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Recently, I looked at these two papers analyzing the excited-state properties of modified DNA bases (2-aminopurine and 8-vinyl-A) and how they are influenced by stacking with natural nucleobases:

  1. Jean, J. M.; Hall, K. B. 2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking. Proceedings of the National Academy of Sciences 2001, 98 (1), 37–41 DOI: 10.1073/pnas.98.1.37.
  2. Kenfack, C. A.; Burger, A.; Mély, Y. Excited-State Properties and Transitions of Fluorescent 8-Vinyl Adenosine in DNA. J. Phys. Chem. B 2006, 110 (51), 26327–26336 DOI: 10.1021/jp064388h.

Briefly, the authors considered dimers comprising the respective modified base and each of the natural bases. The geometries of the individual monomers were optimized using MP2/6-31G(d,p) while maintaining their relative position within in the dimer. Afterwards, the authors examined the excited state properties with TDDFT (B3LYP/6-311+G(d)) to identify dark states that could indicate fluorescence quenching of the modified bases.

I'm not an expert in theoretical chemistry and so I was wondering how the choice of methods here was motivated. In particular, why was MP2 used for geometry optimization and not DFT? Does it have to do with a better description of dispersion interactions by MP2?

For their TDDFT calculations the authors used the 6-311+G(d) basis set. I want to try out some similar calculations using ORCA. According to the manual and online resources from the developers, Ahlrich's basis sets seem to be preferred over Pople style basis sets. Could I expect similar (or better/worse) accuracy with def2-TZVP? It's also triple-zeta and contains polarization functions on heavy atoms, but lacks the diffusion functions that were present in the studies mentioned above. Would these be important anyway in such a case were only valence transitions are investigated?

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    $\begingroup$ Interesting question, but the goal of this site collect general problems/answers that are useful for many people/ It would improve your question if you would briefly summarize the methods and models the two paper use. Most people will not download the paper and read just to understand what you are asking and "Some modified DNA bases" is not enough to understand which interactions might be important from the authros point of view. Also, it would be better if you were focusing on a single question (eg DFT vs MP2) instead of many smaller ones. $\endgroup$ – Greg Jul 9 at 14:48
  • $\begingroup$ Thank you, Greg. I've added a short paragraph describing the methods used in the papers. $\endgroup$ – PracticalChemist Jul 9 at 19:26
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Both papers you refer to used methods which were basically state of the art at their time (Gaussian 98/03 compared to Gaussian 16 today). But that is almost twenty (or fifteen) years ago. Nowadays we thankfully have more developed methods available, and one should check whether the results found back then are still consistent. An (admittedly also a bit outdated) overview can be found here: DFT Functional Selection Criteria.

Long story short: You cannot reliably perform calculations on complexes where non-covalent interactions are dominant. You need to to use a method that treats dispersion at least at an empirically derived level. A popular example is Grimmes DFT-D3 program, which is also available in many ESS codes. (Starting point is The Journal of Chemical Physics 2010, 132 (15), 154104.) In the semi-empirical method xtb a newer version is already implemented.

For that reason I guess (since I only read the methods sections) they used MP2 for molecular structure optimisations, as it recovers dispersion interactions to some degree.

Whether or not DFT is suitable for your investigations, I cannot say. A thorough research of the recent literature will certainly offer far better insight.

The Pople basis sets, while an excellent example to understand the structure of them, are generally a terrible choice for almost everything practical. There are multiple basis sets available, which produce more consistent results, and are better optimised to perform in modern ESS codes. If implementations are missing from you ESS program of choice, you have a high chance to find it in the Basis Set Exchange Library.

For ORCA there are most (if not all) Ahlrichs' def2-variations are available, see the ORCA input library.
I would expect augmented basis sets (ma-def2-XVP or def2-XVPD) are necessary to investigate such complexes.

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    $\begingroup$ Thank your for the detailed answer, Martin! When you say the results should be checked for consistency, do you mean that the geometries should be reoptimized at different levels of theory (e.g. SCS-MP2 or a double hybrid like B2PLYP with D3(BJ) correction, etc.) before evaluating the excited state behavior with different methods? As far as I understood the methods description in the papers, the author's first optimized the monomers individually and then placed them in the dimers in a fixed orientation. Could an improvement of the geometry really be expected in this case? $\endgroup$ – PracticalChemist Jul 10 at 14:28
  • $\begingroup$ @PracticalChemist In those cases it is doubtful to expect a 'better' description of the molecular structure. I don't really understand, why they optimise the monomer structures individually just to place them into a fixed position (from x-ray iirc); I'd assume similar results could have been achieved with single point on x-ray. However, since there are methods available that cover non-covalent interactions, I'd assume the overall description, also in terms of TDDFT or excited states would be better. However, I'm not really an expert on this; more recent literature is more helpful, I guess. $\endgroup$ – Martin - マーチン Jul 18 at 14:55
  • $\begingroup$ I came accross this reference that is complementary to @Martin-マーチン response and you may find helpful: [Lars Goerigk and Nisha Mehta, A Trip to the Density Functional Theory Zoo: Warnings and Recommendations for the User, Australian Journal of Chemistry, 2019.] (doi.org/10.1071/CH19023 $\endgroup$ – PAEP Jul 29 at 19:54

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