Experiment 10: Final Review

You are the consultant

Design, run and report the calculation of a Pd–ligand bond dissociation energy.

At a glance. Three species, and every choice is yours. You will show that you can choose and justify a method, set up the calculations properly, and report the results the way a computational paper would.

Warm-up

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The request

Dissociation of the diphosphinohexatrienepalladium(0) complex. Carbon is black, phosphorus orange, hydrogen white and palladium light blue; dotted lines are dative bonds.

Imagine that a colleague in your department is studying this palladium complex (the structures come from the PdBE2 subset  [1] of the Minnesota 2015B database  [2]) and asks you to calculate the bond dissociation energy of the reaction above. You are in charge of setting up the calculations.

Choose the functional and basis set based on:

• the published literature, for instance these recent benchmarks  [2–11];
• the functionals available in Q-Chem;
• what you learned in Experiments 1–9: basis-set convergence, dispersion, grids, stability analysis.

Remember that every calculation is a compromise between accuracy and computational cost, and the free server stops jobs after 10 minutes. Pd needs an effective core potential (ECP = def2-ECP with the def2 basis sets).

The molecules

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Predict first

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Your method card

Choose every setting and write down why. The card warns you about common pitfalls (double-counting dispersion, grid-sensitive functionals) and estimates whether each job fits in the free server’s 10-minute limit. It then gives you the three Q-Chem inputs for your choice.

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Enter your results

Record the three total energies, SCF cycles and wall times from your outputs, then your bond dissociation energy ΔE = E(Pd(PH₃)₂) + E(C₆H₈) − E(complex).

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Explore your data

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Your report

Write a short report (about 300 words) that:

1. has a title;
2. states the method you chose and why, citing the literature;
3. describes the computational setup completely (program, functional, basis set, ECP, grid, stability analysis, convergence criteria), enough for someone else to reproduce your numbers;
4. presents your results and compares them with the reference value of 16.20 kcal/mol;
5. ends with an appropriate reference section.

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Peer review. Your instructor may ask you to review two classmates’ reports on Canvas with a short rubric: is the method justified, is the setup reproducible, is the comparison with the reference honest?

Submit

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References

[1]

B. B. Averkiev, Y. Zhao, and D. G. Truhlar, J. Mol. Catal. A: Chem. 324, 80 (2010).

[2]

H. S. Yu, X. He, S. L. Li, and D. G. Truhlar, Chem. Sci. 7, 5032 (2016).

[3]

L. Goerigk, A. Hansen, C. Bauer, S. Ehrlich, A. Najibi, and S. Grimme, Phys. Chem. Chem. Phys. 19, 32184 (2017).

[4]

N. Mardirossian and M. Head-Gordon, Mol. Phys. 115, 2315 (2017).

[5]

H. S. Yu, W. Zhang, P. Verma, X. He, and D. G. Truhlar, Phys. Chem. Chem. Phys. 17, 12146 (2015).

[6]

H. S. Yu, X. He, and D. G. Truhlar, J. Chem. Theory Comput. 12, 1280 (2016).

[7]

N. Mehta, M. Casanova-Páez, and L. Goerigk, Phys. Chem. Chem. Phys. 20, 23175 (2018).

[8]

R. Peverati and D. G. Truhlar, Philos. Trans. R. Soc. A 372, 20120476 (2014).

[9]

B. Chan, P. M. W. Gill, and M. Kimura, J. Chem. Theory Comput. 15, 3610 (2019).

[10]

B. Chan, J. Phys. Chem. A 123, 5781 (2019).

[11]

S. Dohm, A. Hansen, M. Steinmetz, S. Grimme, and M. P. Checinski, J. Chem. Theory Comput. 14, 2596 (2018).