Wednesday, September 21, 2016

Enediyne Cyclization on Au(111)

de Oteyza, D. G.; Paz, A. P.; Chen, Y.-C.; Pedramrazi, Z.; Riss, A.; Wickenburg, S.; Tsai, H.-Z.; Fischer, F. R.; Crommei, M. F.; Rubio, A. J. Amer. Chem. Soc. 2016, 138, 10963–10967
Contributed by Steven Bacharach
Reposted from Computational Organic Chemistry with permission

The Bergman cyclization and some competitive reactions are discussed in detail in Chapter 4 of by book. The Bergman cyclization makes the C1-C6 bond from an enediyne. Another, but rarer, option is to make the C1-C5 bond, the Schreiner-Pascal cyclization pathway. de Oteyza and coworkers have examined the competition between these two pathways for 1 on a gold surface, and used STM and computations to identify the reaction pathway.1

The two pathways are shown below. The STM images identify 1 as the reactant on the gold surface and the product is 6. No other product is observed.
Projector augmented wave (PAW) pseudo-potential computations using the PBE functional were performed for the reaction on a Au (111) surface was modeled by a 7 x 7 x 3 supercell. The optimized geometries of the critical points are show in Figure 1.









Figure 1. Optimized geometries of the critical points on the two reaction pathways.

Explicit values of the relative energies are not given in either the paper or the supporting information, but rather a plot shows the relative positions of the critical points. The important points are the following: (a) the barrier for the C1-C5 cyclization is lower than the barrier for the C1-C6 cyclization and 3 is lower in energy than 2; (b) 5 is lower in energy than 6; and (c) the barrier for taking 2 to 6 is significantly below the barrier taking 3 into 5. The barrier for the phenyl migration taking 3 into 5 is so high because of a strong interaction between the carbon radical and a gold atom of the surface. The authors suggest that the two initial cyclizations are reversible, but the very high barrier for forming 5 precludes it from taking place, leaving only the route to 6 as a viable pathway.


(1) de Oteyza, D. G.; Paz, A. P.; Chen, Y.-C.; Pedramrazi, Z.; Riss, A.; Wickenburg, S.; Tsai, H.-Z.; Fischer, F. R.; Crommei, M. F.; Rubio, A. “Enediyne Cyclization on Au(111),” J. Amer. Chem. Soc. 2016138, 10963–10967, DOI: 10.1021/jacs.6b05203.


1: InChI=1S/C22H14/c1-3-9-19(10-4-1)15-17-21-13-7-8-14-22(21)18-16-20-11-5-2-6-12-20/h1-14H
2: InChI=1S/C22H14/c1-3-9-17(10-4-1)21-15-19-13-7-8-14-20(19)16-22(21)18-11-5-2-6-12-18/h1-14H
3: InChI=1S/C22H14/c1-3-9-17(10-4-1)15-22-20-14-8-7-13-19(20)16-21(22)18-11-5-2-6-12-18/h1-14H
4: InChI=1S/C22H14/c1-3-9-17(10-4-1)20-15-19-13-7-8-14-21(19)22(16-20)18-11-5-2-6-12-18/h1-14H
5: InChI=1S/C22H14/c1-3-9-17(10-4-1)15-19-16-22(18-11-5-2-6-12-18)21-14-8-7-13-20(19)21/h1-14H
6: InChI=1S/C22H14/c1-3-9-15(10-4-1)19-17-13-7-8-14-18(17)21-20(22(19)21)16-11-5-2-6-12-16/h1-14H

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Wednesday, September 7, 2016

Redox-Dependent Transformation of a Hydrazinobuckybowl between Curved and Planar Geometries

Higashibayashi, S.; Pandit, P.; Haruki, R.; Adachi, S.-I.; Kumai, R. Angew. Chem. Int. Ed. 2016, 55, 10830-10834
Contributed by Steven Bacharach
Reposted from Computational Organic Chemistry with permission

Higashibayashi and co-workers prepared the hydrazine-substituted Buckyball fragment 1a and also its mono- and deoxidized analogues.1 To interpret their results, they also computed the parent structure 1bat ωB97Xd/6-311+G(d,p).

1a R = tBut
1b R = H
The optimized structure of 1b is a bowl, but a twisted geometry, where the lone pair on each
nitrogen is on the opposite face of the molecule, lies only 1.6 kcal mol-1 higher in energy. The barrier for moving from the bowl to the twist form is 2.0 kcal mol-1. The completely planar structure, which is also a transition state for inversion of the bowl, lies 5.1 kcal mol-1 above the lowest energy bowl structure. The geometries and energies of the conformations are shown in Figure 1.

1b bowl (0.0)

1b twist (1.6)

1b TS (2.0)

1b planar TS (5.11)
Figure 1. ωB97Xd/6-311+G(d,p) optimized
geometry and relative energy (kcal mol-1) of the conformations of 1b.

The mono oxidized 1b.+ structure is also a bowl, but there is no twist form and inversion takes place through a planar structure that is only 0.5 kcal mol-1 above the bowl ground state. The structures and energies of these conformations of 1b.+ are shown in Figure 2.

1b.+ bowl (0.0)

1b.+ planar TS (0.5)
Figure 2. ωB97Xd/6-311+G(d,p) optimized geometry and relative energy (kcal mol-1) of the conformations of 1b.+.

Lastly, the di-oxidized 1b2+ is planar, and its structure is shown in Figure 3.

1b2+ planar
Figure 2. ωB97Xd/6-311+G(d,p) optimized geometry of 1b2+.

These computations corroborate all of the experimental data observed with 1a. What is particularly of note is the fact that the potential energy surface is so dependent on charge state: a three-well potential for the neutral, and two-well potential for the monocation, and a single-well potential for the dication.


(1) Higashibayashi, S.; Pandit, P.; Haruki, R.; Adachi, S.-I.; Kumai, R. “Redox-Dependent
Transformation of a Hydrazinobuckybowl between Curved and Planar Geometries,” Angew. Chem. Int. Ed.201655, 10830-10834, DOI: 10.1002/anie.201605340.


1a: InChI=1S/C40H44N2/c1-37(2,3)21-13-25-26-14-22(38(4,5)6)19-31-32-20-24(40(10,11)12)16-28-27-15-23(39(7,8)9)18-30-29(17-21)33(25)41(34(26)31)42(35(27)30)36(28)32/h13-20H,1-12H3

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Saturday, September 3, 2016

Dynamically Complex [6+4] and [4+2] Cycloadditions in the Biosynthesis of Spinosyn A

Patel, A; Chen, Z. Yang, Z; Gutierrez, O.; Liu, H.-W.; Houk, K. N.; Singleton, D. A.  J. Amer. Chem. Soc. 2016,138, 3631-3634
Contributed by Steven Bacharach
Reposted from Computational Organic Chemistry with permission

Enzyme SpnF is implicated in catalyzing the putative [4+2] cycloaddition taking 1 into 3. Houk, Singleton and co-workers have now examined the mechanism of this transformation in aqueous solution but without the enzyme.1 As might be expected, this mechanism is not straightforward.
Reactant 1, transition states, and products 2 and 3 were optimized at SMD(H2O)/M06-2X/def2-TZVPP//B3LYP-D3(BJ)//6-31+G(d,p). Geometries and relative energies are shown in Figure 1. The reaction1 → 2 is a formal [6+4] cycloaddition, and the reaction 1 → 3 is a formal [4+2] cycloaddition. Interestingly, only a single transition state could be located TS1. It is a bispericyclic TS (see Chapter 4 of my book), where these two pericyclic reaction sort of merge together. After TS1 is traversed the potential energy surface bifurcates, leading to 2 or 3. This is yet again an example of a single TS leading to two different products. (See the many posts I have written on this topic.) The barrier height is 27.6 kcal mol-1, with 2 lying 13.1 kcal mol-1 above 3. However, the steepest descent pathway from TS1 leads to 2. There is a second transition state TScope that describes a Cope rearrangement between 2 and 3. Using the more traditional TS theory description, 1 undergoes a [6+4] cycloaddition to form 2 which then crosses a lower barrier (TScope) to form the thermodynamically favored 3, which is the product observed in the enzymatically catalyzed reaction.

1 (0.0)

TS1 (27.6)

2 (4.0)

3 (-9.1)

Figure 1. B3LYP-D3(BJ)//6-31+G(d,p) optimized geometries and relative energies in kcal mol-1.

Molecular dynamics computations were performed on this system by tracking trajectories starting in the neighborhood of TS1 on a B3LYP-D2/6-31G(d) PES. The results are that 63% of the trajectories end at 2, 25% end at 3, and 12% recross back to reactant 1, suggesting an initial formation ratio for 2:3 of 2.5:1. The reactions are very slow to cross through the “transition zone”, typically 2-3 times longer than for a usual Diels-Alder reaction (see this post).

Once again, we see an example of dynamic effects dictating a reaction mechanism. The authors pose a tantalizing question: Can an enzyme control the outcome of an ambimodal reaction by altering the energy surface such that the steepest downhill path from the transition state leads to the “desired” product(s)? The answer to this question awaits further study.


(1) Patel, A; Chen, Z. Yang, Z; Gutierrez, O.; Liu, H.-W.; Houk, K. N.; Singleton, D. A. “Dynamically
Complex [6+4] and [4+2] Cycloadditions in the Biosynthesis of Spinosyn A,” J. Amer. Chem. Soc. 2016,138, 3631-3634, DOI: 10.1021/jacs.6b00017.


1: InChI=1S/C24H34O5/c1-3-21-15-12-17-23(27)19(2)22(26)16-10-7-9-14-20(25)13-8-5-4-6-11-18-24(28)29-21/h4-11,16,18-21,23,25,27H,3,12-15,17H2,1-2H3/b6-4+,8-5+,9-7+,16-10+,18-11+/t19-,20+,21-,23-/m0/s1
2: InChI=1S/C24H34O5/c1-3-19-8-6-10-22(26)15(2)23(27)20-12-11-17-14-18(25)13-16(17)7-4-5-9-21(20)24(28)29-19/h4-5,7,9,11-12,15-22,25-26H,3,6,8,10,13-14H2,1-2H3/b7-4-,9-5+,12-11+/t15-,16-,17-,18-,19+,20+,21-,22+/m1/s1
3: InChI=1S/C24H34O5/c1-3-19-5-4-6-22(26)15(2)23(27)11-10-20-16(9-12-24(28)29-19)7-8-17-13-18(25)14-21(17)20/h7-12,15-22,25-26H,3-6,13-14H2,1-2H3/b11-10+,12-9+/t15-,16+,17-,18-,19+,20-,21-,22+/m1/s1

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Monday, August 29, 2016

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.

Monday, August 15, 2016

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

Wednesday, August 3, 2016

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

[4+2] TS
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.


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

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Saturday, July 30, 2016

Diverse Optimal Molecular Libraries for Organic Light-Emitting Diodes

This paper uses the property-optimizing ACSESS (PO-ACSESS) method to create a set of diverse set of candidates for organic light-emitting diodes (OLEDs) with efficient blue emissions.  There are over 10$^{60}$ synthetically feasible, low molecular eight organic molecules so it is impossible to do an exhaustive search of this so-called small molecule universe looking for better blue OLEDs. Yang and Beratan have therefore developed PO-ACSESS, a stochastic genetic algorithm to extract a set of diverse molecules with a given set of properties.

PO-ACSESS starts with a set of seed molecules (in this case organic molecules that are known blue emitters) that are then randomly mutated and mated. A mutation may be any of a set of elementary steps such a change in bond order, ring formation, atom addition/deletion, etc. and mating is done by randomly fragmenting the molecules at a rotateable bond followed by re-combination of fragments from different parents. The new molecules that do not meet the desired stability, synthetic-feasibility, and electronic criteria are removed. To enforce diversity, molecules that are too close in chemical space are also removed and the entire process is repeated starting with these molecules. The chemical space distance between two compounds is defined as the distance between compounds based on their descriptors, such as atomic number, Gasteiger−Marsili partial charge, atomic polarizability, and topological steric index.

In the case of blue OLEDs the electronic criteria are a vertical singlet excitation energy in the 2.4−4.1 eV range (blue region), an oscillator strength of ≥0.4, and a singlet-triplet gap ≤ 0.3 eV. “Initially, the threshold is set to a less stringent value … to ensure that the population does not collapse to zero, because of the fitness constraint.” The electronic properties were calculated using semiempirical methods such as AM1, ZINDO/S, and DFTB.

The design process was done in two stages: First PO-ACSESS was used to identify 195 molecules with the desired vertical singlet excitation energies and oscillator strengths.  I could not find any details on what seed molecules were used nor the number of iterations. These 195 molecules where then used as seeds for further optimization of the singlet-triplet gap. This PO-ACSESS search was run for 50 iterations where ∼90 molecules were generated per iteration that satisfied the required singlet-triplet gap constraint, which was completed in 7 days on a 16-core CPU. I’d be very curious to know how many molecule were actually screened as part of the process. Anyway, ∼60 structures with a computed singlet-triplet gap-value of ∼0.3 eV that are predicted to emit in the blue region and to have reasonably high oscillator strengths. 

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