Archive for February, 2018

Strain-promoted cycloaddition to cyclooctyne

Click chemistry has been used in a broad range of applications. The use of metal catalysts has limited its application to biological system, but the development of strain-promoted cycloaddition to cyclooctyne has opened up click chemistry to bioorthogonal labeling.

An interesting variation on this is the use of 1,2-benzoquinone 1 and substituted analogues as the Diels-Alder diene component. Escorihuela and co-workers have reported on the use of this diene with a number of cyclooctyne derivatives, measuring kinetics and also using computations to assess the mechanism.1

Their computations focused on two reactions using cyclooctyne 2 and the cyclopropane-fused analogue 3:

Reaction 1

Reaction 2

They examined these reactions with a variety of density functionals along with some post-HF methods. The transition states of the two reactions are shown in Figure 1. A variety of different density functionals and MP2 are consistent in finding synchronous or nearly synchronous transition states.



Figure 1. B97D/6-311+G(d,p) transition states for Reactions 1 and 2.

In terms of activation energies, all of the DFT methods consistently overestimate the barrier by about 5-10 kcal mol-1, with B97D-D3 doing the best. MP2 drastically underestimates the barriers, though the SOS-MP2 or SCS-MP2 improve the estimate. Both CCSD(T) and MR-AQCC provide estimates of about 8.5 kcal mol-1, still 3-4 kcal mol-1 too high. The agreement between CCSD(T), a single reference method, and MR-AQCC, a multireference method, indicate that the transition states have little multireference character. Given the reasonable estimate of the barrier afforded by B97D-D3, and its tremendous performance advantage over SCS-MP2, CCSD(T) and MR-AQCC, this is the preferred method (at least with current technology) for examining Diels-Alder reactions like these, especially with larger molecules.


1) Escorihuela, J.; Das, A.; Looijen, W. J. E.; van Delft, F. L.; Aquino, A. J. A.; Lischka, H.; Zuilhof, H., "Kinetics of the Strain-Promoted Oxidation-Controlled Cycloalkyne-1,2-quinone Cycloaddition: Experimental and Theoretical Studies." J. Org. Chem. 2018, 83, 244-252, DOI: 10.1021/acs.joc.7b02614.


1: InChI=1S/C6H4O2/c7-5-3-1-2-4-6(5)8/h1-4H

2: InChI=1S/C8H12/c1-2-4-6-8-7-5-3-1/h1-6H2

3: InChI=1S/C9H12/c1-2-4-6-9-7-8(9)5-3-1/h8-9H,3-7H2

4: InChI=1S/C14H16O2/c15-13-11-7-8-12(14(13)16)10-6-4-2-1-3-5-9(10)11/h7-8,11-12H,1-6H2

5: InChI=1S/C15H16O2/c16-14-12-5-6-13(15(14)17)11-4-2-9-7-8(9)1-3-10(11)12/h5-6,8-9,12-13H,1-4,7H2/t8-,9+,12?,13?

cycloadditions &DFT &Diels-Alder Steven Bachrach 19 Feb 2018 No Comments

New Procedure for computing NMR spectra with spin-spin coupling

Computed NMR spectra have become a very useful tool in identifying chemical structures. I have blogged on this multiple times. A recent trend has been the development of computational procedures that lead to computed spectra (again, see that above link). Now, Grimme, Neese and coworkers have offered their approach to computed NMR spectra, including spin-spin splitting.1

Their procedure involves four distinct steps.

  1. Generation of the conformer and rotamer space. This is a critical distinctive element of their method in that they take a number of different tacks for sampling conformational space to insure that they have identified all low-energy structures. This involves a combination of normal mode following, genetic structure crossing (based on genetic algorithms for optimization), and molecular dynamics. Making this all work is their choice of using the computational efficient GFN-xTB2 quantum mechanical method.
  2. The low-energy structures are then subjected to re-optimization at PBEh-3c and then single-point energies obtained at DSD-BLYP-D3/def2-TZVPP including treatment of solvation by COSMO-RS. The low-energy structures that contribute 4% or more of the Boltzmann-weighted population are then carried forward.
  3. Chemical shifts and spin-spin coupling constants are then computed with the PBE0 method and the pcS and pcJ basis sets developed by Jensen for computing NMR shifts.3
  4. Lastly, the chemical shifts and coupling constants are averaged and the spin Hamiltonian is solved.

The paper provides a number of examples of the application of the methodology, all with quite good success. The computer codes to run this method are available for academic use from


1) Grimme, S.; Bannwarth, C.; Dohm, S.; Hansen, A.; Pisarek, J.; Pracht, P.; Seibert, J.; Neese, F., "Fully Automated Quantum-Chemistry-Based Computation of Spin–Spin-Coupled Nuclear Magnetic Resonance Spectra." Angew. Chem. Int. Ed. 2017, 56, 14763-14769, DOI: 10.1002/anie.201708266.

2) Grimme, S.; Bannwarth, C.; Shushkov, P., "A Robust and Accurate Tight-Binding Quantum Chemical Method for Structures, Vibrational Frequencies, and Noncovalent Interactions of Large Molecular Systems Parametrized for All spd-Block Elements (Z = 1–86)." J. Chem. Theory Comput. 2017, 13, 1989-2009, DOI: 10.1021/acs.jctc.7b00118.

3) Jensen, F., "Basis Set Convergence of Nuclear Magnetic Shielding Constants Calculated by Density Functional Methods." J. Chem. Theory Comput. 2008, 4, 719-727, DOI: 10.1021/ct800013z.

Grimme &NMR Steven Bachrach 05 Feb 2018 No Comments