Posts Tagged ‘Chemical polarity’

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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Hypervalence and octet-expansion in trimethylene-λ6-sulfane and related species.

Monday, November 27th, 2017

Previously: “Non-polar” species such as SeMe6, SMe6, ClMe3, ClMe5 all revealed interesting properties for the Se-C, S-C or Cl-C “single” bonds. The latter two examples in particular hinted at internal structures for these single bonds, as manifested by two ELF basins for some of the bonds. Here I take a look at the related molecule where a formal double bond between carbon and the central sulfur atom replacing the single-bond might also hint at octet expansions and hypervalence.

Starting with X=Y=Z=CH2,‡ the calculated (ωB97Xd/Def2-TZVPP) geometry has an interesting chiral D3-symmetric form. The density based ELF-basin centroids are shown below, with each formal C=S π-double bond represented by two ELF basins above and below the C-S axis and with each pair of ELF basins being twisted by 48° with respect to the other two pairs. The total valence shell count around the S is 10.98e and the octet is “expanded” (by ~3e).

The orbital-based NBO approach indicates little utilisation of higher (Rydberg) atomic orbital shells (S: [core]3S(1.13)3p(3.35)3d(0.11)4p(0.02); C: [core]2S(1.15)2p(3.77)3p(0.01)3d(0.01) ). Each S-C bond has a Wiberg bond order of 1.36 (significantly less than a double bond), and the central S has an overall bond index of 4.102. There is a real mis-match between the orbital partitioning (2*1.36 = 2.72e) and the ELF partitioning (2*1.83 = 3.66e) into the S-C bonds. The former indicates that ~two of the twelve valence electrons are entering into anti-bonding orbitals to reduce the total bond index from a possible six to just four, but that they still contribute to the electron-density based ELF disynaptic C-S basins. To cast light on this behaviour, successively one to three of the CH2 groups can be replaced by O.

For each “S=O” bond, we find the ELF basin population more or less halves and electrons instead populate the non-bonding O “lone pairs”. The S-C ELF populations in contrast remain approximately constant. These species therefore have “double” S=C bonds but just “single” S-O bonds. The Rydberg population increases slightly; S: [core]3S(1.06)3p(2.95)3d(0.16)4p(0.02)) and the S bond index is 4.18 for one oxygen and S: [core]3S(0.99)3p(2.67)3d(0.19)4p(0.02) and S bond index 4.16 for two oxygens.

Sulfur trioxide (below) seems best represented by S-O rather than S=O bonds. The Rydberg population is S: [core]3S(0.91)3p(2.41)3d(0.21)4p(0.03) and the S bond index is 4.32.

Just for good measure sulfur trisulfide S(S)3 shows rather lower lone pair population because of course it is less electronegative than oxygen, and hence has a slightly greater S-S ELF basin population. Rydberg, S: [core]3S(1.43)3p(3.73)3d(0.21)4p(0.03) and central S bond index 4.04.

It seems molecules where the electrons in a valence shell exceed the “octet” are only too happy to let the excess electrons leak out into adjacent electronegative atoms as lone pairs, where they are no longer classified as  “shared”. Trimethylene-λ6-sulfane does not have this option and the excess electrons remain in the region of the valence shell, but here they do not contribute to augmenting the bond index at the central atom.  In this specific interpretation, the octet is exceeded, but hypervalence is not induced. It is a slippery concept; one where general agreement about its properties may indeed be difficult to achieve!

‡The FAIR data DOI collection for this post is 10.14469/hpc/3316.

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The dipole moments of highly polar molecules: glycine zwitterion.

Saturday, December 24th, 2016

The previous posts produced discussion about the dipole moments of highly polar molecules. Here to produce some reference points for further discussion I look at the dipole moment of glycine, the classic zwitterion (an internal ion-pair).

Dielectric relaxation studies of glycine–water mixtures yield values that range from 15.7D[1] to 11.9D[2] although these have to be derived using various approximations and assumptions for up to 4 independent Debye processes. Before proceeding to calculations, I looked at the properties of ionized amino acids in the solid state, using the following search query for the Cambridge structure database (CSD). 

The distance measures hydrogen bonds to the carboxylate oxygens and the torsion their orientation. The O…H hydrogen bond distances vary between 1.7-1.85Å, which are short. The orientation of the hydrogen bond can be to the in-plane oxygen “σ-lone pair” (torsion 0 or 180°) and also an out-of-plane ~π form (torsion ~60-90°).

In aqueous solution, it is normally assumed that glycine sustains five such strong H-bonds (three to the H3N+ group and two[3] to the carboxylate anion), forming a polarised “salt bridge” across the ion-pair. Two model types were subjected to calculation using ωB97XD/Def2-TZVPP/SCRF=water. Aqueous glycine without any added explicit water molecules yields a dipole moment of 12.9D (DOI: 10.14469/hpc/2000), which is within the range noted above.‡

The solvated form is shown below, in one specific conformation of the three studied (ωB97XD/Def2-TZVPP/SCRF=water). The calculated O…H hydrogen bond lengths fall into the range revealed from crystal structures. The calculated dipole moments range from 12.6 (DOI: 10.14469/hpc/2007), 15.3 (DOI: 10.14469/hpc/2006) and 14.9D (DOI: 10.14469/hpc/2005), which is a modest increase over the model with no explicit water molecules. The actual dipole is of course a Boltzmann average over these and other as yet unexplored conformations, as well as other values for the number of water molecules.

Given the difficulties in interpreting the dipole moment of a complex Debye system such as hydrated glycine, the agreement between the limited range of solvated models and the measured values seems reasonable, and provides at least some measure of “calibration” for the polar molecules commented on previously.

‡Optimized with the solvent field on. If a vacuum model is used, the proton transfers from the N to the O.

References

  1. M.W. Aaron, and E.H. Grant, "Dielectric relaxation of glycine in water", Transactions of the Faraday Society, vol. 59, pp. 85, 1963. https://doi.org/10.1039/tf9635900085
  2. T. Sato, R. Buchner, . Fernandez, A. Chiba, and W. Kunz, "Dielectric relaxation spectroscopy of aqueous amino acid solutions: dynamics and interactions in aqueous glycine", Journal of Molecular Liquids, vol. 117, pp. 93-98, 2005. https://doi.org/10.1016/j.molliq.2004.08.001
  3. T. Shikata, "Dielectric Relaxation Behavior of Glycine Betaine in Aqueous Solution", The Journal of Physical Chemistry A, vol. 106, pp. 7664-7670, 2002. https://doi.org/10.1021/jp020957j

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Forking “The most polar neutral compound synthesized” into m-benzyne.

Wednesday, December 21st, 2016

A project fork is defined (in computing) as creating a distinct and separate strand from an existing (coding) project. Here I apply the principle to the polar azulene 4 explored in an earlier post, taking m-benzyne as a lower homologue of azulene as my starting point.

m-Benzyne is a less stable 1,3 isomer of o-benzyne (1,2-dehydrobenzene), and is often represented as a 1,3-biradical of 1,3-dehydrobenzene. But, could it be stabilized with cyano and amino groups as shown in 5 above? Here the idea is that charge transfer from the 3-ring to the 5-ring will create a lower homologue of azulene (a well known molecule), with the 3-ring a 4n+2 π-electron aromatic (n=0) and the five ring similarly so (n=1).

I start with the computed (wB97XD/Def2-TZVPP/SCRF=thf) structure of m-benzyne itself, as a closed shell molecule (DOI: 10.14469/hpc/1995). The C-C bond connecting the two rings is long (with a biradical tendency) and hence the conjugation is restricted to the outer periphery. The dipole moment is 0.51D (the dipole vector as shown in blue has the expected direction of polarity).

Now compare this to the substituted version 5; the bond lengths are all more characteristic of aromatic values and most significantly the central bond is as well (DOI: 10.14469/hpc/1996). The dipole moment is augmented thirty fold to 14.6D, which would rank alongside that reported for the most polar neutral molecule.

So I suggest this is substituted “m-benzyne” well worth trying to make and one very much unlikely to have any dispute about the nature of its wavefunction, i.e. biradical or closed shell.

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Posted in Interesting chemistry | 4 Comments »

Forking "The most polar neutral compound synthesized" into m-benzyne.

Wednesday, December 21st, 2016

A project fork is defined (in computing) as creating a distinct and separate strand from an existing (coding) project. Here I apply the principle to the polar azulene 4 explored in an earlier post, taking m-benzyne as a lower homologue of azulene as my starting point.

m-Benzyne is a less stable 1,3 isomer of o-benzyne (1,2-dehydrobenzene), and is often represented as a 1,3-biradical of 1,3-dehydrobenzene. But, could it be stabilized with cyano and amino groups as shown in 5 above? Here the idea is that charge transfer from the 3-ring to the 5-ring will create a lower homologue of azulene (a well known molecule), with the 3-ring a 4n+2 π-electron aromatic (n=0) and the five ring similarly so (n=1).

I start with the computed (wB97XD/Def2-TZVPP/SCRF=thf) structure of m-benzyne itself, as a closed shell molecule (DOI: 10.14469/hpc/1995). The C-C bond connecting the two rings is long (with a biradical tendency) and hence the conjugation is restricted to the outer periphery. The dipole moment is 0.51D (the dipole vector as shown in blue has the expected direction of polarity).

Now compare this to the substituted version 5; the bond lengths are all more characteristic of aromatic values and most significantly the central bond is as well (DOI: 10.14469/hpc/1996). The dipole moment is augmented thirty fold to 14.6D, which would rank alongside that reported for the most polar neutral molecule.

So I suggest this is substituted “m-benzyne” well worth trying to make and one very much unlikely to have any dispute about the nature of its wavefunction, i.e. biradical or closed shell.

1
Henry Rzepa, 2016. [Source]
2
Henry Rzepa, 2016. [Source]

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Posted in Interesting chemistry | 4 Comments »