Tuesday, September 16, 2014

Fullerene Van der Waals Oligomers as Electron Traps

Shubina, T. E.; Sharapa, D. I.; Schubert, C.; Zahn, D.; Halik, M.; Keller, P. A.; Pyne, S. G.; Jennepalli, S.; Guldi, D. M.; Clark, T. J. Am. Chem. Soc. 2014, 136, 10890-10893
Contributed by Steven Bachrach.
Reposted from Computational Organic Chemistry with permission

Clark and co-workers have examined small fullerene clusters for their ability to capture electrons.1 They first looked at the fullerene dimer, comparing the electron affinity of the dimer having a C-C bond between the two cages (about 1.6-1.7 Å between the two cages) 1 and where the two cages are interacting only through van der Waals attractions (around 2.6 Å) 2. The structures and their radical anions were computed at RI-BP86/TZV. The structures of the two radical anions are shown in Figure 1. Interestingly, the radical anion of 2 is actually lower in energy that the radical anion of 1. Comparisons with some other methods are discussed, including a CASSPT2(5,4)/ANO-L-VDZ, computation, that support this result.

1

2

3

4
Figure 1. RI-BP86/TZV optimized geometries of the radical anions of 1-4.
(Be sure to click on these images to be able to manipulate these structures in 3-D!)

This suggests that the added electron is being held between the cages, in an interstitial region. That suggested looking at the trimer and tetramer structures 3 and 4. The radical anions of these two oligomers are also shown in Figure 1. These oligomers show electron affinities of 1 eV greater than for fullerene itself, along with the ability to stabilize the dianion and even the trianion, what the authors call “deep electron traps”.


References

(1) Shubina, T. E.; Sharapa, D. I.; Schubert, C.; Zahn, D.; Halik, M.; Keller, P. A.; Pyne, S. G.; Jennepalli, S.; Guldi, D. M.; Clark, T. "Fullerene Van der Waals Oligomers as Electron Traps," J. Am. Chem. Soc. 2014,136, 10890-10893, DOI: 10.1021/ja505949m.




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Transition State Analysis of Enantioselective Brønsted Base Catalysis Chiral Cyclopropenimines

Bandar, J. S.; Sauer, G. S.; Wulff, W. D.; Lambert, T. H.; Vetticatt, M. J. J. Am. Chem. Soc. 2014, 136, 10700-10707
Contributed by Steven Bachrach.
Reposted from Computational Organic Chemistry with permission

Computational techniques are gaining some traction in helping to understand enantioselective organocatalysis. I talk about a few examples in Chapter 6.3 of my book. Lambert and Vetticatt have now used computations to help understand the role of the catalyst 4 in the Michael addition shown in Scheme 1.1 This reaction proceeds with 99% yield and an ee of 98%.

Scheme 1.

13C kinetic isotope effect studies suggest that the rate determining step is the C-C bond formation (the Michael addition step) which follows the deprotonation of the imine 1 by the catalyst 4.
They performed ONIOM computations to search for transition states of this rate limiting step for the reaction in Scheme 1, using the full molecules. From this ONIOM search, the energies for all transition structures with 5 kcal mol-1 of the lowest energy structure were then obtained at B3LYP/6-31G*. The three lowest energy TS are shown in Figure 1. The two lowest energy structures lead to the major enantiomer, while the third lowest energy structure leads to the minor enantiomer. These energies lead to a prediction of an ee of 92%, in reasonable agreement with the experiment. The computed kinetic isotope effects are in nice agreement with experiment, supporting this step as the overall rate limiting step.

TSs leading to the S isomer

TS1
(0.0)

TS2
(0.9)
TS leading to the R isomer

TS3
(1.7)
Table 1. ONIOM optimized geometries of the three lowest energy TSs. Relative energy (kcal mol-1) in parenthesis.

Analysis of what factors are important in determining the ee is complicated and ultimately the authors are unable to provide a simple explanation. They properly note that
The observation that the major enantiomer (S) is formed from two very geometrically distinct transition structures … suggests that the prediction of enantioselectivity for other reactions … will require a full consideration of all possible transition state assemblies. (emphasis mine)
I agree with this sentiment, pessimistic as it may be. Answering this type of question is likely to remain very challenging for years to come.


References

1) Bandar, J. S.; Sauer, G. S.; Wulff, W. D.; Lambert, T. H.; Vetticatt, M. J. "Transition State Analysis of Enantioselective Brønsted Base Catalysis Chiral Cyclopropenimines," J. Am. Chem. Soc. 2014136, 10700-10707, DOI: 10.1021/ja504532d.


InChIs

1: InChI=1S/C20H23NO/c1-20(2,3)14-18(22)15-21-19(16-10-6-4-7-11-16)17-12-8-5-9-13-17/h4-13H,14-15H2,1-3H3
InChIKey=UZCWUGCTNCNJHI-UHFFFAOYSA-N
2: InChI=1S/C4H6O2/c1-3-4(5)6-2/h3H,1H2,2H3
InChIKey=BAPJBEWLBFYGME-UHFFFAOYSA-N
3: InChI=1S/C24H29NO3/c1-24(2,3)17-21(26)20(15-16-22(27)28-4)25-23(18-11-7-5-8-12-18)19-13-9-6-10-14-19/h5-14,20H,15-17H2,1-4H3/t20-/m0/s1
InChIKey=KTASCPHNNZODSX-FQEVSTJZSA-N
4: InChI=1S/C37H57N3/c1-2-30(28-29-18-8-3-9-19-29)38-35-36(39(31-20-10-4-11-21-31)32-22-12-5-13-23-32)37(35)40(33-24-14-6-15-25-33)34-26-16-7-17-27-34/h3,8-9,18-19,30-34H,2,4-7,10-17,20-28H2,1H3/t30-/m1/s1
InChIKey=GEHSIGXXLTVFFG-SSEXGKCCSA-N



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Thursday, September 4, 2014

8π-Electron Tautomeric Benziphthalocyanine: A Functional Near-Infrared Dye with Tunable Aromaticity

Toriumi, N.; Muranaka, A.; Hirano, K.; Yoshida, K.; Hashizume, D.; Uchiyama, M. Angew. Chem. Int. Ed. 2014, 53, 7814-7818
Contributed by Steven Bachrach.
Reposted from Computational Organic Chemistry with permission

Muranaka and Uchiyama have prepared an 18π-electron system that exhibits variable aromaticity in its tautomeric forms.1 The synthesized benziphthalacyanine 1 shows upfield resonances in the 1H NMR for the internal hydrogens: 1.89 ppm for the C-H proton and 4.67 ppm for the N-H proton. This indicates some weak diatropicity.


To address this interesting magnetic property, they reported B3LYP/6-31+G(d) computations on the model system 2 in its phenol 2p and quinoidal 2q tautomeric forms.


The optimized structures are shown in Figure 1. The phenol form 2p has NICS(0) and NICS(1) values of -6.77 and -6.04 ppm, respectively, indicating only modest aromaticity. However, the NICS values for the quinoidal from 2q are much more negative, -11.43 (NICS(0)) and -10.10 (NICS(1)) ppm, indicating a more significant aromatic character. The calculated chemical shift of the internal C-H is most telling: for 2q it is -4.55ppm but for 2p it is 0.97 ppm, in good agreement with experiment. Thus, 1 has an 18π-electron modestly aromatic periphery, with the phenol form dominant. There is no evidence of a 20π-electron periphery.

2p

2q
Figure 1. B3LYP/6-31+G(d) optimized geometries of 2p and 2q.

(Note that the supporting materials have a missing carbon in 2q and I have made a guess at its proper location – so this is not quite the optimized structure! Once again, a statement about the quality of SI!)


References

(1) Toriumi, N.; Muranaka, A.; Hirano, K.; Yoshida, K.; Hashizume, D.; Uchiyama, M. "18π-Electron Tautomeric Benziphthalocyanine: A Functional Near-Infrared Dye with Tunable Aromaticity," Angew. Chem. Int. Ed. 201453, 7814-7818, DOI: 10.1002/anie.201404020.


InChIs

1: InChI=1S/C108H125N7O2/c1-57(2)75-31-25-32-76(58(3)4)87(75)43-69-49-93-95(51-71(69)45-89-79(61(9)10)35-27-36-80(89)62(11)12)105-111-103(93)109-99-55-100(102(117)56-101(99)116)110-104-94-50-70(44-88-77(59(5)6)33-26-34-78(88)60(7)8)72(46-90-81(63(13)14)37-28-38-82(90)64(15)16)52-96(94)106(112-104)114-108-98-54-74(48-92-85(67(21)22)41-30-42-86(92)68(23)24)73(53-97(98)107(113-105)115-108)47-91-83(65(17)18)39-29-40-84(91)66(19)20/h25-42,49-68,116-117H,43-48H2,1-24H3,(H,109,110,111,112,113,114,115)
InChIKey=LCYQUXHUTZWPDZ-UHFFFAOYSA-N

2p: InChI=1S/C30H17N7O2/c38-23-14-24(39)22-13-21(23)31-25-15-7-1-3-9-17(15)27(33-25)35-29-19-11-5-6-12-20(19)30(37-29)36-28-18-10-4-2-8-16(18)26(32-22)34-28/h1-14,38-39H,(H,31,32,33,34,35,36,37)
InChIKey=JBKUPBCBFUTSRM-UHFFFAOYSA-N

2q: InChI=1S/C30H17N7O2/c38-23-14-24(39)22-13-21(23)31-25-15-7-1-3-9-17(15)27(33-25)35-29-19-11-5-6-12-20(19)30(37-29)36-28-18-10-4-2-8-16(18)26(32-22)34-28/h1-14H,(H3,31,32,33,34,35,36,37,38,39)
InChIKey=PSSSGMKTDQVWLR-UHFFFAOYSA-N



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Sunday, August 31, 2014

Interactive Chemical Reactivity Exploration

Moritz P. Haag, Alain C. Vaucher, Maël Bosson, Stéphane Redon, Markus Reiher arXiv:1405.4036 [physics.chem-ph]
Contributed by +Jan Jensen

Figure 12 from the paper

"... it is still a major task to explore reaction mechanisms for molecular systems of even medium size (say, one to a few hundred atoms). ... The trial- and-error approach currently applied (guessing the important structures and refining them with local optimization methods) requires experience, luck, and time."
This paper provides a very innovative solution to this problem by interfacing a haptic device (a Phantom Desktop), the DFTB method, and the SAMSON visualization program to create a tool to interactively find intermediates and transition states.  

A haptic device is a force-feedback device that simulates a sense of touch based on computational data - in this case the forces on atoms computed by the DFTB method. This, in essence, allows you to provide physically force the reaction to occur. The premise is that this more intuitive approach to molecular modeling will make it easier for non-experts to quickly and thoroughly explore the reactivity of the system of interest. 

In order for this to work convincingly the computational method has to be fast enough to provide real-time feedback on the millisecond timescale and computers and approximate QM methods are now fast enough to provide this. As the user explores the potential energy surface key structures are automatically saved together with their energy and gradient.    

Applying this method leads to interesting practical challenges.  For example, the Phantom Desktop can only manipulate a single point, so many atomic degrees of freedom must be combined and some degree of automatic energy minimization must be included for most of the atoms. Then there is the "evasive adaption" of the system which naturally favors low energy structures, e.g. by moving atoms out of the way rather than reacting. 

I for one would very much like to get my hands on this setup and try this for myself.  Also, this really seems like an invaluable teaching tool! It seems like the many years of study required to build up a chemical intuition of reactivity could be replaced by a few weeks with this device!  Finally, there is the opportunity of citizen- or crowd sourced-science where non-scientists could help find novel reaction paths, much like fold.it for the protein folding problem.


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Wednesday, August 27, 2014

Covalent Hypercoordination: Can Carbon Bind Five Methyl Ligands?

McKee, W. C.; Agarwal, J.; Schaefer, H. F.; Schleyer, P. v. R. Angew. Chem. Int. Ed. 2014, 53, 7875-7878
Contributed by Steven Bachrach.
Reposted from Computational Organic Chemistry with permission

Trying to get carbon to bond in unnatural ways seems to be a passion for many organic chemists! Schleyer has been interested in unusual carbon structures for decades and he and Schaefer now report a molecule with a pentacoordinate carbon bound to five other carbon atoms. Their proposed target is pentamethylmethane cation C(CH3)5+ 1.1 The optimized geometry of 1, which has C3h symmetry, at MP2/cc-pVTZ is shown in Figure 1. The bonds from the central carbon to the equatorial carbon are a rather long 1.612 Å, but the bonds to the axial carbon are even longer, namely 1.736 Å. Bader analysis shows five bond critical points, each connecting the central carbon to one of the methyl carbons. Wiberg bond index and MO analysis suggests that the central carbon is tetravalent, with a 2-electron-3-center bond involving the central and axial carbons.

1

TS1

TS2
Figure 1. MP2/cc-pVTZ optimized geometries of 1 and dissociation transition states.

So while 1 is a local energy minimum, it sits in a very shallow well. One computed dissociation path, which passes through TS1 (Figure 1) on its way to 2-methyl-butyl cation and methane has a barrier of only 1.65 kcal mol-1 (CCSD(T)/CBS + ZPE). A second dissociation pathway goes through TS2 to t-butyl cation and ethane with a barrier of only 1.34 kcal mol-1. Worse still is that the free energy estimates suggest “spontaneous dissociation … through both pathways”.

Undoubtedly, this will not be the last word on trying to torture a poor carbon atom.

References

(1) McKee, W. C.; Agarwal, J.; Schaefer, H. F.; Schleyer, P. v. R. "Covalent Hypercoordination: Can Carbon Bind Five Methyl Ligands?," Angew. Chem. Int. Ed. 201453, 7875-7878, DOI: 10.1002/anie.201403314.

InChIs

1: InChI=1S/C6H15/c1-6(2,3,4)5/h1-5H3/q+1
InChIKey=GGCBGJZCTGZYFV-UHFFFAOYSA-N




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Tuesday, August 12, 2014

Torquoselective Ring Opening of Fused Cyclobutenamides: Evidence for a Cis,Trans-Cyclooctadienone Intermediate

Wang, X.-N.; Krenske, E. H.; Johnston, R. C.; Houk, K. N.; Hsung, R. P.  J. Am. Chem. Soc. 2014, 136, 9802-9805
Contributed by Steven Bachrach.
Reposted from Computational Organic Chemistry with permission

Houk’s theory of torquoselectivity is a great achievement of computational chemistry, as told in Chapter 4.6 of the second edition of my book. Houk, in a collaboration with Krenske and Hsung, now report on an application of torquoselectivity in the formation of a cis-trans-cyclooctadienone intermediate.1

The proposed reaction is shown in Scheme 1, where the bicyclic compound undergoes a conrotatory ring opening in just one orientation to form the E,E-cyclooctadienone, which can then ring close to product.

Scheme 1.

Houk ran M06-2x//6-311+G(d,p)//B3LYP/6-31G(d) computations on the model system 1, passing over the two torquodistinctive transition states TSEE and TSZZ, and on to produce the two cyclooctadienones2EE and 2ZZ, respectively. As seen in Figure 1, the barrier through TSEE is favored by 9.8 kcal mol-1, and leads to the much more favorable cycloocatadienone 2EE.

1
0.0

TSEE
32.3

2EE
9.4

TSZZ
42.1

2ZZ
21.0

TS2
47.5
Figure 1. B3LYP/6-31G(d) optimized structures and relative free energies (kcal mol-1) at M06-2x//6-311+G(d,p)//B3LYP/6-31G(d).

Ring closure taking TSEE to product goes through TS2 (Figure 1), with a very high barrier, 47.5 kcal mol-1above reactant, suggesting that this path is not likely to occur. Instead, they propose that 2EE is first protonated (2EEH+) and then cyclizes through TS2H(Figure 2). This barrier is only 6.2 kcal mol-1, some 44 kcal mol-1 lower than the neutral process through TS2.

2EEH+

TS2H+
Figure 2. B3LYP/6-31G(d) optimized structures

References

(1) Wang, X.-N.; Krenske, E. H.; Johnston, R. C.; Houk, K. N.; Hsung, R. P. "Torquoselective Ring Opening of Fused Cyclobutenamides: Evidence for a Cis,Trans-Cyclooctadienone Intermediate," J. Am. Chem. Soc.2014136, 9802-9805, DOI: 10.1021/ja502252t.


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Sunday, August 10, 2014

Ionic materials and van der Waals

Bučko, Tomáš, Sébastien Lebègue, Jürgen Hafner, and János G. Ángyán. "Improved density dependent correction for the description of London dispersion forces." Journal of Chemical Theory and Computation 9, (2013): 4293-4299.

Bučko, Tomáš, Sébastien Lebègue, János G. Ángyán, and Jürgen Hafner. "Extending the applicability of the Tkatchenko-Scheffler dispersion correction via iterative Hirshfeld partitioning." The Journal of Chemical Physics 141, (2014): 034114.

Contributed by David Bowler
Reposted from Atomistic Computer Simulations with permission

One of the areas which has grown explosively in DFT in recent years is modelling van der Waals interactions (I’ve written about this before). The semi-empirical approach originated by Tkatchenko and Scheffler[1] (normally known as TS) uses the calculated DFT charge density, which is divided between the atoms in the system to give an effective volume occupied by each atom; the ratio of this volume to a free atom volume is then used to rescale the C6 coefficients and polarisabilities found for free atoms. This brings us to an ever-present problem with ab initio methods: how to divide a continuous charge density or wavefunction between the atoms in the system.

TS use Hirshfeld partitioning[2], which creates a distance-dependent weight for each atom according to the ratio between the free atom charge density for the atom and the sum of free atom charge densities for the whole system. This can be used to give a volume and hence the relevant vdW quantities (see Eq. 7-9 in [1] for more detail). But this is not the only way to divide space (and hence charge density) between atoms: Voronoi polyhedra, Bader’s atoms-in-molecules[3], and Becke’s integral partitioning[4] are only some of the methods in common use, along with Mulliken charges as a way of assigning charge to atoms. We discuss these methods in Section 17.2 of the book, and show an example of how different methods and basis sets can change the charge by more than half an electron.

The papers I want to discuss in this blog[5,6] address another problem with the Hirshfeld approach: as it uses free, neutral atoms as the references to divide the charge density, it performs poorly for ionic materials. Instead, they use an update of Hirshfeld partitioning which iterates the charge density decomposition, and interpolates between reference densities of the free atoms in different charge states. It is a relatively small change to make to the process, but has a very strong effect on ionic materials, improving agreement with experiment and high-level theory markedly[5].

Whenever a change is made to an approach, it is important to characterise the effect on the existing performance; in an extensive follow-up paper, the authors do this[6], looking at an large collection of test systems. The main criticism that can be made of the new, iterative approach is that it worsens the modelling of molecular interactions (particularly those which have an obvious van der Waals component). However, the improvement of other systems, particularly ionic solids and molecules interacting with charges on surfaces, is sufficiently strong that this would be well worth using in most circumstances. The authors make the parameters they have used clear (k point meshes, plane wave cutoffs), and the approach is available in VASP (though I would have preferred to have seen it made freely available!).

[1] Phys. Rev. Lett. 102, 073005 (2009) DOI:10.1103/PhysRevLett.102.073005
[2] Theor. Chim. Acta 44, 129 (1977) DOI:10.1007/BF00549096
[3] R. F. W. Bader, Atoms in Molecules: A Quantum Theory, Oxford University Press (1990).
[4] J. Chem. Phys., 88, 2547 (1988) DOI:10.1063/1.454033
[5] J. Chem. Theory Comput. 9, 4293 (2013) DOI:10.1021/ct400694h
[6] J. Chem. Phys. 141, 034114 (2014) DOI:10.1063/1.4890003