Ab Initio Calculation of Rate Constants for Molecule–Surface Reactions with Chemical Accuracy

GiovanniMaria Piccini, Maristella Alessio, and Joachim Sauer (2016)

Contributed by Jan Jensen

Piccini et al. reproduce experimental rate constants for the reactions of methanol with ethene, propene, and trans-2-butene catalyzed by an acidic zeolite (H-MFI), to within one order of magnitude. Key to this is the inclusion of anharmonic effects using the method I highlighted earlier, but it should be noted that the reaction is biomolecular so entropy effects may be larger than for unimolecular reactions such as most enzyme catalysed reactions. However, anharmonic effects also changed the activation enthalpy by as much as 8 kJ/mol.

The PBE/plane wave electronic energy is corrected using MP2/CBS computed for a smaller systems plus a CCSD(T)/TZVP correction computed on an even smaller system.  Such corrections are becoming increasingly feasible for many problems and this study shows that the usual harmonic treatment of the vibrational free energy may become the limiting factor in terms of accuracy. However, anharmonic methods such as the one used here must be implemented, in a black box-fashion, in at least one of the major quantum chemistry packages before we'll see them widely applied.

See also this highlight of the article



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Effect of Complex-Valued Optimal Orbitals on Atomization Energies with the Perdew–Zunger Self-Interaction Correction to Density Functional Theory

Susi Lehtola, Elvar Ö. Jónsson, and Hannes Jónsson J. Chem. Theory Comput. in press (2016)

Contributed by David Bowler
Reposted from Atomistic Computer Simulations with permission

One of the biggest problems facing DFT is that of self-interaction: each electron effectively interacts with itself, because the potential derives from the total charge density of the system. This is not an issue for the exact (unknown) density functional, or for Hartree-Fock, but is the cause of significant error in many DFT functionals. Approaches such as DFT+U[1],[2],[3] and hybrid functionals (far too many to reference !) are aimed in part at fixing this problem.

Probably the earliest attempt to remove this error is the self-interaction correction of Perdew and Zunger[4] which corrects the potential for each Kohn-Sham orbital, complicating the calculation considerably over a standard DFT calculation. (Ironically, this paper, which has over 11,000 citations, is best known for its appendix C, where a parameterisation of the LDA XC energy is given.) However, this process is notoriously slow to converge and is not widely used.

A recent paper[5] showed that, even for isolated molecules, complex orbitals were required to achieve convergence, and this approach has now been tested for atomisation energies of a standard set of 140 molecules[6]. The tests compare the new complex SIC implementation against the standard, real implementation, as well as various GGAs, hybrid functionals and meta-GGAs. The complex SIC, when coupled with the PBEsol functional[7], gives good results (though ironically the PBEsol functional was developed to improve PBE for solids). Not surprisingly, the best results are from hybrids, but meta-GGA improves the energies almost as well.

This study highlights the problem with DFT at the moment: there are many different approaches, which often work well for specific problems. SIC is cheaper than hybrid calculations, and can be important for charge transfer problems (and Rydberg states). The results for convergence and complex orbitals are interesting, but based on these results, I would use meta-GGA for atomisation energies, as a good compromise between accuracy and cost (almost the same as GGA).

[1] Phys. Rev. B 52, R5467 (1995) DOI:10.1103/PhysRevB.52.R5467

[2] Phys. Rev. B 57, 1505 (1998) DOI:10.1103/PhysRevB.57.1505

[3] Int. J. Quantum Chemistry 114, 14 (2014) DOI:10.1002/qua.24521

[4] Phys. Rev. B. 23, 5048 (1981) DOI:10.1103/PhysRevB.23.5048

[5] J. Chem. Theory Comput. 12, 3195 (2016) DOI:10.1021/acs.jctc.6b00347

[6] J. Chem. Theory Comput. in press (2016) DOI:10.1021/acs.jctc.6b00622

[7] Phys. Rev. Lett. 100, 136406 (2008) DOI:10.1103/PhysRevLett.100.136406

A Total Synthesis of Paeoveitol

Xu, L.; Liu, F.; Xu, L.-W.; Gao, Z.; Zhao, Y.-M. Org. Lett. 2016, ASAP
Contributed by Steven Bacharach
Reposted from Computational Organic Chemistry with permission

Xu, Liu, Xu, Gao, and Zhao report a very efficient synthesis of paeoveitol 1 by the [4+2]-cycloaddition of paeveitol D 2 with the o-quinone methide 3.¹ What is interesting here is the selectivity of this reaction. In principle the cyloadditon can give four products (2 different regioisomeric additions along with endo/exo selectivity) and it could also proceed via a Michael addition.

They performed PCM(CH₂Cl₂)/M06-2x/6-311+G(d,p) computations on the reaction of 2 with 3 and located two different transition states for the Michael addition and the four cycloaddition transition states. The lowest energy Michael and cycloaddition transition states are shown in Figure 1. The barrier for the cycloaddition is 17.6 kcal mol^-1, 2.5 kcal mol^-1 below that of the Michael addition. The barriers for the other cycloaddition paths are at more than 10 kcal mol^-1 above the one shown. This cycloaddition TS is favored by a strong intermolecular hydrogen bond and by π-π-stacking. In agreement with experiment, it is the transition state that leads to the observed product.

Michael TS (20.1)

[4+2] TS (17.6)

Figure 1. Optimized geometries of the lowest energy TSs for the Michael and [4+2]cycloaddtion routes. Barrier heights (kcal mol^-1) are listed in parenthesis.

References

(1) Xu, L.; Liu, F.; Xu, L.-W.; Gao, Z.; Zhao, Y.-M. "A Total Synthesis of Paeoveitol," Org. Lett. 2016, ASAP, DOI: 10.1021/acs.orglett.6b01736.

paeoveitol 1: InChI=1S/C21H24O3/c1-5-21-10-14-6-11(2)17(22)8-15(14)13(4)20(21)24-19-7-12(3)18(23)9-16(19)21/h6-9,13,20,22-23H,5,10H2,1-4H3/t13-,20-,21-/m1/s1
InChIKey=LCLFTLPUJXVULB-OBVPDXSSSA-N

paeveitol D 

2: InChI=1S/C9H10O2/c1-3-7-5-8(10)6(2)4-9(7)11/h3-5,10H,1-2H3/b7-3+
InChIKey=KWDDAFOCZGDLEG-XVNBXDOJSA-N

3: InChI=1S/C9H10O2/c1-3-7-5-8(10)6(2)4-9(7)11/h3-5,10H,1-2H3/b7-3+
InChIKey=KWDDAFOCZGDLEG-XVNBXDOJSA-N

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