Archive for September, 2009

Charge-shift bonding

Shaik, Wu and Hiberty have proposed a third bond type, and they have a nice review article in Nature Chemistry.1 Along with the long-standing concepts of the covalent bond and the ionic bond, they add a third category: the charge-shift bond.

The valence bond wavefunction for the diatomic A-B is written as

Ψ(VB) = c1φcov(A-B) + c2φion(A+B) + c3φion(AX+)

Typically one of these terms dominates and we call the bond covalent if c1 is the largest coefficient or ionic if either c2 or c3 is the largest term. The bond dissociation energy (De) is the difference in energy of the total VB wavefunction (above) and the energy of the separate radicals A. and B.. One can determine the energy due to just a single component of the total VB wavefunction. One might expect that for a covalent bond, the bond dissociation energy derived from just the c1φcov(A-B) term would be close to De. For many covalent bonds this is true. However, Shaik and co-authors show a number of bonds where this is not true. For example, in the F-F bond, the covalent term is destabilizing. Rather, it is the resonance energy due to the mixing of the 3 VB terms that leads to bond formation. Shaik, Wu and Hiberty call this the “charge-shift bond”. They describe a number of examples of typically understood homonuclear and heteronuclear covalent bonds that are in fact charge-shift bonds, and an example of an ionic bond that really is charge-shift.

They argue that the charge-shift bond manifests as a consequence of the virial theorem. When an atom participates in a bond, its size gets smaller and this results in an increase in its kinetic energy. If the atom gets very small, then a substantial resultant change in the potential energy must occur, and this is the charge-shift bond. This also occurs in bonds involving atoms with many lone pairs; the lone-pair bond-weakening effect also causes a rise in kinetic energy that must be offset.

The authors speculate that many more examples of the charge-shift bond are waiting to be uncovered. It will be interesting if this concept catches hold and how quickly it will incorporated into general chemistry textbooks.


(1) Shaik, S.; Danovich, D.; Wu, W.; Hiberty, P. C., "Charge-shift bonding and its manifestations in chemistry," Nature Chem., 2009, 1, 443-449, DOI: 10.1038/nchem.327

Bond Dissociation Energy Steven Bachrach 28 Sep 2009 2 Comments

Bifurcation on a terpene synthesis pathway

Unusual potential energy surfaces are a theme of this blog and my book (see chapter 7). Examples might include bifurcations and valley inflection points and often lead to unusual dynamics. Tantillo has now reported a bifurcation on the PES for terpene synthesis, specifically the pathway for synthesis of abietadiene.1

Tantillo discusses two possible cation rearrangement pathways. The first is pretty ordinary, but in the second, the precursor cation 1 can rearrange through either of two transition states 2a or 2b (Scheme 1). The IRC computation from 2a connects back to 1, but in the forward direction it connects to another transition state 3. This TS (3) connects products 4 and 5. These structures are drawn in Figure 1.

Thus, the potential energy surface displays a bifurcation, and one might expect unusual dynamic effects to operate.

Scheme 1




Figure 1. B3LYP/6-31+G(d,p) optimized transition structures of 2-3.1


(1) Hong, Y. J.; Tantillo, D. J., "A potential energy surface bifurcation in terpene biosynthesis," Nature Chem. 2009, 1, 384-389 DOI: 10.1038/nchem.287.

Dynamics Steven Bachrach 21 Sep 2009 5 Comments

Pentacoordinate Carbon?

One of the great longstanding dreams of synthetic and theoretical organic chemists is to prepare a stable molecule containing a pentacoordinate carbon atom. Bickelhaupt and co-workers propose a novel series of compounds that hint that this might be possible.1

Their attack is to first find a CR3 radical that is stable in its planar form. The nitrile group perfectly satisfies this goal. Next they look at the series of compounds X-C(CN)3-X (1) where X is a halogen, searching for a stable D3h structure. This is found with the halogens: Br, I, and At, at the ZORA-OLYP/TZ2P level. Seems like case closed, except that inspection of the supporting materials shows that the nature of the D3h structure is sensitive to computational method. So, with the larger basis set ZORA-OLYP/QZ4P or with ZORA-OPBE/TZ2P, only the I and At compounds are local D3h minima. And with ZORA-M06/TZ2P, only the At compound is a local minimum. The authors do mention these points at the end of the article. So, what we have here is a tantalizing suggestion for how to prepare a hypercoordinate carbon species, but further computational (and experimental) work is clearly needed.

1: X = F, Cl, Br, I, At


(1) Pierrefixe, S. C. A. H.; van Stralen, S. J. M.; van Strale, J. N. P.; Guerra, C. F.; Bickelhaupt, F. M., "Hypervalent Carbon Atom: "Freezing" the SN2 Transition State," Angew. Chem. Int. Ed., 2009, 48, 6469-6471, DOI: 10.1002/anie.200902125


1(F): InChI=1/C4F2N3/c5-4(6,1-7,2-8)3-9/q-1, InChIKey=LBDHZXPWKBFYBC-UHFFFAOYAX

1(Cl): InChI=1/C4Cl2N3/c5-4(6,1-7,2-8)3-9/q-1, InChIKey=NMFGEVWEEWBFSS-UHFFFAOYAU

1(Br): InChI=1/C4Br2N3/c5-4(6,1-7,2-8)3-9/q-1, InChIKey=FHKJQJBDHAEQES-UHFFFAOYAC

1(I): InChI=1/C4I2N3/c5-4(6,1-7,2-8)3-9/q-1, InChIKey=FWKBAUUEXUSUNH-UHFFFAOYAO

1(At): InChI=1/C4At2N3/c5-4(6,1-7,2-8)3-9/q-1, InChIKey=BJQBFKCUAROAAS-UHFFFAOYAK

Uncategorized Steven Bachrach 15 Sep 2009 13 Comments

Data sharing

Nature has a special feature on data sharing, including an editorial and commentaries advocating for both pre- and post-publication of data. I have long been an advocate of data sharing, especially in the post-publication sense (I would argue this is really concurrent-publication data sharing) – and one can read my latest commentary in the Journal of Cheminformatics (DOI: 10.1186/1758-2946-1-2.

Data sharing has been slow in chemistry. Peter Murray-Rust and Henry rzepa have been the major advocates for enhanced publication – see their blogs (PMR and HSR) and lots of publications. Tony Williams (blog) has been advocating for more deposition of data within ChemSpider, and some positive response have occurred. But journals and AUTHORS have been slow to change – supporting materials is often lacking important information and is rarely of useful form – and I consider pdf to be just a slice above “non-useful”. We need to continue to evangelize this issue!

E-publishing Steven Bachrach 10 Sep 2009 No Comments

C6F6.+ — bond stretch isomerism

Bond-stretch isomerism refers to isomers that differ simply in their bond lengths. Seppelt and coworkers suggests that the hexafluorobenzne radical cation C6F6.+ exhibits bond-stretch isomerism.1

The oxidized C6F6 with O2+SbF11 and obtained C6F6.+Sb­2F11 as a crystalline solid. X-ray diffraction identified 2 structures. B3LYP/TZPP computations confirmed the identity of two isomers, a “quinoid” form 1 and a “bisallyl” form 2, shown in Figure 1. The two structures are nearly degenerate, with 1 predicted to be 0.09 kcal mol-1 more stable than 2. The computed two unique C-C bond lengths are 1.371 and 1.427 Å in 1 and 1.449 and 1.389 Å in 2, and these distance agree well with the X-ray experimental values.

1 – quinoid

2 – bisallyl

Figure 1. UB3LYP/6-311+G(d) optimized structures of 1 and 2. Note once again the article and supporting materials lacked the full description of these structures!)

The potential energy surface in the neighborhood of these two isomers is like that of a sombrero. The two isomers lie in the circular trough and movement around this trough is nearly flat. The peak of the sombrero is the D6h structure, which is a transition state interconverting 1 and 2, with a barrier of 3 kcal mol-1.

1 and 2 are clear examples of bond-stretch isomerism, though it is likely that the complexation with the counter ion is what freezes out the rapid interconversion of the two.


(1) Shorafa, H.; Mollenhauer, D.; Paulus, B.; Seppelt, K., "The Two Structures of the Hexafluorobenzene Radical Cation C6F6.+," Angew. Chem. Int. Ed. 2009, 48, 5845-5847, DOI: 10.1002/anie.200900666

Uncategorized Steven Bachrach 08 Sep 2009 1 Comment

Fantastic optical activity of an octaphyrin

The octaphyrin 1 has been prepared and its crystal structure and electronic circular dichroism (ECD) spectra reported.1 The x-ray structure identified the compound as having the M,M helical structure. The optical rotation however could not be determined.


Rzepa now reports the computed ECD spectrum and optical activity of 1 and some related compounds.2 These computed spectra were obtained using TD0DFT with the B3LYP/6-31G(d) method with the CPCM treatment of the dichloromethane solvent. (The structure of 1 and other computed properties are available from the enhanced web table that Rzepa has deposited with the article (here). Once again this material seems to be available only to subscribers! My repeated discussions with ACS Pubs people that these “web objects” should be treated as data and not as copyrighted materials have fallen on deaf ears.) The computed ECD spectrum matches nicely with the experimental one, except that the signs at 570 and 620 nm are opposite. Rzepa suggests that either the compound is really of P,P configuration or the authors of experimental work have erroneously switched their assignments.

The computed value of [α]D of 1 is about -4000 °, with the negative sign in agreement with the sign for [α]D of M-hexahelicene. However, what is truly fantastic is the magnitude of the optical activity of the dication of 1 produced by loss of 2 electrons. This dication should be aromatic and it is predicted to have [α]1000 = -31597°!


(1) Werner, A.; Michels, M.; Zander, L.; Lex, J.; Vogel, E., ""Figure Eight" Cyclooctapyrroles: Enantiomeric Separation and Determination of the Absolute Configuration of a Binuclear Metal Complex," Angew. Chem. Int. Ed. 1999, 38, 3650-3653, DOI: 10.1002/(SICI)1521-3773(19991216)38:24<3650::AID-ANIE3650>3.0.CO;2-F

(2) Rzepa, H. S., "The Chiro-optical Properties of a Lemniscular Octaphyrin," Org. Lett. 2009, 11, 3088–3091DOI: 10.1021/ol901172g

Aromaticity &Optical Rotation Steven Bachrach 01 Sep 2009 2 Comments