As every year this month we had the yearly Mexican Reunion on Theoretical Physical Chemistry organized by prominent researchers in the field, such as Dr. Emilio Orgaz (UNAM), Dr. Alberto Vela (CINVESTAV) and many other. Over 150 different works were presented during this edition which took place in Juriquilla, Querétaro at one of the many campuses of the National Autonomous University of Mexico scattered all around the country. Below you can see some pictures from the talks and the first poster session.
This time we contributed with a small poster on a mechanism proposed by Howard Diaz (an undergrad student from UAEM) on the equilibrium transformation of dihydrocinolines into 1-amino-indoles by an intramolecular rearrangement. May this post also serve as the starting point of a -mini-tutorial on how to evaluate a mechanism theoretically using QST3 and IRC in implicitly solvated environments (PCM)
The equilibrium under study and the proposed mechanism by which it occurs, originally proposed by Frontana-Uribe et al. looks a bit like this:
The energy profile, in which all transition states were calculated with the QST3 method, is presented below, calculated at various levels of theory. Also, the Internal Reaction Coordinate (IRC) connecting both states was calculated and is shown further below in the full poster.
From this results we believe that a new mechanistic proposal is needed since the energy barrier for the first step is quite high (~60 kcal/mol) and hence a bit unlikely to occur through that transition state. Nevertheless this is a first approach to elucidating a mechanism and the more knowledge about it the higher the control will be on this chemical transformation.
A full version of the poster is shown below for your convenience (Spanish). See you all at the next RMFQT in Morelia 2014!
How to calculate the Delta G of solvation? This is a question that I get a lot in this blog, so it is about time I wrote a (mini)post on it, and at the same time put an end to this posting drought which has lasted for quite a few months due to a lot of pending work with which I’ve had to catch up. Therefore, this is another post in the series of SCRF calculations that are so popular in this blog. For the other posts on this subjects remember to click here and here.
SMD is the keyword you want to use when performing a Self Consistent Reaction Field (SCRF) calculation with G09. This keyword was only made available in this last version of the program and it corresponds to Truhlar’s and coworkers solvation model which is recommended by Gaussian itself as the preferred model to calculate Delta G of solvation. The syntax used is the standard way used in any other Gaussian input files as follows:
# 'route section keywords' SCRF=SMD
Separately, we must either perform a gas phase calculation or use the DoVacuum keyword within the same SCRF input, and then take the energy difference between gas phase and solvated models.
# 'route section keywords' SCRF=(SMD,DoVacuum)
No solvation or cavity model should be defined since, by definition, SMD will use the IEFPCM model which is a synonym for PCM.
As opposed to the previous versions of Gaussian, the output energy already contains all corrections, this is why we must take the difference between both values (remember to calculate them both at the same level of theory if calculated separately!). Nevertheless, when using the SMD keyword we get a separate line, just below the energy, stating the SMD-CDS non electrostatic value in kCal/mol.
The radii were also defined in the original paper by Truhlar; I’m not sure if using the keyword RADII with any of its options yields a different result or if it even ends in an error. Its worth the try!
Some calculation variations are not available when using SMD, such as Dis (calculation of the solute-solvent dispersion interaction energy), Rep (solute-solvent repulsion interaction energy) and Cav (inclusion of the solute cavitation energy in the total energy). I guess the reason for this might be that the SMD model is highly parametrized.
Have you found any issue with any item listed above? Pleases share your thoughts in the comments section below. As usual I hope this post was useful and that you all rate it, like it and comment.
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. It is now replaced by DoVacuum which should be included in the SCRF options as SCRF=(DoVacuum,etc.). However, the absolute solvation energy now requires a gas-phase optimization along with a frequency calculation followed by the same calculations with the SCRF=SMD option in the desired solvent and with the appropriate variables.
Gaussian 03 used to calculate and report non-electrostatic contributions to the solvation energy, however they were not included in the total energy nor during optimization procedures. These non-electrosatic interactions are no longer calculated in the default. In order to include these terms during the SCF procedure, and to have them reported separately, the SCRF=SMD option should be used.
My previous post on PCM mentioned the usage of the options OFac=0.8 & RMin=0.5 as part of the additional input. These ‘magic numbers’ (I hate the term) were used to modify the way by which the overlapping spheres were treated in order to create the surface which in turn defined the cavity. G09 uses a new algorithm to make the overlaps generate a smoother surface. I recommend to use the default values before including ‘magic parameters’.
All the default values which G03 used can be retrieved with the G03Defaults keyword, but it is strongly suggested to use it only for comparison with calculations previously done with the older version.
As with some other so-called ‘white papers’ this post will be further improved as more information arises during my own calculations. Thanks for reading! Please comment/like/share this post, as well as others in the blog, if you found useful the information within.
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.
Gaussian 03, the popular electronic structure calculation suite of programs, includes the necessary modules for performing calculations in a solvated environment using the continuum models approximations. Among such models, the Polarizable Continuum Model (PCM) is one of the most widely used methods since it meets a good compromise between accuracy and computation time. Nevertheless, Gaussian may not be the best option for performing such calculations (as opposed to other programs as COSMO) but it still can be very useful when used properly. Unfortunately there is a lack of specific info in the literature regarding the usage of the different variables involved in the cavity generation for G03; the newest version, G09, includes some improvements on the corresponding codes making PCM calculations more achievable. While browsing the CCL archives, it is common to find more questions than answers and usually the same questions are posted over and over by different users over time. This post will get updated as needed.
I hope with this post I can summarize most of the common problems found in Gaussian regarding implicit solvation calculations as well as their respective solutions. Some of the solutions come from Gaussian technical support itself, so my best advise is always to address your questions directly to them. Keywords are typed in capital letters, variables in italics.
Implicit solvent calculations imply the generation of a vacuum cavity inside a continuous and homogeneous dielectric field. The simplest model to do this is Onsager’s in which the molecule is treated as a dipole inside a spherical cavity (SCRF=DIPOLE in Gaussian use along the VOLUME keyword to generate the optimum radius for such cavity.) PCM calculations generate a cavity that relates more closely to the molecule’s shape by placing spheres on each atom or groups of atoms. Check the Gaussian link at the bottom of this post for further info; this is a troubleshooting post, not a tutorial on PCM.
Some common errors and their solutions
In order to get a better definition of a cavity it has been recommended to use the option SCRF=(READ,model,SOLVENT=solvent) with the following parameters to be read at the end of the input file:
Additionally we may include a third line indicating the kind of radii to be used on each atom to generate a sphere around it, the default option is Radii=UA0 (Topological United Atoms model) which treats functional groups as a single sphere. Including this line with Radii=UFF; Radii=Pauling or Radii=Bondi will treat each atom independently, which is very useful to use when some H atoms lye outside the UAKS sphere. The error message associated with this problem is: “Error message, treat H atom explicitly” see below
-> BldSpC: Error generating genealogic tree for sphere 309 at level 15
According to Gaussian’s Help Desk, this is a numerical error in the generation of the cavity. The use of fewer spheres (implicit H atoms for instance) is recomended, so if you are using RADII=PAULING or BONDI, delete that line. It is also recommended to use the NOSYMM keyword on the route section. This problem seems to have been addressed in G09.
-> Too many tesserae. Increase the MxTs.
Try using the TSNUM keyword in the route section as SCRF=(TSNUM=num,…) This will modify the number of tiles to describe each sphere that makes the cavity.
-> AdVTs1: ISph= 500 is engulfed by JSph= 501 but Ae( 500) is not yet zero! Error in link301
Generation of cavity fails. Try using a different radii model (RADII=…) and/or the NOSYMMCAV keyword at the end of the file, via the SCRF=(Read,…) option. Also using the NOSYMM keyword in the route section can work. Once again using the OFAC=0.8 and RMIN=0.5 parameters is useful.
-> UA0: Hydrogen 40 is unbound. Keep it explicit at all point on the …
-> UA0: potential energy surface to get meaningful results.
The location of a certain H atom (number 40 in this case) lies outside the cavity placed on a functional group, so it must be treated explicitly by either changing the RADII= model or by placing a sphere on that particular atom alone through the SPHEREONH=40 (40 for this example) option via SCRF=(Read,…)
Additional remarks and suggestions
- The use of spheres on functional groups is suggested for calculating energies, but for geometry optimization the use of a more sophisticated model in generating the cavity is encouraged.
- Always pay attention to the value of the density lying outside the cavity, i.e. inside the dielectric. In G03 this value is labeled as “error on total polarization charges”. As a rule of thumb this value should be less than 0.05 for the calculation to be acceptable.
- Just in case you are using a very old version of Gaussian, be aware that the keyword COSMORS doesn’t launch a COSMO-RS calculation (thermodynamics of solutes and solvents) but a CPCM calculation in a format that can be post-processed by COSMO software.
- PCM calculations are highly parametrized so it’s useful to always have an experimental reference to which you can validate your choices in each calculation.
If you found interesting or helpful information in this post, please leave a comment however short. This will encourage me to keep gathering and posting this kind of information which in turn may be of help for other users, thanks.