The most favorable conformation of a carboxylic acid is the Z form. In fact, the E form is rarely found. Schreiner now offers an explanation for why this is so.¹

Photolysis of matrix-deposited benzoic acid revealed only the Z form (1Z). However, photolysis of deuterated benzoic acid did reveal the E form 1E, however it disappeared with a half-life of 12 minutes on argon at 11 K and 20 K. The lack of temperature dependence, and the huge isotope effect suggested that the isomerization proceeds via tunneling.

The tunneling rate was computed by generating the reaction path at CCSD(T)/cc-pVTZ with
MP2/cc-pVDZ zero point energy. This gave a half-life of 2.8 h for the deuterium species and 10^-5 min for the proton species. A Hammet-like relationship could be produced for the half-lives of para-substituted benzoic acids. Interestingly, a nice correlation is found between the computed width of the tunneling barrier and the half life with σ-donating ability.

References

(1) Amiri, S.; Reisenauer, H. P.; Schreiner, P. R., "Electronic Effects on Atom Tunneling: Conformational Isomerization of Monomeric Para-Substituted Benzoic Acid Derivatives," J. Am. Chem. Soc., 2010, 132 , 15902–15904, DOI: 10.1021/ja107531y

InChIs

Benzoic acid: InChI=1/C7H6O2/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H,8,9)/f/h8H
InChIKey=WPYMKLBDIGXBTP-FZOZFQFYCI

How is the aromaticity of benzene affected by nitrogen substitution? Are pyridine and pyrimidine more or less aromatic than benzene? This question has been addressed many times, and Schleyer adds to this discussion with a B3LYP/6-311+G** study of the entire series of azines.¹ Analysis of the aromaticity is based on a two metrics: NICS(0)_πzz and extra cyclic resonance energy (ECRE). The NICS(0) _πzz value is now the ring current measurement advocated by Schleyer as it only includes the π orbitals and uses the tensor component perpendicular to the ring. ECRE is obtained by comparing block-localized energies of the azine to appropriate acyclic references.

Interestingly, both metrics give the same result, namely, that the aromaticity of benzene and all of the azines 1-6 are essentially equally aromatic.

References

(1) Wang, Y.; Wu, J. I. C.; Li, Q.; Schleyer, P. v. R., "Aromaticity and Relative Stabilities of Azines," Org. Lett., 2010, 12, 4824-4827, DOI: 10.1021/ol102012d

InChIs

1: InChI=1/C5H5N/c1-2-4-6-5-3-1/h1-5H
InChIKey=JUJWROOIHBZHMG-UHFFFAOYAY

2a: InChI=1/C4H4N2/c1-2-4-6-5-3-1/h1-4H
InChIKey=PBMFSQRYOILNGV-UHFFFAOYAA

2b: InChI=1/C4H4N2/c1-2-5-4-6-3-1/h1-4H
InChIKey=CZPWVGJYEJSRLH-UHFFFAOYAT

2c: InChI=1/C4H4N2/c1-2-6-4-3-5-1/h1-4H
InChIKey=KYQCOXFCLRTKLS-UHFFFAOYAV

3a: InChI=1/C3H3N3/c1-2-4-6-5-3-1/h1-3H
InChIKey=JYEUMXHLPRZUAT-UHFFFAOYAF

3b: InChI=1/C3H3N3/c1-2-5-6-3-4-1/h1-3H
InChIKey=FYADHXFMURLYQI-UHFFFAOYAY

3c: InChI=1/C3H3N3/c1-4-2-6-3-5-1/h1-3H
InChIKey=JIHQDMXYYFUGFV-UHFFFAOYAG

4a: InChI=1/C2H2N4/c1-2-4-6-5-3-1/h1-2H
InChIKey=DPOPAJRDYZGTIR-UHFFFAOYAI

4b: InChI=1/C2H2N4/c1-3-2-5-6-4-1/h1-2H
InChIKey=ZFXBERJDEUDDMX-UHFFFAOYAH

4c: InChI=1/C2H2N4/c1-3-5-2-6-4-1/h1-2H
InChIKey=HTJMXYRLEDBSLT-UHFFFAOYAH

5: InChI=1/CHN5/c1-2-4-6-5-3-1/h1H
InChIKey=ALAGDBVXZZADSN-UHFFFAOYAQ

6: InChI=1/N6/c1-2-4-6-5-3-1
InChIKey=YRBKSJIXFZPPGF-UHFFFAOYAK

Henry Rzepa’s response¹ to the reported detection and x-ray structure of 1,3-dimethylcyclobutadiene² has now been published. He takes a different tack than those take by Alabugin³ and Scheschkewitz⁴ in refuting the analysis of this work (see this earlier post). Rzepa discuses computations to evaluate the possible lifetime of 1,3-dimethylcyclobutadiene in the vicinity of CO₂. In particular, he examines the barrier for the allowed [4+2] cycloaddition to give back the lactone 1 (Reaction 1), which was photolyzed in the experiment to produce the cyclobutadiene and CO₂ species in the first place.

The gas phase free energy barrier at 175 K (the experimental condition) computed at ωB97XD/6-311G(d,p) is 16.8 kcal mol^-1, which is sufficiently high to limit this back reaction. Embedding this into a water continuum lowers the barrier to 12.9 kcal mol^-1.

But the experiment has these species embedded inside a calixarene host along with guanidinum
cations. The cation could associate with the CO₂ (indicated in Reaction 1 as X), and inclusion of a guanidinium in the gas phase, reduces the barrier to 3.3 kcal mol^-1. Rerunning this computation now with a water continuum produce an intermediate zwitterion formed by making the C-C bond, and the second step makes the C-O bond.

Finally, modeling the reaction with guanidium inside a calixarene host leads to a barrier of 8 kcal
mol^-1, 10.5 kcal mol^-1 with water continuum. Rzepa concludes that recombination of 1,3-dimethylcyclobutadiene and CO₂ to give 1 should be too fast on the timescale of the experiment for observation of the cyclobutadiene. This argument, along with the two previous papers, strongly casts doubt on the original claim.

I should point out that Henry has deposited all the structures in a nice enhanced table. You may need a subscription to get to this – I have not checked the access conditions.

References

(1) Rzepa, H. S., "Can 1,3-dimethylcyclobutadiene and carbon dioxide co-exist inside
a supramolecular cavity?," Chem. Commun. 2011, ASAP, DOI: 10.1039/C0CC04023A

(2) Legrand, Y.-M.; van der Lee, A.; Barboiu, M., "Single-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene by Confinement in a Crystalline Matrix," Science 2010, 329, 299-302, DOI: 10.1126/science.1188002.

(3) Alabugin, I. V.; Gold, B.; Shatruk, M.; Kovnir, K., "Comment on "Single-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene by Confinement in a Crystalline Matrix"," Science, 2010, 330, 1047, DOI: 10.1126/science.1196188.

(4) Scheschkewitz, D., "Comment on "Single-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene by Confinement in a Crystalline Matrix"," Science, 2010, 330, 1047, DOI: 10.1126/science.1195752.

InChIs

1: InChI=1/C7H8O2/c1-4-3-7(2)5(4)6(8)9-7/h3,5H,1-2H3
InChIKey=GLYAMHMFKKLRAL-UHFFFAOYAT

1,3-dimethylcyclobutadiene: InChI=1/C6H8/c1-5-3-6(2)4-5/h3-4H,1-2H3
InChIKey=ADQGKIKNUMJFSL-UHFFFAOYAU

I just attended Science Online 2011, an “unconference” that focuses on online tools and resources for science, especially in the social media aspect of science. A great deal of the discussions related to communication of science to the non-science community, with calls for more activism and clear voices to articulate the actions and processes of science clearly to the lay audience.

For the more technical minded, there were a few discussions of open data, data sharing, open notebook science and the like.

The conference was wonderfully organized in a great located (the Sigma Xi building in the Research Triangle Park). Bora and Anton are to be congratulated for putting together a meeting the way most of us want to have meetings – reasonably priced, meals included, buses to a from the hotels and venues, lots of time to mingle and talk, real discussion inside the sessions, etc.

Nonetheless, I came away from the meeting more depressed than when I arrived. This is a conference with a lot of younger people – I was amongst the old crowd. But I was really struck by a couple of attitudes that were quite pervasive in the rooms.

First, many people were advocating for open data and data sharing – admirable goals that I fully support. But the driving force was to make the data discoverable through Google – a decidedly non-Open organization. I was surprised by the complete capitulation to the edifice of Google. I was amazed that so many scientists (along with a slew of science journalists) who believed that Google was the way to search for science and information. In chemistry, this is so clearly not true, as specialized databases provide much better information, faster and cleaner than Google or Bing. Relying on a commercial service that is inherently not designed with science information in mind seems doomed from the start. Google is not going to be the tool for doing a substructure search. Furthermore, over the past couple of years I feel that Google has lost its mojo – when was the last time you were excited by a Google product? Google wave? and look where that is now…

Second, I was really struck once again by the very different practices, concerns, and cultures within the different disciplines of science. What chemists are doing and thinking and what they need is different than the biologists and the physicists and the geoscientists, etc. Solutions in one area will not necessarily transcribe over to another. We chemists should be thinking about what the web technologies can do for us and work for us. We might want to glance a peak at what are brethren are up to, but only for ideas and not as models to emulate.

The last observation is really much more pessimistic. I was greatly taken by the lack of risk-taking being expressed by so many people in the crowd. Academics young and old were advising to be careful with your blogging, tenure and promotion is solely driven by publications and grants, worry about a comment leading to some sort of retribution. People were advocating for the anonymous comment, the pseudonym-using blogger as a way of protecting oneself from the unnamed backlash that would destroy a career. Would we accept a journal that published articles with no attribution of the authors? Then why are we able to accept a comment to an article without an attribution? I was amazed at the view that science research communication tis solely through the journal – no thoughts on alternatives, no impetus to use new media to change how scholarly research is being conducted (except of course by the very small number of Open Notebook Science people at the meeting!). The status quo is well entrenched today and I worry that with the attitude expressed by younger scientists here, that we are doomed to continue these practices in the future. Now there was some undercurrent of distress that the current system was not ideal, but the lack of desire to take a risk, to put yourself out there, to express an opinion, to do something different means, I worry, that when these folks are tenured and in a position of more security they will continue to advise the next generation to act the same way.

We are the ones that run science. If we as community want to communicate and collaborate in different ways than that within the entrenched community, then we need to make it happen. Where are the risk-takers, those willing to stand up and say “we need to change. The old models no longer are serving us. We need to use (twitter, blogs, enhanced media, video, data sharing, open source software, etc) to enable our science – to bring disparate groups together to solve important problems. And we will make this happen.”

Small energy differences pose a serious challenge for computation. The focal point analysis of Allen and Schaefer is one approach towards solving this problem, with energies extrapolated to the complete basis set limit at the HF and MP2 levels, and then corrections added on for higher-order effects.

These authors have applied the method to the conformations of alanine (similar to their previous study on cysteine – see this post).¹ There are two low energy conformers 1 and 2. The CCSD(T)/cc-pVTZ structures are shown in Figure 1. The HF/CBS estimate places 2 below 1, but this is reveres at MP2. With the correction for CCSD and CCSD(T), and core electrons, the energy gap is only 0.45 kJ mol^-1, favoring 1. Zero-point vibrational energy favors 1 by 1.66 kJ mol^-1, for a prediction that 1 is 2.11 kJ mol^-1 lower in energy than 2. It is interesting that most of this energy difference arises from differences in their ZPVE.

1

2

Figure 1. CCSD(T)/cc-pVTZ optimized geometries of the two lowest energy conformations of alanine.

The article also discusses the structures of these to conformers, obtained through a combination of theoretical treatment and revisiting the limited experimental measurements.

References

(1) Jaeger, H. M.; Schaefer, H. F.; Demaison, J.; Csaszar, A. G.; Allen, W. D., "Lowest-Lying Conformers of Alanine: Pushing Theory to Ascertain Precise Energetics and Semiexperimental R_e Structures," J. Chem. Theory Comput., 2010, 6, 3066-3078, DOI: 10.1021/ct1000236

InChIs

Alanine: InChI=1/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1/f/h5H
InChIKey=QNAYBMKLOCPYGJ-SNQCPAJUDI

An IUPAC commission has delivered a technical report on the definition of the hydrogen bond. Unfortunately, it does not as yet seem to be available through Pure and Applied Chemistry, but one of its lead authors, Gautum Desiraju, has written a personal perspective in the first issue of this year’s Angewandte Chemie.¹

Hydrogen bonding may be to some extent within the eye of the beholder. If the “hydrogen bond” is worth less than a single kcal mol^-1, how does that really differ from van der Waals interactions or London dispersion? If the interaction is upwards to 40 kcal mol^-1, do we benefit from not simply calling that a bond? Further complexity comes in the nature of the hydrogen bond: is it simply strong dipole-dipole attraction? Does it possess some covalent character? What is its dispersion component? And can it have some charge transfer character? Is it perhaps some or all of these? Or does the particular environment dictate the nature?

Desiraju argues really for as broad a swath as possible, and the new definition borrows from Pauling’s original definition:

Under certain conditions an atom of hydrogen is attracted by rather strong forces to two atoms, instead of only one, so that it may be considered to be acting as a bond between them

ads in a dash of the Pimentel and McClellan definition:

(1) There is evidence of a bonds and (2) there is evidence that this bond specifically involves a hydrogen atom already bonded to another atom

to come up with

The hydrogen bond is an attractive interaction between a hydrogen atom from a molecule or molecular fragment X-H in which X is more electronegative than H, and an atom or a group of atoms in the same or different molecule, in which there is evidence of bond formation. A typical hydrogen bond may be depicted as X-H^…Y-Z, where the three dots denote the bond. X-H represents the hydrogen bond donor. The acceptor may be an atom or an anion Y or a fragment or molecule Y-Z, where Y is bonded to Z. In specific cases X and Y can be the same with both X-H and Y-H bonds being equal. In any event, the acceptor is an electron-rich region such as, but not limited to, a lone pair in Y or a π-bonded pair in Y-Z.

Broad enough to cover just about everything! But it demands “evidence of bond formation” and the commission spells out a series of experiments/computations that might provide this evidence. One might wonder if this list is acceptable and complete.

While I think this is an interesting and necessary step forward, debate on hydrogen bonding is sure to rage on!

References

(1) Desiraju, G. R., "A Bond by Any Other Name," Angew. Chem. Int. Ed. 2011, 50, 52-59, DOI: 10.1002/anie.201002960

Interacting bis-allyl radicals are the topic of a computational study by Gleiter and Borden.¹ The new twist is to have the two allyl groups interact through a cyclobutyl, cyclopentyl or cyclohexyl ring, as in 1-3.

The degree of interaction of the radical electrons is evaluated with a number of metrics. First, the singlet-triplet energy gap is computed at CASSCF(6,6)/6-31G(d) and UB3LYP/6-31G(d). A larger gap is suggestive of strong interaction between the two allyl radicals. Next, the <S²> value of the UB3LYP wavefunction will be 0 for a pure singlet, which occurs when the radicals are strongly interacting. A value near 1 suggests an electron localized into each allyl fragment. Lastly, the natural orbital occupation numbers (NOON) of the two highest lying orbitals would be 2 and 0 for the pure interacting state and each would be 1 for the non-interacting state. The B3LYP/6-31G(d) optimized geometries of 1-3 are shown in Figure 1. The values of each metric are listed in Table 1.

1	2
3

Figure 1. B3LYP/6-31G(d) optimized geometries of 1-3.

Table 1. Metrics for evaluating the allyl interaction in 1-3.

The different metrics are all consistent. The allyl radicals are strongly interacting in 1, with a low lying singlet state. The interaction is significantly lessened in 2 and smaller still in 3. The authors argue these differences in terms of the molecular orbital interactions between the allyl fragments and the central ring fragment.

References

(1) Lovitt, C. F.; Dong, H.; Hrovat, D. A.; Gleiter, R.; Borden, W. T., "Through-Bond Interactions in the Diradical Intermediates Formed in the Rearrangements of Bicyclo[n.m.0]alkatetraenes," J. Am. Chem. Soc., 2010, 132, 14617-14624, DOI: ja106329t

InChIs

1: InChI=1/C10H10/c1-3-7-9-5-2-6-10(7)8(9)4-1/h1-10H
InChIKey=QQZALYREQJSRLB-UHFFFAOYAA

2: InChI=1/C11H12/c1-3-8-7-9-4-2-6-11(8)10(9)5-1/h1-6,8-11H,7H2
InChIKey=XHSRXRHTBHVJQX-UHFFFAOYAV

3: InChI=1/C12H14/c1-3-9-7-12-6-2-5-11(9)8-10(12)4-1/h1-6,9-12H,7-8H2
InChIKey=JFNCWTOWDGQJLS-UHFFFAOYAA

Mosey has a nice follow-up study on the origin of Woodward-Hoffman forbidden ring opening of cyclobutene under mechanical stress.¹ (See this blog post discussing the earlier work of Martinez.²) Pulling on cis substituents of a cyclobutene causes the ring to open in a disrotatory fashion. Normally, the WH forbidden pathway is accessed by photolysis which creates a new electronic state. Mosey asks if this same mechanism is occurring during mechanical stress.

On the face of things, this seems unlikely; how can a mechanical force lead to a new electronic state? CASSCF computations with either no applied external force or with varying sized external forces and IRC computations help answer this question. Without an external force, a diradical (or at least a species with high diradical character – and this could be the transition state) is found along the disrotatory pathway. This same diradical is found regardless of the size of the externally applied mechanical force. What does change is the position of the TS along the pathway: as the force increases, the TS becomes earlier, and the reaction barrier diminishes. No change in the electronic state is affected by the applied mechanical stress.

References

(1) Kochhar, G. S.; Bailey, A.; Mosey, N. J., "Competition between Orbitals and Stress in Mechanochemistry," Angew. Chem. Int. Ed., 2010, 49, 7452-7455, DOI: 10.1002/anie.201003978

(2) Ong, M. T.; Leiding, J.; Tao, H.; Virshup, A. M.; Martinez, T. J., "First Principles Dynamics and Minimum Energy Pathways for Mechanochemical Ring Opening of Cyclobutene," J. Am. Chem. Soc., 2009, 131, 6377-6379, DOI: 10.1021/ja8095834

Proton and hydrogen transfers can be catalyzed by many things. Da Silva shows that carboxylic acids can catalyze the hydrogen shift that converts an enol into a carbonyl species.¹ The specific example is the ethenol to acetaldehyde tautomerization. This reaction has a barrier of 56.6 kcal mol^-1 (computed using the composite method G3SX).

With formic acid as the catalyst, the reactant is the hydrogen-bonded complex of ethanol with formic acid and the product is the complex of acetaldehyde with formic acid. The transition state is shown in Figure 1. The barrier is only 5.6 kcal mol^-1, a significant reduction. da Silva discusses how carboxylic acids might be catalyzing the enol-keto tautomerization in the troposphere and also in combustion reactions.

Figure 1. B3LYP/6-31G(2df,p) optimized TS of the formic acid catalyzed enol-keto tautomerization of acetaldehyde.

References

(1) da Silva, G., "Carboxylic Acid Catalyzed Keto-Enol Tautomerizations in the Gas Phase," Angew. Chem. Int. Ed., 2010, 49, 7523-7525, DOI: 10.1002/anie.201003530

Bader has been advocating for his topological electron density method (also called AIM for “atoms in molecules”) as the answer to most fundamental chemical issues for a couple of decades now. He summarizes his position regarding molecular structure in a recent paper.¹ Here he argues that physics (meaning quantum mechanics) provides a way to uniquely and non-arbitrarily define molecular structure. The atom is defined by the volume enclosed by zero-flux surfaces around a nucleus. The bond path indicates which atoms bind together.

He is careful to indicate that the chemical bond, used in a sort of intuitive way by most chemists, is ill-defined, beyond or outside of physics. His “bond” (or “binding”) is simply the bond path – indicating a pair of interacting atoms.

Bader really wants the union of the bond paths to correspond with the general notion of a bonded molecular structure. He suggests that for all cases, the chemical bonds in a molecule are always observed as bond paths within the electron density. This may be true so far – but certainly we have not examined (computationally nor experimentally) the electron density of all compounds! Equally bothersome is that bond paths occur between atoms for which most chemists would consider to be non-bonded – like between the ortho hydrogens of biphenyl or between hydrogens across the bay region of phenanthrene (see this post). He argues that the barrier for biphenyl rotation arises from the stretching of the C-C bond when the rings become co-planar, but why does this bond stretch in the first place?

While Bader is certainly allowed to call the bond path a “bond”; the question remains whether this definition offers improvements or advantages concerning how we think about and understand molecules, their properties and reactions. To me, this remains an open question.

References

(1) Bader, R. F. W., "Definition of Molecular Structure: By Choice or by Appeal to Observation?," J. Phys. Chem. A 2010, 114, 7431-7444, DOI: 10.1021/jp102748b