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Aromaticity-induced basicity.

Wednesday, April 18th, 2018

The molecules below were discussed in the previous post as examples of highly polar but formally neutral molecules, a property induced by aromatisation of up to three rings. Since e.g. compound 3 is known only in its protonated phenolic form, here I take a look at the basicity of the oxygen in these systems to see if deprotonation of the ionic phenol form to the neutral polar form is viable.

The equilibrium being considered is shown below for compound 2:

The energetics of this equilibrium shown below, computed at the ωB97XD/Def2-TZVPPD/SCRF=water level and for which the FAIR data DOI is 10.14469/hpc/4073

For 1: X=Cl, the energy is shown below as a function of the O….H distance. Proton abstraction from HCl is exothermic by ~25 kcal/mol.

For 2: X=Cl, the exothermicity increases by only ~5 kcal/mol , despite the apparent aromatisation of a further ring. It is also worth noting that this is greater basicity than that of e.g. water, where around 4-5 water molecules acting in concert are required to deprotonate HCl.For 1: X=OH, the proton abstraction from water is mildly endothermic by about 13 kcal/mol; indeed there is no energy minimum for carbonyl protonation and instead a relatively strong hydrogen bond to the water is formed instead.

For 2: X=OH the endothermicity is reduced to ~9 kcal/mol.

For 1: X=CH3, deprotonation of methane is now strongly endothermic by ~40 kcal/mol.

So the molecules 1 – 2 above are clearly not superbases, which perhaps augers well for being able to deprotonate the ionic phenols into these neutral but highly polar molecules.

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A record polarity for a neutral compound?

Friday, April 13th, 2018

In several posts a year or so ago I considered various suggestions for the most polar neutral molecules, as measured by the dipole moment. A record had been claimed[1] for a synthesized molecule of ~14.1±0.7D. I pushed this to a calculated 21.7D for an admittedly hypothetical and unsynthesized molecule. Here I propose a new family of compounds which have the potential to extend the dipole moment for a formally neutral molecule up still further.

These molecules derive from a well-known class of molecule known as ortho-quinomethides. If the methide part is substituted with an electron donating substituent such as an amino group in 3, a push-pull opportunity now arises, which is strongly driven by aromatisation of the quinomethide ring. This allows one to design “neutral” molecules such as 1 and 2, which now contain respectively two and three rings that will be aromatised by the process. The aromatisation stabilization energy is balanced of course by an opposing increase in energy resulting from charge separation. You can observe that partially aromatising three independent rings as in 2 can drive a great deal of charge separation. One may indeed wonder how much charge separation can be sustained before a triplet instability occurs, driving the molecule back to being neutral. In the case of 2, the wavefunction is in fact stable to such an open shell state, but higher homologues may not be. An aspect worth investing!

1 2
DM 12.3 DM 31.5
DOI: 10.14469/hpc/4004 DOI: 10.14469/hpc/4059

Molecule 1 does have some precedent in 3[2] but this system exists as a phenol, having abstracted a proton from an acid and leaving behind the acid anion, as per below for 1. Any attempts to deprotonate this phenol with a superstrong base were unreported.

Unsurprisingly therefore, molecules such as 1 and 2 could be regarded as even more highly potent bases than 3, driven again by further aromatisation. The properties of such a potential superbase will be investigated in the next post.

References

  1. J. Wudarczyk, G. Papamokos, V. Margaritis, D. Schollmeyer, F. Hinkel, M. Baumgarten, G. Floudas, and K. Müllen, "Hexasubstituted Benzenes with Ultrastrong Dipole Moments", Angewandte Chemie International Edition, vol. 55, pp. 3220-3223, 2016. https://doi.org/10.1002/anie.201508249
  2. N.R. Candeias, L.F. Veiros, C.A.M. Afonso, and P.M.P. Gois, "Water: A Suitable Medium for the Petasis Borono‐Mannich Reaction", European Journal of Organic Chemistry, vol. 2009, pp. 1859-1863, 2009. https://doi.org/10.1002/ejoc.200900056

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How FAIR are the data associated with the 2017 Molecules-of-the-Year?

Wednesday, March 7th, 2018

C&EN has again run a vote for the 2017 Molecules of the year. Here I take a look not just at these molecules, but at how FAIR (Findable, Accessible, Interoperable and Reusable) the data associated with these molecules actually is.

I went about finding out as follows:

  1. The article DOI for all seven candidates was linked to the C&EN site.
  2. From there I manually tracked down the Supporting information
  3. Some of this SI gave a CCDC deposition number for crystal structure data for the molecule in question. The easiest way of going directly to the data was to use the search.datacite.org search engine and to enter the keywords CCDC + deposition number. This gives a DOI for the data, examples of which are included in the table below.
  4. In other examples, I used the CSD Conquest search program and entered the names of 2-3 of the authors of the articles. This also worked well.
  5. Most of the SI files, downloaded as PDF files also had static images of NMR spectra included. This is not active data, and hence does not fulfil the F and I of FAIR, and probably the A as well. None of it is FAIR as defined by my post here although it is actually really easy to make it so. One of the examples had ~116 spectra so unFAIRed.
  6. In another example there was also computational data, included simply as a set of XYZ coordinates and again contained in the PDF file. This too is not really FAIR, since one has to know how to extract it from this container and repurpose it. It also represents a tiny subset of the data potentially available.
How FAIR are the data associated with the 2017 Molecules-of-the-Year?
# Title Article DOI Data DOI
1 Persulfurated Coronene: A New Generation of “Sunflower” 10.1021/jacs.6b12630 Data available only as PDF
Hosted by Figshare
The SI also has its own DOI:
10.1021/jacs.6b12630.s001
2 A Truncated Molecular Star 10.1021/jacs.6b12630 Crystal structure data:
10.5517/ccdc.csd.cc1nb303
3 Synthesis of trinorbornane 10.1039/c7cc06273g Crystal structure data:
10.5517/ccdc.csd.cc1p7806
4 Braiding a molecular knot with eight crossings 10.1126/science.aal1619 Crystal structure data:
10.5517/ccdc.csd.cc1m85y0
5 Unique physicochemical and catalytic properties dictated by the B3NO2 ring system 10.1038/nchem.2708 Crystal structure data:
10.5517/ccdc.csd.cc1lkff0
6 Total synthesis of mycobacterial arabinogalactan containing 92 monosaccharide units 10.1038/ncomms148510 116 NMR spectra available only as PDF. No crystal structure
7 Nitrogen Lewis Acids 10.1021/jacs.6b12360 NMR spectra available only as PDF.
Computed coordinates available only as PDF
Crystal structures data:
CCDC 1457983-1457987,1458000-1458001
e.g. 10.5517/ccdc.csd.cc1ky4qc
10.5517/ccdc.csd.cc1ky4rd

The FAIRness of the data for these molecules of the year is largely rescued by the crystal structure data deposited with the CCDC in their CSD database and rendered F of FAIR by the persistent identifiers such as the (parochial) deposition numbers or the more general DOI. Now if the NMR and computational data were also covered in this way, we would be making great progress. There are of course many other types of data included with these examples, and procedures for making such data also FAIR have to be worked out by the community.

In order to construct the table above, I had to put about two hours of effort into tracking down the items (and this only because I have done this sort of search before). Perhaps next year I might persuade C&EN to include such a table in their own article!

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What are the highest bond indices for main group and transition group elements?

Sunday, March 4th, 2018

A bond index (BI) approximately measures the totals of the bond orders at any given atom in a molecule. Here I ponder what the maximum values might be for elements with filled valence shells.

Following Lewis in 1916[1] who proposed that the full valence shell for main group elements should be 2 (for the first two elements) and 8 (the “octet“), Bohr (1922[2]), Langmuir (1919-1921[3]) and Bury (1921[4]) extended this rule to include 18 (the transition series) and 32 (the lanthanides and actinides). If we assume no contributions from higher Rydberg shells (thus 3s, 3p, 3d for carbon etc) and an electron pair model for orbital population (which amounts to the single-determinantal model), then the maximum bond index for hydrogen (and helium) would be 1, it would be 4 for main group elements, and then what?

For the special case of hydrogen, I have previously identified (for a hypothetical species) a bond index of 1.33, due mostly to a high Rydberg occupancy of 1.19e. The more normal BI is <1.0, as noted for this hexacoordinated hydride system. My current estimate for the maximum bond index for main group elements is <4.5. Thus for SF6, it has the value of ~4.33 and that includes a modest occupancy of Rydberg shells of 0.36e = 0.18 BI. Exclude these and it is close to 4.

Move on from group 16 to group 6 and you get compounds such as Me4CrCrMe44- or ReMe82- where the metal bond indices are ~6.5.‡ Compounds such as Cr(Me)6 (BI = 5.6)  and W(Me)6 (BI = 6.1) are rather lower. This is a long way from 18/2 = 9. The lanthanides and actinides[5] are unlikely to reveal many large BIs (32/2= 16 maximum value) since they are often ionic and the wavefunctions may be too complex to allow a simple index such as a BI to be safely computed.

So if we are hunting for record BIs, the transition elements are the place to hunt. Can a BI of 6.5 be beaten? Can it even approach 9, its maximum value? Does anyone know of candidate molecules? 

‡FAIR Data doi: 10.14469/hpc/3352.

References

  1. G.N. Lewis, "THE ATOM AND THE MOLECULE.", Journal of the American Chemical Society, vol. 38, pp. 762-785, 1916. https://doi.org/10.1021/ja02261a002
  2. N. Bohr, "Der Bau der Atome und die physikalischen und chemischen Eigenschaften der Elemente", Zeitschrift f�r Physik, vol. 9, pp. 1-67, 1922. https://doi.org/10.1007/bf01326955
  3. I. Langmuir, "Types of Valence", Science, vol. 54, pp. 59-67, 1921. https://doi.org/10.1126/science.54.1386.59
  4. C.R. Bury, "LANGMUIR'S THEORY OF THE ARRANGEMENT OF ELECTRONS IN ATOMS AND MOLECULES.", Journal of the American Chemical Society, vol. 43, pp. 1602-1609, 1921. https://doi.org/10.1021/ja01440a023
  5. P. Pyykkö, C. Clavaguéra, and J. Dognon, "The 32‐Electron Principle", Computational Methods in Lanthanide and Actinide Chemistry, pp. 401-424, 2015. https://doi.org/10.1002/9781118688304.ch15

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Hypervalent or not? A fluxional triselenide.

Saturday, February 24th, 2018

Another post inspired by a comment on an earlier one; I had been discussing compounds of the type I.In (n=4,6) as possible candidates for hypervalency. The comment suggests the below as a similar analogue, deriving from observations made in 1989.[1]

This compound was investigated using 77Se NMR, with the following conclusions:

  1. The compound is fluxional, with the lines at room temperature broadened compared to those at -50°C.
  2. At -50°C the peaks are sharp enough to discern 1JSe-Se couplings, with multiplicities and integrations that suggest a central Se is surrounded by four equivalent further Se atoms, with shifts of 655.1 and 251.2 ppm.
  3. The magnitude of this 1JSe-Se coupling (391 Hz) leads to the suggestion of a considerable contribution of a resonance form with Se=Se bonds (structure 2 above).
  4. This was supported by 2J13C-77Se couplings which also imply a symmetrically coordinated central  Se.
  5. Thus the two resonance forms 1 or 2 above were suggested as the predominant form at -50°C, with an increasing incursion of the open chain isomer 3 at higher temperatures giving rise to the observed fluxional dynamic behaviour.
  6. One may surmise from these results that the central Se is certainly hypercoordinated and by the classical interpretations hypervalent.

Here are some calculations (R=H), at the ωB97XD/Def2-TZVPP/SCRF=chloroform level.‡ In red are the calculated Wiberg Se-Se bond orders, which give little indication of any Se=Se double bond character. 

The calculated 77Se shifts are shown in magenta, with the observed values being 655 and 255 ppm. The match is not good, the errors were 120 and 20.5 ppm.†  However calculated shifts for elements adjacent to e.g. Se or Br etc suffer from relativistic effects such as spin orbit coupling.[2] Thus the shift for the central Se, surrounded by four other Se atoms is likely to have a significant error, but the error for the four other Se atoms should be less. The reverse is true.

However, all the calculations of this species (up to Def2-TZVPPD basis set) showed this symmetric form of D2h symmetry to actually be a transition state, as per below.

There is a minimum with the structure below in which one pair of Se-Se lengths are longer than the other pair and for which the free energy is 6.5 kcal/mol lower. The Wiberg bond orders for the two sets of Se-Se bonds are now 0.16 and 0.86, which very much corresponds to structure 3 above.

Assuming that this compound is fluxional even at -50°C, the average of the pairs of Se atoms gives calculated shifts of 667 ppm (655 obs) whilst the central Se is 204.6 ppm (251 obs). The latter, influenced by two especially short Se-Se distances, is likely to have a very large spin-orbit coupling error, whilst for the former the error will be smaller (13C shifts adjacent to one Br typically have induced calculated errors of about 14 ppm[2]).

At this point I searched the Cambridge structure database for Se coordinated by four other Se atoms. A close analogue[3] has the structure shown below, in which pairs of Se-Se interactions have unequal bond lengths, the shorter being ~2.45Å. This matches the calculation above reasonably well.

Reconciling these various observations, we might assume that even at -50°C the fluxional behaviour has not been frozen out. Given that the fluxional barrier is only 6.5 kcal/mol, it is unlikely that the spectrum could be measured at a sufficiently low temperature to reveal not two sets of Se signals in the ratio 4:1 but three in the ratio 2:2:1. The spin-spin couplings reported presumably are a result of averaging a genuine 1JSe-Se coupling with a through space coupling.

So it appears that the analysis of the 77Se NMR reported in this article [1] may not be quite what it seems. A better interpretation is that structure 3 is the most realistic. This means no hypercoordination for the Se, never mind hypervalence!

‡FAIR data at DOI: 10.14469/hpc/3724. †The original reference, Me2Se was incorrectly calculated without solvation by chloroform. The values shown here are now corrected from those shown in the original post.

References

  1. Y. Mazaki, and K. Kobayashi, "Structure and intramolecular dynamics of bis(diisobutylselenocarbamoyl) triselenide as identified in solution by the 77Se-NMR spectroscopy", Tetrahedron Letters, vol. 30, pp. 2813-2816, 1989. https://doi.org/10.1016/s0040-4039(00)99132-9
  2. D.C. Braddock, and H.S. Rzepa, "Structural Reassignment of Obtusallenes V, VI, and VII by GIAO-Based Density Functional Prediction", Journal of Natural Products, vol. 71, pp. 728-730, 2008. https://doi.org/10.1021/np0705918
  3. R.O. Gould, C.L. Jones, W.J. Savage, and T.A. Stephenson, "Crystal and molecular structure of bis(NN-diethyldiselenocarbamato)-selenium(II)", Journal of the Chemical Society, Dalton Transactions, pp. 908, 1976. https://doi.org/10.1039/dt9760000908

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Is (hν)3 an allotrope of light?

Friday, February 23rd, 2018

A little while ago I pondered allotropic bromine, or Br(Br)3. But this is a far wackier report[1] of a molecule of light.

The preparation and detection of dimer and trimer bound photon states is pure physics; probably considered by the physicists themselves as NOT chemistry. It is certainly true, as a chemist,  that I understood only a little of the article. But chemistry uses photons extensively in the area we call photochemistry. We represent photons as hν, and hence (hν)3.

This molecular light has some fascinating properties. One is that it travels around 100,000 times slower than the usual speed of light. Another is the estimate of the photon-photon binding energies, which are ~1010 times smaller than in diatomic molecules such as NaCl and H2. I await with interest to see whether this new state of light will achieve any interesting chemistry.

References

  1. Q. Liang, A.V. Venkatramani, S.H. Cantu, T.L. Nicholson, M.J. Gullans, A.V. Gorshkov, J.D. Thompson, C. Chin, M.D. Lukin, and V. Vuletić, "Observation of three-photon bound states in a quantum nonlinear medium", Science, vol. 359, pp. 783-786, 2018. https://doi.org/10.1126/science.aao7293

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Hypervalent Helium – not!

Friday, February 16th, 2018

Last year, this article[1] attracted a lot of attention as the first example of molecular helium in the form of Na2He. In fact, the helium in this species has a calculated‡ bond index of only 0.15 and it is better classified as a sodium electride with the ionisation induced by pressure and the presence of helium atoms. The helium is neither valent, nor indeed hypervalent (the meanings are in fact equivalent for this element). In a separate blog posted in 2013, I noted a cobalt carbonyl complex containing a hexacoordinate hydrogen in the form of hydride, H–. A comment appended to this blog insightfully asked about the isoelectronic complex containing He instead of H–. Here, rather belatedly, I respond to this comment!

The complex [HCo6(CO)15]– has a calculated bond index at the hydrogen of 0.988 and a calculated NMR chemical shift of 21.6 ppm (ωB97XD/Def2-TZVPPD calculation) compared to a measured value of 23.2 ppm. Despite being six-coordinate, the hydride has a bond index that does not exceed one (it is not hypervalent).

So here is the neutral helium analogue. The He bond index emerges as 0.71 at the geometry of the hydride complex. Compare this with the bond index of 0.15 calculated for Na2He and it would be fair to say that at this geometry, the helium in [HeCo6(CO)15] would have a greater claim to be a molecular compound. Back in 2010, extrapolating from a series of posts here, I had speculated[2] about other molecular species of He, including the di-cation below. This has a He bond index of 0.54, rather less than that in [HeCo6(CO)15] but much more than in Na2He. It is also vibrationally stable.

But now, [HeCo6(CO)15] goes “pear-shaped” (why do pears have such a bad press?). I started a process of optimizing the geometry of this complex (ωB97Xd/Def2-TZVPPD). Slowly, the He started to creep out of the centre of the complex and emerge from the cavity. After about 100 steps it reached the geometry shown below, at which point the Wiberg bond index has dropped to 0.62 and still going down. I think it might take a few more steps to be completely expelled, but I have stopped the geometry optimisation at this stage.

So helium appears not to be valent in [HeCo6(CO)15]. However, I have yet to try Ne, which is both larger and softer. I will post results here.

‡All data at 10.14469/hpc/3587.

References

  1. X. Dong, A.R. Oganov, A.F. Goncharov, E. Stavrou, S. Lobanov, G. Saleh, G. Qian, Q. Zhu, C. Gatti, V.L. Deringer, R. Dronskowski, X. Zhou, V.B. Prakapenka, Z. Konôpková, I.A. Popov, A.I. Boldyrev, and H. Wang, "A stable compound of helium and sodium at high pressure", Nature Chemistry, vol. 9, pp. 440-445, 2017. https://doi.org/10.1038/nchem.2716
  2. H.S. Rzepa, "The rational design of helium bonds", Nature Chemistry, vol. 2, pp. 390-393, 2010. https://doi.org/10.1038/nchem.596

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Silicon drug analogues.

Sunday, January 14th, 2018

I don’t normally write about the pharmaceutical industry, but I was intrigued by several posts by Derek Lowe (who does cover this area) on the topic of creating new drugs by deuterating existing ones. Thus he covered the first deuterated drug receiving FDA approval last year, having first reviewed the concept back in 2009. So when someone introduced me to sila-haloperidol, I checked to see if Derek had written about it. Apparently not, so here are a few details.

The idea appears to take a well-known drug, in this case haloperidol and selectively replacing a carbon atom with a silicon atom to form silahaloperidol.[1] The compound was actually reported in 2004 (see data citation 10.5517/cc7yhc0) but its drug-like properties were only reported four years later in 2008. Haloperidol itself has some undesirable side-effects, including those due to the metabolic products of the drug and so there are certainly reasons for trying to reduce these. Here are the main conclusions:

  1. The sila drug shows a significantly higher affinity for hD2 receptors (Table 1).
  2. Silahaloperidol exhibits higher subtype selectivity at dopamine and σ receptors
  3. The substitution by silicon has little effect on physico-chemical profiles
  4. The in-vivo half-life of the sila analogue was 3.6 times shorter (~18 minutes).
  5. An almost three-fold inhibitory effect against CYP3A4 was noted.
  6. The sila-drug displayed “a completely altered metabolic fate while otherwise maintaining a similar pharmacokinetic profile”.

These do seem to add up to a promising route for optimising drug activities. The authors themselves note the “great potential” for drug design. A review in 2017[2] concurs. So along with deuterated drugs, perhaps siladrugs are ones to watch in the future!

References

  1. R. Tacke, F. Popp, B. Müller, B. Theis, C. Burschka, A. Hamacher, M. Kassack, D. Schepmann, B. Wünsch, U. Jurva, and E. Wellner, "Sila‐Haloperidol, a Silicon Analogue of the Dopamine (D <sub>2</sub> ) Receptor Antagonist Haloperidol: Synthesis, Pharmacological Properties, and Metabolic Fate", ChemMedChem, vol. 3, pp. 152-164, 2008. https://doi.org/10.1002/cmdc.200700205
  2. R. Ramesh, and D.S. Reddy, "Quest for Novel Chemical Entities through Incorporation of Silicon in Drug Scaffolds", Journal of Medicinal Chemistry, vol. 61, pp. 3779-3798, 2017. https://doi.org/10.1021/acs.jmedchem.7b00718

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Hypervalent hydrogen?

Saturday, January 13th, 2018

I discussed the molecule the molecule CH3F2- a while back. It was a very rare computed example of a system where the added two electrons populate the higher valence shells known as Rydberg orbitals as an alternative to populating the C-F antibonding σ-orbital to produce CH3– and F–. The net result was the creation of a weak C-F “hyperbond”, in which the C-F region has an inner conventional bond, with an outer “sheath” encircling the first bond. But this system very easily dissociates to CH3– and F– and is hardly a viable candidate for experimental detection.  In an effort to “tune” this effect to see if a better candidate for such detection might be found, I tried CMe3F2-. Here is its story.

The calculation‡ is at the ωB97XD/Def2-TZVPPD/SCRF=water level (water is here used as an approximate model for a condensed environment, helping to bind the two added electrons).

  1. An NBO (Natural Bond orbital) analysis reveals a total Rydberg orbital population of 1.186e and the following bond indices; F 0.853, C 3.977, C(methyl) 4.051, H(*3) 1.332. The latter corresponds to the three methyl hydrogens aligned antiperiplanar to the C-F bond.
  2. To put this value into context, the hydrogen in the FHF– anion has an NBO H bond index of 0.724, and the bridging hydrogens in diborane only have a value of 0.988. Even the hexa-coordinate hydride system [Co6H(CO)15]– discussed in an earlier blog  has an H bond index of just 0.86. Actually, coordination of six or even higher for hydrogen is no longer rare; some 28 crystal structures of the type HM6 (M=metal) are known (it would be useful to find out if any of the other 27 such structures might have a hydrogen bond index >1).
  3. Next, the ELF analysis (Electron localisation function), analysed firstly using the excellent MultiWFN program.[1]

    This reveals an attractor basin integrating to 1.663e and located along the axis of the F-C bond and extended into the region of the three antiperiplanar methyl hydrogens. The C-F bond itself only supports a basin of 0.729e, typical of the fairly ionic C-F bond. The covalent C-Me bonds are also pretty normal, as are the other hydrogens.
  4. I also show ELF analysis using the alternative TopMod program[2]; the numerical values on this diagram are the calculated bond lengths in Å. The basin integrations are very similar to those obtained using MultiWFN.

    The Wiberg bond orders of the three H…H regions shown connected by dashed lines above are 0.154, which contributes to the bond index of >1 at these three hydrogens.
  5. The predicted 1H chemical shift of these three “hypervalent” hydrogens is +3.0 ppm, whilst the other six methyl hydrogens are at -0.87ppm.

So changing CH3F2- to CMe3F2- has dramatically changed the bonding picture that emerges, rather than a fine-tuning. The C-F is no longer a “hyperbond”, although the Rydberg occupancy of 1.186e remains unusually large. Most of the additional electrons have fled the torus surrounding the C-F bond and relocated to the exo-region of that bond where they now influence the three antiperiplanar methyl hydrogens. A two-electron-three-centre interaction if you like, but with the electron basin occupying a tetrahedral vertex rather than the triatom centroid.

I end with a challenge. Is it possible to find “real” molecules containing hydrogen where the formal bond index for at least one hydrogen exceeds 1.0 significantly, thus making it hypervalent? 

‡The calculations are all collected at FAIR doi; 10.14469/hpc/3372.

References

  1. T. Lu, and F. Chen, "Multiwfn: A multifunctional wavefunction analyzer", Journal of Computational Chemistry, vol. 33, pp. 580-592, 2011. https://doi.org/10.1002/jcc.22885
  2. S. Noury, X. Krokidis, F. Fuster, and B. Silvi, "Computational tools for the electron localization function topological analysis", Computers & Chemistry, vol. 23, pp. 597-604, 1999. https://doi.org/10.1016/s0097-8485(99)00039-x

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Multispectral Chiral Imaging with a Metalens.

Saturday, January 6th, 2018

The title here is from an article on metalenses[1] which caught my eye.

Metalenses are planar and optically thin layers which can be manufactured using a single-step lithographic process. This contrasts with traditional lenses that are not flat and where the optical properties result from very accurately engineered curvatures, which in turn are expensive to manufacture. Metalenses can have built into them many interesting optical properties, including light polarisation and dispersion. Nanoengineering has now resulted[1] in a metalens which can simultaneously present two images of opposite helicity of an object within the same field of view.

What is the relevance to chemistry? Well, a well-known chiroptical technique is known as electronic circular dichroism (ECD). At its simplest, it probes the difference in absorption by a chiral molecule of UV and visible light with opposite circular polarisation. This difference plotted as a function of the wavelength of the light is known as the ECD response. Importantly, this response can also be calculated for either enantiomer of the chiral molecule and hence the absolute configuration can be assigned on the basis of which calculated response matches the observed spectrum. Because the difference in response to the two polarisations of the light (Δε) is actually very small, the ECD technique is intrinsically less sensitive than e.g. normal UV/Visible spectra and this requires the use of expensive instruments to record that small difference. Chiral metalenses offer an interesting future opportunity to create new forms of ECD instrument, perhaps ones that are far more sensitive. In turn, this could lower the costs of acquiring ECD functionality in the standard laboratory (see [2] for an application in teaching laboratories). Very possibly, the most expensive component would in fact then be the computational simulations required to match up with the experimental spectrum!

When metalenses were first introduced, they were only able to lens a limited range of wavelengths. In another article by the same group[3] they now announce a new generation of metalens that covers the region 470 to 670 nm. This excludes the UV regions (<300nm) or the IR regions (>1200nm). The latter covers another important chiroptical instrumental technique known as vibrational circular dichroism, or VCD. As with ECD, the VCD response of a chiral molecule can be pretty well calculated using quantum chemistry and indeed often the VCD method is the only one that can successfully be used to assign absolute molecular configurations.[4] Unfortunately, VCD instruments are even more expensive than ECD ones, again largely due to the intrinsic insensitivity and the need to accumulate data using Fourier Transform methods over many hours. Few chemistry departments have such an instrument. So I will keep an eye out for when an effective chiral metalens operating in infra-red regions is announced! The prospect of routine VCD analyses is tantalising! 

 

References

  1. M. Khorasaninejad, W.T. Chen, A.Y. Zhu, J. Oh, R.C. Devlin, D. Rousso, and F. Capasso, "Multispectral Chiral Imaging with a Metalens", Nano Letters, vol. 16, pp. 4595-4600, 2016. https://doi.org/10.1021/acs.nanolett.6b01897
  2. K.K.(. Hii, H.S. Rzepa, and E.H. Smith, "Asymmetric Epoxidation: A Twinned Laboratory and Molecular Modeling Experiment for Upper-Level Organic Chemistry Students", Journal of Chemical Education, vol. 92, pp. 1385-1389, 2015. https://doi.org/10.1021/ed500398e
  3. W.T. Chen, A.Y. Zhu, V. Sanjeev, M. Khorasaninejad, Z. Shi, E. Lee, and F. Capasso, "A broadband achromatic metalens for focusing and imaging in the visible", Nature Nanotechnology, vol. 13, pp. 220-226, 2018. https://doi.org/10.1038/s41565-017-0034-6
  4. J.I. Murray, N.J. Flodén, A. Bauer, N.D. Fessner, D.L. Dunklemann, O. Bob‐Egbe, H.S. Rzepa, T. Bürgi, J. Richardson, and A.C. Spivey, "Kinetic Resolution of 2‐Substituted Indolines by <i>N</i>‐Sulfonylation using an Atropisomeric 4‐DMAP‐<i>N</i>‐oxide Organocatalyst", Angewandte Chemie International Edition, vol. 56, pp. 5760-5764, 2017. https://doi.org/10.1002/anie.201700977

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