Yet more on the benzene dimer. Lesczynski has optimized 9 different benzene dimer configurations, shown in Scheme 1.¹ There are two T-shaped isomers, where a hydrogen from one benzene interacts with the center of the π-cloud of the second. There are two bent versions of the T-shape, called Bent-T-shape. There are two sandwich configurations and two variants where the benzenes are parallel but displaced. Lastly, they report on a new variant, the V-shape configuration. (Once again, the author has not deposited the structures and so I can’t produce interactive figures!)

Scheme 1

The structures were optimized at MP2/aug-cc-pVDZ and then single point energies computed at MP4(SDTQ)/aug-cc-pVDZ and corrected for basis set superposition error. I list these energies in Table 1. They authors note that in comparison with CCSD(T) computations one has to adjust the amount of BSSE correction – which just supports my long-held contention that the standard counterpoise correction overcompensates and that we really have no reliable way of correcting for BSSE.

Table 1. Dimerization energies (kcal mol^-1) at MP4(SDTQ)/aug-cc-pVDZ.¹

The relative energies of the 9 configurations are similar, indicating a very flat potential energy surface. The lowest energy structure is BT-2, and the V-shape configuration is the least favorable of the nine geometries examined.

References

(1) Dinadayalane, T. C.; Leszczynski, J., "Geometries and stabilities of various configurations of benzene dimer: details of novel V-shaped structure revealed " Struct. Chem. 2009, 20, 11-20, DOI: 10.1007/s11224-009-9411-6.

The Alonso group has once again shown the power of the combination of molecular beam Fourier transform microwave spectroscopy (MB-FTMW) coupled with computations. They examined ephedrine, norephedrine and pseudoephedrine and determined the low energy conformations of each.¹ I discuss just the ephedrine case here, but similar results were obtained for the other two compounds.

1

Ephedrine (1) has six potential conformations, differing by the rotation about the C-C bond and the orientation of the methyl group on the nitrogen. They optimized the 6 conformers at MP2/6-311+G(d,p) and corrected the energies for zero-point vibrational energies computed at B3LYP/6-311++G(d,p). The rotational constants and diagonal elements of the ¹⁴N quadrupole coupling tensor were computed and obtained by experiment. The comparison of these values (shown in Table 1) made possible the identification of three low energy conformers, labeled as AGa, AGb, and GGa. The structures are shown in Figure 1.

Table 1. Experimental and computed^a spectroscopic constants for three conformers of ephedrine.¹

AGa (0.0)	AGb (1.35)
GGa (0.73)

Figure 1. MP2/6-311+G(d,p) computed structures and relative energies (kcal mol^-1) of the three conformers of ephedrine.¹

The agreement between the experimental and computed spectroscopic values is very good, less than 1.5% for the rotational constants. This excellent agreement makes possible the identification of these three conformers. The experimental population ratio of N(AGa):N(GGa):N(AGb) is 20:4:1, in nice agreement with the computed values. Of structural interest here is the intramolecular O-H^…N hydrogen bond in each conformer. The authors also suggest a weak hydrogen bond-like interaction between the N-H and the benzene π-system.

References

(1) Alonso, J. L.; Sanz, M. E.; Lopez, J. C.; Cortijo, V., "Conformational Behavior of Norephedrine, Ephedrine, and Pseudoephedrine," J. Am. Chem. Soc., 2009, 131, 4320-4326, DOI: 10.1021/ja807674q.

InChIs

1: InChI=1/C10H15NO/c1-8(11-2)10(12)9-6-4-3-5-7-9/h3-8,10-12H,1-2H3/t8-,10-/m0/s1
InChIKey=KWGRBVOPPLSCSI-WPRPVWTQBH

The importance of dynamics in simple reactions is made yet again in a recent study by Doubleday and Houk in 1,3-dipolar cycloadditions.¹ They looked at the reaction of acetylene or ethylene with either nitrous oxide, diazonioazanide, or methanediazonium. The transition state for these 6 reactions all show a concerted reaction. The transition vector has three major components; (a) symmetric formation/cleavage of the two new σ bonds, (b) bending of the dipolar component, or (c) symmetric bending of the hydrogens of ethylene or acetylene.

Classical trajectories were traced from the transition state back to reactant and forward to product. In the approach of the two fragments, the dipole bend vibrates, but then after the TS, it needs to bend quickly to close the 5-member ring. This means that the bending mode effectively has to “turn a corner” in phase space, and without energy in this mode, the molecules will simple bounce off of each other. Analysis of the reactants indicates significant vibrational excitation of the dipole bending mode.

References

(1) Xu, L.; Doubleday, C. E.; Houk, K. N., "Dynamics of 1,3-Dipolar Cycloaddition Reactions of Diazonium Betaines to Acetylene and Ethylene: Bending Vibrations Facilitate Reaction," Angew. Chem. Int. Ed. 2009, 48, 2746-2748, DOI: 10.1002/anie.200805906

I blogged on Bickelhaput’s examination of the stability of kinked vs. linear polycyclic aromatics¹ in this post. Bickelhaupt argued against any H^…H stabilization across the bay region, a stabilization that Matta and Bader² argued is present based on the fact that there is a bond path linking the two hydrogens.

Grimme and Erker have now added to this story.³ They prepared the dideuterated phenanthrene 1 and obtained its IR and Raman spectra. The splitting of the symmetric (a₁) and asymmetric (b₁) vibrational frequencies is very small 9-12 cm^-1. The computed splitting are in the same range, with very small variation with the computational methodology employed. The small splitting argues against any significant interaction between the two hydrogen (deuterium) atoms. Further, the sign of the coupling between the two vibrations indicates a repulsive interaction between the two atoms. These authors argue that the vibrational splitting is almost entirely due to conventional weak van der Waals interactions, and that there is no “bond” between the two atoms, despite the fact that a bond path connects them. This bond path results simply from two (electron density) basins forced to butt against each other by the geometry of the molecule as a whole.

References

(1) Poater, J.; Visser, R.; Sola, M.; Bickelhaupt, F. M., "Polycyclic Benzenoids: Why Kinked is More Stable than Straight," J. Org. Chem. 2007, 72, 1134-1142, DOI: 10.1021/jo061637p

(2) Matta, C. F.; Hernández-Trujillo, J.; Tang, T.-H.; Bader, R. F. W., "Hydrogen-Hydrogen Bonding: A Stabilizing Interaction in Molecules and Crystals," Chem. Eur. J. 2003, 9, 1940-1951, DOI: 10.1002/chem.200204626

(3) Grimme, S.; Mück-Lichtenfeld, C.; Erker, G.; Kehr, G.; Wang, H.; Beckers, H. W., H., "When Do Interacting Atoms Form a Chemical Bond? Spectroscopic Measurements and Theoretical Analyses of Dideuteriophenanthrene," Angew. Chem. Int. Ed. 2009, 48, 2592-2595, DOI: 10.1002/anie.200805751

InChIs

1: InChI=1/C14H10/c1-3-7-13-11(5-1)9-10-12-6-2-4-8-14(12)13/h1-10H/i7D,8D
InChIKey=YNPNZTXNASCQKK-QTQOOCSTEC

Another diversion from the main theme of this blog.

I have been an advocate for a revolution in chemistry publication making use of the technologies available on the net. My latest polemic on this topic is “Chemistry publication – making the revolution” (DOI: 10.1186/1758-2946-1-2) where I advocate for inclusion of more data within articles, enhancing the reader experience by being able to manipulate the data in the same way that the author did. I argue for development of tools that will enable publication of data, along with chemical semantics. Peter Murray-Rust has blogged on perhaps the first step in this direction: Chem4Word.

I ran across a very interesting article on a similar topic in Learned Publishing. The article is “Semantic Publishing: the coming revolution in scientific journal publishing” by David Shotten (DOI: 10.1087/2009202, also available from this repository). Shotten is in the zoology department and so comes to the semantic web with a different perspective, yet arrives at a similar place that I and Peter Murray-Rust and Henry Rzepa (and other chemists) have been advocating. Shotten advocates for “live data” and semantic markup – and cites Project Prospect (the RSC markup of chemical documents built on PMR’s work) as an example of this. Shotten includes a link to a sample zoology article that his group has “enhanced” and there are a lot of clever additions that chemistry publishers would be well served to examine – links to data, cloud tagging, customizable references, etc. Check out the enhanced document here.

Perhaps a growing push for “enhanced publication” from many disciplines will spur on action among the major publishers!

Gronert¹ has published a scathing criticism of the concept of “protobranching” (see my previous blog post) put forth by Schleyer, Houk and Ma² – SHM for short. As a review, protobranching is the term coined by SHM for attractive 1,3-interactions in alkanes. They argue that these attractive 1,3-interactions are the reason for the energetic stability of the branched alkanes over the straight-chain alkanes. Their argument largely rests on the fact that Reaction 1 is exothermic by 2.8 kcal mol^-1.

2 CH₂CH₃ → CH₄ + CH₃CH₂CH₃           Reaction 1

Gronert’s arguments are many and I will discuss only some of them. First, he notes that choosing ethane and methane as the reference molecules leads to all alkanes being stabilized. The stabilization energy of n-heptane is 5.7 kcal mol^-1 and that of n-heptane is 14.1 kcal mol^-1; is this a difference that is meaningful? Under the protobranching method, the stabilization energies of norbornane and n-heptane are quite similar (13.8 and 14.1 kcal mol^-1, respectively) – does that mean they are equally strained? Similarly, protobranching leads to an extraordinary prediction for the resonance energy of benzene: 69 kcal mol^-1. (I find these arguments quite compelling – the use of protobranching extenuates to magnitude of many chemical effects like ring strain, π-conjugation and resonance energy to the point that they become unusable.)

Gronert notes that the C-C-C angle in propane is larger than 109.5°, suggestive of a repulsive force, and one that is in fact much larger than suggested by SHM. The “attractive interaction” is not reproduced in intermolecular models. He points out the SHM attribute the attractive 1,3-interaction in alkenes to hyperconjugation and not to protobranching, and further notes that SHM correct for the strength of the C-H bond in ethyne but not for the C_sp-C bond in propyne, nor do they make any such corrections for the alkenes.

But Gronert’s main complaint rests on the fact that there is simply no evidence for an attractive 1,3-interaction. All previous suggestions for this have been refuted by many others over the past 30 years. SHM’s main support rests on the ability to fit the thermodynamic trends, but Gronert points out that many other possibilities exist for doing so, including a repulsive model. There is ample evidence to support a repulsive interaction. It seems to me that Schleyer, Houk and Ma have their work cut out for them to carefully rebut Gronert’s arguments.

References

(1) Gronert, S., "The Folly of Protobranching: Turning Repulsive Interactions into Attractive Ones and Rewriting the Strain/Stabilization Energies of Organic Chemistry," Chem. Eur. J. 2009, DOI: 10.1002/chem.200800282

(2) Wodrich, M. D.; Wannere, C. S.; Mo, Y.; Jarowski, P. D.; Houk, K. N.; Schleyer, P. v. R., "The Concept of Protobranching and Its Many Paradigm Shifting Implications for Energy Evaluations," Chem. Eur. J. 2007, 13, 7731-7744, DOI: 10.1002/chem.200700602