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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.

Delta G of solvation in Gaussian09


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

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.

References

A. V. Marenich, C. J. Cramer, and D. G. Truhlar, “Universal solvation model based on solute electron density and a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions,” J. Phys. Chem. B, 113 (2009) 6378-96.
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