there you can see which transition is the most important.
3) Request the density of the Nth state of interest to be recovered from the checkpoint file with the following route section:

# TD(Read,Root=N) LOT Density=Current Guess=Read Geom=AllCheck

replace N for the Nth state which caught your eye in step number 2) and LOT for the Level of Theory you’ve been using in the previous steps. That should give you the dipole moment for the structure of the Nth excited state and you can compare it with the one in the ground state calculated in 1). Again, if density=current is not used, only properties of N=1 will be printed.

NIST CCCBDB – Vibrational Scaling Factors & ThermoChem Data


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

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

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

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

XXVIII International Materials Research Congress


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.

Dr. López-Honorato and I have been working for a number of years now on the design application of various kinds of materials that can eliminate arsenic species from drinking water supplies, an ever present problem in northern Mexico in South West US. So far we have successfully explored the idea of using calix[n]arenes hosts for various arsenic (V) oxides and their derivatives, but now his group has been thoroughly exploring the use of graphene and graphene oxide (GO) to perform the task.

Our joint work is a wonderful example of what theory and experiment and achieve when working hand-in-hand. During this invited talk I had the opportunity to speak about the modeling side of graphene oxide, in which we’ve been able to rationalize why polar solvents seem to be -counterintuitively- more efficient than non-polar solvents to exfoliate graphene sheets from graphite through attrition milling, as well as to understand the electronic mechanism by which UV light radiation degrades GO without significantly diminishing there arsenic-adsorbing properties. All these results are part of an upcoming paper so more details will come ahead.

Thanks to Dr. Eddie López for his invitation and the opportunity provided to meet old friends and make new ones within the wonderful world of scientific collaborations.

Post Calculation Addition of Empirical Dispersion – Fixing interaction energies


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. Basis set extrapolation methods and inclusion of electronic correlation with MP2 methods yield excellent results but they are not nonetheless almost as time consuming as CC. DFT methods in general are terrible and still are the most widely used tools for electronic structure calculations due to their competitive computing times and the wide availability of schemes for including  terms which help describe various kinds of interactions. The most important ingredients needed to get a decent to good interaction energies values calculated with DFT methods are correlation and dispersion. The first part can be recreated by a good correlation functional and the use of empirical dispersion takes care of the latter shortcoming, dramatically improving the results for interaction energies even for lousy functionals such as the infamous B3LYP. The results still wont be of benchmark quality but still the deviations from the gold standard will be shortened significantly, thus becoming more quantitatively reliable.

There is an online tool for calculating and adding the empirical dispersion from Grimme’s group to a calculation which originally lacked it. In the link below you can upload your calculation, select the basis set and functionals employed originally in it, the desired damping model and you get in return the corrected energy through a geometrical-Counterpoise correction and Grimme’s empirical dispersion function, D3, of which I have previously written here.

The gCP-D3 Webservice is located at: http://wwwtc.thch.uni-bonn.de/

The platform is entirely straightforward to use and it works with xyz, turbomole, orca and gaussian output files. The concept is very simple, a both gCP and D3 contributions are computed in the selected basis set and added to the uncorrected DFT (or HF) energy (eq. 1)

eq1 (1)

If you’re trying to calculate interaction energies, remember to perform these corrections for every component in your supramolecular assembly (eq. 2)

eq2(2)

Here’s a screen capture of the outcome after uploading a G09 log file for the simplest of options B3LYP/6-31G(d), a decomposed energy is shown at the left while a 3D interactive Jmol rendering of your molecule is shown at the right. Also, various links to the literature explaining the details of these calculations are available in the top menu.

Figure1

I’m currently writing a book chapter on methods for calculating ineraction energies so expect many more posts like this. A special mention to Dr. Jacinto Sandoval, who is working with us as a postdoc researcher, for bringing this platform to my attention, I was apparently living under a rock.

 

DFT Textbook in Spanish by Dr. José Cerón-Carrasco


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.

test

For young scientists learning English is a must nowadays but it shouldn’t shy students away from learning science in their own native tongues. To that end, the noble effort by Dr. José Cerón-Carrasco from Universidad Católica San Antonio de Murcia, in Spain, of writing a DFT textbook in Spanish constitutes a remarkable resource for Spanish-speaking computational chemistry students because it is not only a clear and concise introduction to ab initio and DFT methods but because it was also self published and written directly in Spanish. His book “Introducción a los métodos DFT: Descifrando B3LYP sin morir en el intento” is now available in Amazon. Dr. Cerón-Carrasco was very kind to invite me to write a prologue for his book, I’m very thankful to him for this opportunity.

Así que para los estudiantes hispanoparlantes hay ahora un muy valioso recurso para aprender DFT sin morir en el intento gracias al esfuerzo y la mente del Dr. José Pedro Cerón Carrasco a quien le agradezco haberme compartido la primicia de su libro

¡Salud y olé!

XVI Mexican Meeting on Phys.Chem.


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. Gustavo Mondragón gave a talk about his progress on his photosynthesis research linking to the previous work of María Eugenia Sandoval already presented in previous editions; kudos to Gustavo for performing remarkably and thanks to all those who gave us their valuable feedback and criticism. Also, five posters were presented successfully, I can only thank the entire team for representing our laboratory in such an admirable way, and a special mention to the junior members, I hope this was the first of many scientific events they attend and may you deeply enjoy each one of them.

Among the invited speakers, the RMFQT had the honor to welcome Prof. John Perdew (yes, the P in PBE); the team took the opportunity of getting a lovely picture with him.

Here is the official presentation of the newest members of our group:

Alejandra Barrera (hyperpolarizabilty calculations on hypothetical poly-calyx[n]arenes for the search of NLO materials)

img_8255

Fernando Uribe (Interaction energy calculations for non-canonical nucleotides)

img_8254

Juan Guzmán (Reaction mechanisms calculations for catalyzed organic reactions)

img_8259

We thank the organizing committee for giving us the opportunity to actively participate in this edition of the RMFQT, we eagerly await for next year as every year.

 

Dealing with Spin Contamination


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. In open shell systems, unrestricted calculations have a complete set of orbitals for the electrons with alpha spin and another set for those with beta spin. Spin contamination arises from the fact that wavefunctions obtained from unrestricted calculations are no longer eigenfunctions of the total spin operator <S^2>. In other words, one obtains an artificial mixture of spin states; up until now we’re dealing only with single reference methods. With each step of the SCF procedure the value of <S^2> is calculated and compared to s(s+1) where s is half the number of unpaired electrons (0.75 for a radical and 2.0 for triplets, and so on); if a large deviation between these two numbers is found, the then calculation stops.

Gaussian includes an annihilation step during SCF to reduce the amount of spin contamination but it’s not 100% reliable. Spin contaminated wavefunctions aren’t reliable and lead to errors in geometries, energies and population analyses.

One solution to overcome spin contamination is using Restricted Open Shell calculations (ROHF, ROMP2, etc.) for which singly occupied orbitals is used for the unpaired electrons and doubly occupied ones for the rest. These calculations are far more expensive than the unrestricted ones and energies for the unpaired electrons (the interesting ones) are unreliable, specially spin polarization is lost since dynamical correlation is hardly accounted for. The IOP(5/14=2) in Gaussian uses the annihilated wavefunction for the population analysis if acceptable but since Mulliken’s method is not reliable either I don’t advice it anyway. 

The case of DFT is different since rho.alpha and rho.beta can be separated (similarly to the case of unrestricted ab initio calculations), but the fact that both densities are built of Kohn-Sham orbitals and not true canonical orbitals, compensates the contamination somehow. That is not to say that it never shows up in DFT calculations but it is usually less severe, of course for the case of hybrid functional the more HF exchange is included the more important spin contamination may become. 

So, in short, for spin contaminated wavefunctions you want to change from restricted to unrestricted and if that doesn’t work then move to Restricted Open Shell; if using DFT you can use the same scheme and also try changing from hybrid to pure orbitals at the cost of CPU time. There is a last option which is using spin projection methods but I’ll discuss that in a following post. 

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:

$\displaystyle E_{\rm disp} = -\frac{1}{2} \sum_{i=1}^{N_{at}} \sum_{j=1}^{N_{at...
...{6ij}} {r_{ij,{L}}^6} +f_{d,8}(r_{ij,L})\,\frac{C_{8ij}} {r_{ij,L}^8} \right ),$

where coefficients $ C_{6ij}$ are adjusted depending on the geometry of atoms i and j. The damping D3 function for is:

$\displaystyle f_{d,n}(r_{ij}) = \frac{s_n}{1+6(r_{ij}/(s_{R,n}R_{0ij}))^{-\alpha_{n}}},$

where the values of s are adjustable parameters fit for the exchange-correlation functionals used in each calculation.

Fluorescent Chemosensors for Chloride in Water – Sensors and Actuators B: Chemical


A new publication is now available in which we calculated the binding properties of a fluorescent water-soluble chemosensor for halides which is specially sensitive for chloride. Once again, we were working in collaboration with an experimental group who is currently involved in developing all kinds of sustainable chemosensors.

The electronic structure of the chromophore was calculated at the M06-2X/6-311++G(d,p) level of theory under the SMD solvation model (water) at various pH levels which was achieved simply by changing the protonation and charges upon the ligand. Wiberg bond indexes from the Natural Population Analysis showed strong interactions between the chloride ion and the chromophore. Also, Fukui indexes were calculated in order to find the most probable binding sites. A very interesting feature of this compound is its ability to form a cavity without being a macrocycle! I deem it a cavity because of the intramolecular interactions which prevent the entrance of solvent molecules but that can be reversibly disrupted for the inclusion of an anion. In the figure below you can observe the remarkable quenching effect chloride has on the anion.

Sensors

A quick look to the Frontier Molecular Orbitals (FMO’s) show that the chloride anion acts as an electron donor to the sensor.

Frontier Molecular Orbitals

Frontier Molecular Orbitals

If you are interested in more details please check: Bazany-Rodríguez, I. J., Martínez-Otero, D., Barroso-Flores, J., Yatsimirsky, A. K., & Dorazco-González, A. (2015). Sensitive water-soluble fluorescent chemosensor for chloride based on a bisquinolinium pyridine-dicarboxamide compound. Sensors and Actuators B: Chemical, 221, 1348–1355. http://doi.org/10.1016/j.snb.2015.07.031

Thanks to Dr. Alejandro Dorazco from CCIQS for asking me to join him in this project which currently includes some other join ventures in the realm of molecular recognition.

New paper in JPC-A


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! This time at the Journal of Physical Chemistry A as a follow up to this other paper published last year on JPC-C. Back then we reported the development of a selective sensor for Hg(II); this sensor consisted on 1-amino-8-naphthol-3,6-disulphonic acid (H-Acid) covalently bound to a modified silica SBA-15 surface. H-Acid is fluorescent and we took advantage of the fact that, when in the presence of Hg(II) in aqueous media, its fluorescence is quenched but not with other ions, even with closely related ions such as Zn(II) and Cd(II). In this new report we delve into the electronic reasons behind the quenching process by calculating the most important electronic transitions with the framework laid by the Time Dependent Density Functional Theory (TD-DFT) at the PBE0/cc-pVQZ level of theory (we also included an electron core potential on the heavy metal atoms in order to decrease the time of each calculation). One of the things I personally liked about this work is the combination of different techniques that were used to assess the photochemical phenomenon at hand; some of those techniques included calculation of various bond orders (Mayer, Fuzzy, Wiberg, delocalization indexes), time dependent DFT and charge transfer delocalizations. Although we calculated all these various different descriptors to account for changes in the electronic structure of the ligand which lead to the fluorescence quenching, only delocalization indexes as calculated with QTAIM were used to draw conclusion, while the rest are collected in the SI section.

jpca

Thanks a lot to my good friend and collaborator Dr. Pezhman Zarabadi-Poor for all his work, interest and insight into the rationalization of this phenomenon. This is our second paper published together. By the way, if any of you readers is aware of a way to finance a postdoc stay for Pezhman here at our lab, please send us a message because right now funding is scarce and we’d love to keep bringing you many more interesting papers.

For our research group this was the fourth paper published during 2014. We can only hope (and work hard) to have at least five next year without compromising their quality. I’m setting the goal to be 6 papers; we’ll see in a year if we delivered or not.

I’d like to also take this opportunity to thank all the readers of this little blog of mine for your visits and your live demonstrations of appreciation at various local and global meetings such as the ACS meeting in San Francisco and WATOC14 in Chile, it means a lot to me to know that the things I write are read; if I were to make any New Year’s resolutions it would be to reply quicker to questions posted because if you took the time to write I should take the time to reply.

I wish you all the best for 2015 in and out of the lab!

%d bloggers like this: